Toward a better understanding of nonoccupational sound exposures and associated health impacts: Methods of the Apple Hearing Study.

Globally, noise exposure from occupational and nonoccupational sources is common, and, as a result, noise-induced hearing loss affects tens of millions of people. Occupational noise exposures have been studied and regulated for decades, but nonoccupational sound exposures are not well understood. The nationwide Apple Hearing Study, launched using the Apple research app in November 2019 (Apple Inc., Cupertino, CA), is characterizing the levels at which participants listen to headphone audio content, as well as their listening habits. This paper describes the methods of the study, which collects data from several types of hearing tests and uses the Apple Watch noise app to measure environmental sound levels and cardiovascular metrics. Participants, all of whom have consented to participate and share their data, have already contributed nearly 300 × 106 h of sound measurements and 200 000 hearing assessments. The preliminary results indicate that environmental sound levels have been higher, on average, than headphone audio, about 10% of the participants have a diagnosed hearing loss, and nearly 20% of the participants have hearing difficulty. The study's analyses will promote understanding of the overall exposures to sound and associated impacts on hearing and cardiovascular health. This study also demonstrates the feasibility of collecting clinically relevant exposure and health data outside of traditional research settings.

Passive Nocturnal Physiologic Monitoring Enables Early Detection of Exacerbations in Children with Asthma. A Proof-of-Concept Study.

RATIONALE: Asthma management depends on prompt identification of symptoms, which challenges both patients and providers. In asthma, a misapprehension of health between exacerbations can compromise compliance. Thus, there is a need for a tool that permits objective longitudinal monitoring without increasing the burden of patient compliance. OBJECTIVES: We sought to determine whether changes in nocturnal physiology are associated with asthma symptoms in pediatric patients. METHODS: Using a contactless bed sensor, nocturnal heart rate (HR), respiratory rate, relative stroke volume, and movement in children with asthma 5-18 years of age (n = 16) were recorded. Asthma symptoms and asthma control test (ACT) score were reported every 2 weeks. Random forest model was used to identify physiologic parameters associated with asthma symptoms. Elastic net regression was used to identify variables associated with ACT score. MEASUREMENTS AND MAIN RESULTS: The model on the full cohort performed with sensitivity of 47.2%, specificity of 96.3%, and accuracy of 87.4%; HR and respiratory parameters were the most important variables in this model. The model predicted asthma symptoms 35% of the time on the day before perception of symptoms, and 100% of the time for a select subject for which the model performed with greater sensitivity. Multivariable and bivariable analyses demonstrated significant association between HR and respiratory rate parameters and ACT score. CONCLUSIONS: Nocturnal physiologic changes correlate with asthma symptoms, supporting the notion that nocturnal physiologic monitoring represents an objective diagnostic tool capable of longitudinally assessing disease control and predicting asthma exacerbations in children with asthma at home.

Ligand pose and orientational sampling in molecular docking.

Molecular docking remains an important tool for structure-based screening to find new ligands and chemical probes. As docking ambitions grow to include new scoring function terms, and to address ever more targets, the reliability and extendability of the orientation sampling, and the throughput of the method, become pressing. Here we explore sampling techniques that eliminate stochastic behavior in DOCK3.6, allowing us to optimize the method for regularly variable sampling of orientations. This also enabled a focused effort to optimize the code for efficiency, with a three-fold increase in the speed of the program. This, in turn, facilitated extensive testing of the method on the 102 targets, 22,805 ligands and 1,411,214 decoys of the Directory of Useful Decoys-Enhanced (DUD-E) benchmarking set, at multiple levels of sampling. Encouragingly, we observe that as sampling increases from 50 to 500 to 2000 to 5000 to 20,000 molecular orientations in the binding site (and so from about 1×10(10) to 4×10(10) to 1×10(11) to 2×10(11) to 5×10(11) mean atoms scored per target, since multiple conformations are sampled per orientation), the enrichment of ligands over decoys monotonically increases for most DUD-E targets. Meanwhile, including internal electrostatics in the evaluation ligand conformational energies, and restricting aromatic hydroxyls to low energy rotamers, further improved enrichment values. Several of the strategies used here to improve the efficiency of the code are broadly applicable in the field.

Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking.

A key metric to assess molecular docking remains ligand enrichment against challenging decoys. Whereas the directory of useful decoys (DUD) has been widely used, clear areas for optimization have emerged. Here we describe an improved benchmarking set that includes more diverse targets such as GPCRs and ion channels, totaling 102 proteins with 22886 clustered ligands drawn from ChEMBL, each with 50 property-matched decoys drawn from ZINC. To ensure chemotype diversity, we cluster each target's ligands by their Bemis-Murcko atomic frameworks. We add net charge to the matched physicochemical properties and include only the most dissimilar decoys, by topology, from the ligands. An online automated tool (http://decoys.docking.org) generates these improved matched decoys for user-supplied ligands. We test this data set by docking all 102 targets, using the results to improve the balance between ligand desolvation and electrostatics in DOCK 3.6. The complete DUD-E benchmarking set is freely available at http://dude.docking.org.