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Parsimonious Histograms
(2010)
The dissertation is concerned with the construction of data driven histograms. Histograms are the most elementary density estimators at all. However, they require the specification of the number and width of the bins. This thesis provides two new construction methods delivering adaptive histograms where the required parameters are determined automatically. Both methods follow the principle of parsimony, i.e. the histograms are solutions of predetermined optimization problems. In both cases, but under different aspects, the number of bins is minimized. The dissertation presents the algorithms that solve the optimization problems and illustrates them by a number of numerical experiments. Important properties of the estimators are shown. Finally, the new developed methods are compared with standard methods by an extensive simulation study. By means of synthetic samples of different size and distribution the histograms are evaluated by special performance criteria. As one main result, the proposed methods yield histograms with considerably fewer bins and with an excellent ability of peak detection.
With the development of new functional genomics methods that can access the whole genome, transcriptome, proteome and metabolome more comprehensive insights in cellular processes are possible. Largely based on these advances, our knowledge about molecular constituents for many organisms is increasing at a tremendous rate. Until today, the genomes of several organisms including pathogenic bacteria are already sequenced and pave the way for metabolic network constructions. Interest in metabolomics, the global profiling of metabolites in a cell, tissue or organism, has been rapidly increased. A range of analytical techniques, including nuclear magnetic resonance (NMR) spectroscopy, gas chromatography–mass spectrometry (GC–MS), liquid chromatography–mass spectrometry (LC–MS), Fourier Transform mass spectrometry (FT–MS), high performance liquid chromatography (HPLC) are required in order to maximize the number of metabolites that can be identified in a matrix. With the help of microbial metabolomics (qualification and quantification of a huge variety of metabolites from a bacterium) deciphering of the bacterial metabolism is feasible. The metabolome pipeline or workflow encompasses the processes of (i) sample generation and preparation, (ii) establishment of analytical techniques (iii) collection of analytical data, raw data pre-processing, (iv) data analysis and (v) data integration into biological questions. The present work contributes to the above mentioned steps in a metabolomics workflow. A specific focus was set to the exo- and endometabolome analysis of Gram-positive bacteria
Deciphering the entire protein complement of a living cell together with the elucidation of dynamic processes on protein level are the main goals of proteomics as it is used today. To achieve this goal, namely the elucidation of dynamic processes of the entire bacterial cell, we have developed strategies and distinct workflows to cover the most proteins in different subcellular localizations in bacteria together with a stable isotopes labeling approach to follow temporal and spatial changes in different proteomic subfractions. In this work, it has been shown that the use of mass spectrometry based in vivo quantitation techniques and the application of subcellular and chromatographic fractionation has lead to a new level of qualitative and quantitative proteomics data. Emphasizing on the studies revealing the dynamics of the bacterial physiology on a time resolved base, both spatial and temporal processes can be monitored to obtain knowledge on physiological processes in a depth that has not been reached before in comparable global studies.
A central point of this thesis is the investigation of surface structure and surface forces, which are created by single layers of linear polyelectrolytes (PE). In detail, the properties of cationic poly(allylamine)hydrochloride (PAH) and poly-l-lysine (PLL) and anionic sodium poly(styrene sulfonate) (PSS) are determined, which have been physisorbed onto oppositely charged silica surfaces in presence of a predefined salt concentration IAds. For these investigations, a new averaging method for colloidal probe (CP) force profiles is developed, which leads to an ultimate force resolution of 1 pN after the data processing, (signal to noise ratio of > 1000). Furthermore, a new kind of tapping mode imaging is presented (so called colloidal probe tapping mode, CPTM), which uses a CP instead of a sharp tip and hence which allows to resolve lateral inhomogeneously distributed surface forces. The basics to understand such-like obtained tapping mode images are developed. For adsorption from salt-free solution (IAds = 0) the dominance of an electrostatic double layer repulsion is observed, which is commonly attributed to the adsorption of the PE chains into a rather flat and compact layer and which is in full agreement with theoretical predictions and enormous experimental data available in literature. However, even a small addition of salt to the deposition solution (i.e. IAds > 1 mM NaCl) introduces a new contribution to the surface force, which is attributed to PE chains that are non-flatly physisorbed. Using scaling considerations, it is shown for all investigated PE that this non-flat conformation can be described by brush-like chain adsorption (cf. Section 3.3.5); other conformations like mushroom or pancake are excluded (cf. Section 5.3). Interestingly, these non-flatly physisorbed chains combine properties of neutral and PE brushes: (i) The force is very well described by the theory of Alexander and de Gennes (AdG, cf. Section 5.4). By fitting the AdG force law to the data, it is possible to determine the (brush) thickness L of the PE layer and the average distance s between brush-like physisorbed chains. Although the chains are charged the electrostatic contribution to the surface forces is too small to be noticeable (cf. Section 5.4.2). (ii) The thickness L of this PE layer is much larger compared to the compact layer (observed for salt-free adsorption) and is also subject to a pronounced swelling and shrinking if the bulk salt concentration I is decreased or increased, respectively. Surprisingly, all measurements indicate that L follows a scaling law known for salted end-grafted PE brushes, i.e. L ~ N (I s^2)^(-1/3) (with N denoting the degree of polymerization). Furthermore, the osmotic brush phase is never observed in the experiments, but chain stretching up to 1 / 3 of the contour length is regularly achieved. CPTM imaging applied to PSS shows that the brush-like physisorbed chains are not homogenously distributed over the surface, but form brush domains which coexist with flatly physisorbed chains (cf. sections 5.5 and 5.6). This clearly shows that PSS generally physisorbs in two distinct phases, which differ in conformation (flat vs. brush) and the surface force caused (electrostatic vs. steric repulsion). The force profile of the two phase system is in good approximation simply the superposition of a steric and an electrostatic repulsion, whereby their respective contribution to the composed force profile is given by their area fraction. The quantitative analysis reveals that L and s of the brush phase are independent on IAds. This is remarkable, as a change in IAds is known to induce a continuous transition between a stretched (low IAds) and coiled chain conformation (high IAds) in the deposition solution (cf. [Fleer1993, Yashiro2002]). Hence, one can conclude that the conformation in solution does not necessarily correspond to the conformation after adsorption. It is also shown that the area fraction A of the brush domains strongly depends on N and IAds. For example, for constant N the scaling relation A ~ sqrt(IAds) is determined, which is very similar to the common observation that the surface coverage %Gamma of adsorbed PE layers increases also with %Gamma ~ sqrt(IAds) [Schmitt1996, Cosgrove1986, Ahrens2001, Yim2000, Gopinadhan2007, Cornelson2010]. This suggest that brush-like physisorbed PE chains are responsible for the increase in %Gamma. In fact, Section 5.6 shows that the mass of the brush phase is approx. 0.5 mg/m² which is comparable to the increase in %Gamma reported in literature for IAds = 1 M NaCl [Cosgrove1986, Schmitt1996, Ahrens2001]. As a change in IAds does not affect L and s, but solely the brush area fraction A, it is argued in Section 5.6 that an increase in IAds can be understood as a phase transition from the (disordered) flat phase towards the (ordered and extended) brush phase. Here, further theoretical considerations would be desirable.
This thesis presents the results of experimental investigations of the vertical and lateral properties of polyelectrolyte multilayer films (PEMs) adsorbed on a solid support. PEMs are a new class of organic thin films based on self-assembly layer-by-layer (LbL) processes of oppositely charged polyelectrolytes (charged polymers). The LbL assembly technique allows precise control of film thickness within a few nanometers and makes PEM systems especially interesting for technical applications. Thin films are prepared by alternating exposure of a hydrophilic substrate to solutions of oppositely charged polyelectrolytes. In this work, synthetic polycation poly (allylamine hydrochloride) (PAH) and polyanion poly (styrene sulfonate) (PSS) have been used. Range and amplitude of the electrostatic force during PEM build-up, has been shielded by use of high salt concentration in the deposition solution. As a foundation of any theory, role of non-elecrostatic (secondary) forces is explored. Four complementary methods have been combined to investigate the properties and composition of PEMs. X-ray reflectivity is sensitive to electron density gradients, and therefore provides information about film thickness, average electron density and interfacial roughness between materials of different electron densities (like PEM and air). Neutrons are the unique probe that is sensitive to the internal order of the multilayers (scattering length density variation) due to selective deuteration of the layers (PSS replaced by PSS_d). Therefore neutron reflectivity at V6 beamline, at the research reactor BER II, Helmholtz Centre for Materials and Energy (former Hahn-Meitner-Institute), was used in this work. Ultraviolet-visible (UV-Vis) light induces the characteristic absorption peak of polyelectrolytes and metallic nanoparticles, therefore with UV-Vis absorption spectroscopy is possible to probe the aggregation of metallic nanoparticles embedded into PEM by measuring their absorption spectra (imaginary part of the refraction index). Atomic force microscopy (AFM) allows to observe lateral structures at nano-level and to obtain surface topology of the films. Application of only small forces (pN) is achieved by use of a intermittent contact (tapping) mode in air. Summarizing the main results, the unambiguous parametrization of the investigated system for neutron reflectivity measurements enables to obtain detailed information about internal interfaces. New approach for polyelectrolyte multilayer architectures consisting of thick protonated and deuterated blocks can be used in order to distinguish different zones of the thin film growth which can be described as precursor and core zones. Thus, almost no bound water is found in precursor layers at 0% relative humidity, which suggests that water is mobile and the precursor layer is not in the glassy state like in the central zone of the PEM. Swelling behaviour of the PEMs (reversibility of the swelling) can be understood in terms of equilibrium reactions. Explored influence of temperature and type of salt used during preparation contributes to a better understanding of the formation of PEMs. The dependence of the film thickness on preparation temperature, concentration and the type of salt can be described by the hydrophobic nature of the effect. Experimental observations demonstrate that it is possible to decrease both the range and the amplitude of the electrostatic force by using an ion concentration of at least 0.1 mol/L in the solution. The role of secondary interactions such as hydrophobic attraction of the chains that can overcome electrostatic repulsion and become the major contributing factor for the layer formation and resulting structures is emphasized.
Peatlands cover only about 3% of the terrestrial surface but are significant players in the global carbon (C) cycle and the climate system, since they store roughly one quarter of the global soil carbon (C) and are among the largest natural sources of methane (CH4). Since the resulting feedbacks on the climate system are uncertain, research efforts aim at identifying key processes and quantifying the C exchange from ecosystem to regional and global scales. To identify peatland ecosystem dynamics requires analysis of yet different scales. The key scale for their C dynamics is the microform scale, which is the smallest entity of the system. To estimate ecosystem dynamics, up-scaling from the microform scale is needed. Up-scaling demands (1) a correct estimation of the spatial heterogeneity and (2) the correct aggregation. In this thesis, the traditional spatial weighting of microform fluxes by the microform distribution is evaluated by (1) analyzing the flux calculation procedure, (2) investigating the effect of the resolution of the landcover maps on the up-scaling and by (3) cross-evaluating the up-scaling result with the directly measured ecosystem flux. Eventually, it is evaluated how these dynamics are considered in a mechanistic ecosystem model (LPJ-WHyMe). CH4 fluxes were measured on the microform scale with the closed chamber technique and on the ecosystem scale with the eddy covariance (EC) technique. The quantification of microform fluxes relies on the correct flux calculation. Since only few gas samples are taken during the closure period, traditionally the linear regression is applied when calculating CH4 fluxes from chamber measurements. Still, the chamber itself affects the diffusion gradient between peat and chamber atmosphere resulting in a theoretically non-linear concentration increase in the chamber. Using data with six data points per measurement from different microform types it is tested whether the linear or exponential regression fits the data better. In the majority of cases, the linear regression fits best. However, the exponential concentration change might still not be detectable resulting in an underestimation of the ’real‘ flux and the test of different techniqes to estimate the slope of a non-linear function with small sample amounts is recommended. To define the spatial heterogeneity of the peatland surface, the application of remote sensing techniques offer the advantage of supplying area-wide information with less uncertainty when compared to vegetation mapping along transects. However, the required resolution to resolve the microform distribution is <1m which in this study was derived from near-aerial photography. Besides for up-scaling, the resulting high-resolution landcover map was used in combination with a footprint model to analyze (1) the effect of landcover on the directly measured ecosystem flux and (2) its spatial representativeness. It was shown that fluctuations of the measured ecosystem flux over periods of several days could be explained by changes of the landcover composition in the source area of the EC measurements. The estimated budget was slightly biased towards the higher emissions from lawns which could be corrected. Still, the seasonal ecosystem CH4 budget was higher than the estimate derived from the up-scaling of microform fluxes. This is most likely due to an underestimation of microform fluxes by the chamber technique. Generally, the budget estimate derived from EC measurements was more accurate, i.e., characterized by less uncertainty than the up-scaled estimate. The developed approach depends on (1) identification and accurate measurements of all relevant microform types and (2) on spatial information which should be smaller than the footprint size of the EC measurements and available on the scale relevant for the studied process, i.e., the microform scale. The demonstrated effect of microform dynamics on the ecosystem flux highlights the importance of dealing with spatial heterogeneity of ecosystems in mechanistic modelling. For example, in LPJ-WHyMe, the ecosystem flux is simulated with mean input variables as water table level. To investigate its model performance, flux data from the rather homogeneous peatland margin and the more heterogeneous peatland centre were compared with the model output. At the homogeneous peatland margin, the ecosystem flux was clearly dominated (with a contribution of 91%) by one microform flux. In this case, one water table level as input variable could be used to estimate the ecosystem flux. However, for a heterogeneous site such as the peatland centre in this study, only one mean water table would simulate a mean microform flux but not the ecosystem flux. Consequently, it is recommended to incorporate at least one high-emitting and one low-emitting microform type in the model to increase the model performance.
This work proposes and experimentally evaluates a new method and the first prototypic design of an apparatus for the objective assessment of peripheral dynamic stereovision. Peripheral dynamic stereovision is understood as the ability to perceive, recognize and observe moving objects in the visual periphery without sacrificing foveal fixation, i.e. shifting the line of sight (e.g. moving the eyes or the head) and loosing attention to the scene of interest. The presence of stereopsis on top further enhances the perceptive quality by adding the third dimension with judgment of depth and estimation of relative spatial positions as central clues for orientation, coordinative interaction and navigation in space. Based on findings that moving stereoscopic contours can induce distinctive optokinetic reactions, a panoramic stimulus pattern was rotated round subjects’ heads. Designed after the Frisby Stereotest, solely the binocular parallax resulting from the plate thickness carries stereoscopic information, excluding all other depth clues. A specially fitted goggle frame assured correct binocular alignment of the subjects adding objectivity. In first experiments, voluntary reactions (pushing a buzzer button) and involuntarily triggered ocular responses have been registered. The Performance Level (PL) and Confidence Ratio (CR) were introduced as benchmarks for voluntary reactions. Despite larger spreads, the PL averaged at 60 % while an elevated CR confirmed a low error rate of 16 % and thus high overall credibility. Poor performance of available recording hard- and software, in many cases, rendered the analysis of involuntary ocular reactions less exhaustive. It was however observable that objects that appear in the periphery of the visual field triggered the onset of nystagmoid search and tracking mechanisms. Finally, mean peripheral locations of subjects’ active reactions have been established at 30 degrees. The outcome of this pilot study in principle confirmed basic feasibility, conceptual validity and practical applicability of this novel method. Prospective fields of application with raised demands on peripheral dynamic stereopsis have been identified and critically assessed. The applicative possibilities and exclusive advantages of this test combining the assessment of stereopsis and dynamic visual field testing have not been matched by solutions published so far. Before however commercialization should be aimed at, design-related issues, including the implementation of electrophysiological ocular measurements, need to be addressed first to lead the post-prototype development to higher diagnostic expressiveness and reliability.
To uncover the genetic structure of Populus euphratica forests along the Tarim River in Xinjiang, China, a PCR set of eight microsatellite markers was established. 18 primer pairs originally developed for P. tremuloides and P. trichocarpa were screened for amplification in P. euphratica. The eight most variable loci were selected for further genotyping experiments. Subsequently, two multiplex PCR assays, each containing four loci, were set up and optimized. Three populations containing altogether 436 trees were used to characterize the selected loci. The set was found to be moderately polymorphic (mean expected heterozygosity = 0.57). The resolution was sufficient to discriminate even siblings with high confidence (PID = 1.81x10-5). Cumulative exclusion probabilities were 0.89 (single parent), 0.98 (paternity), and 1.00 (parent pair) and proved the set’s suitability for parentage analysis. Practical and theoretical analysis of consequences of genotyping errors in this semi-clonal plant showed that the vast majority of errors (62.1%) lead to division of identical genotypes. Merging of different genotypes was found to be a very rare case (0.4%). This always leads to an overestimation of genotypes. A similarity threshold of one allele difference between two genotypes to be regarded as being identical lead to an underestimation of clonal richness and genotype number of one per cent compared to an overestimation of more than 20 per cent without such a threshold. Allowing a certain amount of variation is therefore expected to reflect the clonal structure better than an analysis that considers exact matches only. Using a combination of morphological and molecular analyses, a first study demonstrated that root suckers are clearly distinguished from seedlings in their root architecture. Root suckering starts when trees are 10–15 years old and bridges distances of up to 40 m at a time. Root suckers depend on their parent tree for at least five years and are expected to have a higher mortality than generatively grown trees. Molecular analysis of old growth stands revealed a highly variable proportion of clonal growth between different stands. In the study area, the proportion of clonality decreases with distance to the main river bed (R = 0.31 at the site closest to the main river, R = 0.97 at the site farthest away from the river). An analysis of the history of river movements at different sites indicates a dependency of clonal growth on the frequency of ground water replenishment by the yearly floods. Genetic differentiation among the stands in the study area is low (FST = 0.055), and isolation by distance was not detectable (P = 0.058). Also, the river does not function as a vector for directed gene flow in downstream direction (P > 0.11). The forests are therefore considered to be one large panmictic metapopulation with unrestricted gene flow. Clonal growth does not lead to higher final stand densities (P = 0.99) and is obviously not of crucial importance for stand survival. Furthermore, analysis of vitality measures and size differences indicate that root suckers are in disadvantage both in vitality and in survival rate compared to seedlings. In this light, a possible function of clonal growth as a luxury strategy to enhance a genetic individual’s reproduction success under good site conditions can be discussed. The genetic structure of the (meta)population bears direct implications for management and conversation of the Tugai forest in Xinjiang. Due to the low degree of differentiation and the unhindered gene flow even small, fragmented, or isolated populations have conservational value, thereby clearly answering the SLOSS question (a single large or several small protected areas) in the latter sense. More than that, non-clonal stands with the highest amount of genotypic diversity can be easily identified on satellite and aerial images. Selection of such stands for conservation is therefore possible without expensive and time-consuming molecular analyses.
Diabetes mellitus has been linked with an increased risk for oral diseases, especially periodontitis. However, studies results were not consistent. The present study was conducted to evaluate whether both type 1 (T1DM) and type 2 diabetes mellitus (T2DM) are associated with increased prevalence and extent of periodontal disease and tooth loss compared with non-diabetic subjects within a homogeneous adult study population. T1DM, T2DM and non-diabetic subjects were recruited from the population-based Study of Health in Pomerania (SHIP). Additionally, T1DM subjects were retrieved from a Diabetes Centre in the same region. The total study population comprised 145 T1DM and 2,647 non-diabetic subjects aged 20-59 years, and 182 T2DM and 1,314 non-diabetic subjects aged 50-81 years. Multivariable regression revealed an association between T1DM and mean attachment loss (B=0.40 [95% CI; 0.19, 0.61], adjusted). Also, T1DM was positively associated with increased number of missing teeth after full adjustment (p<0.001). The association between T1DM and tooth loss was enhanced in subjects aged 40-49 and 50-59 years (p for interaction=0.01). In T2DM subjects, mean attachment loss was significantly higher compared with non-diabetic subjects (B=0.47 [95% CI; 0.21, 0.73], adjusted). The effect of T2DM was significantly enhanced in 60-69-years-old subjects (p for interaction=0.04). The association between T2DM and number of missing teeth was not statistically significant after adjustment (p=0.25). Analyses showed that the effect of T2DM on tooth loss was pronounced in females compared with males (p for interaction=0.01). In accordance with previous literature, present results suggested that periodontal diseases and tooth loss can been seen as a complication of both types of diabetes. Generally, periodontal diseases are preventable and treatable. Therefore, appropriate goals and strategies for improving periodontal health in subjects with diabetes need to be developed. Further, early detection and careful managed therapeutics with the physician and dentist working hand-in-hand may prove beneficial to the patient–s general health.
The objectives of the present work are to relate the spatial distribution of benthic macrofauna in the Baltic Sea to patterns in environmental variables describing near-bottom hydrographical conditions and sediment characteristics, analyzing the data for two various spatial extents. The first case study is devoted to an exploratory statistical description of the prevailing ecological structure within the limited area attached to the region of the Mecklenburg Bight. Key environmental descriptors of spatial distribution of macrofaunal communities were disclosed within the area of investigation: water depth, regarded as a proxy for other environmental factors, and total organic content. Distinct benthic assemblages that are discriminated by particular species (Hydrobia ulvae–Scoloplos armiger, Lagis koreni–Mysella bidentata and Capitella capitata–Halicryptus spinulosus) were defined. Each assemblage is related to different spatial subarea and is characterized by a certain variability of environmental factors. This study represented the basis for the predictive modelling of species distribution in the selected investigation area, which constituted the next part of the investigation. Species-specific models predicting the probability of occurrence relative to environmental and sedimentological characteristics were developed for 29 representative macrofaunal species using a logistic regression modelling approach. Subsequently, the technique for a predictive modelling of species distributions in response to abiotic parameters based on single-factor logistic regression models, utilizing Akaike’s information criterion (AIC) and Akaike weights for multimodel inference, was used. Thus, probabilities of occurrence for selected exemplary species (Arctica islandica, Hediste diversicolor, Pygospio elegans, Tubificoides benedii and Scoloplos armiger) were modelled and mapped. Finally, the investigation proceeded on a large spatial scale. The discriminating ability of such factors as salinity, bathymetry, and sediment characteristics (considered only generally due to the lack of more detailed data) to explain the occurrence of typical macrozoobenthic species on the Baltic Sea-wide extend was tested. Full coverage macrofauna distribution maps, though being increasingly demanded, are generally lacking, with information being merely restricted to point observations. In contrast to spatial interpolation, periled by presence of short distance changes in community structure and dependence of the result on density of the samples, predictive habitat suitability modelling allows to objectively produce distribution maps at a level of detail limited only by the availability and resolution of the environmental data. Various literature sources and available databases were analyzed in respect to the information on macrozoobenthos distribution in the Baltic Sea, resulting in the compilation of an extensive list of taxa and an inventory dataset on species distribution for the whole Baltic Sea. The study demonstrates the need to analyze species’ relationships in gradient systems such as the Baltic Sea and provides a basis for a tool to predict natural and anthropogenic forced changes in species distribution.