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<p>Cognitive psychologists have long known that there are limitations on human information processing abilities. As such we must constantly attend to relevant information in our environment, sometimes for further processing, at the expense of other information. Visual search tasks have been used extensively by researchers who seek to understand the consequences that this selective attention process has on memory. It has been argued that the priming effects observed in efficient visual search tasks reflect specialized, short-term memory representations that differ markedly from the memory representations believed to produce priming effects in other performance tasks. To the extent that this is true, researchers must adopt a necessary level of complexity in terms of the memory models used to explain the full range of human behavior. The empirical goal of this thesis was to provide a rigorous examination of priming effects in efficient visual search, in order to determine whether such effects can be explained by reference to general, well-studied memory mechanisms that have yielded significant explanatory power in other attention and performance tasks. The results of the experiments reported here suggest that general, well-studied memory principles may be a suitable candidate explanation for priming effects in efficient visual search.</p> / Doctor of Philosophy (PhD)

This thesis investigates predictions from prominent conflict theories of cognitive control that information experienced under high conflict conditions should be better encoded. More specifically, recent research suggests that selectively attending to relevant stimuli while ignoring conflicting stimuli can lead to better memory. These ideas have been broadly discussed in the desirable difficulty literature – described by instances where increasing difficulty during initial task performance leads to better later memory. As a growing number of studies have attempted to produce these effects with mixed success, calls for more focused investigations into the underlying mechanisms have been made. This encoding benefit for high-control-demand or high-difficulty situations has been broadly conceptualized as a task-general property, where all activated representations should be better encoded. The goal of this thesis was to investigate whether memory-enhancing effects of difficulty manipulations depend on inducing additional cognitive control at particular information processing stages. This thesis documents some of the first work showing that the within-task locus of conflict and attentional control is critical to whether later memory benefits are seen – conflict/control focused on semantic item representation produces better memory, but conflict/control focused away from item representations at response selection gives no memory benefit. These findings and theory are then extended to physiological measures of pupil dilation and sequential (Grattron-like) conflict/control situations. This thesis proposes a stage-specific conflict-encoding model which complements and extends current leading theories of conflict-driven cognitive control. / Dissertation / Doctor of Philosophy (PhD) / There is an intuitive notion that making a learning experience hard will hinder memory of that information later on. Contrary to this belief, in certain circumstances, making learning difficult can actually enhance the memory of that information – this has been termed desirable difficulty. The issue with these desirable difficulties is that they are only sometimes effective. Originally it was proposed that general task-wide difficulty would lead to an enhancement in memory. This thesis, however, provides evidence suggesting that task difficulty is stage-specific in nature, meaning that for the difficulty to enhance memory, the difficulty needs to be at a specific stage of cognitive processing. For difficulty to have a beneficial effect on memory, the particular difficulty needs to focus an individual’s attention on the core meaning of what they are trying to remember, or else the difficulty will direct attention away from this important information causing a possible decrease in memory. These findings provide a framework for how and when to use difficulty as a means to enhance learning.

In the past two decades, molecular cell biology has transitioned from a traditional descriptive science into a quantitative science that systematically measures cellular dynamics on different levels of genome, transcriptome and proteome. Along with this transition emerges the interdisciplinary field of systems biology, which aims to unravel complex interactions in biological systems through integrating experimental data into qualitative or quantitative models and computer simulations. In this dissertation, we applied various systems biology tools to investigate two important problems with respect to cellular activation dynamics and reprograming. Specifically, in the first section of the dissertation, we focused on lipopolysaccharide (LPS)-mediated priming and tolerance: a reprogramming in cytokine production in macrophages pretreated with specific doses of LPS. Though both priming and tolerance are important in the immune system's response to pathogens, the molecular mechanisms still remain unclear. We computationally investigated all network topologies and dynamics that are able to generate priming or tolerance in a generic three-node model. Accordingly, we found three basic priming mechanisms and one tolerance mechanism. Existing experimental evidence support these in silico found mechanisms. In the second part of the dissertation, we applied stochastic modeling and simulations to investigate the phenotypic transition of bacteria E.coli between normally-growing cells and persister cells (growth-arrested phenotype), and how this process can contribute to drug resistance. We built up a complex computational model capturing the molecular mechanism on both single cell level and population level. The paper also proposed a novel way to accelerate the phenotypic transition from persister cells to normally growing cell under resonance activation. The general picture of phenotypic transitions should be applicable to a broader context of biological systems, such as T cell differentiation and stem cell reprogramming. / Ph. D.

This study examined the perceptions of celebrity CEOs potentially transitioning to political candidates. Using Carly Fiorina's campaign for Senator of California, this study identified how young voters perceive celebrity CEOs as politicians, their identification of celebrity CEOs, and the evaluations of CEOs and their companies. Results indicate a more favorable evaluation of Fiorina resulted in a more favorable reaction to Hewlett- Packard. Results also confirm the use of media messages to prime young voters about political candidates. Finally, political party affiliation was found to significantly influence the findings of this study while gender and political cynicism did not. Theoretical implications and areas of future research in celebrity and politics are discussed. / Master of Arts

Corporate Social Responsibility (CSR) in sport is an emerging area of interest among scholars, sport managers, sponsors, fans, and policy-makers (Breitbarth, Walzel, Anagostopoulos, and van Eekeran, 2015). Despite this increased scholarly attention, a gap in literature exists regarding to the effectiveness of the messages disseminated. This study investigated how sports organizations communicate CSR on Twitter by examining the effectiveness of CSR messages disseminated via Twitter by professional baseball teams. Using priming theory and Lang's (2000) Limited Capacity Model for Mediated Message Processing, this study tested the effects of priming and message sequencing on a persons' ability to recognize and recall these CSR messages. While no statistically significant relationships were found, observed results led to strong arguments about the effects of both priming and message sequencing on the effectiveness of CSR messages disseminated by Major League Baseball (MLB) teams in terms of recognition and recall. Additionally, results suggested that traditional media effects paradigms might not be transferable to social media. / Master of Arts

Agricultural activities have significant impacts on global biogeochemical cycles, particularly carbon and nitrogen. Conventional row-crop agriculture accelerates the decomposition of soil organic matter, contributing to atmospheric carbon and declining soil fertility. Planting perennial warm season grasses is a useful management alternative to row crop agriculture because these species have been shown to be effective at increasing soil carbon storage and retaining nitrogen. The objectives of this research were to examine how converting row crops to a native perennial warm season grass (Panicum virgatum L., common name switchgrass) influences the recovery of soil organic matter fractions and nitrogen retention within an agricultural watershed in the Shenandoah Valley of Virginia. Soil samples were analyzed for total carbon and nitrogen, three particulate organic matter fractions, root biomass, mineralizable carbon and nitrogen pools, and microbial biomass. Surprisingly, I observed significant declines in bulk soil organic matter and surface particulate organic matter pools following switchgrass establishment. There were no differences in mineralizable carbon and microbial biomass pools between row crop and switchgrass soils, but labile carbon pools and nitrogen immobilization increased as switchgrass stands matured. These results are potentially due to switchgrass litter inputs stimulating microbial communities and accelerating the decomposition of recalcitrant soil organic matter, leading to declines in soil organic carbon stocks. The results from this study will be used to understand the environmental and economic benefits of implementing switchgrass plantings in agricultural watershed as a means to mitigate agriculturally-induced effects on carbon storage and nitrogen retention in soils. / Master of Science

Mathematical models have long been used to describe complex biological interactions with the aim of predicting mechanistic interactions hard to distinguish from data. This dissertation uses modeling, mathematical analyses, and data fitting techniques to provide hypotheses on the mechanisms of immune response formation and function. The immune system, comprised of the innate and adaptive immune responses, is responsible for protecting the body against invading pathogens, with disease or vaccine induced immune memory leading to fast responses to subsequent infections. While there is some agreement about the underlying mechanisms of adaptive immune memory, innate immune memory is poorly understood. Stimulation with lipopolysaccharide induces differential phenotypes in innate immune cells depending on the strength of the stimulus, such that a secondary lipopolysaccharide encounter of a constant dose results in either strong or weak inflammatory cytokine expression. We model the biochemical kinetics of three molecules involved in macrophages responses to lipopolysaccharide and find that once a macrophage is programed to show a weak inflammatory response this cannot be reverted. Contrarily, a secondary lipopolysaccharide stimulus of a very high dose or applied prior to waning of the effects of the primary stimulus can induce a phenotype switch in macrophages initially programed to show strong inflammatory responses. Some pathogens, such as the hepatitis B virus, have developed strategies that hinder an efficient innate immune response. Hepatitis B virus infection is a worldwide pandemic with approximately 257 million chronically infected people. One beneficial event in disease progression is the seroclearance of hepatitis B e antigen often in combination with hepatitis B antibody formation. We propose mathematical models of within-host interactions and use them to predict that hepatitis B e antibody formation causes hepatitis B e antigen seroclearance and the subsequent reactivation of cytotoxic T cell immune responses. We use the model to quantify the time between antibody formation and antigen clearance and the average monthly hepatocyte turnover during that time. We further expand the study of hepatitis B infection, by investigating the kinetics of the virus under an experimental drug administered during a clinical trial. Available drugs usually fail to induce hepatitis B s antigen clearance, defined as the functional cure point of chronic hepatitis B infections. Drug therapy clinical trials that combined RNA interference drug ARC-520 with entecavir have shown promising results in reducing hepatitis B s antigen titers. We develop pharmacokinetic-pharmacodynamic models describing the mechanistic interactions of the drugs, hepatitis B virus DNA, and virus proteins. We fit the model to clinical trial data and predict that ARC-520 alone is responsible for the reduction of hepatitis B s and e antigens, while entecavir is the driving force behind viral reduction. This work was supported by Simons Foundation, Grant No. 427115, and National Science Foundation, Grant No. 1813011. / Doctor of Philosophy / Mathematical models have long been used to describe complex biological interactions with the aim of predicting interactions that explain observed data and informing new experiments. This dissertation uses modeling, mathematical analyses, and data fitting techniques to provide hypotheses on the mechanisms of immune response formation and function. The immune system, comprised of the innate and adaptive immune responses, is responsible for protecting the body against invading pathogens, such as viruses, bacteria, or fungi. If an immune response to a secondary pathogen encounter differs from the response when the body first encounters the specific pathogen, this is called immune memory. The mechanisms underlying the memory of immune responses are well understood in the context of adaptive immune responses, but less so for innate immune responses. Stimulation with lipopolysaccharide, a cell wall component of many bacteria, programs innate immune cells, such as macrophages, to be in one of two states, called phenotypes, depending on the strength of the stimulus. Based on their phenotype the macrophages show either a weak or strong inflammatory response upon a secondary lipopolysaccharide encounter of a constant dose. We model the biochemical kinetics of three molecules involved in macrophages responses to lipopolysaccharide. We find that once a macrophage is programed to show a weak inflammatory response this cannot be reverted. Contrarily, a secondary lipopolysaccharide stimulus that is either of a very high dose or applied before the effects of the primary stimulus have waned, can induce a phenotype switch in macrophages initially programed to show strong inflammatory responses. Some pathogens, such as the hepatitis B virus, have developed strategies that hinder an efficient innate immune response. Hepatitis B virus infection is a worldwide pandemic with approximately 257 million chronically infected people. Hepatitis B e antigen is a protein that infected liver cells release into blood and that impairs adaptive immune responses. It is considered a beneficial event in disease progression, and called hepatitis B e antigen clearance, when hepatitis B e antigen becomes indetectable in a patient's blood. We propose mathematical models of interactions between liver cells, the virus, hepatitis B e antigens and hepatitis B e antibodies, which neutralize the antigens. We predict that antibody formation causes antigen clearance and a reactivation of immune responses. We furthermore use the model to quantify the time between antibody formation and antigen clearance and the average number of liver cells killed during that time. We further expand the study of hepatitis B infection, by investigating the kinetics of the virus under an experimental drug administered during a clinical trial. Available drugs rarely induce hepatitis B s antigen clearance, but clinical trials that combined a novel drug, called ARC-520, with the commonly used drug entecavir have shown promising results in reducing hepatitis B s antigen titers in the blood of infected patients. Following the clearance of hepatitis B s antigen, a protein that is released by infected cells and impairs adaptive immunity, the body usually has the capability to control the infection without medication. We develop mathematical models describing the interactions of the drugs, hepatitis B virus, and virus proteins. We fit the model to clinical trial data and predict that ARC-520 alone is responsible for the reduction of hepatitis B s and e antigens, while entecavir is the driving force behind viral reduction.

In adults, the availability of certain kinds of cues prior to a recognition task facilitates performance (often called “priming”). Studies have found that conceptual and perceptual priming improves neural efficiency and thus shortens response time in adults. In infant research, various visual and auditory/visual events are used as attention getters to orient the infant to a screen and alert them to upcoming information for their detection, discrimination, and/or recognition. However, the influence of attention-getters on infants’ performance has rarely been systematically evaluated, even though these attention cues could be acting as perceptual/conceptual primes. This study investigated the effect of priming on infants’ preferences for infant-directed speech (IDS) compared to adult-directed speech (ADS). IDS, an inherently social event, can be described as a moderator between attention systems and later language development. Thus, if the attentional network is primed in advance of hearing IDS, it is possible that the magnitude of the IDS preference may change. In this study, 20, 12- to 18-month old infants were provided with either a nonsocial or social prime in an infant-controlled, speech preference procedure with both IDS and ADS speech types. The infant’s total looking duration to IDS relative to ADS was compared for the social versus nonsocial prime condition. Results indicated a main effect for speech and overall IDS preference. However, no significant effect of prime was detected. Results are discussed in terms of future directions to investigate social priming of language in infancy. / Master of Science / In infant research, short duration events are used before the task of interest to orient infants to the screen, increase their attention, and prepare them for the following information to come. These events are called “attention getters” in developmental research, and are used internationally as a way to garner infants’ attention before the main test of interest. Labs use different attention getters based on their prior experience of what works best, and these attention getters vary in content (e.g., social, nonsocial), and format (e.g., audio, visual, audiovisual). The effect of the content of the attention getter on infants’ subsequent performance has never previously been studied, although the content could be acting as a prime for the following task. This study investigated the effect of a social, as opposed to nonsocial, attention getter on infants’ subsequent performance on a speech preference task. Infants (N = 20, 12- to 18-month olds) received both infant-directed speech (IDS; or how caregivers speak to their infants, characterized by shorter sentences, slower rate of speech, and exaggerated vowels) and adult-directed speech (ADS; or how adults speak to other adults, characterized by complex grammar, faster rates of speech, and shorter vowel sounds) which were preceded by either a social (woman saying “Hi Baby” in IDS) or nonsocial (swirling target with chimes) attention getter to investigate their preferences for speech type. It was predicted that infants who received a social prime would demonstrate a stronger preference for IDS over ADS relative to infants who received the nonsocial prime. Results indicated a main effect for speech and overall IDS preference. However, no significant effect of attention getter was detected, and the interaction between speech type and attention getter was not significant. Thus, our predicted results were not supported; the content of the attention getter did not attenuate or augment infants’ speech type preferences. Results are discussed in terms of future directions to better detect social priming in infancy.

A commercial solid matric priming method and an osmotic priming method were used to measure seed priming responses of birdsfoot trefoil, kura clover, and sericea lespedeza. Differences were not observed using standard germination tests, but both priming methods show potential for increased germination rate (P>0.05). Conflicting results for matric and osmotic priming were found in terms of seed storage potential after priming, with matric primed seeds showing higher (P<0.05) germination after accelerated aging and osmotic primed seeds showing significant lower germination(P<0.01). Birdsfoot trefoil benefited from priming, but responses varied by priming treatment, while kura clover showed less response to both priming treatments. In a field study comparing matric primed vs. unprimed seedling emergence, matric priming effects were small and these data suggest that solid matrix priming may be unlikely to improve the field establishment of either species. Aqueous smoke solutions were also tested for effect on seed germination. Differences in final germination percent due to solution type (after exposure to liquid smoke solutions for 10- or 45-min) were not observed. Highest concentration of the 10-min solution treatment reduced (P<0.05) birdsfoot trefoil germination. Greater germination was observed only for 'Perfect Fit' kura clover treated with low or intermediate concentrations of either solution. High concentrations of 10-min smoke water increased time to 50% germination (T50) for all seeds, but some reduction in T50 occurred for kura clovers treated with low (5%) solution concentrations. The 45-min treatments had little effect on germination rates. Applying aqueous smoke solution to seeds at germination did not improve germination responses of these forage legume species. / Master of Science