@article{LiaimerJensenDittmann2016, author = {Liaimer, Anton and Jensen, John B. and Dittmann, Elke}, title = {A Genetic and Chemical Perspective on Symbiotic Recruitment of Cyanobacteria of the Genus Nostoc into the Host Plant Blasia pusilla L.}, series = {Frontiers in microbiology}, volume = {7}, journal = {Frontiers in microbiology}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-302X}, doi = {10.3389/fmicb.2016.01693}, pages = {449 -- 474}, year = {2016}, abstract = {Liverwort Blasia pusilla L. recruits soil nitrogen-fixing cyanobacteria of genus Nostoc as symbiotic partners. In this work we compared Nostoc community composition inside the plants and in the soil around them from two distant locations in Northern Norway. STRR fingerprinting and 16S rDNA phylogeny reconstruction showed a remarkable local diversity among isolates assigned to several Nostoc clades. An extensive web of negative allelopathic interactions was recorded at an agricultural site, but not at the undisturbed natural site. The cell extracts of the cyanobacteria did not show antimicrobial activities, but four isolates were shown to be cytotoxic to human cells. The secondary metabolite profiles of the isolates were mapped by MALDI-TOF MS, and the most prominent ions were further analyzed by Q-TOF for MS/MS aided identification. Symbiotic isolates produced a great variety of small peptide-like substances, most of which lack any record in the databases. Among identified compounds we found microcystin and nodularin variants toxic to eukaryotic cells. Microcystin producing chemotypes were dominating as symbiotic recruits but not in the free-living community. In addition, we were able to identify several novel aeruginosins and banyaside-like compounds, as well as nostocyclopeptides and nosperin.}, language = {en} } @article{DelgrandeSchaubTompits2001, author = {Delgrande, James Patrick and Schaub, Torsten and Tompits, Hans}, title = {A generic compiler for ordered logic programs}, isbn = {3-540-42593-4}, year = {2001}, language = {en} } @article{LontsiGarciaJerezCamiloMolinaVillegasetal.2019, author = {Lontsi, Agostiny Marrios and Garcia-Jerez, Antonio and Camilo Molina-Villegas, Juan and Jose Sanchez-Sesma, Francisco and Molkenthin, Christian and Ohrnberger, Matthias and Kr{\"u}ger, Frank and Wang, Rongjiang and Fah, Donat}, title = {A generalized theory for full microtremor horizontal-to-vertical [H/V(z,f)] spectral ratio interpretation in offshore and onshore environments}, series = {Geophysical journal international}, volume = {218}, journal = {Geophysical journal international}, number = {2}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0956-540X}, doi = {10.1093/gji/ggz223}, pages = {1276 -- 1297}, year = {2019}, abstract = {Advances in the field of seismic interferometry have provided a basic theoretical interpretation to the full spectrum of the microtremor horizontal-to-vertical spectral ratio [H/V(f)]. The interpretation has been applied to ambient seismic noise data recorded both at the surface and at depth. The new algorithm, based on the diffuse wavefield assumption, has been used in inversion schemes to estimate seismic wave velocity profiles that are useful input information for engineering and exploration seismology both for earthquake hazard estimation and to characterize surficial sediments. However, until now, the developed algorithms are only suitable for on land environments with no offshore consideration. Here, the microtremor H/V(z, f) modelling is extended for applications to marine sedimentary environments for a 1-D layered medium. The layer propagator matrix formulation is used for the computation of the required Green's functions. Therefore, in the presence of a water layer on top, the propagator matrix for the uppermost layer is defined to account for the properties of the water column. As an application example we analyse eight simple canonical layered earth models. Frequencies ranging from 0.2 to 50 Hz are considered as they cover a broad wavelength interval and aid in practice to investigate subsurface structures in the depth range from a few meters to a few hundreds of meters. Results show a marginal variation of 8 per cent at most for the fundamental frequency when a water layer is present. The water layer leads to variations in H/V peak amplitude of up to 50 per cent atop the solid layers.}, language = {en} } @article{BaroniTarantola2014, author = {Baroni, Gabriele and Tarantola, S.}, title = {A general probabilistic framework for uncertainty and global sensitivity analysis of deterministic models: A hydrological case study}, series = {Environmental modelling \& software with environment data news}, volume = {51}, journal = {Environmental modelling \& software with environment data news}, publisher = {Elsevier}, address = {Oxford}, issn = {1364-8152}, doi = {10.1016/j.envsoft.2013.09.022}, pages = {26 -- 34}, year = {2014}, abstract = {The present study proposes a General Probabilistic Framework (GPF) for uncertainty and global sensitivity analysis of deterministic models in which, in addition to scalar inputs, non-scalar and correlated inputs can be considered as well. The analysis is conducted with the variance-based approach of Sobol/Saltelli where first and total sensitivity indices are estimated. The results of the framework can be used in a loop for model improvement, parameter estimation or model simplification. The framework is applied to SWAP, a 113 hydrological model for the transport of water, solutes and heat in unsaturated and saturated soils. The sources of uncertainty are grouped in five main classes: model structure (soil discretization), input (weather data), time-varying (crop) parameters, scalar parameters (soil properties) and observations (measured soil moisture). For each source of uncertainty, different realizations are created based on direct monitoring activities. Uncertainty of evapotranspiration, soil moisture in the root zone and bottom fluxes below the root zone are considered in the analysis. The results show that the sources of uncertainty are different for each output considered and it is necessary to consider multiple output variables for a proper assessment of the model. Improvements on the performance of the model can be achieved reducing the uncertainty in the observations, in the soil parameters and in the weather data. Overall, the study shows the capability of the GPF to quantify the relative contribution of the different sources of uncertainty and to identify the priorities required to improve the performance of the model. The proposed framework can be extended to a wide variety of modelling applications, also when direct measurements of model output are not available.}, language = {en} } @article{FedosovSchulzeTarkhanov2001, author = {Fedosov, Boris and Schulze, Bert-Wolfgang and Tarkhanov, Nikolai Nikolaevich}, title = {A general index formula on toric manifolds with conical point}, year = {2001}, language = {en} } @article{DelgrandeSchaubTompits2007, author = {Delgrande, James Patrick and Schaub, Torsten and Tompits, Hans}, title = {A general framework for expressing preferences in causal reasoning and planning}, issn = {0955-792X}, doi = {10.1093/logcom/exm046}, year = {2007}, abstract = {We consider the problem of representing arbitrary preferences in causal reasoning and planning systems. In planning, a preference may be seen as a goal or constraint that is desirable, but not necessary, to satisfy. To begin, we define a very general query language for histories, or interleaved sequences of world states and actions. Based on this, we specify a second language in which preferences are defined. A single preference defines a binary relation on histories, indicating that one history is preferred to the other. From this, one can define global preference orderings on the set of histories, the maximal elements of which are the preferred histories. The approach is very general and flexible; thus it constitutes a base language in terms of which higher-level preferences may be defined. To this end, we investigate two fundamental types of preferences that we call choice and temporal preferences. We consider concrete strategies for these types of preferences and encode them in terms of our framework. We suggest how to express aggregates in the approach, allowing, e.g. the expression of a preference for histories with lowest total action costs. Last, our approach can be used to express other approaches and so serves as a common framework in which such approaches can be expressed and compared. We illustrate this by indicating how an approach due to Son and Pontelli can be encoded in our approach, as well as the language PDDL3.}, language = {en} } @article{HerzschuhWinterWuennemannetal.2006, author = {Herzschuh, Ulrike and Winter, Katja and W{\"u}nnemann, Bernd and Li, Shijie}, title = {A general cooling trend on the central Tibetan Plateau throughout the Holocene recorded by the Lake Zigetang pollen spectra}, series = {Quaternary international : the journal of the International Union for Quaternary Research}, volume = {154}, journal = {Quaternary international : the journal of the International Union for Quaternary Research}, publisher = {Pergamon Press}, address = {Oxford}, issn = {1040-6182}, doi = {10.1016/j.quaint.2006.02.005}, pages = {113 -- 121}, year = {2006}, abstract = {A 741-cm-long laminated sediment core, covering the last 10,800 years was collected from Lake Zigetang, central Tibetan Plateau (90.9 degrees E, 32.0 degrees N, 4560m a.s.l.), and analysed palynologically at 69 horizons. Biome reconstruction suggests a dominance of temperate steppe vegetation (mainly Artemisia and Poaceae) on the central Tibetan Plateau during the first half of the Holocene (10.8-4.4 cal. ka BP), while alpine steppes with desert elements (mainly Cyperaceae, Poaceae, Chenopodiaceae, and characteristic high-alpine herb families) tend to dominate the second half (4.4-0 cal. ka BP). The Artemisia/Cyperaceae ratio-a semi-quantitative measure for summer temperature-indicates a general cooling trend throughout the Holocene. Dense temperate steppe vegetation and maximum desert plant withdrawal, however, indicate that a suitable balance of wet and warm conditions for optimum vegetation growth likely occurred during the middle Holocene (7.3-4.4 cal. ka BP). Severe Early Holocene cold events have been reconstructed for 8.7-8.3 and similar to 7.4 cal. ka BP. (c) 2006 Elsevier Ltd and INQUA. All rights reserved.}, language = {en} } @article{BalazadehSiddiquiAlluetal.2010, author = {Balazadeh, Salma and Siddiqui, Hamad and Allu, Annapurna Devi and Matallana-Ramirez, Lilian Paola and Caldana, Camila and Mehrnia, Mohammad and Zanor, Maria-In{\´e}s and Koehler, Barbara and M{\"u}ller-R{\"o}ber, Bernd}, title = {A gene regulatory network controlled by the NAC transcription factor ANAC092/AtNAC2/ORE1 during salt-promoted senescence}, issn = {0960-7412}, doi = {10.1111/j.1365-313X.2010.04151.x}, year = {2010}, abstract = {P>The onset and progression of senescence are under genetic and environmental control. The Arabidopsis thaliana NAC transcription factor ANAC092 (also called AtNAC2 and ORE1) has recently been shown to control age-dependent senescence, but its mode of action has not been analysed yet. To explore the regulatory network administered by ANAC092 we performed microarray-based expression profiling using estradiol-inducible ANAC092 overexpression lines. Approximately 46\% of the 170 genes up-regulated upon ANAC092 induction are known senescence-associated genes, suggesting that the NAC factor exerts its role in senescence through a regulatory network that includes many of the genes previously reported to be senescence regulated. We selected 39 candidate genes and confirmed their time-dependent response to enhanced ANAC092 expression by quantitative RT-PCR. We also found that the majority of them (24 genes) are up-regulated by salt stress, a major promoter of plant senescence, in a manner similar to that of ANAC092, which itself is salt responsive. Furthermore, 24 genes like ANAC092 turned out to be stage-dependently expressed during seed growth with low expression at early and elevated expression at late stages of seed development. Disruption of ANAC092 increased the rate of seed germination under saline conditions, whereas the opposite occurred in respective overexpression plants. We also detected a delay of salinity-induced chlorophyll loss in detached anac092-1 mutant leaves. Promoter-reporter (GUS) studies revealed transcriptional control of ANAC092 expression during leaf and flower ageing and in response to salt stress. We conclude that ANAC092 exerts its functions during senescence and seed germination through partly overlapping target gene sets.}, language = {en} } @article{SunnaBergquist2003, author = {Sunna, Anwar and Bergquist, Peter L.}, title = {A gene encoding a novel extremely thermostable 1,4-beta-xylanase isolated directly from an environmental DNA sample}, year = {2003}, abstract = {Small-subunit (SSU) rRNA genes (rDNA) were amplified by PCR from a hot pool environmental DNA sample using Bacteria- or Archaea-specific rDNA primers. Unique rDNA types were identified by restriction fragment length polymorphism (RFLP) analysis and representative sequences were determined. Family 10 glycoside hydrolase consensus PCR primers were used to explore the occurrence and diversity of xylanase genes in the hot pool environmental DNA sample. Partial sequences for three different xylanases were obtained and genomic walking PCR (GWPCR), in combination with nested primer pairs, was used to obtained a unique 1,741-bp nucleotide sequence. Analysis of this sequence identified a putative XynA protein encoded by the xynA open reading frame. The single module novel xylanase shared sequence similarity to the family 10 glycoside hydrolases. The purified recombinant enzyme, XynA expressed in E. coli exhibited optimum activity at 100 degrees C and pH 6.0, and was extremely thermostable at 90 degrees C. The enzyme showed high specificity toward different xylans and xylooligosaccharides.}, language = {en} } @article{SchwarteTiedemann2011, author = {Schwarte, Sandra and Tiedemann, Ralph}, title = {A Gene Duplication/Loss Event in the Ribulose-1,5-Bisphosphate-Carboxylase/Oxygenase (Rubisco) Small Subunit Gene Family among Accessions of Arabidopsis thaliana}, series = {Molecular biology and evolution}, volume = {28}, journal = {Molecular biology and evolution}, number = {6}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0737-4038}, doi = {10.1093/molbev/msr008}, pages = {1861 -- 1876}, year = {2011}, abstract = {Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase; EC 4.1.1.39), the most abundant protein in nature, catalyzes the assimilation of CO(2) (worldwide about 10(11) t each year) by carboxylation of ribulose-1,5-bisphosphate. It is a hexadecamer consisting of eight large and eight small subunits. Although the Rubisco large subunit (rbcL) is encoded by a single gene on the multicopy chloroplast genome, the Rubisco small subunits (rbcS) are encoded by a family of nuclear genes. In Arabidopsis thaliana, the rbcS gene family comprises four members, that is, rbcS-1a, rbcS-1b, rbcS-2b, and rbcS-3b. We sequenced all Rubisco genes in 26 worldwide distributed A. thaliana accessions. In three of these accessions, we detected a gene duplication/loss event, where rbcS-1b was lost and substituted by a duplicate of rbcS-2b (called rbcS-2b*). By screening 74 additional accessions using a specific polymerase chain reaction assay, we detected five additional accessions with this duplication/loss event. In summary, we found the gene duplication/loss in 8 of 100 A. thaliana accessions, namely, Bch, Bu, Bur, Cvi, Fei, Lm, Sha, and Sorbo. We sequenced an about 1-kb promoter region for all Rubisco genes as well. This analysis revealed that the gene duplication/loss event was associated with promoter alterations (two insertions of 450 and 850 bp, one deletion of 730 bp) in rbcS-2b and a promoter deletion (2.3 kb) in rbcS-2b* in all eight affected accessions. The substitution of rbcS-1b by a duplicate of rbcS-2b (i.e., rbcS-2b*) might be caused by gene conversion. All four Rubisco genes evolve under purifying selection, as expected for central genes of the highly conserved photosystem of green plants. We inferred a single positive selected site, a tyrosine to aspartic acid substitution at position 72 in rbcS-1b. Exactly the same substitution compromises carboxylase activity in the cyanobacterium Anacystis nidulans. In A. thaliana, this substitution is associated with an inferred recombination. Functional implications of the substitution remain to be evaluated.}, language = {en} } @article{Reich2012, author = {Reich, Sebastian}, title = {A Gaussian-mixture ensemble transform filter}, series = {Quarterly journal of the Royal Meteorological Society}, volume = {138}, journal = {Quarterly journal of the Royal Meteorological Society}, number = {662}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {0035-9009}, doi = {10.1002/qj.898}, pages = {222 -- 233}, year = {2012}, abstract = {We generalize the popular ensemble Kalman filter to an ensemble transform filter, in which the prior distribution can take the form of a Gaussian mixture or a Gaussian kernel density estimator. The design of the filter is based on a continuous formulation of the Bayesian filter analysis step. We call the new filter algorithm the ensemble Gaussian-mixture filter (EGMF). The EGMF is implemented for three simple test problems (Brownian dynamics in one dimension, Langevin dynamics in two dimensions and the three-dimensional Lorenz-63 model). It is demonstrated that the EGMF is capable of tracking systems with non-Gaussian uni- and multimodal ensemble distributions.}, language = {en} } @article{Martykanova2017, author = {Martykanova, Darina}, title = {A Gateway to the World}, series = {Diasporas : circulations, migrations, histoire}, volume = {29}, journal = {Diasporas : circulations, migrations, histoire}, publisher = {Presses Universitaires du Midi}, address = {Toulouse}, issn = {1637-5823}, doi = {10.4000/diasporas.718}, pages = {33 -- 51}, year = {2017}, abstract = {In the second half of the 19th century, the French {\´E}cole centrale des arts et manufactures became one of the engineering schools that enjoyed a worldwide reputation. There were many foreigners among its students. This article focuses on the graduates born in the Ottoman Empire, particularly on Jews and Armenians. It analyses their backgrounds, their common features and their professional careers, tracing their links with other centraliens. The patterns in the Ottoman centraliens' professional trajectories help us picture a world full of opportunities where highly qualified men could cross borders and build careers with ease, but where, at the same time, origins, allegiances, contacts and credentials mattered greatly.}, language = {en} } @article{FusilloTremblayGaensickeetal.2018, author = {Fusillo, Nicola Pietro Gentile and Tremblay, Pier-Emmanuel and G{\"a}nsicke, Boris T. and Manser, Christopher J. and Cunningham, Tim and Cukanovaite, Elena and Hollands, Mark and Marsh, Thomas and Raddi, Roberto and Jordan, Stefan and Toonen, Silvia and Geier, Stephan and Barstow, Martin and Cummings, Jeffrey D.}, title = {A Gaia Data Release 2 catalogue of white dwarfs and a comparison with SDSS}, series = {Monthly notices of the Royal Astronomical Society}, volume = {482}, journal = {Monthly notices of the Royal Astronomical Society}, number = {4}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0035-8711}, doi = {10.1093/mnras/sty3016}, pages = {4570 -- 4591}, year = {2018}, abstract = {We present a catalogue of white dwarf candidates selected from the second data release of Gaia (DR2). We used a sample of spectroscopically confirmed white dwarfs from the Sloan Digital Sky Survey (SDSS) to map the entire space spanned by these objects in the Gaia Hertzsprung-Russell diagram. We then defined a set of cuts in absolute magnitude, colour, and a number of Gaia quality flags to remove the majority of contaminating objects. Finally, we adopt a method analogous to the one presented in our earlier SDSS photometric catalogues to calculate a probability of being a white dwarf (PWD) for all Gaia sources that passed the initial selection. The final catalogue is composed of 486641 stars with calculated PWD from which it is possible to select a sample of ≃260000 high-confidence white dwarf candidates in the magnitude range 8 < G < 21. By comparing this catalogue with a sample of SDSS white dwarf candidates, we estimate an upper limit in completeness of 85 per cent for white dwarfs with G ≤ 20 mag and Teff >7000 K, at high Galactic latitudes (|b| > 20°). However, the completeness drops at low Galactic latitudes, and the magnitude limit of the catalogue varies significantly across the sky as a function of Gaia's scanning law. We also provide the list of objects within our sample with available SDSS spectroscopy. We use this spectroscopic sample to characterize the observed structure of the white dwarf distribution in the H-R diagram.}, language = {en} } @article{EmuoyibofarheAkindeleRonkeetal.2019, author = {Emuoyibofarhe, Justice O. and Akindele, Akinyinka Tosin and Ronke, Babatunde Seyi and Omotosho, Adebayo and Meinel, Christoph}, title = {A Fuzzy Rule-Based Model for Remote Monitoring of Preterm in the Intensive Care Unit of Hospitals}, series = {International Journal of Medical Research \& Health Sciences}, volume = {8}, journal = {International Journal of Medical Research \& Health Sciences}, number = {5}, publisher = {Sumathi}, address = {Trichy}, issn = {2319-5886}, pages = {33 -- 44}, year = {2019}, abstract = {The use of Remote patient monitoring (RPM) systems to monitor critically ill patients in the Intensive Care Unit (ICU) has enabled quality and real-time healthcare management. Fuzzy logic as an approach to designing RPM systems provides a means for encapsulating the subjective decision-making process of medical experts in an algorithm suitable for computer implementation. In this paper, a remote monitoring system for preterm in neonatal ICU incubators is modeled and simulated. The model was designed with 4 input variables (body temperature, heart rate, respiratory rate, and oxygen level saturation), and 1 output variable (action performed represented as ACT). ACT decides whether-an alert is generated or not and also determines the message displayed when a notification is required. ACT classifies the clinical priority of the monitored preterm into 5 different fields: code blue, code red, code yellow, code green, and-code black. The model was simulated using a fuzzy logic toolbox of MATLAB R2015A. About 216 IF_THEN rules were formulated to monitor the inputs data fed into the model. The performance of the model was evaluated using-the confusion matrix to determine the model's accuracy, precision, sensitivity, specificity, and false alarm rate. The-experimental results obtained shows that the fuzzy-based system is capable of producing satisfactory results when used for monitoring and classifying the clinical statuses of neonates in ICU incubators.}, language = {en} } @article{CollenburgWalterBurgertetal.2016, author = {Collenburg, Lena and Walter, Tim and Burgert, Anne and Mueller, Nora and Seibel, Juergen and Japtok, Lukasz and Kleuser, Burkhard and Sauer, Markus and Schneider-Schaulies, Sibylle}, title = {A Functionalized Sphingolipid Analogue for Studying Redistribution during Activation in Living T Cells}, series = {The journal of immunology}, volume = {196}, journal = {The journal of immunology}, publisher = {American Assoc. of Immunologists}, address = {Bethesda}, issn = {0022-1767}, doi = {10.4049/jimmunol.1502447}, pages = {3951 -- 3962}, year = {2016}, abstract = {Sphingolipids are major components of the plasma membrane. In particular, ceramide serves as an essential building hub for complex sphingolipids, but also as an organizer of membrane domains segregating receptors and signalosomes. Sphingomyelin breakdown as a result of sphingomyelinase activation after ligation of a variety of receptors is the predominant source of ceramides released at the plasma membrane. This especially applies to T lymphocytes where formation of ceramide-enriched membrane microdomains modulates TCR signaling. Because ceramide release and redistribution occur very rapidly in response to receptor ligation, novel tools to further study these processes in living T cells are urgently needed. To meet this demand, we synthesized nontoxic, azido-functionalized ceramides allowing for bio-orthogonal click-reactions to fluorescently label incorporated ceramides, and thus investigate formation of ceramide-enriched domains. Azido-functionalized C-6-ceramides were incorporated into and localized within plasma membrane microdomains and proximal vesicles in T cells. They segregated into clusters after TCR, and especially CD28 ligation, indicating efficient sorting into plasma membrane domains associated with T cell activation; this was abolished upon sphingomyelinase inhibition. Importantly, T cell activation was not abrogated upon incorporation of the compound, which was efficiently excluded from the immune synapse center as has previously been seen in Ab-based studies using fixed cells. Therefore, the functionalized ceramides are novel, highly potent tools to study the subcellular redistribution of ceramides in the course of T cell activation. Moreover, they will certainly also be generally applicable to studies addressing rapid stimulation-mediated ceramide release in living cells.}, language = {en} } @article{BeckmannTrudewind1997, author = {Beckmann, J{\"u}rgen and Trudewind, C.}, title = {A functional-analytic perspective on affect and motivation}, year = {1997}, language = {en} } @article{VanDerVenBartschGauteletal.2000, author = {VanDerVen, Peter F. M. and Bartsch, J{\"o}rg and Gautel, Mathias and Jokusch, Harald and F{\"u}rst, Dieter Oswald}, title = {A functional knock-out of titin results in defective myofibril assembly}, year = {2000}, language = {en} } @article{LiChenWangetal.2013, author = {Li, Jian and Chen, You-Peng and Wang, Zi-Neng and Liu, Tie-Bin and Chen, Dan and Dong, Yun-Peng and Hocher, Berthold}, title = {A functional fetal HSD11B2[CA]n microsatellite polymorphism is associated with maternal serum cortisol concentrations in pregnant women}, series = {Kidney \& blood pressure research : official organ of the Gesellschaft f{\"u}r Nephrologie}, volume = {38}, journal = {Kidney \& blood pressure research : official organ of the Gesellschaft f{\"u}r Nephrologie}, number = {1}, publisher = {Karger}, address = {Basel}, issn = {1420-4096}, doi = {10.1159/000355761}, pages = {132 -- 141}, year = {2013}, abstract = {Background/Aims: Cortisol plays an important role during pregnancy. It controls maternal glucose metabolism and fetal development. Cortisol metabolism is partially controlled by the 11b-HSD2. This enzyme is expressed in the kidney and human placenta. The activity of the enzyme is partially controlled by functional polymorphisms: the HSD11B2[CA]n microsatellite polymorphism. The impact of this functional gene polymorphism on cortisol metabolism and potential effects on the newborn's is unknown so far. Methods: In the current prospective birth cohort study in southern Asia, we analyzed the association of the HSD11B2[CA]n microsatellite polymorphisms in 187 mothers and their newborn's on maternal and newborn's serum cortisol concentrations. Results: Using multivariable regression analyses considering known confounding ( gestational age, newborn's gender, the labor uterine contraction states and the timing during the day of blood taking), we showed that the fetal HSD11B2[CA]n microsatellite polymorphisms in the first intron was related to maternal cortisol concentration ( R2=0.26, B=96.27, p=0.007), whereas as the newborn's cortisol concentrations were independent of fetal and maternal HSD11B2[CA] n microsatellite polymorphism. Conclusions: Our study showed for the first time that the fetal HSD11B2[CA]n microsatellite polymorphism of the HSD11B2 gene in healthy uncomplicated human pregnancy is associated with maternal cortisol concentration. This indicates that fetal genes controlling cortisol metabolism may affect maternal cortisol concentration and hence physiology in healthy pregnant women.}, language = {en} } @article{MaerkerPelacaniSchroeder2011, author = {Maerker, Michael and Pelacani, Samanta and Schroeder, Boris}, title = {A functional entity approach to predict soil erosion processes in a small Plio-Pleistocene Mediterranean catchment in Northern Chianti, Italy}, series = {Geomorphology : an international journal on pure and applied geomorphology}, volume = {125}, journal = {Geomorphology : an international journal on pure and applied geomorphology}, number = {4}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0169-555X}, doi = {10.1016/j.geomorph.2010.10.022}, pages = {530 -- 540}, year = {2011}, abstract = {In this paper we evaluate different methods to predict soil erosion processes. We derived different layers of predictor variables for the study area in the Northern Chianti, Italy, describing the soil-lithologic complex, land use, and topographic characteristics. For a subcatchment of the Orme River, we mapped erosion processes by interpreting aerial photographs and field observations. These were classified as erosional response units (ERU), i.e. spatial areas of homogeneous erosion processes. The ERU were used as the response variable in the soil erosion modelling process. We applied two models i) bootstrap aggregation (Random Forest: RF), and ii) stochastic gradient boosting (TreeNet: TN) to predict the potential spatial distribution of erosion processes for the entire Orme River catchment. The models are statistically evaluated using training data and a set of performance parameters such as the area under the receiver operating characteristic curve (AUC), Cohen's Kappa, and pseudo R2. Variable importance and response curves provide further insight into controlling factors of erosion. Both models provided good performance in terms of classification and calibration; however, TN outperformed RF. Similar classes such as active and inactive landslides can be discriminated and well interpreted by considering response curves and relative variable importance. The spatial distribution of the predicted erosion susceptibilities generally follows topographic constraints and is similar for both models. Hence, the model-based delineation of ERU on the basis of soil and terrain information is a valuable tool in geomorphology; it provides insights into factors controlling erosion processes and may allow the extrapolation and prediction of erosion processes in unsurveyed areas.}, language = {en} } @article{KreowskyStabernack2021, author = {Kreowsky, Philipp and Stabernack, Christian Benno}, title = {A full-featured FPGA-based pipelined architecture for SIFT extraction}, series = {IEEE access : practical research, open solutions / Institute of Electrical and Electronics Engineers}, volume = {9}, journal = {IEEE access : practical research, open solutions / Institute of Electrical and Electronics Engineers}, publisher = {Inst. of Electr. and Electronics Engineers}, address = {New York, NY}, issn = {2169-3536}, doi = {10.1109/ACCESS.2021.3104387}, pages = {128564 -- 128573}, year = {2021}, abstract = {Image feature detection is a key task in computer vision. Scale Invariant Feature Transform (SIFT) is a prevalent and well known algorithm for robust feature detection. However, it is computationally demanding and software implementations are not applicable for real-time performance. In this paper, a versatile and pipelined hardware implementation is proposed, that is capable of computing keypoints and rotation invariant descriptors on-chip. All computations are performed in single precision floating-point format which makes it possible to implement the original algorithm with little alteration. Various rotation resolutions and filter kernel sizes are supported for images of any resolution up to ultra-high definition. For full high definition images, 84 fps can be processed. Ultra high definition images can be processed at 21 fps.}, language = {en} } @article{FrielerLevermannElliottetal.2015, author = {Frieler, Katja and Levermann, Anders and Elliott, J. and Heinke, Jens and Arneth, A. and Bierkens, M. F. P. and Ciais, Philippe and Clark, D. B. and Deryng, D. and Doell, P. and Falloon, P. and Fekete, B. and Folberth, Christian and Friend, A. D. and Gellhorn, C. and Gosling, S. N. and Haddeland, I. and Khabarov, N. and Lomas, M. and Masaki, Y. and Nishina, K. and Neumann, K. and Oki, T. and Pavlick, R. and Ruane, A. C. and Schmid, E. and Schmitz, C. and Stacke, T. and Stehfest, E. and Tang, Q. and Wisser, D. and Huber, Veronika and Piontek, Franziska and Warszawski, Lila and Schewe, Jacob and Lotze-Campen, Hermann and Schellnhuber, Hans Joachim}, title = {A framework for the cross-sectoral integration of multi-model impact projections}, series = {Earth system dynamics}, volume = {6}, journal = {Earth system dynamics}, number = {2}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {2190-4979}, doi = {10.5194/esd-6-447-2015}, pages = {447 -- 460}, year = {2015}, abstract = {Climate change and its impacts already pose considerable challenges for societies that will further increase with global warming (IPCC, 2014a, b). Uncertainties of the climatic response to greenhouse gas emissions include the potential passing of large-scale tipping points (e.g. Lenton et al., 2008; Levermann et al., 2012; Schellnhuber, 2010) and changes in extreme meteorological events (Field et al., 2012) with complex impacts on societies (Hallegatte et al., 2013). Thus climate change mitigation is considered a necessary societal response for avoiding uncontrollable impacts (Conference of the Parties, 2010). On the other hand, large-scale climate change mitigation itself implies fundamental changes in, for example, the global energy system. The associated challenges come on top of others that derive from equally important ethical imperatives like the fulfilment of increasing food demand that may draw on the same resources. For example, ensuring food security for a growing population may require an expansion of cropland, thereby reducing natural carbon sinks or the area available for bio-energy production. So far, available studies addressing this problem have relied on individual impact models, ignoring uncertainty in crop model and biome model projections. Here, we propose a probabilistic decision framework that allows for an evaluation of agricultural management and mitigation options in a multi-impact-model setting. Based on simulations generated within the Inter-Sectoral Impact Model Intercomparison Project (ISI-MIP), we outline how cross-sectorally consistent multi-model impact simulations could be used to generate the information required for robust decision making. Using an illustrative future land use pattern, we discuss the trade-off between potential gains in crop production and associated losses in natural carbon sinks in the new multiple crop-and biome-model setting. In addition, crop and water model simulations are combined to explore irrigation increases as one possible measure of agricultural intensification that could limit the expansion of cropland required in response to climate change and growing food demand. This example shows that current impact model uncertainties pose an important challenge to long-term mitigation planning and must not be ignored in long-term strategic decision making.}, language = {en} } @article{EngelmannVasishthEngbertetal.2013, author = {Engelmann, Felix and Vasishth, Shravan and Engbert, Ralf and Kliegl, Reinhold}, title = {A framework for modeling the interaction of syntactic processing and eye movement control}, series = {Topics in cognitive science}, volume = {5}, journal = {Topics in cognitive science}, number = {3}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1756-8757}, doi = {10.1111/tops.12026}, pages = {452 -- 474}, year = {2013}, abstract = {We explore the interaction between oculomotor control and language comprehension on the sentence level using two well-tested computational accounts of parsing difficulty. Previous work (Boston, Hale, Vasishth, \& Kliegl, 2011) has shown that surprisal (Hale, 2001; Levy, 2008) and cue-based memory retrieval (Lewis \& Vasishth, 2005) are significant and complementary predictors of reading time in an eyetracking corpus. It remains an open question how the sentence processor interacts with oculomotor control. Using a simple linking hypothesis proposed in Reichle, Warren, and McConnell (2009), we integrated both measures with the eye movement model EMMA (Salvucci, 2001) inside the cognitive architecture ACT-R (Anderson et al., 2004). We built a reading model that could initiate short Time Out regressions (Mitchell, Shen, Green, \& Hodgson, 2008) that compensate for slow postlexical processing. This simple interaction enabled the model to predict the re-reading of words based on parsing difficulty. The model was evaluated in different configurations on the prediction of frequency effects on the Potsdam Sentence Corpus. The extension of EMMA with postlexical processing improved its predictions and reproduced re-reading rates and durations with a reasonable fit to the data. This demonstration, based on simple and independently motivated assumptions, serves as a foundational step toward a precise investigation of the interaction between high-level language processing and eye movement control.}, language = {en} } @article{IhdePufahlVoelkeretal.2022, author = {Ihde, Sven and Pufahl, Luise and V{\"o}lker, Maximilian and Goel, Asvin and Weske, Mathias}, title = {A framework for modeling and executing task}, series = {Computing : archives for informatics and numerical computation}, volume = {104}, journal = {Computing : archives for informatics and numerical computation}, publisher = {Springer}, address = {Wien}, issn = {0010-485X}, doi = {10.1007/s00607-022-01093-2}, pages = {2405 -- 2429}, year = {2022}, abstract = {As resources are valuable assets, organizations have to decide which resources to allocate to business process tasks in a way that the process is executed not only effectively but also efficiently. Traditional role-based resource allocation leads to effective process executions, since each task is performed by a resource that has the required skills and competencies to do so. However, the resulting allocations are typically not as efficient as they could be, since optimization techniques have yet to find their way in traditional business process management scenarios. On the other hand, operations research provides a rich set of analytical methods for supporting problem-specific decisions on resource allocation. This paper provides a novel framework for creating transparency on existing tasks and resources, supporting individualized allocations for each activity in a process, and the possibility to integrate problem-specific analytical methods of the operations research domain. To validate the framework, the paper reports on the design and prototypical implementation of a software architecture, which extends a traditional process engine with a dedicated resource management component. This component allows us to define specific resource allocation problems at design time, and it also facilitates optimized resource allocation at run time. The framework is evaluated using a real-world parcel delivery process. The evaluation shows that the quality of the allocation results increase significantly with a technique from operations research in contrast to the traditional applied rule-based approach.}, language = {en} } @article{MaoNakamuraViottietal.2016, author = {Mao, Hailiang and Nakamura, Moritaka and Viotti, Corrado and Grebe, Markus}, title = {A Framework for Lateral Membrane Trafficking and Polar Tethering of the PEN3 ATP-Binding Cassette Transporter}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {172}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.16.01252}, pages = {2245 -- 2260}, year = {2016}, abstract = {The outermost cell layer of plants, the epidermis, and its outer (lateral) membrane domain facing the environment are continuously challenged by biotic and abiotic stresses. Therefore, the epidermis and the outer membrane domain provide important selective and protective barriers. However, only a small number of specifically outer membrane-localized proteins are known. Similarly, molecular mechanisms underlying the trafficking and the polar placement of outer membrane domain proteins require further exploration. Here, we demonstrate that ACTIN7 (ACT7) mediates trafficking of the PENETRATION3 (PEN3) outer membrane protein from the trans-Golgi network (TGN) to the plasma membrane in the root epidermis of Arabidopsis (Arabidopsis thaliana) and that actin function contributes to PEN3 endocytic recycling. In contrast to such generic ACT7-dependent trafficking from the TGN, the EXOCYST84b (EXO84b) tethering factor mediates PEN3 outer-membrane polarity. Moreover, precise EXO84b placement at the outer membrane domain itself requires ACT7 function. Hence, our results uncover spatially and mechanistically distinct requirements for ACT7 function during outer lateral membrane cargo trafficking and polarity establishment. They further identify an exocyst tethering complex mediator of outer lateral membrane cargo polarity.}, language = {en} } @article{YangQuehlSack2014, author = {Yang, Haojin and Quehl, Bernhard and Sack, Harald}, title = {A framework for improved video text detection and recognition}, series = {Multimedia tools and applications : an international journal}, volume = {69}, journal = {Multimedia tools and applications : an international journal}, number = {1}, publisher = {Springer}, address = {Dordrecht}, issn = {1380-7501}, doi = {10.1007/s11042-012-1250-6}, pages = {217 -- 245}, year = {2014}, abstract = {Text displayed in a video is an essential part for the high-level semantic information of the video content. Therefore, video text can be used as a valuable source for automated video indexing in digital video libraries. In this paper, we propose a workflow for video text detection and recognition. In the text detection stage, we have developed a fast localization-verification scheme, in which an edge-based multi-scale text detector first identifies potential text candidates with high recall rate. Then, detected candidate text lines are refined by using an image entropy-based filter. Finally, Stroke Width Transform (SWT)- and Support Vector Machine (SVM)-based verification procedures are applied to eliminate the false alarms. For text recognition, we have developed a novel skeleton-based binarization method in order to separate text from complex backgrounds to make it processible for standard OCR (Optical Character Recognition) software. Operability and accuracy of proposed text detection and binarization methods have been evaluated by using publicly available test data sets.}, language = {en} } @article{DelgrandeSchaubTompits2003, author = {Delgrande, James Patrick and Schaub, Torsten and Tompits, Hans}, title = {A framework for compiling preferences in logic programs}, year = {2003}, language = {en} } @article{JareckiTanJenny2020, author = {Jarecki, Jana B. and Tan, Jolene H. and Jenny, Mirjam}, title = {A framework for building cognitive process models}, series = {Psychonomic bulletin \& review : a journal of the Psychonomic Society}, volume = {27}, journal = {Psychonomic bulletin \& review : a journal of the Psychonomic Society}, number = {6}, publisher = {Springer}, address = {New York, NY}, issn = {1069-9384}, doi = {10.3758/s13423-020-01747-2}, pages = {1218 -- 1229}, year = {2020}, abstract = {The termprocess modelis widely used, but rarely agreed upon. This paper proposes a framework for characterizing and building cognitive process models. Process models model not only inputs and outputs but also model the ongoing information transformations at a given level of abstraction. We argue that the following dimensions characterize process models: They have a scope that includes different levels of abstraction. They specify a hypothesized mental information transformation. They make predictions not only for the behavior of interest but also for processes. The models' predictions for the processes can be derived from the input, without reverse inference from the output data. Moreover, the presumed information transformation steps are not contradicting current knowledge of human cognitive capacities. Lastly, process models require a conceptual scope specifying levels of abstraction for the information entering the mind, the proposed mental events, and the behavior of interest. This framework can be used for refining models before testing them or after testing them empirically, and it does not rely on specific modeling paradigms. It can be a guideline for developing cognitive process models. Moreover, the framework can advance currently unresolved debates about which models belong to the category of process models.}, language = {en} } @article{SchlaegelLewis2016, author = {Schl{\"a}gel, Ulrike E. and Lewis, Mark A.}, title = {A framework for analyzing the robustness of movement models to variable step discretization}, series = {Journal of mathematical biology}, volume = {73}, journal = {Journal of mathematical biology}, publisher = {Springer}, address = {Heidelberg}, issn = {0303-6812}, doi = {10.1007/s00285-016-0969-5}, pages = {815 -- 845}, year = {2016}, abstract = {When sampling animal movement paths, the frequency at which location measurements are attempted is a critical feature for data analysis. Important quantities derived from raw data, e.g. travel distance or sinuosity, can differ largely based on the temporal resolution of the data. Likewise, when movement models are fitted to data, parameter estimates have been demonstrated to vary with sampling rate. Thus, biological statements derived from such analyses can only be made with respect to the resolution of the underlying data, limiting extrapolation of results and comparison between studies. To address this problem, we investigate whether there are models that are robust against changes in temporal resolution. First, we propose a mathematically rigorous framework, in which we formally define robustness as a model property. We then use the framework for a thorough assessment of a range of basic random walk models, in which we also show how robustness relates to other probabilistic concepts. While we found robustness to be a strong condition met by few models only, we suggest a new method to extend models so as to make them robust. Our framework provides a new systematic, mathematically founded approach to the question if, and how, sampling rate of movement paths affects statistical inference.}, language = {en} } @article{OberauerKliegl2006, author = {Oberauer, Klaus and Kliegl, Reinhold}, title = {A formal model of capacity limits in working memory}, series = {Journal of Memory and Language}, volume = {55}, journal = {Journal of Memory and Language}, number = {4}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0749-596X}, doi = {10.1016/j.jml.2006.08.009}, pages = {601 -- 626}, year = {2006}, abstract = {A mathematical model of working-memory capacity limits is proposed on the key assumption of mutual interference between items in working memory. Interference is assumed to arise from overwriting of features shared by these items. The model was fit to time-accuracy data of memory-updating tasks from four experiments using nonlinear mixed effect (NLME) models as a framework. The model gave a good account of the data from a numerical and a spatial task version. The performance pattern in a combination of numerical and spatial updating could be explained by variations in the interference parameter: assuming less feature overlap between contents from different domains than between contents from the same domain, the model can account for double dissociations of content domains in dual-task experiments. Experiment 3 extended this idea to similarity within the verbal domain. The decline of memory accuracy with increasing memory load was steeper with phonologically similar than with dissimilar material, although processing speed was faster for the similar material. The model captured the similarity effects with a higher estimated interference parameter for the similar than for the dissimilar condition. The results are difficult to explain with alternative models, in particular models incorporating time-based decay and models assuming limited resource pools.}, language = {en} } @article{Alexiadou2019, author = {Alexiadou, Artemis}, title = {A form-function mismatch?}, series = {Of trees and birds. A Festschrift for Gisbert Fanselow}, journal = {Of trees and birds. A Festschrift for Gisbert Fanselow}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-457-9}, doi = {10.25932/publishup-43223}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-432235}, pages = {107 -- 117}, year = {2019}, language = {en} } @article{MeynersMertensWessigetal.2017, author = {Meyners, Christian and Mertens, Monique and Wessig, Pablo and Meyer-Almes, Franz-Josef}, title = {A Fluorescence-Lifetime-Based Binding Assay for Class IIa Histone Deacetylases}, series = {Chemistry - a European journal}, volume = {23}, journal = {Chemistry - a European journal}, number = {13}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {0947-6539}, doi = {10.1002/chem.201605140}, pages = {3107 -- 3116}, year = {2017}, abstract = {Class IIa histone deacetylases (HDACs) show extremely low enzymatic activity and no commonly accepted endogenous substrate is known today. Increasing evidence suggests that these enzymes exert their effect rather through molecular recognition of acetylated proteins and recruiting other proteins like HDAC3 to the desired target location. Accordingly, class IIa HDACs like bromodomains have been suggested to act as "Readers" of acetyl marks, whereas enzymatically active HDACs of class I or IIb are called "Erasers" to highlight their capability to remove acetyl groups from acetylated histones or other proteins. Small-molecule ligands of class IIa histone deacetylases (HDACs) have gained tremendous attention during the last decade and have been suggested as pharmaceutical targets in several indication areas such as cancer, Huntington's disease and muscular atrophy. Up to now, only enzyme activity assays with artificial chemically activated trifluoroacetylated substrates are in use for the identification and characterization of new active compounds against class IIa HDACs. Here, we describe the first binding assay for this class of HDAC enzymes that involves a simple mix-and-measure procedure and an extraordinarily robust fluorescence lifetime readout based on [1,3]dioxolo[4,5-f]benzodioxole-based ligand probes. The principle of the assay is generic and can also be transferred to class I HDAC8.}, language = {en} } @article{MeynersWawrzinekKraemeretal.2014, author = {Meyners, Christian and Wawrzinek, Robert and Kraemer, Andreas and Hinz, Steffen and Wessig, Pablo and Meyer-Almes, Franz-Josef}, title = {A fluorescence lifetime-based binding assay for acetylpolyamine amidohydrolases from Pseudomonas aeruginosa using a [1,3]dioxolo[4,5-f][1,3]benzodioxole (DBD) ligand probe}, series = {Analytical \& bioanalytical chemistry}, volume = {406}, journal = {Analytical \& bioanalytical chemistry}, number = {20}, publisher = {Springer}, address = {Heidelberg}, issn = {1618-2642}, doi = {10.1007/s00216-014-7886-5}, pages = {4889 -- 4897}, year = {2014}, abstract = {High-throughput assays for drug screening applications have to fulfill particular specifications. Besides the capability to identify even compounds with low potency, one of the major issues is to minimize the number of false-positive hits in a screening campaign in order to reduce the logistic effort for the subsequent cherry picking and confirmation procedure. In this respect, fluorescence lifetime (FLT) appears as an ideal readout parameter that is supposed to be robust against autofluorescent and light-absorbing compounds, the most common source of systematic false positives. The extraordinary fluorescence features of the recently discovered [1,3]dioxolo[4,5-f][1,3]benzodioxole dyes were exploited to develop an FLT-based binding assay with exceptionally robust readout. The assay setup was comprehensively validated and shown to comply not only with all requirements for a powerful high-throughput screening assay but also to be suitable to determine accurate binding constants for inhibitors against enzymes of the histone deacetylase family. Using the described binding assay, the first inhibitors against three members of this enzyme family from Pseudomonas aeruginosa were identified. The compounds were characterized in terms of potency and selectivity profile. The novel ligand probe should also be applicable to other homologues of the histone deacetylase family that are inhibited by N-hydroxy-N'-phenyloctandiamide.}, language = {en} } @article{SharmaRuelensMaggenetal.2017, author = {Sharma, Neha and Ruelens, Philip and Maggen, Thomas and Dochy, Niklas and Torfs, Sanne and Kaufmann, Kerstin and Rohde, Antje and Geuten, Koen}, title = {A Flowering Locus C Homolog Is a Vernalization-Regulated Repressor in Brachypodium and Is Cold Regulated in Wheat}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {173}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {2}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.16.01161}, pages = {1301 -- 1315}, year = {2017}, abstract = {Winter cereals require prolonged cold to transition from vegetative to reproductive development. This process, referred to as vernalization, has been extensively studied in Arabidopsis (Arabidopsis thaliana). In Arabidopsis, a key flowering repressor called FLOWERING LOCUS C (FLC) quantitatively controls the vernalization requirement. By contrast, in cereals, the vernalization response is mainly regulated by the VERNALIZATION genes, VRN1 and VRN2. Here, we characterize ODDSOC2, a recently identified FLC ortholog in monocots, knowing that it belongs to the FLC lineage. By studying its expression in a diverse set of Brachypodium accessions, we find that it is a good predictor of the vernalization requirement. Analyses of transgenics demonstrated that BdODDSOC2 functions as a vernalization-regulated flowering repressor. In most Brachypodium accessions BdODDSOC2 is down-regulated by cold, and in one of the winter accessions in which this down-regulation was evident, BdODDSOC2 responded to cold before BdVRN1. When stably down-regulated, the mechanism is associated with spreading H3K27me3 modifications at the BdODDSOC2 chromatin. Finally, homoeolog-specific gene expression analyses identify TaAGL33 and its splice variant TaAGL22 as the FLC orthologs in wheat (Triticum aestivum) behaving most similar to Brachypodium ODDSOC2. Overall, our study suggests that ODDSOC2 is not only phylogenetically related to FLC in eudicots but also functions as a flowering repressor in the vernalization pathway of Brachypodium and likely other temperate grasses. These insights could prove useful in breeding efforts to refine the vernalization requirement of temperate cereals and adapt varieties to changing climates.}, language = {en} } @article{LangenhanJaegerBaumetal.2022, author = {Langenhan, Jennifer and Jaeger, Carsten and Baum, Katharina and Simon, Mareike and Lisec, Jan}, title = {A flexible tool to correct superimposed mass isotopologue distributions in GC-APCI-MS flux experiments}, series = {Metabolites}, volume = {12}, journal = {Metabolites}, number = {5}, publisher = {MDPI}, address = {Basel}, issn = {2218-1989}, doi = {10.3390/metabo12050408}, pages = {10}, year = {2022}, abstract = {The investigation of metabolic fluxes and metabolite distributions within cells by means of tracer molecules is a valuable tool to unravel the complexity of biological systems. Technological advances in mass spectrometry (MS) technology such as atmospheric pressure chemical ionization (APCI) coupled with high resolution (HR), not only allows for highly sensitive analyses but also broadens the usefulness of tracer-based experiments, as interesting signals can be annotated de novo when not yet present in a compound library. However, several effects in the APCI ion source, i.e., fragmentation and rearrangement, lead to superimposed mass isotopologue distributions (MID) within the mass spectra, which need to be corrected during data evaluation as they will impair enrichment calculation otherwise. Here, we present and evaluate a novel software tool to automatically perform such corrections. We discuss the different effects, explain the implemented algorithm, and show its application on several experimental datasets. This adjustable tool is available as an R package from CRAN.}, language = {en} } @article{ChiarcosDipperGoetzeetal.2008, author = {Chiarcos, Christian and Dipper, Stefanie and G{\"o}tze, Michael and Leser, Ulf and L{\"u}deling, Anke and Ritz, Julia and Stede, Manfred}, title = {A flexible framework for integrating annotations from different tools and tag sets}, issn = {1248-9433}, year = {2008}, abstract = {We present a general framework for integrating annotations from different tools and tag sets. When annotating corpora at multiple linguistic levels, annotators may use different expert tools for different phenomena or types of annotation. These tools employ different data models and accompanying approaches to visualization, and they produce different output formats. For the purposes of uniformly processing these outputs, we developed a pivot format called PAULA, along with converters to and from tool formats. Different annotations are not only integrated at the level of data format, but are also joined on the level of conceptual representation. For this purpose, we introduce OLiA, an ontology of linguistic annotations that mediates between alternative tag sets that cover the same class of linguistic phenomena. All components are integrated in the linguistic information system ANNIS : Annotation tool output is converted to the pivot format PAULA and read into a database where the data can be visualized, queried, and evaluated across multiple layers. For cross-tag set querying and statistical evaluation, ANNIS uses the ontology of linguistic annotations. Finally, ANNIS is also tied to a machine learning component for semiautomatic annotation.}, language = {en} } @article{RoethleinMiettinenIgnatova2015, author = {R{\"o}thlein, Christoph and Miettinen, Markus S. and Ignatova, Zoya}, title = {A flexible approach to assess fluorescence decay functions in complex energy transfer systems}, series = {BMC biophysics}, volume = {8}, journal = {BMC biophysics}, publisher = {BioMed Central}, address = {London}, issn = {2046-1682}, doi = {10.1186/s13628-015-0020-z}, pages = {10}, year = {2015}, abstract = {Background: Time-correlated Forster resonance energy transfer (FRET) probes molecular distances with greater accuracy than intensity-based calculation of FRET efficiency and provides a powerful tool to study biomolecular structure and dynamics. Moreover, time-correlated photon count measurements bear additional information on the variety of donor surroundings allowing more detailed differentiation between distinct structural geometries which are typically inaccessible to general fitting solutions. Results: Here we develop a new approach based on Monte Carlo simulations of time-correlated FRET events to estimate the time-correlated single photon counts (TCSPC) histograms in complex systems. This simulation solution assesses the full statistics of time-correlated photon counts and distance distributions of fluorescently labeled biomolecules. The simulations are consistent with the theoretical predictions of the dye behavior in FRET systems with defined dye distances and measurements of randomly distributed dye solutions. We validate the simulation results using a highly heterogeneous aggregation system and explore the conditions to use this tool in complex systems. Conclusion: This approach is powerful in distinguishing distance distributions in a wide variety of experimental setups, thus providing a versatile tool to accurately distinguish between different structural assemblies in highly complex systems.}, language = {en} } @article{ThomasPfrommerPakmor2021, author = {Thomas, Timon and Pfrommer, Christoph and Pakmor, R{\"u}diger}, title = {A finite volume method for two-moment cosmic ray hydrodynamics on a moving mesh}, series = {Monthly notices of the Royal Astronomical Society}, volume = {503}, journal = {Monthly notices of the Royal Astronomical Society}, number = {2}, publisher = {Oxford University Press}, address = {Oxford}, issn = {0035-8711}, doi = {10.1093/mnras/stab397}, pages = {2242 -- 2264}, year = {2021}, abstract = {We present a new numerical algorithm to solve the recently derived equations of two-moment cosmic ray hydrodynamics (CRHD). The algorithm is implemented as a module in the moving mesh AREPO code. Therein, the anisotropic transport of cosmic rays (CRs) along magnetic field lines is discretized using a path-conservative finite volume method on the unstructured time-dependent Voronoi mesh of AREPO. The interaction of CRs and gyroresonant Alfven waves is described by short time-scale source terms in the CRHD equations. We employ a custom-made semi-implicit adaptive time stepping source term integrator to accurately integrate this interaction on the small light-crossing time of the anisotropic transport step. Both the transport and the source term integration step are separated from the evolution of the magnetohydrodynamical equations using an operator split approach. The new algorithm is tested with a variety of test problems, including shock tubes, a perpendicular magnetized discontinuity, the hydrodynamic response to a CR overpressure, CR acceleration of a warm cloud, and a CR blast wave, which demonstrate that the coupling between CR and magnetohydrodynamics is robust and accurate. We demonstrate the numerical convergence of the presented scheme using new linear and non-linear analytic solutions.}, language = {en} } @article{BuschMeissnerPotthoffetal.2015, author = {Busch, Jan Philip and Meißner, Tobias and Potthoff, Annegret and Bleyl, Steffen and Georgi, Anett and Mackenzie, Katrin and Trabitzsch, Ralf and Werban, Ulrike and Oswald, Sascha}, title = {A field investigation on transport of carbon-supported nanoscale zero-valent iron (nZVI) in groundwater}, series = {Journal of contaminant hydrology}, volume = {181}, journal = {Journal of contaminant hydrology}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0169-7722}, doi = {10.1016/j.jconhyd.2015.03.009}, pages = {59 -- 68}, year = {2015}, abstract = {The application of nanoscale zero-valent iron (nZVI) for subsurface remediation of groundwater contaminants is a promising new technology, which can be understood as alternative to the permeable reactive barrier technique using granular iron. Dechlorination of organic contaminants by zero-valent iron seems promising. Currently, one limitation to widespread deployment is the fast agglomeration and sedimentation of nZVI in colloidal suspensions, even more so when in soils and sediments, which limits the applicability for the treatment of sources and plumes of contamination. Colloid-supported nZVI shows promising characteristics to overcome these limitations. Mobility of Carbo-Iron Colloids (CIC) - a newly developed composite material based on finely ground activated carbon as a carrier for nZVI - was tested in a field application: In this study, a horizontal dipole flow field was established between two wells separated by 53 m in a confined, natural aquifer. The injection/extraction rate was 500 L/h. Approximately 12 kg of CIC was suspended with the polyanionic stabilizer carboxymethyl cellulose. The suspension was introduced into the aquifer at the injection well. Breakthrough of CIC was observed visually and based on total particle and iron concentrations detected in samples from the extraction well. Filtration of water samples revealed a particle breakthrough of about 12\% of the amount introduced. This demonstrates high mobility of CIC particles and we suggest that nZVI carried on CIC can be used for contaminant plume remediation by in-situ formation of reactive barriers. (C) 2015 Elsevier B.V. All rights reserved.}, language = {en} } @article{KrauseBekkeringLindemann2013, author = {Krause, Florian and Bekkering, Harold and Lindemann, Oliver}, title = {A feeling for numbers shared metric for symbolic and tactile numerosities}, series = {Frontiers in psychology}, volume = {4}, journal = {Frontiers in psychology}, number = {3}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-1078}, doi = {10.3389/fpsyg.2013.00007}, pages = {8}, year = {2013}, abstract = {Evidence for an approximate analog system of numbers has been provided by the finding that the comparison of two numerals takes longer and is more error-prone if the semantic distance between the numbers becomes smaller (so-called numerical distance effect). Recent embodied theories suggest that analog number representations are based on previous sensory experiences and constitute therefore a common magnitude metric shared by multiple domains. Here we demonstrate the existence of a cross-modal semantic distance effect between symbolic and tactile numerosities. Participants received tactile stimulations of different amounts of fingers while reading Arabic digits and indicated verbally whether the amount of stimulated fingers was different from the simultaneously presented digit or not. The larger the semantic distance was between the two numerosities, the faster and more accurate participants made their judgments. This cross-modal numerosity distance effect suggests a direct connection between tactile sensations and the concept of numerical magnitude. A second experiment replicated the interaction between symbolic and tactile numerosities and showed that this effect is not modulated by the participants' finger counting habits. Taken together, our data provide novel evidence for a shared metric for symbolic and tactile numerosities as an instance of an embodied representation of numbers.}, language = {en} } @article{BrothersKoehlerAttermeyeretal.2014, author = {Brothers, Soren M. and Koehler, J. and Attermeyer, Katrin and Grossart, Hans-Peter and Mehner, T. and Meyer, N. and Scharnweber, Inga Kristin and Hilt, Sabine}, title = {A feedback loop links brownification and anoxia in a temperate, shallow lake}, series = {Limnology and oceanography}, volume = {59}, journal = {Limnology and oceanography}, number = {4}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0024-3590}, doi = {10.4319/lo.2014.59.4.1388}, pages = {1388 -- 1398}, year = {2014}, abstract = {This study examines a natural, rapid, fivefold increase in dissolved organic carbon (DOC) concentrations in a temperate shallow lake, describing the processes by which increased DOC resulted in anoxic conditions and altered existing carbon cycling pathways. High precipitation for two consecutive years led to rising water levels and the flooding of adjacent degraded peatlands. Leaching from the flooded soils provided an initial increase in DOC concentrations (from a 2010 mean of 12 +/- 1 mg L-1 to a maximum concentration of 53 mg L-1 by June 2012). Increasing water levels, DOC, and phytoplankton concentrations reduced light reaching the sediment surface, eliminating most benthic primary production and promoting anoxia in the hypolimnion. From January to June 2012 there was a sudden increase in total phosphorus (from 57 mg L-1 to 216 mg L-1), DOC (from 24.6 mg L-1 to 53 mg L-1), and iron (from 0.12 mg L-1 to 1.07 mg L-1) concentrations, without any further large fluxes in water levels. We suggest that anoxic conditions at the sediment surface and flooded soils produced a dramatic release of these chemicals that exacerbated brownification and eutrophication, creating anoxic conditions that persisted roughly 6 months below a water depth of 1 m and extended periodically to the water surface. This brownification-anoxia feedback loop resulted in a near-complete loss of macroinvertebrate and fish populations, and increased surface carbon dioxide (CO2) emissions by an order of magnitude relative to previous years.}, language = {en} } @article{XiaoLiuWangetal.2020, author = {Xiao, Shangbin and Liu, Liu and Wang, Wei and Lorke, Andreas and Woodhouse, Jason Nicholas and Grossart, Hans-Peter}, title = {A Fast-Response Automated Gas Equilibrator (FaRAGE) for continuous in situ measurement of CH4 and CO2 dissolved in water}, series = {Hydrology and earth system sciences : HESS}, volume = {24}, journal = {Hydrology and earth system sciences : HESS}, number = {7}, publisher = {European Geosciences Union (EGU) ; Copernicus}, address = {Munich}, issn = {1027-5606}, doi = {10.5194/hess-24-3871-2020}, pages = {3871 -- 3880}, year = {2020}, abstract = {Biogenic greenhouse gas emissions, e.g., of methane (CH4) and carbon dioxide (CO2) from inland waters, contribute substantially to global warming. In aquatic systems, dissolved greenhouse gases are highly heterogeneous in both space and time. To better understand the biological and physical processes that affect sources and sinks of both CH4 and CO2, their dissolved concentrations need to be measured with high spatial and temporal resolution. To achieve this goal, we developed the Fast-Response Automated Gas Equilibrator (FaRAGE) for real-time in situ measurement of dissolved CH4 and CO2 concentrations at the water surface and in the water column. FaRAGE can achieve an exceptionally short response time (t(95\%) = 12 s when including the response time of the gas analyzer) while retaining an equilibration ratio of 62.6\% and a measurement accuracy of 0.5\% for CH4. A similar performance was observed for dissolved CO2 (t(95\%) = 10 s, equilibration ratio 67.1 \%). An equilibration ratio as high as 91.8\% can be reached at the cost of a slightly increased response time (16 s). The FaRAGE is capable of continuously measuring dissolved CO2 and CH4 concentrations in the nM-to-submM (10(-9)-10(-3) mol L-1) range with a detection limit of subnM (10(-10) mol L-1), when coupling with a cavity ring-down greenhouse gas analyzer (Picarro GasScouter). FaRAGE allows for the possibility of mapping dissolved concentration in a "quasi" three-dimensional manner in lakes and provides an inexpensive alternative to other commercial gas equilibrators. It is simple to operate and suitable for continuous monitoring with a strong tolerance for suspended particles. While the FaRAGE is developed for inland waters, it can be also applied to ocean waters by tuning the gas-water mixing ratio. The FaRAGE is easily adapted to suit other gas analyzers expanding the range of potential applications, including nitrous oxide and isotopic composition of the gases.}, language = {en} } @article{ZieheLaskovNolteetal.2004, author = {Ziehe, Andreas and Laskov, Pavel and Nolte, G and M{\"u}ller, Klaus-Robert}, title = {A fast algorithm for joint diagonalization with non-orthogonal transformations and its application to blind source separation}, year = {2004}, abstract = {A new efficient algorithm is presented for joint diagonalization of several matrices. The algorithm is based on the Frobenius-norm formulation of the joint diagonalization problem, and addresses diagonalization with a general, non- orthogonal transformation. The iterative scheme of the algorithm is based on a multiplicative update which ensures the invertibility of the diagonalizer. The algorithm's efficiency stems from the special approximation of the cost function resulting in a sparse, block-diagonal Hessian to be used in the computation of the quasi-Newton update step. Extensive numerical simulations illustrate the performance of the algorithm and provide a comparison to other leading diagonalization methods. The results of such comparison demonstrate that the proposed algorithm is a viable alternative to existing state-of-the-art joint diagonalization algorithms. The practical use of our algorithm is shown for blind source separation problems}, language = {en} } @article{Lledo1997, author = {Lled{\´o}, Fernando}, title = {A family of examples with quantum constraints}, year = {1997}, language = {en} } @article{DemalHeiseReizetal.2019, author = {Demal, Till Joscha and Heise, Melina and Reiz, Benedikt and Dogra, Deepika and Braenne, Ingrid and Reichenspurner, Hermann and M{\"a}nner, J{\"o}rg and Aherrahrou, Zouhair and Schunkert, Heribert and Erdmann, Jeanette and Abdelilah-Seyfried, Salim}, title = {A familial congenital heart disease with a possible multigenic origin involving a mutation in BMPR1A}, series = {Scientific reports}, volume = {9}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-019-39648-7}, pages = {12}, year = {2019}, abstract = {The genetics of many congenital heart diseases (CHDs) can only unsatisfactorily be explained by known chromosomal or Mendelian syndromes. Here, we present sequencing data of a family with a potentially multigenic origin of CHD. Twelve of nineteen family members carry a familial mutation [NM_004329.2:c.1328 G > A (p.R443H)] which encodes a predicted deleterious variant of BMPR1A. This mutation co-segregates with a linkage region on chromosome 1 that associates with the emergence of severe CHDs including Ebstein's anomaly, atrioventricular septal defect, and others. We show that the continuous overexpression of the zebrafish homologous mutation bmpr1aap.R438H within endocardium causes a reduced AV valve area, a downregulation of Wnt/ß-catenin signalling at the AV canal, and growth of additional tissue mass in adult zebrafish hearts. This finding opens the possibility of testing genetic interactions between BMPR1A and other candidate genes within linkage region 1 which may provide a first step towards unravelling more complex genetic patterns in cardiovascular disease aetiology.}, language = {en} } @article{Hassler2006, author = {Haßler, Gerda}, title = {A Fala : normalizaci{\´o}n tard{\´i}a e identidad cultural}, year = {2006}, language = {en} } @article{LassGronau2020, author = {Lass, Sander and Gronau, Norbert}, title = {A factory operating system for extending existing factories to Industry 4.0}, series = {Computers in industry : an international, application oriented research journal}, volume = {115}, journal = {Computers in industry : an international, application oriented research journal}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0166-3615}, doi = {10.1016/j.compind.2019.103128}, pages = {8}, year = {2020}, abstract = {Cyber-physical systems (CPS) have shaped the discussion about Industry 4.0 (I4.0) for some time. To ensure the competitiveness of manufacturing enterprises the vision for the future figures out cyber-physical production systems (CPPS) as a core component of a modern factory. Adaptability and coping with complexity are (among others) potentials of this new generation of production management. The successful transformation of this theoretical construct into practical implementation can only take place with regard to the conditions characterizing the context of a factory. The subject of this contribution is a concept that takes up the brownfield character and describes a solution for extending existing (legacy) systems with CPS capabilities.}, language = {en} } @article{RullensDeligneLaschewskyetal.2005, author = {Rullens, F. and Deligne, N. and Laschewsky, Andr{\´e} and Devillers, M.}, title = {A facile precursor route to transition metal molybdates using a polyzwitterionic matrix bearing simultaneously charged moieties and complexing groups}, issn = {0959-9428}, year = {2005}, abstract = {An unconventional but easily accessible precursor route involving the thermal treatment of hybrid precursors containing an ampholytic polymer matrix is developed to prepare multimetallic oxides of catalytic interest such as transition metal molybdates. A copolymer of diallyldimethylammonium chloride and a functionalized maleamic acid bearing an amine group suited for cation complexation was designed, synthesized and used as a matrix to stabilize inorganic species generated in solution from Ni(NO3)(2)center dot 6H(2)O, Co(NO3)(2)center dot 6H(2)O and/or Mn(NO3)(2)center dot 4H(2)O together with (NH4)(6)Mo(7)O(24)center dot 4H(2)O. UV-vis-NIR as well as C-13-NMR studies suggest that the interactions between the cations and the polymer in solution are mainly electrostatic. Only minor complexation interactions take place under certain conditions. Homogeneous hybrid blends were prepared from these solutions. The presence of a complexing amine group in addition to the charged betaine moieties in the polymer permits stabilization of more than stoichiometric amounts of the metal species in the blends. XRD measurements suggest that the homogeneity in the solid state can be kept up to about 1.5 mol of each metal that is incorporated ( anionic as well as cationic) per mol of repeat units of the copolymer. The blends were calcined under air at 600 degrees C to produce the simple as well as mixed nickel, cobalt and manganese molybdates. Characterization of the final phases by XRD and Raman spectroscopy indicates that the alpha- as well as the beta-molybdate phases can be prepared, and that the mixed structures are solid solutions of the simple NiMoO4, MnMoO4 and CoMoO4. If the precursors engaged are homogeneous, the pH of the precursor solution, the amount of metal that is incorporated in the matrix, and the nature of the polymer matrix seem to exert only a minor influence on the nature of the final phase, which demonstrates the versatility and facile applicability of the method}, language = {en} } @article{HartmanGentzSchilleretal.2018, author = {Hartman, Jan F. and Gentz, Torben and Schiller, Amanda and Greule, Markus and Grossart, Hans-Peter and Ionescu, Danny and Keppler, Frank and Martinez-Cruz, Karla and Sepulveda-Jauregui, Armando and Isenbeck-Schroeter, Margot}, title = {A f ast and sensitive method for the continuous in situ determination of dissolved methane and its delta C-13-isotope ratio in surface waters}, series = {Limnology and Oceanography-methods}, volume = {16}, journal = {Limnology and Oceanography-methods}, number = {5}, publisher = {Wiley}, address = {Hoboken}, issn = {1541-5856}, doi = {10.1002/lom3.10244}, pages = {273 -- 285}, year = {2018}, abstract = {A fast and sensitive method for the continuous determination of methane (CH4) and its stable carbon isotopic values (delta C-13-CH4) in surface waters was developed by applying a vacuum to a gas/liquid exchange membrane and measuring the extracted gases by a portable cavity ring-down spectroscopy analyser (M-CRDS). The M-CRDS was calibrated and characterized for CH4 concentration and delta C-13-CH4 with synthetic water standards. The detection limit of the M-CRDS for the simultaneous determination of CH4 and delta C-13-CH4 is 3.6 nmol L-1 CH4. A measurement precision of CH4 concentrations and delta C-13-CH4 in the range of 1.1\%, respectively, 1.7 parts per thousand (1 sigma) and accuracy (1.3\%, respectively, 0.8 parts per thousand [1 sigma]) was achieved for single measurements and averaging times of 10 min. The response time tau of 57 +/- 5 s allow determination of delta C-13-CH4 values more than twice as fast than other methods. The demonstrated M-CRDS method was applied and tested for Lake Stechlin (Germany) and compared with the headspace-gas chromatography and fast membrane CH4 concentration methods. Maximum CH4 concentrations (577 nmol L-1) and lightest delta C-13-CH4 (-35.2 parts per thousand) were found around the thermocline in depth profile measurements. The M-CRDS-method was in good agreement with other methods. Temporal variations in CH4 concentration and delta C-13-CH4 obtained in 24 h measurements indicate either local methane production/oxidation or physical variations in the thermocline. Therefore, these results illustrate the need of fast and sensitive analyses to achieve a better understanding of different mechanisms and pathways of CH4 formation in aquatic environments.}, language = {en} } @article{Reich2011, author = {Reich, Sebastian}, title = {A dynamical systems framework for intermittent data assimilation}, series = {BIT : numerical mathematics ; the leading applied mathematics journal for all computational mathematicians}, volume = {51}, journal = {BIT : numerical mathematics ; the leading applied mathematics journal for all computational mathematicians}, number = {1}, publisher = {Springer}, address = {Dordrecht}, issn = {0006-3835}, doi = {10.1007/s10543-010-0302-4}, pages = {235 -- 249}, year = {2011}, abstract = {We consider the problem of discrete time filtering (intermittent data assimilation) for differential equation models and discuss methods for its numerical approximation. The focus is on methods based on ensemble/particle techniques and on the ensemble Kalman filter technique in particular. We summarize as well as extend recent work on continuous ensemble Kalman filter formulations, which provide a concise dynamical systems formulation of the combined dynamics-assimilation problem. Possible extensions to fully nonlinear ensemble/particle based filters are also outlined using the framework of optimal transportation theory.}, language = {en} } @article{SchwetlickBackhausEngbert2023, author = {Schwetlick, Lisa and Backhaus, Daniel and Engbert, Ralf}, title = {A dynamical scan-path model for task-dependence during scene viewing}, series = {Psychological review}, volume = {130}, journal = {Psychological review}, number = {3}, publisher = {American Psychological Association}, address = {Washington}, issn = {0033-295X}, doi = {10.1037/rev0000379}, pages = {807 -- 840}, year = {2023}, abstract = {In real-world scene perception, human observers generate sequences of fixations to move image patches into the high-acuity center of the visual field. Models of visual attention developed over the last 25 years aim to predict two-dimensional probabilities of gaze positions for a given image via saliency maps. Recently, progress has been made on models for the generation of scan paths under the constraints of saliency as well as attentional and oculomotor restrictions. Experimental research demonstrated that task constraints can have a strong impact on viewing behavior. Here, we propose a scan-path model for both fixation positions and fixation durations, which include influences of task instructions and interindividual differences. Based on an eye-movement experiment with four different task conditions, we estimated model parameters for each individual observer and task condition using a fully Bayesian dynamical modeling framework using a joint spatial-temporal likelihood approach with sequential estimation. Resulting parameter values demonstrate that model properties such as the attentional span are adjusted to task requirements. Posterior predictive checks indicate that our dynamical model can reproduce task differences in scan-path statistics across individual observers.}, language = {en} }