TY - JOUR A1 - Bauer, Chris A1 - Herwig, Ralf A1 - Lienhard, Matthias A1 - Prasse, Paul A1 - Scheffer, Tobias A1 - Schuchhardt, Johannes T1 - Large-scale literature mining to assess the relation between anti-cancer drugs and cancer types JF - Journal of translational medicine N2 - Background: There is a huge body of scientific literature describing the relation between tumor types and anti-cancer drugs. The vast amount of scientific literature makes it impossible for researchers and physicians to extract all relevant information manually. Methods: In order to cope with the large amount of literature we applied an automated text mining approach to assess the relations between 30 most frequent cancer types and 270 anti-cancer drugs. We applied two different approaches, a classical text mining based on named entity recognition and an AI-based approach employing word embeddings. The consistency of literature mining results was validated with 3 independent methods: first, using data from FDA approvals, second, using experimentally measured IC-50 cell line data and third, using clinical patient survival data. Results: We demonstrated that the automated text mining was able to successfully assess the relation between cancer types and anti-cancer drugs. All validation methods showed a good correspondence between the results from literature mining and independent confirmatory approaches. The relation between most frequent cancer types and drugs employed for their treatment were visualized in a large heatmap. All results are accessible in an interactive web-based knowledge base using the following link: . Conclusions: Our approach is able to assess the relations between compounds and cancer types in an automated manner. Both, cancer types and compounds could be grouped into different clusters. Researchers can use the interactive knowledge base to inspect the presented results and follow their own research questions, for example the identification of novel indication areas for known drugs. KW - Literature mining KW - Anti-cancer drugs KW - Tumor types KW - Word embeddings KW - Database Y1 - 2021 U6 - https://doi.org/10.1186/s12967-021-02941-z SN - 1479-5876 VL - 19 IS - 1 PB - BioMed Central CY - London ER - TY - JOUR A1 - Huang, Yizhen A1 - Richter, Eric A1 - Kleickmann, Thilo A1 - Wiepke, Axel A1 - Richter, Dirk T1 - Classroom complexity affects student teachers’ behavior in a VR classroom JF - Computers & education : an international journal N2 - Student teachers often struggle to keep track of everything that is happening in the classroom, and particularly to notice and respond when students cause disruptions. The complexity of the classroom environment is a potential contributing factor that has not been empirically tested. In this experimental study, we utilized a virtual reality (VR) classroom to examine whether classroom complexity affects the likelihood of student teachers noticing disruptions and how they react after noticing. Classroom complexity was operationalized as the number of disruptions and the existence of overlapping disruptions (multidimensionality) as well as the existence of parallel teaching tasks (simultaneity). Results showed that student teachers (n = 50) were less likely to notice the scripted disruptions, and also less likely to respond to the disruptions in a comprehensive and effortful manner when facing greater complexity. These results may have implications for both teacher training and the design of VR for training or research purpose. This study contributes to the field from two aspects: 1) it revealed how features of the classroom environment can affect student teachers' noticing of and reaction to disruptions; and 2) it extends the functionality of the VR environment-from a teacher training tool to a testbed of fundamental classroom processes that are difficult to manipulate in real-life. KW - Augmented and virtual reality KW - Simulations KW - Improving classroom KW - teaching KW - Media in education KW - Pedagogical issues Y1 - 2021 U6 - https://doi.org/10.1016/j.compedu.2020.104100 SN - 0360-1315 SN - 1873-782X VL - 163 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Hawro, Tomasz A1 - Przybylowicz, Katarzyna A1 - Spindler, Max A1 - Hawro, Marlena A1 - Steć, Michał A1 - Altrichter, Sabine A1 - Weller, Karsten A1 - Magerl, Markus A1 - Reidel, Ulrich A1 - Alarbeed, Ezzat A1 - Alraboni, Ola A1 - Maurer, Marcus A1 - Metz, Martin T1 - The characteristics and impact of pruritus in adult dermatology patients BT - a prospective, cross-sectional study JF - Journal of the American Academy of Dermatology N2 - Background: Pruritus often accompanies chronic skin diseases, exerting considerable burden on many areas of patient functioning; this burden and the features of pruritus remain insufficiently characterized. Objective: To investigate characteristics, including localization patterns, and burden of pruritus in patients with chronic dermatoses. Methods: We recruited 800 patients with active chronic skin diseases. We assessed pruritus intensity, localization, and further characteristics. We used validated questionnaires to assess quality of life, work productivity and activity impairment, anxiety, depression, and sleep quality. Results: Nine out of every 10 patients had experienced pruritus throughout their disease and 73% in the last 7 days. Pruritus often affected the entire body and was not restricted to skin lesions. Patients with moderate to severe pruritus reported significantly more impairment to their sleep quality and work productivity, and they were more depressed and anxious than control individuals and patients with mild or no pruritus. Suicidal ideations were highly prevalent in patients with chronic pruritus (18.5%) and atopic dermatitis (11.8%). Conclusions: Pruritus prevalence and intensity are very high across all dermatoses studied; intensity is linked to impairment in many areas of daily functioning. Effective treatment strategies are urgently required to treat pruritus and the underlying skin disease. ( J Am Acad Dermatol 2021;84:691-700.) KW - activity KW - anxiety KW - depression KW - pruritus KW - quality of life KW - sleep quality KW - suicidal ideations KW - work productivity Y1 - 2021 U6 - https://doi.org/10.1016/J.JAAD.2020.08.035 SN - 0190-9622 SN - 1097-6787 VL - 84 IS - 3 SP - 691 EP - 700 PB - Elsevier CY - Amsterdam [u.a.] ER - TY - JOUR A1 - Middelanis, Robin A1 - Willner, Sven N. A1 - Otto, Christian A1 - Kuhla, Kilian A1 - Quante, Lennart A1 - Levermann, Anders T1 - Wave-like global economic ripple response to Hurricane Sandy JF - Environmental research letters : ERL / Institute of Physics N2 - Tropical cyclones range among the costliest disasters on Earth. Their economic repercussions along the supply and trade network also affect remote economies that are not directly affected. We here simulate possible global repercussions on consumption for the example case of Hurricane Sandy in the US (2012) using the shock-propagation model Acclimate. The modeled shock yields a global three-phase ripple: an initial production demand reduction and associated consumption price decrease, followed by a supply shortage with increasing prices, and finally a recovery phase. Regions with strong trade relations to the US experience strong magnitudes of the ripple. A dominating demand reduction or supply shortage leads to overall consumption gains or losses of a region, respectively. While finding these repercussions in historic data is challenging due to strong volatility of economic interactions, numerical models like ours can help to identify them by approaching the problem from an exploratory angle, isolating the effect of interest. For this, our model simulates the economic interactions of over 7000 regional economic sectors, interlinked through about 1.8 million trade relations. Under global warming, the wave-like structures of the economic response to major hurricanes like the one simulated here are likely to intensify and potentially overlap with other weather extremes. KW - supply chains KW - Hurricane Sandy KW - economic ripples KW - extreme weather KW - impacts KW - loss propagation KW - natural disasters Y1 - 2021 U6 - https://doi.org/10.1088/1748-9326/ac39c0 SN - 1748-9326 VL - 16 IS - 12 PB - IOP Publ. Ltd. CY - Bristol ER - TY - JOUR A1 - Quante, Lennart A1 - Willner, Sven N. A1 - Middelanis, Robin A1 - Levermann, Anders T1 - Regions of intensification of extreme snowfall under future warming JF - Scientific reports N2 - Due to climate change the frequency and character of precipitation are changing as the hydrological cycle intensifies. With regards to snowfall, global warming has two opposing influences; increasing humidity enables intense snowfall, whereas higher temperatures decrease the likelihood of snowfall. Here we show an intensification of extreme snowfall across large areas of the Northern Hemisphere under future warming. This is robust across an ensemble of global climate models when they are bias-corrected with observational data. While mean daily snowfall decreases, both the 99th and the 99.9th percentiles of daily snowfall increase in many regions in the next decades, especially for Northern America and Asia. Additionally, the average intensity of snowfall events exceeding these percentiles as experienced historically increases in many regions. This is likely to pose a challenge to municipalities in mid to high latitudes. Overall, extreme snowfall events are likely to become an increasingly important impact of climate change in the next decades, even if they will become rarer, but not necessarily less intense, in the second half of the century. Y1 - 2021 U6 - https://doi.org/10.1038/s41598-021-95979-4 SN - 2045-2322 VL - 11 IS - 1 PB - Macmillan Publishers Limited, part of Springer Nature CY - Berlin ER - TY - JOUR A1 - Schirrmann, Michael A1 - Landwehr, Niels A1 - Giebel, Antje A1 - Garz, Andreas A1 - Dammer, Karl-Heinz T1 - Early detection of stripe rust in winter wheat using deep residual neural networks JF - Frontiers in plant science : FPLS N2 - Stripe rust (Pst) is a major disease of wheat crops leading untreated to severe yield losses. The use of fungicides is often essential to control Pst when sudden outbreaks are imminent. Sensors capable of detecting Pst in wheat crops could optimize the use of fungicides and improve disease monitoring in high-throughput field phenotyping. Now, deep learning provides new tools for image recognition and may pave the way for new camera based sensors that can identify symptoms in early stages of a disease outbreak within the field. The aim of this study was to teach an image classifier to detect Pst symptoms in winter wheat canopies based on a deep residual neural network (ResNet). For this purpose, a large annotation database was created from images taken by a standard RGB camera that was mounted on a platform at a height of 2 m. Images were acquired while the platform was moved over a randomized field experiment with Pst-inoculated and Pst-free plots of winter wheat. The image classifier was trained with 224 x 224 px patches tiled from the original, unprocessed camera images. The image classifier was tested on different stages of the disease outbreak. At patch level the image classifier reached a total accuracy of 90%. To test the image classifier on image level, the image classifier was evaluated with a sliding window using a large striding length of 224 px allowing for fast test performance. At image level, the image classifier reached a total accuracy of 77%. Even in a stage with very low disease spreading (0.5%) at the very beginning of the Pst outbreak, a detection accuracy of 57% was obtained. Still in the initial phase of the Pst outbreak with 2 to 4% of Pst disease spreading, detection accuracy with 76% could be attained. With further optimizations, the image classifier could be implemented in embedded systems and deployed on drones, vehicles or scanning systems for fast mapping of Pst outbreaks. KW - yellow rust KW - monitoring KW - deep learning KW - wheat crops KW - image recognition KW - camera sensor KW - ResNet KW - smart farming Y1 - 2021 U6 - https://doi.org/10.3389/fpls.2021.469689 SN - 1664-462X VL - 12 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Gautam, Khem Raj A1 - Zhang, Guoqiang A1 - Landwehr, Niels A1 - Adolphs, Julian T1 - Machine learning for improvement of thermal conditions inside a hybrid ventilated animal building JF - Computers and electronics in agriculture : COMPAG online ; an international journal N2 - In buildings with hybrid ventilation, natural ventilation opening positions (windows), mechanical ventilation rates, heating, and cooling are manipulated to maintain desired thermal conditions. The indoor temperature is regulated solely by ventilation (natural and mechanical) when the external conditions are favorable to save external heating and cooling energy. The ventilation parameters are determined by a rule-based control scheme, which is not optimal. This study proposes a methodology to enable real-time optimum control of ventilation parameters. We developed offline prediction models to estimate future thermal conditions from the data collected from building in operation. The developed offline model is then used to find the optimal controllable ventilation parameters in real-time to minimize the setpoint deviation in the building. With the proposed methodology, the experimental building's setpoint deviation improved for 87% of time, on average, by 0.53 degrees C compared to the current deviations. KW - Animal building KW - Natural ventilation KW - Automatically controlled windows KW - Machine learning KW - Optimization Y1 - 2021 U6 - https://doi.org/10.1016/j.compag.2021.106259 SN - 0168-1699 SN - 1872-7107 VL - 187 PB - Elsevier Science CY - Amsterdam [u.a.] ER - TY - JOUR A1 - Camargo, Tibor de A1 - Schirrmann, Michael A1 - Landwehr, Niels A1 - Dammer, Karl-Heinz A1 - Pflanz, Michael T1 - Optimized deep learning model as a basis for fast UAV mapping of weed species in winter wheat crops JF - Remote sensing / Molecular Diversity Preservation International (MDPI) N2 - Weed maps should be available quickly, reliably, and with high detail to be useful for site-specific management in crop protection and to promote more sustainable agriculture by reducing pesticide use. Here, the optimization of a deep residual convolutional neural network (ResNet-18) for the classification of weed and crop plants in UAV imagery is proposed. The target was to reach sufficient performance on an embedded system by maintaining the same features of the ResNet-18 model as a basis for fast UAV mapping. This would enable online recognition and subsequent mapping of weeds during UAV flying operation. Optimization was achieved mainly by avoiding redundant computations that arise when a classification model is applied on overlapping tiles in a larger input image. The model was trained and tested with imagery obtained from a UAV flight campaign at low altitude over a winter wheat field, and classification was performed on species level with the weed species Matricaria chamomilla L., Papaver rhoeas L., Veronica hederifolia L., and Viola arvensis ssp. arvensis observed in that field. The ResNet-18 model with the optimized image-level prediction pipeline reached a performance of 2.2 frames per second with an NVIDIA Jetson AGX Xavier on the full resolution UAV image, which would amount to about 1.78 ha h(-1) area output for continuous field mapping. The overall accuracy for determining crop, soil, and weed species was 94%. There were some limitations in the detection of species unknown to the model. When shifting from 16-bit to 32-bit model precision, no improvement in classification accuracy was observed, but a strong decline in speed performance, especially when a higher number of filters was used in the ResNet-18 model. Future work should be directed towards the integration of the mapping process on UAV platforms, guiding UAVs autonomously for mapping purpose, and ensuring the transferability of the models to other crop fields. KW - ResNet KW - deep residual networks KW - UAV imagery KW - embedded systems KW - crop KW - monitoring KW - image classification KW - site-specific weed management KW - real-time mapping Y1 - 2021 U6 - https://doi.org/10.3390/rs13091704 SN - 2072-4292 VL - 13 IS - 9 PB - MDPI CY - Basel ER - TY - JOUR A1 - Brede, Nuria A1 - Botta, Nicola T1 - On the correctness of monadic backward induction JF - Journal of functional programming N2 - In control theory, to solve a finite-horizon sequential decision problem (SDP) commonly means to find a list of decision rules that result in an optimal expected total reward (or cost) when taking a given number of decision steps. SDPs are routinely solved using Bellman's backward induction. Textbook authors (e.g. Bertsekas or Puterman) typically give more or less formal proofs to show that the backward induction algorithm is correct as solution method for deterministic and stochastic SDPs. Botta, Jansson and Ionescu propose a generic framework for finite horizon, monadic SDPs together with a monadic version of backward induction for solving such SDPs. In monadic SDPs, the monad captures a generic notion of uncertainty, while a generic measure function aggregates rewards. In the present paper, we define a notion of correctness for monadic SDPs and identify three conditions that allow us to prove a correctness result for monadic backward induction that is comparable to textbook correctness proofs for ordinary backward induction. The conditions that we impose are fairly general and can be cast in category-theoretical terms using the notion of Eilenberg-Moore algebra. They hold in familiar settings like those of deterministic or stochastic SDPs, but we also give examples in which they fail. Our results show that backward induction can safely be employed for a broader class of SDPs than usually treated in textbooks. However, they also rule out certain instances that were considered admissible in the context of Botta et al. 's generic framework. Our development is formalised in Idris as an extension of the Botta et al. framework and the sources are available as supplementary material. Y1 - 2021 U6 - https://doi.org/10.1017/S0956796821000228 SN - 1469-7653 SN - 0956-7968 VL - 31 PB - Cambridge University Press CY - Cambridge ER - TY - JOUR A1 - Andjelković, Marko A1 - Chen, Junchao A1 - Simevski, Aleksandar A1 - Schrape, Oliver A1 - Krstić, Miloš A1 - Kraemer, Rolf T1 - Monitoring of particle count rate and LET variations with pulse stretching inverters JF - IEEE transactions on nuclear science : a publication of the IEEE Nuclear and Plasma Sciences Society N2 - This study investigates the use of pulse stretching (skew-sized) inverters for monitoring the variation of count rate and linear energy transfer (LET) of energetic particles. The basic particle detector is a cascade of two pulse stretching inverters, and the required sensing area is obtained by connecting up to 12 two-inverter cells in parallel and employing the required number of parallel arrays. The incident particles are detected as single-event transients (SETs), whereby the SET count rate denotes the particle count rate, while the SET pulsewidth distribution depicts the LET variations. The advantage of the proposed solution is the possibility to sense the LET variations using fully digital processing logic. SPICE simulations conducted on IHP's 130-nm CMOS technology have shown that the SET pulsewidth varies by approximately 550 ps over the LET range from 1 to 100 MeV center dot cm(2) center dot mg(-1). The proposed detector is intended for triggering the fault-tolerant mechanisms within a self-adaptive multiprocessing system employed in space. It can be implemented as a standalone detector or integrated in the same chip with the target system. KW - Particle detector KW - pulse stretching inverters KW - single-event transient KW - (SET) count rate KW - SET pulsewidth distribution Y1 - 2021 U6 - https://doi.org/10.1109/TNS.2021.3076400 SN - 0018-9499 SN - 1558-1578 VL - 68 IS - 8 SP - 1772 EP - 1781 PB - Institute of Electrical and Electronics Engineers CY - New York, NY ER - TY - JOUR A1 - Schrape, Oliver A1 - Andjelkovic, Marko A1 - Breitenreiter, Anselm A1 - Zeidler, Steffen A1 - Balashov, Alexey A1 - Krstić, Miloš T1 - Design and evaluation of radiation-hardened standard cell flip-flops JF - IEEE transactions on circuits and systems : a publication of the IEEE Circuits and Systems Society: 1, Regular papers N2 - Use of a standard non-rad-hard digital cell library in the rad-hard design can be a cost-effective solution for space applications. In this paper we demonstrate how a standard non-rad-hard flip-flop, as one of the most vulnerable digital cells, can be converted into a rad-hard flip-flop without modifying its internal structure. We present five variants of a Triple Modular Redundancy (TMR) flip-flop: baseline TMR flip-flop, latch-based TMR flip-flop, True-Single Phase Clock (TSPC) TMR flip-flop, scannable TMR flip-flop and self-correcting TMR flipflop. For all variants, the multi-bit upsets have been addressed by applying special placement constraints, while the Single Event Transient (SET) mitigation was achieved through the usage of customized SET filters and selection of optimal inverter sizes for the clock and reset trees. The proposed flip-flop variants feature differing performance, thus enabling to choose the optimal solution for every sensitive node in the circuit, according to the predefined design constraints. Several flip-flop designs have been validated on IHP's 130nm BiCMOS process, by irradiation of custom-designed shift registers. It has been shown that the proposed TMR flip-flops are robust to soft errors with a threshold Linear Energy Transfer (LET) from (32.4 MeV.cm(2)/mg) to (62.5 MeV.cm(2)/mg), depending on the variant. KW - Single event effect KW - fault tolerance KW - triple modular redundancy KW - ASIC KW - design flow KW - radhard design Y1 - 2021 U6 - https://doi.org/10.1109/TCSI.2021.3109080 SN - 1549-8328 SN - 1558-0806 SN - 1057-7122 VL - 68 IS - 11 SP - 4796 EP - 4809 PB - Inst. of Electr. and Electronics Engineers CY - New York, NY ER - TY - JOUR A1 - Tavakoli, Hamad A1 - Alirezazadeh, Pendar A1 - Hedayatipour, Ava A1 - Nasib, A. H. Banijamali A1 - Landwehr, Niels T1 - Leaf image-based classification of some common bean cultivars using discriminative convolutional neural networks JF - Computers and electronics in agriculture : COMPAG online ; an international journal N2 - In recent years, many efforts have been made to apply image processing techniques for plant leaf identification. However, categorizing leaf images at the cultivar/variety level, because of the very low inter-class variability, is still a challenging task. In this research, we propose an automatic discriminative method based on convolutional neural networks (CNNs) for classifying 12 different cultivars of common beans that belong to three various species. We show that employing advanced loss functions, such as Additive Angular Margin Loss and Large Margin Cosine Loss, instead of the standard softmax loss function for the classification can yield better discrimination between classes and thereby mitigate the problem of low inter-class variability. The method was evaluated by classifying species (level I), cultivars from the same species (level II), and cultivars from different species (level III), based on images from the leaf foreside and backside. The results indicate that the performance of the classification algorithm on the leaf backside image dataset is superior. The maximum mean classification accuracies of 95.86, 91.37 and 86.87% were obtained at the levels I, II and III, respectively. The proposed method outperforms the previous relevant works and provides a reliable approach for plant cultivars identification. KW - Bean KW - Plant identification KW - Digital image analysis KW - VGG16 KW - Loss KW - functions Y1 - 2021 U6 - https://doi.org/10.1016/j.compag.2020.105935 SN - 0168-1699 SN - 1872-7107 VL - 181 PB - Elsevier CY - Amsterdam [u.a.] ER - TY - JOUR A1 - Cabalar, Pedro A1 - Fandiño, Jorge A1 - Fariñas del Cerro, Luis T1 - Splitting epistemic logic programs JF - Theory and practice of logic programming / publ. for the Association for Logic Programming N2 - Epistemic logic programs constitute an extension of the stable model semantics to deal with new constructs called subjective literals. Informally speaking, a subjective literal allows checking whether some objective literal is true in all or some stable models. As it can be imagined, the associated semantics has proved to be non-trivial, since the truth of subjective literals may interfere with the set of stable models it is supposed to query. As a consequence, no clear agreement has been reached and different semantic proposals have been made in the literature. Unfortunately, comparison among these proposals has been limited to a study of their effect on individual examples, rather than identifying general properties to be checked. In this paper, we propose an extension of the well-known splitting property for logic programs to the epistemic case. We formally define when an arbitrary semantics satisfies the epistemic splitting property and examine some of the consequences that can be derived from that, including its relation to conformant planning and to epistemic constraints. Interestingly, we prove (through counterexamples) that most of the existing approaches fail to fulfill the epistemic splitting property, except the original semantics proposed by Gelfond 1991 and a recent proposal by the authors, called Founded Autoepistemic Equilibrium Logic. KW - knowledge representation and nonmonotonic reasoning KW - logic programming methodology and applications KW - theory Y1 - 2021 U6 - https://doi.org/10.1017/S1471068420000058 SN - 1471-0684 SN - 1475-3081 VL - 21 IS - 3 SP - 296 EP - 316 PB - Cambridge Univ. Press CY - Cambridge [u.a.] ER - TY - JOUR A1 - Everardo Pérez, Flavio Omar A1 - Osorio, Mauricio T1 - Towards an answer set programming methodology for constructing programs following a semi-automatic approach BT - extended and revised version JF - Electronic notes in theoretical computer science N2 - Answer Set Programming (ASP) is a successful rule-based formalism for modeling and solving knowledge-intense combinatorial (optimization) problems. Despite its success in both academic and industry, open challenges like automatic source code optimization, and software engineering remains. This is because a problem encoded into an ASP might not have the desired solving performance compared to an equivalent representation. Motivated by these two challenges, this paper has three main contributions. First, we propose a developing process towards a methodology to implement ASP programs, being faithful to existing methods. Second, we present ASP encodings that serve as the basis from the developing process. Third, we demonstrate the use of ASP to reverse the standard solving process. That is, knowing answer sets in advance, and desired strong equivalent properties, “we” exhaustively reconstruct ASP programs if they exist. This paper was originally motivated by the search of propositional formulas (if they exist) that represent the semantics of a new aggregate operator. Particularly, a parity aggregate. This aggregate comes as an improvement from the already existing parity (xor) constraints from xorro, where lacks expressiveness, even though these constraints fit perfectly for reasoning modes like sampling or model counting. To this end, this extended version covers the fundaments from parity constraints as well as the xorro system. Hence, we delve a little more in the examples and the proposed methodology over parity constraints. Finally, we discuss our results by showing the only representation available, that satisfies different properties from the classical logic xor operator, which is also consistent with the semantics of parity constraints from xorro. KW - answer set programming KW - combinatorial optimization problems KW - parity aggregate operator Y1 - 2020 U6 - https://doi.org/10.1016/j.entcs.2020.10.004 SN - 1571-0661 VL - 354 SP - 29 EP - 44 PB - Elsevier CY - Amsterdam [u.a.] ER - TY - JOUR A1 - Hollmann, Susanne A1 - Frohme, Marcus A1 - Endrullat, Christoph A1 - Kremer, Andreas A1 - D’Elia, Domenica A1 - Regierer, Babette A1 - Nechyporenko, Alina T1 - Ten simple rules on how to write a standard operating procedure JF - PLOS Computational Biology N2 - Research publications and data nowadays should be publicly available on the internet and, theoretically, usable for everyone to develop further research, products, or services. The long-term accessibility of research data is, therefore, fundamental in the economy of the research production process. However, the availability of data is not sufficient by itself, but also their quality must be verifiable. Measures to ensure reuse and reproducibility need to include the entire research life cycle, from the experimental design to the generation of data, quality control, statistical analysis, interpretation, and validation of the results. Hence, high-quality records, particularly for providing a string of documents for the verifiable origin of data, are essential elements that can act as a certificate for potential users (customers). These records also improve the traceability and transparency of data and processes, therefore, improving the reliability of results. Standards for data acquisition, analysis, and documentation have been fostered in the last decade driven by grassroot initiatives of researchers and organizations such as the Research Data Alliance (RDA). Nevertheless, what is still largely missing in the life science academic research are agreed procedures for complex routine research workflows. Here, well-crafted documentation like standard operating procedures (SOPs) offer clear direction and instructions specifically designed to avoid deviations as an absolute necessity for reproducibility. Therefore, this paper provides a standardized workflow that explains step by step how to write an SOP to be used as a starting point for appropriate research documentation. Y1 - 2020 VL - 16 IS - 9 PB - PLOS CY - San Francisco ER - TY - JOUR A1 - Stede, Manfred T1 - From connectives to coherence relations BT - a case study of German contrastrive connectives JF - Revue roumaine de linguistique : RRL = Romanian review of linguistics N2 - The notion of coherence relations is quite widely accepted in general, but concrete proposals differ considerably on the questions of how they should be motivated, which relations are to be assumed, and how they should be defined. This paper takes a "bottom-up" perspective by assessing the contribution made by linguistic signals (connectives), using insights from the relevant literature as well as verification by practical text annotation. We work primarily with the German language here and focus on the realm of contrast. Thus, we suggest a new inventory of contrastive connective functions and discuss their relationship to contrastive coherence relations that have been proposed in earlier work. KW - coherence relation KW - connective KW - contrast KW - concession KW - corpus analysis Y1 - 2020 SN - 0035-3957 VL - 65 IS - 3 SP - 213 EP - 233 PB - Ed. Academiei Române CY - Bucureşti ER - TY - JOUR A1 - Tiwari, Abhishek A1 - Prakash, Jyoti A1 - Groß, Sascha A1 - Hammer, Christian T1 - A large scale analysis of Android BT - Web hybridization JF - The journal of systems and software N2 - Many Android applications embed webpages via WebView components and execute JavaScript code within Android. Hybrid applications leverage dedicated APIs to load a resource and render it in a WebView. Furthermore, Android objects can be shared with the JavaScript world. However, bridging the interfaces of the Android and JavaScript world might also incur severe security threats: Potentially untrusted webpages and their JavaScript might interfere with the Android environment and its access to native features. No general analysis is currently available to assess the implications of such hybrid apps bridging the two worlds. To understand the semantics and effects of hybrid apps, we perform a large-scale study on the usage of the hybridization APIs in the wild. We analyze and categorize the parameters to hybridization APIs for 7,500 randomly selected and the 196 most popular applications from the Google Playstore as well as 1000 malware samples. Our results advance the general understanding of hybrid applications, as well as implications for potential program analyses, and the current security situation: We discovered thousands of flows of sensitive data from Android to JavaScript, the vast majority of which could flow to potentially untrustworthy code. Our analysis identified numerous web pages embedding vulnerabilities, which we exemplarily exploited. Additionally, we discovered a multitude of applications in which potentially untrusted JavaScript code may interfere with (trusted) Android objects, both in benign and malign applications. KW - Android hybrid apps KW - static analysis KW - information flow control Y1 - 2020 U6 - https://doi.org/10.1016/j.jss.2020.110775 SN - 0164-1212 SN - 1873-1228 VL - 170 PB - Elsevier CY - New York ER - TY - JOUR A1 - Bordihn, Henning A1 - Vaszil, György T1 - Deterministic Lindenmayer systems with dynamic control of parallelism JF - International journal of foundations of computer science N2 - M-rate 0L systems are interactionless Lindenmayer systems together with a function assigning to every string a set of multisets of productions that may be applied simultaneously to the string. Some questions that have been left open in the forerunner papers are examined, and the computational power of deterministic M-rate 0L systems is investigated, where also tabled and extended variants are taken into consideration. KW - parallel rewriting KW - Lindenmayer systems KW - restricted parallelism KW - determinism KW - developmental systems KW - formal languages Y1 - 2019 U6 - https://doi.org/10.1142/S0129054120400031 SN - 0129-0541 SN - 1793-6373 VL - 31 IS - 1 SP - 37 EP - 51 PB - World Scientific CY - Singapore ER - TY - JOUR A1 - Bordihn, Henning A1 - Mitrana, Victor T1 - On the degrees of non-regularity and non-context-freeness JF - Journal of computer and system sciences N2 - We study the derivational complexity of context-free and context-sensitive grammars by counting the maximal number of non-regular and non-context-free rules used in a derivation, respectively. The degree of non-regularity/non-context-freeness of a language is the minimum degree of non-regularity/non-context-freeness of context-free/context-sensitive grammars generating it. A language has finite degree of non-regularity iff it is regular. We give a condition for deciding whether the degree of non-regularity of a given unambiguous context-free grammar is finite. The problem becomes undecidable for arbitrary linear context-free grammars. The degree of non-regularity of unambiguous context-free grammars generating non-regular languages as well as that of grammars generating deterministic context-free languages that are not regular is of order Omega(n). Context-free non-regular languages of sublinear degree of non-regularity are presented. A language has finite degree of non-context-freeness if it is context-free. Context-sensitive grammars with a quadratic degree of non-context-freeness are more powerful than those of a linear degree. KW - context-free grammar KW - degree of non-regularity KW - context-sensitive KW - grammar KW - degree of non-context-freeness Y1 - 2020 U6 - https://doi.org/10.1016/j.jcss.2019.09.003 SN - 0022-0000 SN - 1090-2724 VL - 108 SP - 104 EP - 117 PB - Elsevier CY - San Diego, Calif. [u.a.] ER - TY - JOUR A1 - Gebser, Martin A1 - Janhunen, Tomi A1 - Rintanen, Jussi T1 - Declarative encodings of acyclicity properties JF - Journal of logic and computation N2 - Many knowledge representation tasks involve trees or similar structures as abstract datatypes. However, devising compact and efficient declarative representations of such structural properties is non-obvious and can be challenging indeed. In this article, we take a number of acyclicity properties into consideration and investigate various logic-based approaches to encode them. We use answer set programming as the primary representation language but also consider mappings to related formalisms, such as propositional logic, difference logic and linear programming. We study the compactness of encodings and the resulting computational performance on benchmarks involving acyclic or tree structures. KW - acyclicity properties KW - logic-based modeling KW - answer set programming KW - satisfiability Y1 - 2015 U6 - https://doi.org/10.1093/logcom/exv063 SN - 0955-792X SN - 1465-363X VL - 30 IS - 4 SP - 923 EP - 952 PB - Oxford Univ. Press CY - Eynsham, Oxford ER -