Extending cBioPortal for Therapy Recommendation Documentation in Molecular Tumor Boards: Development and Usability Study.

BACKGROUND: In molecular tumor boards (MTBs), patients with rare or advanced cancers are discussed by a multidisciplinary team of health care professionals. Software support for MTBs is lacking; in particular, tools for preparing and documenting MTB therapy recommendations need to be developed. OBJECTIVE: We aimed to implement an extension to cBioPortal to provide a tool for the documentation of therapy recommendations from MTB sessions in a secure and standardized manner. The developed extension should be embedded in the patient view of cBioPortal to enable easy documentation during MTB sessions. The resulting architecture for storing therapy recommendations should be integrable into various hospital information systems. METHODS: On the basis of a requirements analysis and technology analysis for authentication techniques, a prototype was developed and iteratively refined through a user-centered development process. In conclusion, the tool was evaluated via a usability evaluation, including interviews, structured questionnaires, and the System Usability Scale. RESULTS: The patient view of cBioPortal was extended with a new tab that enables users to document MTB sessions and therapy recommendations. The role-based access control was expanded to allow for a finer distinction among the rights to view, edit, and delete data. The usability evaluation showed overall good usability and a System Usability Scale score of 83.57. CONCLUSIONS: This study demonstrates how cBioPortal can be extended to not only visualize MTB patient data but also be used as a documentation platform for therapy recommendations.

Stroke Outcome Related to Initial Volume Status and Diuretic Use.

Background We hypothesized that stroke outcome is related to multiple baseline hydration-related factors including volume contracted state (VCS) and diuretic use. Methods and Results We analyzed a prospective cohort of subjects with ischemic stroke <24 hours of onset enrolled in acute treatment trials within VISTA (Virtual International Stroke Trials Archive). A VCS was defined based on blood urea nitrogen-to-creatinine ratio. The primary end point was modified Rankin Scale score at 90 days. Primary analysis used generalized ordinal logistic regression over the mRS range, adjusted for Totaled Health Risks in Vascular Events score, onset-to-enrollment time, and thrombolytic use. Of 5971 eligible patients with stroke, 42% were taking diuretics at the time of hospitalization, and 44% were in a VCS. Patients in a VCS were older, had more vascular risk factors, were more likely taking diuretics, and had more severe strokes. Diuretic use was associated with both reduced chance of achieving a good functional outcome (odds ratio [OR], 0.57 [95% CI, 0.52-0.63]) and increased mortality at 90 days (OR, 2.30 [95% CI, 2.04-2.61]). VCS was associated with greater mortality 90 days after stroke (OR, 1.53 [95% CI, 1.33-1.76]). There was no evidence of effect modification among the 3 exposures of VCS, diuretic use, or hypokalemia in relation to outcome. Conclusions A VCS at the time of hospitalization was associated with more severe stroke and odds of death but not associated with worse functional outcome when accounting for relevant characteristics. Diuretic use and low serum potassium at the time of stroke onset were associated with worse outcome and may be worthy of further investigation.

Challenges and Experiences Extending the cBioPortal for Cancer Genomics to a Molecular Tumor Board Platform.

In Molecular Tumor Boards (MTBs), therapy recommendations for cancer patients are discussed. To aid decision-making based on the patient's molecular profile, the research platform cBioPortal was extended based on users' requirements. Additionally, a comprehensive dockerized workflow was developed to support the deployment of cBioPortal and connected services. In this work, we present the challenges and experiences of nearly two years of implementing and deploying an MTB platform based on cBioPortal and compare those to findings of a previous study.

Carotid artery atherosclerosis is not associated with hyoid proximity: Results from a cross-sectional and longitudinal cohort study.

INTRODUCTION: Cervical internal carotid artery (ICA) atherosclerotic plaque and stenosis is often asymmetric. We hypothesized that hyoid bone proximity to the ICA also may be asymmetric and may increase the risk of traumatic endothelial injury and accelerate atherosclerotic stenosis. METHODS: A retrospective cross-sectional and longitudinal cohort design evaluated consecutive adult patients at 3 hospitals who underwent repeat computed tomography angiography (CTA) of the neck 2 calendar years apart (01/2000-07/2017). ICA plaque thickness, luminal stenosis, and their progression over time were compared between side with the nearer hyoid wing (proximal side) to the further side (distal side). RESULTS: Sixty-six patients were included with a median age of 64y (IQR 53-73), 37 (56.1%) female, had a median hyoid-ICA distance of 3.06 mm (IQR 1.27-6.20 mm) and median difference between sides of 2.11 mm (IQR 0.70-3.97 mm). The median plaque thickness was 3.5 mm (IQR 2-4) and median stenosis was 10% (IQR 0-33%). Comparing the proximal to distal side, there was no difference in ICA plaque thickness (median 2.5 mm [IQR 1-4] vs. 3.0 mm [IQR 2-4], p = 0.366) or stenosis (7% [IQR 0-31%] vs. 12% [IQR 0-39%], p = 0.21). After a median follow-up of 1002 days (range 392-3397 days), there was no difference in the change in plaque thickness (0.5 cm [IQR 0-1] vs. 0.0 cm [IQR -0.5-0.5], p = 0.21) or stenosis (0% [IQR -2.5-13%] vs. 0% [IQR -6-5%], p = 0.34) between proximal and distal ICAs. CONCLUSIONS: The presence and progression of atherosclerotic plaque and stenosis were unrelated to hyoid-ICA distance in this cross-sectional and longitudinal cohort study.

High resolution q-space imaging studies of water in elastin.

We report on the direct measurement of the molecular diffusion coefficients of water confined to purified bovine nuchal ligament elastin by high resolution q-space NMR imaging. The experimental data indicate that water trapped within an elastin fiber has two distinguishable molecular diffusion coefficients. The component with the slowest mobility has a diffusion coefficient on the order of 10(-6) cm(2)/s that varies inversely with the diffusion time and is seen to reduce near 37 degrees C. The component with higher mobility has a diffusion coefficient reminiscent of free water but is observed to also behave similarly at 37 degrees C. From our experimental data we extract the surface-to-volume ratio of pores within elastin and associated changes as a function of temperature.