Automated Gas Chromatography Peak Alignment: A Deep Learning Approach using Greedy Optimization and Simulation.

The clinical significance of volatile organic compounds (VOC) in detecting diseases has been established over the past decades. Gas chromatography (GC) devices enable the measurement of these VOCs. Chromatographic peak alignment is one of the important yet challenging steps in analyzing chromatogram signals. Traditional semi-automated alignment algorithms require manual intervention by an operator which is slow, expensive and inconsistent. A pipeline is proposed to train a deep-learning model from artificial chromatograms simulated from a small, annotated dataset, and a postprocessing step based on greedy optimization to align the signals.Clinical Relevance- Breath VOCs have been shown to have a significant diagnostic power for various diseases including asthma, acute respiratory distress syndrome and COVID-19. Automatic analysis of chromatograms can lead to improvements in the diagnosis and management of such diseases.

A Comprehensive Comparison of Six Publicly Available Algorithms for Localization of QRS Complex on Electrocardiograph.

The QRS complex is the most prominent feature of the electrocardiogram (ECG) that is used as a marker to identify the cardiac cycles. Identification of QRS complex locations enables arrhythmia detection and heart rate variability estimation. Therefore, accurate and consistent localization of the QRS complex is an important component of automated ECG analysis which is necessary for the early detection of cardiovascular diseases. This study evaluates the performance of six popular publicly available QRS complex detection methods on a large dataset of over half a million ECGs in a diverse population of patients. We found that a deep-learning method that won first place in the 2019 Chinese physiological challenge (CPSC-1) outperforms the remaining five QRS complex detection methods with an F1 score of 98.8% and an absolute sdRR error of 5.5 ms. We also examined the stratified performance of the studied methods on various cardiac conditions. All six methods had a lower performance in the detection of QRS complexes in ECG signals of patients with pacemakers, complete atrioventricular block, or indeterminate cardiac axis. We also concluded that, in the presence of different cardiac conditions, CPSC-1 is more robust than Pan-Tompkins which is the most popular model for QRS complex detection. We expect that this study can potentially serve as a guide for researchers on the appropriate QRS detection method for their target applications.Clinical Relevance-This study highlights the overall performance of publicly available QRS detection algorithms in a large dataset of diverse patients. We showed that there are specific cardiac conditions that are associated with the poor performance of QRS detection algorithms and may adversely influence the performance of algorithms that rely on accurate and reliable QRS detection.

External Validation and Comparison of a General Ward Deterioration Index Between Diversely Different Health Systems.

OBJECTIVES: Implementing a predictive analytic model in a new clinical environment is fraught with challenges. Dataset shifts such as differences in clinical practice, new data acquisition devices, or changes in the electronic health record (EHR) implementation mean that the input data seen by a model can differ significantly from the data it was trained on. Validating models at multiple institutions is therefore critical. Here, using retrospective data, we demonstrate how Predicting Intensive Care Transfers and other UnfoReseen Events (PICTURE), a deterioration index developed at a single academic medical center, generalizes to a second institution with significantly different patient population. DESIGN: PICTURE is a deterioration index designed for the general ward, which uses structured EHR data such as laboratory values and vital signs. SETTING: The general wards of two large hospitals, one an academic medical center and the other a community hospital. SUBJECTS: The model has previously been trained and validated on a cohort of 165,018 general ward encounters from a large academic medical center. Here, we apply this model to 11,083 encounters from a separate community hospital. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: The hospitals were found to have significant differences in missingness rates (> 5% difference in 9/52 features), deterioration rate (4.5% vs 2.5%), and racial makeup (20% non-White vs 49% non-White). Despite these differences, PICTURE's performance was consistent (area under the receiver operating characteristic curve [AUROC], 0.870; 95% CI, 0.861-0.878), area under the precision-recall curve (AUPRC, 0.298; 95% CI, 0.275-0.320) at the first hospital; AUROC 0.875 (0.851-0.902), AUPRC 0.339 (0.281-0.398) at the second. AUPRC was standardized to a 2.5% event rate. PICTURE also outperformed both the Epic Deterioration Index and the National Early Warning Score at both institutions. CONCLUSIONS: Important differences were observed between the two institutions, including data availability and demographic makeup. PICTURE was able to identify general ward patients at risk of deterioration at both hospitals with consistent performance (AUROC and AUPRC) and compared favorably to existing metrics.

Not so robust: Robusta coffee production is highly sensitive to temperature.

Coffea canephora (robusta coffee) is the most heat-tolerant and 'robust' coffee species and therefore considered more resistant to climate change than other types of coffee production. However, the optimum production range of robusta has never been quantified, with current estimates of its optimal mean annual temperature range (22-30°C) based solely on the climatic conditions of its native range in the Congo basin, Central Africa. Using 10 years of yield observations from 798 farms across South East Asia coupled with high-resolution precipitation and temperature data, we used hierarchical Bayesian modeling to quantify robusta's optimal temperature range for production. Our climate-based models explained yield variation well across the study area with a cross-validated mean R2  = .51. We demonstrate that robusta has an optimal temperature below 20.5°C (or a mean minimum/maximum of ≤16.2/24.1°C), which is markedly lower, by 1.5-9°C than current estimates. In the middle of robusta's currently assumed optimal range (mean annual temperatures over 25.1°C), coffee yields are 50% lower compared to the optimal mean of ≤20.5°C found here. During the growing season, every 1°C increase in mean minimum/maximum temperatures above 16.2/24.1°C corresponded to yield declines of ~14% or 350-460 kg/ha (95% credible interval). Our results suggest that robusta coffee is far more sensitive to temperature than previously thought. Current assessments, based on robusta having an optimal temperature range over 22°C, are likely overestimating its suitable production range and its ability to contribute to coffee production as temperatures increase under climate change. Robusta supplies 40% of the world's coffee, but its production potential could decline considerably as temperatures increase under climate change, jeopardizing a multi-billion dollar coffee industry and the livelihoods of millions of farmers.