Search for: All records

Atrial fibrillation (AF) is the most common arrhythmia encountered clinically, and as the population ages, its prevalence is increasing. Although the CHA 2 DS 2 − VASc score is the most used risk-stratification system for stroke risk in AF, it lacks personalization. Patient-specific computer models of the atria can facilitate personalized risk assessment and treatment planning. However, a challenge faced in creating such models is the complexity of the atrial muscle arrangement and its influence on the atrial fiber architecture. This work proposes a semi-automated rule-based algorithm to generate the local fiber orientation in the left atrium (LA). We use the solutions of several harmonic equations to decompose the LA anatomy into subregions. Solution gradients define a two-layer fiber field in each subregion. The robustness of our approach is demonstrated by recreating the fiber orientation on nine models of the LA obtained from AF patients who underwent WATCHMAN device implantation. This cohort of patients encompasses a variety of morphology variants of the left atrium, both in terms of the left atrial appendages (LAAs) and the number of pulmonary veins (PVs). We test the fiber construction algorithm by performing electrophysiology (EP) simulations. Furthermore, this study is the first to compare its results with other rule-based algorithms for the LA fiber architecture definition available in the literature. This analysis suggests that a multi-layer fiber architecture is important to capture complex electrical activation patterns. A notable advantage of our approach is the ability to reconstruct the main LA fiber bundles in a variety of morphologies while solving for a small number of harmonic fields, leading to a comparatively straightforward and reproducible approach. 

Tandem mass spectrometry (MS/MS) is a popular technology for identifying small molecules involved in metabolism, better known as metabolites. Coupled with liquid chromatography (LC), LC-MS/MS instruments first separate, ionize, and fragment metabolites, then measure mass-to-charge ratios (m/z) and intensities of metabolite fragments. Understanding metabolite fragmentation is crucial to develop computational tools for identifying metabolites based on this spectroscopic data. Metabolite fragmentation patterns have large variations making it especially difficult for computer scientists to design and implement metabolite identification approaches. To address this interdisciplinary challenge, this article presents FragView, a web-based application providing the web service for visualizing metabolite fragmentation. Users can break chemical bonds to produce metabolite fragments and export 3D fragment structures for 3D printing. Developing FragView is an opportunity for exposing student participants to this interdisciplinary bioinformatics project. This paper summarizes the experience of training student participants in bootcamps and designing the implementation plan based on student backgrounds. Students were exposed to project meeting discussions on coding and raw data visualization and visited a lab with an LC-MS/MS instrument. FragView is an open source, freely accessible tool, released under the GPLv3 license. We will continue to improve and update FragView in the future based on feedback. 

Subclinical leaflet thrombosis (SLT) is a potentially serious complication of aortic valve replacement with a bioprosthetic valve in which blood clots form on the replacement valve. SLT is associated with increased risk of transient ischemic attacks and strokes and can progress to clinical leaflet thrombosis. SLT following aortic valve replacement also may be related to subsequent structural valve deterioration, which can impair the durability of the valve replacement. Because of the difficulty in clinical imaging of SLT, models are needed to determine the mechanisms of SLT and could eventually predict which patients will develop SLT. To this end, we develop methods to simulate leaflet thrombosis that combine fluid–structure interaction and a simplified thrombosis model that allows for deposition along the moving leaflets. Additionally, this model can be adapted to model deposition or absorption along other moving boundaries. We present convergence results and quantify the model's ability to realize changes in valve opening and pressures. These new approaches are an important advancement in our tools for modeling thrombosis because they incorporate both adhesion to the surface of the moving leaflets and feedback to the fluid–structure interaction.