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.

The ageing European society is placing an added burden on future generations, as the 'elderly-to-working-age-people' ratio is set to steadily increase in the future. Nowadays, quality of life and fitness allows for most older persons to have an active life well into their eighties. Furthermore, many older persons prefer to live in their own house and choose their own lifestyle. The CAALYX system can have a clear impact in increasing older persons' autonomy, by ensuring that they do not need to leave their preferred environment in order to be properly monitored and taken care of.

Recent advances in mobile positioning systems and telecommunications are providing the technology needed for the development of location-aware tele-care applications. This paper introduces CAALYX -Complete Ambient Assisted Living Experiment, an EU-funded project that aims at increasing older people's autonomy and self-confidence by developing a wearable light device capable of measuring specific vital signs of the elderly, detecting falls and location, and communicating automatically in real-time with his/her care provider in case of an emergency, wherever the older person happens to be, at home or outside.

Background Blended treatments, combining digital components with face-to-face (FTF) therapy, are starting to find their way into mental health care. Knowledge on how blended treatments should be set up is, however, still limited. To further explore and optimize blended treatment protocols, it is important to obtain a full picture of what actually happens during treatments when applied in routine mental health care. Objective The aims of this study were to gain insight into the usage of the different components of a blended cognitive behavioral therapy (bCBT) for depression and reflect on actual engagement as compared with intended application, compare bCBT usage between primary and specialized care, and explore different usage patterns. Methods Data used were collected from participants of the European Comparative Effectiveness Research on Internet-Based Depression Treatment project, a European multisite randomized controlled trial comparing bCBT with regular care for depression. Patients were recruited in primary and specialized routine mental health care settings between February 2015 and December 2017. Analyses were performed on the group of participants allocated to the bCBT condition who made use of the Moodbuster platform and for whom data from all blended components were available (n=200). Included patients were from Germany, Poland, the Netherlands, and France; 64.5% (129/200) were female and the average age was 42 years (range 18-74 years). Results Overall, there was a large variability in the usage of the blended treatment. A clear distinction between care settings was observed, with longer treatment duration and more FTF sessions in specialized care and a more active and intensive usage of the Web-based component by the patients in primary care. Of the patients who started the bCBT, 89.5% (179/200) also continued with this treatment format. Treatment preference, educational level, and the number of comorbid disorders were associated with bCBT engagement. Conclusions Blended treatments can be applied to a group of patients being treated for depression in routine mental health care. Rather than striving for an optimal blend, a more personalized blended care approach seems to be the most suitable. The next step is to gain more insight into the clinical and cost-effectiveness of blended treatments and to further facilitate uptake in routine mental health care.

The Adaptive Immune Receptor Repertoire (AIRR) Community is a research-driven group that is establishing a clear set of community-accepted data and metadata standards; standards-based reference implementation tools; and policies and practices for infrastructure to support the deposit, curation, storage, and use of high-throughput sequencing data from B-cell and T-cell receptor repertoires (AIRR-seq data). The AIRR Data Commons is a distributed system of data repositories that utilizes a common data model, a common query language, and common interoperability formats for storage, query, and downloading of AIRR-seq data. Here is described the principal technical standards for the AIRR Data Commons consisting of the AIRR Data Model for repertoires and rearrangements, the AIRR Data Commons (ADC) API for programmatic query of data repositories, a reference implementation for ADC API services, and tools for querying and validating data repositories that support the ADC API. AIRR-seq data repositories can become part of the AIRR Data Commons by implementing the data model and API. The AIRR Data Commons allows AIRR-seq data to be reused for novel analyses and empowers researchers to discover new biological insights about the adaptive immune system.

Technology driven interventions provide us with an increasing amount of fine-grained data about the patient. This data includes regular ecological momentary assessments (EMA) but also response times to EMA questions by a user. When observing this data, we see a huge variation between the patterns exhibited by different patients. Some are more stable while others vary a lot over time. This poses a challenging problem for the domain of artificial intelligence and makes on wondering whether it is possible to predict the future mental state of a patient using the data that is available. In the end, these predictions could potentially contribute to interventions that tailor the feedback to the user on a daily basis, for example by warning a user that a fall-back might be expected during the next days, or by applying a strategy to prevent the fall-back from occurring in the first place.In this work, we focus on short term mood prediction by considering the adherence and usage data as an additional predictor. We apply recurrent neural networks to handle the temporal aspects best and try to explore whether individual, group level, or one single predictive model provides the highest predictive performance (measured using the root mean squared error (RMSE)). We use data collected from patients from five countries who used the ICT4Depression/MoodBuster platform in the context of the EU E-COMPARED project. In total, we used the data from 143 patients (with between 9 and 425 days of EMA data) who were diagnosed with a major depressive disorder according to DSM-IV.Results show that we can make predictions of short term mood change quite accurate (ranging between 0.065 and 0.11). The past EMA mood ratings proved to be the most influential while adherence and usage data did not improve prediction accuracy. In general, group level predictions proved to be the most promising, however differences were not significant.Short term mood prediction remains a difficult task, but from this research we can conclude that sophisticated machine learning algorithms/setups can result in accurate performance. For future work, we want to use more data from the mobile phone to improve predictive performance of short term mood.

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.

In this paper we introduce a new Android library, called ULTEMAT, for the delivery of ecological momentary assessments (EMAs) on mobile devices and we present its use in the MoodBuster app developed in the H2020 E-COMPARED project. We discuss context-aware, or event-based, triggers for the presentation of EMAs and discuss the potential they have to improve the effectiveness of mobile provision of mental health interventions as they allow for the delivery of assessments to the patients when and where these are most appropriate. Following this, we present the abilities of ULTEMAT to use such context-aware triggers to schedule EMAs and we discuss how a similar approach can be used for Ecological Momentary Interventions (EMIs).