TY - JOUR A1 - Schichor, Christian A1 - Albrecht, Valerie A1 - Korte, Benjamin A1 - Buchner, Alexander A1 - Riesenberg, Rainer A1 - Mysliwietz, Josef A1 - Paron, Igor A1 - Motaln, Helena A1 - Turnsek, Tamara Lah A1 - Juerchott, Kathrin A1 - Selbig, Joachim A1 - Tonn, Jörg-Christian T1 - Mesenchymal stem cells and glioma cells form a structural as well as a functional syncytium in vitro JF - Experimental neurology N2 - The interaction of human mesenchymal stem cells (hMSCs) and tumor cells has been investigated in various contexts. HMSCs are considered as cellular treatment vectors based on their capacity to migrate towards a malignant lesion. However, concerns about unpredictable behavior of transplanted hMSCs are accumulating. In malignant gliomas, the recruitment mechanism is driven by glioma-secreted factors which lead to accumulation of both, tissue specific stem cells as well as bone marrow derived hMSCs within the tumor. The aim of the present work was to study specific cellular interactions between hMSCs and glioma cells in vitro. We show, that glioma cells as well as hMSCs differentially express connexins. and that they interact via gap-junctional coupling. Besides this so-called functional syncytium formation, we also provide evidence of cell fusion events (structural syncytium). These complex cellular interactions led to an enhanced migration and altered proliferation of both, tumor and mesenchymal stem cell types in vitro. The presented work shows that glioma cells display signs of functional as well as structural syncytium formation with hMSCs in vitro. The described cellular phenomena provide new insight into the complexity of interaction patterns between tumor cells and host cells. Based on these findings, further studies are warranted to define the impact of a functional or structural syncytium formation on malignant tumors and cell based therapies in vivo. KW - Mesenchymal stem cell KW - Glioma KW - Syncytium KW - Gap junction KW - Fusion Y1 - 2012 U6 - https://doi.org/10.1016/j.expneurol.2011.12.033 SN - 0014-4886 VL - 234 IS - 1 SP - 208 EP - 219 PB - Elsevier CY - San Diego ER - TY - BOOK A1 - Albrecht, Alexander A1 - Naumann, Felix T1 - Understanding cryptic schemata in large extract-transform-load systems N2 - Extract-Transform-Load (ETL) tools are used for the creation, maintenance, and evolution of data warehouses, data marts, and operational data stores. ETL workflows populate those systems with data from various data sources by specifying and executing a DAG of transformations. Over time, hundreds of individual workflows evolve as new sources and new requirements are integrated into the system. The maintenance and evolution of large-scale ETL systems requires much time and manual effort. A key problem is to understand the meaning of unfamiliar attribute labels in source and target databases and ETL transformations. Hard-to-understand attribute labels lead to frustration and time spent to develop and understand ETL workflows. We present a schema decryption technique to support ETL developers in understanding cryptic schemata of sources, targets, and ETL transformations. For a given ETL system, our recommender-like approach leverages the large number of mapped attribute labels in existing ETL workflows to produce good and meaningful decryptions. In this way we are able to decrypt attribute labels consisting of a number of unfamiliar few-letter abbreviations, such as UNP_PEN_INT, which we can decrypt to UNPAID_PENALTY_INTEREST. We evaluate our schema decryption approach on three real-world repositories of ETL workflows and show that our approach is able to suggest high-quality decryptions for cryptic attribute labels in a given schema. N2 - Extract-Transform-Load (ETL) Tools werden häufig beim Erstellen, der Wartung und der Weiterentwicklung von Data Warehouses, Data Marts und operationalen Datenbanken verwendet. ETL Workflows befüllen diese Systeme mit Daten aus vielen unterschiedlichen Quellsystemen. Ein ETL Workflow besteht aus mehreren Transformationsschritten, die einen DAG-strukturierter Graphen bilden. Mit der Zeit entstehen hunderte individueller ETL Workflows, da neue Datenquellen integriert oder neue Anforderungen umgesetzt werden müssen. Die Wartung und Weiterentwicklung von großen ETL Systemen benötigt viel Zeit und manuelle Arbeit. Ein zentrales Problem ist dabei das Verständnis unbekannter Attributnamen in Quell- und Zieldatenbanken und ETL Transformationen. Schwer verständliche Attributnamen führen zu Frustration und hohen Zeitaufwänden bei der Entwicklung und dem Verständnis von ETL Workflows. Wir präsentieren eine Schema Decryption Technik, die ETL Entwicklern das Verständnis kryptischer Schemata in Quell- und Zieldatenbanken und ETL Transformationen erleichtert. Unser Ansatz berücksichtigt für ein gegebenes ETL System die Vielzahl verknüpfter Attributnamen in den existierenden ETL Workflows. So werden gute und aussagekräftige "Decryptions" gefunden und wir sind in der Lage Attributnamen, die aus unbekannten Abkürzungen bestehen, zu "decrypten". So wird z.B. für den Attributenamen UNP_PEN_INT als Decryption UNPAIN_PENALTY_INTEREST vorgeschlagen. Unser Schema Decryption Ansatz wurde für drei ETL-Repositories evaluiert und es zeigte sich, dass unser Ansatz qualitativ hochwertige Decryptions für kryptische Attributnamen vorschlägt. T3 - Technische Berichte des Hasso-Plattner-Instituts für Digital Engineering an der Universität Potsdam - 60 KW - Extract-Transform-Load (ETL) KW - Data Warehouse KW - Datenintegration KW - Extract-Transform-Load (ETL) KW - Data Warehouse KW - Data Integration Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-61257 SN - 978-3-86956-201-8 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - THES A1 - Albrecht, Alexander T1 - Understanding and managing extract-transform-load systems Y1 - 2013 ER - TY - JOUR A1 - Borchert, Florian A1 - Mock, Andreas A1 - Tomczak, Aurelie A1 - Hügel, Jonas A1 - Alkarkoukly, Samer A1 - Knurr, Alexander A1 - Volckmar, Anna-Lena A1 - Stenzinger, Albrecht A1 - Schirmacher, Peter A1 - Debus, Jürgen A1 - Jäger, Dirk A1 - Longerich, Thomas A1 - Fröhling, Stefan A1 - Eils, Roland A1 - Bougatf, Nina A1 - Sax, Ulrich A1 - Schapranow, Matthieu-Patrick T1 - Knowledge bases and software support for variant interpretation in precision oncology JF - Briefings in bioinformatics N2 - Precision oncology is a rapidly evolving interdisciplinary medical specialty. Comprehensive cancer panels are becoming increasingly available at pathology departments worldwide, creating the urgent need for scalable cancer variant annotation and molecularly informed treatment recommendations. A wealth of mainly academia-driven knowledge bases calls for software tools supporting the multi-step diagnostic process. We derive a comprehensive list of knowledge bases relevant for variant interpretation by a review of existing literature followed by a survey among medical experts from university hospitals in Germany. In addition, we review cancer variant interpretation tools, which integrate multiple knowledge bases. We categorize the knowledge bases along the diagnostic process in precision oncology and analyze programmatic access options as well as the integration of knowledge bases into software tools. The most commonly used knowledge bases provide good programmatic access options and have been integrated into a range of software tools. For the wider set of knowledge bases, access options vary across different parts of the diagnostic process. Programmatic access is limited for information regarding clinical classifications of variants and for therapy recommendations. The main issue for databases used for biological classification of pathogenic variants and pathway context information is the lack of standardized interfaces. There is no single cancer variant interpretation tool that integrates all identified knowledge bases. Specialized tools are available and need to be further developed for different steps in the diagnostic process. KW - HiGHmed KW - personalized medicine KW - molecular tumor board KW - data integration KW - cancer therapy Y1 - 2021 U6 - https://doi.org/10.1093/bib/bbab134 SN - 1467-5463 SN - 1477-4054 VL - 22 IS - 6 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Borchert, Florian A1 - Mock, Andreas A1 - Tomczak, Aurelie A1 - Hügel, Jonas A1 - Alkarkoukly, Samer A1 - Knurr, Alexander A1 - Volckmar, Anna-Lena A1 - Stenzinger, Albrecht A1 - Schirmacher, Peter A1 - Debus, Jürgen A1 - Jäger, Dirk A1 - Longerich, Thomas A1 - Fröhling, Stefan A1 - Eils, Roland A1 - Bougatf, Nina A1 - Sax, Ulrich A1 - Schapranow, Matthieu-Patrick T1 - Correction to: Knowledge bases and software support for variant interpretation in precision oncology JF - Briefings in bioinformatics Y1 - 2021 U6 - https://doi.org/10.1093/bib/bbab246 SN - 1467-5463 SN - 1477-4054 VL - 22 IS - 6 PB - Oxford Univ. Press CY - Oxford ER -