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Pressure overload in patients with aortic valve stenosis and volume overload in mitral valve regurgitation trigger specific forms of cardiac remodeling; however, little is known about similarities and differences in myocardial proteome regulation. We performed proteome profiling of 75 human left ventricular myocardial biopsies (aortic stenosis = 41, mitral regurgitation = 17, and controls = 17) using high-resolution tandem mass spectrometry next to clinical and hemodynamic parameter acquisition. In patients of both disease groups, proteins related to ECM and cytoskeleton were more abundant, whereas those related to energy metabolism and proteostasis were less abundant compared with controls. In addition, disease group-specific and sex-specific differences have been observed. Male patients with aortic stenosis showed more proteins related to fibrosis and less to energy metabolism, whereas female patients showed strong reduction in proteostasis-related proteins. Clinical imaging was in line with proteomic findings, showing elevation of fibrosis in both patient groups and sex differences. Disease-and sex-specific proteomic profiles provide insight into cardiac remodeling in patients with heart valve disease and might help improve the understanding of molecular mechanisms and the development of individualized treatment strategies.
HPI Future SOC Lab
(2015)
Das Future SOC Lab am HPI ist eine Kooperation des Hasso-Plattner-Instituts mit verschiedenen Industriepartnern. Seine Aufgabe ist die Ermöglichung und Förderung des Austausches zwischen Forschungsgemeinschaft und Industrie.
Am Lab wird interessierten Wissenschaftlern eine Infrastruktur von neuester Hard- und Software kostenfrei für Forschungszwecke zur Verfügung gestellt. Dazu zählen teilweise noch nicht am Markt verfügbare Technologien, die im normalen Hochschulbereich in der Regel nicht zu finanzieren wären, bspw. Server mit bis zu 64 Cores und 2 TB Hauptspeicher. Diese Angebote richten sich insbesondere an Wissenschaftler in den Gebieten Informatik und Wirtschaftsinformatik. Einige der Schwerpunkte sind Cloud Computing, Parallelisierung und In-Memory Technologien.
In diesem Technischen Bericht werden die Ergebnisse der Forschungsprojekte des Jahres 2015 vorgestellt. Ausgewählte Projekte stellten ihre Ergebnisse am 15. April 2015 und 4. November 2015 im Rahmen der Future SOC Lab Tag Veranstaltungen vor.
Eatomics
(2021)
Quantitative proteomics data are becoming increasingly more available, and as a consequence are being analyzed and interpreted by a larger group of users. However, many of these users have less programming experience. Furthermore, experimental designs and setups are getting more complicated, especially when tissue biopsies are analyzed. Luckily, the proteomics community has already established some best practices on how to conduct quality control, differential abundance analysis and enrichment analysis. However, an easy-to-use application that wraps together all steps for the exploration and flexible analysis of quantitative proteomics data is not yet available. For Eatomics, we utilize the R Shiny framework to implement carefully chosen parts of established analysis workflows to (i) make them accessible in a user-friendly way, (ii) add a multitude of interactive exploration possibilities, and (iii) develop a unique experimental design setup module, which interactively translates a given research hypothesis into a differential abundance and enrichment analysis formula. In this, we aim to fulfill the needs of a growing group of inexperienced quantitative proteomics data analysts. Eatomics may be tested with demo data directly online via https://we.analyzegenomes.com/now/eatomics/or with the user's own data by installation from the Github repository at https://github.com/Millchmaedchen/Eatomics.
Despite advances in machine learning-based clinical prediction models, only few of such models are actually deployed in clinical contexts. Among other reasons, this is due to a lack of validation studies. In this paper, we present and discuss the validation results of a machine learning model for the prediction of acute kidney injury in cardiac surgery patients initially developed on the MIMIC-III dataset when applied to an external cohort of an American research hospital. To help account for the performance differences observed, we utilized interpretability methods based on feature importance, which allowed experts to scrutinize model behavior both at the global and local level, making it possible to gain further insights into why it did not behave as expected on the validation cohort. The knowledge gleaned upon derivation can be potentially useful to assist model update during validation for more generalizable and simpler models. We argue that interpretability methods should be considered by practitioners as a further tool to help explain performance differences and inform model update in validation studies.
Portal Wissen = Health
(2020)
The Coronavirus pandemic has made it very clear how much health and well-being determine our lives. And that science led the way in this regard could not be ignored. At the University of Potsdam, too, many researchers deal with aspects of health maintenance, whether in nutritional sciences, sports and rehabilitation medicine, biochemistry, or psychology. Their research includes supporting chronically ill children and the professional handling of risks, as you can read in this issue of our magazine.
With the establishment of our seventh faculty, the Faculty of Health Sciences, these and many new medical topics are getting more attention at the University of Potsdam. While in the beginning, the “Brandenburg Health Campus” funded by the federal state of Brandenburg was a virtual network of university and non-university research, it is now getting more points of intersection and, not only since COVID-19, a very practical use and plausible to everyone.
The Faculty of Health Sciences, founded in 2018, is supported by three institutions: the University of Potsdam, the Brandenburg Technical University Cottbus-Senftenberg and the Brandenburg Medical School in Neuruppin. They pursue an interdisciplinary approach that holistically develops teaching, transfers new scientific findings from theory to practice and thus further improves overall medical care in Brandenburg. Their vision of being a central platform of research, teaching, and transfer combines socially relevant issues and existing expertise to align them with the needs of people in Brandenburg and use them to their benefit. This interdisciplinary structure has never been more important to advancing patient-oriented basic research and health care models. An innovative concept that can make Brandenburg a pioneer.
In the meantime, the Faculty of Health Sciences has established 16 new professorships at the supporting universities, which are concerned with medicine and healthy aging, health services research, nursing and rehabilitation sciences, and telemedicine. Cardiology and physiology will play a central role as well. In general, the innovative faculty counts on strong interdisciplinary relationships, for example with nutritional sciences and the digital health department at the Digital Engineering Faculty. The role of digitization and well-prepared data in combating the Coronavirus pandemic can also be read about in this issue.
As usual, the research magazine addresses the full range of research at the university: We introduce historian Dominik Geppert, who deals with the history of unified Germany after 1990 embedded in the tensions created by a context of national unification, European integration, and global networking. In a self-experiment, we explored together with a psycholinguist how to research word-finding disorders. Last but not least, we were able to take part in a trip to Namibia, where ecologists from Potsdam examine wildlife management in the threatened savannah. Let them take you where kudu and springbok live!
Portal Wissen = Gesundheit
(2020)
Wie stark Gesundheit und Wohlbefinden unser Leben bestimmen, hat uns die Corona-Pandemie eindringlich vor Augen geführt. Und dass die Wissenschaft in diesem Kontext den Takt vorgibt, war nicht zu überhören. Auch an der Universität Potsdam beschäftigen sich zahlreich Forscherinnen und Forscher mit Fragen der Gesunderhaltung, ob in den Ernährungswissenschaften, der Sport- und Rehabilitationsmedizin, der Biochemie oder der Psychologie. Das Spektrum reicht von der Entwicklung antimikrobieller Polymere und eines Sensors für die Atemgasanalyse bis zur Unterstützung chronisch kranker Kinder und dem kompetenten Umgang mit Risiken, wie in dieser Ausgabe unseres Magazins zu lesen ist.
Mit dem Aufbau unserer siebenten, einer Gesundheitswissenschaften Fakultät rücken solche und viele neue medizinische Themen an der Universität Potsdam stärker in den Fokus. War der vom Land geförderte „Gesundheitscampus Brandenburg“ am Anfang noch ein virtuelles Netzwerk von universitärer und außeruniversitärer Forschung, bekommt es nun mehr und mehr Knotenpunkte und nicht erst seit Corona einen ganz praktischen Nutzen – für jeden nachvollziehbar.
Die 2018 gegründete Fakultät für Gesundheitswissenschaften wird von drei Einrichtungen getragen: der Universität Potsdam, der Brandenburgischen Technischen Universität Cottbus- Senftenberg und der Medizinischen Hochschule Brandenburg in Neuruppin. Gemeinsam verfolgen sie einen fächerübergreifenden Ansatz, der die Lehre ganzheitlich weiterentwickelt, neue wissenschaftliche Erkenntnisse von der Theorie in die Praxis bringt und damit insgesamt die medizinische Versorgung in Brandenburg weiter verbessert. Ihre Vision, zentrale Plattform in Forschung, Lehre und Transfer zu sein, bündelt gesellschaftlich relevante Fragen und vorhandene Expertisen, um sie am Bedarf der Menschen im Land auszurichten und für ihr Wohl einzusetzen. Nie war diese hochschulübergreifende Struktur wichtiger, um patientenorientierte Grundlagenforschung und Modelle der Gesundheitsversorgung voranzutreiben. Ein wegweisendes Konzept, mit dem Brandenburg Vorreiter sein kann.
Inzwischen hat die Fakultät für Gesundheitswissenschaften 16 neue Professuren an den einzelnen Trägerhochschulen etabliert. Es geht um die Medizin und Gesundheit des Alterns, um Versorgungsforschung, Pflege- und Rehabilitationswissenschaften sowie Telemedizin. Auch die Kardiologie und Physiologie werden eine zentrale Rolle spielen. Generell setzt die innovative Fakultät auf starke Querbeziehungen beispielsweise zu den Ernährungswissenschaften oder zum Fachgebiet Digital Health an der Digital Engineering Fakultät. Welche Rolle die Digitalisierung und gut aufbereitete Daten bei der Bekämpfung der Corona-Pandemie spielen, ist ganz aktuell auch in diesem Heft zu erfahren.
Aber natürlich widmet sich das Forschungsmagazin wie stets der ganzen fachlichen Breite der Universität: So stellen wir den Historiker Dominik Geppert vor, der sich mit der Geschichte des vereinigten Deutschlands nach 1990 im Spannungsfeld von nationaler Einigung, europäischer Integration und globaler Vernetzung befasst. Im Selbstversuch haben wir mit einer Psycholinguistin erkundet, wie sich Wortfindungsstörungen erforschen lassen. Ebenfalls einem Test unterzogen wir eine neuartige vegane Milch, die ein findiges Start-up aus Erbsen herstellt. Nicht zuletzt durften wir teilhaben an einer Reise nach Namibia, wo Potsdamer Ökologen das Wildtiermanagement in der bedrohten Savanne untersuchen. Lassen Sie sich von ihnen dorthin mitnehmen, wo sich Kudu und Springbock Gute Nacht sagen!
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.