Bayesian and Frequentist Two-Sample Predictions of the Inverse Weibull Model Based on Generalized Order Statistics

2000 Mathematics Subject Classification: 62E16,62F15, 62H12, 62M20.

Towards the knowledge-based design of universal influenza epitope ensemble vaccines

Motivation: Influenza A viral heterogeneity remains a significant threat due to unpredictable antigenic drift in seasonal influenza and antigenic shifts caused by the emergence of novel subtypes. Annual review of multivalent influenza vaccines targets strains of influenza A and B likely to be predominant in future influenza seasons. This does not induce broad, cross protective immunity against emergent subtypes. Better strategies are needed to prevent future pandemics. Cross-protection can be achieved by activating CD8+ and CD4+ T cells against highly-conserved regions of the influenza genome. We combine available experimental data with informatics-based immunological predictions to help design vaccines potentially able to induce cross-protective T-cells against multiple influenza subtypes. Results: To exemplify our approach we designed two epitope ensemble vaccines comprising highly-conserved and experimentally-verified immunogenic influenza A epitopes as putative non-seasonal influenza vaccines; one specifically targets the US population and the other is a universal vaccine. The USA-specific vaccine comprised 6 CD8+ T cell epitopes (GILGFVFTL, FMYSDFHFI, GMDPRMCSL, SVKEKDMTK, FYIQMCTEL, DTVNRTHQY) and 3 CD4+ epitopes (KGILGFVFTLTVPSE, EYIMKGVYINTALLN, ILGFVFTLTVPSERG). The universal vaccine comprised 8 CD8+ epitopes: (FMYSDFHFI, GILGFVFTL, ILRGSVAHK, FYIQMCTEL, ILKGKFQTA, YYLEKANKI, VSDGGPNLY, YSHGTGTGY) and the same 3 CD4+ epitopes. Our USA-specific vaccine has a population protection coverage (portion of the population potentially responsive to one or more component epitopes of the vaccine, PPC) of over 96% and 95% coverage of observed influenza subtypes. The universal vaccine has a PPC value of over 97% and 88% coverage of observed subtypes.

Converging evidence that common timing processes underlie temporal-order and simultaneity judgments: a model-based analysis

Perception of simultaneity and temporal order is studied with simultaneity judgment (SJ) and temporal-order judgment (TOJ) tasks. In the former, observers report whether presentation of two stimuli was subjectively simultaneous; in the latter, they report which stimulus was subjectively presented first. SJ and TOJ tasks typically give discrepant results, which has prompted the view that performance is mediated by different processes in each task. We looked at these discrepancies from a model that yields psychometric functions whose parameters characterize the timing, decisional, and response processes involved in SJ and TOJ tasks. We analyzed 12 data sets from published studies in which both tasks had been used in within-subjects designs, all of which had reported differences in performance across tasks. Fitting the model jointly to data from both tasks, we tested the hypothesis that common timing processes sustain simultaneity and temporal order judgments, with differences in performance arising from task-dependent decisional and response processes. The results supported this hypothesis, also showing that model psychometric functions account for aspects of SJ and TOJ data that classical analyses overlook. Implications for research on perception of simultaneity and temporal order are discussed.

Fitting model-based psychometric functions to simultaneity and temporal-order judgment data: MATLAB and R routines

Research on temporal-order perception uses temporal-order judgment (TOJ) tasks or synchrony judgment (SJ) tasks in their binary SJ2 or ternary SJ3 variants. In all cases, two stimuli are presented with some temporal delay, and observers judge the order of presentation. Arbitrary psychometric functions are typically fitted to obtain performance measures such as sensitivity or the point of subjective simultaneity, but the parameters of these functions are uninterpretable. We describe routines in MATLAB and R that fit model-based functions whose parameters are interpretable in terms of the processes underlying temporal-order and simultaneity judgments and responses. These functions arise from an independent-channels model assuming arrival latencies with exponential distributions and a trichotomous decision space. Different routines fit data separately for SJ2, SJ3, and TOJ tasks, jointly for any two tasks, or also jointly for the three tasks (for common cases in which two or even the three tasks were used with the same stimuli and participants). Additional routines provide bootstrap p-values and confidence intervals for estimated parameters. A further routine is included that obtains performance measures from the fitted functions. An R package for Windows and source code of the MATLAB and R routines are available as Supplementary Files.

Sustainability Enhancement of a Turbine Vane Manufacturing Cell through Digital Simulation based Design

Modern manufacturing systems should satisfy emerging needs related to sustainable development. The design of sustainable manufacturing systems can be valuably supported by simulation, traditionally employed mainly for time and cost reduction. In this paper, a multi-purpose digital simulation approach is proposed to deal with sustainable manufacturing systems design through Discrete Event Simulation (DES) and 3D digital human modelling. DES models integrated with data on power consumption of the manufacturing equipment are utilized to simulate different scenarios with the aim to improve productivity as well as energy efficiency, avoiding resource and energy waste. 3D simulation based on digital human modelling is employed to assess human factors issues related to ergonomics and safety of manufacturing systems. The approach is implemented for the sustainability enhancement of a real manufacturing cell of the aerospace industry, automated by robotic deburring. Alternative scenarios are proposed and simulated, obtaining a significant improvement in terms of energy efficiency (−87%) for the new deburring cell, and a reduction of energy consumption around −69% for the coordinate measuring machine, with high potential annual energy cost savings and increased energy efficiency. Moreover, the simulation-based ergonomic assessment of human operator postures allows 25% improvement of the workcell ergonomic index.

Towards a performance based design of shear walls based on damage criteria = Vers un dimensionnement performanciel des murs de refend basé sur des critères d'endommagement

Le dimensionnement basé sur la performance (DBP), dans une approche déterministe, caractérise les objectifs de performance par rapport aux niveaux de performance souhaités. Les objectifs de performance sont alors associés à l'état d'endommagement et au niveau de risque sismique établis. Malgré cette approche rationnelle, son application est encore difficile. De ce fait, des outils fiables pour la capture de l'évolution, de la distribution et de la quantification de l'endommagement sont nécessaires. De plus, tous les phénomènes liés à la non-linéarité (matériaux et déformations) doivent également être pris en considération. Ainsi, cette recherche montre comment la mécanique de l'endommagement pourrait contribuer à résoudre cette problématique avec une adaptation de la théorie du champ de compression modifiée et d'autres théories complémentaires. La formulation proposée adaptée pour des charges monotones, cycliques et de type pushover permet de considérer les effets non linéaires liés au cisaillement couplé avec les mécanismes de flexion et de charge axiale. Cette formulation est spécialement appliquée à l'analyse non linéaire des éléments structuraux en béton soumis aux effets de cisaillement non égligeables. Cette nouvelle approche mise en œuvre dans EfiCoS (programme d'éléments finis basé sur la mécanique de l'endommagement), y compris les critères de modélisation, sont également présentés ici. Des calibrations de cette nouvelle approche en comparant les prédictions avec des données expérimentales ont été réalisées pour les murs de refend en béton armé ainsi que pour des poutres et des piliers de pont où les effets de cisaillement doivent être pris en considération. Cette nouvelle version améliorée du logiciel EFiCoS a démontrée être capable d'évaluer avec précision les paramètres associés à la performance globale tels que les déplacements, la résistance du système, les effets liés à la réponse cyclique et la quantification, l'évolution et la distribution de l'endommagement. Des résultats remarquables ont également été obtenus en référence à la détection appropriée des états limites d'ingénierie tels que la fissuration, les déformations unitaires, l'éclatement de l'enrobage, l'écrasement du noyau, la plastification locale des barres d'armature et la dégradation du système, entre autres. Comme un outil pratique d'application du DBP, des relations entre les indices d'endommagement prédits et les niveaux de performance ont été obtenus et exprimés sous forme de graphiques et de tableaux. Ces graphiques ont été développés en fonction du déplacement relatif et de la ductilité de déplacement. Un tableau particulier a été développé pour relier les états limites d'ingénierie, l'endommagement, le déplacement relatif et les niveaux de performance traditionnels. Les résultats ont démontré une excellente correspondance avec les données expérimentales, faisant de la formulation proposée et de la nouvelle version d'EfiCoS des outils puissants pour l'application de la méthodologie du DBP, dans une approche déterministe.

User-centered, research-based design of futuristic intensive care units

Meta-analysis and cross-validation of a hyperglycemic status predictor model based on salivary glucose

Poster presented at the First International Congress of CiiEM - From Basic Sciences To Clinical Research. Egas Moniz, Caparica, Portugal, 27-28 November 2015.

Towards the Knowledge-based Design of Universal Influenza Epitope Ensemble Vaccines

Motivation: Influenza A viral heterogeneity remains a significant threat due to unpredictable antigenic drift in seasonal influenza and antigenic shifts caused by the emergence of novel subtypes. Annual review of multivalent influenza vaccines targets strains of influenza A and B likely to be predominant in future influenza seasons. This does not induce broad, cross protective immunity against emergent subtypes. Better strategies are needed to prevent future pandemics. Cross-protection can be achieved by activating CD8+ and CD4+ T cells against highly-conserved regions of the influenza genome. We combine available experimental data with informatics-based immunological predictions to help design vaccines potentially able to induce cross-protective T-cells against multiple influenza subtypes. Results: To exemplify our approach we designed two epitope ensemble vaccines comprising highlyconserved and experimentally-verified immunogenic influenza A epitopes as putative non-seasonal influenza vaccines; one specifically targets the US population and the other is a universal vaccine. The USA-specific vaccine comprised 6 CD8+ T cell epitopes (GILGFVFTL, FMYSDFHFI, GMDPRMCSL, SVKEKDMTK, FYIQMCTEL, DTVNRTHQY) and 3 CD4+ epitopes (KGILGFVFTLTVPSE, EYIMKGVYINTALLN, ILGFVFTLTVPSERG). The universal vaccine comprised 8 CD8+ epitopes: (FMYSDFHFI, GILGFVFTL, ILRGSVAHK, FYIQMCTEL, ILKGKFQTA, YYLEKANKI, VSDGGPNLY, YSHGTGTGY) and the same 3 CD4+ epitopes. Our USA-specific vaccine has a population protection coverage (portion of the population potentially responsive to one or more component epitopes of the vaccine, PPC) of over 96% and 95% coverage of observed influenza subtypes. The universal vaccine has a PPC value of over 97% and 88% coverage of observed subtypes.

Collaborative Networked Organizations as System of Systems: A Model-Based Engineering Approach

Part 6: Engineering and Implementation of Collaborative Networks

A SCR Model based on Reactor and Engine Experimental Studies for a Cu-zeolite Catalyst

A NOx reduction efficiency higher than 95% with NH3 slip less than 30 ppm is desirable for heavy-duty diesel (HDD) engines using selective catalytic reduction (SCR) systems to meet the US EPA 2010 NOx standard and the 2014-2018 fuel consumption regulation. The SCR performance needs to be improved through experimental and modeling studies. In this research, a high fidelity global kinetic 1-dimensional 2-site SCR model with mass transfer, heat transfer and global reaction mechanisms was developed for a Cu-zeolite catalyst. The model simulates the SCR performance for the engine exhaust conditions with NH3 maldistribution and aging effects, and the details are presented. SCR experimental data were collected for the model development, calibration and validation from a reactor at Oak Ridge National Laboratory (ORNL) and an engine experimental setup at Michigan Technological University (MTU) with a Cummins 2010 ISB engine. The model was calibrated separately to the reactor and engine data. The experimental setup, test procedures including a surrogate HD-FTP cycle developed for transient studies and the model calibration process are described. Differences in the model parameters were determined between the calibrations developed from the reactor and the engine data. It was determined that the SCR inlet NH3 maldistribution is one of the reasons causing the differences. The model calibrated to the engine data served as a basis for developing a reduced order SCR estimator model. The effect of the SCR inlet NO2/NOx ratio on the SCR performance was studied through simulations using the surrogate HD-FTP cycle. The cumulative outlet NOx and the overall NOx conversion efficiency of the cycle are highest with a NO2/NOx ratio of 0.5. The outlet NH3 is lowest for the NO2/NOx ratio greater than 0.6. A combined engine experimental and simulation study was performed to quantify the NH3 maldistribution at the SCR inlet and its effects on the SCR performance and kinetics. The uniformity index (UI) of the SCR inlet NH3 and NH3/NOx ratio (ANR) was determined to be below 0.8 for the production system. The UI was improved to 0.9 after installation of a swirl mixer into the SCR inlet cone. A multi-channel model was developed to simulate the maldistribution effects. The results showed that reducing the UI of the inlet ANR from 1.0 to 0.7 caused a 5-10% decrease in NOx reduction efficiency and 10-20 ppm increase in the NH3 slip. The simulations of the steady-state engine data with the multi-channel model showed that the NH3 maldistribution is a factor causing the differences in the calibrations developed from the engine and the reactor data. The Reactor experiments were performed at ORNL using a Spaci-IR technique to study the thermal aging effects. The test results showed that the thermal aging (at 800°C for 16 hours) caused a 30% reduction in the NH3 stored on the catalyst under NH3 saturation conditions and different axial concentration profiles under SCR reaction conditions. The kinetics analysis showed that the thermal aging caused a reduction in total NH3 storage capacity (94.6 compared to 138 gmol/m3), different NH3 adsorption/desorption properties and a decrease in activation energy and the pre-exponential factor for NH3 oxidation, standard and fast SCR reactions. Both reduction in the storage capability and the change in kinetics of the major reactions contributed to the change in the axial storage and concentration profiles observed from the experiments.

DYNAMIC MODEL BASED STATE ESTIMATION IN A HEAVY DUTY DIESEL AFTERTREATMENT SYSTEM FOR ONBOARD DIAGNOSTICS AND CONTROLS

Estimating un-measurable states is an important component for onboard diagnostics (OBD) and control strategy development in diesel exhaust aftertreatment systems. This research focuses on the development of an Extended Kalman Filter (EKF) based state estimator for two of the main components in a diesel engine aftertreatment system: the Diesel Oxidation Catalyst (DOC) and the Selective Catalytic Reduction (SCR) catalyst. One of the key areas of interest is the performance of these estimators when the catalyzed particulate filter (CPF) is being actively regenerated. In this study, model reduction techniques were developed and used to develop reduced order models from the 1D models used to simulate the DOC and SCR. As a result of order reduction, the number of states in the estimator is reduced from 12 to 1 per element for the DOC and 12 to 2 per element for the SCR. The reduced order models were simulated on the experimental data and compared to the high fidelity model and the experimental data. The results show that the effect of eliminating the heat transfer and mass transfer coefficients are not significant on the performance of the reduced order models. This is shown by an insignificant change in the kinetic parameters between the reduced order and 1D model for simulating the experimental data. An EKF based estimator to estimate the internal states of the DOC and SCR was developed. The DOC and SCR estimators were simulated on the experimental data to show that the estimator provides improved estimation of states compared to a reduced order model. The results showed that using the temperature measurement at the DOC outlet improved the estimates of the CO , NO , NO2 and HC concentrations from the DOC. The SCR estimator was used to evaluate the effect of NH3 and NOX sensors on state estimation quality. Three sensor combinations of NOX sensor only, NH3 sensor only and both NOX and NH3 sensors were evaluated. The NOX only configuration had the worst performance, the NH3 sensor only configuration was in the middle and both the NOX and NH3 sensor combination provided the best performance.

Reconciling Function- and Affordance-Based Design

Traditional engineering design methods are based on Simon's (1969) use of the concept function, and as such collectively suffer from both theoretical and practical shortcomings. Researchers in the field of affordance-based design have borrowed from ecological psychology in an attempt to address the blind spots of function-based design, developing alternative ontologies and design processes. This dissertation presents function and affordance theory as both compatible and complimentary. We first present a hybrid approach to design for technology change, followed by a reconciliation and integration of function and affordance ontologies for use in design. We explore the integration of a standard function-based design method with an affordance-based design method, and demonstrate how affordance theory can guide the early application of function-based design. Finally, we discuss the practical and philosophical ramifications of embracing affordance theory's roots in ecology and ecological psychology, and explore the insights and opportunities made possible by an ecological approach to engineering design. The primary contribution of this research is the development of an integrated ontology for describing and designing technological systems using both function- and affordance-based methods.