A review of network models for HIV spread.

Background: HIV/AIDS has been a global health crisis for over four decades. Network models, which simulate human behavior and intervention impacts, have become an essential tool in guiding HIV prevention strategies and policies. However, no comprehensive survey of network models in HIV research has been conducted.

Mindfulness-Based Stress Reduction for Symptom Management in Older Individuals with HIV-Associated Neurocognitive Disorder.

The growing number of people aging with HIV represents a group vulnerable to the symptom burdens of HIV-associated neurocognitive disorder (HAND). Among younger groups, Mindfulness-Based Stress Reduction (MBSR) has been shown to help people living with HIV manage HIV-related and other life stress, and although there is some theoretical and empirical evidence that it may be effective among those with cognitive deficits, the approach has not been studied in older populations with HAND. Participants (n = 180) 55 years or older with HIV and cognitive impairment were randomly assigned to either an 8-week MBSR arm or a waitlist control.

Designing and analyzing studies of coronavirus disease 2019 and post-acute sequelae of severe acute respiratory syndrome coronavirus 2 among immunocompromised individuals.

Observational studies of coronavirus disease 2019 (COVID-19) among transplant candidates and recipients remain important as immunocompromised patients formed a very small proportion of patients included in COVID-19 trials and large database analyses. We discuss methods that have been used in such analyses to evaluate the impact of vaccination on the risk of symptomatic COVID-19 in such patients and on the probability of developing post-acute sequelae of severe acute respiratory syndrome coronavirus 2 after the onset of infection. We also propose future directions for research and discuss the methods that will be useful to conduct such investigations.

Optimizing campus-wide COVID-19 test notifications with interpretable wastewater time-series features using machine learning models.

During the COVID-19 pandemic, wastewater surveillance of the SARS CoV-2 virus has been demonstrated to be effective for population surveillance at the county level down to the building level. At the University of California, San Diego, daily high-resolution wastewater surveillance conducted at the building level is being used to identify potential undiagnosed infections and trigger notification of residents and responsive testing, but the optimal determinants for notifications are unknown. To fill this gap, we propose a pipeline for data processing and identifying features of a series of wastewater test results that can predict the presence of COVID-19 in residences associated with the test sites.

Post-acute sequelae of COVID-19 in solid organ transplant recipients.

Background: Post-acute sequelae of coronavirus disease 2019 (COVID-19) (PASC), defined as prolonged symptoms following an episode of COVID-19, is not well-characterized in solid organ transplant recipients (SOTR). In this study, we aimed to assess the prevalence of PASC in SOTR, its descriptive characteristics, and associated risk factors.

Methods: We retrospectively identified SOTRs with acute COVID-19 between June 1, 2020 and April 15, 2022, and abstracted demographic and medical history, characteristics of acute COVID-19 illness, and COVID-19 vaccination status.

Framework for converting mechanistic network models to probabilistic models.

There are two prominent paradigms for the modelling of networks: in the first, referred to as the mechanistic approach, one specifies a set of domain-specific mechanistic rules that are used to grow or evolve the network over time; in the second, referred to as the probabilistic approach, one describes a model that specifies the likelihood of observing a given network. Mechanistic models (models developed based on the mechanistic approach) are appealing because they capture scientific processes that are believed to be responsible for network generation; however, they do not easily lend themselves to the use of inferential techniques when compared with probabilistic models. We introduce a general framework for converting a mechanistic network model (MNM) to a probabilistic network model (PNM).

Modeling homophily in dynamic networks with application to HIV molecular surveillance.

Background: Efforts to control the HIV epidemic can benefit from knowledge of the relationships between the characteristics of people who have transmitted HIV and those who became infected by them. Investigation of this relationship is facilitated by the use of HIV genetic linkage analyses, which allows inference about possible transmission events among people with HIV infection. Two persons with HIV (PWH) are considered linked if the genetic distance between their HIV sequences is less than a given threshold, which implies proximity in a transmission network.

Identification of system-level features in HIV migration within a host.

Objective: Identify system-level features in HIV migration within a host across body tissues. Evaluate heterogeneity in the presence and magnitude of these features across hosts.

Method: Using HIV DNA deep sequencing data generated across multiple tissues from 8 people with HIV, we represent the complex dependencies of HIV migration among tissues as a network and model these networks using the family of exponential random graph models (ERGMs).

Impact of antiretroviral therapy intensification with C-C motif chemokine receptor 5 antagonist maraviroc on HIV-associated neurocognitive impairment.

Objectives: Chemokine receptor CCR5 is the principal co-receptor for entry of M-tropic HIV virus into immune cells. It is expressed in the central nervous system and may contribute to neuro-inflammation. The CCR5 antagonist maraviroc (MVC) has been suggested to improve HIV-associated neurocognitive impairment (NCI).

Estimating contact network properties by integrating multiple data sources associated with infectious diseases.

To effectively mitigate the spread of communicable diseases, it is necessary to understand the interactions that enable disease transmission among individuals in a population; we refer to the set of these interactions as a contact network. The structure of the contact network can have profound effects on both the spread of infectious diseases and the effectiveness of control programs. Therefore, understanding the contact network permits more efficient use of resources.

Leveraging Contact Network Information in Clustered Randomized Studies of Contagion Processes.

In a randomized study, leveraging covariates related to the outcome (e.g. disease status) may produce less variable estimates of the effect of exposure.

Network methods and design of randomized trials: Application to investigation of COVID-19 vaccination boosters.

Network science methods can be useful in design, monitoring, and analysis of randomized trials for control of spread of infections. Their usefulness arises from the role of statistical network models in molecular epidemiology and in study design. Computational models, such as agent-based models that propagate disease on simulated contact networks, can be used to investigate the properties of different study designs and analysis plans.

Evaluating the power of the causal impact method in observational studies of HCV treatment as prevention.

Objectives: The causal impact method (CIM) was recently introduced for evaluation of binary interventions using observational time-series data. The CIM is appealing for practical use as it can adjust for temporal trends and account for the potential of unobserved confounding. However, the method was initially developed for applications involving large datasets and hence its potential in small epidemiological studies is still unclear.

A platform trial design for preventive vaccines against Marburg virus and other emerging infectious disease threats.

Background: The threat of a possible Marburg virus disease outbreak in Central and Western Africa is growing. While no Marburg virus vaccines are currently available for use, several candidates are in the pipeline. Building on knowledge and experiences in the designs of vaccine efficacy trials against other pathogens, including SARS-CoV-2, we develop designs of randomized Phase 3 vaccine efficacy trials for Marburg virus vaccines.

Predicting neural deficits in sensorineural hearing loss from word recognition scores.

The current gold standard of clinical hearing assessment includes a pure-tone audiogram combined with a word recognition task. This retrospective study tests the hypothesis that deficits in word recognition that cannot be explained by loss in audibility or cognition may reflect underlying cochlear nerve degeneration (CND). We collected the audiological data of nearly 96,000 ears from patients with normal hearing, conductive hearing loss (CHL) and a variety of sensorineural etiologies including (1) age-related hearing loss (ARHL); (2) neuropathy related to vestibular schwannoma or neurofibromatosis of type 2; (3) Ménière's disease; (4) sudden sensorineural hearing loss (SSNHL), (5) exposure to ototoxic drugs (carboplatin and/or cisplatin, vancomycin or gentamicin) or (6) noise damage including those with a 4-kHz "noise notch" or reporting occupational or recreational noise exposure.

Ensemble clustering of longitudinal bivariate HIV biomarker profiles to group patients by patterns of disease progression.

Unlabelled: This paper describes an ensemble cluster analysis of bivariate profiles of HIV biomarkers, viral load and CD4 cell counts, which jointly measure disease progression. Data are from a prevalent cohort of HIV positive participants in a clinical trial of vitamin supplementation in Botswana. These individuals were HIV positive upon enrollment, but with unknown times of infection.

Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial - BCPP/Ya Tsie trial.

Background: Mathematical models predict that community-wide access to HIV testing-and-treatment can rapidly and substantially reduce new HIV infections. Yet several large universal test-and-treat HIV prevention trials in high-prevalence epidemics demonstrated variable reduction in population-level incidence.

Methods: To elucidate patterns of HIV spread in universal test-and-treat trials, we quantified the contribution of geographic-location, gender, age, and randomized-HIV-intervention to HIV transmissions in the 30-community Ya Tsie trial in Botswana.

Coronavirus disease 2019 vaccination is protective of clinical disease in solid organ transplant recipients.

Background: Clinical effectiveness of coronavirus disease 2019 (COVID-19) vaccination in solid organ transplant recipients (SOTRs) is not well documented despite multiple studies demonstrating sub-optimal immunogenicity.

Methods: We reviewed medical records of eligible SOTRs at a single center to assess vaccination status and identify cases of symptomatic COVID-19 from January 1 to August 12, 2021. We developed a Cox proportional hazards model using the date of vaccination and time since transplantation as a time-varying covariate with age and gender as potential time-invariant confounders.

Effective Human Immunodeficiency Virus Molecular Surveillance Requires Identification of Incident Cases of Infection.

Background: Ending the human immunodeficiency virus (HIV) epidemic requires knowledge of key drivers of spread of HIV infection.

Methods: Between 1996 and 2018, 1119 newly and previously diagnosed, therapy-naive persons with HIV (PWH) from San Diego were followed. A genetic distance-based network was inferred using pol sequences, and genetic clusters grew over time through linkage of sequences from newly observed infections.

Primary Neural Degeneration in Noise-Exposed Human Cochleas: Correlations with Outer Hair Cell Loss and Word-Discrimination Scores.

Animal studies suggest that cochlear nerve degeneration precedes sensory cell degeneration in both noise-induced hearing loss (NIHL) and age-related hearing loss (ARHL), producing a hearing impairment that is not reflected in audiometric thresholds. Here, we investigated the histopathology of human ARHL and NIHL by comparing loss of auditory nerve fibers (ANFs), cochlear hair cells and the stria vascularis in a group of 52 cases with noise-exposure history against an age-matched control group. Although strial atrophy increased with age, there was no effect of noise history.