@article{BeckerCaminitiFiorellaetal.2013, author = {Becker, Martin and Caminiti, Saverio and Fiorella, Donato and Francis, Louise and Gravino, Pietro and Haklay, Mordechai (Muki) and Hotho, Andreas and Loreto, Virrorio and Mueller, Juergen and Ricchiuti, Ferdinando and Servedio, Vito D. P. and Sirbu, Alina and Tria, Franesca}, title = {Awareness and Learning in Participatory Noise Sensing}, series = {PLOS ONE}, volume = {8}, journal = {PLOS ONE}, number = {12}, issn = {1932-6203}, doi = {10.1371/journal.pone.0081638}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-127675}, pages = {e81638}, year = {2013}, abstract = {The development of ICT infrastructures has facilitated the emergence of new paradigms for looking at society and the environment over the last few years. Participatory environmental sensing, i.e. directly involving citizens in environmental monitoring, is one example, which is hoped to encourage learning and enhance awareness of environmental issues. In this paper, an analysis of the behaviour of individuals involved in noise sensing is presented. Citizens have been involved in noise measuring activities through the WideNoise smartphone application. This application has been designed to record both objective (noise samples) and subjective (opinions, feelings) data. The application has been open to be used freely by anyone and has been widely employed worldwide. In addition, several test cases have been organised in European countries. Based on the information submitted by users, an analysis of emerging awareness and learning is performed. The data show that changes in the way the environment is perceived after repeated usage of the application do appear. Specifically, users learn how to recognise different noise levels they are exposed to. Additionally, the subjective data collected indicate an increased user involvement in time and a categorisation effect between pleasant and less pleasant environments.}, language = {en} } @article{BencurovaShityakovSchaacketal.2022, author = {Bencurova, Elena and Shityakov, Sergey and Schaack, Dominik and Kaltdorf, Martin and Sarukhanyan, Edita and Hilgarth, Alexander and Rath, Christin and Montenegro, Sergio and Roth, G{\"u}nter and Lopez, Daniel and Dandekar, Thomas}, title = {Nanocellulose composites as smart devices with chassis, light-directed DNA Storage, engineered electronic properties, and chip integration}, series = {Frontiers in Bioengineering and Biotechnology}, volume = {10}, journal = {Frontiers in Bioengineering and Biotechnology}, issn = {2296-4185}, doi = {10.3389/fbioe.2022.869111}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-283033}, year = {2022}, abstract = {The rapid development of green and sustainable materials opens up new possibilities in the field of applied research. Such materials include nanocellulose composites that can integrate many components into composites and provide a good chassis for smart devices. In our study, we evaluate four approaches for turning a nanocellulose composite into an information storage or processing device: 1) nanocellulose can be a suitable carrier material and protect information stored in DNA. 2) Nucleotide-processing enzymes (polymerase and exonuclease) can be controlled by light after fusing them with light-gating domains; nucleotide substrate specificity can be changed by mutation or pH change (read-in and read-out of the information). 3) Semiconductors and electronic capabilities can be achieved: we show that nanocellulose is rendered electronic by iodine treatment replacing silicon including microstructures. Nanocellulose semiconductor properties are measured, and the resulting potential including single-electron transistors (SET) and their properties are modeled. Electric current can also be transported by DNA through G-quadruplex DNA molecules; these as well as classical silicon semiconductors can easily be integrated into the nanocellulose composite. 4) To elaborate upon miniaturization and integration for a smart nanocellulose chip device, we demonstrate pH-sensitive dyes in nanocellulose, nanopore creation, and kinase micropatterning on bacterial membranes as well as digital PCR micro-wells. Future application potential includes nano-3D printing and fast molecular processors (e.g., SETs) integrated with DNA storage and conventional electronics. This would also lead to environment-friendly nanocellulose chips for information processing as well as smart nanocellulose composites for biomedical applications and nano-factories.}, language = {en} } @article{BrevesDodel2021, author = {Breves, Priska and Dodel, Nicola}, title = {The influence of cybersickness and the media devices' mobility on the persuasive effects of 360° commercials}, series = {Multimedia Tools and Applications}, volume = {80}, journal = {Multimedia Tools and Applications}, number = {18}, issn = {1573-7721}, doi = {10.1007/s11042-021-11057-x}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-269194}, pages = {27299-27322}, year = {2021}, abstract = {With the rise of immersive media, advertisers have started to use 360° commercials to engage and persuade consumers. Two experiments were conducted to address research gaps and to validate the positive impact of 360° commercials in realistic settings. The first study (N = 62) compared the effects of 360° commercials using either a mobile cardboard head-mounted display (HMD) or a laptop. This experiment was conducted in the participants' living rooms and incorporated individual feelings of cybersickness as a moderator. The participants who experienced the 360° commercial with the HMD reported higher spatial presence and product evaluation, but their purchase intentions were only increased when their reported cybersickness was low. The second experiment (N = 197) was conducted online and analyzed the impact of 360° commercials that were experienced with mobile (smartphone/tablet) or static (laptop/desktop) devices instead of HMDs. The positive effects of omnidirectional videos were stronger when participants used mobile devices.}, language = {en} } @article{BuchheimKellerKoetschanetal.2011, author = {Buchheim, Mark A. and Keller, Alexander and Koetschan, Christian and F{\"o}rster, Frank and Merget, Benjamin and Wolf, Matthias}, title = {Internal Transcribed Spacer 2 (nu ITS2 rRNA) Sequence-Structure Phylogenetics: Towards an Automated Reconstruction of the Green Algal Tree of Life}, series = {PLoS ONE}, volume = {6}, journal = {PLoS ONE}, number = {2}, doi = {10.1371/journal.pone.0016931}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-140866}, pages = {e16931}, year = {2011}, abstract = {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.}, language = {en} } @article{BuchinBuchinByrkaetal.2012, author = {Buchin, Kevin and Buchin, Maike and Byrka, Jaroslaw and N{\"o}llenburg, Martin and Okamoto, Yoshio and Silveira, Rodrigo I. and Wolff, Alexander}, title = {Drawing (Complete) Binary Tanglegrams}, series = {Algorithmica}, volume = {62}, journal = {Algorithmica}, doi = {10.1007/s00453-010-9456-3}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-124622}, pages = {309-332}, year = {2012}, abstract = {A binary tanglegram is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential that both trees are drawn without edge crossings and that the inter-tree edges have as few crossings as possible. It is known that finding a tanglegram with the minimum number of crossings is NP-hard and that the problem is fixed-parameter tractable with respect to that number. We prove that under the Unique Games Conjecture there is no constant-factor approximation for binary trees. We show that the problem is NP-hard even if both trees are complete binary trees. For this case we give an O(n 3)-time 2-approximation and a new, simple fixed-parameter algorithm. We show that the maximization version of the dual problem for binary trees can be reduced to a version of MaxCut for which the algorithm of Goemans and Williamson yields a 0.878-approximation.}, language = {en} } @article{BugaScholzKumaretal.2012, author = {Buga, Ana-Maria and Scholz, Claus J{\"u}rgen and Kumar, Senthil and Herndon, James G. and Alexandru, Dragos and Cojocaru, Gabriel Radu and Dandekar, Thomas and Popa-Wagner, Aurel}, title = {Identification of New Therapeutic Targets by Genome-Wide Analysis of Gene Expression in the Ipsilateral Cortex of Aged Rats after Stroke}, series = {PLoS One}, volume = {7}, journal = {PLoS One}, number = {12}, doi = {10.1371/journal.pone.0050985}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-130657}, pages = {e50985}, year = {2012}, abstract = {Background: Because most human stroke victims are elderly, studies of experimental stroke in the aged rather than the young rat model may be optimal for identifying clinically relevant cellular responses, as well for pinpointing beneficial interventions. Methodology/Principal Findings: We employed the Affymetrix platform to analyze the whole-gene transcriptome following temporary ligation of the middle cerebral artery in aged and young rats. The correspondence, heat map, and dendrogram analyses independently suggest a differential, age-group-specific behaviour of major gene clusters after stroke. Overall, the pattern of gene expression strongly suggests that the response of the aged rat brain is qualitatively rather than quantitatively different from the young, i.e. the total number of regulated genes is comparable in the two age groups, but the aged rats had great difficulty in mounting a timely response to stroke. Our study indicates that four genes related to neuropathic syndrome, stress, anxiety disorders and depression (Acvr1c, Cort, Htr2b and Pnoc) may have impaired response to stroke in aged rats. New therapeutic options in aged rats may also include Calcrl, Cyp11b1, Prcp, Cebpa, Cfd, Gpnmb, Fcgr2b, Fcgr3a, Tnfrsf26, Adam 17 and Mmp14. An unexpected target is the enzyme 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 in aged rats, a key enzyme in the cholesterol synthesis pathway. Post-stroke axonal growth was compromised in both age groups. Conclusion/Significance: We suggest that a multi-stage, multimodal treatment in aged animals may be more likely to produce positive results. Such a therapeutic approach should be focused on tissue restoration but should also address other aspects of patient post-stroke therapy such as neuropathic syndrome, stress, anxiety disorders, depression, neurotransmission and blood pressure.}, language = {en} } @article{BoehlerCreignouGalotaetal.2012, author = {B{\"o}hler, Elmar and Creignou, Nadia and Galota, Matthias and Reith, Steffen and Schnoor, Henning and Vollmer, Heribert}, title = {Complexity Classifications for Different Equivalence and Audit Problems for Boolean Circuits}, series = {Logical Methods in Computer Science}, volume = {8}, journal = {Logical Methods in Computer Science}, number = {3:27}, doi = {10.2168/LMCS-8(3:27)2012}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-131121}, pages = {1 -- 25}, year = {2012}, abstract = {We study Boolean circuits as a representation of Boolean functions and conskier different equivalence, audit, and enumeration problems. For a number of restricted sets of gate types (bases) we obtain efficient algorithms, while for all other gate types we show these problems are at least NP-hard.}, language = {en} } @article{CaliskanCrouchGiddinsetal.2022, author = {Caliskan, Aylin and Crouch, Samantha A. W. and Giddins, Sara and Dandekar, Thomas and Dangwal, Seema}, title = {Progeria and aging — Omics based comparative analysis}, series = {Biomedicines}, volume = {10}, journal = {Biomedicines}, number = {10}, issn = {2227-9059}, doi = {10.3390/biomedicines10102440}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-289868}, year = {2022}, abstract = {Since ancient times aging has also been regarded as a disease, and humankind has always strived to extend the natural lifespan. Analyzing the genes involved in aging and disease allows for finding important indicators and biological markers for pathologies and possible therapeutic targets. An example of the use of omics technologies is the research regarding aging and the rare and fatal premature aging syndrome progeria (Hutchinson-Gilford progeria syndrome, HGPS). In our study, we focused on the in silico analysis of differentially expressed genes (DEGs) in progeria and aging, using a publicly available RNA-Seq dataset (GEO dataset GSE113957) and a variety of bioinformatics tools. Despite the GSE113957 RNA-Seq dataset being well-known and frequently analyzed, the RNA-Seq data shared by Fleischer et al. is far from exhausted and reusing and repurposing the data still reveals new insights. By analyzing the literature citing the use of the dataset and subsequently conducting a comparative analysis comparing the RNA-Seq data analyses of different subsets of the dataset (healthy children, nonagenarians and progeria patients), we identified several genes involved in both natural aging and progeria (KRT8, KRT18, ACKR4, CCL2, UCP2, ADAMTS15, ACTN4P1, WNT16, IGFBP2). Further analyzing these genes and the pathways involved indicated their possible roles in aging, suggesting the need for further in vitro and in vivo research. In this paper, we (1) compare "normal aging" (nonagenarians vs. healthy children) and progeria (HGPS patients vs. healthy children), (2) enlist genes possibly involved in both the natural aging process and progeria, including the first mention of IGFBP2 in progeria, (3) predict miRNAs and interactomes for WNT16 (hsa-mir-181a-5p), UCP2 (hsa-mir-26a-5p and hsa-mir-124-3p), and IGFBP2 (hsa-mir-124-3p, hsa-mir-126-3p, and hsa-mir-27b-3p), (4) demonstrate the compatibility of well-established R packages for RNA-Seq analysis for researchers interested but not yet familiar with this kind of analysis, and (5) present comparative proteomics analyses to show an association between our RNA-Seq data analyses and corresponding changes in protein expression.}, language = {en} } @article{CarolusWienrichToerkeetal.2021, author = {Carolus, Astrid and Wienrich, Carolin and T{\"o}rke, Anna and Friedel, Tobias and Schwietering, Christian and Sperzel, Mareike}, title = {'Alexa, I feel for you!' Observers' empathetic reactions towards a conversational agent}, series = {Frontiers in Computer Science}, volume = {3}, journal = {Frontiers in Computer Science}, doi = {10.3389/fcomp.2021.682982}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-258807}, year = {2021}, abstract = {Conversational agents and smart speakers have grown in popularity offering a variety of options for use, which are available through intuitive speech operation. In contrast to the standard dyad of a single user and a device, voice-controlled operations can be observed by further attendees resulting in new, more social usage scenarios. Referring to the concept of 'media equation' and to research on the idea of 'computers as social actors,' which describes the potential of technology to trigger emotional reactions in users, this paper asks for the capacity of smart speakers to elicit empathy in observers of interactions. In a 2 × 2 online experiment, 140 participants watched a video of a man talking to an Amazon Echo either rudely or neutrally (factor 1), addressing it as 'Alexa' or 'Computer' (factor 2). Controlling for participants' trait empathy, the rude treatment results in participants' significantly higher ratings of empathy with the device, compared to the neutral treatment. The form of address had no significant effect. Results were independent of the participants' gender and usage experience indicating a rather universal effect, which confirms the basic idea of the media equation. Implications for users, developers and researchers were discussed in the light of (future) omnipresent voice-based technology interaction scenarios.}, language = {en} } @article{DavidsonDuekingZinneretal.2020, author = {Davidson, Padraig and D{\"u}king, Peter and Zinner, Christoph and Sperlich, Billy and Hotho, Andreas}, title = {Smartwatch-Derived Data and Machine Learning Algorithms Estimate Classes of Ratings of Perceived Exertion in Runners: A Pilot Study}, series = {Sensors}, volume = {20}, journal = {Sensors}, number = {9}, issn = {1424-8220}, doi = {10.3390/s20092637}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-205686}, year = {2020}, abstract = {The rating of perceived exertion (RPE) is a subjective load marker and may assist in individualizing training prescription, particularly by adjusting running intensity. Unfortunately, RPE has shortcomings (e.g., underreporting) and cannot be monitored continuously and automatically throughout a training sessions. In this pilot study, we aimed to predict two classes of RPE (≤15 "Somewhat hard to hard" on Borg's 6-20 scale vs. RPE >15 in runners by analyzing data recorded by a commercially-available smartwatch with machine learning algorithms. Twelve trained and untrained runners performed long-continuous runs at a constant self-selected pace to volitional exhaustion. Untrained runners reported their RPE each kilometer, whereas trained runners reported every five kilometers. The kinetics of heart rate, step cadence, and running velocity were recorded continuously ( 1 Hz ) with a commercially-available smartwatch (Polar V800). We trained different machine learning algorithms to estimate the two classes of RPE based on the time series sensor data derived from the smartwatch. Predictions were analyzed in different settings: accuracy overall and per runner type; i.e., accuracy for trained and untrained runners independently. We achieved top accuracies of 84.8 \% for the whole dataset, 81.8 \% for the trained runners, and 86.1 \% for the untrained runners. We predict two classes of RPE with high accuracy using machine learning and smartwatch data. This approach might aid in individualizing training prescriptions.}, language = {en} }