Common genetic variation and the control of HIV-1 in humans.

To extend the understanding of host genetic determinants of HIV-1 control, we performed a genome-wide association study in a cohort of 2,554 infected Caucasian subjects. The study was powered to detect common genetic variants explaining down to 1.3% of the variability in viral load at set point. We provide overwhelming confirmation of three associations previously reported in a genome-wide study and show further independent effects of both common and rare variants in the Major Histocompatibility Complex region (MHC). We also examined the polymorphisms reported in previous candidate gene studies and fail to support a role for any variant outside of the MHC or the chemokine receptor cluster on chromosome 3. In addition, we evaluated functional variants, copy-number polymorphisms, epistatic interactions, and biological pathways. This study thus represents a comprehensive assessment of common human genetic variation in HIV-1 control in Caucasians.

Using the institutional grammar tool to understand regulatory compliance: The case of Colorado aquaculture

What is the relationship between the design of regulations and levels of individual compliance? To answer this question, Crawford and Ostrom's institutional grammar tool is used to deconstruct regulations governing the aquaculture industry in Colorado, USA. Compliance with the deconstructed regulatory components is then assessed based on the perceptions of the appropriateness of the regulations, involvement in designing the regulations, and intrinsic and extrinsic motivations. The findings suggest that levels of compliance with regulations vary across and within individuals regarding various aspects of the regulatory components. As expected, the level of compliance is affected by the perceived appropriateness of regulations, participation in designing the regulations, and feelings of guilt and fear of social disapproval. Furthermore, there is a strong degree of interdependence among the written components, as identified by the institutional grammar tool, in affecting compliance levels. The paper contributes to the regulation and compliance literature by illustrating the utility of the institutional grammar tool in understanding regulatory content, applying a new Q-Sort technique for measuring individual levels of compliance, and providing a rare exploration into feelings of guilt and fear outside of the laboratory setting. © 2012 Blackwell Publishing Asia Pty Ltd.

Facilitators and barriers to hypertension self-management in urban African Americans: perspectives of patients and family members.

INTRODUCTION: We aimed to inform the design of behavioral interventions by identifying patients' and their family members' perceived facilitators and barriers to hypertension self-management. MATERIALS AND METHODS: We conducted focus groups of African American patients with hypertension and their family members to elicit their views about factors influencing patients' hypertension self-management. We recruited African American patients with hypertension (n = 18) and their family members (n = 12) from an urban, community-based clinical practice in Baltimore, Maryland. We conducted four separate 90-minute focus groups among patients with controlled (one group) and uncontrolled (one group) hypertension, as well as their family members (two groups). Trained moderators used open-ended questions to assess participants' perceptions regarding patient, family, clinic, and community-level factors influencing patients' effective hypertension self-management. RESULTS: Patient participants identified several facilitators (including family members' support and positive relationships with doctors) and barriers (including competing health priorities, lack of knowledge about hypertension, and poor access to community resources) that influence their hypertension self-management. Family members also identified several facilitators (including their participation in patients' doctor's visits and discussions with patients' doctors outside of visits) and barriers (including their own limited health knowledge and patients' lack of motivation to sustain hypertension self-management behaviors) that affect their efforts to support patients' hypertension self-management. CONCLUSION: African American patients with hypertension and their family members reported numerous patient, family, clinic, and community-level facilitators and barriers to patients' hypertension self-management. Patients' and their family members' views may help guide efforts to tailor behavioral interventions designed to improve hypertension self-management behaviors and hypertension control in minority populations.

The neuropsychology of autobiographical memory.

This special issue of Cortex focuses on the relative contribution of different neural networks to memory and the interaction of 'core' memory processes with other cognitive processes. In this article, we examine both. Specifically, we identify cognitive processes other than encoding and retrieval that are thought to be involved in memory; we then examine the consequences of damage to brain regions that support these processes. This approach forces a consideration of the roles of brain regions outside of the frontal, medial-temporal, and diencephalic regions that form a central part of neurobiological theories of memory. Certain kinds of damage to visual cortex or lateral temporal cortex produced impairments of visual imagery or semantic memory; these patterns of impairment are associated with a unique pattern of amnesia that was distinctly different from the pattern associated with medial-temporal trauma. On the other hand, damage to language regions, auditory cortex, or parietal cortex produced impairments of language, auditory imagery, or spatial imagery; however, these impairments were not associated with amnesia. Therefore, a full model of autobiographical memory must consider cognitive processes that are not generally considered 'core processes,' as well as the brain regions upon which these processes depend.

The origin and evolution of phototropins.

Plant phototropism, the ability to bend toward or away from light, is predominantly controlled by blue-light photoreceptors, the phototropins. Although phototropins have been well-characterized in Arabidopsis thaliana, their evolutionary history is largely unknown. In this study, we complete an in-depth survey of phototropin homologs across land plants and algae using newly available transcriptomic and genomic data. We show that phototropins originated in an ancestor of Viridiplantae (land plants + green algae). Phototropins repeatedly underwent independent duplications in most major land-plant lineages (mosses, lycophytes, ferns, and seed plants), but remained single-copy genes in liverworts and hornworts-an evolutionary pattern shared with another family of photoreceptors, the phytochromes. Following each major duplication event, the phototropins differentiated in parallel, resulting in two specialized, yet partially overlapping, functional forms that primarily mediate either low- or high-light responses. Our detailed phylogeny enables us to not only uncover new phototropin lineages, but also link our understanding of phototropin function in Arabidopsis with what is known in Adiantum and Physcomitrella (the major model organisms outside of flowering plants). We propose that the convergent functional divergences of phototropin paralogs likely contributed to the success of plants through time in adapting to habitats with diverse and heterogeneous light conditions.

Thinking Outside the Box: Treating Acute Heart Failure Outside the Hospital to Improve Care and Reduce Admissions.

The management of acute heart failure is shifting toward treatment approaches outside of a traditional hospital setting. Many heart failure providers are now treating patients in less familiar health care settings, such as acute care clinics, emergency departments, and skilled nursing facilities. In this review we describe the current pressures driving change in the delivery of acute heart failure and summarize the evidence regarding treatments for acute heart failure outside of the inpatient setting. We also provide considerations for the design of future treatment strategies to be implemented in alternative care settings.

Structural and Functional Analysis of the Caspase –dependent and –independent Domains of the X-linked Inhibitor of Apoptosis Protein in Inflammatory Breast Cancer Tumor Biology

Inflammatory breast cancer (IBC) is an extremely rare but highly aggressive form of breast cancer characterized by the rapid development of therapeutic resistance leading to particularly poor survival. Our previous work focused on the elucidation of factors that mediate therapeutic resistance in IBC and identified increased expression of the anti-apoptotic protein, X-linked inhibitor of apoptosis protein (XIAP), to correlate with the development of resistance to chemotherapeutics. Although XIAP is classically thought of as an inhibitor of caspase activation, multiple studies have revealed that XIAP can also function as a signaling intermediate in numerous pathways. Based on preliminary evidence revealing high expression of XIAP in pre-treatment IBC cells rather than only subsequent to the development of resistance, we hypothesized that XIAP could play an important signaling role in IBC pathobiology outside of its heavily published apoptotic inhibition function. Further, based on our discovery of inhibition of chemotherapeutic efficacy, we postulated that XIAP overexpression might also play a role in resistance to other forms of therapy, such as immunotherapy. Finally, we posited that targeting of specific redox adaptive mechanisms, which are observed to be a significant barrier to successful treatment of IBC, could overcome therapeutic resistance and enhance the efficacy of chemo-, radio-, and immuno- therapies. To address these hypotheses our objectives were: 1. to determine a role for XIAP in IBC pathobiology and to elucidate the upstream regulators and downstream effectors of XIAP; 2. to evaluate and describe a role for XIAP in the inhibition of immunotherapy; and 3. to develop and characterize novel redox modulatory strategies that target identified mechanisms to prevent or reverse therapeutic resistance.

Using various genomic and proteomic approaches, combined with analysis of cellular viability, proliferation, and growth parameters both in vitro and in vivo, we demonstrate that XIAP plays a central role in both IBC pathobiology in a manner mostly independent of its role as a caspase-binding protein. Modulation of XIAP expression in cells derived from patients prior to any therapeutic intervention significantly altered key aspects IBC biology including, but not limited to: IBC-specific gene signatures; the tumorigenic capacity of tumor cells; and the metastatic phenotype of IBC, all of which are revealed to functionally hinge on XIAP-mediated NFκB activation, a robust molecular determinant of IBC. Identification of the mechanism of XIAP-mediated NFκB activation led to the characterization of novel peptide-based antagonist which was further used to identify that increased NFκB activation was responsible for redox adaptation previously observed in therapy-resistant IBC cells. Lastly, we describe the targeting of this XIAP-NFκB-ROS axis using a novel redox modulatory strategy both in vitro and in vivo. Together, the data presented here characterize a novel and crucial role for XIAP both in therapeutic resistance and the pathobiology of IBC; these results confirm our previous work in acquired therapeutic resistance and establish the feasibility of targeting XIAP-NFκB and the redox adaptive phenotype of IBC as a means to enhance survival of patients.

Enhancing the Visualization of the Peripheral Retina with Wide Field-of-View Optical Coherence Tomography

The goal of my Ph.D. thesis is to enhance the visualization of the peripheral retina using wide-field optical coherence tomography (OCT) in a clinical setting.

OCT has gain widespread adoption in clinical ophthalmology due to its ability to visualize the diseases of the macula and central retina in three-dimensions, however, clinical OCT has a limited field-of-view of 300. There has been increasing interest to obtain high-resolution images outside of this narrow field-of-view, because three-dimensional imaging of the peripheral retina may prove to be important in the early detection of neurodegenerative diseases, such as Alzheimer's and dementia, and the monitoring of known ocular diseases, such as diabetic retinopathy, retinal vein occlusions, and choroid masses.

Before attempting to build a wide-field OCT system, we need to better understand the peripheral optics of the human eye. Shack-Hartmann wavefront sensors are commonly used tools for measuring the optical imperfections of the eye, but their acquisition speed is limited by their underlying camera hardware. The first aim of my thesis research is to create a fast method of ocular wavefront sensing such that we can measure the wavefront aberrations at numerous points across a wide visual field. In order to address aim one, we will develop a sparse Zernike reconstruction technique (SPARZER) that will enable Shack-Hartmann wavefront sensors to use as little as 1/10th of the data that would normally be required for an accurate wavefront reading. If less data needs to be acquired, then we can increase the speed at which wavefronts can be recorded.

For my second aim, we will create a sophisticated optical model that reproduces the measured aberrations of the human eye. If we know how the average eye's optics distort light, then we can engineer ophthalmic imaging systems that preemptively cancel inherent ocular aberrations. This invention will help the retinal imaging community to design systems that are capable of acquiring high resolution images across a wide visual field. The proposed model eye is also of interest to the field of vision science as it aids in the study of how anatomy affects visual performance in the peripheral retina.

Using the optical model from aim two, we will design and reduce to practice a clinical OCT system that is capable of imaging a large (800) field-of-view with enhanced visualization of the peripheral retina. A key aspect of this third and final aim is to make the imaging system compatible with standard clinical practices. To this end, we will incorporate sensorless adaptive optics in order to correct the inter- and intra- patient variability in ophthalmic aberrations. Sensorless adaptive optics will improve both the brightness (signal) and clarity (resolution) of features in the peripheral retina without affecting the size of the imaging system.

The proposed work should not only be a noteworthy contribution to the ophthalmic and engineering communities, but it should strengthen our existing collaborations with the Duke Eye Center by advancing their capability to diagnose pathologies of the peripheral retinal.

Full of Hot Air? Three Examinations of Climate Change in the American Political Information Environment

Climate change is thought to be one of the most pressing environmental problems facing humanity. However, due in part to failures in political communication and how the issue has been historically defined in American politics, discussions of climate change remain gridlocked and polarized. In this dissertation, I explore how climate change has been historically constructed as a political issue, how conflicts between climate advocates and skeptics have been communicated, and what effects polarization has had on political communication, particularly on the communication of climate change to skeptical audiences. I use a variety of methodological tools to consider these questions, including evolutionary frame analysis, which uses textual data to show how issues are framed and constructed over time; Kullback-Leibler divergence content analysis, which allows for comparison of advocate and skeptical framing over time; and experimental framing methods to test how audiences react to and process different presentations of climate change. I identify six major portrayals of climate change from 1988 to 2012, but find that no single construction of the issue has dominated the public discourse defining the problem. In addition, the construction of climate change may be associated with changes in public political sentiment, such as greater pessimism about climate action when the electorate becomes more conservative. As the issue of climate change has become more polarized in American politics, one proposed causal pathway for the observed polarization is that advocate and skeptic framing of climate change focuses on different facets of the issue and ignores rival arguments, a practice known as “talking past.” However, I find no evidence of increased talking past in 25 years of popular newsmedia reporting on the issue, suggesting both that talking past has not driven public polarization or that polarization is occurring in venues outside of the mainstream public discourse, such as blogs. To examine how polarization affects political communication on climate change, I test the cognitive processing of a variety of messages and sources that promote action against climate change among Republican individuals. Rather than identifying frames that are powerful enough to overcome polarization, I find that Republicans exhibit telltale signs of motivated skepticism on the issue, that is, they reject framing that runs counter to their party line and political identity. This result suggests that polarization constrains political communication on polarized issues, overshadowing traditional message and source effects of framing and increasing the difficulty communicators experience in reaching skeptical audiences.

Dissecting the Functional Impacts of Non-Coding Genetic Variation

A large proportion of the variation in traits between individuals can be attributed to variation in the nucleotide sequence of the genome. The most commonly studied traits in human genetics are related to disease and disease susceptibility. Although scientists have identified genetic causes for over 4,000 monogenic diseases, the underlying mechanisms of many highly prevalent multifactorial inheritance disorders such as diabetes, obesity, and cardiovascular disease remain largely unknown. Identifying genetic mechanisms for complex traits has been challenging because most of the variants are located outside of protein-coding regions, and determining the effects of such non-coding variants remains difficult. In this dissertation, I evaluate the hypothesis that such non-coding variants contribute to human traits and diseases by altering the regulation of genes rather than the sequence of those genes. I will specifically focus on studies to determine the functional impacts of genetic variation associated with two related complex traits: gestational hyperglycemia and fetal adiposity. At the genomic locus associated with maternal hyperglycemia, we found that genetic variation in regulatory elements altered the expression of the HKDC1 gene. Furthermore, we demonstrated that HKDC1 phosphorylates glucose in vitro and in vivo, thus demonstrating that HKDC1 is a fifth human hexokinase gene. At the fetal-adiposity associated locus, we identified variants that likely alter VEPH1 expression in preadipocytes during differentiation. To make such studies of regulatory variation high-throughput and routine, we developed POP-STARR, a novel high throughput reporter assay that can empirically measure the effects of regulatory variants directly from patient DNA. By combining targeted genome capture technologies with STARR-seq, we assayed thousands of haplotypes from 760 individuals in a single experiment. We subsequently used POP-STARR to identify three key features of regulatory variants: that regulatory variants typically have weak effects on gene expression; that the effects of regulatory variants are often coordinated with respect to disease-risk, suggesting a general mechanism by which the weak effects can together have phenotypic impact; and that nucleotide transversions have larger impacts on enhancer activity than transitions. Together, the findings presented here demonstrate successful strategies for determining the regulatory mechanisms underlying genetic associations with human traits and diseases, and value of doing so for driving novel biological discovery.

Beyond the Convent Walls: The Local and Japan-wide Activities of Daihongan’s Nuns in the Early Modern Period (c. 1550–1868)

This dissertation examines the social and financial activities of Buddhist nuns to demonstrate how and why they deployed Buddhist doctrines, rituals, legends, and material culture to interact with society outside the convent. By examining the activities of the nuns of the Daihongan convent (one of the two administrative heads of the popular pilgrimage temple, Zenkōji) in Japan’s early modern period (roughly 1550 to 1868) as documented in the convent’s rich archival sources, I shed further light on the oft-overlooked political and financial activities of nuns, illustrate how Buddhist institutions interacted with the laity, provide further nuance to the discussion of how Buddhist women navigated patriarchal sectarian and secular hierarchies, and, within the field of Japanese history, give voice to women who were active outside of the household unit around which early modern Japanese society was organized.

Zenkōji temple, surrounded by the mountains of Nagano, has been one of Japan’s most popular pilgrimage sites since the medieval period. The abbesses of Daihongan, one Zenkōji’s main sub-temples, traveled widely to maintain connections with elite and common laypeople, participated in frequent country-wide displays of Zenkōji’s icon, and oversaw the creation of branch temples in Edo (now Tokyo), Osaka, Echigo (now Niigata), and Shinano (now Nagano). The abbesses of Daihongan were one of only a few women to hold the imperially sanctioned title of eminent person (shōnin 上人) and to wear purple robes. While this means that this Pure Land convent was in some ways not representative of all convents in early modern Japan, Daihongan’s position is particularly instructive because the existence of nuns and monks in a single temple complex allows us to see in detail how monastics of both genders interacted in close quarters.

This work draws heavily from the convent’s archival materials, which I used as a guide in framing my dissertation chapters. In the Introduction I discuss previous works on women in Buddhism. In Chapter 1, I briefly discuss the convent’s history and its place within the Zenkōji temple complex. In Chapter 2, I examine the convent’s regular economic bases and its expenditures. In Chapter 3, I highlight Daihongan’s branch temples and discuss the ways that they acted as nodes in a network connecting people in various areas to Daihongan and Zenkōji, thus demonstrating how a rural religious center extended its sphere of influence in urban settings. In Chapter 4, I discuss the nuns’ travels throughout the country to generate new and maintain old connections with the imperial court in Kyoto, confraternities in Osaka, influential women in the shogun’s castle, and commoners in Edo. In Chapter 5, I examine the convent’s reliance upon irregular means of income such as patronage, temple lotteries, loans, and displays of treasures, and how these were needed to balance irregular expenditures such as travel and the maintenance or reconstruction of temple buildings. Throughout the dissertation I describe Daihongan’s inner social structure comprised of abbesses, nuns, and administrators, and its local emplacement within Zenkōji and Zenkōji’s temple lands.

Exploring these themes sheds light on the lives of Japanese Buddhist nuns in this period. While the tensions between freedom and agency on the one hand and obligations to patrons, subordination to monks, or gender- and status-based restrictions on the other are important, and I discuss them in my work, my primary focus is on the nuns’ activities and lives. Doing so demonstrates that nuns were central figures in ever-changing economic and social networks as they made and maintained connections with the outside world through Buddhist practices and through precedents set centuries before. This research contributes to our understanding of nuns in Japan’s early modern period and will participate in and shape debates on the roles of women in patriarchal religious hierarchies.

Neurosurgical Needs and Assets Assessment of Public Hospitals in Uganda: An Eevaluation of Mulago Hospital to Inform Neurosurgical Program Planning at Mbarara

Background: Since 2007, there has been an ongoing collaboration between Duke University and Mulago National Referral Hospital (NRH) in Kampala, Uganda to increase surgical capacity. This program is prepared to expand to other sites within Uganda to improve neurosurgery outside of Kampala as well. This study assessed the existing progress at Mulago NRH and the neurosurgical needs and assets at two potential sites for expansion. Methods: Three public hospitals were visited to assess needs and assets: Mulago NRH, Mbarara Regional Referral Hospital (RRH), and Gulu RRH. At each site, a surgical capacity tool was administered and healthcare workers were interviewed about perceived needs and assets. A total of 39 interviews were conducted between the three sites. Thematic analysis of the interviews was conducted to identify the reported needs and assets at each hospital. Results: Some improvements are needed to the Duke-Mulago Collaboration model prior to expansion; minor changes to the neurosurgery residency program as well as the method for supply donation and training provided during neurosurgery camps need to examined. Neurosurgery can be implemented at Mbarara RRH currently but the hospital needs a biomedical equipment technician on staff immediately. Gulu RRH is not well positioned for Neurosurgery until there is a CT Scanner somewhere in the Northern Region of Uganda or at the hospital. Conclusions: Neurosurgery is already present in Uganda on a small scale and needs rapid expansion to meet patient needs. This progression is possible with prudent allocation of resources on strategic equipment purchases, human resources including clinical staff and biomedical staff, and changes to the supply chain management system.

Bidding For Parking: The Impact of University Affiliation on Predicting Bid Values in Dutch Auctions of On-Campus Parking Permits

Parking is often underpriced and expanding its capacity is expensive; universities need a better way of reducing congestion outside of building costly parking garages. Demand based pricing mechanisms, such as auctions, offer a possible solution to the problem by promising to reduce parking at peak times. However, faculty, students, and staff at universities have systematically different parking needs, leading to different parking valuations. In this study, I determine the impact university affiliation has on predicting bid values cast in three Dutch Auctions of on-campus parking permits sold at Chapman University in Fall 2010. Using clustering techniques crosschecked with university demographic information to detect affiliation groups, I ran a log-linear regression, finding that university affiliation had a larger effect on bid amount than on lot location and fraction of auction duration. Generally, faculty were predicted to have higher bids whereas students were predicted to have lower bids.

The Pratt Pouch Provides a Three-Fold Access Increase to Antiretroviral Medication for Births outside Health Facilities in Southern Zambia.

INTRODUCTION: Modern day antiretroviral therapy allows HIV+ pregnant women to lower the likelihood of viral transmission to their infants before, during, and after birth from 20-45% to less than 5%. In developing countries, where non-facility births may outnumber facility births, infant access to safe antiretroviral medication during the critical first three days after birth is often limited. A single-dose, polyethylene pouch ("Pratt Pouch") addresses this challenge by allowing the medication to be distributed to mothers during antenatal care. METHODS: The Pratt Pouch was introduced as part of a one year clinical feasibility study in two districts in Southern Province, Zambia. Participating nurses, community health workers, and pharmacists were trained before implementation. Success in achieving improved antiretroviral medication access was assessed via pre intervention and post intervention survey responses by HIV+ mothers. RESULTS: Access to medication for HIV-exposed infants born outside of a health facility increased from 35% (17/51) before the introduction of the pouch to 94% (15/16) after (p<0.05). A non-significant increase in homebirth rates from 33% (pre intervention cohort) to 50% (post intervention cohort) was observed (p>0.05). Results remained below the national average homebirth rate of 52%. Users reported minimal spillage and a high level of satisfaction with the Pratt Pouch. CONCLUSION: The Pratt Pouch enhances access to infant antiretroviral medication in a rural, non-facility birth setting. Wide scale implementation could have a substantial global impact on HIV transmission rates from mother to child.

The Diary of Mary McKeon, an Irish American Domestic Servant in Nineteenth Century America

What did young, single, unaccompanied Irish women experience when immigrating to the United States in the late nineteenth century? In this final project, I will explore primary and secondary sources that address their experiences, focusing on a diary written in 1883 by a young Irish domestic servant working in New Haven, Connecticut. Mary McKeon, a sixteen-year-old girl from County Leitrim, Ireland, recorded her experiences as a domestic servant for two different families, as well as her own personal thoughts. Mary wrote down her personal experiences, providing a glimpse of what her life was like both inside and outside of her employer’s home. Though much of my research will show that many young women like Mary would be subjected to prejudice and discrimination due to their lack of understanding middle-class American values, which would give rise to the “Bridget” stereotype of a brutish, ill-mannered and incompetent domestic servant, not all Irish women experienced that discrimination and prejudice. Mary is one example of a domestic servant that was treated kindly by her employers and her story documents a more positive and supportive environment for this newly arrived young, single immigrant. Her diary also reveals her to be a young woman who worked to improve her language skills and her situation. And, through her diary, we get a glimpse of her strategies for ensuring an active social life, including access to courtship and marriage. By analyzing Mary’s diary and sharing my results in this final project, I hope to provide a more comprehensive view into the lives of these young women.