TY - JOUR A1 - Kiefer, Christian S. A1 - Claes, Andrea R. A1 - Nzayisenga, Jean-Claude A1 - Pietra, Stefano A1 - Stanislas, Thomas A1 - Ikeda, Yoshihisa A1 - Grebe, Markus T1 - Arabidopsis AIP1-2 restricted by WER-mediated patterning modulates planar polarity JF - Development N2 - The coordination of cell polarity within the plane of the tissue layer (planar polarity) is crucial for the development of diverse multicellular organisms. Small Rac/Rho-family GTPases and the actin cytoskeleton contribute to planar polarity formation at sites of polarity establishment in animals and plants. Yet, upstream pathways coordinating planar polarity differ strikingly between kingdoms. In the root of Arabidopsis thaliana, a concentration gradient of the phytohormone auxin coordinates polar recruitment of Rho-of-plant (ROP) to sites of polar epidermal hair initiation. However, little is known about cytoskeletal components and interactions that contribute to this planar polarity or about their relation to the patterning machinery. Here, we show that ACTIN7 (ACT7) represents a main actin isoform required for planar polarity of root hair positioning, interacting with the negative modulator ACTIN-INTERACTING PROTEIN1-2 (AIP1-2). ACT7, AIP1-2 and their genetic interaction are required for coordinated planar polarity of ROP downstream of ethylene signalling. Strikingly, AIP1-2 displays hair cell file-enriched expression, restricted by WEREWOLF (WER)-dependent patterning and modified by ethylene and auxin action. Hence, our findings reveal AIP1-2, expressed under control of the WER-dependent patterning machinery and the ethylene signalling pathway, as a modulator of actin-mediated planar polarity. KW - AIP1 KW - Actin KW - Arabidopsis KW - Patterning KW - Planar polarity Y1 - 2015 UR - http://dev.biologists.org/content/142/1/151.long U6 - https://doi.org/doi: 10.1242/dev.111013 IS - 142 SP - 151 EP - 161 ER - TY - JOUR A1 - Metzler, Ralf A1 - Bauer, Maximilian A1 - Rasmussen, Emil S. A1 - Lomholt, Michael A. T1 - Real sequence effects on the search dynamics of transcription factors on DNA JF - Scientific Reports N2 - Recent experiments show that transcription factors (TFs) indeed use the facilitated diffusion mechanism to locate their target sequences on DNA in living bacteria cells: TFs alternate between sliding motion along DNA and relocation events through the cytoplasm. From simulations and theoretical analysis we study the TF-sliding motion for a large section of the DNA-sequence of a common E. coli strain, based on the two-state TF-model with a fast-sliding search state and a recognition state enabling target detection. For the probability to detect the target before dissociating from DNA the TF-search times self-consistently depend heavily on whether or not an auxiliary operator (an accessible sequence similar to the main operator) is present in the genome section. Importantly, within our model the extent to which the interconversion rates between search and recognition states depend on the underlying nucleotide sequence is varied. A moderate dependence maximises the capability to distinguish between the main operator and similar sequences. Moreover, these auxiliary operators serve as starting points for DNA looping with the main operator, yielding a spectrum of target detection times spanning several orders of magnitude. Auxiliary operators are shown to act as funnels facilitating target detection by TFs. KW - gene regulatory networks KW - biological physics Y1 - 2015 U6 - https://doi.org/10.1038/srep10072 SN - 2045-2322 VL - 5 IS - 10072 PB - Nature Publishing Group CY - London ER - TY - THES A1 - Gaßmöller, René T1 - The interaction of subducted slabs and plume generation zones in geodynamic models Y1 - 2014 ER - TY - JOUR A1 - Haendler, Yair A1 - Kliegl, Reinhold A1 - Adani, Flavia T1 - Discourse accessibility constraints in children´s processing of object relative clauses JF - Frontiers in psychology N2 - Children’s poor performance on object relative clauses has been explained in terms of intervention locality. This approach predicts that object relatives with a full DP head and an embedded pronominal subject are easier than object relatives in which both the head noun and the embedded subject are full DPs. This prediction is shared by other accounts formulated to explain processing mechanisms. We conducted a visual-world study designed to test the off-line comprehension and on-line processing of object relatives in German-speaking 5-year-olds. Children were tested on three types of object relatives, all having a full DP head noun and differing with respect to the type of nominal phrase that appeared in the embedded subject position: another full DP, a 1st- or a 3rd-person pronoun. Grammatical skills and memory capacity were also assessed in order to see whether and how they affect children’s performance. Most accurately processed were object relatives with 1st-person pronoun, independently of children’s language and memory skills. Performance on object relatives with two full DPs was overall more accurate than on object relatives with 3rd-person pronoun. In the former condition, children with stronger grammatical skills accurately processed the structure and their memory abilities determined how fast they were; in the latter condition, children only processed accurately the structure if they were strong both in their grammatical skills and in their memory capacity. The results are discussed in the light of accounts that predict different pronoun effects like the ones we find, which depend on the referential properties of the pronouns. We then discuss which role language and memory abilities might have in processing object relatives with various embedded nominal phrases. KW - child language KW - relative clauses KW - discourse KW - pronouns KW - intervention locality KW - visual-world paradigm Y1 - 2015 U6 - https://doi.org/10.3389/fpsyg.2015.00860 SN - 1664-1078 VL - 6 IS - 860 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Häussler, Jana A1 - Bader, Markus T1 - An interference account of the missing-VP effect JF - Frontiers in psychology N2 - Sentences with doubly center-embedded relative clauses in which a verb phrase (VP) is missing are sometimes perceived as grammatical, thus giving rise to an illusion of grammaticality. In this paper, we provide a new account of why missing-VP sentences, which are both complex and ungrammatical, lead to an illusion of grammaticality, the so-called missing-VP effect. We propose that the missing-VP effect in particular, and processing difficulties with multiply center-embedded clauses more generally, are best understood as resulting from interference during cue-based retrieval. When processing a sentence with double center-embedding, a retrieval error due to interference can cause the verb of an embedded clause to be erroneously attached into a higher clause. This can lead to an illusion of grammaticality in the case of missing-VP sentences and to processing complexity in the case of complete sentences with double center-embedding. Evidence for an interference account of the missing-VP effect comes from experiments that have investigated the missing-VP effect in German using a speeded grammaticality judgments procedure. We review this evidence and then present two new experiments that show that the missing-VP effect can be found in German also with less restricting procedures. One experiment was a questionnaire study which required grammaticality judgments from participants without imposing any time constraints. The second experiment used a self-paced reading procedure and did not require any judgments. Both experiments confirm the prior findings of missing-VP effects in German and also show that the missing-VP effect is subject to a primacy effect as known from the memory literature. Based on this evidence, we argue that an account of missing-VP effects in terms of interference during cue-based retrieval is superior to accounts in terms of limited memory resources or in terms of experience with embedded structures. KW - sentence parsing KW - center embedding KW - grammatical illusion KW - missing-VP effect KW - cue-based retrieval KW - interference KW - German Y1 - 2015 U6 - https://doi.org/10.3389/fpsyg.2015.00766 SN - 1664-1078 VL - 6 IS - 766 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Felser, Claudia A1 - Patterson, Clare A1 - Cunnings, Ian T1 - Structural constraints on pronoun binding and coreference: Evidence from eye movements during reading JF - Frontiers in psychology N2 - A number of recent studies have investigated how syntactic and non-syntactic constraints combine to cue memory retrieval during anaphora resolution. In this paper we investigate how syntactic constraints and gender congruence interact to guide memory retrieval during the resolution of subject pronouns. Subject pronouns are always technically ambiguous, and the application of syntactic constraints on their interpretation depends on properties of the antecedent that is to be retrieved. While pronouns can freely corefer with non-quantified referential antecedents, linking a pronoun to a quantified antecedent is only possible in certain syntactic configurations via variable binding. We report the results from a judgment task and three online reading comprehension experiments investigating pronoun resolution with quantified and non-quantified antecedents. Results from both the judgment task and participants' eye movements during reading indicate that comprehenders freely allow pronouns to corefer with non-quantified antecedents, but that retrieval of quantified antecedents is restricted to specific syntactic environments. We interpret our findings as indicating that syntactic constraints constitute highly weighted cues to memory retrieval during anaphora resolution. KW - pronoun resolution KW - memory retrieval KW - quantification KW - eye movements KW - reading KW - English Y1 - 2015 U6 - https://doi.org/10.3389/fpsyg.2015.00840 SN - 1664-1078 VL - 6 IS - 840 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Metzler, Ralf A1 - Cherstvy, Andrey G. A1 - Chechkin, Aleksei V. A1 - Bodrova, Anna S. T1 - Ultraslow scaled Brownian motion JF - New journal of physics : the open-access journal for physics N2 - We define and study in detail utraslow scaled Brownian motion (USBM) characterized by a time dependent diffusion coefficient of the form . For unconfined motion the mean squared displacement (MSD) of USBM exhibits an ultraslow, logarithmic growth as function of time, in contrast to the conventional scaled Brownian motion. In a harmonic potential the MSD of USBM does not saturate but asymptotically decays inverse-proportionally to time, reflecting the highly non-stationary character of the process. We show that the process is weakly non-ergodic in the sense that the time averaged MSD does not converge to the regular MSD even at long times, and for unconfined motion combines a linear lag time dependence with a logarithmic term. The weakly non-ergodic behaviour is quantified in terms of the ergodicity breaking parameter. The USBM process is also shown to be ageing: observables of the system depend on the time gap between initiation of the test particle and start of the measurement of its motion. Our analytical results are shown to agree excellently with extensive computer simulations. KW - anomalous diffusion KW - stochastic processes KW - ageing Y1 - 2015 U6 - https://doi.org/10.1088/1367-2630/17/6/063038 SN - 1367-2630 VL - 17 IS - 063038 PB - Dt. Physikalische Ges., IOP CY - Bad Honnef, London ER - TY - THES A1 - Müller, Eva Nora T1 - The ecohydrological transfers, interactions and degradation arising from high-intensity storm events Y1 - 2015 ER - TY - THES A1 - Pinchasik, Bat-El Shani T1 - Manipulaton of Microbubbles Inspired by Bubble Use in Nature KW - fff Y1 - 2015 ER - TY - THES A1 - Zhou, Xu T1 - Atmospheric interactions with land surface in the arctic based on regional climate model solutions Y1 - 2014 ER - TY - THES A1 - Hoffmann Robbiani, Sandra T1 - But 7 is yellower than Q, isn't it? BT - The appearance and representation of typographic synaesthesia Y1 - 2015 SN - 978-3-946069-01-0 PB - Hoffmann CY - Darmstadt ER - TY - THES A1 - Prill, Sebastian T1 - Real-Time in vitro toxicity monotoring in a microfluidic bioreactor for drug and chemical safety assessment Y1 - 2015 ER - TY - THES A1 - Kamprath, Martin T1 - A microfoundations perspectives on fresight and business models BT - Competence development and business model design in times of digital industry transformation Y1 - 2014 ER - TY - THES A1 - Kocyan, Alexander T1 - Evolution within the speciose plant group of asparagales BT - insights from molecular and morphological data Y1 - 2014 ER - TY - THES A1 - Gericke, Lutz T1 - Tele-Board - Supporting and analyzing creative collaboration in synchronous and asynchronous scenario Y1 - 2014 ER - TY - JOUR A1 - Lamprecht, Anna-Lena A1 - Margaria, Tiziana ED - Lamprecht, Anna-Lena ED - Margaria, Tiziana T1 - Scientific workflows and XMDD JF - Process design for natural scientists Y1 - 2015 SN - 978-3-662-45006-2 SP - 1 EP - 13 PB - Springer CY - Berlin ER - TY - JOUR A1 - Blaese, Leif T1 - Data mining for unidentified protein squences JF - Process design for natural scientists: an agile model-driven approach N2 - Through the use of next generation sequencing (NGS) technology, a lot of newly sequenced organisms are now available. Annotating those genes is one of the most challenging tasks in sequence biology. Here, we present an automated workflow to find homologue proteins, annotate sequences according to function and create a three-dimensional model. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 73 EP - 87 PB - Springer CY - Berlin ER - TY - JOUR A1 - Schütt, Christine T1 - Identification of differentially expressed genes JF - Process design for natural scientists: an agile model-driven approach N2 - With the jABC it is possible to realize workflows for numerous questions in different fields. The goal of this project was to create a workflow for the identification of differentially expressed genes. This is of special interest in biology, for it gives the opportunity to get a better insight in cellular changes due to exogenous stress, diseases and so on. With the knowledge that can be derived from the differentially expressed genes in diseased tissues, it becomes possible to find new targets for treatment. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 127 EP - 139 PB - Springer CY - Berlin ER - TY - JOUR A1 - Kuntzsch, Christian T1 - Visualization of data transfer paths JF - Process design for natural scientists: an agile model-driven approach N2 - A workflow for visualizing server connections using the Google Maps API was built in the jABC. It makes use of three basic services: An XML-based IP address geolocation web service, a command line tool and the Static Maps API. The result of the workflow is an URL leading to an image file of a map, showing server connections between a client and a target host. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 140 EP - 148 PB - Springer CY - Berlin ER - TY - JOUR A1 - Teske, Daniel T1 - Geocoder accuracy ranking JF - Process design for natural scientists: an agile model-driven approach N2 - Finding an address on a map is sometimes tricky: the chosen map application may be unfamiliar with the enclosed region. There are several geocoders on the market, they have different databases and algorithms to compute the query. Consequently, the geocoding results differ in their quality. Fortunately the geocoders provide a rich set of metadata. The workflow described in this paper compares this metadata with the aim to find out which geocoder is offering the best-fitting coordinate for a given address. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 161 EP - 174 PB - Springer CY - Berlin ER - TY - JOUR A1 - Schulze, Gunnar T1 - Workflow for rapid metagenome analysis JF - Process design for natural scientists: an agile model-driven approach N2 - Analyses of metagenomes in life sciences present new opportunities as well as challenges to the scientific community and call for advanced computational methods and workflows. The large amount of data collected from samples via next-generation sequencing (NGS) technologies render manual approaches to sequence comparison and annotation unsuitable. Rather, fast and efficient computational pipelines are needed to provide comprehensive statistics and summaries and enable the researcher to choose appropriate tools for more specific analyses. The workflow presented here builds upon previous pipelines designed for automated clustering and annotation of raw sequence reads obtained from next-generation sequencing technologies such as 454 and Illumina. Employing specialized algorithms, the sequence reads are processed at three different levels. First, raw reads are clustered at high similarity cutoff to yield clusters which can be exported as multifasta files for further analyses. Independently, open reading frames (ORFs) are predicted from raw reads and clustered at two strictness levels to yield sets of non-redundant sequences and ORF families. Furthermore, single ORFs are annotated by performing searches against the Pfam database Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 88 EP - 100 PB - Springer CY - Berlin ER - TY - THES A1 - Stutz, Franziska T1 - Reading motivation, reading amount, and reading comprehension in the early elementary years Y1 - 2014 ER - TY - THES A1 - Pagel, Jörn T1 - Statistical process-based models for the understanding and prediction of range dynamics Y1 - 2014 ER - TY - BOOK ED - Lambrecht, Anna-Lena ED - Margaria, Tizian T1 - Process design for natural scientists BT - an agile model-driven approach T3 - Communications in computer and information science ; 500 N2 - This book presents an agile and model-driven approach to manage scientific workflows. The approach is based on the Extreme Model Driven Design (XMDD) paradigm and aims at simplifying and automating the complex data analysis processes carried out by scientists in their day-to-day work. Besides documenting the impact the workflow modeling might have on the work of natural scientists, this book serves three major purposes: 1. It acts as a primer for practitioners who are interested to learn how to think in terms of services and workflows when facing domain-specific scientific processes. 2. It provides interesting material for readers already familiar with this kind of tools, because it introduces systematically both the technologies used in each case study and the basic concepts behind them. 3. As the addressed thematic field becomes increasingly relevant for lectures in both computer science and experimental sciences, it also provides helpful material for teachers that plan similar courses. Y1 - 2014 SN - 978-3-662-45005-5 PB - Springer CY - Wiesbaden ER - TY - JOUR A1 - Sens, Henriette T1 - Web-Based map generalization tools put to the test: a jABC workflow JF - Process Design for Natural Scientists: an agile model-driven approach N2 - Geometric generalization is a fundamental concept in the digital mapping process. An increasing amount of spatial data is provided on the web as well as a range of tools to process it. This jABC workflow is used for the automatic testing of web-based generalization services like mapshaper.org by executing its functionality, overlaying both datasets before and after the transformation and displaying them visually in a .tif file. Mostly Web Services and command line tools are used to build an environment where ESRI shapefiles can be uploaded, processed through a chosen generalization service and finally visualized in Irfanview. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 175 EP - 185 PB - Springer CY - Berlin ER - TY - JOUR A1 - Noack, Franziska T1 - CREADED: Colored-Relief application for digital elevation data JF - Process design for natural scientists: an agile model-driven approach N2 - In the geoinformatics field, remote sensing data is often used for analyzing the characteristics of the current investigation area. This includes DEMs, which are simple raster grids containing grey scales representing the respective elevation values. The project CREADED that is presented in this paper aims at making these monochrome raster images more significant and more intuitively interpretable. For this purpose, an executable interactive model for creating a colored and relief-shaded Digital Elevation Model (DEM) has been designed using the jABC framework. The process is based on standard jABC-SIBs and SIBs that provide specific GIS functions, which are available as Web services, command line tools and scripts. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 186 EP - 199 PB - Springer CY - Berlin ER - TY - JOUR A1 - Respondek, Tobias T1 - A workflow for computing potential areas for wind turbines JF - Process design for natural scientists: an agile model-driven approach N2 - This paper describes the implementation of a workflow model for service-oriented computing of potential areas for wind turbines in jABC. By implementing a re-executable model the manual effort of a multi-criteria site analysis can be reduced. The aim is to determine the shift of typical geoprocessing tools of geographic information systems (GIS) from the desktop to the web. The analysis is based on a vector data set and mainly uses web services of the “Center for Spatial Information Science and Systems” (CSISS). This paper discusses effort, benefits and problems associated with the use of the web services. Y1 - 2014 SN - 978-3-662-45005-5 IS - 500 SP - 200 EP - 215 PB - Springer CY - Berlin ER - TY - JOUR A1 - Scheele, Lasse T1 - Location analysis for placing artificial reefs JF - Process design for natural scientists: an agile model-driven approach N2 - Location analyses are among the most common tasks while working with spatial data and geographic information systems. Automating the most frequently used procedures is therefore an important aspect of improving their usability. In this context, this project aims to design and implement a workflow, providing some basic tools for a location analysis. For the implementation with jABC, the workflow was applied to the problem of finding a suitable location for placing an artificial reef. For this analysis three parameters (bathymetry, slope and grain size of the ground material) were taken into account, processed, and visualized with the The Generic Mapping Tools (GMT), which were integrated into the workflow as jETI-SIBs. The implemented workflow thereby showed that the approach to combine jABC with GMT resulted in an user-centric yet user-friendly tool with high-quality cartographic outputs. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 216 EP - 228 PB - Springer CY - Berlin ER - TY - JOUR A1 - Kind, Josephine T1 - Creation of topographic maps JF - Process design for natural scientists: an agile model-driven approach N2 - Location analyses are among the most common tasks while working with spatial data and geographic information systems. Automating the most frequently used procedures is therefore an important aspect of improving their usability. In this context, this project aims to design and implement a workflow, providing some basic tools for a location analysis. For the implementation with jABC, the workflow was applied to the problem of finding a suitable location for placing an artificial reef. For this analysis three parameters (bathymetry, slope and grain size of the ground material) were taken into account, processed, and visualized with the The Generic Mapping Tools (GMT), which were integrated into the workflow as jETI-SIBs. The implemented workflow thereby showed that the approach to combine jABC with GMT resulted in an user-centric yet user-friendly tool with high-quality cartographic outputs. Y1 - 2014 SN - 978-3-662-45005-5 IS - 500 SP - 229 EP - 238 PB - Springer CY - Berlin ER - TY - JOUR A1 - Holler, Robin T1 - GraffDok - a graffiti documentation application JF - Process design for natural scientists: an agile model-driven approach N2 - GraffDok is an application helping to maintain an overview over sprayed images somewhere in a city. At the time of writing it aims at vandalism rather than at beautiful photographic graffiti in an underpass. Looking at hundreds of tags and scribbles on monuments, house walls, etc. it would be interesting to not only record them in writing but even make them accessible electronically, including images. GraffDok’s workflow is simple and only requires an EXIF-GPS-tagged photograph of a graffito. It automatically determines its location by using reverse geocoding with the given GPS-coordinates and the Gisgraphy WebService. While asking the user for some more meta data, GraffDok analyses the image in parallel with this and tries to detect fore- and background – before extracting the drawing lines and make them stand alone. The command line based tool ImageMagick is used here as well as for accessing EXIF data. Any meta data is written to csv-files, which will stay easily accessible and can be integrated in TeX-files as well. The latter ones are converted to PDF at the end of the workflow, containing a table about all graffiti and a summary for each – including the generated characteristic graffiti pattern image. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 239 EP - 251 PB - Springer CY - Berlin ER - TY - BOOK A1 - Thompson, Sandra A. A1 - Fox, Barbara A. A1 - Couper-Kuhlen, Elizabeth T1 - Grammar in everyday talk BT - building responsive actions T3 - Studies in interactional sociolinguistics ; 31 N2 - This book surveys how English speakers use grammar to formulate responses in ordinary conversation. The authors show that speakers build their responses in a variety of ways: the responses can be longer or shorter, repetitive or not, and can be uttered with different intonational 'melodies'"-- "Drawing on everyday telephone and video interactions, this book surveys how English speakers use grammar to formulate responses in ordinary conversation. The authors show that speakers build their responses in a variety of ways: the responses can be longer or shorter, repetitive or not, and can be uttered with different intonational 'melodies'. Focusing on four sequence types: responses to questions ('What time are we leaving?' - 'Seven'), responses to informings ('The May Company are sure having a big sale' - 'Are they?'), responses to assessments ('Track walking is so boring. Even with headphones' - 'It is'), and responses to requests ('Please don't tell Adeline' - 'Oh no I won't say anything'), they argue that an interactional approach holds the key to explaining why some types of utterances in English conversation seem to have something 'missing' and others seem overly wordy. Y1 - 2015 SN - 978-1-107-03102-9 PB - Cambridge Univ. Press CY - Cambridge ER - TY - JOUR A1 - Jäger, Lena Ann A1 - Engelmann, Felix A1 - Vasishth, Shravan T1 - Retrieval interference in reflexive processing BT - Experimental evidence from Mandarin, and computational modeling JF - Frontiers in psychology N2 - We conducted two eye-tracking experiments investigating the processing of the Mandarin reflexive ziji in order to tease apart structurally constrained accounts from standard cue-based accounts of memory retrieval. In both experiments, we tested whether structurally inaccessible distractors that fulfill the animacy requirement of ziji influence processing times at the reflexive. In Experiment 1, we manipulated animacy of the antecedent and a structurally inaccessible distractor intervening between the antecedent and the reflexive. In conditions where the accessible antecedent mismatched the animacy cue, we found inhibitory interference whereas in antecedent-match conditions, no effect of the distractor was observed. In Experiment 2, we tested only antecedent-match configurations and manipulated locality of the reflexive-antecedent binding (Mandarin allows non-local binding). Participants were asked to hold three distractors (animate vs. inanimate nouns) in memory while reading the target sentence. We found slower reading times when animate distractors were held in memory (inhibitory interference). Moreover, we replicated the locality effect reported in previous studies. These results are incompatible with structure-based accounts. However, the cue-based ACT-R model of Lewis and Vasishth (2005) cannot explain the observed pattern either. We therefore extend the original ACT-R model and show how this model not only explains the data presented in this article, but is also able to account for previously unexplained patterns in the literature on reflexive processing. KW - Chinese reflexives KW - ACT-R KW - eye-tracking KW - interference KW - cue-based retrieval KW - computational modeling KW - ziji KW - content-addressable memory Y1 - 2015 U6 - https://doi.org/10.3389/fpsyg.2015.00617 SN - 1664-1078 VL - 6 IS - 617 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Jäger, Lena Ann A1 - Benz, Lena A1 - Roeser, Jens A1 - Dillon, Brian W. A1 - Vasishth, Shravan T1 - Teasing apart retrieval and encoding interference in the processing of anaphors JF - Frontiers in psychology N2 - Two classes of account have been proposed to explain the memory processes subserving the processing of reflexive-antecedent dependencies. Structure-based accounts assume that the retrieval of the antecedent is guided by syntactic tree-configurational information without considering other kinds of information such as gender marking in the case of English reflexives. By contrast, unconstrained cue-based retrieval assumes that all available information is used for retrieving the antecedent. Similarity-based interference effects from structurally illicit distractors which match a non-structural retrieval cue have been interpreted as evidence favoring the unconstrained cue-based retrieval account since cue-based retrieval interference from structurally illicit distractors is incompatible with the structure-based account. However, it has been argued that the observed effects do not necessarily reflect interference occurring at the moment of retrieval but might equally well be accounted for by interference occurring already at the stage of encoding or maintaining the antecedent in memory, in which case they cannot be taken as evidence against the structure-based account. We present three experiments (self-paced reading and eye-tracking) on German reflexives and Swedish reflexive and pronominal possessives in which we pit the predictions of encoding interference and cue-based retrieval interference against each other. We could not find any indication that encoding interference affects the processing ease of the reflexive-antecedent dependency formation. Thus, there is no evidence that encoding interference might be the explanation for the interference effects observed in previous work. We therefore conclude that invoking encoding interference may not be a plausible way to reconcile interference effects with a structure-based account of reflexive processing. KW - anaphors KW - reflexives KW - possessives KW - eye-tracking KW - German KW - Swedish KW - working-memory KW - interference Y1 - 2015 U6 - https://doi.org/10.3389/fpsyg.2015.00506 SN - 1664-1078 VL - 6 IS - 506 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Goychuk, Igor A1 - Goychuk, Andriy T1 - Stochastic Wilson BT - Cowan models of neuronal network dynamics with memory and delay JF - New journal of physics N2 - We consider a simple Markovian class of the stochastic Wilson–Cowan type models of neuronal network dynamics, which incorporates stochastic delay caused by the existence of a refractory period of neurons. From the point of view of the dynamics of the individual elements, we are dealing with a network of non-Markovian stochastic two-state oscillators with memory, which are coupled globally in a mean-field fashion. This interrelation of a higher-dimensional Markovian and lower-dimensional non-Markovian dynamics is discussed in its relevance to the general problem of the network dynamics of complex elements possessing memory. The simplest model of this class is provided by a three-state Markovian neuron with one refractory state, which causes firing delay with an exponentially decaying memory within the two-state reduced model. This basic model is used to study critical avalanche dynamics (the noise sustained criticality) in a balanced feedforward network consisting of the excitatory and inhibitory neurons. Such avalanches emerge due to the network size dependent noise (mesoscopic noise). Numerical simulations reveal an intermediate power law in the distribution of avalanche sizes with the critical exponent around −1.16. We show that this power law is robust upon a variation of the refractory time over several orders of magnitude. However, the avalanche time distribution is biexponential. It does not reflect any genuine power law dependence. KW - neuronal networks KW - stochastic models KW - memory and delay KW - critical avalanche dynamics Y1 - 2015 U6 - https://doi.org/10.1088/1367-2630/17/4/045029 SN - 1367-2630 VL - 17 IS - 4 PB - Deutsche Physikalische Gesellschaft, Institute of Physics CY - Bad Honnef, London ER - TY - JOUR A1 - Wiebking, Christine A1 - Northoff, Georg T1 - Neural activity during interoceptive awareness and its associations with alexithymia BT - An fMRI study in major depressive disorder and non-psychiatric controls JF - Frontiers in psychology N2 - Objective: Alexithymia relates to difficulties recognizing and describing emotions. It has been linked to subjectively increased interoceptive awareness (IA) and to psychiatric illnesses such as major depressive disorder (MDD) and somatization. MDD in turn is characterized by aberrant emotion processing and IA on the subjective as well as on the neural level. However, a link between neural activity in response to IA and alexithymic traits in health and depression remains unclear. Methods: A well-established fMRI task was used to investigate neural activity during IA (heartbeat counting) and exteroceptive awareness (tone counting) in non-psychiatric controls (NC) and MDD. Firstly, comparing MDD and NC, a linear relationship between IA-related activity and scores of the Toronto Alexithymia Scale (TAS) was investigated through whole-brain regression. Secondly, NC were divided by median-split of TAS scores into groups showing low (NC-low) or high (NC-high) alexithymia. MDD and NC-high showed equally high TAS scores. Subsequently, IA-related neural activity was compared on a whole-brain level between the three independent samples (MDD, NC-low, NC-high). Results: Whole-brain regressions between MDD and NC revealed neural differences during IA as a function of TAS-DD (subscale difficulty describing feelings) in the supragenual anterior cingulate cortex (sACC; BA 24/32), which were due to negative associations between TAS-DD and IA-related activity in NC. Contrasting NC subgroups after median-split on a whole-brain level, high TAS scores were associated with decreased neural activity during IA in the sACC and increased insula activity. Though having equally high alexithymia scores, NC-high showed increased insula activity during IA compared to MDD, whilst both groups showed decreased activity in the sACC. Conclusions: Within the context of decreased sACC activity during IA in alexithymia (NC-high and MDD), increased insula activity might mirror a compensatory mechanism in NC-high, which is disrupted in MDD. KW - major depressive disorder KW - alexithymia KW - interoceptive awareness KW - insula KW - sACC KW - fMRI KW - neuroimaging Y1 - 2015 U6 - https://doi.org/10.3389/fpsyg.2015.00589 SN - 1664-1078 VL - 6 IS - 589 PB - Frontiers Research Foundation ER - TY - THES A1 - Sprenger, Heike T1 - Characterization of drought tolerance in potato cultivars for identification of molecular markers Y1 - 2014 ER - TY - THES A1 - Ippen, Christian Justus T1 - Indium phosphide and zinc selenide quantum dots for light-emitting devices BT - relationships between surface structure and device performance Y1 - 2014 ER - TY - THES A1 - Geckin, Vasfiye T1 - The interpretation of logical connections by monolingual and bilingual children Y1 - 2015 ER - TY - THES A1 - Omidbakhshfard, Mohammad Amin T1 - Functional analysis of the role of GRF9 in leaf development and establishment of Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) in Arabidopsis thaliana Y1 - 2014 ER - TY - THES A1 - Omranian, Nooshin T1 - Inferring gene regulatory networks and cellular phases from time-resolved transcriptomics data Y1 - 2014 ER - TY - JOUR A1 - Ghosh, Surya K. A1 - Cherstvy, Andrey G. A1 - Metzler, Ralf ED - Metzler, Ralf T1 - Non-universal tracer diffusion in crowded media of non-inert obstacles JF - Physical Chemistry Chemical Physics N2 - We study the diffusion of a tracer particle, which moves in continuum space between a lattice of excluded volume, immobile non-inert obstacles. In particular, we analyse how the strength of the tracer–obstacle interactions and the volume occupancy of the crowders alter the diffusive motion of the tracer. From the details of partitioning of the tracer diffusion modes between trapping states when bound to obstacles and bulk diffusion, we examine the degree of localisation of the tracer in the lattice of crowders. We study the properties of the tracer diffusion in terms of the ensemble and time averaged mean squared displacements, the trapping time distributions, the amplitude variation of the time averaged mean squared displacements, and the non-Gaussianity parameter of the diffusing tracer. We conclude that tracer–obstacle adsorption and binding triggers a transient anomalous diffusion. From a very narrow spread of recorded individual time averaged trajectories we exclude continuous type random walk processes as the underlying physical model of the tracer diffusion in our system. For moderate tracer–crowder attraction the motion is found to be fully ergodic, while at stronger attraction strength a transient disparity between ensemble and time averaged mean squared displacements occurs. We also put our results into perspective with findings from experimental single-particle tracking and simulations of the diffusion of tagged tracers in dense crowded suspensions. Our results have implications for the diffusion, transport, and spreading of chemical components in highly crowded environments inside living cells and other structured liquids. KW - fluorescence correlation spectroscopy KW - single-particle tracking KW - anomalous diffusion KW - living cells KW - physiological consequences KW - langevin equation KW - infection pathway KW - excluded volume KW - brownian-motion KW - random-walks Y1 - 2014 SN - 1463-9076 VL - 3 IS - 17 SP - 1847 EP - 1858 PB - The Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Heidemann, Birte T1 - Post-agreement belfast : labour, work and the new subalterns in daragh carville's play this other city JF - Reworking postcolonialism : globalization, labour and rights Y1 - 2015 SN - 978-1-137-43592-7 SP - 119 EP - 133 PB - Palgrave Macmillan CY - New York ER - TY - BOOK ED - Malreddy, Pavan Kumar ED - Heidemann, Birte ED - Larsen, Ole Birk ED - Wilson, Janet T1 - Reworking postcolonialism BT - globalization, labour and rights N2 - An interdisciplinary collection of essays, Reworking Postcolonialism explores questions of work, precarity, migration, minority and indigenous rights in relation to contemporary globalization. It focuses on the impact of global market forces on the formation of new subject positions among urban dwellers, exiles, and other disenfranchised communities. Bringing together political, economic and literary approaches to texts and events from across the postcolonial world, the essays collected here investigate the transformative effects of the global dissemination of capital and goods and the movements of people. They call for a revision of existing discourses on rights, entitlements and citizenship. Y1 - 2015 SN - 978-1-137-43592-7 PB - Palgrave Macmillan CY - New York ER - TY - THES A1 - Jacobs, Simone T1 - Biological mechanisms of the association between proportions of fatty acids in erythrocyte membranes and type 2 diabetes risk in the EPIC-Potsdam-Study Y1 - 2015 ER - TY - JOUR A1 - Shin, Jaeoh A1 - Cherstvy, Andrey G. A1 - Metzler, Ralf ED - Metzler, Ralf T1 - Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size JF - Soft Matter N2 - The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible polymer chains in the presence of different degrees of crowding. From the analysis of the looping–unlooping rates and the looping probabilities of the chain ends we show that the presence of small crowders typically slows down the chain dynamics but larger crowders may in fact facilitate the looping. We rationalise these non-trivial and often counterintuitive effects of the crowder size on the looping kinetics in terms of an effective solution viscosity and standard excluded volume. It is shown that for small crowders the effect of an increased viscosity dominates, while for big crowders we argue that confinement effects (caging) prevail. The tradeoff between both trends can thus result in the impediment or facilitation of polymer looping, depending on the crowder size. We also examine how the crowding volume fraction, chain length, and the attraction strength of the contact groups of the polymer chain affect the looping kinetics and hairpin formation dynamics. Our results are relevant for DNA looping in the absence and presence of protein mediation, DNA hairpin formation, RNA folding, and the folding of polypeptide chains under biologically relevant high-crowding conditions. KW - gene-regulation kinetics KW - physiological consequences KW - spatial-organization KW - anomalous diffusion KW - folding kinetics KW - living cells KW - dna coiling KW - in-vitro KW - dynamics KW - mixtures Y1 - 2014 SN - 1744-683X SP - 472 EP - 488 PB - The Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Roder, Phillip A1 - Hille, Carsten ED - Hille, Carsten T1 - ANG-2 for quantitative Na+ determination in living cells by time-resolved fluorescence microscopy JF - Photochemical & Photobiological Sciences N2 - Sodium ions (Na+) play an important role in a plethora of cellular processes, which are complex and partly still unexplored. For the investigation of these processes and quantification of intracellular Na+ concentrations ([Na+]i), two-photon coupled fluorescence lifetime imaging microscopy (2P-FLIM) was performed in the salivary glands of the cockroach Periplaneta americana. For this, the novel Na+-sensitive fluorescent dye Asante NaTRIUM Green-2 (ANG-2) was evaluated, both in vitro and in situ. In this context, absorption coefficients, fluorescence quantum yields and 2P action cross-sections were determined for the first time. ANG-2 was 2P-excitable over a broad spectral range and displayed fluorescence in the visible spectral range. Although the fluorescence decay behaviour of ANG-2 was triexponential in vitro, its analysis indicates a Na+-sensitivity appropriate for recordings in living cells. The Na+-sensitivity was reduced in situ, but the biexponential fluorescence decay behaviour could be successfully analysed in terms of quantitative [Na+]i recordings. Thus, physiological 2P-FLIM measurements revealed a dopamine-induced [Na+]i rise in cockroach salivary gland cells, which was dependent on a Na+-K+-2Cl− cotransporter (NKCC) activity. It was concluded that ANG-2 is a promising new sodium indicator applicable for diverse biological systems. KW - cockroach salivary-glands KW - intracellular na+ KW - sodium green KW - periplaneta-americana KW - ventricular myocytes KW - lifetime microscopy KW - cytosolic sodium KW - acinar-cells KW - hela-cells KW - rat Y1 - 2014 SN - 1474-905X VL - 12 IS - 13 SP - 1699 EP - 1710 PB - The Royal Society of Chemistry CY - Cambridge ER - TY - BOOK A1 - Plattner, Hasso A1 - Leukert, Bernd T1 - The in-memory revolution BT - how sap hana enables business of the future N2 - This book describes the next generation of business applications enabled by SAP's in-memory database, SAP HANA. In particular, the authors show the substantial changes introduced in S4/HANA by switching to SAP HANA. Using numerous examples and use cases from the authors' wealth of real-world experience, it illustrates the quantum leap in performance made possible by the new technology. The book is written by two of the most prominent actors in the area of business application systems: Hasso Plattner, co-founder of SAP and inaugurator of the Hasso Plattner Institute at the University of Potsdam, and Bernd Leukert, member of the Executive Board and the Global Managing Board of SAP. This clearly structured, highly illustrated book takes an exciting new technology and presents the practicality and success of first mover applications. Y1 - 2015 SN - 978-3-319-16672-8 PB - Springer CY - Cham ER - TY - JOUR A1 - Meyer, Sören A1 - Schulz, Jacqueline A1 - Jeibmann, Astrid A1 - Taleshi, Mojtaba S. A1 - Ebert, Franziska A1 - Francesconi, Kevin A1 - Schwerdtle, Tanja ED - Schwerdtle, Tanja T1 - Arsenic-containing hydrocarbons are toxic in the in vivo model Drosophila melanogaster JF - Metallomics N2 - Arsenic-containing hydrocarbons (AsHC) constitute one group of arsenolipids that have been identified in seafood. In this first in vivo toxicity study for AsHCs, we show that AsHCs exert toxic effects in Drosophila melanogaster in a concentration range similar to that of arsenite. In contrast to arsenite, however, AsHCs cause developmental toxicity in the late developmental stages of Drosophila melanogaster. This work illustrates the need for a full characterisation of the toxicity of AsHCs in experimental animals to finally assess the risk to human health related to the presence of arsenolipids in seafood. KW - arsenolipids present KW - cod-liver KW - fatty-acids KW - identification KW - rp-hplc KW - fish KW - oil Y1 - 2014 SN - 1756-5901 SP - 2010 EP - 2014 PB - The Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Schwarze, Thomas A1 - Müller, Holger A1 - Ast, Sandra A1 - Steinbrück, Dörte A1 - Eidner, Sascha A1 - Geißler, Felix A1 - Kumke, Michael Uwe A1 - Holdt, Hans-Jürgen ED - Kumke, Michael Uwe T1 - Fluorescence lifetime-based sensing of sodium by an optode JF - Chemical Communications N2 - We report a 1,2,3-triazol fluoroionophore for detecting Na+ that shows in vitro enhancement in the Na+-induced fluorescence intensity and decay time. The Na+-selective molecule 1 was incorporated into a hydrogel as a part of a fiber optical sensor. This sensor allows the direct determination of Na+ in the range of 1–10 mM by measuring reversible fluorescence decay time changes. KW - ion optodes KW - sensors KW - indicators KW - chromoionophore KW - ionophore KW - membrane KW - switches KW - systems KW - samples KW - green Y1 - 2014 SN - 0022-4936 SN - 0009-241X SP - 14167 EP - 14170 PB - The Royal Society Chemistry CY - Cambridge ER - TY - THES A1 - Schreck, Simon Frederik T1 - Potential energy surfaces, femtosecond dynamics and nonlinear X-Ray-Matter interactions from resonant inelastic soft x-Ray scattering Y1 - 2014 ER -