Effect of blood flow patterns on localized platelet adhesion under physiologic flow conditions using two-dimensional and three-dimensional stent models: An experimental and computational approach

This dissertation presents dynamic flow experiments with fluorescently labeled platelets to allow for spatial observation of wall attachment in inter-strut spacings, to investigate their relationship to flow patterns. Human blood with fluorescently labeled platelets was circulated through an in vitro system that produced physiologic pulsatile flow in (1) a parallel plate blow chamber that contained two-dimensional (2D) stents that feature completely recirculating flow, partially recirculating flow, and completely reattached flow, and (2) a three-dimensional (3D) cylindrical tube that contained stents of various geometric designs. ^ Flow detachment and reattachment points exhibited very low platelet deposition. Platelet deposition was very low in the recirculation regions in the 3D stents unlike the 2D stents. Deposition distal to a strut was always high in 2D and 3D stents. Spirally recirculating regions were found in 3D unlike in 2D stents, where the deposition was higher than at well-separated regions of recirculation. ^

Freeway travel time estimation and prediction using dynamic neural networks

Providing transportation system operators and travelers with accurate travel time information allows them to make more informed decisions, yielding benefits for individual travelers and for the entire transportation system. Most existing advanced traveler information systems (ATIS) and advanced traffic management systems (ATMS) use instantaneous travel time values estimated based on the current measurements, assuming that traffic conditions remain constant in the near future. For more effective applications, it has been proposed that ATIS and ATMS should use travel times predicted for short-term future conditions rather than instantaneous travel times measured or estimated for current conditions. ^ This dissertation research investigates short-term freeway travel time prediction using Dynamic Neural Networks (DNN) based on traffic detector data collected by radar traffic detectors installed along a freeway corridor. DNN comprises a class of neural networks that are particularly suitable for predicting variables like travel time, but has not been adequately investigated for this purpose. Before this investigation, it was necessary to identifying methods for data imputation to account for missing data usually encountered when collecting data using traffic detectors. It was also necessary to identify a method to estimate the travel time on the freeway corridor based on data collected using point traffic detectors. A new travel time estimation method referred to as the Piecewise Constant Acceleration Based (PCAB) method was developed and compared with other methods reported in the literatures. The results show that one of the simple travel time estimation methods (the average speed method) can work as well as the PCAB method, and both of them out-perform other methods. This study also compared the travel time prediction performance of three different DNN topologies with different memory setups. The results show that one DNN topology (the time-delay neural networks) out-performs the other two DNN topologies for the investigated prediction problem. This topology also performs slightly better than the simple multilayer perceptron (MLP) neural network topology that has been used in a number of previous studies for travel time prediction.^

An improved framework for dynamic origin-destination (O-D) matrix estimation

This dissertation aims to improve the performance of existing assignment-based dynamic origin-destination (O-D) matrix estimation models to successfully apply Intelligent Transportation Systems (ITS) strategies for the purposes of traffic congestion relief and dynamic traffic assignment (DTA) in transportation network modeling. The methodology framework has two advantages over the existing assignment-based dynamic O-D matrix estimation models. First, it combines an initial O-D estimation model into the estimation process to provide a high confidence level of initial input for the dynamic O-D estimation model, which has the potential to improve the final estimation results and reduce the associated computation time. Second, the proposed methodology framework can automatically convert traffic volume deviation to traffic density deviation in the objective function under congested traffic conditions. Traffic density is a better indicator for traffic demand than traffic volume under congested traffic condition, thus the conversion can contribute to improving the estimation performance. The proposed method indicates a better performance than a typical assignment-based estimation model (Zhou et al., 2003) in several case studies. In the case study for I-95 in Miami-Dade County, Florida, the proposed method produces a good result in seven iterations, with a root mean square percentage error (RMSPE) of 0.010 for traffic volume and a RMSPE of 0.283 for speed. In contrast, Zhou's model requires 50 iterations to obtain a RMSPE of 0.023 for volume and a RMSPE of 0.285 for speed. In the case study for Jacksonville, Florida, the proposed method reaches a convergent solution in 16 iterations with a RMSPE of 0.045 for volume and a RMSPE of 0.110 for speed, while Zhou's model needs 10 iterations to obtain the best solution, with a RMSPE of 0.168 for volume and a RMSPE of 0.179 for speed. The successful application of the proposed methodology framework to real road networks demonstrates its ability to provide results both with satisfactory accuracy and within a reasonable time, thus establishing its potential usefulness to support dynamic traffic assignment modeling, ITS systems, and other strategies.

A tidal creek water budget: Estimation of groundwater discharge and overland flow using hydrologic modeling in the Southern Everglades

Taylor Slough is one of the natural freshwater contributors to Florida Bay through a network of microtidal creeks crossing the Everglades Mangrove Ecotone Region (EMER). The EMER ecological function is critical since it mediates freshwater and nutrient inputs and controls the water quality in Eastern Florida Bay. Furthermore, this region is vulnerable to changing hydrodynamics and nutrient loadings as a result of upstream freshwater management practices proposed by the Comprehensive Everglades Restoration Program (CERP), currently the largest wetland restoration project in the USA. Despite the hydrological importance of Taylor Slough in the water budget of Florida Bay, there are no fine scale (∼1 km2) hydrodynamic models of this system that can be utilized as a tool to evaluate potential changes in water flow, salinity, and water quality. Taylor River is one of the major creeks draining Taylor Slough freshwater into Florida Bay. We performed a water budget analysis for the Taylor River area, based on long-term hydrologic data (1999–2007) and supplemented by hydrodynamic modeling using a MIKE FLOOD (DHI,http://dhigroup.com/) model to evaluate groundwater and overland water discharges. The seasonal hydrologic characteristics are very distinctive (average Taylor River wet vs. dry season outflow was 6 to 1 during 1999–2006) with a pronounced interannual variability of flow. The water budget shows a net dominance of through flow in the tidal mixing zone, while local precipitation and evapotranspiration play only a secondary role, at least in the wet season. During the dry season, the tidal flood reaches the upstream boundary of the study area during approximately 80 days per year on average. The groundwater field measurements indicate a mostly upwards-oriented leakage, which possibly equals the evapotranspiration term. The model results suggest a high importance of groundwater contribution to the water salinity in the EMER. The model performance is satisfactory during the dry season where surface flow in the area is confined to the Taylor River channel. The model also provided guidance on the importance of capturing the overland flow component, which enters the area as sheet flow during the rainy season. Overall, the modeling approach is suitable to reach better understanding of the water budget in the mangrove region. However, more detailed field data is needed to ascertain model predictions by further calibrating overland flow parameters.

Freeway Travel Time Estimation and Prediction Using Dynamic Neural Networks

Providing transportation system operators and travelers with accurate travel time information allows them to make more informed decisions, yielding benefits for individual travelers and for the entire transportation system. Most existing advanced traveler information systems (ATIS) and advanced traffic management systems (ATMS) use instantaneous travel time values estimated based on the current measurements, assuming that traffic conditions remain constant in the near future. For more effective applications, it has been proposed that ATIS and ATMS should use travel times predicted for short-term future conditions rather than instantaneous travel times measured or estimated for current conditions. This dissertation research investigates short-term freeway travel time prediction using Dynamic Neural Networks (DNN) based on traffic detector data collected by radar traffic detectors installed along a freeway corridor. DNN comprises a class of neural networks that are particularly suitable for predicting variables like travel time, but has not been adequately investigated for this purpose. Before this investigation, it was necessary to identifying methods for data imputation to account for missing data usually encountered when collecting data using traffic detectors. It was also necessary to identify a method to estimate the travel time on the freeway corridor based on data collected using point traffic detectors. A new travel time estimation method referred to as the Piecewise Constant Acceleration Based (PCAB) method was developed and compared with other methods reported in the literatures. The results show that one of the simple travel time estimation methods (the average speed method) can work as well as the PCAB method, and both of them out-perform other methods. This study also compared the travel time prediction performance of three different DNN topologies with different memory setups. The results show that one DNN topology (the time-delay neural networks) out-performs the other two DNN topologies for the investigated prediction problem. This topology also performs slightly better than the simple multilayer perceptron (MLP) neural network topology that has been used in a number of previous studies for travel time prediction.

Improving the predictability of time series by chaotic parameter estimation

Limited literature regarding parameter estimation of dynamic systems has been identified as the central-most reason for not having parametric bounds in chaotic time series. However, literature suggests that a chaotic system displays a sensitive dependence on initial conditions, and our study reveals that the behavior of chaotic system: is also sensitive to changes in parameter values. Therefore, parameter estimation technique could make it possible to establish parametric bounds on a nonlinear dynamic system underlying a given time series, which in turn can improve predictability. By extracting the relationship between parametric bounds and predictability, we implemented chaos-based models for improving prediction in time series. ^ This study describes work done to establish bounds on a set of unknown parameters. Our research results reveal that by establishing parametric bounds, it is possible to improve the predictability of any time series, although the dynamics or the mathematical model of that series is not known apriori. In our attempt to improve the predictability of various time series, we have established the bounds for a set of unknown parameters. These are: (i) the embedding dimension to unfold a set of observation in the phase space, (ii) the time delay to use for a series, (iii) the number of neighborhood points to use for avoiding detection of false neighborhood and, (iv) the local polynomial to build numerical interpolation functions from one region to another. Using these bounds, we are able to get better predictability in chaotic time series than previously reported. In addition, the developments of this dissertation can establish a theoretical framework to investigate predictability in time series from the system-dynamics point of view. ^ In closing, our procedure significantly reduces the computer resource usage, as the search method is refined and efficient. Finally, the uniqueness of our method lies in its ability to extract chaotic dynamics inherent in non-linear time series by observing its values. ^

A mathematical resolution to log transformations and the binning effect in applied processing of data in flow cytometry

This dissertation develops a new mathematical approach that overcomes the effect of a data processing phenomenon known as “histogram binning” inherent to flow cytometry data. A real-time procedure is introduced to prove the effectiveness and fast implementation of such an approach on real-world data. The histogram binning effect is a dilemma posed by two seemingly antagonistic developments: (1) flow cytometry data in its histogram form is extended in its dynamic range to improve its analysis and interpretation, and (2) the inevitable dynamic range extension introduces an unwelcome side effect, the binning effect, which skews the statistics of the data, undermining as a consequence the accuracy of the analysis and the eventual interpretation of the data. ^ Researchers in the field contended with such a dilemma for many years, resorting either to hardware approaches that are rather costly with inherent calibration and noise effects; or have developed software techniques based on filtering the binning effect but without successfully preserving the statistical content of the original data. ^ The mathematical approach introduced in this dissertation is so appealing that a patent application has been filed. The contribution of this dissertation is an incremental scientific innovation based on a mathematical framework that will allow researchers in the field of flow cytometry to improve the interpretation of data knowing that its statistical meaning has been faithfully preserved for its optimized analysis. Furthermore, with the same mathematical foundation, proof of the origin of such an inherent artifact is provided. ^ These results are unique in that new mathematical derivations are established to define and solve the critical problem of the binning effect faced at the experimental assessment level, providing a data platform that preserves its statistical content. ^ In addition, a novel method for accumulating the log-transformed data was developed. This new method uses the properties of the transformation of statistical distributions to accumulate the output histogram in a non-integer and multi-channel fashion. Although the mathematics of this new mapping technique seem intricate, the concise nature of the derivations allow for an implementation procedure that lends itself to a real-time implementation using lookup tables, a task that is also introduced in this dissertation. ^

Surface mean flow and turbulence structure in tropical cyclone winds

Hurricanes are one of the deadliest and costliest natural hazards affecting the Gulf coast and Atlantic coast areas of the United States. An effective way to minimize hurricane damage is to strengthen structures and buildings. The investigation of surface level hurricane wind behavior and the resultant wind loads on structures is aimed at providing structural engineers with information on hurricane wind characteristics required for the design of safe structures. Information on mean wind profiles, gust factors, turbulence intensity, integral scale, and turbulence spectra and co-spectra is essential for developing realistic models of wind pressure and wind loads on structures. The research performed for this study was motivated by the fact that considerably fewer data and validated models are available for tropical than for extratropical storms. ^ Using the surface wind measurements collected by the Florida Coastal Monitoring Program (FCMP) during hurricane passages over coastal areas, this study presents comparisons of surface roughness length estimates obtained by using several estimation methods, and estimates of the mean wind and turbulence structure of hurricane winds over coastal areas under neutral stratification conditions. In addition, a program has been developed and tested to systematically analyze Wall of Wind (WoW) data, that will make it possible to perform analyses of baseline characteristics of flow obtained in the WoW. This program can be used in future research to compare WoW data with FCMP data, as gust and turbulence generator systems and other flow management devices will be used to create WoW flows that match as closely as possible real hurricane wind conditions. ^ Hurricanes are defined as tropical cyclones for which the maximum 1-minute sustained surface wind speeds exceed 74 mph. FCMP data include data for tropical cyclones with lower sustained speeds. However, for the winds analyzed in this study the speeds were sufficiently high to assure that neutral stratification prevailed. This assures that the characteristics of those winds are similar to those prevailing in hurricanes. For this reason in this study the terms tropical cyclones and hurricanes are used interchangeably. ^

Integrated surface-ground water modeling in wetlands with improved methods to simulate vegetative resistance to flow

In topographically flat wetlands, where shallow water table and conductive soil may develop as a result of wet and dry seasons, the connection between surface water and groundwater is not only present, but perhaps the key factor dominating the magnitude and direction of water flux. Due to their complex characteristics, modeling waterflow through wetlands using more realistic process formulations (integrated surface-ground water and vegetative resistance) is an actual necessity. This dissertation focused on developing an integrated surface – subsurface hydrologic simulation numerical model by programming and testing the coupling of the USGS MODFLOW-2005 Groundwater Flow Process (GWF) package (USGS, 2005) with the 2D surface water routing model: FLO-2D (O’Brien et al., 1993). The coupling included the necessary procedures to numerically integrate and verify both models as a single computational software system that will heretofore be referred to as WHIMFLO-2D (Wetlands Hydrology Integrated Model). An improved physical formulation of flow resistance through vegetation in shallow waters based on the concept of drag force was also implemented for the simulations of floodplains, while the use of the classical methods (e.g., Manning, Chezy, Darcy-Weisbach) to calculate flow resistance has been maintained for the canals and deeper waters. A preliminary demonstration exercise WHIMFLO-2D in an existing field site was developed for the Loxahatchee Impoundment Landscape Assessment (LILA), an 80 acre area, located at the Arthur R. Marshall Loxahatchee National Wild Life Refuge in Boynton Beach, Florida. After applying a number of simplifying assumptions, results have illustrated the ability of the model to simulate the hydrology of a wetland. In this illustrative case, a comparison between measured and simulated stages level showed an average error of 0.31% with a maximum error of 2.8%. Comparison of measured and simulated groundwater head levels showed an average error of 0.18% with a maximum of 2.9%. The coupling of FLO-2D model with MODFLOW-2005 model and the incorporation of the dynamic effect of flow resistance due to vegetation performed in the new modeling tool WHIMFLO-2D is an important contribution to the field of numerical modeling of hydrologic flow in wetlands.

Improving Analytical Travel Time Estimation for Transportation Planning Models

This dissertation aimed to improve travel time estimation for the purpose of transportation planning by developing a travel time estimation method that incorporates the effects of signal timing plans, which were difficult to consider in planning models. For this purpose, an analytical model has been developed. The model parameters were calibrated based on data from CORSIM microscopic simulation, with signal timing plans optimized using the TRANSYT-7F software. Independent variables in the model are link length, free-flow speed, and traffic volumes from the competing turning movements. The developed model has three advantages compared to traditional link-based or node-based models. First, the model considers the influence of signal timing plans for a variety of traffic volume combinations without requiring signal timing information as input. Second, the model describes the non-uniform spatial distribution of delay along a link, this being able to estimate the impacts of queues at different upstream locations of an intersection and attribute delays to a subject link and upstream link. Third, the model shows promise of improving the accuracy of travel time prediction. The mean absolute percentage error (MAPE) of the model is 13% for a set of field data from Minnesota Department of Transportation (MDOT); this is close to the MAPE of uniform delay in the HCM 2000 method (11%). The HCM is the industrial accepted analytical model in the existing literature, but it requires signal timing information as input for calculating delays. The developed model also outperforms the HCM 2000 method for a set of Miami-Dade County data that represent congested traffic conditions, with a MAPE of 29%, compared to 31% of the HCM 2000 method. The advantages of the proposed model make it feasible for application to a large network without the burden of signal timing input, while improving the accuracy of travel time estimation. An assignment model with the developed travel time estimation method has been implemented in a South Florida planning model, which improved assignment results.

Development of a dynamic headspace concentration technique for the non-contact sampling of human odor samples and the creation of canine training aids

Human scent and human remains detection canines are used to locate living or deceased humans under many circumstances. Human scent canines locate individual humans on the basis of their unique scent profile, while human remains detection canines locate the general scent of decomposing human remains. Scent evidence is often collected by law enforcement agencies using a Scent Transfer Unit, a dynamic headspace concentration device. The goals of this research were to evaluate the STU-100 for the collection of human scent samples, and to apply this method to the collection of living and deceased human samples, and to the creation of canine training aids. The airflow rate and collection material used with the STU-100 were evaluated using a novel scent delivery method. Controlled Odor Mimic Permeation Systems were created containing representative standard compounds delivered at known rates, improving the reproducibility of optimization experiments. Flow rates and collection materials were compared. Higher air flow rates usually yielded significantly less total volatile compounds due to compound breakthrough through the collection material. Collection from polymer and cellulose-based materials demonstrated that the molecular backbone of the material is a factor in the trapping and releasing of compounds. The weave of the material also affects compound collection, as those materials with a tighter weave demonstrated enhanced collection efficiencies. Using the optimized method, volatiles were efficiently collected from living and deceased humans. Replicates of the living human samples showed good reproducibility; however, the odor profiles from individuals were not always distinguishable from one another. Analysis of the human remains samples revealed similarity in the type and ratio of compounds. Two types of prototype training aids were developed utilizing combinations of pure compounds as well as volatiles from actual human samples concentrated onto sorbents, which were subsequently used in field tests. The pseudo scent aids had moderate success in field tests, and the Odor pad aids had significant success. This research demonstrates that the STU-100 is a valuable tool for dog handlers and as a field instrument; however, modifications are warranted in order to improve its performance as a method for instrumental detection.

Color-based surface reflectance separation for scene illumination estimation and rendering

Given the importance of color processing in computer vision and computer graphics, estimating and rendering illumination spectral reflectance of image scenes is important to advance the capability of a large class of applications such as scene reconstruction, rendering, surface segmentation, object recognition, and reflectance estimation. Consequently, this dissertation proposes effective methods for reflection components separation and rendering in single scene images. Based on the dichromatic reflectance model, a novel decomposition technique, named the Mean-Shift Decomposition (MSD) method, is introduced to separate the specular from diffuse reflectance components. This technique provides a direct access to surface shape information through diffuse shading pixel isolation. More importantly, this process does not require any local color segmentation process, which differs from the traditional methods that operate by aggregating color information along each image plane. ^ Exploiting the merits of the MSD method, a scene illumination rendering technique is designed to estimate the relative contributing specular reflectance attributes of a scene image. The image feature subset targeted provides a direct access to the surface illumination information, while a newly introduced efficient rendering method reshapes the dynamic range distribution of the specular reflectance components over each image color channel. This image enhancement technique renders the scene illumination reflection effectively without altering the scene’s surface diffuse attributes contributing to realistic rendering effects. ^ As an ancillary contribution, an effective color constancy algorithm based on the dichromatic reflectance model was also developed. This algorithm selects image highlights in order to extract the prominent surface reflectance that reproduces the exact illumination chromaticity. This evaluation is presented using a novel voting scheme technique based on histogram analysis. ^ In each of the three main contributions, empirical evaluations were performed on synthetic and real-world image scenes taken from three different color image datasets. The experimental results show over 90% accuracy in illumination estimation contributing to near real world illumination rendering effects. ^

Reducing uncertainties in estimation of wind effects on tall buildings using aerodynamic wind tunnel tests

Tall buildings are wind-sensitive structures and could experience high wind-induced effects. Aerodynamic boundary layer wind tunnel testing has been the most commonly used method for estimating wind effects on tall buildings. Design wind effects on tall buildings are estimated through analytical processing of the data obtained from aerodynamic wind tunnel tests. Even though it is widely agreed that the data obtained from wind tunnel testing is fairly reliable the post-test analytical procedures are still argued to have remarkable uncertainties. This research work attempted to assess the uncertainties occurring at different stages of the post-test analytical procedures in detail and suggest improved techniques for reducing the uncertainties. Results of the study showed that traditionally used simplifying approximations, particularly in the frequency domain approach, could cause significant uncertainties in estimating aerodynamic wind-induced responses. Based on identified shortcomings, a more accurate dual aerodynamic data analysis framework which works in the frequency and time domains was developed. The comprehensive analysis framework allows estimating modal, resultant and peak values of various wind-induced responses of a tall building more accurately. Estimating design wind effects on tall buildings also requires synthesizing the wind tunnel data with local climatological data of the study site. A novel copula based approach was developed for accurately synthesizing aerodynamic and climatological data up on investigating the causes of significant uncertainties in currently used synthesizing techniques. Improvement of the new approach over the existing techniques was also illustrated with a case study on a 50 story building. At last, a practical dynamic optimization approach was suggested for tuning structural properties of tall buildings towards attaining optimum performance against wind loads with less number of design iterations.

Drosophila Flight Stabilization Depends on Apparent Distances in Optic Flow Field

To perform daily flight tasks, insects rely heavily on their visual perception of a dynamic environment. They must process visual signals quickly and accurately and update their behavior. Flies are vulnerable to environmental disturbances, such as gusts of wind blowing them off course, but they may use the altered visual field to compensate and regain their original course. In studies using Drosophila melanogaster, it has been shown that their corrective responses can be analyzed by measuring changes in their wing beats. By enclosing a tethered fly in a cuboidal visual arena displaying a computerized optic flow field, it is possible to calculate the change in wing beat amplitudes from an infrared shadow of its wings using photodiodes and a custom wing beat analyzer. In this experiment, manipulations ofthe optic flow field are used to create a field where points have varying relative forward speed, to study how the insect performs corrective maneuvers. The results show that Drosophila have a stronger corrective response to the quickly moving, apparently near points compared to the slower moving, apparently distant points. This implies the flies are distinguishing points based on their relative speeds, inferring distance, and adjusting their corrective actions with this information.

Advanced methodologies in dynamic traffic assignment modeling of managed lanes

Managed lane strategies are innovative road operation schemes for addressing congestion problems. These strategies operate a lane (lanes) adjacent to a freeway that provides congestion-free trips to eligible users, such as transit or toll-payers. To ensure the successful implementation of managed lanes, the demand on these lanes need to be accurately estimated. Among different approaches for predicting this demand, the four-step demand forecasting process is most common. Managed lane demand is usually estimated at the assignment step. Therefore, the key to reliably estimating the demand is the utilization of effective assignment modeling processes. ^ Managed lanes are particularly effective when the road is functioning at near-capacity. Therefore, capturing variations in demand and network attributes and performance is crucial for their modeling, monitoring and operation. As a result, traditional modeling approaches, such as those used in static traffic assignment of demand forecasting models, fail to correctly predict the managed lane demand and the associated system performance. The present study demonstrates the power of the more advanced modeling approach of dynamic traffic assignment (DTA), as well as the shortcomings of conventional approaches, when used to model managed lanes in congested environments. In addition, the study develops processes to support an effective utilization of DTA to model managed lane operations. ^ Static and dynamic traffic assignments consist of demand, network, and route choice model components that need to be calibrated. These components interact with each other, and an iterative method for calibrating them is needed. In this study, an effective standalone framework that combines static demand estimation and dynamic traffic assignment has been developed to replicate real-world traffic conditions. ^ With advances in traffic surveillance technologies collecting, archiving, and analyzing traffic data is becoming more accessible and affordable. The present study shows how data from multiple sources can be integrated, validated, and best used in different stages of modeling and calibration of managed lanes. Extensive and careful processing of demand, traffic, and toll data, as well as proper definition of performance measures, result in a calibrated and stable model, which closely replicates real-world congestion patterns, and can reasonably respond to perturbations in network and demand properties.^