Discordant responses to antiretroviral treatment: prevalence, risk factors and associated mortality in Rwanda

Mexico AIDS Conference 200

Use of traveling salesman problem solvers in the construction of genetic linkage maps

Includes bibliographical references.2015 Fall.Construction of genetic linkage maps is an important tool for Biology. Researchers use a variety of laboratory techniques to extract genetic marker data from an experimental cross of a species of interest and then use these data to group the markers into chromosomes, and then construct maps of the locations of the markers within the chromosomes. This in turn allows them to determine which sections of the chromosomes are responsible for variation in agricultural, medical or other traits of interest. The current methods of constructing genetic linkage maps are tedious and time-consuming. This thesis presents a method of utilizing the Hamiltonian path problem (HPP) to solve the problem of genetic linkage mapping. Since solvers already exist for the traveling salesman problem (LKH and Concorde), by casting the linkage mapping problem as a HPP we can use these solvers to efficiently find the solution. To do this, the recombination frequencies between genetic markers are treated as internode weights and the TSP solution gives the lowest-cost path through the markers. By adding a dummy marker with zero weight to all other markers, the TSP solution is made equivalent to a HPP. The primary difficulty in constructing a linkage map is the fact that all data sets are noisy: errors in laboratory techniques create uncertainty in the relationships between genetic markers, so a straightforward HPP solution is not sufficient. This thesis describes a method of using the HPP to separate the raw data into clusters so that the researcher can be sure that the chromosomes are well-separated, the clusters can then be assembled into complete chromosomes using existing TSP solvers. The results show that this method produces results which are equally as good as the prevalent software in the field, while drastically decreasing the time required to run an analysis

Flocks, Swarms, Crowds, and Societies: On the Scope and Limits of Cognition

Traditionally, the concept of cognition has been tied to the brain or the nervous system. Recent work in various noncomputational cognitive sciences has enlarged the category of “cognitive phenomena” to include the organism and its environment, distributed cognition across networks of actors, and basic cellular functions. The meaning, scope, and limits of ‘cognition’ are no longer clear or well-defined. In order to properly delimit the purview of the cognitive sciences, there is a strong need for a clarification of the definition of cognition. This paper will consider the outer bounds of that definition. Not all cognitive behaviors of a given organism are amenable to an analysis at the organismic or organism-environment level. In some cases, emergent cognition in collective biological and human social systems arises that is irreducible to the sum cognitions of their constituent entities. The group and social systems under consideration are more extensive and inclusive than those considered in studies of distributed cognition to date. The implications for this ultimately expand the purview of the cognitive sciences and bring back a renewed relevance for anthropology and introduce sociology on the traditional six-pronged interdisciplinary wheel of the cognitive sciences

Polymer and Fullerene Zwitterions: From Synthesis to Solar Cells

This thesis describes the synthesis and applications of hydrophilic conjugated polymers and fullerenes containing dipole-inducing pendent groups. The pendent groups include tertiary amines, sulfobetaine (SB) zwitterions, quaternary ammoniums, and sulfonates, providing solubility in polar solvents. Particular emphasis is placed on zwitterions functalized structures. Suzuki-Miyaura (SM) and Horner-Wadsworth-Emmons (HWE) coupling reactions proved valuable for the preparation of the hydrophilic conjugated polymers, while the Prato reaction afforded the functional fulleropyrrolidines. Ultraviolet photoelectron spectroscopy (UPS) probed the interactions between the hydrophilic conjugated polymers and conductive metal substrates. In particular, UPS revealed that conjugated polymer zwitterions (CPZs) substantially reduce work function (Φ) of metals, represented by a negative interfacial dipole (Δ). Their solubility properties and interactions with metals make CPZs attractive for integration into solar cells, specifically at the interface between a photoactive layer and high Φ metal cathode. This thesis thus provides routes to improve polymer-based solar cell (PSC) technology through the implementation of novel hydrophilic semiconductors. Initial syntheses focused on the preparation of polythiophene with pendent SB groups, producing CPZs that were incorporated into PSCs as cathode modification layers. Tuning the electronic properties of CPZs with different polymer backbones further enhanced their effectiveness as interlayers in PSCs. Diketopyrrolopyrrole (DPP), iso-indigo (iIn) and naphthalene diimide (NDI) were functionalized with SB, followed by SM polymerization to provide the corresponding CPZs. Unprecedented power conversion efficiency (PCE) values (\u3e 10%) were achieved for devices containing the NDI CPZs, and improved electron transport of the interlayers was found central to this efficiency enhancement. Fulleropyrrolidines functionalized with tertiary amines and SB groups represent an alternative, non-polymeric, class of materials studied as interfacial modifiers in PSCs. The intrinsic n-type properties of fullerene provide an ideal platform for such interlayers, and led to state-of-the-art devices with record PCE values, irrespective of the selection of conductive cathode (Al, Ag, Cu and Au), while eliminating the need for precise control over interlayer thickness. Finally, HWE coupling was investigated as a new approach to hydrophilic CPZs. The methodology presented afforded room temperature production of a variety of hydrophilic poly(arylene vinylene)s (PAVs) from water, including zwitterionic, cationic and anionic derivatives. The scope and limitations of the HWE reaction in water is discussed, along with the utility of the resulting PAVs in sensing and PSCs

Voluntary Counselling, HIV Testing and Sexual Behaviour Among Patients with Tuberculosis in a Rural District of Malawi.

OBJECTIVES: A study was conducted in new patients registered with tuberculosis (TB) in a rural district of Malawi in order to 1) verify the acceptability of voluntary counselling and testing for human immunodeficiency virus (HIV) infection; 2) describe sexual behaviour and condom use; and 3) identify socio-demographic and behavioural risk factors associated with 'no condom use'. DESIGN: Cross-sectional study. METHODS: Consecutive patients diagnosed with TB between January and December 2000 were offered voluntary counselling and HIV testing (VCT) and were subsequently interviewed. RESULTS: There were 1,049 new TB patients enrolled in the study. Of these, 1,007 (96%) were pre-test counselled, 955 (91%) underwent HIV testing and 912 (87%) were post-test counselled; 43 (4%) patients refused HIV testing. The overall HIV infection rate was 77%. Of all HIV-positive TB patients, 691 (94%) were put on cotrimoxazole. There were 479 (49%) TB patients who reported sexual encounters, of whom only 6% always used condoms. Unprotected sex was associated with having TB symptoms for over 1 month, having had less than 8 years of school education, being single, divorced or widowed or having sex with the same partner. CONCLUSIONS: Offering VCT to TB patients in this setting has a high acceptance rate and provides an opportunity to strengthen and integrate TB and HIV programmes

Sexually Transmitted Infections and Sexual Behaviour Among Commercial Sex Workers in a Rural District of Malawi.

In Thyolo District, Malawi, a study was conducted among commercial sex workers (CSWs) attending mobile clinics in order to; determine the prevalence and pattern of sexually transmitted infections (STIs), describe sexual behaviour among those who have an STI and identify risk factors associated with 'no condom use'. There were 1817 CSWs, of whom 448 (25%) had an STI. Of these, the commonest infections included 237 (53%) cases of abnormal vaginal discharge, 109 (24%) cases of pelvic inflammatory disease and 95 (21%) cases of genital ulcer disease (GUD). Eighty-seven per cent had sex while symptomatic, 17% without condoms. Having unprotected sex was associated with being married, being involved with commercial sex outside a known rest-house or bar, having a GUD, having fewer than two clients/day, alcohol intake and having had no prior medication for STI. The high levels of STIs, particularly GUDs, and unprotected sex underlines the importance of developing targeted interventions for CSWs and their clients

How health systems in sub-Saharan Africa can benefit from tuberculosis and other infectious disease programmes.

Weak and dysfunctional health systems in low-income countries, particularly in sub-Saharan Africa, are recognised as major obstacles to attaining the health-related Millennium Development Goals by 2015. Some progress is being made towards achieving the targets of Millennium Development Goal 6 for tuberculosis (TB), HIV/AIDS and malaria, with the achievements largely resulting from clearly defined strategies and intervention delivery systems combined with large amounts of external funding. This article is divided into four main sections. The first highlights the crucial elements that are needed in low-income countries in sub-Saharan Africa to deliver good quality health care through general health systems. The second discusses the main characteristics of infectious disease and TB control programmes. The third illustrates how TB control and other infectious disease programmes can help to strengthen these components, particularly in human resources; infrastructure; procurement and distribution; monitoring, evaluation and supervision; leadership and stewardship. The fourth and final section looks at progress made to date at the international level in terms of policy and guidelines, with some specific suggestions about this might be moved forward at the national level. For TB and other infectious disease programmes to drive broad improvements in health care systems and patient care, the lessons that have been learnt must be consciously applied to the broader health system, and sufficient financial input and the engagement of all players are essential

A Drug Dosage Table is a Useful Tool to Facilitate Prescriptions of Antiretroviral Drugs for Children in Thailand.

Scaling up of antiretroviral treatment (ART) for children in countries like Thailand will require decentralization and management by non-specialist doctors. We describe (a) the formulation of a standardized drug dosage table to facilitate antiretroviral drug (ARV) prescriptions for children, (b) the acceptability of such a table among doctors and (c) the safety and efficacy of drug doses in the table. Acceptability was assessed using a questionnaire. Safety and efficacy were assessed on the basis of incidence of adverse effects and virological response to treatment, respectively. Of all doctors (n=18), 17 (94%) found that the table was practical to use, avoided miscalculations and made them more confident with prescriptions. Of 49 children prescribed ARVs, less than 5% had adverse side-effects. All ARV-naïve children achieved undetectable viral loads within six months of ART. In our setting, a standardized drug dosage table provided a simple and reliable tool that facilitated ARV prescriptions for children