@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} }