@incollection{KochPoghossianWegeetal.2018, author = {Koch, Claudia and Poghossian, Arshak and Wege, Christina and Sch{\"o}ning, Michael Josef}, title = {TMV-Based Adapter Templates for Enhanced Enzyme Loading in Biosensor Applications}, series = {Virus-Derived Nanoparticles for Advanced Technologies}, booktitle = {Virus-Derived Nanoparticles for Advanced Technologies}, editor = {Wege, Christina}, publisher = {Humana Press}, address = {New York, NY}, isbn = {978-1-4939-7808-3}, doi = {10.1007/978-1-4939-7808-3}, pages = {553 -- 568}, year = {2018}, abstract = {Nanotubular tobacco mosaic virus (TMV) particles and RNA-free lower-order coat protein (CP) aggregates have been employed as enzyme carriers in different diagnostic layouts and compared for their influence on biosensor performance. In the following, we describe a label-free electrochemical biosensor for improved glucose detection by use of TMV adapters and the enzyme glucose oxidase (GOD). A specific and efficient immobilization of streptavidin-conjugated GOD ([SA]-GOD) complexes on biotinylated TMV nanotubes or CP aggregates was achieved via bioaffinity binding. Glucose sensors with adsorptively immobilized [SA]-GOD, and with [SA]-GOD cross-linked with glutardialdehyde, respectively, were tested in parallel on the same sensor chip. Comparison of these sensors revealed that TMV adapters enhanced the amperometric glucose detection remarkably, conveying highest sensitivity, an extended linear detection range and fastest response times. These results underline a great potential of an integration of virus/biomolecule hybrids with electronic transducers for applications in biosensorics and biochips. Here, we describe the fabrication and use of amperometric sensor chips combining an array of circular Pt electrodes, their loading with GOD-modified TMV nanotubes (and other GOD immobilization methods), and the subsequent investigations of the sensor performance.}, language = {en} } @article{KochPoghossianSchoeningetal.2018, author = {Koch, Claudia and Poghossian, Arshak and Sch{\"o}ning, Michael Josef and Wege, Christian}, title = {Penicillin Detection by Tobacco Mosaic Virus-Assisted Colorimetric Biosensors}, series = {Nanotheranostics}, volume = {2}, journal = {Nanotheranostics}, number = {2}, publisher = {Ivyspring}, address = {Sydney}, issn = {2206-7418}, doi = {10.7150/ntno.22114}, pages = {184 -- 196}, year = {2018}, abstract = {The presentation of enzymes on viral scaffolds has beneficial effects such as an increased enzyme loading and a prolonged reusability in comparison to conventional immobilization platforms. Here, we used modified tobacco mosaic virus (TMV) nanorods as enzyme carriers in penicillin G detection for the first time. Penicillinase enzymes were conjugated with streptavidin and coupled to TMV rods by use of a bifunctional biotin-linker. Penicillinase-decorated TMV particles were characterized extensively in halochromic dye-based biosensing. Acidometric analyte detection was performed with bromcresol purple as pH indicator and spectrophotometry. The TMV-assisted sensors exhibited increased enzyme loading and strongly improved reusability, and higher analysis rates compared to layouts without viral adapters. They extended the half-life of the sensors from 4 - 6 days to 5 weeks and thus allowed an at least 8-fold longer use of the sensors. Using a commercial budget-priced penicillinase preparation, a detection limit of 100 µM penicillin was obtained. Initial experiments also indicate that the system may be transferred to label-free detection layouts.}, language = {en} } @article{KnoxBruggemannGossmannetal.2020, author = {Knox, Ronald and Bruggemann, Andrea and Gossmann, Matthias and Thomas, Ulrich and Horv{\´a}th, Andr{\´a}s and Dragicevic, Elena and Stoelzle-Feix, Sonja and Fertig, Niels and Jung, Alexander and Raman, Aravind Hariharan and Staat, Manfred and Linder, Peter}, title = {Combining physiological relevance and throughput for in vitro cardiac contractility measurement}, series = {Biophysical Journal}, volume = {118}, journal = {Biophysical Journal}, number = {Issue 3, Supplement 1}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0006-3495}, doi = {10.1016/j.bpj.2019.11.3104}, pages = {570a}, year = {2020}, abstract = {Despite increasing acceptance of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) in safety pharmacology, controversy remains about the physiological relevance of existing in vitro models for their mechanical testing. We hypothesize that existing signs of immaturity of the cell models result from an improper mechanical environment. We cultured hiPSC-CMs in a 96-well format on hyperelastic silicone membranes imitating their native mechanical environment, resulting in physiological responses to compound stimuli.We validated cell responses on the FLEXcyte 96, with a set of reference compounds covering a broad range of cellular targets, including ion channel modulators, adrenergic receptor modulators and kinase inhibitors. Acute (10 - 30 min) and chronic (up to 7 days) effects were investigated. Furthermore, the measurements were complemented with electromechanical models based on electrophysiological recordings of the used cell types.hiPSC-CMs were cultured on freely-swinging, ultra-thin and hyperelastic silicone membranes. The weight of the cell culture medium deflects the membranes downwards. Rhythmic contraction of the hiPSC-CMs resulted in dynamic deflection changes which were quantified by capacitive distance sensing. The cells were cultured for 7 days prior to compound addition. Acute measurements were conducted 10-30 minutes after compound addition in standard culture medium. For chronic treatment, compound-containing medium was replaced daily for up to 7 days. Electrophysiological properties of the employed cell types were recorded by automated patch-clamp (Patchliner) and the results were integrated into the electromechanical model of the system.Calcium channel agonist S Bay K8644 and beta-adrenergic stimulator isoproterenol induced significant positive inotropic responses without additional external stimulation. Kinase inhibitors displayed cardiotoxic effects on a functional level at low concentrations. The system-integrated analysis detected alterations in beating shape as well as frequency and arrhythmic events and we provide a quantitative measure of these.}, language = {en} } @incollection{KnottSofroniaGerressenetal.2014, author = {Knott, Thomas C. and Sofronia, Raluca E. and Gerressen, Marcus and Law, Yuen and Davidescu, Arjana and Savii, George G. and Gatzweiler, Karl-Heinz and Staat, Manfred and Kuhlen, Torsten W.}, title = {Preliminary bone sawing model for a virtual reality-based training simulator of bilateral sagittal split osteotomy}, series = {Biomedical simulation : 6th International Symposium, ISBMS 2014, Strasbourg, France, October 16-17, 2014 : proceedings (Lecture notes in computer science : vol. 8789)}, booktitle = {Biomedical simulation : 6th International Symposium, ISBMS 2014, Strasbourg, France, October 16-17, 2014 : proceedings (Lecture notes in computer science : vol. 8789)}, publisher = {Springer}, address = {Cham}, isbn = {978-3-319-12057-7 (Online)}, doi = {10.1007/978-3-319-12057-7_1}, pages = {1 -- 10}, year = {2014}, abstract = {Successful bone sawing requires a high level of skill and experience, which could be gained by the use of Virtual Reality-based simulators. A key aspect of these medical simulators is realistic force feedback. The aim of this paper is to model the bone sawing process in order to develop a valid training simulator for the bilateral sagittal split osteotomy, the most often applied corrective surgery in case of a malposition of the mandible. Bone samples from a human cadaveric mandible were tested using a designed experimental system. Image processing and statistical analysis were used for the selection of four models for the bone sawing process. The results revealed a polynomial dependency between the material removal rate and the applied force. Differences between the three segments of the osteotomy line and between the cortical and cancellous bone were highlighted.}, language = {en} } @article{KnobeGiesenPlateetal.2016, author = {Knobe, M. and Giesen, M. and Plate, S. and Gradl-Dietsch, G. and Buecking, B. and Eschbach, D. and Laack, Walter van and Pape, H.-C.}, title = {The Aachen mobility and balance index to measure physiological falls risk: a comparison with the Tinetti POMA scale}, series = {European Journal Of Trauma And Emergency Surgery}, volume = {42}, journal = {European Journal Of Trauma And Emergency Surgery}, number = {5}, publisher = {Springer}, address = {Berlin}, issn = {1863-9941}, doi = {10.1007/s00068-016-0693-2}, pages = {537 -- 545}, year = {2016}, abstract = {Purpose The most commonly used mobility assessments for screening risk of falls among older adults are rating scales such as the Tinetti performance oriented mobility assessment (POMA). However, its correlation with falls is not always predictable and disadvantages of the scale include difficulty to assess many of the items on a 3-point scale and poor specificity. The purpose of this study was to describe the ability of the new Aachen Mobility and Balance Index (AMBI) to discriminate between subjects with a fall history and subjects without such events in comparison to the Tinetti POMA Scale. Methods For this prospective cohort study, 24 participants in the study group and 10 in the control group were selected from a population of patients in our hospital who had met the stringent inclusion criteria. Both groups completed the Tinetti POMA Scale (gait and balance component) and the AMBI (tandem stance, tandem walk, ten-meter-walk-test, sit-to-stand with five repetitions, 360° turns, timed-up-and-go-test and measurement of the dominant hand grip strength). A history of falls and hospitalization in the past year were evaluated retrospectively. The relationships among the mobility tests were examined with Bland-Altmananalysis. Receiver-operated characteristics curves, sensitivity and specificity were calculated. Results The study showed a strong negative correlation between the AMBI (17 points max., highest fall risk) and Tinetti POMA Scale (28 points max., lowest fall risk; r = -0.78, p < 0.001) with an excellent discrimination between community-dwelling older people and a younger control group. However, there were no differences in any of the mobility and balance measurements between participants with and without a fall history with equal characteristics in test comparison (AMBI vs. Tinetti POMA Scale: AUC 0.570 vs. 0.598; p = 0.762). The Tinetti POMA Scale (cut-off <20 points) showed a sensitivity of 0.45 and a specificity of 0.69, the AMBI a sensitivity of 0.64 and a specificity of 0.46 (cut-off >5 points). Conclusion The AMBI comprises mobility and balance tasks with increasing difficulty as well as a measurement of the dominant hand-grip strength. Its ability to identify fallers was comparable to the Tinetti POMA Scale. However, both measurement sets showed shortcomings in discrimination between fallers and non-fallers based on a self-reported retrospective falls-status.}, language = {en} } @inproceedings{KloeserKohlKraftetal.2021, author = {Kl{\"o}ser, Lars and Kohl, Philipp and Kraft, Bodo and Z{\"u}ndorf, Albert}, title = {Multi-attribute relation extraction (MARE): simplifying the application of relation extraction}, series = {Proceedings of the 2nd International Conference on Deep Learning Theory and Applications - DeLTA}, booktitle = {Proceedings of the 2nd International Conference on Deep Learning Theory and Applications - DeLTA}, isbn = {978-989-758-526-5}, doi = {10.5220/0010559201480156}, pages = {148 -- 156}, year = {2021}, abstract = {Natural language understanding's relation extraction makes innovative and encouraging novel business concepts possible and facilitates new digitilized decision-making processes. Current approaches allow the extraction of relations with a fixed number of entities as attributes. Extracting relations with an arbitrary amount of attributes requires complex systems and costly relation-trigger annotations to assist these systems. We introduce multi-attribute relation extraction (MARE) as an assumption-less problem formulation with two approaches, facilitating an explicit mapping from business use cases to the data annotations. Avoiding elaborated annotation constraints simplifies the application of relation extraction approaches. The evaluation compares our models to current state-of-the-art event extraction and binary relation extraction methods. Our approaches show improvement compared to these on the extraction of general multi-attribute relations.}, language = {en} } @inproceedings{KloeserBuesgenKohletal.2023, author = {Kl{\"o}ser, Lars and B{\"u}sgen, Andr{\´e} and Kohl, Philipp and Kraft, Bodo and Z{\"u}ndorf, Albert}, title = {Explaining relation classification models with semantic extents}, series = {DeLTA 2023: Deep Learning Theory and Applications}, booktitle = {DeLTA 2023: Deep Learning Theory and Applications}, editor = {Conte, Donatello and Fred, Ana and Gusikhin, Oleg and Sansone, Carlo}, publisher = {Springer}, address = {Cham}, isbn = {978-3-031-39058-6 (Print)}, doi = {10.1007/978-3-031-39059-3_13}, pages = {189 -- 208}, year = {2023}, abstract = {In recent years, the development of large pretrained language models, such as BERT and GPT, significantly improved information extraction systems on various tasks, including relation classification. State-of-the-art systems are highly accurate on scientific benchmarks. A lack of explainability is currently a complicating factor in many real-world applications. Comprehensible systems are necessary to prevent biased, counterintuitive, or harmful decisions. We introduce semantic extents, a concept to analyze decision patterns for the relation classification task. Semantic extents are the most influential parts of texts concerning classification decisions. Our definition allows similar procedures to determine semantic extents for humans and models. We provide an annotation tool and a software framework to determine semantic extents for humans and models conveniently and reproducibly. Comparing both reveals that models tend to learn shortcut patterns from data. These patterns are hard to detect with current interpretability methods, such as input reductions. Our approach can help detect and eliminate spurious decision patterns during model development. Semantic extents can increase the reliability and security of natural language processing systems. Semantic extents are an essential step in enabling applications in critical areas like healthcare or finance. Moreover, our work opens new research directions for developing methods to explain deep learning models.}, language = {en} } @inproceedings{KloockSchoening2007, author = {Kloock, Joachim P. and Sch{\"o}ning, Michael Josef}, title = {Heavy metal detection with semiconductor devices based on PLD-prepared chalcogenide glass thin films}, series = {Armenian Journal of Physics}, booktitle = {Armenian Journal of Physics}, issn = {1829-1171}, pages = {95 -- 98}, year = {2007}, language = {en} } @inproceedings{KloockSchubertErmelenkoetal.2006, author = {Kloock, Joachim P. and Schubert, J. and Ermelenko, Y. and Vlasov, Y. G. and Bratov, A. and Sch{\"o}ning, Michael Josef}, title = {Thin-film sensors with chalcogenide glass materials - a general survey}, series = {Biochemical sensing utilisation of micro- and nanotechnologies : Warsaw, [23rd - 26th] November 2005 / ed. by M. Mascini ...}, booktitle = {Biochemical sensing utilisation of micro- and nanotechnologies : Warsaw, [23rd - 26th] November 2005 / ed. by M. Mascini ...}, address = {Warsaw}, pages = {92 -- 97}, year = {2006}, language = {en} } @article{KloockMourzinaErmolenkoetal.2004, author = {Kloock, Joachim P. and Mourzina, Y.G. and Ermolenko, Y. and Doll, T. and Schubert, J. and Sch{\"o}ning, Michael Josef}, title = {Inorganic thin-film sensor membranes with PLD-prepared chalcogenide glasses: Challenges and implementation}, series = {Sensors. 4 (2004), H. 10}, journal = {Sensors. 4 (2004), H. 10}, isbn = {1424-8220}, pages = {156 -- 162}, year = {2004}, language = {en} }