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In this paper we discuss experimental evidence related to the structure and origin of the bosonic spectral function alpha 2F (omega) in high-temperature superconducting (HTSC) cuprates at and near optimal doping. Global properties of alpha 2F (omega), such as number and positions of peaks, are extracted by combining optics, neutron scattering, ARPES and tunnelling measurements. These methods give evidence for strong electron-phonon interaction (EPI) with 1<lambda ep <~ 3.5 in cuprates near optimal doping. We clarify how these results are in favor of the modified Migdal-Eliashberg (ME) theory for HTSC cuprates near optimal doping. In Section 2 we discuss theoretical ingredients—such as strong EPI, strong correlations—which are necessary to explain the mechanism of d-wave pairing in optimally doped cuprates. These comprise the ME theory for EPI in strongly correlated systems which give rise to the forward scattering peak. The latter is supported by the long-range part of EPI due to the weakly screened Madelung interaction in the ionic-metallic structure of layered HTSC cuprates. In this approach EPI is responsible for the strength of pairing while the residual Coulomb interaction and spin fluctuations trigger the d-wave pairing.
Background: Current conventional vaccination approaches do not induce potent CD8 T-cell responses for fighting mostly variable viral diseases such as influenza, avian influenza viruses or HIV. Following our recent study on vaccine penetration by targeting of vaccine to human hair follicular ducts surrounded by Langerhans cells, we tested in the first randomized Phase-Ia trial based on hair follicle penetration (namely transcutaneous route) the induction of virus-specific CD8 T cell responses. Methods and Findings: We chose the inactivated influenza vaccine – a conventional licensed tetanus/influenza (TETAGRIP®) vaccine – to compare the safety and immunogenicity of transcutaneous (TC) versus IM immunization in two randomized controlled, multi-center Phase I trials including 24 healthy-volunteers and 12 HIV-infected patients. Vaccination was performed by application of inactivated influenza vaccine according to a standard protocol allowing the opening of the hair duct for the TC route or needle-injection for the IM route. We demonstrated that the safety of the two routes was similar. We showed the superiority of TC application, but not the IM route, to induce a significant increase in influenza-specific CD8 cytokine-producing cells in healthy-volunteers and in HIV-infected patients. However, these routes did not differ significantly for the induction of influenza-specific CD4 responses, and neutralizing antibodies were induced only by the IM route. The CD8 cell response is thus the major immune response observed after TC vaccination. Conclusions: This Phase Ia clinical trial (Manon05) testing an anti-influenza vaccine demonstrated that vaccines designed for antibody induction by the IM route, generate vaccine-specific CD8 T cells when administered transcutaneously. These results underline the necessity of adapting vaccination strategies to control complex infectious diseases when CD8 cellular responses are crucial. Our work opens up a key area for the development of preventive and therapeutic vaccines for diseases in which CD8 cells play a crucial role.
Purpose. The aim of this prospective longitudinal clinical pilot study was the evaluation of the effect on the Oral Health Impact Profile (OHIP) and patient-centered results of the envelope technique for Connective Tissue Graft (CTG). Methods. Sixteen patients (11 females) 24 to 71 years of age (42.6±11.1) received CTG that had been harvested from the palate and grafted using the envelope technique. Prior to and 3 months after surgery, all patients were examined clinically, completed the OHIP-G49 questionnaire, and were asked to judge the results of surgery. Results. Mean baseline recession depth of 2.5±0.8 mm was reduced by 1.2±0.9 mm (P<.001). Root coverage amounted to 48±39%. In 5 of 16 defects complete root coverage was achieved. Pain at the donor site was more pronounced than at recipient site regarding prevalence (8/6; P=.007), intensity (2.1±2.3/1.1±1.9 [visual analogue scale]; P=.016), and duration (1.4±2.3/0.8±1.4 days; P=.042). Baseline OHIP (15.7±12.1) was decreased by 3.6±8.5 three months after surgery (P=.139). Thirteen patients (81%) would undergo CTG surgery for similar reasons again. Conclusions. Root coverage using CTG according to the envelope technique provided improvement of OHIP as early as 3 months after surgery. Over all, patients were reasonably satisfied with the surgical technique and its results.
In my dissertation I study the transmission of monetary and fiscal policy in New Keynesian DSGE models. In the first chapter we revisit the exchange rate channel in a two-country model of the U.S. and a panel of industrialized countries to analyse how monetary policy transmission in the U.S. changes if it becomes more trade integrated. We find that more openness lowers the sacrifice ratio, although the effect is quantitatively small and depends on the pricing of the firms. In the second chapter we simulate the impact of the U.S. fiscal stimulus package in 2009 on GDP. We find that the government spendingmultiplier is well below 1. The finding is robust to including rule-of-thumb consumers and simulating the stimulus in the recent recession. In the third chapter we collect the fiscal stimulus measures in the eleven biggest countries of the euro area. Then we do a robustness study by simulating the european package in five different models of the euro area. The macroeconomic models vary in terms of backward-looking decision making of the agents and openness. Our findings provide no support for a Keynesian multiplier. Instead they suggest that additional government spending will reduce private spending for consumption and investment purposes. If government spending faces an implementation lag, the initial effect on GDP may even be negative. In the fourth chapter I estimate a DSGE model for Germany and compute forecasts for the debt-to-GDP ratio. I find that the expected economic recovery will lead to a decrease in Germany’s indebtedness in the medium-term given that policy makers stick to the fiscal policy rules.
Lipid rafts are specialized plasma membrane micro-domains highly enriched in cholesterol, sphingolipids and glycosylphosphatidylinositol (GPI) anchored proteins. Lipid rafts are thought to be located in the exofacial leaflet of plasma membranes. Functionally, lipid rafts are involved in intracellular trafficking of proteins and lipids, secretory and endocytotic pathways, signal transduction, inflammation and in cell-surface proteolysis. There has been substantial interest in lipid rafts in brain, both with respect to normal functioning and with certain neurodegenerative diseases. Based on the impact of lipid rafts on multitude biochemical pathways, modulation of lipid rafts is used to study related disease pathways and probably offers a target for pharmacological intervention. Lipid rafts can be targeted by modulation of its main components, namely cholesterol and sphingolipids. Other approaches include the modulation of membrane dynamics and it has been reported that protein-lipid interactions can vary the occurrence and composition of these membrane micro-domains. The present review summarizes the possibilities to modulate lipid rafts with focus on neuronal cells. Keywords: Lipid raft, cholesterol, membrane fluidity, statin, cyclodextrine, docosahexaenoic acid.
Planning problems, like real-world planning and scheduling problems, are complex tasks. As an efficient strategy for handing such problems is the ‘divide and conquer’ strategy has been identified. Each sub problem is then solved independently. Typically the sub problems are solved in a linear way. This approach enables the generation of sub-optimal plans for a number of real world problems. Today, this approach is widely accepted and has been established e.g. in the organizational structure of companies. But existing interdependencies between the sub problems are not sufficiently regarded, as each problem are solved sequentially and no feedback information is given. The field of coordination has been covered by a number of academic fields, like the distributed artificial intelligence, economics or game theory. An important result is, that there exist no method that leads to optimal results in any given coordination problem. Consequently, a suitable coordination mechanism has to be identified for each single coordination problem. Up to now, there exists no process for the selection of a coordination mechanism, neither in the engineering of distributed systems nor in agent oriented software engineering. Within the scope of this work the ECo process is presented, that address exactly this selection problem. The Eco process contains the following five steps. • Modeling of the coordination problem • Defining the coordination requirements • Selection / Design of the coordination mechanism • Implementation • Evaluation Each of these steps is detailed in the thesis. The modeling has to be done to enable a systemic analysis of the coordination problem. Coordination mechanisms have to respect the given situation and the context in which the coordination has to be done. The requirements imposed by the context of the coordination problem are formalized in the coordination requirements. The selection process is driven by these coordination requirements. Using the requirements as a distinction for the selection of a coordination mechanism is a central aspect of this thesis. Additionally these requirements can be used for documentation of design decisions. Therefore, it is reasonable to annotate the coordination mechanisms with the coordination requirements they fulfill and fail to ease the selection process, for a given situation. For that reason we present a new classification scheme for coordination methods within this thesis that classifies existing coordination methods according to a set of criteria that has been identified as important for the distinction between different coordination methods. The implementation phase of the ECo process is supported by the CoPS process and CoPS framework that has been developed within this thesis, as well. The CoPS process structures the design making that has to be done during the implementation phase. The CoPS framework provides a set of basic features software agents need for realizing the selected coordination method. Within the CoPS process techniques are presented for the design and implementation of conversations between agents that can be applied not only within the context of the coordination of planning systems, but for multiagent systems in general. The ECo-CoPS approach has been successfully validated in two case studies from the logistic domain.
Therapy of hemorrhagic shock with following resuscitation-induced liver injury : in vivo study
(2010)
Shock resulting from life-threatening blood-loss (hemorrhagic shock) represents the most frequent injury pattern after a traumatic insult. Hemorrhagic shock induces inflammatory changes, characterized by highly complex pathophysiological pathways often resulting in death. In this study, we establish an experimental in vivo model of H/R in rats and study the mechanisms which determine the hepatic injury after H/R. Furthermore, we show that hemorrhagic shock with following resuscitation is accompanied with release of systemic and local pro-inflammatory mediators, increased infiltration of hepatic neutrophils in the liver, increased oxidative and nitrosative stress, enhanced cell death of both types, apoptosis and necrosis, conspicuous cytoskeletal rearrangements, loss of hepatic integrity and finally high general mortality rates, up to 80%. In addition, the effects of two potential therapeutic interventions to prevent the H/R induced liver injury are explored in a model of H/R in rats. First, the role of JNK and its inhibition by D-JNKI-1 in preservation of hepatic integrity following H/R was analyzed. Second, we investigated the potential of simvastatin to prevent the disturbed inflammatory response and hepatic injury after H/R. The effects of both therapeutic interventions were studied by looking at several inflammatory parameters, markers of oxidative and nitrosative stress, cytoskeleton integrity, microcirculatory parameters, underlying signaling cascades, liver damage and mortality. Highly specific blockade of JNK with the potent, inhibitory peptide D-JNKI-1 revealed the crucial role of the JNK signaling pathway in the H/R induced pathophysiology and strong protective effects of DJNKI- 1 in H/R induced liver injury, when the peptide was applied before and even after hemorrhagic shock. The other therapeutic intervention tested in this study was the use of simvastatin which also revealed protective effects after H/R and even a remarkable improvement in survival after H/R. We show that H/R induced release of pro-inflammatory cytokines, hepatic PMNL infiltration, increased oxidative and nitrosative stress, apoptosis and necrosis can be diminished by treatment with D-JNKI-1 but also with simvastatin in vivo. Furthermore, simvastatin reduces H/R induced cytoskelatal rearrangements, loss of liver integrity and the mortality rate after H/R. The key pathway which underlies these beneficial effects of simvastatin is the Rho kinase pathway. Identification of both mechanisms as well as the effectiveness of both substances provide new insights in the close interaction between hypoxia and the immune system and present a promising basis for the anti-inflammatory, hepatoprotective treatment after H/R.
One of the earliest and most striking observations made about HIV is the extensive genetic variation that the virus has within individual hosts, particularly in the hypervariable regions of the env gene which is divided into 5 variable regions (V1-V5) and 5 more constant (C1-C5) regions. HIV evolves at any time over the course of an individual’s infection and infected individuals harbours a population of genetically related but non-identical viruses that are under constant change and ready to adapt to changes in their environment. These genetically heterogeneous populations of closely related genomes are called quasispecies [65]. Tuberculosis or tubercle forming disease is an acute and/or chronic bacterial infection that primarily attacks the lungs, but which may also affect the kidneys, bones, lymph nodes, and brain. The disease is caused by Mycobacterium tuberculosis (MTB), a slow growing rod-shaped, acid fast bacterium. It is transmitted from person to person through inhalation of bacteria-carrying air droplets. Worldwide, one person out of three is infected with Mycobacterium tuberculosis – two billion people in total. TB currently holds the seventh place in the global ranking of causes of death [73]. In 2008, there were an estimated 9.4 (range, 8.9–9.9 million) million incident cases (equivalent to 139 cases per 100 000 population) of TB globally [75]. A complex biological interplay occurs between M. tuberculosis and HIV in coinfected host that results in the worsening of both pathologies. HIV promotes progression of M. tuberculosis either by endogenous reactivation or exogenous reinfection [77, 78] and, the course of HIV-1 infection is accelerated subsequent to the development of TB [80]. Active TB is associated with an increase in intra-patient HIV-1 diversity both systemically and at the infected lung sites [64,122]. The sustainability or reversal of the HIV-1 quasispecies heterogeneity after TB treatment is not known. Tetanus toxoid vaccinated HIV-1 infected patients developed a transient increase in HIV-1 heterogeneity which was reversed after few weeks [121]. Emergence of a heterogeneous HIV-1 population within a patient may be one of the mechanisms to escape strong immune or drug pressure [65,128]. The existence of better fitting and/or immune escape HIV-variants can lead to an increase in HIV-1 replication [129,130]. It might be that TB favourably selected HIV-1 variants which are sources for consistent HIV-1 replication. Understanding the mechanisms underlying the impacts of TB on HIV-1 is essential for the development of effective measures to reduce TB related morbidity and mortality in HIV-1 infected individuals. In the present study we studied whether the increase in HIV-1 quasispecies diversity during active TB is reversed or preserved throughout the course of antituberculous chemotherapy. For this purpose Two time point HIV-1 quasispecies were evaluated by comparing HIV-1 infected patients with active tuberculosis (HIV-1/TB) and HIV-1 infected patients without tuberculosis (HIV-1/non TB). Plasma samples were obtained from the Frankfurt HIV cohort and HIV-1 RNA was isolated. C2V5 env was amplified by PCR and molecular cloning was performed. Eight to twenty five clones were sequenced from each patient. Various phylogenetic analyses were performed including tree inferences, intra-patient viral diversity and divergence, selective pressure, co-receptor usage prediction and two time point identity of quasispecies comparison using Mantel’s test. We found out from this study that: 1) Active TB sustains HIV-1 quasispecies diversity for longer period 2. Active TB increases the rate of HIV-1 divergence 3) TB might slow down evolution of X4 variants And we concluded that active TB has an impact on HIV-1 viral diversity and divergence over time. The influence of active TB on longitudinal evolution of HIV- 1 may be predominant for R5 viruses. The use of CCR5-coreceptor inhibitors for HIV-1/TB patients as therapeutic approach needs further investigation.
Background: New drugs are constantly sought after to improve the survival of patients with malignant gliomas. The ideal substance would selectively target tumor cells without eliciting toxic side effects. Here, we report on the anti-proliferative, anti-migratory, and anti-invasive properties of the natural, nontoxic compound Curcumin observed in five human glioblastoma (GBM) cell lines in vitro. Methods: We used monolayer wound healing assays, modified Boyden chamber trans-well assays, and cell growth assays to quantify cell migration, invasion, and proliferation in the absence or presence of Curcumin at various concentrations. Levels of the transcription factor phospho-STAT3, a potential target of Curcumin, were determined by sandwich-ELISA. Subsequent effects on transcription of genes regulating the cell cycle were analyzed by quantitative real-time PCR. Effects on apoptosis were determined by caspase assays. Results: Curcumin potently inhibited GBM cell proliferation as well as migration and invasion in all cell lines contingent on dose. Simultaneously, levels of the biologically active phospho-STAT3 were decreased and correlated with reduced transcription of the cell cycle regulating gene c-Myc and proliferation marking Ki-67, pointing to a potential mechanism by which Curcumin slows tumor growth. Conclusions: Curcumin is part of the diet of millions of people every day and is without known toxic side effects. Our data show that Curcumin bears anti-proliferative, anti-migratory, and anti-invasive properties against GBM cells in vitro. These results warrant further in vivo analyses and indicate a potential role of Curcumin in the treatment of malignant gliomas.
This dissertation introduces in chapter 1 a new comparative approach to model-based research and policy analysis by constructing an archive of business cycle models. It includes many well-known models used in academia and at policy institutions. A computational platform is created that allows straightforward comparisons of models’ implications for monetary and fiscal stabilization policies. Chapter 2 applies business cycle models to forecasting. Several New Keynesian models are estimated on historical U.S. data vintages and forecasts are computed for the five most recent recessions. The extent of forecast heterogeneity for models and professional forecasts is analysed. Chapter 3 extends the forecasting analysis to a long sample and to the evaluation of density forecasts. Weighted forecasts are computed using a variety of weighting schemes. The accuracy of forecasts is evaluated and compared to professional forecasts and forecasts from nonstructural time series methods. Chapter 4 adds a new feature to existing business cycle models. Specifically, a medium-scale New Keynesian model is constructed that allows for strategic complementarities in price-setting. The role of trade integration for monetary policy transmission is explored. A new dimension of the exchange rate channel is highlighted by which monetary policy directly impacts domestic inflation. Chapter 5 tests whether simple symmetric monetary policy rules used in most business cycle models are a sufficient description of reality. I use quantile regressions to estimate policy parameters and find asymmetric reactions to inflation, the output gap and past interest rates.
In the following Magisterarbeit I am going to develop a Concept Empiricist model of conceptual thought, which is in its technical core primarily inspired and motivated by Larry Barsalou‘ s Perceptual Symbol Systems Theory (PSST) (1999, 2008a). But it is not a theory of concepts in the genuine sense only, but it also expands naturally on related topics like the ontology of mind and the problem of intentionality. This is not arbitrarily chosen, but a natural consequence of any contemporary Concept Empiricist theory, for those theories are in kind direct outgrowths of an embodied approach to cognition which yields these consequences – the natural extension to related topics – as will be shown. The roadmap for the Magisterarbeit is going to look like this: First I will delineate the embodied cognition framework. Within embodied cognition there is a plethora of differing attempts at explaining the diverse phenomena of higher and lower cognition which differ in the meanwhile tremendously from each other. Therefore it will be very useful to set clear boundaries between the differing approaches, which range from strong neural embodiment on the one side to a very promiscuous extended mind hypothesis on the other side, in order to make a clear case for Concept Empiricism. It will be also very helpful to set my favoured version of grounded cognition off against classical attempts at the phenomena which are to be explained. Following that I am going to present Larry Barsalou‘s Perceptual Symbol Systems Theory in more detail. I will do that to an extent which allows for an appropriate discussion of concept related phenomena, but which is not too lengthy. I will spare the reader with unnecessary psychological or neurobiological details as long as it is not really necessary for explaining or clarifying the phenomena with which I deal here. Having done this I will discuss at great length conceptual meaning. In doing so I will present a presentational theory of meaning which is anti-realist, internalist and imaginistic. In advertising for this theory I will recur to conceptual methods, intuition as well as to the empirical record. Next and related to this I will develop a resemblance based theory of intentionality which differs also widely from the already established theories of intentionality so far given. Indeed it possess a feature which makes it very distinct and this is, besides its reliance on pattern mapping, the statistical grounding of resemblance which allows a cognitive theory of resemblance which is definite and therefore not open to the counterarguments generally mashalled against related theories, which stress the importance of resemblance. A very distinctive feature of this theory of intentionality is additionally that intentionality is seen as a capacity which emerges naturally form the mental mechanism involved. As we will see, this is a distinctive advantage of it in comparison to other proposal in the field. A discussion of the ontology of mental states follows which is however primarily a discussion of mechanistic explanations and Bechtel‘s and McCauley‘s Heuristic Identity Theory (HIT). Those theories from philosophy of science and philosophy of cognitive science do not only deliver models for the ontology of mental states, but also epistemic criteria for evaluating a theory as superior or inferior. Especially the idea of productive continuity plays a role of pivotal importance in my Magisterarbeit. It might be a bit unfortunate that that an important consideration is discussed nearly at the end of the Magisterarbeit, since I refer to it very often, however, I considered it as equally unfortunate to delay the discussion of meaning and intentionality, which is already protruded by the overview chapter and the more technical parts, even more. Therefore I plead the reader to refer to later parts of the Magisterarbeit when it is necessary in order to understand earlier parts. In the course of writing I have gotten second thoughts regarding the adequacy of an ontology of mental states altogether, especially from the background of the theory of meaning and intentionality delivered here. Therefore I tried to accommodate for ontological concepts by means of a tentative phenomenological interpretation of them. Similar ideas influenced my deliberations regarding meaning too. I hope that this transition towards Phenomenology runs smoothly and that the high level of coherence which is my primary concern and something which I always strive for first is preserved. Further, I have dedicated a main chapter of the Magisterarbeit for possible and actual critics of the ideas brought forth by me. Besides the more classic standard objections there you can find a recent critique of the authors on which I refer most often. Naturally I try to refute any single criticism brought forth and I hope that the reader will approve my objection to the objections. I will round off the Magisterarbeit with some concluding remarks and prospects for future research.
Background: The faunal and floral relationship of northward-drifting India with its neighboring continents is of general biogeographic interest as an important driver of regional biodiversity. However, direct biogeographic connectivity of India and Southeast Asia during the Cenozoic remains largely unexplored. We investigate timing, direction and mechanisms of faunal exchange between India and Southeast Asia, based on a molecular phylogeny, molecular clock-derived time estimates and biogeographic reconstructions of the Asian freshwater crab family Gecarcinucidae. Results: Although the Gecarcinucidae are not an element of an ancient Gondwana fauna, their subfamily Gecarcinucinae, and probably also the Liotelphusinae, evolved on the Indian Subcontinent and subsequently dispersed to Southeast Asia. Estimated by a model testing approach, this dispersal event took place during the Middle Eocene, and thus before the final collision of India and the Tibet-part of Eurasia. Conclusions: We postulate that the India and Southeast Asia were close enough for exchange of freshwater organisms during the Middle Eocene, before the final Indian--Eurasian collision. Our data support geological models that assume the Indian plate having tracked along Southeast Asia during its move northwards.
Background: Complex care management is seen as an approach to face the challenges of an ageing society with increasing numbers of patients with complex care needs. The Medical Research Council in the United Kingdom has proposed a framework for the development and evaluation of complex interventions that will be used to develop and evaluate a primary care-based complex care management program for chronically ill patients at high risk for future hospitalization in Germany. Methods and design: We present a multi-method procedure to develop a complex care management program to implement interventions aimed at reducing potentially avoidable hospitalizations for primary care patients with type 2 diabetes mellitus, chronic obstructive pulmonary disease, or chronic heart failure and a high likelihood of hospitalization. The procedure will start with reflection about underlying precipitating factors of hospitalizations and how they may be targeted by the planned intervention (pre-clinical phase). An intervention model will then be developed (phase I) based on theory, literature, and exploratory studies (phase II). Exploratory studies are planned that entail the recruitment of 200 patients from 10 general practices. Eligible patients will be identified using two ways of 'case finding': software based predictive modelling and physicians' proposal of patients based on clinical experience. The resulting subpopulations will be compared regarding healthcare utilization, care needs and resources using insurance claims data, a patient survey, and chart review. Qualitative studies with healthcare professionals and patients will be undertaken to identify potential barriers and enablers for optimal performance of the complex care management program. Discussion: This multi-method procedure will support the development of a primary care-based care management program enabling the implementation of interventions that will potentially reduce avoidable hospitalizations.
The central difference between objectivist cognitivist semantics and embodied cognition consists in the fact that the latter is, in contrast to the former, mindful of binding meaning to context-sensitive mental systems. According to Lakoff/Johnson's experientialism, conceptual structures arise from preconceptual kinesthetic image-schematic and basic-level structures. Gallese and Lakoff introduced the notion of exploiting sensorimotor structures for higherlevel cognition. Three different types of X-schemas realise three types of environmentally embedded simulation: Areas that control movements in peri-personal space; canonical neurons of the ventral premotor cortex that fire when a graspable object is represented; the firing of mirror neurons while perceiving certain movements of conspecifics. ...
In the present work, the problem of protein folding is addressed from the point of view of equilibrium thermodynamics. The conformation of a globular protein in solution at common temperatures is quite complicated without any geometrical symmetry, but it is an ordered state in the sense of its biological activity. This complicated conformation of a single protein molecule is destroyed upon increasing the temperature or by the addition of appropriate chemical agents, as is revealed by the loss of its activity and change of the physical properties, and so on. Once the complicated native structures having biological activity are lost, it would be natural to suppose that the native structure could hardly be restored. Nevertheless, pioneers, such as Anson and Mirsky, recognized as early as in 1925 that this was not always the case. If one defines the folded and unfolded states of a protein as two distinct phases of a system, then under the variation of temperature the system is transformed from one phase state into another and vice versa. The process of protein folding is accompanied by the release or absorption of a certain amount of energy, corresponding to the first-oder-type phase transitions in the bulk. Knowing the partition function of the system one can evaluate its energy and heat capacity under different temperatures. This task was performed in this work. The results of the developed statistical mechanics model were compared with the results of molecular dynamic simulations of alanine poylpeptides. In particular, the dependencies on temperature of the total energy of the system and heat capacity were compared for alanine polypeptides consisting of 21, 30, 40, 50 and 100 amino acids. The good correspondence of the results of the theoretical model with the results of molecular dynamics simulations allowed to validate the assumptions made about the system and to establish the accuracy range of the theory. In order to perform the comparison of the results of theoretical model and the molecular dynamics simulations it is necessary to perform the efficient analysis of the results of molecular dynamics simulations. This task was also addressed in the present work. In particular, different ways to obtain dependence of the heat capacity on temperature from molecular dynamics simulations are discussed and the most efficient one is proposed. The present thesis reports the result of molecular dynamic simulations for not only alanine polypeptides by also for valine and leucine polypeptides. In valine and leucine polypeptides, it is also possible to observe the helix↔random coil transitions with the increase of temperature. The current thesis presents a work that starts with the investigation of the fundamental degrees of freedom in polypeptides that are responsible for the conformational transitions. Then this knowledge is applied for the statistical mechanics description of helix↔coil transitions in polypeptides. Finally, the theoretical formalism is generalized for the case of proteins in water environment and the comparison of the results of the statistical mechanics model with the experimental measurements of the heat capacity on temperature dependencies for two globular proteins is performed. The presented formalism is based on fundamental physical properties of the system and provides the possibility to describe the folding↔unfolding transitions quantitatively. The combination of these two facts is the major novelty of the presented approach in comparison to the existing ones. The “transparent” physical nature of the formalism provides a possibility to further apply it to a large variety of systems and processes. For instance, it can be used for investigation of the influence of the mutations in the proteins on their stability. This task is of primary importance for design of novel proteins and drug delivering molecules in medicine. It can provide further insights into the problem of protein aggregation and formation of amyloids. The problem of protein aggregation is closely associated with various illnesses such as Alzheimer and mad cow disease. With certain modifications, the presented theoretical method can be applied to the description of the protein crystallization process, which is important for the determination of the structure of proteins with X-Rays. There many other possible applications of the ideas described in the thesis. For instance, the similar formalism can be developed for the description of melting and unzipping of DNA, growth of nanotubes, formation of fullerenes, etc.
Functional and structural characterization of Aquifex aeolicus sulfide:quinone oxidoreductase
(2010)
This work presents the first complete structure of the membrane protein sulfide:quinone oxidoreductase (SQR), obtained by X-ray crystallography. Its description is complemented by the results of biochemical and functional experiments. SQRs are ubiquitous flavoprotein disulfide reductases (FDRs), present in all domains of life, including in humans. Their physiological role extends from sulfide detoxification to sulfide-dependent respiration and photosynthesis (in archaea and bacteria), to heavy metal tolerance (in yeast) and possibly to sulfide signalling (in higher eukaryotes). Until now understanding the function of SQRs was difficult because of the poor level of sequence conservation in this enzyme family, the limited functional characterization available and the absence of any structural data. SQR was identified in the native membranes of the hyperthermophilic bacterium Aquifex aeolicus by peptide mass fingerprinting (PMF) and by a spectrophotometric activity assay. The protein was solubilized in the detergent dodecyl-beta-D-maltoside (DDM) and purified to homogeneity in a functionally active state. It binds one FAD molecule per protein monomer and FAD is its only cofactor. Its structure was determined in the “as-purified”, substrate-bound and inhibitor-bound forms at resolutions of 2.3, 2.0 and 2.9 Å, respectively. It is composed of two Rossmann-fold domains and of one membrane-attachment region. Despite the overall monomeric architecture being similar to that of FDRs, the structure reveals properties that had not been observed in FDRs until now and that have strong implications for the SQR catalytic mechanism. Surprisingly, A. aeolicus SQR is trimeric in the crystal structure and in solution, as determined by density-matched analytical ultracentrifugation, cross-linking and single particle electron microscopy. The trimer creates an appropriate surface for binding lipids and thus ensures that SQR exclusively reduces hydrophobic quinones. SQR inserts to a depth of about 12 Å into the membrane as an integral monotopic membrane protein. The interaction is mediated by an amphipathic helix-turn-helix tripodal motif and two lipid clamps. A channel in the membrane-binding domain extends towards the si-side of FAD and represents the quinone-binding site. The quinone ring is sandwiched between the conserved amino acids Phe 385 and Ile 346 and is possibly protonated upon reduction via Glu 318, Lys 382 and/or neighboring solvent molecules. Sulfide polymerization occurs on the re-side of FAD, where the highly conserved Cys 156 and Cys 347 appear to be covalently bound to the putative product of the reaction, a polysulfur chain which takes the form of an S8 ring in some monomers. Finally, the structure shows that FAD is covalently connected to the protein in an unprecedented way, via a putative disulfide bridge between the 8-methyl group of the isoalloxazine moiety and Cys 124. The high resolution insight into the protein and all unexpected structural observations presented in this work suggest that the catalytic mechanism of SQRs is significantly different from that of FDRs. In agreement with the structural and functional data, two reaction schemes are proposed for A. aeolicus SQR. They both provide a detailed description of how sulfide and quinones reach and bind the active site, how electrons are transferred from sulfide to quinone via FAD and how the elongating polysulfur product is attached to the polypeptide and is finally released. The two hypotheses differ in defining the structure of the covalent protein-FAD intermediate that forms during the reaction cycle and whose identity still remains experimentally undetermined. Remarkably, the structure of the active site and the FAD-binding mode of A. aeolicus SQR are not conserved in another SQR structure which also became available recently, that of the archaeon Acidianus ambivalens. The variability in SQRs suggests that not all of these enzymes follow the same catalytic mechanism, despite having been considered homologous. Consequently, the currently available but contradictory sequence-based classifications of the SQR family were revised. A structure-based alignment calculated on the increasing number of available sequences allowed to define new SQR groups and their characteristic sequence fingerprints in agreement with the reported structural and functional data. In conclusion, the results obtained in this work offer for the first time a detailed look into the intriguing but complicated reactions catalysed by SQRs and provide a stimulus for further genetic, biochemical and structural investigation.
On the backdrop of the 2008 financial crisis this paper introduces an understanding of societal crises as a reduction in the meaning production of social entities, which can either be internally or externally provoked. The emergence of constitutions and, more generally, constitutional structures, can be understood as responses to both forms of crisis. This is the case because they are double-edged structures which are simultaneously oriented towards the maintenance of internal order and stability within a given social entity at the same time as they frame the transfer of the meaning components between the social entities and their environments. Thus, the 2008 financial crisis indicates a failure of constitutional bonding. When observed from an overall structural perspective, the reasons for this failure can be traced back to an increased discrepancy between the structural composition of world society and the constitutional structures in place. The crisis reflects a failure to respond to two simultaneous, inter-related and mutually re-inforcing structural transformations. First, there is the increased globalisation, which has led to massive dis-locations in the relative centrality of the different national configurations for the reproductive processes of functional systems. Second, there is a structural transformation of the transnational layer of world society through a reduced reliance on the centre/periphery differentiation and an increased reliance on functional differentiation. One of the many consequences of this development is the emergence of new forms of transnational law and politics. A new constitutional architecture which reflects these transformations is needed in order to ensure an adequate constitutional bonding of economic processes, as well as of other social processes.
Background: Prospective, observational studies that enroll large numbers of patients with few exclusion criteria may better reflect actual ongoing clinical experience than randomized clinical trials. Our purpose was to obtain efficacy and safety information from a cohort of subjects exposed to latanoprost/timolol fixed combination (FC) for [greater than or equal to]18 months using a prospective, observational design. Methods: In all, 577 office-based ophthalmologists in Germany switched 2339 patients with glaucoma or ocular hypertension to latanoprost/timolol FC for medical reasons. Follow-up visits were scheduled for every 6 months over 24 months; physicians followed usual care routines. Intraocular pressure (IOP), visual field status, optic nerve head findings, and adverse events were recorded. Efficacy parameters were evaluated for the per protocol (PP) population; the safety population included subjects receiving [greater than or equal to]1 drop of FC. Physicians rated efficacy, tolerability, and subject compliance at month 24. Results: Of the 2339 subjects switched to latanoprost/timolol FC (safety population), the primary reasons for switching were inadequate IOP reduction (78.2%) and desire to simplify treatment with once-daily dosing (29.4%; multiple reasons possible). In all, 1317 (56.3%) subjects completed the study, and 1028 (44.0%) were included in the PP population. Most discontinuations were due to loss to follow-up. Change in mean IOP from baseline to month 6 was -4.0 +/- 4.31 mmHg, a reduction that was maintained throughout (P<0.05 for change at all time points). By investigator assessments, optic disc parameters and visual field were stable over 24 months, and there was no relationship between IOP reduction over 24 months and development of a visual field defect. More than 90% of physicians rated latanoprost/timolol FC as "very good" or "good" for efficacy (PP population), tolerability, and compliance. The FC was safe and well tolerated. No change in iris color was reported by most subjects (83.1%) at month 24. Conclusions: Over 24 months, latanoprost/timolol FC effectively lowers IOP levels and is well tolerated in patients with glaucoma or ocular hypertension who change from their previous ocular hypotensive therapy for medical reasons. Investigator assessments found optic disc parameters and visual field to be stable throughout 24 months of follow-up.