@article{DietrichKrebsLimanetal.2019,
  author    = {Dietrich, Georg and Krebs, Jonathan and Liman, Leon and Fette, Georg and Ertl, Maximilian and Kaspar, Mathias and St{\"o}rk, Stefan and Puppe, Frank},
  title     = {Replicating medication trend studies using ad hoc information extraction in a clinical data warehouse},
  series = {BMC Medical Informatics and Decision Making},
  volume    = {19},
  journal   = {BMC Medical Informatics and Decision Making},
  doi       = {10.1186/s12911-018-0729-0},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-200409},
  pages     = {15},
  year      = {2019},
  abstract  = {Background Medication trend studies show the changes of medication over the years and may be replicated using a clinical Data Warehouse (CDW). Even nowadays, a lot of the patient information, like medication data, in the EHR is stored in the format of free text. As the conventional approach of information extraction (IE) demands a high developmental effort, we used ad hoc IE instead. This technique queries information and extracts it on the fly from texts contained in the CDW. Methods We present a generalizable approach of ad hoc IE for pharmacotherapy (medications and their daily dosage) presented in hospital discharge letters. We added import and query features to the CDW system, like error tolerant queries to deal with misspellings and proximity search for the extraction of the daily dosage. During the data integration process in the CDW, negated, historical and non-patient context data are filtered. For the replication studies, we used a drug list grouped by ATC (Anatomical Therapeutic Chemical Classification System) codes as input for queries to the CDW. Results We achieve an F1 score of 0.983 (precision 0.997, recall 0.970) for extracting medication from discharge letters and an F1 score of 0.974 (precision 0.977, recall 0.972) for extracting the dosage. We replicated three published medical trend studies for hypertension, atrial fibrillation and chronic kidney disease. Overall, 93\% of the main findings could be replicated, 68\% of sub-findings, and 75\% of all findings. One study could be completely replicated with all main and sub-findings. Conclusion A novel approach for ad hoc IE is presented. It is very suitable for basic medical texts like discharge letters and finding reports. Ad hoc IE is by definition more limited than conventional IE and does not claim to replace it, but it substantially exceeds the search capabilities of many CDWs and it is convenient to conduct replication studies fast and with high quality.},
  language  = {en}
}
@article{SeidlmayerMagesBerbneretal.2019,
  author    = {Seidlmayer, Lea K. and Mages, Christine and Berbner, Annette and Eder-Negrin, Petra and Arias-Loza, Paula Anahi and Kaspar, Mathias and Song, Moshi and Dorn, Gerald W. and Kohlhaas, Michael and Frantz, Stefan and Maack, Christoph and Gerull, Brenda and Dedkova, Elena N.},
  title     = {Mitofusin 2 is essential for IP3-mediated SR/Mitochondria metabolic feedback in ventricular myocytes},
  series = {Frontiers in Physiology},
  volume    = {10},
  journal   = {Frontiers in Physiology},
  number    = {733},
  issn      = {1664-042X},
  doi       = {10.3389/fphys.2019.00733},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-199141},
  year      = {2019},
  abstract  = {Aim: Endothelin-1 (ET-1) and angiotensin II (Ang II) are multifunctional peptide hormones that regulate the function of the cardiovascular and renal systems. Both hormones increase the intracellular production of inositol-1,4,5-trisphosphate (IP\(_3\)) by activating their membrane-bound receptors. We have previously demonstrated that IP\(_3\)-mediated sarcoplasmic reticulum (SR) Ca\(^{2+}\) release results in mitochondrial Ca\(^{2+}\) uptake and activation of ATP production. In this study, we tested the hypothesis that intact SR/mitochondria microdomains are required for metabolic IP\(_3\)-mediated SR/mitochondrial feedback in ventricular myocytes. Methods: As a model for disrupted mitochondrial/SR microdomains, cardio-specific tamoxifen-inducible mitofusin 2 (Mfn2) knock out (KO) mice were used. Mitochondrial Ca\(^{2+}\) uptake, membrane potential, redox state, and ATP generation were monitored in freshly isolated ventricular myocytes from Mfn2 KO mice and their control wild-type (WT) littermates. Results: Stimulation of ET-1 receptors in healthy control myocytes increases mitochondrial Ca\(^{2+}\) uptake, maintains mitochondrial membrane potential and redox balance leading to the enhanced ATP generation. Mitochondrial Ca\(^{2+}\) uptake upon ET-1 stimulation was significantly higher in interfibrillar (IFM) and perinuclear (PNM) mitochondria compared to subsarcolemmal mitochondria (SSM) in WT myocytes. Mfn2 KO completely abolished mitochondrial Ca\(^{2+}\) uptake in IFM and PNM mitochondria but not in SSM. However, mitochondrial Ca2+ uptake induced by beta-adrenergic receptors activation with isoproterenol (ISO) was highest in SSM, intermediate in IFM, and smallest in PNM regions. Furthermore, Mfn2 KO did not affect ISO-induced mitochondrial Ca\(^{2+}\) uptake in SSM and IFM mitochondria; however, enhanced mitochondrial Ca\(^{2+}\) uptake in PNM. In contrast to ET-1, ISO induced a decrease in ATP levels in WT myocytes. Mfn2 KO abolished ATP generation upon ET-1 stimulation but increased ATP levels upon ISO application with highest levels observed in PNM regions. Conclusion: When the physical link between SR and mitochondria by Mfn2 was disrupted, the SR/mitochondrial metabolic feedback mechanism was impaired resulting in the inability of the IP\(_3\)-mediated SR Ca\(^{2+}\) release to induce ATP production in ventricular myocytes from Mfn2 KO mice. Furthermore, we revealed the difference in Mfn2-mediated SR-mitochondrial communication depending on mitochondrial location and type of communication (IP\(_3\)R-mRyR1 vs. ryanodine receptor type 2-mitochondrial calcium uniporter).},
  language  = {en}
}
@article{KasparFetteHankeetal.2021,
  author    = {Kaspar, Mathias and Fette, Georg and Hanke, Monika and Ertl, Maximilian and Puppe, Frank and St{\"o}rk, Stefan},
  title     = {Automated provision of clinical routine data for a complex clinical follow-up study: A data warehouse solution},
  series = {Health Informatics Journal},
  volume    = {28},
  journal   = {Health Informatics Journal},
  number    = {1},
  doi       = {10.1177/14604582211058081},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-260828},
  year      = {2021},
  abstract  = {A deep integration of routine care and research remains challenging in many respects. We aimed to show the feasibility of an automated transformation and transfer process feeding deeply structured data with a high level of granularity collected for a clinical prospective cohort study from our hospital information system to the study's electronic data capture system, while accounting for study-specific data and visits. We developed a system integrating all necessary software and organizational processes then used in the study. The process and key system components are described together with descriptive statistics to show its feasibility in general and to identify individual challenges in particular. Data of 2051 patients enrolled between 2014 and 2020 was transferred. We were able to automate the transfer of approximately 11 million individual data values, representing 95\% of all entered study data. These were recorded in n = 314 variables (28\% of all variables), with some variables being used multiple times for follow-up visits. Our validation approach allowed for constant good data quality over the course of the study. In conclusion, the automated transfer of multi-dimensional routine medical data from HIS to study databases using specific study data and visit structures is complex, yet viable.},
  language  = {en}
}