Adaptive immune receptor repertoires (AIRR) are key targets for biomedical research as they record past and ongoing adaptive immune responses. The capacity of machine learning (ML) to identify complex discriminative sequence patterns renders it an ideal approach for AIRR-based diagnostic and therapeutic discovery. To date, widespread adoption of AIRR ML has been inhibited by a lack of reproducibility, transparency, and interoperability. immuneML ( immuneml.uio.no ) addresses these concerns by implementing each step of the AIRR ML process in an extensible, open-source software ecosystem that is based on fully specified and shareable workflows. To facilitate widespread user adoption, immuneML is available as a command-line tool and through an intuitive Galaxy web interface, and extensive documentation of workflows is provided. We demonstrate the broad applicability of immuneML by (i) reproducing a large-scale study on immune state prediction, (ii) developing, integrating, and applying a novel method for antigen specificity prediction, and (iii) showcasing streamlined interpretability-focused benchmarking of AIRR ML. 1.

Aims: Patients who present with non-ischemic dilated cardiomyopathy (NIDCM) and enhancement on late gadolinium magnetic resonance imaging (LGE-CMR), are at high risk of sudden cardiac death (SCD). Further risk stratification of these patients based on LGE-CMR may be improved through better understanding of fibrosis microstructure. Our aim is to examine variations in fibrosis microstructure based on LGE imaging, and quantify the effect on reentry inducibility and mechanism. Furthermore, we examine the relationship between transmural activation time differences and reentry.Methods and Results: 2D Computational models were created from a single short axis LGE-CMR image, with 401 variations in fibrosis type (interstitial, replacement) and density, as well as presence or absence of reduced conductivity (RC). Transmural activation times (TAT) were measured, as well as reentry incidence and mechanism. Reentries were inducible above specific density thresholds (0.8, 0.6 for interstitial, replacement fibrosis). RC reduced these thresholds (0.3, 0.4 for interstitial, replacement fibrosis) and increased reentry incidence (48 no RC vs. 133 with RC). Reentries were classified as rotor, micro-reentry, or macro-reentry and depended on fibrosis micro-structure. Differences in TAT at coupling intervals 210 and 500ms predicted reentry in the models (sensitivity 89%, specificity 93%). A sensitivity analysis of TAT and reentry incidence showed that these quantities were robust to small changes in the pacing location.Conclusion: Computational models of fibrosis micro-structure underlying areas of LGE in NIDCM provide insight into the mechanisms and inducibility of reentry, and their dependence upon the type and density of fibrosis. Transmural activation times, measured at the central extent of the scar, can potentially differentiate microstructures which support reentry.

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Adaptive immune receptor repertoires (AIRR) are key targets for biomedical research as they record past and ongoing adaptive immune responses. The capacity of machine learning (ML) to identify complex discriminative sequence patterns renders it an ideal approach for AIRR-based diagnostic and therapeutic discovery. To date, widespread adoption of AIRR ML has been inhibited by a lack of reproducibility, transparency, and interoperability. immuneML (immuneml.uio.no) addresses these concerns by implementing each step of the AIRR ML process in an extensible, open-source software ecosystem that is based on fully specified and shareable workflows. To facilitate widespread user adoption, immuneML is available as a command-line tool and through an intuitive Galaxy web interface, and extensive documentation of workflows is provided. We demonstrate the broad applicability of immuneML by (i) reproducing a large-scale study on immune state prediction, (ii) developing, integrating, and applying a novel method for antigen specificity prediction, and (iii) showcasing streamlined interpretability-focused benchmarking of AIRR ML.

The objective of this transformative action research project was to explore and develop sustainable methods to promote female empowerment through science education in rural, disadvantaged sectors of South Africa. In an attempt to achieve this we collaborated with local community members to develop and implement a contextualized science curriculum at a school in the aforementioned setting. As soon as the project was launched it became increasingly clear that although the ideology of 'empowerment through science education' seemed a promising venture, it could also be an extremely complex and often frustrating undertaking. This was especially true when working within an unfamiliar cultural setting. Numerous challenges, such as the lack of teacher motivation, malnutrition amongst the learners, and conflicts stemming from differences between the indigenous knowledge and the western concept of science, greatly impeded the delivery of quality education in the area. These challenges had to be addressed both in pedagogical and practical terms before any attempt towards libratory education could be made. This article sheds light on the complex inter-relationship between the human factor and the organizational and physical infrastructure at a school. It begins with a brief description of the local context and goes on to identify the theoretical underpinnings and chosen methodology for the project. The article concludes with a review of the complexities involved in possible attempts to initiate and foster educational and social transformations in a rural South African setting. We contend that it is essential to first be thoroughly familiar with the background, culture, and needs of any community before any attempts are made towards social justice.

Objectives This study sought to investigate whether shape-based late gadolinium enhancement (LGE) metrics and simulations of re-entrant electrical activity are associated with arrhythmic events in patients with nonischemic dilated cardiomyopathy (NIDCM). Background The presence of LGE predicts life-threatening ventricular arrhythmias in NIDCM; however, risk stratification remains imprecise. LGE shape and simulations of electrical activity may be able to provide additional prognostic information. Methods Cardiac magnetic resonance (CMR)-LGE shape metrics were computed for a cohort of 156 patients with NIDCM and visible LGE and tested retrospectively for an association with an arrhythmic composite endpoint of sudden cardiac death and ventricular tachycardia. Computational models were created from images and used in conjunction with simulated stimulation protocols to assess the potential for re-entry induction in each patient’s scar morphology. A mechanistic analysis of the simulations was carried out to explain the associations. Results During a median follow-up of 1,611 (interquartile range: 881 to 2,341) days, 16 patients (10.3%) met the primary endpoint. In an inverse probability weighted Cox regression, the LGE–myocardial interface area (hazard ratio [HR]: 1.75; 95% confidence interval [CI]: 1.24 to 2.47; p = 0.001), number of simulated re-entries (HR: 1.40; 95% CI: 1.23 to 1.59; p < 0.01) and LGE volume (HR: 1.44; 95% CI: 1.07 to 1.94; p = 0.02) were associated with arrhythmic events. Computational modeling revealed repolarization heterogeneity and rate-dependent block of electrical wavefronts at the LGE–myocardial interface as putative arrhythmogenic mechanisms directly related to the LGE interface area. Conclusions The area of interface between scar and surviving myocardium, as well as simulated re-entrant activity, are associated with an elevated risk of major arrhythmic events in patients with NIDCM and LGE and represent novel risk predictors.

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This paper presents a morphological analysis of fibrotic scarring in non-ischemic dilated cardiomyopathy, and its relationship to electrical instabilities which underlie reentrant arrhythmias. Two dimensional electrophysiological simulation models were constructed from a set of 699 late gadolinium enhanced cardiac magnetic resonance images originating from 157 patients. Areas of late gadolinium enhancement (LGE) in each image were assigned one of 10 possible microstructures, which modelled the details of fibrotic scarring an order of magnitude below the MRI scan resolution. A simulated programmed electrical stimulation protocol tested each model for the possibility of generating either a transmural block or a transmural reentry. The outcomes of the simulations were compared against morphological LGE features extracted from the images. Models which blocked or reentered, grouped by microstructure, were significantly different from one another in myocardial-LGE interface length, number of components and entropy, but not in relative area and transmurality. With an unknown microstructure, transmurality alone was the best predictor of block, whereas a combination of interface length, transmurality and number of components was the best predictor of reentry in linear discriminant analysis.