Phylogenetic analysis of within -host serially-sampled viral data

The primary goal of this dissertation is the study of patterns of viral evolution inferred from serially-sampled sequence data, i.e., sequence data obtained from strains isolated at consecutive time points from a single patient or host. RNA viral populations have an extremely high genetic variability, largely due to their astronomical population sizes within host systems, high replication rate, and short generation time. It is this aspect of their evolution that demands special attention and a different approach when studying the evolutionary relationships of serially-sampled sequence data. New methods that analyze serially-sampled data were developed shortly after a groundbreaking HIV-1 study of several patients from which viruses were isolated at recurring intervals over a period of 10 or more years. These methods assume a tree-like evolutionary model, while many RNA viruses have the capacity to exchange genetic material with one another using a process called recombination. ^ A genealogy involving recombination is best described by a network structure. A more general approach was implemented in a new computational tool, Sliding MinPD, one that is mindful of the sampling times of the input sequences and that reconstructs the viral evolutionary relationships in the form of a network structure with implicit representations of recombination events. The underlying network organization reveals unique patterns of viral evolution and could help explain the emergence of disease-associated mutants and drug-resistant strains, with implications for patient prognosis and treatment strategies. In order to comprehensively test the developed methods and to carry out comparison studies with other methods, synthetic data sets are critical. Therefore, appropriate sequence generators were also developed to simulate the evolution of serially-sampled recombinant viruses, new and more through evaluation criteria for recombination detection methods were established, and three major comparison studies were performed. The newly developed tools were also applied to "real" HIV-1 sequence data and it was shown that the results represented within an evolutionary network structure can be interpreted in biologically meaningful ways. ^

Selecting POS Systems for Table Service Restaurants

A point-of-sale system can enhance decision making, operational control, guest service, and revenues. However, not all POS systems offer the same features and potential for profit improvement. The author discusses those factors which are critical to POS system selection for table service restaurants

Synthesis and Biological Evaluation of Novel Folic Acid Receptor-Targeted, β-Cyclodextrin-Based Drug Complexes for Cancer Treatment

Drug targeting is an active area of research and nano-scaled drug delivery systems hold tremendous potential for the treatment of neoplasms. In this study, a novel cyclodextrin (CD)-based nanoparticle drug delivery system has been assembled and characterized for the therapy of folate receptor-positive [FR(+)] cancer. Water-soluble folic acid (FA)-conjugated CD carriers (FACDs) were successfully synthesized and their structures were confirmed by 1D/2D nuclear magnetic resonance (NMR), matrix-assisted laser desorption ionization time-of-flight mass spectrometer (MALDI-TOF-MS), high performance liquid chromatography (HPLC), Fourier transform infrared spectroscopy (FTIR), and circular dichroism. Drug complexes of adamatane (Ada) and cytotoxic doxorubicin (Dox) with FACD were readily obtained by mixed solvent precipitation. The average size of FACD-Ada-Dox was 1.5–2.5 nm. The host-guest association constant Ka was 1,639 M−1 as determined by induced circular dichroism and the hydrophilicity of the FACDs was greatly enhanced compared to unmodified CD. Cellular uptake and FR binding competitive experiments demonstrated an efficient and preferentially targeted delivery of Dox into FR-positive tumor cells and a sustained drug release profile was seen in vitro. The delivery of Dox into FR(+) cancer cells via endocytosis was observed by confocal microscopy and drug uptake of the targeted nanoparticles was 8-fold greater than that of non-targeted drug complexes. Our docking results suggest that FA, FACD and FACD-Ada-Dox could bind human hedgehog interacting protein that contains a FR domain. Mouse cardiomyocytes as well as fibroblast treated with FACD-Ada-Dox had significantly lower levels of reactive oxygen species, with increased content of glutathione and glutathione peroxidase activity, indicating a reduced potential for Dox-induced cardiotoxicity. These results indicate that the targeted drug complex possesses high drug association and sustained drug release properties with good biocompatibility and physiological stability. The novel FA-conjugated β-CD based drug complex might be promising as an anti-tumor treatment for FR(+) cancer.

Importance-Performance Analysis of Guest Entertainment Technology Amenities in the Lodging Industry

An assessment of how hotel guests view in-room entertainment-technology amenities was conducted to compare the importance of these technologies to how they performed. In-room entertainment technology continues to evolve in the hotel industry. However, given the multitude of entertainment products available in the marketplace today, hoteliers have little understanding of guests’ expectations and of which in-room entertainment-technology amenities will drive guest satisfaction and increase loyalty to the hotel brand. Given that technology is integral to a hotel stay, this study seeks to evaluate the importance and performance of in-room entertainment-technology amenities. Findings indicate that free-to-guest television (FTG TV) and high-speed Internet access were the two most important inroom entertainment-technology amenities when it comes to the selection of a hotel for both leisure and business travelers. The Importance/Satisfaction Matrix presented in the current study showed that many of the in-room entertainment-technology amenities are currently a low priority for guests. Keywords: importance-performance analysis, hotel, in-room entertainment technologies

From Clerk and Cashier to Guest Service Agent

In their study - From Clerk and Cashier to Guest Service Agent - by Nancy J. Allin, Director of Quality Assurance and Training and Kelly Halpine, Assistant Director of Quality Assurance and Training, The Waldorf-Astoria, New York, the authors state at the outset: “The Waldorf-Astoria has taken the positions of registration clerk and cashier and combined them to provide excellent guest service and efficient systems operation. The authors tell how and why the combination works. That thesis statement defines the article, and puts it squarely in the crosshairs of the service category. Allin and Halpine use their positions at the Waldorf-Astoria in New York City to frame their observations “The allocation of staff hours has been a challenge to many front office managers who try their hardest to schedule for the norm but provide excellent, efficient service throughout the peaks,” Allin and Halpine allude. “…the decision [to combine the positions of registration clerk and cashier] was driven by a desire to improve guest service where its impact is most obvious, at the front desk. Cross-trained employees speed the check-in and check-out process by performing both functions, as the traffic at the desk dictates,” the authors say. Making such a move has resulted in positive benefits for both the guests and the hotel. “Benefits to the hotel, in addition to those brought to bear by increased guest satisfaction, include greater flexibility in weekly scheduling and in granting vacations while maintaining adequate staffing at the desk,” say Allin and Halpine . “Another expected outcome, net payroll savings, should also be realized as a consequence of the ability to schedule more efficiently.” The authors point to communication as the key to designing a successful combination such as this, with the least amount of service disruption. They bullet-point what that communication should entail. Issues of seniority, wage and salary rates, organizational charting, filing, scheduling, possible probationary periods, position titles, and physical layouts are all discussed. “It is critical that each of the management issues be addressed and resolved before any training is begun,” Allin and Halpine suggest. “Unresolved issues project confusion and lack of conviction to line employees and the result is frustration and a lack of commitment to the combination process,” they push the thought Allin and Halpine insist: “Once begun, training must be ongoing and consistent.” In the practical sense, the authors provide that authorizing overtime is helpful in accomplishing training. “Training must address the fact that employees will be faced with guest situations which are new to them, for example: an employee previously functioning as a cashier will be faced with walking guests. Specific exercises should be included to address these needs,” say the authors.

Fuzzy Modeling and Control Based Virtual Machine Resource Management

Virtual machines (VMs) are powerful platforms for building agile datacenters and emerging cloud systems. However, resource management for a VM-based system is still a challenging task. First, the complexity of application workloads as well as the interference among competing workloads makes it difficult to understand their VMs’ resource demands for meeting their Quality of Service (QoS) targets; Second, the dynamics in the applications and system makes it also difficult to maintain the desired QoS target while the environment changes; Third, the transparency of virtualization presents a hurdle for guest-layer application and host-layer VM scheduler to cooperate and improve application QoS and system efficiency. This dissertation proposes to address the above challenges through fuzzy modeling and control theory based VM resource management. First, a fuzzy-logic-based nonlinear modeling approach is proposed to accurately capture a VM’s complex demands of multiple types of resources automatically online based on the observed workload and resource usages. Second, to enable fast adaption for resource management, the fuzzy modeling approach is integrated with a predictive-control-based controller to form a new Fuzzy Modeling Predictive Control (FMPC) approach which can quickly track the applications’ QoS targets and optimize the resource allocations under dynamic changes in the system. Finally, to address the limitations of black-box-based resource management solutions, a cross-layer optimization approach is proposed to enable cooperation between a VM’s host and guest layers and further improve the application QoS and resource usage efficiency. The above proposed approaches are prototyped and evaluated on a Xen-based virtualized system and evaluated with representative benchmarks including TPC-H, RUBiS, and TerraFly. The results demonstrate that the fuzzy-modeling-based approach improves the accuracy in resource prediction by up to 31.4% compared to conventional regression approaches. The FMPC approach substantially outperforms the traditional linear-model-based predictive control approach in meeting application QoS targets for an oversubscribed system. It is able to manage dynamic VM resource allocations and migrations for over 100 concurrent VMs across multiple hosts with good efficiency. Finally, the cross-layer optimization approach further improves the performance of a virtualized application by up to 40% when the resources are contended by dynamic workloads.