Refine
Has Fulltext
- yes (580)
Is part of the Bibliography
- yes (580) (remove)
Year of publication
- 2015 (580) (remove)
Document Type
- Journal article (426)
- Doctoral Thesis (145)
- Working Paper (4)
- Conference Proceeding (3)
- Other (1)
- Preprint (1)
Language
- English (580) (remove)
Keywords
- expression (19)
- ATLAS detector (18)
- proton-proton collision (13)
- cancer (11)
- in vitro (11)
- therapy (11)
- Higgs boson (10)
- endothelial cells (9)
- infection (9)
- physics (9)
Institute
- Theodor-Boveri-Institut für Biowissenschaften (87)
- Physikalisches Institut (70)
- Graduate School of Life Sciences (32)
- Institut für Psychologie (31)
- Neurologische Klinik und Poliklinik (27)
- Medizinische Klinik und Poliklinik I (24)
- Medizinische Klinik und Poliklinik II (20)
- Institut für Molekulare Infektionsbiologie (19)
- Institut für Pharmazie und Lebensmittelchemie (17)
- Institut für Theoretische Physik und Astrophysik (16)
Sonstige beteiligte Institutionen
- ATLAS Collaboration (1)
- Adam Opel AG (1)
- Brown University (1)
- CERN (1)
- Center for Nanosystems Chemistry (CNC), Universität Würzburg, Am Hubland, 97074 Würzburg, Germany (1)
- Deutscher Akademischer Austauschdienst (DAAD) (1)
- Deutsches Zentrum für Luft- und Raumfahrt (DLR), Institut für Raumfahrtsysteme (1)
- Institut für Hygiene und Mikrobiologie (1)
- Instituto de Higiene, Universidad de la República, Montevideo, Uruguay (1)
- König-Ludwig-Haus, Orthopedic Clinic, Würzburg (1)
ResearcherID
- B-1911-2015 (1)
- C-2593-2016 (1)
- D-1221-2009 (1)
- N-2030-2015 (1)
- N-3741-2015 (1)
Background:
Heritable bleeding and platelet disorders (BPD) are heterogeneous and frequently have an unknown genetic basis. The BRIDGE-BPD study aims to discover new causal genes for BPD by high throughput sequencing using cluster analyses based on improved and standardised deep, multi-system phenotyping of cases.
Methods:
We report a new approach in which the clinical and laboratory characteristics of BPD cases are annotated with adapted Human Phenotype Ontology (HPO) terms. Cluster analyses are then used to characterise groups of cases with similar HPO terms and variants in the same genes. Results:
We show that 60% of index cases with heritable BPD enrolled at 10 European or US centres were annotated with HPO terms indicating abnormalities in organ systems other than blood or blood-forming tissues, particularly the nervous system. Cases within pedigrees clustered closely together on the bases of their HPO-coded phenotypes, as did cases sharing several clinically suspected syndromic disorders. Cases subsequently found to harbour variants in ACTN1 also clustered closely, even though diagnosis of this recently described disorder was not possible using only the clinical and laboratory data available to the enrolling clinician.
Conclusions:
These findings validate our novel HPO-based phenotype clustering methodology for known BPD, thus providing a new discovery tool for BPD of unknown genetic basis. This approach will also be relevant for other rare diseases with significant genetic heterogeneity.
Parent-of-origin imprints have been implicated in the regulation of neural differentiation and brain development. Previously we have shown that, despite the lack of a paternal genome, human parthenogenetic (PG) embryonic stem cells (hESCs) can form proliferating neural stem cells (NSCs) that are capable of differentiation into physiologically functional neurons while maintaining allele-specific expression of imprinted genes. Since biparental ("normal") hESC-derived NSCs (N NSCs) are targeted by immune cells, we characterized the immunogenicity of PG NSCs. Flow cytometry and immunocytochemistry revealed that both N NSCs and PG NSCs exhibited surface expression of human leukocyte antigen (HLA) class I but not HLA-DR molecules. Functional analyses using an in vitro mixed lymphocyte reaction assay resulted in less proliferation of peripheral blood mononuclear cells (PBMC) with PG compared with N NSCs. In addition, natural killer (NK) cells cytolyzed PG less than N NSCs. At a molecular level, expression analyses of immune regulatory factors revealed higher HLA-G levels in PG compared with N NSCs. In line with this finding, MIR152, which represses HLA-G expression, is less transcribed in PG compared with N cells. Blockage of HLA-G receptors ILT2 and KIR2DL4 on natural killer cell leukemia (NKL) cells increased cytolysis of PG NSCs. Together this indicates that PG NSCs have unique immunological properties due to elevated HLA-G expression.
This thesis deals with the hp-finite element method (FEM) for linear quadratic optimal control problems. Here, a tracking type functional with control costs as regularization shall be minimized subject to an elliptic partial differential equation. In the presence of control constraints, the first order necessary conditions, which are typically used to find optimal solutions numerically, can be formulated as a semi-smooth projection formula. Consequently, optimal solutions may be non-smooth as well. The hp-discretization technique considers this fact and approximates rough functions on fine meshes while using higher order finite elements on domains where the solution is smooth.
The first main achievement of this thesis is the successful application of hp-FEM to two related problem classes: Neumann boundary and interface control problems. They are solved with an a-priori refinement strategy called boundary concentrated (bc) FEM and interface concentrated (ic) FEM, respectively. These strategies generate grids that are heavily refined towards the boundary or interface. We construct an elementwise interpolant that allows to prove algebraic decay of the approximation error for both techniques. Additionally, a detailed analysis of global and local regularity of solutions, which is critical for the speed of convergence, is included. Since the bc- and ic-FEM retain small polynomial degrees for elements touching the boundary and interface, respectively, we are able to deduce novel error estimates in the L2- and L∞-norm. The latter allows an a-priori strategy for updating the regularization parameter in the objective functional to solve bang-bang problems.
Furthermore, we apply the traditional idea of the hp-FEM, i.e., grading the mesh geometrically towards vertices of the domain, for solving optimal control problems (vc-FEM). In doing so, we obtain exponential convergence with respect to the number of unknowns. This is proved with a regularity result in countably normed spaces for the variables of the coupled optimality system.
The second main achievement of this thesis is the development of a fully adaptive hp-interior point method that can solve problems with distributed or Neumann control. The underlying barrier problem yields a non-linear optimality system, which poses a numerical challenge: the numerically stable evaluation of integrals over possibly singular functions in higher order elements. We successfully overcome this difficulty by monitoring the control variable at the integration points and enforcing feasibility in an additional smoothing step. In this work, we prove convergence of an interior point method with smoothing step and derive a-posteriori error estimators. The adaptive mesh refinement is based on the expansion of the solution in a Legendre series. The decay of the coefficients serves as an indicator for smoothness that guides between h- and p-refinement.
The diploid, polymorphic yeast Candida albicans is one of the most important human pathogenic fungi. C. albicans can grow, proliferate and coexist as a commensal on or within the human host for a long time. However, alterations in the host environment can render C. albicans virulent. In this review, we describe the immunological cross-talk between C. albicans and the human innate immune system. We give an overview in form of pairs of human defense strategies including immunological mechanisms as well as general stressors such as nutrient limitation, pH, fever etc. and the corresponding fungal response and evasion mechanisms. Furthermore, Computational Systems Biology approaches to model and investigate these complex interactions are highlighted with a special focus on game-theoretical methods and agent-based models. An outlook on interesting questions to be tackled by Systems Biology regarding entangled defense and evasion mechanisms is given.
Clostridium difficile is the most common cause of antibiotic-associated intestinal infections and a significant cause of morbidity and mortality. Infection with C. difficile requires disruption of the intestinal microbiota, most commonly by antibiotic usage. Therapeutic intervention largely relies on a small number of broad-spectrum antibiotics, which further exacerbate intestinal dysbiosis and leave the patient acutely sensitive to reinfection. Development of novel targeted therapeutic interventions will require a detailed knowledge of essential cellular processes, which represent attractive targets, and species-specific processes, such as bacterial sporulation. Our knowledge of the genetic basis of C. difficile infection has been hampered by a lack of genetic tools, although recent developments have made some headway in addressing this limitation. Here we describe the development of a method for rapidly generating large numbers of transposon mutants in clinically important strains of C. difficile. We validated our transposon mutagenesis approach in a model strain of C. difficile and then generated a comprehensive transposon library in the highly virulent epidemic strain R20291 (027/BI/NAP1) containing more than 70,000 unique mutants. Using transposon-directed insertion site sequencing (TraDIS), we have identified a core set of 404 essential genes, required for growth in vitro. We then applied this technique to the process of sporulation, an absolute requirement for C. difficile transmission and pathogenesis, identifying 798 genes that are likely to impact spore production. The data generated in this study will form a valuable resource for the community and inform future research on this important human pathogen.
Existing models explaining the evolution of sexual dimorphism in the timing of emergence (SDT) in Lepidoptera assume equal mortality rates for males and females. The limiting assumption of equal mortality rates has the consequence that these models are only able to explain the evolution of emergence of males before females, i.e. protandry-the more common temporal sequence of emergence in Lepidoptera. The models fail, however, in providing adaptive explanations for the evolution of protogyny, where females emerge before males, but protogyny is not rare in insects. The assumption of equal mortality rates seems too restrictive for many insects, such as butterflies. To investigate the influence of unequal mortality rates on the evolution of SDT, we present a generalised version of a previously published model where we relax this assumption. We find that longer life-expectancy of females compared to males can indeed favour the evolution of protogyny as a fitness enhancing strategy. Moreover, the encounter rate between females and males and the sex-ratio are two important factors that also influence the evolution of optimal SDT. If considered independently for females and males the predicted strategies can be shown to be evolutionarily stable (ESS). Under the assumption of equal mortality rates the difference between the females' and males' ESS remains typically very small. However, female and male ESS may be quite dissimilar if mortality rates are different. This creates the potential for an 'evolutionary conflict' between females and males. Bagworm moths (Lepidoptera: Psychidae) provide an exemplary case where life-history attributes are such that protogyny should indeed be the optimal emergence strategy from the males' and females' perspectives: (i) Female longevity is considerably larger than that of males, (ii) encounter rates between females and males are presumably low, and (iii) females mate only once. Protogyny is indeed the general mating strategy found in the bagworm family.
Theory predicts peculiar features for excited-state dynamics in one dimension (1D) that are difficult to be observed experimentally. Single-walled carbon nanotubes (SWNTs) are an excellent approximation to 1D quantum confinement, due to their very high aspect ratio and low density of defects. Here we use ultrafast optical spectroscopy to probe photogenerated charge-carriers in (6,5) semiconducting SWNTs. We identify the transient energy shift of the highly polarizable S\(_{33}\) transition as a sensitive fingerprint of charge-carriers in SWNTs. By measuring the coherent phonon amplitude profile we obtain a precise estimate of the Stark-shift and discuss the binding energy of the S\(_{33}\) excitonic transition. From this, we infer that charge-carriers are formed instantaneously (<50 fs) even upon pumping the first exciton, S\(_{11}\). The decay of the photogenerated charge-carrier population is well described by a model for geminate recombination in 1D.
High convection volume in online post-dilution haemodiafiltration: relevance, safety and costs
(2015)
Increasing evidence suggests that treatment with online post-dilution haemodiafiltration (HDF) improves clinical outcome in patients with end-stage kidney disease, if compared with haemodialysis (HD). Although the primary analyses of three large randomized controlled trials (RCTs) showed inconclusive results, post hoc analyses of these and previous observational studies comparing online post-dilution HDF with HD showed that the risk of overall and cardiovascular mortality is lowest in patients who are treated with high-volume HDF. As such, the magnitude of the convection volume seems crucial and can be considered as the ‘dose’ of HDF. In this narrative review, the relevance of high convection volume in online post-dilution HDF is discussed. In addition, we briefly touch upon some safety and cost issues.
The Hey protein family, comprising Hey1, Hey2 and HeyL in mammals, conveys Notch signals in many cell types. The helix-loop-helix (HLH) domain as well as the Orange domain, mediate homo- and heterodimerization of these transcription factors. Although distinct interaction partners have been identified so far, their physiological relevance for Hey functions is still largely unclear. Using a tandem affinity purification approach and mass spectrometry analysis we identified members of an ubiquitin E3-ligase complex consisting of FBXO45, PAM and SKP1 as novel Hey1 associated proteins. There is a direct interaction between Hey1 and FBXO45, whereas FBXO45 is needed to mediate indirect Hey1 binding to SKP1. Expression of Hey1 induces translocation of FBXO45 and PAM into the nucleus. Hey1 is a short-lived protein that is degraded by the proteasome, but there is no evidence for FBXO45-dependent ubiquitination of Hey1. On the contrary, Hey1 mediated nuclear translocation of FBXO45 and its associated ubiquitin ligase complex may extend its spectrum to additional nuclear targets triggering their ubiquitination. This suggests a novel mechanism of action for Hey bHLH factors.
Background
Anemia is common and is associated with impaired clinical outcomes in diabetic chronic kidney disease (CKD). It may be explained by reduced erythropoietin (EPO) synthesis, but recent data suggest that EPO-resistance and diminished iron availability due to inflammation contribute significantly. In this cohort study, we evaluated the impact of hepcidin-25—the key hormone of iron-metabolism—on clinical outcomes in diabetic patients with CKD along with endogenous EPO levels.
Methods
249 diabetic patients with CKD of any stage, excluding end-stage renal disease (ESRD), were enrolled (2003–2005), if they were not on EPO-stimulating agent and iron therapy. Hepcidin-25 levels were measured by radioimmunoassay. The association of hepcidin-25 at baseline with clinical variables was investigated using linear regression models. All-cause mortality and a composite endpoint of CKD progression (ESRD or doubling of serum creatinine) were analyzed by Cox proportional hazards models.
Results
Patients (age 67 yrs, 53% male, GFR 51 ml/min, hemoglobin 131 g/L, EPO 13.5 U/L, hepcidin-25 62.0 ng/ml) were followed for a median time of 4.2 yrs. Forty-nine patients died (19.7%) and forty (16.1%) patients reached the composite endpoint. Elevated hepcidin levels were independently associated with higher ferritin-levels, lower EPO-levels and impaired kidney function (all p<0.05). Hepcidin was related to mortality, along with its interaction with EPO, older age, greater proteinuria and elevated CRP (all p<0.05). Hepcidin was also predictive for progression of CKD, aside from baseline GFR, proteinuria, low albumin- and hemoglobin-levels and a history of CVD (all p<0.05).
Conclusions
We found hepcidin-25 to be associated with EPO and impaired kidney function in diabetic CKD. Elevated hepcidin-25 and EPO-levels were independent predictors of mortality, while hepcidin-25 was also predictive for progression of CKD. Both hepcidin-25 and EPO may represent important prognostic factors of clinical outcome and have the potential to further define “high risk” populations in CKD.
Background and Aims
Chronic kidney disease (CKD) is a risk factor for development and progression of heart failure (HF). CKD and HF share common risk factors, but few data exist on the prevalence, signs and symptoms as well as correlates of HF in populations with CKD of moderate severity. We therefore aimed to examine the prevalence and correlates of HF in the German Chronic Kidney Disease (GCKD) study, a large observational prospective study.
Methods and Results
We analyzed data from 5,015 GCKD patients aged 18-74 years with an estimated glomerular filtration rate (eGFR) of <60 ml/min/1.73m\(^{2}\) or with an eGFR >= 60 and overt proteinuria (>500 mg/d). We evaluated a definition of HF based on the Gothenburg score, a clinical HF score used in epidemiological studies (Gothenburg HF), and self-reported HF. Factors associated with HF were identified using multivariable adjusted logistic regression. The prevalence of Gothenburg HF was 43% (ranging from 24% in those with eGFR >90 to 59% in those with eGFR<30 ml/min/1.73m2). The corresponding estimate for self-reported HF was 18% (range 5%-24%). Lower eGFR was significantly and independently associated with the Gothenburg definition of HF (p-trend <0.001). Additional significantly associated correlates included older age, female gender, higher BMI, hypertension, diabetes mellitus, valvular heart disease, anemia, sleep apnea, and lower educational status.
Conclusions
The burden of self-reported and Gothenburg HF among patients with CKD is high. The proportion of patients who meet the criteria for Gothenburg HF in a European cohort of patients with moderate CKD is more than twice as high as the prevalence of self-reported HF. However, because of the shared signs, symptoms and medications of HF and CKD, the Gothenburg score cannot be used to reliably define HF in CKD patients. Our results emphasize the need for early screening for HF in patients with CKD.
PURPOSE:
To evaluate the heart and the Tc-99m-sestamibi biodistribution after statin pretreatment in a rat model of abdominal sepsis.
METHODS:
Twenty-four Wistar rats were randomly distributed into four groups (n=6 per group): 1) sepsis with simvastatin treatment, 2) sepsis with vehicle, 3) sham control with simvastatin and 4) sham control with vehicle. 24 hours after cecal ligation and puncture rats received 1.0MBq of Tc-99m-sestamibi i.v. 30min after, animals were euthanized for ex-vivo tissue counting and myocardium histological analysis.
RESULTS:
Myocardial histologic alterations were not detected 24 hours post-sepsis. There was significantly increased cardiac Tc-99m-sestamibi activity in the sepsis group with simvastatin treatment (1.9\(\pm\)0.3%ID/g, p<0.001) in comparison to the sepsis group+vehicle (1.0\(\pm\)0.2% ID/g), control sham group+ simvastatin (1.2\(\pm\)0.3% ID/g) and control sham group (1.3\(\pm\)0.2% ID/g). Significant Tc-99m-sestamibi activity in liver, kidney and lungs was also detected in the sepsis group treated with simvastatinin comparison to the other groups.
CONCLUSIONS:
Statin treatment altered the biodistribution of Tc-99m-sestamibi with increased cardiac and solid organ activity in rats with abdominal sepsis, while no impact on controls. Increased myocardial tracer activity may be a result of a possible protection effect due to increased tissue perfusion mediated by statins.
Protected areas are the central strategy for preserving biodiversity in the face of overexploitation and global change. To ensure their long-term survival, however, these areas may not be regarded as last havens of wilderness, but as complex social-ecological systems. Modern approaches of protected area (PA) management support this view by balancing conservation and development issues in a sustainable way and adapted to the local context. However, success of these strategies in achieving their aims so far remains limited.
This study therefore aimed at analysing processes and outcomes of PA co-management approaches implemented in a large transfrontier conservation area in West Africa. The W-Arly-Pendjari (WAP) complex spans over more than 30.000 square km in Benin, Burkina Faso and Niger and is composed of approximately 20 subunits. Due to national legal and administrative variety as well as a high diversity of local (project) implementation approaches, the general setting resembled a quasi-experimental design facilitating comparative studies.
A mix of quantitative (e.g. survey of 549 households) and qualitative (e.g. expert interviews, literature review) methods was used to evaluate the institutional and organisational differences of PA management approaches implemented in the different parts of WAP belonging to Benin and Burkina Faso. I included an analysis of contextual factors (e.g. land-cover-change) and ecological data, but concentrated on the role of local resource users within the co-management arrangements and the effectiveness of governance regimes to deliver positive socio-economic outputs. Exploring the question whether promotion of development in PA surroundings indeed stipulates conservation success (and vice versa) remained challenging: the lack of sound ecological data, a general mismatch of spatial scale in existing data sets, as well as the high complexity of realities on the ground made me refrain from using simplified proxy indicators and (statistical) modelling approaches.
I found that the Sudano-Sahelian context is a very difficult one for the implementation of effective participation approaches in the short-term. Political, demographic, socio-economic as well as ecological factors generated a very dynamic situation characterized by limited financial and natural resources as well as weak institutional and organisational settings.
Arenas of interaction were often marked rather by a high degree of distrust and competition than by cooperation among actors. Amid all rhetoric, participation in most cases was hence limited to the transfer of (sparse) information, regulated resource access and financial funds. Options for participation of local resource users in decision-making arenas were generally scarce. Underlying processes were dominated by opacity and often low accountability of actors on all levels. Negative, but also positive affection of local residents by PA existence and management hence was high.
Governance regimes of the complex performed very differently with regard to their ability of effectively empowering local village participatory bodies (vpb), generating and distributing benefits to individuals and village communities as well as providing mechanisms of conflict resolution. People around Pendjari enjoyed a relative wealth of high value benefits, while negative impacts caused by human-wildlife conflicts were widespread around the complex. Autochthonous farmers usually were better integrated in incentive schemes than were newcomers or herders.
While there was functional separation of actors’ roles in all parts of WAP, these roles differed significantly between blocks. Existence and functioning of village participatory bodies ameliorated the situation for local resource users fundamentally, as they acted as cut-points between different networks (governmental hierarchies, private concessionaires and local resource users). Vpbs in the Pendjari region proved to be most advanced in their capacity to push resource users’ claims in action arenas on the micro-level. Via their union, these associations also managed to impact arenas on the meso- and the macro scale.
Project interventions often had catalyst functions to empower local resource users and their vbps. However, they also contributed to social imbalance and intra-organisational competition.
My results represent a snapshot of an ongoing process to establish effective co-governance regimes in the WAP-area. Though I identified a large scope of shortcomings, there were also very promising initiatives underway. This work is therefore meant to foster future research and further positive development by giving guidance scholars and decision-makers form the local to the global level alike.
Background
International collaborative research is a mechanism for improving the development of disease-specific therapies and for improving health at the population level. However, limited data are available to assess the trends in research output related to orphan diseases.
Methods and Findings
We used bibliometric mapping and clustering methods to illustrate the level of fragmentation in myeloma research and the development of collaborative efforts. Publication data from Thomson Reuters Web of Science were retrieved for 2005-2009 and followed until 2013. We created a database of multiple myeloma publications, and we analysed impact and co-authorship density to identify scientific collaborations, developments, and international key players over time. The global annual publication volume for studies on multiple myeloma increased from 1,144 in 2005 to 1,628 in 2009, which represents a 43% increase. This increase is high compared to the 24% and 14% increases observed for lymphoma and leukaemia. The major proportion (> 90% of publications) was from the US and EU over the study period. The output and impact in terms of citations, identified several successful groups with a large number of intra-cluster collaborations in the US and EU. The US-based myeloma clusters clearly stand out as the most productive and highly cited, and the European Myeloma Network members exhibited a doubling of collaborative publications from 2005 to 2009, still increasing up to 2013.
Conclusion and Perspective
Multiple myeloma research output has increased substantially in the past decade. The fragmented European myeloma research activities based on national or regional groups are progressing, but they require a broad range of targeted research investments to improve multiple myeloma health care.
Many fractional quantum Hall wave functions are known to be unique highest-density zero modes of certain "pseudopotential" Hamiltonians. While a systematic method to construct such parent Hamiltonians has been available for the infinite plane and sphere geometries, the generalization to manifolds where relative angular momentum is not an exact quantum number, i.e., the cylinder or torus, remains an open problem. This is particularly true for non-Abelian states, such as the Read-Rezayi series (in particular, the Moore-Read and Read-Rezayi Z\(_3\) states) and more exotic nonunitary (Haldane-Rezayi and Gaffnian) or irrational (Haffnian) states, whose parent Hamiltonians involve complicated many-body interactions. Here, we develop a universal geometric approach for constructing pseudopotential Hamiltonians that is applicable to all geometries. Our method straightforwardly generalizes to the multicomponent SU(n) cases with a combination of spin or pseudospin (layer, subband, or valley) degrees of freedom. We demonstrate the utility of our approach through several examples, some of which involve non-Abelian multicomponent states whose parent Hamiltonians were previously unknown, and we verify the results by numerically computing their entanglement properties.
Purpose:
The purpose of this study was to determine possible genotoxic effects of a new very promising antibacterial/ antiviral drug FS-1.
Methods:
The drug was tested in TA98, TA100, TA102, TA 1535 and TA1537 strains of Salmonella (Ames test) with and without metabolic activation, and also in mouse lymphoma L5178Y cells by means of micronucleus and comet assays. In microbes the drug was tested at concentrations up to 500 \(\mu\)g/plate and in mouse lymphoma cells up to 2,000 \(\mu\)g/ml.
Results:
In both test-systems in all experiments completely negative results were obtained although FS-1 was tested at maximum tolerated doses.
Conclusions:
The drug is not genotoxic. This is advantageous because many antibacterial/antiviral drugs possess such activity.
Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315
(2015)
Background: Burkholderia cenocepacia is a soil-dwelling Gram-negative Betaproteobacterium with an important role as opportunistic pathogen in humans. Infections with B. cenocepacia are very difficult to treat due to their high intrinsic resistance to most antibiotics. Biofilm formation further adds to their antibiotic resistance. B. cenocepacia harbours a large, multi-replicon genome with a high GC-content, the reference genome of strain J2315 includes 7374 annotated genes. This study aims to annotate transcription start sites and identify novel transcripts on a whole genome scale. Methods: RNA extracted from B. cenocepacia J2315 biofilms was analysed by differential RNA-sequencing and the resulting dataset compared to data derived from conventional, global RNA-sequencing. Transcription start sites were annotated and further analysed according to their position relative to annotated genes. Results: Four thousand ten transcription start sites were mapped over the whole B. cenocepacia genome and the primary transcription start site of 2089 genes expressed in B. cenocepacia biofilms were defined. For 64 genes a start codon alternative to the annotated one was proposed. Substantial antisense transcription for 105 genes and two novel protein coding sequences were identified. The distribution of internal transcription start sites can be used to identify genomic islands in B. cenocepacia. A potassium pump strongly induced only under biofilm conditions was found and 15 non-coding small RNAs highly expressed in biofilms were discovered. Conclusions: Mapping transcription start sites across the B. cenocepacia genome added relevant information to the J2315 annotation. Genes and novel regulatory RNAs putatively involved in B. cenocepacia biofilm formation were identified. These findings will help in understanding regulation of B. cenocepacia biofilm formation.
Diabetic kidney disease (DKD) is the most common etiology of chronic kidney disease (CKD) in the industrialized world and accounts for much of the excess mortality in patients with diabetes mellitus. Approximately 45% of U.S. patients with incident end-stage kidney disease (ESKD) have DKD. Independent of glycemic control, DKD aggregates in families and has higher incidence rates in African, Mexican, and American Indian ancestral groups relative to European populations. The Family Investigation of Nephropathy and Diabetes (FIND) performed a genome-wide association study (GWAS) contrasting 6,197 unrelated individuals with advanced DKD with healthy and diabetic individuals lacking nephropathy of European American, African American, Mexican American, or American Indian ancestry. A large-scale replication and trans-ethnic meta-analysis included 7,539 additional European American, African American and American Indian DKD cases and non-nephropathy controls. Within ethnic group meta-analysis of discovery GWAS and replication set results identified genome-wide significant evidence for association between DKD and rs12523822 on chromosome 6q25.2 in American Indians (P = 5.74x10\(^{−9}\)). The strongest signal of association in the trans-ethnic meta-analysis was with a SNP in strong linkage disequilibrium with rs12523822 (rs955333; P = 1.31x10\(^{−8}\)), with directionally consistent results across ethnic groups. These 6q25.2 SNPs are located between the SCAF8 and CNKSR3 genes, a region with DKD relevant changes in gene expression and an eQTL with IPCEF1, a gene co-translated with CNKSR3. Several other SNPs demonstrated suggestive evidence of association with DKD, within and across populations. These data identify a novel DKD susceptibility locus with consistent directions of effect across diverse ancestral groups and provide insight into the genetic architecture of DKD.
Electric shock is a common stimulus for nociception-research and the most widely used reinforcement in aversive associative learning experiments. Yet, nothing is known about the mechanisms it recruits at the periphery. To help fill this gap, we undertook a genome-wide association analysis using 38 inbred Drosophila melanogaster strains, which avoided shock to varying extents. We identified 514 genes whose expression levels and/or sequences covaried with shock avoidance scores. We independently scrutinized 14 of these genes using mutants, validating the effect of 7 of them on shock avoidance. This emphasizes the value of our candidate gene list as a guide for follow-up research. In addition, by integrating our association results with external protein-protein interaction data we obtained a shock avoidance- associated network of 38 genes. Both this network and the original candidate list contained a substantial number of genes that affect mechanosensory bristles, which are hairlike organs distributed across the fly's body. These results may point to a potential role for mechanosensory bristles in shock sensation. Thus, we not only provide a first list of candidate genes for shock avoidance, but also point to an interesting new hypothesis on nociceptive mechanisms.
To unravel the role of single genes underlying certain biological processes, scientists often use amorphic or hypomorphic alleles. In the past, such mutants were often created by chance. Enormous approaches with many animals and massive screening effort for striking phenotypes were necessary to find a needle in the haystack. Therefore at the beginning chemical mutagens or radiation were used to induce mutations in the genome. Later P-element insertions and inaccurate jump-outs enabled the advantage of potential larger deletions or inversions. The mutations were characterized and subsequently kept in smaller populations in the laboratories. Thus additional mutations with unknown background effects could accumulate.
The precision of the knockout through homologous recombination and the additional advantage of being able to generate many useful rescue constructs that can be easily reintegrated into the target locus made us trying an ends-out targeting procedure of the two core clock genes period and timeless in Drosophila melanogaster. Instead of the endogenous region, a small fragment of approximately 100 base pairs remains including an attP-site that can be used as integration site for in vitro created rescue constructs. After a successful ends-out targeting procedure, the locus will be restored with e.g. flies expressing the endogenous gene under the native promoter at the original locus coupled to a fluorescence tag or expressing luciferase.
We also linked this project to other research interests of our work group, like the epigenetic related ADAR-editing project of the Timeless protein, a promising newly discovered feature of time point specific timeless mRNA modification after transcription with yet unexplored consequences. The editing position within the Timeless protein is likewise interesting and not only noticed for the first time. This will render new insights into the otherwise not-satisfying investigation and quest for functional important sequences of the Timeless protein, which anyway shows less homology to other yet characterized proteins.
Last but not least, we bothered with the question of the role of Shaggy on the circadian clock. The impact of an overexpression or downregulation of Shaggy on the pace of the clock is obvious and often described. The influence of Shaggy on Period and Timeless was also shown, but for the latter it is still controversially discussed. Some are talking of a Cryptochrome stabilization effect and rhythmic animals in constant light due to Shaggy overexpression, others show a decrease of Cryptochrome levels under these conditions. Also the constant light rhythmicity of the flies, as it was published, could not be repeated so far. We were able to expose the conditions behind the Cryptochrome stabilization and discuss possibilities for the phenomenon of rhythmicity under constant light due to Shaggy overexpression.
Central nervous system dysfunction is an important cause of morbidity and mortality in patients with human immunodeficiency virus type 1 (HIV-1) infection and acquired immunodeficiency virus syndrome (AIDS). Patients with AIDS are usually affected by HIV-associated encephalitis (HIVE) with viral replication limited to cells of monocyte origin. To examine the molecular mechanisms underlying HIVE-induced dementia, the GSE4755 Affymetrix data were obtained from the Gene Expression Omnibus database and the differentially expressed genes (DEGs) between the samples from AIDS patients with and without apparent features of HIVE-induced dementia were identified. In addition, protein–protein interaction networks were constructed by mapping DEGs into protein–protein interaction data to identify the pathways that these DEGs are involved in. The results revealed that the expression of 1,528 DEGs is mainly involved in the immune response, regulation of cell proliferation, cellular response to inflammation, signal transduction, and viral replication cycle. Heat-shock protein alpha, class A member 1 (HSP90AA1), and fibronectin 1 were detected as hub nodes with degree values >130. In conclusion, the results indicate that HSP90A and fibronectin 1 play important roles in HIVE pathogenesis.
How allopolyploids are able not only to cope but profit from their condition is a question that remains elusive, but is of great importance within the context of successful allopolyploid evolution. One outstanding example of successful allopolyploidy is the endemic Iberian cyprinid Squalius alburnoides. Previously, based on the evaluation of a few genes, it was reported that the transcription levels between diploid and triploid S. alburnoides were similar. If this phenomenon occurs on a full genomic scale, a wide functional "diploidization'' could be related to the success of these polyploids. We generated RNA-seq data from whole juvenile fish and from adult livers, to perform the first comparative quantitative transcriptomic analysis between diploid and triploid individuals of a vertebrate allopolyploid. Together with an assay to estimate relative expression per cell, it was possible to infer the relative sizes of transcriptomes. This showed that diploid and triploid S. alburnoides hybrids have similar liver transcriptome sizes. This in turn made it valid to directly compare the S. alburnoides RNA-seq transcript data sets and obtain a profile of dosage responses across the S. alburnoides transcriptome. We found that 64% of transcripts in juveniles' samples and 44% in liver samples differed less than twofold between diploid and triploid hybrids (similar expression). Yet, respectively 29% and 15% of transcripts presented accurate dosage compensation (PAA/PA expression ratio of 1 instead of 1.5). Therefore, an exact functional diploidization of the triploid genome does not occur, but a significant down regulation of gene expression in triploids was observed. However, for those genes with similar expression levels between diploids and triploids, expression is not globally strictly proportional to gene dosage nor is it set to a perfect diploid level. This quantitative expression flexibility may be a strong contributor to overcome the genomic shock, and be an immediate evolutionary advantage of allopolyploids.
Background
Bone morphogenetic protein (BMP)-2 and growth and differentiation factor (GDF)-5 are two related transforming growth factor (TGF)-β family members with important functions in embryonic development and tissue homeostasis. BMP-2 is best known for its osteoinductive properties whereas GDF-5—as evident from its alternative name, cartilage derived morphogenetic protein 1—plays an important role in the formation of cartilage. In spite of these differences both factors signal by binding to the same subset of BMP receptors, raising the question how these different functionalities are generated. The largest difference in receptor binding is observed in the interaction with the type I receptor BMPR-IA. GDF-5, in contrast to BMP-2, shows preferential binding to the isoform BMPR-IB, which is abrogated by a single amino acid (A57R) substitution. The resulting variant, GDF-5 R57A, represents a “BMP-2 mimic” with respect to BMP receptor binding. In this study we thus wanted to analyze whether the two growth factors can induce distinct signals via an identically composed receptor.
Results
Unexpectedly and dependent on the cellular context, GDF-5 R57A showed clear differences in its activity compared to BMP-2. In ATDC-5 cells, both ligands induced alkaline phosphatase (ALP) expression with similar potency. But in C2C12 cells, the BMP-2 mimic GDF-5 R57A (and also wild-type GDF-5) clearly antagonized BMP-2-mediated ALP expression, despite signaling in both cell lines occurring solely via BMPR-IA. The BMP-2- antagonizing properties of GDF-5 and GDF-5 R57A could also be observed in vivo when implanting BMP-2 and either one of the two GDF-5 ligands simultaneously at heterotopic sites.
Conclusions
Although comparison of the crystal structures of the GDF-5 R57A:BMPR-IAEC- and BMP-2:BMPR-IAEC complex revealed small ligand-specific differences, these cannot account for the different signaling characteristics because the complexes seem identical in both differently reacting cell lines. We thus predict an additional component, most likely a not yet identified GDF-5-specific co-receptor, which alters the output of the signaling complexes. Hence the presence or absence of this component then switches GDF-5′s signaling capabilities to act either similar to BMP-2 or as a BMP-2 antagonist. These findings might shed new light on the role of GDF-5, e.g., in cartilage maintenance and/or limb development in that it might act as an inhibitor of signaling events initiated by other BMPs.
Mimicking female insects to attract male pollinators is an important strategy in sexually deceptive orchids of the genus Ophrys, and some species possess flowers with conspicuous labellum patterns. The function of the variation of the patterns remains unresolved, with suggestions that these enhance pollinator communication. We investigated the possible function of the labellum pattern in Ophrys heldreichii, an orchid species in which the conspicuous and complex labellum pattern contrasts with a dark background. The orchid is pollinated exclusively by males of the solitary bee, Eucera berlandi. Comparisons of labellum patterns revealed that patterns within inflorescences are more similar than those of other conspecific plants. Field observations showed that the males approach at a great speed and directly land on flowers, but after an unsuccessful copulation attempt, bees hover close and visually scan the labellum pattern for up to a minute. Learning experiments conducted with honeybees as an accessible model of bee vision demonstrated that labellum patterns of different plants can be reliably learnt; in contrast, patterns of flowers from the same inflorescence could not be discriminated. These results support the hypothesis that variable labellum patterns in O. heldreichii are involved in flower-pollinator communication which would likely help these plants to avoid geitonogamy.
Eukaryotic cells are considered as evolutionary complex organisms because they possess organelles that enable them to regulate the spatio-temporal organization of cellular processes. Spatio-temporal organization of signal transduction cascades occurs in eukaryotic cells via organization of membrane-associated microdomains or lipid rafts. Lipid rafts are nanoscale-sized domains in the plasma membrane that are constituted by a specific set of lipids and proteins and harbor a number of proteins related to signal transduction and trafficking. The integrity of lipid rafts is important for the assembly and functional coordination of a plethora of signaling networks and associated processes. This integrity is partially mediated by a chaperone protein called flotillin. Disruption of lipid raft integrity, for example via depletion or overproduction of flotillin, alters raft-associated signal transduction cascades and causes severe diseases like Alzheimer’s, Parkinson’s disease or cardiovascular disease.
It was traditionally assumed that a sophisticated compartmentalization of cellular processes like the one exhibited in lipid rafts was exclusive to eukaryotic cells and therefore, lipid rafts have been considered as a hallmark in the evolution of cellular complexity, suggesting that prokaryotic cells were too simple organisms to organize such sophisticated membrane platforms. However, it was recently discovered that bacteria are also able to organize Functional Membrane Microdomains (FMMs) in their cellular membrane that are able to organize and catalyze the functionality of many diverse cellular processes. These FMMs of bacterial membranes contain flotillin-like proteins which play important roles in the organization of FMM-associated cellular processes.
In this dissertation I describe the structural and biological significance of the existence of two distinct flotillin proteins, FloA and FloT, in the FMMs of the bacterial model Bacillus subtilis. Localization studies, proteomic data and transcriptomic analyses show that FloA and FloT are individual scaffold proteins that activate different regulatory programs during bacterial growth. Using the tractable bacterial model system, I show that the functionality of important regulatory proteins, like the protease FtsH or the signaling kinases KinC, PhoR and ResE, is linked to the activity of FMMs and that this is a direct consequence of the scaffold activity of the bacterial flotillins. FloA and FloT distribute heterogeneously along the FMMs of B. subtilis thereby generating a heterogeneous population of FMMs that compartmentalize different signal transduction cascades. Interestingly, diversification of FMMs does not occur randomly, but rather in a controlled spatio-temporal program to ensure the activation of given signaling networks at the right place and time during cell growth.
Dimethyl fumarate (DMF) is approved for disease-modifying treatment of patients with relapsing-remitting multiple sclerosis. Animal experiments suggested that part of its therapeutic effect is due to a reduction of T-cell infiltration of the central nervous system (CNS) by uncertain mechanisms. Here we evaluated whether DMF and its primary metabolite monomethyl fumarate (MMF) modulate pro-inflammatory intracellular signaling and T-cell adhesiveness of nonimmortalized single donor human brain microvascular endothelial cells at low passages. Neither DMF nor MMF at concentrations of 10 or 50 \(\mu\)M blocked the IL-1\(\beta\)-induced nuclear translocation of NF-\(\kappa\)B/p65, whereas the higher concentration of DMF inhibited the nuclear entry of p65 in human umbilical vein endothelium cultured in parallel. DMF and MMF also did not alter the IL-1\(\beta\)-stimulated activation of p38 MAPK in brain endothelium. Furthermore, neither DMF nor MMF reduced the basal or IL-1\(\beta\)-inducible expression of ICAM-1. In accordance, both fumaric acid esters did not reduce the adhesion of activated Jurkat T cells to brain endothelium under basal or inflammatory conditions. Therefore, brain endothelial cells probably do not directly mediate a potential blocking effect of fumaric acid esters on the inflammatory infiltration of the CNS by T cells.
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.
Trypanosoma brucei is a uniflagellated protist and the causative agent of African trypanosomiasis, a neglected tropical disease. The single flagellum of T. brucei is essential to a number of cellular processes such as motility, and has been a longstanding focus of scientific enquiry. A number of cytoskeletal structures are associated with the flagellum in T. brucei, and one such structure—a multiprotein complex containing the repeat motif protein TbMORN1—is the focus of this review. The TbMORN1-containing complex, which was discovered less than ten years ago, is essential for the viability of the mammalian-infective form of T. brucei. The complex has an unusual asymmetric morphology, and is coiled around the flagellum to form a hook shape. Proteomic analysis using the proximity-dependent biotin identification (BioID) technique has elucidated a number of its components. Recent work has uncovered a role for TbMORN1 in facilitating protein entry into the cell, thus providing a link between the cytoskeleton and the endomembrane system. This review summarises the extant data on the complex, highlights the outstanding questions for future enquiry, and provides speculation as to its possible role in a size-exclusion mechanism for regulating protein entry. The review additionally clarifies the nomenclature associated with this topic, and proposes the adoption of the term “hook complex” to replace the former name “bilobe” to describe the complex.
Background:
Evidence that home telemonitoring for patients with chronic heart failure (CHF) offers clinical benefit over usual care is controversial as is evidence of a health economic advantage.
Methods:
Between January 2010 and June 2013, patients with a confirmed diagnosis of CHF were enrolled and randomly assigned to 2 study groups comprising usual care with and without an interactive bi-directional remote monitoring system (Motiva\(^{®}\)). The primary endpoint in CardioBBEAT is the Incremental Cost-Effectiveness Ratio (ICER) established by the groups' difference in total cost and in the combined clinical endpoint "days alive and not in hospital nor inpatient care per potential days in study" within the follow-up of 12 months.
Results:
A total of 621 predominantly male patients were enrolled, whereof 302 patients were assigned to the intervention group and 319 to the control group. Ischemic cardiomyopathy was the leading cause of heart failure. Despite randomization, subjects of the control group were more often in NYHA functional class III-IV, and exhibited peripheral edema and renal dysfunction more often. Additionally, the control and intervention groups differed in heart rhythm disorders. No differences existed regarding risk factor profile, comorbidities, echocardiographic parameters, especially left ventricular and diastolic diameter and ejection fraction, as well as functional test results, medication and quality of life. While the observed baseline differences may well be a play of chance, they are of clinical relevance. Therefore, the statistical analysis plan was extended to include adjusted analyses with respect to the baseline imbalances.
Conclusions:
CardioBBEAT provides prospective outcome data on both, clinical and health economic impact of home telemonitoring in CHF. The study differs by the use of a high evidence level randomized controlled trial (RCT) design along with actual cost data obtained from health insurance companies. Its results are conducive to informed political and economic decision-making with regard to home telemonitoring solutions as an option for health care. Overall, it contributes to developing advanced health economic evaluation instruments to be deployed within the specific context of the German Health Care System.
Based on the work of Eisenberg and Noe [2001], Suzuki [2002], Elsinger [2009] and Fischer [2014], we consider a generalization of Merton's asset valuation approach where n firms are linked by cross-ownership of equities and liabilities. Each firm is assumed to have a single outstanding liability, whereas its assets consist of one system-exogenous asset, as well as system-endogenous assets comprising some fraction of other firms' equity and liability, respectively. Following Fischer [2014], one can obtain no-arbitrage prices of equity and the recovery claims of liabilities as solutions of a fixed point problem, and hence obtain no-arbitrage prices of the `firm value' of each firm, which is the value of the firm's liability plus the firm's equity.
In a first step, we consider the two-firm case where explicit formulae for the no-arbitrage prices of the firm values are available (cf. Suzuki [2002]). Since firm values are derivatives of exogenous asset values, the distribution of firm values at maturity can be determined from the distribution of exogenous asset values. The Merton model and most of its known extensions do not account for the cross-ownership structure of the assets owned by the firm. Therefore the assumption of lognormally distributed exogenous assets leads to lognormally distributed firm values in such models, as the values of the liability and the equity add up to the exogenous asset's value (which has lognormal distribution by assumption). Our work therefore starts from lognormally distributed exogenous assets and reveals how cross-ownership, when correctly accounted for in the valuation process, affects the distribution of the firm value, which is not lognormal anymore. In a simulation study we examine the impact of several parameters (amount of cross-ownership of debt and equity, ratio of liabilities to expected exogenous assets value) on the differences between the distribution of firm values obtained from our model and correspondingly matched lognormal distributions. It becomes clear that the assumption of lognormally distributed firm values may lead to both over- and underestimation of the “true" firm values (within the cross-ownership model) and consequently of bankruptcy risk, too.
In a second step, the bankruptcy risk of one firm within the system is analyzed in more detail in a further simulation study, revealing that the correct incorporation of cross-ownership in the valuation procedure is the more important, the tighter the cross-ownership structure between the two firms. Furthermore, depending on the considered type of cross-ownership (debt or equity), the assumption of lognormally distributed firm values is likely to result in an over- resp. underestimation of the actual probability of default. In a similar vein, we consider the Value-at-Risk (VaR) of a firm in the system, which we calculate as the negative α-quantile of the firm value at maturity minus the firm's risk neutral price in t=0, i.e. we consider the (1-α)100%-VaR of the change in firm value. If we let the cross-ownership fractions (i.e. the fraction that one firm holds of another firm's debt or equity) converge to 1 (which is the supremum of the possible values that cross-ownership fractions can take), we can prove that in a system of two firms, the lognormal model will over- resp. underestimate both univariate and bivariate probabilities of default under cross-ownership of debt only resp. cross-ownership of equity only. Furthermore, we provide a formula that allows us to check for an arbitrary scenario of cross-ownership and any non-negative distribution of exogenous assets whether the approximating lognormal model will over- or underestimate the related probability of default of a firm. In particular, any given non-negative distribution of exogenous asset values (non-degenerate in a certain sense) can be transformed into a new, “extreme" distribution of exogenous assets yielding such a low or high actual probability of default that the approximating lognormal model will over- and underestimate this risk, respectively.
After this analysis of the univariate distribution of firm values under cross-ownership in a system of two firms with bivariately lognormally distributed exogenous asset values, we consider the copula of these firm values as a distribution-free measure of the dependency between these firm values. Without cross-ownership, this copula would be the Gaussian copula. Under cross-ownership, we especially consider the behaviour of the copula of firm values in the lower left and upper right corner of the unit square, and depending on the type of cross-ownership and the considered corner, we either obtain error bounds as to how good the copula of firm values under cross-ownership can be approximated with the Gaussian copula, or we see that the copula of firm values can be written as the copula of two linear combinations of exogenous asset values (note that these linear combinations are not lognormally distributed). These insights serve as a basis for our analysis of the tail dependence coefficient of firm values under cross-ownership. Under cross-ownership of debt only, firm values remain upper tail independent, whereas they become perfectly lower tail dependent if the correlation between exogenous asset values exceeds a certain positive threshold, which does not depend on the exact level of cross-ownership. Under cross-ownership of equity only, the situation is reverse in that firm values always remain lower tail independent, but upper tail independence is preserved if and only if the right tail behaviour of both firms’ values is determined by the right tail behaviour of the firms’ own exogenous asset value instead of the respective other firm’s exogenous asset value.
Next, we return to systems of n≥2 firms and analyze sensitivities of no-arbitrage prices of equity and the recovery claims of liabilities with respect to the model parameters. In the literature, such sensitivities are provided with respect to exogenous asset values by Gouriéroux et al. [2012], and we extend the existing results by considering how these no-arbitrage prices depend on the cross-ownership fractions and the level of liabilities. For the former, we can show that all prices are non-decreasing in any cross-ownership fraction in the model, and by use of a version of the Implicit Function Theorem we can also determine exact derivatives. For the latter, we show that the recovery value of debt and the equity value of a firm are non-decreasing and non-increasing in the firm's nominal level of liabilities, respectively, but the firm value is in general not monotone in the firm's level of liabilities. Furthermore, no-arbitrage prices of equity and the recovery claims of liabilities of a firm are in general non-monotone in the nominal level of liabilities of other firms in the system. If we confine ourselves to one type of cross-ownership (i.e. debt or equity), we can derive more precise relationships. All the results can be transferred to risk-neutral prices before maturity.
Finally, following Gouriéroux et al. [2012] and as a kind of extension to the above sensitivity results, we consider how immediate changes in exogenous asset values of one or more firms at maturity affect the financial health of a system of n initially solvent firms. We start with some theoretical considerations on what we call the contagion effect, namely the change in the endogenous asset value of a firm caused by shocks on the exogenous assets of firms within the system. For the two-firm case, an explicit formula is available, making clear that in general (and in particular under cross-ownership of equity only), the effect of contagion can be positive as well as negative, i.e. it can both, mitigate and exacerbate the change in the exogenous asset value of a firm. On the other hand, we cannot generally say that a tighter cross-ownership structure leads to bigger absolute contagion effects. Under cross-ownership of debt only, firms cannot profit from positive shocks beyond the direct effect on exogenous assets, as the contagion effect is always non-positive. Next, we are concerned with spillover effects of negative shocks on a subset of firms to other firms in the system (experiencing non-negative shocks themselves), driving them into default due to large losses in their endogenous asset values. Extending the results of Glasserman and Young [2015], we provide a necessary condition for the shock to cause such an event. This also yields an upper bound for the probability of such an event. We further investigate how the stability of a system of firms exposed to multiple shocks depends on the model parameters in a simulation study. In doing so, we consider three network types (incomplete, core-periphery and ring network) with simultaneous shocks on some of the firms and wiping out a certain percentage of their exogenous assets. Then we analyze for all three types of cross-ownership (debt only, equity only, both debt and equity) how the shock intensity, the shock size, and network parameters as the number of links in the network and the proportion of a firm's debt or equity held within the system of firms influences several output parameters, comprising the total number of defaults and the relative loss in the sum of firm values, among others. Comparing our results to the studies of Nier et al. [2007], Gai and Kapadia [2010] and Elliott et al. [2014], we can only partly confirm their results with respect to the number of defaults. We conclude our work with a theoretical comparison of the complete network (where each firm holds a part of any other firm) and the ring network with respect to the number of defaults caused by a shock on a single firm, as it is done by Allen and Gale [2000]. In line with the literature, we find that under cross-ownership of debt only, complete networks are “robust yet fragile" [Gai and Kapadia, 2010] in that moderate shocks can be completely withstood or drive the firm directly hit by the shock in default, but as soon as the shock exceeds a certain size, all firms are simultaneously in default. In contrast to that, firms default one by one in the ring network, with the first “contagious default" (i.e. a default of a firm not directly hit by the shock) already occurs for smaller shock sizes than under the complete network.
Breakdown of the blood-brain barrier (BBB) is an early hallmark of multiple sclerosis (MS), a progressive inflammatory disease of the central nervous system. Cell adhesion in the BBB is modulated by sphingosine-1-phosphate (S1P), a signaling protein, via S1P receptors (S1P\(_1\)). Fingolimod phosphate (FTY720-P) a functional S1P\(_1\) antagonist has been shown to improve the relapse rate in relapsing-remitting MS by preventing the egress of lymphocytes from lymph nodes. However, its role in modulating BBB permeabilityin particular, on the tight junction proteins occludin, claudin 5 and ZO-1has not been well elucidated to date. In the present study, FTY720-P did not change the transendothelial electrical resistance in a rat brain microvascular endothelial cell (RBMEC) culture exposed to inflammatory conditions and thus did not decrease endothelial barrier permeability. In contrast, occludin was reduced in RBMEC culture after adding FTY720-P. Additionally, FTY720-P did not alter the amount of endothelial matrix metalloproteinase (MMP)-9 and MMP-2 in RBMEC cultures. Taken together, our observations support the assumption that S1P\(_1\) plays a dual role in vascular permeability, depending on its ligand. Thus, S1P\(_1\) provides a mechanistic basis for FTY720-P-associated disruption of endothelial barrierssuch as the blood-retinal barrierwhich might result in macular edema.
Background
Information extraction techniques that get structured representations out of unstructured data make a large amount of clinically relevant information about patients accessible for semantic applications. These methods typically rely on standardized terminologies that guide this process. Many languages and clinical domains, however, lack appropriate resources and tools, as well as evaluations of their applications, especially if detailed conceptualizations of the domain are required. For instance, German transthoracic echocardiography reports have not been targeted sufficiently before, despite of their importance for clinical trials. This work therefore aimed at development and evaluation of an information extraction component with a fine-grained terminology that enables to recognize almost all relevant information stated in German transthoracic echocardiography reports at the University Hospital of Würzburg.
Methods
A domain expert validated and iteratively refined an automatically inferred base terminology. The terminology was used by an ontology-driven information extraction system that outputs attribute value pairs. The final component has been mapped to the central elements of a standardized terminology, and it has been evaluated according to documents with different layouts.
Results
The final system achieved state-of-the-art precision (micro average.996) and recall (micro average.961) on 100 test documents that represent more than 90 % of all reports. In particular, principal aspects as defined in a standardized external terminology were recognized with f 1=.989 (micro average) and f 1=.963 (macro average). As a result of keyword matching and restraint concept extraction, the system obtained high precision also on unstructured or exceptionally short documents, and documents with uncommon layout.
Conclusions
The developed terminology and the proposed information extraction system allow to extract fine-grained information from German semi-structured transthoracic echocardiography reports with very high precision and high recall on the majority of documents at the University Hospital of Würzburg. Extracted results populate a clinical data warehouse which supports clinical research.
In North Korea, the prevalence of hepatitis B is high due to natural factors, gaps in vaccination, and the lack of antiviral treatment. Aid projects are urgently needed, however impeded by North Korea's political and economical situation and isolation. The feasibility of a joint North Korean and German humanitarian hepatitis B prevention program was assessed. Part 1: Hepatitis B vaccination catch-up campaign. Part 2: Implementation of endoscopic ligation of esophageal varices (EVL) by trainings in Germany and North Korea. By vaccinating 7 million children between 2010 and 2012, the hepatitis B vaccination gap was closed. Coverage of 99.23% was reached. A total of 11 hepatitis B-induced liver cirrhosis patients (mean age 41.1 yr) with severe esophageal varices and previous bleedings were successfully treated by EVL without major complications. A clinical standard operating procedure, a feedback system and a follow-up plan were developed. The bi-modal preventive strategy was implemented successfully. Parts of the project can serve as an example for other low-income countries, however its general transferability is limited due to the special circumstances in North Korea.
Photoinduced processes are nowadays studied with a huge variety of spectroscopic methods. In the liquid phase, transient absorption spectroscopy is probably the most versatile pump–probe technique used to study light-induced molecular phenomena. Optical time-resolved spectroscopy is established in a large number of laboratories and is still further being developed with respect to many technical aspects. Nevertheless, the full potential of shortening the data-acquisition time—necessary for the investigation of rapidly photodegrading samples and observation of macroscopically fast processes—achievable with high-repetition-rate laser systems and shot-to-shot detection was not fully exploited. Especially, shot-to-shot detection is highly beneficial due to the high correlation of subsequent laser pulses.
The development and implementation of 100 kHz broadband shot-to-shot data acquisition was presented in Chapter 3. For an established laser dye as a benchmark system, ultrafast excited-state dynamics were measured for the first time with broadband shot-to-shot detection at 100 kHz. An analysis of both the noise characteristics of the employed laser and the correlation of subsequent pulses quantified the advantage of shot-to-shot data acquisition. In the utilized software environment, the time for measuring a complete data set could be sped up by a factor of three or even higher compared to a laser system working at 1 kHz. So far, the limiting factor is the data processing and the movement of the mechanical delay stage. Nevertheless, the new shot-to-shot detection has the potential to shorten the measurement time up to a factor of 100. The data quality is improved by a factor of three when the hitherto conventional averaging scheme is compared to shot-to-shot acquisition for the same number of laser pulses. The expansion of shot-to-shot data acquisition for high repetition rates will allow studies on sensitive samples as exposure times can strongly be reduced to achieve the same signal-to-noise ratio. In addition, multidimensional spectroscopy can also be extended to high-repetition shot-to-shot readout allowing an efficient recording of data. Therefore, in future experiments, dynamics and couplings in sensitive samples and kinetic processes could be studied in more detail.
Complex photophysical and photochemical phenomena are subject of many fields of research. Many of these multifaceted processes are not yet fully understood. Therefore, a possible approach is the elucidation of single reaction steps with the combination of transient absorption spectroscopy and a suitable, less complex model system. The systematic variation of the model system’s properties and environments, e.g., by chemical substitution or adequate choice of the solvent allows the determination of essential entities and reactivities thereof. Proper knowledge of an individual intermediate step and its determining factors can enhance the understanding of the complete photoreaction process.
The application of transient absorption spectroscopy was shown for the optically-induced electron transfer in a series of donor–acceptor oligomers in Chapter 4. In general, the solvent relaxation times were isolated from the back-electron-transfer dynamics by a global lifetime analysis. For the smallest oligomeric structure where complete charge separation is possible, an ultrafast equilibration leads to charge recombination from the configuration showing the lowest barrier for recombination. The back-electron transfer strongly depends on the utilized solvent. Whereas in dichloromethane the back-electron transfer occurs with the maximum rate in the barrierless optimal region, the dynamics in toluene are governed by a Marcus inverted-region effect. The experimentally observed rates were also estimated by theoretical calculations of the respective barriers. The study did not only successfully unravel charge transfer in the oligomeric systems but also improved the understanding of the electron-transfer properties of larger polymers from an earlier study. Therefore, the combination of length variation and time-resolved spectroscopy is an important step towards the correct prediction of charge-carrier dynamics in macroscopic devices, e.g., for photovoltaics.
The bond dissociation of a carbon-monoxide-releasing molecule in aqueous solution was studied in Chapter 5 as a prototype reaction for the photo-triggered breaking of a bond. It was shown that upon excitation only one carbon-monoxide ligand of the tricarbonyl complex is dissociated. A fraction of the photolyzed molecules restore the intact initial complex by geminate recombination within the temporal resolution of the experiment. However, the recombination could be detected by the hot ground-state infrared absorption of the complex. The detectable dicarbonyl formed upon CO release distributes excess energy from the absorbed photon into low-frequency modes which result in broadened absorption bands like for the recombined tricarbonyl. The free coordination site in the ligand sphere is filled with a solvent water molecule. Despite numerous studies of metal carbonyls studied in alkaneous solutions, the elucidation of the dynamics of a CORM in aqueous solution added another important detail to the photochemistry of this class of compounds. Experiments employing a second ultraviolet pump pulse did not trigger further CO dissociation and hence no formation of a monocarbonyl species; this might either be due to a different release mechanism without a further photochemical step or a strong spectral shift of the dicarbonyl’s absorption. Both reasons could explain why degenerate pump–repump–probe spectroscopy is inefficient. However, further experiments with ultraviolet probe pulses could substantiate whether the intermediate dicarbonyl reacts further photochemically or not. Apart from the model-system character of the CORM for bond dissociation, the study could determine exactly how many CO ligands are initially photolyzed off. Detailed knowledge of the release mechanism will affect the previous use and application as well as the further development of CORMs as therapeutic prodrugs to deliver high local concentrations of CO in cancerous or pathological tissue. Hence, the study of two-photon absorption properties which are important for in vivo applications of CORMs should be the main focus in further spectroscopic experiments.
In Chapter 6, both abovementioned molecular phenomena—electron transfer and bond dissociation—were studied in combination. The photochemistry of a tetrazolium salt was studied in detail in a variety of different solvents. Being a relatively small molecule, the studied tetrazolium cation shows a multifaceted photochemistry and is therefore a textbook example for the combination of ultrafast molecular phenomena studied in different environments. Within femtoseconds, the tetrazolium ring is opened. The biradicalic species is then reduced via uptake of an electron from the solvent. The formation of the ring-open formazan photoproduct from this point of the reaction sequence on was excluded by experiments with acidic pH value of the solution. The ring-open radical is stabilized by ring-closure. The resulting tetrazolinyl radical was already observed in experiments with microsecond time resolution. However, its formation was observed in real time for the first time in this study. Irradiation of a tetrazoliumsalt solution yields different photoproduct distributions depending on the solvent. However, it was shown that all photoproducts have a tetrazolinyl radical as a common precursor on an ultrafast time scale. In combination with studies from the literature, the complete photochemical conversion of a tetrazolium salt was clarified in this study. Apart from the prototype character of the reaction sequence, the reaction mechanism will have impact on research associated with life science where tetrazolium assays are used on a daily basis without taking into account of photochemical conversion of the indicating tetrazolium ion and its photochemically formed reactive intermediates. On the basis of the tetrazolium-ion photochemistry, the rich photochemistry of the formazan photoproduct, including structural rearrangements and subsequent reformation of the tetrazolium ion, might be the subject of future studies.
This thesis shows a method advancement and application of transient absorption spectroscopy to exemplary molecular model systems. The insights into each respective field did not only enlighten singular aspects, but have to be seen in a much larger context. Understanding complex photoinduced processes bottom-up by learning about their constituting steps—microscopically and on an ultrafast time scale—is an ideal method to approach understanding and prediction of phenomena in large molecular systems like biological or artificial architectures as for example used in photosynthetic light-harvesting and photovoltaics.
Within the framework of this thesis, photolysis reactions in the liquid phase were investigated by means of ultrafast optical spectroscopy. Apart from molecular studies dealing with the highly spin-dependent reactivity of diphenylcarbene (DPC) in binary solvent
mixtures and ligand dissociation reactions of so-called CO-releasing molecules (CORMs),
special emphasis was put on the implementation and characterization of methods improving
and extending the signal detection in conventional pump–probe transient absorption setups.
The assumption of DPC being an archetypal triplet-ground-state arylcarbene was recently questioned by matrix-isolation studies at low temperatures. DPC embedded in argon matrices revealed a hitherto unknown reactivity when the carbene environment was modified by small amounts of methanol dopant molecules. To complement these findings with liquid-phase experiments at room temperature, femtosecond pump–probe transient absorption spectroscopy with probing in the visible and ultraviolet regime was employed to unravel primary reaction processes of DPC in solvent mixtures. Supported by quantum chemical simulations conducted by our collaborators, it was shown that a competition between the reaction pathways occurs that not only depends on the solvent molecule near-by but also on its interaction with other solvent molecules. In-depth analysis of the solvation dynamics and the amount of nascent intermediates corroborates the importance of a hydrogen-bonded complex with a protic solvent molecule, in striking analogy to complexes found at cryogenic temperatures.
Probing the transient absorption of molecules in the mid-infrared spectral range benefits from the high chemical specificity of molecules’ vibrational signatures. The technique of chirped-pulse upconversion (CPU) constitutes a promising alternative to standard direct multichannel MCT detection when accessing this spectral detection window. Hence, one chapter of this thesis is dedicated to a direct comparison between both detection methods. By conducting an exemplary pump–probe transient absorption experiment, it became evident, that the additional nonlinear interaction step is responsible for increased noise levels when using CPU. However, a correction procedure capable of removing these additional noise contributions—stemming from the fundamental laser radiation used for upconversion—was successfully tested. Perhaps most importantly for various spectroscopic applications, CPU scored with a significantly extended detection bandwidth owing to the high pixel numbers of modern CCD cameras.
Transition-metal complexes capable of releasing small molecular messengers upon photoactivation are promising sources of gasotransmitters such as carbon monoxide (CO) or nitric oxide (NO) in biological applications. However, only little is known about the characteristic time scales of ligand dissociation in this class of molecules. For this purpose, two complexes were investigated with femtosecond time resolution: [Mn(CO)3(tpm)]Cl with tpm=tris(2-pyrazolyl)methane, a manganese tricarbonyl complex which has proven to be selective and cytotoxic to cancer cells, and [Mo(CO)2(NO)(iPr3tacn)]PF6 with iPr3tacn=1,4,7-triisopropyl-1,4,7-triazacyclononane, a molybdenum complex containing both carbonyl and nitrosyl ligands. By conducting pump–probe transient absorption measurements in different spectral probing windows supported by quantum chemical calculations and linear absorption spectroscopy, it was shown that both complexes are able to release one CO ligand within the first few picoseconds after UV excitation. The results complement existing studies which focused on the molecules’ ligand-releasing properties upon long-term exposure. The additional information gained on an ultrafast time scale provides a comprehensive understanding of individual reaction steps connected with ligand release in this class of molecules. Hence, the studies might create new incentives to develop modified molecules for specific applications.
Feedback efficiency and training effects during alpha band modulation over the sensorimotor cortex
(2015)
Neural oscillations can be measured by electroencephalography (EEG) and these oscillations can be characterized by their frequency, amplitude and phase. The mechanistic properties of neural oscillations and their synchronization are able to explain various aspects of many cognitive functions such as motor control, memory, attention, information transfer across brain regions, segmentation of the sensory input and perception (Arnal and Giraud, 2012). The alpha band frequency is the dominant oscillation in the human brain. This oscillatory activity is found in the scalp EEG at frequencies around 8-13 Hz in all healthy adults (Makeig et al., 2002) and considerable interest has been generated in exploring EEG alpha oscillations with regard to their role in cognitive (Klimesch et al., 1993; Hanselmayr et al., 2005), sensorimotor (Birbaumer, 2006; Sauseng et al., 2009) and physiological (Lehmann, 1971; Niedermeyer, 1997; Kiyatkin, 2010) aspects of human life. The ability to voluntarily regulate the alpha amplitude can be learned with neurofeedback training and offers the possibility to control a brain-computer interface (BCI), a muscle independent interaction channel. BCI research is predominantly focused on the signal processing, the classification and the algorithms necessary to translate brain signals into control commands than on the person interacting with the technical system. The end-user must be properly trained to be able to successfully use the BCI and factors such as task instructions, training, and especially feedback can therefore play an important role in learning to control a BCI (Neumann and Kübler, 2003; Pfurtscheller et al., 2006, 2007; Allison and Neuper, 2010; Friedrich et al., 2012; Kaufmann et al., 2013; Lotte et al., 2013).
The main purpose of this thesis was to investigate how end-users can efficiently be trained to perform alpha band modulation recorded over their sensorimotor cortex. The herein presented work comprises three studies with healthy participants and participants with schizophrenia focusing on the effects of feedback and training time on cortical activation patterns and performance. In the first study, the application of a realistic visual feedback to support end-users in developing a concrete feeling of kinesthetic motor imagery was tested in 2D and 3D visualization modality during a single training session. Participants were able to elicit the typical event-related desynchronisation responses over sensorimotor cortex in both conditions but the most significant decrease in the alpha band power was obtained following the three-dimensional realistic visualization. The second study strengthen the hypothesis that an enriched visual feedback with information about the quality of the input signal supports an easier approach for motor imagery based BCI control and can help to enhance performance. Significantly better performance levels were measurable during five online training sessions in the groups with enriched feedback as compared to a conventional simple visual feedback group, without significant differences in performance between the unimodal (visual) and multimodal (auditory–visual) feedback modality. Furthermore, the last study, in which people with schizophrenia participated in multiple sessions with simple feedback, demonstrated that these patients can learn to voluntarily regulate their alpha band. Compared to the healthy group they required longer training times and could not achieve performance levels as high as the control group. Nonetheless, alpha neurofeedback training lead to a constant increase of the alpha resting power across all 20 training session.
To date only little is known about the effects of feedback and training time on BCI performance and cortical activation patterns. The presented work contributes to the evidence that healthy individuals can benefit from enriched feedback: A realistic presentation can support participants in getting a concrete feeling of motor imagery and enriched feedback, which instructs participants about the quality of their input signal can give support while learning to control the BCI. This thesis demonstrates that people with schizophrenia can learn to gain control of their alpha oscillations recorded over the sensorimotor cortex when participating in sufficient training sessions. In conclusion, this thesis improved current motor imagery BCI feedback protocols and enhanced our understanding of the interplay between feedback and BCI performance.
Background:
Accurate preoperative assessment of the aortic annulus dimension is crucial for successful transcatheter aortic valve implantation (TAVI). In this study we validated a new method using two-dimensional transesophageal echocardiography (2D-TEE) for measurement of the aortic annulus prior to TAVI.
Methods:
We analysed 124 patients who underwent successful TAVI using a self-expandable prosthesis, divided equally into two groups; in the study group we used the cross sectional short axis 2D-TEE for measurement of the aortic annulus and in the control group we used the long axis 2D-TEE.
Results:
Both groups were comparable regarding the clinical parameters. On the other hand, patients in the study group had less left ventricular ejection fraction (38.9 % versus 45.6 %, p = 0.01). The aortic valve annulus was, although not statistically significant, smaller in the study group (21.58 versus 23.28 mm, p = 0.25). Post procedural quantification of the aortic regurgitation revealed that only one patient in both groups had severe aortic regurgitation (AR), in this patient the valve was implanted deep. The incidence of significant AR was higher in the control group (29.0 % versus 12.9 %, p = 0.027).
Conclusions:
Sizing of the aortic valve annulus using cross-sectional 2D-TEE offers a safe and plausible method for patients undergoing TAVI using the self-expandable prosthesis and is significantly superior to using long axis 2D-TEE.
The aim of this study was to explore the applicability of fast MR techniques to routine paediatric abdominopelvic MRI at 1.5 Tesla. "Controlled Aliasing in Parallel Imaging Results in Higher Acceleration-" (CAIPIRINHA-) accelerated contrast-enhanced-T1w 3D FLASH imaging was compared to standard T1w 2D FLASH imaging with breath-holding in 40 paediatric patients and to respiratory-triggered T1w TSE imaging in 10 sedated young children. In 20 nonsedated patients, we compared T2w TIRM to fat-saturated T2w HASTE imaging. Two observers performed an independent and blinded assessment of overall image quality. Acquisition time was reduced by the factor of 15 with CAIPIRINHA-accelerated T1w FLASH and by 7 with T2w HASTE. With CAIPIRINHA and with HASTE, there were significantly less motion artefacts in nonsedated patients. In sedated patients, respiratory-triggered T1w imaging in general showed better image quality. However, satisfactory image quality was achieved with CAIPIRINHA in two sedated patients where respiratory triggering failed. In summary, fast scanning with CAIPIRINHA and HASTE presents a reliable high quality alternative to standard sequences in paediatric abdominal MRI. Paediatric patients, in particular, benefit greatly from fast image acquisition with less breath-hold cycles or shorter sedation.
In interpersonal encounters, individuals often exhibit changes in their own facial expressions in response to emotional expressions of another person. Such changes are often called facial mimicry. While this tendency first appeared to be an automatic tendency of the perceiver to show the same emotional expression as the sender, evidence is now accumulating that situation, person, and relationship jointly determine whether and for which emotions such congruent facial behavior is shown. We review the evidence regarding the moderating influence of such factors on facial mimicry with a focus on understanding the meaning of facial responses to emotional expressions in a particular constellation. From this, we derive recommendations for a research agenda with a stronger focus on the most common forms of encounters, actual interactions with known others, and on assessing potential mediators of facial mimicry. We conclude that facial mimicry is modulated by many factors: attention deployment and sensitivity, detection of valence, emotional feelings, and social motivations. We posit that these are the more proximal causes of changes in facial mimicry due to changes in its social setting.
In summary, we have prepared single-wall carbon nanotube (SWNT) thin films by the method of evaporation-induced self-assembly (EISA). Using the scalable two-plate or lens setups, sorts of different film types or patterns of SWNTs has been successfully fabricated directly from the evaporation of solvents and could be precisely controlled by the concentrations of SWNT in ambient conditions. The special geometry of meniscus as the capillary bridge has not only given rise to a much higher efficiency of fabrication than what previously reported but also allowed us to monitor the pinning and depinning process carefully and further investigate the mechanism underlying the formation of different film morphologies.
In contrast with the conventional "stick-slip" model, we have provided the new dynamical pinning and zipping model for the contact line (CL) behavior. By analyzing the motion of CL and varying deposited patterns, the traditionally so-called "stick" state should be treated as a dynamical pinning process due to the interfacial tension contrast between SWNT-covered and bare silicon surface. Besides, the plausible one-step "slip" motion could be dominated by the zipping-like kink propagation.
In addition, the experiments with heated substrates at higher temperatures between 30°C and 50 °C have shown that the striped pattern could be fabricated by both much lower SWNT and SDS concentrations than that in room temperature, which is consistent with our model of interfacial tension contrast. In this situation, the deposition rate was increased but the quality of SWNT alignment was undermined because the corresponding moving velocity of SWNT was also too fast for SWNTs to rotate when the evaporative rate was high.
The similar results were identified by the SWNT/polymer conjugates dispersed in chloroform under the similar setups and other identical conditions. The typical breathing motion of dynamical pinning and zipping-like propagation for depinning were confirmed by the new suspensions despite that some morphological parameters changed dramatically compared with that from the aqueous solution. For example, the spacing between stripes reached 100 µm ~ 200 µm because the large contact angle contrast between HDMS- and SWNT-covered surface accompanies with the high evaporation rate of chloroform in the pinning and depinning process. Likewise the average CL velocity for fabrication reached around 20 µm/s due to the much higher evaporation rate of chloroform than water.
Using alike suspensions, the modified EISA method called dose-controlled floating evaporative self-assembly (DFES) was employed to implement the self-assembly of SWNTs on the water/air interface and then deposit them on solid substrate by directed floating. Although the stripes were fabricated successfully by drops with certain doses and SWNT concentrations, there inevitably existed randomly oriented SWNTs from the water surface that built networks between the stripes containing well-aligned tubes. In order to slow down the evaporation rate and monitor the process detailedly, we used chlorobenzene as the solvent instead of chloroform and find the typical pinning/depinning movement of the CL. A preliminary analysis of the results in terms of chlorobenzene implied that the CL possibly followed the similar pinning/depinning process in consistence with our model with capillary bridge.
In the last part of the thesis, the primary research on the optical properties of these stripes of ultrahigh purity semiconducting nanotubes was conducted by fluorescence microscopy and photoluminescence excitation (PLE) spectroscopy. The energy transfer of the photogenerated excitons was confirmed between different tube species with controlled band gaps.
In short, the experiments performed in this thesis allowed to gain new insights about the fabrication of large-area SWNT thin films by the cost-effective solution-processed method and most importantly to uncover its intrinsic mechanism as well. Combined with the separation and selection technique like density gradient centrifugation or polyfluorene derivatives assisted method, highly monodisperse semiconducting nanotubes could be deposited into organized, controllable and functional arrays.
Beyond the ambient conditions, precise control for the evaporation under preset temperature and vapor pressure could possibly extend the technique to the industry level. Assisted by some other mature techniques such as roll-to-roll printing, the cost-effective method could be widely used in the manufacture of various thin film devices. More complex 2D or even 3D structures could be designed and accomplished by the method for the functional or stretchable requirements. Further research on the fundamental exciton transition and diffusion in different networks or structures of SWNTs will be the significant precondition for the real applications.
Looking ahead, from the individual carbon nanotube to its thin film, this promising material with outstanding properties had many challenges to overcome before the real-world applications. Thanks to the availability of pure and well-defined materials, the scalable solution-processed approaches for fabrication of thin films should be able to unlock the potential of carbon nanotubes and exploit them in (opto-)electronic devices in the foreseeing future.
To trigger innate behavior, sensory neural networks are pre-tuned to extract biologically relevant stimuli. Many male-female or insect-plant interactions depend on this phenomenon. Especially communication among individuals within social groups depends on innate behaviors. One example is the efficient recruitment of nest mates by successful bumblebee foragers. Returning foragers release a recruitment pheromone in the nest while they perform a ‘dance’ behavior to activate unemployed nest mates. A major component of this pheromone is the sesquiterpenoid farnesol. How farnesol is processed and perceived by the olfactory system, has not yet been identified. It is much likely that processing farnesol involves an innate mechanism for the extraction of relevant information to trigger a fast and reliable behavioral response. To test this hypothesis, we used population response analyses of 100 antennal lobe (AL) neurons recorded in alive bumblebee workers under repeated stimulation with four behaviorally different, but chemically related odorants (geraniol, citronellol, citronellal and farnesol). The analysis identified a unique neural representation of the recruitment pheromone component compared to the other odorants that are predominantly emitted by flowers. The farnesol induced population activity in the AL allowed a reliable separation of farnesol from all other chemically related odor stimuli we tested. We conclude that the farnesol induced population activity may reflect a predetermined representation within the AL-neural network allowing efficient and fast extraction of a behaviorally relevant stimulus. Furthermore, the results show that population response analyses of multiple single AL-units may provide a powerful tool to identify distinct representations of behaviorally relevant odors.
Exploring the transport properties of the three-dimensional topological insulator material HgTe
(2015)
In the present thesis the transport properties of strained bulk HgTe devices are investigated. Strained HgTe forms a 3D TI and is of special interest for studying topological surface states, since it can be grown by MBE in high crystal quality. The low defect density leads to considerable mobility values, well above the mobilities of other TI materials. However, strained HgTe has a small band gap of ca. 20 meV. With respect to possible applications the question is important, under which conditions the surface transport occurs. To answer this question, the HgTe devices are investigated at dilution refrigerator temperatures (T<100 mK) in high magnetic fields of different orientation. The influence of top and back gate electrodes as well as surface protecting layers is discussed.
On the basis of an analysis of the quantum Hall behaviour it is shown that transport is dominated by the topological surface states in a surprisingly large parameter range. A dependence on the applied top gate voltage is presented for the topological surface states. It enables the first demonstration of an odd integer QHE sequence from the surfaces perpendicular to the magnetic field. Furthermore, the p-type QHE from the surface states is observed for the first time in any 3D TI. This is achieved in samples of high surface quality. It is concluded from the gate response that the screening behaviour in 3D TI devices is non-trivial. The transport data are qualitatively analysed by means of intuitive theoretical models.
India's economic rise since the 1990s has been followed by a more prominent global role for the country. Despite economic setbacks in recent years and huge domestic challenges like poverty, caste issues, and gender inequality, India today is almost universally characterised as an “emerging power”. At the same time, the country continues to show an enormous diversity. Thus, exploring emerging India can surely not be confined to economic analysis only. Instead, it is vital to take current developments in domestic and international politics, society, culture, religion, and political thinking into consideration as well. Following an interdisciplinary approach, contributions from Political Science, International Relations, Indology, Political Theory, and Economics are fundamental in order to grasp the country's diversity. This collection assembles eight essays which, individually, serve as working papers reflecting the authors' various research focuses, while collectively composing a multifaceted and multidis-ciplinary picture of emerging India. It thereby reflects the approach the University of Würz-burg’s Centre for Modern India and the Institute for Political Science and Sociology’s India Forum are committed to: bringing together different academic disciplines in order to generate nuanced insights into India’s manifold diversity.
The scope of computational chemistry can be broadened by developing new methods and more efficient algorithms. However, the evaluation of the applicability of the methods for the different fields of chemistry is equally important. In this thesis systems with an unusual and complex electronic structure, such as excitonic states in organic semiconductors, a boron-containing bipolaron and the excited states of pyracene were studied and the applicability of the toolkit of computational chemistry was investigated. Concerning the organic semiconductors the focus was laid on organic solar cells, which are one of the most promising technologies with regard to satisfying the world's need for cheap and environmentally sustainable energy. This is due to the low production and material costs and the possibility of using flexible and transparent devices. However, their efficiency does still not live up to the expectations. Especially the exciton diffusion lengths seem to be significantly too short. In order to arrive at improved modules, a fundamental understanding of the elementary processes occurring in the cell on the molecular and supramolecular level is needed. Computational chemistry can provide insight by separating the different effects and providing models for predictions and prescreenings. In this thesis, the focus was laid on the description of excitonic states in merocyanines and perylene-based dyes taking the influence of the environment into account.
At first, the photochemical isomerization between two configurations of 6-nitro BIPS observed experimentally was studied by first benchmarking several functionals against SCS-ADC(2) in the gas phase and subsequently calculating the excited-state potential energy surface. The geometries obtained from a relaxed scan in the ground state as well as from a scan in the excited state were used. The environment was included using different polarizable continuum models. It was shown that the choice of the model and especially the question of the state specificity of the approach is of vital importance. Using the results of the calculations, a two-dimensional potential energy surface could be constructed that could be used to explain the experimental findings. Furthermore, the importance of the excited-state isomerization as a potential deactivation channel in the exciton transport was pointed out.
Then the assessment of the suitability of different merocyanines for optoelectronic applications with quantum-chemical methods was discussed. At first, the effect of the environment on the geometry, especially on the bond length alternation pattern, was investigated. It was shown that the environment changes the character of the ground-state wave function of several merocyanines qualitatively, which means that the results of gas-phase calculations are meaningless - at least when a comparison with solution or device data is desired. It was demonstrated that using a polarizable continuum model with an effective epsilon, a qualitative agreement between the calculated geometry and the geometry in the crystal structure can be obtained. Therefore, by comparing the bond length alternation in solution and in the crystal, a rough estimate of the effect of the crystal environment can be made.
It was further shown that the connection between the HOMO energy and the open-circuit voltage is not as simple as it is often implied in the literature. It was discussed that it is not clear whether the HOMO of a single molecule or a $\pi$-stack containing several monomers should be used and if the environmental charges of the bulk phase or the interface should be included. Investigating the dependence of the HOMO energy on the stack size yielded no definitive trend. Furthermore, it was discussed that the effect due the optimization of the modules (solvent, bulk heterojunction) during the production masks any potential correlation between the HOMO energy and measured open-circuit values. Therefore, a trend can only be expected for unoptimized bilayer cells. It was concluded that ultimately, the importance of the HOMO energy should not be overestimated.
The correlation between the exciton reorganization energy and the so-called cyanine limit, which is predicted by a simple two-state model, was also discussed. By referring to the results of VB calculations, it was discussed that the correlation indeed exists and is non-negligible, although the effect is not as strong as one might have expected. In this context, a potential application of a VB/MM approach was covered briefly. The importance of the molecular reorganization energy and the device morphology was also discussed.
It was concluded that the optimization of merocyanines for organic optoelectronic devices is inherently a multiparameter problem and one cannot expect to find one particular parameter, which solely controls the efficiency.
The perylene-based dyes were studied with a focus on the description of a potential trapping mechanism involving an intermolecular motion in a dimer. The aim was to find methods which can be applied to larger model systems than a dimer and take the effect of the environment into account. As a test coordinate the longitudinal shift of two monomers against each other was used. At first, it was demonstrated how the character of an excited state in a dimer can be defined and how it can be extracted from a standard quantum-chemical calculation. Then several functionals were benchmarked and their applicability or failure was rationalized using the character analysis. Two recipes could be proposed, which were applied to a constraint optimization (only intermolecular degrees of freedom) in the excited states of the PBI dimer and to the description of the potential energy surfaces of ground and excited states along a longitudinal displacement in the perylene tetramer, respectively.
It was further demonstrated that the semi-empirical OMx methods fail to give an accurate description of the excited-state potential energy surfaces as well as the ground-state surface along the test coordinate. This failure could be attributed to an underestimation of overlap-dependent terms. Consequently, it could be shown that the methods are applicable to large intermolecular distances, where the overlap is negligible. The results of DFT calculations with differently composed basis sets suggested that adding an additional single p-function for each atom should significantly improve the performance.
QM/MM methods are ideally suited to take the effect of the environment on a a dimer model system into account. However, it was shown that standard force fields also give an incorrect description of the interaction between the monomers along the intermolecular coordinate. This failure was attributed to the isotropic atom-atom interaction in the repulsion term of the Lennard-Jones potential. This was corroborated using two simple proof-of-principle anisotropy models. Therefore, a novel force field called OPLS-AA_O was presented that is based on OPLS-AA, but uses an anisotropic model for the repulsion. The model involves the overlap integral between the molecular densities, which are modeled as a sum of atom-centered p-type Gaussian functions. It was shown that using this force field an excellent agreement with the DFT results can be obtained when the correct parameters are used. These parameters, however, are not very generalizable, which was attributed to the simplicity of the model in its current state (using the same exponential parameter for all atoms). As a short excursion, the applicability of an MO-based overlap model was discussed.
It was demonstrated that the repulsion term based on the density overlap can be used to correct the failure of the OMx methods for the ground states. This is in accord with the assumption that an underestimation of the overlap terms is responsible for the failure.
It was shown that OPLS-AA_O also gives an excellent description of the longitudinal shift in a PBI tetramer. Using the tetramer as a test system and applying the recipe obtained in the TDDFT benchmark for the QM-part and OPLS-AA_O for the MM-part in conjunction with an electrostatic embedding scheme, a QM/MM description of the excited states of the PBI dimer including the effect of the environment could be obtained.
In the last chapter the theoretical description of the Bis(borolyl)thiophene dianion and the excited states of pyracene were discussed. The electronic structure of the Bis(borolyl)thiophene dianion - a negative bipolaron - was elucidated using DFT and CASPT2 methods. Furthermore, an estimation of the extent of triplet admixture to the ground state due to spin-orbit coupling was given.
In the second project the S1 and S2 states of pyracene were computed using SCS-CC2 and SCS-ADC(2) and an estimation for the balance between aromaticity and ring strain was given. This also involved computing the vibrational frequencies in the excited states.
In both studies the results of the computations were able to rationalize and complete experimental results.
An efficient and accurate computational framework for solving control problems governed by quantum spin systems is presented. Spin systems are extremely important in modern quantum technologies such as nuclear magnetic resonance spectroscopy, quantum imaging and quantum computing. In these applications, two classes of quantum control problems arise: optimal control problems and exact-controllability problems, with a bilinear con- trol structure. These models correspond to the Schrödinger-Pauli equation, describing the time evolution of a spinor, and the Liouville-von Neumann master equation, describing the time evolution of a spinor and a density operator. This thesis focuses on quantum control problems governed by these models. An appropriate definition of the optimiza- tion objectives and of the admissible set of control functions allows to construct controls with specific properties. These properties are in general required by the physics and the technologies involved in quantum control applications. A main purpose of this work is to address non-differentiable quantum control problems. For this reason, a computational framework is developed to address optimal-control prob- lems, with possibly L1 -penalization term in the cost-functional, and exact-controllability problems. In both cases the set of admissible control functions is a subset of a Hilbert space. The bilinear control structure of the quantum model, the L1 -penalization term and the control constraints generate high non-linearities that make difficult to solve and analyse the corresponding control problems. The first part of this thesis focuses on the physical description of the spin of particles and of the magnetic resonance phenomenon. Afterwards, the controlled Schrödinger- Pauli equation and the Liouville-von Neumann master equation are discussed. These equations, like many other controlled quantum models, can be represented by dynamical systems with a bilinear control structure. In the second part of this thesis, theoretical investigations of optimal control problems, with a possible L1 -penalization term in the objective and control constraints, are consid- ered. In particular, existence of solutions, optimality conditions, and regularity properties of the optimal controls are discussed. In order to solve these optimal control problems, semi-smooth Newton methods are developed and proved to be superlinear convergent. The main difficulty in the implementation of a Newton method for optimal control prob- lems comes from the dimension of the Jacobian operator. In a discrete form, the Jacobian is a very large matrix, and this fact makes its construction infeasible from a practical point of view. For this reason, the focus of this work is on inexact Krylov-Newton methods, that combine the Newton method with Krylov iterative solvers for linear systems, and allows to avoid the construction of the discrete Jacobian. In the third part of this thesis, two methodologies for the exact-controllability of quan- tum spin systems are presented. The first method consists of a continuation technique, while the second method is based on a particular reformulation of the exact-control prob- lem. Both these methodologies address minimum L2 -norm exact-controllability problems. In the fourth part, the thesis focuses on the numerical analysis of quantum con- trol problems. In particular, the modified Crank-Nicolson scheme as an adequate time discretization of the Schrödinger equation is discussed, the first-discretize-then-optimize strategy is used to obtain a discrete reduced gradient formula for the differentiable part of the optimization objective, and implementation details and globalization strategies to guarantee an adequate numerical behaviour of semi-smooth Newton methods are treated. In the last part of this work, several numerical experiments are performed to vali- date the theoretical results and demonstrate the ability of the proposed computational framework to solve quantum spin control problems.
Introduction:
Tofacitinib is an oral Janus kinase inhibitor for the treatment of rheumatoid arthritis (RA). During the clinical development programme, increases in mean serum creatinine (SCr) of approximately 0.07 mg/dL and 0.08 mg/dL were observed which plateaued early. This study assessed changes in measured glomerular filtration rate (mGFR) with tofacitinib relative to placebo in patients with active RA.
Methods:
This was a randomised, placebo-controlled, Phase 1 study (NCT01484561). Patients were aged \(\geq\)18 years with active RA. Patients were randomised 2: 1 to oral tofacitinib 10 mg twice daily (BID) in Period 1 then placebo BID in Period 2 (tofacitinib -> placebo); or oral placebo BID in both Periods (placebo. placebo). Change in mGFR was evaluated by iohexol serum clearance at four time points (run-in, pre-dose in Period 1, Period 1 end, and Period 2 end). The primary endpoint was the change in mGFR from baseline to Period 1 end. Secondary endpoints included: change in mGFR at other time points; change in estimated GFR (eGFR; Cockcroft-Gault equation) and SCr; efficacy; and safety.
Results:
148 patients were randomised to tofacitinib -> placebo (N = 97) or placebo -> placebo (N = 51). Baseline characteristics were similar between groups. A reduction of 8% (90% confidence interval [CI]: 2%, 14%) from baseline in adjusted geometric mean mGFR was observed during tofacitinib treatment in Period 1 vs placebo. During Period 2, mean mGFR returned towards baseline during placebo treatment, and there was no difference between the two treatment groups at the end of the study - ratio (tofacitinib -> placebo/placebo -> placebo) of adjusted geometric mean fold change of mGFR was 1.04 (90% CI: 0.97, 1.11). Post-hoc analyses, focussed on mGFR variability in placebo -> placebo patients, were consistent with this conclusion. At study end, similar results were observed for eGFR and SCr. Clinical efficacy and safety were consistent with prior studies.
Conclusion:
Increases in mean SCr and decreases in eGFR in tofacitinib-treated patients with RA may occur in parallel with decreases in mean mGFR; mGFR returned towards baseline after tofacitinib discontinuation, with no significant difference vs placebo, even after post-hoc analyses. Safety monitoring will continue in ongoing and future clinical studies and routine pharmacovigilance.
Recently, several backpack-mounted systems, also known as personal laser scanning systems, have been developed. They consist of laser scanners or cameras that are carried by a human operator to acquire measurements of the environment while walking. These systems were first designed to overcome the challenges of mapping indoor environments with doors and stairs. While the human operator inherently has the ability to open doors and to climb stairs, the flexible movements introduce irregularities of the trajectory to the system. To compete with other mapping systems, the accuracy of these systems has to be evaluated. In this paper, we present an extensive evaluation of our backpack mobile mapping system in indoor environments. It is shown that the system can deal with the normal human walking motion, but has problems with irregular jittering. Moreover, we demonstrate the applicability of the backpack in a suitable urban scenario.