Plant microRNAs (miRNAs) are short, noncoding RNA molecules that restrict gene expression via posttranscriptional regulation and function in several essential pathways, including development, growth, and stress responses. Accurately identifying miRNAs in populations of small RNA sequencing libraries is a computationally intensive process that has resulted in the misidentification of inaccurately annotated miRNA sequences. In recent years, criteria for miRNA annotation have been refined with the aim to reduce these misannotations. Here, we describe miRador, a miRNA identification tool that utilizes the most up-to-date, community-established criteria for accurate identification of miRNAs in plants. We combined target prediction and Parallel Analysis of RNA Ends (PARE) data to assess the precision of the miRNAs identified by miRador. We compared miRador to other commonly used miRNA prediction tools and found that miRador is at least as precise as other prediction tools while being substantially faster than other tools. miRador should be broadly useful for the plant community to identify and annotate miRNAs in plant genomes.

The Solanaceae or “nightshade” family is an economically important group with remarkable diversity. To gain a better understanding of how the unique biology of the Solanaceae relates to the family’s small RNA (sRNA) genomic landscape, we downloaded over 255 publicly available sRNA data sets that comprise over 2.6 billion reads of sequence data. We applied a suite of computational tools to predict and annotate two major sRNA classes: (1) microRNAs (miRNAs), typically 20- to 22-nucleotide (nt) RNAs generated from a hairpin precursor and functioning in gene silencing and (2) short interfering RNAs (siRNAs), including 24-nt heterochromatic siRNAs typically functioning to repress repetitive regions of the genome via RNA-directed DNA methylation, as well as secondary phased siRNAs and trans-acting siRNAs generated via miRNA-directed cleavage of a polymerase II-derived RNA precursor. Our analyses described thousands of sRNA loci, including poorly understood clusters of 22-nt siRNAs that accumulate during viral infection. The birth, death, expansion, and contraction of these sRNA loci are dynamic evolutionary processes that characterize the Solanaceae family. These analyses indicate that individuals within the same genus share similar sRNA landscapes, whereas comparisons between distinct genera within the Solanaceae reveal relatively few commonalities.

Shortness of breath is often considered a repercussion of aging in older adults, as respiratory illnesses like COPD¹ or respiratory illnesses due to heart-related issues are often misdiagnosed, under-diagnosed or ignored at early stages. Continuous health monitoring using ambient sensors has the potential to ameliorate this problem for older adults at aging-in-place facilities. In this paper, we leverage continuous respiratory health data collected by using ambient hydraulic bed sensors installed in the apartments of older adults in aging-in-place Americare facilities to find data-adaptive indicators related to shortness of breath. We used unlabeled data collected unobtrusively over the span of three years from a COPD-diagnosed individual and used data mining to label the data. These labeled data are then used to train a predictive model to make future predictions in older adults related to shortness of breath abnormality. To pick the continuous changes in respiratory health we make predictions for shorter time windows (60-s). Hence, to summarize each day's predictions we propose an abnormal breathing index (ABI) in this paper. To showcase the trajectory of the shortness of breath abnormality over time (in terms of days), we also propose trend analysis on the ABI quarterly and incrementally. We have evaluated six individual cases retrospectively to highlight the potential and use cases of our approach.

Background: Stigmatizing language is common in clinical notes and can adversely affect the quality of patient care. Natural language processing (NLP) is a promising technology for identifying such language across large volumes of clinical notes in electronic health records. Objective: This study proposes an NLP-driven reduce stigmatizing language (ENGAGE) system to automatically identify and replace stigmatizing language. Methods: Using a mixed methods study, we will extract electronic health record data for patients admitted to 2 large, diverse home health care (HHC) organizations between January 2019 and December 2021. We propose the following 4 aims: aim 1 is to refine the ontology of stigmatizing language in HHC by (1) interviewing a diverse sample of HHC nurses and patients to identify terms to avoid and (2) analyzing clinical notes from various regions in the United States to categorize stigmatizing language. Aim 2 is to determine the best NLP approach for accurately identifying stigmatizing language by training algorithms and comparing their performance to human annotations. Aim 3 is to analyze the prevalence of stigmatizing language based on patients’ race and ethnicity using adjusted statistical analyses of a sample of approximately half a million HHC patients (34% racial and ethnic minority groups). Aim 4 is to develop the NLP-driven ENGAGE system by (1) testing NLP methods (rule based; “delete, retrieve, and generate”; and transformers) for suggesting alternative wording and (2) designing and refining the user interface for clinical trial preparation. Results: We received funding from the National Institute on Minority Health and Health Disparities in September 2023. Recruitment began in May 2024, and as of March 2025, interviews have been completed for 9 enrolled participants. We anticipate completing all study aims by April 2027. Conclusions: This study will leverage extensive data sources to examine stigmatizing language in HHC settings and contribute to the development of systems aimed at effectively reducing the use of such language among HHC nurses. International Registered Report Identifier (IRRID): DERR1-10.2196/69753