On Bayesian estimation of a latent trait model defined by a rank-based likelihood.

Maximum likelihood estimation (frequentist) and Bayesian estimation are two common parameter estimation methods. However, maximum likelihood estimation faces limitations, including the effect of outliers, computational complexity, and issues with ordinal categorical data, leading to biased estimates and inaccurate coverage probabilities. To address these limitations, this study employed a latent trait model with a Bayesian marginal likelihood of rank-based estimation for parameter estimation.

Bayesian rank likelihood-based estimation: An application to low birth weight in Ethiopia.

Background: Low birth weight is a significant risk factor associated with high rates of neonatal and infant mortality, particularly in developing countries. However, most studies conducted on this topic in Ethiopia have small sample sizes, often focusing on specific areas and using standard models employing maximum likelihood estimation, leading to potential bias and inaccurate coverage probability.

Methods: This study used a novel approach, the Bayesian rank likelihood method, within a latent traits model, to estimate parameters and provide a nationwide estimate of low birth weight and its risk factors in Ethiopia.

Pairwise fitting of piecewise mixed models for the joint modeling of multivariate longitudinal outcomes, in a randomized crossover trial.

Many statistical models have been proposed in the literature for the analysis of longitudinal data. One may propose to model two or more correlated longitudinal processes simultaneously, with a goal of understanding their association over time. Joint modeling is then required to carefully study the association structure among the outcomes as well as drawing joint inferences about the different outcomes.

Flexible Bayesian semiparametric mixed-effects model for skewed longitudinal data.

Background: In clinical trials and epidemiological research, mixed-effects models are commonly used to examine population-level and subject-specific trajectories of biomarkers over time. Despite their increasing popularity and application, the specification of these models necessitates a great deal of care when analysing longitudinal data with non-linear patterns and asymmetry. Parametric (linear) mixed-effect models may not capture these complexities flexibly and adequately.

Modified sharp regression discontinuity model to settings with fuzzy variables.

Objective: The goal of this study is to develop a Modified Sharp Regression Discontinuity model to predict alcohol consumption in People Living with Human Immunodeficiency Virus (HIV) and Acquired Immunodeficiency Syndrome (AIDS). Previous studies focused on either fuzzy dependent or fuzzy independent variables separately. However, there is a gap in research that examines the interaction between both types of fuzzy variables thus the model considers both dependent and independent fuzzy variables.

Understanding the Evolving Role of Voluntary Medical Male Circumcision as a Public Health Strategy in Eastern and Southern Africa: Opportunities and Challenges.

Purpose Of Review: Voluntary male medical circumcision (VMMC) has been a cornerstone of HIV prevention in Eastern and Southern Africa (ESA) and is credited in part for declines in HIV incidence seen in recent years. However, these HIV incidence declines change VMMC cost-effectiveness and how it varies across populations.

Recent Findings: Mathematical models project continued cost-effectiveness of VMMC in much of ESA despite HIV incidence declines.

HIV Incidence, Recent HIV Infection, and Associated Factors, Kenya, 2007-2018.

Nationally representative surveys provide an opportunity to assess trends in recent human immunodeficiency virus (HIV) infection based on assays for recent HIV infection. We assessed HIV incidence in Kenya in 2018 and trends in recent HIV infection among adolescents and adults in Kenya using nationally representative household surveys conducted in 2007, 2012, and 2018. To assess trends, we defined a recent HIV infection testing algorithm (RITA) that classified as recently infected (<12 months) those HIV-positive participants that were recent on the HIV-1 limiting antigen (LAg)-avidity assay without evidence of antiretroviral use.

Methods for conducting trends analysis: roadmap for comparing outcomes from three national HIV Population-based household surveys in Kenya (2007, 2012, and 2018).

Background: For assessing the HIV epidemic in Kenya, a series of independent HIV indicator household-based surveys of similar design can be used to investigate the trends in key indicators relevant to HIV prevention and control and to describe geographic and sociodemographic disparities, assess the impact of interventions, and develop strategies. We developed methods and tools to facilitate a robust analysis of trends across three national household-based surveys conducted in Kenya in 2007, 2012, and 2018.

Methods: We used data from the 2007 and 2012 Kenya AIDS Indicator surveys (KAIS 2007 and KAIS 2012) and the 2018 Kenya Population-based HIV Impact Assessment (KENPHIA 2018).

A Flexible Bayesian Parametric Proportional Hazard Model: Simulation and Applications to Right-Censored Healthcare Data.

Survival analysis is a collection of statistical techniques which examine the time it takes for an event to occur, and it is one of the most important fields in biomedical sciences and other variety of scientific disciplines. Furthermore, the computational rapid advancements in recent decades have advocated the application of Bayesian techniques in this field, giving a powerful and flexible alternative to the classical inference. The aim of this study is to consider the Bayesian inference for the generalized log-logistic proportional hazard model with applications to right-censored healthcare data sets.

Forecasting the spread of the COVID-19 pandemic in Kenya using SEIR and ARIMA models.

COVID-19, a coronavirus disease 2019, is an ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The first case in Kenya was identified on March 13, 2020, with the pandemic increasing to about 237,000 confirmed cases and 4,746 deaths by August 2021. We developed an SEIR model forecasting the COVID-19 pandemic in Kenya using an Autoregressive Integrated moving averages (ARIMA) model.

Modelling trends of CD4 counts for patients on antiretroviral therapy (ART): a comprehensive health care clinic in Nairobi, Kenya.

Background: In resource-limited settings, changes in CD4 counts constitute an important component in patient monitoring and evaluation of treatment response as these patients do not have access to routine viral load testing. In this study, we quantified trends on CD4 counts in patients on highly active antiretroviral therapy (HAART) in a comprehensive health care clinic in Kenya between 2011 and 2017. We evaluated the rate of change in CD4 cell count in response to antiretroviral treatment.

Employing phylogenetic tree shape statistics to resolve the underlying host population structure.

Background: Host population structure is a key determinant of pathogen and infectious disease transmission patterns. Pathogen phylogenetic trees are useful tools to reveal the population structure underlying an epidemic. Determining whether a population is structured or not is useful in informing the type of phylogenetic methods to be used in a given study.

Bayesian and Classical Inference for the Generalized Log-Logistic Distribution with Applications to Survival Data.

The generalized log-logistic distribution is especially useful for modelling survival data with variable hazard rate shapes because it extends the log-logistic distribution by adding an extra parameter to the classical distribution, resulting in greater flexibility in analyzing and modelling various data types. We derive the fundamental mathematical and statistical properties of the proposed distribution in this paper. Many well-known lifetime special submodels are included in the proposed distribution, including the Weibull, log-logistic, exponential, and Burr XII distributions.

A Generic SAS Macro for Creating Publication-Quality Three-Way Cross-Tabulations.

Cross-tabulations are a simple but important tool for understanding the distribution of socio-demographic characteristics among participants in epidemiological studies. We developed a generic SAS macro, to create publication-quality tables from cross-tabulations between a factor and a by-group variable given a third variable using survey or non-survey data. The macro also performs two-way cross-tabulations and provides extra features not available in existing procedures such as ability to incorporate parameters for survey design and replication-based variance estimation methods, performing validation checks for input parameters, transparently formatting variable values from character into numeric and allowing for generalizability.

Modeling the Effects of Nonpharmaceutical Interventions on COVID-19 Spread in Kenya.

Mathematical modeling of nonpharmaceutical interventions (NPIs) of coronavirus disease (COVID-19) in Kenya is presented. A susceptible-exposed-infected-recovered (SEIR) compartment model is considered with additional compartments of hospitalized population whose condition is severe or critical and the fatality compartment. The basic reproduction number ( ) is computed by the next-generation matrix approach and later expressed as a time-dependent function so as to incorporate the NPIs into the model.

Age-structured model for COVID-19: Effectiveness of social distancing and contact reduction in Kenya.

Coronavirus disease 2019 is caused by severe acute respiratory syndrome coronavirus 2. Kenya reported its first case on March 13, 2020 and by March 16, 2020 she instituted physical distancing strategies to reduce transmission and flatten the epidemic curve. An age-structured compartmental model was developed to assess the impact of the strategies on COVID-19 severity and burden.

SEIR model for COVID-19 dynamics incorporating the environment and social distancing.

Objective: Coronavirus disease 2019 (COVID-19) is a pandemic respiratory illness spreading from person-to-person caused by a novel coronavirus and poses a serious public health risk. The goal of this study was to apply a modified susceptible-exposed-infectious-recovered (SEIR) compartmental mathematical model for prediction of COVID-19 epidemic dynamics incorporating pathogen in the environment and interventions. The next generation matrix approach was used to determine the basic reproduction number [Formula: see text].

Multi-level challenges and opportunities in providing antiretroviral treatment to adolescents in Kenya.

Adolescents have poor antiretroviral therapy (ART) outcomes due to multi-level factors. Adolescent and youth-friendly services (AYFS) have been implemented to address this. Adolescents on ART and HIV clinic managers were interviewed on their experiences with HIV care provision.

%svy_logistic_regression: A generic SAS macro for simple and multiple logistic regression and creating quality publication-ready tables using survey or non-survey data.

Introduction: Reproducible research is increasingly gaining interest in the research community. Automating the production of research manuscript tables from statistical software can help increase the reproducibility of findings. Logistic regression is used in studying disease prevalence and associated factors in epidemiological studies and can be easily performed using widely available software including SAS, SUDAAN, Stata or R.

The influence of mobility among high-risk populations on HIV transmission in Western Kenya.

Western Kenya suffers a highly endemic and also very heterogeneous epidemic of human immunodeficiency virus (HIV). Although female sex workers (FSW) and their male clients are known to be at high risk for HIV, HIV prevalence across regions in Western Kenya is not strongly correlated with the fraction of women engaged in commercial sex. An agent-based network model of HIV transmission, geographically stratified at the county level, was fit to the HIV epidemic, scale-up of interventions, and populations of FSW in Western Kenya under two assumptions about the potential mobility of FSW clients.

Dynamic spatiotemporal modeling of the infected rate of visceral leishmaniasis in human in an endemic area of Amhara regional state, Ethiopia.

Visceral Leishmaniasis is a very dangerous form of leishmaniasis and, shorn of appropriate diagnosis and handling, it leads to death and physical disability. Depicting the spatiotemporal pattern of disease is important for disease regulator and deterrence strategies. Spatiotemporal modeling has distended broad veneration in recent years.

Effect of climate on incidence of respiratory syncytial virus infections in a refugee camp in Kenya: A non-Gaussian time-series analysis.

Respiratory syncytial virus (RSV) is one of the major causes of acute lower respiratory tract infections (ALRTI) in children. Children younger than 1 year are the most susceptible to RSV infection. RSV infections occur seasonally in temperate climate regions.

Field Evaluation of Dried Blood Spots for HIV-1 Viral Load Monitoring in Adults and Children Receiving Antiretroviral Treatment in Kenya: Implications for Scale-up in Resource-Limited Settings.

Background: The World Health Organization recommends viral load (VL) as the preferred method for diagnosing antiretroviral therapy failure; however, operational challenges have hampered the implementation of VL monitoring in most resource-limited settings. This study evaluated the accuracy of dried blood spot (DBS) VL testing under field conditions as a practical alternative to plasma in determining virologic failure (VF).

Methods: From May to December 2013, paired plasma and DBS specimens were collected from 416 adults and 377 children on antiretroviral therapy for ≥6 months at 12 clinics in Kenya.

Findings of Phlebotomy Practices in Kenya in 2010: Need for Action.

Background: Phlebotomy, a commonly performed medical procedure in healthcare, is essential for disease diagnosis and patient management. However, poorly performed phlebotomy can compromise patient safety, healthcare worker (HCW) safety, and specimen quality. We carried out a study between June and July 2010 to assess knowledge, quality and safety of phlebotomy before implementation of a public-private partnership between Becton, Dickinson and Company and the US President's Emergency Plan for AIDS Relief.