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Search Results: 1 - 10 of 244086 matches for " Robert C. Bailey "
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Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data
Robert C McLeay, Timothy L Bailey
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-165
Abstract: We first define a mathematical framework for Motif Enrichment Analysis that relaxes the requirement that the biologist input a selected set of genes. Instead, the input consists of all regulatory regions, each labeled with the level of a biological signal. We then define and implement a number of motif enrichment analysis methods. Some of these methods require a user-specified signal threshold, some identify an optimum threshold in a data-driven way and two of our methods are threshold-free. We evaluate these methods, along with two existing methods (Clover and PASTAA), using yeast ChIP-chip data. Our novel threshold-free method based on linear regression performs best in our evaluation, followed by the data-driven PASTAA algorithm. The Clover algorithm performs as well as PASTAA if the user-specified threshold is chosen optimally. Data-driven methods based on three statistical tests–Fisher Exact Test, rank-sum test, and multi-hypergeometric test—perform poorly, even when the threshold is chosen optimally. These methods (and Clover) perform even worse when unrestricted data-driven threshold determination is used.Our novel, threshold-free linear regression method works well on ChIP-chip data. Methods using data-driven threshold determination can perform poorly unless the range of thresholds is limited a priori. The limits implemented in PASTAA, however, appear to be well-chosen. Our novel algorithms—AME (Analysis of Motif Enrichment)—are available at http://bioinformatics.org.au/ame/ webcite.Elucidating the mechanisms that control the transcription of genes is one of the major goals of molecular biology. One current approach is to determine whether the regulatory sequences (e.g., promoters) of a set of genes have significantly higher than expected affinity for a regulatory protein or microRNA for which the DNA-binding motif is known. Such a motif is said to be "enriched" in the set of sequences. The regulatory proteins and microRNAs whose motifs are enriched in the s
Male circumcision for HIV prevention: a prospective study of complications in clinical and traditional settings in Bungoma, Kenya
Bailey,Robert C; Egesah,Omar; Rosenberg,Stephanie;
Bulletin of the World Health Organization , 2008, DOI: 10.1590/S0042-96862008000900010
Abstract: objective: male circumcision reduces the risk of hiv acquisition by approximately 60%. male circumcision services are now being introduced in selected populations in sub-saharan africa and further interventions are being planned. a serious concern is whether male circumcision can be provided safely to large numbers of adult males in developing countries. methods: this prospective study was conducted in the bungoma district, kenya, where male circumcision is universally practised. young males intending to undergo traditional or clinical circumcision were identified by a two-stage cluster sampling method. during the july-august 2004 circumcision season, 1007 males were interviewed 30-89 days post- circumcision. twenty-four men were directly observed during and 3, 8, 30 and 90 days post-circumcision, and 298 men underwent clinical exams 45-89 days post-procedure. twenty-one traditional and 20 clinical practitioners were interviewed to assess their experience and training. inventories of health facilities were taken to assess the condition of instruments and supplies necessary for performing safe circumcisions. findings: of 443 males circumcised traditionally, 156 (35.2%) experienced an adverse event compared with 99 of 559 (17.7%) circumcised clinically (odds ratio: 2.53; 95% confidence interval: 1.89-3.38). bleeding and infection were the most common adverse effects, with excessive pain, lacerations, torsion and erectile dysfunction also observed. participants were aged 5 to 21 years and half were sexually active before circumcision. practitioners lacked knowledge and training. proper instruments and supplies were lacking at most health facilities. conclusion: extensive training and resources will be necessary in sub-saharan africa before male circumcision can be aggressively promoted for hiv prevention. two-thirds of african men are circumcised, most by traditional or unqualified practitioners in informal settings. safety of circumcision in communities where it is al
Generalized packing designs
Robert F. Bailey,Andrea C. Burgess
Mathematics , 2011,
Abstract: Generalized $t$-designs, which form a common generalization of objects such as $t$-designs, resolvable designs and orthogonal arrays, were defined by Cameron [P.J. Cameron, A generalisation of $t$-designs, \emph{Discrete Math.}\ {\bf 309} (2009), 4835--4842]. In this paper, we define a related class of combinatorial designs which simultaneously generalize packing designs and packing arrays. We describe the sometimes surprising connections which these generalized designs have with various known classes of combinatorial designs, including Howell designs, partial Latin squares and several classes of triple systems, and also concepts such as resolvability and block colouring of ordinary designs and packings, and orthogonal resolutions and colourings. Moreover, we derive bounds on the size of a generalized packing design and construct optimal generalized packings in certain cases. In particular, we provide methods for constructing maximum generalized packings with $t=2$ and block size $k=3$ or 4.
Women's Beliefs about Male Circumcision, HIV Prevention, and Sexual Behaviors in Kisumu, Kenya
Thomas H. Riess, Maryline M. Achieng', Robert C. Bailey
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0097748
Abstract: It is important to understand how women's sexual practices may be influenced by male circumcision (MC) as an HIV prevention effort. Women's beliefs about MC and sexual behaviour will likely influence the scale-up and uptake of medical MC. We conducted qualitative interviews with 30 sexually active women in Kisumu, Kenya. Women discussed MC related to perceived health benefits, condom use, sexual behaviour, knowledge of susceptibility to HIV and sexually transmitted infections (STIs), circumcision preference, and influence on circumcision uptake. Respondents had a good understanding of the partial protection of MC for acquisition of HIV for men. Women perceived circumcised men as cleaner, carrying fewer diseases, and taking more time to reach ejaculation. Male's circumcision status is a salient factor for women's sexual decision making, including partner choice, and condom use. It will be important that educational information affirms that MC provides only partial protection against female to male transmission of HIV and some STIs; that other HIV and STI prevention methods such as condoms need to be used in conjunction with MC; that MC does not preclude a man from having HIV; and that couples should develop plans for not having sex while the man is healing.
The PrePex Device Is Unlikely to Achieve Cost-Savings Compared to the Forceps-Guided Method in Male Circumcision Programs in Sub-Saharan Africa
Walter Obiero, Marisa R. Young, Robert C. Bailey
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0053380
Abstract: Background Male circumcision (MC) reduces the risk of heterosexual HIV acquisition in men by approximately 60%. MC programs for HIV prevention are currently being scaled-up in fourteen countries in sub-Saharan Africa. The current standard surgical technique for MC in many sub-Saharan African countries is the forceps-guided male circumcision (FGMC) method. The PrePex male circumcision (PMC) method could replace FGMC and potentially reduce MC programming costs. We compared the potential costs of introducing the PrePex device into MC programming to the cost of the forceps-guided method. Methods Data were obtained from the Nyanza Reproductive Health Society (NRHS), an MC service delivery organization in Kenya, and from the Kenya Ministry of Health. Analyses are based on 48,265 MC procedures performed in four Districts in western Kenya from 2009 through 2011. Data were entered into the WHO/UNAIDS Decision Makers Program Planning Tool. The tool assesses direct and indirect costs of MC programming. Various sensitivity analyses were performed. Costs were discounted at an annual rate of 6% and are presented in United States Dollars. Results Not including the costs of the PrePex device or referral costs for men with phimosis/tight foreskin, the costs of one MC surgery were $44.54–$49.02 and $54.52–$55.29 for PMC and FGMC, respectively. Conclusion The PrePex device is unlikely to result in significant cost-savings in comparison to the forceps-guided method. MC programmers should target other aspects of the male circumcision minimum package for improved cost efficiency.
Acceptability of Medical Male Circumcision Among Uncircumcised Men in Kenya One Year After the Launch of the National Male Circumcision Program
Amy Herman-Roloff,Nixon Otieno,Kawango Agot,Jeckoniah Ndinya-Achola,Robert C. Bailey
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0019814
Abstract: Numerous studies have demonstrated that male circumcision (MC) reduces the incidence of the Type-1 human immunodeficiency virus (HIV) among heterosexual men by at least half.
Acceptability of Male Circumcision for the Prevention of HIV/AIDS in the Dominican Republic
Maximo O. Brito,Lilliam M. Caso,Hannabell Balbuena,Robert C. Bailey
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0007687
Abstract: Male circumcision (MC) is an effective strategy to prevent HIV infection in heterosexual men. To our knowledge, there are no studies of the acceptability of this procedure in the Dominican Republic (DR). The main objective of this study was to assess the acceptability of MC to prevent HIV transmission among men ages 18 to 50 years in the Altagracia Province in the Dominican Republic. Because differences in culture and beliefs between Haitians and Dominicans could potentially influence their acceptability of MC, we conducted a comparative analysis based on national origin.
“When I Was Circumcised I Was Taught Certain Things”: Risk Compensation and Protective Sexual Behavior among Circumcised Men in Kisumu, Kenya
Thomas H. Riess,Maryline M. Achieng’,Samuel Otieno,J. O. Ndinya-Achola,Robert C. Bailey
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0012366
Abstract: Male circumcision has been shown to reduce the transmission of HIV from women to men through vaginal sex by approximately 60%. There is concern that men may engage in risk compensation after becoming circumcised, diminishing the benefits of male circumcision.
Male Circumcision in the General Population of Kisumu, Kenya: Beliefs about Protection, Risk Behaviors, HIV, and STIs
Matthew Westercamp,Robert C. Bailey,Elizabeth A. Bukusi,Michele Montandon,Zachary Kwena,Craig R. Cohen
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0015552
Abstract: Using a population-based survey we examined the behaviors, beliefs, and HIV/HSV-2 serostatus of men and women in the traditionally non-circumcising community of Kisumu, Kenya prior to establishment of voluntary medical male circumcision services. A total of 749 men and 906 women participated. Circumcision status was not associated with HIV/HSV-2 infection nor increased high risk sexual behaviors. In males, preference for being or becoming circumcised was associated with inconsistent condom use and increased lifetime number of sexual partners. Preference for circumcision was increased with understanding that circumcised men are less likely to become infected with HIV.
Modelling the public health impact of male circumcision for HIV prevention in high prevalence areas in Africa
Nico JD Nagelkerke, Stephen Moses, Sake J de Vlas, Robert C Bailey
BMC Infectious Diseases , 2007, DOI: 10.1186/1471-2334-7-16
Abstract: Two mathematical models were examined to explore this issue: a random mixing model and a compartmental model that distinguishes risk groups associated with sex work. In the compartmental model, two scenarios were developed, one calculating HIV transmission and prevalence in a context similar to the country of Botswana, and one similar to Nyanza Province, in western Kenya.In both models, male circumcision programs resulted in large and sustained declines in HIV prevalence over time among both men and women. Men benefited somewhat more than women, but prevalence among women was also reduced substantially. With 80% male circumcision uptake, the reductions in prevalence ranged from 45% to 67% in the two "countries", and with 50% uptake, from 25% to 41%. It would take over a decade for the intervention to reach its full effect.Large-scale uptake of male circumcision services in African countries with high HIV prevalence, and where male circumcision is not now routinely practised, could lead to substantial reductions in HIV transmission and prevalence over time among both men and women.UNAIDS estimates that 38.6 million people globally are currently living with HIV, and that in 2005, 4.1 million new HIV infections occurred [1]. Although the life expectancy of people living with HIV has increased substantially with the introduction of anti-retroviral therapy (ART), it is still uncertain whether ART will have a major impact in reducing the spread of HIV[2]. More than two decades after the discovery of HIV, the range of public health measures to control sexual transmission is still limited. The ideal intervention, of course, would be a highly effective vaccine that offers long-lasting protection, but as yet the search for an effective vaccine has proven elusive, and it is by no means certain that one will become available in the foreseeable future.Until recently, the growing evidence for a protective effect of male circumcision (MC) against HIV infection has received compara
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