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During reading, saccadic eye movements are generated to shift words into the center of the visual field for lexical processing. Recently, Krugel and Engbert (Vision Research 50:1532-1539, 2010) demonstrated that within-word fixation positions are largely shifted to the left after skipped words. However, explanations of the origin of this effect cannot be drawn from normal reading data alone. Here we show that the large effect of skipped words on the distribution of within-word fixation positions is primarily based on rather subtle differences in the low-level visual information acquired before saccades. Using arrangements of "x" letter strings, we reproduced the effect of skipped character strings in a highly controlled single-saccade task. Our results demonstrate that the effect of skipped words in reading is the signature of a general visuomotor phenomenon. Moreover, our findings extend beyond the scope of the widely accepted range-error model, which posits that within-word fixation positions in reading depend solely on the distances of target words. We expect that our results will provide critical boundary conditions for the development of visuomotor models of saccade planning during reading.
Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations
(2012)
Background: Flux balance analysis (FBA) together with its extension, dynamic FBA, have proven instrumental for analyzing the robustness and dynamics of metabolic networks by employing only the stoichiometry of the included reactions coupled with adequately chosen objective function. In addition, under the assumption of minimization of metabolic adjustment, dynamic FBA has recently been employed to analyze the transition between metabolic states.
Results: Here, we propose a suite of novel methods for analyzing the dynamics of (internally perturbed) metabolic networks and for quantifying their robustness with limited knowledge of kinetic parameters. Following the biochemically meaningful premise that metabolite concentrations exhibit smooth temporal changes, the proposed methods rely on minimizing the significant fluctuations of metabolic profiles to predict the time-resolved metabolic state, characterized by both fluxes and concentrations. By conducting a comparative analysis with a kinetic model of the Calvin-Benson cycle and a model of plant carbohydrate metabolism, we demonstrate that the principle of regulatory on/off minimization coupled with dynamic FBA can accurately predict the changes in metabolic states.
Conclusions: Our methods outperform the existing dynamic FBA-based modeling alternatives, and could help in revealing the mechanisms for maintaining robustness of dynamic processes in metabolic networks over time.
Background
High blood glucose and diabetes are amongst the conditions causing the greatest losses in years of healthy life worldwide. Therefore, numerous studies aim to identify reliable risk markers for development of impaired glucose metabolism and type 2 diabetes. However, the molecular basis of impaired glucose metabolism is so far insufficiently understood. The development of so called 'omics' approaches in the recent years promises to identify molecular markers and to further understand the molecular basis of impaired glucose metabolism and type 2 diabetes. Although univariate statistical approaches are often applied, we demonstrate here that the application of multivariate statistical approaches is highly recommended to fully capture the complexity of data gained using high-throughput methods.
Methods
We took blood plasma samples from 172 subjects who participated in the prospective Metabolic Syndrome Berlin Potsdam follow-up study (MESY-BEPO Follow-up). We analysed these samples using Gas Chromatography coupled with Mass Spectrometry (GC-MS), and measured 286 metabolites. Furthermore, fasting glucose levels were measured using standard methods at baseline, and after an average of six years. We did correlation analysis and built linear regression models as well as Random Forest regression models to identify metabolites that predict the development of fasting glucose in our cohort.
Results
We found a metabolic pattern consisting of nine metabolites that predicted fasting glucose development with an accuracy of 0.47 in tenfold cross-validation using Random Forest regression. We also showed that adding established risk markers did not improve the model accuracy. However, external validation is eventually desirable. Although not all metabolites belonging to the final pattern are identified yet, the pattern directs attention to amino acid metabolism, energy metabolism and redox homeostasis.
Conclusions
We demonstrate that metabolites identified using a high-throughput method (GC-MS) perform well in predicting the development of fasting plasma glucose over several years. Notably, not single, but a complex pattern of metabolites propels the prediction and therefore reflects the complexity of the underlying molecular mechanisms. This result could only be captured by application of multivariate statistical approaches. Therefore, we highly recommend the usage of statistical methods that seize the complexity of the information given by high-throughput methods.
Portal alumni
(2012)
Das zurückliegende Jahr stand an der Universität Potsdam auch im Zeichen des zwanzigjährigen Jubiläums der Hochschule. Am 15. Juli 1991, wurde sie gegründet und während einer Festwoche feierten Professorinnen und Professoren, Mitarbeiterinnen, Mitarbeiter und Studierende dieses Jubiläum gebührend. Seit der Gründung der größten brandenburgischen Hochschule sind wissenschaftliches Renommee, Ansehen und Attraktivität stetig gewachsen. Gerade in den letzten Jahren hat sie ihr Profil geschärft. Vor allem die Kognitions-, die Geo- und Biowissenschaften sind hier zu nennen. Aber auch die Lehrerbildung besitzt einen hohen Stellenwert. International anerkannte Forschungsbereiche, Wissenschaftspreise, eine erfolgreiche Drittmittelbilanz und nicht zuletzt die bauliche Entwicklung an allen drei Standorten sind sichtbare Indikatoren für die erfolgreiche Entwicklung, die die Universität Potsdam in den letzten zwei Jahrzehnten durchlaufen hat. Die drei ehemaligen Präsidenten sowie verschiedene andere Protagonisten werfen in dieser Ausgabe der Portal Alumni einen Blick auf unterschiedliche Aspekte der zurückliegenden Entwicklung der Universität. Vom Erfolg der Universität zeugt auch die wachsende Zahl der Absolventinnen und Absolventen, die die Universität verlassen. Portal Alumni stellt in der vorliegenden Ausgabe deshalb Absolventen und deren universitäre und berufliche Lebenswege genauer vor und lässt damit zugleich kaleidoskopartig 20 Jahre Studium an der Universität Potsdam Revue passieren.
Portal Wissen = Raum
(2012)
Mit „Portal Wissen“ laden wir Sie ein, die Forschung an der Universität Potsdam zu entdecken und in ihrer Vielfalt kennenzulernen. In der ersten Ausgabe dreht sich alles um „Räume“. Räume, in denen geforscht wird, solche, die es zu erforschen gilt, andere, die durch Wissenschaft zugänglich oder erschlossen werden, aber auch Räume, die Wissenschaft braucht, um sich entfalten zu können. Forschung vermisst Räume: „Wissenschaft wird von Menschen gemacht“, schrieb der Physiker Werner Heisenberg. Umgekehrt lässt sich sagen: Wissenschaft macht Menschen, widmet sich ihnen, beeinflusst sie. Dieser Beziehung ist „Portal Wissen“ nachgegangen. Wir haben Wissenschaftler getroffen, sie gefragt, wie aus ihren Fragen Projekte entstehen, haben sie auf dem oft verschlungenen Weg zum Ziel begleitet. Ein besonderes Augenmerk dieses Heftes gilt den „Kulturellen Begegnungsräumen“, denen ein eigener Profilbereich der Forschung an der Universität Potsdam gewidmet ist.
Forschung hat Räume: Labore, Bibliotheken, Gewächshäuser oder Archive – hier ist Wissenschaft zu Liebe Leserinnen und Leser, Hause. All diese Orte sind so einzigartig wie die Wissenschaftler, die in ihnen arbeiten, oder die Untersuchungen, die hier stattfinden. Erst die Vision davon, wie ein Problem zu lösen ist, macht aus einfachen Zimmern „Laborräume“. Wir haben ihre Türen geöffnet, um zu zeigen, was – und wer – sich dahinter befindet.
Forschung eröffnet Räume: Wenn Wissenschaft erfolgreich ist, bewegt sie uns, bringt uns voran. Auf dem Weg einer wissenschaftlichen Erkenntnis aus dem Labor in den Alltag stehen mitunter Hürden, die meist nicht auf den ersten Blick zu erkennen sind. Auf jeden Fall aber ist ihre Anwendung erster Ausgangspunkt von Wissenschaft, Antrieb und Motivation jedes Forschers. „Portal Wissen“ zeigt, welche „Praxisräume“ sich aus der Übersetzung von Forschungsresultaten ergeben. Dort, wo wir es unbedingt erwarten, und dort, wo vielleicht nicht.
Forschung erschließt Räume: Bei Expeditionen, Feldversuchen und Exkursionen wird nahezu jede Umgebung zum mobilen Labor. So eröffnet Wissenschaft Zugänge auch zu Orten, die auf vielfach andere Weise verschlossen oder unzugänglich scheinen. Wir haben uns in Forscher- Reisetaschen gemogelt, um bei Entdeckungsreisen dabei zu sein, die weit weg – vor allem nach Afrika – führen. Zugleich haben wir beobachtet, wie „Entwicklungsräume“ sich auch von Potsdam aus erschließen lassen oder zumindest ihre Vermessung in Potsdam beginnen kann.
Forschung braucht Räume: Wissenschaft hat zwei Geschlechter, endlich. Noch nie waren so viele Frauen in der Forschung tätig wie derzeit. Ein Grund zum Ausruhen ist dies gleichwohl nicht. Deutschlandweit ist aktuell nur jede fünfte Professur von einer Frau besetzt. „Portal Wissen“ schaut, welche „Entwicklungsräume“ Frauen sich in der Wissenschaft, aber auch darüber hinaus geschaffen haben. Und wo sie ihnen verwehrt werden. Wir wünschen Ihnen eine anregende Lektüre und dass auch Sie einen Raum finden, der Sie inspiriert.
Prof. Dr. Robert Seckler
Vizepräsident für Forschung und wissenschaftlichen Nachwuchs
Background: Detection of immunogenic proteins remains an important task for life sciences as it nourishes the understanding of pathogenicity, illuminates new potential vaccine candidates and broadens the spectrum of biomarkers applicable in diagnostic tools. Traditionally, immunoscreenings of expression libraries via polyclonal sera on nitrocellulose membranes or screenings of whole proteome lysates in 2-D gel electrophoresis are performed. However, these methods feature some rather inconvenient disadvantages. Screening of expression libraries to expose novel antigens from bacteria often lead to an abundance of false positive signals owing to the high cross reactivity of polyclonal antibodies towards the proteins of the expression host. A method is presented that overcomes many disadvantages of the old procedures.
Results: Four proteins that have previously been described as immunogenic have successfully been assessed immunogenic abilities with our method. One protein with no known immunogenic behaviour before suggested potential immunogenicity. We incorporated a fusion tag prior to our genes of interest and attached the expressed fusion proteins covalently on microarrays. This enhances the specific binding of the proteins compared to nitrocellulose. Thus, it helps to reduce the number of false positives significantly. It enables us to screen for immunogenic proteins in a shorter time, with more samples and statistical reliability. We validated our method by employing several known genes from Campylobacter jejuni NCTC 11168.
Conclusions: The method presented offers a new approach for screening of bacterial expression libraries to illuminate novel proteins with immunogenic features. It could provide a powerful and attractive alternative to existing methods and help to detect and identify vaccine candidates, biomarkers and potential virulence-associated factors with immunogenic behaviour furthering the knowledge of virulence and pathogenicity of studied bacteria.
The development of infrared observational facilities has revealed a number of massive stars in obscured environments throughout the Milky Way and beyond. The determination of their stellar and wind properties from infrared diagnostics is thus required to take full advantage of the wealth of observations available in the near and mid infrared. However, the task is challenging. This session addressed some of the problems encountered and showed the limitations and successes of infrared studies of massive stars.
The safe upper limit for inclusion of vitamin A in complete diets for growing dogs is uncertain, with the result that current recommendations range from 5.24 to 104.80 mu mol retinol (5000 to 100 000 IU vitamin A)/4184 kJ (1000 kcal) metabolisable energy (ME). The aim of the present study was to determine the effect of feeding four concentrations of vitamin A to puppies from weaning until 1 year of age. A total of forty-nine puppies, of two breeds, Labrador Retriever and Miniature Schnauzer, were randomly assigned to one of four treatment groups. Following weaning at 8 weeks of age, puppies were fed a complete food supplemented with retinyl acetate diluted in vegetable oil and fed at 1ml oil/100 g diet to achieve an intake of 5.24, 13.10, 78.60 and 104.80 mu mol retinol (5000, 12 500, 75 000 and 100 000 IU vitamin A)/4184 kJ (1000 kcal) ME. Fasted blood and urine samples were collected at 8, 10, 12, 14, 16, 20, 26, 36 and 52 weeks of age and analysed for markers of vitamin A metabolism and markers of safety including haematological and biochemical variables, bone-specific alkaline phosphatase, cross-linked carboxyterminal telopeptides of type I collagen and dual-energy X-ray absorptiometry. Clinical examinations were conducted every 4 weeks. Data were analysed by means of a mixed model analysis with Bonferroni corrections for multiple endpoints. There was no effect of vitamin A concentration on any of the parameters, with the exception of total serum retinyl esters, and no effect of dose on the number, type and duration of adverse events. We therefore propose that 104.80 mu mol retinol (100 000 IU vitamin A)/4184 kJ (1000 kcal) is a suitable safe upper limit for use in the formulation of diets designed for puppy growth.
We present 3D zero-beta ideal MHD simulations of the solar flare/CME event that occurred in Active Region 11060 on 2010 April 8. The initial magnetic configurations of the two simulations are stable nonlinear force-free field and unstable magnetic field models constructed by Su et al. (2011) using the flux rope insertion method. The MHD simulations confirm that the stable model relaxes to a stable equilibrium, while the unstable model erupts as a CME. Comparisons between observations and MHD simulations of the CME are also presented.
Recent PIC simulations of relativistic electron-positron (electron-ion) jets injected into a stationary medium show that particle acceleration occurs in the shocked regions. Simulations show that the Weibel instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields and for particle acceleration. These magnetic fields contribute to the electron’s transverse eflection behind the shock. The “jitter” radiation from deflected electrons in turbulent magnetic fields has properties different from synchrotron radiation calculated in a uniform magnetic field. This jitter radiation may be important for understanding the complex time evolution and/or spectral structure of gamma-ray bursts, relativistic jets in general, and supernova remnants. In order to calculate radiation from first principles and go beyond the standard synchrotron model, we have used PIC simulations. We present synthetic spectra to compare with the spectra obtained from Fermi observations.
Recent studies have claimed the existence of very massive stars (VMS) up to 300 M⊙ in the local Universe. As this finding may represent a paradigm shift for the canonical stellar upper-mass limit of 150 M⊙, it is timely to discuss the status of the data, as well as the far-reaching implications of such objects. We held a Joint Discussion at the General Assembly in Beijing to discuss (i) the determination of the current masses of the most massive stars, (ii) the formation of VMS, (iii) their mass loss, and (iv) their evolution and final fate. The prime aim was to reach broad consensus between observers and theorists on how to identify and quantify the dominant physical processes.
In the late Palaeozoic fore-arc system of north-central Chile at latitudes 31-32 degrees S (from the west to the east) three lithotectonic units are telescoped within a short distance by a Mesozoic strikeslip event (derived peak P-T conditions in brackets): (1) the basally accreted Choapa Metamorphic Complex (CMC; 350-430 degrees C, 6-9 kbar), (2) the frontally accreted Arrayan Formation (AF; 280-320 degrees C, 4-6 kbar) and (3) the retrowedge basin of the Huentelauquen Formation (HF; 280-320 degrees C, 3-4 kbar). In the CMC, Ar-Ar spot ages locally date white-mica formation at peak P-T conditions and during early exhumation at 279-242 Ma. In a local garnet mica-schist intercalation (570-585 degrees C, 11-13 kbar) Ar-Ar spot ages refer to the ascent from the subduction channel at 307-274 Ma. Portions of the CMC were isobarically heated to 510-580 degrees C at 6.6-8.5 kbar. The age of peak P-T conditions in the AF can only vaguely be approximated at >= 310 Ma by relict fission-track ages consistent with the observation that frontal accretion occurred prior to basal accretion. Zircon fission-track dating indicates cooling below similar to 280 degrees C at similar to 248 Ma in the CMC and the AF, when a regional unconformity also formed. Ar-Ar white-mica spot ages in parts of the CMC and within the entire AF and HF point to heterogeneous resetting during Mesozoic extensional and shortening events at similar to 245-240 Ma, similar to 210-200 Ma, similar to 174-159 Ma and similar to 142-127 Ma. The zircon fission-track ages are locally reset at 109-96 Ma. All resetting of Ar-Ar white-mica ages is proposed to have occurred by in situ dissolution/precipitation at low temperature in the presence of locally penetrating hydrous fluids. Hence syn-and postaccretionary events in the fore-arc system can still be distinguished and dated in spite of its complex heterogeneous postaccretional overprint.
This article investigates the nature of preposition copying and preposition pruning structures in present-day English. We begin by illustrating the two phenomena and consider how they might be accounted for in syntactic terms, and go on to explore the possibility that preposition copying and pruning arise for processing reasons. We then report on two acceptability judgement experiments examining the extent to which native speakers of English are sensitive to these types of 'error' in language comprehension. Our results indicate that preposition copying creates redundancy rather than ungrammaticality, whereas preposition pruning creates processing problems for comprehenders that may render it unacceptable in timed (but not necessarily in untimed) judgement tasks. Our findings furthermore illustrate the usefulness of combining corpus studies and experimentally elicited data for gaining a clearer picture of usage and acceptability, and the potential benefits of examining syntactic phenomena from both a theoretical and a processing perspective.
Using the eye-movement monitoring technique in two reading comprehension experiments, this study investigated the timing of constraints on wh-dependencies (so-called island constraints) in first- and second-language (L1 and L2) sentence processing. The results show that both L1 and L2 speakers of English are sensitive to extraction islands during processing, suggesting that memory storage limitations affect L1 and L2 comprehenders in essentially the same way. Furthermore, these results show that the timing of island effects in L1 compared to L2 sentence comprehension is affected differently by the type of cue (semantic fit versus filled gaps) signaling whether dependency formation is possible at a potential gap site. Even though L1 English speakers showed immediate sensitivity to filled gaps but not to lack of semantic fit, proficient German-speaking learners of English as a L2 showed the opposite sensitivity pattern. This indicates that initial wh-dependency formation in L2 processing is based on semantic feature matching rather than being structurally mediated as in L1 comprehension.
SXP 1062 is an exceptional case of a young neutron star in a wind-fed high-mass X-ray binary associated with a supernova remnant. A unique combination of measured spin period, its derivative, luminosity and young age makes this source a key probe for the physics of accretion and neutron star evolution. Theoretical models proposed to explain the properties of SXP 1062 shall be tested with new data.
We present the new multi-threaded version of the state-of-the-art answer set solver clasp. We detail its component and communication architecture and illustrate how they support the principal functionalities of clasp. Also, we provide some insights into the data representation used for different constraint types handled by clasp. All this is accompanied by an extensive experimental analysis of the major features related to multi-threading in clasp.