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Food-drug interactions (FDIs) occur when a food item alters the pharmacokinetics or pharmacodynamics of a drug. FDIs can be clinically relevant, as they can hamper or enhance the therapeutic effects of a drug and impact both their efficacy and their safety. However, knowledge of FDIs in clinical practice is limited. This is partially due to the lack of resources focused on FDIs. Here, we describe FooDrugs, a database that centralizes FDI knowledge retrieved from two different approaches: a natural processing language pipeline that extracts potential FDIs from scientific documents and clinical trials and a molecular similarity approach based on the comparison of gene expression alterations caused by foods and drugs. FooDrugs database stores a total of 3 430 062 potential FDIs, with 1 108 429 retrieved from scientific documents and 2 321 633 inferred from molecular data. This resource aims to provide researchers and clinicians with a centralized repository for potential FDI information that is free and easy to use. Database URL:  https://zenodo.org/records/8192515 Database DOI:  https://doi.org/10.5281/zenodo.6638469., (© The Author(s) 2023. Published by Oxford University Press.)

Background: Mailed fecal immunochemical test (FIT) outreach can improve colorectal cancer screening rates, yet little is known about how to optimize these programs for effectiveness and cost., Methods: PROMPT was a pragmatic, stepped-wedge, cluster-randomized effectiveness trial of mailed FIT outreach. Participants in the standard condition were mailed a FIT and received live telephone reminders to return it. Participants in the enhanced condition also received a tailored advance notification (text message or live phone call) and two automated phone call reminders. The primary outcome was 6-month FIT completion; secondary outcomes were any colorectal cancer screening completion at 6 months, implementation, and program costs., Results: The study included 27,585 participants (80% ages 50-64, 82% Hispanic/Latino; 68% preferred Spanish). A higher proportion of enhanced participants completed FIT at 6 months than standard participants, both in intention-to-treat [+2.8%, 95% confidence interval (CI; 0.4-5.2)] and per-protocol [limited to individuals who were reached; +16.9%, 95% CI (12.3-20.3)] analyses. Text messages and automated calls were successfully delivered to 91% to 100% of participants. The per-patient cost for standard mailed FIT was $10.84. The enhanced program's text message plus automated call reminder cost an additional $0.66; live phone calls plus an automated call reminder cost an additional $10.82 per patient., Conclusions: Adding advance notifications and automated calls to a standard mailed FIT program boosted 6-month FIT completion rates at a small additional per-patient cost., Impact: Enhancements to mailed FIT outreach can improve colorectal cancer screening participation. Future research might test the addition of educational video messaging for screening-naïve adults., (©2023 American Association for Cancer Research.)

The increasing prevalence of diet-related diseases calls for an improvement in nutritional advice. Personalized nutrition aims to solve this problem by adapting dietary and lifestyle guidelines to the unique circumstances of each individual. With the latest advances in technology and data science, researchers can now automatically collect and analyze large amounts of data from a variety of sources, including wearable and smart devices. By combining these diverse data, more comprehensive insights of the human body and its diseases can be achieved. However, there are still major challenges to overcome, including the need for more robust data and standardization of methodologies for better subject monitoring and assessment. Here, we present the AI4Food database (AI4FoodDB), which gathers data from a nutritional weight loss intervention monitoring 100 overweight and obese participants during 1 month. Data acquisition involved manual traditional approaches, novel digital methods and the collection of biological samples, obtaining: (i) biological samples at the beginning and the end of the intervention, (ii) anthropometric measurements every 2 weeks, (iii) lifestyle and nutritional questionnaires at two different time points and (iv) continuous digital measurements for 2 weeks. To the best of our knowledge, AI4FoodDB is the first public database that centralizes food images, wearable sensors, validated questionnaires and biological samples from the same intervention. AI4FoodDB thus has immense potential for fostering the advancement of automatic and novel artificial intelligence techniques in the field of personalized care. Moreover, the collected information will yield valuable insights into the relationships between different variables and health outcomes, allowing researchers to generate and test new hypotheses, identify novel biomarkers and digital endpoints, and explore how different lifestyle, biological and digital factors impact health. The aim of this article is to describe the datasets included in AI4FoodDB and to outline the potential that they hold for precision health research. Database URL https://github.com/AI4Food/AI4FoodDB., (© The Author(s) 2023. Published by Oxford University Press.)

Background: Children with bronchopulmonary dysplasia (BPD) who require invasive home mechanical ventilation (IHMV) are medically vulnerable and experience high caregiving and healthcare costs. Predictors for duration of IHMV in children with BPD remain unclear, which can make prognostication and decision-making challenging., Methods: A retrospective cohort study of children with BPD requiring IHMV was conducted from independent children's hospital records (2005-2021). The primary outcome was IHMV duration, defined as time from initial discharge home on IHMV until cessation of positive pressure ventilation (day and night). Two new variables were included: discharge age corrected for tracheostomy (DACT) (chronological age at discharge minus age at tracheostomy) and level of ventilator support at discharge (minute ventilation per kg per day). Univariable Cox regression was performed with variables of interest compared to IHMV duration. Significant nonlinear factors (p < 0.05) were included in the multivariable analysis., Results: One-hundred-and-nineteen patients used IHMV primarily for BPD. Patient median index hospitalization lasted 12 months (interquartile range [IQR] 8.0,14.4). Once home, half of the patients were weaned off IHMV by 36.0 months and 90% by 52.2 months. Being Hispanic/Latinx ethnicity (hazard ratio [HR] 0.14 (95% confidence interval [CI] 0.04, 0.53), p < 0.01) and having a higher DACT were associated with increased IHMV duration (HR 0.66 (CI 0.43, 0.98), p < 0.05)., Conclusions: Disparity in IHMV duration exists among patients using IHMV after prematurity. Prospective multisite studies that further investigate new analytic variables, such as DACT and level of ventilator support, and address standardization of IHMV care are needed to create more equitable IHMV management strategies., (© 2023 The Authors. Pediatric Pulmonology published by Wiley Periodicals LLC.)

Characterization of gene regulatory networks is fundamental to understanding homeostatic development. This process can be simplified by analyzing relatively simple genomes such as the genome of Drosophila melanogaster. In this work we have developed a computational framework in Drosophila to explore for the presence of gene regulatory circuits between two large groups of transcriptional regulators: the epigenetic group of the Polycomb/trithorax (PcG/trxG) proteins and the microRNAs (miRNAs). We have searched genome-wide for miRNA targets in PcG/trxG transcripts as well as for Polycomb Response Elements (PREs) in miRNA genes. Our results show that 10% of the analyzed miRNAs could be controlling PcG/trxG gene expression, while 40% of those miRNAs are putatively controlled by the selected set of PcG/trxG proteins. The integration of these analyses has resulted in the predicted existence of 3 classes of miRNA-PcG/trxG crosstalk interactions that define potential regulatory circuits. In the first class, miRNA-PcG circuits are defined by miRNAs that reciprocally crosstalk with PcG. In the second, miRNA-trxG circuits are defined by miRNAs that reciprocally crosstalk with trxG. In the third class, miRNA-PcG/trxG shared circuits are defined by miRNAs that crosstalk with both PcG and trxG regulators. These putative regulatory circuits may uncover a novel mechanism in Drosophila for the control of PcG/trxG and miRNAs levels of expression. The computational framework developed here for Drosophila melanogaster can serve as a model case for similar analyses in other species. Moreover, our work provides, for the first time, a new and useful resource for the Drosophila community to consult prior to experimental studies investigating the epigenetic regulatory networks of miRNA-PcG/trxG mediated gene expression., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Background: The molecular pathogenesis of T-cell large granular lymphocytic leukemia (T-LGLL), a mature T-cell leukemia arising commonly from T-cell receptor αβ-positive CD8 + memory cytotoxic T cells, is only partly understood. The role of deregulated methylation in T-LGLL is not well known. We analyzed the epigenetic profile of T-LGLL cells of 11 patients compared to their normal counterparts by array-based DNA methylation profiling. For identification of molecular events driving the pathogenesis of T-LGLL, we compared the differentially methylated loci between the T-LGLL cases and normal T cells with chromatin segmentation data of benign T cells from the BLUEPRINT project. Moreover, we analyzed gene expression data of T-LGLL and benign T cells and validated the results by pyrosequencing in an extended cohort of 17 patients, including five patients with sequential samples., Results: We identified dysregulation of DNA methylation associated with altered gene expression in T-LGLL. Since T-LGLL is a rare disease, the samples size is low. But as confirmed for each sample, hypermethylation of T-LGLL cells at various CpG sites located at enhancer regions is a hallmark of this disease. The interaction of BLC11B and C14orf64 as suggested by in silico data analysis could provide a novel pathogenetic mechanism that needs further experimental investigation., Conclusions: DNA methylation is altered in T-LGLL cells compared to benign T cells. In particular, BCL11B is highly significant differentially methylated in T-LGLL cells. Although our results have to be validated in a larger patient cohort, BCL11B could be considered as a potential biomarker for this leukemia. In addition, altered gene expression and hypermethylation of enhancer regions could serve as potential mechanisms for treatment of this disease. Gene interactions of dysregulated genes, like BLC11B and C14orf64, may play an important role in pathogenic mechanisms and should be further analyzed., (© 2022. The Author(s).)