TY - JOUR A1 - Hirth, Matthias A1 - Seufert, Michael A1 - Lange, Stanislav A1 - Meixner, Markus A1 - Tran-Gia, Phuoc T1 - Performance evaluation of hybrid crowdsensing and fixed sensor systems for event detection in urban environments JF - Sensors N2 - Crowdsensing offers a cost-effective way to collect large amounts of environmental sensor data; however, the spatial distribution of crowdsensing sensors can hardly be influenced, as the participants carry the sensors, and, additionally, the quality of the crowdsensed data can vary significantly. Hybrid systems that use mobile users in conjunction with fixed sensors might help to overcome these limitations, as such systems allow assessing the quality of the submitted crowdsensed data and provide sensor values where no crowdsensing data are typically available. In this work, we first used a simulation study to analyze a simple crowdsensing system concerning the detection performance of spatial events to highlight the potential and limitations of a pure crowdsourcing system. The results indicate that even if only a small share of inhabitants participate in crowdsensing, events that have locations correlated with the population density can be easily and quickly detected using such a system. On the contrary, events with uniformly randomly distributed locations are much harder to detect using a simple crowdsensing-based approach. A second evaluation shows that hybrid systems improve the detection probability and time. Finally, we illustrate how to compute the minimum number of fixed sensors for the given detection time thresholds in our exemplary scenario. KW - crowdsensing KW - event detection KW - detection time simulation KW - performance analysis Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-245245 SN - 1424-8220 VL - 21 IS - 17 ER - TY - JOUR A1 - Scherer, Marc A1 - Fleishman, Sarel J. A1 - Jones, Patrik R. A1 - Dandekar, Thomas A1 - Bencurova, Elena T1 - Computational Enzyme Engineering Pipelines for Optimized Production of Renewable Chemicals JF - Frontiers in Bioengineering and Biotechnology N2 - To enable a sustainable supply of chemicals, novel biotechnological solutions are required that replace the reliance on fossil resources. One potential solution is to utilize tailored biosynthetic modules for the metabolic conversion of CO2 or organic waste to chemicals and fuel by microorganisms. Currently, it is challenging to commercialize biotechnological processes for renewable chemical biomanufacturing because of a lack of highly active and specific biocatalysts. As experimental methods to engineer biocatalysts are time- and cost-intensive, it is important to establish efficient and reliable computational tools that can speed up the identification or optimization of selective, highly active, and stable enzyme variants for utilization in the biotechnological industry. Here, we review and suggest combinations of effective state-of-the-art software and online tools available for computational enzyme engineering pipelines to optimize metabolic pathways for the biosynthesis of renewable chemicals. Using examples relevant for biotechnology, we explain the underlying principles of enzyme engineering and design and illuminate future directions for automated optimization of biocatalysts for the assembly of synthetic metabolic pathways. KW - computational KW - enzyme KW - engineering KW - design KW - biomanufacturing KW - biofuel KW - microbes KW - metabolism Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-240598 SN - 2296-4185 VL - 9 ER - TY - JOUR A1 - Kammerer, Klaus A1 - Göster, Manuel A1 - Reichert, Manfred A1 - Pryss, Rüdiger T1 - Ambalytics: a scalable and distributed system architecture concept for bibliometric network analyses JF - Future Internet N2 - A deep understanding about a field of research is valuable for academic researchers. In addition to technical knowledge, this includes knowledge about subareas, open research questions, and social communities (networks) of individuals and organizations within a given field. With bibliometric analyses, researchers can acquire quantitatively valuable knowledge about a research area by using bibliographic information on academic publications provided by bibliographic data providers. Bibliometric analyses include the calculation of bibliometric networks to describe affiliations or similarities of bibliometric entities (e.g., authors) and group them into clusters representing subareas or communities. Calculating and visualizing bibliometric networks is a nontrivial and time-consuming data science task that requires highly skilled individuals. In addition to domain knowledge, researchers must often provide statistical knowledge and programming skills or use software tools having limited functionality and usability. In this paper, we present the ambalytics bibliometric platform, which reduces the complexity of bibliometric network analysis and the visualization of results. It accompanies users through the process of bibliometric analysis and eliminates the need for individuals to have programming skills and statistical knowledge, while preserving advanced functionality, such as algorithm parameterization, for experts. As a proof-of-concept, and as an example of bibliometric analyses outcomes, the calculation of research fronts networks based on a hybrid similarity approach is shown. Being designed to scale, ambalytics makes use of distributed systems concepts and technologies. It is based on the microservice architecture concept and uses the Kubernetes framework for orchestration. This paper presents the initial building block of a comprehensive bibliometric analysis platform called ambalytics, which aims at a high usability for users as well as scalability. KW - system architecture design KW - bibliometric analysis KW - community detection Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-244916 SN - 1999-5903 VL - 13 IS - 8 ER - TY - JOUR A1 - Oberdörfer, Sebastian A1 - Birnstiel, Sandra A1 - Latoschik, Marc Erich A1 - Grafe, Silke T1 - Mutual Benefits: Interdisciplinary Education of Pre-Service Teachers and HCI Students in VR/AR Learning Environment Design JF - Frontiers in Education N2 - The successful development and classroom integration of Virtual (VR) and Augmented Reality (AR) learning environments requires competencies and content knowledge with respect to media didactics and the respective technologies. The paper discusses a pedagogical concept specifically aiming at the interdisciplinary education of pre-service teachers in collaboration with human-computer interaction students. The students’ overarching goal is the interdisciplinary realization and integration of VR/AR learning environments in teaching and learning concepts. To assist this approach, we developed a specific tutorial guiding the developmental process. We evaluate and validate the effectiveness of the overall pedagogical concept by analyzing the change in attitudes regarding 1) the use of VR/AR for educational purposes and in competencies and content knowledge regarding 2) media didactics and 3) technology. Our results indicate a significant improvement in the knowledge of media didactics and technology. We further report on four STEM learning environments that have been developed during the seminar. KW - interdisciplinary education KW - virtual reality KW - augmented reality KW - serious games KW - learning environments KW - teacher education Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-241612 SN - 2504-284X VL - 6 ER - TY - JOUR A1 - Nagler, Matthias A1 - Nägele, Thomas A1 - Gilli, Christian A1 - Fragner, Lena A1 - Korte, Arthur A1 - Platzer, Alexander A1 - Farlow, Ashley A1 - Nordborg, Magnus A1 - Weckwerth, Wolfram T1 - Eco-Metabolomics and Metabolic Modeling: Making the Leap From Model Systems in the Lab to Native Populations in the Field JF - Frontiers in Plant Science N2 - Experimental high-throughput analysis of molecular networks is a central approach to characterize the adaptation of plant metabolism to the environment. However, recent studies have demonstrated that it is hardly possible to predict in situ metabolic phenotypes from experiments under controlled conditions, such as growth chambers or greenhouses. This is particularly due to the high molecular variance of in situ samples induced by environmental fluctuations. An approach of functional metabolome interpretation of field samples would be desirable in order to be able to identify and trace back the impact of environmental changes on plant metabolism. To test the applicability of metabolomics studies for a characterization of plant populations in the field, we have identified and analyzed in situ samples of nearby grown natural populations of Arabidopsis thaliana in Austria. A. thaliana is the primary molecular biological model system in plant biology with one of the best functionally annotated genomes representing a reference system for all other plant genome projects. The genomes of these novel natural populations were sequenced and phylogenetically compared to a comprehensive genome database of A. thaliana ecotypes. Experimental results on primary and secondary metabolite profiling and genotypic variation were functionally integrated by a data mining strategy, which combines statistical output of metabolomics data with genome-derived biochemical pathway reconstruction and metabolic modeling. Correlations of biochemical model predictions and population-specific genetic variation indicated varying strategies of metabolic regulation on a population level which enabled the direct comparison, differentiation, and prediction of metabolic adaptation of the same species to different habitats. These differences were most pronounced at organic and amino acid metabolism as well as at the interface of primary and secondary metabolism and allowed for the direct classification of population-specific metabolic phenotypes within geographically contiguous sampling sites. KW - eco-metabolomics KW - in situ analysis KW - metabolomics KW - metabolic modeling KW - SNP KW - natural variation KW - Jacobian matrix KW - green systems biology Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-189560 SN - 1664-462X VL - 9 IS - 1556 ER - TY - JOUR A1 - Petschke, Danny A1 - Staab, Torsten E.M. T1 - DLTPulseGenerator: a library for the simulation of lifetime spectra based on detector-output pulses JF - SoftwareX N2 - The quantitative analysis of lifetime spectra relevant in both life and materials sciences presents one of the ill-posed inverse problems and, hence, leads to most stringent requirements on the hardware specifications and the analysis algorithms. Here we present DLTPulseGenerator, a library written in native C++ 11, which provides a simulation of lifetime spectra according to the measurement setup. The simulation is based on pairs of non-TTL detector output-pulses. Those pulses require the Constant Fraction Principle (CFD) for the determination of the exact timing signal and, thus, the calculation of the time difference i.e. the lifetime. To verify the functionality, simulation results were compared to experimentally obtained data using Positron Annihilation Lifetime Spectroscopy (PALS) on pure tin. KW - lifetime spectroscopy KW - signal processing KW - pulse simulation Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-176883 VL - 7 ER - TY - JOUR A1 - Osmanoglu, Özge A1 - Khaled AlSeiari, Mariam A1 - AlKhoori, Hasa Abduljaleel A1 - Shams, Shabana A1 - Bencurova, Elena A1 - Dandekar, Thomas A1 - Naseem, Muhammad T1 - Topological Analysis of the Carbon-Concentrating CETCH Cycle and a Photorespiratory Bypass Reveals Boosted CO\(_2\)-Sequestration by Plants JF - Frontiers in Bioengineering and Biotechnology N2 - Synthetically designed alternative photorespiratory pathways increase the biomass of tobacco and rice plants. Likewise, some in planta–tested synthetic carbon-concentrating cycles (CCCs) hold promise to increase plant biomass while diminishing atmospheric carbon dioxide burden. Taking these individual contributions into account, we hypothesize that the integration of bypasses and CCCs will further increase plant productivity. To test this in silico, we reconstructed a metabolic model by integrating photorespiration and photosynthesis with the synthetically designed alternative pathway 3 (AP3) enzymes and transporters. We calculated fluxes of the native plant system and those of AP3 combined with the inhibition of the glycolate/glycerate transporter by using the YANAsquare package. The activity values corresponding to each enzyme in photosynthesis, photorespiration, and for synthetically designed alternative pathways were estimated. Next, we modeled the effect of the crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (CETCH), which is a set of natural and synthetically designed enzymes that fix CO₂ manifold more than the native Calvin–Benson–Bassham (CBB) cycle. We compared estimated fluxes across various pathways in the native model and under an introduced CETCH cycle. Moreover, we combined CETCH and AP3-w/plgg1RNAi, and calculated the fluxes. We anticipate higher carbon dioxide–harvesting potential in plants with an AP3 bypass and CETCH–AP3 combination. We discuss the in vivo implementation of these strategies for the improvement of C3 plants and in natural high carbon harvesters. KW - CO2-sequestration KW - photorespiration KW - elementary modes KW - synthetic pathways KW - carboxylation KW - metabolic modeling KW - CETCH cycle Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-249260 SN - 2296-4185 VL - 9 ER - TY - JOUR A1 - von Mammen, Sebastian Albrecht A1 - Wagner, Daniel A1 - Knote, Andreas A1 - Taskin, Umut T1 - Interactive simulations of biohybrid systems JF - Frontiers in Robotics and AI N2 - In this article, we present approaches to interactive simulations of biohybrid systems. These simulations are comprised of two major computational components: (1) agent-based developmental models that retrace organismal growth and unfolding of technical scaffoldings and (2) interfaces to explore these models interactively. Simulations of biohybrid systems allow us to fast forward and experience their evolution over time based on our design decisions involving the choice, configuration and initial states of the deployed biological and robotic actors as well as their interplay with the environment. We briefly introduce the concept of swarm grammars, an agent-based extension of L-systems for retracing growth processes and structural artifacts. Next, we review an early augmented reality prototype for designing and projecting biohybrid system simulations into real space. In addition to models that retrace plant behaviors, we specify swarm grammar agents to braid structures in a self-organizing manner. Based on this model, both robotic and plant-driven braiding processes can be experienced and explored in virtual worlds. We present an according user interface for use in virtual reality. As we present interactive models concerning rather diverse description levels, we only ensured their principal capacity for interaction but did not consider efficiency analyzes beyond prototypic operation. We conclude this article with an outlook on future works on melding reality and virtuality to drive the design and deployment of biohybrid systems. KW - biohybrid systems KW - augmented reality KW - virtual reality KW - user interfaces KW - biological development KW - generative systems Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-195755 SN - 2296-9144 VL - 4 ER - TY - JOUR A1 - Appel, Mirjam A1 - Scholz, Claus-Jürgen A1 - Müller, Tobias A1 - Dittrich, Marcus A1 - König, Christian A1 - Bockstaller, Marie A1 - Oguz, Tuba A1 - Khalili, Afshin A1 - Antwi-Adjei, Emmanuel A1 - Schauer, Tamas A1 - Margulies, Carla A1 - Tanimoto, Hiromu A1 - Yarali, Ayse T1 - Genome-Wide Association Analyses Point to Candidate Genes for Electric Shock Avoidance in Drosophila melanogaster JF - PLoS ONE N2 - Electric shock is a common stimulus for nociception-research and the most widely used reinforcement in aversive associative learning experiments. Yet, nothing is known about the mechanisms it recruits at the periphery. To help fill this gap, we undertook a genome-wide association analysis using 38 inbred Drosophila melanogaster strains, which avoided shock to varying extents. We identified 514 genes whose expression levels and/or sequences covaried with shock avoidance scores. We independently scrutinized 14 of these genes using mutants, validating the effect of 7 of them on shock avoidance. This emphasizes the value of our candidate gene list as a guide for follow-up research. In addition, by integrating our association results with external protein-protein interaction data we obtained a shock avoidance- associated network of 38 genes. Both this network and the original candidate list contained a substantial number of genes that affect mechanosensory bristles, which are hairlike organs distributed across the fly's body. These results may point to a potential role for mechanosensory bristles in shock sensation. Thus, we not only provide a first list of candidate genes for shock avoidance, but also point to an interesting new hypothesis on nociceptive mechanisms. KW - functional analysis KW - disruption project KW - natural variation KW - complex traits KW - networks KW - behavior KW - flies KW - temperature KW - genetics KW - painful Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-152006 VL - 10 IS - 5 ER - TY - JOUR A1 - Fisseler, Denis A1 - Müller, Gerfrid G. W. A1 - Weichert, Frank T1 - Web-Based scientific exploration and analysis of 3D scanned cuneiform datasets for collaborative research JF - Informatics N2 - The three-dimensional cuneiform script is one of the oldest known writing systems and a central object of research in Ancient Near Eastern Studies and Hittitology. An important step towards the understanding of the cuneiform script is the provision of opportunities and tools for joint analysis. This paper presents an approach that contributes to this challenge: a collaborative compatible web-based scientific exploration and analysis of 3D scanned cuneiform fragments. The WebGL -based concept incorporates methods for compressed web-based content delivery of large 3D datasets and high quality visualization. To maximize accessibility and to promote acceptance of 3D techniques in the field of Hittitology, the introduced concept is integrated into the Hethitologie-Portal Mainz, an established leading online research resource in the field of Hittitology, which until now exclusively included 2D content. The paper shows that increasing the availability of 3D scanned archaeological data through a web-based interface can provide significant scientific value while at the same time finding a trade-off between copyright induced restrictions and scientific usability. KW - cuneiform KW - 3D viewer KW - WebGL KW - Hittitology KW - 3D collation Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-197958 SN - 2227-9709 VL - 4 IS - 4 ER -