Syndemic health disparities and resilience processes related to HIV transmission risk among African American/Black men in south Florida

Rates of HIV infection continue to climb among minority populations and men who have sex with men (MSM), with African American/Black MSM being especially impacted. Numerous studies have found HIV transmission risk to be associated with many health and social disparities resulting from larger environmental and structural forces. Using anthropological and social environment-based theories of resilience that focus on individual agency and larger social and environmental structures, this dissertation employed a mixed methods design to investigate resilience processes among African American/Black MSM.^ Quantitative analyses compared African American/Black (N=108) and Caucasian/White (N=250) MSM who participated in a previously conducted randomized controlled trial (RCT) of sexual and substance use risk reduction interventions. At RCT study entry, using past 90 day recall periods, there were no differences in unprotected sex frequency, however African American/Black MSM reported higher frequencies of days high (P<0.000), and drugs and sex used in combination (P<0.000), and substance dependence (P<0.000) and lower levels of social support (P<0.024) compared to Caucasian/White MSM. At 12- month follow-up, multi-level statistical models found that African American/Black MSM reduced their frequencies of days high and unprotected sex at greater rates than Caucasian/White MSM (P<0.001).^ Qualitative data collected among a sub-sample of African American/Black MSM from the RCT (N=21) described the men's experiences of living with multiple health and social disparities and the importance of RCT study assessments in facilitating reductions in risk behaviors. A cross-case analysis showed different resilience processes undertaken by men who experienced low socioeconomic status, little family support, and homophobia (N=16) compared to those who did not (N=5).^ The dissertation concludes that resilience processes to HIV transmission risk and related health and social disparities among African American/Black MSM varies and are dependent on specific social environmental factors, including social relationships, structural homophobia, and access to social, economic, and cultural capital. Men define for themselves what it means to be resilient within their social environment. These conclusions suggest that both individual and structural-level resilience-based HIV prevention interventions are needed.^

Pulsed parabolic equation model of acoustic transmission (PPEMAT)

Underwater sound is very important in the field of oceanography where it is used for remote sensing in much the same way that radar is used in atmospheric studies. One way to mathematically model sound propagation in the ocean is by using the parabolic-equation method, a technique that allows range dependent environmental parameters. More importantly, this method can model sound transmission where the source emits either a pure tone or a short pulse of sound. Based on the parabolic approximation method and using the split-step Fourier algorithm, a computer model for underwater sound propagation was designed and implemented. This computer model differs from previous models in its use of the interactive mode, structured programming, modular design, and state-of-the-art graphics displays. In addition, the model maximizes the efficiency of computer time through synchronization of loosely coupled dual processors and the design of a restart capability. Since the model is designed for adaptability and for users with limited computer skills, it is anticipated that it will have many applications in the scientific community.

A novel lossless compression technique for text data

The focus of this thesis is placed on text data compression based on the fundamental coding scheme referred to as the American Standard Code for Information Interchange or ASCII. The research objective is the development of software algorithms that result in significant compression of text data. Past and current compression techniques have been thoroughly reviewed to ensure proper contrast between the compression results of the proposed technique with those of existing ones. The research problem is based on the need to achieve higher compression of text files in order to save valuable memory space and increase the transmission rate of these text files. It was deemed necessary that the compression algorithm to be developed would have to be effective even for small files and be able to contend with uncommon words as they are dynamically included in the dictionary once they are encountered. A critical design aspect of this compression technique is its compatibility to existing compression techniques. In other words, the developed algorithm can be used in conjunction with existing techniques to yield even higher compression ratios. This thesis demonstrates such capabilities and such outcomes, and the research objective of achieving higher compression ratio is attained.

Scaling multimode fibre IM/DD transmission capacity through spatial-spectral multiplexing

Data centre connections can greatly benefit from parallel transmission channels on one multimode fibre (MMF). Shortwave wavelength division multiplexing (SWDM) achieves parallel transmission through spectral multiplexing. Furthermore, MMFs offer a spatial dimension that should be exploited to increase parallel transmission, albeit in a cost-effective way. In this paper, it is shown that SWDM and spatial multiplexing can be combined in intensity modulation and direct detection MMF transmission systems that use selective offset excitation and mode-selective spatial filtering.

56 Gb/s multi-band CAP for data center interconnects up to an 80 km SMF

We present the first (to the best of our knowledge) experimental demonstration of a 56 Gb/s multi-band carrierless amplitude and phase modulation (CAP) signal transmission over an 80-km single-mode fiber link with zero overhead pre-FEC signal recovery and enhanced timing jitter tolerance for optical data center interconnects.

Capacity estimates for optical transmission based on the nonlinear Fourier transform

What is the maximum rate at which information can be transmitted error-free in fibre-optic communication systems? For linear channels, this was established in classic works of Nyquist and Shannon. However, despite the immense practical importance of fibre-optic communications providing for >99% of global data traffic, the channel capacity of optical links remains unknown due to the complexity introduced by fibre nonlinearity. Recently, there has been a flurry of studies examining an expected cap that nonlinearity puts on the information-carrying capacity of fibre-optic systems. Mastering the nonlinear channels requires paradigm shift from current modulation, coding and transmission techniques originally developed for linear communication systems. Here we demonstrate that using the integrability of the master model and the nonlinear Fourier transform, the lower bound on the capacity per symbol can be estimated as 10.7 bits per symbol with 500 GHz bandwidth over 2,000 km.

Quality of transmission estimation in WDM and elastic optical networks accounting for space-spectrum dependencies

We develop a framework for estimating the quality of transmission (QoT) of a new lightpath before it is established, as well as for calculating the expected degradation it will cause to existing lightpaths. The framework correlates the QoT metrics of established lightpaths, which are readily available from coherent optical receivers that can be extended to serve as optical performance monitors. Past similar studies used only space (routing) information and thus neglected spectrum, while they focused on oldgeneration noncoherent networks. The proposed framework accounts for correlation in both the space and spectrum domains and can be applied to both fixed-grid wavelength division multiplexing (WDM) and elastic optical networks. It is based on a graph transformation that exposes and models the interference between spectrum-neighboring channels. Our results indicate that our QoT estimates are very close to the actual performance data, that is, to having perfect knowledge of the physical layer. The proposed estimation framework is shown to provide up to 4 × 10-2 lower pre-forward error correction bit error ratio (BER) compared to theworst-case interference scenario,which overestimates the BER. The higher accuracy can be harvested when lightpaths are provisioned with low margins; our results showed up to 47% reduction in required regenerators, a substantial savings in equipment cost.

Data to Decision in a Dynamic Ocean: Robust Species Distribution Models and Spatial Decision Frameworks

Human use of the oceans is increasingly in conflict with conservation of endangered species. Methods for managing the spatial and temporal placement of industries such as military, fishing, transportation and offshore energy, have historically been post hoc; i.e. the time and place of human activity is often already determined before assessment of environmental impacts. In this dissertation, I build robust species distribution models in two case study areas, US Atlantic (Best et al. 2012) and British Columbia (Best et al. 2015), predicting presence and abundance respectively, from scientific surveys. These models are then applied to novel decision frameworks for preemptively suggesting optimal placement of human activities in space and time to minimize ecological impacts: siting for offshore wind energy development, and routing ships to minimize risk of striking whales. Both decision frameworks relate the tradeoff between conservation risk and industry profit with synchronized variable and map views as online spatial decision support systems.

For siting offshore wind energy development (OWED) in the U.S. Atlantic (chapter 4), bird density maps are combined across species with weights of OWED sensitivity to collision and displacement and 10 km2 sites are compared against OWED profitability based on average annual wind speed at 90m hub heights and distance to transmission grid. A spatial decision support system enables toggling between the map and tradeoff plot views by site. A selected site can be inspected for sensitivity to a cetaceans throughout the year, so as to capture months of the year which minimize episodic impacts of pre-operational activities such as seismic airgun surveying and pile driving.

Routing ships to avoid whale strikes (chapter 5) can be similarly viewed as a tradeoff, but is a different problem spatially. A cumulative cost surface is generated from density surface maps and conservation status of cetaceans, before applying as a resistance surface to calculate least-cost routes between start and end locations, i.e. ports and entrance locations to study areas. Varying a multiplier to the cost surface enables calculation of multiple routes with different costs to conservation of cetaceans versus cost to transportation industry, measured as distance. Similar to the siting chapter, a spatial decisions support system enables toggling between the map and tradeoff plot view of proposed routes. The user can also input arbitrary start and end locations to calculate the tradeoff on the fly.

Essential to the input of these decision frameworks are distributions of the species. The two preceding chapters comprise species distribution models from two case study areas, U.S. Atlantic (chapter 2) and British Columbia (chapter 3), predicting presence and density, respectively. Although density is preferred to estimate potential biological removal, per Marine Mammal Protection Act requirements in the U.S., all the necessary parameters, especially distance and angle of observation, are less readily available across publicly mined datasets.

In the case of predicting cetacean presence in the U.S. Atlantic (chapter 2), I extracted datasets from the online OBIS-SEAMAP geo-database, and integrated scientific surveys conducted by ship (n=36) and aircraft (n=16), weighting a Generalized Additive Model by minutes surveyed within space-time grid cells to harmonize effort between the two survey platforms. For each of 16 cetacean species guilds, I predicted the probability of occurrence from static environmental variables (water depth, distance to shore, distance to continental shelf break) and time-varying conditions (monthly sea-surface temperature). To generate maps of presence vs. absence, Receiver Operator Characteristic (ROC) curves were used to define the optimal threshold that minimizes false positive and false negative error rates. I integrated model outputs, including tables (species in guilds, input surveys) and plots (fit of environmental variables, ROC curve), into an online spatial decision support system, allowing for easy navigation of models by taxon, region, season, and data provider.

For predicting cetacean density within the inner waters of British Columbia (chapter 3), I calculated density from systematic, line-transect marine mammal surveys over multiple years and seasons (summer 2004, 2005, 2008, and spring/autumn 2007) conducted by Raincoast Conservation Foundation. Abundance estimates were calculated using two different methods: Conventional Distance Sampling (CDS) and Density Surface Modelling (DSM). CDS generates a single density estimate for each stratum, whereas DSM explicitly models spatial variation and offers potential for greater precision by incorporating environmental predictors. Although DSM yields a more relevant product for the purposes of marine spatial planning, CDS has proven to be useful in cases where there are fewer observations available for seasonal and inter-annual comparison, particularly for the scarcely observed elephant seal. Abundance estimates are provided on a stratum-specific basis. Steller sea lions and harbour seals are further differentiated by ‘hauled out’ and ‘in water’. This analysis updates previous estimates (Williams & Thomas 2007) by including additional years of effort, providing greater spatial precision with the DSM method over CDS, novel reporting for spring and autumn seasons (rather than summer alone), and providing new abundance estimates for Steller sea lion and northern elephant seal. In addition to providing a baseline of marine mammal abundance and distribution, against which future changes can be compared, this information offers the opportunity to assess the risks posed to marine mammals by existing and emerging threats, such as fisheries bycatch, ship strikes, and increased oil spill and ocean noise issues associated with increases of container ship and oil tanker traffic in British Columbia’s continental shelf waters.

Starting with marine animal observations at specific coordinates and times, I combine these data with environmental data, often satellite derived, to produce seascape predictions generalizable in space and time. These habitat-based models enable prediction of encounter rates and, in the case of density surface models, abundance that can then be applied to management scenarios. Specific human activities, OWED and shipping, are then compared within a tradeoff decision support framework, enabling interchangeable map and tradeoff plot views. These products make complex processes transparent for gaming conservation, industry and stakeholders towards optimal marine spatial management, fundamental to the tenets of marine spatial planning, ecosystem-based management and dynamic ocean management.

Syndemic Health Disparities and Resilience Processes Related to HIV Transmission Risk among African American/Black Men in South Florida

Rates of HIV infection continue to climb among minority populations and men who have sex with men (MSM), with African American/Black MSM being especially impacted. Numerous studies have found HIV transmission risk to be associated with many health and social disparities resulting from larger environmental and structural forces. Using anthropological and social environment-based theories of resilience that focus on individual agency and larger social and environmental structures, this dissertation employed a mixed methods design to investigate resilience processes among African American/Black MSM. Quantitative analyses compared African American/Black (N=108) and Caucasian/White (N=250) MSM who participated in a previously conducted randomized controlled trial (RCT) of sexual and substance use risk reduction interventions. At RCT study entry, using past 90 day recall periods, there were no differences in unprotected sex frequency, however African American/Black MSM reported higher frequencies of days high (P Qualitative data collected among a sub-sample of African American/Black MSM from the RCT (N=21) described the men’s experiences of living with multiple health and social disparities and the importance of RCT study assessments in facilitating reductions in risk behaviors. A cross-case analysis showed different resilience processes undertaken by men who experienced low socioeconomic status, little family support, and homophobia (N=16) compared to those who did not (N=5). The dissertation concludes that resilience processes to HIV transmission risk and related health and social disparities among African American/Black MSM varies and are dependent on specific social environmental factors, including social relationships, structural homophobia, and access to social, economic, and cultural capital. Men define for themselves what it means to be resilient within their social environment. These conclusions suggest that both individual and structural-level resilience-based HIV prevention interventions are needed.

Workforce Patterns and the Prevention of Mother-to-Child Transmission of HIV Option B Cascade in Côte d'Ivoire

Thesis (Master's)--University of Washington, 2016-08

Assessing the Association between Receipt of Antimalarial Drugs and Adverse Pregnancy Outcomes using Pooled Data

Thesis (Ph.D.)--University of Washington, 2016-08

Multi-Disciplinary Applications of Oceanographic Geophysical Data Collection

Thesis (Ph.D.)--University of Washington, 2016-08

Application of meta-analytical probabilistic approach for reliability benefits reflective optimal transmission costing – the case of India

In the deregulated Power markets it is necessary to have a appropriate Transmission Pricing methodology that also takes into account “Congestion and Reliability”, in order to ensure an economically viable, equitable, and congestion free power transfer capability, with high reliability and security. This thesis presents results of research conducted on the development of a Decision Making Framework (DMF) of concepts and data analytic and modelling methods for the Reliability benefits Reflective Optimal “cost evaluation for the calculation of Transmission Cost” for composite power systems, using probabilistic methods. The methodology within the DMF devised and reported in this thesis, utilises a full AC Newton-Raphson load flow and a Monte-Carlo approach to determine, Reliability Indices which are then used for the proposed Meta-Analytical Probabilistic Approach (MAPA) for the evaluation and calculation of the Reliability benefit Reflective Optimal Transmission Cost (ROTC), of a transmission system. This DMF includes methods for transmission line embedded cost allocation among transmission transactions, accounting for line capacity-use as well as congestion costing that can be used for pricing using application of Power Transfer Distribution Factor (PTDF) as well as Bialek’s method to determine a methodology which consists of a series of methods and procedures as explained in detail in the thesis for the proposed MAPA for ROTC. The MAPA utilises the Bus Data, Generator Data, Line Data, Reliability Data and Customer Damage Function (CDF) Data for the evaluation of Congestion, Transmission and Reliability costing studies using proposed application of PTDF and other established/proven methods which are then compared, analysed and selected according to the area/state requirements and then integrated to develop ROTC. Case studies involving standard 7-Bus, IEEE 30-Bus and 146-Bus Indian utility test systems are conducted and reported throughout in the relevant sections of the dissertation. There are close correlation between results obtained through proposed application of PTDF method with the Bialek’s and different MW-Mile methods. The novel contributions of this research work are: firstly the application of PTDF method developed for determination of Transmission and Congestion costing, which are further compared with other proved methods. The viability of developed method is explained in the methodology, discussion and conclusion chapters. Secondly the development of comprehensive DMF which helps the decision makers to analyse and decide the selection of a costing approaches according to their requirements. As in the DMF all the costing approaches have been integrated to achieve ROTC. Thirdly the composite methodology for calculating ROTC has been formed into suits of algorithms and MATLAB programs for each part of the DMF, which are further described in the methodology section. Finally the dissertation concludes with suggestions for Future work.

An IP capable data link layer protocol for narrow band half-duplex packet data radio networks

The wide adaptation of Internet Protocol (IP) as de facto protocol for most communication networks has established a need for developing IP capable data link layer protocol solutions for Machine to machine (M2M) and Internet of Things (IoT) networks. However, the wireless networks used for M2M and IoT applications usually lack the resources commonly associated with modern wireless communication networks. The existing IP capable data link layer solutions for wireless IoT networks provide the necessary overhead minimising and frame optimising features, but are often built to be compatible only with IPv6 and specific radio platforms. The objective of this thesis is to design IPv4 compatible data link layer for Netcontrol Oy's narrow band half-duplex packet data radio system. Based on extensive literature research, system modelling and solution concept testing, this thesis proposes the usage of tunslip protocol as the basis for the system data link layer protocol development. In addition to the functionality of tunslip, this thesis discusses the additional network, routing, compression, security and collision avoidance changes required to be made to the radio platform in order for it to be IP compatible while still being able to maintain the point-to-multipoint and multi-hop network characteristics. The data link layer design consists of the radio application, dynamic Maximum Transmission Unit (MTU) optimisation daemon and the tunslip interface. The proposed design uses tunslip for creating an IP capable data link protocol interface. The radio application receives data from tunslip and compresses the packets and uses the IP addressing information for radio network addressing and routing before forwarding the message to radio network. The dynamic MTU size optimisation daemon controls the tunslip interface maximum MTU size according to the link quality assessment calculated from the radio network diagnostic data received from the radio application. For determining the usability of tunslip as the basis for data link layer protocol, testing of the tunslip interface is conducted with both IEEE 802.15.4 radios and packet data radios. The test cases measure the radio network usability for User Datagram Protocol (UDP) based applications without applying any header or content compression. The test results for the packet data radios reveal that the typical success rate for packet reception through a single-hop link is above 99% with a round-trip-delay of 0.315s for 63B packets.

Transmission electron tomography: quality assessment and enhancement for three-dimensional imaging of nanostructures

Nanotechnology has revolutionised humanity's capability in building microscopic systems by manipulating materials on a molecular and atomic scale. Nan-osystems are becoming increasingly smaller and more complex from the chemical perspective which increases the demand for microscopic characterisation techniques. Among others, transmission electron microscopy (TEM) is an indispensable tool that is increasingly used to study the structures of nanosystems down to the molecular and atomic scale. However, despite the effectivity of this tool, it can only provide 2-dimensional projection (shadow) images of the 3D structure, leaving the 3-dimensional information hidden which can lead to incomplete or erroneous characterization. One very promising inspection method is Electron Tomography (ET), which is rapidly becoming an important tool to explore the 3D nano-world. ET provides (sub-)nanometer resolution in all three dimensions of the sample under investigation. However, the fidelity of the ET tomogram that is achieved by current ET reconstruction procedures remains a major challenge. This thesis addresses the assessment and advancement of electron tomographic methods to enable high-fidelity three-dimensional investigations. A quality assessment investigation was conducted to provide a quality quantitative analysis of the main established ET reconstruction algorithms and to study the influence of the experimental conditions on the quality of the reconstructed ET tomogram. Regular shaped nanoparticles were used as a ground-truth for this study. It is concluded that the fidelity of the post-reconstruction quantitative analysis and segmentation is limited, mainly by the fidelity of the reconstructed ET tomogram. This motivates the development of an improved tomographic reconstruction process. In this thesis, a novel ET method was proposed, named dictionary learning electron tomography (DLET). DLET is based on the recent mathematical theorem of compressed sensing (CS) which employs the sparsity of ET tomograms to enable accurate reconstruction from undersampled (S)TEM tilt series. DLET learns the sparsifying transform (dictionary) in an adaptive way and reconstructs the tomogram simultaneously from highly undersampled tilt series. In this method, the sparsity is applied on overlapping image patches favouring local structures. Furthermore, the dictionary is adapted to the specific tomogram instance, thereby favouring better sparsity and consequently higher quality reconstructions. The reconstruction algorithm is based on an alternating procedure that learns the sparsifying dictionary and employs it to remove artifacts and noise in one step, and then restores the tomogram data in the other step. Simulation and real ET experiments of several morphologies are performed with a variety of setups. Reconstruction results validate its efficiency in both noiseless and noisy cases and show that it yields an improved reconstruction quality with fast convergence. The proposed method enables the recovery of high-fidelity information without the need to worry about what sparsifying transform to select or whether the images used strictly follow the pre-conditions of a certain transform (e.g. strictly piecewise constant for Total Variation minimisation). This can also avoid artifacts that can be introduced by specific sparsifying transforms (e.g. the staircase artifacts the may result when using Total Variation minimisation). Moreover, this thesis shows how reliable elementally sensitive tomography using EELS is possible with the aid of both appropriate use of Dual electron energy loss spectroscopy (DualEELS) and the DLET compressed sensing algorithm to make the best use of the limited data volume and signal to noise inherent in core-loss electron energy loss spectroscopy (EELS) from nanoparticles of an industrially important material. Taken together, the results presented in this thesis demonstrates how high-fidelity ET reconstructions can be achieved using a compressed sensing approach.