<p> Hydroxypropyl guar (HPG) is an effective ingredient in lubricant eye drops used by patients with dry eye disease. The overall goal of the work described in this thesis is to understand the physical-chemical properties of HPG in the presence ofmodel surfaces and solutes with view to understanding the behavior of HPG in the tear film. </p> <p> HPG behaviors are complex because borate ions bind to HPG, which converts nonionic HPG into anionic polyelectrolyte, RPG-borate. The borate binding constants are very low, meaning the charges on RPG-borate are labile. Another consequence ofweak binding is that the equilibrium electrolyte concentration with HPG-borate is relatively high. Mathematical models were developed to predict the structure of HPG-borate as functions of pH. </p> <p> This thesis probes the question "When does HPG-borate behave as an anionic polyelectrolyte?" This work shows that HPG-borate exhibits deviant behaviors of an anionic polyelectrolyte: does not interact with cationic surfactants below the CMC; does not interact with lysozyme (cationic protein), and does not adsorb onto cationic liposomes. By contrast, anionic polyelectrolytes such as carboxymethyl guar display generic behaviors. On the other hand, HPG-borate forms polyelectrolyte complexes with cationic polyelectrolytes at low ionic strength and other work from our laboratory has shown that HPG-borate flocculates cationic polystyrene latex. </p> <p> This complex range of RPG-borate behaviors was rationalized by proposing that the labile nature ofthe charge groups means that the charge density on RPG-borate is regulated by the local electrostatic environment. Near a cationic surface HPG-borate charge density increases whereas near an anionic surface the charge density is lower. </p> <p> Anionic liposome interactions with HPG-borate were characterized. HPG concentrations close to clinical levels induced depletion flocculation ofthe anionic liposomes. This is the first example we have found depletion interactions were proposed for the tear film. </p> <p> To summarize the main implications for the ophthalmic application of HPG are: 1) under ophthalmic conditions HPG-borate behaves as a nonionic water soluble polymer; 2) RPG-borate will adsorb onto hydrophobic domains but will not interact with lysozyme; 3) depletion interactions are important and have the potential to stabilize the lipid layer and destabilize emulsion droplets and other dispersed species in the tear film. </p> / Thesis / Doctor of Philosophy (PhD)

<p> Type IV secretion systems (T4SS) are essential for the virulence of many gram-negative pathogens. The systems studied here comprise eleven VirB proteins in case of Agrobacterium tumefaciens and twelve in case of Brucella suis. The VirB proteins associate in the cell envelope and form a complex that mediates the translocation of virulence factors into host cells. In this report, VirB8, a core component of T4SS, is characterized with regards to its interaction with itself and with other VirB proteins. </p> <p> VirB8 was found to exist in monomer-dimer equilibrium and the self-association was demonstrated by analytical ultracentrifugation, analytical gel filtration, surface plasmon resonance and bacterial two-hybrid assay. The above experiments demonstrated that residues M102, Y105 and E214 o fVirB8 from B. suis are involved in self-association and mutagenesis of these residues led to the impairment of T4SS function in B. suis. Furthermore, this information was utilized to unravel the contribution of VirB8 self-association towards T4SS assembly and function. To this end dimerization variants of VirB8 from Agrobacterium tumefaciens were created and the effects were assessed with purified proteins in vitro. Following this, the effects of VirB8 dimer site changes were assessed in vivo. Introduction of a cysteine residue at the predicted interface (V97C) supported DNA transfer but not T-pilus formation. Variants that reduced the self-association did not support T4SS functions and T-pilus formation. Moreover, VirB2- VirB5 co-fractionated with high molecular mass components from membranes of A. tumefaciens and VirB8 dimerization was shown to be necessary for VirB2 association with the high molecular mass components. Using purified VirB8 and VirB5 it was shown that VirB5 interacts with VirB8 via its globular domain and this interaction dissociates VirB8 dimers. Taking these results together, a mechanistic contribution of VirB8 dimerization to T4SS assembly was proposed. </p> <p> Next, the interactions of VirB8 with other core components (VirB9 and VirBlO) were analyzed by using various in vitro and in vivo experiments. Purified soluble periplasmic domains of VirB8, VirB9 and VirB10 were used in enzyme-linked immunosorbent assays, circular dichroism, and surface plasmon resonance experiments. The pair-wise interactions and self-association of VirB8, VirB9 and VirB 10 were demonstrated with the in vitro experiments. In addition, a ternary complex formation between VirB8, VirB9, and VirBlO was identified. Using the bacterial two-hybrid system, the dynamics of the interactions between VirB8-VirB9-VirB 10 full-length proteins were analyzed demonstrating that VirB9 stimulates VirB8 self-association, but that it inhibits the VirB10-VirB10 as well as the VirB8-VirB10 interaction. Based on these results, a dynamic model for secretion system assembly is proposed where VirB8 plays a role as an assembly factor that is not closely associated with the functional core complex comprising VirB9 and VirB10. </p> <p> The work reported in this thesis advances the understanding of VirB8 self-association and its contribution to T4SS assembly and function. Furthermore, the establishment of the bacterial two-hybrid system to detect VirB interactions has helped identify inhibitors for the VirB8 dimerization through collaboration with Dr. Athanasios Paschos. Moreover, techniques such as ELISA, analytical ultracentrifugation, circular dichroism and surface plasmon resonance will be utilized routinely to characterize other VirB-VirB interactions in future. </p> / Thesis / Doctor of Philosophy (PhD)

<p> In the field of communications electronic plug-in units operating together form a system. In the event of failure a plug-in unit can easily be replaced by another. Each unit consists of electronic components soldered onto a board in a particular pattern. A component may be either a single electronic part such as a transistor or a combination of single parts such as an integrated circuit. Electronic components with similar properties have been grouped into families. This reduces the number of parameters to be estimated from the observations available.</p> <p> The method of maximum likelihood is used to estimate the failure rates of component families. The number of unit failures and the number of units in use observed during measured periods of time and the component family makeup of the observed units are used to make the estimates.</p> <p> The probability of an electronic component from a given component from a given family being acceptable after the production process will be referred to as the component yield for that family. Similarly, the probability of a given type of unit being acceptable after the production process will be referred to as the yield for that type of unit. By taking the logarithms of the yields, the estimation problem can be reduced to the linear problem of estimating logarithms of component family yields. Using unit yields, the total number of each type of unit produced, and the component family makeup of those units produced, component family yields are estimated. The method of maximum likelihood is applied directly to the data and the method of weighted least squares is applied to the linearized problem.</p> / Thesis / Master of Science (MSc)

Indiana University-Purdue University Indianapolis (IUPUI) / Several pathological disorders are characterized by maladaptive decision-making (Dalley & Robbins, 2017). Decision-making tasks, such as Delay Discounting (DD), are used to assess the behavioral manifestations of maladaptive decision-making in both clinical and preclinical settings (de Wit, Flory, Acheson, Mccloskey, & Manuck, 2007). DD measures cognitive impulsivity and broadly refers to the inability to delay gratification (Hamilton et al., 2015). How decisions are made in tasks that measure DD can be understood by assessing patterns of behavior that are observable in the sequences of choices or the statistics that accompany each choice (e.g. response latency). These measures have led to insights that suggest strategies that are used by the agent to facilitate the decision (Linsenbardt, Smoker, Janetsian-Fritz, & Lapish, 2016). The current set of analyses aims to use individual trial data to identify the neural underpinnings associated with strategy transition during DD. A greater understanding of how strategy change occurs at a neural level will be useful for developing cognitive and behavioral strategies aimed at reducing impulsive choice. The rat dorso-medial prefrontal cortex (dmPFC) has been implicated as an important brain region for recognizing the need to change strategy during DD (Powell & Redish, 2016). Using advanced statistical techniques, such as demixed principal component analysis (dPCA), we can then begin to understand how decision representations evolve over the decision- making process to impact behaviors such as strategy change. This study was the first known attempt at using dPCA applied to individual sessions to accurately model how decision representations evolve across individual trials. Evidence exists that representations follow a breakdown and remapping at the individual trial level (Karlsson, Tervo, & Karpova, 2012; Powell & Redish, 2016). Furthermore, these representational changes across individual trials have previously been proposed to act as a signal to change strategies (Powell & Redish, 2016). This study aimed to test the hypothesis that a ‘breakdown’ followed by a ‘remapping’ of the decision representation would act as a signal to change strategy that is observable in the behavior of the animal. To investigate the relationship between trials surrounding the breakdown and/or subsequent remapping of the decision representation and trials surrounding strategy changes, sequences of trials surrounding the breakdown and/or remapping were compared to sequences of 9 trials surrounding the strategy-change trial. Strategy types consisted of either exploiting the immediate lever (IM-Exploit), delay lever (DEL-Exploit), or exploring between the two lever options (Explore). Contrary to the hypothesis, an overall relationship between breakdown and remapping trial sequences were not associated with change-trial sequences. In partial support of the hypothesis however, at the 4-sec delay when the subjective value of the immediate reward was high, a relationship between breakdown sequence and strategy change sequence was detected for when the animal was exploiting the delay lever (e.g. DEL-Exploit strategy). This result suggests that a breakdown in decision representation may act as a signal to prompt strategy change under certain contexts. One notable finding of this study was that the decision representation was much more robust at the 4-sec delay compared to the 8-sec delay, suggesting that decisions at the 4-sec delay contain more context that differentiate the two choice options (immediate or delay). In other words, the encoding of the two choice options was more dissociable at the 4-sec delay compared to the 8-sec delay, which was quantified by measuring the average distance between the two representations (immediate and delay) on a given trial. Given that Wistar rats are equally likely to choose between the immediate and delay choice alternatives at the 8-sec delay (Linsenbardt et al., 2016), this finding provides further support for current prevalent theories of how animals use a cognitive search process to mentally imagine choice alternatives during deliberation. If context which differentiates choice options at the 8-sec delay is less dissociable, it is likely that the cognitive search process would be equally likely to find either choice option. If the choice options are equally likely to be found, it would be assumed that the choice alternatives would also be equally likely to be chosen, which is what has been observed in Wistar rats at the 8-sec delay.

Staphylococcus aureus employs an array of virulence factors to aid in its pathogenesis. A subset of cytotoxins termed bi-component leucocidins have been characterized as important determinants in the host-pathogen interaction in S. aureus infections. While they have been studied over a century, bi-component leucocidins’ complex mechanisms in pathogenesis have not been fully elucidated. Secreted as monomers, with the exception of LukAB/GH, many combinations of the S- (HlgA, HlgC, LukE, LukS, LukA/H) and F- (HlgB, LukD, LukF, LukB/G) components have demonstrated cell lysis via pore formation and a magnified proinflammatory response at sublytic concentrations. While studies have described various host cellular receptors and therapeutic strategies to evade leucocidin binding, a common receptor for all the leucocidins has yet to be classified. Challenges in data extrapolation have occurred due to non-native protein expression methods and species specificity of the leucocidin components. In turn, developing successful therapeutic strategies has proven problematic with a need for multimodal therapy. Thus, our studies aimed to clarify the bi-component leucocidins’ cytotoxic effects on multiple subsets of leukocytes using a native protein expression system and to identify a novel human leukocyte receptor common to all leucocidins. Overall, combinations with HlgA and LukE demonstrated the highest degrees of cytotoxicity against PMNs and PBMCs. Coronin 1A was discovered as a common receptor for all cognate pairs of bi-component leucocidins, except LukAB/GH. In conclusion, our results have expanded the knowledge of the cellular targets for leucocidin cytotoxicity and have described a common leucocidin receptor as a potential therapeutic target against the bi-component leucocidins.

It is a popular practice in the remote-sensing community to apply principal component analysis (PCA) on a higher-dimensional feature space to achieve dimensionality-reduction. Several factors that have led to the popularity of PCA include its simplicity, ease of use, availability as part of popular remote-sensing packages, and optimal nature in terms of mean square error. These advantages have prompted the remote-sensing research community to overlook many limitations of PCA when used as a dimensionality-reduction tool for classification and target-detection applications. This thesis addresses the limitations of PCA when used as a dimensionality-reduction technique for extracting discriminating features from hyperspectral data. Theoretical and experimental analyses are presented to demonstrate that PCA is not necessarily an appropriate feature-extraction method for high-dimensional data when the objective is classification or target-recognition. The influence of certain data-distribution characteristics, such as within-class covariance, between-class covariance, and correlation on PCA transformation, is analyzed in this thesis. The classification accuracies obtained using PCA features are compared to accuracies obtained using other feature-extraction methods like variants of Karhunen-Loève transform and greedy search algorithms on spectral and wavelet domains. Experimental analyses are conducted for both two-class and multi-class cases. The classification accuracies obtained from higher-order PCA components are compared to the classification accuracies of features extracted from different regions of the spectrum. The comparative study done on the classification accuracies that are obtained using above feature-extraction methods, ascertain that PCA may not be an appropriate tool for dimensionality-reduction of certain hyperspectral data-distributions, when the objective is classification or target-recognition.

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