Long COVID, or complications arising from COVID-19 weeks after infection, has become a central concern for public health experts. The United States National Institutes of Health founded the RECOVER initiative to better understand long COVID. We used electronic health records available through the National COVID Cohort Collaborative to characterize the association between SARS-CoV-2 vaccination and long COVID diagnosis. Among patients with a COVID-19 infection between August 1, 2021 and January 31, 2022, we defined two cohorts using distinct definitions of long COVID—a clinical diagnosis (n = 47,404) or a previously described computational phenotype (n = 198,514)—to compare unvaccinated individuals to those with a complete vaccine series prior to infection. Evidence of long COVID was monitored through June or July of 2022, depending on patients’ data availability. We found that vaccination was consistently associated with lower odds and rates of long COVID clinical diagnosis and high-confidence computationally derived diagnosis after adjusting for sex, demographics, and medical history.

Accurate projections of seasonal agricultural output are essential for improving food security. However, the collection of agricultural information through seasonal agricultural surveys is often not timely enough to inform public and private stakeholders about crop status during the growing season. Acquiring timely and accurate crop estimates can be particularly challenging in countries with predominately smallholder farms because of the large number of small plots, intense intercropping, and high diversity of crop types. In this study, we used RGB images collected from unmanned aerial vehicles (UAVs) flown in Rwanda to develop a deep learning algorithm for identifying crop types, specifically bananas, maize, and legumes, which are key strategic food crops in Rwandan agriculture. The model leverages advances in deep convolutional neural networks and transfer learning, employing the VGG16 architecture and the publicly accessible ImageNet dataset for pretraining. The developed model performs with an overall test set F1 of 0.86, with individual classes ranging from 0.49 (legumes) to 0.96 (bananas). Our findings suggest that although certain staple crops such as bananas and maize can be classified at this scale with high accuracy, crops involved in intercropping (legumes) can be difficult to identify consistently. We discuss the potential use cases for the developed model and recommend directions for future research in this area.

Tumor testing for mutations in the epidermal growth factor receptor (EGFR) gene is indicated for all newly diagnosed, metastatic lung cancer patients, who may be candidates for first-line treatment with an EGFR tyrosine kinase inhibitor. Few studies have analyzed population-level testing. We identified clinical, demographic, and regional predictors of EGFR & KRAS testing among Medicare beneficiaries with a new diagnosis of lung cancer in 2011–2013 claims. The outcome variable was whether the patient underwent molecular, EGFR and KRAS testing. Independent variables included: patient demographics, Medicaid status, clinical characteristics, and region where the patient lived. We performed multivariate logistic regression to identify factors that predicted testing. From 2011 to 2013, there was a 19.7% increase in the rate of EGFR testing. Patient zip code had the greatest impact on odds to undergo testing; for example, patients who lived in the Boston, Massachusetts hospital referral region were the most likely to be tested (odds ratio (OR) of 4.94, with a 95% confidence interval (CI) of 1.67–14.62). Patient demographics also impacted odds to be tested. Asian/Pacific Islanders were most likely to be tested (OR 1.63, CI 1.53–1.79). Minorities and Medicaid patients were less likely to be tested. Medicaid recipients had an OR of 0.74 (CI 0.72–0.77). Hispanics and Blacks were also less likely to be tested (OR 0.97, CI 0.78–0.99 and 0.95, CI 0.92–0.99), respectively. Clinical procedures were also correlated with testing. Patients who underwent transcatheter biopsies were 2.54 times more likely to be tested (CI 2.49–2.60) than those who did not undergo this type of biopsy. Despite an overall increase in EGFR testing, there is widespread underutilization of guideline-recommended testing. We observed racial, income, and regional disparities in testing. Precision medicine has increased the complexity of cancer diagnosis and treatment. Targeted interventions and clinical decision support tools are needed to ensure that all patients are benefitting from advances in precision medicine. Without such interventions, precision medicine may exacerbate racial disparities in cancer care and health outcomes.

Background: Although the COVID-19 pandemic has persisted for over 3 years, reinfections with SARS-CoV-2 are not well understood. We aim to characterize reinfection, understand development of Long COVID after reinfection, and compare severity of reinfection with initial infection. Methods: We use an electronic health record study cohort of over 3 million patients from the National COVID Cohort Collaborative as part of the NIH Researching COVID to Enhance Recovery Initiative. We calculate summary statistics, effect sizes, and Kaplan–Meier curves to better understand COVID-19 reinfections. Results: Here we validate previous findings of reinfection incidence (6.9%), the occurrence of most reinfections during the Omicron epoch, and evidence of multiple reinfections. We present findings that the proportion of Long COVID diagnoses is higher following initial infection than reinfection for infections in the same epoch. We report lower albumin levels leading up to reinfection and a statistically significant association of severity between initial infection and reinfection (chi-squared value: 25,697, p-value: <0.0001) with a medium effect size (Cramer’s V: 0.20, DoF = 3). Individuals who experienced severe initial and first reinfection were older in age and at a higher mortality risk than those who had mild initial infection and reinfection. Conclusions: In a large patient cohort, we find that the severity of reinfection appears to be associated with the severity of initial infection and that Long COVID diagnoses appear to occur more often following initial infection than reinfection in the same epoch. Future research may build on these findings to better understand COVID-19 reinfections.

Deductive coding is a widely used qualitative research method for determining the prevalence of themes across documents. While useful, deductive coding is often burdensome and time consuming since it requires researchers to read, interpret, and reliably categorize a large body of unstructured text documents. Large language models (LLMs), like ChatGPT, are a class of quickly evolving AI tools that can perform a range of natural language processing and reasoning tasks. In this study, we explore the use of LLMs to reduce the time it takes for deductive coding while retaining the flexibility of a traditional content analysis. We outline the proposed approach, called LLM-assisted content analysis (LACA), along with an in-depth case study using GPT-3.5 for LACA on a publicly available deductive coding data set. Additionally, we conduct an empirical benchmark using LACA on 4 publicly available data sets to assess the broader question of how well GPT-3.5 performs across a range of deductive coding tasks. Overall, we find that GPT-3.5 can often perform deductive coding at levels of agreement comparable to human coders. Additionally, we demonstrate that LACA can help refine prompts for deductive coding, identify codes for which an LLM is randomly guessing, and help assess when to use LLMs vs. human coders for deductive coding. We conclude with several implications for future practice of deductive coding and related research methods.

Data extraction is a critical but error-prone and labor-intensive task in evidence synthesis. Unlike other artificial intelligence (AI) technologies, large language models (LLMs) do not require labeled training data for data extraction. To compare an AI-assisted versus a traditional, human-only data extraction process. Study within reviews (SWAR) using a prospective, parallel-group comparison with blinded data adjudicators. Workflow validation within 6 ongoing systematic reviews of interventions under real-world conditions. Initial data extraction using an LLM (Claude, versions 2.1, 3.0 Opus, and 3.5 Sonnet) verified by a human reviewer. Concordance, time on task, accuracy, sensitivity, positive predictive value, and error analysis. The 6 systematic reviews in the SWAR yielded 9341 data elements from 63 studies. Concordance between the 2 methods was 77.2% (95% CI, 76.3% to 78.0%). Compared with the reference standard, the AI-assisted approach had an accuracy of 91.0% (CI, 90.4% to 91.6%) and the human-only approach an accuracy of 89.0% (CI, 88.3% to 89.6%). Sensitivities were 89.4% (CI, 88.6% to 90.1%) and 86.5% (CI, 85.7% to 87.3%), respectively, with positive predictive values of 99.2% (CI, 99.0% to 99.4%) and 98.9% (CI, 98.6% to 99.1%). Incorrect data were extracted in 9.0% (CI, 8.4% to 9.6%) of AI-assisted cases and 11.0% (CI, 10.4% to 11.7%) of human-only cases, with corresponding proportions of major errors of 2.5% (CI, 2.2% to 2.8%) versus 2.7% (CI, 2.4% to 3.1%). Missed data items were the most frequent error type in both approaches. The AI-assisted method reduced data extraction time by a median of 41 minutes per study. Assessing concordance and classifying errors required subjective judgment. Consistently tracking time on task was challenging. Data extraction assisted by AI may offer a viable, more efficient alternative to human-only methods. Agency for Healthcare Research and Quality and RTI International.