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Author (up) Amaku, M.; Coutinho, F.A.B.; Massad, E. file  url
  Title Why dengue and yellow fever coexist in some areas of the world and not in others? Type Journal Article
  Year 2011 Publication Bio Systems Abbreviated Journal Biosystems  
  Volume 106 Issue 2-3 Pages 111-120  
  Keywords Adaptive Immunity/*immunology; Aedes/*virology; Africa/epidemiology; Animals; Asia/epidemiology; Computer Simulation; *Demography; Dengue/*epidemiology/immunology/transmission; Humans; Insect Vectors/*virology; *Models, Biological; South America/epidemiology; Species Specificity; Yellow Fever/*epidemiology/immunology/transmission  
  Abstract Urban yellow fever and dengue coexist in Africa but not in Asia and South America. In this paper, we examine four hypotheses (and various combinations thereof) to explain the absence of yellow fever in urban areas of Asia and South America. In addition, we examine an additional hypothesis that offers an explanation of the coexistence of the infections in Africa while at the same time explaining their lack of coexistence in Asia. The hypotheses we tested to explain the nonexistence of yellow fever in Asia are the following: (1) the Asian Aedes aegypti is relatively incompetent to transmit yellow fever; (2) there would exist a competition between dengue and yellow fever viruses within the mosquitoes, as suggested by in vitro studies in which the dengue virus always wins; (3) when an A. aegypti mosquito that is infected by or latent for yellow fever acquires dengue, it becomes latent for dengue due to internal competition within the mosquito between the two viruses; (4) there is an important cross-immunity between yellow fever and other flaviviruses, dengue in particular, such that a person recovered from a bout of dengue exhibits a diminished susceptibility to yellow fever. This latter hypothesis is referred to below as the “Asian hypothesis.” Finally, we hypothesize that: (5) the coexistence of the infections in Africa is due to the low prevalence of the mosquito Aedes albopictus in Africa, as it competes with A. aegypti. We will refer to this latter hypothesis as the “African hypothesis.” We construct a model of transmission that allows all of the above hypotheses to be tested. We conclude that the Asian and the African hypotheses can explain the observed phenomena, whereas other hypotheses fail to do so.  
  Call Number Serial 1532  
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Author (up) Goldfield, G.S.; Adamo, K.B.; Rutherford, J.; Legg, C. file  url
  Title Stress and the relative reinforcing value of food in female binge eaters Type Journal Article
  Year 2008 Publication Physiology & Behavior Abbreviated Journal Physiol Behav  
  Volume 93 Issue 3 Pages 579-587  
  Keywords Adolescent; Adult; Analysis of Variance; Body Mass Index; Body Weight; Bulimia/*physiopathology/*psychology; Computer Simulation; Feeding Behavior/physiology; Female; Food Preferences/physiology; Functional Laterality; Humans; Psychological Theory; *Reinforcement (Psychology); Stress, Psychological/*physiopathology  
  Abstract The purpose of this study was to examine the independent and interactive effects of stress reactivity and binge eating (BE) status on changes in the relative reinforcing value of snack foods. The relative reinforcing value of snack foods was assessed in binge eaters and non-binge eaters across a stress-induction session (after 3-minutes of anticipation of giving a speech) or a control day (after 3-minutes of reading magazines), with order of conditions counterbalanced. Subjects were divided into four groups based on scores on the Binge Eating Scale (BES) and changes in perceived stress: Binge eaters/low stress reactivity (n=12), binge eaters/high stress reactivity (n=10), non-binge eaters/low stress reactivity (n=6), non-binge eaters/high stress reactivity (n=9). Dietary restraint, hunger, disinhibition, and hedonics were measured by self-report. Body composition was estimated by body mass index (BMI=weight in kilograms divided by height in metres squared). The relative reinforcing value of snack food was influenced differently by binge status and stress reactivity in the stress and control conditions (p<0.05). Binge eaters who reacted to stress earned more snack food points (p<0.001) in stress condition, but non-binge eaters who showed high stress reactivity earned less points for snack food in stress condition (p<0.05). This same pattern of results remained after statistically controlling for body mass index (BMI) and dietary restraint. Findings suggest that reactivity to interpersonal or ego-related stress increases the relative reinforcing value of food in binge eaters but decreases the relative reinforcing value of snack food in non-binge eaters, and these findings appear to be independent of dietary restraint and BMI.  
  Call Number Serial 1827  
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Author (up) Joanisse, M.; Gagnon, S.; Voloaca, M. file  url
doi  openurl
  Title The impact of Stereotype Threat on the simulated driving performance of older drivers Type Journal Article
  Year 2013 Publication Accident; Analysis and Prevention Abbreviated Journal Accid Anal Prev  
  Volume 50 Issue Pages 530-538  
  Keywords Aged; Aged, 80 and over; Analysis of Variance; Automobile Driving/*psychology; Chi-Square Distribution; Computer Simulation; Female; Humans; Male; Middle Aged; Ontario; Questionnaires; *Stereotyping; Task Performance and Analysis; User-Computer Interface  
  Abstract Older drivers are perceived as being dangerous and overly cautious by other drivers. We tested the hypothesis that this negative stereotype has a direct influence on the performance of older drivers. Based on the Stereotype Threat literature, we predicted that older driving performance would be altered after exposure to a Stereotype Threat. Sixty-one older drivers aged 65 and above completed a simulated driving assessment course. Prior to testing, half of the participants were told that the objective of the study was to investigate why older adults aged 65 and above were more implicated in on-road accidents (Stereotype Threat condition) and half were showed a neutral statement. Results confirmed that exposure to the threat significantly altered driving performance. Older adults in the Stereotype Threat condition made more driving mistakes than those in the control group. Interestingly, under a Stereotype Threat condition, older adults tended to commit more speeding infractions. We also observed that domain identification (whether driving is deemed important or not) moderated the impact of the threat. Taken together, these results support recent older drivers' performance models suggesting that the interaction between individual and social factors need to be considered when examining older drivers' performance.  
  Call Number Serial 1060  
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Author (up) Kang, J.; Cho, J.; Zhao, H. file  url
doi  openurl
  Title Practical issues in building risk-predicting models for complex diseases Type Journal Article
  Year 2010 Publication Journal of Biopharmaceutical Statistics Abbreviated Journal J Biopharm Stat  
  Volume 20 Issue 2 Pages 415-440  
  Keywords Algorithms; Computer Simulation; Data Interpretation, Statistical; Empirical Research; *Genetic Predisposition to Disease; Genome-Wide Association Study/statistics & numerical data; Humans; *Models, Statistical; Mutation; Odds Ratio; Polymorphism, Single Nucleotide; Reproducibility of Results; Risk Assessment; Risk Factors  
  Abstract Recent genome-wide association studies have identified many genetic variants affecting complex human diseases. It is of great interest to build disease risk prediction models based on these data. In this article, we first discuss statistical challenges in using genome-wide association data for risk predictions, and then review the findings from the literature on this topic. We also demonstrate the performance of different methods through both simulation studies and application to real-world data.  
  Call Number Serial 189  
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Author (up) Mulholland, P.J.; Helton, A.M.; Poole, G.C.; Hall, R.O.; Hamilton, S.K.; Peterson, B.J.; Tank, J.L.; Ashkenas, L.R.; Cooper, L.W.; Dahm, C.N.; Dodds, W.K.; Findlay, S.E.G.; Gregory, S.V.; Grimm, N.B.; Johnson, S.L.; McDowell, W.H.; Meyer, J.L.; Valett, H.M.; Webster, J.R.; Arango, C.P.; Beaulieu, J.J.; Bernot, M.J.; Burgin, A.J.; Crenshaw, C.L.; Johnson, L.T.; Niederlehner, B.R.; O'Brien, J.M.; Potter, J.D.; Sheibley, R.W.; Sobota, D.J.; Thomas, S.M. file  url
  Title Stream denitrification across biomes and its response to anthropogenic nitrate loading Type Journal Article
  Year 2008 Publication Nature Abbreviated Journal Nature  
  Volume 452 Issue 7184 Pages 202-205  
  Keywords Agriculture; Bacteria/metabolism; Computer Simulation; *Ecosystem; Geography; *Human Activities; Nitrates/*analysis/*metabolism; Nitrites/*analysis/*metabolism; Nitrogen/analysis/metabolism; Nitrogen Isotopes; Plants/metabolism; Rivers/*chemistry; Urbanization  
  Abstract Anthropogenic addition of bioavailable nitrogen to the biosphere is increasing and terrestrial ecosystems are becoming increasingly nitrogen-saturated, causing more bioavailable nitrogen to enter groundwater and surface waters. Large-scale nitrogen budgets show that an average of about 20-25 per cent of the nitrogen added to the biosphere is exported from rivers to the ocean or inland basins, indicating that substantial sinks for nitrogen must exist in the landscape. Streams and rivers may themselves be important sinks for bioavailable nitrogen owing to their hydrological connections with terrestrial systems, high rates of biological activity, and streambed sediment environments that favour microbial denitrification. Here we present data from nitrogen stable isotope tracer experiments across 72 streams and 8 regions representing several biomes. We show that total biotic uptake and denitrification of nitrate increase with stream nitrate concentration, but that the efficiency of biotic uptake and denitrification declines as concentration increases, reducing the proportion of in-stream nitrate that is removed from transport. Our data suggest that the total uptake of nitrate is related to ecosystem photosynthesis and that denitrification is related to ecosystem respiration. In addition, we use a stream network model to demonstrate that excess nitrate in streams elicits a disproportionate increase in the fraction of nitrate that is exported to receiving waters and reduces the relative role of small versus large streams as nitrate sinks.  
  Call Number Serial 2107  
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Author (up) Phillips, J.C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R.D.; Kale, L.; Schulten, K. file  url
doi  openurl
  Title Scalable molecular dynamics with NAMD Type Journal Article
  Year 2005 Publication Journal of Computational Chemistry Abbreviated Journal J Comput Chem  
  Volume 26 Issue 16 Pages 1781-1802  
  Keywords Algorithms; Aquaporins/chemistry; Cell Membrane/chemistry; *Computer Simulation; Glycophorin/chemistry; *Models, Biological; *Models, Chemical; Models, Molecular; Repressor Proteins/chemistry; *Software; Software Design; Static Electricity; Ubiquitin/chemistry  
  Abstract NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at  
  Call Number Serial 418  
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Author (up) Podlich, D.W.; Cooper, M. file  url
  Title QU-GENE: a simulation platform for quantitative analysis of genetic models Type Journal Article
  Year 1998 Publication Bioinformatics (Oxford, England) Abbreviated Journal Bioinformatics  
  Volume 14 Issue 7 Pages 632-653  
  Keywords Computer Simulation; Epistasis, Genetic; Genotype; Models, Genetic; Software  
  Abstract MOTIVATION: Classical quantitative genetics theory makes a number of simplifying assumptions in order to develop mathematical expressions that describe the mean and variation (genetic and phenotypic) within and among populations, and to predict how these are expected to change under the influence of external forces. These assumptions are often necessary to render the development of many aspects of the theory mathematically tractable. The availability of high-speed computers today provides opportunity for the use of computer simulation methodology to investigate the implications of relaxing many of the assumptions that are commonly made. RESULTS: QU-GENE (QUantitative-GENEtics) was developed as a flexible computer simulation platform for the quantitative analysis of genetic models. Three features of the QU-GENE software that contribute to its flexibility are (i) the core E(N:K) genetic model, where E is the number of types of environment, N is the number of genes, K indicates the level of epistasis and the parentheses indicate that different N:K genetic models can be nested within types of environments, (ii) the use of a two-stage architecture that separates the definition of the genetic model and genotype-environment system from the detail of the individual simulation experiments and (iii) the use of a series of interactive graphical windows that monitor the progress of the simulation experiments. The E(N:K) framework enables the generation of families of genetic models that incorporate the effects of genotype-by-environment (G x E) interactions and epistasis. By the design of appropriate application modules, many different simulation experiments can be conducted for any genotype-environment system. The structure of the QU-GENE simulation software is explained and demonstrated by way of two examples. The first concentrates on some aspects of the influence of G x E interactions on response to selection in plant breeding, and the second considers the influence of multiple-peak epistasis on the evolution of a four-gene epistatic network.  
  Call Number Serial 19  
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Author (up) Redd, M.; de Castro, J.M. file  url
  Title Social facilitation of eating: effects of social instruction on food intake Type Journal Article
  Year 1992 Publication Physiology & Behavior Abbreviated Journal Physiol Behav  
  Volume 52 Issue 4 Pages 749-754  
  Keywords Adolescent; Adult; Arousal; Computer Simulation; Dietary Fats/administration & dosage; *Eating; Energy Intake; Feeding Behavior/*psychology; Female; Humans; Male; Middle Aged; Motivation; Nutritive Value; *Reinforcement, Social; *Social Facilitation; Social Isolation; Sodium, Dietary/administration & dosage  
  Abstract To investigate whether social influences cause increases in eating behavior, thirty undergraduate psychology students completed a diet diary for three 5-day periods. Subjects were instructed to either eat alone or eat with other people, actively eating with them for two of these periods. For the third period, subjects were instructed to eat as they normally would (with or without other people present). When instructed to eat with others present, subjects overall consumed more food, water, sodium, and alcohol than when they were instructed to eat alone. In the normal condition, food intake was 60% higher when the subjects ate with others present than when they ate alone. These results suggest that social facilitation has a causal influence on eating which increases food intake.  
  Call Number Serial 1647  
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