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Molecular HIV Surveillance (MHS) has been described as key to enabling rapid responses to HIV outbreaks. It operates by linking individuals with genetically similar viral sequences, which forms a network. A major limitation of MHS is that…
Whole genome sequencing of pathogens from multiple hosts in an epidemic offers the potential to investigate who infected whom with unparalleled resolution, potentially yielding important insights into disease dynamics and the impact of…
Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer and the fourth most common cause of cancer-related death worldwide. Understanding the underlying gene mutations in HCC provides great prognostic value for…
Dynamic models have been successfully used in producing estimates of HIV epidemics at national level, due to their epidemiological nature and their ability to simultaneously estimate prevalence, incidence, and mortality rates. Recently, HIV…
Human Papillomaviruses (HPV) are one of the most prevalent sexually transmitted infections (STI) and the most oncogenic viruses known to humans. The vast majority of HPV infections clear in less than 3 years, but the underlying mechanisms,…
Accurate HIV incidence estimation based on individual recent infection status (recent vs long-term infection) is important for monitoring the epidemic, targeting interventions to those at greatest risk of new infection, and evaluating…
Developing antiviral drugs is an exigent task since viruses mutate to overcome the effect of antiviral drugs. As a result, the efficacy of most antiviral drugs is short-lived. To include this effect, we modify the Neumann and Dahari model.…
Detection limits (DLs), where a variable is unable to be measured outside of a certain range, are common in research. Most approaches to handle DLs in the response variable implicitly make parametric assumptions on the distribution of data…
This study conducts a comparative analysis of stochastic and deterministic models to better understand the dynamics of the HIV epidemic across genders. By incorporating gender-specific transmission probabilities and treatment uptake rates,…
A simple deterministic model is proposed to represent the basic aspects concerning the effects of different antiretroviral treatment schedules on HIV incidence and prevalence of affected populations. The model mimics current treatment…
Lymphocyte populations, stimulated in vitro or in vivo, grow as cells divide. Stochastic models are appropriate because some cells undergo multiple rounds of division, some die, and others of the same type in the same conditions do not…
Estimating HIV-1 incidence using biomarker assays in cross-sectional surveys is important for understanding the HIV pandemic. However, the utility of these estimates has been limited by uncertainty about what input parameters to use for…
Large Language Models (LLMs) may portray discrimination towards certain individuals, especially those characterized by multiple attributes (aka intersectional bias). Discovering intersectional bias in LLMs is challenging, as it involves…
Mutational escape from vaccine induced immune responses has thwarted the development of a successful vaccine against AIDS, whose causative agent is HIV, a highly mutable virus. Knowing the virus' fitness as a function of its proteomic…
$\textbf{Background:}$ High mutability of HIV is the driving force of antiretroviral drug resistance, which represents a medical care challenge. $\textbf{Method and Model Equation:}$ To detect the mutability of each gene in the HIV-1…
Mixed-effects quantile regression models are widely used to capture heterogeneous responses in hierarchically structured data. The asymmetric Laplace (AL) distribution has traditionally served as the basis for quantile regression; however,…
The origin of the unusual incubation period distribution in the development of AIDS is largely unresolved. A key factor in understanding the observed distribution of latency periods, as well as the occurrence of infected individuals not…
Hypervariable T-cell receptors (TCR) play a key role in adaptive immunity, recognising a vast diversity of pathogen-derived antigens. High throughput sequencing of TCR repertoires (RepSeq) produces huge datasets of T-cell receptor sequences…
In clinical and epidemiological studies, hazard ratios are often applied to compare treatment effects between two groups for survival data. For competing risks data, the corresponding quantities of interest are cause-specific hazard ratios…
Evaluation of HIV large scale interventions programme is becoming increasingly important, but impact estimates frequently hinge on knowledge of changes in behaviour such as the frequency of condom use (CU) over time, or other self-reported…