Converting Entity-Attribute-Value Data Sources to OMOP's CDM: Lessons Learned.

Clinical data repositories often use entity-attribute-value (EAV) data models. To be valuable for secondary use, these health data can be transformed to the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM). The present paper describes the lessons learned from such an endeavour based on the concept of registering transformation functions on source data elements. We further provide future work directions for follow-up projects.

Adherence to Secondary Prevention Measures after Acute Myocardial Infarction and Its Impact on Patient Outcome-A Nationwide Perspective.

Objectives: Secondary prevention is crucial for reducing morbidity and mortality in patients following acute myocardial infraction (MI). However, adherence to cardiac rehabilitation (CR) and pharmacotherapy remains suboptimal despite strong guideline recommendations. This study investigated the adherence to CR, dual antiplatelet therapy (DAPT), and statins following acute MI and evaluated their impact on patient outcomes from a nationwide perspective in Austria. Methods: In this national observational study, all patients diagnosed with acute MI, defined as STEMI or NSTEMI, between April 2011 and August 2015 in Austria were included. Patient characteristics and comorbidities were derived from the Austrian national health insurance system using ICD-10 codes. Adherence to CR, high-intensity statins, and DAPT was assessed based on health insurance records and pharmacy prescription submissions. Cox Regression hazard analysis was used to explore the impact of non-adherence to CR on mortality. Results: Among 16,518 acute MI patients, only 13.4% adhered to the recommended CR programs, which was associated with a significantly lower risk of mortality (adjusted hazard ratio [HR] 0.73; 95% CI: 0.54-0.98; p = 0.036). In contrast, 66.4% of 23,240 patients did not comply with high-intensity statin therapy, correlating with an increased mortality risk (adjusted HR 1.16; 95% CI: 1.06-1.25; p < 0.001). Furthermore, among 22,331 patients analyzed for DAPT adherence, only 29.3% followed the guidelines, yet this adherence was linked to a 21% reduction in mortality over the observation period (adjusted HR 0.79; 95% CI: 0.72-0.88; p < 0.001). Conclusions: This nationwide study reveals alarmingly low adherence to CR and secondary preventive medications among acute MI patients, which is significantly linked to higher mortality rates. Enhanced efforts to promote awareness and adherence are crucial, involving structured referrals and personalized follow-ups to improve patient outcomes. Addressing these gaps through comprehensive healthcare strategies could substantially enhance cardiovascular health.

Getting ready for the European Health Data Space (EHDS): IDERHA's plan to align with the latest EHDS requirements for the secondary use of health data.

Objective: The European Health Data Space (EHDS) shapes the digital transformation of healthcare in Europe. The EHDS regulation will also accelerate the use of health data for research, innovation, policy-making, and regulatory activities for secondary use of data (known as EHDS2). The Integration of heterogeneous Data and Evidence towards Regulatory and HTA Acceptance (IDERHA) project builds one of the first pan-European health data spaces in alignment with the EHDS2 requirements, addressing lung cancer as a pilot. Methods: In this study, we conducted a comprehensive review of the EHDS regulation, technical requirements for EHDS2, and related projects. We also explored the results of the Joint Action Towards the European Health Data Space (TEHDAS) to identify the framework of IDERHA's alignment with EHDS2. We also conducted an internal webinar and an external workshop with EHDS experts to share expertise on the EHDS requirements and challenges. Results: We identified the lessons learned from the existing projects and the minimum-set of requirements for aligning IDERHA infrastructure with EHDS2, including user journey, concepts, terminologies, and standards. The IDERHA framework (i.e., platform architecture, standardization approaches, documentation, etc.) is being developed accordingly. Discussion: The IDERHA's alignment plan with EHDS2 necessitates the implementation of three categories of standardization for: data discoverability: Data Catalog Vocabulary (DCAT-AP), enabling semantics interoperability: Observational Medical Outcomes Partnership (OMOP), and health data exchange (DICOM and FHIR). The main challenge is that some standards are still being refined, e.g., the extension of the DCAT-AP (HealthDCAT-AP). Additionally, extensions to the Observational Health Data Sciences and Informatics (OHDSI) OMOP Common Data Model (CDM) to represent the patient-generated health data are still needed. Finally, proper mapping between standards (FHIR/OMOP) is a prerequisite for proper data exchange. Conclusions: The IDERHA's plan and our collaboration with other EHDS initiatives/projects are critical in advancing the implementation of EHDS2.

Transforming Documents of the Austrian Nationwide EHR System into the OMOP CDM.

The Austrian nationwide EHR system ELGA can contribute valuable data for research due to its high volume of data and broad population coverage. In order to be applicable in international research projects, transformation to a standardized, research-oriented data model such as the OMOP common data model is essential. In this paper we describe our experience with the corresponding transformation task. Using Python scripts, we implemented a prototypical process that extracts, transforms, maps, and loads fully structured sections of ELGA documents to an OMOP database.

Converting HL7 CDA Based Nationwide Austrian Medication Data to OMOP CDM.

Austria's national Electronic Health Record (EHR) system holds information on medication prescriptions and dispenses in highly structured HL7 Clinical Document Architecture (CDA) documents. Making these data accessible for research is desirable due to their volume and completeness. This work describes our approach of transforming the HL7 CDA data into Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) and highlights a key challenge, namely mapping the Austrian drug terminology to OMOP standard concepts.

Comparison of Convolutional Neural Network Architectures for Robustness Against Common Artefacts in Dermatoscopic Images.

Introduction: Classification of dermatoscopic images via neural networks shows comparable performance to clinicians in experimental conditions but can be affected by artefacts like skin markings or rulers. It is unknown whether specialized neural networks are more robust to artefacts. Objectives: Analyze robustness of 3 neural network architectures, namely ResNet-34, Faster R-CNN and Mask R-CNN. Methods: We identified common artefacts in the HAM10000, PH2 and the 7-point criteria evaluation datasets, and established a template-based method to superimpose artefacts on dermatoscopic images. The HAM10000-dataset with and without superimposed artefacts was used to train the networks, followed by analyzing their robustness against artefacts in test images. Performance was assessed via area under the precision recall curve and classification results. Results: ResNet-34 and Faster R-CNN models trained on regular images perform worse than Mask R-CNN on images with superimposed artefacts. Artefacts added to all tested images led to a decrease in area under the precision-recall curve values of 0.030 for ResNet-34 and 0.045 for Faster R-CNN in comparison to only 0.011 for Mask R-CNN. However, changes in model performance only became significant with 40% or more of the images having superimposed artefacts. A loss in performance occurred when the training was biased by selectively superimposing artefacts on images belonging to a certain class. Conclusions: As Mask R-CNN showed the least decrease in performance when confronted with artefacts, instance segmentation architectures may be helpful to counter the effects of artefacts, warranting further research on related architectures. Our artefact insertion mechanism could be useful for future research.

Efficient Quadrature Squeezing from Biexcitonic Parametric Gain in Atomically Thin Semiconductors.

Modification of electromagnetic quantum fluctuations in the form of quadrature squeezing is a central quantum resource, which can be generated from nonlinear optical processes. Such a process is facilitated by coherent two-photon excitation of the strongly bound biexciton in atomically thin semiconductors. We show theoretically that interfacing an atomically thin semiconductor with an optical cavity makes it possible to harness this two-photon resonance and use the biexcitonic parametric gain to generate squeezed light with input power an order of magnitude below current state-of-the-art devices with conventional third-order nonlinear materials that rely on far off-resonant nonlinearities. Furthermore, the squeezing bandwidth is found to be in the range of several meV. These results identify atomically thin semiconductors as a promising candidate for on-chip squeezed-light sources.

Disentangling Many-Body Effects in the Coherent Optical Response of 2D Semiconductors.

In single-layer (1L) transition metal dichalcogenides, the reduced Coulomb screening results in strongly bound excitons which dominate the linear and the nonlinear optical response. Despite the large number of studies, a clear understanding on how many-body and Coulomb correlation effects affect the excitonic resonances on a femtosecond time scale is still lacking. Here, we use ultrashort laser pulses to measure the transient optical response of 1L-WS2. In order to disentangle many-body effects, we perform exciton line-shape analysis, and we study its temporal dynamics as a function of the excitation photon energy and fluence. We find that resonant photoexcitation produces a blue shift of the A exciton, while for above-resonance photoexcitation the transient response at the optical bandgap is largely determined by a reduction of the exciton oscillator strength. Microscopic calculations based on excitonic Heisenberg equations of motion quantitatively reproduce the nonlinear absorption of the material and its dependence on excitation conditions.

Extending the Austrian National EHR System with Patient-Reported Outcome Data.

The Austrian national Electronic Health Record system ELGA is a population-based infrastructure for health data. However, to date, it does not include patient-reported outcomes. In this paper, we describe on-going work on extending ELGA with patient-reported outcome data. This will be done by linking ELGA with the infrastructure of the Health Outcomes Observatory (H2O) initiative. The focus will be on using ELGA's identifier registry for H2O patients and making H2O outcome data accessible in ELGA via an existing ELGA document type for telemonitoring.

Excitons in Bilayer MoS_{2} Displaying a Colossal Electric Field Splitting and Tunable Magnetic Response.

van der Waals heterostructures composed of transition metal dichalcogenide monolayers (TMDCs) are characterized by their truly rich excitonic properties which are determined by their structural, geometric, and electronic properties: In contrast to pure monolayers, electrons and holes can be hosted in different materials, resulting in highly tunable dipolar many-particle complexes. However, for genuine spatially indirect excitons, the dipolar nature is usually accompanied by a notable quenching of the exciton oscillator strength. Via electric and magnetic field dependent measurements, we demonstrate that a slightly biased pristine bilayer MoS_{2} hosts strongly dipolar excitons, which preserve a strong oscillator strength. We scrutinize their giant dipole moment, and shed further light on their orbital and valley physics via bias-dependent magnetic field measurements.

The ultrafast onset of exciton formation in 2D semiconductors.

The equilibrium and non-equilibrium optical properties of single-layer transition metal dichalcogenides (TMDs) are determined by strongly bound excitons. Exciton relaxation dynamics in TMDs have been extensively studied by time-domain optical spectroscopies. However, the formation dynamics of excitons following non-resonant photoexcitation of free electron-hole pairs have been challenging to directly probe because of their inherently fast timescales. Here, we use extremely short optical pulses to non-resonantly excite an electron-hole plasma and show the formation of two-dimensional excitons in single-layer MoS2 on the timescale of 30 fs via the induced changes to photo-absorption. These formation dynamics are significantly faster than in conventional 2D quantum wells and are attributed to the intense Coulombic interactions present in 2D TMDs. A theoretical model of a coherent polarization that dephases and relaxes to an incoherent exciton population reproduces the experimental dynamics on the sub-100-fs timescale and sheds light into the underlying mechanism of how the lowest-energy excitons, which are the most important for optoelectronic applications, form from higher-energy excitations. Importantly, a phonon-mediated exciton cascade from higher energy states to the ground excitonic state is found to be the rate-limiting process. These results set an ultimate timescale of the exciton formation in TMDs and elucidate the exceptionally fast physical mechanism behind this process.

Exciton-Scattering-Induced Dephasing in Two-Dimensional Semiconductors.

Enhanced Coulomb interactions in monolayer transition metal dichalcogenides cause tightly bound electron-hole pairs (excitons) that dominate their linear and nonlinear optical response. The latter includes bleaching, energy renormalizations, and higher-order Coulomb correlation effects like biexcitons and excitation-induced dephasing. While the first three are extensively studied, no theoretical footing for excitation-induced dephasing in exciton-dominated semiconductors is available so far. In this Letter, we present microscopic calculations based on excitonic Heisenberg equations of motion and identify the coupling of optically pumped excitons to exciton-exciton scattering continua as the leading mechanism responsible for an optical-power-dependent linewidth broadening (excitation-induced dephasing) and sideband formation. Performing time-, momentum-, and energy-resolved simulations, we quantitatively evaluate the exciton-induced dephasing for the most common monolayer transition metal dichalcogenides and find an excellent agreement with recent experiments.

Phonon-Assisted Photoluminescence from Indirect Excitons in Monolayers of Transition-Metal Dichalcogenides.

The photoluminescence (PL) spectrum of transition-metal dichalcogenides (TMDs) shows a multitude of emission peaks below the bright exciton line, and not all of them have been explained yet. Here, we study the emission traces of phonon-assisted recombinations of indirect excitons. To this end, we develop a microscopic theory describing simultaneous exciton, phonon, and photon interaction and including consistent many-particle dephasing. We explain the drastically different PL below the bright exciton in tungsten- and molybdenum-based materials as the result of different configurations of bright and momentum-dark states. In good agreement with experiments, our calculations predict that WSe2 exhibits clearly visible low-temperature PL signals stemming from the phonon-assisted recombination of momentum-dark K-K' excitons.