Mathematical modeling and realistic human simulation of human jogging motion is a very challenging problem. Majority of the current literature is focused on studying walking or running. This work is aimed at bridging the gap in literature due to the lack of research work in three main areas: (1) simulations and experiments on running at speeds lower than 3 m/s, (2) Kinetics of fore-foot strike pattern in jogging and running and (3) the existence of a double support phase in running at slower speeds and its effects. Formulations to simulate natural human jogging are studied and developed. The digital human model used for this work includes 55 degrees of freedom, 6 for global translation and rotation and 49 for the revolute joints to represent the kinematics of the body. Predictive Dynamics methodology is used for dynamic analysis where the problem is formulated as a nonlinear optimization problem. Both, displacement and forces are considered as unknowns and identified by solving the optimization problem. The equations of motion are satisfied by applying them as equality constraints in the formulation. Kinematics analysis of the mechanical system is performed using the Denavit-Haretneberg (DH) method. The zero moment point (ZMP) condition is satisfied during the ground contact phase to achieve dynamic stability. The joint angle profiles are discretized using B-spline interpolation method. The joint torque squared, also termed dynamic effort, and the difference between predicted motion and motion capture data are used as performance measures and minimized in the optimization formulation. The formulation also includes a set of constraints to simulate natural jogging motion. Two formulations are discussed for jogging on a straight path: (1) one-step jogging formulation and (2) one-stride jogging formulation. The one-stride formulation is discussed for clock-wise and counter clock-wise jogging along a curved path. Cause and effect is shown by obtaining simulation results for different loading conditions. The proposed formulation provides realistic human jogging motion and is very robust.

The environment is abundant with visual information. Each moment, this information competes for representation in the brain. From billboards and pop-up ads to smart phones and flat screens, in modern society our attention is constantly drawn from one salient object to the next. Learning how to focus on the objects that are most important for the current task is a major developmental hurdle. Fortunately, rewards help us to learn what is important by providing feedback signals to the brain. Sometimes, in adolescence for example, reward seeking can become the pre-potent response. This can ultimately lead to risky and impulsive behaviors that have devastating consequences. Until recently, little has been known about how rewards operate to influence the focus of attention. In this document, I first demonstrate the robustness of various behavioral paradigms designed to measure reward processing in vision. I found that even mundane rewards, such as images of money, are effective enough to prime the attentional system on the basis of value. Remarkably, this effect extended to images of Monopoly money. This observation suggests that whole classes of visual stimuli, such as food, pornography, commercial logos, corporate brands, or money, each with its own reward salience value, are likely vying for representation in the brain. This work has implications for the growing digital economy as it suggests that novel value systems, such as the digital currency Bitcoin, could eventually become as psychologically relevant as physical currency provided sufficient use and exposure. Likewise, this work has implications for gamification in the industrial setting. Next, I examined the sensitivity of the system to make optimal economic decisions. When faced with an economic choice normative theories of decision-making suggest that the economic actor will choose the response that affords the greatest expected utility. Contrary to this account, I developed a new behavioral paradigm (reward contingent capture) and reveal that the attentional homunculus is a fuzzy mathematician. Specifically, I found that low-level attentional processes conform to the same probability distortions observed in prospect theory. This finding supports a unified value learning mechanism across several domains of cognition and converges with evidence from monkey models. Then, I demonstrate the influence of rewards on high-order search parameters. I found that images of money can implicitly encourage observers to preferentially adopt one of two search strategies – one that values salience versus one that values goals. Together, my results expose two distinct ways in which the very same rewards can affect attentional behavior – by tuning the salience of specific features and by shaping global search mode settings. Lastly, I draw from my empirical results to present a unified model of the manifold role of rewards on visual attention. This model makes clear predictions for clinical applications of rewarded attention paradigms because it incorporates a dimension of complexity upon which learning processes can operate on attention. Thus, future work should acknowledge how individual traits such as developmental trajectory, impulsivity, and risk-seeking factors differentially interact with low- and high-level attentional processes. In sum, this document puts forward the notion that rewards serve a compelling role in visual awareness. The key point however is not that rewards can have an effect on attention but that due to the nature of visual processing, reward signals are likely always tuning attention. In this way we can consider reward salience an attentional currency. This means then that deciding where to attend is a matter of gains and losses.

This dissertation research is an archaeological investigation of the burial practices of the Irish Neolithic (4000-2500 BC) and Bronze Age (2500-1100 BC). Burial data from thirty sites are used in order to understand the relationship between the burial treatment of the dead (inhumation vs. cremation), artifact deposition, and faunal deposition with the age and sex of the dead. In order to understand how environmental variability affected the manner in which people constructed their views on identity, the sites were categorized based on two geographic regions, Region A and Region B. Region A refers to sites located in Co. Dublin, Co. Louth, Co. Meath, Co. Kildare, and Co. Wicklow, an area with many sites clustered together on land that was capable of supporting large communities, agricultural surplus, and is geographically located near important long distance trade routes with Britain and continental Europe. Region B refers to the remaining territory of Ireland. The results of the analyses are used to gain information on how burial was used by past populations to reflect social and economic status and how the communal perspective on status changed over time and how the surrounding environment affected the perspective of the people. Previous research on late prehistoric Irish burials has relied on cultural-historical stereotypes of the past to understand the social and economic trends, lumping all data from Ireland as being the same, and even as the same as burial trends in Britain and continental Europe. Therefore, Neolithic Ireland is assumed to have consisted of egalitarian agricultural-based communities, which transitioned into societies with vertical hierarchy dominated by adult males in the Bronze Age because of the rise of metallurgical practices and long-distance trade (Bradley 2007; Waddell 2010). Typically, research interpretations are generated based on only one line of contextual data, rather than taking into consideration the multiple aspects of burial ritual, and environmental variability amongst sites is not considered a factor in socio-economic influences on burial tradition. This study seeks to demonstrate that by using multiple lines of evidence, regional and local differences of burial tradition can be identified which contradict general stereotypes of both the Neolithic and the Bronze Age. The results of this study show that when multiple lines of evidence from burials are analyzed, general stereotypes of the manner in which socio-economic identity was manifested in the archaeological record during the Neolithic and Bronze Age cannot be applied to Ireland as a whole. Instead, the manner in which individuals are deposited and preserved in burial ritual is governed by isolated local traditions, rather than large, regional traditions. This is the result of regional variability in the environment, the arability of land, and the geographic positioning of sites near long-distance trade routes. This research demonstrates that large-scale explanations of social and economic changes in late prehistory and previous understandings of the role of burial ritual in socio-economic displays of identity need to be questioned and re-examined using more datasets to ensure a more thorough interpretation of the past.

Nanomaterials (materials which have at least one dimensional feature with length less than 100 nanometers), and carbon nanotubes (CNTs) specifically, have exhibited great potential in water treatment. CNTs are cylindrical structures comprising single or multiple concentric graphene sheets and have diameters from less than 1 nanometer (nm) up to 50 nm (one nm is one millionth of a millimeter). Due to their unique and tunable structural, physical, and chemical properties, CNTs are used in environmental remediation as absorbents, catalysts or catalyst supports, membranes, and electrodes. However, a poorly understood determinant of the role of CNTs in water treatment is their interaction with chemical disinfectants (e.g., chlorine, chloramine, and ozone). To address these existing gaps in the environmental fate and reactivity of CNTs, this work establishes whether CNTs represent precursors for halogen and nitrogen containing disinfection byproducts (DBPs), which are products that form during a reaction of a disinfectant with organic matter in the water. In addition, we seek to understand how reaction with disinfectants alters CNT surface chemistry, and in turn impacts their environmental mobility and cytotoxicity. Finally, we determine how NOM and other aquatic variables known to impact DBP formation (e.g., Br−, NOM, and pH) influence the rate and products of CNT reaction with disinfectants. Outcomes of this work contribute to the current understanding of the role of carbon-based species as DBP precursors in disinfection and provide new context as to the environmental significance and implications of CNTs in natural and engineered aquatic systems.

The overarching objective of the investigations discussed herein is the development of a model experimental system for surface-enhanced infrared absorption (SEIRA) spectroscopy, with potential applicability in higher order infrared spectroscopic techniques, specifically, surface-enhanced two-dimensional infrared (SE-2D IR) spectroscopy. Theoretical predictions that accurately predict the stability of functionalized nanoparticles enable guided design of their properties but are often limited by the accuracy of the parameters used as model inputs. Hence, first, such parameterization limitations for the extended DLVO (xDLVO) theory are overcome using a size-dependent Hamaker constant for gold, interfacial surface potentials, and tilt angles of self-assembled monolayers (SAMs), which collectively improves the predictive power of xDLVO theory for modeling nanoparticle stability. Measurements of electrical properties of functionalized gold nanoparticles validate the predictions of xDLVO theory using these new parameterizations illustrating the potential for this approach to improve the design and control of the properties of functionalized gold nanoparticles in various applications. Next, a series of experiments were conducted to elucidate the behavior of various infrared active molecules in the presence of spherical gold nanoparticles of average diameter ∼20 nm. Here, the spectroscopic anomalies, specifically the shifted vibrational frequency and the dispersive lineshape observed in the infrared spectra for SCN- in the presence of gold nanoparticles provide direct evidence of SIERA. Nevertheless, it was evidenced that nanomaterial with plasmonic properties that extends into the infrared wavelengths are imperative in observing efficient infrared enhancements. Hence, nanomaterial indicating plasmonic properties extending into the infrared wavelengths were synthesized via a straightforward, seedless, one-pot synthesis. The gold nanostars prepared here indicated plasmonic behavior clearly extending into the near infrared, with simple plasmonic tunability via changing the buffer concentration used during synthesis. The systematic understanding achieved here in terms of theoretical prediction of nanoparticle stability, origin of infrared spectral anomalies in the presence of nanomaterials, and the preparation of infrared plasmonic material, collectively provides a resilient framework for the further investigation of surface-enhanced infrared spectroscopic techniques including SEIRA and SE-2D IR spectroscopies.

The purpose of this study was to examine the relationship between maternal perceived locus of control (PLOC), perceived self-efficacy (PSE), and mother and child gains during a mother-implemented early language and print awareness program. Thirty mother-child dyads (with typically-developing, preschool-aged children) were randomly assigned to either an immediate-training group (ITG) or a delayed-training control group (DTCG). The mothers in the ITG participated in 4 training sessions over the course of a month. Data about mothers’ use of target strategies, mothers’ responsivity, children’s knowledge of print concepts, and child language samples were collected at baseline, 1-month, and 2-months for both groups. The training program was efficacious, as evidenced by greater gains in the ITG mothers’ target strategy use, responsivity, and children’s knowledge of print concepts as compared to DTCG mothers and children respectively. The ITG children significantly increased the number of different words they produced during their language samples from baseline to follow-up. Mothers with a more external PLOC and/or a lower PSE score tended to use fewer strategies at baseline and make greater gains in strategy use over the course of training. Similarly, children whose mothers had a more external PLOC tended to identify fewer print concepts at baseline and make greater gains during training. Conversely, children whose mothers had a lower sense of PSE tended to use a greater variety of words and have a higher number of different words/number of total words ratio at baseline. The results of this study support the incorporation of maternal PLOC and PSE into evidence-based clinical decision-making and provide avenues for future research.

In this dissertation, I investigate the ways in which the phenomenon of racial and cultural hybridity inform and alter the social, political and cultural fabric of three creole cities of significant colonial influence, namely Saint-Louis of Senegal, Saint-Pierre of Martinique and Jérémie of Haiti during and after the colonial era. In particular, I examine the relevance of the French colonial city not only as a nexus of relational complexity but also as an ambiguous center of attraction and exclusion where multiple identities are created and recreated according to the agendas that influence these constructions. In order to articulate the main hypotheses of my thesis, I explore the key historical and social catalysts that have led to the emergence of Saint-Louis, Saint-Pierre and Jérémie as original creole cities. Through the critical analyses of contemporary literatures from Senegal, Martinique and Haiti by Fanon, Sadji, Boilat, Mandeleau, Confiant, Chamoiseau, Salavina, Bonneville, Moreau de Saint-Méry, Desquiron, and Chauvet and films by Deslauriers and Palcy, I illustrate the dynamics of creolization within the context of the French colonial city. I argue that the city engenders new narratives and interpretations of métissage that scholars have often associated with the enclosed space of the plantation. My dissertation intends to prove that the three French colonial cities of Saint-Louis, Saint-Pierre and Jérémie offer distinct interpretations and practices of processes of cultural and ethnic métissage. I propose that a correlation albeit a dialectical one, exists between the development of the French colonial city and the emergence of the mulattoes as a distinct class, conscious of its economic, sexual and political agency. I suggest that the French colonial city, represents both a starting point and a space of continuity that permits new forms of ethnic and cultural admixture. The articulation of such mixtures is made evident by the strategic positioning and creative agency of the mulatto class within the colonial city. The phenomenon of métissage is certainly not a novel subject as evidenced by the plethora of theories and studies advanced by scholars and intellectuals. My research is thus part of an existing critical literary corpus in Postcolonial and Francophone Studies and is inscribed within the theoretical framework of Creolization. My research observes from a historical, comparative and literary perspective, metis presence and consciousness in three specific spaces where colonial authority has been imposed, challenged, resisted and even overpowered (in the case of Haiti). My study therefore analyses the creative agency articulated by the metis ethnoclass in the colonial city and counters the claim of a passive assimilated group. As an in-between group, mulatto’s access to social, economic and political upward mobility are impeded by their ambiguous positioning within the larger community. Consequently, they resort to unconventional means that I refer to rather as creative ingeniousness in order to survive. Scholars usually focus on these “unconventional” practices as immoral rather than as strategies of self-reinvention and revalorization. As a result, representations of cultural and ethnic interconnections and hybridity are often projected in fragmentary ways. The figure of the metis women for example is overly represented in studies on métissage while metis men receive very little attention. My thesis thus intends to decenter narratives on métissage from the women and implicate equally the creative agency of metis males. My thesis expands on the complexities that inform processes of métissage during pre-colonial Saint-Louis in the early seventeenth century, Saint-Pierre from the period 1870-1902 and Jérémie during the dictatorship of Francois Duvalier. It examines further the city as a space that engenders new narratives and interpretations of the processes of creolization. Processes of métissage or creolization have often been described as the results of violent encounters that were colonial and imperial. Moreover, these clashes were inscribed within the enclosed space of the plantation. The city, representation of European pride and greed is an ambiguous space that attracts even as it excludes. Projected as an active commercial, economic and cultural hub, the city is soon engulfed by mass emigration. That site where the European image and culture is imposed, quickly evolves into a complex and chaotic web of human and material interaction giving rise to a complex creolized atmosphere. I propose that practices of métissage in the city are distinct from those generated in the belly of the slave ships, in the trading houses of Sub-Saharan Africa and on the sugar plantations of the French Antilles. I conclude with a look at the present context of métissage, I rethink the significance of racial and cultural hybridity in relation to contemporary cultural and social theories such as creolization, creoleness, and transculturation in articulating, interpreting and decoding a world in constant transformation.

Human Pegivirus (HPgV; originally called GB virus C) is an RNA virus within the Pegivirus genus of the Flaviviridae that commonly causes persistent infection. Worldwide, approximately 750 million people are infected with HPgV. No causal association between HPgV and disease has been identified; however, several studies found an association between persistent HPgV infection and prolonged survival of HIV-infected individuals that appears to be related to a reduction in host immune activation. HPgV replicates well in vivo (>10 million genome copies/ml plasma) but grows poorly in vitro and systems to study this virus are limited. Consequently, mechanisms of viral persistence and host immune modulation remain poorly characterized, and the primary permissive cell type(s) has not yet been identified. The overall goals of my thesis were to characterize HPgV tropism, effects of HPgV infection on host immune response and mechanisms of viral persistence. Previous studies found HPgV RNA in T and B lymphocytes and ex vivo infected lymphocytes produce viral particles. To further characterize HPgV tropism, we quantified HPgV RNA in highly purified CD4+ and CD8+ T cells, including naïve, central memory, and effector memory populations, and in B cells (CD19+), NK cells (CD56+) cells and monocytes (CD14+) obtained from persistently infected humans using real time RT-PCR. Single genome sequencing was performed on virus within individual cell types to estimate genetic diversity among cell populations. HPgV RNA was present in CD4+ and CD8+ T lymphocytes (9 of 9 subjects), B lymphocytes (7 of 9), NK cells and monocytes (both 4 of 5). HPgV RNA levels were higher in naïve (CD45RA+) CD4+ cells than in central memory and effector memory cells (p<0.01). HPgV sequences were highly conserved between patients (0.117 ± 0.02 substitutions per site) and within subjects (0.006 ± 0.003 substitutions per site). The non-synonymous/synonymous substitution ratio was 0.07 suggesting low selective pressure. CFSE-labeled HPgV RNA-positive microvesicles (SEV) from serum delivered CFSE to uninfected monocytes, NK cells, T and B lymphocytes, and HPgV RNA was transferred to peripheral blood mononuclear cells (PBMCs) with evidence of subsequent viral replication. Thus, HPgV RNA-positive SEV may contribute to delivery of HPgV to PBMCs in vivo, explaining the apparent broad tropism of this persistent human RNA virus. Although HPgV infection reduces NK cell activation in HIV-infected individuals, the mechanism by which this occurs is not characterized. We studied HPgV effects on NK cell non-cytolytic function in HIV-infected people by measuring expression of IL-12 induced interferon gamma (IFNg) and cytolytic function by measuring K562 target-cell induced CD107a and granzyme B. IFNg expression was lower in HIV-HPgV co-infected subjects compared to HIV mono-infected subjects treated with combination antiretroviral therapy (p=0.02). In contrast, cytolytic NK cell functions were not affected by HPgV. Inhibition of IFNg was due to inhibition of tyrosine kinase (Tyk2) by HPgV envelope protein E2. HPgV positive human sera, extracellular vesicles containing E2 protein, recombinant E2 protein and synthetic E2 peptides containing a predicted Tyk2 interacting motif inhibited IL-12-mediated IFNg release by NK cells. Thus HPgV-E2 inhibits NK cell non-cytolytic functions. Inhibition of NK cell-induced proinflammatory/antiviral cytokines may contribute to both HPgV's ability to persist with high viral loads (>10 million genome copies/ml plasma) and reduce immune cell activation. Understanding mechanisms by which HPgV alters immune activation may contribute towards novel immunomodulatory therapies to treat HIV and inflammatory diseases.

Cities have a paradoxical relationship with science fiction literature. On the one hand, critics like Brian Aldiss have called sf a `literature of cities', citing them as the dominant context for speculative fiction. On the other, critics like Gary Wolfe have noted how sf has an "anti-urban frontier mentality" and how sf narratives involving cities often tend to view them as a trap from which the protagonist must escape. This relationship is even more complex in sf works by African American authors, as contemporary African American fiction in general takes the city as the dominant context for black social life and has turned to interrogate "issues of urban community" in the post-Civil Rights era. This dissertation explores the connections between the heterogeneous urban histories of Anglo-European and African American sf authors and the cities they construct. It does so by comparing the portrayal of cities by each group and relating the commonalities and contrasts that emerge from these portrayals to the differences and similarities between African American urban history and Anglo-European urban history. To provide a common ground for comparison, two city typologies are focused on: the `imperial city' that reigns at the heart of sf's many empires, and the empty metropolis of the `dead city' or `ghost city'. The study finds that these narratives all interrogate crises of political and environmental sustainability in urban history, but that the focus of these crises often diverge along the axis of race, with an especially large concentration on the crises related to racially targeted urban renewal programs present in black sf's dead cities and on crises related to black anti-imperialist politics in its imperial cities.

This dissertation describes efforts to improve the oxidative capacity of n-alkane- induced Beauveria bassiana; a fungus and a versatile whole cell biocatalyst used in the biotransformation of steroids. n-Hexadecane was used as the carbon source during the growth of B. bassiana, presumably to induce the expression of oxidative enzymes, thus enhancing the oxidation of unactivated carbons. Dehydroepiandrosterone (DHEA) is an essential endogenous male-hormone and serves as a metabolic intermediate in the production of more potent androgens. Using DHEA as a substrate also provides the opportunity to study the hydroxylation of an unfunctionalized carbon, an attractive reaction that produces valuable intermediates for chemical synthesis. Results showed that exposing and inducing cells in n-hexadecane improves the synthesis of 11α-hydroxy derivatives. Reactions were carried out with cells grown on n-hexadecane, resulting in 65 ± 6.3 % conversion of DHEA to androstenediol (40.3% mM) and 3β,11∝,17β- trihydroxyandrost-5-ene (22.8% mM), as determined by HPLC, NMR and LCMS analyses. However, experiments with non-induced cells resulted in a poor substrate conversion (17%). To extend use of B. bassiana to pharmaceutical applications, it was necessary to optimize reaction conditions such as biocatalyst preparation, substrate concentration, agitation reaction temperature and pH. Higher substrate conversion, selectivity and yield of desired product were achieved with the reactor arrangement of “Resting Cells”. The apparent rate of reaction fits a Michaelis-Menten kinetic model with a maximum reaction rate of 4.45 mM/day, revealing that the transformation of intermediate androstenediol to desired 3β,11∝,17β-trihydroxyandrost-5-ene is the limiting step in the reaction. Interestingly, when a diluted amount of substrate was used, a higher yield of 11∞-hydroxy steroid was achieved. Also, reactions at 26°C with pH ranges between 6.0 and 7.0, resulted in the highest conversion (70%) and the higher product yield (45.8%). The maximum conversion of DHEA (71%) was achieved in experiments with high biomass loading, and the increment of desired product yield (11∝-hydroxy) was directly proportional to the amount of biomass used. Moreover, a high VMax/KM value was achieved with high biomass yields. Interestingly, the changes in biomass yield did not have a considerable effect on reaction selectivity. The main drawbacks of biocatalysis for production of steroids were addressed and approaches to minimize the drawbacks have been presented. The production of desired product (11∝-DHEA) was significantly improved using cells previously adapted to n-hexadecane.