HIV-1 Neutralisation and Other Aspects of the Envelope Glycoprotein

The absence of an effective humoral response contributes to the failure of controlling HIV-1 infection. Methods to elicit a potent neutralising antibody response is still underway and this thesis explores three aspects that can affect neutralisation. The pseudovirus-based assay is now recommended as the standard assay for assessing neutralising antibody response. However, recent studies have reported discrepancies between pseduovirus-based assay and conventional PBMCs or other cell-based assays. The first aim is to investigate possible causes behind this difference. The effect of virus producer cell type and virus platform (pseudovirus vs. replication-competent) was examined and both parameters can affect neutralisation. The second aim was to study the the neutralising antibody response in patients with primary HIV-1 infection. A panel of 6 patients were selected from the SPARTAC clinical trial. Pseudoviruses were constructed with the env gene derived from patient samples at week 0 (baseline) and week 52. The evolutionary history and the neutralisation sensitivity of these primary isolates against a panel of broadly neutralising antibodies and heterologous and autologous sera were studied. The week 52 isolates escaped from antisera neutralisation rapidly, most likely at the glycan level. In addition, viral load was found to correlate directly with intra-patient viral diversity and evolutionary divergence over time. Finally, the effect of Nef on HIV-1 neutralisation was investigated. Recent reports suggest that Nef modifies HIV-1 envelope glycoprotein. Hence, neutralising antibody response might also be modified in the absence of Nef. When subjected to neutralisation with a panel of monoclonal antibodies, the Nef-deleted (ΔNef) HIV-1 was more readily neutralised than the wild-type (WT) virus. Immunoprecipitation assays showed that neutralising antibodies can capture ΔNef virus more efficiently than WT virus. However, the enhanced neutralisation of ΔNef virus was neither due to CD4-down regulation nor difference in glycosylation

Mergers Simulation and Demand Analysis for the U.S. Carbonated Soft Drink Industry

Replaced with revised version of paper on 09/29/09. Former title: Mergers, Price Competition for the U.S. Carbonated Soft Drink Industrydistance metrics, demand, merger simulation, Agribusiness, Industrial Organization, Marketing, L13, C14,

On aggregation bias in structural demand models

Consumer demand analysis attracts considerable attention. It remains an open question, however, whether estimating demand with aggregate data is reliable when disaggregate store-level data is given. Demand models may produce biased results when applied to data aggregated across stores with different pricing strategies. In this study, the graphical model is used to investigate the following question: Do we find the same structure when we fit causal models on sub-groupings of stores, as we find when we fit models on aggregate data from all stores?causal analysis, aggregation bias, Demand and Price Analysis, C01,

Speech-based metadata generation for web map search

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial TechnologiesMetadata is indispensable for data discoverability and interoperability. Most datasets utilize automatic techniques to create metadata; nevertheless, metadata creation still requires manual interventions and editions, yet manually metadata creation is a tedious task. The study proposes a prototype that introduces speech recognition in the metadata creation process. Users can generate content by speaking. Afterward, the prototype transforms it into metadata with JSON-LD format, a popular metadata format and utilized by mainstream search engines. A user study was conducted to understand the impact of speech-based interaction on user performance and user satisfaction. The result showed no signi cant performance di erence between speech-based and typebased by the e ciency, slip rate, and di culty rating evaluation. In the user experience evaluation, participants consider the type-based metadata creation is pragmatic, and speech-based metadata creation is hedonic. It suggests that the mix-mode can complement mutually with the advantages of each and optimize the user experience

Sub-graph based joint sparse graph for sparse code multiple access systems

Sparse code multiple access (SCMA) is a promising air interface candidate technique for next generation mobile networks, especially for massive machine type communications (mMTC). In this paper, we design a LDPC coded SCMA detector by combining the sparse graphs of LDPC and SCMA into one joint sparse graph (JSG). In our proposed scheme, SCMA sparse graph (SSG) defined by small size indicator matrix is utilized to construct the JSG, which is termed as sub-graph based joint sparse graph of SCMA (SG-JSG-SCMA). In this paper, we first study the binary-LDPC (B-LDPC) coded SGJSG- SCMA system. To combine the SCMA variable node (SVN) and LDPC variable node (LVN) into one joint variable node (JVN), a non-binary LDPC (NB-LDPC) coded SG-JSG-SCMA is also proposed. Furthermore, to reduce the complexity of NBLDPC coded SG-JSG-SCMA, a joint trellis representation (JTR) is introduced to represent the search space of NB-LDPC coded SG-JSG-SCMA. Based on JTR, a low complexity joint trellis based detection and decoding (JTDD) algorithm is proposed to reduce the computational complexity of NB-LDPC coded SGJSG- SCMA system. According to the simulation results, SG-JSGSCMA brings significant performance improvement compare to the conventional receiver using the disjoint approach, and it can also outperform a Turbo-structured receiver with comparable complexity. Moreover, the joint approach also has advantages in terms of processing latency compare to the Turbo approaches

Controlled Heterogeneous Nucleation and Growth of Germanium Quantum Dots on Nanopatterned Silicon Dioxide and Silicon Nitride Substrates

Controlled heterogeneous nucleation and growth of Ge quantum dots (QDs) are demonstrated on SiO_2/Si_3N_4 substrates by means of a novel fabrication process of thermally oxidizing nanopatterned SiGe layers. The otherwise random self-assembly process for QDs is shown to be strongly influenced by the nanopatterning in determining both the location and size of the QDs. Ostwald ripening processes are observed under further annealing at the oxidation temperature. Both nanopattern oxidation and Ostwald ripening offer additional mechanisms for lithography for controlling the size and placement of the QDs