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Ausgehend von der typischen IT‐Infrastruktur für E‐Learning an Hochschulen auf der einen Seite sowie vom bisherigen Stand der Forschung zu Personal Learning Environments (PLEs) auf der anderen Seite zeigt dieser Beitrag auf, wie bestehende Werkzeuge bzw. Dienste zusammengeführt und für die Anforderungen der modernen, rechnergestützten Präsenzlehre aufbereitet werden können. Für diesen interdisziplinären Entwicklungsprozess bieten sowohl klassische Softwareentwicklungsverfahren als auch bestehende PLE‐Modelle wenig Hilfestellung an. Der Beitrag beschreibt die in einem campusweiten Projekt an der Universität Potsdam verfolgten Ansätze und die damit erzielten Ergebnisse. Dafür werden zunächst typische Lehr‐/Lern‐bzw. Kommunikations‐Szenarien identifiziert, aus denen Anforderungen an eine unterstützende Plattform abgeleitet werden. Dies führt zu einer umfassenden Sammlung zu berücksichtigender Dienste und deren Funktionen, die gemäß den Spezifika ihrer Nutzung in ein Gesamtsystem zu integrieren sind. Auf dieser Basis werden grundsätzliche Integrationsansätze und technische Details dieses Mash‐Ups in einer Gesamtschau aller relevanten Dienste betrachtet und in eine integrierende Systemarchitektur überführt. Deren konkrete Realisierung mit Hilfe der Portal‐Technologie Liferay wird dargestellt, wobei die eingangs definierten Szenarien aufgegriffen und exemplarisch vorgestellt werden. Ergänzende Anpassungen im Sinne einer personalisierbaren bzw. adaptiven Lern‐(und Arbeits‐)Umgebung werden ebenfalls unterstützt und kurz aufgezeigt.
Dispersion engineered silicon nitride waveguides by geometrical and refractive-index optimization
(2014)
Dispersion engineering in silicon nitride (SiXNY) waveguides is investigated through the optimization of the waveguide transversal dimensions and refractive indices in a multicladding arrangement. Ultraflat dispersion of -84.0 +/- 0.5 ps/nm/km between 1700 and 2440 nm and 1.5 +/- 3 ps/nm/km between 1670 and 2500 nm is numerically demonstrated. It is shown that typical refractive index fluctuations as well as dimension fluctuations during fabrication of the SiXNY waveguides are a limitation for obtaining ultraflat dispersion profiles. Single- and multicladding waveguides are fabricated and their dispersion profiles measured (over nearly 1000 nm) using a low-coherence frequency domain interferometric technique. By appropriate thickness optimization, the zero-dispersion wavelength is tuned over a large spectral range in single-and multicladding waveguides with small refractive index contrast (3%). A flat dispersion profile with +/- 3.2 ps/nm/km variation over 500 nm is obtained in a multicladding waveguide fabricated with a refractive index contrast of 37%. Finally, we generate a nearly three-octave supercontinuum in this dispersion flattened multicladding SiXNY waveguide. (C) 2014 Optical Society of America
Until now, spatially resolved Raman Spectroscopy has required to scan a sample under investigation in a time-consuming step-by-step procedure. Here, we present a technique that allows the capture of an entire Raman image with only one single exposure. The Raman scattering arising from the sample was collected with a fiber-coupled high-performance astronomy spectrograph. The probe head consisting of an array of 20 x 20 multimode fibers was linked to the camera port of a microscope. To demonstrate the high potential of this new concept, Raman images of reference samples were recorded. Entire chemical maps were received without the need for a scanning procedure.
Von Ulfila bis Rekkared
(2014)
Für etwa 200 Jahre, vom Ende des 4. Jahrhunderts bis 589 n. Chr., gehören die Westgoten einem von der Orthodoxie der Reichskirche abweichenden christlichen Bekenntnis an. Auf dem 3. Konzil von Toledo beendet König Rekkared diesen Zustand religiöser Alterität durch die Konversion zum Katholizismus. Die antiken Berichte zeichnen nur vordergründig ein kohärentes Bild des Christentums der Goten. Dagegen weist Eike Faber Widersprüche und Fehler in der Überlieferung nach und bietet eine Reihe neuer Interpretationen an. Die genauere Betrachtung vermag dabei sowohl den dogmatischen Gehalt des Christentums der Goten schärfer zu konturieren als auch die Beweggründe für die Annahme des neuen Glaubens herauszustellen und die traditionelle Datierung dieses Vorgangs zu widerlegen. Schließlich wird deutlich, welche Funktion das fortgesetzte Festhalten an einer demonstrativ anderen religiösen Überzeugung für die Goten hatte. Prägnante Wegmarken der gotischen Geschichte, wie die Bibelübersetzung Ulfilas, die Eroberung und Plünderung Roms 410 n. Chr. oder die demonstrative Aufgabe der religiösen Differenz durch König Rekkared, werden erst durch diesen neuen, umfassenden Kontext verständlich.
Word features in parafoveal vision influence eye movements during reading. The question of whether readers extract semantic information from parafoveal words was studied in 3 experiments by using a gaze-contingent display change technique. Subjects read German sentences containing 1 of several preview words that were replaced by a target word during the saccade to the preview (boundary paradigm). In the 1st experiment the preview word was semantically related or unrelated to the target. Fixation durations on the target were shorter for semantically related than unrelated previews, consistent with a semantic preview benefit. In the 2nd experiment, half the sentences were presented following the rules of German spelling (i.e., previews and targets were printed with an initial capital letter), and the other half were presented completely in lowercase. A semantic preview benefit was obtained under both conditions. In the 3rd experiment, we introduced 2 further preview conditions, an identical word and a pronounceable nonword, while also manipulating the text contrast. Whereas the contrast had negligible effects, fixation durations on the target were reliably different for all 4 types of preview. Semantic preview benefits were greater for pretarget fixations closer to the boundary (large preview space) and, although not as consistently, for long pretarget fixation durations (long preview time). The results constrain theoretical proposals about eye movement control in reading.
Biosensors for the detection of benzaldehyde and g-aminobutyric acid (GABA) are reported using aldehyde oxidoreductase PaoABC from Escherichia coli immobilized in a polymer containing bound low potential osmium redox complexes. The electrically connected enzyme already electrooxidizes benzaldehyde at potentials below −0.15 V (vs. Ag|AgCl, 1 M KCl). The pH-dependence of benzaldehyde oxidation can be strongly influenced by the ionic strength. The effect is similar with the soluble osmium redox complex and therefore indicates a clear electrostatic effect on the bioelectrocatalytic efficiency of PaoABC in the osmium containing redox polymer. At lower ionic strength, the pH-optimum is high and can be switched to low pH-values at high ionic strength. This offers biosensing at high and low pH-values. A “reagentless” biosensor has been formed with enzyme wired onto a screen-printed electrode in a flow cell device. The response time to addition of benzaldehyde is 30 s, and the measuring range is between 10–150 µM and the detection limit of 5 µM (signal to noise ratio 3:1) of benzaldehyde. The relative standard deviation in a series (n = 13) for 200 µM benzaldehyde is 1.9%. For the biosensor, a response to succinic semialdehyde was also identified. Based on this response and the ability to work at high pH a biosensor for GABA is proposed by coimmobilizing GABA-aminotransferase (GABA-T) and PaoABC in the osmium containing redox polymer.
Flexion-extension ratio of trunk peak torque measures and antagonistic activity in males and females
(2014)
Purpose: Mirror therapy can improve motor and sensory functions, but effects of the mirror illusion on primary motor and somatosensory cortex could not be established consistently.
Methods: Fifteen right handed healthy volunteers performed or observed a finger-thumb opposition task. Cerebral activations during normal movement (NOR), mirrored movement (MIR) and movement observation (OBS) by means of a video chain were recorded with functional magnetic resonance imaging (fMRI). Activation sizes in movement > static conditions were identified using SPM8 (p < 0.001, unc.) and attributed to predefined areas employing the Anatomy toolbox 1.8. Laterality indices for the responsive areas were calculated on the basis of the number of activated voxels.
Results: Relevant bilateral BOLD responses were found in primary motor (M1) and somatosensory (S1 - BA 2, 3b and 3a) cortex, premotor and parietal areas and V5. When comparing MIR to NOR, no significant change of contralateral activation in M1 was found, but clearly at S1 with differences between hands.
Conclusion: The mirror illusion does not elicit immediate changes in motor areas, yet there is a direct effect on somatosensory areas, especially for left hand movements. These results suggest different effects of mirror therapy on processing and rehabilitation of motor and sensory function.
This essay approaches T. S. Eliot's Four Quartets (1935-1942) from the perspectives of Eve Kosofsky Sedgwick's critical practice of reparative reading and of Paul Ricoeur's poststructuralist hermeneutics. It demonstrates that Sedgwick's and Ricoeur's approaches can be productively combined to investigate hermeneutic processes in which the textual energy of a dissemination of meaning is redirected by a reparative or integrative impulse. In Four Quartets, this impetus induces the creation of semantic innovation through a violation of semantic pertinence, that is, through novel, tensional and provisional connections between formerly separate textual elements and semantic units.
Environmental change is likely to have a strong impact on biodiversity, and many species may shift their distribution in response. In this study, we aimed at projecting the availability of suitable habitat for an endangered amphibian species, the Fire-bellied toad Bombina bombina, in Brandenburg (north-eastern Germany). We modelled a potential habitat distribution map based on (1) a database with 10,581 presence records for Bombina from the years 1990 to 2009, (2) current estimates for ecogeographical variables (EGVs) and (3) the future projection of these EGVs according to the statistical regional model, respectively, the soil and water integrated model, applying the maximum entropy approach (Maxent). By comparing current and potential future distributions, we evaluated the projected change in distribution of suitable habitats and identified the environmental variables most associated with habitat suitability that turned out to be climatic variables related to the hydrological cycle. Under the applied scenario, our results indicate increasing habitat suitability in many areas and an extended range of suitable habitats. However, even if the environmental conditions in Brandenburg may change as predicted, it is questionable whether the Fire-bellied toad will truly benefit, as dispersal abilities of amphibian species are limited and strongly influenced by anthropogenic disturbances, that is, intensive agriculture, habitat destruction and fragmentation. Furthermore, agronomic pressure is likely to increase on productive areas with fertile soils and high water retention capacities, indeed those areas suitable for B. bombina. All these changes may affect temporary pond hydrology as well as the reproductive success and breeding phenology of toads.
Increasing attempts are made to understand the factors responsible for both the demographic and genetic depletion in amphibian populations. Landscape genetics aims at a spatially explicit correlation of genetic population parameters to landscape features. Using data from the endangered fire-bellied toad Bombina bombina in Brandenburg (Northeastern Germany), we performed an environmental niche factor analysis (ENFA), relating demographic (abundance) and genetic (diversity at 17 microsatellite loci and partial sequences of the mitochondrial control region in 434 individuals from 16 populations) parameters to ecological and anthropogenic variables such as temperature, precipitation, soil wetness, water runoff, vegetation density, and road/traffic impact. We found significant correlations between road disturbance and observed heterozygosity and between soil wetness and mitochondrial diversity. As the influences of the environmental variables can differ between different indicators for genetic diversity, population size and abundance data, our ENFA-based landscape genetics approach allows us to put various aspects of long- versus short term effective population size and genetic connectivity into an ecological and spatially explicit context, enabling potentially even forecast assessment under future environmental scenarios.
Time-Travel-Treasures
(2014)
We isolated and characterized 16 new di- and tetranudeotide microsatellite markers for the critically endangered Asian box turtle genus Cuora, focusing on the "Cuora trifasciata" species complex. The new markers were then used to analyse genetic variability and divergence amongst five described species within this complex, namely C. aurocapitata (n = 18), C. cyclornata (n = 31), C. pani (n = 6), C. trifasciata (n = 58), and C. zhoui (n = 7). Our results support the view that all five species represent valid taxa. Within two species (C. trifasciata and C. cyclornata), two distinct morphotypes were corroborated by microsatellite divergence. For three individuals, morphologically identified as being of hybrid origin, the hybrid status was confirmed by our genetic analysis. Our results confirm the controversial species (Cuora aurocapitata, C. cyclornata) and subspecies/morphotypes (C. cyclornata meieri, C. trifasciata cf. trifasciata) to be genetically distinct, which has critical implications for conservation strategies.
Il ciclo dei trentasei Contorni danteschi del pittore e disegnatore berlinese Giovanni Bonaventura Genelli (1798-1868) rappresenta un interessante tentativo d’interpretare il testo della Commedia alla luce dei principi del classicismo tedesco, sull’esempio di Carstens e di Koch e, in parte di Flaxman da cui però Genelli si distingue per continua ricerca volta ad esprimere la plasticità delle forme. Caratteristica precipua delle sue illustrazioni è inoltre il ricorso continuo sia alla scultura antica che agli affreschi michelangioleschi della Sistina come repertorio iconografico. L’articolo approfondisce questi aspetti con particolare riferimento alle sedici tavole dedicate all’Inferno.
Otto Braun
(2014)
Otto Braun war von 1921 bis 1932 mit kurzen Unterbrechungen Ministerpräsident des Freistaates Preußen. Er war sowohl überzeugter sozialer Demokrat als auch Preuße und betrieb eine entschlossene Reformpolitik, die zwar umstritten war, sich aber stets im Rahmen der Legalität bewegte. Die Grenzen dieses Ansatzes wurden am Ende der Weimarer Republik deutlich, als seine Regierung mit dem sogenannten »Preußenschlag« vom 20. Juli 1932 entmachtet wurde und Braun in Verkennung der neuen machtpolitischen Realitäten vergeblich versuchte, mit legalen Maßnahmen dem illegalen Vorgehen der Reichsregierung entgegenzutreten.
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.
Modern microscopic techniques following the stochastic motion of labelled tracer particles have uncovered significant deviations from the laws of Brownian motion in a variety of animate and inanimate systems. Such anomalous diffusion can have different physical origins, which can be identified from careful data analysis. In particular, single particle tracking provides the entire trajectory of the traced particle, which allows one to evaluate different observables to quantify the dynamics of the system under observation. We here provide an extensive overview over different popular anomalous diffusion models and their properties. We pay special attention to their ergodic properties, highlighting the fact that in several of these models the long time averaged mean squared displacement shows a distinct disparity to the regular, ensemble averaged mean squared displacement. In these cases, data obtained from time averages cannot be interpreted by the standard theoretical results for the ensemble averages. Here we therefore provide a comparison of the main properties of the time averaged mean squared displacement and its statistical behaviour in terms of the scatter of the amplitudes between the time averages obtained from different trajectories. We especially demonstrate how anomalous dynamics may be identified for systems, which, on first sight, appear to be Brownian. Moreover, we discuss the ergodicity breaking parameters for the different anomalous stochastic processes and showcase the physical origins for the various behaviours. This Perspective is intended as a guidebook for both experimentalists and theorists working on systems, which exhibit anomalous diffusion.
New porous materials based on covalently connected monomers are presented. The key step of the synthesis is an acetalisation reaction. In previous years we used acetalisation reactions extensively to build up various molecular rods. Based on this approach, investigations towards porous polymeric materials were conducted by us. Here we wish to present the results of these studies in the synthesis of 1D polyacetals and porous 3D polyacetals. By scrambling experiments with 1D acetals we could prove that exchange reactions occur between different building blocks (evidenced by MALDI-TOF mass spectrometry). Based on these results we synthesized porous 3D polyacetals under the same mild conditions.
Picosecond X-ray absorption spectroscopy (XAS) is used to investigate the electronic and structural dynamics initiated by plasmon excitation of 1.8 nm diameter Au nanoparticles (NPs) functionalised with 1-hexanethiol. We show that 100 ps after photoexcitation the transient XAS spectrum is consistent with an 8% expansion of the Au–Au bond length and a large increase in disorder associated with melting of the NPs. Recovery of the ground state occurs with a time constant of ∼1.8 ns, arising from thermalisation with the environment. Simulations reveal that the transient spectrum exhibits no signature of charge separation at 100 ps and allows us to estimate an upper limit for the quantum yield (QY) of this process to be <0.1.
We study the thermal Markovian diffusion of tracer particles in a 2D medium with spatially varying diffusivity D(r), mimicking recently measured, heterogeneous maps of the apparent diffusion coefficient in biological cells. For this heterogeneous diffusion process (HDP) we analyse the mean squared displacement (MSD) of the tracer particles, the time averaged MSD, the spatial probability density function, and the first passage time dynamics from the cell boundary to the nucleus. Moreover we examine the non-ergodic properties of this process which are important for the correct physical interpretation of time averages of observables obtained from single particle tracking experiments. From extensive computer simulations of the 2D stochastic Langevin equation we present an in-depth study of this HDP. In particular, we find that the MSDs along the radial and azimuthal directions in a circular domain obey anomalous and Brownian scaling, respectively. We demonstrate that the time averaged MSD stays linear as a function of the lag time and the system thus reveals a weak ergodicity breaking. Our results will enable one to rationalise the diffusive motion of larger tracer particles such as viruses or submicron beads in biological cells.
Arsenic-containing hydrocarbons are one group of fat-soluble organic arsenic compounds (arsenolipids) found in marine fish and other seafood. A risk assessment of arsenolipids is urgently needed, but has not been possible because of the total lack of toxicological data. In this study the cellular toxicity of three arsenic-containing hydrocarbons was investigated in cultured human bladder (UROtsa) and liver (HepG2) cells. Cytotoxicity of the arsenic-containing hydrocarbons was comparable to that of arsenite, which was applied as the toxic reference arsenical. A large cellular accumulation of arsenic, as measured by ICP-MS/MS, was observed after incubation of both cell lines with the arsenolipids. Moreover, the toxic mode of action shown by the three arsenic-containing hydrocarbons seemed to differ from that observed for arsenite. Evidence suggests that the high cytotoxic potential of the lipophilic arsenicals results from a decrease in the cellular energy level. This first in vitro based risk assessment cannot exclude a risk to human health related to the presence of arsenolipids in seafood, and indicates the urgent need for further toxicity studies in experimental animals to fully assess this possible risk.
Jüdische Mystik
(2014)
Das Handbuch umreißt das gesamte Spektrum der 2000jährigen Geschichte der Juden auf europäischem Boden. Wissenschaftler aus Europa und den USA haben ihre Forschungsergebnisse allgemein verständlich aufbereitet mit dem Ziel, das Leben und Wirken der Juden, aber auch die ihnen entgegengebrachte Intoleranz und deren Ursachen aufzuzeigen.
Der erste Teil konzentriert sich systematisch auf die Länder und Regionen, in denen Juden siedelten bzw. nach Vertreibungen aus anderen Staaten Aufnahme fanden. Es wird sowohl auf die innere Entwicklung der jüdischen Gemeinden als auch auf die Beziehungen zwischen Juden und der sie umgebenden andersgläubigen Gesellschaft eingegangen.
Der zweite Teil behandelt themenspezifische Schwerpunkte. Gemeindeleben und Religion, Familie und Stellung der Frau, kulturelle und geistige Entwicklung, aber auch Judenfeindschaft der sie umgebenden Gesellschaft – vom Antijudaismus bis zur Shoa und zum Antisemitismus der Gegenwart – werden in großangelegten Beiträgen dargelegt.
This study aims to further mechanistically understand toxic modes of action after chronic inorganic arsenic exposure. Therefore long-term incubation studies in cultured cells were carried out, to display chronically attained changes, which cannot be observed in the generally applied in vitro short-term incubation studies. Particularly, the cytotoxic, genotoxic and epigenetic effects of an up to 21 days incubation of human urothelial (UROtsa) cells with pico- to nanomolar concentrations of iAsIII and its metabolite thio-DMAV were compared. After 21 days of incubation, cytotoxic effects were strongly enhanced in the case of iAsIII and might partly be due to glutathione depletion and genotoxic effects on the chromosomal level. These results are in strong contrast to cells exposed to thio-DMAV. Thus, cells seemed to be able to adapt to this arsenical, as indicated among others by an increase in the cellular glutathione level. Most interestingly, picomolar concentrations of both iAsIII and thio-DMAV caused global DNA hypomethylation in UROtsa cells, which was quantified in parallel by 5-medC immunostaining and a newly established, reliable, high resolution mass spectrometry (HRMS)-based test system. This is the first time that epigenetic effects are reported for thio-DMAV; iAsIII induced epigenetic effects occur in at least 8000 fold lower concentrations as reported in vitro before. The fact that both arsenicals cause DNA hypomethylation at really low, exposure-relevant concentrations in human urothelial cells suggests that this epigenetic effect might contribute to inorganic arsenic induced carcinogenicity, which for sure has to be further investigated in future studies.
Probably no other field of statistical physics at the borderline of soft matter and biological physics has caused such a flurry of papers as polymer translocation since the 1994 landmark paper by Bezrukov, Vodyanoy, and Parsegian and the study of Kasianowicz in 1996. Experiments, simulations, and theoretical approaches are still contributing novel insights to date, while no universal consensus on the statistical understanding of polymer translocation has been reached. We here collect the published results, in particular, the famous–infamous debate on the scaling exponents governing the translocation process. We put these results into perspective and discuss where the field is going. In particular, we argue that the phenomenon of polymer translocation is non-universal and highly sensitive to the exact specifications of the models and experiments used towards its analysis.
Anomalous diffusion is frequently described by scaled Brownian motion (SBM){,} a Gaussian process with a power-law time dependent diffusion coefficient. Its mean squared displacement is ?x2(t)? [similar{,} equals] 2K(t)t with K(t) [similar{,} equals] t[small alpha]-1 for 0 < [small alpha] < 2. SBM may provide a seemingly adequate description in the case of unbounded diffusion{,} for which its probability density function coincides with that of fractional Brownian motion. Here we show that free SBM is weakly non-ergodic but does not exhibit a significant amplitude scatter of the time averaged mean squared displacement. More severely{,} we demonstrate that under confinement{,} the dynamics encoded by SBM is fundamentally different from both fractional Brownian motion and continuous time random walks. SBM is highly non-stationary and cannot provide a physical description for particles in a thermalised stationary system. Our findings have direct impact on the modelling of single particle tracking experiments{,} in particular{,} under confinement inside cellular compartments or when optical tweezers tracking methods are used.
Geocoder accuracy ranking
(2014)
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.
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.
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.
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.
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.
Creation of topographic maps
(2014)
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.
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.
The protein classification workflow described in this report enables users to get information about a novel protein sequence automatically. The information is derived by different bioinformatic analysis tools which calculate or predict features of a protein sequence. Also, databases are used to compare the novel sequence with known proteins.
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
Exploratory Data Analysis
(2014)
In bioinformatics the term exploratory data analysis refers to different methods to get an overview of large biological data sets. Hence, it helps to create a framework for further analysis and hypothesis testing. The workflow facilitates this first important step of the data analysis created by high-throughput technologies. The results are different plots showing the structure of the measurements. The goal of the workflow is the automatization of the exploratory data analysis, but also the flexibility should be guaranteed. The basic tool is the free software R.
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.
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.
Spotlocator is a game wherein people have to guess the spots of where photos were taken. The photos of a defined area for each game are from panoramio.com. They are published at http://spotlocator. drupalgardens.com with an ID. Everyone can guess the photo spots by sending a special tweet via Twitter that contains the hashtag #spotlocator, the guessed coordinates and the ID of the photo. An evaluation is published for all tweets. The players are informed about the distance to the real photo spots and the positions are shown on a map.
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.
In this project I constructed a workflow that takes a DNA sequence as input and provides a phylogenetic tree, consisting of the input sequence and other sequences which were found during a database search. In this phylogenetic tree the sequences are arranged depending on similarities. In bioinformatics, constructing phylogenetic trees is often used to explore the evolutionary relationships of genes or organisms and to understand the mechanisms of evolution itself.
Uno sguardo che renda omogenee le teorie della lingua relative al XVII e al XVIII secolo non può cogliere che a grandi linee la realtà delle concezioni della lingua abbracciate in questo periodo. Il riconoscimento di una teoria cartesiana della lingua come la spiegazione indifferenziata degli sviluppi conseguenti il passaggio da visioni razionalistiche a concezioni orientate ai sensi sono risultato di tale omogeneizzazione, un processo che contempla la realtà solo in parte.
Il pensiero linguistico era contrassegnato da un misto di forme di riflessione di carattere narrativo e di tipo concettuale-razionale che si completavano in modo reciproco. Se l’approccio concettuale tentava di rilevare le proprietà fondamentali della lingua e ordinarle razionalmente, le forme narrative della riflessione linguistica non si rivolgevano alla lingua in quanto oggetto concettuale. Piuttosto la rappresentavano come oggetto da comprendere. Gli approcci narrativi e concettuali alla lingua prevedono differenze discorsive nelle impostazioni teorico-linguistiche. Anche lo stampo del pensiero teoretico-linguistico contribuisce, attraverso tradizioni differenti, alla molteplicità delle vedute teoretico-linguistiche. Per tradizioni intendiamo posizioni dominanti nella riflessione metalinguistica, presenti in contesti regionali, che possono differenziarsi da altre tradizioni. Ad ogni modo, anche il ritardato sviluppo o la ricezione di teorie linguistiche può condurre a differenze caratteristiche. Le teorie linguistiche dell´Illuminismo furono per esempio recepite in Spagna più tardi che in altri Paesi europei. Ciò condusse all’accettazione sincronica di elementi teorici relativi a teorie diverse e consecutive. Se si concentra l’attenzione al di fuori dell’Europa si verrà attratti dallo sviluppo degli approcci analoghi alla riflessione linguistica che trovarono sviluppo in Cina all’inizio del XX secolo.
Unità e diversità sono tuttavia rintracciabili non solo sul piano della conoscenza metalinguistica ma anche sul piano dell’oggetto. Una sfida per la descrizione della lingua orientata alla tradizione greco-latina era rappresentata dalle lingue indigene con le quali si stava iniziando ad entrare in contatto attraverso i viaggi di scoperta e in seguito all’inizio del colonialismo. Da affiancare alla comunicazione esogena della trasmissione metalinguistica dei rapporti nell’ambito delle lingue europee sono presenti anche approcci per una percezione della specificità categoriale delle lingue americane. Sebbene in alcuni casi non verranno riconosciute le giuste categorizzazioni per le lingue descritte, per lo meno verrà assodato che le categorie rese note dalla grammatica latina non sussistono.
Nella ricerca degli ultimi decenni, la rappresentazione di un paradigma della filosofia della lingua del XVII e del XVIII secolo che postordini e subordini universalmente la molteplicità delle lingue a strutture valide di pensiero e che prescriva per la riflessione linguistica categorie fisse di una grammatica generale strettamente orientata alla logica razionalistica è stata più volte relativizzata. In quanto connessa con la fondatezza dell’unità e con l’inalterabilità del genere umano a seconda di spazio e tempo, la tesi che le lingue nella loro natura molteplice possano esistere solo alle dipendenze di una struttura universale del pensiero si lasciava catalogare tra quelle posizioni paradigmatiche sussistenti nell’ambito della filosofia della lingua di allora. Attraverso la conoscenza dell’origine storica dell’evoluzione dell’uomo, di tutti i suoi stili di vita e forme di comunicazione, assume rilievo un’altra posizione paradigmatica che attribuisce alla lingua un influsso formativo sul pensiero.
Attraverso la differenziazione ideologico-filosofica e la specificità nazionale delle sue tesi relative alla lingua in generale e alle lingue storiche in particolare la visione secolarizzata dell’uomo e della società elaborata all’apice dell’Illuminismo si associava allo sviluppo corrispettivo e al cambiamento delle posizioni teorico-linguistiche. Con la proclamazione della lingua e del pensiero come risultati di un lungo sviluppo corrispettivo nella storia dell’umanità viene assegnato nuovo valore alle prese di posizione sulla natura e sull’origine della lingua.
Cette recherche a pour objet l'articulation entre les dimensions anthropologiques et sociologiques de l'anthropologie philosophique de Helmuth Plessner (1892-1985). Elles procèdent selon trois axes. Je m'efforce (1) d'offrir une synthèse de l'anthropologie philosophique plessnerienne afin (2) de reconstituer les conditions de possibilité du social au stade humain de l'organique. Le troisième axe (3) correspond, enfin, à l'analyse des limites structurelles du social à partir de ses deux dimensions constitutives : l'individuel (limites ontogénétiques, comportementales et inter-personnelles) et le collectif (limites culturelles, intra- et inter-culturelles).
Die Migration von etwa einer halben Million Menschen aus westlichen Ländern in die DDR ist wenig erforscht. Dies gilt auch für das Gebiet der Literatur. Was so unterschiedliche Autoren wie Anna Seghers, Arnolt Bronnen, Heinar Kipphardt, Adolf Endler, Wolf Biermann, Gisela Kraft oder Ronald M. Schernikau verbindet, ist, sich einmal für ein Leben in der DDR entschieden zu haben. Einige von ihnen fanden in der sozialistischen Wahlheimat ihre Themen und ihr Publikum: häufig in zunehmender Distanz zur Kulturpolitik, mitunter auch in großer Nähe. Andere kehrten dem Land nach wenigen Jahren enttäuscht oder verbittert wieder den Rücken oder wurden hinausgedrängt. Die Beiträge beschäftigen sich mit den Motiven, Umständen, biographischen Konsequenzen, Selbstdeutungen und literarischen Resultaten der Übersiedlung in die SBZ bzw. in die DDR zwischen 1945 und 1989.
Schriftsteller schreiben nicht weil, sondern obwohl sie trinken. Der Trinker als literarische Figur und der Schriftsteller als Trinker, zwischen diesen beiden Punkten oszilliert das Thema »Alkohol und Literatur«. In typischer Alkoholikermanier bewegen sich die Texte der betreffenden Autoren zwischen alkoholseliger Übertreibung und erstaunlich zarter Empfindsamkeit und sind zugleich Zeichen für eine Flucht vor der tief empfundenen Unmenschlichkeit der modernen Welt sowie dem eigenen Versagensgefühl. Die oft satirischen und zumeist hoch intelligenten Reflexionen der trinkenden Helden geraten in den literarischen Texten zu aberwitzigen Monologen, in denen alle moralischen und geistigen Werte demontiert werden und die Realität nicht nur im Chaos versinkt, sondern gar deren Existenz überhaupt in Frage gestellt wird.
Wer wird Vater und wann?
(2014)
Wir alle sind Nachbarn?
(2014)
Vielheit statt Einheit
(2014)
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.
Inferring gene regulatory networks and cellular phases from time-resolved transcriptomics data
(2014)
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.
Im Folgenden schlage ich ein System gesellschaftlicher Dauerbeobachtung für den internationalen Vergleich von Gesellschaften vor, indem aufgrund einer Auseinandersetzung mit der sozialphilosophischen Diskussion acht Performanzkriterien für den Vergleich von Lebensbedingungen bzw. der „Wohlfahrt der Nationen“ entwickelt werden: Wohlstand und Wachstum; ökologische Nachhaltigkeit; Innovation; soziale Sicherung durch Unterstützungsleistungen im Risikofall sowie vorsorgend durch Bildungsinvestitionen; Anerkennung der Besonderheiten (Frauenfreundlichkeit und Migrantenfreundlichkeit); Gleichheit der Teilhabe; soziale Integration; Autonomie („freedom of choice and capabilities”). – Der Wandel von Wohlstand und Wohlfahrt wird im Kontext der Weltfinanzkrise und der folgenden großen Rezession betrachtet.
In meinem Lehrforschungsprojekt haben wir in einem ersten Schritt ab 2004 die Operationalisierung der gesellschaftlich wünschenswerten Ziele entwickelt und erste Auswertungen für 28 Länder vorgenommen (Holtmann, Dieter u. a.: Zur Performanz von Wohlfahrtsregimen und zu den Unterstützungspotentialen für die verschiedenen Wohlfahrtskonzepte. Potsdam 2006: Universitätsverlag). Im nächsten Schritt haben wir die Operationalisierungen weiterentwickelt und ab 2007 36 Länder in den Vergleich einbezogen (Holtmann, Dieter u.a.: Die Sozialstruktur der Bundesrepublik Deutschland im internationalen Vergleich. Potsdam 20127: Universitätsverlag). Im dritten Schritt haben wir diesen systematischen Ländervergleich durch Fallstudien zu den einzelnen Ländern ergänzt (Holtmann, Dieter u.a.: Die Wohlfahrt der Nationen: 40 Länder-Fallstudien zu den Institutionen und ihrer Performanz. Aachen 2012: Shaker).
In meinem Ansatz gehe ich nicht von einem einheitlichen Pfad der Modernisierung in Richtung Wachstum, Partizipation und Inklusion aus, sondern unterscheide – in Erweiterung der „drei Welten des Wohlfahrtskapitalismus“ von Esping-Andersen (1990) – für die berücksichtigten Länder (u.a. alle EU-Mitglieder) insbesondere folgende sechs verschiedene institutionelle Entwicklungspfade der Modernisierung: Der sozialdemokratisch-universalistische Pfad, der wirtschaftsliberale Pfad, der Status-konservierende Pfad, der „familistische“ Pfad, die Entwicklung der Gruppe der post-sozialistischen Länder, die sich in einem Prozess der Ausdifferenzierung befinden, und den produktivistischen, aufstiegsorientierten Modernisierungspfad Ostasiens. Als Erweiterung über die 36 entwickelten Länder unserer Sozialstrukturvergleiche hinaus berücksichtige ich die fünf Aufsteiger Südkorea, Brasilien, Südafrika, China und Indien sowie mit Kroatien und Serbien ein neues bzw. prospektives EU-Mitglied.
Als gesellschaftliche Teilbereiche zur Analyse der Sozialstrukturen nach der Weltfinanzkrise werden behandelt: Bildung und Bildungsregime; Dienstleistungs-gesellschaften und Erwerbstätigkeit; Wohlfahrtsregime und soziale Sicherung (Bildung und nachsorgende soziale Sicherung); Wohlstand, Einkommen, Vermögen und Armut; Individualisierung und ihre Gegenbewegungen; soziale Ungleichheiten zwischen Frauen und Männern; Bevölkerungsstruktur und Lebensformen; zusammenfassender Vergleich von Lebensbedingungen in den verschiedenen Ländern und Wohlfahrtsregimen.
Concepts and techniques for integration, analysis and visualization of massive 3D point clouds
(2014)
Remote sensing methods, such as LiDAR and image-based photogrammetry, are established approaches for capturing the physical world. Professional and low-cost scanning devices are capable of generating dense 3D point clouds. Typically, these 3D point clouds are preprocessed by GIS and are then used as input data in a variety of applications such as urban planning, environmental monitoring, disaster management, and simulation. The availability of area-wide 3D point clouds will drastically increase in the future due to the availability of novel capturing methods (e.g., driver assistance systems) and low-cost scanning devices. Applications, systems, and workflows will therefore face large collections of redundant, up-to-date 3D point clouds and have to cope with massive amounts of data. Hence, approaches are required that will efficiently integrate, update, manage, analyze, and visualize 3D point clouds. In this paper, we define requirements for a system infrastructure that enables the integration of 3D point clouds from heterogeneous capturing devices and different timestamps. Change detection and update strategies for 3D point clouds are presented that reduce storage requirements and offer new insights for analysis purposes. We also present an approach that attributes 3D point clouds with semantic information (e.g., object class category information), which enables more effective data processing, analysis, and visualization. Out-of-core real-time rendering techniques then allow for an interactive exploration of the entire 3D point cloud and the corresponding analysis results. Web-based visualization services are utilized to make 3D point clouds available to a large community. The proposed concepts and techniques are designed to establish 3D point clouds as base datasets, as well as rendering primitives for analysis and visualization tasks, which allow operations to be performed directly on the point data. Finally, we evaluate the presented system, report on its applications, and discuss further research challenges.
African weakly electric fishes (Mormyridae) underwent an outstanding adaptive radiation (about 200 species), putatively owing to their ability to communicate through species-specific weak electric signals. The electric organ discharge (EOD) is produced by muscle-derived electrocytes organized in piles to form an electric organ. Despite the importance of this trait as a prezygotic isolation mechanism, genomic resources remained limited. We present here a first draft of the skeletal muscle and electric organ transcriptomes from the weakly electric fish species Campylomormyrus compressirostris, obtained using the Illumina HiSeq2000 sequencing technology. Approximately 6.8 Gbp of cDNA sequence data were produced from both tissues, resulting in 57268109 raw reads for the skeletal muscle and 46934923 for the electric organ, and assembled de novo into 46143 and 89270 contigs, respectively. About 50% of both transcriptomes were annotated after protein databases search. The two transcriptomes show similar profiles in terms of Gene Ontology categories composition. We identified several candidate genes which are likely to play a central role in the production and evolution of the electric signal. For most of these genes, and for many other housekeeping genes, we were able to obtain the complete or partial coding DNA sequences (CDS), which can be used for the development of primers to be utilized in qRT-PCR experiments. We present also the complete mitochondrial genome and compare it to those available from other weakly electric fish species. Additionally, we located 1671 SSR-containing regions with their flanking sites and designed the relative primers. This study establishes a first step in the development of genomic tools aimed at understanding the role of electric communication during speciation.