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Institute
- Theodor-Boveri-Institut für Biowissenschaften (115)
- Graduate School of Life Sciences (67)
- Medizinische Klinik und Poliklinik II (45)
- Institut für Anorganische Chemie (44)
- Neurologische Klinik und Poliklinik (36)
- Institut für Organische Chemie (34)
- Institut für Psychologie (34)
- Institut für Informatik (28)
- Institut für Geographie und Geologie (26)
- Klinik und Poliklinik für Anästhesiologie (ab 2004) (25)
Sonstige beteiligte Institutionen
- Siemens AG (2)
- Agricultural Center, BASF SE, 67117 Limburgerhof, Germany (1)
- Center of Excellence for Science and Technology - Integration of Mediterranean region (STIM), Faculty of Science, University of Split, Poljička cesta 35, 2100 Split, Croatia (1)
- Core Unit Systemmedizin (1)
- DFG Forschungsgruppe 2757 / Lokale Selbstregelungen im Kontext schwacher Staatlichkeit in Antike und Moderne (LoSAM) (1)
- Departamento de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain (1)
- Department of Chemistry, Humboldt Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany (1)
- Deutsches Archäologisches Institut (1)
- Deutsches Zentrum für Luft- und Raumfahrt (DLR), Institut für Raumfahrtsysteme (1)
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck, CMBI, Leopold-Franzens University Innsbruck, Austria (1)
Single molecule localization microscopy has seen a remarkable growth since its first
experimental implementations about a decade ago. Despite its technical challenges,
it is already widely used in medicine and biology and is valued as a unique tool
to gain molecular information with high specificity. However, common illumination techniques do not allow the use of single molecule sensitive super-resolution
microscopy techniques such as direct stochastic optical reconstruction microscopy
(dSTORM) for whole cell imaging. In addition, they can potentially alter the
quantitative information.
In this thesis, I combine dSTORM imaging in three dimensions with lattice lightsheet illumination to gain quantitative molecular information from cells unperturbed by the illumination and cover slip effects. Lattice light-sheet illumination
uses optical lattices for beam shaping to restrict the illumination to the detectable
volume. I describe the theoretical background needed for both techniques and detail
the experimental realization of the system as well as the software that I developed
to efficiently evaluate the data.
Eventually, I will present key datasets that demonstrate the capabilities of the
developed microscope system with and without dSTORM. My main goal here was
to use these techniques for imaging the neural cell adhesion molecule (NCAM, also
known as CD56) in whole cells. NCAM is a plasma membrane receptor known to
play a key role in biological processes such as memory and learning. Combining
dSTORM and lattice light-sheet illumination enables the collection of quantitative
data of the distribution of molecules across the whole plasma membrane, and shows
an accumulation of NCAM at cell-cell interfaces. The low phototoxicity of lattice
light-sheet illumination further allows for tracking individual NCAM dimers in living cells, showing a significant dependence of its mobility on the actin skeleton of
the cell.
Wurmb, Thomas ; Scholtes, Katja ; Kolibay, Felix ; Schorscher, Nora ; Ertl, Georg ; Ernestus, Ralf-Ingo ; Vogel, Ulrich ; Franke, Axel ; Kowalzik, Barbara
Mass critical care caused by the severe acute respiratory syndrome corona virus 2 pandemic poses an extreme challenge to hospitals. The primary goal of hospital disaster preparedness and response is to maintain conventional or contingency care for as long as possible. Crisis care must be delayed as long as possible by appropriate measures. Increasing the intensive care unit (ICU) capacities is essential. In order to adjust surge capacity, the reduction of planned, elective patient care is an adequate response. However, this involves numerous problems that must be solved with a sense of proportion. This paper summarises preparedness and response measures recommended to acute care hospitals.
Wurmb, Thomas ; Franke, Axel ; Schorscher, Nora ; Kowalzik, Barbara ; Helm, Matthias ; Bohnen, Renate ; Helmerichs, Jutta ; Grueneisen, Ulrich ; Cwojdzinski, Detlef ; Jung, Georg ; Lücking, Gesa ; Weber, Martin
Purpose
Rescue missions during terrorist attacks are extremely challenging for all rescue forces (police as well as non-police forces) involved. To improve the quality and safety of the rescue missions during an active killing event, it is obligatory to adapt common rescue mission goals and strategies.
Methods
After the recent attacks in Europe, the Federal Office of Civil Protection and Disaster Assistance started an evaluation process on behalf of the Federal Ministry of the Interior and the Federal Ministry of Health. This was done to identify weaknesses, lessons learned and to formulate new adapted guidelines.
Results
The presented bullet point recommendations summarise the basic and most important results of the ongoing evaluation process for the Federal Republic of Germany. The safety of all the rescue forces and survival of the greatest possible number of casualties are the priority goals. Furthermore, the preservation and re-establishment of the socio-political integrity are the overarching goals of the management of active killing events. Strategic incident priorities are to stop the killing and to save as much lives as possible. The early identification and prioritised transportation of casualties with life-threatening non-controllable bleeding are major tasks and the shortest possible on-scene time is an important requirement with respect to safety issues.
Conclusion
With respect to hazard prevention tactics within Germany, we attributed the highest priority impact to the bullet points. The focus of the process has now shifted to intense work about possible solutions for the identified deficits and implementation strategies of such solutions during mass killing incidents.
Multifunctional calcium phosphate based coatings on titanium implants with integrated trace elements
(2020)
Wolf-Brandstetter, C ; Beutner, R ; Hess, R ; Bierbaum, S ; Wagner, K ; Scharnweber, D ; Gbureck, U ; Moseke, C
For decades, the main focus of titanium implants developed to restore bone functionality was on improved osseointegration. Additional antimicrobial properties have now become desirable, due to the risk that rising antibiotic resistance poses for implant-associated infections. To this end, the trace elements of copper and zinc were integrated into calcium phosphate based coatings by electrochemically assisted deposition. In addition to their antimicrobial activity, zinc is reported to attract bone progenitor cells through chemotaxis and thus increase osteogenic differentiation, and copper to stimulate angiogenesis. Quantities of up to 68.9 ± 0.1 μg cm\(^{-2}\) of copper and 56.6 ± 0.4 μg cm\(^{-2}\) of zinc were deposited; co-deposition of both ions did not influence the amount of zinc but slightly increased the amount of copper in the coatings. The release of deposited copper and zinc species was negligible in serum-free simulated body fluid. In protein-containing solutions, a burst release of up to 10 μg ml\(^{-1}\) was observed for copper, while zinc was released continuously for up to 14 days. The presence of zinc was beneficial for adhesion and growth of human mesenchymal stromal cells in a concentration-dependent manner, but cytotoxic effects were already visible for coatings with an intermediate copper content. However, co-deposited zinc could somewhat alleviate the adverse effects of copper. Antimicrobial tests with E. coli revealed a decrease in adherent bacteria on brushite without copper or zinc of 60%, but if the coating contained both ions there was almost no bacterial adhesion after 12 h. Coatings with high zinc content and intermediate copper content had the overall best multifunctional properties.
Excitation energy transport in DNA modelled by multi-chromophoric field-induced surface hopping
(2020)
Absorption of ultraviolet light is known as a major source of carcinogenic mutations of DNA. The underlying processes of excitation energy dissipation are yet not fully understood. In this work we provide a new and generally applicable route for studying the excitation energy transport in multi-chromophoric complexes at an atomistic level. The surface-hopping approach in the frame of the extended Frenkel exciton model combined with QM/MM techniques allowed us to simulate the photodynamics of the alternating (dAdT)10 : (dAdT)10 double-stranded DNA. In accordance with recent experiments, we find that the excited state decay is multiexponential, involving a long and a short component which are due to two distinct mechanisms: formation of long-lived delocalized excitonic and charge transfer states vs. ultrafast decaying localized states resembling those of the bare nucleobases. Our simulations explain all stages of the ultrafast photodynamics including initial photoexcitation, dynamical evolution out of the Franck-Condon region, excimer formation and nonradiative relaxation to the ground state.
This cumulative dissertation is organized as follows:
After the introduction, the second chapter, based on “Asymptotic independence of bivariate order statistics” (2017) by Falk and Wisheckel, is an investigation of the asymptotic dependence behavior of the components of bivariate order statistics. We find that the two components of the order statistics become asymptotically independent for certain combinations of (sequences of) indices that are selected, and it turns out that no further assumptions on the dependence of the two components in the underlying sample are necessary. To establish this, an explicit representation of the conditional distribution of bivariate order statistics is derived.
Chapter 3 is from “Conditional tail independence in archimedean copula models” (2019) by Falk, Padoan and Wisheckel and deals with the conditional distribution of an Archimedean copula, conditioned on one of its components. We show that its tails are independent under minor conditions on the generator function, even if the unconditional tails were dependent. The theoretical findings are underlined by a simulation study and can be generalized to Archimax copulas.
“Generalized pareto copulas: A key to multivariate extremes” (2019) by Falk, Padoan and Wisheckel lead to Chapter 4 where we introduce a nonparametric approach to estimate the probability that a random vector exceeds a fixed threshold if it follows a Generalized Pareto copula. To this end, some theory underlying the concept of Generalized Pareto distributions is presented first, the estimation procedure is tested using a simulation and finally applied to a dataset of air pollution parameters in Milan, Italy, from 2002 until 2017.
The fifth chapter collects some additional results on derivatives of D-norms, in particular a condition for the existence of directional derivatives, and multivariate spacings, specifically an explicit formula for the second-to-last bivariate spacing.
Design choices: Empirical recommendations for designing two-dimensional finger-tracking experiments
(2020)
The continuous tracking of mouse or finger movements has become an increasingly popular research method for investigating cognitive and motivational processes such as decision-making, action-planning, and executive functions. In the present paper, we evaluate and discuss how apparently trivial design choices of researchers may impact participants’ behavior and, consequently, a study’s results. We first provide a thorough comparison of mouse- and finger-tracking setups on the basis of a Simon task. We then vary a comprehensive set of design factors, including spatial layout, movement extent, time of stimulus onset, size of the target areas, and hit detection in a finger-tracking variant of this task. We explore the impact of these variations on a broad spectrum of movement parameters that are typically used to describe movement trajectories. Based on our findings, we suggest several recommendations for best practice that avoid some of the pitfalls of the methodology. Keeping these recommendations in mind will allow for informed decisions when planning and conducting future tracking experiments.
Comprehensive investigation in motor neuron disease is vital not to miss a treatable differential diagnosis. Neuroborreliosis should be considered during an ALS work‐up. However, false‐positive CSF results do occur, and thus, results should be interpreted carefully in context of all clinical test results.
Process model comprehension is essential in order to understand the five Ws (i.e., who, what, where, when, and why) pertaining to the processes of organizations. However, research in this context showed that a proper comprehension of process models often poses a challenge in practice. For this reason, a vast body of research exists studying the factors having an influence on process model comprehension. In order to point research towards a neuro-centric perspective in this context, the paper at hand evaluates the appropriateness of measuring the electrodermal activity (EDA) during the comprehension of process models. Therefore, a preliminary test run and a feasibility study were conducted relying on an EDA and physical activity sensor to record the EDA during process model comprehension. The insights obtained from the feasibility study demonstrated that process model comprehension leads to an increased activity in the EDA. Furthermore, EDA-related results indicated significantly that participants were confronted with a higher cognitive load during the comprehension of complex process models. In addition, the experiences and limitations we learned in measuring the EDA during the comprehension of process models are discussed in this paper. In conclusion, the feasibility study demonstrated that the measurement of the EDA could be an appropriate method to obtain new insights into process model comprehension.
The subject of this thesis is the fabrication and characterization of magnetic topological
insulator layers of (V,Bi,Sb)\(_2\)Te\(_3\) exhibiting the quantum anomalous Hall
effect. A major task was the experimental realization of the quantum anomalous
Hall effect, which is only observed in layers with very specific structural,
electronic and magnetic properties. These properties and their influence on the
quantum anomalous Hall effect are analyzed in detail.
First, the optimal conditions for the growth of pure Bi\(_2\)Te\(_3\) and Sb\(_2\)Te\(_3\) crystal
layers and the resulting structural quality are studied. The crystalline quality of
Bi\(_2\)Te\(_3\) improves significantly at higher growth temperatures resulting in a small
mosaicity-tilt and reduced twinning defects. The optimal growth temperature is
determined as 260\(^{\circ}\)C, low enough to avoid desorption while maintaining a high
crystalline quality.
The crystalline quality of Sb\(_2\)Te\(_3\) is less dependent on the growth temperature.
Temperatures below 230\(^{\circ}\)C are necessary to avoid significant material desorption,
though. Especially for the nucleation on Si(111)-H, a low sticking coefficient is
observed preventing the coalescence of islands into a homogeneous layer.
The influence of the substrate type, miscut and annealing sequence on the growth
of Bi\(_2\)Te\(_3\) layers is investigated. The alignment of the layer changes depending on
the miscut angle and annealing sequence: Typically, layer planes align parallel to
the Si(111) planes. This can enhance the twin suppression due to transfer of the
stacking order from the substrate to the layer at step edges, but results in a step
bunched layer morphology. For specific substrate preparations, however, the layer
planes are observed to align parallel to the surface plane. This alignment avoids
displacement at the step edges, which would cause anti-phase domains. This results
in narrow Bragg peaks in XRD rocking curve scans due to long-range order in
the absence of anti-phase domains. Furthermore, the use of rough Fe:InP(111):B
substrates leads to a strong reduction of twinning defects and a significantly reduced
mosaicity-twist due to the smaller lattice mismatch.
Next, the magnetically doped mixed compound V\(_z\)(Bi\(_{1−x}\)Sb\(_x\))\(_{2−z}\)Te\(_3\) is studied in
order to realize the quantum anomalous Hall effect. The addition of V and Bi to
Sb\(_2\)Te\(_3\) leads to efficient nucleation on the Si(111)-H surface and a closed, homogeneous
layer. Magneto-transport measurements of layers reveal a finite anomalous
Hall resistivity significantly below the von Klitzing constant. The observation of
the quantum anomalous Hall effect requires the complete suppression of parasitic
bulklike conduction due to defect induced carriers. This can be achieved by optimizing
the thickness, composition and growth conditions of the layers.
The growth temperature is observed to strongly influence the structural quality.
Elevated temperatures result in bigger islands, improved crystallographic orientation
and reduced twinning. On the other hand, desorption of primarily Sb is
observed, affecting the thickness, composition and reproducibility of the layers.
At 190\(^{\circ}\)C, desorption is avoided enabling precise control of layer thickness and
composition of the quaternary compound while maintaining a high structural
quality.
It is especially important to optimize the Bi/Sb ratio in the (V,Bi,Sb)\(_2\)Te\(_3\) layers,
since by alloying n-type Bi\(_2\)Te\(_3\) and p-type Sb\(_2\)Te\(_3\) charge neutrality is achieved at
a specific mixing ratio. This is necessary to shift the Fermi level into the magnetic
exchange gap and fully suppress the bulk conduction. The Sb content x furthermore
influences the in-plane lattice constant a significantly. This is utilized to
accurately determine x even for thin films below 10 nm thickness required for the
quantum anomalous Hall effect. Furthermore, x strongly influences the surface
morphology: with increasing x the island size decreases and the RMS roughness
increases by up to a factor of 4 between x = 0 and x = 1.
A series of samples with x varied between 0.56-0.95 is grown, while carefully
maintaining a constant thickness of 9 nm and a doping concentration of 2 at.% V.
Magneto-transport measurements reveal the charge neutral point around x = 0.86
at 4.2 K. The maximum of the anomalous Hall resistivity of 0.44 h/e\(^2\) is observed
at x = 0.77 close to charge neutrality. Reducing the measurement temperature
to 50 mK significantly increases the anomalous Hall resistivity. Several samples
in a narrow range of x between 0.76-0.79 show the quantum anomalous Hall effect
with the Hall resistivity reaching the von Klitzing constant and a vanishing
longitudinal resistivity. Having realized the quantum anomalous Hall effect as the
first group in Europe, this breakthrough enabled us to study the electronic and
magnetic properties of the samples in close collaborations with other groups.
In collaboration with the Physikalisch-Technische Bundesanstalt high-precision
measurements were conducted with detailed error analysis yielding a relative de-
viation from the von Klitzing constant of (0.17 \(\pm\) 0.25) * 10\(^{−6}\). This is published
as the smallest, most precise value at that time, proving the high quality of the
provided samples. This result paves the way for the application of magnetic topological
insulators as zero-field resistance standards.
Non-local magneto-transport measurements were conducted at 15 mK in close
collaboration with the transport group in EP3. The results prove that transport
happens through chiral edge channels. The detailed analysis of small anomalies in
transport measurements reveals instabilities in the magnetic phase even at 15 mK.
Their time dependent nature indicates the presence of superparamagnetic contributions
in the nominally ferromagnetic phase.
Next, the influence of the capping layer and the substrate type on structural properties
and the impact on the quantum anomalous Hall effect is investigated. To
this end, a layer was grown on a semi-insulating Fe:InP(111)B substrate using the
previously optimized growth conditions. The crystalline quality is improved significantly
with the mosaicity twist reduced from 5.4\(^{\circ}\) to 1.0\(^{\circ}\). Furthermore, a layer
without protective capping layer was grown on Si and studied after providing sufficient
time for degradation. The uncapped layer on Si shows perfect quantization,
while the layer on InP deviates by about 5%. This may be caused by the higher
crystalline quality, but variations in e.g. Sb content cannot be ruled out as the
cause. Overall, the quantum anomalous Hall effect seems robust against changes
in substrate and capping layer with only little deviations.
Furthermore, the dependence of the quantum anomalous Hall effect on the thickness
of the layers is investigated. Between 5-8 nm thickness the material typically
transitions from a 2D topological insulator with hybridized top and bottom surface
states to a 3D topological insulator. A set of samples with 6 nm, 8 nm, and
9 nm thickness exhibits the quantum anomalous Hall effect, while 5 nm and 15 nm
thick layers show significant bulk contributions. The analysis of the longitudinal
and Hall conductivity during the reversal of magnetization reveals distinct differences
between different thicknesses. The 6 nm thick layer shows scaling consistent
with the integer quantum Hall effect, while the 9 nm thick layer shows scaling expected
for the topological surface states of a 3D topological insulator. The unique
scaling of the 9 nm thick layer is of particular interest as it may be a result of
axion electrodynamics in a 3D topological insulator.
Subsequently, the influence of V doping on the structural and magnetic properties
of the host material is studied systematically. Similarly to Bi alloying, increased
V doping seems to flatten the layer surface significantly. With increasing V content,
Te bonding partners are observed to increase simultaneously in a 2:3 ratio
as expected for V incorporation on group-V sites. The linear contraction of the
in-plane and out-of-plane lattice constants with increasing V doping is quantitatively
consistent with the incorporation of V\(^{3+}\) ions, possibly mixed with V\(^{4+}\)
ions, at the group-V sites. This is consistent with SQUID measurements showing
a magnetization of 1.3 \(\mu_B\) per V ion.
Finally, magnetically doped topological insulator heterostructures are fabricated
and studied in magneto-transport. Trilayer heterostructures with a non-magnetic
(Bi,Sb)\(_2\)Te\(_3\) layer sandwiched between two magnetically doped layers are predicted
to host the axion insulator state if the two magnetic layers are decoupled and in
antiparallel configuration. Magneto-transport measurements of such a trilayer heterostructure
with 7 nm undoped (Bi,Sb)\(_2\)Te\(_3\) between 2 nm thick layers doped with
1.5 at.% V exhibit a zero Hall plateau representing an insulating state. Similar results
in the literature were interpreted as axion insulator state, but in the absence
of a measurement showing the antiparallel magnetic orientation other explanations
for the insulating state cannot be ruled out.
Furthermore, heterostructures including a 2 nm thin, highly V doped layer region
show an anomalous Hall effect of opposite sign compared to previous samples. A
dependency on the thickness and position of the doped layer region is observed,
which indicates that scattering at the interfaces causes contributions to the anomalous
Hall effect of opposite sign compared to bulk scattering effects.
Many interesting phenomena in quantum anomalous Hall insulators as well as axion
insulators are still not unambiguously observed. This includes Majorana bound
states in quantum anomalous Hall insulator/superconductor hybrid systems and
the topological magneto-electric effect in axion insulators. The limited observation
temperature of the quantum anomalous Hall effect of below 1 K could be increased
in 3D topological insulator/magnetic insulator heterostructures which utilize the
magnetic proximity effect.
The main achievement of this thesis is the reproducible growth and characterization
of (V,Bi,Sb)2Te3 layers exhibiting the quantum anomalous Hall effect. The
detailed study of the structural requirements of the quantum anomalous Hall effect
and the observation of the unique axionic scaling behavior in 3D magnetic
topological insulator layers leads to a better understanding of the nature of this
new quantum state. The high-precision measurements of the quantum anomalous
Hall effect reporting the smallest deviation from the von Klitzing constant
are an important step towards the realization of a zero-field quantum resistance
standard.
This thesis contributes to the understanding of the labor market effects of international trade, with a focus on the effects on wage and earnings inequality. The thesis draws on high-quality micro data and applies modern econometric techniques and theoretical concepts to improve our understanding of the distributional effects of international trade. The thesis focuses on the effects in Germany and the USA.
Winkelbeiner, Nicola ; Wandt, Viktoria K. ; Ebert, Franziska ; Lossow, Kristina ; Bankoglu, Ezgi E. ; Martin, Maximilian ; Mangerich, Aswin ; Stopper, Helga ; Bornhorst, Julia ; Kipp, Anna P. ; Schwerdtle, Tanja
Investigation of processes that contribute to the maintenance of genomic stability is one crucial factor in the attempt to understand mechanisms that facilitate ageing. The DNA damage response (DDR) and DNA repair mechanisms are crucial to safeguard the integrity of DNA and to prevent accumulation of persistent DNA damage. Among them, base excision repair (BER) plays a decisive role. BER is the major repair pathway for small oxidative base modifications and apurinic/apyrimidinic (AP) sites. We established a highly sensitive non-radioactive assay to measure BER incision activity in murine liver samples. Incision activity can be assessed towards the three DNA lesions 8-oxo-2'-deoxyguanosine (8-oxodG), 5-hydroxy-2'-deoxyuracil (5-OHdU), and an AP site analogue. We applied the established assay to murine livers of adult and old mice of both sexes. Furthermore, poly(ADP-ribosyl)ation (PARylation) was assessed, which is an important determinant in DDR and BER. Additionally, DNA damage levels were measured to examine the overall damage levels. No impact of ageing on the investigated endpoints in liver tissue were found. However, animal sex seems to be a significant impact factor, as evident by sex-dependent alterations in all endpoints investigated. Moreover, our results revealed interrelationships between the investigated endpoints indicative for the synergetic mode of action of the cellular DNA integrity maintaining machinery.
In reconstructive and plastic surgery, there exists a growing demand of adequate tissue implants, since currently available strategies for autologous transplantation are limited by complications including transplant failure and donor site morbidity. By developing in vitro and in vivo autologous substitutes for defective tissue sites, adipose tissue engineering can address these challenges, although there are several obstacles to overcome. One of the major limitations is the sufficient vascularization of in vitro engineered large constructs that remains crucial and demanding for functional tissues. Decellularized jejunal segments may represent a suitable scaffolding system with preexisting capillary structures that can be repopulated with human microvascular endothelial cells (hMVECs), and a luminal matrix applicable for the adipogenic differentiation of human adipose-derived stem cells (hASCs). Hence, co-culture of these cells in jejunal segments, utilizing a custom-made bioreactor system, was characterized in terms of vascularization and adipose tissue development. Substantial adipogenesis of hASCs was demonstrated within the jejunal lumen in contrast to non-induced controls, and the increase of key adipogenic markers was verified over time upon induction. The development of major extracellular matrix components of mature adipose tissue, such as laminin and collagen IV, was shown within the scaffold in induced samples. Successful reseeding of the vascular network with hMVECs was demonstrated in long-term culture and co-localization of vascular structures and adipogenically differentiated hASCs was observed. Therefore, these results represent a novel approach for in vitro engineering of vascularized adipose tissue constructs that warrants further investigations in preclinical studies.
Another still existing obstacle in adipose tissue engineering is the insufficient knowledge about the applied cells, for instance the understanding of how cells can be optimally expanded and differentiated for successful engineering of tissue transplants. Even though hASCs can be easily isolated from liposuction of abdominal fat depots, yielding low donor site morbidity, huge numbers of cells are required to entirely seed complex and large 3D matrices or scaffolds. Thus, cells need to be large-scale expanded in vitro on the premise of not losing their differentiation capacity caused by replicative aging. Accordingly, an improved differentiation of hASCs in adipose tissue engineering approaches remains still desirable since most engineered constructs exhibit an inhomogeneous differentiation pattern. For mesenchymal stem cells (MSCs), it has been shown that growth factor application can lead to a significant improvement of both proliferation and differentiation capacity. Especially basic fibroblast growth factor (bFGF) represents a potent mitogen for MSCs, while maintaining or even promoting their osteogenic, chondrogenic and adipogenic differentiation potential. As there are currently different contradictory information present in literature about the applied bFGF concentration and the explicit effect of bFGF on ASC differentiation, here, the effect of bFGF on hASC proliferation and differentiation capacity was investigated at different concentrations and time points in 2D culture. Preculture of hASCs with bFGF prior to adipogenic induction showed a remarkable effect, whereas administration of bFGF during culture did not improve adipogenic differentiation capacity. Furthermore, the observations indicated as mode of action an impact of this preculture on cell proliferation capacity, resulting in increased cellular density at the time of adipogenic induction. The difference in cell density at this time point appeared to be pivotal for increased adipogenic capacity of the cells, which was confirmed in a further experiment employing different seeding densities. Interestingly, furthermore, the obtained results suggested a cell-cell contact-mediated mechanism positively influencing adipogenic differentiation. As a consequence, subsequently, studies were conducted focusing on intercellular communication of these cells, which has hardly been investigated to date.
Despite the multitude of literature on the differentiation capacity of ASCs, little is reported about the physiological properties contributing to and controlling the process of lineage differentiation. Direct intercellular communication between adjacent cells via gap junctions has been shown to modulate differentiation processes in other cell types, with connexin 43 (Cx43) being the most abundant isoform of the gap junction-forming connexins. Thus, in the present study we focused on the expression of Cx43 and gap junctional intercellular communication (GJIC) in hASCs, and its significance for adipogenic differentiation of these cells. Cx43 expression in hASCs was demonstrated histologically and on the gene and protein expression level and was shown to be greatly positively influenced by cell seeding density. Functionality of gap junctions was proven by dye transfer analysis in growth medium. Adipogenic differentiation of hASCs was shown to be also distinctly elevated at higher cell seeding densities. Inhibition of GJIC by 18α-glycyrrhetinic acid significantly compromised adipogenic differentiation, as demonstrated by histology, triglyceride quantification, and adipogenic marker gene expression. Flow cytometry analysis showed a lower proportion of cells undergoing adipogenesis when GJIC was inhibited, further indicating the importance of GJIC in the differentiation process. Altogether, these results demonstrate the impact of direct cell-cell communication via gap junctions on the adipogenic differentiation process of hASCs and may contribute to further integrate direct intercellular crosstalk in rationales for tissue engineering approaches.
In recent years, great progress has been made in the area of Artificial Intelligence (AI) due to the possibilities of Deep Learning which steadily yielded new state-of-the-art results especially in many image recognition tasks.
Currently, in some areas, human performance is achieved or already exceeded.
This great development already had an impact on the area of Optical Music Recognition (OMR) as several novel methods relying on Deep Learning succeeded in specific tasks.
Musicologists are interested in large-scale musical analysis and in publishing digital transcriptions in a collection enabling to develop tools for searching and data retrieving.
The application of OMR promises to simplify and thus speed-up the transcription process by either providing fully-automatic or semi-automatic approaches.
This thesis focuses on the automatic transcription of Medieval music with a focus on square notation which poses a challenging task due to complex layouts, highly varying handwritten notations, and degradation.
However, since handwritten music notations are quite complex to read, even for an experienced musicologist, it is to be expected that even with new techniques of OMR manual corrections are required to obtain the transcriptions.
This thesis presents several new approaches and open source software solutions for layout analysis and Automatic Text Recognition (ATR) for early documents and for OMR of Medieval manuscripts providing state-of-the-art technology.
Fully Convolutional Networks (FCN) are applied for the segmentation of historical manuscripts and early printed books, to detect staff lines, and to recognize neume notations.
The ATR engine Calamari is presented which allows for ATR of early prints and also the recognition of lyrics.
Configurable CNN/LSTM-network architectures which are trained with the segmentation-free CTC-loss are applied to the sequential recognition of text but also monophonic music.
Finally, a syllable-to-neume assignment algorithm is presented which represents the final step to obtain a complete transcription of the music.
The evaluations show that the performances of any algorithm is highly depending on the material at hand and the number of training instances.
The presented staff line detection correctly identifies staff lines and staves with an $F_1$-score of above $99.5\%$.
The symbol recognition yields a diplomatic Symbol Accuracy Rate (dSAR) of above $90\%$ by counting the number of correct predictions in the symbols sequence normalized by its length.
The ATR of lyrics achieved a Character Error Rate (CAR) (equivalently the number of correct predictions normalized by the sentence length) of above $93\%$ trained on 771 lyric lines of Medieval manuscripts and of 99.89\% when training on around 3.5 million lines of contemporary printed fonts.
The assignment of syllables and their corresponding neumes reached $F_1$-scores of up to $99.2\%$.
A direct comparison to previously published performances is difficult due to different materials and metrics.
However, estimations show that the reported values of this thesis exceed the state-of-the-art in the area of square notation.
A further goal of this thesis is to enable musicologists without technical background to apply the developed algorithms in a complete workflow by providing a user-friendly and comfortable Graphical User Interface (GUI) encapsulating the technical details.
For this purpose, this thesis presents the web-application OMMR4all.
Its fully-functional workflow includes the proposed state-of-the-art machine-learning algorithms and optionally allows for a manual intervention at any stage to correct the output preventing error propagation.
To simplify the manual (post-) correction, OMMR4all provides an overlay-editor that superimposes the annotations with a scan of the original manuscripts so that errors can easily be spotted.
The workflow is designed to be iteratively improvable by training better models as soon as new Ground Truth (GT) is available.
Whisnant, Adam W. ; Jürges, Christopher S. ; Hennig, Thomas ; Wyler, Emanuel ; Prusty, Bhupesh ; Rutkowski, Andrzej J. ; L'hernault, Anne ; Djakovic, Lara ; Göbel, Margarete ; Döring, Kristina ; Menegatti, Jennifer ; Antrobus, Robin ; Matheson, Nicholas J. ; Künzig, Florian W. H. ; Mastrobuoni, Guido ; Bielow, Chris ; Kempa, Stefan ; Liang, Chunguang ; Dandekar, Thomas ; Zimmer, Ralf ; Landthaler, Markus ; Grässer, Friedrich ; Lehner, Paul J. ; Friedel, Caroline C. ; Erhard, Florian ; Dölken, Lars
The predicted 80 open reading frames (ORFs) of herpes simplex virus 1 (HSV-1) have been intensively studied for decades. Here, we unravel the complete viral transcriptome and translatome during lytic infection with base-pair resolution by computational integration of multi-omics data. We identify a total of 201 transcripts and 284 ORFs including all known and 46 novel large ORFs. This includes a so far unknown ORF in the locus deleted in the FDA-approved oncolytic virus Imlygic. Multiple transcript isoforms expressed from individual gene loci explain translation of the vast majority of ORFs as well as N-terminal extensions (NTEs) and truncations. We show that NTEs with non-canonical start codons govern the subcellular protein localization and packaging of key viral regulators and structural proteins. We extend the current nomenclature to include all viral gene products and provide a genome browser that visualizes all the obtained data from whole genome to single-nucleotide resolution. Here, using computational integration of multi-omics data, the authors provide a detailed transcriptome and translatome of herpes simplex virus 1 (HSV-1), including previously unidentified ORFs and N-terminal extensions. The study also provides a HSV-1 genome browser and should be a valuable resource for further research.
Weselek, Grit ; Keiner, Silke ; Fauser, Mareike ; Wagenführ, Lisa ; Müller, Julia ; Kaltschmidt, Barbara ; Brandt, Moritz D. ; Gerlach, Manfred ; Redecker, Christoph ; Hermann, Andreas ; Storch, Alexander
The limited proliferative capacity of neuroprogenitor cells (NPCs) within the periventricular germinal niches (PGNs) located caudal of the subventricular zone (SVZ) of the lateral ventricles together with their high proliferation capacity after isolation strongly implicates cell‐extrinsic humoral factors restricting NPC proliferation in the hypothalamic and midbrain PGNs. We comparatively examined the effects of norepinephrine (NE) as an endogenous candidate regulator of PGN neurogenesis in the SVZ as well as the periventricular hypothalamus and the periaqueductal midbrain. Histological and neurochemical analyses revealed that the pattern of NE innervation of the adult PGNs is inversely associated with their in vivo NPC proliferation capacity with low NE levels coupled to high NPC proliferation in the SVZ but high NE levels coupled to low NPC proliferation in hypothalamic and midbrain PGNs. Intraventricular infusion of NE decreased NPC proliferation and neurogenesis in the SVZ‐olfactory bulb system, while pharmacological NE inhibition increased NPC proliferation and early neurogenesis events in the caudal PGNs. Neurotoxic ablation of NE neurons using the Dsp4‐fluoxetine protocol confirmed its inhibitory effects on NPC proliferation. Contrarily, NE depletion largely impairs NPC proliferation within the hippocampus in the same animals. Our data indicate that norepinephrine has opposite effects on the two fundamental neurogenic niches of the adult brain with norepinephrine being a negative regulator of adult periventricular neurogenesis. This knowledge might ultimately lead to new therapeutic approaches to influence neurogenesis in hypothalamus‐related metabolic diseases or to stimulate endogenous regenerative potential in neurodegenerative processes such as Parkinson's disease.
Validation of text information as a general mechanism for detecting inconsistent or false information is an integral part of text comprehension. This study examined how the credibility of the information source affects validation processes. Two experiments investigated combined effects of source credibility and plausibility of information during validation with explicit (ratings) and implicit (reading times) measurements. Participants read short stories with a high-credible versus low-credible person that stated a consistent or inconsistent assertion with general world knowledge. Ratings of plausibility and ratings of source credibility were lower when a credible source stated a world-knowledge inconsistent assertion compared with a low-credible source. Reading times on target sentences and on spillover sentences were slower when a credible source stated an assertion inconsistent with world knowledge compared with a low-credible source, suggesting that source information modulated the validation of implausible information. These results show that source credibility modulates validation and suggest a bidirectional relationship of perceived plausibility and source credibility in the reading process.
Werner, Rudolf A. ; Derlin, Thorsten ; Lapa, Constantin ; Sheikbahaei, Sara ; Higuchi, Takahiro ; Giesel, Frederik L. ; Behr, Spencer ; Drzezga, Alexander ; Kimura, Hiroyuki ; Buck, Andreas K. ; Bengel, Frank M. ; Pomper, Martin G. ; Gorin, Michael A. ; Rowe, Steven P.
Prostate-specific membrane antigen (PSMA)-targeted PET imaging for prostate cancer with \(^{68}\)Ga-labeled compounds has rapidly become adopted as part of routine clinical care in many parts of the world. However, recent years have witnessed the start of a shift from \(^{68}\)Ga- to \(^{18}\)F-labeled PSMA-targeted compounds. The latter imaging agents have several key advantages, which may lay the groundwork for an even more widespread adoption into the clinic. First, facilitated delivery from distant suppliers expands the availability of PET radiopharmaceuticals in smaller hospitals operating a PET center but lacking the patient volume to justify an onsite \(^{68}\)Ge/\(^{68}\)Ga generator. Thus, such an approach meets the increasing demand for PSMA-targeted PET imaging in areas with lower population density and may even lead to cost-savings compared to in-house production. Moreover, \(^{18}\)F-labeled radiotracers have a higher positron yield and lower positron energy, which in turn decreases image noise, improves contrast resolution, and maximizes the likelihood of detecting subtle lesions. In addition, the longer half-life of 110 min allows for improved delayed imaging protocols and flexibility in study design, which may further increase diagnostic accuracy. Moreover, such compounds can be distributed to sites which are not allowed to produce radiotracers on-site due to regulatory issues or to centers without access to a cyclotron. In light of these advantageous characteristics, \(^{18}\)F-labeled PSMA-targeted PET radiotracers may play an important role in both optimizing this transformative imaging modality and making it widely available. We have aimed to provide a concise overview of emerging \(^{18}\)F-labeled PSMA-targeted radiotracers undergoing active clinical development. Given the wide array of available radiotracers, comparative studies are needed to firmly establish the role of the available \(^{18}\)F-labeled compounds in the field of molecular PCa imaging, preferably in different clinical scenarios.