Filter and export

Publications

1004 Publications visible to you, out of a total of 1004
Design of Metadata Services for Clinical Data Interoperability in Germany.
SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

Secondary use of electronic health record (EHR) data requires a detailed description of metadata, especially when data collection and data re-use are organizationally and technically far apart. This … paper describes the concept of the SMITH consortium that includes conventions, processes, and tools for describing and managing metadata using common standards for semantic interoperability. It deals in particular with the chain of processing steps of data from existing information systems and provides an overview of the planned use of metadata, medical terminologies, and semantic services in the consortium.

Authors: M. Lobe, O. Beyan, S. Staubert, F. Meineke, D. Ammon, A. Winter, S. Decker, M. Loffler, T. Kirsten

Date Published: 21st Aug 2019

Publication Type: Journal article

Integrating Heterogeneous Data Sources for Cross-Institutional Data Sharing: Requirements Elicitation and Management in SMITH.
SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

The digitization of health records and cross-institutional data sharing is a necessary precondition to improve clinical research and patient care. The SMITH project unites several university hospitals … and medical faculties in order to provide medical informatics solutions for health data integration and cross-institutional communication. In this paper, we focus on requirements elicitation and management for extracting clinical data from heterogeneous subsystems and data integration based on eHealth standards such as HL7 FHIR and IHE profiles.

Authors: K. Tahar, C. Muller, A. Durschmid, S. Haferkamp, K. Saleh, P. Jurs, S. Staubert, J. E. Gewehr, S. Zenker, D. Ammon, T. Wendt

Date Published: 21st Aug 2019

Publication Type: Journal article

Annotating German Clinical Documents for De-Identification.
SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

We devised annotation guidelines for the de-identification of German clinical documents and assembled a corpus of 1,106 discharge summaries and transfer letters with 44K annotated protected health … information (PHI) items. After three iteration rounds, our annotation team finally reached an inter-annotator agreement of 0.96 on the instance level and 0.97 on the token level of annotation (averaged pair-wise F1 score). To establish a baseline for automatic de-identification on our corpus, we trained a recurrent neural network (RNN) and achieved F1 scores greater than 0.9 on most major PHI categories.

Authors: T. Kolditz, C. Lohr, J. Hellrich, L. Modersohn, B. Betz, M. Kiehntopf, U. Hahn

Date Published: 21st Aug 2019

Publication Type: InProceedings

Towards Structured Data Quality Assessment in the German Medical Informatics Initiative: Initial Approach in the MII Demonstrator Study.
SMITH - Smart Medical Information Technology for Healthcare

Abstract (Expand)

The Demonstrator study aims to analyse comorbidities and rare diseases among patients from German university hospitals within the German Medical Informatics Initiative. This work aimed to design and … determine the feasibility of a model to assess the quality of the claims data used in the study. Several data quality issues were identified affecting small amounts of cases in one of the participating sites. As a next step an extension to all participating sites is planned.

Authors: G. Kamdje-Wabo, T. Gradinger, M. Lobe, R. Lodahl, S. A. Seuchter, U. Sax, T. Ganslandt

Date Published: 21st Aug 2019

Publication Type: Journal article

Clinical and lifestyle related factors influencing whole blood metabolite levels -- A comparative analysis of three large cohorts
Genetical Statistics and Systems Biology

Abstract (Expand)

Objective Human blood metabolites are influenced by a number of lifestyle and environmental factors. Identification of these factors and the proper quantification of their relevance provides insights …s into human biological and metabolic disease processes, is key for standardized translation of metabolite biomarkers into clinical applications, and is a prerequisite for comparability of data between studies. However, so far only limited data exist from large and well-phenotyped human cohorts and current methods for analysis do not fully account for the characteristics of these data. The primary aim of this study was to identify, quantify and compare the impact of a comprehensive set of clinical and lifestyle related factors on metabolite levels in three large human cohorts. To achieve this goal, we improve current methodology by developing a principled analysis approach, which could be translated to other cohorts and metabolite panels. Methods 63 Metabolites (amino acids, acylcarnitines) were quantified by liquid chromatography tandem mass spectrometry in three cohorts (total N~=~16,222). Supported by a simulation study evaluating various analytical approaches, we developed an analysis pipeline including preprocessing, identification, and quantification of factors affecting metabolite levels. We comprehensively identified uni- and multivariable metabolite associations considering 29 environmental and clinical factors and performed metabolic pathway enrichment and network analyses. Results Inverse normal transformation of batch corrected and outlier removed metabolite levels accompanied by linear regression analysis proved to be the best suited method to deal with the metabolite data. Association analyses revealed numerous uni- and multivariable significant associations. 15 of the analyzed 29 factors explained {\textgreater}1{\%} of variance for at least one of the metabolites. Strongest factors are application of steroid hormones, reticulocytes, waist-to-hip ratio, sex, haematocrit, and age. Effect sizes of factors are comparable across studies. Conclusions We introduced a principled approach for the analysis of MS data allowing identification, and quantification of effects of clinical and lifestyle factors with metabolite levels. We detected a number of known and novel associations broadening our understanding of the regulation of the human metabolome. The large heterogeneity observed between cohorts could almost completely be explained by differences in the distribution of influencing factors emphasizing the necessity of a proper confounder analysis when interpreting metabolite associations.

Authors: Carl Beuchel, Susen Becker, Julia Dittrich, Holger Kirsten, Anke Toenjes, Michael Stumvoll, Markus Loeffler, Holger Thiele, Frank Beutner, Joachim Thiery, Uta Ceglarek, Markus Scholz

Date Published: 17th Aug 2019

Publication Type: Not specified

Teratogenic Rubella Virus Alters the Endodermal Differentiation Capacity of Human Induced Pluripotent Stem Cells.
LHA - Leipzig Health Atlas

Abstract (Expand)

The study of congenital virus infections in humans requires suitable ex vivo platforms for the species-specific events during embryonal development. A prominent example for these infections is rubella … virus (RV) which most commonly leads to defects in ear, heart, and eye development. We applied teratogenic RV to human induced pluripotent stem cells (iPSCs) followed by differentiation into cells of the three embryonic lineages (ecto-, meso-, and endoderm) as a cell culture model for blastocyst- and gastrulation-like stages. In the presence of RV, lineage-specific differentiation markers were expressed, indicating that lineage identity was maintained. However, portrait analysis of the transcriptomic expression signatures of all samples revealed that mock- and RV-infected endodermal cells were less related to each other than their ecto- and mesodermal counterparts. Markers for definitive endoderm were increased during RV infection. Profound alterations of the epigenetic landscape including the expression level of components of the chromatin remodeling complexes and an induction of type III interferons were found, especially after endodermal differentiation of RV-infected iPSCs. Moreover, the eye field transcription factors RAX and SIX3 and components of the gene set vasculogenesis were identified as dysregulated transcripts. Although iPSC morphology was maintained, the formation of embryoid bodies as three-dimensional cell aggregates and as such cellular adhesion capacity was impaired during RV infection. The correlation of the molecular alterations induced by RV during differentiation of iPSCs with the clinical signs of congenital rubella syndrome suggests mechanisms of viral impairment of human development.

Authors: N. C. Bilz, E. Willscher, H. Binder, J. Bohnke, M. L. Stanifer, D. Hubner, S. Boulant, U. G. Liebert, C. Claus

Date Published: 10th Aug 2019

Publication Type: Not specified

MEK inhibitor cobimetinib rescues a dRaf mutant lethal phenotype in Drosophila melanogaster
Genetical Statistics and Systems Biology

Abstract (Expand)

Since Drosophila melanogaster has proven to be a useful model system to study phenotypes of oncogenic mutations and to identify new anti-cancer drugs, we generated human BRAFV600E homologous dRaf mutant … (dRaf A572E ) Drosophila melanogaster strains to use these for characterization of mutant phenotypes and exploit these phenotypes for drug testing. For mutant gene expression, the GAL4/UAS expression system was used. dRaf A572E was expressed tissue-specific in the eye, epidermis, heart, wings, secretory glands and in the whole animal. Expression of dRaf A572E under the control of an eye-specific driver led to semi-lethality and a rough eye phenotype. tumor, genetics, molecular biology, BRAF, small molecule inhibitors The vast majority of other tissue-specific and ubiquitous drivers led to a lethal phenotype only. The rough eye phenotype was used to test BRAF inhibitor vemurafenib and MEK1/2 inhibitor cobimetinib. There was no phenotype rescue by this treatment. However, a significant rescue of the lethal phenotype was observed under a gut-specific driver. Here, MEK1/2 inhibitor cobimetinib rescued Drosophila larvae to reach pupal stage in 37% of cases as compared to 1% in control experiments. Taken together, the BRAFV600E homolog dRaf A572E exerts mostly lethal effects in Drosophila. Gut-specific dRaf A572E expression might in future be developed further for drug testing. This article is protected by copyright. All rights reserved.

Authors: Isabelle Pfeifle, Jens Bohnekamp, Anna Volkhardt, Holger Kirsten, Astrid Rohwedder, Andreas Thum, Thomas M. Magin, Manfred Kunz

Date Published: 1st Aug 2019

Publication Type: Journal article

Navigate

Health Atlas - Local Data Hub/Leipzig

The Health Atlas - Local Data Hub/Leipzig is an alliance of medical ontologists, medical systems biologists and clinical trials groups to design and implement a multi-functional and quality-assured atlas. It provides models, data and metadata on specific use cases from medical research fields.

Registered Repository

re3data.org Badge
Powered by
 (v.1.13.0-master)
Health Atlas | Funding and Programmes | Credits | Terms & Conditions | Privacy Policy | Imprint
Copyright © 2008 - 2021 The University of Manchester and HITS gGmbH
Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig

By continuing to use this site you agree to the use of cookies