The efficacy of various machine learning models for multi-class classification of RNA-seq expression data

Late diagnosis and high costs are key factors that negatively impact the care of cancer patients worldwide. Although the availability of biological markers for the diagnosis of cancer type is increasing, costs and reliability of tests currently present a barrier to the adoption of their routine use. There is a pressing need for accurate methods that enable early diagnosis and cover a broad range of cancers. The use of machine learning and RNA-seq expression analysis has shown promise in the classification of cancer type. However, research is inconclusive about which type of machine learning models are optimal. The suitability of five algorithms were assessed for the classification of 17 different cancer types. Each algorithm was fine-tuned and trained on the full array of 18,015 genes per sample, for 4,221 samples (75 % of the dataset). They were then tested with 1,408 samples (25 % of the dataset) for which cancer types were withheld to determine the accuracy of prediction. The results show that ensemble algorithms achieve 100% accuracy in the classification of 14 out of 17 types of cancer. The clustering and classification models, while faster than the ensembles, performed poorly due to the high level of noise in the dataset. When the features were reduced to a list of 20 genes, the ensemble algorithms maintained an accuracy above 95% as opposed to the clustering and classification models.Comment: 12 pages, 4 figures, 3 tables, conference paper: Computing Conference 2019, published at https://link.springer.com/chapter/10.1007/978-3-030-22871-2_6

Inter- and Intra-Observer Variability and the Effect of Experience in Cine-MRI for Adhesion Detection

Cine-MRI for adhesion detection is a promising novel modality that can help the large group of patients developing pain after abdominal surgery. Few studies into its diagnostic accuracy are available, and none address observer variability. This retrospective study explores the inter- and intra-observer variability, diagnostic accuracy, and the effect of experience. A total of 15 observers with a variety of experience reviewed 61 sagittal cine-MRI slices, placing box annotations with a confidence score at locations suspect for adhesions. Five observers reviewed the slices again one year later. Inter- and intra-observer variability are quantified using Fleiss’ (inter) and Cohen’s (intra) κ and percentage agreement. Diagnostic accuracy is quantified with receiver operating characteristic (ROC) analysis based on a consensus standard. Inter-observer Fleiss’ κ values range from 0.04 to 0.34, showing poor to fair agreement. High general and cine-MRI experience led to significantly (p < 0.001) better agreement among observers. The intra-observer results show Cohen’s κ values between 0.37 and 0.53 for all observers, except one with a low κ of −0.11. Group AUC scores lie between 0.66 and 0.72, with individual observers reaching 0.78. This study confirms that cine-MRI can diagnose adhesions, with respect to a radiologist consensus panel and shows that experience improves reading cine-MRI. Observers without specific experience adapt to this modality quickly after a short online tutorial. Observer agreement is fair at best and area under the receiver operating characteristic curve (AUC) scores leave room for improvement. Consistently interpreting this novel modality needs further research, for instance, by developing reporting guidelines or artificial intelligence-based methods

Validation, comparison, and combination of algorithms for automatic detection of pulmonary nodules in computed tomography images: The LUNA16 challenge

Automatic detection of pulmonary nodules in thoracic computed tomography (CT) scans has been an active area of research for the last two decades. However, there have only been few studies that provide a comparative performance evaluation of different systems on a common database. We have therefore set up the LUNA16 challenge, an objective evaluation framework for automatic nodule detection algorithms using the largest publicly available reference database of chest CT scans, the LIDC-IDRI data set. In LUNA16, participants develop their algorithm and upload their predictions on 888 CT scans in one of the two tracks: 1) the complete nodule detection track where a complete CAD system should be developed, or 2) the false positive reduction track where a provided set of nodule candidates should be classified. This paper describes the setup of LUNA16 and presents the results of the challenge so far. Moreover, the impact of combining individual systems on the detection performance was also investigated. It was observed that the leading solutions employed convolutional networks and used the provided set of nodule candidates. The combination of these solutions achieved an excellent sensitivity of over 95% at fewer than 1.0 false positives per scan. This highlights the potential of combining algorithms to improve the detection performance. Our observer study with four expert readers has shown that the best system detects nodules that were missed by expert readers who originally annotated the LIDC-IDRI data. We released this set of additional nodules for further development of CAD systems

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Work-Home Interference

In the present study, we examined the associations among work-home culture (WHC

Decay or collapse:aircraft wake vortices in grid turbulence

Trailing vortices are naturally shed by airplanes and they typically evolve into a counter-rotating vortex pair. Downstream of the aircraft, these vortices can persist for a very long time and extend for several kilometers. This poses a potential hazard to following aircraft, particularly during take-off and landing. Therefore, it is of interest to understand what effects control the decay rate in strength of the trailing vortices. The decay of the aircraft wake vortices is strongly dependent on weather conditions. To simulate an environment of atmospheric turbulence, homogeneous isotropic turbulence is introduced next to localized vortical structure. In this contribution, the effect of external turbulence on the vortex decay will be investigated numerically, using a DNS method, and experimentally. Wind tunnel experiments are carried out using a smoke visualization technique

Dimensions of work-home culture and their relations with the use of work-home arrangements and work-home interaction

This study examined the associations of workhome culture with (a) demographic and organizational characteristics, (b) the use of workhome arrangements, and (c) negative and positive workhome interaction, among 1,179 employees from one public and two private organizations. Substantial support was found for a 2-factor structure of a workhome culture measure differentiating between ‘‘support’’ (employees’ perceptions of organization’s, supervisors’, and colleagues’ responsiveness to workfamily issues and to the use of workhome arrangements) and ‘‘hindrance’’ (employees’ perceptions of career consequences and time demands that may prevent them from using workhome arrangements). This 2-factor structure appeared to be invariant across organizations, gender, and parental status. Significant relationships with organizational characteristics, the use of workhome arrangements, and workhome interaction supported the validity of these two cultural dimensions. It is concluded that if employers want to minimize workhome interference, to optimize positive work home interaction, and to boost the use of workhome arrangements, they should create a workhome culture that is characterized by high support and low hindrance.

CO-RADS:A Categorical CT Assessment Scheme for Patients Suspected of Having COVID-19 Definition and Evaluation

Background: A categorical CT assessment scheme for suspicion of pulmonary involvement of coronavirus disease 2019 (COVID-19 provides a basis for gathering scientific evidence and improved communication with referring physicians. Purpose: To introduce the COVID-19 Reporting and Data System (CO-RADS) for use in the standardized assessment of pulmonary involvement of COVID-19 on unenhanced chest CT images and to report its initial interobserver agreement and performance. Materials and Methods: The Dutch Radiological Society developed CO-RADS based on other efforts for standardization, such as the Lung Imaging Reporting and Data System or Breast Imaging Reporting and Data System. CO-RADS assesses the suspicion for pulmonary involvement of COVID-19 on a scale from 1 (very low) to 5 (very high). The system is meant to be used in patients with moderate to severe symptoms of COVID-19. The system was evaluated by using 105 chest CT scans of patients admitted to the hospital with clinical suspicion of COVID-19 and in whom reverse transcription-polymerase chain reaction (RT-PCR) was performed (mean, 62 years ± 16 [standard deviation]; 61 men, 53 with positive RT-PCR results). Eight observers used CO-RADS to assess the scans. Fleiss k value was calculated, and scores of individual observers were compared with the median of the remaining seven observers. The resulting area under the receiver operating characteristics curve (AUC) was compared with results from RTPCR and clinical diagnosis of COVID-19. Results: There was absolute agreement among observers in 573 (68.2%) of 840 observations. Fleiss k value was 0.47 (95% confidence interval [CI]: 0.45, 0.47), with the highest k value for CO-RADS categories 1 (0.58, 95% CI: 0.54, 0.62) and 5 (0.68, 95% CI: 0.65, 0.72). The average AUC was 0.91 (95% CI: 0.85, 0.97) for predicting RT-PCR outcome and 0.95 (95% CI: 0.91, 0.99) for clinical diagnosis. The false-negative rate for CO-RADS 1 was nine of 161 cases (5.6%; 95% CI: 1.0%, 10%), and the falsepositive rate for CO-RADS category 5 was one of 286 (0.3%; 95% CI: 0%, 1.0%). Conclusion: The coronavirus disease 2019 (COVID-19) Reporting and Data System (CO-RADS) is a categorical assessment scheme for pulmonary involvement of COVID-19 at unenhanced chest CT that performs very well in predicting COVID-19 in patients with moderate to severe symptoms and has substantial interobserver agreement, especially for categories 1 and 5

Observer variability for Lung-RADS categorisation of lung cancer screening CTs: impact on patient management

Objectives: Lung-RADS represents a categorical system published by the American College of Radiology to standardise management in lung cancer screening. The purpose of the study was to quantify how well readers agree in assigning Lung-RADS categories to screening CTs; secondary goals were to assess causes of disagreement and evaluate its impact on patient management. Methods: For the observer study, 80 baseline and 80 follow-up scans were randomly selected from the NLST trial covering all Lung-RADS categories in an equal distribution. Agreement of seven observers was analysed using Cohen’s kappa statistics. Discrepancies were correlated with patient management, test performance and diagnosis of malignancy within the scan year. Results: Pairwise interobserver agreement was substantial (mean kappa 0.67, 95% CI 0.58–0.77). Lung-RADS category disagreement was seen in approximately one-third (29%, 971) of 3360 reading pairs, resulting in different patient management in 8% (278/3360). Out of the 91 reading pairs that referred to scans with a tumour diagnosis within 1 year, discrepancies in only two would have resulted in a substantial management change. Conclusions: Assignment of lung cancer screening CT scans to Lung-RADS categories achieves substantial interobserver agreement. Impact of disagreement on categorisation of malignant nodules was low. Key Points: • Lung-RADS categorisation of low-dose lung screening CTs achieved substantial interobserver agreement. • Major cause for disagreement was assigning a different nodule as risk-dominant. • Disagreement led to a different follow-up time in 8% of reading pairs