A framework for mixed-type multi-outcome prediction with applications in healthcare

Health analysis often involves prediction of multiple outcomes of mixed-type. Existing work is restrictive to either a limited number or specific outcome types. We propose a framework for mixed-type multi-outcome prediction. Our proposed framework proposes a cumulative loss function composed of a specific loss function for each outcome type - as an example, least square (continuous outcome), hinge (binary outcome), poisson (count outcome) and exponential (non-negative outcome). Tomodel these outcomes jointly, we impose a commonality across the prediction parameters through a common matrix-Normal prior. The framework is formulated as iterative optimization problems and solved using an efficient Block coordinate descent method (BCD). We empirically demonstrate both scalability and convergence. We apply the proposed model to a synthetic dataset and then on two real-world cohorts: a Cancer cohort and an Acute Myocardial Infarction cohort collected over a two year period. We predict multiple emergency related outcomes - as example, future emergency presentations (binary), emergency admissions (count), emergency length-of-stay-days (non-negative) and emergency time-to-next-admission-day (non-negative). Weshow that the predictive performance of the proposed model is better than several state-of-the-art baselines.

TEST-ANALYSIS MODEL CORRELATION AND CALIBRATION OF A MULTI-COMPONENT PLASTIC PART

The goal of this project is to learn the necessary steps to create a finite element model, which can accurately predict the dynamic response of a Kohler Engines Heavy Duty Air Cleaner (HDAC). This air cleaner is composed of three glass reinforced plastic components and two air filters. Several uncertainties arose in the finite element (FE) model due to the HDAC’s component material properties and assembly conditions. To help understand and mitigate these uncertainties, analytical and experimental modal models were created concurrently to perform a model correlation and calibration. Over the course of the project simple and practical methods were found for future FE model creation. Similarly, an experimental method for the optimal acquisition of experimental modal data was arrived upon. After the model correlation and calibration was performed a validation experiment was used to confirm the FE models predictive capabilities.

A NATURALISTIC COMPUTATIONAL MODEL OF HUMAN BEHAVIOR IN NAVIGATION AND SEARCH TASKS

Planning, navigation, and search are fundamental human cognitive abilities central to spatial problem solving in search and rescue, law enforcement, and military operations. Despite a wealth of literature concerning naturalistic spatial problem solving in animals, literature on naturalistic spatial problem solving in humans is comparatively lacking and generally conducted by separate camps among which there is little crosstalk. Addressing this deficiency will allow us to predict spatial decision making in operational environments, and understand the factors leading to those decisions. The present dissertation is comprised of two related efforts, (1) a set of empirical research studies intended to identify characteristics of planning, execution, and memory in naturalistic spatial problem solving tasks, and (2) a computational modeling effort to develop a model of naturalistic spatial problem solving. The results of the behavioral studies indicate that problem space hierarchical representations are linear in shape, and that human solutions are produced according to multiple optimization criteria. The Mixed Criteria Model presented in this dissertation accounts for global and local human performance in a traditional and naturalistic Traveling Salesman Problem. The results of the empirical and modeling efforts hold implications for basic and applied science in domains such as problem solving, operations research, human-computer interaction, and artificial intelligence.

DIFFUSE-INTERFACE FIELD APPROACH TO MODELING SELF-ASSEMBLY OF HETEROGENEOUS COLLOIDAL SYSTEMS AND RELATED DIPOLE-DIPOLE INTERACTION PHENOMENA

Colloid self-assembly under external control is a new route to fabrication of advanced materials with novel microstructures and appealing functionalities. The kinetic processes of colloidal self-assembly have attracted great interests also because they are similar to many atomic level kinetic processes of materials. In the past decades, rapid technological progresses have been achieved on producing shape-anisotropic, patchy, core-shell structured particles and particles with electric/magnetic charges/dipoles, which greatly enriched the self-assembled structures. Multi-phase carrier liquids offer new route to controlling colloidal self-assembly. Therefore, heterogeneity is the essential characteristics of colloid system, while so far there still lacks a model that is able to efficiently incorporate these possible heterogeneities. This thesis is mainly devoted to development of a model and computational study on the complex colloid system through a diffuse-interface field approach (DIFA), recently developed by Wang et al. This meso-scale model is able to describe arbitrary particle shape and arbitrary charge/dipole distribution on the surface or body of particles. Within the framework of DIFA, a Gibbs-Duhem-type formula is introduced to treat Laplace pressure in multi-liquid-phase colloidal system and it obeys Young-Laplace equation. The model is thus capable to quantitatively study important capillarity related phenomena. Extensive computer simulations are performed to study the fundamental behavior of heterogeneous colloidal system. The role of Laplace pressure is revealed in determining the mechanical equilibrium of shape-anisotropic particles at fluid interfaces. In particular, it is found that the Laplace pressure plays a critical role in maintaining the stability of capillary bridges between close particles, which sheds light on a novel route to in situ firming compact but fragile colloidal microstructures via capillary bridges. Simulation results also show that competition between like-charge repulsion, dipole-dipole interaction and Brownian motion dictates the degree of aggregation of heterogeneously charged particles. Assembly and alignment of particles with magnetic dipoles under external field is studied. Finally, extended studies on the role of dipole-dipole interaction are performed for ferromagnetic and ferroelectric domain phenomena. The results reveal that the internal field generated by dipoles competes with external field to determine the dipole-domain evolution in ferroic materials.

STUDIES OF FUNCTIONALIZED NANOPARTICLES FOR SMART SELF-ASSEMBLY AND AS CONTROLLED DRUG DELIVERY

This dissertation is related to the studies of functionalized nanoparticles for self-assembly and as controlled drug delivery system. The whole topic is composed of two parts. In the first part, the research was conducted to design and synthesize a new type of ionic peptide-functionalized copolymer conjugates for self-assembly into nanoparticle fibers and 3D scaffolds with the ability of multi-drug loading and governing the release rate of each drug for tissue engineering. The self-assembly study confirmed that such peptide-functionalized amphiphilic copolymers underwent different self-assembly behavior. The bigger nanoparticles were more easily assembled into nanoparticle fibers and 3D scaffolds with larger pore size, while the smaller nanoparticle underwent faster self-assembly to form more compact 3D scaffolds with smaller porosity but more stable structure. Controlled release studies confirmed the ability of governing simultaneous release of different model drugs with independent release rate from a same scaffold. Cytotoxicity tests showed that all synthesized peptides, copolymers and peptide-copolymer conjugates were biocompatible with SW-620 cell lines and NIH3T3 cell lines. This new type of self-assembled scaffolds combined the advantages of peptide nanofibers and versatile controlled release of polymeric nanoparticles to achieve simultaneous multi-drug loading and controlled release of each drug, uniform distribution and flexibility of hydrogel scaffolds. The investigations in second part were first to design and synthesize organic biocide-loaded nanoparticles for low-leaching wood preservation using a cost-effective one-pot method to synthesize amphiphilic chitosan-g-PMMA nanoparticles loading with ~25-28 wt.% of the fungicide tebuconazole with particle size of ~100 nm diameter by FESEM. FESEM analysis confirmed efficient penetration of nanoparticles throughout the treated wooden stake with dimension of 19 × 19 × 455 mm^3. Leaching studies showed that biocide introduced into sapwood via nanoparticles leached only ~9% compared with the amount leached from tebuconazole solution-treated control, while soil jar tests showed that the nanoparticle-treated wood blocks were effectively protected from biological decay tested against G. trabeum, a brown rot fungus. Copper oxide nanoparticles with and without polymer stabilizers were also investigated to use as inorganic wood preservatives to clarify the factor affecting copper leaching from treated wood. Copper oxide nanoparticles with uniform diameters of ~10 nm and ~50 nm were prepared, and the leachates from southern pine sapwood treated with these nanoparticles were analyzed. It was found by TEM and EDS analysis that significant numbers of nanoparticles leached from the treated wood. The 50 nm nanoparticles leached slightly less than a soluble copper salt control, but 10 nm nanoparticles leached substantially more than the control. The effect of polymer stabilizers on nanoparticle leaching was also investigated. Results showed that polymer stabilizers increased leaching. The trends showed that nanoparticle size was a major factor in copper leaching.

The periplasmic domain of the barrel assembly machinery protein A (BamA) from Escherichia coli assists folding of outer membrane protein A

The assembly of outer membranes of the cell wall of Gram-negative bacteria and of various organelles of eukaryotic cells requires the evolutionarily conserved β-barrel-assembly machinery (BAM) complex. This thesis describes the biochemical and biophysical properties of the periplasmic domain of the β-barrel assembly machinery protein A (PD-BamA) of the E. coli BAM complex, its effect on insertion and folding of the Outer membrane protein A (OmpA) into lipid bilayers and the identification of regions of PD-BamA that may be involved in protein-protein interactions. The secondary structure of PD-BamA in mixed lipid bilayers, analyzed by Circular dichroism (CD) spectroscopy, contained less β-sheet at an increased content of phosphatidylglycerol (PG) in the lipid membrane. This result showed membrane binding, albeit only in the presence of negatively charged lipids. Fluorescence spectroscopy demonstrated that PD-BamA only binds to lipid bilayers containing the negatively charged DOPG, confirming the results of CD spectroscopy. PD-BamA did not bind to zwitterionic but overall neutral lipid bilayers. PD-BamA bound to OmpA at a stoichiometry of 1:1. PD-BamA strongly facilitated insertion and folding of OmpA into lipid membranes. Kinetics of PD-BamA mediated folding of OmpA was well described by two parallel folding processes, a fast folding process and a slow folding process, differing by 2-3 orders of magnitude in their rate constants. The folding yields of OmpA depended on the concentration of lipid membranes and also on the lipid head groups. The presence of PD-BamA resulted in increased folding yields of OmpA in negatively charged DOPG, but PD-BamA did not affect the folding kinetics of OmpA into bilayers of zwitterionic but overall neutral lipids. The efficiency of folding and insertion of OmpA into lipid bilayers strongly depended on the ratio PD-BamA/OmpA and was optimal at equimolar concentrations of PD-BamA and OmpA. To examine complexes of unfolded OmpA with PD-BamA in more detail, site-directed spectroscopy was used to explore contact regions in both, PD-BamA and OmpA. Similarly, contact regions were also investigated for another protein complex formed by PD-BamA and the lipoprotein BamD. The obtained data suggest, that the site of interaction on PD-BamA for OmpA might be oriented towards the exterior environment away from the preceding POTRA domains, but that PD-BamA is oriented with its short α-helix α1 of POTRA domain 5 towards the C-terminal end of BamD.

Semi-implicit finite strain constitutive integration and mixed strain/stress control based on intermediate configurations

A new semi-implicit stress integration algorithm for finite strain plasticity (compatible with hyperelas- ticity) is introduced. Its most distinctive feature is the use of different parameterizations of equilibrium and reference configurations. Rotation terms (nonlinear trigonometric functions) are integrated explicitly and correspond to a change in the reference configuration. In contrast, relative Green–Lagrange strains (which are quadratic in terms of displacements) represent the equilibrium configuration implicitly. In addition, the adequacy of several objective stress rates in the semi-implicit context is studied. We para- metrize both reference and equilibrium configurations, in contrast with the so-called objective stress integration algorithms which use coinciding configurations. A single constitutive framework provides quantities needed by common discretization schemes. This is computationally convenient and robust, as all elements only need to provide pre-established quantities irrespectively of the constitutive model. In this work, mixed strain/stress control is used, as well as our smoothing algorithm for the complemen- tarity condition. Exceptional time-step robustness is achieved in elasto-plastic problems: often fewer than one-tenth of the typical number of time increments can be used with a quantifiable effect in accuracy. The proposed algorithm is general: all hyperelastic models and all classical elasto-plastic models can be employed. Plane-stress, Shell and 3D examples are used to illustrate the new algorithm. Both isotropic and anisotropic behavior is presented in elasto-plastic and hyperelastic examples.