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Hidden Markov models (HMMs) have been proposed to model the natural history of diseases while accounting for misclassification in state identification. We introduce a discrete time HMM for human papillomavirus (HPV) and cervical precancer/cancer where the hidden and observed state spaces are defined by all possible combinations of HPV, cytology, and colposcopy results. Because the population of women undergoing cervical cancer screening is heterogeneous with respect to sexual behavior, and therefore risk of HPV acquisition and subsequent precancers, we use a mover‐stayer mixture model that assumes a proportion of the population will stay in the healthy state and are not subject to disease progression. As each state is a combination of three distinct tests that characterize the cervix, partially observed data arise when at least one but not every test is observed. The standard forward‐backward algorithm, used for evaluating the E‐step within the E‐M algorithm for maximum‐likelihood estimation of HMMs, cannot incorporate time points with partially observed data. We propose a new forward‐backward algorithm that considers all possible fully observed states that could have occurred across a participant's follow‐up visits. We apply our method to data from a large management trial for women with low‐grade cervical abnormalities. Our simulation study found that our method has relatively little bias and out preforms simpler methods that resulted in larger bias.

Dinophysis spp. can produce diarrhetic shellfish toxins (DST) including okadaic acid and dinophysistoxins, and some strains can also produce non-diarrheic pectenotoxins. Although DSTs are of human health concern and have motivated environmental monitoring programs in many locations, these monitoring programs often have temporal data gaps (e.g., days without measurements). This paper presents a model for the historical time-series, on a daily basis, of DST-producing toxigenic Dinophysis in 8 monitored locations in western Andalucía over 2015–2020, incorporating measurements of algae counts and DST levels. We fitted a bivariate hidden Markov Model (HMM) incorporating an autoregressive correlation among the observed DST measurements to account for environmental persistence of DST. We then reconstruct the maximum-likelihood profile of algae presence in the water column at daily intervals using the Viterbi algorithm. Using historical monitoring data from Andalucía, the model estimated that potentially toxigenic Dinophysis algae is present at greater than or equal to 250 cells/L between< 1% and>10% of the year depending on the site and year. The historical time-series reconstruction enabled by this method may facilitate future investigations into temporal dynamics of toxigenic Dinophysis blooms.

Background Chronic obstructive pulmonary disease (COPD) is a leading cause of mortality worldwide. Identifying both individual and community risk factors associated with higher mortality is essential to improve outcomes. Few population-based studies of mortality in COPD include both individual characteristics and community risk factors. Objective We used geocoded, patient-level data to describe the associations between individual demographics, neighborhood socioeconomic status, and all-cause mortality. Methods We performed a nationally representative retrospective cohort analysis of all patients enrolled in the Veteran Health Administration with at least one ICD-9 or ICD-10 code for COPD in 2016–2019. We obtained demographic characteristics, comorbidities, and geocoded residential address. Area Deprivation Index and rurality were classified using individual geocoded residential addresses. We used logistic regression models to assess the association between these characteristics and age-adjusted all-cause mortality. Results Of 1,106,163 COPD patients, 33.4% were deceased as of January 2021. In age-adjusted models, having more comorbidities, Black/African American race (OR 1.09 [95% CI: 1.08–1.11]), and higher neighborhood disadvantage (OR 1.30 [95% CI: 1.28–1.32]) were associated with all-cause mortality. Female sex (OR 0.67 [95% CI: 0.65–0.69]), Asian race (OR 0.64, [95% CI: 0.59–0.70]), and living in a more rural area were associated with lower odds of all-cause mortality. After adjusting for age, comorbidities, neighborhood socioeconomic status, and rurality, the association with Black/African American race reversed. Conclusion All-cause mortality in COPD patients is disproportionately higher in patients living in poorer neighborhoods and urban areas, suggesting the impact of social determinants of health on COPD outcomes. Black race was associated with higher age-adjusted all-cause mortality, but this association was abrogated after adjusting for gender, socioeconomic status, comorbidities, and urbanicity. Future studies should focus on exploring mechanisms by which disparities arise and developing interventions to address these.