Advances in Bayesian Optimization with Applications in Aerospace Engineering

Optimization requires the quantities of interest that define objective functions and constraints to be evaluated a large number of times. In aerospace engineering, these quantities of interest can be expensive to compute (e.g., numerically solving a set of partial differential equations), leading to a challenging optimization problem. Bayesian optimization (BO) is a class of algorithms for the global optimization of expensive-to-evaluate functions. BO leverages all past evaluations available to construct a surrogate model. This surrogate model is then used to select the next design to evaluate. This paper reviews two recent advances in BO that tackle the challenges of optimizing expensive functions and thus can enrich the optimization toolbox of the aerospace engineer. The first method addresses optimization problems subject to inequality constraints where a finite budget of evaluations is available, a common situation when dealing with expensive models (e.g., a limited time to conduct the optimization study or limited access to a supercomputer). This challenge is addressed via a lookahead BO algorithm that plans the sequence of designs to evaluate in order to maximize the improvement achieved, not only at the next iteration, but once the total budget is consumed. The second method demonstrates how sensitivity information, such as gradients computed with adjoint methods, can be incorporated into a BO algorithm. This algorithm exploits sensitivity information in two ways: first, to enhance the surrogate model, and second, to improve the selection of the next design to evaluate by accounting for future gradient evaluations. The benefits of the two methods are demonstrated on aerospace examples

ROMOP: a light-weight R package for interfacing with OMOP-formatted electronic health record data.

Objectives:Electronic health record (EHR) data are increasingly used for biomedical discoveries. The nature of the data, however, requires expertise in both data science and EHR structure. The Observational Medical Out-comes Partnership (OMOP) common data model (CDM) standardizes the language and structure of EHR data to promote interoperability of EHR data for research. While the OMOP CDM is valuable and more attuned to research purposes, it still requires extensive domain knowledge to utilize effectively, potentially limiting more widespread adoption of EHR data for research and quality improvement. Materials and methods:We have created ROMOP: an R package for direct interfacing with EHR data in the OMOP CDM format. Results:ROMOP streamlines typical EHR-related data processes. Its functions include exploration of data types, extraction and summarization of patient clinical and demographic data, and patient searches using any CDM vocabulary concept. Conclusion:ROMOP is freely available under the Massachusetts Institute of Technology (MIT) license and can be obtained from GitHub (http://github.com/BenGlicksberg/ROMOP). We detail instructions for setup and use in the Supplementary Materials. Additionally, we provide a public sandbox server containing synthesized clinical data for users to explore OMOP data and ROMOP (http://romop.ucsf.edu)

PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model.

MotivationElectronic health records (EHRs) are quickly becoming omnipresent in healthcare, but interoperability issues and technical demands limit their use for biomedical and clinical research. Interactive and flexible software that interfaces directly with EHR data structured around a common data model (CDM) could accelerate more EHR-based research by making the data more accessible to researchers who lack computational expertise and/or domain knowledge.ResultsWe present PatientExploreR, an extensible application built on the R/Shiny framework that interfaces with a relational database of EHR data in the Observational Medical Outcomes Partnership CDM format. PatientExploreR produces patient-level interactive and dynamic reports and facilitates visualization of clinical data without any programming required. It allows researchers to easily construct and export patient cohorts from the EHR for analysis with other software. This application could enable easier exploration of patient-level data for physicians and researchers. PatientExploreR can incorporate EHR data from any institution that employs the CDM for users with approved access. The software code is free and open source under the MIT license, enabling institutions to install and users to expand and modify the application for their own purposes.Availability and implementationPatientExploreR can be freely obtained from GitHub: https://github.com/BenGlicksberg/PatientExploreR. We provide instructions for how researchers with approved access to their institutional EHR can use this package. We also release an open sandbox server of synthesized patient data for users without EHR access to explore: http://patientexplorer.ucsf.edu.Supplementary informationSupplementary data are available at Bioinformatics online

External dose assessment in the Ukraine following the Chernobyl accident

2014 Spring.Includes bibliographical references.While the physiological effects of radiation exposure have been well characterized in general, it remains unclear what the relationship is between large-scale radiological events and psychosocial behavior outcomes in individuals or populations. To investigate this, the National Science Foundation funded a research project in 2008 at the University of Colorado in collaboration with Colorado State University to expand the knowledge of complex interactions between radiation exposure, perception of risk, and psychosocial behavior outcomes by modeling outcomes for a representative sample of the population of the Ukraine which had been exposed to radiocontaminant materials released by the reactor accident at Chernobyl on 26 April 1986. In service of this project, a methodology (based substantially on previously published models specific to the Chernobyl disaster and the Ukrainian population) was developed for daily cumulative effective external dose and dose rate assessment for individuals in the Ukraine for as a result of the Chernobyl disaster. A software platform was designed and produced to estimate effective external dose and dose rate for individuals based on their age, occupation, and location of residence on each day between 26 April 1986 and 31 December 2009. A methodology was developed to transform published 137Cs soil deposition contour maps from the Comprehensive Atlas of Caesium Deposition on Europe after the Chernobyl Accident into a geospatial database to access these data as a radiological source term. Cumulative effective external dose and dose rate were computed for each individual in a 703-member cohort of Ukrainians randomly selected to be representative of the population of the country as a whole. Error was estimated for the resulting individual dose and dose rate values with Monte Carlo simulations. Distributions of input parameters for the dose assessment methodology were compared to computed dose and dose rate estimates to determine which parameters were driving the computed results. The mean external effective dose for all individuals in the cohort due to exposure to radiocontamination from the Chernobyl accident between 26 April 1986 and 31 December 2009 was found to be 1.2 mSv; the geometric mean was 0.84 mSv with a geometric standard deviation of 2.1. The mean value is well below the mean external effective dose expected due to typical background radiation (which in the United States over this time period would be 12.0 mSv). Sensitivity analysis suggests that the greatest driver of the distribution of individual dose estimates is lack of specific information about the daily behavior of each individual, specifically the portion of time each individual spent indoors (and shielded from radionuclides deposited on the soil) versus outdoors (and unshielded)

Academic Emergency Medicine Physicians' Anxiety Levels, Stressors, and Potential Stress Mitigation Measures During the Acceleration Phase of the COVID-19 Pandemic.

ObjectiveThe objective was to assess anxiety and burnout levels, home life changes, and measures to relieve stress of U.S. academic emergency medicine (EM) physicians during the COVID-19 pandemic acceleration phase.MethodsWe sent a cross-sectional e-mail survey to all EM physicians at seven academic emergency departments. The survey incorporated items from validated stress scales and assessed perceptions and key elements in the following domains: numbers of suspected COVID-19 patients, availability of diagnostic testing, levels of home and workplace anxiety, severity of work burnout, identification of stressors, changes in home behaviors, and measures to decrease provider anxiety.ResultsA total of 426 (56.7%) EM physicians responded. On a scale of 1 to 7 (1 = not at all, 4 = somewhat, and 7 = extremely), the median (interquartile range) reported effect of the pandemic on both work and home stress levels was 5 (4-6). Reported levels of emotional exhaustion/burnout increased from a prepandemic median (IQR) of 3 (2-4) to since the pandemic started a median of 4 (3-6), with a difference in medians of 1.8 (95% confidence interval = 1.7 to 1.9). Most physicians (90.8%) reported changing their behavior toward family and friends, especially by decreasing signs of affection (76.8%). The most commonly cited measures cited to alleviate stress/anxiety were increasing personal protective equipment (PPE) availability, offering rapid COVID-19 testing at physician discretion, providing clearer communication about COVID-19 protocol changes, and assuring that physicians can take leave for care of family and self.ConclusionsDuring the acceleration phase, the COVID-19 pandemic has induced substantial workplace and home anxiety in academic EM physicians, and their exposure during work has had a major impact on their home lives. Measures cited to decrease stress include enhanced availability of PPE, rapid turnaround testing at provider discretion, and clear communication about COVID-19 protocol changes

Academic Emergency Medicine Physicians' Anxiety Levels, Stressors, and Potential Stress Mitigation Measures During the Acceleration Phase of the COVID‐19 Pandemic

ObjectiveThe objective was to assess anxiety and burnout levels, home life changes, and measures to relieve stress of U.S. academic emergency medicine (EM) physicians during the COVID-19 pandemic acceleration phase.MethodsWe sent a cross-sectional e-mail survey to all EM physicians at seven academic emergency departments. The survey incorporated items from validated stress scales and assessed perceptions and key elements in the following domains: numbers of suspected COVID-19 patients, availability of diagnostic testing, levels of home and workplace anxiety, severity of work burnout, identification of stressors, changes in home behaviors, and measures to decrease provider anxiety.ResultsA total of 426 (56.7%) EM physicians responded. On a scale of 1 to 7 (1 = not at all, 4 = somewhat, and 7 = extremely), the median (interquartile range) reported effect of the pandemic on both work and home stress levels was 5 (4-6). Reported levels of emotional exhaustion/burnout increased from a prepandemic median (IQR) of 3 (2-4) to since the pandemic started a median of 4 (3-6), with a difference in medians of 1.8 (95% confidence interval = 1.7 to 1.9). Most physicians (90.8%) reported changing their behavior toward family and friends, especially by decreasing signs of affection (76.8%). The most commonly cited measures cited to alleviate stress/anxiety were increasing personal protective equipment (PPE) availability, offering rapid COVID-19 testing at physician discretion, providing clearer communication about COVID-19 protocol changes, and assuring that physicians can take leave for care of family and self.ConclusionsDuring the acceleration phase, the COVID-19 pandemic has induced substantial workplace and home anxiety in academic EM physicians, and their exposure during work has had a major impact on their home lives. Measures cited to decrease stress include enhanced availability of PPE, rapid turnaround testing at provider discretion, and clear communication about COVID-19 protocol changes

Emergency physician stressors, concerns, and behavioral changes during COVID-19: A longitudinal study.

ObjectivesThe objective was to provide a longitudinal assessment of anxiety levels and work and home concerns of U.S. emergency physicians during the COVID-19 pandemic.MethodsWe performed a longitudinal, cross-sectional email survey of clinically active emergency physicians (attending, fellow, and resident) at seven academic emergency departments. Follow-up surveys were sent 4 to 6 weeks after the initial survey and assessed the following: COVID-19 patient exposure, availability of COVID-19 testing, levels of home and workplace anxiety/stress, changes in behaviors, and performance on a primary care posttraumatic stress disorder screen (PC-PTSD-5). Logistic regression explored factors associated with a high PC-PTSD-5 scale score (≥3), indicating increased risk for PTSD.ResultsOf the 426 surveyed initial respondents, 262 (61.5%) completed the follow-up survey. While 97.3% (255/262) reported treating suspected COVID-19 patients, most physicians (162/262, 61.8%) had not received testing themselves. In follow-up, respondents were most concerned about the relaxing of social distancing leading to a second wave (median score = 6, IQR = 4-7). Physicians reported a consistently high ability to order COVID-19 tests for patients (median score = 6, IQR = 5-7) and access to personal protective equipment (median score = 6, IQR = 5-6). Women physicians were more likely to score ≥ 3 than men on the PC-PTSD-5 screener on the initial survey (43.3% vs. 22.5%; Δ 20.8%, 95% confidence interval [CI] = 9.3% to 31.5%), and despite decreases in overall proportions, this discrepancy remained in follow-up (34.7% vs. 16.8%; Δ 17.9%, 95% CI = 7.1% to 28.1%). In examining the relationship between demographics, living situations, and institution location on having a PC-PTSD-5 score ≥ 3, only female sex was associated with a PC-PTSD-5 score ≥ 3 (adjusted odds ratio = 2.48, 95% CI = 1.28 to 4.79).ConclusionsWhile exposure to suspected COVID-19 patients was nearly universal, stress levels in emergency physicians decreased with time. At both initial and follow-up assessments, women were more likely to test positive on the PC-PTSD-5 screener compared to men

Emergency physician stressors, concerns, and behavioral changes during COVID-19: A longitudinal study.

ObjectivesThe objective was to provide a longitudinal assessment of anxiety levels and work and home concerns of U.S. emergency physicians during the COVID-19 pandemic.MethodsWe performed a longitudinal, cross-sectional email survey of clinically active emergency physicians (attending, fellow, and resident) at seven academic emergency departments. Follow-up surveys were sent 4 to 6 weeks after the initial survey and assessed the following: COVID-19 patient exposure, availability of COVID-19 testing, levels of home and workplace anxiety/stress, changes in behaviors, and performance on a primary care posttraumatic stress disorder screen (PC-PTSD-5). Logistic regression explored factors associated with a high PC-PTSD-5 scale score (≥3), indicating increased risk for PTSD.ResultsOf the 426 surveyed initial respondents, 262 (61.5%) completed the follow-up survey. While 97.3% (255/262) reported treating suspected COVID-19 patients, most physicians (162/262, 61.8%) had not received testing themselves. In follow-up, respondents were most concerned about the relaxing of social distancing leading to a second wave (median score = 6, IQR = 4-7). Physicians reported a consistently high ability to order COVID-19 tests for patients (median score = 6, IQR = 5-7) and access to personal protective equipment (median score = 6, IQR = 5-6). Women physicians were more likely to score ≥ 3 than men on the PC-PTSD-5 screener on the initial survey (43.3% vs. 22.5%; Δ 20.8%, 95% confidence interval [CI] = 9.3% to 31.5%), and despite decreases in overall proportions, this discrepancy remained in follow-up (34.7% vs. 16.8%; Δ 17.9%, 95% CI = 7.1% to 28.1%). In examining the relationship between demographics, living situations, and institution location on having a PC-PTSD-5 score ≥ 3, only female sex was associated with a PC-PTSD-5 score ≥ 3 (adjusted odds ratio = 2.48, 95% CI = 1.28 to 4.79).ConclusionsWhile exposure to suspected COVID-19 patients was nearly universal, stress levels in emergency physicians decreased with time. At both initial and follow-up assessments, women were more likely to test positive on the PC-PTSD-5 screener compared to men

Later high school start time is associated with lower migraine frequency in adolescents.

ObjectiveTo determine whether high school start time is associated with headache frequency in adolescents with migraine.BackgroundAdolescence is marked by a physiologic delayed circadian phase, characterized by later bedtimes and wake times. The American Academy of Pediatrics (AAP) recommends that high schools start no earlier than 8:30 a.m., but most high schools in the United States start earlier. The study hypothesis was that adolescents with migraine whose high schools start at 8:30 a.m. or later (late group) would have lower headache frequency than those whose schools start earlier than 8:30 a.m. (early group).MethodsThis was a cross-sectional Internet survey study of US high schoolers with migraine recruited online through social media. Comparisons were made between the late group and the early group. The primary outcome measure was self-reported headache days/month.ResultsIn total, 1012 respondents constituted the analytic set: n = 503 in the late group versus n = 509 in the early group. Mean (SD) self-reported headache days/month was 4.8 (4.6) versus 7.7 (6.1) in the late and early groups, respectively (p < 0.001); mean difference -2.9 (95% CI -2.2 to -3.6). Mean (SD) self-reported hours of sleep on a school night was 7.9 (0.9) versus 6.9 (1.3), p < 0.001. Adjusting for total hours of sleep, sex, taking a migraine preventive, days of acute medication use, hours of homework, grade level, and missing breakfast, mean (SD) self-reported headache days/month remained lower in the late group than in the early group: 5.8 (95% CI 5.3-6.2) versus 7.1 (95% CI 6.7-7.4), (p < 0.001); mean difference -1.3 (95% CI -1.9 to -0.7).ConclusionAdolescents with migraine who attend high schools that follow AAP recommendations for start times have lower self-reported headache frequency than those whose high schools start before 8:30 a.m. If prospective studies confirm this finding, shifting to a later high school start time may be an effective strategy for migraine prevention in adolescents