@phdthesis{Bauckmann2013,
  author    = {Bauckmann, Jana},
  title     = {Dependency discovery for data integration},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-66645},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {Data integration aims to combine data of different sources and to provide users with a unified view on these data. This task is as challenging as valuable. In this thesis we propose algorithms for dependency discovery to provide necessary information for data integration. We focus on inclusion dependencies (INDs) in general and a special form named conditional inclusion dependencies (CINDs): (i) INDs enable the discovery of structure in a given schema. (ii) INDs and CINDs support the discovery of cross-references or links between schemas. An IND "A in B" simply states that all values of attribute A are included in the set of values of attribute B. We propose an algorithm that discovers all inclusion dependencies in a relational data source. The challenge of this task is the complexity of testing all attribute pairs and further of comparing all of each attribute pair's values. The complexity of existing approaches depends on the number of attribute pairs, while ours depends only on the number of attributes. Thus, our algorithm enables to profile entirely unknown data sources with large schemas by discovering all INDs. Further, we provide an approach to extract foreign keys from the identified INDs. We extend our IND discovery algorithm to also find three special types of INDs: (i) Composite INDs, such as "AB in CD", (ii) approximate INDs that allow a certain amount of values of A to be not included in B, and (iii) prefix and suffix INDs that represent special cross-references between schemas. Conditional inclusion dependencies are inclusion dependencies with a limited scope defined by conditions over several attributes. Only the matching part of the instance must adhere the dependency. We generalize the definition of CINDs distinguishing covering and completeness conditions and define quality measures for conditions. We propose efficient algorithms that identify covering and completeness conditions conforming to given quality thresholds. The challenge for this task is twofold: (i) Which (and how many) attributes should be used for the conditions? (ii) Which attribute values should be chosen for the conditions? Previous approaches rely on pre-selected condition attributes or can only discover conditions applying to quality thresholds of 100\%. Our approaches were motivated by two application domains: data integration in the life sciences and link discovery for linked open data. We show the efficiency and the benefits of our approaches for use cases in these domains.},
  language  = {en}
}
@phdthesis{Bajerski2013,
  author    = {Bajerski, Felizitas},
  title     = {Bacterial communities in glacier forefields of the Larsemann Hills, East Antarctica : structure, development \& adaptation},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-67424},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {Antarctic glacier forfields are extreme environments and pioneer sites for ecological succession. The Antarctic continent shows microbial community development as a natural laboratory because of its special environment, geographic isolation and little anthropogenic influence. Increasing temperatures due to global warming lead to enhanced deglaciation processes in cold-affected habitats and new terrain is becoming exposed to soil formation and accessible for microbial colonisation. This study aims to understand the structure and development of glacier forefield bacterial communities, especially how soil parameters impact the microorganisms and how those are adapted to the extreme conditions of the habitat. To this effect, a combination of cultivation experiments, molecular, geophysical and geochemical analysis was applied to examine two glacier forfields of the Larsemann Hills, East Antarctica. Culture-independent molecular tools such as terminal restriction length polymorphism (T-RFLP), clone libraries and quantitative real-time PCR (qPCR) were used to determine bacterial diversity and distribution. Cultivation of yet unknown species was carried out to get insights in the physiology and adaptation of the microorganisms. Adaptation strategies of the microorganisms were studied by determining changes of the cell membrane phospholipid fatty acid (PLFA) inventory of an isolated bacterium in response to temperature and pH fluctuations and by measuring enzyme activity at low temperature in environmental soil samples. The two studied glacier forefields are extreme habitats characterised by low temperatures, low water availability and small oligotrophic nutrient pools and represent sites of different bacterial succession in relation to soil parameters. The investigated sites showed microbial succession at an early step of soil formation near the ice tongue in comparison to closely located but rather older and more developed soil from the forefield. At the early step the succession is influenced by a deglaciation-dependent areal shift of soil parameters followed by a variable and prevalently depth-related distribution of the soil parameters that is driven by the extreme Antarctic conditions. The dominant taxa in the glacier forefields are Actinobacteria, Acidobacteria, Proteobacteria, Bacteroidetes, Cyanobacteria and Chloroflexi. The connection of soil characteristics with bacterial community structure showed that soil parameter and soil formation along the glacier forefield influence the distribution of certain phyla. In the early step of succession the relative undifferentiated bacterial diversity reflects the undifferentiated soil development and has a high potential to shift according to past and present environmental conditions. With progressing development environmental constraints such as water or carbon limitation have a greater influence. Adapting the culturing conditions to the cold and oligotrophic environment, the number of culturable heterotrophic bacteria reached up to 108 colony forming units per gram soil and 148 isolates were obtained. Two new psychrotolerant bacteria, Herbaspirillum psychrotolerans PB1T and Chryseobacterium frigidisoli PB4T, were characterised in detail and described as novel species in the family of Oxalobacteraceae and Flavobacteriaceae, respectively. The isolates are able to grow at low temperatures tolerating temperature fluctuations and they are not specialised to a certain substrate, therefore they are well-adapted to the cold and oligotrophic environment. The adaptation strategies of the microorganisms were analysed in environmental samples and cultures focussing on extracellular enzyme activity at low temperature and PLFA analyses. Extracellular phosphatases (pH 11 and pH 6.5), β-glucosidase, invertase and urease activity were detected in the glacier forefield soils at low temperature (14°C) catalysing the conversion of various compounds providing necessary substrates and may further play a role in the soil formation and total carbon turnover of the habitat. The PLFA analysis of the newly isolated species C. frigidisoli showed that the cold-adapted strain develops different strategies to maintain the cell membrane function under changing environmental conditions by altering the PLFA inventory at different temperatures and pH values. A newly discovered fatty acid, which was not found in any other microorganism so far, significantly increased at decreasing temperature and low pH and thus plays an important role in the adaption of C. frigidisoli. This work gives insights into the diversity, distribution and adaptation mechanisms of microbial communities in oligotrophic cold-affected soils and shows that Antarctic glacier forefields are suitable model systems to study bacterial colonisation in connection to soil formation.},
  language  = {en}
}
@phdthesis{Badarch2013,
  author    = {Badarch, Kherlen},
  title     = {Integrating new values into Mongolian public management},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-261-2},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-66897},
  school      = {Universit{\"a}t Potsdam},
  pages     = {237},
  year      = {2013},
  abstract  = {This dissertation explores the socio-cultural and institutional environment of the public sector organizations of Mongolia that have strong influence on current public administration reform results. This study applies the Cultural theory and Value theory. The strong hierarchy favoring rule-bounded behavior and collectivism, fatalism accepting an authority as inevitable and uncontrollable, and individualism wishing to have control over own actions are the types of culture common in Mongolian public sector organizations. Accordingly, Mongolian public sector employees transcending their selfish interests, emphasize the well-being of others, protection of order, harmony in relations, life safety and stability. Then self-direction values with emphases on independent thought and action, and creativity are important for them. This socio-cultural context has great implication for work behavior of public employees, for their action to implement the reform policies in government organizations. Thus, the institutional leadership, which produces and protects values, becomes essential for introducing changes in the existing intuitional environment.},
  language  = {de}
}
@phdthesis{Bach2013,
  author    = {Bach, Christoph},
  title     = {Improving statistical seismicity models},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-70591},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {Several mechanisms are proposed to be part of the earthquake triggering process, including static stress interactions and dynamic stress transfer. Significant differences of these mechanisms are particularly expected in the spatial distribution of aftershocks. However, testing the different hypotheses is challenging because it requires the consideration of the large uncertainties involved in stress calculations as well as the appropriate consideration of secondary aftershock triggering which is related to stress changes induced by smaller pre- and aftershocks. In order to evaluate the forecast capability of different mechanisms, I take the effect of smaller--magnitude earthquakes into account by using the epidemic type aftershock sequence (ETAS) model where the spatial probability distribution of direct aftershocks, if available, is correlated to alternative source information and mechanisms. Surface shaking, rupture geometry, and slip distributions are tested. As an approximation of the shaking level, ShakeMaps are used which are available in near real-time after a mainshock and thus could be used for first-order forecasts of the spatial aftershock distribution. Alternatively, the use of empirical decay laws related to minimum fault distance is tested and Coulomb stress change calculations based on published and random slip models. For comparison, the likelihood values of the different model combinations are analyzed in the case of several well-known aftershock sequences (1992 Landers, 1999 Hector Mine, 2004 Parkfield). The tests show that the fault geometry is the most valuable information for improving aftershock forecasts. Furthermore, they reveal that static stress maps can additionally improve the forecasts of off--fault aftershock locations, while the integration of ground shaking data could not upgrade the results significantly. In the second part of this work, I focused on a procedure to test the information content of inverted slip models. This allows to quantify the information gain if this kind of data is included in aftershock forecasts. For this purpose, the ETAS model based on static stress changes, which is introduced in part one, is applied. The forecast ability of the models is systematically tested for several earthquake sequences and compared to models using random slip distributions. The influence of subfault resolution and segment strike and dip is tested. Some of the tested slip models perform very good, in that cases almost no random slip models are found to perform better. Contrastingly, for some of the published slip models, almost all random slip models perform better than the published slip model. Choosing a different subfault resolution hardly influences the result, as long the general slip pattern is still reproducible. Whereas different strike and dip values strongly influence the results depending on the standard deviation chosen, which is applied in the process of randomly selecting the strike and dip values.},
  language  = {en}
}
@phdthesis{Amour2013,
  author    = {Amour, Fr{\´e}d{\´e}ric},
  title     = {3-D modeling of shallow-water carbonate systems : a scale-dependent approach based on quantitative outcrop studies},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-66621},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {The study of outcrop modeling is located at the interface between two fields of expertise, Sedimentology and Computing Geoscience, which respectively investigates and simulates geological heterogeneity observed in the sedimentary record. During the last past years, modeling tools and techniques were constantly improved. In parallel, the study of Phanerozoic carbonate deposits emphasized the common occurrence of a random facies distribution along single depositional domain. Although both fields of expertise are intrinsically linked during outcrop simulation, their respective advances have not been combined in literature to enhance carbonate modeling studies. The present study re-examines the modeling strategy adapted to the simulation of shallow-water carbonate systems, based on a close relationship between field sedimentology and modeling capabilities. In the present study, the evaluation of three commonly used algorithms Truncated Gaussian Simulation (TGSim), Sequential Indicator Simulation (SISim), and Indicator Kriging (IK), were performed for the first time using visual and quantitative comparisons on an ideally suited carbonate outcrop. The results show that the heterogeneity of carbonate rocks cannot be fully simulated using one single algorithm. The operating mode of each algorithm involves capabilities as well as drawbacks that are not capable to match all field observations carried out across the modeling area. Two end members in the spectrum of carbonate depositional settings, a low-angle Jurassic ramp (High Atlas, Morocco) and a Triassic isolated platform (Dolomites, Italy), were investigated to obtain a complete overview of the geological heterogeneity in shallow-water carbonate systems. Field sedimentology and statistical analysis performed on the type, morphology, distribution, and association of carbonate bodies and combined with palaeodepositional reconstructions, emphasize similar results. At the basin scale (x 1 km), facies association, composed of facies recording similar depositional conditions, displays linear and ordered transitions between depositional domains. Contrarily, at the bedding scale (x 0.1 km), individual lithofacies type shows a mosaic-like distribution consisting of an arrangement of spatially independent lithofacies bodies along the depositional profile. The increase of spatial disorder from the basin to bedding scale results from the influence of autocyclic factors on the transport and deposition of carbonate sediments. Scale-dependent types of carbonate heterogeneity are linked with the evaluation of algorithms in order to establish a modeling strategy that considers both the sedimentary characteristics of the outcrop and the modeling capabilities. A surface-based modeling approach was used to model depositional sequences. Facies associations were populated using TGSim to preserve ordered trends between depositional domains. At the lithofacies scale, a fully stochastic approach with SISim was applied to simulate a mosaic-like lithofacies distribution. This new workflow is designed to improve the simulation of carbonate rocks, based on the modeling of each scale of heterogeneity individually. Contrarily to simulation methods applied in literature, the present study considers that the use of one single simulation technique is unlikely to correctly model the natural patterns and variability of carbonate rocks. The implementation of different techniques customized for each level of the stratigraphic hierarchy provides the essential computing flexibility to model carbonate systems. Closer feedback between advances carried out in the field of Sedimentology and Computing Geoscience should be promoted during future outcrop simulations for the enhancement of 3-D geological models.},
  language  = {en}
}
@phdthesis{Adhikari2013,
  author    = {Adhikari, Rishi Ram},
  title     = {Quantification of total microbial biomass and metabolic activity in subsurface sediments},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-67773},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {Metabolically active microbial communities are present in a wide range of subsurface environments. Techniques like enumeration of microbial cells, activity measurements with radiotracer assays and the analysis of porewater constituents are currently being used to explore the subsurface biosphere, alongside with molecular biological analyses. However, many of these techniques reach their detection limits due to low microbial activity and abundance. Direct measurements of microbial turnover not just face issues of insufficient sensitivity, they only provide information about a single specific process but in sediments many different process can occur simultaneously. Therefore, the development of a new technique to measure total microbial activity would be a major improvement. A new tritium-based hydrogenase-enzyme assay appeared to be a promising tool to quantify total living biomass, even in low activity subsurface environments. In this PhD project total microbial biomass and microbial activity was quantified in different subsurface sediments using established techniques (cell enumeration and pore water geochemistry) as well as a new tritium-based hydrogenase enzyme assay. By using a large database of our own cell enumeration data from equatorial Pacific and north Pacific sediments and published data it was shown that the global geographic distribution of subseafloor sedimentary microbes varies between sites by 5 to 6 orders of magnitude and correlates with the sedimentation rate and distance from land. Based on these correlations, global subseafloor biomass was estimated to be 4.1 petagram-C and ~0.6 \% of Earth's total living biomass, which is significantly lower than previous estimates. Despite the massive reduction in biomass the subseafloor biosphere is still an important player in global biogeochemical cycles. To understand the relationship between microbial activity, abundance and organic matter flux into the sediment an expedition to the equatorial Pacific upwelling area and the north Pacific Gyre was carried out. Oxygen respiration rates in subseafloor sediments from the north Pacific Gyre, which are deposited at sedimentation rates of 1 mm per 1000 years, showed that microbial communities could survive for millions of years without fresh supply of organic carbon. Contrary to the north Pacific Gyre oxygen was completely depleted within the upper few millimeters to centimeters in sediments of the equatorial upwelling region due to a higher supply of organic matter and higher metabolic activity. So occurrence and variability of electron acceptors over depth and sites make the subsurface a complex environment for the quantification of total microbial activity. Recent studies showed that electron acceptor processes, which were previously thought to thermodynamically exclude each other can occur simultaneously. So in many cases a simple measure of the total microbial activity would be a better and more robust solution than assays for several specific processes, for example sulfate reduction rates or methanogenesis. Enzyme or molecular assays provide a more general approach as they target key metabolic compounds. Since hydrogenase enzymes are ubiquitous in microbes, the recently developed tritium-based hydrogenase radiotracer assay is applied to quantify hydrogenase enzyme activity as a parameter of total living cell activity. Hydrogenase enzyme activity was measured in sediments from different locations (Lake Van, Barents Sea, Equatorial Pacific and Gulf of Mexico). In sediment samples that contained nitrate, we found the lowest cell specific enzyme activity around 10^(-5) nmol H_(2) cell^(-1) d^(-1). With decreasing energy yield of the electron acceptor used, cell-specific hydrogenase activity increased and maximum values of up to 1 nmol H_(2) cell^(-1) d^(-1) were found in samples with methane concentrations of >10 ppm. Although hydrogenase activity cannot be converted directly into a turnover rate of a specific process, cell-specific activity factors can be used to identify specific metabolism and to quantify the metabolically active microbial population. In another study on sediments from the Nankai Trough microbial abundance and hydrogenase activity data show that both the habitat and the activity of subseafloor sedimentary microbial communities have been impacted by seismic activities. An increase in hydrogenase activity near the fault zone revealed that the microbial community was supplied with hydrogen as an energy source and that the microbes were specialized to hydrogen metabolism.},
  language  = {en}
}
@phdthesis{Abdelfadil2013,
  author    = {Abdelfadil, Khaled Mohamed},
  title     = {Geochemistry of Variscan lamprophyre magmatism in the Saxo-Thuringian Zone},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-68854},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {Lamprophyres are mantle-derived magmatic rocks, commonly occurring as dikes. They are readily identified from their field setting, petrography, chemical and mineralogical composition. These rocks not only provide important information on melting processes in the mantle, but also on geodynamic processes modifying the mantle. There are numerous occurrences of lamprophyres in the Saxo-Thuringian Zone of Variscan Central Europe, which are useful to track the variable effects of the Variscan orogeny on local mantle evolution. This work presents and evaluates the mineralogical, geochemical, and Sr-Nd-Pb isotopic data of late-Variscan calc-alkaline lamprophyres, post-Variscan ultramafic lamprophyres, of alkaline basalt from Lusatia, and, for comparison, of pre-Variscan gabbros. In addition, lithium isotopic signatures combined with Sr-Nd-Pb isotopic data of late-Variscan calc-alkaline lamprophyres from three different Variscan Domains (i.e., Erzgebirge, Lusatia, and Sudetes) are used to assess compositional changes of the mantle during Variscan orogeny.},
  language  = {de}
}