Zero-inflated Poisson regression models for QTL mapping applied to tick-resistance in a Gyr × Holstein F2 population

Now a days, an important and interesting alternative in the control of tick-infestation in cattle is to select resistant animals, and identify the respective quantitative trait loci (QTLs) and DNA markers, for posterior use in breeding programs. The number of ticks/animal is characterized as a discrete-counting trait, which could potentially follow Poisson distribution. However, in the case of an excess of zeros, due to the occurrence of several noninfected animals, zero-inflated Poisson and generalized zero-inflated distribution (GZIP) may provide a better description of the data. Thus, the objective here was to compare through simulation, Poisson and ZIP models (simple and generalized) with classical approaches, for QTL mapping with counting phenotypes under different scenarios, and to apply these approaches to a QTL study of tick resistance in an F2 cattle (Gyr × Holstein) population. It was concluded that, when working with zero-inflated data, it is recommendable to use the generalized and simple ZIP model for analysis. On the other hand, when working with data with zeros, but not zero-inflated, the Poisson model or a data-transformation-approach, such as square-root or Box-Cox transformation, are applicable

Foot-and-mouth disease virus serotypes detected in Tanzania from 2003 to 2010: Conjectured status and future prospects

This study was conducted to investigate the presence of foot-and-mouth disease virus (FMDV) in different geographic locations of Tanzania. Epithelial tissues and fluids (n = 364) were collected from cattle exhibiting oral and foot vesicular lesions suggestive of FMD and submitted for routine FMD diagnosis. The analysis of these samples collected during the period of 2002 and 2010 was performed by serotype-specific antigen capture ELISA to determine the presence of FMDV. The results of this study indicated that 167 out of 364 (46.1%) of the samples contained FMDV antigen. Of the 167 positive samples, 37 (28.4%) were type O, 7 (4.1%) type A, 45 (21.9%) SAT 1 and 79 (45.6%) SAT 2. Two FMDV serotypes (O and SAT 2) were widely distributed throughout Tanzania whilst SAT 1 and A types were only found in the Eastern zone. Our findings suggest that serotypes A, O, SAT 1 and SAT 2 prevail in Tanzania and are associated with the recent FMD outbreaks. The lack of comprehensive animal movement records and inconsistent vaccination programmes make it difficult to determine the exact source of FMD outbreaks or to trace the transmission of the disease over time. Therefore, further collection and analysis of samples from domestic and wild animals are being undertaken to investigate the genetic and antigenic characteristics of the circulating strains, so that a rational method to control FMD in Tanzania and the neighbouring countries can be recommended

Evaluation of knowledge levels amongst village AIDS committees after undergoing HIV educational sessions: results from a pilot study in rural Tanzania

ABSTRACT: BACKGROUND: Village AIDS committees (VAC) were formed by the Tanzanian government in 2003 to provide HIV education to their communities. However, their potential has not been realised due to their limited knowledge and misconceptions surrounding HIV, which could be addressed through training of VAC members. In an attempt to increase HIV knowledge levels and address common misconceptions amongst the VACs, an HIV curriculum was delivered to members in rural north western Tanzania. METHODS: An evaluation of HIV knowledge was conducted prior to and post-delivery of HIV training sessions, within members of three VACs in Kisesa ward. Quantitative surveys were used with several open-ended questions to identify local misconceptions and evaluate HIV knowledge levels. Short educational training sessions covering HIV transmission, prevention and treatment were conducted, with each VAC using quizzes, role-plays and participatory learning and action tools. Post-training surveys occurred up to seven days after the final training session. RESULTS: Before the training, "good" HIV knowledge was higher amongst men than women (p = 0.041), and among those with previous HIV education (p = 0.002). The trade-centre had a faster turn-over of VAC members, and proximity to the trade-centre was associated with a shorter time on the committee.Training improved HIV knowledge levels with more members achieving a "good" score in the post-training survey compared with the baseline survey (p = < 0.001). The training programme was popular, with 100% of participants requesting further HIV training in the future and 51.7% requesting training at three-monthly intervals. CONCLUSIONS: In this setting, a series of HIV training sessions for VACs demonstrated encouraging results, with increased HIV knowledge levels following short educational sessions. Further work is required to assess the success of VAC members in disseminating this HIV education to their communities, as well as up-scaling this pilot study to other regions in Tanzania with different misconceptions

"Half plate of rice to a male casual sexual partner, full plate belongs to the husband": Findings from a qualitative study on sexual behaviour in relation to HIV and AIDS in northern Tanzania

A thorough understanding of the contexts of sexual behaviour of the people who are vulnerable to HIV infection is an important component in the battle against AIDS epidemic. We conducted a qualitative study to investigate perceptions, attitudes and practices of sexually active people in three districts of northern Tanzania with the view of collecting data to inform the formulation of appropriate complementary interventions against HIV and AIDS in the study communities. We conducted 96 semi-structured interviews and 48 focus group discussions with sexually active participants (18-60 years of age) who were selected purposively in two fishing and one non-fishing communities. The study revealed a number of socio-economic and cultural factors which act as structural drivers of HIV epidemic. Mobility and migration were mentioned to be associated with the risk of HIV acquisition and transmission. Sexual promiscuous behaviour was common in all study communities. Chomolea, (a quick transactional sex) was reported to exist in fishing communities, whereas extramarital sex in the bush was reported in non-fishing community which was predominantly Christian and polygamous. Traditional practices such as Kusomboka (death cleansing through unprotected sex) was reported to exist. Other risky sexual behaviour and traditional practices together with their socio-economic and cultural contexts are presented in details and discussed. Knowledge of condom was low as some people mistook them for balloons to play with and as decorations for their living rooms. Acute scarcity of condoms in some remote areas such as vizingani (fishing islands) push some people to make their own condoms locally known as kondomu za pepsi using polythene bags. HIV prevention efforts can succeed by addressing sexual behaviour and its socio-economic and cultural contexts. More innovative, interdisciplinary and productive structural approaches to HIV prevention need to be developed in close collaboration with affected communities and be closely related to policy-making and implementation; to go beyond the limited success of traditional behavioural and biomedical interventions to particularly address the underlying social and structural drivers of HIV risk and vulnerability in the study communities

Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes.

Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries. Rabies is an almost invariably fatal viral disease that causes a large public health and economic burden in Asia and Africa, despite being entirely vaccine preventable. With policy efforts now directed towards achieving a global goal of zero dog-mediated human rabies deaths by 2030, establishing effective surveillance tools is critical. Genomic data can provide important and unique insights into rabies spread and persistence that can direct control efforts. However, capacity for genomic research in low- and middle-income countries is held back by limited laboratory infrastructure, cost, supply chains and other logistical challenges. Here we present and validate an end-to-end workflow to facilitate affordable whole genome sequencing for rabies surveillance utilising nanopore technology. We used this workflow in Kenya, Tanzania and the Philippines to generate rabies virus genomes in two to three days, reducing costs to approximately £60 per genome. This is over half the cost of metagenomic sequencing previously conducted for Tanzanian samples, which involved exporting samples to the UK and a three- to six-month lag time. Ongoing optimization of workflows are likely to reduce these costs further. We also present tools to support routine whole genome sequencing and interpretation for genomic surveillance. Moreover, combined with training workshops to empower scientists in-country, we show that local sequencing capacity can be readily established and sustainable, negating the common misperception that cutting-edge genomic research can only be conducted in high resource laboratories. More generally, we argue that the capacity to harness genomic data is a game-changer for endemic disease surveillance and should precipitate a new wave of researchers from low- and middle-income countries

Paracrine cyclooxygenase-2 activity by macrophages drives colorectal adenoma progression in the Apc Min/+ mouse model of intestinal tumorigenesis

Genetic deletion or pharmacological inhibition of cyclooxygenase (COX)-2 abrogates intestinal adenoma development at early stages of colorectal carcinogenesis. COX-2 is localised to stromal cells (predominantly macrophages) in human and mouse intestinal adenomas. Therefore, we tested the hypothesis that paracrine Cox-2-mediated signalling from macrophages drives adenoma growth and progression in vivo in the ApcMin/+ mouse model of intestinal tumorigenesis. Using a transgenic C57Bl/6 mouse model of Cox-2 over-expression driven by the chicken lysozyme locus (cLys-Cox-2), which directs integration site-independent, copy number-dependent transgene expression restricted to macrophages, we demonstrated that stromal macrophage Cox-2 in colorectal (but not small intestinal) adenomas from cLys-Cox-2 x ApcMin/+ mice was associated with significantly increased tumour size (P = 0.025) and multiplicity (P = 0.025), compared with control ApcMin/+ mice. Transgenic macrophage Cox-2 expression was associated with increased dysplasia, epithelial cell Cox-2 expression and submucosal tumour invasion, as well as increased nuclear β-catenin translocation in dysplastic epithelial cells. In vitro studies confirmed that paracrine macrophage Cox-2 signalling drives catenin-related transcription in intestinal epithelial cells. Paracrine macrophage Cox-2 activity drives growth and progression of ApcMin/+ mouse colonic adenomas, linked to increased epithelial cell β-catenin dysregulation. Stromal cell (macrophage) gene regulation and signalling represent valid targets for chemoprevention of colorectal cancer

Deciphering the Complex Distribution of Human Immunodeficiency Virus Type 1 Subtypes among Different Cohorts in Northern Tanzania.

Increased understanding of the genetic diversity of HIV-1 is challenging but important in the development of an effective vaccine. We aimed to describe the distribution of HIV-1 subtypes in northern Tanzania among women enrolled in studies preparing for HIV-1 prevention trials (hospitality facility-worker cohorts), and among men and women in an open cohort demographic surveillance system (Kisesa cohort). The polymerase encompassing partial reverse transcriptase was sequenced and phylogenetic analysis performed and subtype determined. Questionnaires documented demographic data. We examined factors associated with subtype using multinomial logistic regression, adjusted for study, age, and sex. Among 140 individuals (125 women and 15 men), subtype A1 predominated (54, 39%), followed by C (46, 33%), D (25, 18%) and unique recombinant forms (URFs) (15, 11%). There was weak evidence to suggest different subtype frequencies by study (for example, 18% URFs in the Kisesa cohort versus 5-9% in the hospitality facility-worker cohorts; adjusted relative-risk ratio (aRR) = 2.35 [95% CI 0.59,9.32]; global p = 0.09). Compared to men, women were less likely to have subtype D versus A (aRR = 0.12 [95% CI 0.02,0.76]; global p = 0.05). There was a trend to suggest lower relative risk of subtype D compared to A with older age (aRR = 0.44 [95% CI 0.23,0.85] per 10 years; global p = 0.05). We observed multiple subtypes, confirming the complex genetic diversity of HIV-1 strains circulating in northern Tanzania, and found some differences between cohorts and by age and sex. This has important implications for vaccine design and development, providing opportunity to determine vaccine efficacy in diverse HIV-1 strains

"Now we are in a different time; various bad diseases have come." understanding men's acceptability of male circumcision for HIV prevention in a moderate prevalence setting

Background: Adult male surgical circumcision (MC) has been shown to reduce HIV acquisition in men and is recommended by the WHO for inclusion in comprehensive national HIV prevention programs in high prevalence settings. Only limited research to date has been conducted in countries experiencing moderate burden epidemics, where the acceptability, operational feasibility and potential epidemiological impact of MC remain unclear. Methods. A multi-method qualitative research study was conducted at four sites in Papua New Guinea (PNG), with 24 focus group discussions and 65 in-depth interviews carried out among 276 men. Results: The majority of men were in favour of MC being introduced for HIV prevention in PNG and considered improved genital hygiene, enhanced sexual pleasure and culturally appropriateness key factors in the acceptability of a future intervention. A minority of men were against the introduction of MC, primarily due to concerns regarding sexual risk compensation and that the intervention went against prevailing cultural and religious beliefs. Conclusion: This is one of the first community-based MC acceptability studies conducted in a moderate prevalence setting outside of Africa. Research findings from this study suggest that a future MC program for HIV prevention would be widely accepted by men in PNG

Determinants of access to HIV testing and counselling services among female sex workers in sub-Saharan Africa: a systematic review

Quality appraisal tool. (DOCX 20 kb