WorldWideScience

Sample records for model incorporating enzyme

  1. Molybdenum incorporation in tungsten aldehyde oxidoreductase enzymes from Pyrococcus furiosus

    NARCIS (Netherlands)

    Sevcenco, A.M; Bevers, L.E.; Pinkse, M.W.H.; Krijger, G.C.; Wolterbeek, H.T.; Verhaert, P.D.E.M.; Hagen, W.R.; Hagedoorn, P.L.

    2010-01-01

    The hyperthermophilic archaeon Pyrococcus furiosus expresses five aldehyde oxidoreductase (AOR) enzymes, all containing a tungsto-bispterin cofactor. The growth of this organism is fully dependent on the presence of tungsten in the growth medium. Previous studies have suggested that molybdenum is no

  2. Molybdenum incorporation in tungsten aldehyde oxidoreductase enzymes from Pyrococcus furiosus

    NARCIS (Netherlands)

    Sevcenco, A.M; Bevers, L.E.; Pinkse, M.W.H.; Krijger, G.C.; Wolterbeek, H.T.; Verhaert, P.D.E.M.; Hagen, W.R.; Hagedoorn, P.L.

    2010-01-01

    The hyperthermophilic archaeon Pyrococcus furiosus expresses five aldehyde oxidoreductase (AOR) enzymes, all containing a tungsto-bispterin cofactor. The growth of this organism is fully dependent on the presence of tungsten in the growth medium. Previous studies have suggested that molybdenum is no

  3. Multi-enzyme Process Modeling

    DEFF Research Database (Denmark)

    Andrade Santacoloma, Paloma de Gracia

    The subject of this thesis is to develop a methodological framework that can systematically guide mathematical model building for better understanding of multi-enzyme processes. In this way, opportunities for process improvements can be identified by analyzing simulations of either existing...... are affected (in a positive or negative way) by the presence of the other enzymes and compounds in the media. In this thesis the concept of multi-enzyme in-pot term is adopted for processes that are carried out by the combination of enzymes in a single reactor and implemented at pilot or industrial scale...

  4. Dual-enzyme natural motors incorporating decontamination and propulsion capabilities

    OpenAIRE

    Sattayasamitsathit, S; Kaufmann, K; Galarnyk, M; Vazquez-Duhalt, R.; Wang, J

    2014-01-01

    Self-propelled dual-function biocatalytic motors, consisting of unmodified natural tissue and capable of in-motion bioremediation, are described. These enzyme-rich tissue motors rely on the catalase and peroxidase activities of their Raphanus sativus radish body for their propulsion and remediation actions, respectively. The continuous movement of the biocatalytic tissue motors through the contaminated sample facilitates the dynamic removal of phenolic pollutants. Hydrogen peroxide plays a du...

  5. Four enzymes define the incorporation of coenzyme A in thienamycin biosynthesis.

    Science.gov (United States)

    Freeman, Michael F; Moshos, Kristos A; Bodner, Micah J; Li, Rongfeng; Townsend, Craig A

    2008-08-12

    The enzymatic activities of three proteins encoded by the thienamycin gene cluster of Streptomyces cattleya (ThnR, ThnH, and ThnT) have been shown to incrementally cleave CoA to afford the active side-chain component of the beta-lactam antibiotic thienamycin. These results supersede proposals based on earlier radiochemical incorporation experiments. For 20 years it has been thought that cysteine was directly incorporated into the antibiotic. Specific, stepwise truncation of CoA to 4-phosphopantetheine, pantetheine, and finally cysteamine was observed with ThnR, ThnH, and ThnT, respectively, in a series of coupled enzymatic assays. Pantetheinylated carbapenams were synthesized to address possible thienamycin biosynthetic intermediates and were shown to be effective substrates for the pantetheine-cleaving enzyme ThnT. Finally, a fourth gene, thnF, was shown to encode a protein capable of N-acetylating a model compound containing cysteamine in the presence of acetyl-CoA, consistent with the production of the S. cattleya cometabolite, N-acetylthienamycin. Taken together, these four enzymes are proposed to siphon CoA from primary metabolism to create the side chains for the predominant S. cattleya carbapenems, thienamycin and N-acetylthienamycin, in a process likely to be general for the broader class of these antibiotics.

  6. Incorporating groundwater flow into the WEPP model

    Science.gov (United States)

    William Elliot; Erin Brooks; Tim Link; Sue Miller

    2010-01-01

    The water erosion prediction project (WEPP) model is a physically-based hydrology and erosion model. In recent years, the hydrology prediction within the model has been improved for forest watershed modeling by incorporating shallow lateral flow into watershed runoff prediction. This has greatly improved WEPP's hydrologic performance on small watersheds with...

  7. Multi-enzyme Process Modeling

    DEFF Research Database (Denmark)

    Andrade Santacoloma, Paloma de Gracia

    . In this way the model parameters that drives the main dynamic behavior can be identified and thus a better understanding of this type of processes. In order to develop, test and verify the methodology, three case studies were selected, specifically the bi-enzyme process for the production of lactobionic acid......The subject of this thesis is to develop a methodological framework that can systematically guide mathematical model building for better understanding of multi-enzyme processes. In this way, opportunities for process improvements can be identified by analyzing simulations of either existing...... in the scientific literature. Reliable mathematical models of such multi-catalytic schemes can exploit the potential benefit of these processes. In this way, the best outcome of the process can be obtained understanding the types of modification that are required for process optimization. An effective evaluation...

  8. Effects of Straw Incorporation on Soil Nutrients, Enzymes, and Aggregate Stability in Tobacco Fields of China

    Directory of Open Access Journals (Sweden)

    Jiguang Zhang

    2016-07-01

    Full Text Available To determine the effects of straw incorporation on soil nutrients, enzyme activity, and aggregates in tobacco fields, we conducted experiments with different amounts of wheat and maize straw in Zhucheng area of southeast Shandong province for three years (2010–2012. In the final year of experiment (2012, straw incorporation increased soil organic carbon (SOC and related parameters, and improved soil enzyme activity proportionally with the amount of straw added, except for catalase when maize straw was used. And maize straw incorporation was more effective than wheat straw in the tobacco field. The percentage of aggregates >2 mm increased with straw incorporation when measured by either dry or wet sieving. The mean weight diameter (MWD and geometric mean diameter (GMD in straw incorporation treatments were higher than those in the no-straw control (CK. Maize straw increased soil aggregate stability more than wheat straw with the same incorporation amount. Alkaline phosphatase was significantly and negatively correlated with soil pH. Sucrase and urease were both significantly and positively correlated with soil alkali-hydrolysable N. Catalase was significantly but negatively correlated with soil extractable K (EK. The MWD and GMD by dry sieving had significantly positive correlations with SOC, total N, total K, and EK, but only significantly correlated with EK by wet sieving. Therefore, soil nutrients, metabolic enzyme activity, and aggregate stability might be increased by increasing the SOC content through the maize or wheat straw incorporation. Moreover, incorporation of maize straw at 7500 kg·hm−2 was the best choice to enhance soil fertility in the tobacco area of Eastern China.

  9. Incorporating immigrant flows into microsimulation models.

    Science.gov (United States)

    Duleep, Harriet Orcutt; Dowhan, Daniel J

    2008-01-01

    Building on the research on immigrant earnings reviewed in the first article of this series, "Research on Immigrant Earnings," the preceding article, "Adding Immigrants to Microsimulation Models," linked research results to various issues essential for incorporating immigrant earnings into microsimulation models. The discussions of that article were in terms of a closed system. That is, it examined a system in which immigrant earnings and emigration are forecast for a given population represented in the base sample in the microsimulation model. This article, the last in the series, addresses immigrant earnings projections for open systems--microsimulation models that include projections of future immigration. The article suggests a simple method to project future immigrants and their earnings. Including the future flow of immigrants in microsimulation models can dramatically affect the projected Social Security benefits of some groups.

  10. Incorporating neurophysiological concepts in mathematical thermoregulation models

    Science.gov (United States)

    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 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.

  11. Incorporation of RAM techniques into simulation modeling

    Energy Technology Data Exchange (ETDEWEB)

    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.

  12. Enzyme incorporated microfluidic device for in-situ glucose detection in water-in-air microdroplets.

    Science.gov (United States)

    Piao, Yunxian; Han, Dong Ju; Azad, Mohammad Reza; Park, Minsu; Seo, Tae Seok

    2015-03-15

    Droplet generating microfluidic systems can provide miniaturized bioanalytical tools by using the homogenous and high-throughput droplets as nanoreactors. In this study, we demonstrated a sensitive and in-situ glucose monitoring system using water-in-air droplets in an enzyme incorporated microfluidic device. A thin film structure of a glucose oxidase (GOx) enzyme immobilized hydrogel was constructed in the middle of the microfluidic channel, and nanoliter scaled water-in-air droplets which contain a glucose sample, horseradish peroxidase (HRP), and an Amplex Red substrate were generated by flow focusing of water phase with air. Once the droplets passed through the enzyme trapped hydrogel, the droplets temporarily halted and a GOx mediated catalytic reaction with glucose proceeded, resulting in producing fluorescent resorufin products in the droplets. With optimized conditions such as the thickness of a hydrogel film and the size and flowing rate of droplets, fluorescence intensities of the released droplets linearly increased in proportional to the glucose concentration up to 3mM, and the limit of detection was calculated as 6.64µM. A spiked glucose in a real urine sample was also successfully analyzed, and the functionality of the proposed enzyme immobilized microfluidic chip was maintained for at least two weeks without loss of enzymatic activity and detection sensitivity. Thus, our methodology suggests a novel droplet based glucose sensing chip which can monitor glucose in a real-time and high-throughput manner.

  13. Incorporating infiltration modelling in urban flood management

    Directory of Open Access Journals (Sweden)

    A. S. Jumadar

    2008-06-01

    Full Text Available Increasing frequency and intensity of flood events in urban areas can be linked to increase in impervious area due to urbanization, exacerbated by climate change. The established approach of conveying storm water by conventional drainage systems has contributed to magnification of runoff volume and peak flows beyond those of undeveloped catchments. Furthermore, the continuous upgrading of such conventional systems is costly and unsustainable in the long term. Sustainable drainage systems aim at addressing the adverse effects associated with conventional systems, by mimicking the natural drainage processes, encouraging infiltration and storage of storm water. In this study we model one of the key components of SuDS, the infiltration basins, in order to assert the benefits of the approach. Infiltration modelling was incorporated in the detention storage unit within the one-dimensional urban storm water management model, EPA-SWMM 5.0. By introduction of infiltration modelling in the storage, the flow attenuation performance of the unit was considerably improved. The study also examines the catchment scale impact of both source and regional control storage/infiltration systems. Based on the findings of two case study areas modelled with the proposed options, it was observed that source control systems have a greater and much more natural impact at a catchment level, with respect to flow attenuation, compared to regional control systems of which capacity is equivalent to the sum of source control capacity at the catchment.

  14. Incorporation of salinity in Water Availability Modeling

    Science.gov (United States)

    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.

  15. Incorporation of enzyme concentrations into FBA and identification of optimal metabolic pathways

    Directory of Open Access Journals (Sweden)

    Mukhopadhyay Subhasis

    2008-07-01

    Full Text Available Abstract Background In the present article, we propose a method for determining optimal metabolic pathways in terms of the level of concentration of the enzymes catalyzing various reactions in the entire metabolic network. The method, first of all, generates data on reaction fluxes in a pathway based on steady state condition. A set of constraints is formulated incorporating weighting coefficients corresponding to concentration of enzymes catalyzing reactions in the pathway. Finally, the rate of yield of the target metabolite, starting with a given substrate, is maximized in order to identify an optimal pathway through these weighting coefficients. Results The effectiveness of the present method is demonstrated on two synthetic systems existing in the literature, two pentose phosphate, two glycolytic pathways, core carbon metabolism and a large network of carotenoid biosynthesis pathway of various organisms belonging to different phylogeny. A comparative study with the existing extreme pathway analysis also forms a part of this investigation. Biological relevance and validation of the results are provided. Finally, the impact of the method on metabolic engineering is explained with a few examples. Conclusions The method may be viewed as determining an optimal set of enzymes that is required to get an optimal metabolic pathway. Although it is a simple one, it has been able to identify a carotenoid biosynthesis pathway and the optimal pathway of core carbon metabolic network that is closer to some earlier investigations than that obtained by the extreme pathway analysis. Moreover, the present method has identified correctly optimal pathways for pentose phosphate and glycolytic pathways. It has been mentioned using some examples how the method can suitably be used in the context of metabolic engineering.

  16. Incorporating direct marketing activity into latent attrition models

    NARCIS (Netherlands)

    Schweidel, David A.; Knox, George

    2013-01-01

    When defection is unobserved, latent attrition models provide useful insights about customer behavior and accurate forecasts of customer value. Yet extant models ignore direct marketing efforts. Response models incorporate the effects of direct marketing, but because they ignore latent attrition,

  17. Modelling Fungal Fermentations for Enzyme Production

    DEFF Research Database (Denmark)

    Albæk, Mads Orla; Gernaey, Krist; Hansen, Morten S.

    We have developed a process model of fungal fed-batch fermentations for enzyme production. In these processes, oxygen transfer rate is limiting and controls the substrate feeding rate. The model has been shown to describe cultivations of both Aspergillus oryzae and Trichoderma reesei strains in 550...

  18. Integrating microbial physiology and enzyme traits in the quality model

    Science.gov (United States)

    Sainte-Marie, Julien; Barrandon, Matthieu; Martin, Francis; Saint-André, Laurent; Derrien, Delphine

    2017-04-01

    microbial physiology and enzyme traits can be incorporated in a model based on a continuous representation of the organic matter and evaluate how it can improve our ability to predict soil C cycling. To do so, we analyse the properties of the model by implementing different scenarii and test the sensitivity of its parameters. Agren, G. I., & Bosatta, E. (1998). Theoretical ecosystem ecology: understanding element cycles. Cambridge University Press.

  19. Multiplicative earthquake likelihood models incorporating strain rates

    Science.gov (United States)

    Rhoades, D. A.; Christophersen, A.; Gerstenberger, M. C.

    2017-01-01

    SUMMARYWe examine the potential for strain-rate variables to improve long-term earthquake likelihood models. We derive a set of multiplicative hybrid earthquake likelihood models in which cell rates in a spatially uniform baseline model are scaled using combinations of covariates derived from earthquake catalogue data, fault data, and strain-rates for the New Zealand region. Three components of the strain rate estimated from GPS data over the period 1991-2011 are considered: the shear, rotational and dilatational strain rates. The hybrid model parameters are optimised for earthquakes of M 5 and greater over the period 1987-2006 and tested on earthquakes from the period 2012-2015, which is independent of the strain rate estimates. The shear strain rate is overall the most informative individual covariate, as indicated by Molchan error diagrams as well as multiplicative modelling. Most models including strain rates are significantly more informative than the best models excluding strain rates in both the fitting and testing period. A hybrid that combines the shear and dilatational strain rates with a smoothed seismicity covariate is the most informative model in the fitting period, and a simpler model without the dilatational strain rate is the most informative in the testing period. These results have implications for probabilistic seismic hazard analysis and can be used to improve the background model component of medium-term and short-term earthquake forecasting models.

  20. A Financial Market Model Incorporating Herd Behaviour.

    Science.gov (United States)

    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

  1. Incorporating Resilience into Dynamic Social Models

    Science.gov (United States)

    2016-07-20

    resiliency, computational modeling, computational social science /systems, modeling and simulation 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF...system. The relationships between random variables are given as conditional probability rules. BKBs are represented as a directed graph with...and BKB inferencing methods can be found in Santos et al [20]. 4.1. BKB Definition and Inferencing A BKB is a directed , bipartite graph consisting

  2. Incorporating evolutionary processes into population viability models.

    Science.gov (United States)

    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.

  3. Incorporating 3-dimensional models in online articles

    Science.gov (United States)

    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

  4. Incorporating territory compression into population models

    NARCIS (Netherlands)

    Ridley, J; Komdeur, J; Sutherland, WJ; Sutherland, William J.

    The ideal despotic distribution, whereby the lifetime reproductive success a territory's owner achieves is unaffected by population density, is a mainstay of behaviour-based population models. We show that the population dynamics of an island population of Seychelles warblers (Acrocephalus

  5. Incorporating POS Tagging into Language Modeling

    CERN Document Server

    Heeman, P A; Heeman, Peter A.; Allen, James F.

    1997-01-01

    Language models for speech recognition tend to concentrate solely on recognizing the words that were spoken. In this paper, we redefine the speech recognition problem so that its goal is to find both the best sequence of words and their syntactic role (part-of-speech) in the utterance. This is a necessary first step towards tightening the interaction between speech recognition and natural language understanding.

  6. Seeing & Feeling How Enzymes Work Using Tangible Models

    Science.gov (United States)

    Lau, Kwok-chi

    2013-01-01

    This article presents a tangible model used to help students tackle some misconceptions about enzyme actions, particularly the induced-fit model, enzyme-substrate complementarity, and enzyme inhibition. The model can simulate how substrates induce a change in the shape of the active site and the role of attraction force during enzyme-substrate…

  7. Seeing & Feeling How Enzymes Work Using Tangible Models

    Science.gov (United States)

    Lau, Kwok-chi

    2013-01-01

    This article presents a tangible model used to help students tackle some misconceptions about enzyme actions, particularly the induced-fit model, enzyme-substrate complementarity, and enzyme inhibition. The model can simulate how substrates induce a change in the shape of the active site and the role of attraction force during enzyme-substrate…

  8. Incorporating direct marketing activity into latent attrition models

    NARCIS (Netherlands)

    Schweidel, David A.; Knox, George

    2013-01-01

    When defection is unobserved, latent attrition models provide useful insights about customer behavior and accurate forecasts of customer value. Yet extant models ignore direct marketing efforts. Response models incorporate the effects of direct marketing, but because they ignore latent attrition, th

  9. 40 CFR 174.525 - E. coli B-D-glucuronidase enzyme as a plant-incorporated protectant inert ingredient; exemption...

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false E. coli B-D-glucuronidase enzyme as a... E. coli B-D-glucuronidase enzyme as a plant-incorporated protectant inert ingredient; exemption from the requirement of a tolerance. Residues of E. coli B-D-glucuronidase enzyme are exempt from...

  10. Incorporating Peatland Plant Communities into the Enzymic 'Latch' Hypothesis: Can Vegetation Influence Carbon Storage Mechanisms?

    Science.gov (United States)

    Romanowicz, K. J.; Daniels, A. L.; Potvin, L. R.; Kane, E. S.; Kolka, R. K.; Chimner, R. A.; Lilleskov, E. A.

    2012-12-01

    High water table conditions in peatland ecosystems are known to favor plant production over decomposition and carbon is stored. Dominant plant communities change in response to water table but little is know of how these changes affect belowground carbon storage. One hypothesis known as the enzymic 'latch' proposed by Freeman et al. suggests that oxygen limitations due to high water table conditions inhibit microorganisms from synthesizing specific extracellular enzymes essential for carbon and nutrient mineralization, allowing carbon to be stored as decomposition is reduced. Yet, this hypothesis excludes plant community interactions on carbon storage. We hypothesize that the dominant vascular plant communities, sedges and ericaceous shrubs, will have inherently different effects on peatland carbon storage, especially in response to declines in water table. Sedges greatly increase in abundance following water table decline and create extensive carbon oxidation and mineralization hotspots through the production of deep roots with aerenchyma (air channels in roots). Increased oxidation may enhance aerobic microbial activity including increased enzyme activity, leading to peat subsidence and carbon loss. In contrast, ericaceous shrubs utilize enzymatically active ericoid mycorrhizal fungi that suppress free-living heterotrophs, promoting decreased carbon mineralization by mediating changes in rhizosphere microbial communities and enzyme activity regardless of water table declines. Beginning May 2010, bog monoliths were harvested, housed in mesocosm chambers, and manipulated into three vegetation treatments: unmanipulated (+sedge, +Ericaceae), sedge (+sedge, -Ericaceae), and Ericaceae (-sedge, +Ericaceae). Following vegetation manipulations, two distinct water table manipulations targeting water table seasonal profiles were implemented: (low intra-seasonal variability, higher mean water table; high intra-seasonal variability, lower mean water table). In 2012, peat

  11. Incorporating RTI in a Hybrid Model of Reading Disability

    Science.gov (United States)

    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…

  12. Developing an Enzyme Mediated Soil Organic Carbon Decomposition Model

    Science.gov (United States)

    Mayes, M. A.; Post, W. M.; Wang, G.; Jagadamma, S.; Steinweg, J. M.; Schadt, C. W.

    2012-12-01

    We developed the Microbial-ENzyme-mediated Decomposition (MEND) model in order to mechanistically model the decomposition of soil organic carbon (C). This presentation is an overview of the concept and development of the model and of the design of complementary lab-scale experiments. The model divides soil C into five pools of particulate, mineral-associated, dissolved, microbial, and enzyme organic C (Wang et al. 2012). There are three input types - cellulose, lignin, and dissolved C. Decomposition is mediated via microbial extracellular enzymes using the Michaelis-Menten equation, resulting in the production of a common pool of dissolved organic C. Parameters for the Michaelis-Menten equation are obtained through a literature review (Wang and Post, 2012a). The dissolved C is taken up by microbial biomass and proportioned according to microbial maintenance and growth, which were recalculated according to Wang and Post (2012b). The model allows dissolved C to undergo adsorption and desorption reactions with the mineral-associated C, which was also parameterized based upon a literature review and complementary laboratory experiments. In the lab, four 14C-labeled substrates (cellulose, fatty acid, glucose, and lignin-like) were incubated with either the particulate C pool, the mineral-associated C pool, or to bulk soils. The rate of decomposition was measured via the production of 14CO2 over time, along with incorporation into microbial biomass, production of dissolved C, and estimation of sorbed C. We performed steady-state and dynamic simulations and sensitivity analyses under temperature increases of 1-5°C for a period of 100 y. Simulations indicated an initial decrease in soil organic C consisting of both cellulose and lignin pools. Over longer time intervals (> 6 y), however, a shrinking microbial population, a concomitant decrease in enzyme production, and a decrease in microbial carbon use efficiency together decreased CO2 production and resulted in greater

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  14. Enzyme

    Science.gov (United States)

    Enzymes are complex proteins that cause a specific chemical change in all parts of the body. For ... use them. Blood clotting is another example of enzymes at work. Enzymes are needed for all body ...

  15. Incorporating RTI in a Hybrid Model of Reading Disability

    OpenAIRE

    2014-01-01

    The present study seeks to evaluate a hybrid model of identification that incorporates response-to-intervention (RTI) as a one of the key symptoms of reading disability. The one-year stability of alternative operational definitions of reading disability was examined in a large scale sample of students who were followed longitudinally from first to second grade. The results confirmed previous findings of limited stability for single-criterion based operational definitions of reading disability...

  16. Incorporating the Hayflick Limit into a model of Telomere Dynamics

    CERN Document Server

    Cyrenne, Benoit M

    2013-01-01

    A model of telomere dynamics is proposed and examined. Our model, which extends a previously introduced two-compartment model that incorporates stem cells as progenitors of new cells, imposes the Hayflick Limit, the maximum number of cell divisions that are possible. This new model leads to cell populations for which the average telomere length is not necessarily a monotonically decreasing function of time, in contrast to previously published models. We provide a phase diagram indicating where such results would be expected. In addition, qualitatively different results are obtained for the evolution of the total cell population. Last, in comparison to available leukocyte baboon data, this new model is shown to provide a better fit to biological data.

  17. Incorporating Linguistic Structure into Maximum Entropy Language Models

    Institute of Scientific and Technical Information of China (English)

    FANG GaoLin(方高林); GAO Wen(高文); WANG ZhaoQi(王兆其)

    2003-01-01

    In statistical language models, how to integrate diverse linguistic knowledge in a general framework for long-distance dependencies is a challenging issue. In this paper, an improved language model incorporating linguistic structure into maximum entropy framework is presented.The proposed model combines trigram with the structure knowledge of base phrase in which trigram is used to capture the local relation between words, while the structure knowledge of base phrase is considered to represent the long-distance relations between syntactical structures. The knowledge of syntax, semantics and vocabulary is integrated into the maximum entropy framework.Experimental results show that the proposed model improves by 24% for language model perplexity and increases about 3% for sign language recognition rate compared with the trigram model.

  18. Methods improvements incorporated into the SAPHIRE ASP models

    Energy Technology Data Exchange (ETDEWEB)

    Sattison, M.B.; Blackman, H.S.; Novack, S.D. [Idaho National Engineering Lab., Idaho Falls, ID (United States)] [and others

    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.

  19. A novel fluence map optimization model incorporating leaf sequencing constraints.

    Science.gov (United States)

    Jin, Renchao; Min, Zhifang; Song, Enmin; Liu, Hong; Ye, Yinyu

    2010-02-21

    A novel fluence map optimization model incorporating leaf sequencing constraints is proposed to overcome the drawbacks of the current objective inside smoothing models. Instead of adding a smoothing item to the objective function, we add the total number of monitor unit (TNMU) requirement directly to the constraints which serves as an important factor to balance the fluence map optimization and leaf sequencing optimization process at the same time. Consequently, we formulate the fluence map optimization models for the trailing (left) leaf synchronized, leading (right) leaf synchronized and the interleaf motion constrained non-synchronized leaf sweeping schemes, respectively. In those schemes, the leaves are all swept unidirectionally from left to right. Each of those models is turned into a linear constrained quadratic programming model which can be solved effectively by the interior point method. Those new models are evaluated with two publicly available clinical treatment datasets including a head-neck case and a prostate case. As shown by the empirical results, our models perform much better in comparison with two recently emerged smoothing models (the total variance smoothing model and the quadratic smoothing model). For all three leaf sweeping schemes, our objective dose deviation functions increase much slower than those in the above two smoothing models with respect to the decreasing of the TNMU. While keeping plans in the similar conformity level, our new models gain much better performance on reducing TNMU.

  20. The outer-coordination sphere: incorporating amino acids and peptides as ligands for homogeneous catalysts to mimic enzyme function

    Energy Technology Data Exchange (ETDEWEB)

    Shaw, Wendy J.

    2012-10-09

    Great progress has been achieved in the field of homogeneous transition metal-based catalysis, however, as a general rule these solution based catalysts are still easily outperformed, both in terms of rates and selectivity, by their analogous enzyme counterparts, including structural mimics of the active site. This observation suggests that the features of the enzyme beyond the active site, i.e. the outer-coordination sphere, are important for their exceptional function. Directly mimicking the outer-coordination sphere requires the incorporation of amino acids and peptides as ligands for homogeneous catalysts. This effort has been attempted for many homogeneous catalysts which span the manifold of catalytic reactions and often require careful thought regarding solvent type, pH and characterization to avoid unwanted side reactions or catalyst decomposition. This article reviews the current capability of synthesizing and characterizing this often difficult category of metal-based catalysts. This work was funded by the DOE Office of Science Early Career Research Program through the Office of Basic Energy Sciences. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

  1. Incorporating vegetation feedbacks in regional climate modeling over West Africa

    Science.gov (United States)

    Erfanian, A.; Wang, G.; Yu, M.; Ahmed, K. F.; Anyah, R. O.

    2015-12-01

    Despite major advancements in modeling of the climate system, incorporating vegetation dynamics into climate models is still at the initial stages making it an ongoing research topic. Only few of GCMs participating in CMIP5 simulations included the vegetation dynamics component. Consideration for vegetation dynamics is even less common in RCMs. In this study, RegCM4.3.4-CLM4-CN-DV, a regional climate model synchronously coupled with a land surface component that includes both Carbon-Nitrogen (CN) and Dynamic-Vegetation (DV) processes is used to simulate and project regional climate over West Africa. Due to its unique regional features, West Africa climate is known for being susceptible to land-atmosphere interactions, enhancing the importance of including vegetation dynamics in modeling climate over this region. In this study the model is integrated for two scenarios (present-day and future) using outputs from four GCMs participating in CMIP5 (MIROC, CESM, GFDL and CCSM4) as lateral boundary conditions, which form the basis of a multi-model ensemble. Results of model validation indicates that ensemble of all models outperforms each of individual models in simulating present-day temperature and precipitation. Therefore, the ensemble set is used to analyze the impact of including vegetation dynamics in the RCM on future projection of West Africa's climate. Results from the ensemble analysis will be presented, together with comparison among individual models.

  2. A mathematical model for incorporating biofeedback into human postural control

    Directory of Open Access Journals (Sweden)

    Ersal Tulga

    2013-02-01

    Full Text Available Abstract Background Biofeedback of body motion can serve as a balance aid and rehabilitation tool. To date, mathematical models considering the integration of biofeedback into postural control have represented this integration as a sensory addition and limited their application to a single degree-of-freedom representation of the body. This study has two objectives: 1 to develop a scalable method for incorporating biofeedback into postural control that is independent of the model’s degrees of freedom, how it handles sensory integration, and the modeling of its postural controller; and 2 to validate this new model using multidirectional perturbation experimental results. Methods Biofeedback was modeled as an additional torque to the postural controller torque. For validation, this biofeedback modeling approach was applied to a vibrotactile biofeedback device and incorporated into a two-link multibody model with full-state-feedback control that represents the dynamics of bipedal stance. Average response trajectories of body sway and center of pressure (COP to multidirectional surface perturbations of subjects with vestibular deficits were used for model parameterization and validation in multiple perturbation directions and for multiple display resolutions. The quality of fit was quantified using average error and cross-correlation values. Results The mean of the average errors across all tactor configurations and perturbations was 0.24° for body sway and 0.39 cm for COP. The mean of the cross-correlation value was 0.97 for both body sway and COP. Conclusions The biofeedback model developed in this study is capable of capturing experimental response trajectory shapes with low average errors and high cross-correlation values in both the anterior-posterior and medial-lateral directions for all perturbation directions and spatial resolution display configurations considered. The results validate that biofeedback can be modeled as an additional

  3. A model study of sequential enzyme reactions and electrostatic channeling.

    Science.gov (United States)

    Eun, Changsun; Kekenes-Huskey, Peter M; Metzger, Vincent T; McCammon, J Andrew

    2014-03-14

    We study models of two sequential enzyme-catalyzed reactions as a basic functional building block for coupled biochemical networks. We investigate the influence of enzyme distributions and long-range molecular interactions on reaction kinetics, which have been exploited in biological systems to maximize metabolic efficiency and signaling effects. Specifically, we examine how the maximal rate of product generation in a series of sequential reactions is dependent on the enzyme distribution and the electrostatic composition of its participant enzymes and substrates. We find that close proximity between enzymes does not guarantee optimal reaction rates, as the benefit of decreasing enzyme separation is countered by the volume excluded by adjacent enzymes. We further quantify the extent to which the electrostatic potential increases the efficiency of transferring substrate between enzymes, which supports the existence of electrostatic channeling in nature. Here, a major finding is that the role of attractive electrostatic interactions in confining intermediate substrates in the vicinity of the enzymes can contribute more to net reactive throughput than the directional properties of the electrostatic fields. These findings shed light on the interplay of long-range interactions and enzyme distributions in coupled enzyme-catalyzed reactions, and their influence on signaling in biological systems.

  4. A Simple Structure Model for Enzyme Production by Phanerochaete chrysosporium

    Institute of Scientific and Technical Information of China (English)

    岑沛霖; 郑重鸣; FOOYinDin; JefferyPhilipObbard; 林建平

    2003-01-01

    In order to understand the behavior of ligninolytic enzyme production by white rot fungi Phanerochaete chrysosporium, study on time courses and a mathematical model for the production of lignin peroxidase (LiP) and manganese peroxidase (MnP) of the fungi was undertaken. Based on the Monod-Jacob operon model, the ligninolytic enzyme would be synthesized in the absence of a related repressor. The repressor is assumed to be active in the presence of ammonia nitrogen, and as combined as co-repressor, it causes the inhibition of enzyme synthesis. The model can explain the mechanism of extracellular ligninolytic enzyme production by white rot fungi. The results,as predicted by the model, correspond closely to those observed in experimental studies. In addition, some light is also shed on unmeasured variables, such as the concentrations of repressor and mRNA that are related to the enzyme synthesis.

  5. Safety models incorporating graph theory based transit indicators.

    Science.gov (United States)

    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.

  6. Enzymes/non-enzymes classification model complexity based on composition, sequence, 3D and topological indices.

    Science.gov (United States)

    Munteanu, Cristian Robert; González-Díaz, Humberto; Magalhães, Alexandre L

    2008-09-21

    The huge amount of new proteins that need a fast enzymatic activity characterization creates demands of protein QSAR theoretical models. The protein parameters that can be used for an enzyme/non-enzyme classification includes the simpler indices such as composition, sequence and connectivity, also called topological indices (TIs) and the computationally expensive 3D descriptors. A comparison of the 3D versus lower dimension indices has not been reported with respect to the power of discrimination of proteins according to enzyme action. A set of 966 proteins (enzymes and non-enzymes) whose structural characteristics are provided by PDB/DSSP files was analyzed with Python/Biopython scripts, STATISTICA and Weka. The list of indices includes, but it is not restricted to pure composition indices (residue fractions), DSSP secondary structure protein composition and 3D indices (surface and access). We also used mixed indices such as composition-sequence indices (Chou's pseudo-amino acid compositions or coupling numbers), 3D-composition (surface fractions) and DSSP secondary structure amino acid composition/propensities (obtained with our Prot-2S Web tool). In addition, we extend and test for the first time several classic TIs for the Randic's protein sequence Star graphs using our Sequence to Star Graph (S2SG) Python application. All the indices were processed with general discriminant analysis models (GDA), neural networks (NN) and machine learning (ML) methods and the results are presented versus complexity, average of Shannon's information entropy (Sh) and data/method type. This study compares for the first time all these classes of indices to assess the ratios between model accuracy and indices/model complexity in enzyme/non-enzyme discrimination. The use of different methods and complexity of data shows that one cannot establish a direct relation between the complexity and the accuracy of the model.

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

    Science.gov (United States)

    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.

  8. Incorporating Plant Phenology Dynamics in a Biophysical Canopy Model

    Science.gov (United States)

    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.

  9. A dengue model incorporating saturation incidence and human migration

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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, 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

  11. Structural differences of matrix metalloproteinases. Homology modeling and energy minimization of enzyme-substrate complexes

    DEFF Research Database (Denmark)

    Terp, G E; Christensen, I T; Jørgensen, Flemming Steen

    2000-01-01

    Matrix metalloproteinases are extracellular enzymes taking part in the remodeling of extracellular matrix. The structures of the catalytic domain of MMP1, MMP3, MMP7 and MMP8 are known, but structures of enzymes belonging to this family still remain to be determined. A general approach...... to the homology modeling of matrix metalloproteinases, exemplified by the modeling of MMP2, MMP9, MMP12 and MMP14 is described. The models were refined using an energy minimization procedure developed for matrix metalloproteinases. This procedure includes incorporation of parameters for zinc and calcium ions...... in the AMBER 4.1 force field, applying a non-bonded approach and a full ion charge representation. Energy minimization of the apoenzymes yielded structures with distorted active sites, while reliable three-dimensional structures of the enzymes containing a substrate in active site were obtained. The structural...

  12. Incorporating Phaeocystis into a Southern Ocean ecosystem model

    Science.gov (United States)

    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.

  13. A Systems Biology Framework for Modeling Metabolic Enzyme Inhibition of Mycobacterium Tuberculosis

    Science.gov (United States)

    2009-09-15

    between single nucleotide poly- morphisms and anemia [20]. Kinetics of inhibiting enzymes can be incorporated into such models [21]. However, due to the...mycobactin syn- thesis [53]. Although the effects of this inhibitor in the host environment have not yet been reported, its inhibi- tion of the in vitro...92where vMS and denote the flux of the mycobactin syn- thesis reaction in the presence and in the absence of the sAMS inhibitor, respectively, and is

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

    Science.gov (United States)

    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

  15. Dynamic relationships between microbial biomass, respiration, inorganic nutrients and enzyme activities: informing enzyme based decomposition models

    Directory of Open Access Journals (Sweden)

    Daryl L Moorhead

    2013-08-01

    Full Text Available We re-examined data from a recent litter decay study to determine if additional insights could be gained to inform decomposition modeling. Rinkes et al. (2013 conducted 14-day laboratory incubations of sugar maple (Acer saccharum or white oak (Quercus alba leaves, mixed with sand (0.4% organic C content or loam (4.1% organic C. They measured microbial biomass C, carbon dioxide efflux, soil ammonium, nitrate, and phosphate concentrations, and β-glucosidase (BG, β-N-acetyl-glucosaminidase (NAG, and acid phosphatase (AP activities on days 1, 3, and 14. Analyses of relationships among variables yielded different insights than original analyses of individual variables. For example, although respiration rates per g soil were higher for loam than sand, rates per g soil C were actually higher for sand than loam, and rates per g microbial C showed little difference between treatments. Microbial biomass C peaked on day 3 when biomass-specific activities of enzymes were lowest, suggesting uptake of litter C without extracellular hydrolysis. This result refuted a common model assumption that all enzyme production is constitutive and thus proportional to biomass, and/or indicated that part of litter decay is independent of enzyme activity. The length and angle of vectors defined by ratios of enzyme activities (BG/NAG versus BG/AP represent relative microbial investments in C (length, and N and P (angle acquiring enzymes. Shorter lengths on day 3 suggested low C limitation, whereas greater lengths on day 14 suggested an increase in C limitation with decay. The soils and litter in this study generally had stronger P limitation (angles > 45˚. Reductions in vector angles to < 45˚ for sand by day 14 suggested a shift to N limitation. These relational variables inform enzyme-based models, and are usually much less ambiguous when obtained from a single study in which measurements were made on the same samples than when extrapolated from separate studies.

  16. The Journal of Biological Chemistry, Volume 203, 1953: Enzyme secretion and the incorporation of P32 into phospholipides of pancreas slices.

    Science.gov (United States)

    Hokin, M R; Hokin, L E

    1989-06-01

    1. When enzyme secretion was stimulated by carbamylcholine or acetylcholine (with eserine) in slices of pigeon pancreas, the incorporation of P32 into the phospholipide fraction of the stimulated slices was, after 2 hours, 4.8 to 8.7 (average, 7.0) times greater than the incorporation of P32 into the phospholipides of control slices. Neither respiration nor the incorporation of P32 into acid-soluble phosphate esters was increased. 2. Pilocarpine, which on a weight for weight basis was much less effective than carbamylcholine or acetylcholine in stimulating enzyme secretion in pancreas slices, was also much less effective in stimulating the uptake of P32 into phospholipides. 3. The stimulatory effects of carbamylcholine on both enzyme secretion and the incorporation of P32 into phospholipides were abolished by atropine. 4. The specific activity of the phospholipides from slices incubated anaerobically was less than 5 per cent of that observed aerobically. Anaerobically, carbamylcholine did not stimulate the incorporation of P32 into phospholipides to any significant extent. The specific activity of the acid-soluble phosphate esters after anaerobic incubation was 34 per cent of that found aerobically. 5. Cholinergic drugs had little or no effect on the incorporation of P32 into the phospholipides of the following tissue slices: pigeon and guinea pig liver, guinea pig heart ventricle, pigeon gizzard (smooth muscle), and guinea pig kidney cortex. A relatively slight stimulation of P32 uptake into phospholipides was observed in slices of pigeon brain (65 per cent) and guinea pig brain cortex (40 per cent). 6. Stimulation of amylase synthesis in slices of pigeon pancreas by the addition of a mixture of amino acids had no effect on the incorporation of P32 into phospholipides.

  17. Incorporating Context Dependency of Species Interactions in Species Distribution Models.

    Science.gov (United States)

    Lany, Nina K; Zarnetske, Phoebe L; Gouhier, Tarik C; Menge, Bruce A

    2017-07-01

    Species distribution models typically use correlative approaches that characterize the species-environment relationship using occurrence or abundance data for a single species. However, species distributions are determined by both abiotic conditions and biotic interactions with other species in the community. Therefore, climate change is expected to impact species through direct effects on their physiology and indirect effects propagated through their resources, predators, competitors, or mutualists. Furthermore, the sign and strength of species interactions can change according to abiotic conditions, resulting in context-dependent species interactions that may change across space or with climate change. Here, we incorporated the context dependency of species interactions into a dynamic species distribution model. We developed a multi-species model that uses a time-series of observational survey data to evaluate how abiotic conditions and species interactions affect the dynamics of three rocky intertidal species. The model further distinguishes between the direct effects of abiotic conditions on abundance and the indirect effects propagated through interactions with other species. We apply the model to keystone predation by the sea star Pisaster ochraceus on the mussel Mytilus californianus and the barnacle Balanus glandula in the rocky intertidal zone of the Pacific coast, USA. Our method indicated that biotic interactions between P. ochraceus and B. glandula affected B. glandula dynamics across >1000 km of coastline. Consistent with patterns from keystone predation, the growth rate of B. glandula varied according to the abundance of P. ochraceus in the previous year. The data and the model did not indicate that the strength of keystone predation by P. ochraceus varied with a mean annual upwelling index. Balanus glandula cover increased following years with high phytoplankton abundance measured as mean annual chlorophyll-a. M. californianus exhibited the same

  18. Rhodanese incorporated in Langmuir and Langmuir-Blodgett films of dimyristoylphosphatidic acid: Physical chemical properties and improvement of the enzyme activity.

    Science.gov (United States)

    de Araújo, Felipe Tejada; Caseli, Luciano

    2016-05-01

    Preserving the catalytic activity of enzymes immobilized in bioelectronics devices is essential for optimal performance in biosensors. Therefore, ultrathin films in which the architecture can be controlled at the molecular level are of interest. In this work, the enzyme rhodanese was adsorbed onto Langmuir monolayers of the phospholipid dimyristoylphosphatidic acid and characterized by surface pressure-area isotherms, polarization-modulated infrared reflection-absorption spectroscopy (PM-IRRAS), and Brewster angle microscopy (BAM). The incorporation of the enzyme (5% in mol) in the lipid monolayer expanded the film, providing small surface domains, as visualized by BAM. Also, amide bands could be identified in the PM-IRRAS spectra, confirming the presence of the enzyme at the air-water interface. Structuring of the enzyme into α-helices was identified in the mixed monolayer and was preserved when the film was transferred from the liquid interface to solids supports as Langmuir-Blodgett (LB) films. The enzyme-lipid LB films were then characterized by fluorescence spectroscopy, PM-IRRAS, and atomic force microscopy. Measurements of the catalytic activity towards cyanide showed that the enzyme accommodated in the LB films preserved more than 87% of the enzyme activity in relation to the homogeneous medium. After 1 month, the enzyme in the LB film maintained 85% of the activity in contrast to the homogeneous medium, which 24% of the enzyme activity was kept. The method presented in this work not only points to an enhanced catalytic activity toward cyanide, but also may explain why certain film architectures exhibit an improved performance.

  19. Parameter estimation for models of ligninolytic and cellulolytic enzyme kinetics

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Gangsheng [ORNL; Post, Wilfred M [ORNL; Mayes, Melanie [ORNL; Frerichs, Joshua T [ORNL; Jagadamma, Sindhu [ORNL

    2012-01-01

    While soil enzymes have been explicitly included in the soil organic carbon (SOC) decomposition models, there is a serious lack of suitable data for model parameterization. This study provides well-documented enzymatic parameters for application in enzyme-driven SOC decomposition models from a compilation and analysis of published measurements. In particular, we developed appropriate kinetic parameters for five typical ligninolytic and cellulolytic enzymes ( -glucosidase, cellobiohydrolase, endo-glucanase, peroxidase, and phenol oxidase). The kinetic parameters included the maximum specific enzyme activity (Vmax) and half-saturation constant (Km) in the Michaelis-Menten equation. The activation energy (Ea) and the pH optimum and sensitivity (pHopt and pHsen) were also analyzed. pHsen was estimated by fitting an exponential-quadratic function. The Vmax values, often presented in different units under various measurement conditions, were converted into the same units at a reference temperature (20 C) and pHopt. Major conclusions are: (i) Both Vmax and Km were log-normal distributed, with no significant difference in Vmax exhibited between enzymes originating from bacteria or fungi. (ii) No significant difference in Vmax was found between cellulases and ligninases; however, there was significant difference in Km between them. (iii) Ligninases had higher Ea values and lower pHopt than cellulases; average ratio of pHsen to pHopt ranged 0.3 0.4 for the five enzymes, which means that an increase or decrease of 1.1 1.7 pH units from pHopt would reduce Vmax by 50%. (iv) Our analysis indicated that the Vmax values from lab measurements with purified enzymes were 1 2 orders of magnitude higher than those for use in SOC decomposition models under field conditions.

  20. Differential cumene hydroperoxide sensitivity of cytochrome P-450 enzymes IA1 and IIB1 determined by their way of membrane incorporation.

    Science.gov (United States)

    Balvers, W G; Boersma, M G; Veeger, C; Rietjens, I M

    1992-09-15

    The cytochrome P-450-dependent O-dealkylation of alkoxyresorufins was used to study the effect of cumene hydroperoxide on cytochrome P-450 IIB1 and IA1 in microsomal and reconstituted systems. In liver microsomal systems from respectively phenobarbital and 3-methylcholanthrene pretreated male Wistar rats, cytochrome P-450 IIB1-dependent pentoxyresorufin-O-dealkylation appeared to be more sensitive to cumene hydroperoxide treatment than cytochrome P-450 IA1-dependent ethoxyresorufin-O-dealkylation. This phenomenon was also observed when the cumene hydroperoxide sensitivity of P-450 IIB1 and IA1 was studied in an isosafrole pretreated rat liver microsomal system. The decrease in alkoxy-O-dealkylating activities appeared to proceed by destruction of the cytochrome P-450 component of the enzyme system. Purification and reconstitution of the enzyme system components in a system in which the isolated proteins were not incorporated into a membrane resulted in the disappearance of the difference in sensitivity between the two P-450 enzymes. However, in a reconstituted system with membrane incorporated proteins, again cytochrome P-450 IIB1 expressed a higher sensitivity towards cumene hydroperoxide than cytochrome P-450 IA1. From this it was concluded that the differential cumene hydroperoxide sensitivity of cytochrome P-450 IIB1 and IA1 is not caused by an intrinsic difference in their sensitivity but by a differential effect of membrane incorporation on their cumene hydroperoxide sensitivity.

  1. Development of microbial-enzyme-mediated decomposition model parameters through steady-state and dynamic analyses

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Gangsheng [ORNL; Post, Wilfred M [ORNL; Mayes, Melanie [ORNL

    2013-01-01

    We developed a Microbial-ENzyme-mediated Decomposition (MEND) model, based on the Michaelis-Menten kinetics, that describes the dynamics of physically defined pools of soil organic matter (SOC). These include particulate, mineral-associated, dissolved organic matter (POC, MOC, and DOC, respectively), microbial biomass, and associated exoenzymes. The ranges and/or distributions of parameters were determined by both analytical steady-state and dynamic analyses with SOC data from the literature. We used an improved multi-objective parameter sensitivity analysis (MOPSA) to identify the most important parameters for the full model: maintenance of microbial biomass, turnover and synthesis of enzymes, and carbon use efficiency (CUE). The model predicted an increase of 2 C (baseline temperature =12 C) caused the pools of POC-Cellulose, MOC, and total SOC to increase with dynamic CUE and decrease with constant CUE, as indicated by the 50% confidence intervals. Regardless of dynamic or constant CUE, the pool sizes of POC, MOC, and total SOC varied from 8% to 8% under +2 C. The scenario analysis using a single parameter set indicates that higher temperature with dynamic CUE might result in greater net increases in both POC-Cellulose and MOC pools. Different dynamics of various SOC pools reflected the catalytic functions of specific enzymes targeting specific substrates and the interactions between microbes, enzymes, and SOC. With the feasible parameter values estimated in this study, models incorporating fundamental principles of microbial-enzyme dynamics can lead to simulation results qualitatively different from traditional models with fast/slow/passive pools.

  2. Incorporating Enterprise Risk Management in the Business Model Innovation Process

    OpenAIRE

    Yariv Taran; Harry Boer; Peter Lindgren

    2013-01-01

    Purpose: Relative to other types of innovations, little is known about business model innovation, let alone the process of managing the risks involved in that process. Using the emerging (enterprise) risk management literature, an approach is proposed through which risk management can be embedded in the business model innovation process. Design: The integrated business model innovation risk management model developed in this paper has been tested through an action research study in a Dani...

  3. Incorporating inductances in tissue-scale models of cardiac electrophysiology

    Science.gov (United States)

    Rossi, Simone; Griffith, Boyce E.

    2017-09-01

    In standard models of cardiac electrophysiology, including the bidomain and monodomain models, local perturbations can propagate at infinite speed. We address this unrealistic property by developing a hyperbolic bidomain model that is based on a generalization of Ohm's law with a Cattaneo-type model for the fluxes. Further, we obtain a hyperbolic monodomain model in the case that the intracellular and extracellular conductivity tensors have the same anisotropy ratio. In one spatial dimension, the hyperbolic monodomain model is equivalent to a cable model that includes axial inductances, and the relaxation times of the Cattaneo fluxes are strictly related to these inductances. A purely linear analysis shows that the inductances are negligible, but models of cardiac electrophysiology are highly nonlinear, and linear predictions may not capture the fully nonlinear dynamics. In fact, contrary to the linear analysis, we show that for simple nonlinear ionic models, an increase in conduction velocity is obtained for small and moderate values of the relaxation time. A similar behavior is also demonstrated with biophysically detailed ionic models. Using the Fenton-Karma model along with a low-order finite element spatial discretization, we numerically analyze differences between the standard monodomain model and the hyperbolic monodomain model. In a simple benchmark test, we show that the propagation of the action potential is strongly influenced by the alignment of the fibers with respect to the mesh in both the parabolic and hyperbolic models when using relatively coarse spatial discretizations. Accurate predictions of the conduction velocity require computational mesh spacings on the order of a single cardiac cell. We also compare the two formulations in the case of spiral break up and atrial fibrillation in an anatomically detailed model of the left atrium, and we examine the effect of intracellular and extracellular inductances on the virtual electrode phenomenon.

  4. Photoaffinity labeling of Ras converting enzyme using peptide substrates that incorporate benzoylphenylalanine (Bpa) residues: improved labeling and structural implications.

    Science.gov (United States)

    Kyro, Kelly; Manandhar, Surya P; Mullen, Daniel; Schmidt, Walter K; Distefano, Mark D

    2011-12-15

    Rce1p catalyzes the proteolytic trimming of C-terminal tripeptides from isoprenylated proteins containing CAAX-box sequences. Because Rce1p processing is a necessary component in the Ras pathway of oncogenic signal transduction, Rce1p holds promise as a potential target for therapeutic intervention. However, its mechanism of proteolysis and active site have yet to be defined. Here, we describe synthetic peptide analogues that mimic the natural lipidated Rce1p substrate and incorporate photolabile groups for photoaffinity-labeling applications. These photoactive peptides are designed to crosslink to residues in or near the Rce1p active site. By incorporating the photoactive group via p-benzoyl-l-phenylalanine (Bpa) residues directly into the peptide substrate sequence, the labeling efficiency was substantially increased relative to a previously-synthesized compound. Incorporation of biotin on the N-terminus of the peptides permitted photolabeled Rce1p to be isolated via streptavidin affinity capture. Our findings further suggest that residues outside the CAAX-box sequence are in contact with Rce1p, which has implications for future inhibitor design.

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

    Science.gov (United States)

    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...

  6. Modeling cutinase enzyme regulation in polyethylene terepthalate plastic biodegradation

    Science.gov (United States)

    Apri, M.; Silmi, M.; Heryanto, T. E.; Moeis, M. R.

    2016-04-01

    PET (Polyethylene terephthalate) is a plastic material that is commonly used in our daily life. The high production of PET and others plastics that can be up to three hundred million tons per year, is not matched by its degradation rate and hence leads to environmental pollution. To overcome this problem, we develop a biodegradation system. This system utilizes LC Cutinase enzyme produced by engineered escherichia coli bacteria to degrade PET. To make the system works efficaciously, it is important to understand the mechanism underlying its enzyme regulation. Therefore, we construct a mathematical model to describe the regulation of LC Cutinase production. The stability of the model is analyzed. We show that the designated biodegradation system can give an oscillatory behavior that is very important to control the amount of inclusion body (the miss-folded proteins that reduce the efficiency of the biodegradation system).

  7. Modeling cutinase enzyme regulation in polyethylene terepthalate plastic biodegradation

    Energy Technology Data Exchange (ETDEWEB)

    Apri, M., E-mail: m.apri@math.itb.ac.id; Silmi, M. [Department of Mathematics, Institut Teknologi Bandung, Jalan Ganeca 10 Bandung, 40132 (Indonesia); Heryanto, T. E.; Moeis, M. R. [School of Life Sciences and Technology, Institut Teknologi Bandung, Jalan Ganeca 10 Bandung, 40132 (Indonesia)

    2016-04-06

    PET (Polyethylene terephthalate) is a plastic material that is commonly used in our daily life. The high production of PET and others plastics that can be up to three hundred million tons per year, is not matched by its degradation rate and hence leads to environmental pollution. To overcome this problem, we develop a biodegradation system. This system utilizes LC Cutinase enzyme produced by engineered escherichia coli bacteria to degrade PET. To make the system works efficaciously, it is important to understand the mechanism underlying its enzyme regulation. Therefore, we construct a mathematical model to describe the regulation of LC Cutinase production. The stability of the model is analyzed. We show that the designated biodegradation system can give an oscillatory behavior that is very important to control the amount of inclusion body (the miss-folded proteins that reduce the efficiency of the biodegradation system).

  8. Multiplicity Control in Structural Equation Modeling: Incorporating Parameter Dependencies

    Science.gov (United States)

    Smith, Carrie E.; Cribbie, Robert A.

    2013-01-01

    When structural equation modeling (SEM) analyses are conducted, significance tests for all important model relationships (parameters including factor loadings, covariances, etc.) are typically conducted at a specified nominal Type I error rate ([alpha]). Despite the fact that many significance tests are often conducted in SEM, rarely is…

  9. Incorporating Enterprise Risk Management in the Business Model Innovation Process

    Directory of Open Access Journals (Sweden)

    Yariv Taran

    2013-12-01

    Full Text Available Purpose: Relative to other types of innovations, little is known about business model innovation, let alone the process of managing the risks involved in that process. Using the emerging (enterprise risk management literature, an approach is proposed through which risk management can be embedded in the business model innovation process. Design: The integrated business model innovation risk management model developed in this paper has been tested through an action research study in a Danish company. Findings: The study supports our proposition that the implementation of risk management throughout the innovation process reduces the risks related to the uncertainty and complexity of developing and implementing a new business model. Originality: The study supports the proposition that the implementation of risk management throughout the innovation process reduces the risks related to the uncertainty and complexity of developing and implementing a new business model. The business model risk management model makes managers much more focused on identifying problematic issues and putting explicit plans and timetables into place for resolving/reducing risks, and assists companies in aligning the risk treatment choices made during the

  10. Model for Quantitative Evaluation of Enzyme Replacement Treatment

    Directory of Open Access Journals (Sweden)

    Radeva B.

    2009-12-01

    Full Text Available Gaucher disease is the most frequent lysosomal disorder. Its enzyme replacement treatment was the new progress of modern biotechnology, successfully used in the last years. The evaluation of optimal dose of each patient is important due to health and economical reasons. The enzyme replacement is the most expensive treatment. It must be held continuously and without interruption. Since 2001, the enzyme replacement therapy with Cerezyme*Genzyme was formally introduced in Bulgaria, but after some time it was interrupted for 1-2 months. The dose of the patients was not optimal. The aim of our work is to find a mathematical model for quantitative evaluation of ERT of Gaucher disease. The model applies a kind of software called "Statistika 6" via the input of the individual data of 5-year-old children having the Gaucher disease treated with Cerezyme. The output results of the model gave possibilities for quantitative evaluation of the individual trends in the development of the disease of each child and its correlation. On the basis of this results, we might recommend suitable changes in ERT.

  11. A Constrained CA Model for Planning Simulation Incorporating Institutional Constraints

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    In recent years,it is prevailing to simulate urban growth by means of cellular automata (CA in short) modeling,which is based on selforganizing theories and different from the system dynamic modeling.Since the urban system is definitely complex,the CA models applied in urban growth simulation should take into consideration not only the neighborhood influence,but also other factors influencing urban development.We bring forward the term of complex constrained CA (CC-CA in short) model,which integrates the constrained conditions of neighborhood,macro socio-economy,space and institution.Particularly,the constrained construction zoning,as one institutional constraint,is considered in the CC-CA modeling.In the paper,the conceptual CC-CA model is introduced together with the transition rules.Based on the CC-CA model for Beijing,we discuss the complex constraints to the urban development of,and we show how to set institutional constraints in planning scenario to control the urban growth pattern of Beijing.

  12. Modelling of Permanent Magnet Synchronous Motor Incorporating Core-loss

    Directory of Open Access Journals (Sweden)

    K. Suthamno

    2012-08-01

    Full Text Available This study proposes a dq-axis modelling of a Permanent Magnet Synchronous Motor (PMSM with copper-loss and core-loss taken into account. The proposed models can be applied to PMSM control and drive with loss minimization in simultaneous consideration. The study presents simulation results of direct drive of a PMSM under no-load and loaded conditions using the proposed models with MATLAB codes. Comparisons of the results are made among those obtained from using PSIM and SIMULINK software packages. The comparison results indicate very good agreement.

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

    Science.gov (United States)

    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.

  14. Incorporating concern for relative wealth into economic models

    OpenAIRE

    1995-01-01

    This article develops a simple model that captures a concern for relative standing, or status. This concern is instrumental, in the sense that individuals do not get utility directly from their relative standing, but, rather, the concern is induced because their relative standing affects their consumption of standard commodities. The article investigates the consequences of a concern for relative wealth in models in which individuals are making labor/leisure decisions. The analysis shows how ...

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

    Science.gov (United States)

    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.

  16. The incorporation and validation of empirical crawling data into the buildingEXODUS model

    OpenAIRE

    Muhdi, Rani; Gwynne, Steve; Davis, Jerry

    2009-01-01

    The deterioration of environmental conditions can influence evacuee decisions and their subsequent behaviors. Simulating evacuee behaviors enhances the robustness of engineering procedural designs, improves the accuracy of egress models, and better evaluates the safety of evacuees. The purpose of this paper is to more accurately incorporate and validate evacuee crawling behavior into the buildingEXODUS egress model. Crawling data were incorporated into the model and tested for accurate repres...

  17. Incorporation of alkaline phosphatase into layer-by-layer polyelectrolyte films on the surface of affi-gel heparin beads: physicochemical characterization and evaluation of the enzyme stability.

    Science.gov (United States)

    Derbal, Lylia; Lesot, Hervé; Voegel, Jean Claude; Ball, Vincent

    2003-01-01

    The preparation of functionalized beads in the micrometer size range that can be used to probe the action of immobilized biomolecules on cell cultures during controlled periods of time is of fundamental importance in cell biology. However, the preparation and characterization of such particles is tedious because of their fast sedimentation. It is hence difficult to prepare such beads in a reproducible manner. This highlights the need to prepare an important batch of functionnalized particles and to store them under conditions where the loss of biological activity is minimized. The aim of this paper was to immobilize alkaline phosphatase (AP) as a model enzyme on the surface of Affi-gel heparin beads functionnalized by means of a layer-by-layer (LBL) film made of poly-l-glutamic (PGA) acid and poly-l-lysine (PLL). The enzyme has been adsorbed either on the top of the LBL film or embedded under five polyelectrolyte layers. When embedded, the enzyme was not released in buffer and retained more than 30% of its initial activity after 3 months of storage at 4 degrees C. However, when the enzyme was adsorbed on top of the LBL film, about 80% of the adsorbed enzyme was released in the buffer after a few days of storage. Longer storage did not lead to any further desorption and the remaining enzyme displayed the same evolution of its activity with time as the embedded enzyme. The time evolution of the enzyme activity on the beads is compared with that in solution alone and in the presence of PGA and PLL separately.

  18. Modelling toluene oxidation : Incorporation of mass transfer phenomena

    NARCIS (Netherlands)

    Hoorn, J.A.A.; van Soolingen, J.; Versteeg, G. F.

    2005-01-01

    The kinetics of the oxidation of toluene have been studied in close interaction with the gas-liquid mass transfer occurring in the reactor. Kinetic parameters for a simple model have been estimated on basis of experimental observations performed under industrial conditions. The conclusions for the m

  19. Modelling toluene oxidation : Incorporation of mass transfer phenomena

    NARCIS (Netherlands)

    Hoorn, J.A.A.; van Soolingen, J.; Versteeg, G. F.

    The kinetics of the oxidation of toluene have been studied in close interaction with the gas-liquid mass transfer occurring in the reactor. Kinetic parameters for a simple model have been estimated on basis of experimental observations performed under industrial conditions. The conclusions for the

  20. Modelling toluene oxidation : Incorporation of mass transfer phenomena

    NARCIS (Netherlands)

    Hoorn, J.A.A.; van Soolingen, J.; Versteeg, G. F.

    2005-01-01

    The kinetics of the oxidation of toluene have been studied in close interaction with the gas-liquid mass transfer occurring in the reactor. Kinetic parameters for a simple model have been estimated on basis of experimental observations performed under industrial conditions. The conclusions for the m

  1. Incorporating Uncertainties in Satellite-Derived Chlorophyll into Model Forecasts

    Science.gov (United States)

    2012-10-01

    radiances in the seven visible MODIS channels used in the estimation of the bio-optical products, such as chlorophyll, absorption and backscattering...grazers, nitrate, silicate, ammonium, and two detritus pools. Phytoplankton photosynthesis in the biochemical model is driven by Photosynthetically

  2. Day-to-day route choice modeling incorporating inertial behavior

    NARCIS (Netherlands)

    Essen, van M.A.; Rakha, H.; Vreeswijk, J.D.; Wismans, L.J.J.; Berkum, van E.C.

    2015-01-01

    Accurate route choice modeling is one of the most important aspects when predicting the effects of transport policy and dynamic traffic management. Moreover, the effectiveness of intervention measures to a large extent depends on travelers’ response to the changes these measures cause. As a compleme

  3. Incorporation of Allium sativum in yogurt: In vitro study on inhibition of diabetes- and hypertension-associated enzymes

    Directory of Open Access Journals (Sweden)

    Shabboo Amirdivani Amirdivani

    2015-06-01

    Full Text Available The effects of inclusion of Allium sativum on yogurt formation and subsequent storage (4°C, up to 28 days on proteolysis, microbial activity, the inhibition of a-amylase, a-glucosidase and angiotensin-1 converting enzyme (ACE-1 in vitro were investigated. A. sativum-yogurt showed higher rates of pH reduction and increment of TA than plain-yogurt during incubation at 41°C. Highest proteolysis,  on day 7 showed in A. sativum-yogurt (62.7±0.80 mg/mL, which was 2-flod higher than plain yogurt (31.0±0.96 mg/mL. Bacterial counts in A.sativum-yogurt were higher for Lactobacillus spp. but lower for S. thermophillus (p<0.05 compared to those in plain yogurt throughout refrigerated storage. Highest inhibitory activities for α-amylase were recorded on day 14 of storage for A. sativum- and plain-yogurts (IC50= 13.7±1.99and 26.3±2.15mg respectively; p<0.05 and on day 7 for α-glucosidase (IC50= 120.7±22.71 and 192.3±33.24mg respectively; p<0.05. The highest anti-ACE-I activity was observed on day 7 of refrigerated storage with A. sativum-yogurt (IC50=6.9±0.23mg being more potent than plain-yogurt (IC50=9.7±0.12mg; p<0.05. A. sativum-yogurt was not favoured for overall aroma, sourness and bitterness in the sensory evaluations but recorded the same overall preference as plain yogurt. A. sativum enhanced the fermentation of yogurt in favour of the population of Lactobacillus spp, stimulated proteolysis of milk proteins and increased the in vitro inhibition of key enzymes associated with diabetes and hypertension.

  4. Workforce scheduling: A new model incorporating human factors

    Directory of Open Access Journals (Sweden)

    Mohammed Othman

    2012-12-01

    Full Text Available Purpose: The majority of a company’s improvement comes when the right workers with the right skills, behaviors and capacities are deployed appropriately throughout a company. This paper considers a workforce scheduling model including human aspects such as skills, training, workers’ personalities, workers’ breaks and workers’ fatigue and recovery levels. This model helps to minimize the hiring, firing, training and overtime costs, minimize the number of fired workers with high performance, minimize the break time and minimize the average worker’s fatigue level.Design/methodology/approach: To achieve this objective, a multi objective mixed integer programming model is developed to determine the amount of hiring, firing, training and overtime for each worker type.Findings: The results indicate that the worker differences should be considered in workforce scheduling to generate realistic plans with minimum costs. This paper also investigates the effects of human fatigue and recovery on the performance of the production systems.Research limitations/implications: In this research, there are some assumptions that might affect the accuracy of the model such as the assumption of certainty of the demand in each period, and the linearity function of Fatigue accumulation and recovery curves. These assumptions can be relaxed in future work.Originality/value: In this research, a new model for integrating workers’ differences with workforce scheduling is proposed. To the authors' knowledge, it is the first time to study the effects of different important human factors such as human personality, skills and fatigue and recovery in the workforce scheduling process. This research shows that considering both technical and human factors together can reduce the costs in manufacturing systems and ensure the safety of the workers.

  5. Incorporating Satellite Time-Series Data into Modeling

    Science.gov (United States)

    Gregg, Watson

    2008-01-01

    In situ time series observations have provided a multi-decadal view of long-term changes in ocean biology. These observations are sufficiently reliable to enable discernment of even relatively small changes, and provide continuous information on a host of variables. Their key drawback is their limited domain. Satellite observations from ocean color sensors do not suffer the drawback of domain, and simultaneously view the global oceans. This attribute lends credence to their use in global and regional model validation and data assimilation. We focus on these applications using the NASA Ocean Biogeochemical Model. The enhancement of the satellite data using data assimilation is featured and the limitation of tongterm satellite data sets is also discussed.

  6. Aircraft conceptual design modelling incorporating reliability and maintainability predictions

    OpenAIRE

    Vaziry-Zanjany , Mohammad Ali (F)

    1996-01-01

    A computer assisted conceptual aircraft design program has been developed (CACAD). It has an optimisation capability, with extensive break-down in maintenance costs. CACAD's aim is to optimise the size, and configurations of turbofan-powered transport aircraft. A methodology was developed to enhance the reliability of current aircraft systems, and was applied to avionics systems. R&M models of thermal management were developed and linked with avionics failure rate and its ma...

  7. Incorporating nucleosomes into thermodynamic models of transcription regulation.

    Science.gov (United States)

    Raveh-Sadka, Tali; Levo, Michal; Segal, Eran

    2009-08-01

    Transcriptional control is central to many cellular processes, and, consequently, much effort has been devoted to understanding its underlying mechanisms. The organization of nucleosomes along promoter regions is important for this process, since most transcription factors cannot bind nucleosomal sequences and thus compete with nucleosomes for DNA access. This competition is governed by the relative concentrations of nucleosomes and transcription factors and by their respective sequence binding preferences. However, despite its importance, a mechanistic understanding of the quantitative effects that the competition between nucleosomes and factors has on transcription is still missing. Here we use a thermodynamic framework based on fundamental principles of statistical mechanics to explore theoretically the effect that different nucleosome organizations along promoters have on the activation dynamics of promoters in response to varying concentrations of the regulating factors. We show that even simple landscapes of nucleosome organization reproduce experimental results regarding the effect of nucleosomes as general repressors and as generators of obligate binding cooperativity between factors. Our modeling framework also allows us to characterize the effects that various sequence elements of promoters have on the induction threshold and on the shape of the promoter activation curves. Finally, we show that using only sequence preferences for nucleosomes and transcription factors, our model can also predict expression behavior of real promoter sequences, thereby underscoring the importance of the interplay between nucleosomes and factors in determining expression kinetics.

  8. Enzyme replacement therapy in a mouse model of aspartylglycosaminuria.

    Science.gov (United States)

    Dunder, U; Kaartinen, V; Valtonen, P; Väänänen, E; Kosma, V M; Heisterkamp, N; Groffen, J; Mononen, I

    2000-02-01

    Aspartylglycosaminuria (AGU), the most common lysosomal disorder of glycoprotein degradation, is caused by deficient activity of glycosylasparaginase (AGA). AGA-deficient mice share most of the clinical, biochemical and histopathologic characteristics of human AGU disease. In the current study, recombinant human AGA administered i.v. to adult AGU mice disappeared from the systemic circulation of the animals in two phases predominantly into non-neuronal tissues, which were rapidly cleared from storage compound aspartylglucosamine. Even a single AGA injection reduced the amount of aspartylglucosamine in the liver and spleen of AGU mice by 90% and 80%, respectively. Quantitative biochemical analyses along with histological and immunohistochemical studies demonstrated that the pathophysiologic characteristics of AGU were effectively corrected in non-neuronal tissues of AGU mice during 2 wk of AGA therapy. At the same time, AGA activity increased to 10% of that in normal brain tissue and the accumulation of aspartylglucosamine was reduced by 20% in total brain of the treated animals. Immunohistochemical studies suggested that the corrective enzyme was widely distributed within the brain tissue. These findings suggest that AGU may be correctable by enzyme therapy.-Dunder, U., Kaartinen, V., Valtonen, P., Väänänen, E., Kosma, V.-M., Heisterkamp, N., Groffen, J., Mononen, I. Enzyme replacement therapy in a mouse model of aspartylglycosaminuria.

  9. Models of microbiome evolution incorporating host and microbial selection.

    Science.gov (United States)

    Zeng, Qinglong; Wu, Steven; Sukumaran, Jeet; Rodrigo, Allen

    2017-09-25

    Numerous empirical studies suggest that hosts and microbes exert reciprocal selective effects on their ecological partners. Nonetheless, we still lack an explicit framework to model the dynamics of both hosts and microbes under selection. In a previous study, we developed an agent-based forward-time computational framework to simulate the neutral evolution of host-associated microbial communities in a constant-sized, unstructured population of hosts. These neutral models allowed offspring to sample microbes randomly from parents and/or from the environment. Additionally, the environmental pool of available microbes was constituted by fixed and persistent microbial OTUs and by contributions from host individuals in the preceding generation. In this paper, we extend our neutral models to allow selection to operate on both hosts and microbes. We do this by constructing a phenome for each microbial OTU consisting of a sample of traits that influence host and microbial fitnesses independently. Microbial traits can influence the fitness of hosts ("host selection") and the fitness of microbes ("trait-mediated microbial selection"). Additionally, the fitness effects of traits on microbes can be modified by their hosts ("host-mediated microbial selection"). We simulate the effects of these three types of selection, individually or in combination, on microbiome diversities and the fitnesses of hosts and microbes over several thousand generations of hosts. We show that microbiome diversity is strongly influenced by selection acting on microbes. Selection acting on hosts only influences microbiome diversity when there is near-complete direct or indirect parental contribution to the microbiomes of offspring. Unsurprisingly, microbial fitness increases under microbial selection. Interestingly, when host selection operates, host fitness only increases under two conditions: (1) when there is a strong parental contribution to microbial communities or (2) in the absence of a strong

  10. Amphiphilic poly-N-vinylpyrrolidone nanocarriers with incorporated model proteins

    Energy Technology Data Exchange (ETDEWEB)

    Kuskov, A N [Department of Polymers, D I Mendeleyev University of Chemical Technology, 9 Miusskaya Square, Moscow 125047 (Russian Federation); Villemson, A L [Department of Chemistry, M V Lomonosov Moscow State University, 119992 Moscow (Russian Federation); Shtilman, M I [Department of Polymers, D I Mendeleyev University of Chemical Technology, 9 Miusskaya Square, Moscow 125047 (Russian Federation); Larionova, N I [Department of Chemistry, M V Lomonosov Moscow State University, 119992 Moscow (Russian Federation); Tsatsakis, A M [Medical School, University of Crete, Voutes, 71409 Heraklion, Crete (Greece); Tsikalas, I [Department of Chemistry and Foundation for Research and Technology-Hellas (FORTH), University of Crete, PO Box 2208, Heraklion 71003, Crete (Greece); Rizos, A K [Department of Chemistry and Foundation for Research and Technology-Hellas (FORTH), University of Crete, PO Box 2208, Heraklion 71003, Crete (Greece)

    2007-05-23

    New nanoscaled polymeric carriers have been prepared on the basis of different amphiphilic water-soluble derivatives of poly-N-vinylpyrrolidone (PVP). The polymer self-assembly and interaction with model proteins (Bowman-Birk soybean proteinase inhibitor (BBI) and its hydrophobized derivatives) were studied in aqueous media. The possibility of inclusion of both BBI and hydrophobized oleic acid derivatives of BBI in amphiphilic PVP aggregates was investigated. It was ascertained that polymeric particles of size 50-80 nm were formed in certain concentrations of amphiphilic PVP and poorly soluble dioleic acid derivatives of BBI. Such polymeric aggregates are capable of solubilization of dioleoyl BBI with a concomitant prevention of its inactivation at low pH values.

  11. Amphiphilic poly-N-vinylpyrrolidone nanocarriers with incorporated model proteins

    Science.gov (United States)

    Kuskov, A. N.; Villemson, A. L.; Shtilman, M. I.; Larionova, N. I.; Tsatsakis, A. M.; Tsikalas, I.; Rizos, A. K.

    2007-05-01

    New nanoscaled polymeric carriers have been prepared on the basis of different amphiphilic water-soluble derivatives of poly-N-vinylpyrrolidone (PVP). The polymer self-assembly and interaction with model proteins (Bowman-Birk soybean proteinase inhibitor (BBI) and its hydrophobized derivatives) were studied in aqueous media. The possibility of inclusion of both BBI and hydrophobized oleic acid derivatives of BBI in amphiphilic PVP aggregates was investigated. It was ascertained that polymeric particles of size 50-80 nm were formed in certain concentrations of amphiphilic PVP and poorly soluble dioleic acid derivatives of BBI. Such polymeric aggregates are capable of solubilization of dioleoyl BBI with a concomitant prevention of its inactivation at low pH values.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

  14. Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints

    DEFF Research Database (Denmark)

    Sanchez, Benjamin J.; Zhang, Xi-Cheng; Nilsson, Avlant

    2017-01-01

    Genome-scale metabolic models (GEMs) are widely used to calculate metabolic phenotypes. They rely on defining a set of constraints, the most common of which is that the production of metabolites and/or growth are limited by the carbon source uptake rate. However, enzyme abundances and kinetics......, which act as limitations on metabolic fluxes, are not taken into account. Here, we present GECKO, a method that enhances a GEM to account for enzymes as part of reactions, thereby ensuring that each metabolic flux does not exceed its maximum capacity, equal to the product of the enzyme's abundance...... with stress, or overexpressing a specific pathway. GECKO also allows to directly integrate quantitative proteomics data; by doing so, we significantly reduced flux variability of the model, in over 60% of metabolic reactions. Additionally, the model gives insight into the distribution of enzyme usage between...

  15. Molecular Communication Model for Targeted Drug Delivery in Multiple Disease Sites With Diversely Expressed Enzymes.

    Science.gov (United States)

    Chude-Okonkwo, Uche A K; Malekian, Reza; Maharaj, B T Sunil

    2016-04-01

    Targeted drug delivery (TDD) for disease therapy using liposomes as nanocarriers has received extensive attention in the literature. The liposome's ability to incorporate capabilities such as long circulation, stimuli responsiveness, and targeting characteristics, makes it a versatile nanocarrier. Timely drug release at the targeted site requires that trigger stimuli such as pH, light, and enzymes be uniquely overexpressed at the targeted site. However, in some cases, the targeted sites may not express trigger stimuli significantly, hence, achieving effective TDD at those sites is challenging. In this paper, we present a molecular communication-based TDD model for the delivery of therapeutic drugs to multiple sites that may or may not express trigger stimuli. The nanotransmitter and nanoreceiver models for the molecular communication system are presented. Here, the nanotransmitter and nanoreceiver are injected into the targeted body system's blood network. The compartmental pharmacokinetics model is employed to model the transportation of these therapeutic nanocarriers to the targeted sites where they are meant to anchor before the delivery process commences. We also provide analytical expressions for the delivered drug concentration. The effectiveness of the proposed model is investigated for drug delivery on tissue surfaces. Results show that the effectiveness of the proposed molecular communication-based TDD depends on parameters such as the total transmitter volume capacity, the receiver radius, the diffusion characteristic of the microenvironment of the targeted sites, and the concentration of the enzymes associated with the nanotransmitter and the nanoreceiver designs.

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

    Science.gov (United States)

    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.

  17. Iteration model of starch hydrolysis by amylolytic enzymes.

    Science.gov (United States)

    Wojciechowski, P M; Koziol, A; Noworyta, A

    2001-12-05

    An elaborate computer program to simulate the process of starch hydrolysis by amylolytic enzymes was been developed. It is based on the Monte Carlo method and iteration kinetic model, which predict productive and non-productive amylase complexes with substrates. It describes both multienzymatic and multisubstrate reactions simulating the "real" concentrations of all components versus the time of the depolymerization reaction the number of substrates, intermediate products, and final products are limited only by computer memory. In this work, it is assumed that the "proper" substrate for amylases is the glucoside linkages in starch molecules. Dynamic changes of substrate during the simulation adequately influence the increase or decrease of reaction velocity, as well as the kinetics of depolymerization. The presented kinetic model, can be adapted to describe most enzymatic degradations of a polymer. This computer program has been tested on experimental data obtained for alpha- and beta-amylases.

  18. Excessive Cu and Zn affecting on distribution of the metals and activities of glycolytic and nitrogen incorporating key enzymes in mycelia of ectomycorrhizal fungi Suillus bovinus

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Concentration of copper and zinc in isolated Suillus bovinus mycelia, used nutrient solution and 0.5 mol/L EDTA mycelia washing solution were measured to investigate the distribution of heavy metals in mycelia growth in excess copper or zinc nutrient solution. Treated with zinc, most of added zinc maintained in used solution, and 9.8%/14.6% was in/on mycelia in treatment, and in treetment 2 was 3.9%/8.0%in/on mycelia. In the copper applications, copper stimulated in more than on mycelis, i.e., 25.9%/4.5% in/on mycelia in treatment, and 7%/18.8% in/on mycelia while most of copper retained in used nutrient solution. Certain amount of copper or zinc uptake by mycelia led to pronounced influence on glycolysis and nitrogen incorporating process of Suillus bovinus, while the tested enzymes kept constant in treatment.In crude extracts of copper treatment 2 mycelia, activities of HK, PFK and GS were inhibited and decrease to 63%, 48% and 38% and GlDH ncreased by 68 % of the control, respectively. The behaviors of these tested enzymes toward sinc corresponded in general with that towards copper. The potential protection of Suillus bpvoninus for its host plant under excess copper or zinc threaten was discussed.

  19. Using Unlabeled Data to Improve Inductive Models by Incorporating Transductive Models

    Directory of Open Access Journals (Sweden)

    ShengJun Cheng

    2014-02-01

    Full Text Available This paper shows how to use labeled and unlabeled data to improve inductive models with the help of transductivemodels.We proposed a solution for the self-training scenario. Self- training is an effective semi-supervised wrapper method which can generalize any type of supervised inductive model to the semi-supervised settings. it iteratively refines a inductive model by bootstrap from unlabeled data. Standard self-training uses the classifier model(trained on labeled examples to label and select candidates from the unlabeled training set, which may be problematic since the initial classifier may not be able to provide highly confident predictions as labeled training data is always rare. As a result, it could always suffer from introducing too much wrongly labeled candidates to the labeled training set, which may severely degrades performance. To tackle this problem, we propose a novel self-training style algorithm which incorporate a graph-based transductive model in the self-labeling process. Unlike standard self-training, our algorithm utilizes labeled and unlabeled data as a whole to label and select unlabeled examples for training set augmentation. A robust transductive model based on graph markov random walk is proposed, which exploits manifold assumption to output reliable predictions on unlabeled data using noisy labeled examples. The proposed algorithm can greatly minimize the risk of performance degradation due to accumulated noise in the training set. Experiments show that the proposed algorithm can effectively utilize unlabeled data to improve classification performance.

  20. A new model for in situ nitrogen incorporation into 4H-SiC during epitaxy

    Science.gov (United States)

    Ferro, Gabriel; Chaussende, Didier

    2017-02-01

    Nitrogen doping of 4H-SiC during vapor phase epitaxy is still lacking of a general model explaining the apparently contradictory trends obtained by different teams. In this paper, the evolutions of nitrogen incorporation (on both polar Si and C faces) as a function of the main growth parameters (C/Si ratio, temperature, pressure and growth rate) are reviewed and explained using a model based on surface exchanges between the gas phase and the uppermost 4H-SiC atomic layers. In this model, N incorporation is driven mainly by the transient formation of C vacancies, due to H2 etching, at the surface or near the surface. It is shown that all the growth parameters are influencing the probability of C vacancies formation in a similar manner as they do for N incorporation. The surface exchange model proposes a new framework for explaining the experimental results even beyond the commonly accepted reactor type dependency.

  1. Printable organic thin film transistors for glucose detection incorporating inkjet-printing of the enzyme recognition element

    Science.gov (United States)

    Elkington, D.; Wasson, M.; Belcher, W.; Dastoor, P. C.; Zhou, X.

    2015-06-01

    The effect of device architecture upon the response of printable enzymatic glucose sensors based on poly(3-hexythiophene) (P3HT) organic thin film transistors is presented. The change in drain current is used as the basis for glucose detection and we show that significant improvements in drain current response time can be achieved by modifying the design of the sensor structure. In particular, we show that eliminating the dielectric layer and reducing the thickness of the active layer reduce the device response time considerably. The results are in good agreement with a diffusion based model of device operation, where an initial rapid dedoping process is followed by a slower doping of the P3HT layer from protons that are enzymatically generated by glucose oxidase (GOX) at the Nafion gate electrode. The fitted diffusion data are consistent with a P3HT doping region that is close to the source-drain electrodes rather than located at the P3HT:[Nafion:GOX] interface. Finally, we demonstrate that further improvements in sensor structure and morphology can be achieved by inkjet-printing the GOX layer, offering a pathway to low-cost printed biosensors for the detection of glucose in saliva.

  2. Printable organic thin film transistors for glucose detection incorporating inkjet-printing of the enzyme recognition element

    Energy Technology Data Exchange (ETDEWEB)

    Elkington, D., E-mail: Daniel.Elkington@newcastle.edu.au; Wasson, M.; Belcher, W.; Dastoor, P. C.; Zhou, X. [Centre for Organic Electronics, The University of Newcastle, Callaghan 2308 (Australia)

    2015-06-29

    The effect of device architecture upon the response of printable enzymatic glucose sensors based on poly(3-hexythiophene) (P3HT) organic thin film transistors is presented. The change in drain current is used as the basis for glucose detection and we show that significant improvements in drain current response time can be achieved by modifying the design of the sensor structure. In particular, we show that eliminating the dielectric layer and reducing the thickness of the active layer reduce the device response time considerably. The results are in good agreement with a diffusion based model of device operation, where an initial rapid dedoping process is followed by a slower doping of the P3HT layer from protons that are enzymatically generated by glucose oxidase (GOX) at the Nafion gate electrode. The fitted diffusion data are consistent with a P3HT doping region that is close to the source-drain electrodes rather than located at the P3HT:[Nafion:GOX] interface. Finally, we demonstrate that further improvements in sensor structure and morphology can be achieved by inkjet-printing the GOX layer, offering a pathway to low-cost printed biosensors for the detection of glucose in saliva.

  3. Fungal Morphology in Industrial Enzyme Production - Modelling and Monitoring

    DEFF Research Database (Denmark)

    Quintanilla, D.; Hagemann, T.; Hansen, K.

    2015-01-01

    Filamentous fungi are widely used in the biotechnology industry for the production of industrial enzymes. Thus, considerable work has been done with the purpose of characterizing these processes. The ultimate goal of these efforts is to be able to control and predict fermentation performance...... on the basis of "standardized" measurements in terms of morphology, rheology, viscosity, mass transfer and productivity. However, because the variables are connected or dependent on each other, this task is not trivial. The aim of this review article is to gather available information in order to explain......, and on the way the data is interpreted-i.e. which models were applied. The main filamentous fungi used in industrial fermentation are introduced, ranging from Trichoderma reesei to Aspergillus species. Due to the fact that secondary metabolites, like antibiotics, are not to be considered bulk products, organisms...

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

    Science.gov (United States)

    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.

  5. Incorporation of the capillary hysteresis model HYSTR into the numerical code TOUGH

    Energy Technology Data Exchange (ETDEWEB)

    Niemi, A.; Bodvarsson, G.S.; Pruess, K.

    1991-11-01

    As part of the work performed to model flow in the unsaturated zone at Yucca Mountain Nevada, a capillary hysteresis model has been developed. The computer program HYSTR has been developed to compute the hysteretic capillary pressure -- liquid saturation relationship through interpolation of tabulated data. The code can be easily incorporated into any numerical unsaturated flow simulator. A complete description of HYSTR, including a brief summary of the previous hysteresis literature, detailed description of the program, and instructions for its incorporation into a numerical simulator are given in the HYSTR user`s manual (Niemi and Bodvarsson, 1991a). This report describes the incorporation of HYSTR into the numerical code TOUGH (Transport of Unsaturated Groundwater and Heat; Pruess, 1986). The changes made and procedures for the use of TOUGH for hysteresis modeling are documented.

  6. Bias associated with failing to incorporate dependence on event history in Markov models.

    Science.gov (United States)

    Bentley, Tanya G K; Kuntz, Karen M; Ringel, Jeanne S

    2010-01-01

    When using state-transition Markov models to simulate risk of recurrent events over time, incorporating dependence on higher numbers of prior episodes can increase model complexity, yet failing to capture this event history may bias model outcomes. This analysis assessed the tradeoffs between model bias and complexity when evaluating risks of recurrent events in Markov models. The authors developed a generic episode/relapse Markov cohort model, defining bias as the percentage change in events prevented with 2 hypothetical interventions (prevention and treatment) when incorporating 0 to 9 prior episodes in relapse risk versus a model with 10 such episodes. Magnitude and sign of bias were evaluated as a function of event and recovery risks, disease-specific mortality, and risk function. Bias was positive in the base case for a prevention strategy, indicating that failing to fully incorporate dependence on event history overestimated the prevention's predicted impact. For treatment, the bias was negative, indicating an underestimated benefit. Bias approached zero as the number of tracked prior episodes increased, and the average bias over 10 tracked episodes was greater with the exponential compared with linear functions of relapse risk and with treatment compared with prevention strategies. With linear and exponential risk functions, absolute bias reached 33% and 78%, respectively, in prevention and 52% and 85% in treatment. Failing to incorporate dependence on prior event history in subsequent relapse risk in Markov models can greatly affect model outcomes, overestimating the impact of prevention and treatment strategies by up to 85% and underestimating the impact in some treatment models by up to 20%. When at least 4 prior episodes are incorporated, bias does not exceed 26% in prevention or 11% in treatment.

  7. Modeling fraud detection and the incorporation of forensic specialists in the audit process

    DEFF Research Database (Denmark)

    Sakalauskaite, Dominyka

    Financial statement audits are still comparatively poor in fraud detection. Forensic specialists can play a significant role in increasing audit quality. In this paper, based on prior academic research, I develop a model of fraud detection and the incorporation of forensic specialists in the audit...... process. The intention of the model is to identify the reasons why the audit is weak in fraud detection and to provide the analytical framework to assess whether the incorporation of forensic specialists can help to improve it. The results show that such specialists can potentially improve the fraud...

  8. Incorporating Prior Knowledge for Quantifying and Reducing Model-Form Uncertainty in RANS Simulations

    CERN Document Server

    Wang, Jian-Xun; Xiao, Heng

    2015-01-01

    Simulations based on Reynolds-Averaged Navier--Stokes (RANS) models have been used to support high-consequence decisions related to turbulent flows. Apart from the deterministic model predictions, the decision makers are often equally concerned about the predictions confidence. Among the uncertainties in RANS simulations, the model-form uncertainty is an important or even a dominant source. Therefore, quantifying and reducing the model-form uncertainties in RANS simulations are of critical importance to make risk-informed decisions. Researchers in statistics communities have made efforts on this issue by considering numerical models as black boxes. However, this physics-neutral approach is not a most efficient use of data, and is not practical for most engineering problems. Recently, we proposed an open-box, Bayesian framework for quantifying and reducing model-form uncertainties in RANS simulations by incorporating observation data and physics-prior knowledge. It can incorporate the information from the vast...

  9. Bayseian genomic models for the incorporation of pathway topology knowledge into association studies.

    Science.gov (United States)

    Brisbin, Abra; Fridley, Brooke L

    2013-08-01

    Pathway topology and relationships between genes have the potential to provide information for modeling effects of mRNA gene expression on complex traits. For example, researchers may wish to incorporate the prior belief that "hub" genes (genes with many neighbors) are more likely to influence the trait. In this paper, we propose and compare six Bayesian pathway-based prior models to incorporate pathway topology information into association analyses. Including prior information regarding the relationships among genes in a pathway was effective in somewhat improving detection rates for genes associated with complex traits. Through an extensive set of simulations, we found that when hub (central) effects are expected, the diagonal degree model is preferred; when spoke (edge) effects are expected, the spatial power model is preferred. When there is no prior knowledge about the location of the effect genes in the pathway (e.g., hub versus spoke model), it is worthwhile to apply multiple models, as the model with the best DIC is not always the one with the best detection rate. We also applied the models to pharmacogenomic studies for the drugs gemcitabine and 6-mercaptopurine and found that the diagonal degree model identified an association between 6-mercaptopurine response and expression of the gene SLC28A3, which was not detectable using the model including no pathway information. These results demonstrate the value of incorporating pathway information into association analyses.

  10. Multilevel growth curve models that incorporate a random coefficient model for the level 1 variance function.

    Science.gov (United States)

    Goldstein, Harvey; Leckie, George; Charlton, Christopher; Tilling, Kate; Browne, William J

    2017-01-01

    Aim To present a flexible model for repeated measures longitudinal growth data within individuals that allows trends over time to incorporate individual-specific random effects. These may reflect the timing of growth events and characterise within-individual variability which can be modelled as a function of age. Subjects and methods A Bayesian model is developed that includes random effects for the mean growth function, an individual age-alignment random effect and random effects for the within-individual variance function. This model is applied to data on boys' heights from the Edinburgh longitudinal growth study and to repeated weight measurements of a sample of pregnant women in the Avon Longitudinal Study of Parents and Children cohort. Results The mean age at which the growth curves for individual boys are aligned is 11.4 years, corresponding to the mean 'take off' age for pubertal growth. The within-individual variance (standard deviation) is found to decrease from 0.24 cm(2) (0.50 cm) at 9 years for the 'average' boy to 0.07 cm(2) (0.25 cm) at 16 years. Change in weight during pregnancy can be characterised by regression splines with random effects that include a large woman-specific random effect for the within-individual variation, which is also correlated with overall weight and weight gain. Conclusions The proposed model provides a useful extension to existing approaches, allowing considerable flexibility in describing within- and between-individual differences in growth patterns.

  11. A Physically Based Analytical Model to Predict Quantized Eigen Energies and Wave Functions Incorporating Penetration Effect

    CERN Document Server

    Chowdhury, Nadim; Azim, Zubair Al; Alam, Md Hasibul; Niaz, Iftikhar Ahmad; Khosru, Quazi D M

    2014-01-01

    We propose a physically based analytical compact model to calculate Eigen energies and Wave functions which incorporates penetration effect. The model is applicable for a quantum well structure that frequently appears in modern nano-scale devices. This model is equally applicable for both silicon and III-V devices. Unlike other models already available in the literature, our model can accurately predict all the eigen energies without the inclusion of any fitting parameters. The validity of our model has been checked with numerical simulations and the results show significantly better agreement compared to the available methods.

  12. Study on the Model for Regulation of the Allosteric Enzyme Activity

    Institute of Scientific and Technical Information of China (English)

    LI,Qian-Zhong(李前忠); LUO,Liao-Fu(罗辽复); ZHANG,Li-Rong(张利绒)

    2002-01-01

    The effects of activator molecule and repressive molecule on binding process between allosteric enzyme and substrate are disused by considering the heterotropic effect of the regulating molecule that binds to allosteric enzyme. A model of allosteric enzyme with heterotropic effect is presented. The cooperativity and anticooperativity in the regulation process are studied.

  13. Incorporating Linguistic Rules in Statistical Chinese Language Model for Pinyin-to-character Conversion

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    An N-gram Chinese language model incorporating linguistic rules is presented. By constructing elements lattice, rules information is incorporated in statistical frame. To facilitate the hybrid modeling, novel methods such as MI-based rule evaluating, weighted rule quantification and element-based n-gram probability approximation are presented. Dynamic Viterbi algorithm is adopted to search the best path in lattice. To strengthen the model, transformation-based error-driven rules learning is adopted. Applying proposed model to Chinese Pinyin-to-character conversion, high performance has been achieved in accuracy, flexibility and robustness simultaneously. Tests show correct rate achieves 94.81% instead of 90.53% using bi-gram Markov model alone. Many long-distance dependency and recursion in language can be processed effectively.

  14. A new experimental procedure for incorporation of model contaminants in polymer hosts

    NARCIS (Netherlands)

    Papaspyrides, C.D.; Voultzatis, Y.; Pavlidou, S.; Tsenoglou, C.; Dole, P.; Feigenbaum, A.; Paseiro, P.; Pastorelli, S.; Cruz Garcia, C. de la; Hankemeier, T.; Aucejo, S.

    2005-01-01

    A new experimental procedure for incorporation of model contaminants in polymers was developed as part of a general scheme for testing the efficiency of functional barriers in food packaging. The aim was to progressively pollute polymers in a controlled fashion up to a high level in the range of 100

  15. 75 FR 56487 - Airworthiness Directives; Erickson Air-Crane Incorporated Model S-64F Helicopters

    Science.gov (United States)

    2010-09-16

    ... Federal Aviation Administration 14 CFR Part 39 RIN 2120-AA64 Airworthiness Directives; Erickson Air-Crane... rulemaking (NPRM). SUMMARY: This document proposes adopting a new airworthiness directive (AD) for Erickson Air-Crane Incorporated (Erickson Air-Crane) Model S- 64F helicopters. The AD would require, at...

  16. A new experimental procedure for incorporation of model contaminants in polymer hosts

    NARCIS (Netherlands)

    Papaspyrides, C.D.; Voultzatis, Y.; Pavlidou, S.; Tsenoglou, C.; Dole, P.; Feigenbaum, A.; Paseiro, P.; Pastorelli, S.; Cruz Garcia, C. de la; Hankemeier, T.; Aucejo, S.

    2005-01-01

    A new experimental procedure for incorporation of model contaminants in polymers was developed as part of a general scheme for testing the efficiency of functional barriers in food packaging. The aim was to progressively pollute polymers in a controlled fashion up to a high level in the range of 100

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

    Science.gov (United States)

    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...

  18. The Forced Choice Dilemma: A Model Incorporating Idiocentric/Allocentric Cultural Orientation

    Science.gov (United States)

    Jung, Jae Yup; McCormick, John; Gross, Miraca U. M.

    2012-01-01

    This study developed and tested a new model of the forced choice dilemma (i.e., the belief held by some intellectually gifted students that they must choose between academic achievement and peer acceptance) that incorporates individual-level cultural orientation variables (i.e., vertical allocentrism and vertical idiocentrism). A survey that had…

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

    Science.gov (United States)

    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…

  20. Application of fuzzy sets and cognitive maps to incorporate social science scenarios in integrated assessment models

    NARCIS (Netherlands)

    Kok, de Jean-Luc; Titus, Milan; Wind, Herman G.

    2000-01-01

    Decision-support systems in the field of integrated water management could benefit considerably from social science knowledge, as many environmental changes are human-induced. Unfortunately the adequate incorporation of qualitative social science concepts in a quantitative modeling framework is not

  1. Extending the kinetic solution of the classic Michaelis-Menten model of enzyme action

    OpenAIRE

    BISPO, Jose Ailton Conceicao; Bonafe, Carlos Francisco Sampaio; SOUZA, Volnei Brito de; SILVA, Joao Batista de Almeida e; CARVALHO, Giovani Brandao Mafra de

    2011-01-01

    The principal aim of studies of enzyme-mediated reactions has been to provide comparative and quantitative information on enzyme-catalyzed reactions under distinct conditions. The classic Michaelis-Menten model (Biochem Zeit 49:333, 1913) for enzyme kinetic has been widely used to determine important parameters involved in enzyme catalysis, particularly the Michaelis-Menten constant (K (M) ) and the maximum velocity of reaction (V (max) ). Subsequently, a detailed treatment of the mechanisms ...

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

    Science.gov (United States)

    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. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

  3. Incorporation of composite defects from ultrasonic NDE into CAD and FE models

    Science.gov (United States)

    Bingol, Onur Rauf; Schiefelbein, Bryan; Grandin, Robert J.; Holland, Stephen D.; Krishnamurthy, Adarsh

    2017-02-01

    Fiber-reinforced composites are widely used in aerospace industry due to their combined properties of high strength and low weight. However, owing to their complex structure, it is difficult to assess the impact of manufacturing defects and service damage on their residual life. While, ultrasonic testing (UT) is the preferred NDE method to identify the presence of defects in composites, there are no reasonable ways to model the damage and evaluate the structural integrity of composites. We have developed an automated framework to incorporate flaws and known composite damage automatically into a finite element analysis (FEA) model of composites, ultimately aiding in accessing the residual life of composites and make informed decisions regarding repairs. The framework can be used to generate a layer-by-layer 3D structural CAD model of the composite laminates replicating their manufacturing process. Outlines of structural defects, such as delaminations, are automatically detected from UT of the laminate and are incorporated into the CAD model between the appropriate layers. In addition, the framework allows for direct structural analysis of the resulting 3D CAD models with defects by automatically applying the appropriate boundary conditions. In this paper, we show a working proof-of-concept for the composite model builder with capabilities of incorporating delaminations between laminate layers and automatically preparing the CAD model for structural analysis using a FEA software.

  4. Incorporating sorption/desorption of organic pollutants into river water quality model

    Institute of Scientific and Technical Information of China (English)

    LOU Bao-feng; ZHU Li-zhong; YANG Kun

    2004-01-01

    Preliminary research was conducted about how to incorporate sorption/desorption of organic pollutants with suspended solids and sediments into single-chemical and one-dimensional water quality model of Jinghang Canal.Sedimentation-resuspension coefficient k3 was deduced; characteristics of organic pollutants, concentrations and components of suspended solids/sediments and hydrological and hydraulic conditions were integrated into k3 and further into river water quality model; impact of sorption/desorption of organic pollutants with suspended solids and sediments on prediction function of the model was discussed. Results demonstrated that this impact is pronounced for organic pollutants with relatively large Koc and Kow, especially when they are also conservative and foc of river suspended solids/sediments is high, and that incorporation of sorption/ desorption of organic pollutants into river water quality model can improve its prediction accuracy.

  5. Incorporating Parameter Uncertainty in Bayesian Segmentation Models: Application to Hippocampal Subfield Volumetry

    OpenAIRE

    Iglesias, Juan Eugenio; Sabuncu, Mert Rory; Van Leemput, Koen

    2012-01-01

    Many successful segmentation algorithms are based on Bayesian models in which prior anatomical knowledge is combined with the available image information. However, these methods typically have many free parameters that are estimated to obtain point estimates only, whereas a faithful Bayesian analysis would also consider all possible alternate values these parameters may take. In this paper, we propose to incorporate the uncertainty of the free parameters in Bayesian segmentation models more a...

  6. Incorporating social role theory into topic models for social media content analysis

    OpenAIRE

    Zhao, Wayne Xin; Wang, Jinpeng; He, Yulan; Nie, Jian-Yun; Wen, Ji-Rong; Li, Xiaoming

    2015-01-01

    In this paper, we explore the idea of social role theory (SRT) and propose a novel regularized topic model which incorporates SRT into the generative process of social media content. We assume that a user can play multiple social roles, and each social role serves to fulfil different duties and is associated with a role-driven distribution over latent topics. In particular, we focus on social roles corresponding to the most common social activities on social networks. Our model is instantiate...

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

    Science.gov (United States)

    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

  8. 2-D magnetotelluric modeling using finite element method incorporating unstructured quadrilateral elements

    Science.gov (United States)

    Sarakorn, Weerachai

    2017-04-01

    In this research, the finite element (FE) method incorporating quadrilateral elements for solving 2-D MT modeling was presented. The finite element software was developed, employing a paving algorithm to generate the unstructured quadrilateral mesh. The accuracy, efficiency, reliability, and flexibility of our FE forward modeling are presented, compared and discussed. The numerical results indicate that our FE codes using an unstructured quadrilateral mesh provide good accuracy when the local mesh refinement is applied around sites and in the area of interest, with superior results when compared to other FE methods. The reliability of the developed codes was also confirmed when comparing both analytical solutions and COMMEMI2D model. Furthermore, our developed FE codes incorporating an unstructured quadrilateral mesh showed useful and powerful features such as handling irregular and complex subregions and providing local refinement of the mesh for a 2-D domain as closely as unstructured triangular mesh but it requires less number of elements in a mesh.

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

    Directory of Open Access Journals (Sweden)

    Ismail eAdeniran

    2013-07-01

    Full Text Available Introduction Genetic forms of the Short QT Syndrome (SQTS arise due to cardiac ion channel mutations leading to accelerated ventricular repolarisation, arrhythmias and sudden cardiac death. Results from experimental and simulation studies suggest that changes to refractoriness and tissue vulnerability produce a substrate favourable 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 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, the SQTS mutations produced dramatic reductions in the amplitude of 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 modelling 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.

  10. Modeling physiological processes in plankton on enzyme kinetic principles

    Directory of Open Access Journals (Sweden)

    Ted Packard

    2004-04-01

    Full Text Available Many ecologically important chemical transformations in the ocean are controlled by biochemical enzyme reactions in plankton. Nitrogenase regulates the transformation of N2 to ammonium in some cyanobacteria and serves as the entryway for N2 into the ocean biosphere. Nitrate reductase controls the reduction of NO3 to NO2 and hence new production in phytoplankton. The respiratory electron transfer system in all organisms links the carbon oxidation reactions of intermediary metabolism with the reduction of oxygen in respiration. Rubisco controls the fixation of CO2 into organic matter in phytoplankton and thus is the major entry point of carbon into the oceanic biosphere. In addition to these, there are the enzymes that control CO2 production, NH4 excretion and the fluxes of phosphate. Some of these enzymes have been recognized and researched by marine scientists in the last thirty years. However, until recently the kinetic principles of enzyme control have not been exploited to formulate accurate mathematical equations of the controlling physiological expressions. Were such expressions available they would increase our power to predict the rates of chemical transformations in the extracellular environment of microbial populations whether this extracellular environment is culture media or the ocean. Here we formulate from the principles of bisubstrate enzyme kinetics, mathematical expressions for the processes of NO3 reduction, O2 consumption, N2 fixation, total nitrogen uptake.

  11. Incorporating spatial autocorrelation into species distribution models alters forecasts of climate-mediated range shifts.

    Science.gov (United States)

    Crase, Beth; Liedloff, Adam; Vesk, Peter A; Fukuda, Yusuke; Wintle, Brendan A

    2014-08-01

    Species distribution models (SDMs) are widely used to forecast changes in the spatial distributions of species and communities in response to climate change. However, spatial autocorrelation (SA) is rarely accounted for in these models, despite its ubiquity in broad-scale ecological data. While spatial autocorrelation in model residuals is known to result in biased parameter estimates and the inflation of type I errors, the influence of unmodeled SA on species' range forecasts is poorly understood. Here we quantify how accounting for SA in SDMs influences the magnitude of range shift forecasts produced by SDMs for multiple climate change scenarios. SDMs were fitted to simulated data with a known autocorrelation structure, and to field observations of three mangrove communities from northern Australia displaying strong spatial autocorrelation. Three modeling approaches were implemented: environment-only models (most frequently applied in species' range forecasts), and two approaches that incorporate SA; autologistic models and residuals autocovariate (RAC) models. Differences in forecasts among modeling approaches and climate scenarios were quantified. While all model predictions at the current time closely matched that of the actual current distribution of the mangrove communities, under the climate change scenarios environment-only models forecast substantially greater range shifts than models incorporating SA. Furthermore, the magnitude of these differences intensified with increasing increments of climate change across the scenarios. When models do not account for SA, forecasts of species' range shifts indicate more extreme impacts of climate change, compared to models that explicitly account for SA. Therefore, where biological or population processes induce substantial autocorrelation in the distribution of organisms, and this is not modeled, model predictions will be inaccurate. These results have global importance for conservation efforts as inaccurate

  12. Energy system investment model incorporating heat pumps with thermal storage in buildings and buffer tanks

    DEFF Research Database (Denmark)

    Hedegaard, Karsten; Balyk, Olexandr

    2013-01-01

    options: passive heat storage in the building structure via radiator heating, active heat storage in concrete floors via floor heating, and use of thermal storage tanks for space heating and hot water. It is shown that the model is well qualified for analysing possibilities and system benefits...... be taken into account. In this study, we present a model that facilitates analysing individual heat pumps and complementing heat storages in integration with the energy system, while optimising both investments and operation. The model incorporates thermal building dynamics and covers various heat storage...

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

    Science.gov (United States)

    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.

  14. Modeling fraud detection and the incorporation of forensic specialists in the audit process

    DEFF Research Database (Denmark)

    Sakalauskaite, Dominyka

    Financial statement audits are still comparatively poor in fraud detection. Forensic specialists can play a significant role in increasing audit quality. In this paper, based on prior academic research, I develop a model of fraud detection and the incorporation of forensic specialists in the audit...... process. The intention of the model is to identify the reasons why the audit is weak in fraud detection and to provide the analytical framework to assess whether the incorporation of forensic specialists can help to improve it. The results show that such specialists can potentially improve the fraud...... detection in the audit, but might also cause some negative implications. Overall, even though fraud detection is one of the main topics in research there are very few studies done on the subject of how auditors co-operate with forensic specialists. Thus, the paper concludes with suggestions for further...

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

    Directory of Open Access Journals (Sweden)

    Anandakumari Chandrasekharan Sunil Sekhar

    2016-05-01

    Full Text Available 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.

  16. Going beyond the unitary curve: incorporating richer cognition into agent-based water resources models

    Science.gov (United States)

    Kock, B. E.

    2008-12-01

    The increased availability and understanding of agent-based modeling technology and techniques provides a unique opportunity for water resources modelers, allowing them to go beyond traditional behavioral approaches from neoclassical economics, and add rich cognition to social-hydrological models. Agent-based models provide for an individual focus, and the easier and more realistic incorporation of learning, memory and other mechanisms for increased cognitive sophistication. We are in an age of global change impacting complex water resources systems, and social responses are increasingly recognized as fundamentally adaptive and emergent. In consideration of this, water resources models and modelers need to better address social dynamics in a manner beyond the capabilities of neoclassical economics theory and practice. However, going beyond the unitary curve requires unique levels of engagement with stakeholders, both to elicit the richer knowledge necessary for structuring and parameterizing agent-based models, but also to make sure such models are appropriately used. With the aim of encouraging epistemological and methodological convergence in the agent-based modeling of water resources, we have developed a water resources-specific cognitive model and an associated collaborative modeling process. Our cognitive model emphasizes efficiency in architecture and operation, and capacity to adapt to different application contexts. We describe a current application of this cognitive model and modeling process in the Arkansas Basin of Colorado. In particular, we highlight the potential benefits of, and challenges to, using more sophisticated cognitive models in agent-based water resources models.

  17. Application of fuzzy sets and cognitive maps to incorporate social science scenarios in integrated assessment models

    OpenAIRE

    Kok, de, JMM John; Titus, Milan; Wind, Herman G.

    2000-01-01

    Decision-support systems in the field of integrated water management could benefit considerably from social science knowledge, as many environmental changes are human-induced. Unfortunately the adequate incorporation of qualitative social science concepts in a quantitative modeling framework is not straightforward. The applicability of fuzzy set theory and fuzzy cognitive maps for the integration of qualitative scenarios in a decision–support system was examined for the urbanization of the co...

  18. Incorporation of stochastic engineering models as prior information in Bayesian medical device trials.

    Science.gov (United States)

    Haddad, Tarek; Himes, Adam; Thompson, Laura; Irony, Telba; Nair, Rajesh

    2017-03-10

    Evaluation of medical devices via clinical trial is often a necessary step in the process of bringing a new product to market. In recent years, device manufacturers are increasingly using stochastic engineering models during the product development process. These models have the capability to simulate virtual patient outcomes. This article presents a novel method based on the power prior for augmenting a clinical trial using virtual patient data. To properly inform clinical evaluation, the virtual patient model must simulate the clinical outcome of interest, incorporating patient variability, as well as the uncertainty in the engineering model and in its input parameters. The number of virtual patients is controlled by a discount function which uses the similarity between modeled and observed data. This method is illustrated by a case study of cardiac lead fracture. Different discount functions are used to cover a wide range of scenarios in which the type I error rates and power vary for the same number of enrolled patients. Incorporation of engineering models as prior knowledge in a Bayesian clinical trial design can provide benefits of decreased sample size and trial length while still controlling type I error rate and power.

  19. Incorporation of ICRP-116 eye model into ICRP reference polygonal surface phantoms

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Thang Tat; Yeom, Yeon Soo; Han, Min Cheol; Wang, Zhao Jun; Kim, Han Sung; Kim, Chan Hyeong [Dept. of Nuclear Engineering, Hanyang University, Seoul (Korea, Republic of)

    2015-04-15

    The ICRP adopted a detailed stylized eye model developed by Behrens et al. for evaluation of lens dose coefficients released in ICRP publication 116. However, the dose coefficients were calculated with the stylized eye model modelled into the head of mathematical phantoms not the ICRP reference phantoms, which may cause inconsistency in lens dose assessment. In order to keep consistency in the lens dose assessment, the present study incorporates the ICRP-116 eye model into the currently developing polygonal-mesh-type ICRP reference phantoms which are being converted from the voxel-type ICRP reference phantoms. Then, lens dose values were calculated and compared with those calculated with the mathematical phantom to see how it affects lens doses. The present study incorporated the ICRP-116 eye model into the currently developing polygonal-mesh-type ICRP reference phantoms and showed significant dose differences when compared with ICRP-116 data calculated with the mathematical phantom. We believe that the ICRP reference phantoms including the detailed eye model provide more consistent assessment for eye lens dose.

  20. A code reviewer assignment model incorporating the competence differences and participant preferences

    Directory of Open Access Journals (Sweden)

    Wang Yanqing

    2016-03-01

    Full Text Available A good assignment of code reviewers can effectively utilize the intellectual resources, assure code quality and improve programmers’ skills in software development. However, little research on reviewer assignment of code review has been found. In this study, a code reviewer assignment model is created based on participants’ preference to reviewing assignment. With a constraint of the smallest size of a review group, the model is optimized to maximize review outcomes and avoid the negative impact of “mutual admiration society”. This study shows that the reviewer assignment strategies incorporating either the reviewers’ preferences or the authors’ preferences get much improvement than a random assignment. The strategy incorporating authors’ preference makes higher improvement than that incorporating reviewers’ preference. However, when the reviewers’ and authors’ preference matrixes are merged, the improvement becomes moderate. The study indicates that the majority of the participants have a strong wish to work with reviewers and authors having highest competence. If we want to satisfy the preference of both reviewers and authors at the same time, the overall improvement of learning outcomes may be not the best.

  1. Fully-coupled magnetoelastic model for Galfenol alloys incorporating eddy current losses and thermal relaxation

    Science.gov (United States)

    Evans, Phillip G.; Dapino, Marcelo J.

    2008-03-01

    A general framework is developed to model the nonlinear magnetization and strain response of cubic magnetostrictive materials to 3-D dynamic magnetic fields and 3-D stresses. Dynamic eddy current losses and inertial stresses are modeled by coupling Maxwell's equations to Newton's second law through a nonlinear constitutive model. The constitutive model is derived from continuum thermodynamics and incorporates rate-dependent thermal effects. The framework is implemented in 1-D to describe a Tonpilz transducer in both dynamic actuation and sensing modes. The model is shown to qualitatively describe the effect of increase in magnetic hysteresis with increasing frequency, the shearing of the magnetization loops with increasing stress, and the decrease in the magnetostriction with increasing load stiffness.

  2. Global dynamics of a PDE model for aedes aegypti mosquitoe incorporating female sexual preference

    KAUST Repository

    Parshad, Rana

    2011-01-01

    In this paper we study the long time dynamics of a reaction diffusion system, describing the spread of Aedes aegypti mosquitoes, which are the primary cause of dengue infection. The system incorporates a control attempt via the sterile insect technique. The model incorporates female mosquitoes sexual preference for wild males over sterile males. We show global existence of strong solution for the system. We then derive uniform estimates to prove the existence of a global attractor in L-2(Omega), for the system. The attractor is shown to be L-infinity(Omega) regular and posess state of extinction, if the injection of sterile males is large enough. We also provide upper bounds on the Hausdorff and fractal dimensions of the attractor.

  3. Molecular Modeling of Enzyme Dynamics Towards Understanding Solvent Effects

    DEFF Research Database (Denmark)

    Wedberg, Nils Hejle Rasmus Ingemar

    This thesis describes the development of a molecular simulation methodology to study properties of enzymes in non-aqueous media at fixed thermodynamic water activities. The methodology is applied in a molecular dynamics study of the industrially important enzyme Candida antarctica lipase B (CALB...... integration, while for small systems, it seems to be even better. The method is applied to compute the excess Gibbs energy of the mixtures of water and organic solvents used in the simulations of CALB. This allows to determine the water activity of the simulated systems and thus to compare protein properties......), BMC Struct. Biol., 8) and the approach to fix the water activity which often is used in experimental studies. The water activity is shown to have a profound effect on the structure and dynamics of CALB. Conformational flexibility, for instance, increases with increasing hydration in acetone, t...

  4. A data-driven model for influenza transmission incorporating media effects

    CERN Document Server

    Mitchell, Lewis

    2016-01-01

    Numerous studies have attempted to model the effect of mass media on the transmission of diseases such as influenza, however quantitative data on media engagement has until recently been difficult to obtain. With the recent explosion of "big data" coming from online social media and the like, large volumes of data on a population's engagement with mass media during an epidemic are becoming available to researchers. In this study we combine an online data set comprising millions of shared messages relating to influenza with traditional surveillance data on flu activity to suggest a functional form for the relationship between the two. Using this data we present a simple deterministic model for influenza dynamics incorporating media effects, and show that such a model helps explain the dynamics of historical influenza outbreaks. Furthermore, through model selection we show that the proposed media function fits historical data better than other media functions proposed in earlier studies.

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

    Science.gov (United States)

    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.

  6. Incorporation of the Driver’s Personality Profile in an Agent Model

    Directory of Open Access Journals (Sweden)

    Mian Muhammad Mubasher

    2015-12-01

    Full Text Available Urban traffic flow is a complex system. Behavior of an individual driver can have butterfly effect which can become root cause of an emergent phenomenon such as congestion or accident. Interaction of drivers with each other and the surrounding environment forms the dynamics of traffic flow. Hence global effects of traffic flow depend upon the behavior of each individual driver. Due to several applications of driver models in serious games, urban traffic planning and simulations, study of a realistic driver model is important. Hhence cognitive models of a driver agent are required. In order to address this challenge concepts from cognitive science and psychology are employed to design a computational model of driver cognition which is capable of incorporating law abidance and social norms using big five personality profile.

  7. A data-driven model for influenza transmission incorporating media effects.

    Science.gov (United States)

    Mitchell, Lewis; Ross, Joshua V

    2016-10-01

    Numerous studies have attempted to model the effect of mass media on the transmission of diseases such as influenza; however, quantitative data on media engagement has until recently been difficult to obtain. With the recent explosion of 'big data' coming from online social media and the like, large volumes of data on a population's engagement with mass media during an epidemic are becoming available to researchers. In this study, we combine an online dataset comprising millions of shared messages relating to influenza with traditional surveillance data on flu activity to suggest a functional form for the relationship between the two. Using this data, we present a simple deterministic model for influenza dynamics incorporating media effects, and show that such a model helps explain the dynamics of historical influenza outbreaks. Furthermore, through model selection we show that the proposed media function fits historical data better than other media functions proposed in earlier studies.

  8. A predictive model of community assembly that incorporates intraspecific trait variation.

    Science.gov (United States)

    Laughlin, Daniel C; Joshi, Chaitanya; van Bodegom, Peter M; Bastow, Zachary A; Fulé, Peter Z

    2012-11-01

    Community assembly involves two antagonistic processes that select functional traits in opposite directions. Environmental filtering tends to increase the functional similarity of species within communities leading to trait convergence, whereas competition tends to limit the functional similarity of species within communities leading to trait divergence. Here, we introduce a new hierarchical Bayesian model that incorporates intraspecific trait variation into a predictive framework to unify classic coexistence theory and evolutionary biology with recent trait-based approaches. Model predictions exhibited a significant positive correlation (r = 0.66) with observed relative abundances along a 10 °C gradient in mean annual temperature. The model predicted the correct dominant species in half of the plots, and accurately reproduced species' temperature optimums. The framework is generalizable to any ecosystem as it can accommodate any species pool, any set of functional traits and multiple environmental gradients, and it eliminates some of the criticisms associated with recent trait-based community assembly models.

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

    Science.gov (United States)

    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.

  10. A data-driven model for influenza transmission incorporating media effects

    Science.gov (United States)

    Ross, Joshua V.

    2016-01-01

    Numerous studies have attempted to model the effect of mass media on the transmission of diseases such as influenza; however, quantitative data on media engagement has until recently been difficult to obtain. With the recent explosion of ‘big data’ coming from online social media and the like, large volumes of data on a population’s engagement with mass media during an epidemic are becoming available to researchers. In this study, we combine an online dataset comprising millions of shared messages relating to influenza with traditional surveillance data on flu activity to suggest a functional form for the relationship between the two. Using this data, we present a simple deterministic model for influenza dynamics incorporating media effects, and show that such a model helps explain the dynamics of historical influenza outbreaks. Furthermore, through model selection we show that the proposed media function fits historical data better than other media functions proposed in earlier studies. PMID:27853563

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

    Science.gov (United States)

    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

  12. A model of extracellular enzymes in free-living microbes: Which strategy pays off?

    DEFF Research Database (Denmark)

    Traving, Sachia J; Thygesen, Uffe Høgsbro; Riemann, Lasse

    2015-01-01

    entails potential substrates being reduced to very low concentrations. Free enzymes, on the other hand, generate a radically different substrate field, which suggests significant benefits for the strategy if free cells engage in social foraging or experience high substrate concentrations. Swimming has...... must be utilized efficiently. The model revealed that surface-attached and free enzymes generate unique enzyme and substrate fields, and each deployment strategy has distinctive advantages. For a solitary cell, surface-attached enzymes are suggested to be the most cost-efficient strategy. This strategy...... a slight positive effect for the attached-enzyme strategy, while the effect is negative for the free-enzyme strategy. The results of this study suggest that specific dissolved organic compounds in the ocean likely persist below a threshold concentration impervious to biological utilization. This could help...

  13. A model of extracellular enzymes in free-living microbes: which strategy pays off?

    Science.gov (United States)

    Traving, Sachia J; Thygesen, Uffe H; Riemann, Lasse; Stedmon, Colin A

    2015-11-01

    An initial modeling approach was applied to analyze how a single, nonmotile, free-living, heterotrophic bacterial cell may optimize the deployment of its extracellular enzymes. Free-living cells live in a dilute and complex substrate field, and to gain enough substrate, their extracellular enzymes must be utilized efficiently. The model revealed that surface-attached and free enzymes generate unique enzyme and substrate fields, and each deployment strategy has distinctive advantages. For a solitary cell, surface-attached enzymes are suggested to be the most cost-efficient strategy. This strategy entails potential substrates being reduced to very low concentrations. Free enzymes, on the other hand, generate a radically different substrate field, which suggests significant benefits for the strategy if free cells engage in social foraging or experience high substrate concentrations. Swimming has a slight positive effect for the attached-enzyme strategy, while the effect is negative for the free-enzyme strategy. The results of this study suggest that specific dissolved organic compounds in the ocean likely persist below a threshold concentration impervious to biological utilization. This could help explain the persistence and apparent refractory state of oceanic dissolved organic matter (DOM). Microbial extracellular enzyme strategies, therefore, have important implications for larger-scale processes, such as shaping the role of DOM in ocean carbon sequestration.

  14. A Model of Extracellular Enzymes in Free-Living Microbes: Which Strategy Pays Off?

    Science.gov (United States)

    Thygesen, Uffe H.; Riemann, Lasse; Stedmon, Colin A.

    2015-01-01

    An initial modeling approach was applied to analyze how a single, nonmotile, free-living, heterotrophic bacterial cell may optimize the deployment of its extracellular enzymes. Free-living cells live in a dilute and complex substrate field, and to gain enough substrate, their extracellular enzymes must be utilized efficiently. The model revealed that surface-attached and free enzymes generate unique enzyme and substrate fields, and each deployment strategy has distinctive advantages. For a solitary cell, surface-attached enzymes are suggested to be the most cost-efficient strategy. This strategy entails potential substrates being reduced to very low concentrations. Free enzymes, on the other hand, generate a radically different substrate field, which suggests significant benefits for the strategy if free cells engage in social foraging or experience high substrate concentrations. Swimming has a slight positive effect for the attached-enzyme strategy, while the effect is negative for the free-enzyme strategy. The results of this study suggest that specific dissolved organic compounds in the ocean likely persist below a threshold concentration impervious to biological utilization. This could help explain the persistence and apparent refractory state of oceanic dissolved organic matter (DOM). Microbial extracellular enzyme strategies, therefore, have important implications for larger-scale processes, such as shaping the role of DOM in ocean carbon sequestration. PMID:26253668

  15. An in silico model of the ubiquitin-proteasome system that incorporates normal homeostasis and age-related decline

    Directory of Open Access Journals (Sweden)

    Proctor Carole J

    2007-03-01

    Full Text Available Abstract Background The ubiquitin-proteasome system is responsible for homeostatic degradation of intact protein substrates as well as the elimination of damaged or misfolded proteins that might otherwise aggregate. During ageing there is a decline in proteasome activity and an increase in aggregated proteins. Many neurodegenerative diseases are characterised by the presence of distinctive ubiquitin-positive inclusion bodies in affected regions of the brain. These inclusions consist of insoluble, unfolded, ubiquitinated polypeptides that fail to be targeted and degraded by the proteasome. We are using a systems biology approach to try and determine the primary event in the decline in proteolytic capacity with age and whether there is in fact a vicious cycle of inhibition, with accumulating aggregates further inhibiting proteolysis, prompting accumulation of aggregates and so on. A stochastic model of the ubiquitin-proteasome system has been developed using the Systems Biology Mark-up Language (SBML. Simulations are carried out on the BASIS (Biology of Ageing e-Science Integration and Simulation system and the model output is compared to experimental data wherein levels of ubiquitin and ubiquitinated substrates are monitored in cultured cells under various conditions. The model can be used to predict the effects of different experimental procedures such as inhibition of the proteasome or shutting down the enzyme cascade responsible for ubiquitin conjugation. Results The model output shows good agreement with experimental data under a number of different conditions. However, our model predicts that monomeric ubiquitin pools are always depleted under conditions of proteasome inhibition, whereas experimental data show that monomeric pools were depleted in IMR-90 cells but not in ts20 cells, suggesting that cell lines vary in their ability to replenish ubiquitin pools and there is the need to incorporate ubiquitin turnover into the model. Sensitivity

  16. Incorporating risk attitude into Markov-process decision models: importance for individual decision making.

    Science.gov (United States)

    Cher, D J; Miyamoto, J; Lenert, L A

    1997-01-01

    Most decision models published in the medical literature take a risk-neutral perspective. Under risk neutrality, the utility of a gamble is equivalent to its expected value and the marginal utility of living a given unit of time is the same regardless of when it occurs. Most patients, however, are not risk-neutral. Not only does risk aversion affect decision analyses when tradeoffs between short- and long-term survival are involved, it also affects the interpretation of time-tradeoff measures of health-state utility. The proportional time tradeoff under- or overestimates the disutility of an inferior health state, depending on whether the patient is risk-seeking or risk-averse (it is unbiased if the patient is risk-neutral). The authors review how risk attitude with respect to gambles for survival duration can be incorporated into decision models using the framework of risk-adjusted quality-adjusted life years (RA-QALYs). They present a simple extension of this framework that allows RA-QALYs to be calculated for Markov-process decision models. Using a previously published Markov-process model of surgical vs expectant treatment for benign prostatic hypertrophy (BPH), they show how attitude towards risk affects the expected number of QALYs calculated by the model. In this model, under risk neutrality, surgery was the preferred option. Under mild risk aversion, expectant treatment was the preferred option. Risk attitude is an important aspect of preferences that should be incorporated into decision models where one treatment option has upfront risks of morbidity or mortality.

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

    Science.gov (United States)

    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.

  18. Extension of the QUASAR river water quality model to incorporate dead-zone mixing

    Directory of Open Access Journals (Sweden)

    M. J. Lees

    1998-01-01

    Full Text Available A modification to the well-known water quality model 'Quality Simulation Along River Systems' (QUASAR is presented, extending its utility to real-time forecasting applications such as the management and control of pollution incidents. Two aggregated dead-zone (ADZ parameters, namely time delay and dispersive fraction, are incorporated into the existing model formulation, extending the current continuously stirred tank reactor based model processes to account for advective and active mixing volume dispersive processes. The resulting river water quality model combines the strengths of the QUASAR model, which has proven non-conservative pollutant modelling capabilities, with the accurate advection and dispersion characterisation of the ADZ model. A discrete-time mathematical representation of the governing equations is developed that enables efficient system identification methods of parameter estimation to be utilised. The enhanced water quality model and associated methods of parameter estimation are validated using data from tracer experiments conducted on the River Mimram. The revised model produces accurate predictions of observed concentration-time curves for conservative substances.

  19. Extension of the QUASAR river water quality model to incorporate dead-zone mixing

    Science.gov (United States)

    Lees, M. J.; Camacho, L.; Whitehead, P.

    A modification to the well-known water quality model "Quality Simulation Along River Systems" (QUASAR) is presented, extending its utility to real-time forecasting applications such as the management and control of pollution incidents. Two aggregated dead-zone (ADZ) parameters, namely time delay and dispersive fraction, are incorporated into the existing model formulation, extending the current continuously stirred tank reactor based model processes to account for advective and active mixing volume dispersive processes. The resulting river water quality model combines the strengths of the QUASAR model, which has proven non-conservative pollutant modelling capabilities, with the accurate advection and dispersion characterisation of the ADZ model. A discrete-time mathematical representation of the governing equations is developed that enables efficient system identification methods of parameter estimation to be utilised. The enhanced water quality model and associated methods of parameter estimation are validated using data from tracer experiments conducted on the River Mimram. The revised model produces accurate predictions of observed concentration-time curves for conservative substances.

  20. A molecular dynamics model of rhodamine-labeled phospholipid incorporated into a lipid bilayer

    Science.gov (United States)

    Kyrychenko, Alexander

    2010-01-01

    Phospholipids, labeled covalently by a fluorescent dye, are commonly applied in membrane biophysics. In this work, a molecular dynamics model of sulforhodamine attached covalently to a headgroup of 1,2-dipalmitoyl- sn-glycero-3-phosphoethanolamine is developed. It is found that the incorporation of rhodamine-labeled phospholipids into a DPPC bilayer at the low concentration results in small perturbation of the bilayer. In the dye-labeled membrane, the sulforhodamine moiety binds favorably to a polar membrane interface, forming the tilt angle 44° ± 8° to the bilayer normal. The deep location and binding of a bulk sulforhodamine fluorophore lead, therefore, to some 'softening' of the membrane structure.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  3. Transporter-Enzyme Interplay: Deconvoluting Effects of Hepatic Transporters and Enzymes on Drug Disposition Using Static and Dynamic Mechanistic Models.

    Science.gov (United States)

    Varma, Manthena V; El-Kattan, Ayman F

    2016-07-01

    A large body of evidence suggests hepatic uptake transporters, organic anion-transporting polypeptides (OATPs), are of high clinical relevance in determining the pharmacokinetics of substrate drugs, based on which recent regulatory guidances to industry recommend appropriate assessment of investigational drugs for the potential drug interactions. We recently proposed an extended clearance classification system (ECCS) framework in which the systemic clearance of class 1B and 3B drugs is likely determined by hepatic uptake. The ECCS framework therefore predicts the possibility of drug-drug interactions (DDIs) involving OATPs and the effects of genetic variants of SLCO1B1 early in the discovery and facilitates decision making in the candidate selection and progression. Although OATP-mediated uptake is often the rate-determining process in the hepatic clearance of substrate drugs, metabolic and/or biliary components also contribute to the overall hepatic disposition and, more importantly, to liver exposure. Clinical evidence suggests that alteration in biliary efflux transport or metabolic enzymes associated with genetic polymorphism leads to change in the pharmacodynamic response of statins, for which the pharmacological target resides in the liver. Perpetrator drugs may show inhibitory and/or induction effects on transporters and enzymes simultaneously. It is therefore important to adopt models that frame these multiple processes in a mechanistic sense for quantitative DDI predictions and to deconvolute the effects of individual processes on the plasma and hepatic exposure. In vitro data-informed mechanistic static and physiologically based pharmacokinetic models are proven useful in rationalizing and predicting transporter-mediated DDIs and the complex DDIs involving transporter-enzyme interplay.

  4. Evolutionary Models of Super-Earths and Mini-Neptunes Incorporating Cooling and Mass Loss

    CERN Document Server

    Howe, Alex R

    2015-01-01

    We construct models of the structural evolution of super-Earth- and mini-Neptune-type exoplanets with hydrogen-helium 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 initial envelope mass fraction are the most important factors determining planetary evolution, particular 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 los...

  5. Agent-Based Evacuation Model Incorporating Fire Scene and Building Geometry

    Institute of Scientific and Technical Information of China (English)

    TANG Fangqin; REN Aizhu

    2008-01-01

    A comprehensive description of the key factors affecting evacuations at fire scones is necessary for accurate simulations.An agent-based simulation model which incorporates the fire scene and the building geometry is developed using a fire dynamics simulator (FDS) based on the computational fluid dynamics and geographic information system (GIS) data to model the occupant response.The building entities are generated for FDS simulation while the spatial analysis on GIS data represents the occupant's knowledge of the building.The influence of the fire is based on a hazard assessment of the combustion products.The agent behavior and decisions are affected by environmental features and the fire field.A case study demonstrates that the evacuation model effectively simulates the coexistence and interactions of the major factors including occupants,building geometry,and fire disaster during the evacuation.The results can be used for the assessments of building designs regarding fire safety.

  6. Hidden Markov Models Incorporating Fuzzy Measures and Integrals for Protein Sequence Identification and Alignment

    Institute of Scientific and Technical Information of China (English)

    Niranjan P.Bidargaddi; Madlhu Chetty; Joarder Kamruzzaman

    2008-01-01

    Profile hidden Markov models (HMMs) based on classical HMMs have been widely applied for protein sequence identification. The formulation of the forward and backward variables in profile HMMs is made under statistical independence assumption of the probability theory. We propose a fuzzy profile HMM to overcome the limitations of that assumption and to achieve an improved alignment for protein sequences belonging to a given family. The proposed model fuzzifies the forward and backward variables by incorporating Sugeno fuzzy measures and Choquet integrals, thus further extends the generalized HMM. Based on the fuzzified forwardand backward variables, we propose a fuzzy Baum-Welch parameter estimation al-gorithm for profiles. The strong correlations and the sequence preference involved in the protein structures make this fuzzy architecture based model as a suitable candidate for building profiles of a given family, since the fuzzy set can handle uncertainties better than classical methods.

  7. Some considerations concerning the challenge of incorporating social variables into epidemiological models of infectious disease transmission.

    Science.gov (United States)

    Barnett, Tony; Fournié, Guillaume; Gupta, Sunetra; Seeley, Janet

    2015-01-01

    Incorporation of 'social' variables into epidemiological models remains a challenge. Too much detail and models cease to be useful; too little and the very notion of infection - a highly social process in human populations - may be considered with little reference to the social. The French sociologist Émile Durkheim proposed that the scientific study of society required identification and study of 'social currents'. Such 'currents' are what we might today describe as 'emergent properties', specifiable variables appertaining to individuals and groups, which represent the perspectives of social actors as they experience the environment in which they live their lives. Here we review the ways in which one particular emergent property, hope, relevant to a range of epidemiological situations, might be used in epidemiological modelling of infectious diseases in human populations. We also indicate how such an approach might be extended to include a range of other potential emergent properties to represent complex social and economic processes bearing on infectious disease transmission.

  8. Incorporating evolutionary adaptation in species distribution modelling reduces projected vulnerability to climate change.

    Science.gov (United States)

    Bush, Alex; Mokany, Karel; Catullo, Renee; Hoffmann, Ary; Kellermann, Vanessa; Sgrò, Carla; McEvey, Shane; Ferrier, Simon

    2016-12-01

    Based on the sensitivity of species to ongoing climate change, and numerous challenges they face tracking suitable conditions, there is growing interest in species' capacity to adapt to climatic stress. Here, we develop and apply a new generic modelling approach (AdaptR) that incorporates adaptive capacity through physiological limits, phenotypic plasticity, evolutionary adaptation and dispersal into a species distribution modelling framework. Using AdaptR to predict change in the distribution of 17 species of Australian fruit flies (Drosophilidae), we show that accounting for adaptive capacity reduces projected range losses by up to 33% by 2105. We identify where local adaptation is likely to occur and apply sensitivity analyses to identify the critical factors of interest when parameters are uncertain. Our study suggests some species could be less vulnerable than previously thought, and indicates that spatiotemporal adaptive models could help improve management interventions that support increased species' resilience to climate change. © 2016 John Wiley & Sons Ltd/CNRS.

  9. Affordances perspective and grammaticalization: Incorporation of language, environment and users in the model of semantic paths

    Directory of Open Access Journals (Sweden)

    Alexander Andrason

    2015-12-01

    Full Text Available The present paper demonstrates that insights from the affordances perspective can contribute to developing a more comprehensive model of grammaticalization. The authors argue that the grammaticalization process is afforded differently depending on the values of three contributing parameters: the factor (schematized as a qualitative-quantitative map or a wave of a gram, environment (understood as the structure of the stream along which the gram travels, and actor (narrowed to certain cognitive-epistemological capacities of the users, in particular to the fact of being a native speaker. By relating grammaticalization to these three parameters and by connecting it to the theory of optimization, the proposed model offers a better approximation to realistic cases of grammaticalization: The actor and environment are overtly incorporated into the model and divergences from canonical grammaticalization paths are both tolerated and explicable.

  10. A Fibrocontractive Mechanochemical Model of Dermal Wound Closure Incorporating Realistic Growth Factor Kinetics

    KAUST Repository

    Murphy, Kelly E.

    2012-01-13

    Fibroblasts and their activated phenotype, myofibroblasts, are the primary cell types involved in the contraction associated with dermal wound healing. Recent experimental evidence indicates that the transformation from fibroblasts to myofibroblasts involves two distinct processes: The cells are stimulated to change phenotype by the combined actions of transforming growth factor β (TGFβ) and mechanical tension. This observation indicates a need for a detailed exploration of the effect of the strong interactions between the mechanical changes and growth factors in dermal wound healing. We review the experimental findings in detail and develop a model of dermal wound healing that incorporates these phenomena. Our model includes the interactions between TGFβ and collagenase, providing a more biologically realistic form for the growth factor kinetics than those included in previous mechanochemical descriptions. A comparison is made between the model predictions and experimental data on human dermal wound healing and all the essential features are well matched. © 2012 Society for Mathematical Biology.

  11. A Direct Method for Incorporating Experimental Data into Multiscale Coarse-Grained Models.

    Science.gov (United States)

    Dannenhoffer-Lafage, Thomas; White, Andrew D; Voth, Gregory A

    2016-05-10

    To extract meaningful data from molecular simulations, it is necessary to incorporate new experimental observations as they become available. Recently, a new method was developed for incorporating experimental observations into molecular simulations, called experiment directed simulation (EDS), which utilizes a maximum entropy argument to bias an existing model to agree with experimental observations while changing the original model by a minimal amount. However, there is no discussion in the literature of whether or not the minimal bias systematically and generally improves the model by creating agreement with the experiment. In this work, we show that the relative entropy of the biased system with respect to an ideal target is always reduced by the application of a minimal bias, such as the one utilized by EDS. Using all-atom simulations that have been biased with EDS, one can then easily and rapidly improve a bottom-up multiscale coarse-grained (MS-CG) model without the need for a time-consuming reparametrization of the underlying atomistic force field. Furthermore, the improvement given by the many-body interactions introduced by the EDS bias can be maintained after being projected down to effective two-body MS-CG interactions. The result of this analysis is a new paradigm in coarse-grained modeling and simulation in which the "bottom-up" and "top-down" approaches are combined within a single, rigorous formalism based on statistical mechanics. The utility of building the resulting EDS-MS-CG models is demonstrated on two molecular systems: liquid methanol and ethylene carbonate.

  12. 'Enzyme Test Bench': A biochemical application of the multi-rate modeling

    Science.gov (United States)

    Rachinskiy, K.; Schultze, H.; Boy, M.; Büchs, J.

    2008-11-01

    In the expanding field of 'white biotechnology' enzymes are frequently applied to catalyze the biochemical reaction from a resource material to a valuable product. Evolutionary designed to catalyze the metabolism in any life form, they selectively accelerate complex reactions under physiological conditions. Modern techniques, such as directed evolution, have been developed to satisfy the increasing demand on enzymes. Applying these techniques together with rational protein design, we aim at improving of enzymes' activity, selectivity and stability. To tap the full potential of these techniques, it is essential to combine them with adequate screening methods. Nowadays a great number of high throughput colorimetric and fluorescent enzyme assays are applied to measure the initial enzyme activity with high throughput. However, the prediction of enzyme long term stability within short experiments is still a challenge. A new high throughput technique for enzyme characterization with specific attention to the long term stability, called 'Enzyme Test Bench', is presented. The concept of the Enzyme Test Bench consists of short term enzyme tests conducted under partly extreme conditions to predict the enzyme long term stability under moderate conditions. The technique is based on the mathematical modeling of temperature dependent enzyme activation and deactivation. Adapting the temperature profiles in sequential experiments by optimum non-linear experimental design, the long term deactivation effects can be purposefully accelerated and detected within hours. During the experiment the enzyme activity is measured online to estimate the model parameters from the obtained data. Thus, the enzyme activity and long term stability can be calculated as a function of temperature. The results of the characterization, based on micro liter format experiments of hours, are in good agreement with the results of long term experiments in 1L format. Thus, the new technique allows for both

  13. 'Enzyme Test Bench': A biochemical application of the multi-rate modeling

    Energy Technology Data Exchange (ETDEWEB)

    Rachinskiy, K; Buechs, J [Department of Biochemical Engineering, Sammelbau Biologie, RWTH-Aachen University, D-52074 Aachen (Germany); Schultze, H; Boy, M [BASF Aktiengesellschaft, Ludwigshafen (Germany)], E-mail: buechs@biovt.rwth-aachen.de

    2008-11-01

    In the expanding field of 'white biotechnology' enzymes are frequently applied to catalyze the biochemical reaction from a resource material to a valuable product. Evolutionary designed to catalyze the metabolism in any life form, they selectively accelerate complex reactions under physiological conditions. Modern techniques, such as directed evolution, have been developed to satisfy the increasing demand on enzymes. Applying these techniques together with rational protein design, we aim at improving of enzymes' activity, selectivity and stability. To tap the full potential of these techniques, it is essential to combine them with adequate screening methods. Nowadays a great number of high throughput colorimetric and fluorescent enzyme assays are applied to measure the initial enzyme activity with high throughput. However, the prediction of enzyme long term stability within short experiments is still a challenge. A new high throughput technique for enzyme characterization with specific attention to the long term stability, called 'Enzyme Test Bench', is presented. The concept of the Enzyme Test Bench consists of short term enzyme tests conducted under partly extreme conditions to predict the enzyme long term stability under moderate conditions. The technique is based on the mathematical modeling of temperature dependent enzyme activation and deactivation. Adapting the temperature profiles in sequential experiments by optimum non-linear experimental design, the long term deactivation effects can be purposefully accelerated and detected within hours. During the experiment the enzyme activity is measured online to estimate the model parameters from the obtained data. Thus, the enzyme activity and long term stability can be calculated as a function of temperature. The results of the characterization, based on micro liter format experiments of hours, are in good agreement with the results of long term experiments in 1L format. Thus, the new

  14. Incorporating animal behavior into seed dispersal models: implications for seed shadows.

    Science.gov (United States)

    Russo, Sabrina E; Portnoy, Stephen; Augspurger, Carol K

    2006-12-01

    Seed dispersal fundamentally influences plant population and community dynamics but is difficult to quantify directly. Consequently, models are frequently used to describe the seed shadow (the seed deposition pattern of a plant population). For vertebrate-dispersed plants, animal behavior is known to influence seed shadows but is poorly integrated in seed dispersal models. Here, we illustrate a modeling approach that incorporates animal behavior and develop a stochastic, spatially explicit simulation model that predicts the seed shadow for a primate-dispersed tree species (Virola calophylla, Myristicaceae) at the forest stand scale. The model was parameterized from field-collected data on fruit production and seed dispersal, behaviors and movement patterns of the key disperser, the spider monkey (Ateles paniscus), densities of dispersed and non-dispersed seeds, and direct estimates of seed dispersal distances. Our model demonstrated that the spatial scale of dispersal for this V. calophylla population was large, as spider monkeys routinely dispersed seeds >100 m, a commonly used threshold for long-distance dispersal. The simulated seed shadow was heterogeneous, with high spatial variance in seed density resulting largely from behaviors and movement patterns of spider monkeys that aggregated seeds (dispersal at their sleeping sites) and that scattered seeds (dispersal during diurnal foraging and resting). The single-distribution dispersal kernels frequently used to model dispersal substantially underestimated this variance and poorly fit the simulated seed-dispersal curve, primarily because of its multimodality, and a mixture distribution always fit the simulated dispersal curve better. Both seed shadow heterogeneity and dispersal curve multimodality arose directly from these different dispersal processes generated by spider monkeys. Compared to models that did not account for disperser behavior, our modeling approach improved prediction of the seed shadow of this V

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

    Science.gov (United States)

    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

  16. An approach to incorporate individual personality in modeling fish dispersal across in-stream barriers.

    Science.gov (United States)

    Hirsch, Philipp Emanuel; Thorlacius, Magnus; Brodin, Tomas; Burkhardt-Holm, Patricia

    2017-01-01

    Animal personalities are an important factor that affects the dispersal of animals. In the context of aquatic species, dispersal modeling needs to consider that most freshwater ecosystems are highly fragmented by barriers reducing longitudinal connectivity. Previous research has incorporated such barriers into dispersal models under the neutral assumption that all migrating animals attempt to ascend at all times. Modeling dispersal of animals that do not perform trophic or reproductive migrations will be more realistic if it includes assumptions of which individuals attempt to overcome a barrier. We aimed to introduce personality into predictive modeling of whether a nonmigratory invasive freshwater fish (the round goby, Neogobius melanostomus) will disperse across an in-stream barrier. To that end, we experimentally assayed the personalities of 259 individuals from invasion fronts and established round goby populations. Based on the population differences in boldness, asociability, and activity, we defined a priori thresholds with bolder, more asocial, and more active individuals having a higher likelihood of ascent. We then combined the personality thresholds with swimming speed data from the literature and in situ measurements of flow velocities in the barrier. The resulting binary logistic regression model revealed probabilities of crossing a barrier which depended not only on water flow and fish swimming speed but also on animal personalities. We conclude that risk assessment through predictive dispersal modeling across fragmented landscapes can be advanced by including personality traits as parameters. The inclusion of behavior into modeling the spread of invasive species can help to improve the accuracy of risk assessments.

  17. A constitutive mechanical model for gas hydrate bearing sediments incorporating inelastic mechanisms

    KAUST Repository

    Sánchez, Marcelo

    2016-11-30

    Gas hydrate bearing sediments (HBS) are natural soils formed in permafrost and sub-marine settings where the temperature and pressure conditions are such that gas hydrates are stable. If these conditions shift from the hydrate stability zone, hydrates dissociate and move from the solid to the gas phase. Hydrate dissociation is accompanied by significant changes in sediment structure and strongly affects its mechanical behavior (e.g., sediment stiffenss, strength and dilatancy). The mechanical behavior of HBS is very complex and its modeling poses great challenges. This paper presents a new geomechanical model for hydrate bearing sediments. The model incorporates the concept of partition stress, plus a number of inelastic mechanisms proposed to capture the complex behavior of this type of soil. This constitutive model is especially well suited to simulate the behavior of HBS upon dissociation. The model was applied and validated against experimental data from triaxial and oedometric tests conducted on manufactured and natural specimens involving different hydrate saturation, hydrate morphology, and confinement conditions. Particular attention was paid to model the HBS behavior during hydrate dissociation under loading. The model performance was highly satisfactory in all the cases studied. It managed to properly capture the main features of HBS mechanical behavior and it also assisted to interpret the behavior of this type of sediment under different loading and hydrate conditions.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Directory of Open Access Journals (Sweden)

    Min Chen

    2011-04-01

    Full Text Available 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. Incorporating S-shaped testing-effort functions into NHPP software reliability model with imperfect debugging

    Institute of Scientific and Technical Information of China (English)

    Qiuying Li; Haifeng Li; Minyan Lu

    2015-01-01

    Testing-effort (TE) and imperfect debugging (ID) in the reliability modeling process may further improve the fitting and pre-diction results of software reliability growth models (SRGMs). For describing the S-shaped varying trend of TE increasing rate more accurately, first, two S-shaped testing-effort functions (TEFs), i.e., delayed S-shaped TEF (DS-TEF) and inflected S-shaped TEF (IS-TEF), are proposed. Then these two TEFs are incorporated into various types (exponential-type, delayed S-shaped and in-flected S-shaped) of non-homogeneous Poisson process (NHPP) SRGMs with two forms of ID respectively for obtaining a series of new NHPP SRGMs which consider S-shaped TEFs as wel as ID. Final y these new SRGMs and several comparison NHPP SRGMs are applied into four real failure data-sets respectively for investigating the fitting and prediction power of these new SRGMs. The experimental results show that: (i) the proposed IS-TEF is more suitable and flexible for describing the consumption of TE than the previous TEFs; (i ) incorporating TEFs into the inflected S-shaped NHPP SRGM may be more effective and appropriate compared with the exponential-type and the delayed S-shaped NHPP SRGMs; (i i) the inflected S-shaped NHPP SRGM con-sidering both IS-TEF and ID yields the most accurate fitting and prediction results than the other comparison NHPP SRGMs.

  1. MOLECULAR MODELLING OF HUMAN ALDEHYDE OXIDASE AND IDENTIFICATION OF THE KEY INTERACTIONS IN THE ENZYME-SUBSTRATE COMPLEX

    Directory of Open Access Journals (Sweden)

    Siavoush Dastmalchi

    2005-05-01

    Full Text Available Aldehyde oxidase (EC 1.2.3.1, a cytosolic enzyme containing FAD, molybdenum and iron-sulphur cluster, is a member of non-cytochrome P-450 enzymes called molybdenum hydroxylases which is involved in the metabolism of a wide range of endogenous compounds and many drug substances. Drug metabolism is one of the important characteristics which influences many aspects of a therapeutic agent such as routes of administration, drug interaction and toxicity and therefore, characterisation of the key interactions between enzymes and substrates is very important from drug development point of view. The aim of this study was to generate a three-dimensional model of human aldehyde oxidase (AO in order to assist us to identify the mode of interaction between enzyme and a set of phethalazine/quinazoline derivatives. Both sequence-based (BLAST and inverse protein fold recognition methods (THREADER were used to identify the crystal structure of bovine xanthine dehydrogenase (pdb code of 1FO4 as the suitable template for comparative modelling of human AO. Model structure was generated by aligning and then threading the sequence of human AO onto the template structure, incorporating the associated cofactors, and molecular dynamics simulations and energy minimization using GROMACS program. Different criteria which were measured by the PROCHECK, QPACK, VERIFY-3D were indicative of a proper fold for the predicted structural model of human AO. For example, 97.9 percentages of phi and psi angles were in the favoured and most favoured regions in the ramachandran plot, and all residues in the model are assigned environmentally positive compatibility scores. Further evaluation on the model quality was performed by investigation of AO-mediated oxidation of a set of phthalazine/quinazoline derivatives to develop QSAR model capable of describing the extent of the oxidation. Substrates were aligned by docking onto the active site of the enzyme using GOLD technology and then

  2. Incorporating parameter uncertainty in Bayesian segmentation models: application to hippocampal subfield volumetry.

    Science.gov (United States)

    Iglesias, Juan Eugenio; Sabuncu, Mert Rory; Van Leemput, Koen

    2012-01-01

    Many successful segmentation algorithms are based on Bayesian models in which prior anatomical knowledge is combined with the available image information. However, these methods typically have many free parameters that are estimated to obtain point estimates only, whereas a faithful Bayesian analysis would also consider all possible alternate values these parameters may take. In this paper, we propose to incorporate the uncertainty of the free parameters in Bayesian segmentation models more accurately by using Monte Carlo sampling. We demonstrate our technique by sampling atlas warps in a recent method for hippocampal subfield segmentation, and show a significant improvement in an Alzheimer's disease classification task. As an additional benefit, the method also yields informative "error bars" on the segmentation results for each of the individual sub-structures.

  3. Incorporating Parameter Uncertainty in Bayesian Segmentation Models: Application to Hippocampal Subfield Volumetry

    DEFF Research Database (Denmark)

    Iglesias, J. E.; Sabuncu, M. R.; Van Leemput, Koen

    2012-01-01

    in a recent method for hippocampal subfield segmentation, and show a significant improvement in an Alzheimer’s disease classification task. As an additional benefit, the method also yields informative “error bars” on the segmentation results for each of the individual sub-structures.......Many successful segmentation algorithms are based on Bayesian models in which prior anatomical knowledge is combined with the available image information. However, these methods typically have many free parameters that are estimated to obtain point estimates only, whereas a faithful Bayesian...... analysis would also consider all possible alternate values these parameters may take. In this paper, we propose to incorporate the uncertainty of the free parameters in Bayesian segmentation models more accurately by using Monte Carlo sampling. We demonstrate our technique by sampling atlas warps...

  4. Algorithm for break even availability allocation in process system modification using deterministic valuation model incorporating reliability

    Energy Technology Data Exchange (ETDEWEB)

    Shouri, P.V.; Sreejith, P.S. [Division of Mechanical Engineering, School of Engineering, Cochin University of Science and Technology (CUSAT), Cochin 682 022, Kerala (India)

    2008-06-15

    In the present scenario of energy demand overtaking energy supply, top priority is given for energy conservation programs and policies. As a result, most existing systems are redesigned or modified with a view for improving energy efficiency. Often these modifications can have an impact on process system configuration, thereby affecting process system reliability. The paper presents a model for valuation of process systems incorporating reliability that can be used to determine the change in process system value resulting from system modification. The model also determines the break even system availability and presents an algorithm for allocation of component reliabilities of the modified system based on the break even system availability. The developed equations are applied to a steam power plant to study the effect of various operating parameters on system value. (author)

  5. SIFT and shape information incorporated into fluid model for non-rigid registration of ultrasound images.

    Science.gov (United States)

    Lu, Xuesong; Zhang, Su; Yang, Wei; Chen, Yazhu

    2010-11-01

    Non-rigid registration of ultrasound images takes an important role in image-guided radiotherapy and surgery. Intensity-based method is popular in non-rigid registration, but it is sensitive to intensity variations and has problems with matching small structure features for the existence of speckles in ultrasound images. In this paper, we develop a new algorithm integrating the intensity and feature of ultrasound images. Both global shape information and local keypoint information extracted by scale invariant feature transform (SIFT) are incorporated into intensity similarity measure as the body force of viscous fluid model in a Bayesian framework. Experiments were performed on synthetic and clinical ultrasound images of breast and kidney. It is shown that shape and keypoint information significantly improves fluid model for non-rigid registration, especially for alignment of small structure features in accuracy.

  6. A Loudness Model for Time-Varying Sounds Incorporating Binaural Inhibition

    Directory of Open Access Journals (Sweden)

    Brian C. J. Moore

    2016-12-01

    Full Text Available This article describes a model of loudness for time-varying sounds that incorporates the concept of binaural inhibition, namely, that the signal applied to one ear can reduce the internal response to a signal at the other ear. For each ear, the model includes the following: a filter to allow for the effects of transfer of sound through the outer and middle ear; a short-term spectral analysis with greater frequency resolution at low than at high frequencies; calculation of an excitation pattern, representing the magnitudes of the outputs of the auditory filters as a function of center frequency; application of a compressive nonlinearity to the output of each auditory filter; and smoothing over time of the resulting instantaneous specific loudness pattern using an averaging process resembling an automatic gain control. The resulting short-term specific loudness patterns are used to calculate broadly tuned binaural inhibition functions, the amount of inhibition depending on the relative short-term specific loudness at the two ears. The inhibited specific loudness patterns are summed across frequency to give an estimate of the short-term loudness for each ear. The overall short-term loudness is calculated as the sum of the short-term loudness values for the two ears. The long-term loudness for each ear is calculated by smoothing the short-term loudness for that ear, again by a process resembling automatic gain control, and the overall loudness impression is obtained by summing the long-term loudness across ears. The predictions of the model are more accurate than those of an earlier model that did not incorporate binaural inhibition.

  7. A Loudness Model for Time-Varying Sounds Incorporating Binaural Inhibition.

    Science.gov (United States)

    Moore, Brian C J; Glasberg, Brian R; Varathanathan, Ajanth; Schlittenlacher, Josef

    2016-01-01

    This article describes a model of loudness for time-varying sounds that incorporates the concept of binaural inhibition, namely, that the signal applied to one ear can reduce the internal response to a signal at the other ear. For each ear, the model includes the following: a filter to allow for the effects of transfer of sound through the outer and middle ear; a short-term spectral analysis with greater frequency resolution at low than at high frequencies; calculation of an excitation pattern, representing the magnitudes of the outputs of the auditory filters as a function of center frequency; application of a compressive nonlinearity to the output of each auditory filter; and smoothing over time of the resulting instantaneous specific loudness pattern using an averaging process resembling an automatic gain control. The resulting short-term specific loudness patterns are used to calculate broadly tuned binaural inhibition functions, the amount of inhibition depending on the relative short-term specific loudness at the two ears. The inhibited specific loudness patterns are summed across frequency to give an estimate of the short-term loudness for each ear. The overall short-term loudness is calculated as the sum of the short-term loudness values for the two ears. The long-term loudness for each ear is calculated by smoothing the short-term loudness for that ear, again by a process resembling automatic gain control, and the overall loudness impression is obtained by summing the long-term loudness across ears. The predictions of the model are more accurate than those of an earlier model that did not incorporate binaural inhibition.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  10. Tutorial in medical decision modeling incorporating waiting lines and queues using discrete event simulation.

    Science.gov (United States)

    Jahn, Beate; Theurl, Engelbert; Siebert, Uwe; Pfeiffer, Karl-Peter

    2010-01-01

    In most decision-analytic models in health care, it is assumed that there is treatment without delay and availability of all required resources. Therefore, waiting times caused by limited resources and their impact on treatment effects and costs often remain unconsidered. Queuing theory enables mathematical analysis and the derivation of several performance measures of queuing systems. Nevertheless, an analytical approach with closed formulas is not always possible. Therefore, simulation techniques are used to evaluate systems that include queuing or waiting, for example, discrete event simulation. To include queuing in decision-analytic models requires a basic knowledge of queuing theory and of the underlying interrelationships. This tutorial introduces queuing theory. Analysts and decision-makers get an understanding of queue characteristics, modeling features, and its strength. Conceptual issues are covered, but the emphasis is on practical issues like modeling the arrival of patients. The treatment of coronary artery disease with percutaneous coronary intervention including stent placement serves as an illustrative queuing example. Discrete event simulation is applied to explicitly model resource capacities, to incorporate waiting lines and queues in the decision-analytic modeling example.

  11. Benefits of incorporating spatial organisation of catchments for a semi-distributed hydrological model

    Science.gov (United States)

    Schumann, Andreas; Oppel, Henning

    2017-04-01

    To represent the hydrological behaviour of catchments a model should reproduce/reflect the hydrologically most relevant catchment characteristics. These are heterogeneously distributed within a watershed but often interrelated and subject of a certain spatial organisation. Since common models are mostly based on fundamental assumptions about hydrological processes, the reduction of variance of catchment properties as well as the incorporation of the spatial organisation of the catchment is desirable. We have developed a method that combines the idea of the width-function used for determination of the geomorphologic unit hydrograph with information about soil or topography. With this method we are able to assess the spatial organisation of selected catchment characteristics. An algorithm was developed that structures a watershed into sub-basins and other spatial units to minimise its heterogeneity. The outcomes of this algorithm are used for the spatial setup of a semi-distributed model. Since the spatial organisation of a catchment is not bound to a single characteristic, we have to embed information of multiple catchment properties. For this purpose we applied a fuzzy-based method to combine the spatial setup for multiple single characteristics into a union, optimal spatial differentiation. Utilizing this method, we are able to propose a spatial structure for a semi-distributed hydrological model, comprising the definition of sub-basins and a zonal classification within each sub-basin. Besides the improved spatial structuring, the performed analysis ameliorates modelling in another way. The spatial variability of catchment characteristics, which is considered by a minimum of heterogeneity in the zones, can be considered in a parameter constrained calibration scheme in a case study both options were used to explore the benefits of incorporating the spatial organisation and derived parameter constraints for the parametrisation of a HBV-96 model. We use two benchmark

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

    Science.gov (United States)

    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

  13. Overall challenges in incorporating micro-mechanical models into materials design process

    Science.gov (United States)

    Bennoura, M.; Aboutajeddine, A.

    2016-10-01

    Using materials in engineering design has historically been handled using the paradigm of selecting appropriate materials from the finite set of available material databases. Recent trends, however, have moved toward the tailoring of materials that meet the overall system performance requirements, based on a process called material design. An important building block of this process is micromechanical models that relate microstructure to proprieties. Unfortunately, these models remain short and include a lot of uncertainties from assumptions and idealizations, which, unavoidably, impacts material design strategy. In this work, candidate methods to deal with micromechanical models uncertainties and their drawbacks in material design are investigated. Robust design methods for quantifying uncertainty and managing or mitigating its impact on design performances are reviewed first. These methods include principles for classifying uncertainty, mathematical techniques for evaluating its level degree, and design methods for performing and generating design alternatives, that are relatively insensitive to sources of uncertainty and flexible for admitting design changes or variations. The last section of this paper addresses the limits of the existing approaches from material modelling perspective and identifies the research opportunities to overcome the impediment of incorporating micromechanical models in material design process.

  14. Incorporating experimental design and error into coalescent/mutation models of population history.

    Science.gov (United States)

    Knudsen, Bjarne; Miyamoto, Michael M

    2007-08-01

    Coalescent theory provides a powerful framework for estimating the evolutionary, demographic, and genetic parameters of a population from a small sample of individuals. Current coalescent models have largely focused on population genetic factors (e.g., mutation, population growth, and migration) rather than on the effects of experimental design and error. This study develops a new coalescent/mutation model that accounts for unobserved polymorphisms due to missing data, sequence errors, and multiple reads for diploid individuals. The importance of accommodating these effects of experimental design and error is illustrated with evolutionary simulations and a real data set from a population of the California sea hare. In particular, a failure to account for sequence errors can lead to overestimated mutation rates, inflated coalescent times, and inappropriate conclusions about the population. This current model can now serve as a starting point for the development of newer models with additional experimental and population genetic factors. It is currently implemented as a maximum-likelihood method, but this model may also serve as the basis for the development of Bayesian approaches that incorporate experimental design and error.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  17. Incorporating plant fossil data into species distribution models is not straightforward: Pitfalls and possible solutions

    Science.gov (United States)

    Moreno-Amat, Elena; Rubiales, Juan Manuel; Morales-Molino, César; García-Amorena, Ignacio

    2017-08-01

    The increasing development of species distribution models (SDMs) using palaeodata has created new prospects to address questions of evolution, ecology and biogeography from wider perspectives. Palaeobotanical data provide information on the past distribution of taxa at a given time and place and its incorporation on modelling has contributed to advancing the SDM field. This has allowed, for example, to calibrate models under past climate conditions or to validate projected models calibrated on current species distributions. However, these data also bear certain shortcomings when used in SDMs that may hinder the resulting ecological outcomes and eventually lead to misleading conclusions. Palaeodata may not be equivalent to present data, but instead frequently exhibit limitations and biases regarding species representation, taxonomy and chronological control, and their inclusion in SDMs should be carefully assessed. The limitations of palaeobotanical data applied to SDM studies are infrequently discussed and often neglected in the modelling literature; thus, we argue for the more careful selection and control of these data. We encourage authors to use palaeobotanical data in their SDMs studies and for doing so, we propose some recommendations to improve the robustness, reliability and significance of palaeo-SDM analyses.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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. Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily

    Science.gov (United States)

    Lukk, Tiit; Sakai, Ayano; Kalyanaraman, Chakrapani; Brown, Shoshana D.; Imker, Heidi J.; Song, Ling; Fedorov, Alexander A.; Fedorov, Elena V.; Toro, Rafael; Hillerich, Brandan; Seidel, Ronald; Patskovsky, Yury; Vetting, Matthew W.; Nair, Satish K.; Babbitt, Patricia C.; Almo, Steven C.; Gerlt, John A.; Jacobson, Matthew P.

    2012-01-01

    The rapid advance in genome sequencing presents substantial challenges for protein functional assignment, with half or more of new protein sequences inferred from these genomes having uncertain assignments. The assignment of enzyme function in functionally diverse superfamilies represents a particular challenge, which we address through a combination of computational predictions, enzymology, and structural biology. Here we describe the results of a focused investigation of a group of enzymes in the enolase superfamily that are involved in epimerizing dipeptides. The first members of this group to be functionally characterized were Ala-Glu epimerases in Eschericiha coli and Bacillus subtilis, based on the operon context and enzymological studies; these enzymes are presumed to be involved in peptidoglycan recycling. We have subsequently studied more than 65 related enzymes by computational methods, including homology modeling and metabolite docking, which suggested that many would have divergent specificities;, i.e., they are likely to have different (unknown) biological roles. In addition to the Ala-Phe epimerase specificity reported previously, we describe the prediction and experimental verification of: (i) a new group of presumed Ala-Glu epimerases; (ii) several enzymes with specificity for hydrophobic dipeptides, including one from Cytophaga hutchinsonii that epimerizes D-Ala-D-Ala; and (iii) a small group of enzymes that epimerize cationic dipeptides. Crystal structures for certain of these enzymes further elucidate the structural basis of the specificities. The results highlight the potential of computational methods to guide experimental characterization of enzymes in an automated, large-scale fashion. PMID:22392983

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

    Energy Technology Data Exchange (ETDEWEB)

    Tucker, Susan L., E-mail: sltucker@mdanderson.org [Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Li Minghuan [Department of Radiation Oncology, Shandong Cancer Hospital, Jinan, Shandong (China); Xu Ting; Gomez, Daniel [Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Yuan Xianglin [Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan (China); Yu Jinming [Department of Radiation Oncology, Shandong Cancer Hospital, Jinan, Shandong (China); Liu Zhensheng; Yin Ming; Guan Xiaoxiang; Wang Lie; Wei Qingyi [Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Mohan, Radhe [Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Vinogradskiy, Yevgeniy [University of Colorado School of Medicine, Aurora, Colorado (United States); Martel, Mary [Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Liao Zhongxing [Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas (United States)

    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.

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

    Science.gov (United States)

    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. A neural population model incorporating dopaminergic neurotransmission during complex voluntary behaviors.

    Directory of Open Access Journals (Sweden)

    Stefan Fürtinger

    2014-11-01

    Full Text Available Assessing brain activity during complex voluntary motor behaviors that require the recruitment of multiple neural sites is a field of active research. Our current knowledge is primarily based on human brain imaging studies that have clear limitations in terms of temporal and spatial resolution. We developed a physiologically informed non-linear multi-compartment stochastic neural model to simulate functional brain activity coupled with neurotransmitter release during complex voluntary behavior, such as speech production. Due to its state-dependent modulation of neural firing, dopaminergic neurotransmission plays a key role in the organization of functional brain circuits controlling speech and language and thus has been incorporated in our neural population model. A rigorous mathematical proof establishing existence and uniqueness of solutions to the proposed model as well as a computationally efficient strategy to numerically approximate these solutions are presented. Simulated brain activity during the resting state and sentence production was analyzed using functional network connectivity, and graph theoretical techniques were employed to highlight differences between the two conditions. We demonstrate that our model successfully reproduces characteristic changes seen in empirical data between the resting state and speech production, and dopaminergic neurotransmission evokes pronounced changes in modeled functional connectivity by acting on the underlying biological stochastic neural model. Specifically, model and data networks in both speech and rest conditions share task-specific network features: both the simulated and empirical functional connectivity networks show an increase in nodal influence and segregation in speech over the resting state. These commonalities confirm that dopamine is a key neuromodulator of the functional connectome of speech control. Based on reproducible characteristic aspects of empirical data, we suggest a number

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

    Science.gov (United States)

    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

  5. Discrete Software Reliability Growth Modeling for Errors of Different Severity Incorporating Change-point Concept

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Several software reliability growth models (SRGM) have been developed to monitor the reliability growth during the testing phase of software development. In most of the existing research available in the literatures, it is considered that a similar testing effort is required on each debugging effort. However, in practice, different types of faults may require different amounts of testing efforts for their detection and removal. Consequently, faults are classified into three categories on the basis of severity: simple, hard and complex. This categorization may be extended to r type of faults on the basis of severity. Although some existing research in the literatures has incorporated this concept that fault removal rate (FRR) is different for different types of faults, they assume that the FRR remains constant during the overall testing period. On the contrary, it has been observed that as testing progresses, FRR changes due to changing testing strategy, skill, environment and personnel resources. In this paper, a general discrete SRGM is proposed for errors of different severity in software systems using the change-point concept. Then, the models are formulated for two particular environments. The models were validated on two real-life data sets. The results show better fit and wider applicability of the proposed models as to different types of failure datasets.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Li, Zhen; Bian, Xin; Karniadakis, George Em, E-mail: george-karniadakis@brown.edu [Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912 (United States); Li, Xiantao [Department of Mathematics, Pennsylvania State University, University Park, Pennsylvania 16802 (United States)

    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.

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

    Science.gov (United States)

    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.

  10. A Biomimetic Model of the Outer Plexiform Layer by Incorporating Memristive Devices

    CERN Document Server

    Gelencser, Andras; Toumazou, Christofer; Roska, Tamas

    2011-01-01

    In this paper we present a biorealistic model for the first part of the early vision processing by incorporating memristive nanodevices. The architecture of the proposed network is based on the organisation and functioning of the outer plexiform layer (OPL) in the vertebrate retina. We demonstrate that memristive devices are indeed a valuable building block for neuromorphic architectures, as their highly non-linear and adaptive response could be exploited for establishing ultra-dense networks with similar dynamics to their biological counterparts. We particularly show that hexagonal memristive grids can be employed for faithfully emulating the smoothing-effect occurring at the OPL for enhancing the dynamic range of the system. In addition, we employ a memristor-based thresholding scheme for detecting the edges of grayscale images, while the proposed system is also evaluated for its adaptation and fault tolerance capacity against different light or noise conditions as well as distinct device yields.

  11. Incorporating fragmentation and non-native species into distribution models to inform fluvial fish conservation.

    Science.gov (United States)

    Taylor, Andrew T; Papeş, Monica; Long, James M

    2017-09-06

    Fluvial fishes face increased imperilment from anthropogenic activities, but the specific factors contributing most to range declines are often poorly understood. For example, the shoal bass (Micropterus cataractae) is a fluvial-specialist species experiencing continual range loss, yet how perceived threats have contributed to range loss is largely unknown. We employed species distribution models (SDMs) to disentangle which factors are contributing most to shoal bass range loss by estimating a potential distribution based on natural abiotic factors and by estimating a series of current, occupied distributions that also incorporated variables characterizing land cover, non-native species, and fragmentation intensity (no fragmentation, dams only, and dams and large impoundments). Model construction allowed for interspecific relationships between non-native congeners and shoal bass to vary across fragmentation intensities. Results from the potential distribution model estimated shoal bass presence throughout much of their native basin, whereas models of current occupied distribution illustrated increased range loss as fragmentation intensified. Response curves from current occupied models indicated a potential interaction between fragmentation intensity and the relationship between shoal bass and non-native congeners, wherein non-natives may be favored at the highest fragmentation intensity. Response curves also suggested that free-flowing fragment lengths of > 100 km were necessary to support shoal bass presence. Model evaluation, including an independent validation, suggested models had favorable predictive and discriminative abilities. Similar approaches that use readily-available, diverse geospatial datasets may deliver insights into the biology and conservation needs of other fluvial species facing similar threats. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  12. Models for gibberellic acid transport and enzyme production and transport in the aleurone layer of barley.

    Science.gov (United States)

    O'Brien, Ricky; Fowkes, Nev; Bassom, Andrew P

    2010-11-01

    Gibberellins are growth hormones produced in the embryo of grain released during germination. They promote growth through the production of enzymes in the aleurone layer surrounding the endosperm. These enzymes then diffuse into the endosperm and produce the sugars required by the growing acrospire. Here we model the transport of gibberellins into and along the aleurone layer, the consequent production of enzymes, and their transport into the endosperm. Simple approximate solutions of the governing equations are obtained which suggest that the enzymes are released immediately behind a gibberellin front which travels with almost constant speed along the aleurone layer. The model also suggests that this propagation speed is determined primarily by conditions near the scutellum-aleurone junction, which may enable the embryo to actively control the germination process.

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

    Energy Technology Data Exchange (ETDEWEB)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  15. Incorporation of a Wind Generator Model into a Dynamic Power Flow Analysis

    Directory of Open Access Journals (Sweden)

    Angeles-Camacho C.

    2011-07-01

    Full Text Available Wind energy is nowadays one of the most cost-effective and practical options for electric generation from renewable resources. However, increased penetration of wind generation causes the power networks to be more depend on, and vulnerable to, the varying wind speed. Modeling is a tool which can provide valuable information about the interaction between wind farms and the power network to which they are connected. This paper develops a realistic characterization of a wind generator. The wind generator model is incorporated into an algorithm to investigate its contribution to the stability of the power network in the time domain. The tool obtained is termed dynamic power flow. The wind generator model takes on account the wind speed and the reactive power consumption by induction generators. Dynamic power flow analysis is carried-out using real wind data at 10-minute time intervals collected for one meteorological station. The generation injected at one point into the network provides active power locally and is found to reduce global power losses. However, the power supplied is time-varying and causes fluctuations in voltage magnitude and power fl ows in transmission lines.

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

    Science.gov (United States)

    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…

  17. A Numerical Procedure for Model Identifiability Analysis Applied to Enzyme Kinetics

    DEFF Research Database (Denmark)

    Daele, Timothy, Van; Van Hoey, Stijn; Gernaey, Krist;

    2015-01-01

    exercise, thereby bypassing the challenging task of model structure determination and identification. Parameter identification problems can thus lead to ill-calibrated models with low predictive power and large model uncertainty. Every calibration exercise should therefore be precededby a proper model...... and Pronzato (1997) and which can be easily set up for any type of model. In this paper the proposed approach is applied to the forward reaction rate of the enzyme kinetics proposed by Shin and Kim(1998). Structural identifiability analysis showed that no local structural model problems were occurring......The proper calibration of models describing enzyme kinetics can be quite challenging. In the literature, different procedures are available to calibrate these enzymatic models in an efficient way. However, in most cases the model structure is already decided on prior to the actual calibration...

  18. Hydrogenase Enzymes and Their Synthetic Models: The Role of Metal Hydrides.

    Science.gov (United States)

    Schilter, David; Camara, James M; Huynh, Mioy T; Hammes-Schiffer, Sharon; Rauchfuss, Thomas B

    2016-08-10

    Hydrogenase enzymes efficiently process H2 and protons at organometallic FeFe, NiFe, or Fe active sites. Synthetic modeling of the many H2ase states has provided insight into H2ase structure and mechanism, as well as afforded catalysts for the H2 energy vector. Particularly important are hydride-bearing states, with synthetic hydride analogues now known for each hydrogenase class. These hydrides are typically prepared by protonation of low-valent cores. Examples of FeFe and NiFe hydrides derived from H2 have also been prepared. Such chemistry is more developed than mimicry of the redox-inactive monoFe enzyme, although functional models of the latter are now emerging. Advances in physical and theoretical characterization of H2ase enzymes and synthetic models have proven key to the study of hydrides in particular, and will guide modeling efforts toward more robust and active species optimized for practical applications.

  19. Incorporating an extended dendritic growth model into the CAFE model for rapidly solidified non-dilute alloys

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Jie; Wang, Bo [State Key Laboratory of Advanced Special Steel, Shanghai University, Shanghai 200072 (China); Shanghai Engineering Technology Research Center of Special Casting, Shanghai 201605 (China); Zhao, Shunli [Research Institute, Baoshan Iron & Steel Co., Ltd, Shanghai 201900 (China); Wu, Guangxin [State Key Laboratory of Advanced Special Steel, Shanghai University, Shanghai 200072 (China); Shanghai Engineering Technology Research Center of Special Casting, Shanghai 201605 (China); Zhang, Jieyu, E-mail: zjy6162@staff.shu.edu.cn [State Key Laboratory of Advanced Special Steel, Shanghai University, Shanghai 200072 (China); Shanghai Engineering Technology Research Center of Special Casting, Shanghai 201605 (China); Yang, Zhiliang [State Key Laboratory of Advanced Special Steel, Shanghai University, Shanghai 200072 (China); Shanghai Engineering Technology Research Center of Special Casting, Shanghai 201605 (China)

    2016-05-25

    We have extended the dendritic growth model first proposed by Boettinger, Coriell and Trivedi (here termed EBCT) for microstructure simulations of rapidly solidified non-dilute alloys. The temperature-dependent distribution coefficient, obtained from calculations of phase equilibria, and the continuous growth model (CGM) were adopted in the present EBCT model to describe the solute trapping behaviors. The temperature dependence of the physical properties, which were not used in previous dendritic growth models, were also considered in the present EBCT model. These extensions allow the present EBCT model to be used for microstructure simulations of non-dilute alloys. The comparison of the present EBCT model with the BCT model proves that the considerations of the distribution coefficient and physical properties are necessary for microstructure simulations, especially for small particles with high undercoolings. Finally, the EBCT model was incorporated into the cellular automaton-finite element (CAFE) model to simulate microstructures of gas-atomized ASP30 high speed steel particles that were then compared with experimental results. Both the simulated and experimental results reveal that a columnar dendritic microstructure preferentially forms in small particles and an equiaxed microstructure forms otherwise. The applications of the present EBCT model provide a convenient way to predict the microstructure of non-dilute alloys. - Highlights: • A dendritic growth model was developed considering non-equilibrium distribution coefficient. • The physical properties with temperature dependence were considered in the extended model. • The extended model can be used to non-dilute alloys and the extensions are necessary in small particles. • Microstructure of ASP30 steel was investigated using the present model and verified by experiment.

  20. A land use regression model incorporating data on industrial point source pollution

    Institute of Scientific and Technical Information of China (English)

    Li Chen; Yuming Wang; Peiwu Li; Yaqin Ji; Shaofei Kong; Zhiyong Li; Zhipeng Bai

    2012-01-01

    Advancing the understanding of the spatial aspects of air pollution in the city regional environment is an area where improved methods can be of great benefit to exposure assessment and polcy support.We created land use regression (LUR) models for SO2,NO2 and PM10for Tianjin,China.Traffic volumes,road networks,land use data,population density,meteorological conditions,physical conditions and satellite-derived greenness,brightness and wetness were used for predicting SO2,NO2 and PM10 concentrations.We incorporated data on industrial point sources to improve LUR model performance.In order to consider the impact of different sources,we calculated the PSIndex,LSIndex and area of different land use types (agricultural land,industrial land,commercial land,residential land,green space and water area) within different buffer radii (1 to 20 km).This method makes up for the lack of consideration of source impact based on the LUR model.Remote sensing-derived variables were significantly correlated with gaseous pollutant concentrations such as SO2 and NO2.R2 values of the multiple linear regression equations for SO2,NO2 and PM10 were 0.78,0.89 and 0.84,respectively,and the RMSE values were 0.32,0.18 and 0.21,respectively.Model predictions at validation monitoring sites went well with predictions generally within 15% of measured values.Compared to the relationship between dependent variables and simple variables (such as traffic variables or meteorological condition variables),the relationship between dependent variables and integrated variables was more consistent with a linear relationship.Such integration has a discernable influence on both the overall model prediction and health effects assessment on the spatial distribution of air pollution in the city region.

  1. A land use regression model incorporating data on industrial point source pollution.

    Science.gov (United States)

    Chen, Li; Wang, Yuming; Li, Peiwu; Ji, Yaqin; Kong, Shaofei; Li, Zhiyong; Bai, Zhipeng

    2012-01-01

    Advancing the understanding of the spatial aspects of air pollution in the city regional environment is an area where improved methods can be of great benefit to exposure assessment and policy support. We created land use regression (LUR) models for SO2, NO2 and PM10 for Tianjin, China. Traffic volumes, road networks, land use data, population density, meteorological conditions, physical conditions and satellite-derived greenness, brightness and wetness were used for predicting SO2, NO2 and PM10 concentrations. We incorporated data on industrial point sources to improve LUR model performance. In order to consider the impact of different sources, we calculated the PSIndex, LSIndex and area of different land use types (agricultural land, industrial land, commercial land, residential land, green space and water area) within different buffer radii (1 to 20 km). This method makes up for the lack of consideration of source impact based on the LUR model. Remote sensing-derived variables were significantly correlated with gaseous pollutant concentrations such as SO2 and NO2. R2 values of the multiple linear regression equations for SO2, NO2 and PM10 were 0.78, 0.89 and 0.84, respectively, and the RMSE values were 0.32, 0.18 and 0.21, respectively. Model predictions at validation monitoring sites went well with predictions generally within 15% of measured values. Compared to the relationship between dependent variables and simple variables (such as traffic variables or meteorological condition variables), the relationship between dependent variables and integrated variables was more consistent with a linear relationship. Such integration has a discernable influence on both the overall model prediction and health effects assessment on the spatial distribution of air pollution in the city region.

  2. Incorporating food web dynamics into ecological restoration: A modeling approach for river ecosystems

    Science.gov (United States)

    Bellmore, J. Ryan; Benjamin, Joseph R.; Newsom, Michael; Bountry, Jennifer A.; Dombroski, Daniel

    2017-01-01

    Restoration is frequently aimed at the recovery of target species, but also influences the larger food web in which these species participate. Effects of restoration on this broader network of organisms can influence target species both directly and indirectly via changes in energy flow through food webs. To help incorporate these complexities into river restoration planning we constructed a model that links river food web dynamics to in-stream physical habitat and riparian vegetation conditions. We present an application of the model to the Methow River, Washington (USA), a location of on-going restoration aimed at recovering salmon. Three restoration strategies were simulated: riparian vegetation restoration, nutrient augmentation via salmon carcass addition, and side-channel reconnection. We also added populations of nonnative aquatic snails and fish to the modeled food web to explore how changes in food web structure mediate responses to restoration. Simulations suggest that side-channel reconnection may be a better strategy than carcass addition and vegetation planting for improving conditions for salmon in this river segment. However, modeled responses were strongly sensitive to changes in the structure of the food web. The addition of nonnative snails and fish modified pathways of energy through the food web, which negated restoration improvements. This finding illustrates that forecasting responses to restoration may require accounting for the structure of food webs, and that changes in this structure—as might be expected with the spread of invasive species—could compromise restoration outcomes. Unlike habitat-based approaches to restoration assessment that focus on the direct effects of physical habitat conditions on single species of interest, our approach dynamically links the success of target organisms to the success of competitors, predators, and prey. By elucidating the direct and indirect pathways by which restoration affects target species

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

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

    OpenAIRE

    2015-01-01

    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 influe...

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Yanhua Jiang

    2014-09-01

    Full Text Available 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.

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

    Science.gov (United States)

    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

  10. Exciton delocalization incorporated drift-diffusion model for bulk-heterojunction organic solar cells

    Science.gov (United States)

    Wang, Zi Shuai; Sha, Wei E. I.; Choy, Wallace C. H.

    2016-12-01

    Modeling the charge-generation process is highly important to understand device physics and optimize power conversion efficiency of bulk-heterojunction organic solar cells (OSCs). Free carriers are generated by both ultrafast exciton delocalization and slow exciton diffusion and dissociation at the heterojunction interface. In this work, we developed a systematic numerical simulation to describe the charge-generation process by a modified drift-diffusion model. The transport, recombination, and collection of free carriers are incorporated to fully capture the device response. The theoretical results match well with the state-of-the-art high-performance organic solar cells. It is demonstrated that the increase of exciton delocalization ratio reduces the energy loss in the exciton diffusion-dissociation process, and thus, significantly improves the device efficiency, especially for the short-circuit current. By changing the exciton delocalization ratio, OSC performances are comprehensively investigated under the conditions of short-circuit and open-circuit. Particularly, bulk recombination dependent fill factor saturation is unveiled and understood. As a fundamental electrical analysis of the delocalization mechanism, our work is important to understand and optimize the high-performance OSCs.

  11. Building a Better Model: A Personalized Breast Cancer Risk Model Incorporating Breast Density to Stratify Risk and Improve Application of Resources

    Science.gov (United States)

    2015-12-01

    women with a diagnosis of breast cancer from 2003 to 2012 and enrolled in a larger study on MD were evaluated. Operative and pathology reports were...AD______________ AWARD NUMBER: W81XWH-11-1-0545 TITLE: Building a Better Model: A Personalized Breast Cancer Risk Model Incorporating Breast ...Better Model: A Personalized Breast Cancer Risk Model Incorporating Breast Density to Stratify Risk and Improve Application of Resources 5a. CONTRACT

  12. Thiamin diphosphate-dependent enzymes: from enzymology to metabolic regulation, drug design and disease models.

    Science.gov (United States)

    Bunik, Victoria I; Tylicki, Adam; Lukashev, Nikolay V

    2013-12-01

    Bringing a knowledge of enzymology into research in vivo and in situ is of great importance in understanding systems biology and metabolic regulation. The central metabolic significance of thiamin (vitamin B1 ) and its diphosphorylated derivative (thiamin diphosphate; ThDP), and the fundamental differences in the ThDP-dependent enzymes of metabolic networks in mammals versus plants, fungi and bacteria, or in health versus disease, suggest that these enzymes are promising targets for biotechnological and medical applications. Here, the in vivo action of known regulators of ThDP-dependent enzymes, such as synthetic structural analogs of the enzyme substrates and thiamin, is analyzed in light of the enzymological data accumulated during half a century of research. Mimicking the enzyme-specific catalytic intermediates, the phosphonate analogs of 2-oxo acids selectively inhibit particular ThDP-dependent enzymes. Because of their selectivity, use of these compounds in cellular and animal models of ThDP-dependent enzyme malfunctions improves the validity of the model and its predictive power when compared with the nonselective and enzymatically less characterized oxythiamin and pyrithiamin. In vitro studies of the interaction of thiamin analogs and their biological derivatives with potential in vivo targets are necessary to identify and attenuate the analog selectivity. For both the substrate and thiamin synthetic analogs, in vitro reactivities with potential targets are highly relevant in vivo. However, effective concentrations in vivo are often higher than in vitro studies would suggest. The significance of specific inihibition of the ThDP-dependent enzymes for the development of herbicides, antibiotics, anticancer and neuroprotective strategies is discussed.

  13. Mathematical Modeling of Biosensors Based on an Array of Enzyme Microreactors

    Directory of Open Access Journals (Sweden)

    Juozas Kulys

    2006-04-01

    Full Text Available This paper presents a two-dimensional-in-space mathematical model ofbiosensors based on an array of enzyme microreactors immobilised on a single electrode.The modeling system acts under amperometric conditions. The microreactors were modeledby particles and by strips. The model is based on the diffusion equations containing a non-linear term related to the Michaelis-Menten kinetics of the enzymatic reaction. The modelinvolves three regions: an array of enzyme microreactors where enzyme reaction as well asmass transport by diffusion takes place, a diffusion limiting region where only the diffusiontakes place, and a convective region, where the analyte concentration is maintained constant.Using computer simulation, the influence of the geometry of the microreactors and of thediffusion region on the biosensor response was investigated. The digital simulation wascarried out using the finite difference technique.

  14. Vibrational spectroscopy modeling of a drug in molecular solvents and enzymes

    Science.gov (United States)

    Devereux, Christian J.; Fulfer, Kristen D.; Zhang, Xiaoliu; Kuroda, Daniel G.

    2017-09-01

    Modeling of drugs in enzymes is of immensurable value to many areas of science. We present a theoretical study on the vibrational spectroscopy of Rilpivirine, a HIV reverse transcriptase inhibitor, in conventional solvents and in clinically relevant enzymes. The study is based on vibrational spectroscopy modeling of the drug using molecular dynamics simulations, DFT frequency maps, and theory. The modeling of the infrared lineshape shows good agreement with experimental data for the drug in molecular solvents where the local environment motions define the vibrational band lineshape. On the other hand, the theoretical description of the drug in the different enzymes does not match previous experimental findings indicating that the utilized methodology might not apply to heterogeneous environments. Our findings show that the lack of reproducibility might be associated with the development of the frequency map which does not contain all of the possible interactions observed in such systems.

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

    Science.gov (United States)

    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.

  16. A coarse-grained model for synergistic action of multiple enzymes on cellulose

    Directory of Open Access Journals (Sweden)

    Asztalos Andrea

    2012-08-01

    Full Text Available Abstract Background Degradation of cellulose to glucose requires the cooperative action of three classes of enzymes, collectively known as cellulases. Endoglucanases randomly bind to cellulose surfaces and generate new chain ends by hydrolyzing β-1,4-D-glycosidic bonds. Exoglucanases bind to free chain ends and hydrolyze glycosidic bonds in a processive manner releasing cellobiose units. Then, β-glucosidases hydrolyze soluble cellobiose to glucose. Optimal synergistic action of these enzymes is essential for efficient digestion of cellulose. Experiments show that as hydrolysis proceeds and the cellulose substrate becomes more heterogeneous, the overall degradation slows down. As catalysis occurs on the surface of crystalline cellulose, several factors affect the overall hydrolysis. Therefore, spatial models of cellulose degradation must capture effects such as enzyme crowding and surface heterogeneity, which have been shown to lead to a reduction in hydrolysis rates. Results We present a coarse-grained stochastic model for capturing the key events associated with the enzymatic degradation of cellulose at the mesoscopic level. This functional model accounts for the mobility and action of a single cellulase enzyme as well as the synergy of multiple endo- and exo-cellulases on a cellulose surface. The quantitative description of cellulose degradation is calculated on a spatial model by including free and bound states of both endo- and exo-cellulases with explicit reactive surface terms (e.g., hydrogen bond breaking, covalent bond cleavages and corresponding reaction rates. The dynamical evolution of the system is simulated by including physical interactions between cellulases and cellulose. Conclusions Our coarse-grained model reproduces the qualitative behavior of endoglucanases and exoglucanases by accounting for the spatial heterogeneity of the cellulose surface as well as other spatial factors such as enzyme crowding. Importantly, it captures

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

    Science.gov (United States)

    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…

  18. Using a cognitive architecture in educational and recreational games : How to incorporate a model in your App

    NARCIS (Netherlands)

    Taatgen, Niels A.; de Weerd, Harmen; Reitter, David; Ritter, Frank

    2016-01-01

    We present a Swift re-implementation of the ACT-R cognitive architecture, which can be used to quickly build iOS Apps that incorporate an ACT-R model as a core feature. We discuss how this implementation can be used in an example model, and explore the breadth of possibilities by presenting six Apps

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

    Science.gov (United States)

    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…

  20. A Fault-Cored Anticline Boundary Element Model Incorporating the Combined Fault Slip and Buckling Mechanisms

    Directory of Open Access Journals (Sweden)

    Wen-Jeng Huang

    2016-02-01

    Full Text Available We develop a folding boundary element model in a medium containing a fault and elastic layers to show that anticlines growing over slipping reverse faults can be significantly amplified by mechanical layering buckling under horizontal shortening. Previous studies suggested that folds over blind reverse faults grow primarily during deformation increments associated with slips on the fault during and immediately after earthquakes. Under this assumption, the potential for earthquakes on blind faults can be determined directly from fold geometry because the amount of slip on the fault can be estimated directly from the fold geometry using the solution for a dislocation in an elastic half-space. Studies that assume folds grown solely by slip on a fault may therefore significantly overestimate fault slip. Our boundary element technique demonstrates that the fold amplitude produced in a medium containing a fault and elastic layers with free slip and subjected to layer-parallel shortening can grow to more than twice the fold amplitude produced in homogeneous media without mechanical layering under the same amount of shortening. In addition, the fold wavelengths produced by the combined fault slip and buckling mechanisms may be narrower than folds produced by fault slip in an elastic half space by a factor of two. We also show that subsurface fold geometry of the Kettleman Hills Anticline in Central California inferred from seismic reflection image is consistent with a model that incorporates layer buckling over a dipping, blind reverse fault and the coseismic uplift pattern produced during a 1985 earthquake centered over the anticline forelimb is predicted by the model.

  1. Investigations of the efficiency of enzyme production technologies using modelling tools

    DEFF Research Database (Denmark)

    Albæk, Mads Orla; Gernaey, Krist; Hansen, Morten Skov

    Growing markets and new innovative applications of industrial enzymes leads to increased interest in efficient production of these products. Most industrial enzymes are currently produced in traditional stirred tank reactors in submerged fed batch culture. The limiting parameter in such processes...... fermentations of the filamentous fungus Trichoderma reesei in 550litre pilot scale stirred tank reactors for a range of process conditions. Based on the experimental data a process model has been created, which satisfactory simulates the effect of the changing process conditions: Aeration rate, agitation speed...... and head space pressure. Examples of simulation results and outlines of the future uses of the model will be given....

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

    Science.gov (United States)

    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.

  3. A diagnostic model incorporating P50 sensory gating and neuropsychological tests for schizophrenia.

    Directory of Open Access Journals (Sweden)

    Jia-Chi Shan

    Full Text Available OBJECTIVES: Endophenotypes in schizophrenia research is a contemporary approach to studying this heterogeneous mental illness, and several candidate neurophysiological markers (e.g. P50 sensory gating and neuropsychological tests (e.g. Continuous Performance Test (CPT and Wisconsin Card Sorting Test (WCST have been proposed. However, the clinical utility of a single marker appears to be limited. In the present study, we aimed to construct a diagnostic model incorporating P50 sensory gating with other neuropsychological tests in order to improve the clinical utility. METHODS: We recruited clinically stable outpatients meeting DSM-IV criteria of schizophrenia and age- and gender-matched healthy controls. Participants underwent P50 sensory gating experimental sessions and batteries of neuropsychological tests, including CPT, WCST and Wechsler Adult Intelligence Scale Third Edition (WAIS-III. RESULTS: A total of 106 schizophrenia patients and 74 healthy controls were enrolled. Compared with healthy controls, the patient group had significantly a larger S2 amplitude, and thus poorer P50 gating ratio (gating ratio = S2/S1. In addition, schizophrenia patients had a poorer performance on neuropsychological tests. We then developed a diagnostic model by using multivariable logistic regression analysis to differentiate patients from healthy controls. The final model included the following covariates: abnormal P50 gating (defined as P50 gating ratio >0.4, three subscales derived from the WAIS-III (Arithmetic, Block Design, and Performance IQ, sensitivity index from CPT and smoking status. This model had an adequate accuracy (concordant percentage = 90.4%; c-statistic = 0.904; Hosmer-Lemeshow Goodness-of-Fit Test, p = 0.64>0.05. CONCLUSION: To the best of our knowledge, this is the largest study to date using P50 sensory gating in subjects of Chinese ethnicity and the first to use P50 sensory gating along with other neuropsychological tests

  4. Bayesian hierarchical models for network meta-analysis incorporating nonignorable missingness.

    Science.gov (United States)

    Zhang, Jing; Chu, Haitao; Hong, Hwanhee; Virnig, Beth A; Carlin, Bradley P

    2015-07-28

    Network meta-analysis expands the scope of a conventional pairwise meta-analysis to simultaneously compare multiple treatments, synthesizing both direct and indirect information and thus strengthening inference. Since most of trials only compare two treatments, a typical data set in a network meta-analysis managed as a trial-by-treatment matrix is extremely sparse, like an incomplete block structure with significant missing data. Zhang et al. proposed an arm-based method accounting for correlations among different treatments within the same trial and assuming that absent arms are missing at random. However, in randomized controlled trials, nonignorable missingness or missingness not at random may occur due to deliberate choices of treatments at the design stage. In addition, those undertaking a network meta-analysis may selectively choose treatments to include in the analysis, which may also lead to missingness not at random. In this paper, we extend our previous work to incorporate missingness not at random using selection models. The proposed method is then applied to two network meta-analyses and evaluated through extensive simulation studies. We also provide comprehensive comparisons of a commonly used contrast-based method and the arm-based method via simulations in a technical appendix under missing completely at random and missing at random.

  5. Incorporating organizational factors into probabilistic safety assessment of nuclear power plants through canonical probabilistic models

    Energy Technology Data Exchange (ETDEWEB)

    Galan, S.F. [Dpto. de Inteligencia Artificial, E.T.S.I. Informatica (UNED), Juan del Rosal, 16, 28040 Madrid (Spain)]. E-mail: seve@dia.uned.es; Mosleh, A. [2100A Marie Mount Hall, Materials and Nuclear Engineering Department, University of Maryland, College Park, MD 20742 (United States)]. E-mail: mosleh@umd.edu; Izquierdo, J.M. [Area de Modelado y Simulacion, Consejo de Seguridad Nuclear, Justo Dorado, 11, 28040 Madrid (Spain)]. E-mail: jmir@csn.es

    2007-08-15

    The {omega}-factor approach is a method that explicitly incorporates organizational factors into Probabilistic safety assessment of nuclear power plants. Bayesian networks (BNs) are the underlying formalism used in this approach. They have a structural part formed by a graph whose nodes represent organizational variables, and a parametric part that consists of conditional probabilities, each of them quantifying organizational influences between one variable and its parents in the graph. The aim of this paper is twofold. First, we discuss some important limitations of current procedures in the {omega}-factor approach for either assessing conditional probabilities from experts or estimating them from data. We illustrate the discussion with an example that uses data from Licensee Events Reports of nuclear power plants for the estimation task. Second, we introduce significant improvements in the way BNs for the {omega}-factor approach can be constructed, so that parameter acquisition becomes easier and more intuitive. The improvements are based on the use of noisy-OR gates as model of multicausal interaction between each BN node and its parents.

  6. Conformational preferences of proline derivatives incorporated into vasopressin analogues: NMR and molecular modelling studies.

    Science.gov (United States)

    Sikorska, Emilia; Sobolewski, Dariusz; Kwiatkowska, Anna

    2012-04-01

    In this study, arginine vasopressin analogues modified with proline derivatives - indoline-2-carboxylic acid (Ica), (2S,4R)-4-(naphthalene-2-ylmethyl)pyrrolidine-2-carboxylic acid (Nmp), (2S,4S)-4-aminopyroglutamic acid (APy) and (2R,4S)-4-aminopyroglutamic acid, (Apy) - were examined using NMR spectroscopy and molecular modelling methods. The results have shown that Ica is involved in the formation of the cis peptide bond. Moreover, it reduces to a great extent the conformational flexibility of the peptide. In turn, incorporation of (2S,4R)-Nmp stabilizes the backbone conformation, which is heavily influenced by the pyrrolidine ring. However, the aromatic part of the Nmp side chain exhibits a high degree of conformational freedom. With analogues IV and V, introduction of the 4-aminopyroglumatic acid reduces locally conformational space of the peptides, but it also results in weaker interactions with the dodecylphosphocholine/sodium dodecyl sulphate micelle. Admittedly, both analogues are adsorbed on the micelle's surface but they do not penetrate into its core. With analogue V, the interactions between the peptide and the micelle seem to be so weak that conformational equilibrium is established between different bound states.

  7. Elastic Properties of Natural Sea Surface Films Incorporated with Solid Dust Particles: Model Baltic Sea Studies

    Directory of Open Access Journals (Sweden)

    Adriana Z. Mazurek

    2012-01-01

    Full Text Available Floating dust-originated solid particles at air-water interfaces will interact with one another and disturb the smoothness of such a composite surface affecting its dilational elasticity. To quantify the effect, surface pressure (Π versus film area (A isotherm, and stress-relaxation (Π-time measurements were performed for monoparticulate layers of the model hydrophobic material (of μm-diameter and differentiated hydrophobicity corresponding to the water contact angles (CA ranging from 60 to 140° deposited at surfaces of surfactant-containing original seawater and were studied with a Langmuir trough system. The composite surface dilational modulus predicted from the theoretical approach, in which natural dust load signatures (particle number flux, daily deposition rate, and diameter spectra originated from in situ field studies performed along Baltic Sea near-shore line stations, agreed well with the direct experimentally derived data. The presence of seawater surfactants affected wettability of the solid material which was evaluated with different CA techniques applicable to powdered samples. Surface energetics of the particle-subphase interactions was expressed in terms of the particle removal energy, contact cross-sectional areas, collapse energies, and so forth. The hydrophobic particles incorporation at a sea surface film structure increased the elasticity modulus by a factor K (1.29–1.58. The particle-covered seawater revealed a viscoelastic behavior with the characteristic relaxation times ranging from 2.6 to 68.5 sec.

  8. A generalized cellular automata approach to modeling first order enzyme kinetics

    Indian Academy of Sciences (India)

    Abhishek Dutta; Saurajyoti Kar; Advait Apte; Ingmar Nopens; Denis Constales

    2015-04-01

    Biochemical processes occur through intermediate steps which are associated with the formation of reaction complexes. These enzyme-catalyzed biochemical reactions are inhibited in a number of ways such as inhibitors competing for the binding site directly, inhibitors deforming the allosteric site or inhibitors changing the structure of active substrate. Using an in silico approach, the concentration of various reaction agents can be monitored at every single time step, which are otherwise difficult to analyze experimentally. Cell-based models with discrete state variables, such as Cellular Automata (CA) provide an understanding of the organizational principles of interacting cellular systems to link the individual cell (microscopic) dynamics wit a particular collective (macroscopic) phenomenon. In this study, a CA model representing a first order enzyme kinetics with inhibitor activity is formulated. The framework of enzyme reaction rules described in this study is probabilistic. An extended von Neumann neighborhood with periodic boundary condition is implemented on a two-dimensional (2D) lattice framework. The effect of lattice-size variation is studied followed by a sensitivity analysis of the model output to the probabilistic parameters which represent various kinetic reaction constants in the enzyme kinetic model. This provides a deeper insight into the sensitivity of the CA model to these parameters. It is observed that cellular automata can capture the essential features of a discrete real system, consisting of space, time and state, structured with simple local rules without making complex implementations but resulting in complex but explainable patterns.

  9. Incorporating Geological Effects in Modeling of Revegetation Strategies for Salt-Affected Landscapes.

    Science.gov (United States)

    Clarke; Bell; Hobbs; George

    1999-07-01

    / This paper synthesizes results of research into the impact that major faults have on dryland salinity and the development of revegetation treatments in the wheatbelt of Western Australia. Currently, landscape planning does not routinely incorporate geology, but this research shows that faults can have a dramatic impact on land and stream salinization and on the effectiveness of revegetation treatments, and evidence exists that other geological features can have a similar influence. This research shows that faults can be identified from airborne magnetic data, they can be assigned a characteristic hydraulic conductivity based on simple borehole tests, and four other geological features that are expected to affect land and stream salinity could be identified in airborne geophysical data. A geological theme map could then be created to which characteristic hydraulic conductivities could be assigned for use in computer groundwater models to improve prediction of the effectiveness of revegetation treatments and thus enhance the landscape planning process. The work highlights the difficulties of using standard sampling and statistical techniques to investigate regional phenomena and presents an integrated approach combining small-scale sampling with broad-scale observations to provide input into a modeling exercise. It is suggested that such approaches are vital if landscape- and regional-scale processes are to be understood and managed. The way in which the problem is perceived (holistically or piecemeal) affects the way treatments are designed and their effectiveness: past approaches have failed to integrate the various scales and processes involved. Effective solutions require an integrated holistic response.KEY WORDS: Dryland salinity; Geology; Landscape; Revegetation integrationhttp://link.springer-ny.com/link/service/journals/00267/bibs/24n1p99.html

  10. Modelling in situ enzyme potential of soils: a tool to predict soil respiration from agricultural fields

    Science.gov (United States)

    Shahbaz Ali, Rana; Poll, Christian; Demyan, Scott; Nkwain Funkuin, Yvonne; Ingwersen, Joachim; Wizemann, Hans-Dieter; Kandeler, Ellen

    2014-05-01

    The fate of soil organic carbon (SOC) is one of the largest uncertainties in predicting future climate and terrestrial ecosystem functions. Extra-cellular enzymes, produced by microorganisms, perform the very first step in SOC degradation and serve as key components in global carbon cycling. Very little information is available about the seasonal variation in the temperature sensitivity of soil enzymes. Here we aim to model in situ enzyme potentials involved in the degradation of either labile or recalcitrant organic compounds to understand the temporal variability of degradation processes. To identify the similarities in seasonal patterns of soil respiration and in situ enzyme potentials, we compared the modelled in situ enzyme activities with weekly measured soil CO2 emissions. Arable soil samples from two different treatments (4 years fallow and currently vegetated plots; treatments represent range of carbon input into soil) were collected every month from April, 2012 to April, 2013, from two different study regions (Kraichgau and Swabian Alb) in Southwest Germany. The vegetation plots were under crop rotation in both study areas. We measured activities of three enzymes including β-glucosidase, xylanase and phenoloxidase at five different temperatures. We also measured soil microbial biomass in form of microbial carbon (Cmic). Land-use and area had significant effects (P < 0.001) on the microbial biomass; fallow plots having less Cmic than vegetation plots. Potential activities of β-glucosidase (P < 0.001) and xylanase (P < 0.01) were significantly higher in the vegetation plots of the Swabian Alb region than in the Kraichgau region. In both study areas, enzyme activities were higher during vegetation period and lower during winter which points to the importance of carbon input and/or temperature and soil moisture. We calculated the temperature sensitivity (Q10) of enzyme activities based on laboratory measurements of enzyme activities at a range of incubation

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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 ...

  13. Evaluation of the energy efficiency of enzyme fermentation by mechanistic modeling

    DEFF Research Database (Denmark)

    Albaek, Mads O.; Gernaey, Krist V.; Hansen, Morten S.

    2012-01-01

    Modeling biotechnological processes is key to obtaining increased productivity and efficiency. Particularly crucial to successful modeling of such systems is the coupling of the physical transport phenomena and the biological activity in one model. We have applied a model for the expression...... prediction. At different rates of agitation and aeration as well as headspace pressure, we can predict the energy efficiency of oxygen transfer, a key process parameter for economical production of industrial enzymes. An inverse relationship between the productivity and energy efficiency of the process...... was found. This modeling approach can be used by manufacturers to evaluate the enzyme fermentation process for a range of different process conditions with regard to energy efficiency....

  14. A model-based framework for design of intensified enzyme-based processes

    DEFF Research Database (Denmark)

    Román-Martinez, Alicia

    This thesis presents a generic and systematic model-based framework to design intensified enzyme-based processes. The development of the presented methodology was motivated by the needs of the bio-based industry for a more systematic approach to achieve intensification in its production plants wi...

  15. Discrimination among eight modified michaelis-menten kinetics models of cellulose hydrolysis with a large range of substrate/enzyme ratios: inhibition by cellobiose.

    Science.gov (United States)

    Bezerra, Rui M F; Dias, Albino A

    2004-03-01

    The kinetics of exoglucanase (Cel7A) from Trichoderma reesei was investigated in the presence of cellobiose and 24 different enzyme/Avicel ratios for 47 h, in order to establish which of the eight available kinetic models best explained the factors involved. The heterogeneous catalysis was studied and the kinetic parameters were estimated employing integrated forms of Michaelis-Menten equations through the use of nonlinear least squares. It was found that cellulose hydrolysis follows a model that takes into account competitive inhibition by cellobiose (final product) with the following parameters: Km = 3.8 mM, Kic = 0.041 mM, kcat = 2 h-1 (5.6 x 10-4 s-1). Other models, such as mixed type inhibition and those incorporating improvements concerning inhibition by substrate and parabolic inhibition, increased the modulation performance very slightly. The results support the hypothesis that nonproductive enzyme substrate complexes, parabolic inhibition, and enzyme inactivation (Selwyn test) are not the principal constraints in enzymatic cellulose hydrolysis. Under our conditions, the increment in hydrolysis was not significant for substrate/enzyme ratios <6.5.

  16. Enzymatic hydration activity assessed by selective spectrophotometric detection of alcohols: a novel screening assay using oleate hydratase as a model enzyme.

    Science.gov (United States)

    Hiseni, Aida; Medici, Rosario; Arends, Isabel W C E; Otten, Linda G

    2014-06-01

    Hydroxy fatty acids (HFAs) are high-added-value compounds, which are incorporated in polymers, lubricants, emulsifiers and stabilizers and have potential medicinal use. In nature, HFAs are regio-specifically synthesized by several enzymes, including P450 monooxygenases, lipoxygenases, hydratases, 12-hydroxylases, and diol synthases. The growing demand for HFAs warrants the development of simple and efficient analytical methods that enable high-throughput detection of the hydroxylated product in the presence of its unsaturated precursor. Herein a novel high-throughput assay for the detection of alcohols is described using oleate hydratase (OHase, EC 4.2.1.53) from Elizabethkingia meningoseptica as the model enzyme. The developed assay is based on the selective spectrophotometric detection of alkyl nitrites formed upon the reaction between the hydroxyl group and nitrous acid. The assay proved to discriminate between unsaturated fatty acids as well as small cyclic and acyclic unsaturated alkenes and their corresponding alcohols. Lower detection limits were 1.5-3 mM with excellent Z'-factors. Enzymatic reactions using OHase with oleic acid resulted in somewhat lower Z-factors for various enzyme preparations. This small scale assay can enable fast discovery of new microorganisms or improved enzymes from mutant libraries and will be useful for biocatalytic strategies involving fatty acid (de)hydrating enzymes.

  17. A passive movement method for parameter estimation of a musculo-skeletal arm model incorporating a modified hill muscle model.

    Science.gov (United States)

    Yu, Tung Fai; Wilson, Adrian J

    2014-05-01

    In this paper we present an experimental method of parameterising the passive mechanical characteristics of the bicep and tricep muscles in vivo, by fitting the dynamics of a two muscle arm model incorporating anatomically meaningful and structurally identifiable modified Hill muscle models to measured elbow movements. Measurements of the passive flexion and extension of the elbow joint were obtained using 3D motion capture, from which the elbow angle trajectories were determined and used to obtain the spring constants and damping coefficients in the model through parameter estimation. Four healthy subjects were used in the experiments. Anatomical lengths and moment of inertia values of the subjects were determined by direct measurement and calculation. There was good reproducibility in the measured arm movement between trials, and similar joint angle trajectory characteristics were seen between subjects. Each subject had their own set of fitted parameter values determined and the results showed good agreement between measured and simulated data. The average fitted muscle parallel spring constant across all subjects was 143 N/m and the average fitted muscle parallel damping constant was 1.73 Ns/m. The passive movement method was proven to be successful, and can be applied to other joints in the human body, where muscles with similar actions are grouped together. Copyright © 2013 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

  18. Modeling the Interaction between β-Amyloid Aggregates and Choline Acetyltransferase Activity and Its Relation with Cholinergic Dysfunction through Two-Enzyme/Two-Compartment Model

    Directory of Open Access Journals (Sweden)

    Hedia Fgaier

    2015-01-01

    Full Text Available The effect of β-amyloid aggregates on activity of choline acetyltransferase (ChAT which is responsible for synthesizing acetylcholine (ACh in human brain is investigated through the two-enzyme/two-compartment (2E2C model where the presynaptic neuron is considered as compartment 1 while both the synaptic cleft and the postsynaptic neuron are considered as compartment 2 through suggesting three different kinetic mechanisms for the inhibition effect. It is found that the incorporation of ChAT inhibition by β-amyloid aggregates into the 2E2C model is able to yield dynamic solutions for concentrations of generated β-amyloid, ACh, choline, acetate, and pH in addition to the rates of ACh synthesis and ACh hydrolysis in compartments 1 and 2. It is observed that ChAT activity needs a high concentration of β-amyloid aggregates production rate. It is found that ChAT activity is reduced significantly when neurons are exposed to high levels of β-amyloid aggregates leading to reduction in levels of ACh which is one of the most significant physiological symptoms of AD. Furthermore, the system of ACh neurocycle is dominated by the oscillatory behavior when ChAT enzyme is completely inhibited by β-amyloid. It is observed that the direct inactivation of ChAT by β-amyloid aggregates may be a probable mechanism contributing to the development of AD.

  19. A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosis

    Directory of Open Access Journals (Sweden)

    Reifman Jaques

    2009-09-01

    Full Text Available Abstract Background Because metabolism is fundamental in sustaining microbial life, drugs that target pathogen-specific metabolic enzymes and pathways can be very effective. In particular, the metabolic challenges faced by intracellular pathogens, such as Mycobacterium tuberculosis, residing in the infected host provide novel opportunities for therapeutic intervention. Results We developed a mathematical framework to simulate the effects on the growth of a pathogen when enzymes in its metabolic pathways are inhibited. Combining detailed models of enzyme kinetics, a complete metabolic network description as modeled by flux balance analysis, and a dynamic cell population growth model, we quantitatively modeled and predicted the dose-response of the 3-nitropropionate inhibitor on the growth of M. tuberculosis in a medium whose carbon source was restricted to fatty acids, and that of the 5'-O-(N-salicylsulfamoyl adenosine inhibitor in a medium with low-iron concentration. Conclusion The predicted results quantitatively reproduced the experimentally measured dose-response curves, ranging over three orders of magnitude in inhibitor concentration. Thus, by allowing for detailed specifications of the underlying enzymatic kinetics, metabolic reactions/constraints, and growth media, our model captured the essential chemical and biological factors that determine the effects of drug inhibition on in vitro growth of M. tuberculosis cells.

  20. Homology modeling and functional sites prediction of azoreductase enzyme from the cyanobacterium Nostoc sp. PCC7120.

    Science.gov (United States)

    Devi, Philem Priyadarshini; Adhikari, Samrat

    2012-12-01

    Industrial dyes such as azodyes are potential environmental pollutants causing deleterious health hazards complications. These dyes are potentially degraded by azoreductase enzyme which is widely distributed in bacteria and also cyanobacteria. The azoreductase enzymes from cyanobacteria have not been explored in detail. Hence this enzyme from Nostoc sp. PCC 7120 has been addressed in detail in the present study considering to explore the physico-chemical properties, evolutionary relationships, functional sites and structural properties using various bioinformatics tools. Four conserved regions were obtained from the multiple sequence analysis. The multiple sequence alignment showed conserved regions at different stretches from 1-11, 40-57, 82-120 and 161-177 amino acid residues. These regions could be used for designing degenerate primers or probes for PCR-based amplification or hybridization-based detection of azoreductase sequences from different source organisms. Domain analysis and functional site prediction showed the presence of functional sites and domain such as flavodoxin like fold responsible for enzyme activity. 3D model was constructed and the best model was selected and validated. Superimposition of the final structure and the template showed variations in certain regions which might be involved in the accommodation of various dyes. Our results may be helpful for further investigations like docking studies as well as in vivo and in vitro conditions although these predictions still need to be studied.

  1. 76 FR 66617 - Airworthiness Directives; Erickson Air-Crane Incorporated Model S-64F Helicopters

    Science.gov (United States)

    2011-10-27

    ...-026-AD; Amendment 39-16835; AD 2011-21-12] RIN 2120-AA64 Airworthiness Directives; Erickson Air-Crane.... SUMMARY: We are adopting a new airworthiness directive (AD) for the Erickson Air-Crane (Erickson Air-Crane..., 2011. ADDRESSES: For service information identified in this AD, contact Erickson Air-Crane Incorporated...

  2. Incorporating food web dynamics into ecological restoration: a modeling approach for river ecosystems

    Science.gov (United States)

    J. Ryan Bellmore; Joseph R. Benjamin; Michael Newsom; Jennifer A. Bountry; Daniel Dombroski

    2017-01-01

    Restoration is frequently aimed at the recovery of target species, but also influences the larger food web in which these species participate. Effects of restoration on this broader network of organisms can influence target species both directly and indirectly via changes in energy flow through food webs. To help incorporate these complexities into river restoration...

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

    Science.gov (United States)

    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…

  4. Stabilized enzymes in continuous gas phase reactions

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Fangxiao; LeJeune, K.; Yang, Zhen [Univ. of Pittsburgh, PA (United States)] [and others

    1995-12-01

    We are assessing the utility of enzymes to catalyze reactions in a continuous gas phase reactor. First, alcohol dehydrogenase has been used to oxidize an unsaturated alcohol, 3-methyl-2-buten-1-ol (UOL), to the corresponding unsaturated aldehyde, 3-methyl-2-butenal (UAL). Cofactor NAD{sup +} was regenerated by concomitant acetone reduction to isopropyl alcohol. Second, organophosphorus hydrolase (OPH) has been used to hydrolyze pesticide vapors. In order to control enzyme hydration level, enzyme water adsorption isotherms at different temperature have been studied. Huttig`s isotherm model has been found suitable to describe adsorption behavior. The influence of enzyme hydration level, enzyme loading on glass beads, reaction temperature and flow rate on enzymatic reaction rate and biocatalyst stability were investigated. Reaction kinetics were studied and a kinetic model was proposed. We will also report our attempts to further stabilize enzymes for use in gas reactions by incorporating them into polymer matrices.

  5. Student Collaboration in a Series of Integrated Experiments to Study Enzyme Reactor Modeling with Immobilized Cell-Based Invertase

    Science.gov (United States)

    Taipa, M. A^ngela; Azevedo, Ana M.; Grilo, Anto´nio L.; Couto, Pedro T.; Ferreira, Filipe A. G.; Fortuna, Ana R. M.; Pinto, Ine^s F.; Santos, Rafael M.; Santos, Susana B.

    2015-01-01

    An integrative laboratory study addressing fundamentals of enzyme catalysis and their application to reactors operation and modeling is presented. Invertase, a ß-fructofuranosidase that catalyses the hydrolysis of sucrose, is used as the model enzyme at optimal conditions (pH 4.5 and 45 °C). The experimental work involves 3 h of laboratory time…

  6. New types of experimental data shape the use of enzyme kinetics for dynamic network modeling.

    Science.gov (United States)

    Tummler, Katja; Lubitz, Timo; Schelker, Max; Klipp, Edda

    2014-01-01

    Since the publication of Leonor Michaelis and Maude Menten's paper on the reaction kinetics of the enzyme invertase in 1913, molecular biology has evolved tremendously. New measurement techniques allow in vivo characterization of the whole genome, proteome or transcriptome of cells, whereas the classical enzyme essay only allows determination of the two Michaelis-Menten parameters V and K(m). Nevertheless, Michaelis-Menten kinetics are still commonly used, not only in the in vitro context of enzyme characterization but also as a rate law for enzymatic reactions in larger biochemical reaction networks. In this review, we give an overview of the historical development of kinetic rate laws originating from Michaelis-Menten kinetics over the past 100 years. Furthermore, we briefly summarize the experimental techniques used for the characterization of enzymes, and discuss web resources that systematically store kinetic parameters and related information. Finally, describe the novel opportunities that arise from using these data in dynamic mathematical modeling. In this framework, traditional in vitro approaches may be combined with modern genome-scale measurements to foster thorough understanding of the underlying complex mechanisms.

  7. Repeated oral dosing of TAS-102 confers high trifluridine incorporation into DNA and sustained antitumor activity in mouse models.

    Science.gov (United States)

    Tanaka, Nozomu; Sakamoto, Kazuki; Okabe, Hiroyuki; Fujioka, Akio; Yamamura, Keisuke; Nakagawa, Fumio; Nagase, Hideki; Yokogawa, Tatsushi; Oguchi, Kei; Ishida, Keiji; Osada, Akiko; Kazuno, Hiromi; Yamada, Yukari; Matsuo, Kenichi

    2014-12-01

    TAS-102 is a novel oral nucleoside antitumor agent containing trifluridine (FTD) and tipiracil hydrochloride (TPI). The compound improves overall survival of colorectal cancer (CRC) patients who are insensitive to standard chemotherapies. FTD possesses direct antitumor activity since it inhibits thymidylate synthase (TS) and is itself incorporated into DNA. However, the precise mechanisms underlying the incorporation into DNA and the inhibition of TS remain unclear. We found that FTD-dependent inhibition of TS was similar to that elicited by fluorodeoxyuridine (FdUrd), another clinically used nucleoside analog. However, washout experiments revealed that FTD-dependent inhibition of TS declined rapidly, whereas FdUrd activity persisted. The incorporation of FTD into DNA was significantly higher than that of other antitumor nucleosides. Additionally, orally administered FTD had increased antitumor activity and was incorporated into DNA more effectively than continuously infused FTD. When TAS-102 was administered, FTD gradually accumulated in tumor cell DNA, in a TPI-independent manner, and significantly delayed tumor growth and prolonged survival, compared to treatment with 5-FU derivatives. TAS-102 reduced the Ki-67-positive cell fraction, and swollen nuclei were observed in treated tumor tissue. The amount of FTD incorporation in DNA and the antitumor activity of TAS-102 in xenograft models were positively and significantly correlated. These results suggest that TAS-102 exerts its antitumor activity predominantly due to its DNA incorporation, rather than as a result of TS inhibition. The persistence of FTD in the DNA of tumor cells treated with TAS-102 may underlie its ability to prolong survival in cancer patients.

  8. Phage lytic enzymes: a history

    Institute of Scientific and Technical Information of China (English)

    David; Trudil

    2015-01-01

    There are many recent studies regarding the efficacy of bacteriophage-related lytic enzymes: the enzymes of ‘bacteria-eaters’ or viruses that infect bacteria. By degrading the cell wall of the targeted bacteria, these lytic enzymes have been shown to efficiently lyse Gram-positive bacteria without affecting normal flora and non-related bacteria. Recent studies have suggested approaches for lysing Gram-negative bacteria as well(Briersa Y, et al., 2014). These enzymes include: phage-lysozyme, endolysin, lysozyme, lysin, phage lysin, phage lytic enzymes, phageassociated enzymes, enzybiotics, muralysin, muramidase, virolysin and designations such as Ply, PAE and others. Bacteriophages are viruses that kill bacteria, do not contribute to antimicrobial resistance, are easy to develop, inexpensive to manufacture and safe for humans, animals and the environment. The current focus on lytic enzymes has been on their use as anti-infectives in humans and more recently in agricultural research models. The initial translational application of lytic enzymes, however, was not associated with treating or preventing a specifi c disease but rather as an extraction method to be incorporated in a rapid bacterial detection assay(Bernstein D, 1997).The current review traces the translational history of phage lytic enzymes–from their initial discovery in 1986 for the rapid detection of group A streptococcus in clinical specimens to evolving applications in the detection and prevention of disease in humans and in agriculture.

  9. A computational model incorporating neural stem cell dynamics reproduces glioma incidence across the lifespan in the human population.

    Directory of Open Access Journals (Sweden)

    Roman Bauer

    Full Text Available Glioma is the most common form of primary brain tumor. Demographically, the risk of occurrence increases until old age. Here we present a novel computational model to reproduce the probability of glioma incidence across the lifespan. Previous mathematical models explaining glioma incidence are framed in a rather abstract way, and do not directly relate to empirical findings. To decrease this gap between theory and experimental observations, we incorporate recent data on cellular and molecular factors underlying gliomagenesis. Since evidence implicates the adult neural stem cell as the likely cell-of-origin of glioma, we have incorporated empirically-determined estimates of neural stem cell number, cell division rate, mutation rate and oncogenic potential into our model. We demonstrate that our model yields results which match actual demographic data in the human population. In particular, this model accounts for the observed peak incidence of glioma at approximately 80 years of age, without the need to assert differential susceptibility throughout the population. Overall, our model supports the hypothesis that glioma is caused by randomly-occurring oncogenic mutations within the neural stem cell population. Based on this model, we assess the influence of the (experimentally indicated decrease in the number of neural stem cells and increase of cell division rate during aging. Our model provides multiple testable predictions, and suggests that different temporal sequences of oncogenic mutations can lead to tumorigenesis. Finally, we conclude that four or five oncogenic mutations are sufficient for the formation of glioma.

  10. Incorporating wind availability into land use regression modelling of air quality in mountainous high-density urban environment.

    Science.gov (United States)

    Shi, Yuan; Lau, Kevin Ka-Lun; Ng, Edward

    2017-08-01

    Urban air quality serves as an important function of the quality of urban life. Land use regression (LUR) modelling of air quality is essential for conducting health impacts assessment but more challenging in mountainous high-density urban scenario due to the complexities of the urban environment. In this study, a total of 21 LUR models are developed for seven kinds of air pollutants (gaseous air pollutants CO, NO2, NOx, O3, SO2 and particulate air pollutants PM2.5, PM10) with reference to three different time periods (summertime, wintertime and annual average of 5-year long-term hourly monitoring data from local air quality monitoring network) in Hong Kong. Under the mountainous high-density urban scenario, we improved the traditional LUR modelling method by incorporating wind availability information into LUR modelling based on surface geomorphometrical analysis. As a result, 269 independent variables were examined to develop the LUR models by using the "ADDRESS" independent variable selection method and stepwise multiple linear regression (MLR). Cross validation has been performed for each resultant model. The results show that wind-related variables are included in most of the resultant models as statistically significant independent variables. Compared with the traditional method, a maximum increase of 20% was achieved in the prediction performance of annual averaged NO2 concentration level by incorporating wind-related variables into LUR model development. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. A Mass Balance Model for Designing Green Roof Systems that Incorporate a Cistern for Re-Use

    OpenAIRE

    Manoj Chopra; Martin Wanielista; Mike Hardin

    2012-01-01

    Green roofs, which have been used for several decades in many parts of the world, offer a unique and sustainable approach to stormwater management. Within this paper, evidence is presented on water retention for an irrigated green roof system. The presented green roof design results in a water retention volume on site. A first principle mass balance computer model is introduced to assist with the design of these green roof systems which incorporate a cistern to capture and reuse runoff waters...

  12. 3D structure prediction of lignolytic enzymes lignin peroxidase and manganese peroxidase based on homology modelling

    Directory of Open Access Journals (Sweden)

    SWAPNIL K. KALE

    2016-04-01

    Full Text Available Lignolytic enzymes have great biotechnological value in biopulping, biobleaching, and bioremediation. Manganese peroxidase (EC 1:11:1:13 and lignin peroxidase (EC 1:11:1:14 are extracellular and hem-containing peroxidases that catalyze H2O2-dependent oxidation of lignin. Because of their ability to catalyse oxidation of a wide range of organic compounds and even some inorganic compounds, they got tremendous industrial importance. In this study, 3D structure of lignin and manganese peroxidase has been predicted on the basis of homology modeling using Swiss PDB workspace. The physicochemical properties like molecular weight, isoelectric point, Grand average of hydropathy, instability and aliphatic index of the target enzymes were performed using Protparam. The predicted secondary structure of MnP has 18 helices and 6 strands, while LiP has 20 helices and 4 strands. Generated 3D structure was visualized in Pymol. The generated model for MnP and LiP has Z-score Qmean of 0.01 and -0.71, respectively. The predicted models were validated through Ramachandran Plot, which indicated that 96.1 and 95.5% of the residues are in most favored regions for MnP and LiP respectively. The quality of predicted models were assessed and confirmed by VERIFY 3D, PROCHECK and ERRAT. The modeled structure of MnP and LiP were submitted to the Protein Model Database.

  13. Ab initio modeling of point defects, self-diffusion, and incorporation of impurities in thorium

    Science.gov (United States)

    Daroca, D. Pérez

    2017-02-01

    Research on Generation-IV nuclear reactors has boosted the investigation of thorium as nuclear fuel. By means of first-principles calculations within the framework of density functional theory, structural properties and phonon dispersion curves of Th are obtained. These results agreed very well with previous ones. The stability and formation energies of vacancies, interstitial and divacancies are studied. It is found that vacancies are the energetically preferred defects. The incorporation energies of He, Xe, and Kr atoms in Th defects are analyzed. Self-diffusion, migration paths and activation energies are also calculated.

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

    Science.gov (United States)

    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. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. Enzyme as catalytic wheel powered by a Markovian engine: conformational coupling and barrier surfing models

    Science.gov (United States)

    Tsong, Tian Yow; Chang, Cheng-Hung

    2005-05-01

    We examine a typical Michaelis-Menten Enzyme (MME) and redress it to form a transducer of free energy, and electric, acoustic, or other types of energy. This amendment and extension is necessary in lieu of recent experiments in which enzymes are shown to perform pump, motor, and locomotion functions resembling their macroscopic counterparts. Classical textbook depicts enzyme, or an MME, as biocatalyst which can enhance the rate of a chemical reaction by lowering the activation barrier but cannot shift the thermodynamic equilibrium of the biochemical reaction. An energy transducer, on the other hand, must also be able to harvest, store, or divert energy and in doing so alter the chemical equilibrium, change the energy form, fuel an energy consuming process, or perform all these functions stepwise in one catalytic turnover. The catalytic wheel presented in this communication is both a catalyst and an energy transducer and can perform all these tasks with ease. A Conformational Coupling Model for the rotary motors and a Barrier Surfing Model for the track-guided stepping motors and transporters, are presented and compared. It is shown that the core engine of the catalytic wheel, or a Brownian motor, is a Markovian engine. It remains to be seen if this core engine is the basic mechanism for a wide variety of bio-molecular energy transducers, as well as certain other dynamic systems, for example, the Parrondo's Games.

  16. Modelling the Effects of Ageing Time of Starch on the Enzymatic Activity of Three Amylolytic Enzymes

    Directory of Open Access Journals (Sweden)

    Nelson P. Guerra

    2012-01-01

    Full Text Available The effect of increasing ageing time (t of starch on the activity of three amylolytic enzymes (Termamyl, San Super, and BAN was investigated. Although all the enzymatic reactions follow michaelian kinetics, vmax decreased significantly (P<0.05 and KM increased (although not always significantly with the increase in t. The conformational changes produced in the starch chains as a consequence of the ageing seemed to affect negatively the diffusivity of the starch to the active site of the enzymes and the release of the reaction products to the medium. A similar effect was observed when the enzymatic reactions were carried out with unaged starches supplemented with different concentrations of gelatine [G]. The inhibition in the amylolytic activities was best mathematically described by using three modified forms of the Michaelis-Menten model, which included a term to consider, respectively, the linear, exponential, and hyperbolic inhibitory effects of t and [G].

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  18. Incorporating Transmission Into Causal Models of Infectious Diseases for Improved Understanding of the Effect and Impact of Risk Factors.

    Science.gov (United States)

    Paynter, Stuart

    2016-03-15

    Conventional measures of causality (which compare risks between exposed and unexposed individuals) do not factor in the population-scale dynamics of infectious disease transmission. We used mathematical models of 2 childhood infections (respiratory syncytial virus and rotavirus) to illustrate this problem. These models incorporated 3 causal pathways whereby malnutrition could act to increase the incidence of severe infection: increasing the proportion of infected children who develop severe infection, increasing the children's susceptibility to infection, and increasing infectiousness. For risk factors that increased the proportion of infected children who developed severe infection, the population attributable fraction (PAF) calculated conventionally was the same as the PAF calculated directly from the models. However, for risk factors that increased transmission (by either increasing susceptibility to infection or increasing infectiousness), the PAF calculated directly from the models was much larger than that predicted by the conventional PAF calculation. The models also showed that even when conventional studies find no association between a risk factor and an outcome, risk factors that increase transmission can still have a large impact on disease burden. For a complete picture of infectious disease causality, transmission effects must be incorporated into causal models.

  19. Incorporation of Failure Into an Orthotropic Three-Dimensional Model with Tabulated Input Suitable for Use in Composite Impact Problems

    Science.gov (United States)

    Goldberg, Robert K.; Carney, Kelly S.; Dubois, Paul; Hoffarth, Canio; Khaled, Bilal; Shyamsunder, Loukham; Rajan, Subramaniam; Blankenhorn, Gunther

    2017-01-01

    The need for accurate material models to simulate the deformation, damage and failure of polymer matrix composites under impact conditions is becoming critical as these materials are gaining increased use in the aerospace and automotive communities. The aerospace community has identified several key capabilities which are currently lacking in the available material models in commercial transient dynamic finite element codes. To attempt to improve the predictive capability of composite impact simulations, a next generation material model is being developed for incorporation within the commercial transient dynamic finite element code LS-DYNA. The material model, which incorporates plasticity, damage and failure, utilizes experimentally based tabulated input to define the evolution of plasticity and damage and the initiation of failure as opposed to specifying discrete input parameters such as modulus and strength. The plasticity portion of the orthotropic, three-dimensional, macroscopic composite constitutive model is based on an extension of the Tsai-Wu composite failure model into a generalized yield function with a non-associative flow rule. For the damage model, a strain equivalent formulation is used to allow for the uncoupling of the deformation and damage analyses. In the damage model, a semi-coupled approach is employed where the overall damage in a particular coordinate direction is assumed to be a multiplicative combination of the damage in that direction resulting from the applied loads in various coordinate directions. For the failure model, a tabulated approach is utilized in which a stress or strain based invariant is defined as a function of the location of the current stress state in stress space to define the initiation of failure. Failure surfaces can be defined with any arbitrary shape, unlike traditional failure models where the mathematical functions used to define the failure surface impose a specific shape on the failure surface. In the current

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

    Science.gov (United States)

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

    2015-01-01

    Nanofibers were prepared from polycaprolactone, polylactide and polyvinyl alcohol using Nanospider(TM) 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.

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

    Directory of Open Access Journals (Sweden)

    Jakub Hrib

    2015-09-01

    Full Text Available 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.

  2. Experiment of Enzyme Kinetics Using Guided Inquiry Model for Enhancing Generic Science Skills

    Science.gov (United States)

    Amida, N.; Supriyanti, F. M. T.; Liliasari

    2017-02-01

    This study aims to enhance generic science skills of students using guided inquiry model through experiments of enzyme kinetics. This study used quasi-experimental methods, with pretest-posttestnonequivalent control group design. Subjects of this study were chemistry students enrolled in biochemistry lab course, consisted of 18 students in experimental class and 19 students in control class. Instrument in this study were essay test that involves 5 indicators of generic science skills (i.e. direct observation, causality, symbolic language, mathematical modeling, and concepts formation) and also student worksheets. The results showed that the experiments of kinetics enzyme using guided inquiry model have been enhance generic science skills in high category with a value of average of 0.77. Four indicators classified in the high category are direct observation, causality, symbolic language, and mathematical modeling with the value of 0,73 0,70; 0,96; dan 0,85. Meanwhile, indicator of concepts formation in the medium category with a value of 0.62

  3. A Mass Balance Model for Designing Green Roof Systems that Incorporate a Cistern for Re-Use

    Directory of Open Access Journals (Sweden)

    Manoj Chopra

    2012-11-01

    Full Text Available Green roofs, which have been used for several decades in many parts of the world, offer a unique and sustainable approach to stormwater management. Within this paper, evidence is presented on water retention for an irrigated green roof system. The presented green roof design results in a water retention volume on site. A first principle mass balance computer model is introduced to assist with the design of these green roof systems which incorporate a cistern to capture and reuse runoff waters for irrigation of the green roof. The model is used to estimate yearly stormwater retention volume for different cistern storage volumes. Additionally, the Blaney and Criddle equation is evaluated for estimation of monthly evapotranspiration rates for irrigated systems and incorporated into the model. This is done so evapotranspiration rates can be calculated for regions where historical data does not exist, allowing the model to be used anywhere historical weather data are available. This model is developed and discussed within this paper as well as compared to experimental results.

  4. A new multi-wavelength model-based method for determination of enzyme kinetic parameters

    Indian Academy of Sciences (India)

    Mohammad-Hossein Sorouraddin; Kaveh Amini; Abdolhossein Naseri; Javad Vallipour; Jalal Hanaee; Mohammad-Reza Rashidi

    2010-09-01

    Lineweaver–Burk plot analysis is the most widely used method to determine enzyme kinetic parameters. In the spectrophotometric determination of enzyme activity using the Lineweaver–Burk plot, it is necessary to find a wavelength at which only the substrate or the product has absorbance without any spectroscopic interference of the other reaction components. Moreover, in this method, different initial concentrations of the substrate should be used to obtain the initial velocities required for Lineweaver–Burk plot analysis. In the present work, a multi-wavelength model-based method has been developed and validated to determine Michaelis–Menten constants for some enzyme reactions. In this method, a selective wavelength region and several experiments with different initial concentrations of the substrate are not required. The absorbance data of the kinetic assays are fitted by non-linear regression coupled to the numeric integration of the related differential equation. To indicate the applicability of the proposed method, the Michaelis–Menten constants for the oxidation of phenanthridine, 6-deoxypenciclovir and xanthine by molybdenum hydroxylases were determined using only a single initial concentration of the substrate, regardless of any spectral overlap.

  5. A new multi-wavelength model-based method for determination of enzyme kinetic parameters.

    Science.gov (United States)

    Sorouraddin, Mohammad-Hossein; Amini, Kaveh; Naseri, Abdolhossein; Vallipour, Javad; Hanaee, Jalal; Rashidi, Mohammad-Reza

    2010-09-01

    Lineweaver-Burk plot analysis is the most widely used method to determine enzyme kinetic parameters. In the spectrophotometric determination of enzyme activity using the Lineweaver-Burk plot, it is necessary to find a wavelength at which only the substrate or the product has absorbance without any spectroscopic interference of the other reaction components. Moreover, in this method, different initial concentrations of the substrate should be used to obtain the initial velocities required for Lineweaver-Burk plot analysis. In the present work, a multi-wavelength model-based method has been developed and validated to determine Michaelis-Menten constants for some enzyme reactions. In this method, a selective wavelength region and several experiments with different initial concentrations of the substrate are not required. The absorbance data of the kinetic assays are fitted by non-linear regression coupled to the numeric integration of the related differential equation. To indicate the applicability of the proposed method, the Michaelis-Menten constants for the oxidation of phenanthridine, 6-deoxypenciclovir and xanthine by molybdenum hydroxylases were determined using only a single initial concentration of the substrate, regardless of any spectral overlap.

  6. Investigation of a growth model incorporating density dependence for the mackerel management plan simulations

    NARCIS (Netherlands)

    Brunel, T.P.A.

    2015-01-01

    This report presents a framework to model density dependent growth for the North East Atlantic mackerel. The model used is the classical von Bertalanffy equation, but modified so that growth is reduced when stock size increases. The model developed was able to reproduce quite closely the trends in t

  7. Investigation of a growth model incorporating density dependence for the mackerel management plan simulations

    NARCIS (Netherlands)

    Brunel, T.P.A.

    2015-01-01

    This report presents a framework to model density dependent growth for the North East Atlantic mackerel. The model used is the classical von Bertalanffy equation, but modified so that growth is reduced when stock size increases. The model developed was able to reproduce quite closely the trends in

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

    Science.gov (United States)

    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.

  9. Micellar Effects on Nucleophilic Addition Reaction and Applicability of Enzyme Catalysis Model

    Directory of Open Access Journals (Sweden)

    R. K. London Singh

    2012-01-01

    Full Text Available This study describes the effect of anionic and cationic micelles on nucleophilic addition reaction of rosaniline hydrochloride (RH with hydroxide under pseudo-first order condition. Strong inhibitory effect is observed due to SDS micelle, whereas CTAB catalysed the reaction. This is explained on the basis of electrostatic and hydrophobic interactions which are simultaneously operating in the reaction system. The kinetic data obtained is quantitatively analysed by applying the positive cooperativity model of enzyme catalysis. Binding constants and influence of counterions on the reaction have also been investigated.

  10. Incorporating shape constraints in generalized additive modelling of the height-diameter relationship for Norway spruce

    Directory of Open Access Journals (Sweden)

    Natalya Pya

    2016-02-01

    Full Text Available Background: Measurements of tree heights and diameters are essential in forest assessment and modelling. Tree heights are used for estimating timber volume, site index and other important variables related to forest growth and yield, succession and carbon budget models. However, the diameter at breast height (dbh can be more accurately obtained and at lower cost, than total tree height. Hence, generalized height-diameter (h-d models that predict tree height from dbh, age and other covariates are needed. For a more flexible but biologically plausible estimation of covariate effects we use shape constrained generalized additive models as an extension of existing h-d model approaches. We use causal site parameters such as index of aridity to enhance the generality and causality of the models and to enable predictions under projected changeable climatic conditions. Methods: We develop unconstrained generalized additive models (GAM and shape constrained generalized additive models (SCAM for investigating the possible effects of tree-specific parameters such as tree age, relative diameter at breast height, and site-specific parameters such as index of aridity and sum of daily mean temperature during vegetation period, on the h-d relationship of forests in Lower Saxony, Germany. Results: Some of the derived effects, e.g. effects of age, index of aridity and sum of daily mean temperature have significantly non-linear pattern. The need for using SCAM results from the fact that some of the model effects show partially implausible patterns especially at the boundaries of data ranges. The derived model predicts monotonically increasing levels of tree height with increasing age and temperature sum and decreasing aridity and social rank of a tree within a stand. The definition of constraints leads only to marginal or minor decline in the model statistics like AIC. An observed structured spatial trend in tree height is modelled via 2-dimensional surface

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

    Science.gov (United States)

    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.

  12. Systems pharmacology modeling of drug‐induced hyperbilirubinemia: Differentiating hepatotoxicity and inhibition of enzymes/transporters

    Science.gov (United States)

    Battista, C; Woodhead, JL; Stahl, SH; Mettetal, JT; Watkins, PB; Siler, SQ; Howell, BA

    2017-01-01

    Elevations in serum bilirubin during drug treatment may indicate global liver dysfunction and a high risk of liver failure. However, drugs also can increase serum bilirubin in the absence of hepatic injury by inhibiting specific enzymes/transporters. We constructed a mechanistic model of bilirubin disposition based on known functional polymorphisms in bilirubin metabolism/transport. Using physiologically based pharmacokinetic (PBPK) model‐predicted drug exposure and enzyme/transporter inhibition constants determined in vitro, our model correctly predicted indinavir‐mediated hyperbilirubinemia in humans and rats. Nelfinavir was predicted not to cause hyperbilirubinemia, consistent with clinical observations. We next examined a new drug candidate that caused both elevations in serum bilirubin and biochemical evidence of liver injury in rats. Simulations suggest that bilirubin elevation primarily resulted from inhibition of transporters rather than global liver dysfunction. We conclude that mechanistic modeling of bilirubin can help elucidate underlying mechanisms of drug‐induced hyperbilirubinemia, and thereby distinguish benign from clinically important elevations in serum bilirubin. PMID:28074467

  13. The angiotensin converting enzyme inhibitor captopril protects nigrostriatal dopamine neurons in animal models of parkinsonism.

    Science.gov (United States)

    Sonsalla, Patricia K; Coleman, Christal; Wong, Lai-Yoong; Harris, Suzan L; Richardson, Jason R; Gadad, Bharathi S; Li, Wenhao; German, Dwight C

    2013-12-01

    Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by a prominent loss of nigrostriatal dopamine (DA) neurons with an accompanying neuroinflammation. The peptide angiotensin II (AngII) plays a role in oxidative-stress induced disorders and is thought to mediate its detrimental actions via activation of AngII AT1 receptors. The brain renin-angiotensin system is implicated in neurodegenerative disorders including PD. Blockade of the angiotensin converting enzyme or AT1 receptors provides protection in acute animal models of parkinsonism. We demonstrate here that treatment of mice with the angiotensin converting enzyme inhibitor captopril protects the striatum from acutely administered 1-methyl-4-phenyl-1,2,3,6-tetrahydropyrine (MPTP), and that chronic captopril protects the nigral DA cell bodies from degeneration in a progressive rat model of parkinsonism created by the chronic intracerebral infusion of 1-methyl-4-phenylpyridinium (MPP+). The accompanying activation of microglia in the substantia nigra of MPP+-treated rats was reduced by the chronic captopril treatment. These findings indicate that captopril is neuroprotective for nigrostriatal DA neurons in both acute and chronic rodent PD models. Targeting the brain AngII pathway may be a feasible approach to slowing neurodegeneration in PD. © 2013.

  14. An Application of Combined Model for Tehran Metropolitan Area Incorporating Captive Travel Behavior

    Directory of Open Access Journals (Sweden)

    Shahriar A. Zargari

    2009-01-01

    Full Text Available To overcome deficiencies of the sequential transportation planning approach, this research applies a Combined Trip Distribution and Assignment Model (CTDAM for the simultaneous prediction. The proposed combined model can itself be reformulated as an Equivalent Minimization Problem (EMP. When applying the Evans algorithm to the EMP, the CTDAM is expected to be usable in a realistic application. The objective of this research is to compare the conventional sequential procedure and CTDAM by applying both models to a large urban transportation network for captive trip purposes. Several evaluation measures were utilized to compare the results and confirm that the proposed model can efficiently satisfy several convergence criterions. It became clear that the User Equilibrium (UE assignment in the proposed model can be obtained relatively swifter than the Sequential Model (SM and can be efficiently used in large transportation networks. Furthermore, the comparing results point out the performance of the CTDAM is significantly better than SM.

  15. Incorporating Floating Surface Objects into a Fully Dispersive Surface Wave Model

    Science.gov (United States)

    2016-04-19

    solutions and a VOF model for a 2D floating box and with laboratory measurements of wave generation by a ver- tically oscillating sphere. A steep...breaking waves or sud - en surface impacts. These simplifications also considerably reduce he computational requirements of the model. The Pressure...recently, erakhti et al. (2015) carried out extensive model validations of HWAVE against laboratory data. The focus of their study was to xamine the

  16. Incorporating Latent Variables into Discrete Choice Models - A Simultaneous Estimation Approach Using SEM Software

    Directory of Open Access Journals (Sweden)

    Dirk Temme

    2008-12-01

    Full Text Available Integrated choice and latent variable (ICLV models represent a promising new class of models which merge classic choice models with the structural equation approach (SEM for latent variables. Despite their conceptual appeal, applications of ICLV models in marketing remain rare. We extend previous ICLV applications by first estimating a multinomial choice model and, second, by estimating hierarchical relations between latent variables. An empirical study on travel mode choice clearly demonstrates the value of ICLV models to enhance the understanding of choice processes. In addition to the usually studied directly observable variables such as travel time, we show how abstract motivations such as power and hedonism as well as attitudes such as a desire for flexibility impact on travel mode choice. Furthermore, we show that it is possible to estimate such a complex ICLV model with the widely available structural equation modeling package Mplus. This finding is likely to encourage more widespread application of this appealing model class in the marketing field.

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

    Science.gov (United States)

    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.

  18. Modeling transformation of soil organic matter through the soil enzyme activity

    Science.gov (United States)

    Tregubova, Polina; Vladimirov, Artem; Vasilyeva, Nadezda

    2017-04-01

    The sensitivity of soil heterotrophic respiration to changing environmental conditions is widely investigated nowadays but still remain extremely controversial. The mechanisms are still needed to reveal. In this work we model soil C and N biogeochemical cycles based on general principles of soil carbon and nitrogen dynamics with focusing on biochemical processes occurring in the soil based on well known classes of enzymes and organic compounds that they can transform. According to classic theories, exoenzymes and endoenzymes of bacteria and fungi as stable over a long period catalytic components play a significant role in degradation of plant and animal residues, decomposition of biopolymers of different sizes, humification processes and in releasing of labile compounds essential for the microorganism and plant growth and germination. We test the model regimes sensitivity to such environmental factors as temperature and moisture. Modeling the directions and patterns of soil biochemical activity is important for evaluation of soil agricultural productivity as well as its ecological functions.

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

    Science.gov (United States)

    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…

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

    Science.gov (United States)

    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 ...

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

    Directory of Open Access Journals (Sweden)

    A. Pathirana

    2008-11-01

    Full Text Available 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  3. Incorporating Fuzzy Systems Modeling and Possibility Theory in Hydrogeological Uncertainty Analysis

    Science.gov (United States)

    Faybishenko, B.

    2008-12-01

    Hydrogeological predictions are subject to numerous uncertainties, including the development of conceptual, mathematical, and numerical models, as well as determination of their parameters. Stochastic simulations of hydrogeological systems and the associated uncertainty analysis are usually based on the assumption that the data characterizing spatial and temporal variations of hydrogeological processes are random, and the output uncertainty is quantified using a probability distribution. However, hydrogeological systems are often characterized by imprecise, vague, inconsistent, incomplete or subjective information. One of the modern approaches to modeling and uncertainty quantification of such systems is based on using a combination of statistical and fuzzy-logic uncertainty analyses. The aims of this presentation are to: (1) present evidence of fuzziness in developing conceptual hydrogeological models, and (2) give examples of the integration of the statistical and fuzzy-logic analyses in modeling and assessing both aleatoric uncertainties (e.g., caused by vagueness in assessing the subsurface system heterogeneities of fractured-porous media) and epistemic uncertainties (e.g., caused by the selection of different simulation models) involved in hydrogeological modeling. The author will discuss several case studies illustrating the application of fuzzy modeling for assessing the water balance and water travel time in unsaturated-saturated media. These examples will include the evaluation of associated uncertainties using the main concepts of possibility theory, a comparison between the uncertainty evaluation using probabilistic and possibility theories, and a transformation of the probabilities into possibilities distributions (and vice versa) for modeling hydrogeological processes.

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

    Science.gov (United States)

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

    Science.gov (United States)

    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,…

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

    Science.gov (United States)

    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.

  7. Incorporating sediment compaction into a gravitationally self-consistent model for ice age sea-level change

    Science.gov (United States)

    Ferrier, Ken L.; Austermann, Jacqueline; Mitrovica, Jerry X.; Pico, Tamara

    2017-10-01

    Sea-level changes are of wide interest because they regulate coastal hazards, shape the sedimentary geologic record and are sensitive to climate change. In areas where rivers deliver sediment to marine deltas and fans, sea-level changes are strongly modulated by the deposition and compaction of marine sediment. Deposition affects sea level by increasing the elevation of the seafloor, by perturbing crustal elevation and gravity fields and by reducing the volume of seawater through the incorporation of water into sedimentary pore space. In a similar manner, compaction affects sea level by lowering the elevation of the seafloor and by purging water out of sediments and into the ocean. Here we incorporate the effects of sediment compaction into a gravitationally self-consistent global sea-level model by extending the approach of Dalca et al. (2013). We show that incorporating compaction requires accounting for two quantities that are not included in the Dalca et al. (2013) analysis: the mean porosity of the sediment and the degree of saturation in the sediment. We demonstrate the effects of compaction by modelling sea-level responses to two simplified 122-kyr sediment transfer scenarios for the Amazon River system, one including compaction and one neglecting compaction. These simulations show that the largest effect of compaction is on the thickness of the compacting sediment, an effect that is largest where deposition rates are fastest. Compaction can also produce minor sea-level changes in coastal regions by influencing shoreline migration and the location of seawater loading, which perturbs crustal elevations. By providing a tool for modelling gravitationally self-consistent sea-level responses to sediment compaction, this work offers an improved approach for interpreting the drivers of past sea-level changes.

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

    Science.gov (United States)

    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.

  9. A spatial model for conflict incorporating within- and between-actor effects

    Science.gov (United States)

    Knipl, Diána; Davies, Toby; Baudains, Peter

    2017-10-01

    The application of ecological models to human conflict scenarios has given rise to a number of models which describe antagonistic relationships between adversaries. Recent work demonstrates that the spatial disaggregation of such models is not only well-motivated but also gives rise to interesting dynamic behaviour, particularly with respect to the spatial distribution of resources. One feature which is largely absent from previous models, however, is the ability of an adversary to coordinate activity across its various locations. Most immediately, this corresponds to the notion of 'support' - the reallocation of resources from one site to another according to need - which plays an important role in real-world conflict. In this paper, we generalise a spatially-disaggregated form of the classic Richardson model of conflict escalation by adding a cross-location interaction term for the within-adversary dynamics at each location. We explore the model analytically, giving conditions for the stability of the balanced equilibrium state. We then also carry out a number of numerical simulations which correspond to stylised real-world conflict scenarios. Potential further applications of the model, and its implications for policy, are then discussed.

  10. A LabVIEW model incorporating an open-loop arterial impedance and a closed-loop circulatory system.

    Science.gov (United States)

    Cole, R T; Lucas, C L; Cascio, W E; Johnson, T A

    2005-11-01

    While numerous computer models exist for the circulatory system, many are limited in scope, contain unwanted features or incorporate complex components specific to unique experimental situations. Our purpose was to develop a basic, yet multifaceted, computer model of the left heart and systemic circulation in LabVIEW having universal appeal without sacrificing crucial physiologic features. The program we developed employs Windkessel-type impedance models in several open-loop configurations and a closed-loop model coupling a lumped impedance and ventricular pressure source. The open-loop impedance models demonstrate afterload effects on arbitrary aortic pressure/flow inputs. The closed-loop model catalogs the major circulatory waveforms with changes in afterload, preload, and left heart properties. Our model provides an avenue for expanding the use of the ventricular equations through closed-loop coupling that includes a basic coronary circuit. Tested values used for the afterload components and the effects of afterload parameter changes on various waveforms are consistent with published data. We conclude that this model offers the ability to alter several circulatory factors and digitally catalog the most salient features of the pressure/flow waveforms employing a user-friendly platform. These features make the model a useful instructional tool for students as well as a simple experimental tool for cardiovascular research.

  11. Forest type mapping using incorporation of spatial models and ETM+ data.

    Science.gov (United States)

    Joibary, Shaban Shataee; Darvishsefat, Ali A; Kellenberger, Tobias W

    2007-07-15

    Results of former researches have shown that spectrally based analysis alone could not satisfy forest type classification in mountainous mixed forests. Forest type based on composed different parameters such as topography elements like aspect, elevation and slop. These elements that are affected on occurrences of forest type can be stated as spatial distribution models. Using ancillary data integrated with spectral data could help to separate forest type. In order to find the abilities of using topographic spatial predictive models to improve forest type classification, an investigation was carried out to classify forest type using ETM+ data in a part of northern forests of Iran. The Tasseled Cap, Ratioing transformations and Principal Component Analysis were applied to the spectral bands. The best spectral and predictive data sets for classifying forest type using maximum likelihood classification were chosen using the Bhattacharya seperability index. Primary analysis between forest type and topographic parameters showed that elevation and aspect are most correlated with the occurrences of type. Probability occurrence rates of forest type were extracted in the aspect; elevation, integrated aspect and elevation as well as homogeneous units structured on elevation and aspect classes. Based on occurrence rates of forest type, spatial predictive distribution models were generated for each type individually. Classification of the best spectral data sets was accomplished by maximum likelihood classifier and using these spatial predictive models. Results were assessed using a sample ground truth of forest type. This study showed that spatial predictive models could considerably improve the results compared with spectral data alone from 49 to 60%. Among spatial models used, the spatial predictive models constructed based on the homogeneous units could improve results in comparison to other models. Applying other parameters related to forest type like soil maps would

  12. Periglacial processes incorporated into a long-term landscape evolution model

    DEFF Research Database (Denmark)

    Andersen, Jane Lund; Egholm, D.L.; Knudsen, Mads Faurschou

    relating frost-cracking intensity to the mean annual air temperature (MAAT). The model integrates temperature variations in the subsurface following an annually oscillating surface temperature. Hales and Roering (2007) assumed that frost-cracking intensity is a simple function of the temperature gradient...... allows us to couple the frost-cracking model to a long- term landscape evolution model where surface elevation, sediment thickness, and air temperature evolve through time. This enables us to explore the spatial distribution of frost cracking in realistic landscapes, and to study the slow feedbacks...

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

    Science.gov (United States)

    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.

  14. Incorporating Protein Biosynthesis into the Saccharomyces cerevisiae Genome-scale Metabolic Model

    DEFF Research Database (Denmark)

    Olivares Hernandez, Roberto

    Based on stoichiometric biochemical equations that occur into the cell, the genome-scale metabolic models can quantify the metabolic fluxes, which are regarded as the final representation of the physiological state of the cell. For Saccharomyces Cerevisiae the genome scale model has been......, translation initiation, translation elongation, translation termination, translation elongation, and mRNA decay. Considering these information from the mechanisms of transcription and translation, we will include this stoichiometric reactions into the genome scale model for S. Cerevisiae to obtain the first...

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  16. Moving college students to a better understanding of substrate specificity of enzymes through utilizing multimedia pre-training and an interactive enzyme model

    Science.gov (United States)

    Saleh, Mounir R.

    Scientists' progress in understanding enzyme specificity uncovered a complex natural phenomenon. However, not all of the currently available biology textbooks seem to be up to date on this progress. Students' understanding of how enzymes work is a core requirement in biochemistry and biology tertiary education. Nevertheless, current pre-college science education does not provide students with enough biochemical background to enable them to understand complex material such as this. To bridge this gap, a multimedia pre-training presentation was prepared to fuel the learner's prior knowledge with discrete facts necessary to understand the presented concept. This treatment is also known to manage intrinsic cognitive load during the learning process. An interactive instructional enzyme model was also built to motivate students to learn about substrate specificity of enzymes. Upon testing the effect of this combined treatment on 111 college students, desirable learning outcomes were found in terms of cognitive load, motivation, and achievement. The multimedia pre-training group reported significantly less intrinsic cognitive load, higher motivation, and demonstrated higher transfer performance than the control and post-training groups. In this study, a statistical mediation model is also proposed to explain how cognitive load and motivation work in concert to foster learning from multimedia pre-training. This type of research goes beyond simple forms of "what works" to a deeper understanding of "how it works", thus enabling informed decisions for multimedia instructional design. Multimedia learning plays multiple roles in science education. Therefore, science learners would be some of the first to benefit from improving multimedia instructional design. Accordingly, complex scientific phenomena can be introduced to college students in a motivating, informative, and cognitively efficient learning environment.

  17. Incorporating seepage losses into a 1D unsteady model of floods in ...

    African Journals Online (AJOL)

    2015-07-04

    Joseph et al., 2004): (i) runoff volume and velocity; (ii) channel geometry; (iii) ... of seepage on different turbulent characteristics for an open channel flow. ..... Comparison of flow profiles calculated by present model with MIKE 11.

  18. Radmap: ''as-built'' cad models incorporating geometrical, radiological and material information

    Energy Technology Data Exchange (ETDEWEB)

    Piotrowski, L. [Electricite de France (EDF/DRD), 78 - Chatou (France); Lubawy, J.L. [Electricite de France (EDF/CNEPE), 37 - Tours (France)

    2001-07-01

    EDF intends to achieve successful and cost-effective dismantling of its obsolete nuclear plants. To reach this goal, EDF is currently extending its ''as-built'' 3-D modelling system to also include the location and characteristics of gamma sources in the geometrical models of its nuclear installations. The resulting system (called RADMAP) is a complete CAD chain covering 3-D and gamma data acquisitions, CAD modelling and exploitation of the final model. Its aim is to describe completely the geometrical and radiological state of a particular nuclear environment. This paper presents an overall view of RADMAP. The technical and functional characteristics of each element of the chain are indicated and illustrated using real (EDF) environments/applications. (author)

  19. Simulation of a severe convective storm using a numerical model with explicitly incorporated aerosols

    Science.gov (United States)

    Lompar, Miloš; Ćurić, Mladjen; Romanic, Djordje

    2017-09-01

    Despite an important role the aerosols play in all stages of cloud lifecycle, their representation in numerical weather prediction models is often rather crude. This paper investigates the effects the explicit versus implicit inclusion of aerosols in a microphysics parameterization scheme in Weather Research and Forecasting (WRF) - Advanced Research WRF (WRF-ARW) model has on cloud dynamics and microphysics. The testbed selected for this study is a severe mesoscale convective system with supercells that struck west and central parts of Serbia in the afternoon of July 21, 2014. Numerical products of two model runs, i.e. one with aerosols explicitly (WRF-AE) included and another with aerosols implicitly (WRF-AI) assumed, are compared against precipitation measurements from surface network of rain gauges, as well as against radar and satellite observations. The WRF-AE model accurately captured the transportation of dust from the north Africa over the Mediterranean and to the Balkan region. On smaller scales, both models displaced the locations of clouds situated above west and central Serbia towards southeast and under-predicted the maximum values of composite radar reflectivity. Similar to satellite images, WRF-AE shows the mesoscale convective system as a merged cluster of cumulonimbus clouds. Both models over-predicted the precipitation amounts; WRF-AE over-predictions are particularly pronounced in the zones of light rain, while WRF-AI gave larger outliers. Unlike WRF-AI, the WRF-AE approach enables the modelling of time evolution and influx of aerosols into the cloud which could be of practical importance in weather forecasting and weather modification. Several likely causes for discrepancies between models and observations are discussed and prospects for further research in this field are outlined.

  20. Incorporation of a Generalized Data Assimilation Module within a Global Photospheric Flux Transport Model

    Science.gov (United States)

    2016-03-31

    National Laboratory (LANL). The main outcome of this research effort is the state-of- the- art data assimilative photospheric flux transport model now...input to WSA. Such comparisons were made with the assistance of a University of New Mexico graduate student/Summer AFRL Space Scholar so that WSA...advance state-of-the- art 3-D MHD CORHEL coronal and solar wind model. In year seven (2014) significant progress was made in is this area. Figure 41

  1. A rat experimental model of glaucoma incorporating rapid-onset elevation of intraocular pressure

    OpenAIRE

    Smedowski, Adrian; Pietrucha-Dutczak, Marita; Kaarniranta, Kai; Lewin-Kowalik, Joanna

    2014-01-01

    Glaucoma is a chronic disease that causes structural and functional damage to retinal ganglion cells (RGC). The currently employed therapeutic options are not sufficient to prevent vision loss in patients with glaucoma; therefore, there is a need to develop novel therapies, which requires the creation of functional, repeatable and easy-to-utilize animal models for use in pre-clinical studies. The currently available models ensure only low to moderate damage in optic nerves, with high variatio...

  2. Improving River Flow Predictions from the NOAA NCRFC Forecasting Model by Incorporating Satellite Observations

    Science.gov (United States)

    Tuttle, S. E.; Jacobs, J. M.; Restrepo, P. J.; Deweese, M. M.; Connelly, B.; Buan, S.

    2016-12-01

    The NOAA National Weather Service North Central River Forecast Center (NCRFC) is responsible for issuing river flow forecasts for parts of the Upper Mississippi, Great Lakes, and Hudson Bay drainages, including the Red River of the North basin (RRB). The NCRFC uses an operational hydrologic modeling infrastructure called the Community Hydrologic Prediction System (CHPS) for its operational forecasts, which currently links the SNOW-17 snow accumulation and ablation model, to the Sacramento-Soil Moisture Accounting (SAC-SMA) rainfall-runoff model, to a number of hydrologic and hydraulic flow routing models. The operational model is lumped and requires only area-averaged precipitation and air temperature as inputs. NCRFC forecasters use observational data of hydrological state variables as a source of supplemental information during forecasting, and can use professional judgment to modify the model states in real time. In a few recent years (e.g. 2009, 2013), the RRB exhibited unexpected anomalous hydrologic behavior, resulting in overestimation of peak flood discharge by up to 70% and highlighting the need for observations with high temporal and spatial coverage. Unfortunately, observations of hydrological states (e.g. soil moisture, snow water equivalent (SWE)) are relatively scarce in the RRB. Satellite remote sensing can fill this need. We use Minnesota's Buffalo River watershed within the RRB as a test case and update the operational CHPS model using modifications based on satellite observations, including AMSR-E SWE and SMOS soil moisture estimates. We evaluate the added forecasting skill of the satellite-enhanced model compared to measured streamflow using hindcasts from 2010-2013.

  3. Enhanced stability of car-following model upon incorporation of short-term driving memory

    Science.gov (United States)

    Liu, Da-Wei; Shi, Zhong-Ke; Ai, Wen-Huan

    2017-06-01

    Based on the full velocity difference model, a new car-following model is developed to investigate the effect of short-term driving memory on traffic flow in this paper. Short-term driving memory is introduced as the influence factor of driver's anticipation behavior. The stability condition of the newly developed model is derived and the modified Korteweg-de Vries (mKdV) equation is constructed to describe the traffic behavior near the critical point. Via numerical method, evolution of a small perturbation is investigated firstly. The results show that the improvement of this new car-following model over the previous ones lies in the fact that the new model can improve the traffic stability. Starting and breaking processes of vehicles in the signalized intersection are also investigated. The numerical simulations illustrate that the new model can successfully describe the driver's anticipation behavior, and that the efficiency and safety of the vehicles passing through the signalized intersection are improved by considering short-term driving memory.

  4. Dynamic Modelling Reveals 'Hotspots' on the Pathway to Enzyme-Substrate Complex Formation.

    Directory of Open Access Journals (Sweden)

    Shane E Gordon

    2016-03-01

    Full Text Available Dihydrodipicolinate synthase (DHDPS catalyzes the first committed step in the diaminopimelate pathway of bacteria, yielding amino acids required for cell wall and protein biosyntheses. The essentiality of the enzyme to bacteria, coupled with its absence in humans, validates DHDPS as an antibacterial drug target. Conventional drug design efforts have thus far been unsuccessful in identifying potent DHDPS inhibitors. Here, we make use of contemporary molecular dynamics simulation and Markov state models to explore the interactions between DHDPS from the human pathogen Staphylococcus aureus and its cognate substrate, pyruvate. Our simulations recover the crystallographic DHDPS-pyruvate complex without a priori knowledge of the final bound structure. The highly conserved residue Arg140 was found to have a pivotal role in coordinating the entry of pyruvate into the active site from bulk solvent, consistent with previous kinetic reports, indicating an indirect role for the residue in DHDPS catalysis. A metastable binding intermediate characterized by multiple points of intermolecular interaction between pyruvate and key DHDPS residue Arg140 was found to be a highly conserved feature of the binding trajectory when comparing alternative binding pathways. By means of umbrella sampling we show that these binding intermediates are thermodynamically metastable, consistent with both the available experimental data and the substrate binding model presented in this study. Our results provide insight into an important enzyme-substrate interaction in atomistic detail that offers the potential to be exploited for the discovery of more effective DHDPS inhibitors and, in a broader sense, dynamic protein-drug interactions.

  5. Correlation between enzyme activity and substrate storage in a cell culture model system for Gaucher disease.

    Science.gov (United States)

    Schueler, U H; Kolter, T; Kaneski, C R; Zirzow, G C; Sandhoff, K; Brady, R O

    2004-01-01

    Gaucher disease, the most common sphingolipidosis, is caused by a decreased activity of glucosylceramide beta-glucosidase, resulting in the accumulation of glucosylceramide in macrophage-derived cells known as Gaucher cells. Much of the storage material is thought to originate from the turnover of cell membranes, such as phagocytosed red and white blood cells. In this study, an in vitro model of Gaucher disease was developed by treating the murine macrophage cell line J774 with a specific inhibitor of glucosylceramide beta-glucosidase, conduritol B-epoxide, and feeding red blood cell ghosts, in order to mimic the disease state. It was found in this model system that glucosylceramide beta-glucosidase activity could be reduced to about 11-15% of the normal control level before increased storage of glucosylceramide occurred. This in vitro system allows insight into the correlation between enzyme activity and lipid storage as predicted by the theory of residual enzyme activity that was proposed by Conzelmann and Sandhoff.

  6. Incorporation of the time aspect into the liability-threshold model for case-control-family data

    DEFF Research Database (Denmark)

    Cederkvist, Luise; Holst, Klaus K.; Andersen, Klaus K.

    2017-01-01

    Familial aggregation and the role of genetic and environmental factors can be investigated through family studies analysed using the liability-threshold model. The liability-threshold model ignores the timing of events including the age of disease onset and right censoring, which can lead...... to estimates that are difficult to interpret and are potentially biased. We incorporate the time aspect into the liability-threshold model for case-control-family data following the same approach that has been applied in the twin setting. Thus, the data are considered as arising from a competing risks setting...... and inverse probability of censoring weights are used to adjust for right censoring. In the case-control-family setting, recognising the existence of competing events is highly relevant to the sampling of control probands. Because of the presence of multiple family members who may be censored at different...

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  9. Incorporating rainfall uncertainty in a SWAT model: the river Zenne basin (Belgium) case study

    Science.gov (United States)

    Tolessa Leta, Olkeba; Nossent, Jiri; van Griensven, Ann; Bauwens, Willy

    2013-04-01

    The European Union Water Framework Directive (EU-WFD) called its member countries to achieve a good ecological status for all inland and coastal water bodies by 2015. According to recent studies, the river Zenne (Belgium) is far from this objective. Therefore, an interuniversity and multidisciplinary project "Towards a Good Ecological Status in the river Zenne (GESZ)" was launched to evaluate the effects of wastewater management plans on the river. In this project, different models have been developed and integrated using the Open Modelling Interface (OpenMI). The hydrologic, semi-distributed Soil and Water Assessment Tool (SWAT) is hereby used as one of the model components in the integrated modelling chain in order to model the upland catchment processes. The assessment of the uncertainty of SWAT is an essential aspect of the decision making process, in order to design robust management strategies that take the predicted uncertainties into account. Model uncertainty stems from the uncertainties on the model parameters, the input data (e.g, rainfall), the calibration data (e.g., stream flows) and on the model structure itself. The objective of this paper is to assess the first three sources of uncertainty in a SWAT model of the river Zenne basin. For the assessment of rainfall measurement uncertainty, first, we identified independent rainfall periods, based on the daily precipitation and stream flow observations and using the Water Engineering Time Series PROcessing tool (WETSPRO). Secondly, we assigned a rainfall multiplier parameter for each of the independent rainfall periods, which serves as a multiplicative input error corruption. Finally, we treated these multipliers as latent parameters in the model optimization and uncertainty analysis (UA). For parameter uncertainty assessment, due to the high number of parameters of the SWAT model, first, we screened out its most sensitive parameters using the Latin Hypercube One-factor-At-a-Time (LH-OAT) technique

  10. Predictors of hepatitis B cure using gene therapy to deliver DNA cleavage enzymes: a mathematical modeling approach.

    Directory of Open Access Journals (Sweden)

    Joshua T Schiffer

    Full Text Available Most chronic viral infections are managed with small molecule therapies that inhibit replication but are not curative because non-replicating viral forms can persist despite decades of suppressive treatment. There are therefore numerous strategies in development to eradicate all non-replicating viruses from the body. We are currently engineering DNA cleavage enzymes that specifically target hepatitis B virus covalently closed circular DNA (HBV cccDNA, the episomal form of the virus that persists despite potent antiviral therapies. DNA cleavage enzymes, including homing endonucleases or meganucleases, zinc-finger nucleases (ZFNs, TAL effector nucleases (TALENs, and CRISPR-associated system 9 (Cas9 proteins, can disrupt specific regions of viral DNA. Because DNA repair is error prone, the virus can be neutralized after repeated cleavage events when a target sequence becomes mutated. DNA cleavage enzymes will be delivered as genes within viral vectors that enter hepatocytes. Here we develop mathematical models that describe the delivery and intracellular activity of DNA cleavage enzymes. Model simulations predict that high vector to target cell ratio, limited removal of delivery vectors by humoral immunity, and avid binding between enzyme and its DNA target will promote the highest level of cccDNA disruption. Development of de novo resistance to cleavage enzymes may occur if DNA cleavage and error prone repair does not render the viral episome replication incompetent: our model predicts that concurrent delivery of multiple enzymes which target different vital cccDNA regions, or sequential delivery of different enzymes, are both potentially useful strategies for avoiding multi-enzyme resistance. The underlying dynamics of cccDNA persistence are unlikely to impact the probability of cure provided that antiviral therapy is given concurrently during eradication trials. We conclude by describing experiments that can be used to validate the model, which

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  13. A kinematic wave model in Lagrangian coordinates incorporating capacity drop: Application to homogeneous road stretches and discontinuities

    Science.gov (United States)

    Yuan, Kai; Knoop, Victor L.; Hoogendoorn, Serge P.

    2017-01-01

    On freeways, congestion always leads to capacity drop. This means the queue discharge rate is lower than the pre-queue capacity. Our recent research findings indicate that the queue discharge rate increases with the speed in congestion, that is the capacity drop is strongly correlated with the congestion state. Incorporating this varying capacity drop into a kinematic wave model is essential for assessing consequences of control strategies. However, to the best of authors' knowledge, no such a model exists. This paper fills the research gap by presenting a Lagrangian kinematic wave model. "Lagrangian" denotes that the new model is solved in Lagrangian coordinates. The new model can give capacity drops accompanying both of stop-and-go waves (on homogeneous freeway section) and standing queues (at nodes) in a network. The new model can be applied in a network operation. In this Lagrangian kinematic wave model, the queue discharge rate (or the capacity drop) is a function of vehicular speed in traffic jams. Four case studies on links as well as at lane-drop and on-ramp nodes show that the Lagrangian kinematic wave model can give capacity drops well, consistent with empirical observations.

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

    Science.gov (United States)

    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

  15. High-resolution Continental Scale Land Surface Model incorporating Land-water Management in United States

    Science.gov (United States)

    Shin, S.; Pokhrel, Y. N.

    2016-12-01

    Land surface models have been used to assess water resources sustainability under changing Earth environment and increasing human water needs. Overwhelming observational records indicate that human activities have ubiquitous and pertinent effects on the hydrologic cycle; however, they have been crudely represented in large scale land surface models. In this study, we enhance an integrated continental-scale land hydrology model named Leaf-Hydro-Flood to better represent land-water management. The model is implemented at high resolution (5km grids) over the continental US. Surface water and groundwater are withdrawn based on actual practices. Newly added irrigation, water diversion, and dam operation schemes allow better simulations of stream flows, evapotranspiration, and infiltration. Results of various hydrologic fluxes and stores from two sets of simulation (one with and the other without human activities) are compared over a range of river basin and aquifer scales. The improved simulations of land hydrology have potential to build consistent modeling framework for human-water-climate interactions.

  16. Analytical solutions for a soil vapor extraction model that incorporates gas phase dispersion and molecular diffusion

    Science.gov (United States)

    Huang, Junqi; Goltz, Mark N.

    2017-06-01

    To greatly simplify their solution, the equations describing radial advective/dispersive transport to an extraction well in a porous medium typically neglect molecular diffusion. While this simplification is appropriate to simulate transport in the saturated zone, it can result in significant errors when modeling gas phase transport in the vadose zone, as might be applied when simulating a soil vapor extraction (SVE) system to remediate vadose zone contamination. A new analytical solution for the equations describing radial gas phase transport of a sorbing contaminant to an extraction well is presented. The equations model advection, dispersion (including both mechanical dispersion and molecular diffusion), and rate-limited mass transfer of dissolved, separate phase, and sorbed contaminants into the gas phase. The model equations are analytically solved by using the Laplace transform with respect to time. The solutions are represented by confluent hypergeometric functions in the Laplace domain. The Laplace domain solutions are then evaluated using a numerical Laplace inversion algorithm. The solutions can be used to simulate the spatial distribution and the temporal evolution of contaminant concentrations during operation of a soil vapor extraction well. Results of model simulations show that the effect of gas phase molecular diffusion upon concentrations at the extraction well is relatively small, although the effect upon the distribution of concentrations in space is significant. This study provides a tool that can be useful in designing SVE remediation strategies, as well as verifying numerical models used to simulate SVE system performance.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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. Periglacial processes incorporated into a long-term landscape evolution model

    DEFF Research Database (Denmark)

    Andersen, Jane Lund; Egholm, D.L.; Knudsen, Mads Faurschou

    relating frost-cracking intensity to the mean annual air temperature (MAAT). The model integrates temperature variations in the subsurface following an annually oscillating surface temperature. Hales and Roering (2007) assumed that frost-cracking intensity is a simple function of the temperature gradient......Little is known about the long-term influence of periglacial processes on landscape evolution in cold areas, even though the efficiency of frost cracking on the breakdown of rocks has been documented by observations and experiments. Cold-room laboratory experiments show that a continuous water...... by their model and the elevation of scree deposits in the Southern Alps, New Zealand. This result suggests a link between frost-cracking efficiency and long-term landscape evolution and thus merits further investigations. Anderson et al. (2012) expanded this early model by including the effects of latent heat...

  20. Modeling & Informatics at Vertex Pharmaceuticals Incorporated: our philosophy for sustained impact

    Science.gov (United States)

    McGaughey, Georgia; Patrick Walters, W.

    2016-11-01

    Molecular modelers and informaticians have the unique opportunity to integrate cross-functional data using a myriad of tools, methods and visuals to generate information. Using their drug discovery expertise, information is transformed to knowledge that impacts drug discovery. These insights are often times formulated locally and then applied more broadly, which influence the discovery of new medicines. This is particularly true in an organization where the members are exposed to projects throughout an organization, such as in the case of the global Modeling & Informatics group at Vertex Pharmaceuticals. From its inception, Vertex has been a leader in the development and use of computational methods for drug discovery. In this paper, we describe the Modeling & Informatics group at Vertex and the underlying philosophy, which has driven this team to sustain impact on the discovery of first-in-class transformative medicines.

  1. The design of a wind tunnel VSTOL fighter model incorporating turbine powered engine simulators

    Science.gov (United States)

    Bailey, R. O.; Maraz, M. R.; Hiley, P. E.

    1981-01-01

    A wind-tunnel model of a supersonic VSTOL fighter aircraft configuration has been developed for use in the evaluation of airframe-propulsion system aerodynamic interactions. The model may be employed with conventional test techniques, where configuration aerodynamics are measured in a flow-through mode and incremental nozzle-airframe interactions are measured in a jet-effects mode, and with the Compact Multimission Aircraft Propulsion Simulator which is capable of the simultaneous simulation of inlet and exhaust nozzle flow fields so as to allow the evaluation of the extent of inlet and nozzle flow field coupling. The basic configuration of the twin-engine model has a geometrically close-coupled canard and wing, and a moderately short nacelle with nonaxisymmetric vectorable exhaust nozzles near the wing trailing edge, and may be converted to a canardless configuration with an extremely short nacelle. Testing is planned to begin in the summer of 1982.

  2. Incorporation of leaf nitrogen observations for biochemical and environmental modeling of photosynthesis and evapotranspiration

    DEFF Research Database (Denmark)

    Boegh, E; Gjetterman, B; Abrahamsen, P

    2007-01-01

    relation to photosynthetic (Rubisco) capacity should also be known to quantify leaf N impacts on canopy photosynthesis. In this study, impacts of the amount and vertical distribution of leaf N contents on canopy photosynthesis were investigated by combining field measurements and photosynthesis modelling....... While most canopy photosynthesis models assume an exponential vertical profile of leaf N contents in the canopy, the field measurements showed that well-fertilized fields may have a uniform or exponential profile, and senescent canopies have reduced levels of N contents in upper leaves. The sensitivity...... of simulated canopy photosynthesis to the different (observed) N profiles was examined using a multi-layer sun/shade biochemically based photosynthesis model and found to be important; ie. for a well-fertilized barley field, the use of exponential instead of uniform vertical N profiles increased the annual...

  3. Eatwell Guide: modelling the dietary and cost implications of incorporating new sugar and fibre guidelines

    DEFF Research Database (Denmark)

    Scarborough, Peter; Kaur, Asha; Cobiac, Linda

    2016-01-01

    Objectives To model food group consumption and price of diet associated with achieving UK dietary recommendations while deviating as little as possible from the current UK diet, in order to support the redevelopment of the UK food-based dietary guidelines (now called the Eatwell Guide). Design...... Optimisation modelling, minimising an objective function of the difference between population mean modelled and current consumption of 125 food groups, and constraints of nutrient and food-based recommendations. Setting The UK. Population Adults aged 19 years and above from the National Diet and Nutrition...... Survey 2008–2011. Main outcome measures Proportion of diet consisting of major foods groups and price of the optimised diet. Results The optimised diet has an increase in consumption of ‘potatoes, bread, rice, pasta and other starchy carbohydrates’ (+69%) and ‘fruit and vegetables’ (+54%) and reductions...

  4. Incorporation of leaf nitrogen observations for biochemical and environmental modeling of photosynthesis and evapotranspiration

    DEFF Research Database (Denmark)

    Boegh, E; Gjetterman, B; Abrahamsen, P

    2007-01-01

    relation to photosynthetic (Rubisco) capacity should also be known to quantify leaf N impacts on canopy photosynthesis. In this study, impacts of the amount and vertical distribution of leaf N contents on canopy photosynthesis were investigated by combining field measurements and photosynthesis modelling....... While most canopy photosynthesis models assume an exponential vertical profile of leaf N contents in the canopy, the field measurements showed that well-fertilized fields may have a uniform or exponential profile, and senescent canopies have reduced levels of N contents in upper leaves. The sensitivity...... of simulated canopy photosynthesis to the different (observed) N profiles was examined using a multi-layer sun/shade biochemically based photosynthesis model and found to be important; ie. for a well-fertilized barley field, the use of exponential instead of uniform vertical N profiles increased the annual...

  5. Modeling & Informatics at Vertex Pharmaceuticals Incorporated: our philosophy for sustained impact

    Science.gov (United States)

    McGaughey, Georgia; Patrick Walters, W.

    2017-03-01

    Molecular modelers and informaticians have the unique opportunity to integrate cross-functional data using a myriad of tools, methods and visuals to generate information. Using their drug discovery expertise, information is transformed to knowledge that impacts drug discovery. These insights are often times formulated locally and then applied more broadly, which influence the discovery of new medicines. This is particularly true in an organization where the members are exposed to projects throughout an organization, such as in the case of the global Modeling & Informatics group at Vertex Pharmaceuticals. From its inception, Vertex has been a leader in the development and use of computational methods for drug discovery. In this paper, we describe the Modeling & Informatics group at Vertex and the underlying philosophy, which has driven this team to sustain impact on the discovery of first-in-class transformative medicines.

  6. Novel Method for Incorporating Model Uncertainties into Gravitational Wave Parameter Estimates

    CERN Document Server

    Moore, Christopher J

    2014-01-01

    Posterior distributions on parameters computed from experimental data using Bayesian techniques are only as accurate as the models used to construct them. In many applications these models are incomplete, which both reduces the prospects of detection and leads to a systematic error in the parameter estimates. In the analysis of data from gravitational wave detectors, for example, accurate waveform templates can be computed using numerical methods, but the prohibitive cost of these simulations means this can only be done for a small handful of parameters. In this work a novel method to fold model uncertainties into data analysis is proposed; the waveform uncertainty is analytically marginalised over using with a prior distribution constructed by using Gaussian process regression to interpolate the waveform difference from a small training set of accurate templates. The method is well motivated, easy to implement, and no more computationally expensive than standard techniques. The new method is shown to perform...

  7. Modeling of lithium-sulfur batteries incorporating the effect of Li2S precipitation

    Science.gov (United States)

    Ren, Y. X.; Zhao, T. S.; Liu, M.; Tan, P.; Zeng, Y. K.

    2016-12-01

    In this work, we present a one-dimensional model for the discharge behavior of lithium-sulfur (Li-S) batteries. In addition to the consideration of multiple-step polysulfide dissolution and reductions, the surface nucleation and growth kinetics coupled with electrochemical reactions is particularly exploited for describing the Li2S precipitation. Unlike previous models that overlook the rate-dependent precipitation phenomenon, our model reveals that discrete Li2S particle growth becomes suppressed at higher rates, resulting in smaller Li2S precipitates with a more uniform particle size distribution and a limited discharge capacity. Experimental discharge curves and discharge product observation adequately confirm our numerical results. It is further predicted that promoting the growth of Li2S particles, including lowering the initial nucleation rate and providing a suitable amount of initial nucleation sites, can efficiently prolong the Li-S battery's discharge capacity.

  8. Enzyme hydrolysis of plasma proteins in a CSTR ultrafiltration reactor: Performances and modeling.

    Science.gov (United States)

    Bressollier, P; Petit, J M; Julien, R

    1988-05-01

    By investigating the effects of four operating variables-volume (V), Ultrafiltration flux (J), enzyme concentration (E), and substrate concentration (S)-on capacity (K) and conversion rate (epsilon) of a hollow fiber CSTR, the performances of the CSTR and the kinetic constants of the reaction were determined. A model which takes into account the course of fractional conversion (X) according to the modified space-time parameter, tau (integrated form of V, J, S, and E), was devised by employing the relationship to integrate the equation for the reaction rate of the CSTR and the expression of the modified space time. Correlation of this model and the experimentally obtained results demonstrates that the characteristics for an ultrafiltration membrane reactor for enzymatic hydrolysis by alcalase of plasma proteins are close to those of an ideal CSTR. Optimal scaling up, however, remains dependent on the compromise which may be obtained between capacity and the conversion rate.

  9. A model-based framework for design of intensified enzyme-based processes

    DEFF Research Database (Denmark)

    Román-Martinez, Alicia

    This thesis presents a generic and systematic model-based framework to design intensified enzyme-based processes. The development of the presented methodology was motivated by the needs of the bio-based industry for a more systematic approach to achieve intensification in its production plants...... space is reduced to locate the candidate process options, giving an optimal design where further experimental efforts can be focused on. The application of a generic and systematic model-based framework is illustrated through a case study involving the production of an important intermediate...... without an excessive investment in experimental resources. Process intensification has recently gained a lot of attention since it is a holistic approach to design safer, cleaner, smaller, cheaper and more efficient processes. This dissertation proposes a methodological approach to achieve intensification...

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Qiushi, E-mail: qiushi@clemson.edu [Glenn Department of Civil Engineering, Clemson University, Clemson, SC 29634 (United States); Ostien, Jakob T., E-mail: jtostie@sandia.gov [Mechanics of Materials Dept. 8256, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969 (United States); Hansen, Glen, E-mail: gahanse@sandia.gov [Computational Multiphysics Dept. 1443, Sandia National Laboratories, P.O. Box 5800, Albuquerque, NM 87185-1321 (United States)

    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 J{sub 2} 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.

  12. Anti-BlyS antibody reduces the immune reaction against enzyme and enhances the efficacy of enzyme replacement therapy in Fabry disease model mice.

    Science.gov (United States)

    Sato, Yohei; Ida, Hiroyuki; Ohashi, Toya

    2017-02-02

    Formation of antibodies against a therapeutic enzyme is an important complication during enzyme replacement therapy (ERT) for lysosomal storage diseases. Fabry disease (FD) is caused by a deficiency of alpha-galactosidase (GLA), which results in the accumulation of globotriaosylceramide (GL-3). We have shown immune tolerance induction (ITI) during ERT in FD model mice by using an anti-B lymphocyte stimulator (anti-BlyS) antibody (belimumab). A single dose of the anti-BlyS antibody temporarily lowered the percentage of B cells and IgG antibody titer against recombinant human GLA. Administration of a low maintenance dose of the anti-BlyS antibody suppressed the B cell population and immunotolerance was induced in 20% of mice, but antibody formation could not be prevented. We then increased the maintenance dose of the anti-BlyS antibody and immunotolerance was induced in 50% of mice. Therapeutic enzyme distribution and clearance of GL-3 were also enhanced by a high maintenance dose of the anti-BlyS antibody.

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

    Science.gov (United States)

    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.

  14. An Improved Atmospheric Vector Radiative Transfer Model Incorporating Rough Ocean Boundaries

    Institute of Scientific and Technical Information of China (English)

    FAN Xue-Hua; CHEN Hong-Bin; HAN Zhi-Gang; LIN Long-Fu

    2010-01-01

    The radiative transfer model (RT3), a vector radiative transfer (VRT) scheme in a plane-parallel at-mosphere, was bounded by a rough ocean surface in this study. The boundary problem was solved using a Fourier series decomposition of the radiation field as a function of the azimuth. For the case of a rough ocean surface, the decomposition was obtained by developing both the Fresnel reflection matrix and the probability distribution of the water facet orientation as Fourier series. The effect of shadowing by ocean surface waves was also considered in the boundary condition. The VRT model can compute the intensity and degree of polarization of the light at the top of the atmosphere (TOA), the ocean surface, and any level of the atmosphere in the ocean-atmosphere system. The results obtained by our model are in good agreement with those computed by Ahmad's model. The simulated results showed that the shadow effects of wave facets on the intensity and the degree of polarization are negligible except at the ocean surface near the grazing angle, possi-bly because we did not consider the effect of white caps.

  15. An explicit surface-potential-based MOSFET model incorporating the quantum mechanical effects

    Science.gov (United States)

    Basu, Dipanjan; Dutta, Aloke K.

    2006-07-01

    An explicit surface-potential-based MOSFET model has been proposed in this work here, which takes into account the quantum mechanical effects that arise in deep-submicron MOSFETs. The coupled Schrödinger's and Poisson's equations have been solved by using a variational wave function approach, as proposed by Fang and Howard. The resulting surface potential model is analytical, technology mapped, and completely continuous over the entire range of operation. The surface potential and the inversion charge density calculated using the proposed model show good match with the results of the numerical simulations obtained from a self-consistent Schrödinger-Poisson solver for a wide range of substrate doping and oxide thickness. The simulated values of the drain current match closely with the experimental results published elsewhere. The device small-signal parameters, e.g., transconductance, output conductance, etc., pass the standard benchmark tests suggested by Suyama and Tsividis qualitatively, thereby validating the approach of the model presented.

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

    Science.gov (United States)

    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.

  17. Development of a mission-based funding model for undergraduate medical education: incorporation of quality.

    Science.gov (United States)

    Stagnaro-Green, Alex; Roe, David; Soto-Greene, Maria; Joffe, Russell

    2008-01-01

    Increasing financial pressures, along with a desire to realign resources with institutional priorities, has resulted in the adoption of mission-based funding (MBF) at many medical schools. The lack of inclusion of quality and the time and expense in developing and implementing mission based funding are major deficiencies in the models reported to date. In academic year 2002-2003 New Jersey Medical School developed a model that included both quantity and quality in the education metric and that was departmentally based. Eighty percent of the undergraduate medical education allocation was based on the quantity of undergraduate medical education taught by the department ($7.35 million), and 20% ($1.89 million) was allocated based on the quality of the education delivered. Quality determinations were made by the educational leadership based on student evaluations and departmental compliance with educational administrative requirements. Evolution of the model has included the development of a faculty oversight committee and the integration of peer evaluation in the determination of educational quality. Six departments had a documented increase in quality over time, and one department had a transient decrease in quality. The MBF model has been well accepted by chairs, educational leaders, and faculty and has been instrumental in enhancing the stature of education at our institution.

  18. Incorporating Religiosity into a Developmental Model of Positive Family Functioning across Generations

    Science.gov (United States)

    Spilman, Sarah K.; Neppl, Tricia K.; Donnellan, M. Brent; Schofield, Thomas J.; Conger, Rand D.

    2013-01-01

    This study evaluated a developmental model of intergenerational continuity in religiosity and its association with observed competency in romantic and parent-child relationships across 2 generations. Using multi-informant data from the Family Transitions Project, a 20-year longitudinal study of families that began during early adolescence (N =…

  19. Incorporating Logistics in Freight Transport Demand Models: State-of-the-Art and Research Opportunities

    NARCIS (Netherlands)

    Tavasszy, L.A.; Ruijgrok, K.; Davydenko, I.

    2012-01-01

    Freight transport demand is a demand derived from all the activities needed to move goods between locations of production to locations of consumption, including trade, logistics and transportation. A good representation of logistics in freight transport demand models allows us to predict the effects

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

    Science.gov (United States)

    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...

  1. Incorporating Religiosity into a Developmental Model of Positive Family Functioning across Generations

    Science.gov (United States)

    Spilman, Sarah K.; Neppl, Tricia K.; Donnellan, M. Brent; Schofield, Thomas J.; Conger, Rand D.

    2013-01-01

    This study evaluated a developmental model of intergenerational continuity in religiosity and its association with observed competency in romantic and parent-child relationships across 2 generations. Using multi-informant data from the Family Transitions Project, a 20-year longitudinal study of families that began during early adolescence (N =…

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

    Science.gov (United States)

    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…

  3. Predicting the Term Structure of Interest Rates: Incorporating parameter uncertainty, model uncertainty and macroeconomic information

    NARCIS (Netherlands)

    M.D. de Pooter (Michiel); F. Ravazzolo (Francesco); D.J.C. van Dijk (Dick)

    2007-01-01

    textabstractWe forecast the term structure of U.S. Treasury zero-coupon bond yields by analyzing a range of models that have been used in the literature. We assess the relevance of parameter uncertainty by examining the added value of using Bayesian inference compared to frequentist estimation

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

    Science.gov (United States)

    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 ...

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

    Science.gov (United States)

    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.

  6. Incorporating Protein Biosynthesis into the Saccharomyces cerevisiae Genome-scale Metabolic Model

    DEFF Research Database (Denmark)

    Olivares Hernandez, Roberto

    by a rapidly growing cell. To extend the model including protein synthesis, from the survey of the available literature was possible to identify a few enzymatic reactions and gene functions in the early steps of gene expression for proteins: mRNA transcription, mRNA processing, mRNA export out of the nucleus...

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

    Science.gov (United States)

    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…

  8. Novel method for incorporating model uncertainties into gravitational wave parameter estimates.

    Science.gov (United States)

    Moore, Christopher J; Gair, Jonathan R

    2014-12-19

    Posterior distributions on parameters computed from experimental data using Bayesian techniques are only as accurate as the models used to construct them. In many applications, these models are incomplete, which both reduces the prospects of detection and leads to a systematic error in the parameter estimates. In the analysis of data from gravitational wave detectors, for example, accurate waveform templates can be computed using numerical methods, but the prohibitive cost of these simulations means this can only be done for a small handful of parameters. In this Letter, a novel method to fold model uncertainties into data analysis is proposed; the waveform uncertainty is analytically marginalized over using with a prior distribution constructed by using Gaussian process regression to interpolate the waveform difference from a small training set of accurate templates. The method is well motivated, easy to implement, and no more computationally expensive than standard techniques. The new method is shown to perform extremely well when applied to a toy problem. While we use the application to gravitational wave data analysis to motivate and illustrate the technique, it can be applied in any context where model uncertainties exist.

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

    Science.gov (United States)

    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.…

  10. Sensitizing effect of Z,Z-bilirubin IXα and its photoproducts on enzymes in model solutions

    Science.gov (United States)

    Plavskii, V. Yu.; Mostovnikov, V. A.; Tret'yakova, A. I.; Mostovnikova, G. R.

    2008-05-01

    In model systems, we have studied side effects which may be induced by light during phototherapy of hyperbilirubinemia (jaundice) in newborn infants, with the aim of reducing the Z,Z-bilirubin IXα (Z,Z-BR IXα) level. We have shown that the sensitizing effect of Z,Z-BR IXα, localized at strong binding sites of the human serum albumin (HSA) macromolecule, is primarily directed at the amino acid residues of the carrier protein and does not involve the molecules of the enzyme (lactate dehydrogenase (LDH)) present in the buffer solution. The detected photodynamic damage to LDH is due to sensitization by bilirubin photoisomers, characterized by lower HSA association constants and located (in contrast to native Z,Z-BR IXα) on the surface of the HSA protein globule. Based on study of the spectral characteristics of the photoproducts of Z,Z-BR IXα and comparison of their accumulation kinetics in solution and the enzyme photo-inactivation kinetics, we concluded that the determining role in sensitized damage to LDH is played by lumirubin. The photosensitization effect depends on the wavelength of the radiation used for photoconversion of bilirubin. When (at the beginning of exposure) we make sure that identical numbers of photons are absorbed by the pigment in the different spectral ranges, the side effect is minimal for radiation corresponding to the long-wavelength edge of the bilirubin absorption band. We have shown that for a bilirubin/HSA concentration ratio >2 (when some of the pigment molecules are sorbed on the surface of the protein globule), the bilirubin can act as a photosensitizing agent for the enzyme present in solution. We discuss methods for reducing unfavorable side effects of light on the body of newborn infants during phototherapy of hyperbilirubinemia.

  11. A multi-component model of the developing retinocollicular pathway incorporating axonal and synaptic growth.

    Directory of Open Access Journals (Sweden)

    Keith B Godfrey

    2009-12-01

    Full Text Available During development, neurons extend axons to different brain areas and produce stereotypical patterns of connections. The mechanisms underlying this process have been intensively studied in the visual system, where retinal neurons form retinotopic maps in the thalamus and superior colliculus. The mechanisms active in map formation include molecular guidance cues, trophic factor release, spontaneous neural activity, spike-timing dependent plasticity (STDP, synapse creation and retraction, and axon growth, branching and retraction. To investigate how these mechanisms interact, a multi-component model of the developing retinocollicular pathway was produced based on phenomenological approximations of each of these mechanisms. Core assumptions of the model were that the probabilities of axonal branching and synaptic growth are highest where the combined influences of chemoaffinity and trophic factor cues are highest, and that activity-dependent release of trophic factors acts to stabilize synapses. Based on these behaviors, model axons produced morphologically realistic growth patterns and projected to retinotopically correct locations in the colliculus. Findings of the model include that STDP, gradient detection by axonal growth cones and lateral connectivity among collicular neurons were not necessary for refinement, and that the instructive cues for axonal growth appear to be mediated first by molecular guidance and then by neural activity. Although complex, the model appears to be insensitive to variations in how the component developmental mechanisms are implemented. Activity, molecular guidance and the growth and retraction of axons and synapses are common features of neural development, and the findings of this study may have relevance beyond organization in the retinocollicular pathway.

  12. Modeling Ear-Canal Acoustics, Incorporating Visco-Thermal Effects and the Influence of the Middle Ear

    Science.gov (United States)

    Gowdy, Lauren E.; Withnell, Robert H.

    2011-11-01

    The ear canal, below about 6 kHz, is well described by a uniform cylinder (sound propagates predominantly as plane waves) with the middle ear being a non-rigid termination. A non-rigid termination can be viewed as altering, as a function of frequency, the acoustic length and radius of the cylinder. It is generally assumed that sound transmission in the ear canal over this frequency range is lossless. This paper presents a method for calculating the influence of visco-thermal losses and the middle ear on ear canal acoustics. The acoustic input impedance was derived from sound pressure measurements in the ear canal and then a nonlinear least-square-fit to the data with a one-dimensional model incorporating visco-thermal losses generated length, radius, and middle ear impedance parameters. It was found that a rigid wall assumption for visco-thermal calculations was insufficient to account for damping in the ear canal. The properties of the ear canal wall (not being a rigid, low-friction surface), incorporated into visco-thermal losses as a scaling factor, provided a better fit to the data. Viscous and thermal losses were both found to affect sound propagation in the ear canal, viscous losses being more significant, altering the acoustic input impedance of the ear primarily in the region of the standing wave frequency. The model data suggests that the middle ear influences ear canal acoustics up to about 3 kHz.

  13. A density dependent delayed predator-prey model with Beddington-DeAngelis type function response incorporating a prey refuge

    Science.gov (United States)

    Tripathi, Jai Prakash; Abbas, Syed; Thakur, Manoj

    2015-05-01

    This paper describes a predator-prey model incorporating a prey refuge. The feeding rate of consumers (predators) per consumer (i.e. functional response) is considered to be of Beddington-DeAngelis type. The Beddington-DeAngelis functional response is similar to the Holling-type II functional response but contains an extra term describing mutual interference by predators. We investigate the role of prey refuge and degree of mutual interference among predators in the dynamics of system. The dynamics of the system is discussed mainly from the point of view of permanence and stability. We obtain conditions that affect the persistence of the system. Local and global asymptotic stability of various equilibrium solutions is explored to understand the dynamics of the model system. The global asymptotic stability of positive interior equilibrium solution is established using suitable Lyapunov functional. The dynamical behaviour of the delayed system is further analyzed through incorporating discrete type gestation delay of predator. It is found that Hopf bifurcation occurs when the delay parameter τ crosses some critical value. The analytical results found in the paper are illustrated with the help of numerical examples.

  14. Incorporation of water vapor transfer in the JULES land surface model: Implications for key soil variables and land surface fluxes

    Science.gov (United States)

    Garcia Gonzalez, Raquel; Verhoef, Anne; Luigi Vidale, Pier; Braud, Isabelle

    2012-05-01

    This study focuses on the mechanisms underlying water and heat transfer in upper soil layers, and their effects on soil physical prognostic variables and the individual components of the energy balance. The skill of the JULES (Joint UK Environment Simulator) land surface model (LSM) to simulate key soil variables, such as soil moisture content and surface temperature, and fluxes such as evaporation, is investigated. The Richards equation for soil water transfer, as used in most LSMs, was updated by incorporating isothermal and thermal water vapor transfer. The model was tested for three sites representative of semiarid and temperate arid climates: the Jornada site (New Mexico, USA), Griffith site (Australia), and Audubon site (Arizona, USA). Water vapor flux was found to contribute significantly to the water and heat transfer in the upper soil layers. This was mainly due to isothermal vapor diffusion; thermal vapor flux also played a role at the Jornada site just after rainfall events. Inclusion of water vapor flux had an effect on the diurnal evolution of evaporation, soil moisture content, and surface temperature. The incorporation of additional processes, such as water vapor flux among others, into LSMs may improve the coupling between the upper soil layers and the atmosphere, which in turn could increase the reliability of weather and climate predictions.

  15. Incorporating the influence of sub-grid heterogeneity in regional-scale contaminant transport models

    CERN Document Server

    Baeumer, Boris; Schumer, Rina

    2013-01-01

    Numerical transport models based on the advection-dispersion equation (ADE) are built on the assumption that sub-grid cell transport is Fickian such that dispersive spreading around the average velocity is symmetric and without significant tailing on the front edge of a solute plume. However, anomalous diffusion in the form of super-diffusion due to preferential pathways in an aquifer has been observed in field data, challenging the assumption of Fickian dispersion at the local scale. This study develops a fully Lagrangian method to simulate sub-grid super-diffusion in a multi-dimensional regional-scale transport. The underlying concept is based on previous observations that solutions to space-fractional ADEs, which can describe super-diffusive dispersion, can be obtained by transforming solutions of classical ADEs. The transformations are equivalent to randomizing particle travel time or relative velocity for each model time step. Here, the time randomizing procedure known as subordination is applied to flow...

  16. Incorporating social contact data in spatio-temporal models for infectious disease spread

    CERN Document Server

    Meyer, Sebastian

    2015-01-01

    Routine public health surveillance of notifiable infectious diseases gives rise to weekly counts of reported cases - possibly stratified by region and/or age group. A well-established approach to the statistical analysis of such surveillance data are endemic-epidemic time-series models. The temporal dependence inherent to communicable diseases is thereby taken into account by an observation-driven formulation conditioning on past counts. Additional spatial dynamics in areal-level counts are largely driven by human travel and can be captured by power-law weights based on the order of adjacency. However, social contacts are highly assortative also with respect to age. For example, characteristic pathways of directly transmitted pathogens are linked to childcare facilities, schools and nursing homes. We therefore investigate how a spatio-temporal endemic-epidemic model can be extended to take social contact data into account. The approach is illustrated in a case study on norovirus gastroenteritis in Berlin, 201...

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

    Science.gov (United States)

    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.

  18. A Dynamic Economic Dispatch Model Incorporating Wind Power Based on Chance Constrained Programming

    Directory of Open Access Journals (Sweden)

    Wushan Cheng

    2014-12-01

    Full Text Available In order to maintain the stability and security of the power system, the uncertainty and intermittency of wind power must be taken into account in economic dispatch (ED problems. In this paper, a dynamic economic dispatch (DED model based on chance constrained programming is presented and an improved particle swarm optimization (PSO approach is proposed to solve the problem. Wind power is regarded as a random variable and is included in the chance constraint. New formulation of up and down spinning reserve constraints are presented under expectation meaning. The improved PSO algorithm combines a feasible region adjustment strategy with a hill climbing search operation based on the basic PSO. Simulations are performed under three distinct test systems with different generators. Results show that both the proposed DED model and the improved PSO approach are effective.

  19. Incorporating prediction models in the SelfLet framework: a plugin approach

    CERN Document Server

    Calcavecchia, Nicolo' Maria

    2010-01-01

    A complex pervasive system is typically composed of many cooperating \\emph{nodes}, running on machines with different capabilities, and pervasively distributed across the environment. These systems pose several new challenges such as the need for the nodes to manage autonomously and dynamically in order to adapt to changes detected in the environment. To address the above issue, a number of autonomic frameworks has been proposed. These usually offer either predefined self-management policies or programmatic mechanisms for creating new policies at design time. From a more theoretical perspective, some works propose the adoption of prediction models as a way to anticipate the evolution of the system and to make timely decisions. In this context, our aim is to experiment with the integration of prediction models within a specific autonomic framework in order to assess the feasibility of such integration in a setting where the characteristics of dynamicity, decentralization, and cooperation among nodes are import...

  20. Incorporation of Advanced Activation Treatments into CESM/CAM5: Model Evaluation and Impacts on Aerosol Indirect Forcing

    Science.gov (United States)

    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

  1. A SEASONAL INFLUENZA THEORY AND MATHEMATICAL MODEL INCORPORATING METEOROLOGICAL AND SOCIO- BEHAVIORAL FACTORS

    Institute of Scientific and Technical Information of China (English)

    Zhixiang ZHOU

    2009-01-01

    On the basis of a comprehensive literature review and data analysis of global influenza surveillance,a transmission theory based numerical model is developed to understand the causative factors of influenza seasonality and the biodynamical mechanisms of seasonal flu. The model is applied to simulate the seasonality and weekly activity of influenza in different areas across all continents and climate zones around the world. Model solution and the good matches between model output and actual influenza indexes affirm that influenza activity is highly auto-correlative and relies on determinants of a broad spectrum. Internal dynamic resonance; variations of meteorological elements (solar radiation,precipitation and dewpoint); socio-behavioral influences and herd immunity to circulating strains prove to be the critical explanatory thctors of the seasonality and weekly activity of influenza. In all climate regions,influenza activity is proportional to the exponential of the number of days with precipitation and to the negative exponential of quarter power of sunny hours. Influenza activity is a negative exponential function of dewpoint in temperate and arctic regions and an exponential function of the absolute deviation of dewpoint from its annual mean in the tropics. Epidemics of seasonal influenza could be deemed as the consequence of the dynamic resonance and interactions of determinants. Early interventions (such as opportune vaccination,prompt social distancing,and maintaining incidence well below a baseline) are key to the control and prevention of seasonal influenza. Moderate amount of sunlight exposure or Vitamin D supplementation during rainy and short-day photoperiod seasons,more outdoor activities,and appropriate indoor dewpoint deserve great attention in influenza prevention. To a considerable degree,the study reveals the mechanism of inlluenza seasonality,demonstrating a potential for influenza activity projection. The concept and algorithm can be explored

  2. Finite Element Surface Registration Incorporating Curvature, Volume Preservation, and Statistical Model Information

    Directory of Open Access Journals (Sweden)

    Thomas Albrecht

    2013-01-01

    Full Text Available 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.

  3. Incorporating microbial ecology into the metabolic modelling of polyphosphate accumulating organisms and glycogen accumulating organisms.

    Science.gov (United States)

    Oehmen, A; Carvalho, G; Lopez-Vazquez, C M; van Loosdrecht, M C M; Reis, M A M

    2010-09-01

    In the enhanced biological phosphorus removal (EBPR) process, the competition between polyphosphate accumulating organisms (PAO) and glycogen accumulating organisms (GAO) has been studied intensively in recent years by both microbiologists and engineers, due to its important effects on phosphorus removal performance and efficiency. This study addresses the impact of microbial ecology on assessing the PAO-GAO competition through metabolic modelling, focussing on reviewing recent developments, discussion of how the results from molecular studies can impact the way we model the process, and offering perspectives for future research opportunities based on unanswered questions concerning PAO and GAO metabolism. Indeed, numerous findings that are seemingly contradictory could in fact be explained by the metabolic behaviour of different sub-groups of PAOs and/or GAOs exposed to different environmental and operational conditions. Some examples include the glycolysis pathway (i.e. Embden-Meyerhof-Parnas (EMP) vs. Entner-Doudoroff (ED)), denitrification capacity, anaerobic tricarboxylic acid (TCA) cycle activity and PAOs' ability to adjust their metabolism to e.g. a GAO-like metabolism. Metabolic modelling may further yield far-reaching influences on practical applications as well, and serves as a bridge between molecular/biochemical research studies and the optimisation of wastewater treatment plant operation. Copyright © 2010 Elsevier Ltd. All rights reserved.

  4. Incorporating temporal heterogeneity in environmental conditions into a somatic growth model

    Science.gov (United States)

    Dzul, Maria C.; Yackulic, Charles B.; Korman, Josh; Yard, Michael D.; Muehlbauer, Jeffrey D.

    2017-01-01

    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.

  5. A rat experimental model of glaucoma incorporating rapid-onset elevation of intraocular pressure

    Science.gov (United States)

    Smedowski, Adrian; Pietrucha-Dutczak, Marita; Kaarniranta, Kai; Lewin-Kowalik, Joanna

    2014-01-01

    Glaucoma is a chronic disease that causes structural and functional damage to retinal ganglion cells (RGC). The currently employed therapeutic options are not sufficient to prevent vision loss in patients with glaucoma; therefore, there is a need to develop novel therapies, which requires the creation of functional, repeatable and easy-to-utilize animal models for use in pre-clinical studies. The currently available models ensure only low to moderate damage in optic nerves, with high variation in the outcomes and poor repeatability. We have developed an effective and reproducible rat glaucoma model based on a previous idea for a “Bead Model” in mice, which could be useful in future glaucoma research. Additionally, in an attempt to achieve rapid elevation of Intraocular Pressure (IOP), we included an initial “high-pressure injury” as part of this method, which serves as the equivalent of a severe glaucoma attack. These modifications made it possible to achieve longer lasting IOP elevation with chronic damage of retinal ganglion cells. PMID:25081302

  6. A Partition-Based Active Contour Model Incorporating Local Information for Image Segmentation

    Directory of Open Access Journals (Sweden)

    Jiao Shi

    2014-01-01

    Full Text Available 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. A partition-based active contour model incorporating local information for image segmentation.

    Science.gov (United States)

    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.

  8. Incorporating institutions and collective action into a sociohydrological model of flood resilience

    Science.gov (United States)

    Yu, David J.; Sangwan, Nikhil; Sung, Kyungmin; Chen, Xi; Merwade, Venkatesh

    2017-02-01

    Stylized sociohydrological models have mainly used social memory aspects such as community awareness or sensitivity to connect hydrologic change and social response. However, social memory alone does not satisfactorily capture the details of how human behavior is translated into collective action for water resources governance. Nor is it the only social mechanism by which the two-way feedbacks of sociohydrology can be operationalized. This study contributes toward bridging of this gap by developing a sociohydrological model of a flood resilience that includes two additional components: (1) institutions for collective action, and (2) connections to an external economic system. Motivated by the case of community-managed flood protection systems (polders) in coastal Bangladesh, we use the model to understand critical general features that affect long-term resilience of human-flood systems. Our findings suggest that occasional adversity can enhance long-term resilience. Allowing some hydrological variability to enter into the polder can increase its adaptive capacity for resilience through the preservation of social norm for collective action. Further, there are potential trade-offs associated with optimization of flood resistance through structural measures. By reducing sensitivity to floods, the system may become more fragile under the double impact of floods and economic change.

  9. Information spreading on mobile communication networks: A new model that incorporates human behaviors

    Science.gov (United States)

    Ren, Fei; Li, Sai-Ping; Liu, Chuang

    2017-03-01

    Recently, there is a growing interest in the modeling and simulation based on real social networks among researchers in multi-disciplines. Using an empirical social network constructed from the calling records of a Chinese mobile service provider, we here propose a new model to simulate the information spreading process. This model takes into account two important ingredients that exist in real human behaviors: information prevalence and preferential spreading. The fraction of informed nodes when the system reaches an asymptotically stable state is primarily determined by information prevalence, and the heterogeneity of link weights would slow down the information diffusion. Moreover, the sizes of blind clusters which consist of connected uninformed nodes show a power-law distribution, and these uninformed nodes correspond to a particular portion of nodes which are located at special positions in the network, namely at the edges of large clusters or inside the clusters connected through weak links. Since the simulations are performed on a real world network, the results should be useful in the understanding of the influences of social network structures and human behaviors on information propagation.

  10. Absorbed dose evaluation based on a computational voxel model incorporating distinct cerebral structures

    Energy Technology Data Exchange (ETDEWEB)

    Brandao, Samia de Freitas; Trindade, Bruno; Campos, Tarcisio P.R. [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil)]. E-mail: samiabrandao@gmail.com; bmtrindade@yahoo.com; campos@nuclear.ufmg.br

    2007-07-01

    Brain tumors are quite difficult to treat due to the collateral radiation damages produced on the patients. Despite of the improvements in the therapeutics protocols for this kind of tumor, involving surgery and radiotherapy, the failure rate is still extremely high. This fact occurs because tumors can not often be totally removed by surgery since it may produce some type of deficit in the cerebral functions. Radiotherapy is applied after the surgery, and both are palliative treatments. During radiotherapy the brain does not absorb the radiation dose in homogeneous way, because the various density and chemical composition of tissues involved. With the intention of evaluating better the harmful effects caused by radiotherapy it was developed an elaborated cerebral voxel model to be used in computational simulation of the irradiation protocols of brain tumors. This paper presents some structures function of the central nervous system and a detailed cerebral voxel model, created in the SISCODES program, considering meninges, cortex, gray matter, white matter, corpus callosum, limbic system, ventricles, hypophysis, cerebellum, brain stem and spinal cord. The irradiation protocol simulation was running in the MCNP5 code. The model was irradiated with photons beam whose spectrum simulates a linear accelerator of 6 MV. The dosimetric results were exported to SISCODES, which generated the isodose curves for the protocol. The percentage isodose curves in the brain are present in this paper. (author)

  11. Kinetic model for the co-action of beta-amylase and debranching enzymes in the production of maltose.

    Science.gov (United States)

    Jiahua, Z

    1999-03-05

    The kinetics of the hydrolysis of starch with beta-amylase and debranching enzymes was studied. The hydrolysis of the alpha-1, 6-glycoside bonds of the substrate by debranching enzymes does not create any new nonreducing ends, so debranching enzyme promotes the action of beta-amylase not by increasing the concentration of the substrate of beta-amylase but by increasing the linear linkage portion of the substrate. The introduction of an effective chain length function was used to formulate a kinetic model.

  12. A Mock Circulatory System Incorporating a Compliant 3D-Printed Anatomical Model to Investigate Pulmonary Hemodynamics.

    Science.gov (United States)

    Knoops, Paul G M; Biglino, Giovanni; Hughes, Alun D; Parker, Kim H; Xu, Linzhang; Schievano, Silvia; Torii, Ryo

    2017-07-01

    A realistic mock circulatory system (MCS) could be a valuable in vitro testbed to study human circulatory hemodynamics. The objective of this study was to design a MCS replicating the pulmonary arterial circulation, incorporating an anatomically representative arterial model suitable for testing clinically relevant scenarios. A second objective of the study was to ensure the system's compatibility with magnetic resonance imaging (MRI) for additional measurements. A latex pulmonary arterial model with two generations of bifurcations was manufactured starting from a 3D-printed mold reconstructed from patient data. The model was incorporated into a MCS for in vitro hydrodynamic measurements. The setup was tested under physiological pulsatile flow conditions and results were evaluated using wave intensity analysis (WIA) to investigate waves traveling in the arterial system. Increased pulmonary vascular resistance (IPVR) was simulated as an example of one pathological scenario. Flow split between right and left pulmonary artery was found to be realistic (54 and 46%, respectively). No substantial difference in pressure waveform was observed throughout the various generations of bifurcations. Based on WIA, three main waves were identified in the main pulmonary artery (MPA), that is, forward compression wave, backward compression wave, and forward expansion wave. For IPVR, a rise in mean pressure was recorded in the MPA, within the clinical range of pulmonary arterial hypertension. The feasibility of using the MCS in the MRI scanner was demonstrated with the MCS running 2 h consecutively while acquiring preliminary MRI data. This study shows the development and verification of a pulmonary MCS, including an anatomically correct, compliant latex phantom. The setup can be useful to explore a wide range of hemodynamic questions, including the development of patient- and pathology-specific models, considering the ease and low cost of producing rapid prototyping molds, and the

  13. Incorporation of Fuzzy Sets and Earned Value Management into a Cost-Time Trade-off Model

    Directory of Open Access Journals (Sweden)

    Mostafa Salari

    2014-01-01

    Full Text Available Time-cost trade-off (TCT problem is a well-known subject in the project scheduling contexts. None of previous studies in this area of research emphasize on the incorporation of the TCT problem into the started project’s performance in order to present a comprehensive model for scheduling and controlling the project in its whole life. The aim of this paper is to provide a novel control mechanism which includes scheduling the project prior to start date, monitoring the project’s performance through the execution, predicting future performance of the project, determining the necessity for re-scheduling, and providing an approach for re-scheduling of the project. In the proposed model, several options with specific time and cost have been considered for the initiation of each activity. These options make different paths for the construction of the project. Due to vagueness and imprecision presented in real case projects, the time and cost behavior for each option has been presumed as fuzzy numbers. Earned Value Management (EVM has been then utilized for measuring project performance and ultimately, statistical modeling has been also employed in predicting the future trend of EVM’s indices. The model has resulted in selection of the best path for implementation purpose among all available paths. Moreover, the proposed model provides the advantage of assessing the possibility of rescheduling process. An illustrative case has been studied to analyze the application of the proposed model .

  14. Incorporation of SemiSpan SuperSonic Transport (S4T) Aeroservoelastic Models into SAREC-ASV Simulation

    Science.gov (United States)

    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.

  15. Modelling and analysis of an open-loop induction motor drive incorporating the effect of inverter dead-time

    Indian Academy of Sciences (India)

    Anirudh Guha; G Narayanan

    2016-02-01

    The objective of this paper is to study the influence of inverter dead-time on steady as well as dynamic operation of an open-loop induction motor drive fed from a voltage source inverter (VSI). Towards this goal, this paper presents a systematic derivation of a dynamic model for an inverter-fed induction motor, incorporating the effect of inverter dead-time, in the synchronously revolving dq reference frame. Simulation results based on this dynamic model bring out the impact of inverter dead-time on both the transient response and steady-state operation of the motor drive. For the purpose of steady-state analysis, the dynamic model of the motor drive is used to derive a steady-state model, which is found to be non-linear. The steady-state model shows that the impact of dead-time can be seen as an additional resistance in the stator circuit, whose value depends on the stator current. Towards precise evaluation of this dead-time equivalent resistance, an analytical expression is proposed for the same in terms of inverter dead-time, switching frequency, modulation index and load impedance. The notion of dead-time equivalent resistance is shown to simplify the solution of the non-linear steady-state model. The analytically evaluated steady-state solutions are validated through numerical simulations and experiments.

  16. Bayesian random effect models incorporating real-time weather and traffic data to investigate mountainous freeway hazardous factors.

    Science.gov (United States)

    Yu, Rongjie; Abdel-Aty, Mohamed; Ahmed, Mohamed

    2013-01-01

    Freeway crash occurrences are highly influenced by geometric characteristics, traffic status, weather conditions and drivers' behavior. For a mountainous freeway which suffers from adverse weather conditions, it is critical to incorporate real-time weather information and traffic data in the crash frequency study. In this paper, a Bayesian inference method was employed to model one year's crash data on I-70 in the state of Colorado. Real-time weather and traffic variables, along with geometric characteristics variables were evaluated in the models. Two scenarios were considered in this study, one seasonal and one crash type based case. For the methodology part, the Poisson model and two random effect models with a Bayesian inference method were employed and compared in this study. Deviance Information Criterion (DIC) was utilized as a comparison factor. The correlated random effect models outperformed the others. The results indicate that the weather condition variables, especially precipitation, play a key role in the crash occurrence models. The conclusions imply that different active traffic management strategies should be designed based on seasons, and single-vehicle crashes have different crash mechanism compared to multi-vehicle crashes.

  17. A 3-D probabilistic stability model incorporating the variability of root reinforcement

    Science.gov (United States)

    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.

  18. Incorporating the user perspective into a proposed model for assessing success of SHS implementations

    Directory of Open Access Journals (Sweden)

    Hans Holtorf

    2015-10-01

    Full Text Available Modern energy can contribute to development in multiple ways while approximately 20% of world's populations do not yet have access to electricity. Solar Home Systems (SHSs consists of a PV module, a charge controller and a battery supply in the range of 100 Wh/d in Sunbelt countries. The question addressed in this paper is how SHS users approach success of their systems and how these user's views can be integrated in to an existing model of success. Information was obtained on the user's approach to their SHSs by participatory observation, interviews with users and by self-observation undertaken by the lead author while residing under SHS electricity supply conditions. It was found that success of SHSs from the users' point of view is related to the ability of these systems to reduce the burdens of supplying energy services to homesteads. SHSs can alleviate some energy supply burdens, and they can improve living conditions by enabling communication on multiple levels and by addressing convenience and safety concerns. However, SHSs do not contribute to the energy services which are indispensable for survival, nor to the thermal energy services required and desired in dwellings of Sunbelt countries. The elements of three of the four components of our previously proposed model of success have been verified and found to be appropriate, namely the user's self-set goals, their importance and SHSs' success factors. The locally appropriate, and scientifically satisfactory, measurement of the level of achievement of self-set goals, the fourth component of our model of success, remains an interesting area for future research.

  19. Eatwell Guide: modelling the dietary and cost implications of incorporating new sugar and fibre guidelines

    Science.gov (United States)

    Scarborough, Peter; Cobiac, Linda; Owens, Paul; Parlesak, Alexandr; Sweeney, Kate; Rayner, Mike

    2016-01-01

    Objectives To model food group consumption and price of diet associated with achieving UK dietary recommendations while deviating as little as possible from the current UK diet, in order to support the redevelopment of the UK food-based dietary guidelines (now called the Eatwell Guide). Design Optimisation modelling, minimising an objective function of the difference between population mean modelled and current consumption of 125 food groups, and constraints of nutrient and food-based recommendations. Setting The UK. Population Adults aged 19 years and above from the National Diet and Nutrition Survey 2008–2011. Main outcome measures Proportion of diet consisting of major foods groups and price of the optimised diet. Results The optimised diet has an increase in consumption of ‘potatoes, bread, rice, pasta and other starchy carbohydrates’ (+69%) and ‘fruit and vegetables’ (+54%) and reductions in consumption of ‘beans, pulses, fish, eggs, meat and other proteins’ (−24%), ‘dairy and alternatives’ (−21%) and ‘foods high in fat and sugar’ (−53%). Results within food groups show considerable variety (eg, +90% for beans and pulses, −78% for red meat). The modelled diet would cost £5.99 (£5.93 to £6.05) per adult per day, very similar to the cost of the current diet: £6.02 (£5.96 to £6.08). The optimised diet would result in increased consumption of n-3 fatty acids and most micronutrients (including iron and folate), but decreased consumption of zinc and small decreases in consumption of calcium and riboflavin. Conclusions To achieve the UK dietary recommendations would require large changes in the average diet of UK adults, including in food groups where current average consumption is well within the recommended range (eg, processed meat) or where there are no current recommendations (eg, dairy). These large changes in the diet will not lead to significant changes in the price of the diet. PMID:28003292

  20. Approximate solution of a model of biological immune responses incorporating delay.

    Science.gov (United States)

    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.

  1. Two-site adsolubilization model of incorporation of fluoromonomers into fluorosurfactants formed on cotton fabric.

    Science.gov (United States)

    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.

  2. An expanded Notch-Delta model exhibiting long-range patterning and incorporating MicroRNA regulation.

    Directory of Open Access Journals (Sweden)

    Jerry S Chen

    2014-06-01

    Full Text Available 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.

  3. Quantifying the regional water footprint of biofuel production by incorporating hydrologic modeling

    Science.gov (United States)

    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.

  4. A stage structured mosquito model incorporating effects of precipitation and daily temperature fluctuations.

    Science.gov (United States)

    Wang, Xia; Tang, Sanyi; Cheke, Robert A

    2016-12-21

    An outbreak of dengue fever in Guangdong province in 2014 was the most serious outbreak ever recorded in China. Given the known positive correlation between the abundance of mosquitoes and the number of dengue fever cases, a stage structured mosquito model was developed to investigate the cause of the large abundance of mosquitoes in 2014 and its implications for outbreaks of the disease. Data on the Breteau index (number of containers positive for larvae per 100 premises investigated), temperature and precipitation were used for model fitting. The egg laying rate, the development rate and the mortality rates of immatures and adults were obtained from the estimated parameters. Moreover, effects of daily fluctuations of temperature on these parameters were obtained and the effects of temperature and precipitation were analyzed by simulations. Our results indicated that the abundance of mosquitoes depended not only on the total annual precipitation but also on the distribution of the precipitation. The daily mean temperature had a nonlinear relationship with the abundance of mosquitoes, and large diurnal temperature differences can reduce the abundance of mosquitoes. In addition, effects of increasing precipitation and temperature were interdependent. Our findings suggest that the large abundance of mosquitoes in 2014 was mainly caused by the distribution of the precipitation. In the perspective of mosquito control, our results reveal that it is better to clear water early and spray insecticide between April and August in case of limited resources.

  5. INCORPORATING PRIOR BELIEF IN THE GENERAL PATH MODEL: A COMPARISON OF INFORMATION SOURCES

    Directory of Open Access Journals (Sweden)

    JAMIE COBLE

    2014-12-01

    Full Text Available The general path model (GPM is one approach for performing degradation-based, or Type III, prognostics. The GPM fits a parametric function to the collected observations of a prognostic parameter and extrapolates the fit to a failure threshold. This approach has been successfully applied to a variety of systems when a sufficient number of prognostic parameter observations are available. However, the parametric fit can suffer significantly when few data are available or the data are very noisy. In these instances, it is beneficial to include additional information to influence the fit to conform to a prior belief about the evolution of system degradation. Bayesian statistical approaches have been proposed to include prior information in the form of distributions of expected model parameters. This requires a number of run-to-failure cases with tracked prognostic parameters; these data may not be readily available for many systems. Reliability information and stressor-based (Type I and Type II, respectively prognostic estimates can provide the necessary prior belief for the GPM. This article presents the Bayesian updating framework to include prior information in the GPM and compares the efficacy of including different information sources on two data sets.

  6. On the tectonics and metallogenesis of West Africa: a model incorporating new geophysical data

    Science.gov (United States)

    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.

  7. In silico molecular modeling of neuraminidase enzyme H1N1 avian influenza virus and docking with zanamivir ligands

    Directory of Open Access Journals (Sweden)

    Muthiyan Ramachandran

    2012-12-01

    Full Text Available Objective: Neuraminidase is an enzyme aspartic protease that is essential for the life cycle of H1N1. Methods: Constructed a model of Neuraminidase enzyme the 3D structure as template using with Modeller software. The Neuraminidase enzyme model was predicted and validated by Procheck, What check, Errat, Verify-3D and AutoDock web server for reliability. Results: The Modeller homology-modeling algorithm was demonstrated excellent accuracy in blind predictions. The Neuraminidase enzyme model built with little, 35% identity could be accurate enough to be successfully used in receptor based rational drug design. The closest homologue with the highest sequence identity 100% was selected. Zanamivir drug and analogues were retrieved from PubChem database, as well as subjected to docking interaction with Neuraminidase enzyme used AutoDock programme. Based on the root mean square deviation and lowest binding energy values the best docking orientation was selected. The better lowest binding energy value -6.91 was selected of CID_25209232. Conclusions: This study will be used in broad screening of inhibitors of the protein. However, further implemented experimental and clinical verification is needed to establishment these analogues as drug.

  8. A Simple Biomineralization Model to Explain Li, Mg, and Sr Incorporation into Aragonitic Foraminifera and Corals

    Science.gov (United States)

    Marchitto, T. M.; Bryan, S. P.; Montagna, P.

    2011-12-01

    The relationships between growth temperature and individual metal/Ca ratios in biogenic aragonites may be fundamentally perturbed by at least two processes: Ca pumping and Rayleigh fractionation. We suggest that the ratio Li/Mg is insensitive to both processes. Theoretically this is because the two elements experience negligible leakage through the Ca pump and very low partitioning into aragonite, leading to relatively constant Li/Mg in the calcifying fluid. This behavior may be related to the small ionic radii of both elements compared to Ca. As a result, Li/Mg is well explained by the temperature dependence of Li and Mg partitioning into inorganic aragonite, lending promise to its utility as a paleothermometer. Coral Sr/Ca is shown to be consistent with this model if the Ca pump is leaky with respect to Sr.

  9. A Compliant Bistable Mechanism Design Incorporating Elastica Buckling Beam Theory and Pseudo-Rigid-Body Model

    DEFF Research Database (Denmark)

    Sönmez, Ümit; Tutum, Cem Celal

    2008-01-01

    In this work, a new compliant bistable mechanism design is introduced. The combined use of pseudo-rigid-body model (PRBM) and the Elastica buckling theory is presented for the first time to analyze the new design. This mechanism consists of the large deflecting straight beams, buckling beams......, and a slider. The kinematic analysis of this new mechanism is studied, using nonlinear Elastica buckling beam theory, the PRBM of a large deflecting cantilever beam, the vector loop closure equations, and numerically solving nonlinear algebraic equations. A design method of the bistable mechanism...... and the buckling Elastica solution for an original compliant mechanism kinematic analysis. New compliant mechanism designs are presented to highlight where such combined kinematic analysis is required....

  10. Teaching For Art Criticism: Incorporating Feldman’s Critical Analysis Learning Model In Students’ Studio Practice

    Directory of Open Access Journals (Sweden)

    Maithreyi Subramaniam

    2016-01-01

    Full Text Available 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. Pearson Correlation Coefficient was used to find out the correlation between students’ studio practice and art critical ability scores. The findings showed most students performed slightly better than average in the critical analyses and performed best in selecting analysis among the four dimensions assessed. In the context of the students’ studio practice and critical ability, findings showed there are some connections between the students’ art critical ability and studio practice.

  11. A model for hydraulic redistribution incorporating coupled soil-root moisture transport

    Directory of Open Access Journals (Sweden)

    G. G. Amenu

    2007-10-01

    Full Text Available One of the adaptive strategies of vegetation, particularly in water limited ecosystems, is the development of deep roots and the use of hydraulic redistribution which enables them to make optimal use of resources available throughout the soil column. Hydraulic redistribution refers to roots acting as a preferential pathway for the movement of water from wet to dry soil layers driven by the moisture gradient – be it from the shallow to deep layers or vice versa. This occurs during the nighttime while during the daytime moisture movement is driven to fulfill the transpiration demand at the canopy. In this study, we develop a model to investigate the effect of hydraulic redistribution by deep roots on the terrestrial climatology. Sierra Nevada eco-region is chosen as the study site which has wet winters and dry summers. Hydraulic redistribution enables the movement of moisture from the upper soil layers to deeper zones during the wet months and this moisture is then available to meet the transpiration demand during the late dry season. It results in significant alteration of the profiles of soil moisture and water uptake as well as increase in the canopy transpiration, carbon assimilation, and the associated water-use-efficiency during the dry summer season. This also makes the presence of roots in deeper soil layers much more important than their proportional abundance would otherwise dictate. Comparison with observations of latent heat from a flux tower demonstrates improved predictability and provides validation of the model results. Hydraulic redistribution serves as a mechanism for the interaction between the variability of deep layer soil-moisture and the land-surface climatology and could have significant implications for seasonal and sub-seasonal climate prediction.

  12. A model for hydraulic redistribution incorporating coupled soil-root moisture transport

    Directory of Open Access Journals (Sweden)

    G. G. Amenu

    2008-01-01

    Full Text Available One of the adaptive strategies of vegetation, particularly in water limited ecosystems, is the development of deep roots and the use of hydraulic redistribution which enables them to make optimal use of resources available throughout the soil column. Hydraulic redistribution refers to roots acting as a preferential pathway for the movement of water from wet to dry soil layers driven by the moisture gradient – be it from the shallow to deep layers or vice versa. This occurs during the nighttime while during the daytime moisture movement is driven to fulfill the transpiration demand at the canopy. In this study, we develop a model to investigate the effect of hydraulic redistribution by deep roots on the terrestrial climatology. Sierra Nevada eco-region is chosen as the study site which has wet winters and dry summers. Hydraulic redistribution enables the movement of moisture from the upper soil layers to deeper zones during the wet months and this moisture is then available to meet the transpiration demand during the late dry season. It results in significant alteration of the profiles of soil moisture and water uptake as well as increase in the canopy transpiration, carbon assimilation, and the associated water-use-efficiency during the dry summer season. This also makes the presence of roots in deeper soil layers much more important than their proportional abundance would otherwise dictate. Comparison with observations of latent heat from a flux tower demonstrates improved predictability and provides validation of the model results. Hydraulic redistribution serves as a mechanism for the interaction between the variability of deep layer soil-moisture and the land-surface climatology and could have significant implications for seasonal and sub-seasonal climate prediction.

  13. The identification of enzyme targets for the optimization of a valine producing Corynebacterium glutamicum strain using a kinetic model.

    Science.gov (United States)

    Magnus, Jørgen Barsett; Oldiges, Marco; Takors, Ralf

    2009-01-01

    The enzyme targets for the rational optimization of a Corynebacterium glutamicum strain constructed for valine production are identified by analyzing the control of flux in the valine/leucine pathway. The control analysis is based on measurements of the intracellular metabolite concentrations and on a kinetic model of the reactions in the investigated pathway. Data-driven and model-based methods are used and evaluated against each other. The approach taken gives a quantitative evaluation of the flux control and it is demonstrated how the understanding of flux control is used to reach specific recommendations for strain optimization. The flux control coefficients (FCCs) with respect to the valine excretion rate were calculated, and it was found that the control is distributed mainly between the acetohydroxyacid synthase enzyme (FCC = 0.32), the branched chain amino acid transaminase (FCC = 0.27), and the exporting translocase (FCC = 0.43). The availability of the precursor pyruvate has substantial influence on the valine flux, whereas the cometabolites are less important as demonstrated by the calculation of the respective response coefficients. The model is further used to make in-silico predictions of the change in valine flux following a change in enzyme level. A doubling of the enzyme level of valine translocase will result in an increase in valine flux of 31%. By optimizing the enzyme levels with respect to valine flux it was found that the valine flux can be increased by a factor 2.5 when the optimal enzyme levels are implemented.

  14. DYNAMIC MODELLING AND ADVANCED PREDICTIVE CONTROL OF A CONTINUOUS PROCESS OF ENZYME PURIFICATION

    Directory of Open Access Journals (Sweden)

    Dechechi E.C.

    1997-01-01

    Full Text Available A dynamic mathematical model, simulation and computer control of a Continuous Affinity Recycle Extraction (CARE process, a protein purification technique based on protein adsorption on solid-phase adsorbents is described in this work. This process, consisting of three reactors, is a multivariable process with considerable time delay in the on-line analyses of the controlled variable. An advanced predictive control configuration, specifically the Dynamic Matrix Control (DMC, was applied. The DMC algorithm was applied in process schemes where the aim was to maintain constant the enzyme concentration in the outlet of the third reactor. The performance of the DMC controller was analyzed in the feed-flow disturbances and the results are presented.

  15. Modeling the role of covalent enzyme modification in Escherichia coli nitrogen metabolism

    Science.gov (United States)

    Kidd, Philip B.; Wingreen, Ned S.

    2010-03-01

    In the bacterium Escherichia coli, the enzyme glutamine synthetase (GS) converts ammonium into the amino acid glutamine. GS is principally active when the cell is experiencing nitrogen limitation, and its activity is regulated by a bicyclic covalent modification cascade. The advantages of this bicyclic-cascade architecture are poorly understood. We analyze a simple model of the GS cascade in comparison to other regulatory schemes and conclude that the bicyclic cascade is suboptimal for maintaining metabolic homeostasis of the free glutamine pool. Instead, we argue that the lag inherent in the covalent modification of GS slows the response to an ammonium shock and thereby allows GS to transiently detoxify the cell, while maintaining homeostasis over longer times.

  16. A battery model that fully couples mechanics and electrochemistry at both particle and electrode levels by incorporation of particle interaction

    Science.gov (United States)

    Wu, Bin; Lu, Wei

    2017-08-01

    This paper develops a multi-scale mechanical-electrochemical model which enables fully coupled mechanics and electrochemistry at both particle and electrode levels. At the particle level, solid diffusion is modeled using a generalized chemical potential to capture the effects of mechanical stress and phase transformation. At the electrode level, the stress arising from particle interaction is incorporated in a continuum model. This particle interaction stress is in addition to the traditional concept of intercalation stress inside isolated particles. The particle and continuum electrode levels are linked by the particle interaction stress as loads on the particle surface, and by consideration of stress on the electrochemical reaction rate on the particle surface. The effect of mechanical stress on electrochemical reaction results in a stress-dependent over-potential between particle and electrolyte. Stress gradient in an electrode leads to inhomogeneous intercalation/deintercalation currents for particles depending on their interaction stress with neighbors, resulting in stress gradient induced inhomogeneous state of charge. Conversely, non-uniform intercalation/deintercalation currents in an electrode lead to stress between particles. With this model we have an important finding: an electrochemically inactive region in an electrode causes stress built-up. This model provides a powerful tool to address various problems such as fracture in-between particles.

  17. Incorporating Groundwater Dynamics and Surface/Subsurface Runoff Mechanisms in Regional Climate Modeling over River Basins in China

    Institute of Scientific and Technical Information of China (English)

    QIN Peihua; XIE Zhenghui; YUAN Xing

    2013-01-01

    To improve the capability of numerical modeling of climate-groundwater interactions,a groundwater component and new surface/subsurface runoff schemes were incorporated into the regional climate model RegCM3,renamed RegCM3_Hydro.20-year simulations from both models were used to investigate the effects of groundwater dynamics and surface/subsurface runoff parameterizations on regional climate over seven river basins in China.A comparison of results shows that RegCM3_Hydro reduced the positive biases of annual and summer (June,July,August) precipitation over six river basins,while it slightly increased the bias over the Huaihe River Basin in eastern China.RegCM3_Hydro also reduced the cold bias of surface air temperature from RegCM3 across years,especially for the Haihe and the Huaihe river basins,with significant bias reductions of 0.80℃ and 0.88℃,respectively.The spatial distribution and seasonal variations of water table depth were also well captured.With the new surface and subsurface runoff schemes,RegCM3_Hydro increased annual surface runoff by 0.11-0.62 mm d-1 over the seven basins.Though previous studies found that incorporating a groundwater component tends to increase soil moisture due to the consideration of upward groundwater recharge,our present work shows that the modified runoff schemes cause less infiltration,which outweigh the recharge from groundwater and result in drier soil,and consequently cause less latent heat and more sensible heat over most of the basins.

  18. Incorporation of advanced aerosol activation treatments into CESM/CAM5: model evaluation and impacts on aerosol indirect effects

    Science.gov (United States)

    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

  19. An innovative land use regression model incorporating meteorology for exposure analysis.

    Science.gov (United States)

    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.

  20. TOWARD MORE REALISTIC ANALYTIC MODELS OF THE HELIOTAIL: INCORPORATING MAGNETIC FLATTENING VIA DISTORTION FLOWS

    Energy Technology Data Exchange (ETDEWEB)

    Kleimann, Jens; Fichtner, Horst [Ruhr-Universität Bochum, Fakultät für Physik und Astronomie, Institut für Theoretische Physik IV, Bochum (Germany); Röken, Christian [Universität Regensburg, Fakultät für Mathematik, Regensburg (Germany); Heerikhuisen, Jacob, E-mail: jk@tp4.rub.de, E-mail: hf@tp4.rub.de, E-mail: christian.roeken@mathematik.uni-regensburg.de, E-mail: jacob.heerikhuisen@uah.edu [Department of Space Science and Center for Space Plasma and Aeronomic Research, University of Alabama in Huntsville, Huntsville, AL 35899 (United States)

    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.

  1. A heat transfer model for incorporating carbon foam fabrics in firefighter's garment

    Science.gov (United States)

    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.

  2. Modelling how incorporation of divalent cations affects calcite wettability–implications for biomineralisation and oil recovery

    Science.gov (United States)

    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.

  3. Searching for the true diet of marine predators: incorporating Bayesian priors into stable isotope mixing models.

    Directory of Open Access Journals (Sweden)

    André Chiaradia

    Full Text Available 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 δ(15N and δ(13C 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.

  4. Incorporating the gut microbiota into models of human and non-human primate ecology and evolution.

    Science.gov (United States)

    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.

  5. Incorporating induced seismicity in the 2014 United States National Seismic Hazard Model: results of the 2014 workshop and sensitivity studies

    Science.gov (United States)

    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

  6. Development of Advanced Continuum Models that Incorporate Nanomechanical Deformation into Engineering Analysis.

    Energy Technology Data Exchange (ETDEWEB)

    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

  7. Incorporating transportation network modeling tools within transportation economic impact studies of disasters

    Directory of Open Access Journals (Sweden)

    Yi Wen

    2014-08-01

    Full Text Available Transportation system disruption due to a disaster results in "ripple effects" throughout the entire transportation system of a metropolitan region. Many researchers have focused on the economic costs of transportation system disruptions in transportation-related industries, specifïcally within commerce and logistics, in the assessment of the regional economic costs. However, the foundation of an assessment of the regional economic costs of a disaster needs to include the evaluation of consumer surplus in addition to the direct cost for reconstruction of the regional transportation system. The objective of this study is to propose a method to estimate the regional consumer surplus based on indirect economic costs of a disaster on intermodal transportation systems in the context of diverting vehicles and trains. The computational methods used to assess the regional indirect economic costs sustained by the highway and railroad system can utilize readily available state departments of transportation (DOTs and metropolitan planning organizations (MPOs traffic models allowing prioritization of regional recovery plans after a disaster and strengthening of infrastructure before a disaster. Hurricane Katrina is one of the most devastating hurricanes in the history of the United States. Due to the significance of Hurricane Katrina, a case study is presented to evaluate consumer surplus in the Gulf Coast Region of Mississippi. Results from the case study indicate the costs of rerouting and congestion delays in the regional highway system and the rent costs of right-of-way in the regional railroad system are major factors of the indirect costs in the consumer surplus.

  8. Image quality analysis of high-density diffuse optical tomography incorporating a subject-specific head model

    Directory of Open Access Journals (Sweden)

    Yuxuan eZhan

    2012-05-01

    Full Text Available High-density diffuse optical tomography (HD-DOT methods have shown significant improvement in localization accuracy and image resolution compared to traditional topographic near infrared spectroscopy (NIRS of the human brain. In this work we provide a comprehensive evaluation of image quality in visual cortex mapping via a simulation study with the use of an anatomical head model derived from MRI data of a human subject. A model of individual head anatomy provides the surface shape and internal structure that allow for the construction of a more realistic physical model for the forward problem, as well as the use of a structural constraint in the inverse problem. The HD-DOT model utilized here incorporates multiple source-detector separations with continuous-wave data with added noise based on experimental results. To evaluate image quality we quantify the localization error and localized volume at half maximum (LVHM throughout a region of interest (ROI within the visual cortex and systematically analyze the use of whole brain tissue spatial constraint within image reconstruction. Our results demonstrate that an image quality with less than 10 mm in localization error and 1000 m3 in LVHM can be obtained up to 13 mm below the scalp surface with a typical unconstrained reconstruction and up to 18 mm deep when a spatial constraint based on the brain tissue is utilized.

  9. Photocatalytic degradation and reactor modeling of 17α-ethynylestradiol employing titanium dioxide-incorporated foam concrete.

    Science.gov (United States)

    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.

  10. Global Hopf bifurcation analysis of an susceptible-infective-removed epidemic model incorporating media coverage with time delay.

    Science.gov (United States)

    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.

  11. Modeling of pharmacokinetics of cocaine in human reveals the feasibility for development of enzyme therapies for drugs of abuse.

    Directory of Open Access Journals (Sweden)

    Fang Zheng

    Full Text Available A promising strategy for drug abuse treatment is to accelerate the drug metabolism by administration of a drug-metabolizing enzyme. The question is how effectively an enzyme can actually prevent the drug from entering brain and producing physiological effects. In the present study, we have developed a pharmacokinetic model through a combined use of in vitro kinetic parameters and positron emission tomography data in human to examine the effects of a cocaine-metabolizing enzyme in plasma on the time course of cocaine in plasma and brain of human. Without an exogenous enzyme, cocaine half-lives in both brain and plasma are almost linearly dependent on the initial cocaine concentration in plasma. The threshold concentration of cocaine in brain required to produce physiological effects has been estimated to be 0.22±0.07 µM, and the threshold area under the cocaine concentration versus time curve (AUC value in brain (denoted by AUC2(∞ required to produce physiological effects has been estimated to be 7.9±2.7 µM·min. It has been demonstrated that administration of a cocaine hydrolase/esterase (CocH/CocE can considerably decrease the cocaine half-lives in both brain and plasma, the peak cocaine concentration in brain, and the AUC2(∞. The estimated maximum cocaine plasma concentration which a given concentration of drug-metabolizing enzyme can effectively prevent from entering brain and producing physiological effects can be used to guide future preclinical/clinical studies on cocaine-metabolizing enzymes. Understanding of drug-metabolizing enzymes is key to the science of pharmacokinetics. The general insights into the effects of a drug-metabolizing enzyme on drug kinetics in human should be valuable also in future development of enzyme therapies for other drugs of abuse.

  12. Enzyme catalysis: tool to make and break amygdalin hydrogelators from renewable resources: a delivery model for hydrophobic drugs.

    Science.gov (United States)

    Vemula, Praveen Kumar; Li, Jun; John, George

    2006-07-12

    We report a novel approach for the controlled delivery of an antiinflammatory, chemopreventive drug by an enzyme-triggered drug release mechanism via the degradation of encapsulated hydrogels. The hydro- and organogelators are synthesized in high yields from renewable resources by using regioselective enzyme catalysis, and a known chemopreventive and antiinflammatory drug, i.e., curcumin, is used for the model study. The release of the drug occurred at physiological temperature, and control of the drug release rate is achieved by manipulating the enzyme concentration and/or temperature. The byproducts formed after the gel degradation were characterized and clearly demonstrated the site specificity of degradation of the gelator by enzyme catalysis. The present approach could have applications in developing cost-effective controlled drug delivery vehicles from renewable resources, with a potential impact on pharmaceutical research and molecular design and delivery strategies.

  13. Segmenting multiple overlapping objects via a hybrid active contour model incorporating shape priors: applications to digital pathology

    Science.gov (United States)

    Ali, Sahirzeeshan; Madabhushi, Anant

    2011-03-01

    Active contours and active shape models (ASM) have been widely employed in image segmentation. A major limitation of active contours, however, is in their (a) inability to resolve boundaries of intersecting objects and to (b) handle occlusion. Multiple overlapping objects are typically segmented out as a single object. On the other hand, ASMs are limited by point correspondence issues since object landmarks need to be identified across multiple objects for initial object alignment. ASMs are also are constrained in that they can usually only segment a single object in an image. In this paper, we present a novel synergistic boundary and region-based active contour model that incorporates shape priors in a level set formulation. We demonstrate an application of these synergistic active contour models using multiple level sets to segment nuclear and glandular structures on digitized histopathology images of breast and prostate biopsy specimens. Unlike previous related approaches, our model is able to resolve object overlap and separate occluded boundaries of multiple objects simultaneously. The energy functional of the active contour is comprised of three terms. The first term comprises the prior shape term, modeled on the object of interest, thereby constraining the deformation achievable by the active contour. The second term, a boundary based term detects object boundaries from image gradients. The third term drives the shape prior and the contour towards the object boundary based on region statistics. The results of qualitative and quantitative evaluation on 100 prostate and 14 breast cancer histology images for the task of detecting and segmenting nuclei, lymphocytes, and glands reveals that the model easily outperforms two state of the art segmentation schemes (Geodesic Active Contour (GAC) and Roussons shape based model) and resolves up to 92% of overlapping/occluded lymphocytes and nuclei on prostate and breast cancer histology images.

  14. Towards a Predictive Thermodynamic Model of Oxidation States of Uranium Incorporated in Fe (hydr) oxides

    Energy Technology Data Exchange (ETDEWEB)

    Bagus, Paul S. [Univ. of North Texas, Denton, TX (United States)

    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

  15. 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

    Energy Technology Data Exchange (ETDEWEB)

    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

  16. Restoration of glyoxalase enzyme activity precludes cognitive dysfunction in a mouse model of Alzheimer's disease.

    Science.gov (United States)

    More, Swati S; Vartak, Ashish P; Vince, Robert

    2013-02-20

    Pathologically high brain levels of reactive dicarbonyls such as methylglyoxal or glyoxal initiate processes that lead ultimately to neurodegeneration, presented clinically as Alzheimer's disease and other cognitive or motor impairment disorders. Methylglyoxal and glyoxal result from glycolysis and normal metabolic pathways. Their reaction products with proteins (advanced glycation end products), and their primary chemical toxicities are both linked unequivocally to the primary pathologies of Alzheimer's disease, namely, amyloid plaques and neurofibrillary tangles. Generation of dicarbonyls is countered through the reduction of dicarbonyls by the glutathione-dependent glyoxalase enzyme system. Although glyoxalase-I is overexpressed in early and middle stages of Alzheimer's disease, glutathione depletion in the Alzheimer's afflicted brain cripples its efficacy. Due to the lack of a suitable pharmacological tool, the restoration of glyoxalase enzyme activity in pre-Alzheimer's or manifest Alzheimer's remains yet unvalidated as a means for anti-Alzheimer's therapy development. Disclosed herein are the results of a preclinical study into the therapeutic efficacy of ψ-GSH, a synthetic cofactor of glyoxalase, in mitigating Alzheimer's indicators in a transgenic mouse model (APP/PS1) that is predisposed to Alzheimer's disease. ψ-GSH administration completely averts the development of spatial mnemonic and long-term cognitive/cued-recall impairment. Amyloid β deposition and oxidative stress indicators are drastically reduced in the ψ-GSH-treated APP/PS1 mouse. ψ-GSH lacks discernible toxicity at strikingly high doses of 2000 mg/kg. The hypothesis that restoring brain glyoxalase activity would ameliorate neurogeneration stands validated, thus presenting a much needed new target for design of anti-Alzheimer's therapeutics. Consequently, ψ-GSH is established as a candidate for drug-development.

  17. Incorporation of expert variability into breast cancer treatment recommendation in designing clinical protocol guided fuzzy rule system models.

    Science.gov (United States)

    Garibaldi, Jonathan M; Zhou, Shang-Ming; Wang, Xiao-Ying; John, Robert I; Ellis, Ian O

    2012-06-01

    It has been often demonstrated that clinicians exhibit both inter-expert and intra-expert variability when making difficult decisions. In contrast, the vast majority of computerized models that aim to provide automated support for such decisions do not explicitly recognize or replicate this variability. Furthermore, the perfect consistency of computerized models is often presented as a de facto benefit. In this paper, we describe a novel approach to incorporate variability within a fuzzy inference system using non-stationary fuzzy sets in order to replicate human variability. We apply our approach to a decision problem concerning the recommendation of post-operative breast cancer treatment; specifically, whether or not to administer chemotherapy based on assessment of five clinical variables: NPI (the Nottingham Prognostic Index), estrogen receptor status, vascular invasion, age and lymph node status. In doing so, we explore whether such explicit modeling of variability provides any performance advantage over a more conventional fuzzy approach, when tested on a set of 1310 unselected cases collected over a fourteen year period at the Nottingham University Hospitals NHS Trust, UK. The experimental results show that the standard fuzzy inference system (that does not model variability) achieves overall agreement to clinical practice around 84.6% (95% CI: 84.1-84.9%), while the non-stationary fuzzy model can significantly increase performance to around 88.1% (95% CI: 88.0-88.2%), p<0.001. We conclude that non-stationary fuzzy models provide a valuable new approach that may be applied to clinical decision support systems in any application domain.

  18. Thermal remote sensing of surface soil water content with partial vegetation cover for incorporation into climate models

    Science.gov (United States)

    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.

  19. Research and Application of Fire Forecasting Model for Electric Transmission Lines Incorporating Meteorological Data and Human Activities

    Directory of Open Access Journals (Sweden)

    Jiazheng Lu

    2016-01-01

    Full Text Available Recently, there is a rise in frequency of fires which pose a serious threat to the safety operation of electric transmission lines. Several ultrahigh voltage (UHV electric transmission lines, including Fufeng line, Jinsu line, Longzheng line, and Changnan line, showed many times tripping or bipolar latching caused by fire disasters. Fire disasters have tended to be the biggest threat to the safety operation of electric transmission lines and even can cause power grid collapse in some severe situations. Researchers have made much research on fires forecasting. However, these studies are mainly concentrated on predicting fires based on measured or forecasting meteorological data and do not take into account the effect of human activities. In fact, fire disasters have a very close relationship with human activities. In our research, a fire prediction model is proposed incorporating meteorological data as well as human activities. And this model is applied in Hunan province and Anhui province, which seriously suffer from fire disasters. The results show that the model has good prediction precision and can be a powerful tool for practical application.

  20. Thermal remote sensing of surface soil water content with partial vegetation cover for incorporation into climate models

    Science.gov (United States)

    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.

  1. A hierarchy of dynamic plume models incorporating uncertainty: Volume 5, Pennsylvania State University mesoscale model (PSU-MM): Final report

    Energy Technology Data Exchange (ETDEWEB)

    Lewellen, W.S.; Sykes, R.I.; Parker, S.F.; Henn, D.S.; Seaman, N.L.; Stauffer, D.R.; Warner, T.T.

    1989-02-01

    An existing mesoscale model (the Penn State University/National Center for Atmospheric Research mesoscale model) was extended for use with a PUFF-type plume model. By including a fine-mesh 2 km nested-grid and the assimilation of 4-dimensional data, horizontally variable hourly-average meteorological conditions can be simulated up to 300 km downwind of stack emissions in complex terrain. In 4 days of tests (32 90-minute periods) against meteorological observations obtained in moderately complex terrain, wind-speed uncertainties are usually less than 3.3 m/s, and direction errors are less than 40/degree/ for winds less than 1 m/s. The performance of this model was also compared on 3 days (20 hours) with a locally homogeneous meteorological data assimilation model when both were coupled to a new second order closure integrated puff model (SCIPUFF). Use of the new mesoscale model slightly reduced the deviations between simulated and observed concentrations of SF/sub 6/ tracer, even within 50 km. At distances longer than 50 km (not tested) it is expected that use of the mesoscale model would further improve dispersion simulations. 8 refs., 26 figs., 6 tabs.

  2. Modelling sediment dynamics due to hillslope-river interactions : incorporating fluvial behaviour in landscape evolution model LAPSUS

    NARCIS (Netherlands)

    Baartman, Jantiene E. M.; van Gorp, Wouter; Temme, Arnaud J. A. M.; Schoorl, Jeroen M.

    2012-01-01

    Landscape evolution models (LEMs) simulate the three-dimensional development of landscapes over time. Different LEMs have different foci, e.g. erosional behaviour, river dynamics, the fluvial domain, hillslopes or a combination. LEM LAPSUS is a relatively simple cellular model operating on timescale

  3. A model of canopy photosynthesis incorporating protein distribution through the canopy and its acclimation to light, temperature and CO2

    Science.gov (United States)

    Johnson, Ian R.; Thornley, John H. M.; Frantz, Jonathan M.; Bugbee, Bruce

    2010-01-01

    Background and Aims The distribution of photosynthetic enzymes, or nitrogen, through the canopy affects canopy photosynthesis, as well as plant quality and nitrogen demand. Most canopy photosynthesis models assume an exponential distribution of nitrogen, or protein, through the canopy, although this is rarely consistent with experimental observation. Previous optimization schemes to derive the nitrogen distribution through the canopy generally focus on the distribution of a fixed amount of total nitrogen, which fails to account for the variation in both the actual quantity of nitrogen in response to environmental conditions and the interaction of photosynthesis and respiration at similar levels of complexity. Model A model of canopy photosynthesis is presented for C3 and C4 canopies that considers a balanced approach between photosynthesis and respiration as well as plant carbon partitioning. Protein distribution is related to irradiance in the canopy by a flexible equation for which the exponential distribution is a special case. The model is designed to be simple to parameterize for crop, pasture and ecosystem studies. The amount and distribution of protein that maximizes canopy net photosynthesis is calculated. Key Results The optimum protein distribution is not exponential, but is quite linear near the top of the canopy, which is consistent with experimental observations. The overall concentration within the canopy is dependent on environmental conditions, including the distribution of direct and diffuse components of irradiance. Conclusions The widely used exponential distribution of nitrogen or protein through the canopy is generally inappropriate. The model derives the optimum distribution with characteristics that are consistent with observation, so overcoming limitations of using the exponential distribution. Although canopies may not always operate at an optimum, optimization analysis provides valuable insight into plant acclimation to environmental

  4. Polyol specificity of recombinant Arabidopsis thaliana sorbitol dehydrogenase studied by enzyme kinetics and in silico modeling

    Directory of Open Access Journals (Sweden)

    María Francisca eAguayo

    2015-02-01

    Full Text Available Polyols are enzymatically-produced plant compounds which can act as compatible solutes during periods of abiotic stress. NAD+-dependent SORBITOL DEHYDROGENASE (SDH, E.C. 1.1.1.14 from Arabidopsis thaliana L. (AtSDH is capable of oxidizing several polyols including sorbitol, ribitol and xylitol. In the present study, enzymatic assays using recombinant AtSDH demonstrated a higher specificity constant for xylitol compared to sorbitol and ribitol, all of which are C2 (S and C4 (R polyols. Enzyme activity was reduced by preincubation with ethylenediaminetetraacetic acid (EDTA, indicating a requirement for zinc ions. In humans, it has been proposed that sorbitol becomes part of a pentahedric coordination sphere of the catalytic zinc during the reaction mechanism. In order to determine the validity of this pentahedric coordination model in a plant SDH, homology modeling and Molecular Dynamics simulations of AtSDH ternary complexes with the three polyols were performed using crystal structures of human and Bemisia argentifolii (Genn. (Hemiptera: Aleyrodidae SDHs as scaffolds. The results indicate that the differences in interaction with structural water molecules correlate very well with the observed enzymatic parameters, validate the proposed pentahedric coordination of the catalytic zinc ion in a plant SDH, and provide an explanation for why AtSDH shows a preference for polyols with a chirality of C2 (S and C4 (R.

  5. Multiscale modeling of biological functions: from enzymes to molecular machines (Nobel Lecture).

    Science.gov (United States)

    Warshel, Arieh

    2014-09-15

    A detailed understanding of the action of biological molecules is a pre-requisite for rational advances in health sciences and related fields. Here, the challenge is to move from available structural information to a clear understanding of the underlying function of the system. In light of the complexity of macromolecular complexes, it is essential to use computer simulations to describe how the molecular forces are related to a given function. However, using a full and reliable quantum mechanical representation of large molecular systems has been practically impossible. The solution to this (and related) problems has emerged from the realization that large systems can be spatially divided into a region where the quantum mechanical description is essential (e.g. a region where bonds are being broken), with the remainder of the system being represented on a simpler level by empirical force fields. This idea has been particularly effective in the development of the combined quantum mechanics/molecular mechanics (QM/MM) models. Here, the coupling between the electrostatic effects of the quantum and classical subsystems has been a key to the advances in describing the functions of enzymes and other biological molecules. The same idea of representing complex systems in different resolutions in both time and length scales has been found to be very useful in modeling the action of complex systems. In such cases, starting with coarse grained (CG) representations that were originally found to be very useful in simulating protein folding, and augmenting them with a focus on electrostatic energies, has led to models that are particularly effective in probing the action of molecular machines. The same multiscale idea is likely to play a major role in modeling of even more complex systems, including cells and collections of cells.

  6. Homology modeling of mosquito cytochrome P450 enzymes involved in pyrethroid metabolism: insights into differences in substrate selectivity

    Directory of Open Access Journals (Sweden)

    Rongnoparut Pornpimol

    2011-09-01

    Full Text Available Abstract Background Cytochrome P450 enzymes (P450s have been implicated in insecticide resistance. Anopheles minumus mosquito P450 isoforms CYP6AA3 and CYP6P7 are capable of metabolizing pyrethroid insecticides, however CYP6P8 lacks activity against this class of compounds. Findings Homology models of the three An. minimus P450 enzymes were constructed using the multiple template alignment method. The predicted enzyme model structures were compared and used for molecular docking with insecticides and compared with results of in vitro enzymatic assays. The three model structures comprise common P450 folds but differences in geometry of their active-site cavities and substrate access channels are prominent. The CYP6AA3 model has a large active site allowing it to accommodate multiple conformations of pyrethroids. The predicted CYP6P7 active site is more constrained and less accessible to binding of pyrethroids. Moreover the predicted hydrophobic interface in the active-site cavities of CYP6AA3 and CYP6P7 may contribute to their substrate selectivity. The absence of CYP6P8 activity toward pyrethroids appears to be due to its small substrate access channel and the presence of R114 and R216 that may prevent access of pyrethroids to the enzyme heme center. Conclusions Differences in active site topologies among CYPAA3, CYP6P7, and CYP6P8 enzymes may impact substrate binding and selectivity. Information obtained using homology models has the potential to enhance the understanding of pyrethroid metabolism and detoxification mediated by P450 enzymes.

  7. Incorporating Field Studies into Species Distribution and Climate Change Modelling: A Case Study of the Koomal Trichosurus vulpecula hypoleucus (Phalangeridae).

    Science.gov (United States)

    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

  8. Numerical Modeling of Regional Windblown Dust in the Pacific Northwest:Incorporation of an Improved Dust Emission Model

    Science.gov (United States)

    Sundram, I.; Claiborn, C.; Strand, T.; Lamb, B.; Chandler, D.; Saxton, K.

    2003-12-01

    Soil erosion by wind is a serious consequence of dryland agriculture in eastern Washington where the main adverse effects are loss of nutrient rich soil, reduced visibility during dust storms and regional air quality impacts in downwind populated areas. A multidisciplinary research effort to study windblown dust in central and eastern Washington was initiated under the Columbia Plateau PM 10 (CP 3) program. As part of this study, wind erosion and windblown dust emissions were measured in impacted population centers and a transport and dispersion model was developed for the region. The modeling system includes the use of a prognostic meteorological model, Mesoscale Metorological Model Version 5 (MM5), coupled with the CALMET/CALGRID Eularian modeling pair and a new dust emission module (EMIT-PM), developed specifically for this region from extensive soil sampling, portable wind tunnel measurements and intensive field campaigns. Surface wind observations were integrated into the diagnostic meteorological model, CALMET, along with wind fields generated by MM5 for six dust storm events that occurred in November 1990, October 1991, September 1993, November 1993, August 1996 and September 1999. Area dust emissions were generated using the CALMET wind fields along with detailed soil and land use maps in the EMIT-PM model and these hourly, gridded emissions were then used in CALGRID, which calculated hourly averaged concentrations of PM10 (particulate matter of aerodynamic diameter < 10 μ m) throughout the modeling domain. The predicted 24-hour average concentrations compared favorably to observed concentrations that were measured at selected locations within the modeling domain. For all the simulated events, with the exception of the August 1996 event, ratios of observed to predicted concentrations were within a range of 0.5 to 6.0. Because these ratios' were obtained without the need for a calibrated dust constant, it appears that the EMIT-PM provides an improved

  9. Modeling the coverage of an AFM tip by enzymes and its application in nanobiosensors.

    Science.gov (United States)

    Amarante, Adriano M; Oliveira, Guedmiller S; Bueno, Carolina C; Cunha, Richard A; Ierich, Jéssica C M; Freitas, Luiz C G; Franca, Eduardo F; Oliveira, Osvaldo N; Leite, Fábio L

    2014-09-01

    A stochastic simulation of adsorption processes was developed to simulate the coverage of an atomic force microscope (AFM) tip with enzymes represented as rigid polyhedrons. From geometric considerations of the enzyme structure and AFM tip, we could estimate the average number of active sites available to interact with substrate molecules in the bulk. The procedure was exploited to determine the interaction force between acetyl-CoA carboxylase enzyme (ACC enzyme) and its substrate diclofop, for which steered molecular dynamics (SMD) was used. The theoretical force of (1.6±0.5) nN per enzyme led to a total force in remarkable agreement with the experimentally measured force with AFM, thus demonstrating the usefulness of the procedure proposed here to assist in the interpretation of nanobiosensors experiments.

  10. Stochastic modeling of phosphorus transport in the Three Gorges Reservoir by incorporating variability associated with the phosphorus partition coefficient

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Lei; Fang, Hongwei; Xu, Xingya; He, Guojian; Zhang, Xuesong; Reible, Danny

    2017-08-01

    Phosphorus (P) fate and transport plays a crucial role in the ecology of rivers and reservoirs in which eutrophication is limited by P. A key uncertainty in models used to help manage P in such systems is the partitioning of P to suspended and bed sediments. By analyzing data from field and laboratory experiments, we stochastically characterize the variability of the partition coefficient (Kd) and derive spatio-temporal solutions for P transport in the Three Gorges Reservoir (TGR). We formulate a set of stochastic partial different equations (SPDEs) to simulate P transport by randomly sampling Kd from the measured distributions, to obtain statistical descriptions of the P concentration and retention in the TGR. The correspondence between predicted and observed P concentrations and P retention in the TGR combined with the ability to effectively characterize uncertainty suggests that a model that incorporates the observed variability can better describe P dynamics and more effectively serve as a tool for P management in the system. This study highlights the importance of considering parametric uncertainty in estimating uncertainty/variability associated with simulated P transport.

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

    CERN Document Server

    van Hulten, Marco; Middag, Rob; de Baar, Hein; Gehlen, Marion; Dutay, Jean-Claude; Tagliabue, Alessandro

    2014-01-01

    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 ~40{\\deg}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 usin...

  12. Fuzzy Case-Based Reasoning in Product Style Acquisition Incorporating Valence-Arousal-Based Emotional Cellular Model

    Directory of Open Access Journals (Sweden)

    Fuqian Shi

    2012-01-01

    Full Text Available Emotional cellular (EC, proposed in our previous works, is a kind of semantic cell that contains kernel and shell and the kernel is formalized by a triple- L = , where P denotes a typical set of positive examples relative to word-L, d is a pseudodistance measure on emotional two-dimensional space: valence-arousal, and δ is a probability density function on positive real number field. The basic idea of EC model is to assume that the neighborhood radius of each semantic concept is uncertain, and this uncertainty will be measured by one-dimensional density function δ. In this paper, product form features were evaluated by using ECs and to establish the product style database, fuzzy case based reasoning (FCBR model under a defined similarity measurement based on fuzzy nearest neighbors (FNN incorporating EC was applied to extract product styles. A mathematical formalized inference system for product style was also proposed, and it also includes uncertainty measurement tool emotional cellular. A case study of style acquisition of mobile phones illustrated the effectiveness of the proposed methodology.

  13. Incorporating moisture content in modeling the surface energy balance of debris-covered Changri Nup Glacier, Nepal

    Science.gov (United States)

    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

  14. Incorporating a Generic Model of Subcutaneous Insulin Absorption into the AIDA v4 Diabetes Simulator 3. Early Plasma Insulin Determinations

    Science.gov (United States)

    Lehmann, Eldon D.; Tarín, Cristina; Bondia, Jorge; Teufel, Edgar; Deutsch, Tibor

    2009-01-01

    Introduction AIDA is an interactive educational diabetes simulator that has been available without charge via the Internet for over 12 years. Recent articles have described the incorporation of a novel generic model of insulin absorption into AIDA as a way of enhancing its capabilities. The basic model components to be integrated have been overviewed, with the aim being to provide simulations of regimens utilizing insulin analogues, as well as insulin doses greater than 40 IU (the current upper limit within the latest release of AIDA [v4.3a]). Some preliminary calculated insulin absorption results have also recently been described. Methods This article presents the first simulated plasma insulin profiles from the integration of the generic subcutaneous insulin absorption model, and the currently implemented model in AIDA for insulin disposition. Insulin absorption has been described by the physiologically based model of Tarín and colleagues. A single compartment modeling approach has been used to specify how absorbed insulin is distributed in, and eliminated from, the human body. To enable a numerical solution of the absorption model, a spherical subcutaneous depot for the injected insulin dose has been assumed and spatially discretized into shell compartments with homogeneous concentrations, having as its center the injection site. The number of these compartments will depend on the dose and type of insulin. Insulin inflow arises as the sum of contributions to the different shells. For this report the first bench testing of plasma insulin determinations has been done. Results Simulated plasma insulin profiles are provided for currently available insulin preparations, including a rapidly acting insulin analogue (e.g., lispro/Humalog or aspart/Novolog), a short-acting (regular) insulin preparation (e.g., Actrapid), intermediate-acting insulins (both Semilente and neutral protamine Hagedorn types), and a very long-acting insulin analogue (e.g., glargine/Lantus), as

  15. Evaluating the Capacity of Global CO2 Flux and Atmospheric Transport Models to Incorporate New Satellite Observations

    Science.gov (United States)

    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

  16. A modified Wright-Fisher model that incorporates Ne: A variant of the standard model with increased biological realism and reduced computational complexity.

    Science.gov (United States)

    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

  17. Production of manganese peroxidase and laccase in a solid-state bioreactor and modeling of enzyme production kinetics.

    Science.gov (United States)

    Moilanen, Ulla; Winquist, Erika; Mattila, Tuomas; Hatakka, Annele; Eerikäinen, Tero

    2015-01-01

    Lignin-modifying enzymes have various promising applications such as biobleaching, biopulping, the functionalization of lignocellulosic materials, the modification of wood fibers, the remediation of contaminated soil and effluents, as well as improvement of the enzymatic hydrolysis of lignocellulosic substrates. In this study, the production of laccase and manganese peroxidase (MnP) in solid-state cultivation was examined. Oat husks were used as an inexpensive substrate for the white-rot fungus Cerrena unicolor PM170798 (FBCC 387). The addition of a fines fraction (consisting of oat flour and finely ground husks) enhanced MnP production fivefold and laccase production almost threefold. The enzyme production was studied first on a 100 g scale, and the cultivation experiments were then repeated at a larger laboratory-scale (4 kg) in a solid-state bioreactor. High enzyme activity levels were obtained (MnP: 340 nkat g(-1) DM, laccase: 470 nkat g(-1) DM). In addition, the correlation between the CO2 evolution rate and enzyme production was mathematically modeled from the bioreactor experimental data. The model parameters could be used to predict enzyme production.

  18. Recent Progresses in Incorporating Human Land-Water Management into Global Land Surface Models Toward Their Integration into Earth System Models

    Science.gov (United States)

    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.

  19. Directed Ligand Passage Over the Surface of Diffusion-Controlled Enzymes: A Cellular Automata Model

    CERN Document Server

    Ghaemi, M; Sarbolouki, M N; Ghaemi, Mehrdad; Rezaei-Ghaleh, Nasrollah; Sarbolouki, Mohammad-Nabi

    2004-01-01

    The rate-limiting step of some enzymatic reactions is a physical step, i.e. diffusion. The efficiency of such reactions can be improved through an increase in the arrival rate of the substrate molecules, e.g. by a directed passage of substrate (ligand) to active site after its random encounter with the enzyme surface. Herein, we introduce a cellular automata model simulating the ligand passage over the protein surface to its destined active site. The system is simulated using the lattice gas automata with probabilistic transition rules. Different distributions of amino acids over the protein surface are examined. For each distribution, the hydration pattern is achieved and the mean number of iteration steps needed for the ligand to arrive at the active site calculated. Comparison of results indicates that the rate at which ligand arrives at the active site is clearly affected by the distribution of amino acids outside the active side. Such a process can facilitate the ligand diffusion towards the active site ...

  20. Modelling Gaucher disease progression: long-term enzyme replacement therapy reduces the incidence of splenectomy and bone complications.

    Science.gov (United States)

    van Dussen, Laura; Biegstraaten, Marieke; Dijkgraaf, Marcel Gw; Hollak, Carla Em

    2014-07-24

    Long-term complications and associated conditions of type 1 Gaucher Disease (GD) can include splenectomy, bone complications, pulmonary hypertension, Parkinson disease and malignancies. Enzyme replacement therapy (ERT) reverses cytopenia and reduces organomegaly. To study the effects of ERT on long-term complications and associated conditions, the course of Gaucher disease was modelled.

  1. A neural network for incorporating the thermal effect on the magnetic hysteresis of the 3F3 material using the Jiles–Atherton model

    Energy Technology Data Exchange (ETDEWEB)

    Nouicer, A., E-mail: nouicer_abdelmadjid@yahoo.fr [Electrical engineering department, University of Skikda, BP26 Route Elhadaik, Skikda 21000 (Algeria); Nouicer, E., E-mail: n_elamine@yahoo.fr [Department of physics, University of Constantine1, Route Ain Elbey, Constantine 25000 (Algeria); Feliachi, Mouloud, E-mail: mouloud.feliachi@univ-nantes.fr [IREENA-Université de Nantes, PRES-L’UNAM, IUT, Saint-Nazaire (France)

    2015-01-01

    The present paper deals with the temperature dependent modeling approach for the generation of hysteresis loops of ferromagnetic materials. The physical model is developed to study the effect of temperature on the magnetic hysteresis loop using the Jiles–Atherton (J–A) model. The thermal effects were incorporated through temperature dependent hysteresis parameters of JA model. The temperature-dependent J–A model was validated by measurements made on the ferrite material. The results of proposed model were in good agreement with the measurements. - Highlights: • We incorporate the thermal effect on the magnetic hysteresis of the 3F3 material. • We use the Jiles–Atherton model. • A neural network is used to learn the variation of M{sub s} and H{sub c} with the temperature. • k≈H{sub c}, the rest of the J–A model parameters (α, c) are calculated analytically. • The parameter a is treated as a constant.

  2. In Situ Measurement, Characterization, and Modeling of Two-Phase Pressure Drop Incorporating Local Water Saturation in PEMFC Gas Channels

    Science.gov (United States)

    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

  3. First steps in incorporating data-driven modelling to flood early warning in Norway's Flood Forecasting Service

    Science.gov (United States)

    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.

  4. Pharmacological kynurenine 3-monooxygenase enzyme inhibition significantly reduces neuropathic pain in a rat model.

    Science.gov (United States)

    Rojewska, Ewelina; Piotrowska, Anna; Makuch, Wioletta; Przewlocka, Barbara; Mika, Joanna

    2016-03-01

    Recent studies have highlighted the involvement of the kynurenine pathway in the pathology of neurodegenerative diseases, but the role of this system in neuropathic pain requires further extensive research. Therefore, the aim of our study was to examine the role of kynurenine 3-monooxygenase (Kmo), an enzyme that is important in this pathway, in a rat model of neuropathy after chronic constriction injury (CCI) to the sciatic nerve. For the first time, we demonstrated that the injury-induced increase in the Kmo mRNA levels in the spinal cord and the dorsal root ganglia (DRG) was reduced by chronic administration of the microglial inhibitor minocycline and that this effect paralleled a decrease in the intensity of neuropathy. Further, minocycline administration alleviated the lipopolysaccharide (LPS)-induced upregulation of Kmo mRNA expression in microglial cell cultures. Moreover, we demonstrated that not only indirect inhibition of Kmo using minocycline but also direct inhibition using Kmo inhibitors (Ro61-6048 and JM6) decreased neuropathic pain intensity on the third and the seventh days after CCI. Chronic Ro61-6048 administration diminished the protein levels of IBA-1, IL-6, IL-1beta and NOS2 in the spinal cord and/or the DRG. Both Kmo inhibitors potentiated the analgesic properties of morphine. In summary, our data suggest that in neuropathic pain model, inhibiting Kmo function significantly reduces pain symptoms and enhances the effectiveness of morphine. The results of our studies show that the kynurenine pathway is an important mediator of neuropathic pain pathology and indicate that Kmo represents a novel pharmacological target for the treatment of neuropathy.

  5. Osteogenesis imperfecta model peptides: incorporation of residues replacing Gly within a triple helix achieved by renucleation and local flexibility.

    Science.gov (United States)

    Xiao, Jianxi; Madhan, Balaraman; Li, Yingjie; Brodsky, Barbara; Baum, Jean

    2011-07-20

    Missense mutations, which replace one Gly with a larger residue in the repeating sequence of the type I collagen triple helix, lead to the hereditary bone disorder osteogenesis imperfecta (OI). Previous studies suggest that these mutations may interfere with triple-helix folding. NMR was used to investigate triple-helix formation in a series of model peptides where the residue replacing Gly, as well as the local sequence environment, was varied. NMR measurement of translational diffusion coefficients allowed the identification of partially folded species. When Gly was replaced by Ala, the Ala residue was incorporated into a fully folded triple helix, whereas replacement of Gly by Ser or Arg resulted in the presence of some partially folded species, suggesting a folding barrier. Increasing the triple-helix stability of the sequence N-terminal to a Gly-to-Ser replacement allowed complete triple-helix folding, whereas with the substitution of Arg, with its large side chain, the peptide achieved full folding only after flexible residues were introduced N-terminal to the mutation site. These studies shed light on the factors important for accommodation of Gly mutations within the triple helix and may relate to the varying severity of OI.

  6. Structural differences of matrix metalloproteinases. Homology modeling and energy minimization of enzyme-substrate complexes

    DEFF Research Database (Denmark)

    Terp, G E; Christensen, I T; Jørgensen, Flemming Steen

    2000-01-01

    in the AMBER 4.1 force field, applying a non-bonded approach and a full ion charge representation. Energy minimization of the apoenzymes yielded structures with distorted active sites, while reliable three-dimensional structures of the enzymes containing a substrate in active site were obtained. The structural...... differences between the eight enzyme-substrate complexes were studied with particular emphasis on the active site, and possible sites for obtaining selectivity among the MMP's are discussed. Differences in the P1' pocket are well-documented and have been extensively exploited in inhibitor design. The present......Matrix metalloproteinases are extracellular enzymes taking part in the remodeling of extracellular matrix. The structures of the catalytic domain of MMP1, MMP3, MMP7 and MMP8 are known, but structures of enzymes belonging to this family still remain to be determined. A general approach...

  7. Compartmental and enzyme kinetic modeling to elucidate the biotransformation pathway of a centrally acting antitrypanosomal prodrug.

    Science.gov (United States)

    Generaux, Claudia N; Ainslie, Garrett R; Bridges, Arlene S; Ismail, Mohamed A; Boykin, David W; Tidwell, Richard R; Thakker, Dhiren R; Paine, Mary F

    2013-02-01

    DB868 [2,5-bis [5-(N-methoxyamidino)-2-pyridyl] furan], a prodrug of the diamidine DB829 [2,5-bis(5-amidino-2-pyridyl) furan], has demonstrated efficacy in murine models of human African trypanosomiasis. A cross-species evaluation of prodrug bioconversion to the active drug is required to predict the disposition of prodrug, metabolites, and active drug in humans. The phase I biotransformation of DB868 was elucidated using liver microsomes and sandwich-cultured hepatocytes from humans and rats. All systems produced four NADPH-dependent metabolites via O-demethylation (M1, M2) and N-dehydroxylation (M3, M4). Compartmental kinetic modeling of the DB868 metabolic pathway suggested an unusual N-demethoxylation reaction that was supported experimentally. A unienzyme Michaelis-Menten model described the kinetics of M1 formation by human liver microsomes (HLMs) (K(m), 11 μM; V(max), 340 pmol/min/mg), whereas a two-enzyme model described the kinetics of M1 formation by rat liver microsomes (RLMs) (K(m1), 0.5 μM; V(max1), 12 pmol/min/mg; K(m2), 27 μM; V(max2), 70 pmol/min/mg). Human recombinant CYP1A2, CYP3A4, and CYP4F2, rat recombinant Cyp1a2 and Cyp2d2, and rat purified Cyp4f1 catalyzed M1 formation. M2 formation by HLMs exhibited allosteric kinetics (S(50), 18 μM; V(max), 180 pmol/mg), whereas M2 formation by RLMs was negligible. Recombinant CYP1A2/Cyp1a2 catalyzed M2 formation. DB829 was detected in trace amounts in HLMs at the end of the 180-min incubation and was detected readily in sandwich-cultured hepatocytes from both species throughout the 24-h incubation. These studies demonstrated that DB868 biotransformation to DB829 is conserved between humans and rats. An improved understanding of species differences in the kinetics of DB829 formation would facilitate preclinical development of a promising antitrypanosomal prodrug.

  8. Incorporating uncertainty into the ranking of SPARROW model nutrient yields from Mississippi/Atchafalaya River basin watersheds

    Science.gov (United States)

    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

  9. Predicting Drug Extraction in the Human Gut Wall: Assessing Contributions from Drug Metabolizing Enzymes and Transporter Proteins using Preclinical Models.

    Science.gov (United States)

    Peters, Sheila Annie; Jones, Christopher R; Ungell, Anna-Lena; Hatley, Oliver J D

    2016-06-01

    Intestinal metabolism can limit oral bioavailability of drugs and increase the risk of drug interactions. It is therefore important to be able to predict and quantify it in drug discovery and early development. In recent years, a plethora of models-in vivo, in situ and in vitro-have been discussed in the literature. The primary objective of this review is to summarize the current knowledge in the quantitative prediction of gut-wall metabolism. As well as discussing the successes of current models for intestinal metabolism, the challenges in the establishment of good preclinical models are highlighted, including species differences in the isoforms; regional abundances and activities of drug metabolizing enzymes; the interplay of enzyme-transporter proteins; and lack of knowledge on enzyme abundances and availability of empirical scaling factors. Due to its broad specificity and high abundance in the intestine, CYP3A is the enzyme that is frequently implicated in human gut metabolism and is therefore the major focus of this review. A strategy to assess the impact of gut wall metabolism on oral bioavailability during drug discovery and early development phases is presented. Current gaps in the mechanistic understanding and the prediction of gut metabolism are highlighted, with suggestions on how they can be overcome in the future.

  10. Pectic enzymes

    NARCIS (Netherlands)

    Benen, J.A.E.; Voragen, A.G.J.; Visser, J.

    2003-01-01

    The pectic enzymes comprise a diverse group of enzymes. They consist of main-chain depolymerases and esterases active on methyl- and acetylesters of galacturonosyl uronic acid residues. The depolymerizing enzymes comprise hydrolases as wel as lyases

  11. Pectic enzymes

    NARCIS (Netherlands)

    Benen, J.A.E.; Voragen, A.G.J.; Visser, J.

    2003-01-01

    The pectic enzymes comprise a diverse group of enzymes. They consist of main-chain depolymerases and esterases active on methyl- and acetylesters of galacturonosyl uronic acid residues. The depolymerizing enzymes comprise hydrolases as wel as lyases

  12. Biochemical characterization, homology modeling and docking studies of ornithine delta-aminotransferase--an important enzyme in proline biosynthesis of plants.

    Science.gov (United States)

    Sekhar, P Nataraj; Amrutha, R Naga; Sangam, Shubhada; Verma, D P S; Kishor, P B Kavi

    2007-11-01

    Ornithine delta-aminotransferase (OAT) is an important enzyme in proline biosynthetic pathway and is implicated in salt tolerance in higher plants. OAT transaminates ornithine to pyrroline 5-carboxylate, which is further catalyzed to proline by pyrroline 5-carboxylate reductase. The Vigna aconitifolia OAT cDNA, encoding a polypeptide of 48.1 kDa, was expressed in Escherichia coli and the enzyme was partially characterized following its purification using (NH(4))(2)SO(4) precipitation and gel filtration techniques. Optimal activity of the enzyme was observed at a temperature of 25 degrees C and pH 8.0. The enzyme appeared to be a monomer and exhibited high activity at 4mM ornithine. Proline did not show any apparent effect but isoleucine, valine and serine inhibited the activity when added into the assay mixture along with ornithine. Omission of pyridoxal 5'-phosphate from the reaction mixture reduced the activity of this enzyme by 60%. To further evaluate these biochemical observations, homology modeling of the OAT was performed based on the crystal structure of the ornithine delta-aminotransferase from humans (PDB code 1OAT) by using the software MODELLER6v2. With the aid of the molecular mechanics and dynamics methods, the final model was obtained and assessed subsequently by PROCHECK and VERIFY-3D graph. With this model, a flexible docking study with the substrate and inhibitors was performed and the results indicated that Gly106 and Lys256 in OAT are the important determinant residues in binding as they have strong hydrogen bonding contacts with the substrate and inhibitors. These observations are in conformity with the results obtained from experimental investigations.

  13. The non-specific inhibition of enzymes by environmental pollutants: a study of a model system towards the development of electrochemical biosensor arrays.

    Science.gov (United States)

    Young, S J; Hart, J P; Dowman, A A; Cowell, D C

    2001-12-01

    Previous research has shown that lactate dehydrogenase (LDH) was competitively inhibited by pentachlorophenol (PCP) and a modified assay produced a detection limit of 1 microM (270 microg l(-1)). This work used spectrophotometric rate-determination but in order to move towards biosensor development the selected detection method was electrochemical. The linkage of LDH to lactate oxidase (LOD) provided the electroactive species, hydrogen peroxide. This could be monitored using a screen-printed carbon electrode (SPCE) incorporating the mediator, cobalt phthalocyanine, at a potential of +300 mV (vs. Ag/AgCl). A linked LDH/LOD system was optimised with respect to inhibition by PCP. It was found that the SPCE support material, PVC, acted to reduce inhibition, possibly by combining with PCP. A cellulose acetate membrane removed this effect. Inhibition of the system was greatest at enzyme activities of 5 U ml(-1) LDH and 0.8 U ml(-1) LOD in reactions containing 246 microM pyruvate and 7.5 microM NADPH. PCP detection limits were an EC(10) of 800 nM (213 microg l(-1)) and a minimum inhibition detectable (MID) limit of 650 nM (173 microg l(-1)). The inclusion of a third enzyme, glucose dehydrogenase (GDH), provided cofactor recycling to enable low concentrations of NADPH to be incorporated within the assay. NADPH was reduced from 7.5 to 2 microM. PCP detection limits were obtained for an assay containing 5 U ml(-1) LDH, 0.8 U ml(-1) LOD and 0.1 U ml(-1) GDH with 246 microM pyruvate, 400 mM glucose and 2 microM NADPH. The EC(10) limit was 150 nM (39.9 microg l(-1)) and the MID was 100 nM (26.6 microg l(-1)). The design of the inhibition assays discussed has significance as a model for other enzymes and moves forward the possibility of an electrochemical biosensor array for pollution monitoring.

  14. Enzyme assays.

    Science.gov (United States)

    Reymond, Jean-Louis; Fluxà, Viviana S; Maillard, Noélie

    2009-01-07

    Enzyme assays are analytical tools to visualize enzyme activities. In recent years a large variety of enzyme assays have been developed to assist the discovery and optimization of industrial enzymes, in particular for "white biotechnology" where selective enzymes are used with great success for economically viable, mild and environmentally benign production processes. The present article highlights the aspects of fluorogenic and chromogenic substrates, sensors, and enzyme fingerprinting, which are our particular areas of interest.

  15. Forizymes - functionalised artificial forisomes as a platform for the production and immobilisation of single enzymes and multi-enzyme complexes.

    Science.gov (United States)

    Visser, Franziska; Müller, Boje; Rose, Judith; Prüfer, Dirk; Noll, Gundula A

    2016-01-01

    The immobilisation of enzymes plays an important role in many applications, including biosensors that require enzyme activity, stability and recyclability in order to function efficiently. Here we show that forisomes (plant-derived mechanoproteins) can be functionalised with enzymes by translational fusion, leading to the assembly of structures designated as forizymes. When forizymes are expressed in the yeast Saccharomyces cerevisiae, the enzymes are immobilised by the self-assembly of forisome subunits to form well-structured protein bodies. We used glucose-6-phosphate dehydrogenase (G6PDH) and hexokinase 2 (HXK2) as model enzymes for the one-step production and purification of catalytically active forizymes. These structures retain the typical stimulus-response reaction of the forisome and the enzyme remains active even after multiple assay cycles, which we demonstrated using G6PDH forizymes as an example. We also achieved the co-incorporation of both HXK2 and G6PDH in a single forizyme, facilitating a two-step reaction cascade that was 30% faster than the coupled reaction using the corresponding enzymes on different forizymes or in solution. Our novel forizyme immobilisation technique therefore not only combines the sensory properties of forisome proteins with the catalytic properties of enzymes but also allows the development of multi-enzyme complexes for incorporation into technical devices.

  16. Substrate reduction augments the efficacy of enzyme therapy in a mouse model of Fabry disease.

    Directory of Open Access Journals (Sweden)

    John Marshall

    Full Text Available Fabry disease is an X-linked glycosphingolipid storage disorder caused by a deficiency in the activity of the lysosomal hydrolase α-galactosidase A (α-gal. This deficiency results in accumulation of the glycosphingolipid globotriaosylceramide (GL-3 in lysosomes. Endothelial cell storage of GL-3 frequently leads to kidney dysfunction, cardiac and cerebrovascular disease. The current treatment for Fabry disease is through infusions of recombinant α-gal (enzyme-replacement therapy; ERT. Although ERT can markedly reduce the lysosomal burden of GL-3 in endothelial cells, variability is seen in the clearance from several other cell types. This suggests that alternative and adjuvant therapies may be desirable. Use of glucosylceramide synthase inhibitors to abate the biosynthesis of glycosphingolipids (substrate reduction therapy, SRT has been shown to be effective at reducing substrate levels in the related glycosphingolipidosis, Gaucher disease. Here, we show that such an inhibitor (eliglustat tartrate, Genz-112638 was effective at lowering GL-3 accumulation in a mouse model of Fabry disease. Relative efficacy of SRT and ERT at reducing GL-3 levels in Fabry mouse tissues differed with SRT being more effective in the kidney, and ERT more efficacious in the heart and liver. Combination therapy with ERT and SRT provided the most complete clearance of GL-3 from all the tissues. Furthermore, treatment normalized urine volume and uromodulin levels and significantly delayed the loss of a nociceptive response. The differential efficacies of SRT and ERT in the different tissues indicate that the combination approach is both additive and complementary suggesting the possibility of an improved therapeutic paradigm in the management of Fabry disease.

  17. Investigation of realistic PET simulations incorporating tumor patient's specificity using anthropomorphic models: creation of an oncology database.

    Science.gov (United States)

    Papadimitroulas, Panagiotis; Loudos, George; Le Maitre, Amandine; Hatt, Mathieu; Tixier, Florent; Efthimiou, Nikos; Nikiforidis, George C; Visvikis, Dimitris; Kagadis, George C

    2013-11-01

    The GATE Monte Carlo simulation toolkit is used for the implementation of realistic PET simulations incorporating tumor heterogeneous activity distributions. The reconstructed patient images include noise from the acquisition process, imaging system's performance restrictions and have limited spatial resolution. For those reasons, the measured intensity cannot be simply introduced in GATE simulations, to reproduce clinical data. Investigation of the heterogeneity distribution within tumors applying partial volume correction (PVC) algorithms was assessed. The purpose of the present study was to create a simulated oncology database based on clinical data with realistic intratumor uptake heterogeneity properties. PET/CT data of seven oncology patients were used in order to create a realistic tumor database investigating the heterogeneity activity distribution of the simulated tumors. The anthropomorphic models (NURBS based cardiac torso and Zubal phantoms) were adapted to the CT data of each patient, and the activity distribution was extracted from the respective PET data. The patient-specific models were simulated with the Monte Carlo Geant4 application for tomography emission (GATE) in three different levels for each case: (a) using homogeneous activity within the tumor, (b) using heterogeneous activity distribution in every voxel within the tumor as it was extracted from the PET image, and (c) using heterogeneous activity distribution corresponding to the clinical image following PVC. The three different types of simulated data in each case were reconstructed with two iterations and filtered with a 3D Gaussian postfilter, in order to simulate the intratumor heterogeneous uptake. Heterogeneity in all generated images was quantified using textural feature derived parameters in 3D according to the ground truth of the simulation, and compared to clinical measurements. Finally, profiles were plotted in central slices of the tumors, across lines with heterogeneous

  18. A neural network for incorporating the thermal effect on the magnetic hysteresis of the 3F3 material using the Jiles-Atherton model

    Science.gov (United States)

    Nouicer, A.; Nouicer, E.; Feliachi, Mouloud

    2015-01-01

    The present paper deals with the temperature dependent modeling approach for the generation of hysteresis loops of ferromagnetic materials. The physical model is developed to study the effect of temperature on the magnetic hysteresis loop using the Jiles-Atherton (J-A) model. The thermal effects were incorporated through temperature dependent hysteresis parameters of JA model. The temperature-dependent J-A model was validated by measurements made on the ferrite material. The results of proposed model were in good agreement with the measurements.

  19. Application of fuzzy sets and cognitive maps to incorporate social science scenarios in integrated assessment models: A case study of urbanization in Ujung Pandang, Indonesia.

    NARCIS (Netherlands)

    de Kok, Jean-Luc; Titus, Milan; Wind, H.G.

    2000-01-01

    Decision-support systems in the field of integrated water management could benefit considerably from social science knowledge, as many environmental changes are human-induced. Unfortunately the adequate incorporation of qualitative social science concepts in a quantitative modeling framework is not

  20. Incorporating biologic measurements (SF(2), CFE) into a tumor control probability model increases their prognostic significance: a study in cervical carcinoma treated with radiation therapy.

    Science.gov (United States)

    Buffa, F M; Davidson, S E; Hunter, R D; Nahum, A E; West, C M

    2001-08-01

    To assess whether incorporation of measurements of surviving fraction at 2 Gy (SF(2)) and colony-forming efficiency (CFE) into a tumor control probability (tcp) model increases their prognostic significance. Measurements of SF(2) and CFE were available from a study on carcinoma of the cervix treated with radiation alone. These measurements, as well as tumor volume, dose, and treatment time, were incorporated into a Poisson tcp model (tcp(alpha,rho)). Regression analysis was performed to assess the prognostic power of tcp(alpha,rho) vs. the use of either tcp models with biologic parameters fixed to best-fit estimates (but incorporating individual dose, volume, and treatment time) or the use of SF(2) and CFE measurements alone. In a univariate regression analysis of 44 patients, tcp(alpha,rho) was a better prognostic factor for both local control and survival (p CFE alone (p = 0.015 for local control, p = 0.38 for survival). In multivariate analysis, tcp(alpha,rho) emerged as the most important prognostic factor for local control (p CFE was still a significant independent prognostic factor for local control, whereas SF(2) was not. The sensitivities of tcp(alpha,rho) and SF(2) as predictive tests for local control were 87% and 65%, respectively. Specificities were 70% and 77%, respectively. A Poisson tcp model incorporating individual SF(2), CFE, dose, tumor volume, and treatment time was found to be the best independent prognostic factor for local control and survival in cervical carcinoma patients.

  1. Molecular view modeling of atmospheric organic particulate matter: Incorporating molecular structure and co-condensation of water

    Science.gov (United States)

    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

  2. Protective Potential of Antioxidant Enzymes as Vaccines for Schistosomiasis in a Non-Human Primate Model

    Science.gov (United States)

    Carvalho-Queiroz, Claudia; Nyakundi, Ruth; Ogongo, Paul; Rikoi, Hitler; Egilmez, Nejat K.; Farah, Idle O.; Kariuki, Thomas M.; LoVerde, Philip T.

    2015-01-01

    Schistosomiasis remains a major cause of morbidity in the world. The challenge today is not so much in the clinical management of individual patients, but rather in population-based control of transmission in endemic areas. Despite recent large-scale efforts, such as integrated control programs aimed at limiting schistosomiasis by improving education and sanitation, molluscicide treatment programs and chemotherapy with praziquantel, there has only been limited success. There is an urgent need for complementary approaches, such as vaccines. We demonstrated previously that anti-oxidant enzymes, such as Cu–Zn superoxide dismutase (SOD) and glutathione S peroxidase (GPX), when administered as DNA-based vaccines induced significant levels of protection in inbred mice, greater than the target 40% reduction in worm burden compared to controls set as a minimum by the WHO. These results led us to investigate if immunization of non-human primates with antioxidants would stimulate an immune response that could confer protection as a prelude study for human trials. Issues of vaccine toxicity and safety that were difficult to address in mice were also investigated. All baboons in the study were examined clinically throughout the study and no adverse reactions occurred to the immunization. When our outbred baboons were vaccinated with two different formulations of SOD (SmCT-SOD and SmEC-SOD) or one of GPX (SmGPX), they showed a reduction in worm number to varying degrees, when compared with the control group. More pronounced, vaccinated animals showed decreased bloody diarrhea, days of diarrhea, and egg excretion (transmission), as well as reduction of eggs in the liver tissue and in the large intestine (pathology) compared to controls. Specific IgG antibodies were present in sera after immunizations and 10 weeks after challenge infection compared to controls. Peripheral blood mononuclear cells, mesenteric, and inguinal node cells from vaccinated animals proliferated and

  3. Mathematical modelling of a single-line flow-injection analysis systems with single-layer enzyme electrode detection. Pt. 3; Experimental verification of the model

    Energy Technology Data Exchange (ETDEWEB)

    Kolev, S.D. (Sofia Univ. (Bulgaria). Khimicheski Fakultet); Nagy, Geza; Pungor, Ernoe (Budapesti Mueszaki Egyetem, Budapest (Hungary). Altalanos es Analitikai Kemia Tanszek)

    1991-11-20

    Glucose and urea electrodes, prepared by two different enzyme immobilization techniques and used as detectors in a single-line flow-injection manifold, were experimentally investigated for elucidating the influence of their most important parameters, i.e., the initial substrate concentration in the sample, the enzyme concentration in the reaction layer and its thickness and the buffer concentration, on the output signal. The results obtained were compared with the theoretical predictions based on simulations of the model for single-line flow-injection systems with single-layer enzyme electrode detection. The good qualitative agreement which was observed is a convincing experimental verification of this model and the guidelines for the production of flow-through biocatalytic electrodes with optimum design based upon it. (author). 12 refs.; 6 figs.

  4. Incorporation of the electron energy equation into the hybrid Monte Carlo - fluid model for glow discharge: the applicability and reliability of the model

    Science.gov (United States)

    Eylenceoglu, Ender; Rafatov, Ismail; Kudryavtsev, Anatoly

    2016-09-01

    A modification of the conventional hybrid Monte Carlo - fluid model for glow discharge, which incorporates the electron energy equation, is considered. In the proposed model electrons are separated into two groups, namely, high energetic fast and low energetic slow (bulk) electrons. Density profiles of ions, slow electrons, and meta-stable particles are determined from the solution of corresponding continuity equations. Fast electrons, which are responsible for ionization and excitation events in the discharge, are simulated by the Monte-Carlo method. The temperature profile for slow electrons is obtained from the solution of the energy balance equation. The transport (mobility and diffusion) coefficients as well as the reaction rates for slow electrons are determined as functions of the electron temperature. Test calculations are carried out for the direct current glow discharge in argon within two-dimensional geometry. Comparison of the computed results with those obtained from the conventional fluid and hybrid models and the experimental data is done, the applicability and reliability of the proposed model is studied in details.