@phdthesis{Trompelt2010, author = {Trompelt, Helena}, title = {Production of regular and non-regular verbs : evidence for a lexical entry complexity account}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-061-8}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-42120}, school = {Universit{\"a}t Potsdam}, pages = {x, 168}, year = {2010}, abstract = {The incredible productivity and creativity of language depends on two fundamental resources: a mental lexicon and a mental grammar. Rules of grammar enable us to produce and understand complex phrases we have not encountered before and at the same time constrain the computation of complex expressions. The concepts of the mental lexicon and mental grammar have been thoroughly tested by comparing the use of regular versus non-regular word forms. Regular verbs (e.g. walk-walked) are computed using a suffixation rule in a neural system for grammatical processing; non-regular verbs (run-ran) are retrieved from associative memory. The role of regularity has only been explored for the past tense, where regularity is overtly visible. To explore the representation and encoding of regularity as well as the inflectional processes involved in the production of regular and non-regular verbs, this dissertation investigated three groups of German verbs: regular, irregular and hybrid verbs. Hybrid verbs in German have completely regular conjugation in the present tense and irregular conjugation in the past tense. Articulation latencies were measured while participants named pictures of actions, producing the 3rd person singular of regular, hybrid, and irregular verbs in present and past tense. Studying the production of German verbs in past and present tense, this dissertation explored the complexity of lexical entries as a decisive factor in the production of verbs.}, language = {en} } @book{JannVeit2010, author = {Jann, Werner and Veit, Sylvia}, title = {Politicisation of administration or bureaucratisation of politics? : The case of Germany}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45163}, publisher = {Universit{\"a}t Potsdam}, year = {2010}, abstract = {Der Aufsatz befasst sich mit der Frage, ob sich eine wachsende Politisierung der Ministerialb{\"u}rokratie und eine zunehmende B{\"u}rokratisierung der Politik in einer Hybridisierung der Karriereverl{\"a}ufe von Spitzenbeamten und Exekutivpolitikern auf Bundes- und Landesebene in Deutschland nachweisen l{\"a}sst.}, language = {en} } @phdthesis{Gentsch2010, author = {Gentsch, Rafael}, title = {Complex bioactive fiber systems by means of electrospinning}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44900}, school = {Universit{\"a}t Potsdam}, year = {2010}, abstract = {Nanofibrous mats are interesting scaffold materials for biomedical applications like tissue engineering due to their interconnectivity and their size dimension which mimics the native cell environment. Electrospinning provides a simple route to access such fiber meshes. This thesis addresses the structural and functional control of electrospun fiber mats. In the first section, it is shown that fiber meshes with bimodal size distribution could be obtained in a single-step process by electrospinning. A standard single syringe set-up was used to spin concentrated poly(ε-caprolactone) (PCL) and poly(lactic-co-glycolic acid) (PLGA) solutions in chloroform and meshes with bimodal-sized fiber distribution could be directly obtained by reducing the spinning rate at elevated humidity. Scanning electron microscopy (SEM) and mercury porosity of the meshes suggested a suitable pore size distribution for effective cell infiltration. The bimodal fiber meshes together with unimodal fiber meshes were evaluated for cellular infiltration. While the micrometer fibers in the mixed meshes generate an open pore structure, the submicrometer fibers support cell adhesion and facilitate cell bridging on the large pores. This was revealed by initial cell penetration studies, showing superior ingrowth of epithelial cells into the bimodal meshes compared to a mesh composed of unimodal 1.5 μm fibers. The bimodal fiber meshes together with electrospun nano- and microfiber meshes were further used for the inorganic/organic hybrid fabrication of PCL with calcium carbonate or calcium phosphate, two biorelevant minerals. Such composite structures are attractive for the potential improvement of properties such as stiffness or bioactivity. It was possible to encapsulate nano and mixed sized plasma-treated PCL meshes to areas > 1 mm2 with calcium carbonate using three different mineralization methods including the use of poly(acrylic acid). The additive seemed to be useful in stabilizing amorphous calcium carbonate to effectively fill the space between the electrospun fibers resulting in composite structures. Micro-, nano- and mixed sized fiber meshes were successfully coated within hours by fiber directed crystallization of calcium phosphate using a ten-times concentrated simulated body fluid. It was shown that nanofibers accelerated the calcium phosphate crystallization, as compared to microfibers. In addition, crystallizations performed at static conditions led to hydroxyapatite formations whereas in dynamic conditions brushite coexisted. In the second section, nanofiber functionalization strategies are investigated. First, a one-step process was introduced where a peptide-polymer-conjugate (PLLA-b-CGGRGDS) was co-spun with PLGA in such a way that the peptide is enriched on the surface. It was shown that by adding methanol to the chloroform/blend solution, a dramatic increase of the peptide concentration at the fiber surface could be achieved as determined by X-ray photoelectron spectroscopy (XPS). Peptide accessibility was demonstrated via a contact angle comparison of pure PLGA and RGD-functionalized fiber meshes. In addition, the electrostatic attraction between a RGD-functionalized fiber and a silica bead at pH ~ 4 confirmed the accessibility of the peptide. The bioactivity of these RGD-functionalized fiber meshes was demonstrated using blends containing 18 wt\% bioconjugate. These meshes promoted adhesion behavior of fibroblast compared to pure PLGA meshes. In a second functionalization approach, a modular strategy was investigated. In a single step, reactive fiber meshes were fabricated and then functionalized with bioactive molecules. While the electrospinning of the pure reactive polymer poly(pentafluorophenyl methacrylate) (PPFPMA) was feasible, the inherent brittleness of PPFPMA required to spin a PCL blend. Blends and pure PPFPMA showed a two-step functionalization kinetics. An initial fast reaction of the pentafluorophenyl esters with aminoethanol as a model substance was followed by a slow conversion upon further hydrophilization. This was analysed by UV/Vis-spectroscopy of the pentaflurorophenol release upon nucleophilic substitution with the amines. The conversion was confirmed by increased hydrophilicity of the resulting meshes. The PCL/PPFPMA fiber meshes were then used for functionalization with more complex molecules such as saccharides. Aminofunctionalized D-Mannose or D-Galactose was reacted with the active pentafluorophenyl esters as followed by UV/Vis spectroscopy and XPS. The functionality was shown to be bioactive using macrophage cell culture. The meshes functionalized with D-Mannose specifically stimulated the cytokine production of macrophages when lipopolysaccharides were added. This was in contrast to D-Galactose- or aminoethanol-functionalized and unfunctionalized PCL/PPFPMA fiber mats.}, language = {en} } @book{OPUS4-4353, title = {EUCHIS '99 : proceedings of the 3rd international conference of the European Chitin Society, Potsdam, Germany, Aug. 31 - Sept. 3, 1999}, isbn = {978-3-980649-45-2}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45492}, publisher = {Universit{\"a}t Potsdam}, year = {2000}, abstract = {Contents: Production and Applications of Chitin and Chitosan Krill as a promising raw material for the production of chitin in Europe - Containerized plant for producing chitin - Preparation and characterization of chitosan from Mucorales - Chitosan from Absidia orchidis - Scaling up of lactic acid fermentation of prawn wastes in packed-bed column reactor for chitin recovery - Preparation of chitin by acetic acid fermentation - Inter-source reproducibility of the chitin deacetylation process - Comparative analysis of chitosans from insects and crustacea - Effect of the rate of deacetylation on the physico-chemical properties of cuttlefish chitosan - Deacetylation of chitin by fungal enzymes - Production of partially degraded chitosan with desired molecular weight - Chitin-containing materials Mycoton for wounds treatment - Biological activity of selected forms of chitosan - Application of chitosan on the preservation quality of cut flowers - Preparation and characterization of chitosan films: application in cell cultures - Transport phenomena in chitin gels - Symplex membranes of chitosan and sulphoethylcellulose - Preparation and use of chitosan-Ca pectinate pellets - Bioseparation of protein from cheese whey by using chitosan coagulation and ultrafiltration membranes - Preparation of silk fibroin/chitosan fiber - Preparation of paper sheets containing microcrystalline chitosan - Applications of chitosan in textile printing - Permanent modification of fibrous materials with biopolymers - Ion exchanger from chitosan - Chitosan in waste water treatment - The immobilization of tyrosinase on chitin and chitosan and its possible use in wastewater treatment - Utilization of modified chitosan in aqueous system treatment Biomaterials Chemical and preclinical studies on 6-oxychitin - Diverse biological effects of fungal chitin-glucan complex - Effect of concentration of neutralizing agent on chitosan membrane properties - Preliminary investigation of the compatibility of a chitosan-based peritoneal dialysis solution - Influence of chitosan on the growth of several cellular lines - A new chitosan containing phosphonic group with chelating properties - Biocompatibility of chitin materials using cell culture method Oral Administration of Chitosan Recent results in the oral administration of chitosan - Reduction of absorption of dietary lipids and cholesterol by chitosan, its derivatives and special formulations - Chitosan in weight reduction: results from a large scale consumer study - Conformation of chitosan ascorbic acid salt - Trimethylated chitosans as safe absorption enhancers for transmucosal delivery of peptide drugs - Chitosan derivates as intestinal penetration enhancers of the peptide drug buserelin in vivo and in vitro - Chitosan microparticles for oral vaccination: optimization and characterization - Effect of chitosan in enhancing drug delivery across buccal mucosa - Influence of chitosans on permeability of human intestinal epithelial (Caco-2) cells: The effect of molecular weight, degree of deacetylation and exposure time - Oral polymeric N-acetyl-D-glucosamine as potential treatment for patients with osteoarthritis - Clinicoimmunological efficiency of the chitin-containing drug Mycoton in complex treatment of a chronic hepatitis - Interactions of chitin, chitosan, N-laurylchitosan, and N-dimethylaminopropyl chitosan with olive oil - The chitin-containing preparation Mycoton in a pediatric gastroenterology case - Antifungal activity and release behaviour of cross-linked chitosan films incorporated with chlorhexidine gluconate - Release of N-acetyl-D-glucosamine from chitosan in saliva - Physical and Physicochemical Properties Recent approach of metal binding by chitosan and derivatives - As(V) sorption on molybdate-impregnated chitosan gel beads (MICB) - Influence of medium pH on the biosorption of heavy metals by chitin-containing sorbent Mycoton - Comparative studies on molecular chain parameters of polyelectrolyte chains: the stiffness parameter B and temperature coefficient of intrinsic viscosity of chitosans and poly(diallyldimethylammonium chloride) - Crystalline behavior of chitosan - The relationship between the crystallinity and degree of deacetylation of chitin from crab shell - Reversible water-swellable chitin gel: modulation of swellability - Syneresis aspects of chitosan based gel systems - In situ chitosan gelation using the enzyme tyrosinase - Preparation and characterization of controlling pore size chitosan membranes - Fabrication of porous chitin matrices - Changes of polydispersity and limited molecular weight of ultrasonic treated chitosan - A statistical evaluation of IR spectroscopic methods to determine the degree of acetylation of ?-chitin and chitosan - Products of alkaline hydrolysis of dibutyrylchitin: chemical composition and DSC investigation - Chitosan emulsification properties Chemistry of Chitin and Chitosan Chemically modified chitinous materials: preparation and properties - Progress on the modification of chitosan - The graft copolymerization of chitosan with methyl acrylate using an organohalide-manganese carbonyl coinitiator system - Grafting of 4-vinylpyridine, maleic acid and maleic anhydride onto chitin and chitosan - Peptide synthesis on chitosan/chitin - Graft copolymerization of methyl methacrylate onto mercapto-chitin - Thermal depolymerization of chitosan salts - Radiolysis and sonolysis of chitosan - two convenient techniques for a controlled reduction of molecular weight - Thermal and UV degradation of chitosan - Heat-induced physicochemical changes in highly deacetylated chitosan - Chitosan fiber and its chemical N-modification at the fiber state for use as functional materials - Preparation of a fiber reactive chitosan derivative with enhanced microbial activity - Chromatographic separation of rare earths with complexane types of chemically modified chitosan - The effects of detergents on chitosan - Chitosan-alginate PEC films prepared from chitosan of different molecular weights - Enzymology of Chitin and Chitosan Biosynthesis and Degradation Enzymes of chitin metabolism for the design of antifungals - Enzymatic degradation of chitin by microorganisms - Kinetic behaviours of chitinase isozymes - An acidic chitinase from gizzards of broiler (Gallus gallus L.) - On the contribution of conserved acidic residues to catalytic activity of chitinase B from Serratia marcescens - Detection, isolation and preliminary characterisation of a new hyperthermophilic chitinase from the anaerobic archaebacterium Thermococcus chitonophagus - Biochemical and genetic engineering studies on chitinase A from Serratia marcescens - Induction of chitinase production by Serratia marcescens, using a synthetic N-acetylglucosamine derivative - Libraries of chito-oligosaccharides of mixed acetylation patterns and their interactions with chitinases - Approaches towards the design of new chitinase inhibitors - Allosamidin inhibits the fragmentation and autolysis of Penicillium chrysogenum - cDNA encoding chitinase in the midge, Chironomus tentans - Extraction and purification of chitosanase from Bacillus cereus - Substrate binding mechanism of chitosanase from Streptomyces sp. N174 - Chitosanase-catalyzed hydrolysis of 4-methylumbelliferyl ?-chitotrioside - A rust fungus turns chitin into chitosan upon plant tissue colonization to evade recognition by the host - Antibiotic kanosamine is an inhibitor of chitin biosynthesis in fungi - PCR amplification of chitin deacetylase genes - Amplification of antifungal effect of GlcN-6-P synthase and chitin synthase inhibitors - ?-N-Acetylhexosaminidases: two enzyme families, two mechanisms - Purification and characterisation of chitin deacetylase from Absidia orchidis - Effect of aluminium ion on hydrolysis reaction of carboxymethyl- and dihydroxypropyl-chitin with lysozyme - Structure and function relatioship of human N-acetyl-D-glucosamine 2-epimerase (renin binding protein) - Identification of active site residue(s)}, language = {en} } @phdthesis{Esther2010, author = {Esther, Alexandra}, title = {Investigating mechanisms maintaining plant species diversity in fire prone Mediterranean-type vegetation using spatially-explicit simulation models}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44632}, school = {Universit{\"a}t Potsdam}, year = {2010}, abstract = {Fire prone Mediterranean-type vegetation systems like those in the Mediterranean Basin and South-Western Australia are global hot spots for plant species diversity. To ensure management programs act to maintain these highly diverse plant communities, it is necessary to get a profound understanding of the crucial mechanisms of coexistence. In the current literature several mechanisms are discussed. The objective of my thesis is to systematically explore the importance of potential mechanisms for maintaining multi-species, fire prone vegetation by modelling. The model I developed is spatially-explicit, stochastic, rule- and individual-based. It is parameterised on data of population dynamics collected over 18 years in the Mediterranean-type shrublands of Eneabba, Western Australia. From 156 woody species of the area seven plant traits have been identified to be relevant for this study: regeneration mode, annual maximum seed production, seed size, maximum crown diameter, drought tolerance, dispersal mode and seed bank type. Trait sets are used for the definition of plant functional types (PFTs). The PFT dynamics are simulated annual by iterating life history processes. In the first part of my thesis I investigate the importance of trade-offs for the maintenance of high diversity in multi-species systems with 288 virtual PFTs. Simulation results show that the trade-off concept can be helpful to identify non-viable combinations of plant traits. However, the Shannon Diversity Index of modelled communities can be high despite of the presence of 'supertypes'. I conclude, that trade-offs between two traits are less important to explain multi-species coexistence and high diversity than it is predicted by more conceptual models. Several studies show, that seed immigration from the regional seed pool is essential for maintaining local species diversity. However, systematical studies on the seed rain composition to multi-species communities are missing. The results of the simulation experiments, as presented in part two of this thesis, show clearly, that without seed immigration the local species community found in Eneabba drifts towards a state with few coexisting PFTs. With increasing immigration rates the number of simulated coexisting PFTs and Shannon diversity quickly approaches values as also observed in the field. Including the regional seed input in the model is suited to explain more aggregated measures of the local plant community structure such as species richness and diversity. Hence, the seed rain composition should be implemented in future studies. In the third part of my thesis I test the sensitivity of Eneabba PFTs to four different climate change scenarios, considering their impact on both local and regional processes. The results show that climate change clearly has the potential to alter the number of dispersed seeds for most of the Eneabba PFTs and therefore the source of the 'immigrants' at the community level. A classification tree analysis shows that, in general, the response to climate change was PFT-specific. In the Eneabba sand plains sensitivity of a PFT to climate change depends on its specific trait combination and on the scenario of environmental change i.e. development of the amount of rainfall and the fire frequency. This result emphasizes that PFT-specific responses and regional process seed immigration should not be ignored in studies dealing with the impact of climate change on future species distribution. The results of the three chapters are finally analysed in a general discussion. The model is discussed and improvements and suggestions are made for future research. My work leads to the following conclusions: i) It is necessary to support modelling with empirical work to explain coexistence in species-rich plant communities. ii) The chosen modelling approach allows considering the complexity of coexistence and improves the understanding of coexistence mechanisms. iii) Field research based assumptions in terms of environmental conditions and plant life histories can relativise the importance of more hypothetic coexistence theories in species-rich systems. In consequence, trade-offs can play a lower role than predicted by conceptual models. iv) Seed immigration is a key process for local coexistence. Its alteration because of climate change should be considered for prognosis of coexistence. Field studies should be carried out to get data on seed rain composition.}, language = {en} } @misc{KoseskaZaikinKurthsetal.2009, author = {Koseska, Aneta and Zaikin, Alexey and Kurths, J{\"u}rgen and Garc{\´i}a-Ojalvo, Jordi}, title = {Timing cellular decision making under noise via cell-cell communication}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45260}, year = {2009}, abstract = {Many cellular processes require decision making mechanisms, which must act reliably even in the unavoidable presence of substantial amounts of noise. However, the multistable genetic switches that underlie most decision-making processes are dominated by fluctuations that can induce random jumps between alternative cellular states. Here we show, via theoretical modeling of a population of noise-driven bistable genetic switches, that reliable timing of decision-making processes can be accomplished for large enough population sizes, as long as cells are globally coupled by chemical means. In the light of these results, we conjecture that cell proliferation, in the presence of cell-cell communication, could provide a mechanism for reliable decision making in the presence of noise, by triggering cellular transitions only when the whole cell population reaches a certain size. In other words , the summation performed by the cell population would average out the noise and reduce its detrimental impact.}, language = {en} } @misc{SzymanskiJozefczukNikoloskietal.2009, author = {Szymanski, Jedrzej and Jozefczuk, Szymon and Nikoloski, Zoran and Selbig, Joachim and Nikiforova, Victoria and Catchpole, Gareth and Willmitzer, Lothar}, title = {Stability of metabolic correlations under changing environmental conditions in Escherichia coli : a systems approach}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45253}, year = {2009}, abstract = {Background: Biological systems adapt to changing environments by reorganizing their cellula r and physiological program with metabolites representing one important response level. Different stresses lead to both conserved and specific responses on the metabolite level which should be reflected in the underl ying metabolic network. Methodology/Principal Findings: Starting from experimental data obtained by a GC-MS based high-throughput metabolic profiling technology we here develop an approach that: (1) extracts network representations from metabolic conditiondependent data by using pairwise correlations, (2) determines the sets of stable and condition-dependent correlations based on a combination of statistical significance and homogeneity tests, and (3) can identify metabolites related to the stress response, which goes beyond simple ob servation s about the changes of metabolic concentrations. The approach was tested with Escherichia colias a model organism observed under four different environmental stress conditions (cold stress, heat stress, oxidative stress, lactose diau xie) and control unperturbed conditions. By constructing the stable network component, which displays a scale free topology and small-world characteristics, we demonstrated that: (1) metabolite hubs in this reconstructed correlation networks are significantly enriched for those contained in biochemical networks such as EcoCyc, (2) particular components of the stable network are enriched for functionally related biochemical path ways, and (3) ind ependently of the response scale, based on their importance in the reorganization of the cor relation network a set of metabolites can be identified which represent hypothetical candidates for adjusting to a stress-specific response. Conclusions/Significance: Network-based tools allowed the identification of stress-dependent and general metabolic correlation networks. This correlation-network-ba sed approach does not rely on major changes in concentration to identify metabolites important for st ress adaptation, but rather on the changes in network properties with respect to metabolites. This should represent a useful complementary technique in addition to more classical approaches.}, language = {en} } @misc{WienhoeferGermerLindenmaieretal.2009, author = {Wienh{\"o}fer, Jan and Germer, Kai and Lindenmaier, Falk and F{\"a}rber, Arne and Zehe, Erwin}, title = {Applied tracers for the observation of subsurface stormflow at the hillslope scale}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45246}, year = {2009}, abstract = {Rain fall-runoff response in temperate humid headwater catchments is mainly controlled by hydrolo gical processes at the hillslope scale. Applied tracer experiments with fluore scent dye and salt tracers are well known tools in groundwater studies at the large scale and vadose zone studies at the plot scale, where they provide a means to characterise subsurface flow. We extend this approach to the hillslope scale to investigate saturated and unsaturated flow path s concertedly at a forested hill slope in the Austrian Alps. Dye staining experiments at the plot scale revealed that crack s and soil pipe s function as preferential flow path s in the fine-textured soils of the study area, and these preferenti al flow structures were active in fast subsurface transport of tracers at the hillslope scale. Breakthrough curves obtained under steady flow conditions could be fitted well to a one-dimensional convection-dispersion model. Under natural rain fall a positive correlation of tracer concentrations to the transient flows was observed. The results of this study demon strate qualitative and quantitative effects of preferential flow feature s on subsurface stormflow in a temperate humid headwater catchment. It turn s out that , at the hill slope scale, the interaction s of structures and processes are intrinsically complex, which implies that attempts to model such a hillslope satisfactorily require detailed investigation s of effective structures and parameters at the scale of interest.}, language = {en} } @misc{MellWartenburgerMarschneretal.2009, author = {Mell, Thomas and Wartenburger, Isabell and Marschner, Alexander and Villringer, Arno and Reischies, Friedel M. and Heekeren, Hauke R.}, title = {Altered function of ventral striatum during reward-based decision making in old age}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45235}, year = {2009}, abstract = {Normal aging is associated with a decline in different cognitive domains and local structural atrophy as well as decreases in dopamine concentration and receptor density. To date, it is largely unknown how these reductions in dopaminergic neurotransmission affect human brain regions responsible for reward-based decision making in older adults. Using a learning criterion in a probabilistic object reversal task, we found a learning stage by age interaction in the dorsolateral prefrontal cortex (dIPFC) during decision making. While young adults recruited the dlPFC in an early stage of learning reward associations, older adults recruited the dlPFC when reward associations had already been learned. Furthermore, we found a reduced change in ventral striatal BOLD signal in older as compared to younger adults in response to high probability rewards. Our data are in line with behavioral evidence that older adults show altered stimulus-reward learning and support the view of an altered fronto-striatal interaction during reward-based decision making in old age, which contributes to prolonged learning of reward associations.}, language = {en} } @misc{ChildsNikoloskiMayetal.2009, author = {Childs, Liam H. and Nikoloski, Zoran and May, Patrick and Walther, Dirk}, title = {Identification and classification of ncRNA molecules using graph properties}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45192}, year = {2009}, abstract = {The study of non-coding RNA genes has received increased attention in recent years fuelled by accumulating evidence that larger portions of genomes than previously acknowledged are transcribed into RNA molecules of mostly unknown function, as well as the discovery of novel non-coding RNA types and functional RNA elements. Here, we demonstrate that specific properties of graphs that represent the predicted RNA secondary structure reflect functional information. We introduce a computational algorithm and an associated web-based tool (GraPPLE) for classifying non-coding RNA molecules as functional and, furthermore, into Rfam families based on their graph properties. Unlike sequence-similarity-based methods and covariance models, GraPPLE is demonstrated to be more robust with regard to increasing sequence divergence, and when combined with existing methods, leads to a significant improvement of prediction accuracy. Furthermore, graph properties identified as most informative are shown to provide an understanding as to what particular structural features render RNA molecules functional. Thus, GraPPLE may offer a valuable computational filtering tool to identify potentially interesting RNA molecules among large candidate datasets.}, language = {en} } @misc{CoxMarisSoetartetal.2009, author = {Cox, Tom and Maris, Tom and Soetart, Karline and Conley, Daniel and van Damme, Stefan and Meire, Patrick and Middelburg, Jack J. and Vos, Matthijs and Struyf, Eric}, title = {A macro-tidal freshwater ecosystem recovering from hypereutrophication : the Schelde lease study}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45180}, year = {2009}, abstract = {We report a 40 year record of eutrophication and hypoxia on an estuarine ecosystem and its recovery from hypereutrophication. After decades of high inorganic nutrient concentrations and recurring anoxia and hypoxia, we observe a paradoxical increase in chlorophyll-a concentrations with decreasing nutrient inputs. We hypothesise that algal growth was inhibited due to hypereutrophication, either by elevated ammonium concentrations, severe hypoxia or the production of harmful substances in such a reduced environment. We study the dynamics of a simple but realistic mathematical model, incorporating the assumption of algal growth inhibition. It shows a high algal biomass, net oxygen production equilibrium with low ammonia inputs, and a low algal biomass, net oxygen consumption equilibrium with high ammonia inputs. At intermediate ammonia inputs it displays two alternative stable states. Although not intentional, the numerical output of this model corresponds to observations, giving extra support for assumption of algal growth inhibition. Due to potential algal growth inhibition, the recovery of hypereutrophied systems towards a classical eutrophied state, will need reduction of waste loads below certain thresholds and will be accompanied by large fluctuations in oxygen concentrations. We conclude that also flow-through systems, heavily influenced by external forcings which partly mask internal system dynamics, can display multiple stable states.}, language = {en} } @misc{ZiegeMahlowHennigeSulzetal.2009, author = {Ziege, Madlen and Mahlow, Kristin and Hennige-Sulz, Carmen and Kronmarck, Claudia and Tiedemann, Ralph and Streit, Bruno and Plath, Martin}, title = {Audience effects in the Atlantic molly (Poecilia mexicana) : prudent male mate choice in response to perceived sperm competition risk?}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45171}, year = {2009}, abstract = {Background: Multidirectional interactions in social networks can have a profound effect on mate choice behavior; e.g., Poecilia mexicana males show weaker expression of mating preferences when being observed by a rival. This may be an adaptation to reduce sperm competition risk, which arises because commonly preferred female phenotypes will receive attention also from surrounding males, and/or because other males can copy the focal male's mate choice. Do P. mexicana males indeed respond to perceived sperm competition risk? We gave males a choice between two females and repeated the tests under one of the following conditions: (1) an empty transparent cylinder was presented (control); (2) another ("audience") male inside the cylinder observed the focal male throughout the 2nd part, or (3) the audience male was presented only before the tests, but could not eavesdrop during the actual choice tests (non-specific sperm competition risk treatments); (4) the focal male could see a rival male interact sexually with the previously preferred, or (5) with the non-preferred female before the 2nd part of the tests (specific sperm competition risk treatments). Results: The strength of individual male preferences declined slightly also during the control treatment (1). However, this decrease was more than two-fold stronger in audience treatment (2), i.e., with non-specific sperm competition risk including the possibility for visual eavesdropping by the audience male. No audience effect was found in treatments (3) and (5), but a weak effect was also observed when the focal male had seen the previously preferred female sexually interact with a rival male (treatment 4; specific sperm competition risk). Conclusion: When comparing the two 'non-specific sperm competition risk' treatments, a very strong effect was found only when the audience male could actually observe the focal male during mate choice [treatment (2)]. This suggests that focal males indeed attempt to conceal their mating preferences so as to prevent surrounding males from copying their mate choice. When there is no potential for eavesdropping [treatment (3)], non-specific specific sperm competition risk seems to play a minor or no role. Our results also show that P. mexicana males tend to share their mating effort more equally among females when the resource value of their previously preferred mate decreases after mating with a rival male (perceived specific sperm competition risk), but this effect is comparatively weak.}, language = {en} } @misc{GaertnerSteinfathAndorfetal.2009, author = {G{\"a}rtner, Tanja and Steinfath, Matthias and Andorf, Sandra and Lisec, Jan and Meyer, Rhonda C. and Altmann, Thomas and Willmitzer, Lothar and Selbig, Joachim}, title = {Improved heterosis prediction by combining information on DNA- and metabolic markers}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45132}, year = {2009}, abstract = {Background: Hybrids represent a cornerstone in the success story of breeding programs. The fundamental principle underlying this success is the phenomenon of hybrid vigour, or heterosis. It describes an advantage of the offspring as compared to the two parental lines with respect to parameters such as growth and resistance against abiotic or biotic stress. Dominance, overdominance or epistasis based models are commonly used explanations. Conclusion/Significance: The heterosis level is clearly a function of the combination of the parents used for offspring production. This results in a major challenge for plant breeders, as usually several thousand combinations of parents have to be tested for identifying the best combinations. Thus, any approach to reliably predict heterosis levels based on properties of the parental lines would be highly beneficial for plant breeding. Methodology/Principal Findings: Recently, genetic data have been used to predict heterosis. Here we show that a combination of parental genetic and metabolic markers, identified via feature selection and minimum-description-length based regression methods, significantly improves the prediction of biomass heterosis in resulting offspring. These findings will help furthering our understanding of the molecular basis of heterosis, revealing, for instance, the presence of nonlinear genotype-phenotype relationships. In addition, we describe a possible approach for accelerated selection in plant breeding.}, language = {en} } @phdthesis{Abed2010, author = {Abed, Jamil}, title = {An iterative approach to operators on manifolds with singularities}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44757}, school = {Universit{\"a}t Potsdam}, year = {2010}, abstract = {We establish elements of a new approach to ellipticity and parametrices within operator algebras on manifolds with higher singularities, only based on some general axiomatic requirements on parameter-dependent operators in suitable scales of spaes. The idea is to model an iterative process with new generations of parameter-dependent operator theories, together with new scales of spaces that satisfy analogous requirements as the original ones, now on a corresponding higher level. The "full" calculus involves two separate theories, one near the tip of the corner and another one at the conical exit to infinity. However, concerning the conical exit to infinity, we establish here a new concrete calculus of edge-degenerate operators which can be iterated to higher singularities.}, language = {en} } @misc{DurekSchudomaWeckwerthetal.2009, author = {Durek, Pawel and Schudoma, Christian and Weckwerth, Wolfram and Selbig, Joachim and Walther, Dirk}, title = {Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45129}, year = {2009}, abstract = {Background: Phosphorylation of proteins plays a crucial role in the regulation and activation of metabolic and signaling pathways and constitutes an important target for pharmaceutical intervention. Central to the phosphorylation process is the recognition of specific target sites by protein kinases followed by the covalent attachment of phosphate groups to the amino acids serine, threonine, or tyrosine. The experimental identification as well as computational prediction of phosphorylation sites (P-sites) has proved to be a challenging problem. Computational methods have focused primarily on extracting predictive features from the local, one-dimensional sequence information surrounding phosphorylation sites. Results: We characterized the spatial context of phosphorylation sites and assessed its usability for improved phosphorylation site predictions. We identified 750 non-redundant, experimentally verified sites with three-dimensional (3D) structural information available in the protein data bank (PDB) and grouped them according to their respective kinase family. We studied the spatial distribution of amino acids around phosphorserines, phosphothreonines, and phosphotyrosines to extract signature 3D-profiles. Characteristic spatial distributions of amino acid residue types around phosphorylation sites were indeed discernable, especially when kinase-family-specific target sites were analyzed. To test the added value of using spatial information for the computational prediction of phosphorylation sites, Support Vector Machines were applied using both sequence as well as structural information. When compared to sequence-only based prediction methods, a small but consistent performance improvement was obtained when the prediction was informed by 3D-context information. Conclusion: While local one-dimensional amino acid sequence information was observed to harbor most of the discriminatory power, spatial context information was identified as relevant for the recognition of kinases and their cognate target sites and can be used for an improved prediction of phosphorylation sites. A web-based service (Phos3D) implementing the developed structurebased P-site prediction method has been made available at http://phos3d.mpimp-golm.mpg.de.}, language = {en} } @misc{ReusserBlumeSchaeflietal.2009, author = {Reusser, Dominik and Blume, Theresa and Schaefli, Bettina and Zehe, Erwin}, title = {Analysing the temporal dynamics of model performance for hydrological models}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45114}, year = {2009}, abstract = {The temporal dynamics of hydrological model performance gives insights into errors that cannot be obtained from global performance measures assigning a single number to the fit of a simulated time series to an observed reference series. These errors can include errors in data, model parameters, or model structure. Dealing with a set of performance measures evaluated at a high temporal resolution implies analyzing and interpreting a high dimensional data set. This paper presents a method for such a hydrological model performance assessment with a high temporal resolution and illustrates its application for two very different rainfall-runoff modeling case studies. The first is the Wilde Weisseritz case study, a headwater catchment in the eastern Ore Mountains, simulated with the conceptual model WaSiM-ETH. The second is the Malalcahuello case study, a headwater catchment in the Chilean Andes, simulated with the physicsbased model Catflow. The proposed time-resolved performance assessment starts with the computation of a large set of classically used performance measures for a moving window. The key of the developed approach is a data-reduction method based on self-organizing maps (SOMs) and cluster analysis to classify the high-dimensional performance matrix. Synthetic peak errors are used to interpret the resulting error classes. The final outcome of the proposed method is a time series of the occurrence of dominant error types. For the two case studies analyzed here, 6 such error types have been identified. They show clear temporal patterns, which can lead to the identification of model structural errors.}, language = {en} } @misc{SchroederLissoLangeetal.2009, author = {Schr{\"o}der, Florian and Lisso, Janina and Lange, Peggy and M{\"u}ssig, Carsten}, title = {The extracellular EXO protein mediates cell expansion in Arabidopsis leaves}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45107}, year = {2009}, abstract = {Background: The EXO (EXORDIUM) gene was identified as a potential mediator of brassinosteroid (BR)-promoted growth. It is part of a gene family with eight members in Arabidopsis. EXO gene expression is under control of BR, and EXO overexpression promotes shoot and root growth. In this study, the consequences of loss of EXO function are described. Results: The exo loss of function mutant showed diminished leaf and root growth and reduced biomass production. Light and scanning electron microscopy analyses revealed that impaired leaf growth is due to reduced cell expansion. Epidermis, palisade, and spongy parenchyma cells were smaller in comparison to the wild-type. The exo mutant showed reduced brassinolide-induced cotyledon and hypocotyl growth. In contrast, exo roots were significantly more sensitive to the inhibitory effect of synthetic brassinolide. Apart from reduced growth, exo did not show severe morphological abnormalities. Gene expression analyses of leaf material identified genes that showed robust EXO-dependent expression. Growth-related genes such as WAK1, EXP5, and KCS1, and genes involved in primary and secondary metabolism showed weaker expression in exo than in wild-type plants. However, the vast majority of BR-regulated genes were normally expressed in exo. HA- and GFP-tagged EXO proteins were targeted to the apoplast. Conclusion: The EXO gene is essential for cell expansion in leaves. Gene expression patterns and growth assays suggest that EXO mediates BR-induced leaf growth. However, EXO does not control BR-levels or BR-sensitivity in the shoot. EXO presumably is involved in a signalling process which coordinates BR-responses with environmental or developmental signals. The hypersensitivity of exo roots to BR suggests that EXO plays a diverse role in the control of BR responses in the root.}, language = {en} } @misc{SzarzynskaSobkowiakPantetal.2009, author = {Szarzynska, Bogna and Sobkowiak, Lukasz and Pant, Bikram Datt and Balazadeh, Salma and Scheible, Wolf-R{\"u}diger and M{\"u}ller-R{\"o}ber, Bernd and Jarmolowski, Artur and Szweykowska-Kulinska, Zofia}, title = {Gene structures and processing of Arabidopsis thaliana HYL1-dependent pri-miRNAs}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45085}, year = {2009}, abstract = {Arabidopsis thaliana HYL1 is a nuclear doublestranded RNA-binding protein involved in the maturation of pri-miRNAs. A quantitative real-time PCR platform for parallel quantification of 176 primiRNAs was used to reveal strong accumulation of 57 miRNA precursors in the hyl1 mutant that completely lacks HYL1 protein. This approach enabled us for the first time to pinpoint particular members of MIRNA family genes that require HYL1 activity for efficient maturation of their precursors. Moreover, the accumulation of miRNA precursors in the hyl1 mutant gave us the opportunity to carry out 3' and 5' RACE experiments which revealed that some of these precursors are of unexpected length. The alignment of HYL1- dependent miRNA precursors to A. thaliana genomic sequences indicated the presence of introns in 12 out of 20 genes studied. Some of the characterized intron-containing pri-miRNAs undergo alternative splicing such as exon skipping or usage of alternative 5' splice sites suggesting that this process plays a role in the regulation of miRNA biogenesis. In the hyl1 mutant intron-containing pri-miRNAs accumulate alongside spliced primiRNAs suggesting the recruitment of HYL1 into the miRNA precursor maturation pathway before their splicing occurs.}, language = {en} } @misc{RianoPachonNagelNeigenfindetal.2009, author = {Riano-Pachon, Diego Mauricio and Nagel, Axel and Neigenfind, Jost and Wagner, Robert and Basekow, Rico and Weber, Elke and M{\"u}ller-R{\"o}ber, Bernd and Diehl, Svenja and Kersten, Birgit}, title = {GabiPD : the GABI primary database - a plant integrative "omics" database}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45075}, year = {2009}, abstract = {The GABI Primary Database, GabiPD (http:// www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyze and visualize primary information from GABI projects. GabiPD constitutes a repository and analysis platform for a wide array of heterogeneous data from high-throughput experiments in several plant species. Data from different 'omics' fronts are incorporated (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from 14 different model or crop species. We have developed the concept of GreenCards for textbased retrieval of all data types in GabiPD (e.g. clones, genes, mutant lines). All data types point to a central Gene GreenCard, where gene information is integrated from genome projects or NCBI UniGene sets. The centralized Gene GreenCard allows visualizing ESTs aligned to annotated transcripts as well as displaying identified protein domains and gene structure. Moreover, GabiPD makes available interactive genetic maps from potato and barley, and protein 2DE gels from Arabidopsis thaliana and Brassica napus. Gene expression and metabolic-profiling data can be visualized through MapManWeb. By the integration of complex data in a framework of existing knowledge, GabiPD provides new insights and allows for new interpretations of the data.}, language = {en} } @misc{LamprechtMargariaSteffen2009, author = {Lamprecht, Anna-Lena and Margaria, Tiziana and Steffen, Bernhard}, title = {Bio-jETI : a framework for semantics-based service composition}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45066}, year = {2009}, abstract = {Background: The development of bioinformatics databases, algorithms, and tools throughout the last years has lead to a highly distributedworld of bioinformatics services. Without adequatemanagement and development support, in silico researchers are hardly able to exploit the potential of building complex, specialized analysis processes from these services. The Semantic Web aims at thoroughly equipping individual data and services with machine-processable meta-information, while workflow systems support the construction of service compositions. However, even in this combination, in silico researchers currently would have to deal manually with the service interfaces, the adequacy of the semantic annotations, type incompatibilities, and the consistency of service compositions. Results: In this paper, we demonstrate by means of two examples how Semantic Web technology together with an adequate domain modelling frees in silico researchers from dealing with interfaces, types, and inconsistencies. In Bio-jETI, bioinformatics services can be graphically combined to complex services without worrying about details of their interfaces or about type mismatches of the composition. These issues are taken care of at the semantic level by Bio-jETI's model checking and synthesis features. Whenever possible, they automatically resolve type mismatches in the considered service setting. Otherwise, they graphically indicate impossible/incorrect service combinations. In the latter case, the workflow developermay either modify his service composition using semantically similar services, or ask for help in developing the missing mediator that correctly bridges the detected type gap. Newly developed mediators should then be adequately annotated semantically, and added to the service library for later reuse in similar situations. Conclusion: We show the power of semantic annotations in an adequately modelled and semantically enabled domain setting. Using model checking and synthesis methods, users may orchestrate complex processes from a wealth of heterogeneous services without worrying about interfaces and (type) consistency. The success of this method strongly depends on a careful semantic annotation of the provided services and on its consequent exploitation for analysis, validation, and synthesis. We are convinced that these annotations will become standard, as they will become preconditions for the success and widespread use of (preferred) services in the Semantic Web}, language = {en} } @misc{LiTaubert2009, author = {Li, Zhonghao and Taubert, Andreas}, title = {Cellulose/gold nanocrystal hybrids via an ionic liquid/aqueous precipitation route}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45046}, year = {2009}, abstract = {Injection of a mixture of HAuCl4 and cellulose dissolved in the ionic liquid (IL) 1-butyl-3-methylimidazolium chloride [Bmim]Cl into aqueous NaBH4 leads to colloidal gold nanoparticle/cellulose hybrid precipitates. This process is a model example for a very simple and generic approach towards (noble) metal/cellulose hybrids, which could find applications in sensing, sterile filtration, or as biomaterials.}, language = {en} } @misc{SchumannTeraoGarattinietal.2009, author = {Schumann, Silvia and Terao, Mineko and Garattini, Enrico and Saggu, Miguel and Lendzian, Friedhelm and Hildebrandt, Peter and Leimk{\"u}hler, Silke}, title = {Site directed mutagenesis of amino acid residues at the active site of mouse aldehyde oxidase AOX1}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45030}, year = {2009}, abstract = {Mouse aldehyde oxidase (mAOX1) forms a homodimer and belongs to the xanthine oxidase family of molybdoenzymes which are characterized by an essential equatorial sulfur ligand coordinated to the molybdenum atom. In general, mammalian AOs are characterized by broad substrate specificity and an yet obscure physiological function. To define the physiological substrates and the enzymatic characteristics of mAOX1, we established a system for the heterologous expression of the enzyme in Eschericia coli. The recombinant protein showed spectral features and a range of substrate specificity similar to the native protein purified from mouse liver. The EPR data of recombinant mAOX1 were similar to those of AO from rabbit liver, but differed from the homologous xanthine oxidoreductase enzymes. Site-directed mutagenesis of amino acids Val806, Met884 and Glu1265 at the active site resulted in a drastic decrease in the oxidation of aldehydes with no increase in the oxidation of purine substrates. The double mutant V806E/M884R and the single mutant E1265Q were catalytically inactive enzymes regardless of the aldehyde or purine substrates tested. Our results show that only Glu1265 is essential for the catalytic activity by initiating the base-catalyzed mechanism of substrate oxidation. In addition, it is concluded that the substrate specificity of molybdo-flavoenzymes is more complex and not only defined by the three characterized amino acids in the active site.}, language = {en} } @misc{KroellerWarschburger2009, author = {Kr{\"o}ller, Katja and Warschburger, Petra}, title = {Maternal feeding strategies and child's food intake : considering weight and demographic influences using structural equation modeling}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45023}, year = {2009}, abstract = {Background: Research concerning child's food intake have considered various influencing factors, for example parental feeding strategies, demographic and weight factors. At this time, however, there are few findings that explore these factors simultaneously. Accordingly, the aim of this study was to test a structural equation model regarding the associations between maternal feeding strategies and child's food intake. Methods: 556 mothers and their children between 1 and 10 years of age participated in this crosssectional study. Besides socio-demographic and weight data, the mothers were asked about their feeding strategies as well as their child's food intake. Results: The well-fitting model explained 73\% of the variance in the child's consumption of healthy and 34\% of unhealthy food. In addition to the effect of the mother's social status and the child's age, a rewarding and modeling feeding behavior significantly influenced the child's food intake. Conclusion: The results highlight the relevance of maternal feeding behavior on the child's food intake. In terms of preventing eating- or weight-related problems, the findings indicate the usefulness of training parents in explicit modeling behavior and avoiding food as a reward.}, language = {en} } @misc{KuglerKoehlerPalmeetal.2009, author = {Kugler, Annette and K{\"o}hler, Barbara and Palme, Klaus and Wolff, Patricia and Dietrich, Petra}, title = {Salt-dependent regulation of a CNG channel subfamily in Arabidopsis}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45019}, year = {2009}, abstract = {Background: In Arabidopsis thaliana, the family of cyclic nucleotide-gated channels (CNGCs) is composed of 20 members. Previous studies indicate that plant CNGCs are involved in the control of growth processes and responses to abiotic and biotic stresses. According to their proposed function as cation entry pathways these channels contribute to cellular cation homeostasis, including calcium and sodium, as well as to stress-related signal transduction. Here, we studied the expression patterns and regulation of CNGC19 and CNGC20, which constitute one of the five CNGC subfamilies. Results: GUS, GFP and luciferase reporter assays were used to study the expression of CNGC19 and CNGC20 genes from Arabidopsis thaliana in response to developmental cues and salt stress. CNGC19 and CNGC20 were differentially expressed in roots and shoots. The CNGC19 gene was predominantly active in roots already at early growth stages. Major expression was observed in the phloem. CNGC20 showed highest promoter activity in mesophyll cells surrounding the veins. Its expression increased during development and was maximal in mature and senescent leaves. Both genes were upregulated in the shoot in response to elevated NaCl but not mannitol concentrations. While in the root, CNGC19 did not respond to changes in the salt concentration, in the shoot it was strongly upregulated in the observed time frame (6-72 hours). Salt-induction of CNGC20 was also observed in the shoot, starting already one hour after stress treatment. It occurred with similar kinetics, irrespective of whether NaCl was applied to roots of intact plants or to the petiole of detached leaves. No differences in K and Na contents of the shoots were measured in homozygous T-DNA insertion lines for CNGC19 and CNGC20, respectively, which developed a growth phenotype in the presence of up to 75 mM NaCl similar to that of the wild type. Conclusion: Together, the results strongly suggest that both channels are involved in the salinity response of different cell types in the shoot. Upon salinity both genes are upregulated within hours. CNGC19 and CNGC20 could assist the plant to cope with toxic effects caused by salt stress, probably by contributing to a re-allocation of sodium within the plant.}, language = {en} } @misc{ZhangIgnatova2009, author = {Zhang, Gong and Ignatova, Zoya}, title = {Generic algorithm to predict the speed of translational elongation : implications for protein biogenesis}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45007}, year = {2009}, abstract = {Synonymous codon usage and variations in the level of isoaccepting tRNAs exert a powerful selective force on translation fidelity. We have developed an algorithm to evaluate the relative rate of translation which allows large-scale comparisons of the non-uniform translation rate on the protein biogenesis. Using the complete genomes of Escherichia coli and Bacillus subtilis we show that stretches of codons pairing to minor tRNAs form putative sites to locally attenuate translation; thereby the tendency is to cluster in near proximity whereas long contiguous stretches of slow-translating triplets are avoided. The presence of slow-translating segments positively correlates with the protein length irrespective of the protein abundance. The slow-translating clusters are predominantly located down-stream of the domain boundaries presumably to fine-tune translational accuracy with the folding fidelity of multidomain proteins. Translation attenuation patterns at highly structurally and functionally conserved domains are preserved across the species suggesting a concerted selective pressure on the codon selection and species-specific tRNA abundance in these regions.}, language = {en} } @misc{HaynBeirleHamprechtetal.2009, author = {Hayn, Michael and Beirle, Steffen and Hamprecht, Fred A. and Platt, Ulrich and Menze, Bj{\"o}rn H. and Wagner, Thomas}, title = {Analysing spatio-temporal patterns of the global NO2-distribution retrieved from GOME satellite observations using a generalized additive model}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44999}, year = {2009}, abstract = {With the increasing availability of observational data from different sources at a global level, joint analysis of these data is becoming especially attractive. For such an analysis - oftentimes with little prior knowledge about local and global interactions between the different observational variables at hand - an exploratory, data-driven analysis of the data may be of particular relevance. In the present work we used generalized additive models (GAM) in an exemplary study of spatio-temporal patterns in the tropospheric NO2-distribution derived from GOME satellite observations (1996 to 2001) at global scale. We focused on identifying correlations between NO2 and local wind fields, a quantity which is of particular interest in the analysis of spatio-temporal interactions. Formulating general functional, parametric relationships between the observed NO2 distribution and local wind fields, however, is difficult - if not impossible. So, rather than following a modelbased analysis testing the data for predefined hypotheses (assuming, for example, sinusoidal seasonal trends), we used a GAM with non-parametric model terms to learn this functional relationship between NO2 and wind directly from the data. The NO2 observations showed to be affected by winddominated processes over large areas. We estimated the extent of areas affected by specific NO2 emission sources, and were able to highlight likely atmospheric transport "pathways". General temporal trends which were also part of our model - weekly, seasonal and linear changes - showed to be in good agreement with previous studies and alternative ways of analysing the time series. Overall, using a non-parametric model provided favorable means for a rapid inspection of this large spatio-temporal NO2 data set, with less bias than parametric approaches, and allowing to visualize dynamical processes of the NO2 distribution at a global scale.}, language = {en} } @misc{KartalEbenhoeh2009, author = {Kartal, {\"O}nder and Ebenh{\"o}h, Oliver}, title = {Ground state robustness as an evolutionary design principle in signaling networks}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44982}, year = {2009}, abstract = {The ability of an organism to survive depends on its capability to adapt to external conditions. In addition to metabolic versatility and efficient replication, reliable signal transduction is essential. As signaling systems are under permanent evolutionary pressure one may assume that their structure reflects certain functional properties. However, despite promising theoretical studies in recent years, the selective forces which shape signaling network topologies in general remain unclear. Here, we propose prevention of autoactivation as one possible evolutionary design principle. A generic framework for continuous kinetic models is used to derive topological implications of demanding a dynamically stable ground state in signaling systems. To this end graph theoretical methods are applied. The index of the underlying digraph is shown to be a key topological property which determines the so-called kinetic ground state (or off-state) robustness. The kinetic robustness depends solely on the composition of the subdigraph with the strongly connected components, which comprise all positive feedbacks in the network. The component with the highest index in the feedback family is shown to dominate the kinetic robustness of the whole network, whereas relative size and girth of these motifs are emphasized as important determinants of the component index. Moreover, depending on topological features, the maintenance of robustness differs when networks are faced with structural perturbations. This structural off-state robustness, defined as the average kinetic robustness of a network's neighborhood, turns out to be useful since some structural features are neutral towards kinetic robustness, but show up to be supporting against structural perturbations. Among these are a low connectivity, a high divergence and a low path sum. All results are tested against real signaling networks obtained from databases. The analysis suggests that ground state robustness may serve as a rationale for some structural peculiarities found in intracellular signaling networks.}, language = {en} } @misc{EbenhoehHandorf2009, author = {Ebenh{\"o}h, Oliver and Handorf, Thomas}, title = {Functional classification of genome-scale metabolic networks}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44975}, year = {2009}, abstract = {We propose two strategies to characterize organisms with respect to their metabolic capabilities. The first, investigative, strategy describes metabolic networks in terms of their capability to utilize different carbon sources, resulting in the concept of carbon utilization spectra. In the second, predictive, approach minimal nutrient combinations are predicted from the structure of the metabolic networks, resulting in a characteristic nutrient profile. Both strategies allow for a quantification of functional properties of metabolic networks, allowing to identify groups of organisms with similar functions. We investigate whether the functional description reflects the typical environments of the corresponding organisms by dividing all species into disjoint groups based on whether they are aerotolerant and/or photosynthetic. Despite differences in the underlying concepts, both measures display some common features. Closely related organisms often display a similar functional behavior and in both cases the functional measures appear to correlate with the considered classes of environments. Carbon utilization spectra and nutrient profiles are complementary approaches toward a functional classification of organism-wide metabolic networks. Both approaches contain different information and thus yield different clusterings, which are both different from the classical taxonomy of organisms. Our results indicate that a sophisticated combination of our approaches will allow for a quantitative description reflecting the lifestyles of organisms.}, language = {en} } @misc{deCastroGaedkeBoenigk2009, author = {de Castro, Francisco and Gaedke, Ursula and Boenigk, Jens}, title = {Reverse evolution : driving forces behind the loss of acquired photosynthetic traits}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44968}, year = {2009}, abstract = {Background: The loss of photosynthesis has occurred often in eukaryotic evolution, even more than its acquisition, which occurred at least nine times independently and which generated the evolution of the supergroups Archaeplastida, Rhizaria, Chromalveolata and Excavata. This secondary loss of autotrophic capability is essential to explain the evolution of eukaryotes and the high diversity of protists, which has been severely underestimated until recently. However, the ecological and evolutionary scenarios behind this evolutionary ''step back'' are still largely unknown. Methodology/Principal Findings: Using a dynamic model of heterotrophic and mixotrophic flagellates and two types of prey, large bacteria and ultramicrobacteria, we examine the influence of DOC concentration, mixotroph's photosynthetic growth rate, and external limitations of photosynthesis on the coexistence of both types of flagellates. Our key premises are: large bacteria grow faster than small ones at high DOC concentrations, and vice versa; and heterotrophic flagellates are more efficient than the mixotrophs grazing small bacteria (both empirically supported). We show that differential efficiency in bacteria grazing, which strongly depends on cell size, is a key factor to explain the loss of photosynthesis in mixotrophs (which combine photosynthesis and bacterivory) leading to purely heterotrophic lineages. Further, we show in what conditions an heterotroph mutant can coexist, or even out-compete, its mixotrophic ancestor, suggesting that bacterivory and cell size reduction may have been major triggers for the diversification of eukaryotes. Conclusions/Significance: Our results suggest that, provided the mixotroph's photosynthetic advantage is not too large, the (small) heterotroph will also dominate in nutrient-poor environments and will readily invade a community of mixotrophs and bacteria, due to its higher efficiency exploiting the ultramicrobacteria. As carbon-limited conditions were presumably widespread throughout Earth history, such a scenario may explain the numerous transitions from phototrophy to mixotrophy and further to heterotrophy within virtually all major algal lineages. We challenge prevailing concepts that affiliated the evolution of phagotrophy with eutrophic or strongly light-limited environments only.}, language = {en} } @misc{DambacherRolfsGoellneretal.2009, author = {Dambacher, Michael and Rolfs, Martin and G{\"o}llner, Kristin and Kliegl, Reinhold and Jacobs, Arthur M.}, title = {Event-related potentials reveal rapid verification of predicted visual input}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44953}, year = {2009}, abstract = {Human information processing depends critically on continuous predictions about upcoming events, but the temporal convergence of expectancy-based top-down and input-driven bottom-up streams is poorly understood. We show that, during reading, event-related potentials differ between exposure to highly predictable and unpredictable words no later than 90 ms after visual input. This result suggests an extremely rapid comparison of expected and incoming visual information and gives an upper temporal bound for theories of top-down and bottom-up interactions in object recognition.}, language = {en} } @misc{MayChristianKempaetal.2009, author = {May, Patrick and Christian, Jan-Ole and Kempa, Stefan and Walther, Dirk}, title = {ChlamyCyc : an integrative systems biology database and web-portal for Chlamydomonas reinhardtii}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44947}, year = {2009}, abstract = {Background: The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern highthroughput technologies there is an imperative need to integrate large-scale data sets from highthroughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism. Results: In the framework of the German Systems Biology initiative GoFORSYS, a pathway database and web-portal for Chlamydomonas (ChlamyCyc) was established, which currently features about 250 metabolic pathways with associated genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification. Conclusion: ChlamyCyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de.}, language = {en} } @misc{Buerger2009, author = {B{\"u}rger, Gerd}, title = {Dynamically vs. empirically downscaled medium-range precipitation forecasts}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44939}, year = {2009}, abstract = {For three small, mountainous catchments in Germany two medium-range forecast systems are compared that predict precipitation for up to 5 days in advance. One system is composed of the global German weather service (DWD) model, GME, which is dynamically downscaled using the COSMO-EU regional model. The other system is an empirical (expanded) downscaling of the ECMWF model IFS. Forecasts are verified against multi-year daily observations, by applying standard skill scores to events of specified intensity. All event classes are skillfully predicted by the empirical system for up to five days lead time. For the available prediction range of one to two days it is superior to the dynamical system.}, language = {en} } @misc{BlumeZeheBronstert2009, author = {Blume, Theresa and Zehe, Erwin and Bronstert, Axel}, title = {Use of soil moisture dynamics and patterns at different spatio-temporal scales for the investigation of subsurface flow processes}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44924}, year = {2009}, abstract = {Spatial patterns as well as temporal dynamics of soil moisture have a major influence on runoff generation. The investigation of these dynamics and patterns can thus yield valuable information on hydrological processes, especially in data scarce or previously ungauged catchments. The combination of spatially scarce but temporally high resolution soil moisture profiles with episodic and thus temporally scarce moisture profiles at additional locations provides information on spatial as well as temporal patterns of soil moisture at the hillslope transect scale. This approach is better suited to difficult terrain (dense forest, steep slopes) than geophysical techniques and at the same time less cost-intensive than a high resolution grid of continuously measuring sensors. Rainfall simulation experiments with dye tracers while continuously monitoring soil moisture response allows for visualization of flow processes in the unsaturated zone at these locations. Data was analyzed at different spacio-temporal scales using various graphical methods, such as space-time colour maps (for the event and plot scale) and binary indicator maps (for the long-term and hillslope scale). Annual dynamics of soil moisture and decimeterscale variability were also investigated. The proposed approach proved to be successful in the investigation of flow processes in the unsaturated zone and showed the importance of preferential flow in the Malalcahuello Catchment, a datascarce catchment in the Andes of Southern Chile. Fast response times of stream flow indicate that preferential flow observed at the plot scale might also be of importance at the hillslope or catchment scale. Flow patterns were highly variable in space but persistent in time. The most likely explanation for preferential flow in this catchment is a combination of hydrophobicity, small scale heterogeneity in rainfall due to redistribution in the canopy and strong gradients in unsaturated conductivities leading to self-reinforcing flow paths.}, language = {en} } @misc{MwinyiMeyerBleidornetal.2009, author = {Mwinyi, Adina and Meyer, Achim and Bleidorn, Christoph and Lieb, Bernhard and Bartolomaeus, Thomas and Podsiadlowski, Lars}, title = {Mitochondrial genome sequence and gene order of Sipunculus nudus give additional support for an inclusion of Sipuncula into Annelida}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44916}, year = {2009}, abstract = {Background: Mitochondrial genomes are a valuable source of data for analysing phylogenetic relationships. Besides sequence information, mitochondrial gene order may add phylogenetically useful information, too. Sipuncula are unsegmented marine worms, traditionally placed in their own phylum. Recent molecular and morphological findings suggest a close affinity to the segmented Annelida. Results: The first complete mitochondrial genome of a member of Sipuncula, Sipunculus nudus, is presented. All 37 genes characteristic for metazoan mtDNA were detected and are encoded on the same strand. The mitochondrial gene order (protein-coding and ribosomal RNA genes) resembles that of annelids, but shows several derivations so far found only in Sipuncula. Sequence based phylogenetic analysis of mitochondrial protein-coding genes results in significant bootstrap support for Annelida sensu lato, combining Annelida together with Sipuncula, Echiura, Pogonophora and Myzostomida. Conclusion: The mitochondrial sequence data support a close relationship of Annelida and Sipuncula. Also the most parsimonious explanation of changes in gene order favours a derivation from the annelid gene order. These results complement findings from recent phylogenetic analyses of nuclear encoded genes as well as a report of a segmental neural patterning in Sipuncula.}, language = {en} } @misc{BleidornPodsiadlowskiZhongetal.2009, author = {Bleidorn, Christoph and Podsiadlowski, Lars and Zhong, Min and Eeckhaut, Igor and Hartmann, Stefanie and Halanych, Kenneth M. and Tiedemann, Ralph}, title = {On the phylogenetic position of Myzostomida : can 77 genes get it wrong?}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44893}, year = {2009}, abstract = {Background: Phylogenomic analyses recently became popular to address questions about deep metazoan phylogeny. Ribosomal proteins (RP) dominate many of these analyses or are, in some cases, the only genes included. Despite initial hopes, hylogenomic analyses including tens to hundreds of genes still fail to robustly place many bilaterian taxa. Results: Using the phylogenetic position of myzostomids as an example, we show that phylogenies derived from RP genes and mitochondrial genes produce incongruent results. Whereas the former support a position within a clade of platyzoan taxa, mitochondrial data recovers an annelid affinity, which is strongly supported by the gene order data and is congruent with morphology. Using hypothesis testing, our RP data significantly rejects the annelids affinity, whereas a platyzoan relationship is significantly rejected by the mitochondrial data. Conclusion: We conclude (i) that reliance of a set of markers belonging to a single class of macromolecular complexes might bias the analysis, and (ii) that concatenation of all available data might introduce conflicting signal into phylogenetic analyses. We therefore strongly recommend testing for data incongruence in phylogenomic analyses. Furthermore, judging all available data, we consider the annelid affinity hypothesis more plausible than a possible platyzoan affinity for myzostomids, and suspect long branch attraction is influencing the RP data. However, this hypothesis needs further confirmation by future analyses.}, language = {en} } @misc{BlenauHauserCazzamalietal.2006, author = {Blenau, Wolfgang and Hauser, Frank and Cazzamali, Giuseppe and Williamson, Michael and Grimmelikhuijzen, Cornelis J. P.}, title = {A review of neurohormone GPCRs present in the fruitfly Drosophila melanogaster and the honey bee Apis mellifera}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44326}, year = {2006}, abstract = {G protein-coupled receptor (GPCR) genes are large gene families in every animal, sometimes making up to 1-2\% of the animal's genome. Of all insect GPCRs, the neurohormone (neuropeptide, protein hormone, biogenic amine) GPCRs are especially important, because they, together with their ligands, occupy a high hierarchic position in the physiology of insects and steer crucial processes such as development, reproduction, and behavior. In this paper, we give a review of our current knowledge on Drosophila melanogaster GPCRs and use this information to annotate the neurohormone GPCR genes present in the recently sequenced genome from the honey bee Apis mellifera. We found 35 neuropeptide receptor genes in the honey bee (44 in Drosophila) and two genes, coding for leucine-rich repeats-containing protein hormone GPCRs (4 in Drosophila). In addition, the honey bee has 19 biogenic amine receptor genes (21 in Drosophila). The larger numbers of neurohormone receptors in Drosophila are probably due to gene duplications that occurred during recent evolution of the fly. Our analyses also yielded the likely ligands for 40 of the 56 honey bee neurohormone GPCRs identified in this study. In addition, we made some interesting observations on neurohormone GPCR evolution and the evolution and co-evolution of their ligands. For neuropeptide and protein hormone GPCRs, there appears to be a general co-evolution between receptors and their ligands. This is in contrast to biogenic amine GPCRs, where evolutionarily unrelated GPCRs often bind to the same biogenic amine, suggesting frequent ligand exchanges ("ligand hops") during GPCR evolution. (c) 2006 Elsevier Ltd. All rights reserved.}, language = {en} } @techreport{OPUS4-4236, type = {Working Paper}, title = {Tax systems and tax harmonisation in the East African Community (EAC)}, series = {Finanzwissenschaftliche Diskussionsbeitr{\"a}ge}, journal = {Finanzwissenschaftliche Diskussionsbeitr{\"a}ge}, number = {60}, editor = {Petersen, Hans-Georg}, issn = {1864-1431}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44693}, pages = {128}, year = {2010}, abstract = {In the first part of the report of the GTZ expert group an overview on the basics of integration and tax harmonisation within a common market is given. Chapter II. concentrates on the problems of national and international tax law regarding double taxation before the harmonisation process within the EU is described in detail. This process is not a best practice example but at least the experiences made in the course of the last five decades are interesting enough and might contribute important information for regions, which more or less recently have started a similar endeavour. The harmonisation needs are discussed for value added taxation (VAT), excise taxation, and income taxation. The problems of tax administrations, procedures laws, taxpayers' rights and obligations as well as tax compliance are also taken into consideration. The second part of the study reviews the national tax systems within the EAC member countries. Before the single taxes are described in more detail, the macroeconomic situation is illuminated by some basic figures and the current stand of the inner-community integration analysed. Then the single tax bases and tax rates are confronted to shed some light on the necessities for the development of a common market within the near future. Again the value added tax laws, excise taxes and income taxes are discussed in detail, while regarding the latter the focus is on company taxation. For a better systematic analysis the national tax laws are confronted within an overview. The chapter is closed with a summary of the tax rates applied and a rough estimation of the tax burdens within the Partner States. The third part of this report contains the policy recommendations of the expert group following the same structures as the chapters before and presenting the results for the VAT, the excises and the corporate income tax (CIT). Additionally the requirements for tax procedures and administration as well as problems of transparency and information exchange are discussed in detail before the strategic recommendations are derived in close relation to the experiences made within the EU harmonisation process. The recommendations are based on the following normative arguments: (1) Tax harmonisation is a basic requirement for economic integration. (2) Equality of taxation is an imperative of tax justice and demands the avoidance of double taxation as well as the combat of tax evasion and corruption. (3) The avoidance of harmful tax competition between the Partner States. (4) The strengthening of taxpayers' rights in tax procedures. Hence, all kinds of income, goods and services should be taxed once and only once.}, language = {en} } @book{GellerHirschfeldBracha2010, author = {Geller, Felix and Hirschfeld, Robert and Bracha, Gilad}, title = {Pattern Matching for an object-oriented and dynamically typed programming language}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-065-6}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-43035}, publisher = {Universit{\"a}t Potsdam}, pages = {81}, year = {2010}, abstract = {Pattern matching is a well-established concept in the functional programming community. It provides the means for concisely identifying and destructuring values of interest. This enables a clean separation of data structures and respective functionality, as well as dispatching functionality based on more than a single value. Unfortunately, expressive pattern matching facilities are seldomly incorporated in present object-oriented programming languages. We present a seamless integration of pattern matching facilities in an object-oriented and dynamically typed programming language: Newspeak. We describe language extensions to improve the practicability and integrate our additions with the existing programming environment for Newspeak. This report is based on the first author's master's thesis.}, language = {en} } @misc{SchweizerBluemkeBrandetal.2010, author = {Schweizer, Geoffrey and Bluemke, Matthias and Brand, Ralf and Kahlert, Daniela}, title = {Exercise might be good for me, but I don't feel good about it : do automatic associations predict exercise behavior?}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-42510}, year = {2010}, abstract = {Models employed in exercise psychology highlight the role of reflective processes for explaining behavior change. However, as discussed in social cognition literature, information-processing models also consider automatic processes (dual-process models). To examine the relevance of automatic processing in exercise psychology, we used a priming task to assess the automatic evaluations of exercise stimuli in physically active sport and exercise majors (n = 32), physically active nonsport majors (n = 31), and inactive students (n = 31). Results showed that physically active students responded faster to positive words after exercise primes, whereas inactive students responded more rapidly to negative words. Priming task reaction times were successfully used to predict reported amounts of exercise in an ordinal regression model. Findings were obtained only with experiential items reflecting negative and positive consequences of exercise. The results illustrate the potential importance of dual-process models in exercise psychology.}, language = {en} } @misc{ScholtkaSchneiderMelcheretal.2009, author = {Scholtka, Bettina and Schneider, Mandy and Melcher, Ralph and Katzenberger, Tiemo and Friedrich, Daniela and Berghof-J{\"a}ger, Kornelia and Scheppach, Wolfgang and Steinberg, Pablo}, title = {A gene marker panel covering the Wnt and the Ras-Raf-MEK-MAPK signalling pathways allows to detect gene mutations in 80\% of early (UICC I) colon cancer stages in humans}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44587}, year = {2009}, abstract = {Background: Very recently a gene marker panel that allows the mutational analysis of APC, CTNNB1, B-RAF and K-RAS was conceived. The aim of the present study was to use the 4-gene marker panel covering the Wnt and Ras-Raf-MEK-MAPK signalling pathways to determine the percentage of sporadic colorectal carcinomas (CRC) carrying at least one of the four above-mentioned genes in a mutated form alone and/or in combination with microsatellite instability (MSI) and to compare the sensitivity of the gene marker panel used in this study with that of gene marker panels previously reported in the scientific literature. Methods: CTNNB1 and B-RAF were screened by PCR-single-strand conformation polymorphism analysis and K-RAS gene mutations by restriction fragment length polymorphism analysis. For the mutational analysis of the APC gene mutation cluster region (codons 1243-1567) direct DNA sequencing was performed. The U.S. National Cancer Institute microsatellite panel (BAT25, BAT26, D2S123, D5S346 and D17S250) was used for MSI analysis. Results: It could be shown that about 80\% of early stage CRC (UICC stages I and II) and over 90\% of CRC in the UICC stage IV carried at least one mutated gene and/or showed MSI. No significant increase in the gene mutation frequencies could be determined when comparing tumours in the UICC stage I with those in UICC stage IV. Conclusions: When compared with previously published gene marker panels the 4-gene marker panel used in the present study shows an excellent performance, allowing to detect genetic alterations in 80-90\% of human sporadic CRC samples analyzed.}, language = {en} } @misc{ScholtkaKuehnelTaugneretal.2009, author = {Scholtka, Bettina and K{\"u}hnel, Dana and Taugner, Felicitas and Steinberg, Pablo}, title = {Inflammation does not precede or accompany the induction of perneoplastic lesions in the colon of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine-fed rats}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44570}, year = {2009}, abstract = {Heterocyclic aromatic amines (HCAs) are formed in meat cooked at high temperatures for a long time or over an open flame. In this context 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), the most abundant HCA in cooked meat, has been suggested to be involved in colon and prostate carcinogenesis. In the latter case it has been reported that: (1) roughly 50\% of Fischer F344 male rats treated with PhIP develop carcinomas in the ventral prostate lobe at 1 year of age; (2) inflammation precedes prostatic intraepithelial neoplasia in PhIP-fed rats; (3) inflammation specifically occurs in the ventral prostate lobe of PhIP-fed rats. To test whether PhIP by itself leads to inflammation in the colon and whether a human-relevant concentration of PhIP is able to induce preneoplastic lesions in the colon, male F344 rats were fed 0.1 or 100 ppm PhIP for up to 10 months and thereafter the colon tissue was analyzed histochemically. In none of the experimental groups signs of acute or chronic colonic inflammation were observed. 0.1 ppm PhIP leads to the development of hyperplastic and dysplastic lesions in the colon of single animals, but the incidence of these lesions does not reach a statistical significance. In contrast, in rats fed 100 ppm PhIP for 10 months hyperplastic and dysplastic colonic lesions were induced in a statistically significant number of animals. It is concluded that: (1) the induction of preneoplastic lesions in rat colon by PhIP is not preceded or accompanied by an inflammatory process; (2) a human-relevant concentration of PhIP alone is not sufficient to initiate colon carcinogenesis in rats.}, language = {en} } @misc{PeterYenesewTwinomuhwezietal.2009, author = {Peter, Martin G. and Yenesew, Abiy and Twinomuhwezi, Hannington and Kabaru, Jacques M. and Akala, Hoseah M. and Kiremire, Bernard T. and Heydenreich, Matthias and Eyase, Fredrick and Waters, Norman C. and Walsh, Douglas S.}, title = {Antiplasmodial and larvicidal flavonoids from Derris trifoliata}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44614}, year = {2009}, abstract = {From the dichloromethane-methanol (1:1) extract of the seed pods of Derris trifoliata, a new flavanone derivative (S)-lupinifolin 4´-methyl ether was isolated. In addition, the known flavonoids lupinifolin and rotenone were identified. The structures were determined on the basis of spectroscopic evidence. Lupinfolin showed moderate in vitro antiplasmodial activity against the D6 (chloroquine-sensitive) and W2 (chloroquineresistant) strains of Plasmodium falciparum. The different parts of this plant showed larvicidal activities against Aedes aegypti and rotenoids were identified as the active principles.}, language = {en} } @misc{PeterMuivaYenesewetal.2009, author = {Peter, Martin G. and Muiva, Lois M. and Yenesew, Abiy and Derese, Solomon and Heydenreich, Matthias and Akala, Hoseah M. and Eyase, Fredrick and Waters, Norman C. and Mutai, Charles and Keriko, Joseph M. and Walsh, Douglas S.}, title = {Antiplasmodial β-hydroxydihydrochalcone from seedpods of Tephrosia elata}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44437}, year = {2009}, abstract = {From the seedpods of Tephrosia elata, a new β-hydroxydihydrochalcone named (S)-elatadihydrochalcone was isolated. In addition, the known flavonoids obovatachalcone, obovatin, obovatin methyl ether and deguelin were identified. The structures were determined on the basis of spectroscopic evidence. The crude extract and the flavonoids obtained from the seedpods of this plant showed antiplasmodial activities. The literature NMR data on β-hydroxydihydrochalcones is reviewed and the identity of some of the compounds assigned β-hydroxydihydrochalcone skeleton is questioned.}, language = {en} } @misc{BlenauRotteWitteetal.2009, author = {Blenau, Wolfgang and Rotte, Cathleen and Witte, Jeannine and Baumann, Otto and Walz, Bernd}, title = {Source, topography and excitatory effects of GABAergic innervation in cockroach salivary glands}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44353}, year = {2009}, abstract = {Cockroach salivary glands are innervated by dopaminergic and serotonergic neurons. Both transmitters elicit saliva secretion. We studied the distribution pattern of neurons containing gamma-aminobutyric acid ( GABA) and their physiological role. Immunofluorescence revealed a GABA-immunoreactive axon that originates within the subesophageal ganglion at the salivary neuron 2 (SN2) and this extends within the salivary duct nerve towards the salivary gland. GABA-positive fibers form a network on most acinar lobules and a dense plexus in the interior of a minor fraction of acinar lobules. Co-staining with anti-synapsin revealed that some putative GABAergic terminals seem to make pre-synaptic contacts with GABA-negative release sites. Many putative GABAergic release sites are at some distance from other synapses and at distance from the acinar tissue. Intracellular recordings from isolated salivary glands have revealed that GABA does not affect the basolateral membrane potential of the acinar cells directly. When applied during salivary duct nerve stimulation, GABA enhances the electrical response of the acinar cells and increases the rates of fluid and protein secretion. The effect on electrical cell responses is mimicked by the GABA(B) receptor agonists baclofen and SKF97541, and blocked by the GABAB receptor antagonists CGP52432 and CGP54626. These findings indicate that GABA has a modulatory role in the control of salivation, acting presynaptically on serotonergic and/or dopaminergic neurotransmission.}, language = {en} } @misc{BlenauMustardHamiltonetal.2003, author = {Blenau, Wolfgang and Mustard, Julie A. and Hamilton, Ingrid S. and Ward, Vernon K. and Ebert, Paul R. and Mercer, Alison R.}, title = {Analysis of two D1-like dopamine receptors from the honey bee Apis mellifera reveals agonist-independent activity}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44378}, year = {2003}, abstract = {Dopamine is found in many invertebrate organisms, including insects, however, the mechanisms through which this amine operates remain unclear. We have expressed two dopamine receptors cloned from honey bee (AmDOP1 and AmDOP2) in insect cells (Spodoptera frugiperda), and compared their pharmacology directly using production of cAMP as a functional assay. In each assay, AmDOP1 receptors required lower concentrations of dopamine and 6,7-ADTN for maximal activation than AmDOP2 receptors. Conversely, butaclamol and cis(Z)-flupentixol were more potent at blocking the cAMP response mediated through AmDOP2 than AmDOP1 receptors. Expression of AmDOP1, but not AmDOP2, receptors significantly increased levels of cAMP even in the absence of ligand. This constitutive activity was blocked by cis(Z)-flupentixol. This work provides the first evidence of a constitutively activated dopamine receptor in invertebrates and suggests that although AmDOP1 and AmDOP2 share much less homology than their vertebrate counterparts, they display a number of functional parallels with the mammalian D1-like dopamine receptors.}, language = {en} } @misc{BlenauBaumann2003, author = {Blenau, Wolfgang and Baumann, Arnd}, title = {Aminergic signal transduction in invertebrates : focus on tyramine and octopamine receptors}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44271}, year = {2003}, abstract = {Electro-chemical signal transduction is the basis of communication between n eurons and their target cells. An important group of neuroactive substances that are released by action potentials from neurons are the biogenic amines. These a re small organic molecules that bind to specific receptors located in the target cell membrane. Once activated these receptors cause changes in the intracellula r concentration of second messengers, i.e. cyclic nucleotides, phosphoinositides , or Ca2+, leading to slow but long-lasting cellular responses. Biochemical, pha rmacological, physiological, and molecular biological approaches have unequivoca lly shown that biogenic amines are important regulators of cellular function in both vertebrates and invertebrates. In this review, we will concentrate on the p roperties of two biogenic amines and their receptors that were originally identi fied in invertebrates: tyramine and octopamine. }, language = {en} } @book{NastanskyStrohe2010, author = {Nastansky, Andreas and Strohe, Hans Gerhard}, title = {The impact of changes in asset prices on real economic activity : a cointegration analysis for Germany}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-43762}, publisher = {Universit{\"a}t Potsdam}, year = {2010}, abstract = {This paper reviews theoretical and empirical evidence of asset price movements impact on the real economic activity. A key channel is the wealth effect on consumption. Fluctuations in stock prices and housing prices influence the households wealth and could have important impacts on households consumption. In addition, stock prices may affect corporate sector investments and property prices may affect building activity. Here, the method of cointegration is used to estimate the wealth effect and the investment effect in aggregate time series for Germany after the Reunification in 1990. Moreover, we discuss the role of asset prices in the monetary policy strategy of the ECB.}, language = {en} } @book{OPUS4-4172, title = {Baset - Bubastis - Tell Basta}, series = {Arcus: Berichte aus Arch{\"a}ologie, Baugeschichte und Nachbargebieten}, journal = {Arcus: Berichte aus Arch{\"a}ologie, Baugeschichte und Nachbargebieten}, number = {9}, editor = {Tietze, Christian and Lange, Eva}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {3-937786-55-4}, issn = {0947-1081}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-43783}, publisher = {Universit{\"a}t Potsdam}, pages = {107}, year = {2005}, language = {en} } @book{SmirnovReijersNugterenetal.2010, author = {Smirnov, Sergey and Reijers, Hajo A. and Nugteren, Thijs and Weske, Mathias}, title = {Business process model abstraction : theory and practice}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-054-0}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41782}, publisher = {Universit{\"a}t Potsdam}, pages = {17}, year = {2010}, abstract = {Business process management aims at capturing, understanding, and improving work in organizations. The central artifacts are process models, which serve different purposes. Detailed process models are used to analyze concrete working procedures, while high-level models show, for instance, handovers between departments. To provide different views on process models, business process model abstraction has emerged. While several approaches have been proposed, a number of abstraction use case that are both relevant for industry and scientifically challenging are yet to be addressed. In this paper we systematically develop, classify, and consolidate different use cases for business process model abstraction. The reported work is based on a study with BPM users in the health insurance sector and validated with a BPM consultancy company and a large BPM vendor. The identified fifteen abstraction use cases reflect the industry demand. The related work on business process model abstraction is evaluated against the use cases, which leads to a research agenda.}, language = {en} } @phdthesis{Wilke2010, author = {Wilke, Franziska Daniela Helena}, title = {Quantifying crystalline exhumation in the Himalaya}, doi = {10.25932/publishup-4119}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-43138}, school = {Universit{\"a}t Potsdam}, pages = {IV, 99}, year = {2010}, abstract = {In 1915, Alfred Wegener published his hypotheses of plate tectonics that revolutionised the world for geologists. Since then, many scientists have studied the evolution of continents and especially the geologic structure of orogens: the most visible consequence of tectonic processes. Although the morphology and landscape evolution of mountain belts can be observed due to surface processes, the driving force and dynamics at lithosphere scale are less well understood despite the fact that rocks from deeper levels of orogenic belts are in places exposed at the surface. In this thesis, such formerly deeply-buried (ultra-) high-pressure rocks, in particular eclogite facies series, have been studied in order to reveal details about the formation and exhumation conditions and rates and thus provide insights into the geodynamics of the most spectacular orogenic belt in the world: the Himalaya. The specific area investigated was the Kaghan Valley in Pakistan (NW Himalaya). Following closure of the Tethyan Ocean by ca. 55-50 Ma, the northward subduction of the leading edge of India beneath the Eurasian Plate and subsequent collision initiated a long-lived process of intracrustal thrusting that continues today. The continental crust of India - granitic basement, Paleozoic and Mesozoic cover series and Permo-Triassic dykes, sills and lavas - has been buried partly to mantle depths. Today, these rocks crop out as eclogites, amphibolites and gneisses within the Higher Himalayan Crystalline between low-grade metamorphosed rocks (600-640°C/ ca. 5 kbar) of the Lesser Himalaya and Tethyan sediments. Beside tectonically driven exhumation mechanisms the channel flow model, that describes a denudation focused ductile extrusion of low viscosity material developed in the middle to lower crust beneath the Tibetan Plateau, has been postulated. To get insights into the lithospheric and crustal processes that have initiated and driven the exhumation of this (ultra-) high-pressure rocks, mineralogical, petrological and isotope-geochemical investigations have been performed. They provide insights into 1) the depths and temperatures to which these rocks were buried, 2) the pressures and temperatures the rocks have experienced during their exhumation, 3) the timing of these processes 4) and the velocity with which these rocks have been brought back to the surface. In detail, through microscopical studies, the identification of key minerals, microprobe analyses, standard geothermobarometry and modelling using an effective bulk rock composition it has been shown that published exhumation paths are incomplete. In particular, the eclogites of the northern Kaghan Valley were buried to depths of 140-100 km (36-30 kbar) at 790-640°C. Subsequently, cooling during decompression (exhumation) towards 40-35 km (17-10 kbar) and 630-580°C has been superseded by a phase of reheating to about 720-650°C at roughly the same depth before final exhumation has taken place. In the southern-most part of the study area, amphibolite facies assemblages with formation conditions similar to the deduced reheating phase indicate a juxtaposition of both areas after the eclogite facies stage and thus a stacking of Indian Plate units. Radiometric dating of zircon, titanite and rutile by U-Pb and amphibole and micas by Ar-Ar reveal peak pressure conditions at 47-48 Ma. With a maximum exhumation rate of 14 cm/a these rocks reached the crust-mantle boundary at 40-35 km within 1 Ma. Subsequent exhumation (46-41 Ma, 40-35 km) decelerated to ca. 1 mm/a at the base of the continental crust but rose again to about 2 mm/a in the period of 41-31 Ma, equivalent to 35-20 km. Apatite fission track (AFT) and (U-Th)/He ages from eclogites, amphibolites, micaschists and gneisses yielded moderate Oligocene to Miocene cooling rates of about 10°C/Ma in the high altitude northern parts of the Kaghan Valley using the mineral-pair method. AFT ages are of 24.5±3.8 to 15.6±2.1 Ma whereas apatite (U-Th)/He analyses yielded ages between 21.0±0.6 and 5.3±0.2 Ma. The southern-most part of the Valley is dominated by younger late Miocene to Pliocene apatite fission track ages of 7.6±2.1 and 4.0±0.5 Ma that support earlier tectonically and petrologically findings of a juxtaposition and stack of Indian Plate units. As this nappe is tectonically lowermost, a later distinct exhumation and uplift driven by thrusting along the Main Boundary Thrust is inferred. A multi-stage exhumation path is evident from petrological, isotope-geochemical and low temperature thermochronology investigations. Buoyancy driven exhumation caused an initial rapid exhumation: exhumation as fast as recent normal plate movements (ca. 10 cm/a). As the exhuming units reached the crust-mantle boundary the process slowed down due to changes in buoyancy. Most likely, this exhumation pause has initiated the reheating event that is petrologically evident (e.g. glaucophane rimmed by hornblende, ilmenite overgrowth of rutile). Late stage processes involved widespread thrusting and folding with accompanied regional greenschist facies metamorphism, whereby contemporaneous thrusting on the Batal Thrust (seen by some authors equivalent to the MCT) and back sliding of the Kohistan Arc along the inverse reactivated Main Mantle Thrust caused final exposure of these rocks. Similar circumstances have been seen at Tso Morari, Ladakh, India, 200 km further east where comparable rock assemblages occur. In conclusion, as exhumation was already done well before the initiation of the monsoonal system, climate dependent effects (erosion) appear negligible in comparison to far-field tectonic effects.}, language = {en} } @misc{Fruebing2008, type = {Master Thesis}, author = {Fr{\"u}bing, Judith}, title = {The third generation of Indians in Britain : cultural identity and cultural change}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-42668}, school = {Universit{\"a}t Potsdam}, year = {2008}, abstract = {Over the last decades Britain´s ethnic minorities have successfully established themselves in a multicultural society. In particular, Indian - Hindu communities generally improved their social and economic situation. In this context, the third generation of British Indians is now growing up. In contrast to the previous generation of the Indian diaspora, these children grow up in an established ethnic community, which learned to retain its religion, traditions and culture in a foreign environment. At the same time, these children are part of the multicultural British society. Based on the academic discussion about the second generation of immigrated ethnic communities, when the youth often suffered from cultural differences, racism and discrimination and therefore rejected aspects of their culture of origin, this paper assumes that the loss of the culture of origin further increases in the third generation. This thesis follows the main theories about the connection between generation and integration. It is believed that the preference of western culture influences the personal, ethnic and cultural identity of young people. This leads to the rejection of traditional bonds. Before introducing this thesis various theoretical concepts are discussed which are inevitable for the comprehension of the diasporic situation in which British Indian youngsters grow up. As part of the worldwide Asian Indian diaspora Indian families in Britain maintain manifold links to Indian communities in various countries. Particularly, the link to India plays a decisive role; the subcontinent is referred to as an abstract homeland, especially by the first generation. While the grandparents strongly adhere to their Indian culture and Hindu religion, the second generation already generated cultural change. In this process various cultural values of the Indian ethnic community have been questioned and modified. Further, the second generation pushed the integration into the British society by giving up the dependence on the ethnic network. This paper is based on a hybrid and fluent definition of culture. This definition also applies to the underlying understanding of identity and ethnicity. Due to migration, cultural contact and the multilocality of the diaspora, diasporic and post-diasporic identities and cultures are characterized by hybridity, heterogeneity, fragmentation and flexibility. Particularly, in the younger generation - though dependent on a number of social and structural factors - cultural change and mixture happen; in this process new ethnicities and identities evolve. In the second and third part of this paper the thesis of loss of culture of origin is refuted on the basis of findings from empirical research. British - Indian youngsters in London have been questioned for the study. Half of the youngsters are related to a sampradaya, a Hindu sect. This enables the author to compare youngsters who do not belong to a particular religious group with those who are included into a religious and / or ethnic community through a sampradaya. The analysis of the findings which are based on qualitative and quantitative social research shows that the young people have great interest in their culture of origin and that they aim to maintain this culture in the diaspora. They identify as Indian and are proud of their cultural differences. In this, they differ from the second generation. In contrast to the generation of their grandparents the Indian identity of the third generation is not based on nostalgic memories. They confirm and emphasize their postdiasporic difference in a western multicultural society. The findings from the survey hereby exceed the thesis from Hansen's theory about the rediscovery of the culture of origin in the third generation. The comparison of both groups shows that in the context of the differentiation of postmodern and postcolonial communities also ethnic groups become increasingly differentiated. Therefore, the Indian heritage and culture does not play the same role for every young British Indian.}, language = {en} } @book{Dambacher2010, author = {Dambacher, Michael}, title = {Bottom-up and top-down processes in reading : influences of frequency and predictability on event-related potentials and eye movements}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-059-5}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-42024}, publisher = {Universit{\"a}t Potsdam}, pages = {239}, year = {2010}, abstract = {In reading, word frequency is commonly regarded as the major bottom-up determinant for the speed of lexical access. Moreover, language processing depends on top-down information, such as the predictability of a word from a previous context. Yet, however, the exact role of top-down predictions in visual word recognition is poorly understood: They may rapidly affect lexical processes, or alternatively, influence only late post-lexical stages. To add evidence about the nature of top-down processes and their relation to bottom-up information in the timeline of word recognition, we examined influences of frequency and predictability on event-related potentials (ERPs) in several sentence reading studies. The results were related to eye movements from natural reading as well as to models of word recognition. As a first and major finding, interactions of frequency and predictability on ERP amplitudes consistently revealed top-down influences on lexical levels of word processing (Chapters 2 and 4). Second, frequency and predictability mediated relations between N400 amplitudes and fixation durations, pointing to their sensitivity to a common stage of word recognition; further, larger N400 amplitudes entailed longer fixation durations on the next word, a result providing evidence for ongoing processing beyond a fixation (Chapter 3). Third, influences of presentation rate on ERP frequency and predictability effects demonstrated that the time available for word processing critically co-determines the course of bottom-up and top-down influences (Chapter 4). Fourth, at a near-normal reading speed, an early predictability effect suggested the rapid comparison of top-down hypotheses with the actual visual input (Chapter 5). The present results are compatible with interactive models of word recognition assuming that early lexical processes depend on the concerted impact of bottom-up and top-down information. We offered a framework that reconciles the findings on a timeline of word recognition taking into account influences of frequency, predictability, and presentation rate (Chapter 4).}, language = {en} } @phdthesis{Huber2010, author = {Huber, Veronika Emilie Charlotte}, title = {Climate impact on phytoplankton blooms in shallow lakes}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-42346}, school = {Universit{\"a}t Potsdam}, year = {2010}, abstract = {Lake ecosystems across the globe have responded to climate warming of recent decades. However, correctly attributing observed changes to altered climatic conditions is complicated by multiple anthropogenic influences on lakes. This thesis contributes to a better understanding of climate impacts on freshwater phytoplankton, which forms the basis of the food chain and decisively influences water quality. The analyses were, for the most part, based on a long-term data set of physical, chemical and biological variables of a shallow, polymictic lake in north-eastern Germany (M{\"u}ggelsee), which was subject to a simultaneous change in climate and trophic state during the past three decades. Data analysis included constructing a dynamic simulation model, implementing a genetic algorithm to parameterize models, and applying statistical techniques of classification tree and time-series analysis. Model results indicated that climatic factors and trophic state interactively determine the timing of the phytoplankton spring bloom (phenology) in shallow lakes. Under equally mild spring conditions, the phytoplankton spring bloom collapsed earlier under high than under low nutrient availability, due to a switch from a bottom-up driven to a top-down driven collapse. A novel approach to model phenology proved useful to assess the timings of population peaks in an artificially forced zooplankton-phytoplankton system. Mimicking climate warming by lengthening the growing period advanced algal blooms and consequently also peaks in zooplankton abundance. Investigating the reasons for the contrasting development of cyanobacteria during two recent summer heat wave events revealed that anomalously hot weather did not always, as often hypothesized, promote cyanobacteria in the nutrient-rich lake studied. The seasonal timing and duration of heat waves determined whether critical thresholds of thermal stratification, decisive for cyanobacterial bloom formation, were crossed. In addition, the temporal patterns of heat wave events influenced the summer abundance of some zooplankton species, which as predators may serve as a buffer by suppressing phytoplankton bloom formation. This thesis adds to the growing body of evidence that lake ecosystems have strongly responded to climatic changes of recent decades. It reaches beyond many previous studies of climate impacts on lakes by focusing on underlying mechanisms and explicitly considering multiple environmental changes. Key findings show that climate impacts are more severe in nutrient-rich than in nutrient-poor lakes. Hence, to develop lake management plans for the future, limnologists need to seek a comprehensive, mechanistic understanding of overlapping effects of the multi-faceted human footprint on aquatic ecosystems.}, language = {en} } @phdthesis{Ruehling2008, author = {R{\"u}hling, Markus}, title = {Substitution effect through fiscal transfers?! : incidence of the Peruvian property tax}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-42100}, school = {Universit{\"a}t Potsdam}, year = {2008}, abstract = {Whether the results of fiscal transfers have positive or negative implications depends upon the incentives that transfer systems create for both central and local governments. The complexity and ambiguity of the relationship between fiscal transfers and tax revenues of local governments is one of the main causes why research projects, even in the same country, come to different results. This investigation is seriously questioning the often stated substitution effect based only on an analysis of aggregated data and finally rejects in the qualitative part of this research (using survey techniques) a substitution effect in the majority of the assessed municipalities. While most theories are modeling governments as tax-maximizers (Leviathan) or as being prone to fiscal laziness, this investigation shows that mayors react to a whole set of incentives. Most mayors react rational and rather pragmatically in respect to the incentives and constraints which are established by the particular context of a municipality, the central government and their own personality/identity/interests. While the yield on property tax in Peru is low, there are no signs that increases in transfers have had, on average, a negative impact on their revenue generation. On an individual basis there exist mayors who are revenue maximizers, others who are substituting revenues and others who show apathy. Many engage in property tax. While rural or small municipalities have limited potential, property taxes are the main revenue sources for the Peruvian urban municipalities, rising on average 10\% during the last five years. The property tax in Peru accounts for less than 0.2\% of GDP, which compared to the Latin American average, is extremely low. In 2002, property tax was collecting nationwide about 10\% of the overall budget of local governments. In 2006, the share was closer to 6\% due to windfall transfers. The property tax can enhance accountability at the local level and has important impacts on urban spatial development. It is also important considering that most charges or transfers are earmarked such that property tax yields can cover discretionary finances. The intergovernmental fiscal transfers can be described as a patchwork of political liabilities of the past rather than connected with thorough compensation or service improvement functions. The fiscal base of local governments in Peru remains small for the municipalities and the incentive structure to enhance property tax revenues is far from optimal. The central government and sector institutions, which are in the Peruvian institutional design of the property tax responsible for the enablement environment, can reinforce local tax efforts. In the past the central government permanently changed the rules of the game, giving municipalities reduced predictability of policy choices. There are no relevant signs that a stronger property tax is captured by Peruvian interest groups. Since the central government has responsibility for tax regulation and partly valuation there has been little debate about financial issues on the local political agenda. Most council members are therefore not familiar with tax issues. If the central government did not set the tax rate and valuation then there would probably be a more vigorous public debate and an electorate that was better informed about local politics. Elected mayors (as political and administrative leaders) are not counterbalanced and held in check by an active council and/or by vigorous local political parties. Local politics are concentrated on the mayor, electoral rules, the institutional design and political culture - all of which are not helpful in increasing the degree of influence that citizens and associations have upon collective decision-making at the local level. The many alternations between democracy and autocracy have not been helpful in building strong institutions at the local level. Property tax revenues react slowly and the institutional context matters because an effective tax system as a public good can only be created if actors have long time horizons. The property tax has a substantial revenue potential, however, since municipalities are going through a transfer bonanza, it is especially difficult to make a plea for increasing their own revenue base. Local governments should be the proponents of property tax reform, but they have, in Peru, little policy clout because the municipal associations are dispersed and there exists little relevant information concerning important local policy issues.}, language = {en} } @phdthesis{Aichner2009, author = {Aichner, Bernhard}, title = {Aquatic macrophyte-derived biomarkers as palaeolimnological proxies on the Tibetan Plateau}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-42095}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {The Tibetan Plateau is the largest elevated landmass in the world and profoundly influences atmospheric circulation patterns such as the Asian monsoon system. Therefore this area has been increasingly in focus of palaeoenvironmental studies. This thesis evaluates the applicability of organic biomarkers for palaeolimnological purposes on the Tibetan Plateau with a focus on aquatic macrophyte-derived biomarkers. Submerged aquatic macrophytes have to be considered to significantly influence the sediment organic matter due to their high abundance in many Tibetan lakes. They can show highly 13C-enriched biomass because of their carbon metabolism and it is therefore crucial for the interpretation of δ13C values in sediment cores to understand to which extent aquatic macrophytes contribute to the isotopic signal of the sediments in Tibetan lakes and in which way variations can be explained in a palaeolimnological context. Additionally, the high abundance of macrophytes makes them interesting as potential recorders of lake water δD. Hydrogen isotope analysis of biomarkers is a rapidly evolving field to reconstruct past hydrological conditions and therefore of special relevance on the Tibetan Plateau due to the direct linkage between variations of monsoon intensity and changes in regional precipitation / evaporation balances. A set of surface sediment and aquatic macrophyte samples from the central and eastern Tibetan Plateau was analysed for composition as well as carbon and hydrogen isotopes of n-alkanes. It was shown how variable δ13C values of bulk organic matter and leaf lipids can be in submerged macrophytes even of a single species and how strongly these parameters are affected by them in corresponding sediments. The estimated contribution of the macrophytes by means of a binary isotopic model was calculated to be up to 60\% (mean: 40\%) to total organic carbon and up to 100\% (mean: 66\%) to mid-chain n-alkanes. Hydrogen isotopes of n-alkanes turned out to record δD of meteoric water of the summer precipitation. The apparent enrichment factor between water and n-alkanes was in range of previously reported ones (≈-130 per mille) at the most humid sites, but smaller (average: -86 per mille) at sites with a negative moisture budget. This indicates an influence of evaporation and evapotranspiration on δD of source water for aquatic and terrestrial plants. The offset between δD of mid- and long-chain n-alkanes was close to zero in most of the samples, suggesting that lake water as well as soil and leaf water are affected to a similar extent by those effects. To apply biomarkers in a palaeolimnological context, the aliphatic biomarker fraction of a sediment core from Lake Koucha (34.0° N; 97.2° E; eastern Tibetan Plateau) was analysed for concentrations, δ13C and δD values of compounds. Before ca. 8 cal ka BP, the lake was dominated by aquatic macrophyte-derived mid-chain n-alkanes, while after 6 cal ka BP high concentrations of a C20 highly branched isoprenoid compound indicate a predominance of phytoplankton. Those two principally different states of the lake were linked by a transition period with high abundances of microbial biomarkers. δ13C values were relatively constant for long-chain n-alkanes, while mid-chain n-alkanes showed variations between -23.5 to -12.6 per mille. Highest values were observed for the assumed period of maximum macrophyte growth during the late glacial and for the phytoplankton maximum during the middle and late Holocene. Therefore, the enriched values were interpreted to be caused by carbon limitation which in turn was induced by high macrophyte and primary productivity, respectively. Hydrogen isotope signatures of mid-chain n-alkanes have been shown to be able to track a previously deduced episode of reduced moisture availability between ca. 10 and 7 cal ka BP, indicated by a 20 per mille shift towards higher δD values. Indications for cooler episodes at 6.0, 3.1 and 1.8 cal ka BP were gained from drops of biomarker concentrations, especially microbial-derived hopanoids, and from coincidental shifts towards lower δ13C values. Those episodes correspond well with cool events reported from other locations on the Tibetan Plateau as well as in the Northern Hemisphere. To conclude, the study of recent sediments and plants improved the understanding of factors affecting the composition and isotopic signatures of aliphatic biomarkers in sediments. Concentrations and isotopic signatures of the biomarkers in Lake Koucha could be interpreted in a palaeolimnological context and contribute to the knowledge about the history of the lake. Aquatic macrophyte-derived mid-chain n-alkanes were especially useful, due to their high abundance in many Tibetan Lakes and their ability to record major changes of lake productivity and palaeo-hydrological conditions. Therefore, they have the potential to contribute to a fuller understanding of past climate variability in this key region for atmospheric circulation systems.}, language = {en} } @book{OPUS4-4066, title = {Baset - Bubastis - Tell Basta}, series = {Arcus: Berichte aus Arch{\"a}ologie, Baugeschichte und Nachbargebieten}, journal = {Arcus: Berichte aus Arch{\"a}ologie, Baugeschichte und Nachbargebieten}, number = {8}, editor = {Tietze, Christian and Lange, Eva}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-937786-31-5}, issn = {0947-1081}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-42682}, publisher = {Universit{\"a}t Potsdam}, pages = {201}, year = {2005}, abstract = {Inhalt: Habachi, Labib: Tell Basta Chapter 1: Introductory: Bubatis and its monuments Chapter II: The temple of Pepi I [I]: Description Chapter III: The temple of Pepi [III]: Finds and importance Chapter IV: General notes on the great temple [I]: Mihos temple and entrance hall Chapter V: General notes on the great temple [II]: Festival hall and hypostyle hall Chapter VI: General notes on the great temple [III]: The temple of Nektanebos (Nekht-har-hebi) Chapter VII: Work outside the temples Chapter VIII: Blocks transferred to Bubastis Chapter IX: Blocks removed from Bubastis Farid, Shafik: Preliminary report on the excavations of the antiquities department at Tell Basta}, language = {en} } @phdthesis{Chirvasa2010, author = {Chirvasa, Mihaela}, title = {Finite difference methods for 1st Order in time, 2nd order in space, hyperbolic systems used in numerical relativity}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-42135}, school = {Universit{\"a}t Potsdam}, year = {2010}, abstract = {This thesis is concerned with the development of numerical methods using finite difference techniques for the discretization of initial value problems (IVPs) and initial boundary value problems (IBVPs) of certain hyperbolic systems which are first order in time and second order in space. This type of system appears in some formulations of Einstein equations, such as ADM, BSSN, NOR, and the generalized harmonic formulation. For IVP, the stability method proposed in [14] is extended from second and fourth order centered schemes, to 2n-order accuracy, including also the case when some first order derivatives are approximated with off-centered finite difference operators (FDO) and dissipation is added to the right-hand sides of the equations. For the model problem of the wave equation, special attention is paid to the analysis of Courant limits and numerical speeds. Although off-centered FDOs have larger truncation errors than centered FDOs, it is shown that in certain situations, off-centering by just one point can be beneficial for the overall accuracy of the numerical scheme. The wave equation is also analyzed in respect to its initial boundary value problem. All three types of boundaries - outflow, inflow and completely inflow that can appear in this case, are investigated. Using the ghost-point method, 2n-accurate (n = 1, 4) numerical prescriptions are prescribed for each type of boundary. The inflow boundary is also approached using the SAT-SBP method. In the end of the thesis, a 1-D variant of BSSN formulation is derived and some of its IBVPs are considered. The boundary procedures, based on the ghost-point method, are intended to preserve the interior 2n-accuracy. Numerical tests show that this is the case if sufficient dissipation is added to the rhs of the equations.}, language = {en} } @phdthesis{Borchert2010, author = {Borchert, Manuela}, title = {Interactions between aqueous fluids and silicate melts : equilibration, partitioning and complexation of trace elements}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-42088}, school = {Universit{\"a}t Potsdam}, year = {2010}, abstract = {The origin and evolution of granites has been widely studied because granitoid rocks constitute a major portion of the Earth's crust. The formation of granitic magma is, besides temperature mainly triggered by the water content of these rocks. The presence of water in magmas plays an important role due to the ability of aqueous fluids to change the chemical composition of the magma. The exsolution of aqueous fluids from melts is closely linked to a fractionation of elements between the two phases. Then, aqueous fluids migrate to shallower parts of the Earth's crust because of it's lower density compared to that of melts and adjacent rocks. This process separates fluids and melts, and furthermore, during the ascent, aqueous fluids can react with the adjacent rocks and alter their chemical signature. This is particularly impor- tant during the formation of magmatic-hydrothermal ore deposits or in the late stages of the evolution of magmatic complexes. For a deeper insight to these processes, it is essential to improve our knowledge on element behavior in such systems. In particular, trace elements are used for these studies and petrogenetic interpretations because, unlike major elements, they are not essential for the stability of the phases involved and often reflect magmatic processes with less ambiguity. However, for the majority of important trace elements, the dependence of the geochemical behavior on temperature, pressure, and in particular on the composition of the system are only incompletely or not at all experimentally studied. Former studies often fo- cus on the determination of fluid-melt partition coefficients (Df/m=cfluid/cmelt) of economically interesting elements, e.g., Mo, Sn, Cu, and there are some partitioning data available for ele- ments that are also commonly used for petrological interpretations. At present, no systematic experimental data on trace element behavior in fluid-melt systems as function of pressure, temperature, and chemical composition are available. Additionally, almost all existing data are based on the analysis of quenched phases. This results in substantial uncertainties, particularly for the quenched aqueous fluid because trace element concentrations may change upon cooling. The objective of this PhD thesis consisted in the study of fluid-melt partition coefficients between aqueous solutions and granitic melts for different trace elements (Rb, Sr, Ba, La, Y, and Yb) as a function of temperature, pressure, salinity of the fluid, composition of the melt, and experimental and analytical approach. The latter included the refinement of an existing method to measure trace element concentrations in fluids equilibrated with silicate melts di- rectly at elevated pressures and temperatures using a hydrothermal diamond-anvil cell and synchrotron radiation X-ray fluorescence microanalysis. The application of this in-situ method enables to avoid the main source of error in data from quench experiments, i.e., trace element concentration in the fluid. A comparison of the in-situ results to data of conventional quench experiments allows a critical evaluation of quench data from this study and literature data. In detail, starting materials consisted of a suite of trace element doped haplogranitic glasses with ASI varying between 0.8 and 1.4 and H2O or a chloridic solution with m NaCl/KCl=1 and different salinities (1.16 to 3.56 m (NaCl+KCl)). Experiments were performed at 750 to 950◦C and 0.2 or 0.5 GPa using conventional quench devices (externally and internally heated pressure vessels) with different quench rates, and at 750◦C and 0.2 to 1.4 GPa with in-situ analysis of the trace element concentration in the fluids. The fluid-melt partitioning data of all studied trace elements show 1. a preference for the melt (Df/m < 1) at all studied conditions, 2. one to two orders of magnitude higher Df/m using chloridic solutions compared to experiments with H2O, 3. a clear dependence on the melt composition for fluid-melt partitioning of Sr, Ba, La, Y, and Yb in experiments using chloridic solutions, 4. quench rate-related differences of fluid-melt partition coefficients of Rb and Sr, and 5. distinctly higher fluid-melt partitioning data obtained from in-situ experiments than from comparable quench runs, particularly in the case of H2O as starting solution. The data point to a preference of all studied trace elements for the melt even at fairly high salinities, which contrasts with other experimental studies, but is supported by data from studies of natural co-genetically trapped fluid and melt inclusions. The in-situ measurements of trace element concentrations in the fluid verify that aqueous fluids will change their composition upon cooling, which is in particular important for Cl free systems. The distinct differences of the in-situ results to quench data of this study as well as to data from the literature signify the im- portance of a careful fluid sampling and analysis. Therefore, the direct measurement of trace element contents in fluids equilibrated with silicate melts at elevated PT conditions represents an important development to obtain more reliable fluid-melt partition coefficients. For further improvement, both the aqueous fluid and the silicate melt need to be analyzed in-situ because partitioning data that are based on the direct measurement of the trace element content in the fluid and analysis of a quenched melt are still not completely free of quench effects. At present, all available data on element complexation in aqueous fluids in equilibrium with silicate melts at high PT are indirectly derived from partitioning data, which involves in these experiments assumptions on the species present in the fluid. However, the activities of chemical components in these partitioning experiments are not well constrained, which is required for the definition of exchange equilibria between melt and fluid species. For example, the melt-dependent variation of partition coefficient observed for Sr imply that this element can not only be complexed by Cl- as suggested previously. The data indicate a more complicated complexation of Sr in the aqueous fluid. To verify this hypothesis, the in-situ setup was also used to determine strontium complexation in fluids equilibrated with silicate melts at desired PT conditions by the application of X-ray absorption near edge structure (XANES) spectroscopy. First results show a strong effect of both fluid and melt composition on the resulting XANES spectra, which indicates different complexation environments for Sr.}, language = {en} } @phdthesis{Dokić2009, author = {Dokić, Jadranka}, title = {Quantum mechanical study of molecular switches : electronic structure, kinetics and dynamical aspects}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41796}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {Molecular photoswitches are attracting much attention lately mostly because of their possible applications in nano technology, and their role in biology. One of the widely studied representatives of photochromic molecules is azobenzene (AB). With light, by a static electric field, or with tunneling electrons this specie can be "switched" from the flat and energetically more stable trans form, into the compact cis form. The back reaction can be induced optically or thermally. Quantum chemical calculations, mostly based on density functional theory, on the AB molecule, AB derivatives and related systems are presented. All the calculations were done for isolated species, however, with implications for latest experimental results aiming at the switching of surface mounted ABs. In some of these experiments, it is assumed that the switching process is substrate mediated, by attaching an electron or a hole to the adsorbate forming short-lived anion or cation resonances. Therefore, we calculated also cationic and anionic ABs in this work. An influence of external electric fields on the potential energy surfaces, was also studied. Further, by the type, number and positioning of various substituent groups, systematic changes on activation energies and rates for the thermal cis-to-trans isomerization can be enforced. The nature of the transition state for ground state isomerization was investigated. Applying Eyring's transition state theory, trends in activation energies and rates were predicted and are, where a comparison was possible, in good agreement with experimental data. Further, thermal isomerization was studied in solution, for which a polarizable continuum model was employed. The influence of substitution and an environment leaves its traces on structural properties of molecules and quantitative appearance of calculated UV/Vis spectra, as well. Finally, an explicit treatment of a solid substrate was demonstrated for the conformational switching, by scanning tunneling microscope, of a 1,5-cyclooctadiene (COD) molecule at a Si(001) surface, treated by a cluster model. At first, we studied energetics and potential energy surfaces along relevant switching coordinates by quantum chemical calculations, followed by the switching dynamics using wave packet methods. We show that, in spite the simplicity of the model, our calculations support the switching of adsorbed COD, by inelastic electron tunneling at low temperatures.}, language = {en} } @book{Lkhagvadorj2010, author = {Lkhagvadorj, Ariunaa}, title = {Fiscal federalism and decentralization in Mongolia}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-053-3}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41768}, publisher = {Universit{\"a}t Potsdam}, pages = {178}, year = {2010}, abstract = {Fiscal federalism has been an important topic among public finance theorists in the last four decades. There is a series of arguments that decentralization of governments enhances growth by improving allocation efficiency. However, the empirical studies have shown mixed results for industrialized and developing countries and some of them have demonstrated that there might be a threshold level of economic development below which decentralization is not effective. Developing and transition countries have developed a variety of forms of fiscal decentralization as a possible strategy to achieve effective and efficient governmental structures. A generalized principle of decentralization due to the country specific circumstances does not exist. Therefore, decentralization has taken place in different forms in various countries at different times, and even exactly the same extent of decentralization may have had different impacts under different conditions. The purpose of this study is to investigate the current state of the fiscal decentralization in Mongolia and to develop policy recommendations for the efficient and effective intergovernmental fiscal relations system for Mongolia. Within this perspective the analysis concentrates on the scope and structure of the public sector, the expenditure and revenue assignment as well as on the design of the intergovernmental transfer and sub-national borrowing. The study is based on data for twenty-one provinces and the capital city of Mongolia for the period from 2000 to 2009. As a former socialist country Mongolia has had a highly centralized governmental sector. The result of the analysis below revealed that the Mongolia has introduced a number of decentralization measures, which followed a top down approach and were slowly implemented without any integrated decentralization strategy in the last decade. As a result Mongolia became de-concentrated state with fiscal centralization. The revenue assignment is lacking a very important element, for instance significant revenue autonomy given to sub-national governments, which is vital for the efficient service delivery at the local level. According to the current assignments of the expenditure and revenue responsibilities most of the provinces are unable to provide a certain national standard of public goods supply. Hence, intergovernmental transfers from the central jurisdiction to the sub-national jurisdictions play an important role for the equalization of the vertical and horizontal imbalances in Mongolia. The critical problem associated with intergovernmental transfers is that there is not a stable, predictable and transparent system of transfer allocation. The amount of transfers to sub-national governments is determined largely by political decisions on ad hoc basis and disregards local differences in needs and fiscal capacity. Thus a fiscal equalization system based on the fiscal needs of the provinces should be implemented. The equalization transfers will at least partly offset the regional disparities in revenues and enable the sub-national governments to provide a national minimum standard of local public goods.}, language = {en} } @book{KunzeStrohe2010, author = {Kunze, Karl-Kuno and Strohe, Hans Gerhard}, title = {Time-varying persistence in the German stock market}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-42046}, publisher = {Universit{\"a}t Potsdam}, year = {2010}, abstract = {This paper studies the persistence of daily returns of 21 German stocks from 1960 to 2008. We apply a widely used test based upon the modified R/S-Method by Lo [1991]. As an extension to Lux [1996] and Carbone et al. [2004] and in analogy to moving average or moving volatility, the statistics is calculated for moving windows of length 4, 8, and 16 years for every time series. Periods of persistence or long memory in returns can be found in some but not all time series. Robustness of results is verified by investigating stationarity and short memory effects.}, language = {en} } @book{BauckmannLeserNaumann2010, author = {Bauckmann, Jana and Leser, Ulf and Naumann, Felix}, title = {Efficient and exact computation of inclusion dependencies for data integration}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-048-9}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41396}, publisher = {Universit{\"a}t Potsdam}, pages = {36}, year = {2010}, abstract = {Data obtained from foreign data sources often come with only superficial structural information, such as relation names and attribute names. Other types of metadata that are important for effective integration and meaningful querying of such data sets are missing. In particular, relationships among attributes, such as foreign keys, are crucial metadata for understanding the structure of an unknown database. The discovery of such relationships is difficult, because in principle for each pair of attributes in the database each pair of data values must be compared. A precondition for a foreign key is an inclusion dependency (IND) between the key and the foreign key attributes. We present with Spider an algorithm that efficiently finds all INDs in a given relational database. It leverages the sorting facilities of DBMS but performs the actual comparisons outside of the database to save computation. Spider analyzes very large databases up to an order of magnitude faster than previous approaches. We also evaluate in detail the effectiveness of several heuristics to reduce the number of necessary comparisons. Furthermore, we generalize Spider to find composite INDs covering multiple attributes, and partial INDs, which are true INDs for all but a certain number of values. This last type is particularly relevant when integrating dirty data as is often the case in the life sciences domain - our driving motivation.}, language = {en} } @book{AlnemrPolyvyanyyAbuJarouretal.2010, author = {Alnemr, Rehab and Polyvyanyy, Artem and AbuJarour, Mohammed and Appeltauer, Malte and Hildebrandt, Dieter and Thomas, Ivonne and Overdick, Hagen and Sch{\"o}bel, Michael and Uflacker, Matthias and Kluth, Stephan and Menzel, Michael and Schmidt, Alexander and Hagedorn, Benjamin and Pascalau, Emilian and Perscheid, Michael and Vogel, Thomas and Hentschel, Uwe and Feinbube, Frank and Kowark, Thomas and Tr{\"u}mper, Jonas and Vogel, Tobias and Becker, Basil}, title = {Proceedings of the 4th Ph.D. Retreat of the HPI Research School on Service-oriented Systems Engineering}, editor = {Meinel, Christoph and Plattner, Hasso and D{\"o}llner, J{\"u}rgen Roland Friedrich and Weske, Mathias and Polze, Andreas and Hirschfeld, Robert and Naumann, Felix and Giese, Holger}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-036-6}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-40838}, publisher = {Universit{\"a}t Potsdam}, pages = {Getr. Z{\"a}hlung}, year = {2010}, language = {en} } @phdthesis{Krebs2009, author = {Krebs, Jonas}, title = {Molecular and physiological characterisation of selected DOF transcription factors in the model plant Arabidopsis thaliana}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41831}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {About 2,000 of the more than 27,000 genes of the genetic model plant Arabidopsis thaliana encode for transcription factors (TFs), proteins that bind DNA in the promoter region of their target genes and thus act as transcriptional activators and repressors. Since TFs play essential roles in nearly all biological processes, they are of great scientific and biotechnological interest. This thesis concentrated on the functional characterisation of four selected members of the Arabidopsis DOF-family, namely DOF1.2, DOF3.1, DOF3.5 and DOF5.2, which were selected because of their specific expression pattern in the root tip, a region that comprises the stem cell niche and cells for the perception of environmental stimuli. DOF1.2, DOF3.1 and DOF3.5 are previously uncharacterized members of the Arabidopsis DOF-family, while DOF5.2 has been shown to be involved in the phototrophic flowering response. However, its role in root development has not been described so far. To identify biological processes regulated by the four DOF proteins in detail, molecular and physiological characterization of transgenic plants with modified levels of DOF1.2, DOF3.1, DOF3.5 and DOF5.2 expression (constitutive and inducible over-expression, artificial microRNA) was performed. Additionally expression patterns of the TFs and their target genes were analyzed using promoter-GUS lines and publicly available microarray data. Finally putative protein-protein interaction partners and upstream regulating TFs were identified using the yeast two-hybrid and one-hybrid system. This combinatorial approach revealed distinct biological functions of DOF1.2, DOF3.1, DOF3.5 and DOF5.2 in the context of root development. DOF1.2 and DOF3.5 are specifically and exclusively expressed in the root cap, including the central root cap (columella) and the lateral root cap, organs which are essential to direct oriented root growth. It could be demonstrated that both genes work in the plant hormone auxin signaling pathway and have an impact on distal cell differentiation. Altered levels of gene expression lead to changes in auxin distribution, abnormal cell division patterns and altered root growth orientation. DOF3.1 and DOF5.2 share a specific expression pattern in the organizing centre of the root stem cell niche, called the quiescent centre. Both genes redundantly control cell differentiation in the root´s proximal meristem and unravel a novel transcriptional regulation pathway for genes enriched in the QC cells. Furthermore this work revealed a novel bipartite nuclear localisation signal being present in the protein sequence of the DOF TF family from all sequenced plant species. Summing up, this work provides an important input into our knowledge about the role of DOF TFs during root development. Future work will concentrate on revealing the exact regulatory networks of DOF1.2, DOF3.1, DOF3.5 and DOF5.2 and their possible biotechnological applications.}, language = {en} } @phdthesis{Werth2010, author = {Werth, Susanna}, title = {Calibration of the global hydrological model WGHM with water mass variations from GRACE gravity data}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41738}, school = {Universit{\"a}t Potsdam}, year = {2010}, abstract = {Since the start-up of the GRACE (Gravity Recovery And Climate Experiment) mission in 2002 time dependent global maps of the Earth's gravity field are available to study geophysical and climatologically-driven mass redistributions on the Earth's surface. In particular, GRACE observations of total water storage changes (TWSV) provide a comprehensive data set for analysing the water cycle on large scales. Therefore they are invaluable for validation and calibration of large-scale hydrological models as the WaterGAP Global Hydrology Model (WGHM) which simulates the continental water cycle including its most important components, such as soil, snow, canopy, surface- and groundwater. Hitherto, WGHM exhibits significant differences to GRACE, especially for the seasonal amplitude of TWSV. The need for a validation of hydrological models is further highlighted by large differences between several global models, e.g. WGHM, the Global Land Data Assimilation System (GLDAS) and the Land Dynamics model (LaD). For this purpose, GRACE links geodetic and hydrological research aspects. This link demands the development of adequate data integration methods on both sides, forming the main objectives of this work. They include the derivation of accurate GRACE-based water storage changes, the development of strategies to integrate GRACE data into a global hydrological model as well as a calibration method, followed by the re-calibration of WGHM in order to analyse process and model responses. To achieve these aims, GRACE filter tools for the derivation of regionally averaged TWSV were evaluated for specific river basins. Here, a decorrelation filter using GRACE orbits for its design is most efficient among the tested methods. Consistency in data and equal spatial resolution between observed and simulated TWSV were realised by the inclusion of all most important hydrological processes and an equal filtering of both data sets. Appropriate calibration parameters were derived by a WGHM sensitivity analysis against TWSV. Finally, a multi-objective calibration framework was developed to constrain model predictions by both river discharge and GRACE TWSV, realised with a respective evolutionary method, the ε-Non-dominated-Sorting-Genetic-Algorithm-II (ε-NSGAII). Model calibration was done for the 28 largest river basins worldwide and for most of them improved simulation results were achieved with regard to both objectives. From the multi-objective approach more reliable and consistent simulations of TWSV within the continental water cycle were gained and possible model structure errors or mis-modelled processes for specific river basins detected. For tropical regions as such, the seasonal amplitude of water mass variations has increased. The findings lead to an improved understanding of hydrological processes and their representation in the global model. Finally, the robustness of the results is analysed with respect to GRACE and runoff measurement errors. As a main conclusion obtained from the results, not only soil water and snow storage but also groundwater and surface water storage have to be included in the comparison of the modelled and GRACE-derived total water budged data. Regarding model calibration, the regional varying distribution of parameter sensitivity suggests to tune only parameter of important processes within each region. Furthermore, observations of single storage components beside runoff are necessary to improve signal amplitudes and timing of simulated TWSV as well as to evaluate them with higher accuracy. The results of this work highlight the valuable nature of GRACE data when merged into large-scale hydrological modelling and depict methods to improve large-scale hydrological models.}, language = {en} } @phdthesis{Ganesan2010, author = {Ganesan, Lakshmi Meena}, title = {Coupling of the electrical, mechanical and optical response in polymer/liquid-crystal composites}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41572}, school = {Universit{\"a}t Potsdam}, year = {2010}, abstract = {Micrometer-sized liquid-crystal (LC) droplets embedded in a polymer matrix may enable optical switching in the composite film through the alignment of the LC director along an external electric field. When a ferroelectric material is used as host polymer, the electric field generated by the piezoelectric effect can orient the director of the LC under an applied mechanical stress, making these materials interesting candidates for piezo-optical devices. In this work, polymer-dispersed liquid crystals (PDLCs) are prepared from poly(vinylidene fluoride-trifluoroethylene) (P(VDF-TrFE)) and a nematic liquid crystal (LC). The anchoring effect is studied by means of dielectric relaxation spectroscopy. Two dispersion regions are observed in the dielectric spectra of the pure P(VDF-TrFE) film. They are related to the glass transition and to a charge-carrier relaxation, respectively. In PDLC films containing 10 and 60 wt\% LC, an additional, bias-field-dependent relaxation peak is found that can be attributed to the motion of LC molecules. Due to the anchoring effect of the LC molecules, this relaxation process is slowed down considerably, when compared with the related process in the pure LC. The electro-optical and piezo-optical behavior of PDLC films containing 10 and 60 wt\% LCs is investigated. In addition to the refractive-index mismatch between the polymer matrix and the LC molecules, the interaction between the polymer dipoles and the LC molecules at the droplet interface influences the light-scattering behavior of the PDLC films. For the first time, it was shown that the electric field generated by the application of a mechanical stress may lead to changes in the transmittance of a PDLC film. Such a piezo-optical PDLC material may be useful e.g. in sensing and visualization applications. Compared to a non-polar matrix polymer, the polar matrix polymer exhibits a strong interaction with the LC molecules at the polymer/LC interface which affects the electro-optical effect of the PDLC films and prevents a larger increase in optical transmission.}, language = {en} } @phdthesis{Ishebabi2010, author = {Ishebabi, Harold}, title = {Architecture synthesis for adaptive multiprocessor systems on chip}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41316}, school = {Universit{\"a}t Potsdam}, year = {2010}, abstract = {This thesis presents methods for automated synthesis of flexible chip multiprocessor systems from parallel programs targeted at FPGAs to exploit both task-level parallelism and architecture customization. Automated synthesis is necessitated by the complexity of the design space. A detailed description of the design space is provided in order to determine which parameters should be modeled to facilitate automated synthesis by optimizing a cost function, the emphasis being placed on inclusive modeling of parameters from application, architectural and physical subspaces, as well as their joint coverage in order to avoid pre-constraining the design space. Given a parallel program and a set of an IP library, the automated synthesis problem is to simultaneously (i) select processors (ii) map and schedule tasks to them, and (iii) select one or several networks for inter-task communications such that design constraints and optimization objectives are met. The research objective in this thesis is to find a suitable model for automated synthesis, and to evaluate methods of using the model for architectural optimizations. Our contributions are a holistic approach for the design of such systems, corresponding models to facilitate automated synthesis, evaluation of optimization methods using state of the art integer linear and answer set programming, as well as the development of synthesis heuristics to solve runtime challenges.}, language = {en} } @phdthesis{Childs2010, author = {Childs, Liam H.}, title = {Bioinformatics approaches to analysing RNA mediated regulation of gene expression}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41284}, school = {Universit{\"a}t Potsdam}, year = {2010}, abstract = {The genome can be considered the blueprint for an organism. Composed of DNA, it harbours all organism-specific instructions for the synthesis of all structural components and their associated functions. The role of carriers of actual molecular structure and functions was believed to be exclusively assumed by proteins encoded in particular segments of the genome, the genes. In the process of converting the information stored genes into functional proteins, RNA - a third major molecule class - was discovered early on to act a messenger by copying the genomic information and relaying it to the protein-synthesizing machinery. Furthermore, RNA molecules were identified to assist in the assembly of amino acids into native proteins. For a long time, these - rather passive - roles were thought to be the sole purpose of RNA. However, in recent years, new discoveries have led to a radical revision of this view. First, RNA molecules with catalytic functions - thought to be the exclusive domain of proteins - were discovered. Then, scientists realized that much more of the genomic sequence is transcribed into RNA molecules than there are proteins in cells begging the question what the function of all these molecules are. Furthermore, very short and altogether new types of RNA molecules seemingly playing a critical role in orchestrating cellular processes were discovered. Thus, RNA has become a central research topic in molecular biology, even to the extent that some researcher dub cells as "RNA machines". This thesis aims to contribute towards our understanding of RNA-related phenomena by applying Bioinformatics means. First, we performed a genome-wide screen to identify sites at which the chemical composition of DNA (the genotype) critically influences phenotypic traits (the phenotype) of the model plant Arabidopsis thaliana. Whole genome hybridisation arrays were used and an informatics strategy developed, to identify polymorphic sites from hybridisation to genomic DNA. Following this approach, not only were genotype-phenotype associations discovered across the entire Arabidopsis genome, but also regions not currently known to encode proteins, thus representing candidate sites for novel RNA functional molecules. By statistically associating them with phenotypic traits, clues as to their particular functions were obtained. Furthermore, these candidate regions were subjected to a novel RNA-function classification prediction method developed as part of this thesis. While determining the chemical structure (the sequence) of candidate RNA molecules is relatively straightforward, the elucidation of its structure-function relationship is much more challenging. Towards this end, we devised and implemented a novel algorithmic approach to predict the structural and, thereby, functional class of RNA molecules. In this algorithm, the concept of treating RNA molecule structures as graphs was introduced. We demonstrate that this abstraction of the actual structure leads to meaningful results that may greatly assist in the characterization of novel RNA molecules. Furthermore, by using graph-theoretic properties as descriptors of structure, we indentified particular structural features of RNA molecules that may determine their function, thus providing new insights into the structure-function relationships of RNA. The method (termed Grapple) has been made available to the scientific community as a web-based service. RNA has taken centre stage in molecular biology research and novel discoveries can be expected to further solidify the central role of RNA in the origin and support of life on earth. As illustrated by this thesis, Bioinformatics methods will continue to play an essential role in these discoveries.}, language = {en} } @inproceedings{OPUS4-3955, title = {Proceedings of the 23rd Workshop on (Constraint) Logic Programming 2009}, editor = {Geske, Ulrich and Wolf, Armin}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-026-7}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-37977}, pages = {187}, year = {2010}, abstract = {The workshops on (constraint) logic programming (WLP) are the annual meeting of the Society of Logic Programming (GLP e.V.) and bring together researchers interested in logic programming, constraint programming, and related areas like databases, artificial intelligence and operations research. The 23rd WLP was held in Potsdam at September 15 - 16, 2009. The topics of the presentations of WLP2009 were grouped into the major areas: Databases, Answer Set Programming, Theory and Practice of Logic Programming as well as Constraints and Constraint Handling Rules.}, language = {en} } @book{OPUS4-3946, title = {Proceedings of the 9th Workshop on Aspects, Components, and Patterns for Infrastructure Software (ACP4IS '10)}, editor = {Adams, Bram and Haupt, Michael and Lohmann, Daniel}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-043-4}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41221}, publisher = {Universit{\"a}t Potsdam}, pages = {47}, year = {2010}, abstract = {Aspect-oriented programming, component models, and design patterns are modern and actively evolving techniques for improving the modularization of complex software. In particular, these techniques hold great promise for the development of "systems infrastructure" software, e.g., application servers, middleware, virtual machines, compilers, operating systems, and other software that provides general services for higher-level applications. The developers of infrastructure software are faced with increasing demands from application programmers needing higher-level support for application development. Meeting these demands requires careful use of software modularization techniques, since infrastructural concerns are notoriously hard to modularize. Aspects, components, and patterns provide very different means to deal with infrastructure software, but despite their differences, they have much in common. For instance, component models try to free the developer from the need to deal directly with services like security or transactions. These are primary examples of crosscutting concerns, and modularizing such concerns are the main target of aspect-oriented languages. Similarly, design patterns like Visitor and Interceptor facilitate the clean modularization of otherwise tangled concerns. Building on the ACP4IS meetings at AOSD 2002-2009, this workshop aims to provide a highly interactive forum for researchers and developers to discuss the application of and relationships between aspects, components, and patterns within modern infrastructure software. The goal is to put aspects, components, and patterns into a common reference frame and to build connections between the software engineering and systems communities.}, language = {en} } @phdthesis{Lkhagvadorj2009, author = {Lkhagvadorj, Ariunaa}, title = {Fiscal federalism and decentralization in Mongolia}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41196}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {Fiscal federalism has been an important topic among public finance theorists in the last four decades. There is a series of arguments that decentralization of governments enhances growth by improving allocation efficiency. However, the empirical studies have shown mixed results for industrialized and developing countries and some of them have demonstrated that there might be a threshold level of economic development below which decentralization is not effective. Developing and transition countries have developed a variety of forms of fiscal decentralization as a possible strategy to achieve effective and efficient governmental structures. A generalized principle of decentralization due to the country specific circumstances does not exist. Therefore, decentralization has taken place in different forms in various countries at different times, and even exactly the same extent of decentralization may have had different impacts under different conditions. The purpose of this study is to investigate the current state of the fiscal decentralization in Mongolia and to develop policy recommendations for the efficient and effective intergovernmental fiscal relations system for Mongolia. Within this perspective the analysis concentrates on the scope and structure of the public sector, the expenditure and revenue assignment as well as on the design of the intergovernmental transfer and sub-national borrowing. The study is based on data for twenty-one provinces and the capital city of Mongolia for the period from 2000 to 2009. As a former socialist country Mongolia has had a highly centralized governmental sector. The result of the analysis below revealed that the Mongolia has introduced a number of decentralization measures, which followed a top down approach and were slowly implemented without any integrated decentralization strategy in the last decade. As a result Mongolia became de-concentrated state with fiscal centralization. The revenue assignment is lacking a very important element, for instance significant revenue autonomy given to sub-national governments, which is vital for the efficient service delivery at the local level. According to the current assignments of the expenditure and revenue responsibilities most of the provinces are unable to provide a certain national standard of public goods supply. Hence, intergovernmental transfers from the central jurisdiction to the sub-national jurisdictions play an important role for the equalization of the vertical and horizontal imbalances in Mongolia. The critical problem associated with intergovernmental transfers is that there is not a stable, predictable and transparent system of transfer allocation. The amount of transfers to sub-national governments is determined largely by political decisions on ad hoc basis and disregards local differences in needs and fiscal capacity. Thus a fiscal equalization system based on the fiscal needs of the provinces should be implemented. The equalization transfers will at least partly offset the regional disparities in revenues and enable the sub-national governments to provide a national minimum standard of local public goods.}, language = {en} } @phdthesis{Bojdys2009, author = {Bojdys, Michael Janus}, title = {On new allotropes and nanostructures of carbon nitrides}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41236}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {In the first section of the thesis graphitic carbon nitride was for the first time synthesised using the high-temperature condensation of dicyandiamide (DCDA) - a simple molecular precursor - in a eutectic salt melt of lithium chloride and potassium chloride. The extent of condensation, namely next to complete conversion of all reactive end groups, was verified by elemental microanalysis and vibrational spectroscopy. TEM- and SEM-measurements gave detailed insight into the well-defined morphology of these organic crystals, which are not based on 0D or 1D constituents like known molecular or short-chain polymeric crystals but on the packing motif of extended 2D frameworks. The proposed crystal structure of this g-C3N4 species was derived in analogy to graphite by means of extensive powder XRD studies, indexing and refinement. It is based on sheets of hexagonally arranged s-heptazine (C6N7) units that are held together by covalent bonds between C and N atoms. These sheets stack in a graphitic, staggered fashion adopting an AB-motif, as corroborated by powder X-ray diffractometry and high-resolution transmission electron microscopy. This study was contrasted with one of many popular - yet unsuccessful - approaches in the last 30 years of scientific literature to perform the condensation of an extended carbon nitride species through synthesis in the bulk. The second section expands the repertoire of available salt melts introducing the lithium bromide and potassium bromide eutectic as an excellent medium to obtain a new phase of graphitic carbon nitride. The combination of SEM, TEM, PXRD and electron diffraction reveals that the new graphitic carbon nitride phase stacks in an ABA' motif forming unprecedentedly large crystals. This section seizes the notion of the preceding chapter, that condensation in a eutectic salt melt is the key to obtain a high degree of conversion mainly through a solvatory effect. At the close of this chapter ionothermal synthesis is seen established as a powerful tool to overcome the inherent kinetic problems of solid state reactions such as incomplete polymerisation and condensation in the bulk especially when the temperature requirement of the reaction in question falls into the proverbial "no man's land" of classical solvents, i.e. above 250 to 300 °C. The following section puts the claim to the test, that the crystalline carbon nitrides obtained from a salt melt are indeed graphitic. A typical property of graphite - namely the accessibility of its interplanar space for guest molecules - is transferred to the graphitic carbon nitride system. Metallic potassium and graphitic carbon nitride are converted to give the potassium intercalation compound, K(C6N8)3 designated according to its stoichiometry and proposed crystal structure. Reaction of the intercalate with aqueous solvents triggers the exfoliation of the graphitic carbon nitride material and - for the first time - enables the access of singular (or multiple) carbon nitride sheets analogous to graphene as seen in the formation of sheets, bundles and scrolls of carbon nitride in TEM imaging. The thus exfoliated sheets form a stable, strongly fluorescent solution in aqueous media, which shows no sign in UV/Vis spectroscopy that the aromaticity of individual sheets was subject to degradation. The final section expands on the mechanism underlying the formation of graphitic carbon nitride by literally expanding the distance between the covalently linked heptazine units which constitute these materials. A close examination of all proposed reaction mechanisms to-date in the light of exhaustive DSC/MS experiments highlights the possibility that the heptazine unit can be formed from smaller molecules, even if some of the designated leaving groups (such as ammonia) are substituted by an element, R, which later on remains linked to the nascent heptazine. Furthermore, it is suggested that the key functional groups in the process are the triazine- (Tz) and the carbonitrile- (CN) group. On the basis of these assumptions, molecular precursors are tailored which encompass all necessary functional groups to form a central heptazine unit of threefold, planar symmetry and then still retain outward functionalities for self-propagated condensation in all three directions. Two model systems based on a para-aryl (ArCNTz) and para-biphenyl (BiPhCNTz) precursors are devised via a facile synthetic procedure and then condensed in an ionothermal process to yield the heptazine based frameworks, HBF-1 and HBF-2. Due to the structural motifs of their molecular precursors, individual sheets of HBF-1 and HBF-2 span cavities of 14.2 {\AA} and 23.0 {\AA} respectively which makes both materials attractive as potential organic zeolites. Crystallographic analysis confirms the formation of ABA' layered, graphitic systems, and the extent of condensation is confirmed as next-to-perfect by elemental analysis and vibrational spectroscopy.}, language = {en} } @phdthesis{Lampert2009, author = {Lampert, Astrid}, title = {Airborne lidar observations of tropospheric arctic clouds}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41211}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {Due to the unique environmental conditions and different feedback mechanisms, the Arctic region is especially sensitive to climate changes. The influence of clouds on the radiation budget is substantial, but difficult to quantify and parameterize in models. In the framework of the PhD, elastic backscatter and depolarization lidar observations of Arctic clouds were performed during the international Arctic Study of Tropospheric Aerosol, Clouds and Radiation (ASTAR) from Svalbard in March and April 2007. Clouds were probed above the inaccessible Arctic Ocean with a combination of airborne instruments: The Airborne Mobile Aerosol Lidar (AMALi) of the Alfred Wegener Institute for Polar and Marine Research provided information on the vertical and horizontal extent of clouds along the flight track, optical properties (backscatter coefficient), and cloud thermodynamic phase. From the data obtained by the spectral albedometer (University of Mainz), the cloud phase and cloud optical thickness was deduced. Furthermore, in situ observations with the Polar Nephelometer, Cloud Particle Imager and Forward Scattering Spectrometer Probe (Laboratoire de M{\´e}t{\´e}orologie Physique, France) provided information on the microphysical properties, cloud particle size and shape, concentration, extinction, liquid and ice water content. In the thesis, a data set of four flights is analyzed and interpreted. The lidar observations served to detect atmospheric structures of interest, which were then probed by in situ technique. With this method, an optically subvisible ice cloud was characterized by the ensemble of instruments (10 April 2007). Radiative transfer simulations based on the lidar, radiation and in situ measurements allowed the calculation of the cloud forcing, amounting to -0.4 W m-2. This slight surface cooling is negligible on a local scale. However, thin Arctic clouds have been reported more frequently in winter time, when the clouds' effect on longwave radiation (a surface warming of 2.8 W m-2) is not balanced by the reduced shortwave radiation (surface cooling). Boundary layer mixed-phase clouds were analyzed for two days (8 and 9 April 2007). The typical structure consisting of a predominantly liquid water layer on cloud top and ice crystals below were confirmed by all instruments. The lidar observations were compared to European Centre for Medium-Range Weather Forecasts (ECMWF) meteorological analyses. A change of air masses along the flight track was evidenced in the airborne data by a small completely glaciated cloud part within the mixed-phase cloud system. This indicates that the updraft necessary for the formation of new cloud droplets at cloud top is disturbed by the mixing processes. The measurements served to quantify the shortcomings of the ECMWF model to describe mixed-phase clouds. As the partitioning of cloud condensate into liquid and ice water is done by a diagnostic equation based on temperature, the cloud structures consisting of a liquid cloud top layer and ice below could not be reproduced correctly. A small amount of liquid water was calculated for the lowest (and warmest) part of the cloud only. Further, the liquid water content was underestimated by an order of magnitude compared to in situ observations. The airborne lidar observations of 9 April 2007 were compared to space borne lidar data on board of the satellite Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO). The systems agreed about the increase of cloud top height along the same flight track. However, during the time delay of 1 h between the lidar measurements, advection and cloud processing took place, and a detailed comparison of small-scale cloud structures was not possible. A double layer cloud at an altitude of 4 km was observed with lidar at the West coast in the direct vicinity of Svalbard (14 April 2007). The cloud system consisted of two geometrically thin liquid cloud layers (each 150 m thick) with ice below each layer. While the upper one was possibly formed by orographic lifting under the influence of westerly winds, or by the vertical wind shear shown by ECMWF analyses, the lower one might be the result of evaporating precipitation out of the upper layer. The existence of ice precipitation between the two layers supports the hypothesis that humidity released from evaporating precipitation was cooled and consequently condensed as it experienced the radiative cooling from the upper layer. In summary, a unique data set characterizing tropospheric Arctic clouds was collected with lidar, in situ and radiation instruments. The joint evaluation with meteorological analyses allowed a detailed insight in cloud properties, cloud evolution processes and radiative effects.}, language = {en} } @phdthesis{Yin2010, author = {Yin, Fan}, title = {Mathematic approaches for the calibration of the CHAMP satellite magnetic field measurements}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41201}, school = {Universit{\"a}t Potsdam}, year = {2010}, abstract = {CHAMP (CHAllenging Minisatellite Payload) is a German small satellite mission to study the earth's gravity field, magnetic field and upper atmosphere. Thanks to the good condition of the satellite so far, the planned 5 years mission is extended to year 2009. The satellite provides continuously a large quantity of measurement data for the purpose of Earth study. The measurements of the magnetic field are undertaken by two Fluxgate Magnetometers (vector magnetometer) and one Overhauser Magnetometer (scalar magnetometer) flown on CHAMP. In order to ensure the quality of the data during the whole mission, the calibration of the magnetometers has to be performed routinely in orbit. The scalar magnetometer serves as the magnetic reference and its readings are compared with the readings of the vector magnetometer. The readings of the vector magnetometer are corrected by the parameters that are derived from this comparison, which is called the scalar calibration. In the routine processing, these calibration parameters are updated every 15 days by means of scalar calibration. There are also magnetic effects coming from the satellite which disturb the measurements. Most of them have been characterized during tests before launch. Among them are the remanent magnetization of the spacecraft and fields generated by currents. They are all considered to be constant over the mission life. The 8 years of operation experience allow us to investigate the long-term behaviors of the magnetometers and the satellite systems. According to the investigation, it was found that for example the scale factors of the FGM show obvious long-term changes which can be described by logarithmic functions. The other parameters (offsets and angles between the three components) can be considered constant. If these continuous parameters are applied for the FGM data processing, the disagreement between the OVM and the FGM readings is limited to \pm1nT over the whole mission. This demonstrates, the magnetometers on CHAMP exhibit a very good stability. However, the daily correction of the parameter Z component offset of the FGM improves the agreement between the magnetometers markedly. The Z component offset plays a very important role for the data quality. It exhibits a linear relationship with the standard deviation of the disagreement between the OVM and the FGM readings. After Z offset correction, the errors are limited to \pm0.5nT (equivalent to a standard deviation of 0.2nT). We improved the corrections of the spacecraft field which are not taken into account in the routine processing. Such disturbance field, e.g. from the power supply system of the satellite, show some systematic errors in the FGM data and are misinterpreted in 9-parameter calibration, which brings false local time related variation of the calibration parameters. These corrections are made by applying a mathematical model to the measured currents. This non-linear model is derived from an inversion technique. If the disturbance field of the satellite body are fully corrected, the standard deviation of scalar error \triangle B remains about 0.1nT. Additionally, in order to keep the OVM readings a reliable standard, the imperfect coefficients of the torquer current correction for the OVM are redetermined by solving a minimization problem. The temporal variation of the spacecraft remanent field is investigated. It was found that the average magnetic moment of the magneto-torquers reflects well the moment of the satellite. This allows for a continuous correction of the spacecraft field. The reasons for the possible unknown systemic error are discussed in this thesis. Particularly, both temperature uncertainties and time errors have influence on the FGM data. Based on the results of this thesis the data processing of future magnetic missions can be designed in an improved way. In particular, the upcoming ESA mission Swarm can take advantage of our findings and provide all the auxiliary measurements needed for a proper recovery of the ambient magnetic field.}, language = {en} } @phdthesis{Cabral2009, author = {Cabral, Juliano Sarmento}, title = {Demographic processes determining the range dynamics of plant species, and their consequences for biodiversity maintenance in the face of environmental change}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41188}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {The present thesis aims to introduce process-based model for species range dynamics that can be fitted to abundance data. For this purpose, the well-studied Proteaceae species of the South African Cape Floristic Region (CFR) offer a great data set to fit process-based models. These species are subject to wildflower harvesting and environmental threats like habitat loss and climate change. The general introduction of this thesis presents shortly the available models for species distribution modelling. Subsequently, it presents the feasibility of process-based modelling. Finally, it introduces the study system as well as the objectives and layout. In Chapter 1, I present the process-based model for range dynamics and a statistical framework to fit it to abundance distribution data. The model has a spatially-explicit demographic submodel (describing dispersal, reproduction, mortality and local extinction) and an observation submodel (describing imperfect detection of individuals). The demographic submodel links species-specific habitat models describing the suitable habitat and process-based demographic models that consider local dynamics and anemochoric seed dispersal between populations. After testing the fitting framework with simulated data, I applied it to eight Proteaceae species with different demographic properties. Moreover, I assess the role of two other demographic mechanisms: positive (Allee effects) and negative density-dependence. Results indicate that Allee effects and overcompensatory local dynamics (including chaotic behaviour) seem to be important for several species. Most parameter estimates quantitatively agreed with independent data. Hence, the presented approach seemed to suit the demand of investigating non-equilibrium scenarios involving wildflower harvesting (Chapter 2) and environmental change (Chapter 3). The Chapter 2 addresses the impacts of wildflower harvesting. The chapter includes a sensitivity analysis over multiple spatial scales and demographic properties (dispersal ability, strength of Allee effects, maximum reproductive rate, adult mortality, local extinction probability and carrying capacity). Subsequently, harvesting effects are investigated on real case study species. Plant response to harvesting showed abrupt threshold behavior. Species with short-distance seed dispersal, strong Allee effects, low maximum reproductive rate, high mortality and high local extinction are most affected by harvesting. Larger spatial scales benefit species response, but the thresholds become sharper. The three case study species supported very low to moderate harvesting rates. Summarizing, demographic knowledge about the study system and careful identification of the spatial scale of interest should guide harvesting assessments and conservation of exploited species. The sensitivity analysis' results can be used to qualitatively assess harvesting impacts for poorly studied species. I investigated in Chapter 3 the consequences of past habitat loss, future climate change and their interaction on plant response. I use the species-specific estimates of the best model describing local dynamics obtained in Chapter 1. Both habitat loss and climate change had strong negative impacts on species dynamics. Climate change affected mainly range size and range filling due to habitat reductions and shifts combined with low colonization. Habitat loss affected mostly local abundances. The scenario with both habitat loss and climate change was the worst for most species. However, this impact was better than expected by simple summing of separate effects of habitat loss and climate change. This is explained by shifting ranges to areas less affected by humans. Range size response was well predicted by the strength of environmental change, whereas range filling and local abundance responses were better explained by demographic properties. Hence, risk assessments under global change should consider demographic properties. Most surviving populations were restricted to refugia, serving as key conservation focus.The findings obtained for the study system as well as the advantages, limitations and potentials of the model presented here are further discussed in the General Discussion. In summary, the results indicate that 1) process-based demographic models for range dynamics can be fitted to data; 2) demographic processes improve species distribution models; 3) different species are subject to different processes and respond differently to environmental change and exploitation; 4) density regulation type and Allee effects should be considered when investigating range dynamics of species; 5) the consequences of wildflower harvesting, habitat loss and climate change could be disastrous for some species, but impacts vary depending on demographic properties; 6) wildflower harvesting impacts varies over spatial scale; 7) The effects of habitat loss and climate change are not always additive.}, language = {en} } @phdthesis{Todt2009, author = {Todt, Helge Tobias}, title = {Hydrogen-deficient central stars of planetary nebulae}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41047}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {Central stars of planetary nebulae are low-mass stars on the brink of their final evolution towards white dwarfs. Because of their surface temperature of above 25,000 K their UV radiation ionizes the surrounding material, which was ejected in an earlier phase of their evolution. Such fluorescent circumstellar gas is called a "Planetary Nebula". About one-tenth of the Galactic central stars are hydrogen-deficient. Generally, the surface of these central stars is a mixture of helium, carbon, and oxygen resulting from partial helium burning. Moreover, most of them have a strong stellar wind, similar to massive Pop-I Wolf-Rayet stars, and are in analogy classified as [WC]. The brackets distinguish the special type from the massive WC stars. Qualitative spectral analyses of [WC] stars lead to the assumption of an evolutionary sequence from the cooler, so-called late-type [WCL] stars to the very hot, early-type [WCE] stars. Quantitative analyses of the winds of [WC] stars became possible by means of computer programs that solve the radiative transfer in the co-moving frame, together with the statistical equilibrium equations for the population numbers. First analyses employing models without iron-line blanketing resulted in systematically different abundances for [WCL] and [WCE] stars. While the mass ratio of He:C is roughly 40:50 for [WCL] stars, it is 60:30 in average for [WCE] stars. The postulated evolution from [WCL] to [WCE] however could only lead to an increase of carbon, since heavier elements are built up by nuclear fusion. In the present work, improved models are used to re-analyze the [WCE] stars and to confirm their He:C abundance ratio. Refined models, calculated with the Potsdam WR model atmosphere code (PoWR), account now for line-blanketing due to iron group elements, small scale wind inhomogeneities, and complex model atoms for He, C, O, H, P, N, and Ne. Referring to stellar evolutionary models for the hydrogen-deficient [WC] stars, Ne and N abundances are of particular interest. Only one out of three different evolutionary channels, the VLTP scenario, leads to a Ne and N overabundance of a few percent by mass. A VLTP, a very late thermal pulse, is a rapid increase of the energy production of the helium-burning shell, while hydrogen burning has already ceased. Subsequently, the hydrogen envelope is mixed with deeper layers and completely burnt in the presence of C, He, and O. This results in the formation of N and Ne. A sample of eleven [WCE] stars has been analyzed. For three of them, PB 6, NGC 5189, and [S71d]3, a N overabundance of 1.5\% has been found, while for three other [WCE] stars such high abundances of N can be excluded. In the case of NGC 5189, strong spectral lines of Ne can be reproduced qualitatively by our models. At present, the Ne mass fraction can only be roughly estimated from the Ne emission lines and seems to be in the order of a few percent by mass. Furthermore, using a diagnostic He-C line pair, the He:C abundance ratio of 60:30 for [WCE] stars is confirmed. Within the framework of the analysis, a new class of hydrogen-deficient central stars has been discovered, with PB 8 as its first member. Its atmospheric mixture resembles rather that of the massive WNL stars than of the [WC] stars. The determined mass fractions H:He:C:N:O are 40:55:1.3:2:1.3. As the wind of PB 8 contains significant amounts of O and C, in contrast to WN stars, a classification as [WN/WC] is suggested.}, language = {en} } @book{WistSchaeferVogleretal.2010, author = {Wist, Dominic and Schaefer, Mark and Vogler, Walter and Wollowski, Ralf}, title = {STG decomposition : internal communication for SI implementability}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-037-3}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-40786}, publisher = {Universit{\"a}t Potsdam}, pages = {36}, year = {2010}, abstract = {STG decomposition is a promising approach to tackle the complexity problems arising in logic synthesis of speed independent circuits, a robust asynchronous (i.e. clockless) circuit type. Unfortunately, STG decomposition can result in components that in isolation have irreducible CSC conflicts. Generalising earlier work, it is shown how to resolve such conflicts by introducing internal communication between the components via structural techniques only.}, language = {en} } @phdthesis{Ballato2009, author = {Ballato, Paolo}, title = {Tectonic and climatic forcing in orogenic processes : the foreland basin point of view, Alborz mountains, N Iran}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41068}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {Systeme von Vorlandbecken repr{\"a}sentieren bedeutende geologische Archive und dienen dem Verst{\"a}ndnis von R{\"u}ckkopplungen zwischen oberfl{\"a}chennahen und tektonischen Prozessen. Außerdem dokumentieren sie die Entwicklung unmittelbar angrenzender Bergketten. Die sediment{\"a}ren Abfolgen in Vorlandbecken reflektieren das Gleichgewicht zwischen tektonischer Subsidenz, der Bildung langzeitlichen Akkommodationsraumes und des Sedimenteintrages, welcher wiederum die Wirksamkeit von Erosions- und Massenneuverteilungsprozessen wiederspiegelt. Um die Effekte von Klima und Tektonik in einem solchen System zu erforschen, untersuchte ich die Oligo-Mioz{\"a}nen Sedimente in den Vorlandbecken der s{\"u}dlichen Elburs Bergkette, einem intrakontinentalen Gebirge in Nord-Iran, das im Zuge der Arabisch-Eurasischen Kontinent-Kollision herausgehoben wurde. In dieser Studie der Vorlandbeckensedimente wurden Datierungstechniken angewandt (40Ar/39Ar, (U-Th)/He Thermochronologie und Magnetostratigraphie), die Sedimente und deren Herkunft analysiert und die Tonmineralogie, sowie Sauerstoff- und Kohlenstoffisotope untersucht. Die Ergebnisse zeigen, dass auf einer Zeitskala von 105 bis 106 Jahren eine systematische Korrelation zwischen „coarsening upward" Zyklen und den sediment{\"a}ren Akkumulationsraten besteht. W{\"a}hrend sukzessiver {\"U}berschiebungsphasen werden die durch Hebung der Bergkette bereitgestellten groben Kornfraktionen in proximale Bereiche des Beckens geliefert und feink{\"o}rnige Fazies in distalen Beckenregionen abgelagert. Variationen in der Sedimentherkunft in Phasen gr{\"o}ßerer tektonischer Aktivit{\"a}t zeugen von erosionaler Abdeckung und/oder der Umorganisation nat{\"u}rlicher Entw{\"a}sserungsstrukturen. Außerdem zeigen die Untersuchungen an stabilen Isotopen, dass die verst{\"a}rkte tektonische Aktivit{\"a}t das Anwachsen der Topographie f{\"o}rderte und damit die Wirksamkeit einer topographischen Barriere erh{\"o}hte. Wenn aufgrund nachlassender Beckenabsenkung die grobe Kornfraktion nicht vollst{\"a}ndig im Nahbereich des Beckens aufgenommen werden kann breitet sie sich in ferne Beckenregionen aus. Im Elburs wird die verringerte Subsidenz durch eine interne Hebung des Vorlandes hervorgerufen und ist mit einer lateralen Stapelung von Flussbetten assoziiert. Dokumentiert wird dies anhand konsequenten Schichtwachstums, tektonischer Schr{\"a}gstellung und sediment{\"a}rer Umlagerung. Gleichzeitig nehmen die Sedimentationsraten zu. Die Sauerstoff-Isotope der Pal{\"a}ob{\"o}den zeigen, dass dieser Anstieg mit einer Phase feuchteren Klimas einhergeht, wodurch Oberfl{\"a}chenprozesse effizienter werden und Heraushebungssraten steigen, was eine positive R{\"u}ckkopplung erzeugt. Des Weiteren zeigen die isotopischen und sediment{\"a}ren Daten, dass seit 10-9 Millionen Jahren (Ma) das Klima durch saisonalen Anstieg der Niederschl{\"a}ge zunehmend feuchter wurde. Da bedeutende klimatische Ver{\"a}nderungen zu dieser Zeit auch im Mittelmeerraum und Asien beobachtet wurden, ist anzunehmen, dass die klimatische Ver{\"a}nderung, die im Elburs Gebirge beobachtet wird, h{\"o}chstwahrscheinlich {\"A}nderungen der atmosph{\"a}rischen Zirkulationen der n{\"o}rdlichen Hemisph{\"a}re reflektiert. Aus den Ergebnissen dieser Studie lassen sich zus{\"a}tzliche Implikationen f{\"u}r die Entwicklung des Elburs Gebirges und die Arabisch-Eurasische kontinentale Kollisionszone ableiten. Die orogen-weite Hauptdeformation propagierte nicht gleichm{\"a}ßig nach S{\"u}den, sondern seit dem Oligoz{\"a}n schrittweise vorw{\"a}rts und r{\"u}ckw{\"a}rts. Insbesondere von ~17,5 bis 6,2 Ma wurde das Gebirge durch eine Kombination aus frontaler Akkretion und interner Keildeformation in Schritten von 0,7 bis 2 Millionen Jahren herausgehoben. Dar{\"u}ber hinaus deuten die Sedimentherkunftsdaten darauf hin, dass sich noch vor 10-9 Ma die Haupteinengungsrichtung von NW-SE nach NNE-SSW ver{\"a}nderte. Regional erlaubt die Geschichte der untersuchten Becken und angrenzenden Gebirgsz{\"u}ge R{\"u}ckschl{\"u}sse auf ein neues geodynamisches Model zur Entwicklung der Arabisch-Eurasischen kontinentalen Kollisionszone. Zahlreiche Sedimentbecken des Elburs Gebirges und anderer Lokalit{\"a}ten der Arabisch-Eurasischen Deformationszone belegen einen Wechsel von einem tensionalen zu einem kompressionalen tektonischen Regime vor ~36 Ma . Dieser Wechsel k{\"o}nnte den Beginn der Subduktion von gedehnter arabischer kontinentaler Lithosph{\"a}re unter Zentral-Iran bedeuten, was zu einer moderaten Plattenkopplung und Deformation von Unter- sowie Oberplatte gef{\"u}hrt hat. Der Anstieg der Deformationsraten im s{\"u}dlichen Elburs Gebirge seit ~17,5 Ma l{\"a}sst vermuten, dass die Oberplatte, wahrscheinlich aufgrund steigender Plattenkopplung, seit dem fr{\"u}hen Mioz{\"a}n signifikant deformiert wurde. Diese Ver{\"a}nderung k{\"o}nnte der Subduktion m{\"a}chtigerer arabischer kontinentaler Lithosph{\"a}re zugeschrieben werden und den Anfang echter kontinentaler Kollision bedeuten. Dieses Model erkl{\"a}rt daher die Zeitverz{\"o}gerung zwischen der Initiation der Arabisch-Eurasischen kontinentalen Kollision (Eoz{\"a}n-Oligoz{\"a}n) and dem Beginn ausgedehnter Deformation in der Kollisionszone (Mioz{\"a}n).}, language = {en} } @phdthesis{Knebe2008, author = {Knebe, Alexander}, title = {Computational cosmology}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41147}, school = {Universit{\"a}t Potsdam}, year = {2008}, abstract = {"Computational Cosmology" is the modeling of structure formation in the Universe by means of numerical simulations. These simulations can be considered as the only "experiment" to verify theories of the origin and evolution of the Universe. Over the last 30 years great progress has been made in the development of computer codes that model the evolution of dark matter (as well as gas physics) on cosmic scales and new research discipline has established itself. After a brief summary of cosmology we will introduce the concepts behind such simulations. We further present a novel computer code for numerical simulations of cosmic structure formation that utilizes adaptive grids to efficiently distribute the work and focus the computing power to regions of interests, respectively. In that regards we also investigate various (numerical) effects that influence the credibility of these simulations and elaborate on the procedure of how to setup their initial conditions. And as running a simulation is only the first step to modelling cosmological structure formation we additionally developed an object finder that maps the density field onto galaxies and galaxy clusters and hence provides the link to observations. Despite the generally accepted success of the cold dark matter cosmology the model still inhibits a number of deviations from observations. Moreover, none of the putative dark matter particle candidates have yet been detected. Utilizing both the novel simulation code and the halo finder we perform and analyse various simulations of cosmic structure formation investigating alternative cosmologies. These include warm (rather than cold) dark matter, features in the power spectrum of the primordial density perturbations caused by non-standard inflation theories, and even modified Newtonian dynamics. We compare these alternatives to the currently accepted standard model and highlight the limitations on both sides; while those alternatives may cure some of the woes of the standard model they also inhibit difficulties on their own. During the past decade simulation codes and computer hardware have advanced to such a stage where it became possible to resolve in detail the sub-halo populations of dark matter halos in a cosmological context. These results, coupled with the simultaneous increase in observational data have opened up a whole new window on the concordance cosmogony in the field that is now known as "Near-Field Cosmology". We will present an in-depth study of the dynamics of subhaloes and the development of debris of tidally disrupted satellite galaxies.1 Here we postulate a new population of subhaloes that once passed close to the centre of their host and now reside in the outer regions of it. We further show that interactions between satellites inside the radius of their hosts may not be negliable. And the recovery of host properties from the distribution and properties of tidally induced debris material is not as straightforward as expected from simulations of individual satellites in (semi-)analytical host potentials.}, language = {en} } @phdthesis{Kopka2008, author = {Kopka, Joachim}, title = {Applied metabolome analysis : exploration, development and application of gas chromatography-mass spectrometry based metabolite profiling technologies}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-40597}, school = {Universit{\"a}t Potsdam}, year = {2008}, abstract = {The uptake of nutrients and their subsequent chemical conversion by reactions which provide energy and building blocks for growth and propagation is a fundamental property of life. This property is termed metabolism. In the course of evolution life has been dependent on chemical reactions which generate molecules that are common and indispensable to all life forms. These molecules are the so-called primary metabolites. In addition, life has evolved highly diverse biochemical reactions. These reactions allow organisms to produce unique molecules, the so-called secondary metabolites, which provide a competitive advantage for survival. The sum of all metabolites produced by the complex network of reactions within an organism has since 1998 been called the metabolome. The size of the metabolome can only be estimated and may range from less than 1,000 metabolites in unicellular organisms to approximately 200,000 in the whole plant kingdom. In current biology, three additional types of molecules are thought to be important to the understanding of the phenomena of life: (1) the proteins, in other words the proteome, including enzymes which perform the metabolic reactions, (2) the ribonucleic acids (RNAs) which constitute the so-called transcriptome, and (3) all genes of the genome which are encoded within the double strands of desoxyribonucleic acid (DNA). Investigations of each of these molecular levels of life require analytical technologies which should best enable the comprehensive analysis of all proteins, RNAs, et cetera. At the beginning of this thesis such analytical technologies were available for DNA, RNA and proteins, but not for metabolites. Therefore, this thesis was dedicated to the implementation of the gas chromatography - mass spectrometry technology, in short GC-MS, for the in-parallel analysis of as many metabolites as possible. Today GC-MS is one of the most widely applied technologies and indispensable for the efficient profiling of primary metabolites. The main achievements and research topics of this work can be divided into technological advances and novel insights into the metabolic mechanisms which allow plants to cope with environmental stresses. Firstly, the GC-MS profiling technology has been highly automated and standardized. The major technological achievements were (1) substantial contributions to the development of automated and, within the limits of GC-MS, comprehensive chemical analysis, (2) contributions to the implementation of time of flight mass spectrometry for GC-MS based metabolite profiling, (3) the creation of a software platform for reproducible GC-MS data processing, named TagFinder, and (4) the establishment of an internationally coordinated library of mass spectra which allows the identification of metabolites in diverse and complex biological samples. In addition, the Golm Metabolome Database (GMD) has been initiated to harbor this library and to cope with the increasing amount of generated profiling data. This database makes publicly available all chemical information essential for GC-MS profiling and has been extended to a global resource of GC-MS based metabolite profiles. Querying the concentration changes of hundreds of known and yet non-identified metabolites has recently been enabled by uploading standardized, TagFinder-processed data. Long-term technological aims have been pursued with the central aims (1) to enhance the precision of absolute and relative quantification and (2) to enable the combined analysis of metabolite concentrations and metabolic flux. In contrast to concentrations which provide information on metabolite amounts, flux analysis provides information on the speed of biochemical reactions or reaction sequences, for example on the rate of CO2 conversion into metabolites. This conversion is an essential function of plants which is the basis of life on earth. Secondly, GC-MS based metabolite profiling technology has been continuously applied to advance plant stress physiology. These efforts have yielded a detailed description of and new functional insights into metabolic changes in response to high and low temperatures as well as common and divergent responses to salt stress among higher plants, such as Arabidopsis thaliana, Lotus japonicus and rice (Oryza sativa). Time course analysis after temperature stress and investigations into salt dosage responses indicated that metabolism changed in a gradual manner rather than by stepwise transitions between fixed states. In agreement with these observations, metabolite profiles of the model plant Lotus japonicus, when exposed to increased soil salinity, were demonstrated to have a highly predictive power for both NaCl accumulation and plant biomass. Thus, it may be possible to use GC-MS based metabolite profiling as a breeding tool to support the selection of individual plants that cope best with salt stress or other environmental challenges.}, language = {en} } @phdthesis{Decker2009, author = {Decker, Gero}, title = {Design and analysis of process choreographies}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-40761}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {With the rise of electronic integration between organizations, the need for a precise specification of interaction behavior increases. Information systems, replacing interaction previously carried out by humans via phone, faxes and emails, require a precise specification for handling all possible situations. Such interaction behavior is described in process choreographies. Choreographies enumerate the roles involved, the allowed interactions, the message contents and the behavioral dependencies between interactions. Choreographies serve as interaction contract and are the starting point for adapting existing business processes and systems or for implementing new software components. As a thorough analysis and comparison of choreography modeling languages is missing in the literature, this thesis introduces a requirements framework for choreography languages and uses it for comparing current choreography languages. Language proposals for overcoming the limitations are given for choreography modeling on the conceptual and on the technical level. Using an interconnection modeling style, behavioral dependencies are defined on a per-role basis and different roles are interconnected using message flow. This thesis reveals a number of modeling "anti-patterns" for interconnection modeling, motivating further investigations on choreography languages following the interaction modeling style. Here, interactions are seen as atomic building blocks and the behavioral dependencies between them are defined globally. Two novel language proposals are put forward for this modeling style which have already influenced industrial standardization initiatives. While avoiding many of the pitfalls of interconnection modeling, new anomalies can arise in interaction models. A choreography might not be realizable, i.e. there does not exist a set of interacting roles that collectively realize the specified behavior. This thesis investigates different dimensions of realizability.}, language = {en} } @phdthesis{Jechow2009, author = {Jechow, Andreas}, title = {Tailoring the emission of stripe-array diode lasers with external cavities to enable nonlinear frequency conversion}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-031-1}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-39653}, school = {Universit{\"a}t Potsdam}, pages = {ii, 139}, year = {2009}, abstract = {A huge number of applications require coherent radiation in the visible spectral range. Since diode lasers are very compact and efficient light sources, there exists a great interest to cover these applications with diode laser emission. Despite modern band gap engineering not all wavelengths can be accessed with diode laser radiation. Especially in the visible spectral range between 480 nm and 630 nm no emission from diode lasers is available, yet. Nonlinear frequency conversion of near-infrared radiation is a common way to generate coherent emission in the visible spectral range. However, radiation with extraordinary spatial temporal and spectral quality is required to pump frequency conversion. Broad area (BA) diode lasers are reliable high power light sources in the near-infrared spectral range. They belong to the most efficient coherent light sources with electro-optical efficiencies of more than 70\%. Standard BA lasers are not suitable as pump lasers for frequency conversion because of their poor beam quality and spectral properties. For this purpose, tapered lasers and diode lasers with Bragg gratings are utilized. However, these new diode laser structures demand for additional manufacturing and assembling steps that makes their processing challenging and expensive. An alternative to BA diode lasers is the stripe-array architecture. The emitting area of a stripe-array diode laser is comparable to a BA device and the manufacturing of these arrays requires only one additional process step. Such a stripe-array consists of several narrow striped emitters realized with close proximity. Due to the overlap of the fields of neighboring emitters or the presence of leaky waves, a strong coupling between the emitters exists. As a consequence, the emission of such an array is characterized by a so called supermode. However, for the free running stripe-array mode competition between several supermodes occurs because of the lack of wavelength stabilization. This leads to power fluctuations, spectral instabilities and poor beam quality. Thus, it was necessary to study the emission properties of those stripe-arrays to find new concepts to realize an external synchronization of the emitters. The aim was to achieve stable longitudinal and transversal single mode operation with high output powers giving a brightness sufficient for efficient nonlinear frequency conversion. For this purpose a comprehensive analysis of the stripe-array devices was done here. The physical effects that are the origin of the emission characteristics were investigated theoretically and experimentally. In this context numerical models could be verified and extended. A good agreement between simulation and experiment was observed. One way to stabilize a specific supermode of an array is to operate it in an external cavity. Based on mathematical simulations and experimental work, it was possible to design novel external cavities to select a specific supermode and stabilize all emitters of the array at the same wavelength. This resulted in stable emission with 1 W output power, a narrow bandwidth in the range of 2 MHz and a very good beam quality with M²<1.5. This is a new level of brightness and brilliance compared to other BA and stripe-array diode laser systems. The emission from this external cavity diode laser (ECDL) satisfied the requirements for nonlinear frequency conversion. Furthermore, a huge improvement to existing concepts was made. In the next step newly available periodically poled crystals were used for second harmonic generation (SHG) in single pass setups. With the stripe-array ECDL as pump source, more than 140 mW of coherent radiation at 488 nm could be generated with a very high opto-optical conversion efficiency. The generated blue light had very good transversal and longitudinal properties and could be used to generate biphotons by parametric down-conversion. This was feasible because of the improvement made with the infrared stripe-array diode lasers due to the development of new physical concepts.}, language = {en} } @phdthesis{GuedesCorrea2009, author = {Guedes Corr{\^e}a, Luiz Gustavo}, title = {Evolutionary and functional analysis of transcription factors controlling leaf development}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-40038}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {Leaves are the main photosynthetic organs of vascular plants, and leaf development is dependent on a proper control of gene expression. Transcription factors (TFs) are global regulators of gene expression that play essential roles in almost all biological processes among eukaryotes. This PhD project focused on the characterization of the sink-to-source transition of Arabidopsis leaves and on the analysis of TFs that play a role in early leaf development. The sink-to-source transition occurs when the young emerging leaves (net carbon importers) acquire a positive photosynthetic balance and start exporting photoassimilates. We have established molecular and physiological markers (i.e., CAB1 and CAB2 expression levels, AtSUC2 and AtCHoR expression patterns, chlorophyll and starch levels, and photosynthetic electron transport rates) to identify the starting point of the transition, especially because the sink-to-source is not accompanied by a visual phenotype in contrast to other developmental transitions, such as the mature-to-senescent transition of leaves. The sink-to-source transition can be divided into two different processes: one light dependent, related to photosynthesis and light responses; and one light independent or impaired, related to the changes in the vascular tissue that occur when leaves change from an import to an export mode. Furthermore, starch, but not sucrose, has been identified as one of the potential signalling molecules for this transition. The expression level of 1880 TFs during early leaf development was assessed by qRTPCR, and 153 TFs were found to exhibit differential expression levels of at least 5-fold. GRF, MYB and SRS are TF families, which are overrepresented among the differentially expressed TFs. Additionally, processes like cell identity acquisition, formation of the epidermis and leaf development are overrepresented among the differentially expressed TFs, which helps to validate the results obtained. Two of these TFs were further characterized. bZIP21 is a gene up-regulated during the sink-to-source and mature-to-senescent transitions. Its expression pattern in leaves overlaps with the one observed for AtCHoR, therefore it constitutes a good marker for the sink-to-source transition. Homozygous null mutants of bZIP21 could not be obtained, indicating that the total absence of bZIP21 function may be lethal to the plant. Phylogenetic analyses indicate that bZIP21 is an orthologue of Liguleless2 from maize. In these analyses, we identified that the whole set of bZIPs in plants originated from four founder genes, and that all bZIPs from angiosperms can be classified into 13 groups of homologues and 34 Possible Groups of Orthologues (PoGOs). bHLH64 is a gene highly expressed in early sink leaves, its expression is downregulated during the mature-to-senescent transition. Null mutants of bHLH64 are characterized by delayed bolting when compared to the wild-type; this indicates a possible delay in the sink-to-source transition or the retention of a juvenile identity. A third TF, Dof4, was also characterized. Dof4 is neither differentially expressed during the sink-to-source nor during the senescent-to-mature transition, but a null mutant of Dof4 develops bigger leaves than the wild-type and forms a greater number of siliques. The Dof4 null mutant has proven to be a good background for biomass accumulation analysis. Though not overrepresented during the sink-to-source transition, NAC transcription factors seem to contribute significantly to the mature-to-senescent transition. Twenty two NACs from Arabidopsis and 44 from rice are differentially expressed during late stages of leaf development. Phylogenetic analyses revealed that most of these NACs cluster into three big groups of homologues, indicating functional conservation between eudicots and monocots. To prove functional conservation of orthologues, the expression of ten NAC genes of barley was analysed. Eight of the ten NAC genes were found to be differentially expressed during senescence. The use of evolutionary approaches combined with functional studies is thus expected to support the transfer of current knowledge of gene control gained in model species to crops.}, language = {en} } @phdthesis{Rafler2009, author = {Rafler, Mathias}, title = {Gaussian loop- and P{\´o}lya processes : a point process approach}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-029-8}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-38706}, school = {Universit{\"a}t Potsdam}, pages = {ix, 162}, year = {2009}, abstract = {This thesis considers on the one hand the construction of point processes via conditional intensities, motivated by the partial Integration of the Campbell measure of a point process. Under certain assumptions on the intensity the existence of such a point process is shown. A fundamental example turns out to be the P{\´o}lya sum process, whose conditional intensity is a generalisation of the P{\´o}lya urn dynamics. A Cox process representation for that point process is shown. A further process considered is a Poisson process of Gaussian loops, which represents a noninteracting particle system derived from the discussion of indistinguishable particles. Both processes are used to define particle systems locally, for which thermodynamic limits are determined.}, language = {en} } @phdthesis{Mailer2009, author = {Mailer, Tina}, title = {Neon, Helium and Argon isotope systematics of the Hawaiian hotspot}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-39633}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {This study presents noble gas compositions (He, Ne, Ar, Kr, and Xe) of lavas from several Hawaiian volcanoes. Lavas from the Hawaii Scientific Drilling Project (HSDP) core, surface samples from Mauna Kea, Mauna Loa, Kilauea, Hualalai, Kohala and Haleakala as well as lavas from a deep well on the summit of Kilauea were investigated. Noble gases, especially helium, are used as tracers for mantle reservoirs, based on the assumption that high 3He/4He ratios (>8 RA) represent material from the deep and supposedly less degassed mantle, whereas lower ratios (~ 8 RA) are thought to represent the upper mantle. Shield stage Mauna Kea, Kohala and Kilauea lavas yielded MORB-like to moderately high 3He/4He ratios, while 3He/4He ratios in post-shield stage Haleakala lavas are MORB-like. Few samples show 20Ne/22Ne and 21Ne/22Ne ratios different from the atmospheric values, however, Mauna Kea and Kilauea lavas with excess in mantle Ne agree well with the Loihi-Kilauea line in a neon three-isotope plot, whereas one Kohala sample plots on the MORB correlation line. The values in the 4He/40Ar* (40Ar* denotes radiogenic Ar) versus 4He diagram imply open system fractionation of He from Ar, with a deficiency in 4He. Calculated 4He/40Ar*, 3He/22Nes (22NeS denotes solar Ne) and 4He/21Ne ratios for the sample suite are lower than the respective production and primordial ratios, supporting the observation of a fractionation of He from the heavier noble gases, with a depletion of He with respect to Ne and Ar. The depletion of He is interpreted to be partly due to solubility controlled gas loss during magma ascent. However, the preferential He loss suggests that He is more incompatible than Ne and Ar during magmatic processes. In a binary mixing model, the isotopic He and Ne pattern are best explained by a mixture of a MORB-like end-member with a plume like or primordial end-member with a fractionation in 3He/22Ne, represented by a curve parameter r of 15 (r=(³He/²²Ne)MORB/(³He/²²Ne)PLUME or PRIMORDIAL). Whether the high 3He/4He ratios in Hawaiian lavas are indicative of a primitive component within the Hawaiian plume or are rather a product of the crystal-melt- partitioning behavior during partial melting remains to be resolved.}, language = {en} } @phdthesis{Karabudak2009, author = {Karabudak, Engin}, title = {Development of MWL-AUC / CCD-C-AUC / SLS-AUC detectors for the analytical ultracentrifuge}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-39921}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {Analytical ultracentrifugation (AUC) has made an important contribution to polymer and particle characterization since its invention by Svedberg (Svedberg and Nichols 1923; Svedberg and Pederson 1940) in 1923. In 1926, Svedberg won the Nobel price for his scientific work on disperse systems including work with AUC. The first important discovery performed with AUC was to show the existence of macromolecules. Since that time AUC has become an important tool to study polymers in biophysics and biochemistry. AUC is an absolute technique that does not need any standard. Molar masses between 200 and 1014 g/mol and particle size between 1 and 5000 nm can be detected by AUC. Sample can be fractionated into its components due to its molar mass, particle size, structure or density without any stationary phase requirement as it is the case in chromatographic techniques. This very property of AUC earns it an important status in the analysis of polymers and particles. The distribution of molar mass, particle sizes and densities can be measured with the fractionation. Different types of experiments can give complementary physicochemical parameters. For example, sedimentation equilibrium experiments can lead to the study of pure thermodynamics. For complex mixtures, AUC is the main method that can analyze the system. Interactions between molecules can be studied at different concentrations without destroying the chemical equilibrium (Kim et al. 1977). Biologically relevant weak interactions can also be monitored (K ≈ 10-100 M-1). An analytical ultracentrifuge experiment can yield the following information: • Molecular weight of the sample • Number of the components in the sample if the sample is not a single component • Homogeneity of the sample • Molecular weight distribution if the sample is not a single component • Size and shape of macromolecules \& particles • Aggregation \& interaction of macromolecules • Conformational changes of macromolecules • Sedimentation coefficient and density distribution Such an extremely wide application area of AUC allows the investigation of all samples consisting of a solvent and a dispersed or dissolved substance including gels, micro gels, dispersions, emulsions and solutions. Another fact is that solvent or pH limitation does not exist for this method. A lot of new application areas are still flourishing, although the technique is 80 years old. In 1970s, 1500 AUC were operational throughout the world. At those times, due to the limitation in detection technologies, experimental results were obtained with photographic records. As time passed, faster techniques such as size exclusion chromatography (SEC), light scattering (LS) or SDS-gel electrophoresis occupied the same research fields with AUC. Due to these relatively new techniques, AUC began to loose its importance. In the 1980s, only a few AUC were in use throughout the world. In the beginning of the 1990s a modern AUC -the Optima XL-A - was released by Beckman Instruments (Giebeler 1992). The Optima XL-A was equipped with a modern computerized scanning absorption detector. The addition of Rayleigh Interference Optics is introduced which is called XL-I AUC. Furthermore, major development in computers made the analysis easier with the help of new analysis software. Today, about 400 XL-I AUC exist worldwide. It is usually applied in the industry of pharmacy, biopharmacy and polymer companies as well as in academic research fields such as biochemistry, biophysics, molecular biology and material science. About 350 core scientific publications which use analytical ultracentrifugation are published every year (source: SciFinder 2008 ) with an increasing number of references (436 reference in 2008). A tremendous progress has been made in method and analysis software after digitalization of experimental data with the release of XL-I. In comparison to the previous decade, data analysis became more efficient and reliable. Today, AUC labs can routinely use sophisticated data analysis methods for determination of sedimentation coefficient distributions (Demeler and van Holde 2004; Schuck 2000; Stafford 1992), molar mass distributions (Brookes and Demeler 2008; Brookes et al. 2006; Brown and Schuck 2006), interaction constants (Cao and Demeler 2008; Schuck 1998; Stafford and Sherwood 2004), particle size distributions with Angstrom resolution (C{\"o}lfen and Pauck 1997) and the simulations determination of size and shape distributions from sedimentation velocity experiments (Brookes and Demeler 2005; Brookes et al. 2006). These methods are also available in powerful software packages that combines various methods, such as, Ultrascan (Demeler 2005), Sedift/Sedphat (Schuck 1998; Vistica et al. 2004) and Sedanal (Stafford and Sherwood 2004). All these powerful packages are free of charge. Furthermore, Ultrascans source code is licensed under the GNU Public License (http://www.gnu.org/copyleft/gpl.html). Thus, Ultrascan can be further improved by any research group. Workshops are organized to support these software packages. Despite of the tremendous developments in data analysis, hardware for the system has not developed much. Although there are various user developed detectors in research laboratories, they are not commercially available. Since 1992, only one new optical system called "the fluorescence optics" (Schmidt and Reisner, 1992, MacGregor et al. 2004, MacGregor, 2006, Laue and Kroe, in press) has been commercialized. However, except that, there has been no commercially available improvement in the optical system. The interesting fact about the current hardware of the XL-I is that it is 20 years old, although there has been an enormous development in microelectronics, software and in optical systems in the last 20 years, which could be utilized for improved detectors. As examples of user developed detector, Bhattacharyya (Bhattacharyya 2006) described a Multiwavelength-Analytical Ultracentrifuge (MWL-AUC), a Raman detector and a small angle laser light scattering detector in his PhD thesis. MWL-AUC became operational, but a very high noise level prevented to work with real samples. Tests with the Raman detector were not successful due to the low light intensity and thus high integration time is required. The small angle laser light scattering detector could only detect latex particles but failed to detect smaller particles and molecules due to low sensitivity of the detector (a photodiode was used as detector). The primary motivation of this work is to construct a detector which can measure new physico-chemical properties with AUC with a nicely fractionated sample in the cell. The final goal is to obtain a multiwavelength detector for the AUC that measures complementary quantities. Instrument development is an option for a scientist only when there is a huge potential benefit but there is no available commercial enterprise developing appropriate equipment, or if there is not enough financial support to buy it. The first case was our motivation for developing detectors for AUC. Our aim is to use today's technological advances in microelectronics, programming, mechanics in order to develop new detectors for AUC and improve the existing MWL detector to routine operation mode. The project has multiple aspects which can be listed as mechanical, electronical, optical, software, hardware, chemical, industrial and biological. Hence, by its nature it is a multidisciplinary project. Again by its nature it contains the structural problem of its kind; the problem of determining the exact discipline to follow at each new step. It comprises the risk of becoming lost in some direction. Having that fact in mind, we have chosen the simplest possible solution to any optical, mechanical, electronic, software or hardware problem we have encountered and we have always tried to see the overall picture. In this research, we have designed CCD-C-AUC (CCD Camera UV/Vis absorption detector for AUC) and SLS-AUC (Static Light Scattering detector for AUC) and tested them. One of the SLS-AUC designs produced successful test results, but the design could not be brought to the operational stage. However, the operational state Multiwavelength Analytical Ultracentrifuge (MWL-AUC) AUC has been developed which is an important detector in the fields of chemistry, biology and industry. In this thesis, the operational state Multiwavelength Analytical Ultracentrifuge (MWL-AUC) AUC is to be introduced. Consequently, three different applications of MWL-AUC to the aforementioned disciplines shall be presented. First of all, application of MWL-AUC to a biological system which is a mixture of proteins lgG, aldolase and BSA is presented. An application of MWL-AUC to a mass-produced industrial sample (β-carotene gelatin composite particles) which is manufactured by BASF AG, is presented. Finally, it is shown how MWL-AUC will impact on nano-particle science by investigating the quantum size effect of CdTe and its growth mechanism. In this thesis, mainly the relation between new technological developments and detector development for AUC is investigated. Pioneering results are obtained that indicate the possible direction to be followed for the future of AUC. As an example, each MWL-AUC data contains thousands of wavelengths. MWL-AUC data also contains spectral information at each radial point. Data can be separated to its single wavelength files and can be analyzed classically with existing software packages. All the existing software packages including Ultrascan, Sedfit, Sedanal can analyze only single wavelength data, so new extraordinary software developments are needed. As a first attempt, Emre Brookes and Borries Demeler have developed mutliwavelength module in order to analyze the MWL-AUC data. This module analyzes each wavelength separately and independently. We appreciate Emre Brookes and Borries Demeler for their important contribution to the development of the software. Unfortunately, this module requires huge amount of computer power and does not take into account the spectral information during the analysis. New software algorithms are needed which take into account the spectral information and analyze all wavelengths accordingly. We would like also invite the programmers of Ultrascan, Sedfit, Sedanal and the other programs, to develop new algorithms in this direction.}, language = {en} } @phdthesis{Kirschbaum2009, author = {Kirschbaum, Michael}, title = {A microfluidic approach for the initiation and investigation of surface-mediated signal transduction processes on a single-cell level}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-39576}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {For the elucidation of the dynamics of signal transduction processes that are induced by cellular interactions, defined events along the signal transduction cascade and subsequent activation steps have to be analyzed and then also correlated with each other. This cannot be achieved by ensemble measurements because averaging biological data ignores the variability in timing and response patterns of individual cells and leads to highly blurred results. Instead, only a multi-parameter analysis at a single-cell level is able to exploit the information that is crucially needed for deducing the signaling pathways involved. The aim of this work was to develop a process line that allows the initiation of cell-cell or cell-particle interactions while at the same time the induced cellular reactions can be analyzed at various stages along the signal transduction cascade and correlated with each other. As this approach requires the gentle management of individually addressable cells, a dielectrophoresis (DEP)-based microfluidic system was employed that provides the manipulation of microscale objects with very high spatiotemporal precision and without the need of contacting the cell membrane. The system offers a high potential for automation and parallelization. This is essential for achieving a high level of robustness and reproducibility, which are key requirements in order to qualify this approach for a biomedical application. As an example process for intercellular communication, T cell activation has been chosen. The activation of the single T cells was triggered by contacting them individually with microbeads that were coated with antibodies directed against specific cell surface proteins, like the T cell receptor-associated kinase CD3 and the costimulatory molecule CD28 (CD; cluster of differentiation). The stimulation of the cells with the functionalized beads led to a rapid rise of their cytosolic Ca2+ concentration which was analyzed by a dual-wavelength ratiometric fluorescence measurement of the Ca2+-sensitive dye Fura-2. After Ca2+ imaging, the cells were isolated individually from the microfluidic system and cultivated further. Cell division and expression of the marker molecule CD69 as a late activation event of great significance were analyzed the following day and correlated with the previously recorded Ca2+ traces for each individual cell. It turned out such that the temporal profile of the Ca2+ traces between both activated and non-activated cells as well as dividing and non-dividing cells differed significantly. This shows that the pattern of Ca2+ signals in T cells can provide early information about a later reaction of the cell. As isolated cells are highly delicate objects, a precondition for these experiments was the successful adaptation of the system to maintain the vitality of single cells during and after manipulation. In this context, the influences of the microfluidic environment as well as the applied electric fields on the vitality of the cells and the cytosolic Ca2+ concentration as crucially important physiological parameters were thoroughly investigated. While a short-term DEP manipulation did not affect the vitality of the cells, they showed irregular Ca2+ transients upon exposure to the DEP field only. The rate and the strength of these Ca2+ signals depended on exposure time, electric field strength and field frequency. By minimizing their occurrence rate, experimental conditions were identified that caused the least interference with the physiology of the cell. The possibility to precisely control the exact time point of stimulus application, to simultaneously analyze short-term reactions and to correlate them with later events of the signal transduction cascade on the level of individual cells makes this approach unique among previously described applications and offers new possibilities to unravel the mechanisms underlying intercellular communication.}, language = {en} } @phdthesis{BivigouKoumba2009, author = {Bivigou Koumba, Achille Mayelle}, title = {Design, Synthesis and Characterisation of Amphiphilic Symmetrical triblock copolymers by the RAFT process : their self-organisation in dilute and concentrated aqueous solutions}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-39549}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {This work presents the synthesis and the self-assembly of symmetrical amphiphilic ABA and BAB triblock copolymers in dilute, semi-concentrated and highly concentrated aqueous solution. A series of new bifunctional bistrithiocarbonates as RAFT agents was used to synthesise these triblock copolymers, which are characterised by a long hydrophilic middle block and relatively small, but strongly hydrophobic end blocks. As hydrophilic A blocks, poly(N-isopropylacrylamide) (PNIPAM) and poly(methoxy diethylene glycol acrylate) (PMDEGA) were employed, while as hydrophobic B blocks, poly(4-tert-butyl styrene), polystyrene, poly(3,5-dibromo benzyl acrylate), poly(2-ethylhexyl acrylate), and poly(octadecyl acrylate) were explored as building blocks with different hydrophobicities and glass transition temperatures. The five bifunctional trithiocarbonates synthesised belong to two classes: the first are RAFT agents, which position the active group of the growing polymer chain at the outer ends of the polymer (Z-C(=S)-S-R-S-C(=S)-Z, type I). The second class places the active groups in the middle of the growing polymer chain (R-S-C(=S)-Z-C(=S)-S-R, type II). These RAFT agents enable the straightforward synthesis of amphiphilic triblock copolymers in only two steps, allowing to vary the nature of the hydrophobic blocks as well as the length of the hydrophobic and hydrophilic blocks broadly with good molar mass control and narrow polydispersities. Specific side reactions were observed among some RAFT agents including the elimination of ethylenetrithiocarbonate in the early stage of the polymerisation of styrene mediated by certain agents of the type II, while the use of the RAFT agents of type I resulted in retardation of the chain extension of PNIPAM with styrene. These results underline the need of a careful choice of RAFT agents for a given task. The various copolymers self-assemble in dilute and semi-concentrated aqueous solution into small flower-like micelles. No indication for the formation of micellar clusters was found, while only at high concentration, physical hydrogels are formed. The reversible thermoresponsive behaviour of the ABA and BAB type copolymer solutions in water with A made of PNIPAM was examined by turbidimetry and dynamic light scattering (DLS). The cloud point of the copolymers was nearly identical to the cloud point of the homopolymer and varied between 28-32 °C with concentrations from 0.01 to 50 wt\%. This is attributed to the formation of micelles where the hydrophobic blocks are shielded from a direct contact with water, so that the hydrophobic interactions of the copolymers are nearly the same as for pure PNIPAM. Dynamic light scattering measurements showed the presence of small micelles at ambient temperature. The aggregate size dramatically increased above the cloud point, indicating a change of aggregate morphology into clusters due to the thermosensitivity of the PNIPAM block. The rheological behaviour of the amphiphilic BAB triblock copolymers demonstrated the formation of hydrogels at high concentrations, typically above 30-35 wt\%. The minimum concentration to induce hydrogels decreased with the increasing glass transition temperatures and increasing length of the end blocks. The weak tendency to form hydrogels was attributed to a small share of bridged micelles only, due to the strong segregation regime occurring. In order to learn about the role of the nature of the thermoresponsive block for the aggregation, a new BAB triblock copolymer consisting of short polystyrene end blocks and PMDEGA as stimuli-responsive middle block was prepared and investigated. Contrary to PNIPAM, dilute aqueous solutions of PMDEGA and of its block copolymers showed reversible phase transition temperatures characterised by a strong dependence on the polymer composition. Moreover, the PMDEGA block copolymer allowed the formation of physical hydrogels at lower concentration, i.e. from 20 wt\%. This result suggests that PMDEGA has a higher degree of water-swellability than PNIPAM.}, language = {en} } @phdthesis{Itonaga2009, author = {Itonaga, Naomi}, title = {White storks (Ciconia ciconia) of Eastern Germany: age-dependent breeding ability, and age- and density-dependent effects on dispersal behavior}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-39052}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {Dispersal behavior plays an important role for the geographical distribution and population structure of any given species. Individual's fitness, reproductive and competitive ability, and dispersal behavior can be determined by the age of the individual. Age-dependent as well as density-dependent dispersal patterns are common in many bird species. In this thesis, I first present age-dependent breeding ability and natal site fidelity in white storks (Ciconia ciconia); migratory birds breeding in large parts of Europe. I predicted that both the proportion of breeding birds and natal site fidelity increase with the age. After the seventies of the last century, following a steep population decline, a recovery of the white stork population has been observed in many regions in Europe. Increasing population density in the white stork population in Eastern Germany especially after 1983 allowed examining density- as well as age-dependent breeding dispersal patterns. Therefore second, I present whether: young birds show more often and longer breeding dispersal than old birds, and frequency of dispersal events increase with the population density increase, especially in the young storks. Third, I present age- and density-dependent dispersal direction preferences in the give population. I asked whether and how the major spring migration direction interacts with dispersal directions of white storks: in different age, and under different population densities. The proportion of breeding individuals increased in the first 22 years of life and then decreased suggesting, the senescent decay in aging storks. Young storks were more faithful to their natal sites than old storks probably due to their innate migratory direction and distance. Young storks dispersed more frequently than old storks in general, but not for longer distance. Proportion of dispersing individuals increased significantly with increasing population densities indicating, density- dependent dispersal behavior in white storks. Moreover, the finding of a significant interaction effects between the age of dispersing birds and year (1980-2006) suggesting, older birds dispersed more from their previous nest sites over time due to increased competition. Both young and old storks dispersed along their spring migration direction; however, directional preferences were different in young storks and old storks. Young storks tended to settle down before reaching their previous nest sites (leading to the south-eastward dispersal) while old birds tended to keep migrating along the migration direction after reaching their previous nest sites (leading to the north-westward dispersal). Cues triggering dispersal events may be age-dependent. Changes in the dispersal direction over time were observed. Dispersal direction became obscured during the second half of the observation period (1993-2006). Increase in competition may affect dispersal behavior in storks. I discuss the potential role of: age for the observed age-dependent dispersal behavior, and competition for the density dependent dispersal behavior. This Ph.D. thesis contributes significantly to the understanding of population structure and geographical distribution of white storks. Moreover, presented age- and density (competition)-dependent dispersal behavior helps understanding underpinning mechanisms of dispersal behavior in bird species.}, language = {en} } @phdthesis{Dall'Aglio2009, author = {Dall'Aglio, Aldo}, title = {Constraining the UV background with the proximity effect}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-38713}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {After the epoch of reionisation the intergalactic medium (IGM) is kept at a high photoionisation level by the cosmic UV background radiation field. Primarily composed of the integrated contribution of quasars and young star forming galaxies, its intensity is subject to spatial and temporal fluctuations. In particular in the vicinity of luminous quasars, the UV radiation intensity grows by several orders of magnitude. Due to an enhanced UV radiation up to a few Mpc from the quasar, the ionised hydrogen fraction significantly increases and becomes visible as a reduced level of absorption in the HI Lyman alpha (Ly-alpha) forest. This phenomenon is known as the proximity effect and it is the main focus of this thesis. Modelling the influence on the IGM of the quasar radiation, one is able to determine the UV background intensity at a specific frequency (J_nu_0), or equivalently, its photoionisation rate (Gamma_b). This is of crucial importance for both theoretical and observational cosmology. Thus far, the proximity effect has been investigated primarily by combining the signal of large samples of quasars, as it has been regarded as a statistical phenomenon. Only a handful of studies tried to measure its signature on individual lines of sight, albeit focusing on one sight line only. Our aim is to perform a systematic investigation of large samples of quasars searching for the signature of the proximity effect, with a particular emphasis on its detection on individual lines of sight. We begin this survey with a sample of 40 high resolution (R~45000), high signal to noise ratio (S/N~70) quasar spectra at redshift 2.12.3. In spite of the low resolution and limited S/N we detect the proximity effect on about 98\\% of the quasars at a high significance level. Thereby we are able to determine the evolution of the UV background photoionisation rate within the redshift range 2 6.0\$) and show mass-loss rates and wind characteristics typical for radiation-driven winds. By comparison with stellar evolutionary models (Meynet \\& Maeder 2003a; Langer et al. 1994), the initial masses were estimated and indicate that the Quintuplet WN stars are descendants from the most massive O stars with \$M_\text{init} > 60 M_\odot\$ and their ages correspond to a cluster age of 3-5\,million years. The analysis of the individual WN stars revealed an average extinction of \$A_K =3.1 \pm 0.5\$\,mag (\$A_V = 27 \pm 4\$) towards the Quintuplet cluster. This extinction was applied to derive the stellar luminosities of the remaining early-type and late-type stars in the catalog and a Hertzsprung-Russell diagram could be compiled. Surprisingly, two stellar populations are found, a group of main sequence OB stars and a group of evolved late-type stars, i.e. red supergiants (RSG). The main sequence stars indicate a cluster age of 4 million years, which would be too young for red supergiants to be already present. A star formation event lasting for a few million years might possibly explain the Quintuplet's population and the cluster would still be considered coeval. However, the unexpected and simultaneous presence of red supergiants and Wolf-Rayet stars in the cluster points out that the details of star formation and cluster evolution are not yet well understood for the Quintuplet cluster.}, language = {en} } @phdthesis{Breitenbach2009, author = {Breitenbach, Sebastian Franz Martin}, title = {Changes in monsoonal precipitation and atmospheric circulation during the Holocene reconstructed from stalagmites from Northeastern India}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-37807}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {Recent years witnessed a vast advent of stalagmites as palaeoclimate archives. The multitude of geochemical and physical proxies and a promise of a precise and accurate age model greatly appeal to palaeoclimatologists. Although substantial progress was made in speleothem-based palaeoclimate research and despite high-resolution records from low-latitudinal regions, proving that palaeo-environmental changes can be archived on sub-annual to millennial time scales our comprehension of climate dynamics is still fragmentary. This is in particular true for the summer monsoon system on the Indian subcontinent. The Indian summer monsoon (ISM) is an integral part of the intertropical convergence zone (ITCZ). As this rainfall belt migrates northward during boreal summer, it brings monsoonal rainfall. ISM strength depends however on a variety of factors, including snow cover in Central Asia and oceanic conditions in the Indic and Pacific. Presently, many of the factors influencing the ISM are known, though their exact forcing mechanism and mutual relations remain ambiguous. Attempts to make an accurate prediction of rainfall intensity and frequency and drought recurrence, which is extremely important for South Asian countries, resemble a puzzle game; all interaction need to fall into the right place to obtain a complete picture. My thesis aims to create a faithful picture of climate change in India, covering the last 11,000 ka. NE India represents a key region for the Bay of Bengal (BoB) branch of the ISM, as it is here where the monsoon splits into a northwestward and a northeastward directed arm. The Meghalaya Plateau is the first barrier for northward moving air masses and receives excessive summer rainfall, while the winter season is very dry. The proximity of Meghalaya to the Tibetan Plateau on the one hand and the BoB on the other hand make the study area a key location for investigating the interaction between different forcings that governs the ISM. A basis for the interpretation of palaeoclimate records, and a first important outcome of my thesis is a conceptual model which explains the observed pattern of seasonal changes in stable isotopes (d18O and d2H) in rainfall. I show that although in tropical and subtropical regions the amount effect is commonly called to explain strongly depleted isotope values during enhanced rainfall, alone it cannot account for observed rainwater isotope variability in Meghalaya. Monitoring of rainwater isotopes shows no expected negative correlation between precipitation amount and d18O of rainfall. In turn I find evidence that the runoff from high elevations carries an inherited isotopic signature into the BoB, where during the ISM season the freshwater builds a strongly depleted plume on top of the marine water. The vapor originating from this plume is likely to memorize' and transmit further very negative d18O values. The lack of data does not allow for quantication of this plume effect' on isotopes in rainfall over Meghalaya but I suggest that it varies on seasonal to millennial timescales, depending on the runoff amount and source characteristics. The focal point of my thesis is the extraction of climatic signals archived in stalagmites from NE India. High uranium concentration in the stalagmites ensured excellent age control required for successful high-resolution climate reconstructions. Stable isotope (d18O and d13C) and grey-scale data allow unprecedented insights into millennial to seasonal dynamics of the summer and winter monsoon in NE India. ISM strength (i. e. rainfall amount) is recorded in changes in d18Ostalagmites. The d13C signal, reflecting drip rate changes, renders a powerful proxy for dry season conditions, and shows similarities to temperature-related changes on the Tibetan Plateau. A sub-annual grey-scale profile supports a concept of lower drip rate and slower stalagmite growth during dry conditions. During the Holocene, ISM followed a millennial-scale decrease of insolation, with decadal to centennial failures resulting from atmospheric changes. The period of maximum rainfall and enhanced seasonality corresponds to the Holocene Thermal Optimum observed in Europe. After a phase of rather stable conditions, 4.5 kyr ago, the strengthening ENSO system dominated the ISM. Strong El Nino events weakened the ISM, especially when in concert with positive Indian Ocean dipole events. The strongest droughts of the last 11 kyr are recorded during the past 2 kyr. Using the advantage of a well-dated stalagmite record at hand I tested the application of laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) to detect sub-annual to sub-decadal changes in element concentrations in stalagmites. The development of a large ablation cell allows for ablating sample slabs of up to 22 cm total length. Each analyzed element is a potential proxy for different climatic parameters. Combining my previous results with the LAICP- MS-generated data shows that element concentration depends not only on rainfall amount and associated leaching from the soil. Additional factors, like biological activity and hydrogeochemical conditions in the soil and vadose zone can eventually affect the element content in drip water and in stalagmites. I present a theoretical conceptual model for my study site to explain how climatic signals can be transmitted and archived in stalagmite carbonate. Further, I establish a first 1500 year long element record, reconstructing rainfall variability. Additionally, I hypothesize that volcanic eruptions, producing large amounts of sulfuric acid, can influence soil acidity and hence element mobilization.}, language = {en} } @phdthesis{Baczyński2009, author = {Baczyński, Krzysztof Konrad}, title = {Buckling instabilities of semiflexible filaments in biological systems}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-37927}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {In dieser Arbeit werden Knickinstabilit{\"a}ten von Filamenten in biologischen Systemen untersucht. Das Zytoskelett von Zellen ist aus solchen Filamenten aufgebaut. Sie sind f{\"u}r die mechanische Stabilit{\"a}t der Zelle verantwortlich und spielen eine große Rolle bei intrazellul{\"a}ren Transportprozessen durch molekulare Motoren, die verschiedene Lasten wie beispielsweise Organellen entlang der Filamente des Zytoskeletts transportieren. Filamente sind semiflexible Polymere, deren Biegeenergie {\"a}hnlich groß ist wie die thermische Energie, so dass sie auch als elastische Balken auf der Nanoskala gesehen werden k{\"o}nnen, die signifikante thermische Fluktuationen zeigen. Wie ein makroskopischer elastischer Balken k{\"o}nnen auch Filamente eine mechanische Knickinstabilit{\"a}t unter Kompression zeigen. Im ersten Teil dieser Arbeit wird untersucht, wie diese Instabilit{\"a}t durch thermische Fluktuationen der Filamente beeinflusst wird. In Zellen k{\"o}nnen Kompressionskr{\"a}fte durch molekulare Motoren erzeugt werden. Das geschieht zum Beispiel w{\"a}hrend der Zellteilung in der mitotischen Spindel. Im zweiten Teil der Arbeit untersuchen wir, wie die stochastische Natur einer von Motoren generierten Kraft die Knickinstabilit{\"a}t von Filamenten beeinflusst. Zun{\"a}chst stellen wir kurz das Problem von Knickinstabilit{\"a}ten auf der makroskopischen Skala dar und f{\"u}hren ein Modell f{\"u}r das Knicken von Filamenten oder elastischen St{\"a}ben in zwei Raumdimensionen und in Anwesenheit thermischer Fluktuationen ein. Wir pr{\"a}sentieren eine analytische L{\"o}sung f{\"u}r Knickinstabilit{\"a}ten in Anwesenheit thermischer Fluktuationen, die auf einer Renormierungsgruppenrechnung im Rahmen des nichtlinearen Sigma-Models basiert. Wir integrieren die kurzwelligen Fluktuationen aus, um eine effektive Theorie f{\"u}r die langwelligen Moden zu erhalten, die die Knickinstabilit{\"a}t bestimmen. Wir berechnen die {\"A}nderung der kritischen Kraft f{\"u}r die Knickinstabilit{\"a}t und zeigen, dass die thermischen Fluktuationen in zwei Raumdimensionen zu einer Zunahme der kritischen Kraft f{\"u}hren. Außerdem zeigen wir, dass thermische Fluktuationen im geknickten Zustand zu einer Zunahme der mittleren projizierten L{\"a}nge des Filaments in Richtung der wirkenden Kraft f{\"u}hren. Als Funktion der Konturl{\"a}nge des Filaments besitzt die mittlere projizierte L{\"a}nge eine Spitze an der Knickinstabilit{\"a}t, die durch thermische Fluktuationen abgerundet wird. Unser Hauptresultat ist die Beobachtung, dass ein geknicktes Filament unter dem Einfluss thermischer Fluktuationen gestreckt wird, d.h. dass seine mittlere projizierte L{\"a}nge in Richtung der Kompressionskraft auf Grund der thermischen Fluktuationen zunimmt. Unsere analytischen Resultate werden durch Monte-Carlo Simulationen der Knickinstabilit{\"a}t semiflexibler Filamente in zwei Raumdimensionen best{\"a}tigt. Wir f{\"u}hren auch Monte-Carlo Simulationen in h{\"o}heren Raumdimensionen durch und zeigen, dass die Zunahme der projizierten L{\"a}nge unter dem Einfluss thermischer Fluktuationen weniger ausgepr{\"a}gt ist und stark von der Wahl der Randbedingungen abh{\"a}ngt. Im zweiten Teil der Arbeit formulieren wir ein Modell f{\"u}r die Knickinstabilit{\"a}t semiflexibler Filamente unter dem Einfluss molekularer Motoren. Wir untersuchen ein System, in dem sich eine Gruppe von Motoren entlang eines fixierten Filaments bewegt, und dabei ein zweites Filament als Last tr{\"a}gt. Das Last-Filament wird gegen eine Wand gedr{\"u}ckt und knickt. W{\"a}hrend des Knickvorgangs k{\"o}nnen die Motoren, die die Kraft auf das Filament generieren, stochastisch von dem Filament ab- und an das Filament anbinden. Wir formulieren ein stochastisches Model f{\"u}r dieses System und berechnen die "mean first passage time", d.h. die mittlere Zeit f{\"u}r den {\"U}bergang von einem Zustand, in dem alle Motoren gebundenen sind zu einem Zustand, in dem alle Motoren abgebunden sind. Dieser {\"U}bergang entspricht auch einem {\"U}bergang aus dem gebogenen zur{\"u}ck in einen ungebogenen Zustand des Last-Filaments. Unser Resultat zeigt, dass f{\"u}r gen{\"u}gend kurze Mikrotubuli die Bewegung der Motoren von der durch das Last-Filament generierten Kraft beeinflusst wird. Diese Ergebnisse k{\"o}nnen in zuk{\"u}nftigen Experimenten {\"u}berpr{\"u}ft werden.}, language = {en} } @phdthesis{SennemaSkowronek2009, author = {Sennema-Skowronek, Anke}, title = {The use of focus markers in second language word processing}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-37237}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {There are many factors which make speaking and understanding a second language (L2) a highly complex challenge. Skills and competencies in in both linguistic and metalinguistic areas emerge as parts of a multi-faceted, flexible concept underlying bilingual/multilingual communication. On the linguistic level, a combination of an extended knowledge of idiomatic expressions, a broad lexical familiarity, a large vocabulary size, and the ability to deal with phonetic distinctions and fine phonetic detail has been argued necessary for effective nonnative comprehension of spoken language. The scientific interest in these factors has also led to more interest in the L2's information structure, the way in which information is organised and packaged into informational units, both within and between clauses. On a practical level, the information structure of a language can offer the means to assign focus to a certain element considered important. Speakers can draw from a rich pool of linguistic means to express this focus, and listeners can in turn interpret these to guide them to the highlighted information which in turn facilitates comprehension, resulting in an appropriate understanding of what has been said. If a speaker doesn't follow the principles of information structure, and the main accent in a sentence is placed on an unimportant word, then there may be inappropriate information transfer within the discourse, and misunderstandings. The concept of focus as part of the information structure of a language, the linguistic means used to express it, and the differential use of focus in native and nonnative language processing are central to this dissertation. Languages exhibit a wide range of ways of directing focus, including by prosodic means, by syntactic constructions, and by lexical means. The general principles underlying information structure seem to contrast structurally across different languages, and they can also differ in the way they express focus. In the context of L2 acquisition, characteristics of the L1 linguistic system are argued to influence the acquisition of the L2. Similarly, the conceptual patterns of information structure of the L1 may influence the organization of information in the L2. However, strategies and patterns used to exploit information structure for succesful language comprehension in the native L1, may not apply at all, or work in different ways or todifferent degrees in the L2. This means that L2 learners ideally have to understand the way that information structure is expressed in the L2 to fully use the information structural benefit in the L2. The knowledge of information structural requirements in the L2 could also imply that the learner would have to make adjustments regarding the use of information structural devices in the L2. The general question is whether the various means to mark focus in the learners' native language are also accessible in the nonnative language, and whether a L1-L2 transfer of their usage should be considered desirable. The current work explores how information structure helps the listener to discover and structure the forms and meanings of the L2. The central hypothesis is that the ability to access information structure has an impact on the level of the learners' appropriateness and linguistic competence in the L2. Ultimately, the ability to make use of information structure in the L2 is believed to underpin the L2 learners' ability to effectively communicate in the L2. The present study investigated how use of focus markers affects processing speed and word recall recall in a native-nonnative language comparison. The predominant research question was whether the type of focus marking leads to more efficient and accurate word processing in marked structures than in unmarked structures, and whether differences in processing patterns can be observed between the two language conditions. Three perception studies were conducted, each concentrating on one of the following linguistic parameters: 1. Prosodic prominence: Does prosodic focus conveyed by sentence accent and by word position facilitate word recognition? 2. Syntactical means: Do cleft constructions result in faster and more accurate word processing? 3. Lexical means: Does focus conveyed by the particles even/only (German: sogar/nur) facilitate word processing and word recall? Experiments 2 and 3 additionally investigated the contribution of context in the form of preceding questions. Furthermore, they considered accent and its facilitative effect on the processing of words which are in the scope of syntactic or lexical focus marking. All three experiments tested German learners of English in a native German language condition and in English as their L2. Native English speakers were included as a control for the English language condition. Test materials consisted of single sentences, all dealing with bird life. Experiment 1 tested word recognition in three focus conditions (broad focus, narrow focus on the target, and narrow focus on a constituent than the target) in one condition using natural unmanipulated sentences, and in the other two conditions using spliced sentences. Experiment 2 (effect of syntactic focus marking) and Experiment 3 (effect of lexical focus marking) used phoneme monitoring as a measure for the speed of word processing. Additionally, a word recall test (4AFC) was conducted to assess the effective entry of target-bearing words in the listeners' memory. Experiment 1: Focus marking by prosodic means Prosodic focus marking by pitch accent was found to highlight important information (Bolinger, 1972), making the accented word perceptually more prominent (Klatt, 1976; van Santen \& Olive, 1990; Eefting, 1991; Koopmans-van Beinum \& van Bergem, 1989). However, accent structure seems to be processed faster in native than in nonnative listening (Akker\& Cutler, 2003, Expt. 3). Therefore, it is expected that prosodically marked words are better recognised than unmarked words, and that listeners can exploit accent structure better for accurate word recognition in their L1 than they do in the L2 (L1 > L2). Altogether, a difference in word recognition performance in L1 listening is expected between different focus conditions (narrow focus > broad focus). Results of Experiments 1 show that words were better recognized in native listening than in nonnative listening. Focal accent, however, doesn't seem to help the German subjects recognize accented words more accurately, in both the L1 and the L2. This could be due to the focus conditions not being acoustically distinctive enough. Results of experiments with spliced materials suggest that the surrounding prosodic sentence contour made listeners remember a target word and not the local, prosodic realization of the word. Prosody seems to indeed direct listeners' attention to the focus of the sentence (see Cutler, 1976). Regarding the salience of word position, VanPatten (2002; 2004) postulated a sentence location principle for L2 processing, stating a ranking of initial > final > medial word position. Other evidence mentions a processing adantage of items occurring late in the sentence (Akker \& Cutler, 2003), and Rast (2003) observed in an English L2 production study a trend of an advantage of items occurring at the outer ends of the sentence. The current Experiment 1 aimed to keep the length of the sentences to an acceptable length, mainly to keep the task in the nonnative lnaguage condition feasable. Word length showed an effect only in combination with word position (Rast, 2003; Rast \& Dommergues, 2003). Therefore, word length was included in the current experiment as a secondary factor and without hypotheses. Results of Experiment 1 revealed that the length of a word doesn't seem to be important for its accurate recognition. Word position, specifically the final position, clearly seems to facilitate accurate word recognition in German. A similar trend emerges in condition English L2, confirming Klein (1984) and Slobin (1985). Results don't support the sentence location principle of VanPatten (2002; 2004). The salience of the final position is interpreted as recency effect (Murdock, 1962). In addition, the advantage of the final position may benefit from the discourse convention that relevant background information is referred to first, and then what is novel later (Haviland \& Clark, 1974). This structure is assumed to cue the listener as to what the speaker considers to be important information, and listeners might have reacted according to this convention. Experiment 2: Focus marking by syntactic means Atypical syntactic structures often draw listeners' attention to certain information in an utterance, and the cleft structure as a focus marking device appears to be a common surface feature in many languages (Lambrecht, 2001). Surface structure influences sentence processing (Foss \& Lynch, 1969; Langford \& Holmes, 1979), which leads to competing hypotheses in Experiment 2: on the one hand, the focusing effect of the cleft construction might reduce processing times. On the other, cleft constructions in German were found to be used less to mark fo than in English (Ahlemeyer \& Kohlhof, 1999; Doherty, 1999; E. Klein, 1988). The complexity of the constructions, and the experience from the native language might work against an advantage of the focus effect in the L2. Results of Experiment 2 show that the cleft structure is an effective device to mark focus in German L1. The processing advantage is explained by the low degree of structural markedness of cleft structures: listeners use the focus function of sentence types headed by the dummy subject es (English: it) due to reliance on 'safe' subject-prominent SVO-structures. The benefit of cleft is enhanced when the sentences are presented with context, suggesting a substantial benefit when focus effects of syntactic surface structure and coherence relation between sentences are integrated. Clefts facilitate word processing for English native speakers. Contrary to German L1, the marked cleft construction doesn't reduce processing times in English L2. The L1-L2 difference was interpreted as a learner problem of applying specific linguistic structures according to the principles of information structure in the target language. Focus marking by cleft did not help German learners in native or in nonnative word recall. This could be attributed to the phonological similarity of the multiple choice options (Conrad \& Hull, 1964), and to a long time span between listening and recall (Birch \& Garnsey, 1995; McKoon et al., 1993). Experiment 3: Focus marking by lexical means Focus particles are elements of structure that can indicate focus (K{\"o}nig, 1991), and their function is to emphasize a certain part of the sentence (Paterson et al., 1999). I argue that the focus particles even/only (German: sogar/nur) evoke contrast sets of alternatives resp. complements to the element in focus (Ni et al., 1996), which causes interpretations of context. Therefore, lexical focus marking isn't expected to lead to faster word processing. However, since different mechanisms of encoding seem to underlie word memory, a benefit of the focusing function of particles is expected to show in the recall task: due to focus particles being a preferred and well-used feature for native speakers of German, a transfer of this habitualness is expected, resulting in a better recall of focused words. Results indicated that focus particles seem to be the weakest option to mark focus: Focus marking by lexical particle don't seem to reduce word processing times in either German L1, English L2, or in English L1. The presence of focus particles is likely to instantiate a complex discourse model which lets the listener await further modifying information (Liversedge et al., 2002). This semantic complexity might slow down processing. There are no indications that focus particles facilitate native language word recall in German L1 and English L1. This could be because focus particles open sets of conditions and contexts that enlarge the set of representations in listeners rather than narrowing it down to the element in the scope of the focus particle. In word recall, the facilitative effect of focus particles emerges only in the nonnative language condition. It is suggested that L2 learners, when faced with more demanding tasks in an L2, use a broad variety of means that identify focus for a better representation of novel words in the memory. In Experiments 2 and 3, evidence suggests that accent is an important factor for efficient word processing and accurate recall in German L1 and English L1, but less so in English L2. This underlines the function of accent as core speech parameter and consistent cue to the perception of prominence native language use (see Cutler \& Fodor, 1979; Pitt \& Samuel, 1990a; Eriksson et al., 2002; Akker \& Cutler, 2003); the L1-L2 difference is attributed to patterns of expectation that are employed in the L1 but not (yet?) in the L2. There seems to exist a fine-tuned sensitivity to how accents are distributed in the native language, listeners expect an appropriate distribution and interpret it accordingly (Eefting, 1991). This pleads for accent placement as extremely important to L2 proficiency; the current results also suggest that accent and its relationship with other speech parameters has to be newly established in the L2 to fully reveal its benefits for efficient processing of speech. There is evidence that additional context facilitates processing of complex syntactic structures but that a surplus of information has no effect if the sentence construction is less challenging for the listener. The increased amount of information to be processed seems to impede better word recall, particularly in the L2. Altogether, it seems that focus marking devices and context can combine to form an advantageous alliance: a substantial benefit in processing efficiency is found when parameters of focus marking and sentence coherence are integrated. L2 research advocates the beneficial aspects of providing context for efficient L2 word learning (Lawson \& Hogben, 1996). The current thesis promotes the view that a context which offers more semantic, prosodic, or lexical connections might compensate for the additional processing load that context constitutes for the listeners. A methodological consideration concerns the order in which language conditions are presented to listeners, i.e., L1-L2 or L2-L1. Findings suggest that presentation order could enforce a learning bias, with the performance in the second experiment being influenced by knowledge acquired in the first (see Akker \& Cutler, 2003). To conclude this work: The results of the present study suggest that information structure is more accessible in the native language than it is in the nonnative language. There is, however, some evidence that L2 learners have an understanding of the significance of some information-structural parameters of focus marking. This has a beneficial effect on processing efficiency and recall accuracy; on the cognitive side it illustrates the benefits and also the need of a dynamic exchange of information-structural organization between L1 and L2. The findings of the current thesis encourage the view that an understanding of information structure can help the learner to discover and categorise forms and meanings of the L2. Information structure thus emerges as a valuable resource to advance proficiency in a second language.}, language = {en} } @phdthesis{Hiller2009, author = {Hiller, Matthias}, title = {Sample preparation of membrane proteins suitable for solid-state MAS NMR and development of assignment strategies}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-37246}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {Although the basic structure of biological membranes is provided by the lipid bilayer, most of the specific functions are carried out by membrane proteins (MPs) such as channels, ion-pumps and receptors. Additionally, it is known, that mutations in MPs are directly or indirectly involved in many diseases. Thus, structure determination of MPs is of major interest not only in structural biology but also in pharmacology, especially for drug development. Advances in structural biology of membrane proteins (MPs) have been strongly supported by the success of three leading techniques: X-ray crystallography, electron microscopy and solution NMR spectroscopy. However, X-ray crystallography and electron microscopy, require highly diffracting 3D or 2D crystals, respectively. Today, structure determination of non-crystalline solid protein preparations has been made possible through rapid progress of solid-state MAS NMR methodology for biological systems. Castellani et. al. solved and refined the first structure of a microcrystalline protein using only solid-state MAS NMR spectroscopy. These successful application open up perspectives to access systems that are difficult to crystallise or that form large heterogeneous complexes and insoluble aggregates, for example ligands bound to a MP-receptor, protein fibrils and heterogeneous proteins aggregates. Solid-state MAS NMR spectroscopy is in principle well suited to study MP at atomic resolution. In this thesis, different types of MP preparations were tested for their suitability to be studied by solid-state MAS NMR. Proteoliposomes, poorly diffracting 2D crystals and a PEG precipitate of the outer membrane protein G (OmpG) were prepared as a model system for large MPs. Results from this work, combined with data found in the literature, show that highly diffracting crystalline material is not a prerequirement for structural analysis of MPs by solid-state MAS NMR. Instead, it is possible to use non-diffracting 3D crystals, MP precipitates, poorly diffracting 2D crystals and proteoliposomes. For the latter two types of preparations, the MP is reconstituted into a lipid bilayer, which thus allows the structural investigation in a quasi-native environment. In addition, to prepare a MP sample for solid-state MAS NMR it is possible to use screening methods, that are well established for 3D and 2D crystallisation of MPs. Hopefully, these findings will open a fourth method for structural investigation of MP. The prerequisite for structural studies by NMR in general, and the most time consuming step, is always the assignment of resonances to specific nuclei within the protein. Since the last few years an ever-increasing number of assignments from solid-state MAS NMR of uniformly carbon and nitrogen labelled samples is being reported, mostly for small proteins of up to around 150 amino acids in length. However, the complexity of the spectra increases with increasing molecular weight of the protein. Thus the conventional assignment strategies developed for small proteins do not yield a sufficiently high degree of assignment for the large MP OmpG (281 amino acids). Therefore, a new assignment strategy to find starting points for large MPs was devised. The assignment procedure is based on a sample with [2,3-13C, 15N]-labelled Tyr and Phe and uniformly labelled alanine and glycine. This labelling pattern reduces the spectral overlap as well as the number of assignment possibilities. In order to extend the assignment, four other specifically labelled OmpG samples were used. The assignment procedure starts with the identification of the spin systems of each labelled amino acid using 2D 13C-13C and 3D NCACX correlation experiments. In a second step, 2D and 3D NCOCX type experiments are used for the sequential assignment of the observed resonances to specific nuclei in the OmpG amino acid sequence. Additionally, it was shown in this work, that biosynthetically site directed labelled samples, which are normally used to observe long-range correlations, were helpful to confirm the assignment. Another approach to find assignment starting points in large protein systems, is the use of spectroscopic filtering techniques. A filtering block that selects methyl resonances was used to find further assignment starting points for OmpG. Combining all these techniques, it was possible to assign nearly 50 \% of the observed signals to the OmpG sequence. Using this information, a prediction of the secondary structure elements of OmpG was possible. Most of the calculated motifs were in good aggreement with the crystal structures of OmpG. The approaches presented here should be applicable to a wide variety of MPs and MP-complexes and should thus open a new avenue for the structural biology of MPs.}, language = {en} }