TY - JOUR A1 - Fathy, Moustafa A1 - Darwish, Mostafa A. A1 - Abdelhamid, Al-Shaimaa M. A1 - Alrashedy, Gehad M. A1 - Othman, Othman Ali A1 - Naseem, Muhammad A1 - Dandekar, Thomas A1 - Othman, Eman M. T1 - Kinetin ameliorates cisplatin-induced hepatotoxicity and lymphotoxicity via attenuating oxidative damage, cell apoptosis and inflammation in rats JF - Biomedicines N2 - Though several previous studies reported the in vitro and in vivo antioxidant effect of kinetin (Kn), details on its action in cisplatin-induced toxicity are still scarce. In this study we evaluated, for the first time, the effects of kinetin in cisplatin (cp)- induced liver and lymphocyte toxicity in rats. Wistar male albino rats were divided into nine groups: (i) the control (C), (ii) groups 2,3 and 4, which received 0.25, 0.5 and 1 mg/kg kinetin for 10 days; (iii) the cisplatin (cp) group, which received a single intraperitoneal injection of CP (7.0 mg/kg); and (iv) groups 6, 7, 8 and 9, which received, for 10 days, 0.25, 0.5 and 1 mg/kg kinetin or 200 mg/kg vitamin C, respectively, and Cp on the fourth day. CP-injected rats showed a significant impairment in biochemical, oxidative stress and inflammatory parameters in hepatic tissue and lymphocytes. PCR showed a profound increase in caspase-3, and a significant decline in AKT gene expression. Intriguingly, Kn treatment restored the biochemical, redox status and inflammatory parameters. Hepatic AKT and caspase-3 expression as well as CD95 levels in lymphocytes were also restored. In conclusion, Kn mitigated oxidative imbalance, inflammation and apoptosis in CP-induced liver and lymphocyte toxicity; therefore, it can be considered as a promising therapy. KW - cisplatin KW - hepatotoxicity KW - lymphotoxicity KW - oxidative stress KW - AKT KW - CD95 KW - caspase-3 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-281686 SN - 2227-9059 VL - 10 IS - 7 ER - TY - JOUR A1 - Kempf, Sebastian A1 - Krug, Markus A1 - Puppe, Frank T1 - KIETA: Key-insight extraction from scientific tables JF - Applied Intelligence N2 - An important but very time consuming part of the research process is literature review. An already large and nevertheless growing ground set of publications as well as a steadily increasing publication rate continue to worsen the situation. Consequently, automating this task as far as possible is desirable. Experimental results of systems are key-insights of high importance during literature review and usually represented in form of tables. Our pipeline KIETA exploits these tables to contribute to the endeavor of automation by extracting them and their contained knowledge from scientific publications. The pipeline is split into multiple steps to guarantee modularity as well as analyzability, and agnosticim regarding the specific scientific domain up until the knowledge extraction step, which is based upon an ontology. Additionally, a dataset of corresponding articles has been manually annotated with information regarding table and knowledge extraction. Experiments show promising results that signal the possibility of an automated system, while also indicating limits of extracting knowledge from tables without any context. KW - table extraction KW - table understanding KW - ontology KW - key-insight extraction KW - information extraction Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-324180 SN - 0924-669X VL - 53 IS - 8 ER - TY - JOUR A1 - Steinhaeusser, Sophia C. A1 - Oberdörfer, Sebastian A1 - von Mammen, Sebastian A1 - Latoschik, Marc Erich A1 - Lugrin, Birgit T1 - Joyful adventures and frightening places – designing emotion-inducing virtual environments JF - Frontiers in Virtual Reality N2 - Virtual environments (VEs) can evoke and support emotions, as experienced when playing emotionally arousing games. We theoretically approach the design of fear and joy evoking VEs based on a literature review of empirical studies on virtual and real environments as well as video games’ reviews and content analyses. We define the design space and identify central design elements that evoke specific positive and negative emotions. Based on that, we derive and present guidelines for emotion-inducing VE design with respect to design themes, colors and textures, and lighting configurations. To validate our guidelines in two user studies, we 1) expose participants to 360° videos of VEs designed following the individual guidelines and 2) immerse them in a neutral, positive and negative emotion-inducing VEs combining all respective guidelines in Virtual Reality. The results support our theoretically derived guidelines by revealing significant differences in terms of fear and joy induction. KW - virtual reality KW - virtual environments KW - immersion KW - emotions KW - design Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-284831 SN - 2673-4192 VL - 3 ER - TY - JOUR A1 - Landeck, Maximilian A1 - Alvarez Igarzábal, Federico A1 - Unruh, Fabian A1 - Habenicht, Hannah A1 - Khoshnoud, Shiva A1 - Wittmann, Marc A1 - Lugrin, Jean-Luc A1 - Latoschik, Marc Erich T1 - Journey through a virtual tunnel: Simulated motion and its effects on the experience of time JF - Frontiers in Virtual Reality N2 - This paper examines the relationship between time and motion perception in virtual environments. Previous work has shown that the perception of motion can affect the perception of time. We developed a virtual environment that simulates motion in a tunnel and measured its effects on the estimation of the duration of time, the speed at which perceived time passes, and the illusion of self-motion, also known as vection. When large areas of the visual field move in the same direction, vection can occur; observers often perceive this as self-motion rather than motion of the environment. To generate different levels of vection and investigate its effects on time perception, we developed an abstract procedural tunnel generator. The generator can simulate different speeds and densities of tunnel sections (visibly distinguishable sections that form the virtual tunnel), as well as the degree of embodiment of the user avatar (with or without virtual hands). We exposed participants to various tunnel simulations with different durations, speeds, and densities in a remote desktop and a virtual reality (VR) laboratory study. Time passed subjectively faster under high-speed and high-density conditions in both studies. The experience of self-motion was also stronger under high-speed and high-density conditions. Both studies revealed a significant correlation between the perceived passage of time and perceived self-motion. Subjects in the virtual reality study reported a stronger self-motion experience, a faster perceived passage of time, and shorter time estimates than subjects in the desktop study. Our results suggest that a virtual tunnel simulation can manipulate time perception in virtual reality. We will explore these results for the development of virtual reality applications for therapeutic approaches in our future work. This could be particularly useful in treating disorders like depression, autism, and schizophrenia, which are known to be associated with distortions in time perception. For example, the tunnel could be therapeutically applied by resetting patients’ time perceptions by exposing them to the tunnel under different conditions, such as increasing or decreasing perceived time. KW - passage of time KW - illusion of self-motion KW - vection KW - virtual tunnel KW - therapeutic application KW - virtual reality KW - extended reality (XR) Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-301519 SN - 2673-4192 VL - 3 ER - TY - JOUR A1 - Karl, Stefan A1 - Dandekar, Thomas T1 - Jimena: Efficient computing and system state identification for genetic regulatory networks JF - BMC Bioinformatics N2 - Background: Boolean networks capture switching behavior of many naturally occurring regulatory networks. For semi-quantitative modeling, interpolation between ON and OFF states is necessary. The high degree polynomial interpolation of Boolean genetic regulatory networks (GRNs) in cellular processes such as apoptosis or proliferation allows for the modeling of a wider range of node interactions than continuous activator-inhibitor models, but suffers from scaling problems for networks which contain nodes with more than ~10 inputs. Many GRNs from literature or new gene expression experiments exceed those limitations and a new approach was developed. Results: (i) As a part of our new GRN simulation framework Jimena we introduce and setup Boolean-tree-based data structures; (ii) corresponding algorithms greatly expedite the calculation of the polynomial interpolation in almost all cases, thereby expanding the range of networks which can be simulated by this model in reasonable time. (iii) Stable states for discrete models are efficiently counted and identified using binary decision diagrams. As application example, we show how system states can now be sampled efficiently in small up to large scale hormone disease networks (Arabidopsis thaliana development and immunity, pathogen Pseudomonas syringae and modulation by cytokinins and plant hormones). Conclusions: Jimena simulates currently available GRNs about 10-100 times faster than the previous implementation of the polynomial interpolation model and even greater gains are achieved for large scale-free networks. This speed-up also facilitates a much more thorough sampling of continuous state spaces which may lead to the identification of new stable states. Mutants of large networks can be constructed and analyzed very quickly enabling new insights into network robustness and behavior. KW - Boolean function KW - genetic regulatory network KW - interpolation KW - stable state KW - binary decision diagram KW - Boolean tree Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-128671 VL - 14 ER - TY - JOUR A1 - Krupitzer, Christian A1 - Eberhardinger, Benedikt A1 - Gerostathopoulos, Ilias A1 - Raibulet, Claudia T1 - Introduction to the special issue “Applications in Self-Aware Computing Systems and their Evaluation” JF - Computers N2 - The joint 1st Workshop on Evaluations and Measurements in Self-Aware Computing Systems (EMSAC 2019) and Workshop on Self-Aware Computing (SeAC) was held as part of the FAS* conference alliance in conjunction with the 16th IEEE International Conference on Autonomic Computing (ICAC) and the 13th IEEE International Conference on Self-Adaptive and Self-Organizing Systems (SASO) in Umeå, Sweden on 20 June 2019. The goal of this one-day workshop was to bring together researchers and practitioners from academic environments and from the industry to share their solutions, ideas, visions, and doubts in self-aware computing systems in general and in the evaluation and measurements of such systems in particular. The workshop aimed to enable discussions, partnerships, and collaborations among the participants. This special issue follows the theme of the workshop. It contains extended versions of workshop presentations as well as additional contributions. KW - self-aware computing systems KW - quality evaluation KW - measurements KW - quality assurance KW - autonomous KW - self-adaptive KW - self-managing systems Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-203439 SN - 2073-431X VL - 9 IS - 1 ER - TY - JOUR A1 - Buchheim, Mark A. A1 - Keller, Alexander A1 - Koetschan, Christian A1 - Förster, Frank A1 - Merget, Benjamin A1 - Wolf, Matthias T1 - Internal Transcribed Spacer 2 (nu ITS2 rRNA) Sequence-Structure Phylogenetics: Towards an Automated Reconstruction of the Green Algal Tree of Life JF - PLoS ONE N2 - Background: Chloroplast-encoded genes (matK and rbcL) have been formally proposed for use in DNA barcoding efforts targeting embryophytes. Extending such a protocol to chlorophytan green algae, though, is fraught with problems including non homology (matK) and heterogeneity that prevents the creation of a universal PCR toolkit (rbcL). Some have advocated the use of the nuclear-encoded, internal transcribed spacer two (ITS2) as an alternative to the traditional chloroplast markers. However, the ITS2 is broadly perceived to be insufficiently conserved or to be confounded by introgression or biparental inheritance patterns, precluding its broad use in phylogenetic reconstruction or as a DNA barcode. A growing body of evidence has shown that simultaneous analysis of nucleotide data with secondary structure information can overcome at least some of the limitations of ITS2. The goal of this investigation was to assess the feasibility of an automated, sequence-structure approach for analysis of IT2 data from a large sampling of phylum Chlorophyta. Methodology/Principal Findings: Sequences and secondary structures from 591 chlorophycean, 741 trebouxiophycean and 938 ulvophycean algae, all obtained from the ITS2 Database, were aligned using a sequence structure-specific scoring matrix. Phylogenetic relationships were reconstructed by Profile Neighbor-Joining coupled with a sequence structure-specific, general time reversible substitution model. Results from analyses of the ITS2 data were robust at multiple nodes and showed considerable congruence with results from published phylogenetic analyses. Conclusions/Significance: Our observations on the power of automated, sequence-structure analyses of ITS2 to reconstruct phylum-level phylogenies of the green algae validate this approach to assessing diversity for large sets of chlorophytan taxa. Moreover, our results indicate that objections to the use of ITS2 for DNA barcoding should be weighed against the utility of an automated, data analysis approach with demonstrated power to reconstruct evolutionary patterns for highly divergent lineages. KW - RBCL Gene-sequences KW - Colonial volvocales chlorophyta KW - 26S RDNA Data KW - Land plants KW - Molecular systematics KW - Secondary structure KW - Nuclear RDNA KW - DNA KW - Barcodes KW - Dasycladales chlorophyta KW - Profile distances Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-140866 VL - 6 IS - 2 ER - TY - JOUR A1 - Prakash, Subash A1 - Unnikrishnan, Vishnu A1 - Pryss, Rüdiger A1 - Kraft, Robin A1 - Schobel, Johannes A1 - Hannemann, Ronny A1 - Langguth, Berthold A1 - Schlee, Winfried A1 - Spiliopoulou, Myra T1 - Interactive system for similarity-based inspection and assessment of the well-being of mHealth users JF - Entropy N2 - Recent digitization technologies empower mHealth users to conveniently record their Ecological Momentary Assessments (EMA) through web applications, smartphones, and wearable devices. These recordings can help clinicians understand how the users' condition changes, but appropriate learning and visualization mechanisms are required for this purpose. We propose a web-based visual analytics tool, which processes clinical data as well as EMAs that were recorded through a mHealth application. The goals we pursue are (1) to predict the condition of the user in the near and the far future, while also identifying the clinical data that mostly contribute to EMA predictions, (2) to identify users with outlier EMA, and (3) to show to what extent the EMAs of a user are in line with or diverge from those users similar to him/her. We report our findings based on a pilot study on patient empowerment, involving tinnitus patients who recorded EMAs with the mHealth app TinnitusTips. To validate our method, we also derived synthetic data from the same pilot study. Based on this setting, results for different use cases are reported. KW - medical analytics KW - condition prediction KW - ecological momentary assessment KW - visual analytics KW - time series Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-252333 SN - 1099-4300 VL - 23 IS - 12 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 - Hurtienne, Jörn T1 - Inter-coder reliability of categorising force-dynamic events in human-technology interaction N2 - Two studies are reported that investigate how readily accessible and applicable ten force-dynamic categories are to novices in describing short episodes of human-technology interaction (Study 1) and that establish a measure of inter-coder reliability when re-classifying these episodes into force-dynamic categories (Study 2). The results of the first study show that people can easily and confidently relate their experiences with technology to the definitions of force-dynamic events (e.g. “The driver released the handbrake” as an example of restraint removal). The results of the second study show moderate agreement between four expert coders across all ten force-dynamic categories (Cohen’s kappa = .59) when re-classifying these episodes. Agreement values for single force-dynamic categories ranged between ‘fair’ and ‘almost perfect’, i.e. between kappa = .30 and .95. Agreement with the originally intended classifications of study 1 was higher than the pure inter-coder reliabilities. Single coders achieved an average kappa of .71, indicating substantial agreement. Using more than one coder increased kappas to almost perfect: up to .87 for four coders. A qualitative analysis of the predicted versus the observed number of category confusions revealed that about half of the category disagreement could be predicted from strong overlaps in the definitions of force-dynamic categories. From the quantitative and qualitative results, guidelines are derived to aid the better training of coders in order to increase inter-coder reliability. KW - inter-coder reliability KW - force dynamics KW - image schemas KW - humantechnology interaction Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-194127 SN - 2197-2796 SN - 2197-2788 N1 - This publication is with permission of the rights owner freely accessible due to an Alliance licence and a national licence (funded by the DFG, German Research Foundation) respectively. VL - 1 IS - 1 ER -