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In the present thesis the MBE growth and sample characterization of HgTe structures is investigated
and discussed. Due to the first experimental discovery of the quantum Spin Hall effect
(QSHE) in HgTe quantum wells, this material system attains a huge interest in the spintronics
society. Because of the long history of growing Hg-based heterostructures here at the Experimentelle
Physik III in Würzburg, there are very good requirements to analyze this material
system more precisely and in new directions. Since in former days only doped HgTe quantum
wells were grown, this thesis deals with the MBE growth in the (001) direction of undoped
HgTe quantum wells, surface located quantum wells and three dimensional bulk layers. All
Hg-based layers were grown on CdTe substrates which generate strain in the layer stack and
provide therefore new physical effects. In the same time, the (001) CdTe growth was investigated
on n-doped (001) GaAs:Si because the Japanese supplier of CdTe substrates had a
supply bottleneck due to the Tohoku earthquake and its aftermath in 2011.
After a short introduction of the material system, the experimental techniques were demonstrated
and explained explicitly. After that, the experimental part of this thesis is displayed.
So, the investigation of the (001) CdTe growth on (001) GaAs:Si is discussed in chapter 4.
Firstly, the surface preparation of GaAs:Si by oxide desorption is explored and analyzed.
Here, rapid thermal desorption of the GaAs oxide with following cool down in Zn atmosphere
provides the best results for the CdTe due to small holes at the surface, while e.g. an atomic
flat GaAs buffer deteriorates the CdTe growth quality. The following ZnTe layer supplies the
(001) growth direction of the CdTe and exhibits best end results of the CdTe for 30 seconds
growth time at a flux ratio of Zn/Te ~ 1/1.2. Without this ZnTe layer, CdTe will grow in the
(111) direction. However, the main investigation is here the optimization of the MBE growth
of CdTe. The substrate temperature, Cd/Te flux ratio and the growth time has to be adjusted
systematically. Therefore, a complex growth process is developed and established. This optimized
CdTe growth process results in a RMS roughness of around 2.5 nm and a FWHM value
of the HRXRD w-scan of 150 arcsec. Compared to the literature, there is no lower FWHM
value traceable for this growth direction. Furthermore, etch pit density measurements show
that the surface crystallinity is matchable with the commercial CdTe substrates (around 1x10^4
cm^(-2)). However, this whole process is not completely perfect and offers still room for improvements.
The growth of undoped HgTe quantum wells was also a new direction in research in contrast
to the previous n-doped grown HgTe quantum wells. Here in chapter 5, the goal of very low
carrier densities was achieved and therefore it is now possible to do transport experiments in
the n - and p - region by tuning the gate voltage. To achieve this high sample quality, very precise
growth of symmetric HgTe QWs and their HRXRD characterization is examined. Here,
the quantum well thickness can now determined accurate to under 0.3 nm. Furthermore, the transport analysis of different quantum well thicknesses shows that the carrier density and
mobility increase with rising HgTe layer thickness. However, it is found out that the band
gap of the HgTe QW closes indirectly at a thickness of 11.6 nm. This is caused by the tensile
strained growth on CdTe substrates. Moreover, surface quantum wells are studied. These
quantum wells exhibit no or a very thin HgCdTe cap. Though, oxidization and contamination
of the surface reduces here the carrier mobility immensely and a HgCdTe layer of around 5 nm
provides the pleasing results for transport experiments with superconductors connected to the
topological insulator [119]. A completely new achievement is the realization of MBE growth
of HgTe quantum wells on CdTe/GaAs:Si substrates. This is attended by the optimization of
the CdTe growth on GaAs:Si. It exposes that HgTe quantum wells grown in-situ on optimized
CdTe/GaAs:Si show very nice transport data with clear Hall plateaus, SdH oscillations, low
carrier densities and carrier mobilities up to 500 000 cm^2/Vs. Furthermore, a new oxide etching
process is developed and analyzed which should serve as an alternative to the standard
HCl process which generates volcano defects at some time. However, during the testing time
the result does not differ in Nomarski, HRXRD, AFM and transport measurements. Here,
long-time tests or etching and mounting in nitrogen atmosphere may provide new elaborate
results.
The main focus of this thesis is on the MBE growth and standard characterization of HgTe bulk
layers and is discussed in chapter 6. Due to the tensile strained growth on lattice mismatched
CdTe, HgTe bulk opens up a band gap of around 22 meV at the G-point and exhibits therefore
its topological surface states. The analysis of surface condition, roughness, crystalline quality,
carrier density and mobility via Nomarski, AFM, XPS, HRXRD and transport measurements
is therefore included in this work. Layer thickness dependence of carrier density and mobility
is identified for bulk layer grown directly on CdTe substrates. So, there is no clear correlation
visible between HgTe layer thickness and carrier density or mobility. So, the carrier density is
almost constant around 1x10^11 cm^(-2) at 0 V gate voltage. The carrier mobility of these bulk
samples however scatters between 5 000 and 60 000 cm^2/Vs almost randomly. Further experiments
should be made for a clearer understanding and therefore the avoidance of unusable
bad samples.But, other topological insulator materials show much higher carrier densities and
lower mobility values. For example, Bi2Se3 exhibits just density values around 1019 cm^(-2)
and mobility values clearly below 5000 cm2/Vs. The carrier density however depends much
on lithography and surface treatment after growth. Furthermore, the relaxation behavior and
critical thickness of HgTe grown on CdTe is determined and is in very good agreement with
theoretical prediction (d_c = 155 nm). The embedding of the HgTe bulk layer between HgCdTe
layers created a further huge improvement. Similar to the quantum well structures the carrier
mobility increases immensely while the carrier density levels at around 1x10^11 cm^(-2) at 0
V gate voltage as well. Additionally, the relaxation behavior and critical thickness of these
barrier layers has to be determined. HgCdTe grown on commercial CdTe shows a behavior as
predicted except the critical thickness which is slightly higher than expected (d_c = 850 nm).
Otherwise, the relaxation of HgCdTe grown on CdTe/GaAs:Si occurs in two parts. The layer
is fully strained up to 250 nm. Between 250 nm and 725 nm the HgCdTe film starts to relax
randomly up to 10 %. The relaxation behavior for thicknesses larger than 725 nm occurs than
linearly to the inverse layer thickness. A explanation is given due to rough interface conditions
and crystalline defects of the CdTe/GaAs:Si compared to the commercial CdTe substrate. HRXRD and AFM data support this statement. Another point is that the HgCdTe barriers protect the active HgTe layer and because of the high carrier mobilities the Hall measurements provide new transport data which have to be interpreted more in detail in the future. In addition, HgTe bulk samples show very interesting transport data by gating the sample from the top and the back. It is now possible to manipulate the carrier densities of the top and bottom surface states almost separately. The back gate consisting of the n-doped GaAs substrate and the thick insulating CdTe buffer can tune the carrier density for Delta(n) ~ 3x10^11 cm^(-2). This is sufficient to tune the Fermi energy from the p-type into the n-type region [138].
In this thesis it is shown that strained HgTe bulk layers exhibit superior transport data by embedding between HgCdTe barrier layers. The n-doped GaAs can here serve as a back gate.
Furthermore, MBE growth of high crystalline, undoped HgTe quantum wells shows also new
and extended transport output. Finally, it is notable that due to the investigated CdTe growth
on GaAs the Hg-based heterostructure MBE growth is partially independent from commercial
suppliers.
In this work, Emilio de’ Cavalieri’s musical sources will serve as a platform in an attempt to overcome the lack of explicit original guidance and guidelines of performance practice of early basso continuo. It will offer a methodology that will allow the unraveling of implicit theory and practice hidden in the music sources themselves. The methodology of this work is based on the fact that Cavalieri’s Rappresentatione di Anima e di Corpo (Rome, 1600) is printed using a unique continuo notation, which is detailed, precise, and coherent—more so than any other contemporaneous printed source. Through thorough investigation of this continuo notation, it will be possible to enrich our practical as well as theoretical knowledge of the early basso continuo. A wide range of evidences will emerge, covering a wide spectrum, from general questions of instrumentation up to the very notes that should be played. Using a special notation for illustration, I will demonstrate how Cavalieri’s basso continuo figuration, when combined with the known rules of counterpoint, is at times equivalent to written-out realizations.
As part of this study, different models of contrapuntal phenomena will be analyzed, mainly in the context of cadences but also in the context of other progressions that deserve to be recognized as formulas. Their theoretical structure will be uncovered as well as their actual application in music and their manner of execution. The prevalence of each phenomenon will be examined in order to distinguish common and recurrent phenomena from rarely-used formulas. In order to do this, and due to problematic historical terminology, it will be necessary to create a set of new terms inspired by Cavalieri’s notation. Those terms will not be solely relevant to Cavalieri’s music; the models were made flexible so that they may prove useful for future discussions or studies of early continuo in general.
Out of the known early basso continuo sources, a “mini-compendium” of practical implications will be extracted in order to exhaust the practical knowledge implicit in them. This endeavor will be concluded with a list of rules and general advice drawn from the sources, but it will also reveal some problematic aspects of these sources.
This endeavor will make it possible to compare the “new” implicit practical information deduced in this study with the explicit known continuo sources, and assess to what extant Cavalieri’s continuo practices illuminate and complement the known knowledge from previously-studied yet opaque sources of basso continuo.
The focus of this dissertation is on Cavalieri’s music, but the findings proposed here will be traced so as to illuminate the broader realm of the early Baroque and the 17th century musical style at large. Finally, this new research about Cavalieri’s music and continuo, along reevaluating of its place among the common continuo sources, calls for redistribution of source materials on the traditional “shelf” of early basso continuo sources.
Aspergillus fumigatus is the most common cause for invasive fungal infections, a disease associated with high mortality in immune-compromised patients. CD1d-restricted invariant Natural Killer T (iNKT) cells compose a small subset of T cells known to impact the immune response towards various infectious pathogens. To investigate the role of human iNKT cells during A. fumigatus infection, we studied their activation as determined by CD69 expression and cytokine production in response to distinct fungal morphotypes in the presence of different CD1d⁺ antigen presenting cells using flow cytometry and multiplex ELISA. Among CD1d⁺ subpopulations, CD1d⁺CD1c⁺ mDCs showed the highest potential to activate iNKT cells on a per cell basis. The presence of A. fumigatus decreased this effect of CD1d⁺CD1c⁺ mDCs on iNKT cells and led to reduced secretion of TNF-α, G-CSF and RANTES. Production of other Th1 and Th2 cytokines was not affected by the fungus, suggesting an immune-modulating function for human iNKT cells during A. fumigatus infection.
The controlled shaping of ultrashort laser pulses is a powerful technology and applied in many laser laboratories today. Most of the used pulse shapers are only able to produce linearly polarized pulses shaped in amplitude and phase. Some devices are also capable of producing limited time-varying polarization profiles, but they are not able to control the amplitude. However, for some state-of-the-art non-linear time-resolved methods, such as polarization-enhanced two-dimensional spectroscopy, the possibility of controlling the amplitude and the polarization simultaneously is desirable.
Over the last years, different concepts have been developed to overcome these restrictions and to manipulate the complete vector-field of an ultrashort laser pulse with independent control over all four degrees of freedom - phase, amplitude, orientation, and ellipticity. The aim of this work was to build such a vector-field shaper. While the basic concept used for our setup is based on previous designs reported in the literature, the goal was to develop an optimized optical design that minimizes artifacts, allowing for the generation of predefined polarization pulse sequences with the highest achievable accuracy.
In Chapter 3, different approaches reported in the literature for extended and unrestricted vector-field control were examined and compared in detail. Based on this analysis, we decided to follow the approach of modulating the spectral phase and amplitude of two perpendicularly polarized pulses independently from each other in two arms of an interferometer and recombining them to a single laser pulse to gain control over the complete vector field.
As described in Chapter 4, the setup consists of three functional groups: i) an optical component to generate and recombine the two polarized beams, ii) a 4f setup, and iii) a refracting telescope to direct the two beams under two different angles of incidence onto the grating of the 4f setup in a common-path geometry. This geometry was chosen to overcome potential phase instabilities of an interferometric vector-field shaper. Manipulating the two perpendicularly polarized pulses simultaneously within one 4f setup and using adjacent pixel groups of the same liquid-crystal spatial light modulator (LC SLM) for the two polarizations has the advantages that only a single dual-layer LC SLM is required and that a robust and compact setup was achieved. The shaping capabilities of the presented design were optimized by finding the best parameters for the setup through numerical calculations to adjust the frequency distributions for a broad spectrum of 740 – 880 nm. Instead of using a Wollaston prism as in previous designs, a thin-film polarizer (TFP) is utilized to generate and recombine the two orthogonally polarized beams. Artifacts such as angular dispersion and phase distortions along the beam profile which arise when a Wollaston prism is used were discussed. Furthermore, it was shown by ray-tracing simulations that in combination with a telescope and the 4f setup, a significant deformation of the beam profile would be present when using a Wollaston prism since a separation of the incoming and outgoing beam in height is needed. The ray-tracing simulations also showed that most optical aberrations of the setup are canceled out when the incoming and outgoing beams propagate in the exact same plane by inverting the beam paths. This was realized by employing a TFP in the so-called crossed-polarizer arrangement which has also the advantage that the polarization-dependent efficiencies of the TFP and the other optics are automatically compensated and that a high extinction ratio in the order of 15000:1 is reached. Chromatic aberrations are, however, not compensated by the crossed-polarizer arrangement. The ray-tracing simulations confirmed that these chromatic aberrations are mainly caused by the telescope and not by the cylindrical lens of the 4f setup. Nevertheless, in the experimentally used wavelength range of 780 – 816 nm, only minor distortions of the beam profile were observed, which were thus considered to be negligible in the presented setup.
The software implementation of the pulse shaper was reviewed in Chapter 5 of this thesis. In order to perform various experiments, five different parameterizations, accounting for the extended shaping capabilities of a vector-field shaper, were developed. The Pixel Basis, the Spectral Basis, and the Spectral Taylor Basis can generally be used in combination with an optimization algorithm and are therefore well suited for quantum control experiments. For multidimensional spectroscopy, the Polarized Four-Pulse Basis was established. With this parameterization pulse sequences with up to four subpulses can be created. The polarization state of each subpulse can be specified and the relative intensity, phase, and temporal delay between consecutive subpulses can be controlled. In addition, different software programs were introduced in Chapter 5 which are required to perform the experiments conducted in this work.
The experimental results were presented in Chapter 6. The frequency distribution across the LC SLM was measured proving that the optimal frequency distribution was realized experimentally. Furthermore, the excellent performance of the TFP was verified. In general, satellite pulses are emitted from the TFP due to multiple internal reflections. Various measurements demonstrated that these pulses are temporally separated by at least 4.05 ps from the main pulse and that they have vanishing intensity. The phase stability between the two arms of the presented common-path setup σ = 28.3 mrad (λ/222) over 60 minutes. To further improve this stability over very long measurement times, an on-the-fly phase reduction and stabilization (OPRAS) routine utilizing the pulse shaper itself was developed. This routine automatically produces a compressed pulse with a minimized relative phase between the two polarization components. A phase stability of σ = 31.9 mrad (λ/197) over nearly 24 hours was measured by employing OPRAS. Various pulse sequences exceeding the capabilities of conventional pulse shapers were generated and characterized. The experimental results proved that shaped pulses with arbitrary phase, amplitude, and polarization states can be created. In all cases very high agreement between the target parameters and the experimental data was achieved.
For the future use of the setup also possible modifications were suggested. These are not strictly required, but all of them could further improve the performance and flexibility of the setup. Firstly, it was illustrated how a “dual-output” of the setup can be realized. With this modification it would be possible to use the main intensity of the shaped pulse for an experiment while using a small fraction to characterize the pulse or to perform OPRAS simultaneously. Secondly, the basic idea of replacing the telescope by focusing mirrors in order to eliminate the chromatic aberrations was presented. Regarding the different parameterizations for vector-field shaping, some modifications increasing the flexibility of the implemented bases and the realization of a von Neumann Basis for the presented setup were proposed. In future experiments, the vector-field shaper will be used in conjunction with a photoemission electron microscope (PEEM). This approach combines the temporal resolution provided by ultrashort laser pulses with the high spatial resolution gained by electron microscopy in order to perform two-dimensional spectroscopy and coherent control on nanostructures with polarization-shaped femtosecond laser pulses. In combination with other chiral-sensitive experimental setups implemented earlier in our group, the vector-field shaper opens up new perspectives for chiral femtochemistry and chiral control.
The designed vector-field shaper meets all requirements to generate high-precision polarization-shaped multipulse sequences. These can be used to perform numerous polarization-sensitive experiments. Employing the OPRAS routine, a quasi-infinitely long phase stability is achieved and complex and elaborated long-term measurements can be carried out. The fact that OPRAS demands no additional hardware and that only a single dual-layer LC SLM and inexpensive optics are required allows the building of a vector-field shaper at comparatively low costs. We hope that with the detailed insights into the optical design process as well as into the software implementation given in this thesis, vector-field shaping will become a standard technique just as conventional pulse shaping in the upcoming years.
Following the early experiences in aviation, medical simulation has rapidly
evolved into one of the most novel educational tools of the last three decades. In addition to its
use in training individuals or teams in crisis resource management, simulation has been studied as
a tool to evaluate technical and non-technical skills of individuals as well as, more recently,
entire medical teams.
It is usually fairly difficult to obtain clinical reference data from critical events to refute
claims that the management of actual events fell below what could reasonably be expected and we
demonstrated the use of rank order statistics to calculate quantiles with confidence limits for
management times of critical obstetrical events using data from realistic simulation. This approach
could be used to describe the distribution of treatment times in order to assist in deciding what
performance may constitute an outlier. It can also identify particular challenges of clinical
practice and allow the development of educational curricula. While the information derived from
simulation has to be interpreted with a high degree of caution for a clinical context, it may
represent a further ‘added value’ or important step in establishing simulation as a training tool
and to provide information that could be used in an appropriate clinical context for adverse
events. Large amounts of data (such as from a simulation registry) would allow the calculation of
acceptable confidence intervals for the required
outcome parameters as well as actual tolerance limits.
In this work, Emilio de’ Cavalieri’s musical sources will serve as a platform in an attempt to overcome the lack of explicit original guidance and guidelines of performance practice of early basso continuo. It will offer a methodology that will allow the unraveling of implicit theory and practice hidden in the music sources themselves. The methodology of this work is based on the fact that Cavalieri’s Rappresentatione di Anima e di Corpo (Rome, 1600) is printed using a unique continuo notation, which is detailed, precise, and coherent—more so than any other contemporaneous printed source. Through thorough investigation of this continuo notation, it will be possible to enrich our practical as well as theoretical knowledge of the early basso continuo. A wide range of evidences will emerge, covering a wide spectrum, from general questions of instrumentation up to the very notes that should be played. Using a special notation for illustration, I will demonstrate how Cavalieri’s basso continuo figuration, when combined with the known rules of counterpoint, is at times equivalent to written-out realizations.
As part of this study, different models of contrapuntal phenomena will be analyzed, mainly in the context of cadences but also in the context of other progressions that deserve to be recognized as formulas. Their theoretical structure will be uncovered as well as their actual application in music and their manner of execution. The prevalence of each phenomenon will be examined in order to distinguish common and recurrent phenomena from rarely-used formulas. In order to do this, and due to problematic historical terminology, it will be necessary to create a set of new terms inspired by Cavalieri’s notation. Those terms will not be solely relevant to Cavalieri’s music; the models were made flexible so that they may prove useful for future discussions or studies of early continuo in general.
Out of the known early basso continuo sources, a “mini-compendium” of practical implications will be extracted in order to exhaust the practical knowledge implicit in them. This endeavor will be concluded with a list of rules and general advice drawn from the sources, but it will also reveal some problematic aspects of these sources.
This endeavor will make it possible to compare the “new” implicit practical information deduced in this study with the explicit known continuo sources, and assess to what extant Cavalieri’s continuo practices illuminate and complement the known knowledge from previously-studied yet opaque sources of basso continuo.
The focus of this dissertation is on Cavalieri’s music, but the findings proposed here will be traced so as to illuminate the broader realm of the early Baroque and the 17th century musical style at large. Finally, this new research about Cavalieri’s music and continuo, along reevaluating of its place among the common continuo sources, calls for redistribution of source materials on the traditional “shelf” of early basso continuo sources.
Environmental interlinked problems such as human-induced land cover change, water scarcity, loss in soil fertility, and anthropogenic climate change are expected to affect the viability of agriculture and increase food insecurity in many developing countries. Climate change is certainly the most serious of these challenges for the twenty-first century. The poorest regions of the world – tropical West Africa included – are the most vulnerable due to their high dependence on climate and weather sensitive activities such as agriculture, and the widespread poverty that limits the institutional and economic capacities to adapt to the new stresses brought about by climate change. Climate change is already acting negatively on the poor smallholders of tropical West Africa whose livelihoods dependent mainly on rain-fed agriculture that remains the cornerstone of the economy in the region. Adaptation of the agricultural systems to climate change effects is, therefore, crucial to secure the livelihoods of these rural communities. Since information is a key for decision-making, it is important to provide well-founded information on the magnitude of the impacts in order to design appropriate and sustainable adaptation strategies.
Considering the case of agricultural production in the Republic of Benin, this study aims at using large-scale climatic predictors to assess the potential impacts of past and future climate change on agricultural productivity at a country scale in West Africa. Climate signals from large-scale circulation were used because state-of-the art regional climate models (RCM) still do not perfectly resolve synoptic and mesoscale convective processes. It was hypothesised that in rain-fed systems with low investments in agricultural inputs, yield variations are widely governed by climatic factors. Starting with pineapple, a perennial fruit crops, the study further considered some annual crops such as cotton in the group of fibre crops, maize, sorghum and rice in the group of cereals, cowpeas and groundnuts belonging to the legume crops, and cassava and yams which are root and tuber crops. Thus the selected crops represented the three known groups of photosynthetic pathways (i.e. CAM, C3, and C4 plants).
In the study, use was made of the historical agricultural yield statistics for the Republic of Benin, observed precipitation and mean near-surface air temperature data from the Climatic Research Unit (CRU TS 3.1) and the corresponding variables simulated by the regional climate model (RCM) REMO. REMO RCM was driven at its boundaries by the global climate model ECHAM 5. Simulations with different greenhouse gas concentrations (SRES-A1B and B1 emission scenarios) and transient land cover change scenarios for present-day and future conditions were considered. The CRU data were submitted to empirical orthogonal functions analysis over the north hemispheric part of Africa to obtain large-scale observed climate predictors and associated consistent variability modes. REMO RCM data for the same region were projected on the derived climate patterns to get simulated climate predictors. By means of cross-validated Model Output Statistics (MOS) approach combined with Bayesian model averaging (BMA) techniques, the observed climate predictors and the crop predictand were further on used to derive robust statistical relationships. The robust statistical crop models perform well with high goodness-of-fit coefficients (e.g. for all combined crop models: 0.49 ≤ R2 ≤ 0.99; 0.28 ≤ Brier-Skill-Score ≤ 0.90).
Provided that REMO RCM captures the main features of the real African climate system and thus is able to reproduce its inter-annual variability, the time-independent statistical transfer functions were then used to translate future climate change signal from the simulated climate predictors into attainable crop yields/crop yield changes. The results confirm that precipitation and air temperature governed agricultural production in Benin in general, and particularly, pineapple yield variations are mainly influenced by temperature. Furthermore, the projected yield changes under future anthropogenic climate change during the first-half of the 21st century amount up to -12.5% for both maize and groundnuts, and -11%, -29%, -33% for pineapple, cassava, and cowpeas respectively. Meanwhile yield gain of up to +10% for sorghum and yams, +24% for cotton, and +39% for rice are expected. Over the time period 2001 – 2050, on average the future yield changes range between -3% and -13% under REMO SRES–B1 (GHG)+LCC, -2% and -11% under REMO SRES–A1B (GHG only),and -3% and -14% under REMO SRES–A1B (GHG)+LCC for pineapple, maize, sorghum, groundnuts, cowpeas and cassava. In the meantime for yams, cotton and rice, the average yield gains lie in interval of about +2% to +7% under REMO SRES–B1 (GHG)+LCC, +0.1% and +12% under REMO SRES–A1B (GHG only), and +3% and +10% under REMO SRES–A1B (GHG)+LCC. For sorghum, although the long-term average future yield depicts a reduction there are tendencies towards increasing yields in the future. The results also reveal that the increases in mean air temperature more than the changes in precipitation patterns are responsible for the projected yield changes. As well the results suggest that the reductions in pineapple yields cannot be attributed to the land cover/land use changes across sub-Saharan Africa. The production of groundnuts and in particular yams and cotton will profit from the on-going land use/land cover changes while the other crops will face detrimental effects.
Henceforth, policymakers should take effective measures to limit the on-going land degradation processes and all other anthropogenic actions responsible for temperature increase. Biotechnological improvement of the cultivated crop varieties towards development of set of seed varieties adapted to hotter and dry conditions should be included in the breeding pipeline programs. Amongst other solutions, application of appropriate climate-smart agricultural practices and conservation agriculture are also required to offset the negative impacts of climate change in agriculture.
Kinetic assessment by in vitro approaches - A contribution to reduce animals in toxicity testing
(2015)
The adoption of directives and regulations by the EU requires the development of alternative testing strategies as opposed to animal testing for risk assessment of xenobiotics. Additionally, high attrition rates of drugs late in the discovery phase demand improvement of current test batteries applied in the preclinical phase within the pharmaceutical area. These issues were taken up by the EU founded 7th Framework Program “Predict-IV”; with the overall goal to improve the predictability of safety of an investigational product, after repeated exposure, by integration of “omics” technologies applied on well established in vitro approaches. Three major target organs for drug-induced toxicity were in focus: liver, kidney and central nervous system. To relate obtained dynamic data with the in vivo situation, kinetics of the test compounds have to be evaluated and extrapolated by physiologically based pharmacokinetic modeling.
This thesis assessed in vitro kinetics of the selected test compounds (cyclosporine A, adefovir dipivoxil and cisplatinum) regarding their reliability and relevance to respective in vivo pharmacokinetics. Cells were exposed daily or every other day to the test compounds at two concentration levels (toxic and non-toxic) for up to 14 days. Concentrations of the test compounds or their major biotransformation products were determined by LC-MS/MS or ICP-MS in vehicle, media, cells and plastic adsorption samples generated at five different time-points on the first and the last treatment day.
Cyclosporine A bioaccumulation was evident in primary rat hepatocytes (PRH) at the high concentration, while efficient biotransformation mediated by CYP3A4 and CYP3A5 was determined in primary human hepatocytes (PHH) and HepaRG cells. The lower biotransformation in PRH is in accordance with observation made in vivo with the rat being a poor model for CYP3A biotransformation. Further, inter-assay variability was noticed in PHH caused by biological variability in CYP3A4 and CYP3A5 activity in human donors. The inter-assay variability observed for PRH and HepaRG cells was a result of differences between vehicles regarding their cyclosporine A content. Cyclosporine A biotransformation was more prominent in HepaRG cells due to stable and high CYP3A4 and CYP3A5 activity. In addition, in vitro clearances were calculated and scaled to in vivo. All scaled in vitro clearances were overestimated (PRH: 10-fold, PHH: 2-fold, HepaRG cells: 2-fold). These results should be proven by physiologically-based pharmacokinetic modeling and additional experiments, in order to verify that these overestimations are constant for each system and subsequently can be diminished by implementation of further scaling factors.
Brain cell cultures, primary neuronal culture of mouse cortex cells and primary aggregating rat brain cells, revealed fast achieved steady state levels of cyclosporine A. This indicates a chemical distribution of cyclosporine A between the aqueous and organic phases and only minor involvement of biological processes such as active transport and biotransformation. Hence, cyclosporine A uptake into cells is presumably transport mediated, supported by findings of transporter experiments performed on a parallel artificial membrane and Caco-2 cells. Plastic adsorption of cyclosporine A was significant, but different for each model, and should be considered by physiologically based pharmacokinetic modeling.
Kinetics of adefovir dipivoxil highlights the limits of in vitro approaches. Active transporters are required for adefovir uptake, but were not functional in RPTECT/TERT1. Therefore, adefovir uptake was limited to passive diffusion of adefovir dipivoxil, which itself degrades time-dependently under culture conditions.
Cisplatinum kinetics, studied in RPTEC/TERT1 cells, indicated intracellular enrichment of platinum, while significant bioaccumulation was not noted. This could be due to cisplatinum not reaching steady state levels within 14 days repeated exposure. As shown in vivo, active transport occurred from the basolateral to apical side, but with lower velocity. Hence, obtained data need to be modeled to estimate cellular processes, which can be scaled and compared to in vivo.
Repeated daily exposure to two different drug concentrations makes it possible to account for bioaccumulation at toxic concentrations or biotransformation/extrusion at non-toxic concentrations. Potential errors leading to misinterpretation of data were reduced by analyses of the vehicles as the applied drug concentrations do not necessarily correspond to the nominal concentrations. Finally, analyses of separate compartments (medium, cells, plastic) give insights into a compound’s distribution, reduce misprediction of cellular processes, e.g. biotransformation, and help to interpret kinetic data. On the other hand, the limits of in vitro approaches have also been pointed out. For correct extrapolation to in vivo, it is essential that the studied in vitro system exhibits the functionality of proteins, which play a key role in the specific drug induced toxicity. Considering the benefits and limitations, it is worth to validate this long-term treatment experimental set-up and expand it on co-culture systems and on organs-on-chips with regard to alternative toxicity testing strategies for repeated dose toxicity studies.
The purpose of confidence and prediction intervals is to provide an interval estimation for an unknown distribution parameter or the future value of a phenomenon. In many applications, prior knowledge about the distribution parameter is available, but rarely made use of, unless in a Bayesian framework. This thesis provides exact frequentist confidence intervals of minimal volume exploiting prior information. The scheme is applied to distribution parameters of the binomial and the Poisson distribution. The Bayesian approach to obtain intervals on a distribution parameter in form of credibility intervals is considered, with particular emphasis on the binomial distribution. An application of interval estimation is found in auditing, where two-sided intervals of Stringer type are meant to contain the mean of a zero-inflated population. In the context of time series analysis, covariates are supposed to improve the prediction of future values. Exponential smoothing with covariates as an extension of the popular forecasting method exponential smoothing is considered in this thesis. A double-seasonality version of it is applied to forecast hourly electricity load under the use of meteorological covariates. Different kinds of prediction intervals for exponential smoothing with covariates are formulated.
The main objective of this thesis was the design and synthesis of perylene bisimide dyes with sufficient water-solubility for the construction of self-assembled architectures in aqueous solutions. Beside these tasks another goal of this project was the control over the self-assembly process in terms of aggregate size and helicity, respectively. Within this thesis an appropriate synthesis for spermine-functionalized perylene bisimide dyes was developed and conducted successfully. The characterization of these building blocks and their course of self-assembly were investigated by NMR, UV/Vis and fluorescence spectroscopy as well as by atomic force and transmission electron microscopy. For the better understanding of the experimental results theoretical calculations were performed.