ObjectivesCurrent mortality prediction models used in the intensive care unit (ICU) have a limited role for specific diseases such as influenza, and we aimed to establish an explainable machine learning (ML) model for predicting mortality in critically ill influenza patients using a real-world severe influenza data set.Study designA cross-sectional retrospective multicentre study in TaiwanSettingEight medical centres in Taiwan.ParticipantsA total of 336 patients requiring ICU-admission for virology-proven influenza at eight hospitals during an influenza epidemic between October 2015 and March 2016.Primary and secondary outcome measuresWe employed extreme gradient boosting (XGBoost) to establish the prediction model, compared the performance with logistic regression (LR) and random forest (RF), demonstrated the feature importance categorised by clinical domains, and used SHapley Additive exPlanations (SHAP) for visualised interpretation.ResultsThe data set contained 76 features of the 336 patients with severe influenza. The severity was apparently high, as shown by the high Acute Physiology and Chronic Health Evaluation II score (22, 17 to 29) and pneumonia severity index score (118, 88 to 151). XGBoost model (area under the curve (AUC): 0.842; 95% CI 0.749 to 0.928) outperformed RF (AUC: 0.809; 95% CI 0.629 to 0.891) and LR (AUC: 0.701; 95% CI 0.573 to 0.825) for predicting 30-day mortality. To give clinicians an intuitive understanding of feature exploitation, we stratified features by the clinical domain. The cumulative feature importance in the fluid balance domain, ventilation domain, laboratory data domain, demographic and symptom domain, management domain and severity score domain was 0.253, 0.113, 0.177, 0.140, 0.152 and 0.165, respectively. We further used SHAP plots to illustrate associations between features and 30-day mortality in critically ill influenza patients.ConclusionsWe used a real-world data set and applied an ML approach, mainly XGBoost, to establish a practical and explainable mortality prediction model in critically ill influenza patients.

Introduction: Healthcare-associated pneumonia (HCAP) is a relatively new category of pneumonia. It refers to infections that occur prior to hospital admission in patients with specific risk factors following contact or exposure to a healthcare environment. There is currently no scoring index to predict the outcomes of HCAP patients. We applied and compared different community acquired pneumonia (CAP) scoring indices to predict 30-day mortality and 3-day and 14-day intensive care unit (ICU) admission in patients with HCAP. Methods: We conducted a retrospective cohort study based on an inpatient database from six medical centers, recruiting a total of 444 patients with HCAP between 1 January 2007 and 31 December 2007. Pneumonia severity scoring indices including PSI (pneumonia severity index), CURB 65 (confusion, urea, respiratory rate, blood pressure, age 65), IDSA/ATS (Infectious Diseases Society of America/American Thoracic Society), modified ATS rule, SCAP (severe community acquired pneumonia), SMART-COP (systolic blood pressure, multilobar involvement, albumin, respiratory rate, tachycardia, confusion, oxygenation, pH), SMRT-CO (systolic blood pressure, multilobar involvement, respiratory rate, tachycardia, confusion, oxygenation), and SOAR (systolic blood pressure, oxygenation, age, respiratory rate) were calculated for each patient. Patient characteristics, co-morbidities, pneumonia pathogen culture results, length of hospital stay (LOS), and length of ICU stay were also recorded.

Background: High glycemic variability (GV) is common in critically ill patients; however, the prevalence and mortality association with early GV in patients with sepsis remains unclear.Methods: This retrospective cohort study was conducted in a medical intensive care unit (ICU) in central Taiwan. Patients in the ICU with sepsis between January 2014 and December 2015 were included for analysis. All of these patients received protocol-based management, including blood sugar monitoring every 2 h for the first 24 h of ICU admission. Mean amplitude of glycemic excursions (MAGE) and coefficient of variation (CoV) were used to assess GV. Results:A total of 452 patients (mean age 71.4 ± 14.7 years; 76.7% men) were enrolled for analysis. They were divided into high GV (43.4%, 196/452) and low GV (56.6%, 256/512) groups using MAGE 65 mg/dL as the cut-off point. Patients with high GV tended to have higher HbA1c (6.7 ± 1.8% vs. 5.9 ± 0.9%, p < 0.01) and were more likely to have diabetes mellitus (DM) (50.0% vs. 23.4%, p < 0.01) compared with those in the low GV group. Kaplan-Meier analysis showed that a high GV was associated with increased 30-day mortality (log-rank test, p = 0.018). The association remained strong in the non-DM (log-rank test, p = 0.035), but not in the DM (log-rank test, p = 0.254) group. Multivariate Cox proportional hazard regression analysis identified that high APACHE II score (adjusted hazard ratio (aHR) 1.045, 95% confidence interval (CI) 1.013-1.078), high serum lactate level at 0 h (aHR 1.009, 95% CI 1.003-1.014), having chronic airway disease (aHR 0.478, 95% CI 0.302-0.756), high mean day 1 glucose (aHR 1.008, 95% CI 1.000-1.016), and high MAGE (aHR 1.607, 95% CI 1.008-2.563) were independently associated with increased 30-day mortality. The association with 30-day mortality remained consistent when using CoV to assess GV. Conclusions:We found that approximately 40% of the septic patients had a high early GV, defined as MAGE > 65 mg/dL. Higher GV within 24 h of ICU admission was independently associated with increased 30-day mortality. These findings highlight the need to monitor GV in septic patients early during an ICU admission.

Deciphering the structure of gene regulatory networks across the tree of life remains one of the major challenges in postgenomic biology. We present a novel ChIP-seq workflow for the archaea using the model organism Halobacterium salinarum sp. NRC-1 and demonstrate its application for mapping the genome-wide binding sites of natively expressed transcription factors. This end-to-end pipeline is the first protocol for ChIP-seq in archaea, with methods and tools for each stage from gene tagging to data analysis and biological discovery. Genome-wide binding sites for transcription factors with many binding sites (TfbD) are identified with sensitivity, while retaining specificity in the identification the smaller regulons (bacteriorhodopsin-activator protein). Chromosomal tagging of target proteins with a compact epitope facilitates a standardized and cost-effective workflow that is compatible with high-throughput immunoprecipitation of natively expressed transcription factors. The Pique package, an open-source bioinformatics method, is presented for identification of binding events. Relative to ChIP-Chip and qPCR, this workflow offers a robust catalog of protein–DNA binding events with improved spatial resolution and significantly decreased cost. While this study focuses on the application of ChIP-seq in H. salinarum sp. NRC-1, our workflow can also be adapted for use in other archaea and bacteria with basic genetic tools.