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Objective To assess the change in inpatient radiotherapy related to COVID-19 lockdown measures during the first wave of the pandemic in 2020. Methods We included cases hospitalized between January 1 and August 31, 2018–2020, with a primary ICD-10 diagnosis of C00–C13, C32 (head and neck cancer, HNC) and C53 (cervical cancer, CC). Data collection was conducted within the Medical Informatics Initiative. Outcomes were fractions and admissions. Controlling for decreasing hospital admissions during holidays, calendar weeks of 2018/2019 were aligned to Easter 2020. A lockdown period (LP; 16/03/2020–02/08/2020) and a return-to-normal period (RNP; 04/05/2020–02/08/2020) were defined. The study sample comprised a control (admission 2018/19) and study cohort (admission 2020). We computed weekly incidence and IR ratios from generalized linear mixed models. Results We included 9365 (CC: 2040, HNC: 7325) inpatient hospital admissions from 14 German university hospitals. For CC, fractions decreased by 19.97% in 2020 compared to 2018/19 in the LP. In the RNP the reduction was 28.57% (p p Conclusion Related to the COVID-19 lockdown in an inpatient setting, radiotherapy for HNC treatment became a more frequently applied modality, while admissions of CC cases decreased.

Neben der prospektiven Versorgungsforschung mit ihrem qualitativen und quantitativen Ansatz sind retrospektive Datenquellen essenziell zur Beurteilung von Prozessen im Gesundheitswesen. In Deutschland ermoglichen strukturelle Veranderungen in den Krebsregistern bzw. die Etablierung neuer Datenquellen interessante Moglichkeiten fur die Versorgungsforschung. So wurde mit der Medizininformatik-Initiative eine Vernetzung klinischer Einrichtungen aufgebaut, womit sich schnelle, sektorubergreifende und lebensnahe Analysen realisieren lassen. Durch die Neustrukturierung der Krebsregister sollen bevolkerungsbasierte Erhebungen im onkologischen Bereich vereinfacht und die Detailtreue der Daten erhoht werden. Die Folgen der COVID-19-Pandemie (Coronavirus-Krankheit 2019) im onkologischen Bereich lassen sich dabei uber das neu geschaffene Nationale Pandemie Kohorten Netz (NAPKON), ein Zusammenschluss universitarer und nichtuniversitarer Gesundheitsdienstleister, abbilden. Durch die Einbeziehung der Akteure im Gesundheitswesen und unter der Mitwirkung prospektiver Studien lasst sich damit ein umfassendes Bild des onkologischen Versorgungsgeschehens in Deutschland zeichnen.

Quantification of DNA methylation in neoplastic cells is crucial both from mechanistic and diagnostic perspectives. However, such measurements are prone to different experimental biases. Polymerase chain reaction (PCR) bias results in an unequal recovery of methylated and unmethylated alleles at the sample preparation step. Post-PCR biases get introduced additionally by the readout processes. Correcting the biases is more practicable than optimising experimental conditions, as demonstrated previously. However, utilisation of our earlier developed algorithm strongly necessitates automation. Here, we present two R packages: rBiasCorrection, the core algorithms to correct biases; and BiasCorrector, its web-based graphical user interface frontend. The software detects and analyses experimental biases in calibration DNA samples at a single base resolution by using cubic polynomial and hyperbolic regression. The correction coefficients from the best regression type are employed to compensate for the bias. Three common technologies-bisulphite pyrosequencing, next-generation sequencing and oligonucleotide microarrays-were used to comprehensively test BiasCorrector. We demonstrate the accuracy of BiasCorrector's performance and reveal technology-specific PCR- and post-PCR biases. BiasCorrector effectively eliminates biases regardless of their nature, locus, the number of interrogated methylation sites and the detection method, thus representing a user-friendly tool for producing accurate epigenetic results.

COVID-19 has challenged the healthcare systems worldwide. To quickly identify successful diagnostic and therapeutic approaches large data sharing approaches are inevitable. Though organizational clinical data are abundant, many of them are available only in isolated silos and largely inaccessible to external researchers. To overcome and tackle this challenge the university medicine network (comprising all 36 German university hospitals) has been founded in April 2020 to coordinate COVID-19 action plans, diagnostic and therapeutic strategies and collaborative research activities. 13 projects were initiated from which the CODEX project, aiming at the development of a Germany-wide Covid-19 Data Exchange Platform, is presented in this publication. We illustrate the conceptual design, the stepwise development and deployment, first results and the current status.

Objectives To evaluate whether neural networks can distinguish between seropositive RA, seronegative RA, and PsA based on inflammatory patterns from hand MRIs and to test how psoriasis patients with subclinical inflammation fit into such patterns. Methods ResNet neural networks were utilized to compare seropositive RA vs PsA, seronegative RA vs PsA, and seropositive vs seronegative RA with respect to hand MRI data. Results from T1 coronal, T2 coronal, T1 coronal and axial fat-suppressed contrast-enhanced (CE), and T2 fat-suppressed axial sequences were used. The performance of such trained networks was analysed by the area under the receiver operating characteristics curve (AUROC) with and without presentation of demographic and clinical parameters. Additionally, the trained networks were applied to psoriasis patients without clinical arthritis. Results MRI scans from 649 patients (135 seronegative RA, 190 seropositive RA, 177 PsA, 147 psoriasis) were fed into ResNet neural networks. The AUROC was 75% for seropositive RA vs PsA, 74% for seronegative RA vs PsA, and 67% for seropositive vs seronegative RA. All MRI sequences were relevant for classification, however, when deleting contrast agent–based sequences the loss of performance was only marginal. The addition of demographic and clinical data to the networks did not provide significant improvements for classification. Psoriasis patients were mostly assigned to PsA by the neural networks, suggesting that a PsA-like MRI pattern may be present early in the course of psoriatic disease. Conclusion Neural networks can be successfully trained to distinguish MRI inflammation related to seropositive RA, seronegative RA, and PsA.

Background: Assessing the uncertainty of diagnostic findings is essential for advising patients. Previous research has demonstrated the difficulty of computing the expected correctness of positive or negative results, although clinical decision support (CDS) tools promise to facilitate adequate interpretations. Objectives: To teach the potential utility of CDS tools to medical students, we designed an interactive software module that computes and visualizes relevant probabilities from typical inputs. Methods: We reviewed the literature on recommended graphical approaches and decided to support contingency tables, plain table formats, tree diagrams, and icon arrays. Results: We implemented these functions in a single-page web application, which was configured to complement our local learning management system where students also access interpretation tasks. Conclusion: Our technical choices promoted a rapid implementation. We intend to explore the utility of the tool during some upcoming courses. Future developments could also model a more complex clinical reality where the likelihood of alternative diagnoses is estimated from sets of clinical investigations.

Assessing the uncertainty of diagnostic findings is essential for advising patients. Previous research has demonstrated the difficulty of computing the expected correctness of positive or negative results, although clinical decision support (CDS) tools promise to facilitate adequate interpretations.To teach the potential utility of CDS tools to medical students, we designed an interactive software module that computes and visualizes relevant probabilities from typical inputs.We reviewed the literature on recommended graphical approaches and decided to support contingency tables, plain table formats, tree diagrams, and icon arrays.We implemented these functions in a single-page web application, which was configured to complement our local learning management system where students also access interpretation tasks.Our technical choices promoted a rapid implementation. We intend to explore the utility of the tool during some upcoming courses. Future developments could also model a more complex clinical reality where the likelihood of alternative diagnoses is estimated from sets of clinical investigations.

The aim of this study is to evaluate the use of a natural language processing (NLP) software to extract medication statements from unstructured medical discharge letters.Ten randomly selected discharge letters were extracted from the data warehouse of the University Hospital Erlangen (UHE) and manually annotated to create a gold standard. The AHD NLP tool, provided by MIRACUM's industry partner was used to annotate these discharge letters. Annotations by the NLP tool where then compared to the gold standard on two levels: phrase precision (whether or not the whole medication statement has been identified correctly) and token precision (whether or not the medication name has been identified correctly within correctly discovered medication phrases).The NLP tool detected medication related phrases with an overall F-measure of 0.852. The medication name has been identified correctly with an overall F-measure of 0.936.This proof-of-concept study is a first step towards an automated scalable evaluation system for MIRACUM's industry partner's NLP tool by using a gold standard. Medication phrases and names have been correctly identified in most cases by the NLP system. Future effort needs to be put into extending and validating the gold standard.

Semantic interoperability is a major challenge in multi-center data sharing projects, a challenge that the German Initiative for Medical Informatics is taking up. With respect to laboratory data, enriching site-specific tests and measurements with LOINC codes appears to be a crucial step in supporting cross-institutional research. However, this effort is very time-consuming, as it requires expert knowledge of local site specifics. To ease this process, we developed a generic manual collaborative terminology mapping tool, the MIRACUM Mapper. It allows the creation of arbitrary mapping workflows involving different user roles. A mapping workflow with two user roles has been implemented at University Hospital Erlangen to support the local LOINC mapping. Additionally, the MIRACUM LabVisualizeR provides summary statistics and visualizations of analyte data. We developed a toolbox that facilitates the collaborative creation of mappings and streamlines the review as well as the validation process. The two tools are available under an open source license.

Introduction: The aim of this study is to evaluate the use of a natural language processing (NLP) software to extract medication statements from unstructured medical discharge letters. Methods: Ten randomly selected discharge letters were extracted from the data warehouse of the University Hospital Erlangen (UHE) and manually annotated to create a gold standard. The AHD NLP tool, provided by MIRACUM’s industry partner was used to annotate these discharge letters. Annotations by the NLP tool where then compared to the gold standard on two levels: phrase precision (whether or not the whole medication statement has been identified correctly) and token precision (whether or not the medication name has been identified correctly within correctly discovered medication phrases). Results: The NLP tool detected medication related phrases with an overall F-measure of 0.852. The medication name has been identified correctly with an overall F-measure of 0.936. Discussion: This proof-of-concept study is a first step towards an automated scalable evaluation system for MIRACUM’s industry partner’s NLP tool by using a gold standard. Medication phrases and names have been correctly identified in most cases by the NLP system. Future effort needs to be put into extending and validating the gold standard.

Semantic interoperability is a major challenge in multi-center data sharing projects, a challenge that the German Initiative for Medical Informatics is taking up. With respect to laboratory data, enriching site-specific tests and measurements with LOINC codes appears to be a crucial step in supporting cross-institutional research. However, this effort is very time-consuming, as it requires expert knowledge of local site specifics. To ease this process, we developed a generic manual collaborative terminology mapping tool, the MIRACUM Mapper. It allows the creation of arbitrary mapping workflows involving different user roles. A mapping workflow with two user roles has been implemented at University Hospital Erlangen to support the local LOINC mapping. Additionally, the MIRACUM LabVisualizeR provides summary statistics and visualizations of analyte data. We developed a toolbox that facilitates the collaborative creation of mappings and streamlines the review as well as the validation process. The two tools are available under an open source license.

Data quality (DQ) is an important prerequisite for secondary use of electronic health record (EHR) data in clinical research, particularly with regards to progressing towards a learning health system, one of the MIRACUM consortium's goals. Following the successful integration of the i2b2 research data repository in MIRACUM, we present a standardized and generic DQ framework.Already established DQ evaluation methods do not cover all of MIRACUM's requirements.A data quality analysis plan was developed to assess common data quality dimensions for demographic-, condition-, procedure- and department-related variables of MIRACUM's research data repository.A data quality analysis (DQA) tool was developed using R scripts packaged in a Docker image with all the necessary dependencies and R libraries for easy distribution. It integrates with the i2b2 data repository at each MIRACUM site, executes an analysis on the data and generates a DQ report.Our DQA tool brings the analysis to the data and thus meets the MIRACUM data protection requirements. It evaluates established DQ dimensions of data repositories in a standardized and easily distributable way. This analysis allowed us to reveal and revise inconsistencies in earlier versions of the ETL jobs. The framework is portable, easy to deploy across different sites and even further adaptable to other database schemes.The presented framework provides the first step towards a unified, standardized and harmonized EHR DQ assessment in MIRACUM. DQ issues can now be systematically identified by individual hospitals to subsequently implement site- or consortium-wide feedback loops to increase data quality.

Searching for patient cohorts in electronic patient data often requires the definition of temporal constraints between the selection criteria. However, beyond a certain degree of temporal complexity, the non-graphical, form-based approaches implemented in current translational research platforms may be limited when modeling such constraints. In our opinion, there is a need for an easily accessible and implementable, fully graphical method for creating temporal queries. We aim to respond to this challenge with a new graphical notation. Based on Allen's time interval algebra, it allows for modeling temporal queries by arranging simple horizontal bars depicting symbolic time intervals. To make our approach applicable to complex temporal patterns, we apply two extensions: with duration intervals, we enable the inference about relative temporal distances between patient events, and with time interval modifiers, we support counting and excluding patient events, as well as constraining numeric values. We describe how to generate database queries from this notation. We provide a prototypical implementation, consisting of a temporal query modeling frontend and an experimental backend that connects to an i2b2 system. We evaluate our modeling approach on the MIMIC-III database to demonstrate that it can be used for modeling typical temporal phenotyping queries.

To take full advantage of decision support, machine learning, and patient-level prediction models, it is important that models are not only created, but also deployed in a clinical setting. The KETOS platform demonstrated in this work implements a tool for researchers allowing them to perform statistical analyses and deploy resulting models in a secure environment.The proposed system uses Docker virtualization to provide researchers with reproducible data analysis and development environments, accessible via Jupyter Notebook, to perform statistical analysis and develop, train and deploy models based on standardized input data. The platform is built in a modular fashion and interfaces with web services using the Health Level 7 (HL7) Fast Healthcare Interoperability Resources (FHIR) standard to access patient data. In our prototypical implementation we use an OMOP common data model (OMOP-CDM) database. The architecture supports the entire research lifecycle from creating a data analysis environment, retrieving data, and training to final deployment in a hospital setting.We evaluated the platform by establishing and deploying an analysis and end user application for hemoglobin reference intervals within the University Hospital Erlangen. To demonstrate the potential of the system to deploy arbitrary models, we loaded a colorectal cancer dataset into an OMOP database and built machine learning models to predict patient outcomes and made them available via a web service. We demonstrated both the integration with FHIR as well as an example end user application. Finally, we integrated the platform with the open source DataSHIELD architecture to allow for distributed privacy preserving data analysis and training across networks of hospitals.The KETOS platform takes a novel approach to data analysis, training and deploying decision support models in a hospital or healthcare setting. It does so in a secure and privacy-preserving manner, combining the flexibility of Docker virtualization with the advantages of standardized vocabularies, a widely applied database schema (OMOP-CDM), and a standardized way to exchange medical data (FHIR).