Re-imagining Yerevan in the post-Soviet era: Urban symbolism and narratives of the nation in the landscape of Armenia's capital

The urban landscape of Yerevan has experienced tremendous changes since the collapse of the Soviet Union and Armenia’s independence in 1991. Domestic and foreign investments have poured into Yerevan’s building sector, converting many downtown neighborhoods into sleek modern districts that now cater to foreign investors, tourists, and the newly rich Armenian nationals. Large portions of the city’s green parks and other public spaces have been commercialized for private and exclusive use, creating zones that are accessible only to the affluent. In this dissertation I explore the rapidly transforming landscape of Yerevan and its connections to the development of contemporary Armenian national identity. This research was guided by principles of ethnographic inquiry, and I employed diverse methods, including document and archival research, structured and semi-structured interviews and content analysis of news media. I also used geographic information systems (GIS) and satellite images to represent and visualize the stark transformations of spaces in Yerevan. Informed by and contributing to three literatures—on the relationship between landscape and identity formation, on the construction of national identity, and on Soviet and post-Soviet cities—this dissertation investigates how messages about contemporary Armenian national identity are being expressed via the transforming landscape of Armenia’s national capital. In it I describe the ways in which abrupt transformations have resulted in the physical and symbolic eviction of residents, introducing fierce public debates about belonging and exclusion within the changing urban context. I demonstrate that the new additions to Yerevan’s landscape and the symbolic messages that they carry are hotly contested by many long-time residents, who struggle for inclusion of their opinions and interests in the process of re-imagining their national capital. This dissertation illustrates many of the trends that are apparent in post-Soviet and post-Socialist space, while at the same time exposing some unique characteristics of the Armenian case.

An integrated multi-agent framework for optimizing time, cost and environmental impact of construction processes

Environmentally conscious construction has received a significant amount of research attention during the last decades. Even though construction literature is rich in studies that emphasize the importance of environmental impact during the construction phase, most of the previous studies failed to combine environmental analysis with other project performance criteria in construction. This is mainly because most of the studies have overlooked the multi-objective nature of construction projects. In order to achieve environmentally conscious construction, multi-objectives and their relationships need to be successfully analyzed in the complex construction environment. The complex construction system is composed of changing project conditions that have an impact on the relationship between time, cost and environmental impact (TCEI) of construction operations. Yet, this impact is still unknown by construction professionals. Studying this impact is vital to fulfill multiple project objectives and achieve environmentally conscious construction. This research proposes an analytical framework to analyze the impact of changing project conditions on the relationship of TCEI. This study includes green house gas (GHG) emissions as an environmental impact category. The methodology utilizes multi-agent systems, multi-objective optimization, analytical network process, and system dynamics tools to study the relationships of TCEI and support decision-making under the influence of project conditions. Life cycle assessment (LCA) is applied to the evaluation of environmental impact in terms of GHG. The mixed method approach allowed for the collection and analysis of qualitative and quantitative data. Structured interviews of professionals in the highway construction field were conducted to gain their perspectives in decision-making under the influence of certain project conditions, while the quantitative data were collected from the Florida Department of Transportation (FDOT) for highway resurfacing projects. The data collected were used to test the framework. The framework yielded statistically significant results in simulating project conditions and optimizing TCEI. The results showed that the change in project conditions had a significant impact on the TCEI optimal solutions. The correlation between TCEI suggested that they affected each other positively, but in different strengths. The findings of the study will assist contractors to visualize the impact of their decision on the relationship of TCEI.

A novel 3-D segmentation algorithm for anatomic liver and tumor volume calculations for liver cancer treatment planning

Three-Dimensional (3-D) imaging is vital in computer-assisted surgical planning including minimal invasive surgery, targeted drug delivery, and tumor resection. Selective Internal Radiation Therapy (SIRT) is a liver directed radiation therapy for the treatment of liver cancer. Accurate calculation of anatomical liver and tumor volumes are essential for the determination of the tumor to normal liver ratio and for the calculation of the dose of Y-90 microspheres that will result in high concentration of the radiation in the tumor region as compared to nearby healthy tissue. Present manual techniques for segmentation of the liver from Computed Tomography (CT) tend to be tedious and greatly dependent on the skill of the technician/doctor performing the task. ^ This dissertation presents the development and implementation of a fully integrated algorithm for 3-D liver and tumor segmentation from tri-phase CT that yield highly accurate estimations of the respective volumes of the liver and tumor(s). The algorithm as designed requires minimal human intervention without compromising the accuracy of the segmentation results. Embedded within this algorithm is an effective method for extracting blood vessels that feed the tumor(s) in order to plan effectively the appropriate treatment. ^ Segmentation of the liver led to an accuracy in excess of 95% in estimating liver volumes in 20 datasets in comparison to the manual gold standard volumes. In a similar comparison, tumor segmentation exhibited an accuracy of 86% in estimating tumor(s) volume(s). Qualitative results of the blood vessel segmentation algorithm demonstrated the effectiveness of the algorithm in extracting and rendering the vasculature structure of the liver. Results of the parallel computing process, using a single workstation, showed a 78% gain. Also, statistical analysis carried out to determine if the manual initialization has any impact on the accuracy showed user initialization independence in the results. ^ The dissertation thus provides a complete 3-D solution towards liver cancer treatment planning with the opportunity to extract, visualize and quantify the needed statistics for liver cancer treatment. Since SIRT requires highly accurate calculation of the liver and tumor volumes, this new method provides an effective and computationally efficient process required of such challenging clinical requirements.^

A Customer's Expectation and Perception of Hotel Service Quality in Cyprus

In recent years, hotels in Cyprus have encountered difficult economic times due to increasing customer demands and strong internal industry development competition. The hospitality industry’s main concern globally is to serve its customer S needs and desires, most of which are addressed through personal services. Hence, the hotel businesses that are able to provide quality services to its ever-demanding customers in a warm and efficient manner are those businesses which will be more likely to obtain a long term competitive advantage over their rivals. Ironically, the quality of services frequently cannot fully appreciated until something goes wrong, and then, the poor quality of services can have long lasting lingering effects on the customer base and, hence, often is translated into a loss of business. Nevertheless, since the issue of delivery of hospitality services always involves people, this issue must center around the management of the human resource factor, and in particular, on the way which interacts with itself and with guests, as service encounters. In the eyes of guests, hospitality businesses will be viewed successful or failure, depending on [he cumulative impact of the service encounters they have experienced on a personal level. Finally, since hotels are offering intangible and perishable personal service encounters, managing these services must be a paramount concern of any hotel business. As a preliminary exercise, visualize when you have last visited a hotel, or a restaurant, and then, ask yourself these questions: What did you feel about the quality of the experience? Was it a memorable one, which you would recommend it to others, or there were certain things, which could have made the difference? Thus, the way personalized services are provided can make the deference in attracting arid retaining long-term customers

A model for continuous measurement of drilled shaft diameter during construction

Non-Destructive Testing (NDT) of deep foundations has become an integral part of the industry's standard manufacturing processes. It is not unusual for the evaluation of the integrity of the concrete to include the measurement of ultrasonic wave speeds. Numerous methods have been proposed that use the propagation speed of ultrasonic waves to check the integrity of concrete for drilled shaft foundations. All such methods evaluate the integrity of the concrete inside the cage and between the access tubes. The integrity of the concrete outside the cage remains to be considered to determine the location of the border between the concrete and the soil in order to obtain the diameter of the drilled shaft. It is also economic to devise a methodology to obtain the diameter of the drilled shaft using the Cross-Hole Sonic Logging system (CSL). Performing such a methodology using the CSL and following the CSL tests is performed and used to check the integrity of the inside concrete, thus allowing the determination of the drilled shaft diameter without having to set up another NDT device.^ This proposed new method is based on the installation of galvanized tubes outside the shaft across from each inside tube, and performing the CSL test between the inside and outside tubes. From the performed experimental work a model is developed to evaluate the relationship between the thickness of concrete and the ultrasonic wave properties using signal processing. The experimental results show that there is a direct correlation between concrete thicknesses outside the cage and maximum amplitude of the received signal obtained from frequency domain data. This study demonstrates how this new method to measuring the diameter of drilled shafts during construction using a NDT method overcomes the limitations of currently-used methods. ^ In the other part of study, a new method is proposed to visualize and quantify the extent and location of the defects. It is based on a color change in the frequency amplitude of the signal recorded by the receiver probe in the location of defects and it is called Frequency Tomography Analysis (FTA). Time-domain data is transferred to frequency-domain data of the signals propagated between tubes using Fast Fourier Transform (FFT). Then, distribution of the FTA will be evaluated. This method is employed after CSL has determined the high probability of an anomaly in a given area and is applied to improve location accuracy and to further characterize the feature. The technique has a very good resolution and clarifies the exact depth location of any void or defect through the length of the drilled shaft for the voids inside the cage. ^ The last part of study also evaluates the effect of voids inside and outside the reinforcement cage and corrosion in the longitudinal bars on the strength and axial load capacity of drilled shafts. The objective is to quantify the extent of loss in axial strength and stiffness of drilled shafts due to presence of different types of symmetric voids and corrosion throughout their lengths.^

The Application of Fluorescent Nanocrystals to Study the Distribution of Neuropeptides in the Aedes Aegypti Mosquito

Semiconductor nanocrystals, also known as quantum dots (QDs), have been used in studies involving mice and human tissues, but never before in research on insects. We used QDs to study the distribution of two neuropeptides in the Aedes aegypti mosquito, the vector of both dengue and yellow fever. These neuropeptides play a significant role in the production of juvenile hormone, a hormone that controls biting behavior, metamorphosis, and reproduction throughout the life of the mosquito. The two neuropeptides allatostatin-C (AS-C) and allatotropin (AT) function as inhibitory (AS-C) and stimulatory (AT) regulators of juvenile hormone synthesis in the corpus allatum gland. In other insects, they also affect heart rate, gut movement, and nutrient uptake. Conjugating these neuropeptides to quantum dots via a streptavidinlbiotin link, we were able to expose the mosquito corpus allatum and abdomen to allatostatin-C and allatotropin and then to visualize their distribution under UV light using confocal and compound light microscopy. Histological sections of the whole mosquito, incubations of tissues with conjugates (in vitro), and microinjections of conjugates into the mosquito (in vivo) were performed. The results showed that quantum dots can be used to detect neuropeptide distribution in the mosquito. The more we understand about these neuropeptides and juvenile hormone, the more we can contribute to stopping the spread of infectious diseases, such as dengue and yellow fever.

Expression of Bf/C2 Gene(S) in the Japanese Medaka Fish

Complement factor B and C2 are two central serine proteases of the alternative and classical complement pathways, respectively, that serve as the catalytic subunits of the C3 convertase. Research has been completed using a female Japanese medaka fish, (Oryzias latipes), and other teleost and elasmobrach species in order to isolate eDNA clones and perform linkage analysis of the Bf/C2 gene(s). To further analyze the evolution of the complement system in teleosts, different tissues than the ones from previous studies of medaka fish were analyzed for the constitutive gene expression of factor B and C2. Bf/C2 sequences were amplified by reverse transcription-polymerase chain reaction with primers corresponding to the common amino acid sequences shared by mammalian Bf and C2. Agarose gel electrophoresis was used to visualize sample bands and to calculate the concentration of gene expression of the Bf/C2 gene(s) in each tissue. All five tissue types, kidney, liver, muscle, testis, and spleen from a male medaka fish demonstrated Bf/C2 gene(s) expression, confirming that the messages of Bf/C2 gene(s) are distributed throughout the medaka fish. Tissues of the spleen, liver, and kidney contained the highest concentrations of expression of Bf/C2 gene( s ), while tissues of the muscle and testis contained the lowest concentrations. This research also determined that RT-PCR allowed for more sensitive analysis of gene expression than other molecular biology techniques such as Northern blotting analysis.

Diatom-based Models for Inferring Hydrology and Periphyton Abundance in a Subtropical Karstic Wetland: Implications for Ecosystem-Scale Bioassessment

We developed diatom-based prediction models of hydrology and periphyton abundance to inform assessment tools for a hydrologically managed wetland. Because hydrology is an important driver of ecosystem change, hydrologic alterations by restoration efforts could modify biological responses, such as periphyton characteristics. In karstic wetlands, diatoms are particularly important components of mat-forming calcareous periphyton assemblages that both respond and contribute to the structural organization and function of the periphyton matrix. We examined the distribution of diatoms across the Florida Everglades landscape and found hydroperiod and periphyton biovolume were strongly correlated with assemblage composition. We present species optima and tolerances for hydroperiod and periphyton biovolume, for use in interpreting the directionality of change in these important variables. Predictions of these variables were mapped to visualize landscape-scale spatial patterns in a dominant driver of change in this ecosystem (hydroperiod) and an ecosystem-level response metric of hydrologic change (periphyton biovolume). Specific diatom assemblages inhabiting periphyton mats of differing abundance can be used to infer past conditions and inform management decisions based on how assemblages are changing. This study captures diatom responses to wide gradients of hydrology and periphyton characteristics to inform ecosystem-scale bioassessment efforts in a large wetland.

Design and Development of Geographical Information System (GIS) Map for Nuclear Waste Streams

A nuclear waste stream is the complete flow of waste material from origin to treatment facility to final disposal. The objective of this study was to design and develop a Geographic Information Systems (GIS) module using Google Application Programming Interface (API) for better visualization of nuclear waste streams that will identify and display various nuclear waste stream parameters. A proper display of parameters would enable managers at Department of Energy waste sites to visualize information for proper planning of waste transport. The study also developed an algorithm using quadratic Bézier curve to make the map more understandable and usable. Microsoft Visual Studio 2012 and Microsoft SQL Server 2012 were used for the implementation of the project. The study has shown that the combination of several technologies can successfully provide dynamic mapping functionality. Future work should explore various Google Maps API functionalities to further enhance the visualization of nuclear waste streams.

A responsabilidade enunciativa em artigos científicos de pesquisadores iniciantes e contribuições para o ensino da produção textual na graduação

This thesis investigates materialization strategies of non-assumption of enunciation responsibility and inscription of an authorial voice in scientific articles produced by initial researchers in Linguistics. The specific focus lays on identify, describe and interpret: i) linguistics marks that assign enunciation responsibility; ii) the positions taken by the first speaker-enunciator (L1/E1) in relation to points of view (PoV) imputed to second enunciators (e2); and iii) the linguistic marks that assign the formulation of themselves' PoV. As a practical deployment, it is proposed to discuss how to teach taking into account text discursive strategies regarding to enunciation responsibility and also authorship in academic and scientific texts. Our research corpus is formed by eight scientific essays and they were selected in a renamed Linguistics scientific magazine which is high evaluated by Qualis/CAPES (Brazil Science Agency). The methodology follows the assumptions of a qualitative research, and an it has such an interpretative basis, even though it takes support in a quantitative approach, too. Theoretically, we based this research on Textual Analysis of Speech and linguistics theories about linguistic enunciation area. The results show two kinds of movements in PoV management: imputation and responsibility. In imputation contexts, the most recursive linguistic marks were reported speech, indirect speech, reported speech with “that”, modalization in reported speech (in enunciation with “according to”, “in agreement with”, “for”), beyond that we see certain points of non-coincidences of speech, specifically the non-coincidence of the speech itself. The way those linguistic marks occur in the text point out three kinds of enunciation positions that are assumed by L1/E1 in relation to PoV of e2: agreement, disagreement and a pseudo neutrality. It was clearly recursive the imputation followed by agreement (explicit or not), this perspective puts other’s voices to defend a speech assumed like own authorship. In speech responsibility contexts, we observed such a formulation of inner PoV that results from theoretical findings undertaken by novice researchers (revealing how he/she interpreted concepts of the theory) or arising from their research data, allowing them to express with more autonomy and without reporting to speeches from e2. Based on those data, we can say that, in text by initial researchers, the authorship is strongly built upon PoV and also dependent from others' words (theory and the scholars quoted there), taking into account that many contexts in which we can observe agreement position, PoV formulations with words taken from e2 and assumed as own words by syntactic integration, the comments about what the other says, the absence of explanations and additions, as well as a data analysis that could show agreement with the theory used to support the work. These results allow us to visualize how initial researcher dialogs with the theoretical enunciation sources he or she takes as support and how he/she displays the status of a subject doing a research and positioning himself/herself as a researcher/author in the scientific field. In assuming the reported speech, when quoting, as a resource that allows the enunciation responsibility and also when doing evidence to the positions of speaker-enunciator in relation do reported PoV, this suggests to a textual-discursive treatment of quoting in academic and scientific text, in a context of teaching that gives attention to the development of communication skills of initial researcher and that can contribute to insert and interact students in the scientific field.

A responsabilidade enunciativa em artigos científicos de pesquisadores iniciantes e contribuições para o ensino da produção textual na graduação

This thesis investigates materialization strategies of non-assumption of enunciation responsibility and inscription of an authorial voice in scientific articles produced by initial researchers in Linguistics. The specific focus lays on identify, describe and interpret: i) linguistics marks that assign enunciation responsibility; ii) the positions taken by the first speaker-enunciator (L1/E1) in relation to points of view (PoV) imputed to second enunciators (e2); and iii) the linguistic marks that assign the formulation of themselves' PoV. As a practical deployment, it is proposed to discuss how to teach taking into account text discursive strategies regarding to enunciation responsibility and also authorship in academic and scientific texts. Our research corpus is formed by eight scientific essays and they were selected in a renamed Linguistics scientific magazine which is high evaluated by Qualis/CAPES (Brazil Science Agency). The methodology follows the assumptions of a qualitative research, and an it has such an interpretative basis, even though it takes support in a quantitative approach, too. Theoretically, we based this research on Textual Analysis of Speech and linguistics theories about linguistic enunciation area. The results show two kinds of movements in PoV management: imputation and responsibility. In imputation contexts, the most recursive linguistic marks were reported speech, indirect speech, reported speech with “that”, modalization in reported speech (in enunciation with “according to”, “in agreement with”, “for”), beyond that we see certain points of non-coincidences of speech, specifically the non-coincidence of the speech itself. The way those linguistic marks occur in the text point out three kinds of enunciation positions that are assumed by L1/E1 in relation to PoV of e2: agreement, disagreement and a pseudo neutrality. It was clearly recursive the imputation followed by agreement (explicit or not), this perspective puts other’s voices to defend a speech assumed like own authorship. In speech responsibility contexts, we observed such a formulation of inner PoV that results from theoretical findings undertaken by novice researchers (revealing how he/she interpreted concepts of the theory) or arising from their research data, allowing them to express with more autonomy and without reporting to speeches from e2. Based on those data, we can say that, in text by initial researchers, the authorship is strongly built upon PoV and also dependent from others' words (theory and the scholars quoted there), taking into account that many contexts in which we can observe agreement position, PoV formulations with words taken from e2 and assumed as own words by syntactic integration, the comments about what the other says, the absence of explanations and additions, as well as a data analysis that could show agreement with the theory used to support the work. These results allow us to visualize how initial researcher dialogs with the theoretical enunciation sources he or she takes as support and how he/she displays the status of a subject doing a research and positioning himself/herself as a researcher/author in the scientific field. In assuming the reported speech, when quoting, as a resource that allows the enunciation responsibility and also when doing evidence to the positions of speaker-enunciator in relation do reported PoV, this suggests to a textual-discursive treatment of quoting in academic and scientific text, in a context of teaching that gives attention to the development of communication skills of initial researcher and that can contribute to insert and interact students in the scientific field.

Geographic Visualization in Archaeology

Archaeologists are often considered frontrunners in employing spatial approaches within the social sciences and humanities, including geospatial technologies such as geographic information systems (GIS) that are now routinely used in archaeology. Since the late 1980s, GIS has mainly been used to support data collection and management as well as spatial analysis and modeling. While fruitful, these efforts have arguably neglected the potential contribution of advanced visualization methods to the generation of broader archaeological knowledge. This paper reviews the use of GIS in archaeology from a geographic visualization (geovisual) perspective and examines how these methods can broaden the scope of archaeological research in an era of more user-friendly cyber-infrastructures. Like most computational databases, GIS do not easily support temporal data. This limitation is particularly problematic in archaeology because processes and events are best understood in space and time. To deal with such shortcomings in existing tools, archaeologists often end up having to reduce the diversity and complexity of archaeological phenomena. Recent developments in geographic visualization begin to address some of these issues, and are pertinent in the globalized world as archaeologists amass vast new bodies of geo-referenced information and work towards integrating them with traditional archaeological data. Greater effort in developing geovisualization and geovisual analytics appropriate for archaeological data can create opportunities to visualize, navigate and assess different sources of information within the larger archaeological community, thus enhancing possibilities for collaborative research and new forms of critical inquiry.

At surface behaviour of juvenile and female southern elephant seals from King George Island from expeditions JUB1996 and JUB1997

Between December 1996 and February 1997, weaned pups and postmoult female southern elephant seals (Mirounga leonina) were fitted with satellite transmitters at King George Island (South Shetlands). Of the nine adult females tracked for more than two months, three stayed in a localized area between the South Shetlands and the South Orkneys. The other six females travelled southwest along the coast of the Antarctic Peninsula up to the Bellingshausen Sea. Two of them then moved far northeast and hauled out on South Georgia in October. One female was last located north of the South Shetlands in March 1998. In total, eight females were again sighted on King George Island and six of the transmitters removed. The tracks of the weaners contrasted with those of the adults. In January, five juveniles left King George Island for the Pacific sector ranging about four weeks in the open sea west of the De Gerlache Seamounts. Three of them returned to the tip of the Antarctic Peninsula in June, of which one was last located on the Patagonian Shelf in November 1997. A computer animation was developed to visualize the animal movements in relation to the extent and concentration of sea ice. The juveniles avoided sea ice while the adults did not. The latter displayed behavioural differences in using the pack ice habitat during winter. Some females adjusted their movement patterns to the pulsating sea ice fringe in far-distant foraging areas while others ranged in closed pack ice of up to 100 %. The feeding grounds of adult female elephant seals are more closely associated with the pack ice zone than previously assumed.

Biochemical and Structural Studies on PrfA, the Transcriptional Regulator of Virulence in Listeria monocytogenes

Abstract

Listeria monocytogenes is a gram-positive soil saprophytic bacterium that is capable of causing fatal infection in humans. The main virulence regulator PrfA, a member of the Crp/FNR family of transcriptional regulators, activates the expression of essential proteins required for host cell invasion and cell-to-cell spread. The mechanism of PrfA activation and the identity of its small molecule coactivator have remained a mystery for more than 20 years, but it is hypothesized that PrfA shares mechanistic similarity to the E. coli cAMP binding protein, Crp. Crp activates gene expression by binding cAMP, increasing the DNA binding affinity of the protein and causing a significant DNA bend that facilitates RNA polymerase binding and downstream gene activation. Our data suggests PrfA activates virulence protein expression through a mechanism distinct from the canonical Crp activation mechanism that involves a combination of cysteine residue reduction and glutathione (GSH) binding.

Listeria lacking glutathione synthase (ΔgshF) is avirulent in mice; however virulence is rescued when the bacterium expresses the constitutively active PrfA mutant G145S. Interestingly, Listeria expressing a PrfA mutant in which its four cysteines are mutated to alanine (Quad PrfA), demonstrate a 30-fold decrease in virulence. The Quad and ΔgshF double mutant strains are avirulent. DNA-binding affinity, measured through fluorescence polarization assays, indicate reduction of the cysteine side chains is sufficient to allow PrfA to binds its physiological promoters Phly and PactA with low nanomolar affinity. Oxidized PrfA binds the promoters poorly.

Unexpectedly, Quad also binds promoter DNA with nanomolar affinity, suggesting that the cysteines play a role in transcription efficiency in addition to DNA binding. Both PrfA and Quad bind GSH at physiologically relevant and comparable affinities, however GSH did not affect DNA binding in either case. Thermal denaturation assays suggest that Quad and wild-type PrfA differ structurally upon binding GSH, which supports the in vivo difference in infection between the regulator and its mutant.

Structures of PrfA in complex with cognate DNA, determined through X-ray crystallography, further support the disparity between PrfA and Crp activation mechanisms as two structures of reduced PrfA bound to Phly (PrfA-Phly30 and PrfA-Phly24) suggest the DNA adopts a less bent DNA conformation when compared to Crp-cAMP- DNA. The structure of Quad-Phly30 confirms the DNA-binding data as the protein-DNA complex adopts the same overall conformation as PrfA-Phly.

From these results, we hypothesize a two-step activation mechanism wherein PrfA, oxidized upon cell entry and unable to bind DNA, is reduced upon its intracellular release and binds DNA, causing a slight bend in the promoter and small increase in transcription of PrfA-regulated genes. The structures of PrfA-Phly30 and PrfA-Phly24 likely visualize this intermediate complex. Increasing concentrations of GSH shift the protein to a (PrfA-GSH)-DNA complex which is fully active transcriptionally and is hypothesized to resemble closely the transcriptionally active structure of the cAMP-(Crp)-DNA complex. Thermal denaturation results suggest Quad PrfA is deficient in this second step, which explains the decrease in virulence and implicates the cysteine residues as critical for transcription efficiency. Further structural and biochemical studies are on-going to clarify this mechanism of activation.

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.