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Publikation Discovering fundamental principles of antibody repertoires by large-scale systems and network analysis(ETH, 2017) Miho, Enkelejda05 - Forschungs- oder ArbeitsberichtPublikation Backtrainer. Computer-aided therapy system with augmented feedback for the lower back(SciTePress, 2009) Brodbeck, Dominique; Degen, Markus; Stanimirov, Michael; Kool, Jan; Scheermesser, Mandy; Oesch, Peter; Neuhaus, Cornelia; Azevedo, Luis; Londral, AnaLow back pain is an important problem in industrialized countries. Two key factors limit the effectiveness of physiotherapy: low compliance of patients with repetitive movement exercises, and inadequate awareness of patients of their own posture. The Backtrainer system addresses these problems by real-time monitoring of the spine position, by providing a framework for most common physiotherapy exercises for the low back, and by providing feedback to patients in a motivating way. A minimal sensor configuration was identified as two inertial sensors that measure the orientation of the lower back at two points with three degrees of freedom. The software was designed as a flexible platform to experiment with different hardware, and with various feedback modalities. Basic exercises for two types of movements are provided: mobilizing and stabilizing. We developed visual feedback - abstract as well as in the form of a virtual reality game - and complemented the on-screen graphics with an ambient feedback device. The system was evaluated during five weeks in a rehabilitation clinic with 26 patients and 15 physiotherapists. Subjective satisfaction of subjects was good, and we interpret the results as encouraging indication for the adoption of such a therapy support system by both patients and therapists.04B - Beitrag KonferenzschriftPublikation A mobile collaboration and decision support system for the medical emergency departement(SciTePress, 2012) Brodbeck, Dominique; Degen, Markus; Reiss, Maximilian; Conchon, Emmanuel; Correia, Carlos; Fred, Ana; Gamboa, HugoA hospital emergency department is a complex work environment, where the availability of the right information at the right time is crucial for efficient and safe operation. The current technology in use for communication and information management is mostly based on telephones and stationary personal computers. Modern smartphones with their computational power, voice, image, and video capabilities have the potential to play a significant role in improving the flow of information in the emergency department. We developed a system that explicitly supports the work flows of an emergency department. In addition to mobile access to patient data and notifications about the availability of diagnostic findings, it provides the possibility to supply media captured on-site to the patient record, and directly supports the consultation process.04B - Beitrag KonferenzschriftPublikation Using membrane-supported liquid–liquid extraction for the measurement of extraction kinetics(Swiss Chemical Society, 2011) Riedl, Wolfgang; Mollet, Daniel; Grundler, GerhardMembrane-supported liquid–liquid extraction uses artificial membranes for the generation of a phase interface between the two liquid phases involved in extraction. Additional equipment for the generation of droplets as well as phase separation afterwards is no longer necessary. Since the membranes used for this special type of extraction are quite well described concerning thickness, porosity, tortuosity and material it is possible to generate information about the diffusion coefficient of the component to be extracted within the preferred solvent from extraction trails easily. This article describes an experimental set-up for both the proof of principle of membrane-supported liquid–liquid extraction and, using a dedicated computer-aided data treatment, how to calculate the overall mass transfer coefficient as well as the diffusion coefficient for a given system within moderate testing duration.01A - Beitrag in wissenschaftlicher ZeitschriftPublikation Energy-related chemical research at the universities of applied sciences(Swiss Chemical Society, 2013) Riedl, Wolfgang; Fischer, Fabian; Marti, Roger; Brühwiler, DominikAn overview of current activities in the field of energy-related chemical research at the Swiss Universities of Applied Sciences is presented.01A - Beitrag in wissenschaftlicher ZeitschriftPublikation Sustainable Chemistry at the Universities of Applied Sciences(Swiss Chemical Society, 2012) Sanglard, Pauline; Rogano, Frank; Naef, Olivier; Riedl, Wolfgang; Crelier, Simon; Fischer, Fabian; Morganti, Franziska; Hinderling, ChristianAn overview of activities in the field of sustainable or 'green' chemistry at the Universities of Applied Sciences in Switzerland is presented.01A - Beitrag in wissenschaftlicher ZeitschriftPublikation Reinigungseffektivität und Kavitationsrauschpegel bei Ultraschall-unterstützter wässriger Reinigung von Medizinprodukten(2012) Jung, Christiane; Budesa, Boris; Fässler, Fabian; Uehlinger, Robert; Müller, Thomas; Schaffner, Patrik; Bläsi, Simon; de Wild, Michael04B - Beitrag KonferenzschriftPublikation Computational strategies for dissecting the high-dimensional complexity of adaptive immune repertoires(Frontiers Research Foundation, 2018) Miho, Enkelejda; Yermanos, Alexander; Weber, Cédric R.; Berger, Christoph T.; Reddy, Sai T.; Greiff, VictorThe adaptive immune system recognizes antigens via an immense array of antigen binding antibodies and T-cell receptors, the immune repertoire. The interrogation of immune repertoires is of high relevance for understanding the adaptive immune response in disease and infection (e.g., autoimmunity, cancer, HIV). Adaptive immune receptor repertoire sequencing (AIRR-seq) has driven the quantitative and molecular-level profiling of immune repertoires, thereby revealing the high-dimensional complexity of the immune receptor sequence landscape. Several methods for the computational and statistical analysis of large-scale AIRR-seq data have been developed to resolve immune repertoire complexity and to understand the dynamics of adaptive immunity. Here, we review the current research on (i) diversity, (ii) clustering and network, (iii) phylogenetic, and (iv) machine learning methods applied to dissect, quantify, and compare the architecture, evolution, and specificity of immune repertoires. We summarize outstanding questions in computational immunology and propose future directions for systems immunology toward coupling AIRR-seq with the computational discovery of immunotherapeutics, vaccines, and immunodiagnostics.01A - Beitrag in wissenschaftlicher ZeitschriftPublikation Synthetic standards combined with error and bias correction improve the accuracy and quantitative resolution of antibody repertoire sequencing in human naïve and memory B cells(Frontiers Research Foundation, 20.06.2018) Friedensohn, Simon; Lindner, John M.; Cornacchione, Vanessa; Iazeolla, Mariavittoria; Miho, Enkelejda; Zingg, Andreas; Meng, Simon; Traggiai, Elisabetta; Reddy, Sai T.High-throughput sequencing of immunoglobulin (Ig) repertoires (Ig-seq) is a powerful method for quantitatively interrogating B cell receptor sequence diversity. When applied to human repertoires, Ig-seq provides insight into fundamental immunological questions, and can be implemented in diagnostic and drug discovery projects. However, a major challenge in Ig-seq is ensuring accuracy, as library preparation protocols and sequencing platforms can introduce substantial errors and bias that compromise immunological interpretation. Here, we have established an approach for performing highly accurate human Ig-seq by combining synthetic standards with a comprehensive error and bias correction pipeline. First, we designed a set of 85 synthetic antibody heavy-chain standards (in vitro transcribed RNA) to assess correction workflow fidelity. Next, we adapted a library preparation protocol that incorporates unique molecular identifiers (UIDs) for error and bias correction which, when applied to the synthetic standards, resulted in highly accurate data. Finally, we performed Ig-seq on purified human circulating B cell subsets (naïve and memory), combined with a cellular replicate sampling strategy. This strategy enabled robust and reliable estimation of key repertoire features such as clonotype diversity, germline segment, and isotype subclass usage, and somatic hypermutation. We anticipate that our standards and error and bias correction pipeline will become a valuable tool for researchers to validate and improve accuracy in human Ig-seq studies, thus leading to potentially new insights and applications in human antibody repertoire profiling.01A - Beitrag in wissenschaftlicher ZeitschriftPublikation Large-scale network analysis reveals the sequence space architecture of antibody repertoires(Nature, 01.12.2019) Miho, Enkelejda; Roškar, Rok; Greiff, Victor; Reddy, Sai T.The architecture of mouse and human antibody repertoires is defined by the sequence similarity networks of the clones that compose them. The major principles that define the architecture of antibody repertoires have remained largely unknown. Here, we establish a high-performance computing platform to construct large-scale networks from comprehensive human and murine antibody repertoire sequencing datasets (>100,000 unique sequences). Leveraging a network-based statistical framework, we identify three fundamental principles of antibody repertoire architecture: reproducibility, robustness and redundancy. Antibody repertoire networks are highly reproducible across individuals despite high antibody sequence dissimilarity. The architecture of antibody repertoires is robust to the removal of up to 50–90% of randomly selected clones, but fragile to the removal of public clones shared among individuals. Finally, repertoire architecture is intrinsically redundant. Our analysis provides guidelines for the large-scale network analysis of immune repertoires and may be used in the future to define disease-associated and synthetic repertoires.01A - Beitrag in wissenschaftlicher Zeitschrift