FAIRification of health-related data using semantic web technologies in the Swiss Personalized Health Network

The Swiss Personalized Health Network (SPHN) is a government-funded initiative developing federated infrastructures for a responsible and efficient secondary use of health data for research purposes in compliance with the FAIR principles (Findable, Accessible, Interoperable and Reusable). We built a common standard infrastructure with a fit-for-purpose strategy to bring together health-related data and ease the work of both data providers to supply data in a standard manner and researchers by enhancing the quality of the collected data. As a result, the SPHN Resource Description Framework (RDF) schema was implemented together with a data ecosystem that encompasses data integration, validation tools, analysis helpers, training and documentation for representing health metadata and data in a consistent manner and reaching nationwide data interoperability goals. Data providers can now efficiently deliver several types of health data in a standardised and interoperable way while a high degree of flexibility is granted for the various demands of individual research projects. Researchers in Switzerland have access to FAIR health data for further use in RDF triplestores.

[RECUR - Establishment of An Automated Digital Registry for Patients with Recurrent Stones in the Upper Urinary Tract]

Kidney stones, like cardiovascular diseases and diabetes mellitus, affect a large number of people. Patients suffer from acute pain, repeated hospitalizations and associated secondary diseases, such as arterial hypertension and renal insufficiency. This results in considerable costs for the society and its health care system. The recurrence rate is as high as 50%. The registry for RECurrent URolithiasis (RECUR) aims to fill existing evidence gaps. The prospective and longitudinal RECUR registry is funded by the German Ministry of Education and Science (BMBF). It is based on the digital infrastructure of the German Medical Informatics Initiative (MII). RECUR aims to include patients that have suffered from more than one stone occurrence and treated at any one of the ten participating university hospitals of the MIRACUM consortium. The intention is to obtain new information on risk factors and to evaluate different diagnosis and treatment algorithms. Along with the data form the patient's Electronic Health Records (EHR), the RECUR project will also collect Patient Reported Outcomes data from patients with recurrent kidney stones. These data will be collected at participating sites using digital questionnaires via a smartphone app. These data will be merged with medical data from the hospital information systems and saved in the MII research data repositories. The RECUR registry has a model character due to its fully federated, digital approach. This allows the recruitment of many patients, the collection of a wide range of data and their processing with low administrative and personnel costs.

International Comparisons of Harmonized Laboratory Value Trajectories to Predict Severe COVID-19: Leveraging the 4CE Collaborative Across 342 Hospitals and 6 Countries: A Retrospective Cohort Study

Objectives

To perform an international comparison of the trajectory of laboratory values among hospitalized patients with COVID-19 who develop severe disease and identify optimal timing of laboratory value collection to predict severity across hospitals and regions.

Design

Retrospective cohort study.

Setting

The Consortium for Clinical Characterization of COVID-19 by EHR (4CE), an international multi-site data-sharing collaborative of 342 hospitals in the US and in Europe.

Participants

Patients hospitalized with COVID-19, admitted before or after PCR-confirmed result for SARS-CoV-2.

Primary and secondary outcome measures

Patients were categorized as "ever-severe" or "never-severe" using the validated 4CE severity criteria. Eighteen laboratory tests associated with poor COVID-19-related outcomes were evaluated for predictive accuracy by area under the curve (AUC), compared between the severity categories. Subgroup analysis was performed to validate a subset of laboratory values as predictive of severity against a published algorithm. A subset of laboratory values (CRP, albumin, LDH, neutrophil count, D-dimer, and procalcitonin) was compared between North American and European sites for severity prediction.

Results

Of 36,447 patients with COVID-19, 19,953 (43.7%) were categorized as ever-severe. Most patients (78.7%) were 50 years of age or older and male (60.5%). Longitudinal trajectories of CRP, albumin, LDH, neutrophil count, D-dimer, and procalcitonin showed association with disease severity. Significant differences of laboratory values at admission were found between the two groups. With the exception of D-dimer, predictive discrimination of laboratory values did not improve after admission. Sub-group analysis using age, D-dimer, CRP, and lymphocyte count as predictive of severity at admission showed similar discrimination to a published algorithm (AUC=0.88 and 0.91, respectively). Both models deteriorated in predictive accuracy as the disease progressed. On average, no difference in severity prediction was found between North American and European sites.

Conclusions

Laboratory test values at admission can be used to predict severity in patients with COVID-19. Prediction models show consistency across international sites highlighting the potential generalizability of these models.

Towards Implementation of OMOP in a German University Hospital Consortium

Background  In 2015, the German Federal Ministry of Education and Research initiated a large data integration and data sharing research initiative to improve the reuse of data from patient care and translational research. The Observational Medical Outcomes Partnership (OMOP) common data model and the Observational Health Data Sciences and Informatics (OHDSI) tools could be used as a core element in this initiative for harmonizing the terminologies used as well as facilitating the federation of research analyses across institutions.

Objective  To realize an OMOP/OHDSI-based pilot implementation within a consortium of eight German university hospitals, evaluate the applicability to support data harmonization and sharing among them, and identify potential enhancement requirements.

Methods  The vocabularies and terminological mapping required for importing the fact data were prepared, and the process for importing the data from the source files was designed. For eight German university hospitals, a virtual machine preconfigured with the OMOP database and the OHDSI tools as well as the jobs to import the data and conduct the analysis was provided. Last, a federated/distributed query to test the approach was executed.

Results  While the mapping of ICD-10 German Modification succeeded with a rate of 98.8% of all terms for diagnoses, the procedures could not be mapped and hence an extension to the OMOP standard terminologies had to be made.

Overall, the data of 3 million inpatients with approximately 26 million conditions, 21 million procedures, and 23 million observations have been imported.

A federated query to identify a cohort of colorectal cancer patients was successfully executed and yielded 16,701 patient cases visualized in a Sunburst plot.

Conclusion  OMOP/OHDSI is a viable open source solution for data integration in a German research consortium. Once the terminology problems can be solved, researchers can build on an active community for further development.

Regional Differences in Thrombectomy Rates : Secondary use of Billing Codes in the MIRACUM (Medical Informatics for Research and Care in University Medicine) Consortium

BACKGROUND AND PURPOSE

Mechanical thrombectomy, in addition to intravenous (i.v.) thrombolysis is recommended for treatment of acute stroke in patients with large vessel occlusions (LVO) in the anterior circulation up to 6 h after symptom onset. We compared thrombectomy rates of eight university hospitals of the MIRACUM consortium to analyze the implementation of this guideline in clinical routine.

METHODS

Anonymized billing data in a standardized format were loaded into a local i2b2 data warehouse by applying already existing extract, transform and load (ETL) routines. A locally executed uniform SQL (structured query language) query delivered aggregated site data for all inpatients with a discharge diagnosis of ischemic stroke (ICD-10 I63) containing counts for type of acute treatment, type of admission and age groups, which were centrally analyzed with R.

RESULTS

From 2014 to 2016, the thrombectomy rate almost doubled from a mean of 4.7% to 9.6%, although significant differences between centers exist (range in 2016: 5.8-17%). The number of drip-and-ship procedures increased in 3 out of 8 centers. There was no evidence for a decrease in thrombectomy rates during weekends/holiday or among patients older than 80 years, but this age group is more likely to receive i.v. recombinant tissue plasminogen activator (rtPA).

CONCLUSION

The observed increase of thrombectomy rates and drip-and-ship procedures without a significant difference between weekdays and weekends or patients of different ages is substantiating a rapid implementation of stroke guidelines within the analyzed neurovascular centers. The prototype of the MIRACUM Data Integration Center already contributes to health services research in Germany.

Improved concept and first results of an auditory single-switch BCI for the future use in disorders of consciousness patients

A promising approach to establish basic communication for disorders of consciousness (DOC) patients, is the application of Brain-Computer Interface (BCI) systems, especially the use of single-switch BCIs (ssBCIs). Recently we proposed the concept of a novel auditory ssBCI paradigm and presented first classification results. In this study we report on the evaluation of four different modifications of the original paradigm with the intention to increase the suitability. Therefore we investigated different sound types and the inclusion of additional spatial information. Finally, the classification investigation with the most encouraging modifications shows an enhancement compared to our original paradigm, within healthy subjects, implicating better results for the future use in DOC patients.

Detection of mental imagery and attempted movements in patients with disorders of consciousness using EEG

Further development of an EEG based communication device for patients with disorders of consciousness (DoC) could benefit from addressing the following gaps in knowledge—first, an evaluation of different types of motor imagery; second, an evaluation of passive feet movement as a mean of an initial classifier setup; and third, rapid delivery of biased feedback. To that end we investigated whether complex and/or familiar mental imagery, passive, and attempted feet movement can be reliably detected in patients with DoC using EEG recordings, aiming to provide them with a means of communication. Six patients in a minimally conscious state (MCS) took part in this study. The patients were verbally instructed to perform different mental imagery tasks (sport, navigation), as well as attempted feet movements, to induce distinctive event-related (de)synchronization (ERD/S) patterns in the EEG. Offline classification accuracies above chance level were reached in all three tasks (i.e., attempted feet, sport, and navigation), with motor tasks yielding significant (p < 0.05) results more often than navigation (sport: 10 out of 18 sessions; attempted feet: 7 out of 14 sessions; navigation: 4 out of 12 sessions). The passive feet movements, evaluated in one patient, yielded mixed results: whereas time-frequency analysis revealed task-related EEG changes over neurophysiological plausible cortical areas, the classification results were not significant enough (p < 0.05) to setup an initial classifier for the detection of attempted movements. Concluding, the results presented in this study are consistent with the current state of the art in similar studies, to which we contributed by comparing different types of mental tasks, notably complex motor imagery and attempted feet movements, within patients. Furthermore, we explored new venues, such as an evaluation of passive feet movement as a mean of an initial classifier setup, and rapid delivery of biased feedback.

Evaluation of healthy EEG responses for spelling through listener-assisted scanning

We investigated whether listener-assisted scanning, an alternative communication method for persons with severe motor and visual impairments but preserved cognitive skills, could be used for spelling with EEG. To that end spoken letters were presented sequentially, and the participants made selections by performing motor execution/imagery or a cognitive task. The motor task was a brisk dorsiflexion of both feet, and the cognitive task was related to working memory and perception of human voice. The motor imagery task yielded the most promising results with respect to letter selection accuracy, albeit with a large variation in individual performance. The cognitive task yielded significant ( p = 0.05) albeit moderate results. Closer inspection of grand average ERPs for the cognitive task revealed task-related modulation of a late negative component, which is novel in the auditory BCI literature. Guidelines for further development are presented.

An independent SSVEP-based brain-computer interface in locked-in syndrome

OBJECTIVE

Steady-state visually evoked potential (SSVEP)-based brain-computer interfaces (BCIs) allow healthy subjects to communicate. However, their dependence on gaze control prevents their use with severely disabled patients. Gaze-independent SSVEP-BCIs have been designed but have shown a drop in accuracy and have not been tested in brain-injured patients. In the present paper, we propose a novel independent SSVEP-BCI based on covert attention with an improved classification rate. We study the influence of feature extraction algorithms and the number of harmonics. Finally, we test online communication on healthy volunteers and patients with locked-in syndrome (LIS).

APPROACH

Twenty-four healthy subjects and six LIS patients participated in this study. An independent covert two-class SSVEP paradigm was used with a newly developed portable light emitting diode-based 'interlaced squares' stimulation pattern.

MAIN RESULTS

Mean offline and online accuracies on healthy subjects were respectively 85 ± 2% and 74 ± 13%, with eight out of twelve subjects succeeding to communicate efficiently with 80 ± 9% accuracy. Two out of six LIS patients reached an offline accuracy above the chance level, illustrating a response to a command. One out of four LIS patients could communicate online.

SIGNIFICANCE

We have demonstrated the feasibility of online communication with a covert SSVEP paradigm that is truly independent of all neuromuscular functions. The potential clinical use of the presented BCI system as a diagnostic (i.e., detecting command-following) and communication tool for severely brain-injured patients will need to be further explored.

An adaptive P300-based control system

An adaptive P300 brain-computer interface (BCI) using a 12 × 7 matrix explored new paradigms to improve bit rate and accuracy. During online use, the system adaptively selects the number of flashes to average. Five different flash patterns were tested. The 19-flash paradigm represents the typical row/column presentation (i.e. 12 columns and 7 rows). The 9- and 14-flash A and B paradigms present all items of the 12 × 7 matrix three times using either 9 or 14 flashes (instead of 19), decreasing the amount of time to present stimuli. Compared to 9-flash A, 9-flash B decreased the likelihood that neighboring items would flash when the target was not flashing, thereby reducing the interference from items adjacent to targets. 14-flash A also reduced the adjacent item interference and 14-flash B additionally eliminated successive (double) flashes of the same item. Results showed that the accuracy and bit rate of the adaptive system were higher than those of the non-adaptive system. In addition, 9- and 14-flash B produced significantly higher performance than their respective A conditions. The results also show the trend that the 14-flash B paradigm was better than the 19-flash pattern for naive users.

Asynchronous steady-state visual evoked potential based BCI control of a 2-DoF artificial upper limb

A brain-computer interface (BCI) provides a direct connection between the human brain and a computer. One type of BCI can be realized using steady-state visual evoked potentials (SSVEPs), resulting from repetitive stimulation. The aim of this study was the realization of an asynchronous SSVEP-BCI, based on canonical correlation analysis, suitable for the control of a 2-degrees of freedom (DoF) hand and elbow neuroprosthesis. To determine whether this BCI is suitable for the control of 2-DoF neuroprosthetic devices, online experiments with a virtual and a robotic limb feedback were conducted with eight healthy subjects and one tetraplegic patient. All participants were able to control the artificial limbs with the BCI. In the online experiments, the positive predictive value (PPV) varied between 69% and 83% and the false negative rate (FNR) varied between 1% and 17%. The spinal cord injured patient achieved PPV and FNR values within one standard deviation of the mean for all healthy subjects.