610 Medizin, Gesundheit
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The Logical Observation Identifiers, Names and Codes (LOINC) is a common terminology used for standardizing laboratory terms. Within the consortium of the HiGHmed project, LOINC is one of the central terminologies used for health data sharing across all university sites. Therefore, linking the LOINC codes to the site-specific tests and measures is one crucial step to reach this goal. In this work we report our ongoing efforts in implementing LOINC to our laboratory information system and research infrastructure, as well as our challenges and the lessons learned. 407 local terms could be mapped to 376 LOINC codes of which 209 are already available to routine laboratory data. In our experience, mapping of local terms to LOINC is a widely manual and time consuming process for reasons of language and expert knowledge of local laboratory procedures.
The German Corona Consensus (GECCO) established a uniform dataset in FHIR format for exchanging and sharing interoperable COVID-19 patient specific data between health information systems (HIS) for universities. For sharing the COVID-19 information with other locations that use openEHR, the data are to be converted in FHIR format. In this paper, we introduce our solution through a web-tool named “openEHR-to-FHIR” that converts compositions from an openEHR repository and stores in their respective GECCO FHIR profiles. The tool provides a REST web service for ad hoc conversion of openEHR compositions to FHIR profiles.
Purpose: Radiology reports mostly contain free-text, which makes it challenging to obtain structured data. Natural language processing (NLP) techniques transform free-text reports into machine-readable document vectors that are important for creating reliable, scalable methods for data analysis. The aim of this study is to classify unstructured radiograph reports according to fractures of the distal fibula and to find the best text mining method.
Materials & Methods: We established a novel German language report dataset: a designated search engine was used to identify radiographs of the ankle and the reports were manually labeled according to fractures of the distal fibula. This data was used to establish a machine learning pipeline, which implemented the text representation methods bag-of-words (BOW), term frequency-inverse document frequency (TF-IDF), principal component analysis (PCA), non-negative matrix factorization (NMF), latent Dirichlet allocation (LDA), and document embedding (doc2vec). The extracted document vectors were used to train neural networks (NN), support vector machines (SVM), and logistic regression (LR) to recognize distal fibula fractures. The results were compared via cross-tabulations of the accuracy (acc) and area under the curve (AUC).
Results: In total, 3268 radiograph reports were included, of which 1076 described a fracture of the distal fibula. Comparison of the text representation methods showed that BOW achieved the best results (AUC = 0.98; acc = 0.97), followed by TF-IDF (AUC = 0.97; acc = 0.96), NMF (AUC = 0.93; acc = 0.92), PCA (AUC = 0.92; acc = 0.9), LDA (AUC = 0.91; acc = 0.89) and doc2vec (AUC = 0.9; acc = 0.88). When comparing the different classifiers, NN (AUC = 0,91) proved to be superior to SVM (AUC = 0,87) and LR (AUC = 0,85).
Conclusion: An automated classification of unstructured reports of radiographs of the ankle can reliably detect findings of fractures of the distal fibula. A particularly suitable feature extraction method is the BOW model.
Key Points:
- The aim was to classify unstructured radiograph reports according to distal fibula fractures.
- Our automated classification system can reliably detect fractures of the distal fibula.
- A particularly suitable feature extraction method is the BOW model.
The Wnt signaling pathway has been associated with many essential cell processes. This study aims to examine the effects of Wnt signaling on proliferation of cultured HEK293T cells. Cells were incubated with Wnt3a, and the activation of the Wnt pathway was followed by analysis of the level of the β-catenin protein and of the expression levels of the target genes MYC and CCND1. The level of β-catenin protein increased up to fourfold. While the mRNA levels of c-Myc and cyclin D1 increased slightly, the protein levels increased up to a factor of 1.5. Remarkably, MTT and BrdU assays showed different results when measuring the proliferation rate of Wnt3a stimulated HEK293T cells. In the BrdU assays an increase of the proliferation rate could be detected, which correlated to the applied Wnt3a concentration. Oppositely, this correlation could not be shown in the MTT assays. The MTT results, which are based on the mitochondrial activity, were confirmed by analysis of the succinate dehydrogenase complex by immunofluorescence and by western blotting. Taken together, our study shows that Wnt3a activates proliferation of HEK293 cells. These effects can be detected by measuring DNA synthesis rather than by measuring changes of mitochondrial activity.
Harmonisation of German Health Care Data Using the OMOP Common Data Model – A Practice Report
(2023)
Data harmonization is an important step in large-scale data analysis and for generating evidence on real world data in healthcare. With the OMOP common data model, a relevant instrument for data harmonization is available that is being promoted by different networks and communities. At the Hannover Medical School (MHH) in Germany, an Enterprise Clinical Research Data Warehouse (ECRDW) is established and harmonization of that data source is the focus of this work. We present MHH’s first implementation of the OMOP common data model on top of the ECRDW data source and demonstrate the challenges concerning the mapping of German healthcare terminologies to a standardized format.
Building a well-founded understanding of the concepts, tasks and limitations of IT in all areas of society is an essential prerequisite for future developments in business and research. This applies in particular to the healthcare sector and medical research, which are affected by the noticeable advances in digitization. In the transfer project “Zukunftslabor Gesundheit” (ZLG), a teaching framework was developed to support the development of further education online courses in order to teach heterogeneous groups of learners independent of location and prior knowledge. The study at hand describes the development and components of the framework.
Pathologists need to identify abnormal changes in tissue. With the developing digitalization, the used tissue slides are stored digitally. This enables pathologists to annotate the region of interest with the support of software tools. PathoLearn is a web-based learning platform explicitly developed for the teacher-student scenario, where the goal is that students learn to identify potential abnormal changes. Artificial intelligence (AI) and machine learning (ML) have become very important in medicine. Many health sectors already utilize AI and ML. This will only increase in the future, also in the field of pathology. Therefore, it is important to teach students the fundamentals and concepts of AI and ML early in their studies. Additionally, creating and training AI generally requires knowledge of programming and technical details. This thesis evaluates how this boundary can be overcome by comparing existing end-to-end AI platforms and teaching tools for AI. It was shown that a visual programming editor offers a fitting abstraction for creating neural networks without programming. This was extended with real-time collaboration to enable students to work in groups. Additionally, an automatic training feature was implemented, removing the necessity to know technical details about training neural networks.
After kidney transplantation graft rejection must be prevented. Therefore, a multitude of parameters of the patient is observed pre- and postoperatively. To support this process, the Screen Reject research project is developing a data warehouse optimized for kidney rejection diagnostics. In the course of this project it was discovered that important information are only available in form of free texts instead of structured data and can therefore not be processed by standard ETL tools, which is necessary to establish a digital expert system for rejection diagnostics. Due to this reason, data integration has been improved by a combination of methods from natural language processing and methods from image processing. Based on state-of-the-art data warehousing technologies (Microsoft SSIS), a generic data integration tool has been developed. The tool was evaluated by extracting Banff-classification from 218 pathology reports and extracting HLA mismatches from about 1700 PDF files, both written in german language.
Purpose: The calculation of aggregated composite measures is a widely used strategy to reduce the amount of data on hospital report cards. Therefore, this study aims to elicit and compare preferences of both patients as well as referring physicians regarding publicly available hospital quality information.
Methods: Based on systematic literature reviews as well as qualitative analysis, two discrete choice experiments (DCEs) were applied to elicit patients’ and referring physicians’ preferences. The DCEs were conducted using a fractional factorial design. Statistical data analysis was performed using multinomial logit models.
Results: Apart from five identical attributes, one specific attribute was identified for each study group, respectively. Overall, 322 patients (mean age 68.99) and 187 referring physicians (mean age 53.60) were included. Our models displayed significant coefficients for all attributes (p < 0.001 each). Among patients, “Postoperative complication rate” (20.6%; level range of 1.164) was rated highest, followed by “Mobility at hospital discharge” (19.9%; level range of 1.127), and ‘‘The number of cases treated” (18.5%; level range of 1.045). In contrast, referring physicians valued most the ‘‘One-year revision surgery rate’’ (30.4%; level range of 1.989), followed by “The number of cases treated” (21.0%; level range of 1.372), and “Postoperative complication rate” (17.2%; level range of 1.123).
Conclusion: We determined considerable differences between both study groups when calculating the relative value of publicly available hospital quality information. This may have an impact when calculating aggregated composite measures based on consumer-based weighting.
Chronic kidney disease is one of the main causes of mortality worldwide. It affects more than 800 million patients globally, accounting for approximately 10% of the general population. The significant burden of the disease prompts healthcare systems to implement adequate preventive and therapeutic measures. This systematic review and meta-analysis aimed to provide a concise summary of the findings published in the existing body of research about the influence that mobile health technology has on the outcomes of patients with the disease. A comprehensive systematic literature review was conducted from inception until March 1st, 2023. This systematic review and meta-analysis included all clinical trials that compared the efficacy of mobile app-based educational programs to that of more conventional educational treatment for the patients. Eleven papers were included in the current analysis, representing 759 CKD patients. 381 patients were randomly assigned to use the mobile apps, while 378 individuals were assigned to the control group. The mean systolic blood pressure was considerably lower in the mobile app group (MD -4.86; 95%-9.60, -0.13; p=0.04). Meanwhile, the mean level of satisfaction among patients who used the mobile app was considerably greater (MD 0.75; 95% CI 0.03, 1.46; p=0.04). Additionally, the mean self-management scores in the mobile app groups were significantly higher (SMD 0.534; 95% CI 0.201, 0.867; p=0.002). Mobile health applications are potentially valuable interventions for patients. This technology improved the self-management of the disease, reducing the mean levels of systolic blood pressure with a high degree of patient satisfaction.