1
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Ulrich H, Macherius A, Kunkel U, Sengl M, Letzel T. Novel PFAS-specific monitoring approach for highly impacted surface waters. Chemosphere 2024; 349:140893. [PMID: 38072205 DOI: 10.1016/j.chemosphere.2023.140893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/27/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023]
Abstract
In regulatory environmental monitoring programs, only a very small fraction of the vast number of per- and polyfluoroalkyl substances (PFAS) are investigated by target analysis. Therefore, non-target analysis (NTA) studies are increasingly conducted to detect unknown or unnoticed PFAS. These studies are often based on a few grab samples. Thus, discontinuously emitted PFAS from industrial batch processes might be easily overlooked. To address this deficiency and obtain in-depth information on the occurrence and temporal trend of PFAS in surface water impacted by treated industrial waste water, a comprehensive target and NTA study was implemented for 29 months. Elevated PFAS concentrations with up to 10.8 μg L-1 were detected in the river water by target analysis. In addition to PFAS target analysis, the water samples were analyzed by liquid chromatography-high-resolution tandem mass spectrometry (LC-HRMS/MS). Data processing strategies and various filtering steps were applied to prioritize PFAS. Substances were identified by comparing data to available internal and external PFAS suspect lists, a fragment ion and neutral loss list, and spectral libraries. Several compounds were unequivocally identified based on reference standards. Fifty-five PFAS were (tentatively) identified using NTA. Of those, 43 could be assigned to 13 different homologous series. Partly fluorinated short-chain carboxylic acids (H-PFCA) and sulfonic acids (H-PFSA) were predominantly found in addition to perfluoroalkyl carboxylic acids (PFCA) and the alkyl ether carboxylic acid DONA. To the best of our knowledge, 12 PFAS were reported in surface water for the first time. Signal intensities of individual PFAS and signal ratios varied widely over time, which may indicate batch operations leading to discontinuous emission. Results and insights from this screening approach on PFAS can be used to optimize forthcoming surface water monitoring programs by including newly identified PFAS and selecting appropriate sampling intervals.
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Affiliation(s)
- H Ulrich
- Bavarian Environment Agency, Demollstr. 31, 82407 Wielenbach, Germany; Technical University of Munich (Chair of Urban Water Systems Engineering), Am Coulombwall 3, 85748 Garching bei München, Germany.
| | - A Macherius
- Bavarian Environment Agency, Buergermeister-Ulrich-Straße 160, 86179 Augsburg, Germany.
| | - U Kunkel
- Bavarian Environment Agency, Buergermeister-Ulrich-Straße 160, 86179 Augsburg, Germany.
| | - M Sengl
- Bavarian Environment Agency, Buergermeister-Ulrich-Straße 160, 86179 Augsburg, Germany.
| | - T Letzel
- Technical University of Munich (Chair of Urban Water Systems Engineering), Am Coulombwall 3, 85748 Garching bei München, Germany; Analytisches Forschungsinstitut fuer Non-Target Screening (AFIN-TS) GmbH, Augsburg, Germany.
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2
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Ulrich H, Anywar M, Kinast B, Schreiweis B. Large-Scale Standardized Image Integration for Secondary Use Research Projects. Stud Health Technol Inform 2024; 310:174-178. [PMID: 38269788 DOI: 10.3233/shti230950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Imaging techniques are a cornerstone of today's medicine and can be crucial for a successful therapy. But in addition, the generated imaging series are an important resource for new informatics' methods, especially in the field of artificial intelligence. This paper describes the success of integrating clinical routine imaging data into a standardized format for research purposes. Thus, we designed an integration flow and successfully implemented it in the local data integration center of University Hospital Schleswig-Holstein. The flow integrates imaging series and radiological reports from the primary system into an openEHR repository with enrichment by semantic codes for better findability and retrieval using HL7 FHIR. As a result, 6.6 million radiological studies with 29 million image series are now available for further medical (informatics) research.
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Affiliation(s)
- Hannes Ulrich
- Institute for Medical Informatics and Statistics, Kiel University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel and Lübeck, Schleswig-Holstein, Germany
| | - Michael Anywar
- Institute for Medical Informatics and Statistics, Kiel University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel and Lübeck, Schleswig-Holstein, Germany
| | - Benjamin Kinast
- Institute for Medical Informatics and Statistics, Kiel University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel and Lübeck, Schleswig-Holstein, Germany
| | - Björn Schreiweis
- Institute for Medical Informatics and Statistics, Kiel University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel and Lübeck, Schleswig-Holstein, Germany
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3
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Nuñez-Rios JD, Ulrich H, Díaz-Muñoz M, Lameu C, Vázquez-Cuevas FG. Purinergic system in cancer stem cells. Purinergic Signal 2023:10.1007/s11302-023-09976-5. [PMID: 37966629 DOI: 10.1007/s11302-023-09976-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 10/25/2023] [Indexed: 11/16/2023] Open
Abstract
Accumulating evidence supports the idea that cancer stem cells (CSCs) are those with the capacity to initiate tumors, generate phenotypical diversity, sustain growth, confer drug resistance, and orchestrate the spread of tumor cells. It is still controversial whether CSCs originate from normal stem cells residing in the tissue or cancer cells from the tumor bulk that have dedifferentiated to acquire stem-like characteristics. Although CSCs have been pointed out as key drivers in cancer, knowledge regarding their physiology is still blurry; thus, research focusing on CSCs is essential to designing novel and more effective therapeutics. The purinergic system has emerged as an important autocrine-paracrine messenger system with a prominent role at multiple levels of the tumor microenvironment, where it regulates cellular aspects of the tumors themselves and the stromal and immune systems. Recent findings have shown that purinergic signaling also participates in regulating the CSC phenotype. Here, we discuss updated information regarding CSCs in the purinergic system and present evidence supporting the idea that elements of the purinergic system expressed by this subpopulation of the tumor represent attractive pharmacological targets for proposing innovative anti-cancer therapies.
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Affiliation(s)
- J D Nuñez-Rios
- Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México (UNAM), Boulevard Juriquilla #3001, Juriquilla Querétaro, Querétaro, CP 76230, México
| | - H Ulrich
- Department of Biochemistry, Chemistry Institute, University of São Paulo (USP), São Paulo, Brazil
| | - M Díaz-Muñoz
- Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México (UNAM), Boulevard Juriquilla #3001, Juriquilla Querétaro, Querétaro, CP 76230, México
| | - C Lameu
- Department of Biochemistry, Chemistry Institute, University of São Paulo (USP), São Paulo, Brazil
| | - F G Vázquez-Cuevas
- Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México (UNAM), Boulevard Juriquilla #3001, Juriquilla Querétaro, Querétaro, CP 76230, México.
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4
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Schüttler C, Ulrich H. Support of Young Talent in the GMDS. Stud Health Technol Inform 2023; 302:484-485. [PMID: 37203726 DOI: 10.3233/shti230182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The German Association for Medical Informatics, Biometry and Epidemiology (GMDS) aims to develop subject-specific methods, which are then to be applied in collaboration with various medical domains. Furthermore, the support of young scientists is an essential field of activity of the GMDS, since the need for junior staff has increased due to the acceleration in medical digitization. A specially established Presidential Commission strives to promote young talents and scientists in the above-mentioned disciplines. For this purpose, various strategies and concepts are elaborated in regular meetings and finally implemented. These include online formats such as a lecture series on research-related topics, as well as events such as summer schools and PhD symposia.
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Affiliation(s)
| | - Hannes Ulrich
- Institute for Medical Informatics and Statistics, Kiel University and University Hospital Schleswig-Holstein, Germany
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5
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Bennett AM, Ulrich H, van Damme P, Wiedekopf J, Johnson AEW. MIMIC-IV on FHIR: converting a decade of in-patient data into an exchangeable, interoperable format. J Am Med Inform Assoc 2023; 30:718-725. [PMID: 36688534 PMCID: PMC10018258 DOI: 10.1093/jamia/ocad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/01/2022] [Accepted: 01/16/2023] [Indexed: 01/24/2023] Open
Abstract
OBJECTIVE Convert the Medical Information Mart for Intensive Care (MIMIC)-IV database into Health Level 7 Fast Healthcare Interoperability Resources (FHIR). Additionally, generate and publish an openly available demo of the resources, and create a FHIR Implementation Guide to support and clarify the usage of MIMIC-IV on FHIR. MATERIALS AND METHODS FHIR profiles and terminology system of MIMIC-IV were modeled from the base FHIR R4 resources. Data and terminology were reorganized from the relational structure into FHIR according to the profiles. Resources generated were validated for conformance with the FHIR profiles. Finally, FHIR resources were published as newline delimited JSON files and the profiles were packaged into an implementation guide. RESULTS The modeling of MIMIC-IV in FHIR resulted in 25 profiles, 2 extensions, 35 ValueSets, and 34 CodeSystems. An implementation guide encompassing the FHIR modeling can be accessed at mimic.mit.edu/fhir/mimic. The generated demo dataset contained 100 patients and over 915 000 resources. The full dataset contained 315 000 patients covering approximately 5 840 000 resources. The final datasets in NDJSON format are accessible on PhysioNet. DISCUSSION Our work highlights the challenges and benefits of generating a real-world FHIR store. The challenges arise from terminology mapping and profiling modeling decisions. The benefits come from the extensively validated openly accessible data created as a result of the modeling work. CONCLUSION The newly created MIMIC-IV on FHIR provides one of the first accessible deidentified critical care FHIR datasets. The extensive real-world data found in MIMIC-IV on FHIR will be invaluable for research and the development of healthcare applications.
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Affiliation(s)
- Alex M Bennett
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Hannes Ulrich
- Institute for Medical Informatics and Statistics, Kiel University and University Hospital Center Schleswig-Holstein, Campus Kiel, Germany
| | - Philip van Damme
- Department of Medical Informatics, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health, Digital Health & Methodology, Amsterdam, The Netherlands
| | - Joshua Wiedekopf
- IT Center for Clinical Research, University of Lübeck and University Hospital Center Schleswig-Holstein, Campus Lübeck, Germany
| | - Alistair E W Johnson
- Corresponding Author: Alistair E. W. Johnson, Child Health Evaluative Sciences, The Hospital for Sick Children, 686 Bay St., Toronto, ON M5G 0A4, Canada;
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6
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Eysenbach G, Ulrich H, Bergh B, Schreiweis B. Functional Requirements for Medical Data Integration into Knowledge Management Environments: Requirements Elicitation Approach Based on Systematic Literature Analysis. J Med Internet Res 2023; 25:e41344. [PMID: 36757764 PMCID: PMC9951079 DOI: 10.2196/41344] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/24/2022] [Accepted: 11/17/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND In patient care, data are historically generated and stored in heterogeneous databases that are domain specific and often noninteroperable or isolated. As the amount of health data increases, the number of isolated data silos is also expected to grow, limiting the accessibility of the collected data. Medical informatics is developing ways to move from siloed data to a more harmonized arrangement in information architectures. This paradigm shift will allow future research to integrate medical data at various levels and from various sources. Currently, comprehensive requirements engineering is working on data integration projects in both patient care- and research-oriented contexts, and it is significantly contributing to the success of such projects. In addition to various stakeholder-based methods, document-based requirement elicitation is a valid method for improving the scope and quality of requirements. OBJECTIVE Our main objective was to provide a general catalog of functional requirements for integrating medical data into knowledge management environments. We aimed to identify where integration projects intersect to derive consistent and representative functional requirements from the literature. On the basis of these findings, we identified which functional requirements for data integration exist in the literature and thus provide a general catalog of requirements. METHODS This work began by conducting a literature-based requirement elicitation based on a broad requirement engineering approach. Thus, in the first step, we performed a web-based systematic literature review to identify published articles that dealt with the requirements for medical data integration. We identified and analyzed the available literature by applying the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. In the second step, we screened the results for functional requirements using the requirements engineering method of document analysis and derived the requirements into a uniform requirement syntax. Finally, we classified the elicited requirements into a category scheme that represents the data life cycle. RESULTS Our 2-step requirements elicitation approach yielded 821 articles, of which 61 (7.4%) were included in the requirement elicitation process. There, we identified 220 requirements, which were covered by 314 references. We assigned the requirements to different data life cycle categories as follows: 25% (55/220) to data acquisition, 35.9% (79/220) to data processing, 12.7% (28/220) to data storage, 9.1% (20/220) to data analysis, 6.4% (14/220) to metadata management, 2.3% (5/220) to data lineage, 3.2% (7/220) to data traceability, and 5.5% (12/220) to data security. CONCLUSIONS The aim of this study was to present a cross-section of functional data integration-related requirements defined in the literature by other researchers. The aim was achieved with 220 distinct requirements from 61 publications. We concluded that scientific publications are, in principle, a reliable source of information for functional requirements with respect to medical data integration. Finally, we provide a broad catalog to support other scientists in the requirement elicitation phase.
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Affiliation(s)
- G Eysenbach
- Institute for Medical Informatics and StatisticsKiel University and University Hospital Schleswig-HolsteinKielGermany
| | - Hannes Ulrich
- Institute for Medical Informatics and Statistics, Kiel University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Björn Bergh
- Institute for Medical Informatics and Statistics, Kiel University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Björn Schreiweis
- Institute for Medical Informatics and Statistics, Kiel University and University Hospital Schleswig-Holstein, Kiel, Germany
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7
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Anywar M, Schreiweis B, Ulrich H. Strategies and Recommendation for Data Loading of FHIR-Based Data Marts with Focus on GDPR Compliance. Stud Health Technol Inform 2022; 298:127-131. [PMID: 36073470 DOI: 10.3233/shti220921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Interoperability and portability of healthcare data to enable research in the healthcare sector is an important factor towards precision medicine and a learning health system. With many safety-nets put in place like the European General Data Protection Regulation, and local standards like the broad consent set up by the German Medical Informatics Initiative, management and compliance to these standards across all systems and clinical data repositories becomes a daunting task. An appropriate process needs to be established especially when patient data is transferred to and from different systems and standards. On extraction and transforming, an appropriate method of loading the modified data to a destination where it can be read and accessed needs to be established besides functional compliance by the repository systems. This paper makes recommendations in relation to data load strategies while working with FHIR server-based data marts.
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Affiliation(s)
- Michael Anywar
- Institute for Medical Informatics and Statistics, Kiel University and University Hospital Center Schleswig-Holstein, Campus Kiel, Germany
| | - Björn Schreiweis
- Institute for Medical Informatics and Statistics, Kiel University and University Hospital Center Schleswig-Holstein, Campus Kiel, Germany
| | - Hannes Ulrich
- Institute for Medical Informatics and Statistics, Kiel University and University Hospital Center Schleswig-Holstein, Campus Kiel, Germany
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8
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Wiedekopf J, Ulrich H, Drenkhahn C, Kock-Schoppenhauer AK, Ingenerf J. TermiCron - Bridging the Gap Between FHIR Terminology Servers and Metadata Repositories. Stud Health Technol Inform 2022; 290:71-75. [PMID: 35672973 DOI: 10.3233/shti220034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The large variability of data models, specifications, and interpretations of data elements is particular to the healthcare domain. Achieving semantic interoperability is the first step to enable reuse of healthcare data. To ensure interoperability, metadata repositories (MDR) are increasingly used to manage data elements on a structural level, while terminology servers (TS) manage the ontologies, terminologies, coding systems and value sets on a semantic level. In practice, however, this strict separation is not always followed; instead, semantical information is stored and maintained directly in the MDR, as a link between both systems is missing. This may be reasonable up to a certain level of complexity, but it quickly reaches its limitations with increasing complexity. The goal of this approach is to combine both components in a compatible manner. We present TermiCron, a synchronization engine that provides synchronized value sets from TS in MDRs, including versioning and annotations. Prototypical results were shown for the terminology server Ontoserver and two established MDR systems. Bridging the semantic and structural gap between the two infrastructure components, this approach enables shared use of metadata and reuse of corresponding health information by establishing a clear separation of the two systems and thus serves to strengthen reuse as well as to increase quality.
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Affiliation(s)
- Joshua Wiedekopf
- IT Center for Clinical Research (ITCR-L), University of Lübeck, Germany
| | - Hannes Ulrich
- IT Center for Clinical Research (ITCR-L), University of Lübeck, Germany
| | - Cora Drenkhahn
- IT Center for Clinical Research (ITCR-L), University of Lübeck, Germany
| | | | - Josef Ingenerf
- IT Center for Clinical Research (ITCR-L), University of Lübeck, Germany.,Institute of Medical Informatics, University of Lübeck, Germany
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9
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Löbe M, Ulrich H, Beger C, Bender T, Bauer C, Sax U, Ingenerf J, Winter A. Improving Findability of Digital Assets in Research Data Repositories Using the W3C DCAT Vocabulary. Stud Health Technol Inform 2022; 290:61-65. [PMID: 35672971 DOI: 10.3233/shti220032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Research data management requires stable, trustworthy repositories to safeguard scientific research results. In this context, rich markup with metadata is crucial for the discoverability and interpretability of the relevant resources. SEEK is a web-based software to manage all important artifacts of a research project, including project structures, involved actors, documents and datasets. SEEK is organized along the ISA model (Investigation - Study - Assay). It offers several machine-readable serializations, including JSON and RDF. In this paper, we extend the power of RDF serialization by leveraging the W3C Data Catalog Vocabulary (DCAT). DCAT was specifically designed to improve interoperability between digital assets on the Web and enables cross-domain markup. By using community-consented gold standard vocabularies and a formal knowledge description language, findability and interoperability according to the FAIR principles are significantly improved.
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Affiliation(s)
- Matthias Löbe
- Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Leipzig, Germany
| | - Hannes Ulrich
- Institut für Medizinische Informatik, University of Lübeck, Lübeck, Germany
| | - Christoph Beger
- Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Leipzig, Germany
| | | | | | - Ulrich Sax
- University Medical Center Göttingen, Göttingen, Germany
- Campus Institute Data Science (CIDAS) Göttingen, Germany
| | - Josef Ingenerf
- Institut für Medizinische Informatik, University of Lübeck, Lübeck, Germany
| | - Alfred Winter
- Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Leipzig, Germany
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10
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Ulrich H, Uzunova H, Handels H, Ingenerf J. Proposal of Semantic Annotation for German Metadata Using Bidirectional Recurrent Neural Networks. Stud Health Technol Inform 2022; 294:357-361. [PMID: 35612096 DOI: 10.3233/shti220474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The distributed nature of our digital healthcare and the rapid emergence of new data sources prevents a compelling overview and the joint use of new data. Data integration, e.g., with metadata and semantic annotations, is expected to overcome this challenge. In this paper, we present an approach to predict UMLS codes to given German metadata using recurrent neural networks. The augmentation of the training dataset using the Medical Subject Headings (MeSH), particularly the German translations, also improved the model accuracy. The model demonstrates robust performance with 75% accuracy and aims to show that increasingly sophisticated machine learning tools can already play a significant role in data integration.
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Affiliation(s)
- Hannes Ulrich
- IT Center for Clinical Research (ITCR-L), University of Lübeck, Germany
| | - Hristina Uzunova
- German Research Center for Artificial Intelligence, Lübeck, Germany
| | - Heinz Handels
- German Research Center for Artificial Intelligence, Lübeck, Germany
- Institute of Medical Informatics, University of Lübeck, Germany
| | - Josef Ingenerf
- IT Center for Clinical Research (ITCR-L), University of Lübeck, Germany
- Institute of Medical Informatics, University of Lübeck, Germany
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11
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Wiedekopf J, Drenkhahn C, Rosenau L, Ulrich H, Kock-Schoppenhauer AK, Ingenerf J. TerminoDiff - Detecting Semantic Differences in HL7 FHIR CodeSystems. Stud Health Technol Inform 2022; 294:362-366. [PMID: 35612097 DOI: 10.3233/shti220475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
While HL7 FHIR and its terminology package have seen a rapid uptake by the research community, in no small part due to the wide availability of tooling and resources, there are some areas where tool availability is still lacking. In particular, the comparison of terminological resources, which supports the work of terminologists and implementers alike, has not yet been sufficiently addressed. Hence, we present TerminoDiff, an application to semantically compare FHIR R4 CodeSystem resources. Our tool considers differences across all levels required, i.e. metadata and concept differences, as well as differences in the edge graph, and surfaces them in a visually digestible fashion.
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Affiliation(s)
- Joshua Wiedekopf
- Institute of Medical Informatics, University of Lübeck, Lübeck, Germany
- IT Center for Clinical Research, University of Lübeck, Lübeck, Germany
| | - Cora Drenkhahn
- Institute of Medical Informatics, University of Lübeck, Lübeck, Germany
- IT Center for Clinical Research, University of Lübeck, Lübeck, Germany
| | - Lorenz Rosenau
- Institute of Medical Informatics, University of Lübeck, Lübeck, Germany
- IT Center for Clinical Research, University of Lübeck, Lübeck, Germany
| | - Hannes Ulrich
- Institute of Medical Informatics, University of Lübeck, Lübeck, Germany
- IT Center for Clinical Research, University of Lübeck, Lübeck, Germany
| | | | - Josef Ingenerf
- Institute of Medical Informatics, University of Lübeck, Lübeck, Germany
- IT Center for Clinical Research, University of Lübeck, Lübeck, Germany
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12
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Ulrich H, Kock-Schoppenhauer AK, Deppenwiese N, Gött R, Kern J, Lablans M, Majeed RW, Stöhr MR, Stausberg J, Varghese J, Dugas M, Ingenerf J. Understanding the Nature of Metadata: Systematic Review. J Med Internet Res 2022; 24:e25440. [PMID: 35014967 PMCID: PMC8790684 DOI: 10.2196/25440] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/28/2021] [Accepted: 10/14/2021] [Indexed: 01/11/2023] Open
Abstract
Background Metadata are created to describe the corresponding data in a detailed and unambiguous way and is used for various applications in different research areas, for example, data identification and classification. However, a clear definition of metadata is crucial for further use. Unfortunately, extensive experience with the processing and management of metadata has shown that the term “metadata” and its use is not always unambiguous. Objective This study aimed to understand the definition of metadata and the challenges resulting from metadata reuse. Methods A systematic literature search was performed in this study following the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines for reporting on systematic reviews. Five research questions were identified to streamline the review process, addressing metadata characteristics, metadata standards, use cases, and problems encountered. This review was preceded by a harmonization process to achieve a general understanding of the terms used. Results The harmonization process resulted in a clear set of definitions for metadata processing focusing on data integration. The following literature review was conducted by 10 reviewers with different backgrounds and using the harmonized definitions. This study included 81 peer-reviewed papers from the last decade after applying various filtering steps to identify the most relevant papers. The 5 research questions could be answered, resulting in a broad overview of the standards, use cases, problems, and corresponding solutions for the application of metadata in different research areas. Conclusions Metadata can be a powerful tool for identifying, describing, and processing information, but its meaningful creation is costly and challenging. This review process uncovered many standards, use cases, problems, and solutions for dealing with metadata. The presented harmonized definitions and the new schema have the potential to improve the classification and generation of metadata by creating a shared understanding of metadata and its context.
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Affiliation(s)
- Hannes Ulrich
- IT Center for Clinical Research, University of Lübeck, Lübeck, Germany.,Institute of Medical Informatics, University of Lübeck, Lübeck, Germany
| | | | - Noemi Deppenwiese
- Chair of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Robert Gött
- Department Epidemiology of Health Care and Community Health, Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Jori Kern
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany.,Complex Data Processing in Medical Informatics, University Medical Center Mannheim, Mannheim, Germany
| | - Martin Lablans
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany.,Complex Data Processing in Medical Informatics, University Medical Center Mannheim, Mannheim, Germany
| | - Raphael W Majeed
- Universities of Giessen and Marburg Lung Center, German Center for Lung Research, Justus-Liebig-University, Giessen, Germany.,Institute of Medical Informatics, University Hospital RWTH Aachen, Aachen, Germany
| | - Mark R Stöhr
- Universities of Giessen and Marburg Lung Center, German Center for Lung Research, Justus-Liebig-University, Giessen, Germany
| | - Jürgen Stausberg
- Institute of Medical Informatics, Biometry and Epidemiology, Faculty of Medicine, University of Duisburg-Essen, Essen, Germany
| | - Julian Varghese
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, Heidelberg University Hospital, Heidelberg, Germany
| | - Josef Ingenerf
- IT Center for Clinical Research, University of Lübeck, Lübeck, Germany.,Institute of Medical Informatics, University of Lübeck, Lübeck, Germany
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Ulrich H, Behrend P, Wiedekopf J, Drenkhahn C, Kock-Schoppenhauer AK, Ingenerf J. Hands on the Medical Informatics Initiative Core Data Set - Lessons Learned from Converting the MIMIC-IV. Stud Health Technol Inform 2021; 283:119-126. [PMID: 34545827 DOI: 10.3233/shti210549] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
With the steady increase in the connectivity of the healthcare system, new requirements and challenges are emerging. In addition to the seamless exchange of data between service providers on a national level, the local legacy data must also meet the new requirements. For this purpose, the applications used must be tested securely and sufficiently. However, the availability of suitable and realistic test data is not always given. Therefore, this study deals with the creation of test data based on real electronic health record data provided by the Medical Information Mart for Intensive Care (MIMIC-IV) database. In addition to converting the data to the current FHIR R4, conversion to the core data sets of the German Medical Informatics Initiative was also presented and made available. The test data was generated to simulate a legacy data transfer. Moreover, four different FHIR servers were tested for performance. This study is the first step toward comparable test scenarios around shared datasets and promotes comparability among providers on a national level.
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Affiliation(s)
- Hannes Ulrich
- IT Center for Clinical Research (ITCR-L), University of Lübeck, Lübeck, Germany
| | - Paul Behrend
- IT Center for Clinical Research (ITCR-L), University of Lübeck, Lübeck, Germany
| | - Joshua Wiedekopf
- IT Center for Clinical Research (ITCR-L), University of Lübeck, Lübeck, Germany
| | - Cora Drenkhahn
- IT Center for Clinical Research (ITCR-L), University of Lübeck, Lübeck, Germany
| | | | - Josef Ingenerf
- IT Center for Clinical Research (ITCR-L), University of Lübeck, Lübeck, Germany.,Institute of Medical Informatics, University of Lübeck, Lübeck, Germany
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14
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Banach A, Ulrich H, Kroll B, Kiel A, Ingenerf J, Kock-Schoppenhauer AK. APERITIF - Automatic Patient Recruiting for Clinical Trials Based on HL7 FHIR. Stud Health Technol Inform 2021; 281:58-62. [PMID: 34042705 DOI: 10.3233/shti210120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Clinical trials are carried out to prove the safety and effectiveness of new interventions and therapies. As diseases and their causes continue to become more specific, so do inclusion and exclusion criteria for trials. Patient recruitment has always been a challenge, but with medical progress, it becomes increasingly difficult to achieve the necessary number of cases. In Germany, the Medical Informatics Initiative is planning to use the central application and registration office to conduct feasibility analyses at an early stage and thus to identify suitable project partners. This approach aims to technically adapt/integrate the envisioned infrastructure in such a way that it can be used for trial case number estimation for the planning of multicenter clinical trials. We have developed a fully automated solution called APERITIF that can identify the number of eligible patients based on free-text eligibility criteria, taking into account the MII core data set and based on the FHIR standard. The evaluation showed a precision of 62.64 % for inclusion criteria and a precision of 66.45 % for exclusion criteria.
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Affiliation(s)
- Alexandra Banach
- IT Center for Clinical Research, Lübeck, University of Lübeck, Germany
| | - Hannes Ulrich
- IT Center for Clinical Research, Lübeck, University of Lübeck, Germany
| | - Björn Kroll
- IT Center for Clinical Research, Lübeck, University of Lübeck, Germany
| | - Alexander Kiel
- LIFE - Leipzig Research Centre for Civilization Diseases, University of Leipzig, Germany
| | - Josef Ingenerf
- IT Center for Clinical Research, Lübeck, University of Lübeck, Germany.,Institute of Medical Informatics, University of Lübeck, Germany
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15
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Ulrich H, Germer S, Kock-Schoppenhauer AK, Kern J, Lablans M, Ingenerf J. A Smart Mapping Editor for Standardised Data Transformation. Stud Health Technol Inform 2020; 270:1185-1186. [PMID: 32570571 DOI: 10.3233/shti200354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The integration of heterogeneous healthcare data sources is a necessary process to enable the secondary use valuable information in clinical research. Data integration is time-consuming for data stewards. The transformation using predefined rules for data harmonization can reduce the time-consuming and error-prone work and ease the data integration at various sites. In our study, we examined various script(ing) languages to find the most suitable candidate for definition of transformation rules and implement a smart editor which supports the data stewards in selecting rules reusing them. Thereby, it also provides an automatic and seamless documentation to strengthen the reliability of the defined transformation rules.
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Affiliation(s)
- Hannes Ulrich
- IT Center for Clinical Research, University of Lübeck, Germany
| | | | | | - Jori Kern
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
| | - Martin Lablans
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
| | - Josef Ingenerf
- IT Center for Clinical Research, University of Lübeck, Germany.,Institute of Medical Informatics, University of Lübeck, Germany
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16
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Kock-Schoppenhauer AK, Kroll B, Lambarki M, Ulrich H, Stahl-Toyota S, Habermann JK, Duhm-Harbeck P, Ingenerf J, Lablans M. One Step Away from Technology but One Step Towards Domain Experts-MDRBridge: A Template-Based ISO 11179-Compliant Metadata Processing Pipeline. Methods Inf Med 2019; 58:e72-e79. [PMID: 31853911 DOI: 10.1055/s-0039-3399579] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
BACKGROUND Secondary use of routine medical data relies on a shared understanding of given information. This understanding is achieved through metadata and their interconnections, which can be stored in metadata repositories (MDRs). The necessity of an MDR is well understood, but the local work on metadata is a time-consuming and challenging process for domain experts. OBJECTIVE To support the identification, collection, and provision of metadata in a predefined structured manner to foster consolidation. A particular focus is placed on user acceptance. METHODS We propose a software pipeline MDRBridge as a practical intermediary for metadata capture and processing, based on MDRSheet, an ISO 11179-3 compliant template using popular spreadsheet software. It serves as a practical mediator for metadata acquisition and processing in a broader pipeline. Due to the different origins of the metadata, both manual entry and automatic extractions from application systems are supported. To enable the export of collected metadata into external MDRs, a mapping of ISO 11179 to Clinical Data Interchange Standards Consortium (CDISC) Operational Data Model (ODM) was developed. RESULTS MDRSheet is embedded in the processing pipeline MDRBridge and delivers metadata in the CDISC ODM format for further use in MDRs. This approach is used to interactively unify core datasets, import existing standard datasets, and automatically extract all defined data elements from source systems. The involvement of clinical domain experts improved significantly due to minimal changes within their usual work routine. CONCLUSION A high degree of acceptance was achieved by adapting the working methods of clinical domain experts. The designed process is capable of transforming all relevant data elements according to the ISO 11179-3 format. MDRSheet is used as an intermediate format to present the information at a glance and to allow editing or supplementing by domain experts.
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Affiliation(s)
| | - B Kroll
- IT Center for Clinical Research, University of Lübeck, Germany
| | - M Lambarki
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
| | - H Ulrich
- IT Center for Clinical Research, University of Lübeck, Germany
| | - S Stahl-Toyota
- Medical Informatics for Translational Oncology, German Cancer Research Center, Heidelberg, Germany
| | - J K Habermann
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck & University Clinical Center Schleswig-Holstein, Campus Lübeck, Germany.,Interdisciplinary Center for Biobanking-Lübeck (ICB-L), University of Lübeck, Germany
| | - P Duhm-Harbeck
- IT Center for Clinical Research, University of Lübeck, Germany
| | - J Ingenerf
- Institute of Medical Informatics, University of Lübeck, Germany
| | - M Lablans
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
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17
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Ulrich H, Mlinarić M, Kohler E. Explaining healthcare among unaccompanied minor refugees: a realist review. Eur J Public Health 2019. [DOI: 10.1093/eurpub/ckz185.418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Introduction
Existing research on psychosocial care of unaccompanied minor refugees (UMRs) mainly focusses on socio-epidemiological accounts and qualitative evidence from the perspective of experts in the field of psychosocial care. In contrast, knowledge concerning differing context factors as well as underlying mechanisms of current healthcare barriers, which could inform policy recommendations, are rather scant.
Methods
To synthesize scientific evidence and gray literature dealing with the field of psychosocial healthcare of UMRs, a realist review (RR) was conducted following six methodological steps of RAMESES publication standards for realist synthesis. Based on a iterative search of keywords “UMR”, “UMF”, “UMA” and “mental health care” in electronic databases PubMed, GBV and Web of Science we gained access to 974 texts from 2005 to 2019. Screend studies and reports were systematically reviewed according rigor and relevance, which included n = 53 documents for realist synthesis with theory-informed context-mechanism-outcome configurations (CMOs).
Results
UMRs have a high prevalence risk for posttraumatic stress disorders and they face manifold institutional, cultural, ethical, juridical, and language-based barriers of care. A dominant and multiple CMO highlight residence status (C1), which limits access of UMRs to healthcare (M1) and produces psychosocially related mental health outcomes (O1). Residence status (C1) may also trigger mechanisms of structural or at least perceived discrimination (M2), which mediates undersupply of UMRs (O2).
Conclusions
The inclusion of lay perspectives and an intersectional approach could inform health services research and practitioners. The reflection of UMR’s social positions between categorical constructs of resilience and vulnerability, discriminatory discourses of othering, and restrictive health policies may guide policy recommendations to potentially reduce persistent disadvantages.
Key messages
The inclusion of lay perspectives and an intersectional approach could inform UMR related health services research and practitioners. The reflection of UMR’s social positions (between categories, discourses, and health policies) may guide policy recommendations to potentially reduce persistent disadvantages.
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Affiliation(s)
- H Ulrich
- Institut für Medizinische Soziologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - M Mlinarić
- Institut für Medizinische Soziologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - E Kohler
- Institut für Medizinische Soziologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
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18
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Baptista MS, Alves MJM, Arantes GM, Armelin HA, Augusto O, Baldini RL, Basseres DS, Bechara EJH, Bruni-Cardoso A, Chaimovich H, Colepicolo Neto P, Colli W, Cuccovia IM, Da-Silva AM, Di Mascio P, Farah SC, Ferreira C, Forti FL, Giordano RJ, Gomes SL, Gueiros Filho FJ, Hoch NC, Hotta CT, Labriola L, Lameu C, Machini MT, Malnic B, Marana SR, Medeiros MHG, Meotti FC, Miyamoto S, Oliveira CC, Souza-Pinto NC, Reis EM, Ronsein GE, Salinas RK, Schechtman D, Schreier S, Setubal JC, Sogayar MC, Souza GM, Terra WR, Truzzi DR, Ulrich H, Verjovski-Almeida S, Winck FV, Zingales B, Kowaltowski AJ. Where do we aspire to publish? A position paper on scientific communication in biochemistry and molecular biology. ACTA ACUST UNITED AC 2019; 52:e8935. [PMID: 31482979 PMCID: PMC6719344 DOI: 10.1590/1414-431x20198935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/19/2019] [Indexed: 11/21/2022]
Abstract
The scientific publication landscape is changing quickly, with an enormous increase in options and models. Articles can be published in a complex variety of journals that differ in their presentation format (online-only or in-print), editorial organizations that maintain them (commercial and/or society-based), editorial handling (academic or professional editors), editorial board composition (academic or professional), payment options to cover editorial costs (open access or pay-to-read), indexation, visibility, branding, and other aspects. Additionally, online submissions of non-revised versions of manuscripts prior to seeking publication in a peer-reviewed journal (a practice known as pre-printing) are a growing trend in biological sciences. In this changing landscape, researchers in biochemistry and molecular biology must re-think their priorities in terms of scientific output dissemination. The evaluation processes and institutional funding for scientific publications should also be revised accordingly. This article presents the results of discussions within the Department of Biochemistry, University of São Paulo, on this subject.
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Affiliation(s)
- M S Baptista
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - M J M Alves
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - G M Arantes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - H A Armelin
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - O Augusto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - R L Baldini
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - D S Basseres
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - E J H Bechara
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - A Bruni-Cardoso
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - H Chaimovich
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - P Colepicolo Neto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - W Colli
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - I M Cuccovia
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - A M Da-Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - P Di Mascio
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - S C Farah
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - C Ferreira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - F L Forti
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - R J Giordano
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - S L Gomes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - F J Gueiros Filho
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - N C Hoch
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - C T Hotta
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - L Labriola
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - C Lameu
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - M T Machini
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - B Malnic
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - S R Marana
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - M H G Medeiros
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - F C Meotti
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - S Miyamoto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - C C Oliveira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - N C Souza-Pinto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - E M Reis
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - G E Ronsein
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - R K Salinas
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - D Schechtman
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - S Schreier
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - J C Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - M C Sogayar
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - G M Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - W R Terra
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - D R Truzzi
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - H Ulrich
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - S Verjovski-Almeida
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - F V Winck
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - B Zingales
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - A J Kowaltowski
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
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19
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Ulrich H, Kern J, Kock-Schoppenhauer AK, Lablans M, Ingenerf J. Towards a Federation of Metadata Repositories: Addressing Technical Interoperability. Stud Health Technol Inform 2019; 267:74-80. [PMID: 31483257 DOI: 10.3233/shti190808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The utilisation of metadata repositories increasingly promotes secondary use of routinely collected data. However, this has not yet solved the problem of data exchange across organisational boundaries. The local description of a metadata set must also be exchangeable for flawless data exchange. In previous work, a metadata exchange language QL4MDR was developed. This work aimed to examine the applicability of this exchange language. For this purpose, existing MDR implementations were identified and systematically inspected and roughly divided into two categories to distinguish between data integration and query integration. It has been shown that all the implementations can be adapted to QL4MDR. The integration of metadata is an important first step; it enables the exchange of information, which is so urgently needed for the further processing of instance data, from the metadata mappings to the transformation rules.
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Affiliation(s)
- Hannes Ulrich
- IT Center for Clinical Research, University of Lübeck, Germany
| | - Jori Kern
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
| | | | - Martin Lablans
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
| | - Josef Ingenerf
- IT Center for Clinical Research, University of Lübeck, Germany
- Institute of Medical Informatics, University of Lübeck, Germany
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20
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Abstract
Metadata matching is an important step towards integrating heterogeneous healthcare data and facilitating secondary use. MDRCupid supports this step by providing a configurable metadata matching toolbox incorporating lexical and statistical matching approaches. The matching configuration can be adapted to different purposes by manually selecting algorithms and their weights or by using the optimization module with corresponding training data. The toolbox can be accessed as a web service via programming or user interface. For every selected metadata element, the metadata elements with the highest similarity scores are presented to the user and can be manually confirmed via the user interface, while the programming interface uses a similarity threshold to select corresponding elements. An HL7 FHIR ConceptMap is used to save the matches. Manually confirmed matches may be used as new training data for the optimizer to improve the matching parameters further.
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Affiliation(s)
- Noemi Deppenwiese
- IT Center for Clinical Research, Lübeck (ITCR-L), University of Lübeck, Germany
| | - Petra Duhm-Harbeck
- IT Center for Clinical Research, Lübeck (ITCR-L), University of Lübeck, Germany
| | - Josef Ingenerf
- IT Center for Clinical Research, Lübeck (ITCR-L), University of Lübeck, Germany.,Institute of Medical Informatics, University of Lübeck, Germany
| | - Hannes Ulrich
- IT Center for Clinical Research, Lübeck (ITCR-L), University of Lübeck, Germany
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21
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Kock-Schoppenhauer AK, Bruland P, Kadioglu D, Brammen D, Ulrich H, Kulbe K, Duhm-Harbeck P, Ingenerf J. Scientific Challenge in eHealth: MAPPATHON, a Metadata Mapping Challenge. Stud Health Technol Inform 2019; 264:1516-1517. [PMID: 31438209 DOI: 10.3233/shti190512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Scientific challenges based on benchmark data enable the comparison and evaluation of different algorithms and take place regularly in scientific disciplines like medical image processing, text mining or genetics. The idea of a challenge is rarely applied within the eHealth community. Mappathon is a metadata mapping challenge that asks for methods to find corresponding data elements within similar datasets and to correlate data elements among each other.
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Affiliation(s)
| | - Philipp Bruland
- Institute of Medical Informatics, University of Münster, Germany
| | - Dennis Kadioglu
- Medical Informatics Group, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Dominik Brammen
- Department of Anesthesiology, University of Magdeburg, Germany
| | - Hannes Ulrich
- IT Center for Clinical Research, Lübeck, University of Lübeck, Germany
| | - Kerstin Kulbe
- Institute of Medical Informatics, University of Lübeck, Germany
| | | | - Josef Ingenerf
- IT Center for Clinical Research, Lübeck, University of Lübeck, Germany.,Institute of Medical Informatics, University of Lübeck, Germany
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22
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Ulrich H, Kern J, Tas D, Kock-Schoppenhauer AK, Ückert F, Ingenerf J, Lablans M. QL 4MDR: a GraphQL query language for ISO 11179-based metadata repositories. BMC Med Inform Decis Mak 2019; 19:45. [PMID: 30885183 PMCID: PMC6421684 DOI: 10.1186/s12911-019-0794-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/06/2019] [Indexed: 11/30/2022] Open
Abstract
Background Heterogeneous healthcare instance data can hardly be integrated without harmonizing its schema-level metadata. Many medical research projects and organizations use metadata repositories to edit, store and reuse data elements. However, existing metadata repositories differ regarding software implementation and have shortcomings when it comes to exchanging metadata. This work aims to define a uniform interface with a technical interlingua between the different MDR implementations in order to enable and facilitate the exchange of metadata, to query over distributed systems and to promote cooperation. To design a unified interface for multiple existing MDRs, a standardized data model must be agreed on. The ISO 11179 is an international standard for the representation of metadata, and since most MDR systems claim to be at least partially compliant, it is suitable for defining an interface thereupon. Therefore, each repository must be able to define which parts can be served and the interface must be able to handle highly linked data. GraphQL is a data access layer and defines query techniques designed to navigate easily through complex data structures. Results We propose QL4MDR, an ISO 11179-3 compatible GraphQL query language. The GraphQL schema for QL4MDR is derived from the ISO 11179 standard and defines objects, fields, queries and mutation types. Entry points within the schema define the path through the graph to enable search functionalities, but also the exchange is promoted by mutation types, which allow creating, updating and deleting of metadata. QL4MDR is the foundation for the uniform interface, which is implemented in a modern web-based interface prototype. Conclusions We have introduced a uniform query interface for metadata repositories combining the ISO 11179 standard for metadata repositories and the GraphQL query language. A reference implementation based on the existing Samply.MDR was implemented. The interface facilitates access to metadata, enables better interaction with metadata as well as a basis for connecting existing repositories. We invite other ISO 11179-based metadata repositories to take this approach into account.
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Affiliation(s)
- H Ulrich
- IT Center for Clinical Research, University of Lübeck, Lübeck, Germany.
| | - J Kern
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
| | - D Tas
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
| | | | - F Ückert
- Medical Informatics in Translational Oncology, German Cancer Research Center, Heidelberg, Germany
| | - J Ingenerf
- IT Center for Clinical Research, University of Lübeck, Lübeck, Germany.,Institute of Medical Informatics, University of Lübeck, Lübeck, Germany
| | - M Lablans
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
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23
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Dimpfel W, Spüler M, Pierau FK, Ulrich H. Thioctic Acid Induces Dose-Dependent Sprouting of Neurites
in Cultured Rat Neuroblastoma Cells. ACTA ACUST UNITED AC 2019. [DOI: 10.1159/000480918] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Kang D, Apel W, Arteaga-Velázquez J, Bekk K, Bertaina M, Blümer J, Bozdog H, Brancus I, Cantoni E, Chiavassa A, Cossavella F, Daumiller K, de Souza V, Di Pierro F, Doll P, Engel R, Fuhrmann D, Gherghel-Lascu A, Gils H, Glasstetter R, Grupen C, Haungs A, Heck D, Hörandel J, Huber D, Huege T, Kampert KH, Klages H, Link K, Łuczak P, Mathes H, Mayer H, Milke J, Mitrica B, Morello C, Oehlschläger J, Ostapchenko S, Palmieri N, Pierog T, Rebel H, Roth M, Schieler H, Schoo S, Schröder F, Sima O, Toma G, Trinchero G, Ulrich H, Weindl A, Wochele J, Zabierowski J. Recent results from the KASCADE-Grande data analysis. EPJ Web Conf 2019. [DOI: 10.1051/epjconf/201920804005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
KASCADE, together with its extension KASCADE-Grande measured individual air showers of cosmic rays in the primary energy range of 100 TeV to 1 EeV. The data collection was fully completed at the end of 2013 and the experiment was dismantled. However, the data analysis is still in progress. Recently, we published a new result on upper limits to the flux of ultra-high energy gamma rays, which set constraints on some fundamental astrophysical models. We also use the data to investigate the validity of the new hadronic interactions models like SIBYLL version 2.3c or EPOS-LHC. In addition, we updated and improved the webbased platform of the KASCADE Cosmic Ray Data Centre (KCDC), where now the data from KASCADE and KASCADE-Grande of more than 20 years measurements is available, including corresponding Monte-Carlo simulated events based on three different hadronic interaction models. In this contribution, recent results from KASCADE-Grande and the update of KCDC is briefly discussed.
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Arteaga-Velázquez J, Rivera-Rangel D, Apel W, Bekk K, Bertaina M, Blümer J, Bozdog H, Brancus I, Cantoni E, Chiavassa A, Cossavella F, Daumiller K, de Souza V, Di Pierro F, Doll P, Engel R, Fuhrmann D, Gherghel-Lascu A, Gils H, Glasstetter R, Grupen C, Haungs A, Heck D, Hörandel J, Huege T, Kampert K, Kang D, Klages H, Link K, Łuczak P, Mathes H, Mayer H, Milke J, Mitrica B, Morello C, Oehlschläger J, Ostapchenko S, Pierog T, Rebel H, Roth M, Schieler H, Schoo S, Schröder F, Sima O, Toma G, Trinchero G, Ulrich H, Weindl A, Wochele J, Zabierowski J. Study of themuon content of high-energy air showers with KASCADE-Grande. EPJ Web Conf 2019. [DOI: 10.1051/epjconf/201920806003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we report measurements on the muon content (Eth > 230 MeV) of extensive air showers (EAS) induced by cosmic rays with primary energy from 10 PeV up to 1 EeV performed with the KASCADE-Grande experiment. The measurements are confronted with SIBYLL 2.3. The results are focused on the dependence of the total muon number and the lateral density distribution of muons in EAS on the zenith angle and the total number of charged particles in the shower. We also present updated results of a detailed study of the attenuation length of shower muons, which reveal a deviation between the measured data and the predictions of the post-LHC hadronic interaction models SIBYLL 2.3, QGSJET-II-04 and EPOS-LHC.
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Chiavassa A, Apel W, Arteaga-Velázquez J, Bekk K, Bertaina M, Blümer J, Bozdog H, Brancus I, Cantoni E, Cossavella F, Daumiller K, de Souza V, Di Pierro F, Doll P, Engel R, Fuhrmann D, Gherghel-Lascu A, Gils H, Glasstetter R, Grupen C, Haungs A, Heck D, Hörandel J, Huber D, Huege T, Kampert KH, Kang D, Klages H, Link K, Łuczak P, Mathes H, Mayer H, Milke J, Mitrica B, Morello C, Oehlschläger J, Ostapchenko S, Palmieri N, Pierog T, Rebel H, Roth M, Schieler H, Schoo S, Schröder F, Sima O, Toma G, Trinchero G, Ulrich H, Weindl A, Wochele J, Zabierowski J. Summary of the main results of the KASCADE and KASCADE-Grande experiments. EPJ Web Conf 2019. [DOI: 10.1051/epjconf/201920803002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The KASCADE and KASCADE-Grande experiments operated in KIT-Campus North, Karlsruhe (Germany) from 1993 to 2012. The two experiments studied primary cosmic rays in the energy range from 1014 eV to 1018 eV, investigating the change of slope of the spectrum detected at 2 - 4 × 1015 eV, the so called knee. We briefly review the performance of the experiments and then the main results obtained in the operation of both experiments: the test of hadronic interaction models, the all particle primary spectrum, the elemental composition of primary cosmic rays (with the first claim of a knee-like feature of the heavy primaries spectrum) and the search for large scale anisotropies.
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Ribeiro DE, Glaser T, Oliveira-Giacomelli Á, Ulrich H. Purinergic receptors in neurogenic processes. Brain Res Bull 2018; 151:3-11. [PMID: 30593881 DOI: 10.1016/j.brainresbull.2018.12.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 11/28/2018] [Accepted: 12/20/2018] [Indexed: 12/19/2022]
Abstract
Neurogenesis is a process of generating functional neurons, which occurs during embryonic and adult stages in mammals. While neurogenesis during development phase is characterized by intensive proliferation activity in all regions of the brain to form the architecture and neural function of the nervous system, adult neurogenesis occurs with less intensity in two brain regions and is involved in the maintenance of neurogenic niches, local repair, memory and cognitive functions in the hippocampus. Taking such differences into account, the understanding of molecular mechanisms involved in cell differentiation in developmental stages and maintenance of the nervous system is an important research target. Although embryonic and adult neurogenesis presents several differences, signaling through purinergic receptors participates in this process throughout life. For instance, while embryonic neurogenesis involves P2X7 receptor down-regulation and calcium waves triggered by P2Y1 receptor stimulation, adult neurogenesis may be enhanced by increased activity of A2A and P2Y1 receptors and impaired by A1, P2Y13 and P2X7 receptor stimulation.
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Affiliation(s)
- D E Ribeiro
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-900, Av. Prof. Lineu Prestes, 748, São Paulo, SP, Brazil
| | - T Glaser
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-900, Av. Prof. Lineu Prestes, 748, São Paulo, SP, Brazil
| | - Á Oliveira-Giacomelli
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-900, Av. Prof. Lineu Prestes, 748, São Paulo, SP, Brazil
| | - H Ulrich
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-900, Av. Prof. Lineu Prestes, 748, São Paulo, SP, Brazil.
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Andersen B, Kasparick M, Ulrich H, Franke S, Schlamelcher J, Rockstroh M, Ingenerf J. Connecting the clinical IT infrastructure to a service-oriented architecture of medical devices. ACTA ACUST UNITED AC 2018; 63:57-68. [PMID: 29272252 DOI: 10.1515/bmt-2017-0021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 10/13/2017] [Indexed: 11/15/2022]
Abstract
The new medical device communication protocol known as IEEE 11073 SDC is well-suited for the integration of (surgical) point-of-care devices, so are the established Health Level Seven (HL7) V2 and Digital Imaging and Communications in Medicine (DICOM) standards for the communication of systems in the clinical IT infrastructure (CITI). An integrated operating room (OR) and other integrated clinical environments, however, need interoperability between both domains to fully unfold their potential for improving the quality of care as well as clinical workflows. This work thus presents concepts for the propagation of clinical and administrative data to medical devices, physiologic measurements and device parameters to clinical IT systems, as well as image and multimedia content in both directions. Prototypical implementations of the derived components have proven to integrate well with systems of networked medical devices and with the CITI, effectively connecting these heterogeneous domains. Our qualitative evaluation indicates that the interoperability concepts are suitable to be integrated into clinical workflows and are expected to benefit patients and clinicians alike. The upcoming HL7 Fast Healthcare Interoperability Resources (FHIR) communication standard will likely change the domain of clinical IT significantly. A straightforward mapping to its resource model thus ensures the tenability of these concepts despite a foreseeable change in demand and requirements.
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Affiliation(s)
- Björn Andersen
- Institute of Medical Informatics, University of Lübeck, 23562 Lübeck, Germany
| | - Martin Kasparick
- Institute of Applied Microelectronics and Computer Engineering, University of Rostock, 18119 Rostock, Germany
| | - Hannes Ulrich
- IT for Clinical Research, University of Lübeck, 23562 Lübeck, Germany
| | - Stefan Franke
- Innovation Center Computer-Assisted Surgery, University of Leipzig, 04103 Leipzig, Germany
| | - Jan Schlamelcher
- OFFIS - Institute for Information Technology, R&D Division Health, 26121 Oldenburg, Germany
| | - Max Rockstroh
- Innovation Center Computer-Assisted Surgery, University of Leipzig, 04103 Leipzig, Germany
| | - Josef Ingenerf
- Institute of Medical Informatics, University of Lübeck, 23562 Lübeck, Germany
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Nascimento I, Lima M, Mavri J, Smuc T, Nery A, Peterka M, Sogayar M, Ulrich H. P18 Targeting Lung Cancer Initiating Cells by Aptamers. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.07.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Ulrich H, Kock-Schoppenhauer AK, Duhm-Harbeck P, Ingenerf J. Using Graph Tools on Metadata Repositories. Stud Health Technol Inform 2018; 253:55-59. [PMID: 30147040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
To exchange data across several sites or to interpret it at a later point in time, it is necessary to create a general understanding of the data. As a standard practice, this understanding is achieved through metadata. These metadata are usually stored in relational databases, so-called metadata repositories (MDR). Typical functions of such an MDR include pure storage, administration and other specific metadata functionalities such as finding relations among data elements. This results in a multitude of connections between the data elements, which can be described as highly interconnected graphs. To use alternative databases such as graph databases for modelling and visualisation it has already been proven to be beneficial in previous studies. The objective of this work is to evaluate how on-board techniques rely on matching and mapping using a graph database. Different datasets relating to cancer were entered, and algorithms for metadata management were applied.
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Affiliation(s)
- Hannes Ulrich
- IT Center for Clinical Research, Lübeck (ITCR-L), University of Lübeck, Germany
| | | | - Petra Duhm-Harbeck
- IT Center for Clinical Research, Lübeck (ITCR-L), University of Lübeck, Germany
| | - Josef Ingenerf
- IT Center for Clinical Research, Lübeck (ITCR-L), University of Lübeck, Germany
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Kock-Schoppenhauer AK, Hartung L, Ulrich H, Duhm-Harbeck P, Ingenerf J. Practical Extension of Provenance to Healthcare Data Based on the W3C PROV Standard. Stud Health Technol Inform 2018; 253:28-32. [PMID: 30147034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Secondary use of healthcare data is dependent on the availability of provenance data for assessing its quality, reliability or trustworthiness. Usually, instance-level data that might be communicated by HL7 interfaces entail limited metadata about involved software systems, persons or organizations bearing responsibility for those systems. This paper proposes a strategy for capturing interoperable provenance data needed by data stewards for assessing healthcare data that are reused in a research context. Aimed at a realistic level of granularity even system-level metadata will support a data steward trying to trace the origins or provenance of healthcare data that have been transferred to the research context. Those metadata are extracted from the 3LGM2-system, used for modelling hospital information systems. Based on the W3C provenance specification interrelated activities, entities and agents can be integrated and stored in RDF triple stores and therefore queried and visualized.
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Affiliation(s)
| | - Lina Hartung
- Institute of Medical Informatics, University of Lübeck, Germany
| | - Hannes Ulrich
- IT Center for Clinical Research, Lübeck (ITCR-L), University of Lübeck, Germany
| | - Petra Duhm-Harbeck
- IT Center for Clinical Research, Lübeck (ITCR-L), University of Lübeck, Germany
| | - Josef Ingenerf
- IT Center for Clinical Research, Lübeck (ITCR-L), University of Lübeck, Germany
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Kern J, Tas D, Ulrich H, Schmidt EE, Ingenerf J, Ückert F, Lablans M. A Method to Use Metadata in Legacy Web Applications: The Samply.MDR.Injector. Stud Health Technol Inform 2018; 253:45-49. [PMID: 30147038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Whenever medical data is integrated from multiple sources, it is regarded good practice to separate data from information about its meaning, such as designations, definitions or permissible values (in short: metadata). However, the ways in which applications work with metadata are imperfect: Many applications do not support fetching metadata from externalized sources such as metadata repositories. In order to display human-readable metadata in any application, we propose not to change the application, but to provide a library that makes a change to the user interface. The goal of this work is to provide a way to "inject" the meaning of metadata keys into the web-based frontend of an application to make it "metadata aware".
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Affiliation(s)
- Jori Kern
- Medical Informatics in Translational Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Deniz Tas
- Medical Informatics in Translational Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Hannes Ulrich
- IT Center for Clinical Research, University of Lübeck, Germany
| | - Esther E Schmidt
- Medical Informatics in Translational Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Josef Ingenerf
- IT Center for Clinical Research, University of Lübeck, Germany
| | - Frank Ückert
- Medical Informatics in Translational Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Martin Lablans
- Medical Informatics in Translational Oncology, German Cancer Research Center, Heidelberg, Germany
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Kock-Schoppenhauer AK, Ulrich H, Wagen-Zink S, Duhm-Harbeck P, Ingenerf J, Neuhaus P, Dugas M, Bruland P. Compatibility Between Metadata Standards: Import Pipeline of CDISC ODM to the Samply.MDR. Stud Health Technol Inform 2018; 247:221-225. [PMID: 29677955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The establishment of a digital healthcare system is a national and community task. The Federal Ministry of Education and Research in Germany is providing funding for consortia consisting of university hospitals among others participating in the "Medical Informatics Initiative". Exchange of medical data between research institutions necessitates a place where meta information for this data is made accessible. Within these consortia different metadata registry solutions were chosen. To promote interoperability between these solutions, we have examined whether the portal of Medical Data Models is eligible for managing and communicating metadata and relevant information across different data integration centres of the Medical Informatics Initiative and beyond. Apart from the MDM-portal, some ISO 11179-based systems such as Samply.MDR as well as openEHR-based solutions are going to be applyed. In this paper, we have focused on the creation of a mapping model between the CDISC ODM standard and the Samply.MDR import format. In summary, it can be stated that the mapping model is feasible and promote the exchangeability between different metadata registry approaches.
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Affiliation(s)
| | - Hannes Ulrich
- IT Center for Clinical Research, Lübeck (ITCR-L), University of Lübeck, Germany
| | - Stefanie Wagen-Zink
- IT Center for Clinical Research, Lübeck (ITCR-L), University of Lübeck, Germany
| | - Petra Duhm-Harbeck
- IT Center for Clinical Research, Lübeck (ITCR-L), University of Lübeck, Germany
| | - Josef Ingenerf
- IT Center for Clinical Research, Lübeck (ITCR-L), University of Lübeck, Germany
| | - Philipp Neuhaus
- Institute of Medical Informatics, University of Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Germany
| | - Philipp Bruland
- Institute of Medical Informatics, University of Münster, Germany
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Arteaga-Velázquez J, Rivera-Rangel D, Apel W, Bekk K, Bertaina M, Blümer J, Bozdog H, Brancus I, Cantoni E, Chiavassa A, Cossavella F, Daumiller K, Souza VD, Pierro FD, Doll P, Engel R, Fuhrmann D, Gherghel-Lascu A, Gils H, Glasstetter R, Grupen C, Haungs A, Heck D, Hörandel J, Huege T, Kampert K, Kang D, Klages H, Link K, Łuczak P, Mathes H, Mayer H, Milke J, Mitrica B, Morello C, Oehlschläger J, Ostapchenko S, Pierog T, Rebel H, Roth M, Schieler H, Schoo S, Schröder F, Sima O, Toma G, Trinchero G, Ulrich H, Weindl A, Wochele J, Zabierowski J. Tests of the SIBYLL 2.3 high-energy hadronic interaction model using the KASCADE-Grande muon data. EPJ Web of Conferences 2018. [DOI: 10.1051/epjconf/201817207003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The KASCADE-Grande observatory was a ground-based air shower array dedicated to study the energy and composition of cosmic rays in the energy interval E = 1 PeV –1 EeV. The experiment consisted of different detector systems which allowed the simultaneous measurement of distinct components of air showers (EAS), such as the muon content. In this contribution, we study the total muon number and the lateral density distribution of muons in EAS detected by KASCADE-Grande as a function of the zenith angle and the total number of charged particles. The attenuation length of the muon content of EAS is also measured. The results are compared with the predictions of the SIBYLL 2.3 high-energy hadronic interaction model.
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Affiliation(s)
- R.R. Resende
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, SP, Brazil
- Departamento de Fisiologia e Biofísica, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
| | - H.A.M. Torres
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo 04023-062, SP, Brazil
| | - K.K. Yuahasi
- Departamento de Neurologia e Neurocirurgia, Universidade Federal de São Paulo, São Paulo, SP, Brazil. Present address
| | - P Majumder
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, SP, Brazil
| | - H Ulrich
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, SP, Brazil
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Martínez-Ramírez AS, Díaz-Muñoz M, Battastini AM, Campos-Contreras A, Olvera A, Bergamin L, Glaser T, Jacintho Moritz CE, Ulrich H, Vázquez-Cuevas FG. Cellular Migration Ability Is Modulated by Extracellular Purines in Ovarian Carcinoma SKOV-3 Cells. J Cell Biochem 2017; 118:4468-4478. [PMID: 28464260 DOI: 10.1002/jcb.26104] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 04/28/2017] [Indexed: 12/14/2022]
Abstract
Extracellular nucleotides and nucleosides have emerged as important elements regulating tissue homeostasis. Acting through specific receptors, have the ability to control gene expression patterns to direct cellular fate. We observed that SKOV-3 cells express the ectonucleotidases: ectonucleotide pyrophosphatase 1 (ENPP1), ecto-5'-nucleotidase (NT5E), and liver alkaline phosphatase (ALPL). Strikingly, in pulse and chase experiments supplemented with ATP, SKOV-3 cells exhibited low catabolic efficiency in the conversion of ADP into AMP, but they were efficient in converting AMP into adenosine. Since these cells release ATP, we proposed that the conversion of ADP into AMP is a regulatory node associated with the migratory ability and the mesenchymal characteristics shown by SKOV-3 cells under basal conditions. The landscape of gene expression profiles of SKOV-3 cell cultures treated with apyrase or adenosine demonstrated similarities (e.g., decrease FGF16 transcript) and differences (e.g., the negative regulation of Wnt 2, and 10B by adenosine). Thus, in SKOV-3 we analyzed the migratory ability and the expression of epithelium to mesenchymal transition (EMT) markers in response to apyrase. Apyrase-treatment favored the epithelial-like phenotype, as revealed by the re-location of E-cadherin to the cell to cell junctions. Pharmacological approaches strongly suggested that the effect of Apyrase involved the accumulation of extracellular adenosine; this notion was strengthened when the incubation of the SKOV-3 cell with α,β-methylene ADP (CD73 inhibitor) or adenosine deaminase was sufficient to abolish the effect of apyrase on cell migration. Overall, adenosine signaling is a fine tune mechanism in the control of cell phenotype in cancer. J. Cell. Biochem. 118: 4468-4478, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- A S Martínez-Ramírez
- Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Boulevard Juriquilla 3001, Juriquilla Querétaro, CP 76230, Querétaro, México
| | - M Díaz-Muñoz
- Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Boulevard Juriquilla 3001, Juriquilla Querétaro, CP 76230, Querétaro, México
| | - A M Battastini
- Departamento de Bioquímica, Instituto de Ciências Básicas e da Saúde, UFRGS, Porto Alegre, RS, Brazil
| | - A Campos-Contreras
- Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Boulevard Juriquilla 3001, Juriquilla Querétaro, CP 76230, Querétaro, México
| | - A Olvera
- Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Boulevard Juriquilla 3001, Juriquilla Querétaro, CP 76230, Querétaro, México
| | - L Bergamin
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, Sao Paulo, 05508-900, Brazil
| | - T Glaser
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, Sao Paulo, 05508-900, Brazil
| | - C E Jacintho Moritz
- Departamento de Bioquímica, Instituto de Ciências Básicas e da Saúde, UFRGS, Porto Alegre, RS, Brazil
| | - H Ulrich
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, Sao Paulo, 05508-900, Brazil
| | - F G Vázquez-Cuevas
- Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Boulevard Juriquilla 3001, Juriquilla Querétaro, CP 76230, Querétaro, México
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Kock-Schoppenhauer AK, Kamann C, Ulrich H, Duhm-Harbeck P, Ingenerf J. Linked Data Applications Through Ontology Based Data Access in Clinical Research. Stud Health Technol Inform 2017; 235:131-135. [PMID: 28423769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Clinical care and research data are widely dispersed in isolated systems based on heterogeneous data models. Biomedicine predominantly makes use of connected datasets based on the Semantic Web paradigm. Initiatives like Bio2RDF created Resource Description Framework (RDF) versions of Omics resources, enabling sophisticated Linked Data applications. In contrast, electronic healthcare records (EHR) data are generated and processed in diverse clinical subsystems within hospital information systems (HIS). Usually, each of them utilizes a relational database system with a different proprietary schema. Semantic integration and access to the data is hardly possible. This paper describes ways of using Ontology Based Data Access (OBDA) for bridging the semantic gap between existing raw data and user-oriented views supported by ontology-based queries. Based on mappings between entities of data schemas and ontologies data can be made available as materialized or virtualized RDF triples ready for querying and processing. Our experiments based on CentraXX for biobank and study management demonstrate the advantages of abstracting away from low level details and semantic mediation. Furthermore, it becomes clear that using a professional platform for Linked Data applications is recommended due to the inherent complexity, the inconvenience to confront end users with SPARQL, and scalability and performance issues.
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Affiliation(s)
| | - Christian Kamann
- IT for Clinical Research, Lübeck (ITCR-L), University of Lübeck, Germany
| | - Hannes Ulrich
- IT for Clinical Research, Lübeck (ITCR-L), University of Lübeck, Germany
| | - Petra Duhm-Harbeck
- IT for Clinical Research, Lübeck (ITCR-L), University of Lübeck, Germany
| | - Josef Ingenerf
- IT for Clinical Research, Lübeck (ITCR-L), University of Lübeck, Germany
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Haungs A, Apel W, Arteaga-Velázquez J, Bekk K, Bertaina M, Blümer J, Bozdog H, Brancus I, Cantoni E, Chiavassa A, Cossavella F, Daumiller K, Souza VD, Pierro FD, Doll P, Engel R, Fuhrmann D, Gherghel-Lascu A, Gils H, Glasstetter R, Grupen C, Heck D, Hörandel J, Huege T, Kampert KH, Kang D, Klages H, Link K, Łuczak P, Mathes H, Mayer H, Milke J, Mitrica B, Morello C, Oehlschläger J, Ostapchenko S, Pierog T, Rebel H, Roth M, Schieler H, Schoo S, Schröder F, Sima O, Toma G, Trinchero G, Ulrich H, Weindl A, Wochele J, Zabierowski J. KASCADE-Grande: Composition studies in the view of the post-LHC hadronic interaction models. EPJ Web Conf 2017. [DOI: 10.1051/epjconf/201714513001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Ulrich H, Kock-Schoppenhauer AK, Andersen B, Ingenerf J. Analysis of Annotated Data Models for Improving Data Quality. Stud Health Technol Inform 2017; 243:190-194. [PMID: 28883198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The public Medical Data Models (MDM) portal with more than 9.000 annotated forms from clinical trials and other sources provides many research opportunities for the medical informatics community. It is mainly used to address the problem of heterogeneity by searching, mediating, reusing, and assessing data models, e. g. the semi-interactive curation of core data records in a special domain. Furthermore, it can be used as a benchmark for evaluating algorithms that create, transform, annotate, and analyse structured patient data. Using CDISC ODM for syntactically representing all data models in the MDM portal, there are semi-automatically added UMLS CUIs at several ODM levels like ItemGroupDef, ItemDef, or CodeList item. This can improve the interpretability and processability of the received information, but only if the coded information is correct and reliable. This raises the question how to assure that semantically similar datasets are also processed and classified similarly. In this work, a (semi-)automatic approach to analyse and assess items, questions, and data elements in clinical studies is described. The approach uses a hybrid evaluation process to rate and propose semantic annotations for under-specified trial items. The evaluation algorithm operates with the commonly used NLM MetaMap to provide UMLS support and corpus-based proposal algorithms to link datasets from the provided CDISC ODM item pool.
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Affiliation(s)
- Hannes Ulrich
- IT for Clinical Research, Lübeck (ITCR-L), University of Lübeck, Germany
| | | | - Björn Andersen
- Institute of Medical Informatics, University of Lübeck, Germany
| | - Josef Ingenerf
- IT for Clinical Research, Lübeck (ITCR-L), University of Lübeck, Germany
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40
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Affiliation(s)
- H.E. Reymore
- The Upjohn Company D. S. Gilmore Research Laboratories North Haven, CT 06473
| | - R.J. Lockwood
- The Upjohn Company D. S. Gilmore Research Laboratories North Haven, CT 06473
| | - H. Ulrich
- The Upjohn Company D. S. Gilmore Research Laboratories North Haven, CT 06473
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41
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Affiliation(s)
- H. Ulrich
- The Upjohn Company Donald S. Gilmore Research Labs North Haven, Ct 06473
| | - H.W. Bonk
- The Upjohn Company Donald S. Gilmore Research Labs North Haven, Ct 06473
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42
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Ulrich H, Kock AK, Duhm-Harbeck P, Habermann JK, Ingenerf J. Metadata Repository for Improved Data Sharing and Reuse Based on HL7 FHIR. Stud Health Technol Inform 2016; 228:162-166. [PMID: 27577363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Unreconciled data structures and formats are a common obstacle to the urgently required sharing and reuse of data within healthcare and medical research. Within the North German Tumor Bank of Colorectal Cancer, clinical and sample data, based on a harmonized data set, is collected and can be pooled by using a hospital-integrated Research Data Management System supporting biobank and study management. Adding further partners who are not using the core data set requires manual adaptations and mapping of data elements. Facing this manual intervention and focusing the reuse of heterogeneous healthcare instance data (value level) and data elements (metadata level), a metadata repository has been developed. The metadata repository is an ISO 11179-3 conformant server application built for annotating and mediating data elements. The implemented architecture includes the translation of metadata information about data elements into the FHIR standard using the FHIR Data Element resource with the ISO 11179 Data Element Extensions. The FHIR-based processing allows exchange of data elements with clinical and research IT systems as well as with other metadata systems. With increasingly annotated and harmonized data elements, data quality and integration can be improved for successfully enabling data analytics and decision support.
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Affiliation(s)
- Hannes Ulrich
- Institute of Medical Informatics, University of Lübeck, Germany
| | | | | | - Jens K Habermann
- Interdisciplinary Center for Biobanking-Lübeck, University of Lübeck, Germany
| | - Josef Ingenerf
- Institute of Medical Informatics, University of Lübeck, Germany
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Andersen B, Ulrich H, Rehmann D, Kock AK, Wrage JH, Ingenerf J. Reporting Device Observations for semantic interoperability of surgical devices and clinical information systems. Annu Int Conf IEEE Eng Med Biol Soc 2015; 2015:1725-1728. [PMID: 26736610 DOI: 10.1109/embc.2015.7318710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Service-oriented medical device architectures make the progress from interdisciplinary research projects to international standardisation: A new set of IEEE 11073 proposals shall pave the way to industry acceptance. This expected availability of device observations in a standardised representation enables secondary usage if interoperability with clinical information systems can be achieved. The Device Observation Reporter (DOR) described in this work is a gateway that connects these realms. After a user chooses a selection of signals from different devices in the digital operating room, the DOR records these semantically described values for a specified duration. Upon completion, the signals descriptions and values are transformed to Health Level Seven version 2 messages and sent to a hospital information system/electronic health record system within the clinical IT network. The successful integration of device data for documentation and usage in clinical information systems can further leverage the novel device communication standard proposals. Complementing these, an Integrating the Healthcare Enterprise profile will aid commercial implementers in achieving interoperability. Their solutions could incorporate clinical knowledge to autonomously select signal combinations and generate reports of diagnostic and interventional procedures, thus saving time and effort for surgical documentation.
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Łuczak P, Apel W, Arteaga-Velázquez J, Bekk K, Bertaina M, Blümer J, Bozdog H, Brancus I, Cantoni E, Chiavassa A, Cossavella F, Curcio C, Daumiller K, Souza VD, Pierro FD, Doll P, Engel R, Engler J, Fuchs B, Fuhrmann D, Gils H, Glasstetter R, Grupen C, Haungs A, Heck D, Hörandel J, Huber D, Huege T, Kampert KH, Kang D, Klages H, Link K, Ludwig M, Mathes H, Mayer H, Melissas M, Milke J, Mitrica B, Morello C, Oehlschläger J, Ostapchenko S, Palmieri N, Petcu M, Pierog T, Rebel H, Roth M, Schieler H, Schoo S, Schröder F, Sima O, Toma G, Trinchero G, Ulrich H, Weindl A, Wochele J, Zabierowski J. The 〈 ln A 〉 study with the Muon tracking detector in the KASCADE-Grande experiment – comparison of hadronic interaction models. EPJ Web of Conferences 2015. [DOI: 10.1051/epjconf/20159913001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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45
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Arteaga-Velázquez J, Apel W, Bekk K, Bertaina M, Blümer J, Bozdog H, Brancus I, Cantoni E, Chiavassa A, Cossavella F, Daumiller K, Souza VD, Pierro FD, Doll P, Engel R, Engler J, Fuchs B, Fuhrmann D, Gherghel-Lascu A, Gils H, Glasstetter R, Grupen C, Haungs A, Heck D, Hörandel J, Huber D, Huege T, Kampert KH, Kang D, Klages H, Link K, Łuczak P, Mathes H, Mayer H, Milke J, Mitrica B, Morello C, Oehlschläger J, Ostapchenko S, Palmieri N, Petcu M, Pierog T, Rebel H, Roth M, Schieler H, Schoo S, Schröder F, Sima O, Toma G, Trinchero G, Ulrich H, Weindl A, Wochele J, Zabierowski J. Confronting the EPOS-LHC model predictions on the charged particle and muon attenuation lengths of EAS with the measurements of the KASCADE-Grande observatory. EPJ Web of Conferences 2015. [DOI: 10.1051/epjconf/20159912002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Ulrich H, Bocsi J, Glaser T, Tárnok A. Cytometry in the brain: studying differentiation to diagnostic applications in brain disease and regeneration therapy. Cell Prolif 2014; 47:12-9. [PMID: 24450810 DOI: 10.1111/cpr.12087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 11/02/2013] [Indexed: 12/30/2022] Open
Abstract
During brain development, a population of uniform embryonic cells migrates and differentiates into a large number of neural phenotypes - origin of the enormous complexity of the adult nervous system. Processes of cell proliferation, differentiation and programmed death of no longer required cells, do not occur only during embryogenesis, but are also maintained during adulthood and are affected in neurodegenerative and neuropsychiatric disease states. As neurogenesis is an endogenous response to brain injury, visible as proliferation (of to this moment silent stem or progenitor cells), its further stimulation can present a treatment strategy in addition to stem cell transfer for cell regeneration therapy. Concise techniques for studying such events in vitro and in vivo permit understanding of underlying mechanisms. Detection of subtle physiological alterations in brain cell proliferation and neurogenesis can be explored, that occur during environmental stimulation, exercise and ageing. Here, we have collected achievements in the field of basic research on applications of cytometry, including automated imaging for quantification of morphological or fluorescence-based parameters in cell cultures, towards imaging of three-dimensional brain architecture together with DNA content and proliferation data. Multi-parameter and more recently in vivo flow cytometry procedures, have been developed for quantification of phenotypic diversity and cell processes that occur during brain development as well as in adulthood, with importance for therapeutic approaches.
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Affiliation(s)
- H Ulrich
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, São Paulo, S.P 05508-900, Brazil
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Torres-Rivera W, Pérez D, Park KY, Carrasco M, Platt MO, Eterović VA, Ferchmin PA, Ulrich H, Martins AH. Kinin-B2 receptor exerted neuroprotection after diisopropylfluorophosphate-induced neuronal damage. Neuroscience 2013; 247:273-9. [PMID: 23735753 DOI: 10.1016/j.neuroscience.2013.05.054] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 05/23/2013] [Accepted: 05/24/2013] [Indexed: 02/06/2023]
Abstract
The kinin-B2 receptor (B2BKR) activated by its endogenous ligand bradykinin participates in various metabolic processes including the control of arterial pressure and inflammation. Recently, functions for this receptor in brain development and protection against glutamate-provoked excitotoxicity have been proposed. Here, we report neuroprotective properties for bradykinin against organophosphate poisoning using acute hippocampal slices as an in vitro model. Following slice perfusion for 10min with diisopropylfluorophosphate (DFP) to initiate the noxious stimulus, responses of pyramidal neurons upon an electric impulse were reduced to less than 30% of control amplitudes. Effects on synaptic-elicited population spikes were reverted when preparations had been exposed to bradykinin 30min after challenging with DFP. Accordingly, bradykinin-induced population spike recovery was abolished by HOE-140, a B2BKR antagonist. However, the kinin-B1 receptor (B1BKR) agonist Lys-des-Arg(9)-bradykinin, inducing the phosphorylation of mitogen-activated protein kinase (MEK/MAPK) and cell death, abolished bradykinin-mediated neuroprotection, an effect, which was reverted by the ERK inhibitor PD98059. In agreement with pivotal B1BKR functions in this process, antagonism of endogenous B1BKR activity alone was enough for restoring population spike activity. On the other hand pralidoxime, an oxime, reactivating acetylcholinesterase (AChE) after organophosphate poisoning, induced population spike recovery after DFP exposure in the presence of bradykinin and Lys-des-Arg(9)-bradykinin. Lys-des-Arg(9)-bradykinin did not revert protection exerted by pralidoxime, however when instead bradykinin and Ly-des-Arg(9)-bradykinin were superfused together, recovery of population spikes diminished. These findings again confirm the neuroprotective feature of bradykinin, which is, diminished by its endogenous metabolites, stimulating the B1BKR, providing a novel understanding of the physiological roles of these receptors.
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Affiliation(s)
- W Torres-Rivera
- Department of Biochemistry, Universidad Central del Caribe, Bayamón, PR 00956, USA
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48
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Apel WD, Arteaga-Velàzquez JC, Bekk K, Bertaina M, Blümer J, Bozdog H, Brancus IM, Cantoni E, Chiavassa A, Cossavella F, Daumiller K, de Souza V, Di Pierro F, Doll P, Engel R, Engler J, Finger M, Fuchs B, Fuhrmann D, Gils HJ, Glasstetter R, Grupen C, Haungs A, Heck D, Hörandel JR, Huber D, Huege T, Kampert KH, Kang D, Klages HO, Link K, Łuczak P, Ludwig M, Mathes HJ, Mayer HJ, Melissas M, Milke J, Mitrica B, Morello C, Oehlschläger J, Ostapchenko S, Palmieri N, Petcu M, Pierog T, Rebel H, Roth M, Schieler H, Schoo S, Schröder FG, Sima O, Toma G, Trinchero GC, Ulrich H, Weindl A, Wochele J, Wommer M, Zabierowski J. Ankle-like feature in the energy spectrum of light elements of cosmic rays observed with KASCADE-Grande. Int J Clin Exp Med 2013. [DOI: 10.1103/physrevd.87.081101] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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49
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Arteaga-Velázquez J, Apel W, Bekk K, Bertaina M, Blümer J, Bozdog H, Brancus I, Cantoni E, Chiavassa A, Cossavella F, Daumiller K, de Souza V, Di Pierro F, Doll P, Engel R, Engler J, Finger M, Fuchs B, Fuhrmann D, Gils H, Glasstetter R, Grupen C, Haungs A, Heck D, Hörandel J, Huber D, Huege T, Kampert KH, Kang D, Klages H, Link K, Łuczak P, Ludwig M, Mathes H, Mayer H, Melissas M, Milke J, Mitrica B, Morello C, Oehlschläger J, Ostapchenko S, Palmieri N, Petcu M, Pierog T, Rebel H, Roth M, Schieler H, Schoo S, Schröder FG, Sima O, Toma G, Trinchero G, Ulrich H, Weindl A, Wochele J, Wommer M, Zabierowski J. Test of hadronic interaction models with the KASCADE-Grande muon data. EPJ Web of Conferences 2013. [DOI: 10.1051/epjconf/20135207002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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50
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Apel WD, Arteaga-Velázquez JC, Bekk K, Bertaina M, Blümer J, Bozdog H, Brancus IM, Buchholz P, Cantoni E, Chiavassa A, Cossavella F, Daumiller K, de Souza V, Di Pierro F, Doll P, Engel R, Engler J, Finger M, Fuhrmann D, Ghia PL, Gils HJ, Glasstetter R, Grupen C, Haungs A, Heck D, Hörandel JR, Huber D, Huege T, Isar PG, Kampert KH, Kang D, Klages HO, Link K, Łuczak P, Ludwig M, Mathes HJ, Mayer HJ, Melissas M, Milke J, Mitrica B, Morello C, Navarra G, Oehlschläger J, Ostapchenko S, Over S, Palmieri N, Petcu M, Pierog T, Rebel H, Roth M, Schieler H, Schröder FG, Sima O, Toma G, Trinchero GC, Ulrich H, Weindl A, Wochele J, Wommer M, Zabierowski J. Kneelike structure in the spectrum of the heavy component of cosmic rays observed with KASCADE-Grande. Phys Rev Lett 2011; 107:171104. [PMID: 22107501 DOI: 10.1103/physrevlett.107.171104] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 08/25/2011] [Indexed: 05/31/2023]
Abstract
We report the observation of a steepening in the cosmic ray energy spectrum of heavy primary particles at about 8×10(16) eV. This structure is also seen in the all-particle energy spectrum, but is less significant. Whereas the "knee" of the cosmic ray spectrum at 3-5×10(15) eV was assigned to light primary masses by the KASCADE experiment, the new structure found by the KASCADE-Grande experiment is caused by heavy primaries. The result is obtained by independent measurements of the charged particle and muon components of the secondary particles of extensive air showers in the primary energy range of 10(16) to 10(18) eV. The data are analyzed on a single-event basis taking into account also the correlation of the two observables.
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Affiliation(s)
- W D Apel
- Institut für Kernphysik, Karlsruher Institut für Technologie, Karlsruhe, Germany
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