Evaluating and Improving Reverse Engineering Tools

Developers tend to leave some important steps and actions (e.g. properly designing the system's architecture, code review and testing) out of the software development process, and use risky practices (e.g. the copy-paste technique) so that the software can be released as fast as possible. However, these practices may turn out to be critical from the viewpoint of maintainability of the software system. In such cases, a cost-effective solution might be to re-engineer the system. Re-engineering consists of two stages, namely reverse-engineering information from the current system and, based on this information, forward-engineering the system to a new form. In this way, successful re-engineering significantly depends on the reverse engineering phase. Therefore, it is vital to guarantee correctness, and to improve the results of the reverse engineering step. Otherwise, the re-engineering of the software system could fail due to the bad results of reverse engineering. The above issues motivated us to develop a method which extends and improves one of our reverse engineering tools, and to develop benchmarks and to perform experiments on evaluating and comparing reverse engineering tools

Utilization Of Fermentation And Purification Strategies To Enhance The Yield Of BmR1 Antigen

Brugia Rapid merupakan UJian diagnostik komersial yang digunakan untuk mengesan jangkitan terhadap Brugia malayi dan Brugia timori (filariasis brugia). Brugia Rapid TM is an established diagnostic test that is commercially available. to detect infection to both B. malayi and B. timori infections (brugian filariasis).

Particle Swarm Optimization

Particle swarm optimization (PSO) is a population based stochastic optimization technique influenced by the social behavior of bird flocking or fish schooling.PSO shares many similarities with evolutionary computation techniques such as Genetic Algorithms (GA). The system is initialized with a population of random solutions and searches for optima by updating generations. However, unlike GA, PSO has no evolution operators such as crossover and mutation. In PSO, the potential solutions, called particles, fly through the problem space by following the current optimum particles. This book represents the contributions of the top researchers in this field and will serve as a valuable tool for professionals in this interdisciplinary field

Harnessing Knowledge to Ensure Food Safety: Opportunities to Improve the Nation\u27s Food Safety Information Infrastructure

Those working in the food industry face an abundance of information generated by diverse institutions and individuals. Ensuring the safety of food is critically important to the public\u27s health and a challenge for policy-makers seeking to enhance the government\u27s role in this arena. Although the food industry has an inherent duty to make food safe, the effectiveness of what they do is highly dependent on the quality of the information they receive on potential hazards and good practices. In this context, the Robert Wood Johnson Foundation funded a project under the auspices of the Food Safety Research Consortium to examine and make recommendations for improving the food safety information infrastructure (FSII). Through this initiative, a collection of food safety experts met for a series of workshops to discuss information needs around food safety. Key Findings: Establish a national FSII policy and program. Build a database for tracking research and data collection. Provide broader public access to journal articles and to complete data from research projects. Create a networking Web site. In this report, whose recommendations are based on those workshop discussions, the authors explore the constraints facing today\u27s FSII. These include the diversity of the information currently available, the plethora of information sources, and the numerous agencies and actors involved in generating data

Automated Low-Cost Malaria Detection System in Thin Blood Slide Images Using Mobile Phones

Malaria, a deadly disease which according to the World Health Organisation (WHO) is responsible for the fatal illness in 200 million people around the world in 2010, is diagnosed using peripheral blood examination. The work undertaken in this research programme aims to develop an automated malaria parasite-detection system, using microscopic-image processing, that can be incorporated onto mobile phones. In this research study, the main objective is to achieve the performance equal to or better than the manual microscopy, which is the gold standard in malaria diagnosis, in order to produce a reliable automated diagnostic platform without expert intervention, for the effective treatment and eradication of the deadly disease. The work contributed to the field of mathematical morphology by proposing a novel method called the Annular Ring Ratio transform for blood component identification. It has also proposed an automated White Blood Cell and Red Blood Cell differentiation algorithm, which when combined with ARR transform method, has wide applications not only for malaria diagnosis but also for many blood related analysis involving microscopic examination. The research has undertaken investigations on infected cell identification which aids in the calculation of parasitemia, the measure of infection. In addition, an automated diagnostic tool to detect the sexual stage (gametocytes) of the species P.falciparum for post-treatment malaria diagnosis was developed. Furthermore, a parallel investigation was carried out on automated malaria diagnosis on fluorescent thin blood films and a WBC and infected cell differentiation algorithm was proposed. Finally, a mobile phone application based on the morphological image processing algorithms proposed in this thesis was developed. A complete malaria diagnostic unit using the mobile phones attached to a portable microscope was set up which has enormous potential not only for malaria diagnosis but also for the blood parasitological field where advancement in medical diagnostics using cellular smart phone technology is widely acknowledged

Biochemical characterisation of trans-sialidases from Trypanosoma congolense

The work compiled here aimed at biochemically characterising trans-sialidase (TS) genes from Trypanosoma congolense, the most prevalent causative agent of animal African trypanosomiasis, also called nagana. Using published partial TS sequences as starting queries, database at the Welcome Trust Sanger Institute (WTSI) was queried and TS1 genes identified. This is a multi-copy gene group comprising 11 members. Members were cloned and recombinant protein expressed in fibroblasts and purified proteins assayed for enzyme activities (Publication 1/Chapter 1). All TS1 variants were found to be active TS enzymes, transferring Sia from donor fetuin to the lactose acceptor substrate and could resialylate asialofetuin up to 50%. Use of synthetic substrates revealed poor specific activities. Further searches on WTSI using TconTS1 gene variants as queries revealed 3 other TS genes, TconTS2, TconTS3 and TconTS4, all conserving the critical amino acids required in activity. A further 3 distantly related genes, this latter group is presumed inactive due to lack of conservation of critical amino acids (Publication 2/Chapter 3). TS/sialidase ratios confirmed the former to be active trans-sialidases but with differing specific activities. A mouse monoclonal antibody raised from native proteins probably containing other TconTS and not only TconTS1 reacted with both TconTS1 and TconTS2, two of the proteins with the highest specific activities. Incidentally, the epitope for the antibody is localised on the lectin domain (LD) in both enzymes. Phylogenetic analysis using the LD grouped TconTS1 and TconTS2 together while the use of catalytic domain (CD) grouped them separately. This suggests a possible role for the LD in enzyme activities and hence pathology of nagana. To gain knowledge on the role of TS in pathogenesis of nagana, blood glycoconjugates were employed as substrates and activities of TS gene characterised (Manuscript/Chapter 4). All TconTS proteins transferred Sia from serum-bound glycoconjugates to lactose. In absence of lactose, TconTS1 and TconTS2 released free Sia from the serum-glycoconjugates, possibly explaining the high amounts of free Sia observed in blood and serum of animals suffering nagana. TconTS3 showed an unidentified product peak in presence of serum-bound Sia and lactose, while 3 unidentified signals probably representing serum-glycoconjugates inherent in serum were altered by TconTS2. Collectively, the above indicate the possibility of acceptor and donor preferences and show that expressing more than one TS gene at a time could be beneficial to the parasite. Since TS genes are expressed in two different hosts systems; the Glossina insect vector and the mammalian hosts with different pH systems, pH optima for the enzymes was studied. TconTS2 exhibited a wide pH optima that would make it active in both host systems

Biochemical characterisation of trans-sialidases from Trypanosoma congolense

The work compiled here aimed at biochemically characterising trans-sialidase (TS) genes from Trypanosoma congolense, the most prevalent causative agent of animal African trypanosomiasis, also called nagana. Using published partial TS sequences as starting queries, database at the Welcome Trust Sanger Institute (WTSI) was queried and TS1 genes identified. This is a multi-copy gene group comprising 11 members. Members were cloned and recombinant protein expressed in fibroblasts and purified proteins assayed for enzyme activities (Publication 1/Chapter 1). All TS1 variants were found to be active TS enzymes, transferring Sia from donor fetuin to the lactose acceptor substrate and could resialylate asialofetuin up to 50%. Use of synthetic substrates revealed poor specific activities. Further searches on WTSI using TconTS1 gene variants as queries revealed 3 other TS genes, TconTS2, TconTS3 and TconTS4, all conserving the critical amino acids required in activity. A further 3 distantly related genes, this latter group is presumed inactive due to lack of conservation of critical amino acids (Publication 2/Chapter 3). TS/sialidase ratios confirmed the former to be active trans-sialidases but with differing specific activities. A mouse monoclonal antibody raised from native proteins probably containing other TconTS and not only TconTS1 reacted with both TconTS1 and TconTS2, two of the proteins with the highest specific activities. Incidentally, the epitope for the antibody is localised on the lectin domain (LD) in both enzymes. Phylogenetic analysis using the LD grouped TconTS1 and TconTS2 together while the use of catalytic domain (CD) grouped them separately. This suggests a possible role for the LD in enzyme activities and hence pathology of nagana. To gain knowledge on the role of TS in pathogenesis of nagana, blood glycoconjugates were employed as substrates and activities of TS gene characterised (Manuscript/Chapter 4). All TconTS proteins transferred Sia from serum-bound glycoconjugates to lactose. In absence of lactose, TconTS1 and TconTS2 released free Sia from the serum-glycoconjugates, possibly explaining the high amounts of free Sia observed in blood and serum of animals suffering nagana. TconTS3 showed an unidentified product peak in presence of serum-bound Sia and lactose, while 3 unidentified signals probably representing serum-glycoconjugates inherent in serum were altered by TconTS2. Collectively, the above indicate the possibility of acceptor and donor preferences and show that expressing more than one TS gene at a time could be beneficial to the parasite. Since TS genes are expressed in two different hosts systems; the Glossina insect vector and the mammalian hosts with different pH systems, pH optima for the enzymes was studied. TconTS2 exhibited a wide pH optima that would make it active in both host systems

High Throughput Screening to Identify, Develop and Analyse Inositol Phosphorylceramide Synthase Inhibitors as Novel Antileishmanials

Leishmaniasis and Human African trypanosomiasis are tropical diseases caused by kinetoplastid parasites that together affect over 12 million people, with an estimated 400 million at risk worldwide. Both are potentially fatal, yet the current treatments available are expensive and many have toxic side effects. Emerging resistance to many current drugs is also a concern; novel therapeutic agents are therefore urgently required. One novel target for drug discovery previously identified in the group is sphingolipid synthesis. Sphingolipids are ubiquitous biomolecules found in nature and are both structural membrane components and signalling molecules. Inositol phosphorylceramide synthase (IPCS) is an essential enzyme involved in kinetoplastid sphingolipid synthesis that has no mammalian equivalent, making it an attractive drug target. Whilst specific inhibitors of the fungal IPCS are known, they are unsuitable as pharmaceuticals. The overall aim of this project was to identify novel inhibitors of this enzyme that could be further investigated as potential antikinetoplastid drugs. The first stage involved the construction of Saccharomyces cerevisiae strains as expression systems of the kinetoplastid IPCS enzymes. The strain complemented with the Leishmania major enzyme was subsequently used in the development and optimisation of a robust high throughput screening (HTS)-compatible assay. This was used to screen the 1.8 million compound library stored at the GlaxoSmithKline research site in Tres Cantos in what is believed to be the largest screening project undertaken by an academic group to date. 500 compounds were identified as selective inhibitors of the L. major IPCS enzyme, and 216 of these were selected for additional investigation. Further compound triage was achieved by means of a screening process involving multiple in cellulo assays against both Leishmania parasites and mammalian cells. Six compounds demonstrating both high potency and selectivity were identified. Following additional biochemical testing, the two most potent compounds were found to share a common benzazepane chemical structure. Investigation of analogues of these compounds permitted the identification of preliminary structure-activity relationship data, which identified several possible avenues for further investigation

Microsystems for parasite enrichment

The aim of this project was to develop a lab-on-chip platform upon which activities in engineering and parasitology can be brought together to create new low cost diagnostic technologies for Human African Trypanosomiasis, a disease also known as sleeping sickness, for use in resource-poor environments like Sub-Saharan Africa. Filtration and separation of particles is essential for many biochemical and analytical assays. This work describes the development of novel techniques to enhance the separation/enrichment of parasites from whole blood. Techniques like chemotaxis, inertial microfluidics and density based separation were used to achieve the separation/enrichment. This thesis describes (i) development of an assay to confirm the chemotaxis of Trypanosoma brucei towards higher concentrations of glucose, (ii) designing, fabrication and use of inertial microfluidic device for continuous sorting of trypanosomes from blood cells, (iii) density based separation of trypanosomes from whole blood using a two phase Dextran-Ficoll system, and (iv) density based enrichment of trypanosomes using surface acoustic waves. This work represents an important step towards improving the detection of trypanosomes in blood for which microscopy is still considered to be the gold standard