@misc{LinKhajooeiEngeletal.2012, author = {Lin, Chiao-I and Khajooei, Mina and Engel, Tilman and Nair, Alexandra and Heikkila, Mika and Kaplick, Hannes and Mayer, Frank}, title = {The effect of chronic ankle instability on muscle activations in lower extremities}, series = {Postprints der Universit{\"a}t Potsdam : Humanwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Humanwissenschaftliche Reihe}, issn = {1866-8364}, doi = {10.25932/publishup-51563}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-515632}, pages = {17}, year = {2012}, abstract = {Background/Purpose Muscular reflex responses of the lower extremities to sudden gait disturbances are related to postural stability and injury risk. Chronic ankle instability (CAI) has shown to affect activities related to the distal leg muscles while walking. Its effects on proximal muscle activities of the leg, both for the injured- (IN) and uninjured-side (NON), remain unclear. Therefore, the aim was to compare the difference of the motor control strategy in ipsilateral and contralateral proximal joints while unperturbed walking and perturbed walking between individuals with CAI and matched controls. Materials and methods In a cross-sectional study, 13 participants with unilateral CAI and 13 controls (CON) walked on a split-belt treadmill with and without random left- and right-sided perturbations. EMG amplitudes of muscles at lower extremities were analyzed 200 ms after perturbations, 200 ms before, and 100 ms after (Post100) heel contact while walking. Onset latencies were analyzed at heel contacts and after perturbations. Statistical significance was set at alpha≤0.05 and 95\% confidence intervals were applied to determine group differences. Cohen's d effect sizes were calculated to evaluate the extent of differences. Results Participants with CAI showed increased EMG amplitudes for NON-rectus abdominus at Post100 and shorter latencies for IN-gluteus maximus after heel contact compared to CON (p<0.05). Overall, leg muscles (rectus femoris, biceps femoris, and gluteus medius) activated earlier and less bilaterally (d = 0.30-0.88) and trunk muscles (bilateral rectus abdominus and NON-erector spinae) activated earlier and more for the CAI group than CON group (d = 0.33-1.09). Conclusion Unilateral CAI alters the pattern of the motor control strategy around proximal joints bilaterally. Neuromuscular training for the muscles, which alters motor control strategy because of CAI, could be taken into consideration when planning rehabilitation for CAI.}, language = {en} } @misc{EbertLamprechtSteffenetal.2012, author = {Ebert, Birgitta E. and Lamprecht, Anna-Lena and Steffen, Bernhard and Blank, Lars M.}, title = {Flux-P}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1054}, issn = {1866-8372}, doi = {10.25932/publishup-47669}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-476696}, pages = {872 -- 890}, year = {2012}, abstract = {Quantitative knowledge of intracellular fluxes in metabolic networks is invaluable for inferring metabolic system behavior and the design principles of biological systems. However, intracellular reaction rates can not often be calculated directly but have to be estimated; for instance, via 13C-based metabolic flux analysis, a model-based interpretation of stable carbon isotope patterns in intermediates of metabolism. Existing software such as FiatFlux, OpenFLUX or 13CFLUX supports experts in this complex analysis, but requires several steps that have to be carried out manually, hence restricting the use of this software for data interpretation to a rather small number of experiments. In this paper, we present Flux-P as an approach to automate and standardize 13C-based metabolic flux analysis, using the Bio-jETI workflow framework. Exemplarily based on the FiatFlux software, it demonstrates how services can be created that carry out the different analysis steps autonomously and how these can subsequently be assembled into software workflows that perform automated, high-throughput intracellular flux analysis of high quality and reproducibility. Besides significant acceleration and standardization of the data analysis, the agile workflow-based realization supports flexible changes of the analysis workflows on the user level, making it easy to perform custom analyses.}, language = {en} } @misc{CaliendoHogenacker2012, author = {Caliendo, Marco and Hogenacker, Jens}, title = {The German labor market after the Great Recession}, series = {Postprints der Universit{\"a}t Potsdam : Wirtschafts- und Sozialwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Wirtschafts- und Sozialwissenschaftliche Reihe}, number = {129}, issn = {1867-5808}, doi = {10.25932/publishup-43519}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-435195}, pages = {26}, year = {2012}, abstract = {The reaction of the German labor market to the Great Recession 2008/09 was relatively mild - especially compared to other countries. The reason lies not only in the specific type of the recession - which was favorable for the German economy structure - but also in a series of labor market reforms initiated between 2002 and 2005 altering, inter alia, labor supply incentives. However, irrespective of the mild response to the Great Recession, there are a number of substantial future challenges the German labor market will soon have to face. Female labor supply still lies well below that of other countries and a massive demographic change over the next 50 years will have substantial effects on labor supply as well as the pension system. In addition, due to a skill-biased technological change over the next decades, firms will face problems of finding employees with adequate skills. The aim of this paper is threefold. First, we outline why the German labor market reacted in such a mild fashion, describe current economic trends of the labor market in light of general trends in the European Union, and reveal some of the main associated challenges. Thereafter, the paper analyzes recent reforms of the main institutional settings of the labor market which influence labor supply. Finally, based on the status quo of these institutional settings, the paper gives a brief overview of strategies to combat adequately the challenges in terms of labor supply and to ensure economic growth in the future.}, language = {en} } @misc{KrippendorffOyarzunHuisinga2012, author = {Krippendorff, Ben-Fillippo and Oyarz{\´u}n, Diego A. and Huisinga, Wilhelm}, title = {Predicting the F(ab)-mediated effect of monoclonal antibodies in vivo by combining cell-level kinetic and pharmacokinetic modelling}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {958}, issn = {1866-8372}, doi = {10.25932/publishup-43105}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431051}, pages = {125 -- 139}, year = {2012}, abstract = {Cell-level kinetic models for therapeutically relevant processes increasingly benefit the early stages of drug development. Later stages of the drug development processes, however, rely on pharmacokinetic compartment models while cell-level dynamics are typically neglected. We here present a systematic approach to integrate cell-level kinetic models and pharmacokinetic compartment models. Incorporating target dynamics into pharmacokinetic models is especially useful for the development of therapeutic antibodies because their effect and pharmacokinetics are inherently interdependent. The approach is illustrated by analysing the F(ab)-mediated inhibitory effect of therapeutic antibodies targeting the epidermal growth factor receptor. We build a multi-level model for anti-EGFR antibodies by combining a systems biology model with in vitro determined parameters and a pharmacokinetic model based on in vivo pharmacokinetic data. Using this model, we investigated in silico the impact of biochemical properties of anti-EGFR antibodies on their F(ab)-mediated inhibitory effect. The multi-level model suggests that the F(ab)-mediated inhibitory effect saturates with increasing drug-receptor affinity, thereby limiting the impact of increasing antibody affinity on improving the effect. This indicates that observed differences in the therapeutic effects of high affinity antibodies in the market and in clinical development may result mainly from Fc-mediated indirect mechanisms such as antibody-dependent cell cytotoxicity.}, language = {en} } @misc{LarhlimiDavidSelbigetal.2012, author = {Larhlimi, Abdelhalim and David, Laszlo and Selbig, Joachim and Bockmayr, Alexander}, title = {F2C2}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {921}, issn = {1866-8372}, doi = {10.25932/publishup-43243}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-432431}, pages = {11}, year = {2012}, abstract = {Background: Flux coupling analysis (FCA) has become a useful tool in the constraint-based analysis of genome-scale metabolic networks. FCA allows detecting dependencies between reaction fluxes of metabolic networks at steady-state. On the one hand, this can help in the curation of reconstructed metabolic networks by verifying whether the coupling between reactions is in agreement with the experimental findings. On the other hand, FCA can aid in defining intervention strategies to knock out target reactions. Results: We present a new method F2C2 for FCA, which is orders of magnitude faster than previous approaches. As a consequence, FCA of genome-scale metabolic networks can now be performed in a routine manner. Conclusions: We propose F2C2 as a fast tool for the computation of flux coupling in genome-scale metabolic networks. F2C2 is freely available for non-commercial use at https://sourceforge.net/projects/f2c2/files/.}, language = {en} } @misc{Lenhard2012, author = {Lenhard, Michael}, title = {All's well that ends well}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {906}, issn = {1866-8372}, doi = {10.25932/publishup-43803}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-438035}, pages = {9 -- 11}, year = {2012}, abstract = {The transition from cell proliferation to cell expansion is critical for determining leaf size. Andriankaja et al. (2012) demonstrate that in leaves of dicotyledonous plants, a basal proliferation zone is maintained for several days before abruptly disappearing, and that chloroplast differentiation is required to trigger the onset of cell expansion.}, language = {en} } @misc{DallmeyerClaussenWangetal.2012, author = {Dallmeyer, Anne and Claussen, Martin and Wang, Yongbo and Herzschuh, Ulrike}, title = {Spatial variability of Holocene changes in the annual precipitation pattern}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {905}, issn = {1866-8372}, doi = {10.25932/publishup-43277}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-432771}, pages = {20}, year = {2012}, abstract = {This study provides a detailed analysis of the mid-Holocene to present-day precipitation change in the Asian monsoon region. We compare for the first time results of high resolution climate model simulations with a standardised set of mid-Holocene moisture reconstructions. Changes in the simulated summer monsoon characteristics (onset, withdrawal, length and associated rainfall) and the mechanisms causing the Holocene precipitation changes are investigated. According to the model, most parts of the Indian subcontinent received more precipitation (up to 5 mm/day) at mid-Holocene than at present-day. This is related to a stronger Indian summer monsoon accompanied by an intensified vertically integrated moisture flux convergence. The East Asian monsoon region exhibits local inhomogeneities in the simulated annual precipitation signal. The sign of this signal depends on the balance of decreased pre-monsoon and increased monsoon precipitation at mid-Holocene compared to present-day. Hence, rainfall changes in the East Asian monsoon domain are not solely associated with modifications in the summer monsoon circulation but also depend on changes in the mid-latitudinal westerly wind system that dominates the circulation during the pre-monsoon season. The proxy-based climate reconstructions confirm the regional dissimilarities in the annual precipitation signal and agree well with the model results. Our results highlight the importance of including the pre-monsoon season in climate studies of the Asian monsoon system and point out the complex response of this system to the Holocene insolation forcing. The comparison with a coarse climate model simulation reveals that this complex response can only be resolved in high resolution simulations.}, language = {en} } @misc{ChengVicente2012, author = {Cheng, Lisa Lai-Shen and Vicente, Luis}, title = {Verb doubling in Mandarin Chinese}, series = {Postprints der Universit{\"a}t Potsdam : Humanwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Humanwissenschaftliche Reihe}, number = {629}, issn = {1866-8364}, doi = {10.25932/publishup-43688}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-436880}, pages = {1 -- 37}, year = {2012}, abstract = {This article examines two so-far-understudied verb doubling constructions in Mandarin Chinese, viz., verb doubling clefts and verb doubling lian…dou. We show that these constructions have the same internal syntax as regular clefts and lian…dou sentences, the doubling effect being epiphenomenal; therefore, we classify them as subtypes of the general cleft and lian…dou constructions, respectively, rather than as independent constructions. Additionally, we also show that, as in many other languages with comparable constructions, the two instances of the verb are part of a single movement chain, which has the peculiarity of allowing Spell-Out of more than one link.}, language = {en} } @misc{PowellLenhard2012, author = {Powell, Anahid E. and Lenhard, Michael}, title = {Control of organ size in plants}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {898}, issn = {1866-8372}, doi = {10.25932/publishup-43802}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-438029}, pages = {10}, year = {2012}, abstract = {The size of plant organs, such as leaves and flowers, is determined by an interaction of genotype and environmental influences. Organ growth occurs through the two successive processes of cell proliferation followed by cell expansion. A number of genes influencing either or both of these processes and thus contributing to the control of final organ size have been identified in the last decade. Although the overall picture of the genetic regulation of organ size remains fragmentary, two transcription factor/microRNA-based genetic pathways are emerging in the control of cell proliferation. However, despite this progress, fundamental questions remain unanswered, such as the problem of how the size of a growing organ could be monitored to determine the appropriate time for terminating growth. While genetic analysis will undoubtedly continue to advance our knowledge about size control in plants, a deeper understanding of this and other basic questions will require including advanced live-imaging and mathematical modeling, as impressively demonstrated by some recent examples. This should ultimately allow the comparison of the mechanisms underlying size control in plants and in animals to extract common principles and lineage-specific solutions.}, language = {en} } @misc{WojcinskiDupontSchmidtetal.2012, author = {Wojcinski, Sebastian and Dupont, Jennifer and Schmidt, Werner and Cassel, Michael and Hillemanns, Peter}, title = {Real-time ultrasound elastography in 180 axillary lymph nodes}, series = {Postprints der Universit{\"a}t Potsdam : Humanwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Humanwissenschaftliche Reihe}, number = {626}, issn = {1866-8364}, doi = {10.25932/publishup-43158}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431584}, pages = {12}, year = {2012}, abstract = {Background To determine the general appearance of normal axillary lymph nodes (LNs) in real-time tissue sonoelastography and to explore the method′s potential value in the prediction of LN metastases. Methods Axillary LNs in healthy probands (n=165) and metastatic LNs in breast cancer patients (n=15) were examined with palpation, B-mode ultrasound, Doppler and sonoelastography (assessment of the elasticity of the cortex and the medulla). The elasticity distributions were compared and sensitivity (SE) and specificity (SP) were calculated. In an exploratory analysis, positive and negative predictive values (PPV, NPV) were calculated based upon the estimated prevalence of LN metastases in different risk groups. Results In the elastogram, the LN cortex was significantly harder than the medulla in both healthy (p=0.004) and metastatic LNs (p=0.005). Comparing healthy and metastatic LNs, there was no difference in the elasticity distribution of the medulla (p=0.281), but we found a significantly harder cortex in metastatic LNs (p=0.006). The SE of clinical examination, B-mode ultrasound, Doppler ultrasound and sonoelastography was revealed to be 13.3\%, 40.0\%, 14.3\% and 60.0\%, respectively, and SP was 88.4\%, 96.8\%, 95.6\% and 79.6\%, respectively. The highest SE was achieved by the disjunctive combination of B-mode and elastographic features (cortex >3mm in B-mode or blue cortex in the elastogram, SE=73.3\%). The highest SP was achieved by the conjunctive combination of B-mode ultrasound and elastography (cortex >3mm in B-mode and blue cortex in the elastogram, SP=99.3\%). Conclusions Sonoelastography is a feasible method to visualize the elasticity distribution of LNs. Moreover, sonoelastography is capable of detecting elasticity differences between the cortex and medulla, and between metastatic and healthy LNs. Therefore, sonoelastography yields additional information about axillary LN status and can improve the PPV, although this method is still experimental.}, language = {en} } @misc{JingAmbroseKnoxetal.2012, author = {Jing, Runchun and Ambrose, Michael A. and Knox, Maggie R. and Smykal, Petr and Hybl, Miroslav and Ramos, {\´A}. and Caminero, Constantino and Burstin, Judith and Duc, Gerard and van Soest, L. J. M. and Święcicki, W. K. and Pereira, M. Graca and Vishnyakova, Margarita and Davenport, Guy F. and Flavell, Andrew J. and Ellis, T. H. Noel}, title = {Genetic diversity in European Pisum germplasm collections}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {871}, issn = {1866-8372}, doi = {10.25932/publishup-43474}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-434743}, pages = {367 -- 380}, year = {2012}, abstract = {The distinctness of, and overlap between, pea genotypes held in several Pisum germplasm collections has been used to determine their relatedness and to test previous ideas about the genetic diversity of Pisum. Our characterisation of genetic diversity among 4,538 Pisum accessions held in 7 European Genebanks has identified sources of novel genetic variation, and both reinforces and refines previous interpretations of the overall structure of genetic diversity in Pisum. Molecular marker analysis was based upon the presence/absence of polymorphism of retrotransposon insertions scored by a high-throughput microarray and SSAP approaches. We conclude that the diversity of Pisum constitutes a broad continuum, with graded differentiation into sub-populations which display various degrees of distinctness. The most distinct genetic groups correspond to the named taxa while the cultivars and landraces of Pisum sativum can be divided into two broad types, one of which is strongly enriched for modern cultivars. The addition of germplasm sets from six European Genebanks, chosen to represent high diversity, to a single collection previously studied with these markers resulted in modest additions to the overall diversity observed, suggesting that the great majority of the total genetic diversity collected for the Pisum genus has now been described. Two interesting sources of novel genetic variation have been identified. Finally, we have proposed reference sets of core accessions with a range of sample sizes to represent Pisum diversity for the future study and exploitation by researchers and breeders.}, language = {en} } @misc{AdamBovend'EerdtDoorenetal.2012, author = {Adam, Jos J. and Bovend'Eerdt, Thamar J. H. and Dooren, Fleur E. P. van and Fischer, Martin H. and Pratt, Jay}, title = {The closer the better}, series = {Postprints der Universit{\"a}t Potsdam : Humanwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Humanwissenschaftliche Reihe}, number = {607}, issn = {1866-8364}, doi = {10.25932/publishup-43296}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-432963}, pages = {1533 -- 1538}, year = {2012}, abstract = {A growing literature has suggested that processing of visual information presented near the hands is facilitated. In this study, we investigated whether the near-hands superiority effect also occurs with the hands moving. In two experiments, participants performed a cyclical bimanual movement task requiring concurrent visual identification of briefly presented letters. For both the static and dynamic hand conditions, the results showed improved letter recognition performance with the hands closer to the stimuli. The finding that the encoding advantage for near-hand stimuli also occurred with the hands moving suggests that the effect is regulated in real time, in accordance with the concept of a bimodal neural system that dynamically updates hand position in external space.}, language = {en} } @misc{KruegelVituEngbert2012, author = {Kr{\"u}gel, Andr{\´e} and Vitu, Fran{\c{c}}oise and Engbert, Ralf}, title = {Fixation positions after skipping saccades}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {856}, issn = {1866-8372}, doi = {10.25932/publishup-43288}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-432887}, pages = {1556 -- 1561}, year = {2012}, abstract = {During reading, saccadic eye movements are generated to shift words into the center of the visual field for lexical processing. Recently, Krugel and Engbert (Vision Research 50:1532-1539, 2010) demonstrated that within-word fixation positions are largely shifted to the left after skipped words. However, explanations of the origin of this effect cannot be drawn from normal reading data alone. Here we show that the large effect of skipped words on the distribution of within-word fixation positions is primarily based on rather subtle differences in the low-level visual information acquired before saccades. Using arrangements of "x" letter strings, we reproduced the effect of skipped character strings in a highly controlled single-saccade task. Our results demonstrate that the effect of skipped words in reading is the signature of a general visuomotor phenomenon. Moreover, our findings extend beyond the scope of the widely accepted range-error model, which posits that within-word fixation positions in reading depend solely on the distances of target words. We expect that our results will provide critical boundary conditions for the development of visuomotor models of saccade planning during reading.}, language = {en} } @misc{KleessenNikoloski2012, author = {Kleessen, Sabrina and Nikoloski, Zoran}, title = {Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {852}, issn = {1866-8372}, doi = {10.25932/publishup-43112}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431128}, pages = {15}, year = {2012}, abstract = {Background: Flux balance analysis (FBA) together with its extension, dynamic FBA, have proven instrumental for analyzing the robustness and dynamics of metabolic networks by employing only the stoichiometry of the included reactions coupled with adequately chosen objective function. In addition, under the assumption of minimization of metabolic adjustment, dynamic FBA has recently been employed to analyze the transition between metabolic states. Results: Here, we propose a suite of novel methods for analyzing the dynamics of (internally perturbed) metabolic networks and for quantifying their robustness with limited knowledge of kinetic parameters. Following the biochemically meaningful premise that metabolite concentrations exhibit smooth temporal changes, the proposed methods rely on minimizing the significant fluctuations of metabolic profiles to predict the time-resolved metabolic state, characterized by both fluxes and concentrations. By conducting a comparative analysis with a kinetic model of the Calvin-Benson cycle and a model of plant carbohydrate metabolism, we demonstrate that the principle of regulatory on/off minimization coupled with dynamic FBA can accurately predict the changes in metabolic states. Conclusions: Our methods outperform the existing dynamic FBA-based modeling alternatives, and could help in revealing the mechanisms for maintaining robustness of dynamic processes in metabolic networks over time.}, language = {en} } @misc{HischeLarhlimiSchwarzetal.2012, author = {Hische, Manuela and Larhlimi, Abdelhalim and Schwarz, Franziska and Fischer-Rosinsk{\´y}, Antje and Bobbert, Thomas and Assmann, Anke and Catchpole, Gareth S. and Pfeiffer, Andreas F. H. and Willmitzer, Lothar and Selbig, Joachim and Spranger, Joachim}, title = {A distinct metabolic signature predictsdevelopment of fasting plasma glucose}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {850}, issn = {1866-8372}, doi = {10.25932/publishup-42740}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-427400}, pages = {12}, year = {2012}, abstract = {Background High blood glucose and diabetes are amongst the conditions causing the greatest losses in years of healthy life worldwide. Therefore, numerous studies aim to identify reliable risk markers for development of impaired glucose metabolism and type 2 diabetes. However, the molecular basis of impaired glucose metabolism is so far insufficiently understood. The development of so called 'omics' approaches in the recent years promises to identify molecular markers and to further understand the molecular basis of impaired glucose metabolism and type 2 diabetes. Although univariate statistical approaches are often applied, we demonstrate here that the application of multivariate statistical approaches is highly recommended to fully capture the complexity of data gained using high-throughput methods. Methods We took blood plasma samples from 172 subjects who participated in the prospective Metabolic Syndrome Berlin Potsdam follow-up study (MESY-BEPO Follow-up). We analysed these samples using Gas Chromatography coupled with Mass Spectrometry (GC-MS), and measured 286 metabolites. Furthermore, fasting glucose levels were measured using standard methods at baseline, and after an average of six years. We did correlation analysis and built linear regression models as well as Random Forest regression models to identify metabolites that predict the development of fasting glucose in our cohort. Results We found a metabolic pattern consisting of nine metabolites that predicted fasting glucose development with an accuracy of 0.47 in tenfold cross-validation using Random Forest regression. We also showed that adding established risk markers did not improve the model accuracy. However, external validation is eventually desirable. Although not all metabolites belonging to the final pattern are identified yet, the pattern directs attention to amino acid metabolism, energy metabolism and redox homeostasis. Conclusions We demonstrate that metabolites identified using a high-throughput method (GC-MS) perform well in predicting the development of fasting plasma glucose over several years. Notably, not single, but a complex pattern of metabolites propels the prediction and therefore reflects the complexity of the underlying molecular mechanisms. This result could only be captured by application of multivariate statistical approaches. Therefore, we highly recommend the usage of statistical methods that seize the complexity of the information given by high-throughput methods.}, language = {en} } @misc{HoppeBiervonNickischRosenegk2012, author = {Hoppe, Sebastian and Bier, Frank Fabian and von Nickisch-Rosenegk, Markus}, title = {Microarray-based method for screening of immunogenic proteins from bacteria}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {726}, issn = {1866-8372}, doi = {10.25932/publishup-42981}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-429815}, pages = {12}, year = {2012}, abstract = {Background: Detection of immunogenic proteins remains an important task for life sciences as it nourishes the understanding of pathogenicity, illuminates new potential vaccine candidates and broadens the spectrum of biomarkers applicable in diagnostic tools. Traditionally, immunoscreenings of expression libraries via polyclonal sera on nitrocellulose membranes or screenings of whole proteome lysates in 2-D gel electrophoresis are performed. However, these methods feature some rather inconvenient disadvantages. Screening of expression libraries to expose novel antigens from bacteria often lead to an abundance of false positive signals owing to the high cross reactivity of polyclonal antibodies towards the proteins of the expression host. A method is presented that overcomes many disadvantages of the old procedures. Results: Four proteins that have previously been described as immunogenic have successfully been assessed immunogenic abilities with our method. One protein with no known immunogenic behaviour before suggested potential immunogenicity. We incorporated a fusion tag prior to our genes of interest and attached the expressed fusion proteins covalently on microarrays. This enhances the specific binding of the proteins compared to nitrocellulose. Thus, it helps to reduce the number of false positives significantly. It enables us to screen for immunogenic proteins in a shorter time, with more samples and statistical reliability. We validated our method by employing several known genes from Campylobacter jejuni NCTC 11168. Conclusions: The method presented offers a new approach for screening of bacterial expression libraries to illuminate novel proteins with immunogenic features. It could provide a powerful and attractive alternative to existing methods and help to detect and identify vaccine candidates, biomarkers and potential virulence-associated factors with immunogenic behaviour furthering the knowledge of virulence and pathogenicity of studied bacteria.}, language = {en} } @misc{MartinsBergemannBestenlehneretal.2012, author = {Martins, Fabrice and Bergemann, Maria and Bestenlehner, Joachim M. and Crowther, Paul A. and Hamann, Wolf-Rainer and Najarro, Francisco and Nieva, Maria Fernanda and Przybilla, Norbert and Freimanis, Juris and Hou, Weizhen and Kaper, Lex}, title = {SpS5 - II. Stellar and wind parameters}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {688}, issn = {1866-8372}, doi = {10.25932/publishup-41495}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-414956}, pages = {9}, year = {2012}, abstract = {The development of infrared observational facilities has revealed a number of massive stars in obscured environments throughout the Milky Way and beyond. The determination of their stellar and wind properties from infrared diagnostics is thus required to take full advantage of the wealth of observations available in the near and mid infrared. However, the task is challenging. This session addressed some of the problems encountered and showed the limitations and successes of infrared studies of massive stars.}, language = {en} } @misc{MorrisSaltRailaetal.2012, author = {Morris, Penelope J. and Salt, Carina and Raila, Jens and Brenten, Thomas and Kohn, Barbara and Schweigert, Florian J. and Zentek, J{\"u}rgen}, title = {Safety evaluation of vitamin A in growing dogs}, series = {Potsprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Potsprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {686}, doi = {10.25932/publishup-41492}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-414929}, pages = {10}, year = {2012}, abstract = {The safe upper limit for inclusion of vitamin A in complete diets for growing dogs is uncertain, with the result that current recommendations range from 5.24 to 104.80 mu mol retinol (5000 to 100 000 IU vitamin A)/4184 kJ (1000 kcal) metabolisable energy (ME). The aim of the present study was to determine the effect of feeding four concentrations of vitamin A to puppies from weaning until 1 year of age. A total of forty-nine puppies, of two breeds, Labrador Retriever and Miniature Schnauzer, were randomly assigned to one of four treatment groups. Following weaning at 8 weeks of age, puppies were fed a complete food supplemented with retinyl acetate diluted in vegetable oil and fed at 1ml oil/100 g diet to achieve an intake of 5.24, 13.10, 78.60 and 104.80 mu mol retinol (5000, 12 500, 75 000 and 100 000 IU vitamin A)/4184 kJ (1000 kcal) ME. Fasted blood and urine samples were collected at 8, 10, 12, 14, 16, 20, 26, 36 and 52 weeks of age and analysed for markers of vitamin A metabolism and markers of safety including haematological and biochemical variables, bone-specific alkaline phosphatase, cross-linked carboxyterminal telopeptides of type I collagen and dual-energy X-ray absorptiometry. Clinical examinations were conducted every 4 weeks. Data were analysed by means of a mixed model analysis with Bonferroni corrections for multiple endpoints. There was no effect of vitamin A concentration on any of the parameters, with the exception of total serum retinyl esters, and no effect of dose on the number, type and duration of adverse events. We therefore propose that 104.80 mu mol retinol (100 000 IU vitamin A)/4184 kJ (1000 kcal) is a suitable safe upper limit for use in the formulation of diets designed for puppy growth.}, language = {en} } @misc{SuKliemvanBallegooijenetal.2012, author = {Su, Yingna and Kliem, Bernhard and van Ballegooijen, Adriaan and Deluca, Edward}, title = {Numerical simulations of the CME on 2010 April 8}, series = {Solar and Astrophysical Dynamos and Magnetic Activity}, journal = {Solar and Astrophysical Dynamos and Magnetic Activity}, number = {674}, issn = {1866-8372}, doi = {10.25932/publishup-41488}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-414887}, pages = {575 -- 576}, year = {2012}, abstract = {We present 3D zero-beta ideal MHD simulations of the solar flare/CME event that occurred in Active Region 11060 on 2010 April 8. The initial magnetic configurations of the two simulations are stable nonlinear force-free field and unstable magnetic field models constructed by Su et al. (2011) using the flux rope insertion method. The MHD simulations confirm that the stable model relaxes to a stable equilibrium, while the unstable model erupts as a CME. Comparisons between observations and MHD simulations of the CME are also presented.}, language = {en} } @misc{NishikawaZhangChoietal.2012, author = {Nishikawa, K.-I. and Zhang, B. and Choi, E. J. and Min, K. W. and Niemiec, J. and Medvedev, M. and Hardee, P. and Mizuno, Y. and Nordlund, A. and Frederiksen, J. and Sol, H. and Pohl, Martin and Hartmann, D. H. and Fishman, G.J.}, title = {Radiation from accelerated particles in shocks}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {600}, issn = {1866-8372}, doi = {10.25932/publishup-41312}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-413128}, pages = {371 -- 372}, year = {2012}, abstract = {Recent PIC simulations of relativistic electron-positron (electron-ion) jets injected into a stationary medium show that particle acceleration occurs in the shocked regions. Simulations show that the Weibel instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields and for particle acceleration. These magnetic fields contribute to the electron's transverse eflection behind the shock. The "jitter" radiation from deflected electrons in turbulent magnetic fields has properties different from synchrotron radiation calculated in a uniform magnetic field. This jitter radiation may be important for understanding the complex time evolution and/or spectral structure of gamma-ray bursts, relativistic jets in general, and supernova remnants. In order to calculate radiation from first principles and go beyond the standard synchrotron model, we have used PIC simulations. We present synthetic spectra to compare with the spectra obtained from Fermi observations.}, language = {en} }