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Sonstige beteiligte Institutionen
- IZKF Nachwuchsgruppe Geweberegeneration für muskuloskelettale Erkrankungen (5)
- Bernhard-Heine-Centrum für Bewegungsforschung (4)
- Zentraleinheit Klinische Massenspektrometrie (3)
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- Arizona State University, Tempe, Arizona, USA (1)
Despite belonging to the best described patterns in ecology, the mechanisms driving biodiversity along broad-scale climatic gradients, like the latitudinal gradient in diversity, remain poorly understood. Because of their high biodiversity, restricted spatial ranges, the continuous change in abiotic factors with altitude and their worldwide occurrence, mountains constitute ideal study systems to elucidate the predictors of global biodiversity patterns. However, mountain ecosystems are increasingly threatened by human land use and climate change. Since the consequences of such alterations on mountainous biodiversity and related ecosystem services are hardly known, research along elevational gradients is also of utmost importance from a conservation point of view. In addition to classical biodiversity research focusing on taxonomy, the significance of studying functional traits and their prominence in biodiversity ecosystem functioning (BEF) relationships is increasingly acknowledged. In this dissertation, I explore the patterns and drivers of mammal and dung beetle diversity along elevational and land use gradients on Mt. Kilimanjaro, Tanzania. Furthermore, I investigate the predictors of dung decomposition by dung beetles under different extinction scenarios.
Mammals are not only charismatic, they also fulfil important roles in ecosystems. They provide important ecosystem services such as seed dispersal and nutrient cycling by turning over high amounts of biomass. In chapter II, I show that mammal diversity and community biomass both exhibited a unimodal distribution with elevation on Mt.Kilimanjaro and were mainly impacted by primary productivity, a measure of the total food abundance, and the protection status of study plots. Due to their large size and endothermy, mammals, in contrast to most arthopods, are theoretically predicted to be limited by food availability. My results are in concordance with this prediction. The significantly higher diversity and biomass in the Kilimanjaro National Park and in other conservation areas underscore the important role of habitat protection is vital for the conservation of large mammal biodiversity on tropical mountains.
Dung beetles are dependent on mammals since they rely upon mammalian dung as a food and nesting resource. Dung beetles are also important ecosystem service providers: they play an important role in nutrient cycling, bioturbation, secondary seed dispersal and parasite suppression. In chapter III, I show that dung beetle diversity declined with elevation while dung beetle abundance followed a hump-shaped pattern along the elevational gradient. In contrast to mammals, dung beetle diversity was primarily predicted by temperature. Despite my attempt to accurately quantifiy mammalian dung resources by calculating mammalian defecation rates, I did not find an influence of dung resource availability on dung beetle richness. Instead, higher temperature translated into higher dung beetle diversity.
Apart from being important ecosystem service providers, dung beetles are also model organisms for BEF studies since they rely on a resource which can be quantified easily. In chapter IV, I explore dung decomposition by dung beetles along the elevational gradient by means of an exclosure experiment in the presence of the whole dung beetle community, in the absence of large dung beetles and without any dung beetles. I show that dung decomposition was the highest when the dung could be decomposed by the whole dung beetle community, while dung decomposition was significantly reduced in the sole presence of small dung beetles and the lowest in the absence of dung beetles. Furthermore, I demonstrate that the drivers of dung decomposition were depend on the intactness of the dung beetle community. While body size was the most important driver in the presence of the whole dung beetle community, species richness gained in importance when large dung beetles were excluded. In the most perturbed state of the system with no dung beetles present, temperature was the sole driver of dung decomposition. In conclusion, abiotic drivers become more important predictors of ecosystem services the more the study system is disturbed.
In this dissertation, I exemplify that the drivers of diversity along broad-scale climatic gradients on Mt. Kilimanjaro depend on the thermoregulatory strategy of organisms. While mammal diversity was mainly impacted by food/energy resources, dung beetle diversity was mainly limited by temperature. I also demonstrate the importance of protected areas for the preservation of large mammal biodiversity. Furthermore, I show that large dung beetles were disproportionately important for dung decomposition as dung decomposition significantly decreased when large dung beetles were excluded. As regards land use, I did not detect an overall effect on dung beetle and mammal diversity nor on dung beetle-mediated dung decomposition. However, for the most specialised mammal trophic guilds and dung beetle functional groups, negative land use effects were already visible. Even though the current moderate levels of land use on Mt. Kilimanjaro can sustain high levels of biodiversity, the pressure of the human population on Mt. Kilimanjaro is increasing and further land use intensification poses a great threat to biodiversity. In synergy wih land use, climate change is jeopardizing current patterns and levels of biodiversity with the potential to displace communities, which may have unpredictable consequences for ecosystem service provisioning in the future.
Spatiotemporal dynamics of freshwater macrophytes in Bavarian lakes under environmental change
(2022)
Macrophytes are key components of freshwater ecosystems because they provide habitat, food, and improve the water quality. Macrophyte are vulnerable to environmental change as their physiological processes depend on changing environmental factors, which themselves vary within a geographical region and along lake depth. Their spatial distribution is not well understood and their importance is publicly little-known. In this thesis, I have investigated the spatiotemporal dynamics of freshwater macrophytes in Bavarian lakes to understand their diversity pattern along different scales and to predict and communicate potential consequences of global change on their richness.
In the introduction (Chapter 1), I provide an overview of the current scientific knowledge of the species richness patterns of macrophytes in freshwater lakes, the influences of climate and land-use change on macrophyte growth, and different modelling approaches of macrophytes.
The main part of the thesis starts with a study about submerged and emergent macrophyte species richness in natural and artificial lakes of Bavaria (Chapter 2). By analysing publicly available monitoring data, I have found a higher species richness of submerged macrophytes in natural lakes than in artificial lakes. Furthermore, I showed that the richness of submerged species is better explained by physio-chemical lake parameters than the richness of emergent species. In Chapter 3, I considered that submerged macrophytes grow along a depth gradient that provides a sharp environmental gradient on a short spatial scale. This study is the first comparative assessment of the depth diversity gradient (DDG) of macrophytes. I have found a hump-shaped pattern of different diversity components. Generalised additive mixed-effect models indicate that the shape of the DDG is influenced mainly by light quality, light quantity, layering depth, and lake area. I could not identify a general trend of the DDG within recent years, but single lakes show trends leading into different directions. In Chapter 4, I used a mechanistic eco-physiological model to explore changes in the distribution of macrophyte species richness under different scenarios of environmental conditions across lakes and with depths. I could replicate the hump-shaped pattern of potential species richness along depth. Rising temperature leads to increased species richness in all lake types, and depths. The effect of turbidity and nutrient change depends on depth and lake type. Traits that characterise “loser species” under increased turbidity and nutrients are a high light consumption and a high sensibility to disturbances. “Winner species” can be identified by a high biomass production. In Chapter 5, I discuss the image problem of macrophytes. Unawareness, ignorance, and the poor accessibility of macrophytes can lead to conflicts of use. I assumed that an increased engagement and education could counteract this. Because computer games can transfer knowledge interactively while creating an immersive experience, I present in the chapter an interactive single-player game for children.
Finally, I discuss the findings of this thesis in the light of their implications for ecological theory, their implications for conservation, and future research ideas (Chapter 6). The findings help to understand the regional distribution and the drivers of macrophyte species richness. By applying eco-physiological models, multiple environmental shaping factors for species richness were tested and scenarios of climate and land-use change were explored.
Background: Anemia remains one of the most common comorbidities in intensive care patients worldwide. The cause of anemia is often multifactorial and triggered by underlying disease, comorbidities, and iatrogenic factors, such as diagnostic phlebotomies. As anemia is associated with a worse outcome, especially in intensive care patients, unnecessary iatrogenic blood loss must be avoided. Therefore, this scoping review addresses the amount of blood loss during routine phlebotomies in adult (>17 years) intensive care patients and whether there are factors that need to be improved in terms of patient blood management (PBM). Methods: A systematic search of the Medline Database via PubMed was conducted according to PRISMA guidelines. The reported daily blood volume for diagnostics and other relevant information from eligible studies were charted. Results: A total of 2167 studies were identified in our search, of which 38 studies met the inclusion criteria (9 interventional studies and 29 observational studies). The majority of the studies were conducted in the US (37%) and Canada (13%). An increasing interest to reduce iatrogenic blood loss has been observed since 2015. Phlebotomized blood volume per patient per day was up to 377 mL. All interventional trials showed that the use of pediatric-sized blood collection tubes can significantly reduce the daily amount of blood drawn. Conclusion: Iatrogenic blood loss for diagnostic purposes contributes significantly to the development and exacerbation of hospital-acquired anemia. Therefore, a comprehensive PBM in intensive care is urgently needed to reduce avoidable blood loss, including blood-sparing techniques, regular advanced training, and small-volume blood collection tubes.
Herpes Simplex Virus type 1 (HSV-1) is an ubiquitous neurotropic human pathogen that infects a large majority of the world’s population. It is the causative agent of the common cold sore but also responsible for life-threatening infections (e.g., encephalitis), particularly in immunocompromised individuals and neonates. Like other herpesviruses, HSV-1 takes over the cellular RNA machinery to facilitate productive infection while efficiently shutting down host gene expression by targeting multiple steps of RNA metabolism. The two viral proteins, vhs and ICP27, play a crucial role in this process. Delivered by the tegument of the incoming virus, the virion host shut-off (vhs) endonuclease rapidly starts cleaving both cellular and viral mRNAs. With the onset of viral gene expression, the HSV-1 immediate-early protein ICP27 promotes the expression of viral early and late genes through various mechanisms, including mRNA processing, export, and translation.
Prior research by the Dölken lab demonstrated that lytic HSV-1 infection results in the disruption of transcription termination (DoTT) of most cellular genes by the viral ICP27 protein. This significantly contributes to HSV-1 induced host shut-off. DoTT results in transcription for tens of thousands of nucleotides beyond poly(A) sites and into downstream genes. Interestingly, this was found to be accompanied by a dramatic increase in chromatin accessibility downstream of the affected poly(A) sites. This is consistent with the formation of extensive downstream open chromatin regions (dOCR) and indicative of impaired histone repositioning in the wake of RNA polymerase II (Pol II) downstream of the affected poly(A) sites.
In my PhD thesis, I demonstrate that dOCR formation is dependent on the viral ICP22 protein when poly(A) read-through transcription is triggered by the ectopic expression of ICP27 or salt stress. I show that dOCR formation occurs when a high level of transcriptional activity arises downstream of genes due to the HSV-1-induced DoTT. To investigate whether histone composition is affected downstream of genes, I established the ChIPmentation approach to study associated changes and the influence of DoTT and dOCR formation on major histone modification marks. In HSV-1 WT infection, dOCR formation was reflected in alterations of canonical H1 histone downstream of affected genes, which was absent in ICP22 infection. To elucidate the underlying molecular mechanism, two major histone chaperones SPT6 and FACT (SPT16 and SSRP1), which govern histone repositioning and may thus play a role in H1 homeostasis, were extensively studied. Both histone chaperones have been recently shown to be recruited to the viral genome by interactions with ICP22 protein. To investigate whether the depletion of SSRP1 or SPT6 would complement the loss of ICP22 to induce dOCR, T-HF cells with doxycycline-inducible knock-down of either of the two factors were generated. ATAC-seq analysis revealed that the interaction between the two histone chaperones and ICP22 is not involved in HSV-1-induced dOCR formation, suggesting the involvement of other proteins. In summary, this work sheds new light on a fundamental molecular mechanism of the cellular transcriptional machinery that is manipulated by the concerted actions of the two HSV-1 immediate-early proteins ICP22 and ICP27.
The “active self” approach suggests that any object we manipulate voluntarily and foreseeably becomes part of our “self” in the sense that we feel control over this object (sense of agency) and experience it as belonging to our own body (sense of ownership). While there is considerable evidence that we can indeed experience both a sense of agency and a sense of ownership over a broad variety of objects when we control these through our actions, the approach has also been criticized for exaggerating the flexibility of the human self. In this thesis, I investigate the influence that the relationship between the body movements controlling an object and the movements of the object itself has on the process of integrating an object into the self. I demonstrate that fully controlling an object is not sufficient for it to be integrated into the self since both explicit and implicit measures of the sense of agency and the sense of ownership indicate less or no integration when body movements are transformed into inverted object movements. Furthermore, I show that such inversions lead to the downregulation of sensory signals either from the body or from the controlled object in order to deal with the conflicting multisensory information when performing such actions. I argue that this downregulation is the underlying factor behind the diminished or eliminated integration of inverted body and object movements and I discuss further pathways for possible future studies building up on these findings.
This thesis includes measurements that were recorded by cooperation partners. The EPR spec‐ trosa mentioned in section 5.2 were recorded by Michael Auth from the Dyakonov Group (Ex‐ perimental Physics VI, Julius‐Maximilians‐Universität, Würzburg). The TREFISH experiments and transient absorption in section 5.4 spectra were performed by Jašinskas et al. from the V. Gulbi‐ nas group (Center for Physical Sciences and Technology, Vilnius, Lithuania). This dissertation investigated the interactions of semiconducting single‐walled carbon nanotubes (SWNTs) of (6,5) chirality with their environment. Shear‐mixing provided high‐quality SWNT sus‐ pensions, which was complemented by various film preparation techniques. These techniques were in turn used to prepare heterostructures with MoS2 and hBN, which were examined with a newly constructed photoluminescence microscope specifically for this purpose. Finally, the change of spectral properties of SWNTs upon doping was investigated in more detail, as well as the behaviour of charge carriers in the tubes themselves. To optimise the SWNT sample preparation techniques that supplied the other experiments, the sample quality of shear‐mixed preparations was compared with that of sonicated samples. It was found that the quantum efficiency of sheared suspensions exceeds that of sonicated suspensions as soon as the sonication time exceeds 30 min. The higher PLQY is due to the lower defect concentration in shear‐mixed samples. Via transient absorption, a mean lifetime of 17.3 ps and a mean distance between defects of 192.1 nm could be determined. Furthermore, it was found that the increased efficiency of horn sonication is probably not only due to higher shear forces acting on the SWNT bundles but also that the shortening of PFO‐BPy strands plays a significant role. Sonication of very long polymer strands significantly increased their effectiveness in shear mixing. While previous approaches could only achieve very low concentrations of SWNTs in suspensions, pre‐sonicated polymer yielded results which were comparable with much shorter PFO‐BPy batches. Reference experiments also showed that different aggregation processes are relevant during production and further processing. Initial reprocessing of carbon nanotube raw material requires 7 h sonication time and over 24 h shear mixing before no increase in carbon nano concentration is detectable. However, only a few minutes of sonication or shear mixing are required when reprocessing the residue produced during the separation of the slurry. This discrepancy indicates that different aggregates are present, with markedly different aggregation properties. To study low‐dimensional heterostructures, a PL microscope was set up with the ability to ob‐ serve single SWNTs as well as monolayers of other low‐dimensional systems. Furthermore, sam‐ ples were prepared which bring single SWNTs into contact with 2D materials such as h‐BN andMoS2 layers and the changes in the photoluminescence spectrum were documented. For h‐BN, it was observed whether previous methods for depositing SWNTs could be transferred for photo‐ luminescence spectroscopy. SWNTs were successfully deposited on monolayers via a modified drip coating, with the limitation that SWNTs aggregate more at the edges of the monolayers. Upon contact of SWNTs with MoS2, significant changes in the emission properties of the mono‐ layers were observed. The fluorescence, which was mainly dominated by excitons, was shifted towards trion emission. Reference experiments excluded PFO‐BPy and toluene as potential causes. Based on the change in the emission behaviour of MoS2, the most plausible explanation is a photoinduced charge transfer leading to delocalised charge carriers on MoS2. In contrast, on SWNTs, the introduction of additional charges would constitute a quenching centre, which would quench their PL emission, making them undetectable in the PL image. In the last chapter, the electronic properties of doped SWNTs and the behaviour of charge carri‐ ers inside the tubes should be investigated. First, the change in the conductivity of SWNT films with increasing doping levels was docu‐ mented. The resistance of the films drops drastically at minimum doping. After the initial in‐ troduction of charges, the resistance drops with increasing dopant concentration according to a double logarithmic curve. The initial drop could be due to a reduction of contact resistances within the SWNT network film, but this could not be further investigated within the scope of this PhD thesis. In cooperation with Andreas Sperlich and Michael Auth, the spin concentration of SWNTs at different doping levels was determined. The obtained concentrations were compared with the carrier concentrations determined from PL and absorption spectra. At low spin densities, good agreement with previous models was found. Furthermore, the presence of isolated spins strongly suggests a localised charge carrier distribution at temperatures around 10 K. When the charge density is increased, the spin density deviates significantly from the charge carrier con‐ centration. This discrepancy is attributed to the increasing delocalisation of charge carriers at high charge densities and the interactions of neighbouring spins. These results strongly indicate the existence of localised charge carriers in SWNTs at low temperatures. Next, the effect of doping on the Raman spectra of SWNT suspensions was investigated. In gen‐ eral, doping is expected to reduce the intensity of the Raman bands, i.e. a consequence of the reduced resonance gain due to bleaching of the S2 transition. However, similar to the resistivity measurements, the oscillator strength of the G+ band drops sharply in the first doping steps. It was also found that the G+ band decreases more than would be expected due to loss of reso‐ nance condition. Furthermore, the G‐ is bleached faster than the G+ band. All these anomalies suggest that resonance enhancement is not the only relevant effect. Another much faster deac‐ tivation path for the excitons may be introduced by doping. This would leave less time for the scattering process to occur and reduce the oscillator strength of the Raman bands. In cooperation with Vidmantas et al., the photoinduced charge carrier behaviour of SWNT/PCBM films was investigated. The required films were prepared by drop coating. The SWNT suspen‐ sions required for this were obtained from sheared SWNT preparations. Using transient absorp‐ tion and TREFISH, a number of charge transfer effects were identified and their dynamics in‐ vestigated: the recombination of neutral excitons (< 50 ps), the electron transfer from carbon nanotubes to PCBM molecules (< 1 ps), the decay of charge‐transfer excitons (∼200 ps), the recombination of charge carriers between charge‐transfer excitons (1 ns to 4 ns) and finally the propagation through the SWNT network (∼20 ns)
Nanodiamond (ND) is a versatile and promising material for bio-applications. Despite many efforts, agglomeration of nanodiamond and the non-specific adsorption of proteins on the ND surface when exposed to bio-fluids remains a major obstacle for biomedical applications. An assortment of branched and linear molecules with superior ability to colloidally stabilize nanoparticles in salt and cell media environment, for up to 30 days, was attached to the ND’s surface.
The building box system with azide as external groups offers a huge variety of binding with many molecules, such as drugs, dyes or targeting molecules, is possible. Clicking, for instance, zwitterions moieties to the chain protects ND surface from protein corona forming when the particles get in contact with biofluids containing proteins.
Thermogravimetric analysis results of the ND surface loading show a significant prevention of up to 98 % of the protein adsorption compared with NDs without zwitterionic headgroups and long colloidal stability when tetraethylene glycol (TEG) are attached to the surface.
The versatility of the modular system to bind not only zwitterionic chains but also clickable functional molecules to fluorescent nanodiamonds (fNDs) demonstrates the potential of the system at the nanodiamond. Using defect structures, such as nitrogen-vacancy (NV) centers, diamond particles, due to their widely non-toxic behavior, can be used as fNDs for photostable labeling, bioimaging and nanoscale sensing in living cells and organisms. To functionalize the fND surface a novel milling technique with diazonium salts was established to perform grafting on poorly reactive HPHT fNDs yielding in high surface loading and high negative zeta potential.
Combining the benefits of TEG and zwitterion containing groups with antibody enabled nucleus targeting ability on fND confirms the enhanced colloidal stability in living cells experiments for the first time. Furthermore, the results indicate an improved corona repulsion compared with fND without zwitterion containing headgroups. As a result, the circulation times were enlarged from 4 (fND without zwitterion chain but with antibody) to 17 (with antibody and zwitterion chains) hours.
In non-biomedical applications, the modular system can be used as a probe for heavy metals by binding it to dyes. Detection of metals in different environments with high selectivity and specificity is one of the prerequisites of the fight against environmental pollution with these elements. Pyrenes are well suited and known for fluorescence sensing in different media.
The applied sensing principle typically relies on the formation of intra- and intermolecular excimers, which is however limiting the sensitivity range due to masking of e.g. quenching effects by the excimer emission. This study shows a highly selective, structurally rigid chemical sensor based on the monomer fluorescence of pyrene moieties bearing triazole groups.
This probe can quantitatively detect Cu2+, Pb2+ and Hg2+ in organic solvents over a broad concentration range, even in the presence of ubiquitous ions such as Na+, K+, Ca2+ and Mg2+. The strongly emissive sensor’s fluorescence with a long lifetime of 165 ns is quenched by a 1:1 complex formation upon addition of metal ions in acetonitrile. Upon addition of a tenfold excess of the metal ion to the sensor, agglomerates with a diameter of about 3 nm are formed. Due to complex interactions in the system, conventional linear correlations are not observed for all concentrations. Therefore, a critical comparison between the conventional Job plot interpretation, the method of Benesi-Hildebrand, and a non-linear fit is presented. The reported system enables the specific and robust sensing of medically and environmentally relevant ions in the health-relevant nM range and could be used e.g. for the monitoring of the respective ions in waste streams.
Nonetheless, often these waste streams end up in sensitive aquacultures, where such sensor technology only works if the probe is water-soluble to monitor the spread and formation of environmental damage from heavy metals. Many chemosensors only work quantitatively in specific solvents and under highly pure conditions. In this thesis a method to stabilize water-insoluble chemosensors on nanodiamonds in saline water while maintaining the sensor efficacy and specificityas as well as colloidal stability is presented. Additionally, the sensor capability is retained in organic solvents. This study provides insight into the absorptivity of pyrene derivatives to the nanodiamond surface and a way to reversibly desorb them.
Moreover, the system proves that in presence of 95 % oxygen atmosphere while the fluoresce measurement the results of the do not vary from the one in argon atmosphere. Furthermore, the presence of common ions in water do not disturb the colloidal stability of the NDs and also no influence the sensor functionality and thus is highly promising candidate for measurement without cumbersome preparation steps.
The future of water-derived hydrogen as the “sustainable energy source” straightaway bets on the success of the sluggish oxygen-generating half-reaction. The endeavor to emulate the natural photosystem II for efficient water oxidation has been extended across the spectrum of organic and inorganic combinations. However, the achievement has so far been restricted to homogeneous catalysts rather than their pristine heterogeneous forms. The poor structural understanding and control over the mechanistic pathway often impede the overall development. Herein, we have synthesized a highly crystalline covalent organic framework (COF) for chemical and photochemical water oxidation. The interpenetrated structure assures the catalyst stability, as the catalyst’s performance remains unaltered after several cycles. This COF exhibits the highest ever accomplished catalytic activity for such an organometallic crystalline solid-state material where the rate of oxygen evolution is as high as ∼26,000 μmol L\(^{–1}\) s\(^{–1}\) (second-order rate constant k ≈ 1650 μmol L s\(^{–1}\) g\(^{–2}\)). The catalyst also proves its exceptional activity (k ≈ 1600 μmol L s\(^{–1}\) g\(^{–2}\)) during light-driven water oxidation under very dilute conditions. The cooperative interaction between metal centers in the crystalline network offers 20–30-fold superior activity during chemical as well as photocatalytic water oxidation as compared to its amorphous polymeric counterpart.
The Amduat is one of the most important Netherworld Books which was recorded in various kinds of Ancient Egyptian sources since the beginning of the 18th dynasty, especially the walls of the royal tombs. The main theme of the Amduat is the journey of the sun god through the underworld where the solar bark and its crew is the central scene of the journey. The study focuses on finding the reasons of choosing the crew’s members who manage the sun bark’s journey in the Amduat. It also aims at illustrating the functions and responsibilities of each crew member. Following a historical approach, the study analyzes the Pyramid Texts and Coffin Texts as the most important documents before the New Kingdom, and proceeding to the inscriptions and writings of the monuments which contain portrayals and inscriptions of the Amduat in the New Kingdom. Furthermore, it sheds some light on the solar cycle’s main features and primary aspects, and tries to scrutinize the date, meaning, and symbolisms of the Amduat and its indications in the earlier sources.
Background: Treatment options for NAFLD are still limited. Bariatric surgery, such as Roux-en-Y gastric bypass (RYGB), has been shown to improve metabolic and histologic markers of NAFLD. Glucagon-like-peptide-1 (GLP-1) analogues lead to improvements in phase 2 clinical trials. We directly compared the effects of RYGB with a treatment using liraglutide and/or peptide tyrosine tyrosine 3-36 (PYY\(_{3-36}\)) in a rat model for early NAFLD. Methods: Obese male Wistar rats (high-fat diet (HFD)-induced) were randomized into the following treatment groups: RYGB, sham-operation (sham), liraglutide (0.4 mg/kg/day), PYY\(_{3-36}\) (0.1 mg/kg/day), liraglutide+PYY\(_{3-36}\), and saline. After an observation period of 4 weeks, liver samples were histologically evaluated, ELISAs and RNA sequencing + RT-qPCRs were performed. Results: RYGB and liraglutide+PYY\(_{3-36}\) induced a similar body weight loss and, compared to sham/saline, marked histological improvements with significantly less steatosis. However, only RYGB induced significant metabolic improvements (e.g., adiponectin/leptin ratio 18.8 ± 11.8 vs. 2.4 ± 1.2 in liraglutide+PYY\(_{3-36}\)- or 1.4 ± 0.9 in sham-treated rats). Furthermore, RNA sequencing revealed a high number of differentially regulated genes in RYGB treated animals only. Conclusions: The combination therapy of liraglutide+PYY\(_{3-36}\) partly mimics the positive effects of RYGB on weight reduction and on hepatic steatosis, while its effects on metabolic function lack behind RYGB.
After implementing a reliable mass spectrometry based kinetic study the indole conjugation with different organometallic indoles led to questions about the electronical and sterical influences on reactivity. The substitution pattern of the ferrocene functionalized indoles at the six-membered ring determines the electron density on the C3 atom, which reacts with the formed Schiff base. Since the experimental results showed the exact opposite trend, covalent docking studies were performed elucidating the importance of surface interactions. These studies were in harmony with the experimental results and determined lysine 33 as most preferable conjugation site as well as substitution in 6-position as most favourable pattern. The amine motif in compounds 6, 7 and 8 proofed to be easily fragmented by the ESI method used. The amide linker in 10 remains intact but shows a lower conversion. Those two inherent characteristics are however preferable for well-defined and site-specific bioconjugation. The synthesis and evaluation of piano stool complex derivatives with manganese and rhenium metal centre 15, 16, 18 and 22 gave additional guidance by the interpretation of applicable structural motifs. The electron-withdrawing carbonyl groups lead to the hindrance of fulvene formation and thus to no fragmentation as seen with the ferrocene group. The total conversion is low compared to 8, only 22 shows a good enough conversion to mainly monoconjugate of 45% and a possible radio-labelling application as 99mTc analogue. As consequence manganese complexes with a stable facial tricarbonyl unit and a tridentate chelator with 4-, 5- and 6-substituted aminomethylindole conjugated through an amide bond were synthesized and consecutively evaluated. The resulting organometallic indole derivatives 29, 30 and 31 all showed a total conversion around 40% similar to 16, but at the same time a rate constant in the range of 10-4 s-1 like the organic indole. Besides the similar conversion, the rate constants followed the trend of the 6-substituted derivative as fastest and then 5- and 4- substituted derivative with decreasing reactivity. For underlining the usage as technetium label for the best out of the series 31, a rhenium analogue was prepared. The resulting compound 32 was especially interesting, because the conversion was even higher than the 70% of 8 with a total of 88%. Additionally, the rate constant was a tenfold higher as well. This rendered compound 32 as best possible 99mTc analogue for further application as radio-label. After the success of 32 and realizing the sterical benefits resulting from the flexible tridentate ligand-system, substitution at the five-membered ring was explored. The complexes 33, 34 and 35 are based on indole-2-carboxylic acid and with the difference of the length of the alkyl spacer between amide and complex to probe for the influence and sterical hindrance, but all three derivatives showed no conjugation which excludes functionalization in 2-position. As the C3 is used for the actual bioconjugation, the last possible derivatization was realized on the indole-N1 by using 1-(3-bromopropyl)indole as building block during the synthesis of the ligand-system. The corresponding manganese 36 and rhenium 37 complexes both showed similar properties of a moderate conversion like 22 and a rate constant in the range of 10-5 s-1. In conclusion the rhenium complex 32 with the 6-substitution pattern at the tridentate indole-bearing ligand remains the most promising structure.
The here developed liquid chromatography coupled mass spectrometry-based assay for the determination of inhibitory activity of drug candidates against the 3CLpro of the sever acute respiratory syndrome coronavirus type 2 was successfully implemented and especially designed to give, due to the available absorption spectra and corresponding mass traces, further insight in the otherwise through fluorescence resonance energy transfer-based assays neglected influences on the inhibition results. Starting with a literature-known quinolone containing covalent inhibitor 42 an N1-methylated derivative 43 and their analogues 44 and 45 in which the benzoic acid was exchanged for ferrocene carboxylic acid were synthesized. The inhibition of 3CLpro was evaluated by the concentration of initial 15mer peptide left after incubation and for that purpose the for 280 nm defined molar attenuation coefficient of (26.41±0.59) L*mol-1*cm-1 determined and used. The results showed a reaction of DL dithiothreitol with the less stable benzoic acid esters leading to a moderate inhibitory effect. The methylation in N1-position showed an increase in stability. The methylated and with ferrocene carboxylic acid functionalized derivative showed a complete inhibition during the timeframe of the assay. In search of a fluorescent and therefore traceable inhibitor, 4 hydroxycoumarin was used to synthesize the analogue with benzoic acid 49 and ferrocene carboxylic acid 50. Both derivatives were less stable than their analogues but exhibited the same trend of a more stable ferrocene-derived compound, which exerted a higher inhibition as well. After preparing and testing the model thioester 53 and showing an inactivation of the established inhibitor ebselen, it was concluded that the reaction with DL dithiothreitol reduces the concentration of active intact inhibitor and therefore decreases the inhibition rate during the assay. The next step was proofing the reducing agent as non-essential for the fast assay conducted in a timeframe of 5 min to circumvent the negative influence of DL dithiothreitol. By excluding every inhibition-altering part, the resulting method is the perfect tool for precise statements in relation of inhibitory activity. Then the inhibition assay was repeated for ebselen and the best out of the here introduced organometallic inhibitors 45. Both give equivalent results of a complete inhibition during the measurement. The implemented liquid chromatography coupled mass spectrometry-based assay has many advantages over the fluorescence resonance energy transfer-based assays in which all the information and insight accumulated by the evaluation of uv/vis traces and mass spectra are not available leading to wrong or deviating results regarding the inhibitory capacity of inhibitor candidates.
Squamous cell carcinomas (SCC) frequently have an exceptionally high mutational burden. As consequence, they rapidly develop resistance to platinum-based chemotherapy and overall survival is limited. Novel therapeutic strategies are therefore urgently required. SCC express ∆Np63, which regulates the Fanconi Anemia (FA) DNA-damage response in cancer cells, thereby contributing to chemotherapy-resistance. Here we report that the deubiquitylase USP28 is recruited to sites of DNA damage in cisplatin-treated cells. ATR phosphorylates USP28 and increases its enzymatic activity. This phosphorylation event is required to positively regulate the DNA damage repair in SCC by stabilizing ∆Np63. Knock-down or inhibition of USP28 by a specific inhibitor weakens the ability of SCC to cope with DNA damage during platin-based chemotherapy. Hence, our study presents a novel mechanism by which ∆Np63 expressing SCC can be targeted to overcome chemotherapy resistance. Limited treatment options and low response rates to chemotherapy are particularly common in patients with squamous cancer. The SCC specific transcription factor ∆Np63 enhances the expression of Fanconi Anemia genes, thereby contributing to recombinational DNA repair and Cisplatin resistance. Targeting the USP28-∆Np63 axis in SCC tones down this DNA damage response pathways, thereby sensitizing SCC cells to cisplatin treatment.
Background
Prostate cancer (PCa) is the most frequent cancer in men. The prognosis of PCa is heterogeneous with many clinically indolent tumors and rare highly aggressive cases. Reliable tissue markers of prognosis are lacking. Active cholesteryl ester synthesis has been associated with prostate cancer aggressiveness. Sterol-O-Acyl transferases (SOAT) 1 and 2 catalyze cholesterol esterification in humans.
Objective
To investigate the value of SOAT1 and SOAT2 tissue expression as prognostic markers in high risk PCa.
Patients and Methods
Formalin-fixed paraffin-embedded tissue samples from 305 high risk PCa cases treated with radical prostatectomy were analyzed for SOAT1 and SOAT2 protein expression by semi-quantitative immunohistochemistry. The Kaplan-Meier method and Cox proportional hazards modeling were used to compare outcome.
Main Outcome Measure
Biochemical recurrence (BCR) free survival.
Results
SOAT1 expression was high in 73 (25%) and low in 219 (75%; not evaluable: 13) tumors. SOAT2 was highly expressed in 40 (14%) and at low levels in 249 (86%) samples (not evaluable: 16). By Kaplan-Meier analysis, we found significantly shorter median BCR free survival of 93 months (95% confidence interval 23.6-123.1) in patients with high SOAT1 vs. 134 months (112.6-220.2, Log-rank p < 0.001) with low SOAT1. SOAT2 expression was not significantly associated with BCR. After adjustment for age, preoperative PSA, tumor stage, Gleason score, resection status, lymph node involvement and year of surgery, high SOAT1 but not SOAT2 expression was associated with shorter BCR free survival with a hazard ratio of 2.40 (95% CI 1.57-3.68, p < 0.001). Time to clinical recurrence and overall survival were not significantly associated with SOAT1 and SOAT2 expression CONCLUSIONS: SOAT1 expression is strongly associated with BCR free survival alone and after multivariable adjustment in high risk PCa. SOAT1 may serve as a histologic marker of prognosis and holds promise as a future treatment target.
Multiple myeloma remains a largely incurable disease of clonally expanding malignant plasma cells. The bone marrow microenvironment harbors treatment-resistant myeloma cells, which eventually lead to disease relapse in patients. In the bone marrow, CD4\(^{+}\)FoxP3\(^{+}\) regulatory T cells (Tregs) are highly abundant amongst CD4\(^{+}\) T cells providing an immune protective niche for different long-living cell populations, e.g., hematopoietic stem cells. Here, we addressed the functional role of Tregs in multiple myeloma dissemination to bone marrow compartments and disease progression. To investigate the immune regulation of multiple myeloma, we utilized syngeneic immunocompetent murine multiple myeloma models in two different genetic backgrounds. Analyzing the spatial immune architecture of multiple myeloma revealed that the bone marrow Tregs accumulated in the vicinity of malignant plasma cells and displayed an activated phenotype. In vivo Treg depletion prevented multiple myeloma dissemination in both models. Importantly, short-term in vivo depletion of Tregs in mice with established multiple myeloma evoked a potent CD8 T cell- and NK cell-mediated immune response resulting in complete and stable remission. Conclusively, this preclinical in-vivo study suggests that Tregs are an attractive target for the treatment of multiple myeloma.
Chapter 1 – General introduction
Anthropogenic land-use and climate change are the major drivers of the global biodiversity loss. Yet, biodiversity is essential for human well-being, as we depend on the availability of potable water, sufficient food and further benefits obtained from nature. Each species makes a somewhat unique contribution to these ecosystem services. Furthermore, species tolerate environmental stressors, such as climate change, differently. Thus, biodiversity is both the "engine" and the "insurance" for human well-being in a changing climate. Here, I investigate the effects of temperature and land use on herbivory (Chapter 2), predation (Chapter 3) and pest control (Chapter 4), and at the same time identify features of habitats (e.g. plant richness, proximity to different habitat types) and landscapes (e.g. landscape diversity, proportion of oilseed rape area) as potential management targets in an adaptation strategy to climate change. Finally, I discuss the similarities and differences between factors influencing herbivory, predation and pest control, while placing the observations in the context of climate change as a multifaceted phenomenon, and highlighting starting points for sustainable insect pest management (Chapter 5).
Chapter 2 – Plant richness, land use and temperature differently shape invertebrate leaf-chewing herbivory on major plant functional groups
Invertebrate herbivores are temperature-sensitive. Rising temperatures increase their metabolic rates and thus their demand for carbon-rich relative to protein-rich resources, which can lead to changes in the diets of generalist herbivores. Here, we quantified leaf-area loss to chewing invertebrates among three plant functional groups (legumes, non-leguminous forbs and grasses), which largely differ in C:N (carbon:nitrogen) ratio. This reseach was conducted along spatial temperature and land-use gradients in open herbaceous vegetation adjacent to different habitat types (forest, grassland, arable field, settlement). Herbivory largely differed among plant functional groups and was higher on legumes than forbs and grasses, except in open areas in forests. There, herbivory was similar among plant functional groups and on legumes lower than in grasslands. Also the presence of many plant families lowered herbivory on legumes. This suggests that open areas in forests and diverse vegetation provide certain protection against leaf damage to some plant families (e.g. legumes). This could be used as part of a conservation strategy for protected species. Overall, the effects of the dominant habitat type in the vicinity and diverse vegetation outweighed those of temperature and large-scale land use (e.g. grassland proportion, landscape diversity) on herbivory of legumes, forbs and grasses at the present time.
Chapter 3 – Landscape diversity and local temperature, but not climate, affect arthropod predation among habitat types
Herbivorous insects underlie top-down regulation by arthropod predators. Thereby, predation rates depend on predator community composition and behaviour, which is shaped by temperature, plant richness and land use. How the interaction of these factors affects the regulatory performance of predators was unknown. Therefore, we assessed arthropod predation rates on artificial caterpillars along temperature, and land-use gradients. On plots with low local mean temperature (≤ 7°C) often not a single caterpillar was attacked, which may be due to the temperature-dependent inactivity of arthropods. However, multi-annual mean temperature, plant richness and the dominant habitat type in the vicinity did not substantially affect arthropod predation rates. Highest arthropod predation rates were observed in diverse landscapes (2-km scale) independently of the locally dominanting habitat type. As landscape diversity, but not multi-annual mean temperature, affected arthropod predation rates, the diversification of landscapes may also support top-down regulation of herbivores independent of moderate increases of multi-annual mean temperature in the near future.
Chapter 4 – Pest control and yield of winter oilseed rape depend on spatiotemporal crop-cover dynamics and flowering onset: implications for global warming
Winter oilseed rape is an important oilseed crop in Europe, yet its seed yield is diminished through pests such as the pollen beetle and stem weevils. Damage from pollen beetles depends on pest abundances, but also on the timing of infestation relative to crop development as the bud stage is particularly vulnerable. The development of both oilseed rape and pollen beetles is temperature-dependent, while temperature effects on pest abundances are yet unknown, which brings opportunities and dangers to oilseed rape cropping under increased temperatures. We obtained measures of winter oilseed rape (flowering time, seed yield) and two of its major pests (pollen beetle, stem weevils) for the first time along both land-use and temperature gradients. Infestation with stem weevils was not influenced by any temperature or land-use aspect considered, and natural pest regulation of pollen beetles in terms of parasitism rates of pollen beetle larvae was low (< 30%), except on three out of 29 plots. Nonetheless, we could identify conditions favouring low pollen beetle abundances per plant and high seed yields. Low pollen beetle densities were favoured by a constant oilseed rape area relative to the preceding year (5-km scale), whereas a strong reduction in area (> 40%) caused high pest densities (concentration effect). This occurred more frequently in warmer regions, due to drought around sowing, which contributed to increased pollen beetle numbers in those regions. Yet, in warmer regions, oilseed rape flowered early, which possibly led to partial escape from pollen beetle infestation in the most vulnerable bud stage. This is also suggested by higher seed yields of early flowering oilseed rape fields, but not per se at higher temperatures. Thus, early flowering (e.g. cultivar selection) and the interannual coordination of oilseed rape area offer opportunities for environmental-friendly pollen beetle management.
Chapter 5 – General discussion
Anthropogenic land-use and climate change are major threats to biodiversity, and consequently to ecosystem functions, although I could show that ecosystem functions such as herbivory and predation barely responded to temperature along a spatial gradient at present time. Yet, it is important to keep several points in mind: (i) The high rate of climate warming likely reduces the time that species will have to adapt to temperature in the future; (ii) Beyond mean temperatures, many aspects of climate will change; (iii) The compensation of biodiversity loss through functional redundancy in arthropod communities may be depleted at some point; (iv) Measures of ecosystem functions are limited by methodological filters, so that changes may be captured incompletely. Although much uncertainty of the effects of climate and land-use change on ecosystem functions remains, actions to halt biodiversity loss and to interfere with natural processes in an environmentally friendly way, e.g. reduction of herbivory on crops, are urgently needed. With this thesis, I contribute options to the environment-friendly regulation of herbivory, which are at least to some extent climate resilient, and at the same time make a contribution to halt biodiversity loss. Yet, more research and a transformation process is needed to make human action more sustainable. In terms of crop protection, this means that the most common method of treating pests with fast-acting pesticides is not necessarily the most sustainable. To realize sustainable strategies, collective efforts will be needed targeted at crop damage prevention through reducing pest populations and densities in the medium to long term. The sooner we transform human action from environmentally damaging to biodiversity promoting, the higher is our insurance asset that secures human well-being under a changing climate.
Chimeric antigen receptors (CARs) are able to specifically direct T cells to tumor antigens and therapy with anti-CD19 CARs has already cured cancer patients with B-cell lymphomas who have undergone long-term therapy non-successful. Despite this impressive result, the therapy is currently only approved as a last treatment option for blood cancers due to its life-threatening deficiencies. For patient safety and to enable additional application such as the treatment of solid tumors, CAR-T cells must be controllable, e. g. by chemically programmable CARs (cpCARs) regulated by hapten-like compounds.
This thesis reports the synthesis and characterization of such hapten-like compounds. In the first step, seven different warheads with two different spacers were bound to biotin in order to find a suitable warhead for programming the cpCAR.
In a second step, synthetic routes for the three pharmacophores folate, c(RGD), and an RGD peptidomimetic were developed. The routes allow the modification of the pharmacophores with one of the warheads from the first step. CuAAC was chosen as a bioorthogonal approach to link pharmacophores and warheads.
In total, three different pharmacophores were modified with the 1,3-diketone motif of compound 21 leading to 112, 113 and 128. Activation of the T-cell signaling cascade was tested after binding of these hapten-like compounds to the cpCAR in the presence of suitable target structures. For 112, only a slight, non-significant, activation of the T-cell signaling cascade was observed, whereas for 113 and 128, a significant activation of the T-cell signaling cascade was observed.
The poor solubility of the folate compounds led to alternative strategies. Folic acid was exchanged by pteroic acid and the bifunctional, linear compounds were enlarged to trifunctional dendrimers.
Besides the reported regioisomer in 112, a second one, which was not reported to date, occurred by the cyclization of the linear RGD pentapeptide leading to 113.
After the reported synthesis of an RGD peptidomimetic analogous to 128 could not be reproduced, a new synthetic route was developed. It also consists of 17 steps, but reduces the number of linear steps from 13 to 10. Moreover, the developed route contains an asymmetric hydrogenation step and is, compared to the published one, more flexible by the use of the copper-catalyzed azide-alkyne cycloaddition (CuAAC). In addition, an unknown reaction was observed. Instead of the formation of a Schiff base in the reductive amination of 129, an insertion of propargylamine occurred forming 131. The reaction is almost quantitative and in high purity. After requiring no purification, it could be predestined for industrial purposes, such as the synthesis of N-functionalized 1,2-dihydroquinolines or as a building block with various orthogonal functional groups.
Besides the sulfonamide 16, the diketone (21, 27, 31) and lactam compounds (39 – 41), experiments on adapter molecules with further warheads were performed. In the synthesis of a proadapter approach, in which the warhead is formed only after the retro-aldol reaction catalyzed by the mAb, 6 of 10 steps were successfully performed. A newly developed synthesis to keto-sulfonyl and keto-sulfoxide compounds could not be completed but was performed on a small scale to the point of keto-sulfonyl and keto-sulfoxide. Furthermore, a universal synthesis route was designed to allow the introduction of the warhead at the end of the synthesis by acylation. Thus, after 5 shared steps, 3 of them in quantitative yield, different warheads may be introduced. Moreover, this also facilitates the purification and the analysis of the compounds by the absence of tautomerism or labile groups. However, the acylation experiments were not successful with either the acid cyanide or the Weinreb amide.
In summary, this thesis has proven that the 1,3-diketone motif is a suitable warhead for programming the cpCAR, which was developed by Hudecek et al. (unpublished data). The hapten-like compounds 112, 113 and 128 simultaneously bind to integrin ${\alpha}_v{\beta}_3$ and the cpCAR activating the T-cell signaling cascade. The modular synthesis strategy and the use of the bioorthogonal CuAAC allow straightforward access to these valuable immunotherapeutics but revealed the need for an additional purification step to remove copper ions.
Background and Purpose
The standard treatment of glioblastoma patients consists of surgery followed by normofractionated radiotherapy (NFRT) with concomitant and adjuvant temozolomide chemotherapy. Whether accelerated hyperfractionated radiotherapy (HFRT) yields comparable results to NFRT in combination with temozolomide has only sparsely been investigated. The objective of this study was to compare NFRT with HFRT in a multicenter analysis.
Materials and Methods
A total of 484 glioblastoma patients from four centers were retrospectively pooled and analyzed. Three-hundred-ten and 174 patients had been treated with NFRT (30 × 1.8 Gy or 30 × 2 Gy) and HFRT (37 × 1.6 Gy or 30 × 1.8 Gy twice/day), respectively. The primary outcome of interest was overall survival (OS) which was correlated with patient-, tumor- and treatment-related variables via univariable and multivariable Cox frailty models. For multivariable modeling, missing covariates were imputed using multiple imputation by chained equations, and a sensitivity analysis was performed on the complete-cases-only dataset.
Results
After a median follow-up of 15.7 months (range 0.8-88.6 months), median OS was 16.9 months (15.0-18.7 months) in the NFRT group and 14.9 months (13.2-17.3 months) in the HFRT group (p = 0.26). In multivariable frailty regression, better performance status, gross-total versus not gross-total resection, MGMT hypermethylation, IDH mutation, smaller planning target volume and salvage therapy were significantly associated with longer OS (all p < 0.01). Treatment differences (HFRT versus NFRT) had no significant effect on OS in either univariable or multivariable analysis.
Conclusions
Since HFRT with temozolomide was not associated with worse OS, we assume HFRT to be a potential option for patients wishing to shorten their treatment time.
For the past 20 years, chronic kidney disease (CKD) has remained one of the major causes of death worldwide. Cardiovascular events account for approximately 50% of deaths in CKD patients, underscoring the clinical relevance of the observed cardiac changes. These changes define uremic cardiomyopathy (UCM) and include left-ventricular hypertrophy (LVH), LV dilatation, and LV systolic and diastolic dysfunction. LVH is seen as the primary manifestation of UCM and is caused by a multitude of different systems including in-creased pre- and afterload and the renin-angiotensin system (RAS). More recent studies found that myocardial dysfunction is apparent before changes in the ventricular geome-try, like hypertrophy, occur to the uremic heart. This leads to the conclusion that LVH is not the cause of cardiac dysfunction, but one of the alterations caused by factors related to the uremic state itself. Among these factors that are independent of pressure and vol-ume overload, are cardiotonic steroids as well as the parathyroid hormone and the endo-thelin (ET-1) system. But we suggest a different substance to play an important role in UCM: Urea. Patients in end-stage renal disease (ESRD) display increased oxidative stress and urea has been found to increase levels of oxidative stress, at least in endothelial cells. Therefore, we investigated the effect that elevated urea levels, as seen in patients undergoing dialysis, have on cardiomyocytes. As the oxidative stress in a cell is regulated by mitochondrial processes, we suspected the mitochondrial orchestrator PGC-1α to play an important role.
The uremic heart is in a state of elevated oxidative stress. This has been presented by multiple authors before. By conducting immunofluorescent staining for reactive oxygen species (ROS), we tried to replicate their findings and illustrate elevated levels of ROS. As the fluorescence analysis did not bear significant results, we approached oxidative stress from a different angle: Via mass spectrometry, we looked at the amino acids methionine, cysteine and betaine which are highly involved in sustaining the oxidative balance in the cell. Our findings in the media of urea-treated HL-1 cells lead us to the conclusion, that these cardiomyocytes were in a state of low antioxidative resources.
Next, to find the intracellular mechanisms that connect uremia to oxidative stress and compromised energetics, we investigated possible downstream effectors of uremia. The urea-treated cardiomyocytes exhibited significant alterations regarding upstream effec-tors of PGC-1α: The protein kinases Akt and Erk were expressed and phosphorylated dif-ferently in a western blot analysis of uremic h9c2 cells and in mice with induced kidney failure. To combine these findings regarding the protein kinases Akt and Erk and oxidative stress, the Erk/p38 pathways seems conclusive (figure 20). This pathway links uremia and oxidative stress to intracellular effectors that have been found to influence the develop-ment of uremic cardiomyopathy.
Another life-threatening alteration in uremic cardiomyopathy is a corrupted cardiac func-tion. The myocardium of uremic patients has shown to be more susceptible to ischemic damage and most patients receiving dialysis experience repeated episodes of intradialytic impairments in cardiac function. The urea-treated cardiomyocytes had a significantly higher oxygen consumption rate due to an inefficiently increased metabolism, most likely caused by an increased level of uncoupling.
Taken together, the results of this study indicate that urea by itself plays a role in the de-velopment of uremic cardiomyopathy. So-called high-physiologic levels of urea have led to a mitochondrial inefficiency and an increase of oxidative stress in cardiomyocytes. The protein kinases Akt and Erk may work as effectors of urea to induce these changes via the Erk/p38 pathway. It seems very likely that the mitochondrial changes are mediated by the mitochondrial orchestrator PGC-1α. These observations might lead to further studies in-vestigating urea levels in dialysis patients. In the future, these might lead to a change of practice regarding tolerated urea levels in dialysis and help reduce the cardiac mortality of patients with chronic kidney disease.
A sequentialquadratic Hamiltonian schemefor solving open-loop differential Nash games is proposed and investigated. This method is formulated in the framework of the Pontryagin maximum principle and represents an efficient and robust extension of the successive approximations strategy for solving optimal control problems. Theoretical results are presented that prove the well-posedness of the proposed scheme, and results of numerical experiments are reported that successfully validate its computational performance.
This paper argues that applied ethics can itself be morally problematic. As illustrated by the case of Peter Singer’s criticism of social practice, morally loaded communication by applied ethicists can lead to protests, backlashes, and aggression. By reviewing the psychological literature on self-image, collective identity, and motivated reasoning three categories of morally problematic consequences of ethical criticism by applied ethicists are identified: serious psychological discomfort, moral backfiring, and hostile conflict. The most worrisome is moral backfiring: psychological research suggests that ethical criticism of people’s central moral convictions can reinforce exactly those attitudes. Therefore, applied ethicists unintentionally can contribute to a consolidation of precisely those social circumstances that they condemn to be unethical. Furthermore, I argue that the normative concerns raised in this paper are not dependent on the commitment to one specific paradigm in moral philosophy. Utilitarianism, Aristotelian virtue ethics, and Rawlsian contractarianism all provide sound reasons to take morally problematic consequences of ethical criticism seriously. Only the case of deontological ethics is less clear-cut. Finally, I point out that the issues raised in this paper provide an excellent opportunity for further interdisciplinary collaboration between applied ethics and social sciences. I also propose strategies for communicating ethics effectively.
Objectives
Magnesium phosphate-based cements begin to catch more attention as bone substitute materials and especially as alternatives for the more commonly used calcium phosphates. In bone substitutes for augmentation purposes, atraumatic materials with good biocompatibility and resorbability are favorable. In the current study, we describe the in vivo testing of novel bone augmentation materials in form of spherical granules based on a calcium-doped magnesium phosphate (CaMgP) cement.
Materials and Methods
Granules with diameters between 500 and 710 μm were fabricated via the emulsification of CaMgP cement pastes in a lipophilic liquid. As basic material, two different CaMgP formulations were used. The obtained granules were implanted into drill hole defects at the distal femoral condyle of 27 New Zealand white rabbits for 6 and 12 weeks. After explantation, the femora were examined via X-ray diffraction analysis, histological staining, radiological examination, and EDX measurement.
Results
Both granule types display excellent biocompatibility without any signs of inflammation and allow for proper bone healing without the interposition of connective tissue. CaMgP granules show a fast and continuous degradation and enable fully adequate bone regeneration.
Conclusions
Due to their biocompatibility, their degradation behavior, and their completely spherical morphology, these CaMgP granules present a promising bone substitute material for bone augmentation procedures, especially in sensitive areas.
Clinical Relevance
The mostly insufficient local bone supply after tooth extractions complicates prosthetic dental restoration or makes it even impossible. Therefore, bone augmentation procedures are oftentimes inevitable. Spherical CaMgP granules may represent a valuable bone replacement material in many situations.
Objectives
Posttraumatic stress disorder (PTSD) is triggered by extremely stressful environmental events and characterized by high emotional distress, re-experiencing of trauma, avoidance and hypervigilance. The present study uses polygenic risk scores (PRS) derived from the UK Biobank (UKBB) mega-cohort analysis as part of the PGC PTSD GWAS effort to determine the heritable basis of PTSD in the South Eastern Europe (SEE)-PTSD cohort. We further analyzed the relation between PRS and additional disease-related variables, such as number and intensity of life events, coping, sex and age at war on PTSD and CAPS as outcome variables.
Methods
Association of PRS, number and intensity of life events, coping, sex and age on PTSD were calculated using logistic regression in a total of 321 subjects with current and remitted PTSD and 337 controls previously subjected to traumatic events but not having PTSD. In addition, PRS and other disease-related variables were tested for association with PTSD symptom severity, measured by the Clinician Administrated PTSD Scale (CAPS) by liner regression. To assess the relationship between the main outcomes PTSD diagnosis and symptom severity, each of the examined variables was adjusted for all other PTSD related variables.
Results
The categorical analysis showed significant polygenic risk in patients with remitted PTSD and the total sample, whereas no effects were found on symptom severity. Intensity of life events as well as the individual coping style were significantly associated with PTSD diagnosis in both current and remitted cases. The dimensional analyses showed as association of war-related frequency of trauma with symptom severity, whereas the intensity of trauma yielded significant results independently of trauma timing in current PTSD.
Conclusions
The present PRS application in the SEE-PTSD cohort confirms modest but significant polygenic risk for PTSD diagnosis. Environmental factors, mainly the intensity of traumatic life events and negative coping strategies, yielded associations with PTSD both categorically and dimensionally with more significant p-values. This suggests that, at least in the present cohort of war-related trauma, the association of environmental factors and current individual coping strategies with PTSD psychopathology was stronger than the polygenic risk.
Purpose
Patients suffering from aggressive systemic peripheral lymphoma with primary central nervous system involvement (PCL) are a rare and sparsely investigated population. Recommended treatment regimens include a combination of intrathecal and systemic chemotherapy as well as whole brain radiotherapy while offering relatively poor survival.
Methods
We conducted a single-center retrospective study that analyzed safety and outcome of 4 + 4 cycles Rituximab (R)-CHOP and R-high-dose Methotrexate (HD-MTX) for newly diagnosed, transplant-eligible patients ("Ping-Pong"), followed by Cytarabine (AraC)/Thiotepa (TT), BCNU/TT, and autologous hematologic stem cell transplantation (aHSCT). We retrospectively analyzed a set of 16 patients with high-intermediate or high-risk IPI status.
Results
Overall response rate to Ping-Pong was 100% measured by CT/MRI, including 93.75% complete remissions after BCNU/TT followed by PBSCT. One patient failed to qualify for high-dose chemotherapy due to progression when receiving Cytarabine/TT. All patients experienced grade III adverse events, 3 of them a grade IV adverse event. Estimated progression-free survival is 93.75% after a 4.8-year follow-up currently.
Conclusion
Our study suggests high effectivity of R-CHOP with mid-cycle MTX with aHSCT consolidation towards acceptable OS results in this challenging patient population.
Creativity, specifically divergent thinking, has been shown to benefit from unrestrained walking. Despite these findings, it is not clear if it is the lack of restriction that leads to the improvement. Our goal was to explore the effects of motor restrictions on divergent thinking for different movement states. In addition, we assessed whether spontaneous eye blinks, which are linked to motor execution, also predict performance. In experiment 1, we compared the performance in Guilford's alternate uses task (AUT) during walking vs. sitting, and analysed eye blink rates during both conditions. We found that AUT scores were higher during walking than sitting. Albeit eye blinks differed significantly between movement conditions (walking vs. sitting) and task phase (baseline vs. thinking vs. responding), they did not correlate with task performance. In experiment 2 and 3, participants either walked freely or in a restricted path, or sat freely or fixated on a screen. When the factor restriction was explicitly modulated, the effect of walking was reduced, while restriction showed a significant influence on the fluency scores. Importantly, we found a significant correlation between the rate of eye blinks and creativity scores between subjects, depending on the restriction condition. Our study shows a movement state-independent effect of restriction on divergent thinking. In other words, similar to unrestrained walking, unrestrained sitting also improves divergent thinking. Importantly, we discuss a mechanistic explanation of the effect of restriction on divergent thinking based on the increased size of the focus of attention and the consequent bias towards flexibility.
Systemic sclerosis (SSc) is a severe chronic disease with a broad spectrum of clinical manifestations. SSc displays disturbed lymphocyte homeostasis. Immunosuppressive medications targeting T or B cells can improve disease manifestations. SSc clinical manifestations and immunosuppressive medication in itself can cause changes in lymphocyte subsets. The aim of this study was to investigate peripheral lymphocyte homeostasis in SSc with regards to the immunosuppression and to major organ involvement. 44 SSc patients and 19 healthy donors (HD) were included. Immunophenotyping of peripheral whole blood by fluorescence-activated cell sorting was performed. Cytokine secretions of stimulated B cell cultures were measured. SSc patients without immunosuppression compared to HD displayed lower γδ T cells, lower T helper cells (CD3+/CD4+), lower transitional B cells (CD19+/CD38++/CD10+/IgD+), lower pre-switched memory B cells (CD19+/CD27+/IgD+), and lower post-switched memory B cells (CD19+/CD27+/IgD-). There was no difference in the cytokine production of whole B cell cultures between SSc and HD. Within the SSc cohort, mycophenolate intake was associated with lower T helper cells and lower NK cells (CD56+/CD3-). The described differences in peripheral lymphocyte subsets between SSc and HD generate further insight in SSc pathogenesis. Lymphocyte changes under effective immunosuppression indicate how lymphocyte homeostasis in SSc might be restored.
Adrenocortical carcinoma (ACC) is a rare, aggressive cancer with still partially unknown pathogenesis, heterogenous clinical behaviour and no effective treatment for advanced stages. Therefore, there is an urgent clinical unmet need for better prognostication strategies, innovative therapies and significant improvement of the management of the individual patients. In this review, we summarize available studies on molecular prognostic markers and markers predictive of response to standard therapies as well as newly proposed drug targets in sporadic ACC. We include in vitro studies and available clinical trials, focusing on alterations at the DNA, RNA and epigenetic levels. We also discuss the potential of biomarkers to be implemented in a clinical routine workflow for improved ACC patient care.
Observing physicians acting with different levels of empathy modulates later assessed pain tolerance
(2022)
Objectives
The patient–physician relationship is essential for treatment success. Previous studies demonstrated that physicians who behave empathic in their interaction with patients have a positive effect on health outcomes. In this study, we investigated if the mere perception of physicians as empathic/not empathic modulates pain despite an emotionally neutral interaction with the patients.
Methods
N = 60 women took part in an experimental study that simulated a clinical interaction. In the paradigm, each participant watched two immersive 360° videos via a head-mounted display from a patient’s perspective. The physicians in the videos behaved either empathic or not empathic towards a third person. Importantly, these physicians remained emotionally neutral in the subsequent virtual interaction with the participants. Finally, participants received a controlled, painful pressure stimulus within the narratives of the videos.
Results
The physicians in the high compared with the low empathy videos were rated as more empathic and more likable, indicating successful experimental manipulation. In spite of later neutral behaviour of physicians, this short observation of physicians’ behaviour towards a third person was sufficient to modulate pain tolerance of the participants.
Conclusions
The finding of this study that the mere observation of physicians’ behaviour towards a third person modulates pain, despite a neutral direct interaction with the participants, has important clinical implications. Further, the proposed paradigm enables investigating aspects of patient–physician communication that are difficult to examine in a clinical setting.
Background
Cancer patients' mental health and quality of life can be improved through professional support according to their needs. In previous analyses of the UNSAID study, we showed that a relevant proportion of cancer patients did not express their needs during the admission interview of inpatient rehabilitation. We now examine trajectories of mental health, quality of life, and utilization of professional help in cancer patients with unexpressed needs.
Methods
We enrolled 449 patients with breast, prostate, and colon cancer at beginning (T0) and end (T1) of a 3-week inpatient rehabilitation and 3 (T2) and 9 (T3) months after discharge. We explored depression (PHQ-2), anxiety (GAD-2), emotional functioning (EORTC QLQ-C30), fear of progression (FoP-Q-SF), and global quality of life (EORTC QLQ-C30) using structuring equation models. Furthermore, we evaluated self-reports about expressing needs and utilization of professional help at follow-up.
Results
Patients with unexpressed needs (24.3%, n = 107) showed decreased mental health compared to other patients (e.g., depression: d T0 = 0.32, d T1-T3 = 0.39). They showed a significant decline in global quality of life at discharge and follow-up (d = 0.28). Furthermore, they had a higher need for support (Cramer's V T2 = 0.10, T3 = 0.15), talked less about their needs (Cramer’s V T2 = 0.18), and made less use of different health care services at follow-up.
Conclusion
Unexpressed needs in cancer patients may be a risk factor for decreased mental health, quality of life, and non-utilization of professional help in the long term. Further research should clarify causal relationships and focus on this specific group of patients to improve cancer care.
Charge transfer in ternary solar cells employing two fullerene derivatives: where do electrons go?
(2022)
Earlier reports demonstrated that ternary organic solar cells (OSC) made of donor polymers (D) blended with different mixtures of fullerene acceptors (A : A) performed very similarly. This finding is surprising, as the corresponding fullerene LUMO levels are slightly different, which might result in decisive differences in the charge transfer step. We investigate ternary OSC (D : A : A) made of the donor polymer P3HT with stoichiometric mixtures of different fullerene derivatives, PC\(_{60}\)BM : PC\(_{70}\)BM and PC\(_{70}\)BM : IC\(_{60}\)BA, respectively. Using quantitative electron paramagnetic resonance (EPR) we can distinguish between positive and negative polarons, localized on the specific molecules. We found that after the initial charge transfer step, the electrons are re-distributed over two nearby acceptors in agreement with their stoichiometry and their relative LUMO energy difference. Remarkably, the measured ΔLUMO differences in fullerene mixtures are reduced by an order of magnitude compared to that of the pristine materials, i. e., below 1 meV for PC\(_{60}\)BM : PC\(_{70}\)BM and (20±5) meV for PC\(_{70}\)BM : IC\(_{60}\)BA. Furthermore, we found that this reduced ΔLUMO explains the shift in open circuit voltage for D : A : A organic solar cells. We attribute these findings to hybridization, leading to an effective fullerene LUMO. Consequently, multi-acceptor blends are indeed a viable option for photodetectors and solar cells, as they combine the best electron acceptor and light absorbing properties.
The multi-agent therapy “VDT-PACE” represents an established regimen in relapsed/refractory multiple myeloma (RRMM). Here, we report on our experience with a “modified VDT-PACE” incorporating new generation anti-MM agents daratumumab and carfilzomib (“Dara-KDT-P(A)CE”). We retrospectively analyzed 38 patients with RRMM treated with “Dara-KDT-P(A)CE”. The median age was 62 (range 45–82) years, and the patients were heavily pretreated with a median of 5 (range 2–12) prior lines of therapy. Twenty-one (55%) patients suffered from penta-refractory MM. High-risk cytogenetics was present in 31 (81%) patients. The patients received a median of 2 (range 1–10) cycles of this therapy, and the overall response rate (ORR) was 70%. Patients with penta-refractory MM and high-risk cytogenetics showed similar ORR of 65% and 79%, respectively. The median progression-free survival (PFS) and overall survival were 4.1 (95% CI 2.7–5.4) and 8.4 (95% CI 6.7–10.0) months, respectively. Patients with lactate dehydrogenase >250 IU/L showed significantly shorter PFS in comparison with others patients (p = 0.006). We used this regimen as bridging therapy prior to chimeric antigen receptor T-cell infusion in four patients. In conclusion, “Dara-KDT-P(A)CE” is an effective salvage therapy for patients with heavily pretreated, multi-refractory, high-risk RRMM lacking alternative options.
The neuropeptide pigment-dispersing factor (PDF) plays a prominent role in the circadian clock of many insects including honey bees. In the honey bee brain, PDF is expressed in about 15 clock neurons per hemisphere that lie between the central brain and the optic lobes. As in other insects, the bee PDF neurons form wide arborizations in the brain, but certain differences are evident. For example, they arborize only sparsely in the accessory medulla (AME), which serves as important communication center of the circadian clock in cockroaches and flies. Furthermore, all bee PDF neurons cluster together, which makes it impossible to distinguish individual projections. Here, we investigated the developing bee PDF network and found that the first three PDF neurons arise in the third larval instar and form a dense network of varicose fibers at the base of the developing medulla that strongly resembles the AME of hemimetabolous insects. In addition, they send faint fibers toward the lateral superior protocerebrum. In last larval instar, PDF cells with larger somata appear and send fibers toward the distal medulla and the medial protocerebrum. In the dorsal part of the medulla serpentine layer, a small PDF knot evolves from which PDF fibers extend ventrally. This knot disappears during metamorphosis and the varicose arborizations in the putative AME become fainter. Instead, a new strongly stained PDF fiber hub appears in front of the lobula. Simultaneously, the number of PDF neurons increases and the PDF neuronal network in the brain gets continuously more complex.
Dye–dye interactions affect the optical and electronic properties in organic semiconductor films of light harvesting and detecting optoelectronic applications. This review elaborates how to tailor these properties of organic semiconductors for organic solar cells (OSCs) and organic photodiodes (OPDs). While these devices rely on similar materials, the demands for their optical properties are rather different, the former requiring a broad absorption spectrum spanning from the UV over visible up to the near‐infrared region and the latter an ultra‐narrow absorption spectrum at a specific, targeted wavelength. In order to design organic semiconductors satisfying these demands, fundamental insights on the relationship of optical properties are provided depending on molecular packing arrangement and the resultant electronic coupling thereof. Based on recent advancements in the theoretical understanding of intermolecular interactions between slip‐stacked dyes, distinguishing classical J‐aggregates with predominant long‐range Coulomb coupling from charge transfer (CT)‐mediated or ‐coupled J‐aggregates, whose red‐shifts are primarily governed by short‐range orbital interactions, is suggested. Within this framework, the relationship between aggregate structure and functional properties of representative classes of dye aggregates is analyzed for the most advanced OSCs and wavelength‐selective OPDs, providing important insights into the rational design of thin‐film optoelectronic materials.
Background: Acute respiratory failure is the most important organ dysfunction of COVID-19 patients. While non-invasive ventilation (NIV) and high-flow nasal cannula (HFNC) oxygen are frequently used, efficacy and safety remain uncertain. Benefits and harms of awake prone positioning (APP) in COVID-19 patients are unknown. Methods: We searched for randomized controlled trials (RCTs) comparing HFNC vs. NIV and APP vs. standard care. We meta-analyzed data for mortality, intubation rate, and safety. Results: Five RCTs (2182 patients) were identified. While it remains uncertain whether HFNC compared to NIV alters mortality (RR: 0.92, 95% CI 0.65–1.33), HFNC may increase rate of intubation or death (composite endpoint; RR 1.22, 1.03–1.45). We do not know if HFNC alters risk for harm. APP compared to standard care probably decreases intubation rate (RR 0.83, 0.71–0.96) but may have little or no effect on mortality (RR: 1.08, 0.51–2.31). Conclusions: Certainty of evidence is moderate to very low. There is no compelling evidence for either HFNC or NIV, but both carry substantial risk for harm. The use of APP probably has benefits although mortality appears unaffected.
(1) Background: Data on coronavirus 2 infection during pregnancy vary. We aimed to describe maternal characteristics and clinical presentation of SARS-CoV-2 positive women requiring intensive care treatment for COVID-19 during pregnancy and postpartum period based on data of a comprehensive German surveillance system in obstetric patients. (2) Methods: Data from COVID-19 Related Obstetric and Neonatal Outcome Study (CRONOS), a prospective multicenter registry for SARS-CoV-2 positive pregnant women, was analyzed with respect to ICU treatment. All women requiring intensive care treatment for COVID-19 were included and compared regarding maternal characteristics, course of disease, as well as maternal and neonatal outcomes. (3) Results: Of 2650 cases in CRONOS, 101 women (4%) had a documented ICU stay. Median maternal age was 33 (IQR, 30–36) years. COVID-19 was diagnosed at a median gestational age of 33 (IQR, 28–35) weeks. As the most invasive form of COVID-19 treatment interventions, patients received either continuous monitoring of vital signs without further treatment requirement (n = 6), insufflation of oxygen (n = 30), non-invasive ventilation (n = 22), invasive ventilation (n = 28), or escalation to extracorporeal membrane oxygenation (n = 15). No significant clinical differences were identified between patients receiving different forms of ventilatory support for COVID-19. Prevalence of preterm delivery was significantly higher in women receiving invasive respiratory treatments. Four women died of COVID-19 and six fetuses were stillborn. (4) Conclusions: Our cohort shows that progression of COVID-19 is rare in pregnant and postpartum women treated in the ICU. Preterm birth rate is high and COVID-19 requiring respiratory support increases the risk of poor maternal and neonatal outcome.
Introduction: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) profoundly impacts hemostasis and microvasculature. In the light of the dilemma between thromboembolic and hemorrhagic complications, in the present paper, we systematically investigate the prevalence, mortality, radiological subtypes, and clinical characteristics of intracranial hemorrhage (ICH) in coronavirus disease (COVID-19) patients. Methods: Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we performed a systematic review of the literature by screening the PubMed database and included patients diagnosed with COVID-19 and concomitant ICH. We performed a pooled analysis, including a prospectively collected cohort of critically ill COVID-19 patients with ICH, as part of the PANDEMIC registry (Pooled Analysis of Neurologic Disorders Manifesting in Intensive Care of COVID-19). Results: Our literature review revealed a total of 217 citations. After the selection process, 79 studies and a total of 477 patients were included. The median age was 58.8 years. A total of 23.3% of patients experienced the critical stage of COVID-19, 62.7% of patients were on anticoagulation and 27.5% of the patients received ECMO. The prevalence of ICH was at 0.85% and the mortality at 52.18%, respectively. Conclusion: ICH in COVID-19 patients is rare, but it has a very poor prognosis. Different subtypes of ICH seen in COVID-19, support the assumption of heterogeneous and multifaceted pathomechanisms contributing to ICH in COVID-19. Further clinical and pathophysiological investigations are warranted to resolve the conflict between thromboembolic and hemorrhagic complications in the future.
Point-spread function engineering for single-molecule localization microscopy in brain slices
(2022)
Single-molecule localization microscopy (SMLM) is the method of choice to study biological specimens on a nanoscale level. Advantages of SMLM imply its superior specificity due to targeted molecular fluorescence labeling and its enhanced tissue preservation compared to electron microscopy, while reaching similar resolution. To reveal the molecular organization of protein structures in brain tissue, SMLM moves to the forefront: Instead of investigating brain slices with a thickness of a few µm, measurements of intact neuronal assemblies (up to 100 µm in each dimension) are required. As proteins are distributed in the whole brain volume and can move along synapses in all directions, this method is promising in revealing arrangements of neuronal protein markers. However, diffraction-limited imaging still required for the localization of the fluorophores is prevented by sample-induced distortion of emission pattern due to optical aberrations in tissue slices from non-superficial planes. In particular, the sample causes wavefront dephasing, which can be described as a summation of Zernike polynomials. To recover an optimal point spread function (PSF), active shaping can be performed by the use of adaptive optics. The aim of this thesis is to establish a setup using a deformable mirror and a wavefront sensor to actively shape the PSF to correct the wavefront phases in a super-resolution microscope setup. Therefore, fluorescence-labeled proteins expressed in different anatomical regions in brain tissue will be used as experiment specimen. Resolution independent imaging depth in slices reaching tens of micrometers is aimed.
Due to a usually late diagnosis, drug resistance and early metastases, pancreatic ductal adenocarcinoma (PDAC) is the seventh leading cause of global cancer deaths. Thus, there is an urgent need to develop new therapeutic concepts. Two different approaches have in recent years become the focus of intense research: (1) targeting cancer-associated metabolic rearrangements, and (2) targeting genetic vulnerabilities with combination therapy. Both concepts potentially have advantages such as increased efficacy, which decreases the likelihood of therapy-resistance, and reduced side effects, that are often associated with high concentrations of chemotherapeutic drugs. Autophagy is an evolutionary conserved signalling pathway that regulates cellular homeostasis. Regarding cancer, autophagy can either promote or suppress tumor growth. However, mouse models that allow genetic regulation of autophagy in established tumor tissue are not yet established. Therefore, we analysed new inducible shRNA mouse models targeting Atg5 or Atg7 with regard to functionality and toxicity. Both, shRNA Atg5- and shRNA Atg7-mediated knockdown anteceded functional autophagy impairment, and revealed unexpected profound phenotypic differences. Knockdown of Atg5 neither impaired the animal nor caused any grossly or microscopically detectable organ damage, whereas knockdown of Atg7 caused pancreatic destruction and eventually death. It is currently unclear whether mice died as a result of exocrine or endocrine collapse or due to a combination of both. The presented mouse models are highly potent RNAi mice that allow widespread and regulable inhibition of autophagy upon administration of doxycycline and provide a valuable and versatile toolbox for future autophagy and cancer research. In PDAC, argininosuccinate synthase 1 (ASS1) deficiency has been associated with higher recurrence rates, shorter disease-free survival, and shorter overall survival. During cancer development, rate-limiting enzymes of de novo arginine synthesis, like ASS1 or OTC, are downregulated via epigenetic silencing of their respective promotor. Known as ‘arginine auxotrophy‘, loss of these essential enzymes results in dependence on extracellular arginine. Based on this assumption, sensitivity of various cell lines to arginine deprivation was reported. However, the underlying mechanism is still unclear and the anti-tumor effects of the monotherapy are not sufficient to completely abrogate cancer cells. Therefore, the effects of arginine deprivation via rhArgI-PEG5000 were investigated in murine and human PDAC cells. In this study, we highlighted that arginine deprivation induced profound alterations such as autophagosome accumulation, induction of senescence and the ISR in pancreatic cancer cells. These alterations are potential genetic vulnerabilities that can be targeted by additional means to induce tumor cell death.
RNA molecules play diverse roles in biological systems. Post-transcriptional RNA modifications and dynamic structures enhance the functional diversity of RNA. A prerequisite for studying their biological significance is the availability of reliable methods for the detection of RNA modifications and structures. Several promising approaches have been developed in the last few decades; however, efficient, and versatile tools are still required to study the dynamic features of RNA. This thesis focuses on the development of nucleic acid catalysts as a tool to address the current needs in studying RNA. The major part of this thesis aimed at the development of deoxyribozymes as a tool for the detection of RNA modifications. Using in vitro selection from a random DNA library, we found deoxyribozymes that are sensitive to N 6 -isopentenyladenosine (i6A), a native tRNA modification and structural analogue of m6A. The in vitro evolution identified three classes of DNA enzymes: AA, AB08, and AC17 DNAzymes that showed distinct response to i6A modification and showed strong discrimination between structural analogues, i.e., m6A and i6A. In the continuation of the project, we attempted to develop RNA-cleaving deoxyribozymes that differentially respond to monomethylated cytidine isomers, 3-methylcytidine (m3C), N4 - methylcytidine (m4C), and 5-methylcytidine (m5C). Several deoxyribozymes were identified from in vitro selection, which are selective for a specific methylated cytidine isomer. The characterization of AL112, AM101, AN05, and AK104 catalysts confirmed the successful evolution of modification-specific and general deoxyribozymes that showed a broad substrate scope. In order to accelerate the DNAzymes discovery, a high throughput sequencing method (DZ-seq) was established that directly quantifies the RNA cleavage activity and cleavage site from deep sequencing data. The libraries contained information about cleavage status, cleavage site and sequence of deoxyribozymes and RNA substrate. The fraction cleaved (FC) data obtained from Dz-seq was validated for a subset of deoxyribozmes using conventional gel based kinetic assay and showed a good linear correlation (R2 = 0.91). Dz-seq possesses a great potential for the discovery of novel deoxyribozymes for the analysis of various RNA modifications in the future. The second objective of the current study was the development of structure-specific RNA labeling ribozymes. Here, we attempted to develop ribozymes that targets RNA of interest by structure-specific interaction rather than base-pairing and focused on a specific RNA G-quadruplex as the target. Two subsequent selection experiments led to the identification of the adenylyltransferase ribozymes AO10.2 and AR9. The partial characterization of these catalysts showed that A010.2 was unable to recognize intact BCL2 structure, but it turned out as the first reported trans-active ribozyme that efficiently labeled uridine in a defined substrate RNA hybridized to the ribozyme. The other ribozyme AR9 was shown to serve as a trans-active, self-labeling ribozyme that catalyzed adenylyl transferase reaction in the presence of the intact BCL2 sequence. Based on these preliminary findings, we envision that AR9 could potentially serve as a reporter RNA by self-labeling in the presence of an RNA G-quadruplex. However, both AO10.2 and AR9 still require more detailed characterization for their potential applications.
Tribenzotriquinacene (TBTQ) is a polycyclic aromatic framework with a particularly rigid, C3v symmetrical, bowl-shaped core bearing three mutually fused indane wings. It has been discussed as a defect center for a nanographene by Kuck and colleagues. Therefore, extended TBTQ structures are promising models for saturated defect structures in graphene and graphene like molecules and could be used to investigate the role of defects for the electronic properties of graphene. With this motivation, three different pi-extended TBTQ derivatives have been synthesized in this work. Several different Scholl reaction conditions were tried to obtain fully annulated product of hexaphenyl substituted TBTQ. The desired benzannulated TBTQ derivative could not be obtained due to unfavourable electron density in the respective positions of the molecule and increased reactivity of the bay position of the precursor. As an another method for benzannulation is the on-surface synthesis of graphene flakes and can be carried out using electron beams e.g. in a tunneling microscope (STM). According to our previous research, the parent system TBTQ and centro-methyl TBTQ on silver and gold surfaces showed that the gas phase deposition of these molecules gives rise to the formation of highly ordered two-dimensional assemblies with unique structural features. This shows the feasibility for the formation of defective graphene networks starting from the parent structures. Therefore, the same deposition technique was used to deposit Me-TBTQ(OAc)3Ph6, and investigate the molecular self-assembly properties directly on the surface of Cu (111). In summary, the substrate temperature dependent self-assembly of Me-TBTQ(OAc)3Ph6 molecules on Cu(111), shows the following evolution of orientations. At room temperature, molecules form dimers, which construct a higher-coverage honeycomb lattice. Furthermore, one of the acetyl group located in the bay positions of the TBTQ core is cleaved and the remaining two induce the metal-molecule interaction. It was presumed that by increasing the temperature to 393 K, the remaining acetyl and methyl groups would beeliminated from the molecular structure.In addition, the smaller TBTQ-Ph6 molecules preferably lie flat on Cu(111) crystal and allowing the molecules to settle into a C3-symmetry and form a dense hexagonal structure.
This dissertation describes the synthesis of an unsymmetrically-substituted triarylborane. This term describes a three-coordinate boron atom that is bound to three different aromatic systems, namely 2,6-dimethylphenyl, mesityl, and 4-(N,N-dimethylamino)-2,6-dimethylphenyl. It is also demonstrated that the amine functionality can be converted with methyl triflate into an ammonium moiety. The investigation of photophysical and electrochemical properties of this compound in comparison with the non-aminated and di-aminated analogues of the triarylborane is described besides other investigations of e. g. singlet oxygen sensitization, rotational barriers, and fundamental DFT calculations. Based on these investigations, selectively mono-, bis- and tris-dimethylamino- and trimethylammonium-substituted bis-triarylborane bithiophene chromophores were synthesized and their photophysical, and electrochemical properties were investigated together with the water solubility and singlet oxygen sensitizing efficiency of the cationic compounds Cat1+, Cat2+, Cat(i)2+, and Cat3+. Comparing these properties with the results obtained for the mono-triarylboranes reveals a large influence of the bridging unit on the investigated properties of the bis-triarylboranes. In addition, the interaction of the cationic bis-triarylboranes with different polynucleotides were investigated in buffered solutions as well as the ability of these selectively charged compounds to enter and localize within organelles of human lung carcinoma and normal lung cells. All these investigations demonstrate that the number of charges and their distribution influences the interactions and staining properties as well as most of the other properties investigated.
In addition, preliminary investigations on H2O2-cleavable boronate esters in the presence of stochiometric amounts of H2O2 are described for three different aryl boronate esters.
This thesis focuses on investigating magneto-transport properties of a ferromagnetic topological insulator (V,Bi,Sb)2Te3. This material is most famously known for exhibiting the quantum anomalous Hall effect, a novel quantum state of matter that has opened up possibilities for potential applications in quantum metrology as a quantum standard of resistance, as well as for academic investigations into unusual magnetic properties and axion electrodynamics. All of those aspects are investigated in the thesis.
The digital transformation facilitates new forms of collaboration between companies along the supply chain and between companies and consumers. Besides sharing information on centralized platforms, blockchain technology is often regarded as a potential basis for this kind of collaboration. However, there is much hype surrounding the technology due to the rising popularity of cryptocurrencies, decentralized finance (DeFi), and non-fungible tokens (NFTs). This leads to potential issues being overlooked. Therefore, this thesis aims to investigate, highlight, and address the current weaknesses of blockchain technology: Inefficient consensus, privacy, smart contract security, and scalability.
First, to provide a foundation, the four key challenges are introduced, and the research objectives are defined, followed by a brief presentation of the preliminary work for this thesis.
The following four parts highlight the four main problem areas of blockchain. Using big data analytics, we extracted and analyzed the blockchain data of six major blockchains to identify potential weaknesses in their consensus algorithm. To improve smart contract security, we classified smart contract functionalities to identify similarities in structure and design. The resulting taxonomy serves as a basis for future standardization efforts for security-relevant features, such as safe math functions and oracle services. To challenge privacy assumptions, we researched consortium blockchains from an adversary role. We chose four blockchains with misconfigured nodes and extracted as much information from those nodes as possible. Finally, we compared scalability solutions for blockchain applications and developed a decision process that serves as a guideline to improve the scalability of their applications.
Building on the scalability framework, we showcase three potential applications for blockchain technology. First, we develop a token-based approach for inter-company value stream mapping. By only relying on simple tokens instead of complex smart-contracts, the computational load on the network is expected to be much lower compared to other solutions. The following two solutions use offloading transactions and computations from the main blockchain. The first approach uses secure multiparty computation to offload the matching of supply and demand for manufacturing capacities to a trustless network. The transaction is written to the main blockchain only after the match is made. The second approach uses the concept of payment channel networks to enable high-frequency bidirectional micropayments for WiFi sharing. The host gets paid for every second of data usage through an off-chain channel. The full payment is only written to the blockchain after the connection to the client gets terminated.
Finally, the thesis concludes by briefly summarizing and discussing the results and providing avenues for further research.
Breaking inversion symmetry in crystalline solids enables the formation of spin-polarized electronic states by spin-orbit coupling without the need for magnetism. A variety of interesting physical phenomena related to this effect have been intensively investigated in recent years, including the Rashba effect, topological insulators and Weyl semimetals. In this work, the interplay of inversion symmetry breaking and spin-orbit coupling and, in particular their general influence on the character of electronic states, i.e., on the spin and orbital degrees of freedom, is investigated experimentally. Two different types of suitable model systems are studied: two-dimensional surface states for which the Rashba effect arises from the inherently broken inversion symmetry at the surface, and a Weyl semimetal, for which inversion symmetry is broken in the three-dimensional crystal structure. Angle-resolved photoelectron spectroscopy provides momentum-resolved access to the spin polarization and the orbital composition of electronic states by means of photoelectron spin detection and dichroism with polarized light. The experimental results shown in this work are also complemented and supported by ab-initio density functional theory calculations and simple model considerations.
Altogether, it is shown that the breaking of inversion symmetry has a decisive influence on the Bloch wave function, namely, the formation of an orbital angular momentum. This mechanism is, in turn, of fundamental importance both for the physics of the surface Rashba effect and the topology of the Weyl semimetal TaAs.
An enduring engineering problem is the creation of unreliable software leading to unreliable systems. One reason for this is source code is written in a complicated manner making it too hard for humans to review and understand. Complicated code leads to other issues beyond dependability, such as expanded development efforts and ongoing difficulties with maintenance, ultimately costing developers and users more money.
There are many ideas regarding where blame lies in the reation of buggy and unreliable systems. One prevalent idea is the selected life cycle model is to blame. The oft-maligned “waterfall” life cycle model is a particularly popular recipient of blame. In response, many organizations changed their life cycle model in hopes of addressing these issues. Agile life cycle models have become very popular, and they promote communication between team members and end users. In theory, this communication leads to fewer misunderstandings and should lead to less complicated and more reliable code.
Changing the life cycle model can indeed address communications ssues, which can resolve many problems with understanding requirements.
However, most life cycle models do not specifically address coding practices or software architecture. Since lifecycle models do not address the structure of the code, they are often ineffective at addressing problems related to code complicacy.
This dissertation answers several research questions concerning software complicacy, beginning with an investigation of traditional metrics and static analysis to evaluate their usefulness as measurement tools. This dissertation also establishes a new concept in applied linguistics by creating a measurement of software complicacy based on linguistic economy. Linguistic economy describes the efficiencies of speech, and this thesis shows the applicability of linguistic economy to software. Embedded in each topic is a discussion
of the ramifications of overly complicated software, including the relationship of complicacy to software faults. Image recognition using machine learning is also investigated as a potential method of identifying problematic source code.
The central part of the work focuses on analyzing the source code of hundreds of different projects from different areas. A static analysis was performed on the source code of each project, and traditional software metrics were calculated. Programs were also analyzed using techniques developed by linguists to measure expression and statement complicacy and identifier complicacy. Professional software engineers were also directly surveyed to understand mainstream perspectives.
This work shows it is possible to use traditional metrics as indicators of potential project bugginess. This work also discovered it is possible to use image recognition to identify problematic pieces of source code. Finally, this work discovered it is possible to use linguistic methods to determine which statements and expressions are least desirable and more complicated for programmers.
This work’s principle conclusion is that there are multiple ways to discover traits indicating a project or a piece of source code has characteristics of being buggy. Traditional metrics and static analysis can be used to gain some understanding of software complicacy and bugginess potential. Linguistic economy demonstrates a new tool for measuring software complicacy, and machine learning can predict where bugs may lie in source code. The significant implication of this work is developers can recognize when a project is becoming buggy and take practical steps to avoid creating buggy projects.
To investigate trabeculopuncture (TP) for predicting the outcome of ab interno trabeculectomy (AIT). Ex vivo porcine anterior segments were perfused and sequentially underwent two procedures, TP and AIT. We concluded that a 10% reduction in IOP after TP can be used to predict the success (>20% IOP decrease) of AIT in porcine eyes. As porcine eyes share many similarities with human eyes, our findings may have implications on the validity of this test as a predictor for surgical outcomes of AITs in humans.
Purpose: The threat of national and international terrorism remains high. Preparation is the key requirement for the resilience of hospitals and out-of-hospital rescue forces. The scientific evidence for defining medical and tactical strategies often feeds on the analysis of real incidents and the lessons learned derived from them. This systematic review of the literature aims to identify and systematically report lessons learned from terrorist attacks since 2001.
Methods: PubMed was used as a database using predefined search strategies and eligibility criteria. All countries that are part of the Organization for Economic Cooperation and Development (OECD) were included. The time frame was set between 2001 and 2018.
Results: 68 articles were included in the review. From these, 616 lessons learned were extracted and summarized into 15 categories. The data shows that despite the difference in attacks, countries, and casualties involved, many of the lessons learned are similar. We also found that the pattern of lessons learned is repeated continuously over the time period studied.
Conclusions: The lessons from terrorist attacks since 2001 follow a certain pattern and remained constant over time. Therefore, it seems to be more accurate to talk about lessons identified rather than lessons learned. To save as many victims as possible, protect rescue forces from harm, and to prepare hospitals at the best possible level it is important to implement the lessons identified in training and preparation.
1 Summary
Left ventricular (LV) ejection fraction (EF) and global longitudinal strain (GLS) are the most commonly used measures of LV function. Yet, they are highly dependent on loading conditions since higher afterload yields lower systolic deformation and thereby a lower LVEF and GLS – despite presumably unchanged LV myocardial contractile strength. Invasive pressure-volume loop measurements represent the reference standard to assess LV function, also considering loading conditions. However, this procedure cannot be used in serial investigations or large sample populations due to its invasive nature. The novel concept of echocardiography-derived assessment of myocardial work (MyW) is based on LV pressure-strain loops, may be a valuable alternative to overcome these challenges, and may also be used with relative ease in large populations. As MyW also accounts for afterload, it is considered less load-dependent than LVEF and GLS.
The current PhD work addresses the application and clinical characterization of MyW, an innovative echocardiographic tool. As the method is new, we focused on four main topics:
(a) To establish reference values for MyW indices, i.e., Global Work Index (GWI), Global Constructive Work (GCW), Global Wasted Work (GWW), and Global Work Efficiency (GWE); we addressed a wide age range and evaluated the association of MyW indices with age, sex and other clinical and echocardiography parameters in apparently cardiovascular healthy individuals.
(b) To investigate the impact of cardiovascular (CV) risk factors on MyW indices and characterize the severity of subclinical LV deterioration in the general population.
(c) To assess the association of the LV geometry, i.e., LV mass and dimensions, with MyW indices.
(d) To evaluate in-hospital dynamics of MyW indices in patients hospitalized for acute heart failure (AHF).
For the PhD thesis, we could make use of two larger cohorts:
The STAAB population-based cohort study prospectively recruited and phenotyped a representative sample (5,000 individuals) of the general population of the City of Würzburg, aged 30-79 years and free from symptomatic heart failure at the time of inclusion. We focused on the first half of the study sample (n=2473 individuals), which fulfilled the anticipated strata regarding age and sex.
The Acute Heart Failure (AHF) Registry is a prospective clinical registry recruiting and phenotyping consecutive patients admitted for decompensated AHF to the Department of Medicine I, University Hospital Würzburg, and observing the natural course of the disease. The AHF Registry focuses on the pathophysiological understanding, particularly in relation to the early phase after cardiac decompensation, with the aim to improve diagnosis and better-tailored treatment of patients with AHF. For the current study, we concentrated on patients who provided pairs of echocardiograms acquired early after index hospital admission and prior to discharge.
The main findings of the PhD thesis were:
From the STAAB cohort study, we determined the feasibility of large-scale MyW derivation and the accuracy of the method. We established reference values for MyW indices based on 779 analyzable, apparently healthy participants (mean age 49 ± 10 years, 59% women), who were in sinus rhythm, free from CV risk factors or CV disease, and had no significant LV valve disease. Apart from GWI, there were no associations of other MyW indices with sex. Further, we found a disparate association with age, where MyW showed stable values until the age of 45 years, with an upward shift occurring beyond the age of 45. A higher age decade was associated with higher GWW and lower GWE, respectively. MyW indices only correlated weakly with common echocardiographic parameters, suggesting that MyW may add incremental information to clinically established parameters.
Further analyses from the STAAB cohort study contributed to a better understanding of the impact of CV risk factors on MyW indices and the association of LV geometry with LV performance. We demonstrated that CV risk factors impacted selectively on GCW and GWW. Hypertension appears to profoundly compromise the work of the myocardium, in particular, by increasing both GCW and GWW. The LV in hypertension seems to operate at a higher energy level yet lower efficiency. Other classical CV risk factors (Diabetes mellitus, Obesity, Dyslipidemia, Smoking) – independent of blood pressure – impacted consistently and adversely on GCW but did not affect GWW. Further, all CV risk factors affected GWE adversely.
We observed that any deviation from a normal LV geometric profile was associated with alterations on MyW. Of note, MyW was sensitive to early changes in LV mass and dimensions. Individuals with normal LV geometry yet established arterial hypertension exhibited a MyW pattern that is typically found in LV hypertrophy. Therefore, such a pattern might serve as an early sign of myocardial damage in hypertensive heart disease and might aid in risk stratification and primary prevention.
From the AHF Registry, we selected individuals with serial in-hospital echocardiograms and described in-hospital changes in myocardial performance during recompensation. In patients presenting with a reduced ejection fraction (HFrEF), decreasing N-terminal pro-natriuretic peptide (NT-proBNP) levels as a surrogate of successful recompensation were associated with an improvement in GCW and GWI and consecutively in GWE. In contrast, in patients presenting with a preserved ejection fraction (HFpEF), there was no significant change in GCW and GWI. However, unsuccessful recompensation, i.e., no change or an increase in NT-proBNP levels, was associated with an increase in GWW. This suggests a differential myocardial response to de- and recompensation depending on the HF phenotype.
Further, GWW as a surrogate of inappropriate LV energy consumption was elevated in all patients with AHF (compared to reference values) and was not associated with conventional markers as LVEF or NT-proBNP. In an exploratory analysis, GWW predicted the risk of death or rehospitalization within six months after discharge. Hence, GWW might carry incremental information beyond conventional markers of HF severity.
Time-to-Live (TTL) caches decouple the occupancy of objects in cache through object-specific validity timers. Stateof- the art techniques provide exact methods for the calculation of object-specific hit probabilities given entire cache hierarchies with random inter-cache network delays. The system hit probability is a provider-centric metric as it relates to the origin offload, i.e., the decrease in the number of requests that are served by the content origin server. In this paper we consider a user-centric metric, i.e., the response time, which is shown to be structurally different from the system hit probability. Equipped with the state-of-theart exact modeling technique using Markov-arrival processes we derive expressions for the expected object response time and pave a way for its optimization under network delays.
In scientific research, the independent reproduction of experiments is the source of trust. Detailed documentation is required to enable experiment reproduction. Reproducibility awards were created to honor the increased documentation effort. In this work, we propose a novel approach toward reproducible research—a structured experimental workflow that allows the creation of reproducible experiments without requiring additional efforts of the researcher. Moreover, we present our own testbed and toolchain, namely, plain orchestrating service (pos), which enables the creation of such experimental workflows. The experiment is documented by our proposed, fully scripted experiment structure. In addition, pos provides scripts enabling the automation of the bundling and release of all experimental artifacts. We provide an interactive environment where pos experiments can be executed and reproduced, available at https://gallenmu.github.io/single-server-experiment.
LoRaWAN Network Planning in Smart Environments: Towards Reliability, Scalability, and Cost Reduction
(2022)
The goal in this work is to present a guidance for LoRaWAN planning to improve overall reliability for message transmissions and scalability. At the end, the cost component is discussed. Therefore, a five step approach is presented that helps to plan a LoRaWAN deployment step by step: Based on the device locations, an initial gateway placement is suggested followed by in-depth frequency and channel access planning. After an initial planning phase, updates for channel access and the initial gateway planning is suggested that should also be done periodically during network operation. Since current gateway placement approaches are only studied with random channel access, there is a lot of potential in the cell planning phase. Furthermore, the performance of different channel access approaches is highly related on network load, and thus cell size and sensor density. Last, the influence of different cell planning ideas on expected costs are discussed.
Civil society organizations only started to be considered a sector in the 1970s in the United States. Amitai Etzioni pioneered the use of the expression third sector, which became common in academic and political literature. However, in the United States, the non-profit sector concept gradually became more robust and was spread internationally based on the studies conducted by Lester Salomon and associated researchers.
The theory built on the concept of the non-profit sector is strongly related to the North American cultural context, marked by the tradition of philanthropy and volunteerism, but with little importance given to associative and cooperative organizations.
The non-profit sector is implicitly or explicitly conceived as part of the private sphere. In contrast, theoretical currents such as liberal communitarianism, the theories of cooperation, common goods, social capital, European social economy, and the Latin American solidarity economy highlight the primacy of cooperation in solving collective problems. These theories underpin the associative approach of the third sector and link it to the community, not to the market.
This paper argues that the associative approach is more appropriate for international studies on the third sector and the relevance of self-organization. The third sector, i.e., the set of organizations created and maintained by civil society, is the inheritor of the millennial associative tradition, including both entities whose values are compatible with the common good and those with particularistic values, authoritarian and contrary to human rights. The third sector is not entirely virtuous, but it is a vital sector for solving great human problems.
Lightning has fascinated humanity since the beginning of our existence. Different types of lightning like sprites and blue jets were discovered, and many more are theorized. However, it is very likely that these phenomena are not exclusive to our home planet. Venus’s dense and active atmosphere is a place where lightning is to be expected. Missions like Venera, Pioneer, and Galileo have carried instruments to measure electromagnetic activity. These measurements have indeed delivered results. However, these results are not clear. They could be explained by other effects like cosmic rays, plasma noise, or spacecraft noise. Furthermore, these lightning seem different from those we know from our home planet. In order to tackle these issues, a different approach to measurement is proposed. When multiple devices in different spacecraft or locations can measure the same atmospheric discharge, most other explanations become increasingly less likely. Thus, the suggested instrument and method of VELEX incorporates multiple spacecraft. With this approach, the question about the existence of lightning on Venus could be settled.
The first step towards aerial planetary exploration has been made. Ingenuity shows extremely promising results, and new missions are already underway. Rotorcraft are capable of flight. This capability could be utilized to support the last stages of Entry, Descent, and Landing. Thus, mass and complexity could be scaled down.
Autorotation is one method of descent. It describes unpowered descent and landing, typically performed by helicopters in case of an engine failure. MAPLE is suggested to test these procedures and understand autorotation on other planets. In this series of experiments, the Ingenuity helicopter is utilized. Ingenuity would autorotate a ”mid-air-landing” before continuing with normal flight. Ultimately, the collected data shall help to understand autorotation on Mars and its utilization for interplanetary exploration.
Shannon channel capacity estimation, based on large packet length is used in traditional Radio Resource Management (RRM) optimization. This is good for the normal transmission of data in a wired or wireless system. For industrial automation and control, rather short packages are used due to the short-latency requirements. Using Shannon’s formula leads in this case to inaccurate RRM solutions, thus another formula should be used to optimize radio resources in short block-length packet transmission, which is the basic of Ultra-Reliable Low-Latency Communications (URLLCs). The stringent requirement of delay Quality of Service (QoS) for URLLCs requires a link-level channel model rather than a physical level channel model. After finding the basic and accurate formula of the achievable rate of short block-length packet transmission, the RRM optimization problem can be accurately formulated and solved under the new constraints of URLLCs. In this short paper, the current mathematical models, which are used in formulating the effective transmission rate of URLLCs, will be briefly explained. Then, using this rate in RRM for URLLC will be discussed.
We attempt to identify sequences of signaling dialogs, to strengthen our understanding of the signaling behavior of IoT devices by examining a dataset containing over 270.000 distinct IoT devices whose signaling traffic has been observed over a 31-day period in a 2G network [4]. We propose a set of rules that allows the assembly of signaling dialogs into so-called sessions in order to identify common patterns and lay the foundation for future research in the areas of traffic modeling and anomaly detection.
This work proposes a novel approach to disperse dense transmission intervals and reduce bursty traffic patterns without the need for centralized control. Furthermore, by keeping the mechanism as close to the Long Range Wide Area Network (LoRaWAN) standard as possible the suggested mechanism can be deployed within existing networks and can even be co-deployed with other devices.
Utilizing multiple access technologies such as 5G, 4G, and Wi-Fi within a coherent framework is currently standardized by 3GPP within 5G ATSSS. Indeed, distributing packets over multiple networks can lead to increased robustness, resiliency and capacity. A key part of such a framework is the multi-access proxy, which transparently distributes packets over multiple paths. As the proxy needs to serve thousands of customers, scalability and performance are crucial for operator deployments. In this paper, we leverage recent advancements in data plane programming, implement a multi-access proxy based on the MP-DCCP tunneling approach in P4 and hardware accelerate it by deploying the pipeline on a smartNIC. This is challenging due to the complex scheduling and congestion control operations involved. We present our pipeline and data structures design for congestion control and packet scheduling state management. Initial measurements in our testbed show that packet latency is in the range of 25 μs demonstrating the feasibility of our approach.
Future mobile communication networks, such as 5G and beyond, can benefit from Virtualized Network Functions (VNFs) when deployed on cloud infrastructures to achieve elasticity and scalability. However, new challenges arise as to managing states of Network Functions (NFs). Especially control plane VNFs, which are mainly found in cellular core networks like the 5G Core (5GC), received little attention since the shift towards virtualizing NFs. Most existing solutions for these core networks are often complex, intrusive, and are seldom compliant with the standard. With the emergence of 5G campus networks, UEs will be mainly machine-type devices. These devices communicate more deterministically, bringing new opportunities for elaborated state management. This work presents an emulation environment to perform rigorous measurements on state access patterns. The emulation comes with a fully parameterized Markov model for the UE to examine a wide variety of different devices. These measurements can then be used as a solid base for designing an efficient, simple, and standard conform state management solution that brings us further towards stateless core networks.
Tactile Internet aims at allowing perceived real-time interactions between humans and machines. This requires satisfying a stringent latency requirement of haptic data streams whose data rates vary drastically as the results of perceptual codecs. This introduces a complex problem for the underlying network infrastructure to fulfill the pre-defined level of Quality of Service (QoS). However, novel networking hardware with data plane programming capability allows processing packets differently and opens up a new opportunity. For example, a dynamic and network-aware resource management strategy can help satisfy the QoS requirements of different priority flows without wasting precious bandwidth. This paper introduces virtual queues for service differentiation between different types of traffic streams, leveraging protocol independent switch architecture (PISA). We propose coordinating the management of all the queues and dynamically adapting their sizes to minimize packet loss and delay due to network congestion and ensure QoS compliance.
This document presents a networking latency measurement setup that focuses on affordability and universal applicability, and can provide sub-microsecond accuracy. It explains the prerequisites, hardware choices, and considerations to respect during measurement. In addition, it discusses the necessity for exhaustive latency measurements when dealing with high availability and low latency requirements. Preliminary results show that the accuracy is within ±0.02 μs when used with the Intel I350-T2 network adapter.
In time-sensitive networks (TSN) based on 802.1Qbv, i.e., the time-aware Shaper (TAS) protocol, precise transmission schedules and, paths are used to ensure end-to-end deterministic communication. Such resource reservations for data flows are usually established at the startup time of an application and remain untouched until the flow ends. There is no way to migrate existing flows easily to alternative paths without inducing additional delay or wasting resources. Therefore, some of the new flows cannot be embedded due to capacity limitations on certain links which leads to sub-optimal flow assignment. As future networks will need to support a large number of lowlatency flows, accommodating new flows at runtime and adapting existing flows accordingly becomes a challenging problem. In this extended abstract we summarize a previously published paper of us [1]. We combine software-defined networking (SDN), which provides better control of network flows, with TSN to be able to seamlessly migrate time-sensitive flows. For that, we formulate an optimization problem and propose different dynamic path configuration strategies under deterministic communication requirements. Our simulation results indicate that regularly reconfiguring the flow assignments can improve the latency of time-sensitive flows and can increase the number of flows embedded in the network around 4% in worst-case scenarios while still satisfying individual flow deadlines.
This paper gives an overview of our recent activities in the field of satellite communication networks, including an introduction to geostationary satellite systems and Low Earth Orbit megaconstellations. To mitigate the high latencies of geostationary satellite networks, TCP-splitting Performance Enhancing Proxies are deployed. However, these cannot be applied in the case of encrypted transport headers as it is the case for VPNs or QUIC. We summarize performance evaluation results from multiple measurement campaigns. In a recently concluded project, multipath communication was used to combine the advantages of very heterogeneous communication paths: low data rate, low latency (e.g., DSL light) and high data rate, high latency (e.g., geostationary satellite).
Today’s advanced Internet-of-Things applications raise technical challenges on cloud, edge, and fog computing. The design of an efficient, virtualized, context-aware, self-configuring orchestration system of a fog computing system constitutes a major development effort within this very innovative area of research. In this paper we describe the architecture and relevant implementation aspects of a cloudless resource monitoring system interworking with an SDN/NFV infrastructure. It realizes the basic monitoring component of the fundamental MAPE-K principles employed in autonomic computing. Here we present the hierarchical layering and functionality within the underlying fog nodes to generate a working prototype of an intelligent, self-managed orchestrator for advanced IoT applications and services. The latter system has the capability to monitor automatically various performance aspects of the resource allocation among multiple hosts of a fog computing system interconnected by SDN.
The increased occurrence of Software-Defined-Networking (SDN) not only improves the dynamics and maintenance of network architectures, but also opens up new use cases and application possibilities. Based on these observations, we propose a new network topology consisting of a star and a ring topology. This hybrid topology will be called wheel topology in this paper. We have considered the static characteristics of the wheel topology and compare them with known other topologies.
A series of monomeric chirally substituted indolenine squaraine monomers were successfully synthesized and utilized for the construction of various oligo- and polymers, in order to study their chiroptical properties in terms of exciton chirality. The quaternary carbon atom at the 3-position of the indolenine subunit, as well as the alkyl side chain attached to the indolenine nitrogen were selected as the most suitable site for chiral functionalization.
For the C(3)-chiral derivatives, two synthetic routes depending on the desired substitution at the stereogenic center were established. The chiral side chains were prepared via Evans asymmetric alkylation where the resulting branching point at the 2 position constituted the chiral center. While the chiral substitution only had minor effects on the linear optical properties and geometric structure of the chromophore, all compounds exhibited a distinct and measurable CD signal that correlated with the distance of the chiral center to the central chromophore.
Polymers bearing chiral side chains exhibited a solvent- and temperature-dependent helix-coil equilibrium, which was influenced by the type of side chain used. CD spectroscopy revealed the helical conformation to possess a preferred twist sense, and temperature-dependent measurements showed the degree of homohelicity to be nearly complete in certain cases. Furthermore, a CPL signal was able to be obtained for the helical conformer of one polymer.
Various (co)oligo- and polymers comprising the C(3)-chiral monomers only displayed a solvent-independent J-type absorption behavior and thus did not form helical conformations in solution. CD spectroscopy revealed a solvent-dependent adoption of quasi-enantiomeric conformers, which was elucidated by quantum chemical TDDFT calculations.
With the miniaturization of satellites a fundamental change took place in the space industry. Instead of single big monolithic satellites nowadays more and more systems are envisaged consisting of a number of small satellites to form cooperating systems in space. The lower costs for development and launch as well as the spatial distribution of these systems enable the implementation of new scientific missions and commercial services.
With this paradigm shift new challenges constantly emerge for satellite developers, particularly in the area of wireless communication systems and network protocols.
Satellites in low Earth orbits and ground stations form dynamic space-terrestrial networks. The characteristics of these networks differ fundamentally from those of other networks.
The resulting challenges with regard to communication system design, system analysis, packet forwarding, routing and medium access control as well as challenges concerning the reliability and efficiency of wireless communication links are addressed in this thesis.
The physical modeling of space-terrestrial networks is addressed by analyzing existing satellite systems and communication devices, by evaluating measurements and by implementing a simulator for space-terrestrial networks.
The resulting system and channel models were used as a basis for the prediction of the dynamic network topologies, link properties and channel interference. These predictions allowed for the implementation of efficient routing and medium access control schemes for space-terrestrial networks. Further, the implementation and utilization of software-defined ground stations is addressed, and a data upload scheme for the operation of small satellite formations is presented.
Hard X-ray Properties of Relativistically Beamed Jets from Radio- and Gamma-Ray-Bright Blazars
(2022)
In this work I characterize the hard X-ray properties of blazars, active galactic nuclei with highly beamed emission, which are notoriously hard to detect in this energy range. I employ pre-defined samples of beamed AGN: the radio-selected MOJAVE and TANAMI samples, as well as the most recent gamma-ray-selected Fermi/LAT 4LAC catalog. The hard X-ray data is extracted from the 105-month all-sky survey maps of the Swift/BAT (Burst Alert Telescope) in the energy band of 20 keV to 100 keV. A great majority of both the MOJAVE and TANAMI samples are significantly detected, with signal-to noise ratios of the sources often just below the X-ray catalog signal thresholds. All blazar sub-types (FSRQs, BL Lacs) and radio galaxies show characteristic ranges of X-ray flux, luminosity, and photon index. Their properties are correlated with the corresponding SED's shape / peak frequency. The LogN-LogS distributions of the samples show a scarcity of blazars in the middle and lower X-ray flux range, indicating differing evolutionary paths between radio and X-ray emission, which is also suggested by the corresponding luminosity functions. Compared to the radio samples, the 4LAC sources are on average significantly less bright in the BAT band since this range often coincides with the spectral gap region between the two big SED emission bumps. Also, the spectral shapes differ notably, especially for the sub-type of BL Lacs. Using the parameter space of X-ray and gamma-ray photon indices, 35 blazar candidate sources can be assigned to either the FSRQ or BL Lac type with high certainty. The reason why many blazars are weak in this energy band can be traced back to a number of factors: the selection bias of the initial sample, differential evolution of the X-rays and the wavelengths in which the sample is defined, and the limited sensitivity of the observing instruments.
This thesis studies connections between quantum information measures and geometric features of spacetimes within the AdS/CFT correspondence. These studies are motivated by the idea that spacetime can be thought of as an effect emerging from an underlying entanglement structure in the AdS/CFT correspondence. In particular, I study generalized entanglement measures in two-dimensional conformal field theories and their holographic duals. Unlike the ordinary entanglement entropy of a spatial subregion typically used in the AdS/CFT context, the generalization considered here measures correlations between different fields as well as between spatial degrees of freedom. I present a new gauge invariant definition of the generalized entanglement entropy applicable to both mixed and pure states as well as explicit results for thermal states of the S_N-orbifold theory of the D1/D5 system. Along the way, I develop computation techniques for conformal blocks on the torus and apply them to the calculation of the ordinary entanglement entropy for large central charge CFTs at finite size and finite temperature. The generalized Ryu-Takayanagi formula arising from these studies provides further support for the idea that entanglement and geometry are intrinsically linked in AdS/CFT. The results show that the holographic dual to the generalized entanglement entropy given by the length of a geodesic winding around black hole horizons or naked singularities probes subregions of spacetime that are inaccessible to Ryu-Takayanagi surfaces, thereby solving the puzzle of how these features of the spacetime are encoded in the boundary theory. Furthermore, I investigate quantum circuits embedded in two-dimensional conformal field theories as well as computational complexity measures therein. These investigations are motivated by conjectures relating computational complexity in conformal field theories to geometric features of black hole geometries. In this thesis, I study quantum circuits built up from conformal transformations. I investigate examples of computational complexity measures in these circuits related to geometric actions on coadjoint orbits of the Virasoro group and to the Fubini-Study metric. I then work out relations between these computational complexity measures and the dual gravitational theory. Moreover, I construct a bulk dual to the circuits in consideration and use this construction to study geometric realizations of computational complexity measures from first principles. The results of this part on the one hand rule out some possibilities for dual realizations of computational complexity in two-dimensional CFTs put forward in previous work while on the other hand providing a new robust dual realization of a computational complexity measure based on the Fubini-Study distance.
Anxiety research is one of the major psychological research domains and looks back on decades of research activity. Traditionally, novel theories and approaches are tested utilizing animal models. One way to study inherent anxiety in rodents is the elevated plus-maze (EPM). The EPM is a plus-shaped platform with two closed, i.e., walled, arms and two open unwalled arms. If given the opportunity to freely explore the apparatus, rodents instinctively avoid the open arms to protect themselves from predators. Hence, they spent less time on open and more time on closed arms, which is behaviorally associated with general anxiety. In the course of the pharmacological validation, it was found that this exploratory pattern can be reversed by anxiolytic substances, e.g., benzodiazepines, or potentiated by anxiogenics. One of the significant advantages of the EPM is that no prior training session is required in contrast to conditioning studies, thus allowing to observe natural behavior. Therefore, together with the economic and uncomplicated setup, the EPM has become a standard preclinical rodent anxiety test over the decades. In order to validate these rodent anxiety tests, there have recently been attempts to retranslate them to humans. A paramount of cross-species validation is not only the simple transferability of these animal tests but also the observation of anxiety behaviors that are evolutionarily conserved across species. Accordingly, it could be possible to conclude various factors associated with the etiology and maintenance of anxiety disorders in humans. So far, convincing translations of the EPM to humans are still lacking. For that reason, the primary aim of this dissertation is to retranslate the EPM throughout three studies and to evaluate cross-species validity critically. Secondly, the undertaken studies are set out to observe ambulatory activity equivalent to rodent EPM behavior, i.e., open arm avoidance. Thirdly, the undertaken studies aimed to assess the extent to which trait anxiety influences human exploratory activity on the platform to associate it with the assumption that rodent EPM-behavior is a reflection of general anxiety. Finally, virtual reality (VR) was the method of choice to maintain the economic advantage and adjust the EPM size to humans. Study 1 (N = 30) was set up to directly transfer the rodent EPM regarding test design and experimental procedure using a Computer Automatic Virtual Environment (CAVE). The results revealed that humans unlike rodents display a general open arms approach during free exploration. However, open arm avoidance was associated with high trait anxiety and acrophobia (fear of height), which was initially assessed as a control variable due to the virtual platform height. Regression analyses and subjective anxiety ratings hinted at a more significant influence of acrophobia on open arm avoidance. In addition, it was assumed that the open arms approach might have resulted from claustrophobic tendencies experienced in the closed arms due to the high walls. Study 2 (N = 61) sought to differentiate the influence of trait anxiety and acrophobia and adapt the virtual EPM to humans. Therefore, parts of the platform held a semi-transparent grid-floor texture, and the wall height on the closed arms was reduced to standard handrail level. Moreover, participants were priorly screened to exclude clinically significant levels of acrophobia, claustrophobia, and agoraphobia. The data on general exploratory activity showed no arm preference. Regression analyses confirmed that acrophobia is related to open arm avoidance, corroborating the finding of Study 1. Surprisingly, for trait anxiety, the result of Study 1 could not be replicated. Instead, for trait anxiety, no significant effect was found indicating that predominantly fear of heights shapes human EPM behavior even on a subclinical stage. In Study 3 (N = 57), the EPM was embedded into a city setting to 1) create a more natural human environment and 2) eliminate height. Furthermore, a head-mounted display was utilized for VR presentation, and arousal ratings were introduced. Participants were screened for high and low levels of trait anxiety and agoraphobia, and claustrophobia. Replicating the findings of Study 2, no difference in open and closed arm activity was observed, and no effect was found in relationship with trait anxiety. The data on anxiety ratings and claustrophobia suggest a positive correlation indicating that in this city EPM, claustrophobic tendencies might play a role in closed arm avoidance. In summary, this thesis added valuable insights into the retranslation of a well-established standard anxiety test used in rodents. However, it also majorly challenges current findings on the cross-species validity of the EPM. Various explanatory models for the results are critically discussed and associated with clinical implications concerning future research.
Wilms tumor (WT) is the most common renal tumor in childhood. Among others, MYCN copy number gain and MYCN P44L and MAX R60Q mutations have been identified in WT. The proto-oncogene MYCN encodes a transcription factor that requires dimerization with MAX to activate transcription of numerous target genes. MYCN gain has been associated with adverse prognosis. The MYCN P44L and MAX R60Q mutations, located in either the transactivating or basic helix-loop-helix domain, respectively, are predicted to be damaging by different pathogenicity prediction tools. These mutations have been reported in several other cancers and remain to be functionally characterized.
In order to further describe these events in WT, we screened both mutations in a large cohort of unselected WT patients, to check for an association of the mutation status with certain histological or clinical features. MYCN P44L and MAX R60Q revealed frequencies of 3 % and 0.9 % and also were significantly associated to higher risk of relapse and metastasis, respectively. Furthermore, to get a better understanding of the MAX mutational landscape in WT, over 100 WT cases were analyzed by Sanger sequencing to identify other eventual MAX alterations in its coding sequence. R60Q remained the only MAX CDS alteration described in WT to date.
To analyze the potential functional consequences of these mutations, we used a doxycycline-inducible system to overexpress each mutant in HEK293 cells. This biochemical characterization identified a reduced transcriptional activation potential for MAX R60Q, while the MYCN P44L mutation did not change activation potential or protein stability. The protein interactome of N-MYC-P44L was likewise not altered as shown by mass spectrometric analyses of purified N-MYC complexes. However, we could identify a number of novel N-MYC partner proteins, several of these known for their oncogenic potential. Their correlated expression in WT samples suggested a role in WT oncogenesis and they expand the range of potential biomarkers for WT stratification and targeting, especially for high-risk WT.
To safely navigate their environment, flying insects rely on visual cues, such as optic flow. Which cues insects can extract from their environment depends closely on the spatial and temporal response properties of their visual system. These in turn can vary between individuals that differ in body size. How optic flow-based flight control depends on the spatial structure of visual cues, and how this relationship scales with body size, has previously been investigated in insects with apposition compound eyes. Here, we characterised the visual flight control response limits and their relationship to body size in an insect with superposition compound eyes: the hummingbird hawkmoth Macroglossum stellatarum. We used the hawkmoths' centring response in a flight tunnel as a readout for their reception of translational optic flow stimuli of different spatial frequencies. We show that their responses cut off at different spatial frequencies when translational optic flow was presented on either one, or both tunnel walls. Combined with differences in flight speed, this suggests that their flight control was primarily limited by their temporal rather than spatial resolution. We also observed strong individual differences in flight performance, but no correlation between the spatial response cutoffs and body or eye size.
At the beginning of their foraging careers, Cataglyphis desert ants calibrate their compass systems and learn the visual panorama surrounding the nest entrance. For that, they perform well-structured initial learning walks. During rotational body movements (pirouettes), naïve ants (novices) gaze back to the nest entrance to memorize their way back to the nest. To align their gaze directions, they rely on the geomagnetic field as a compass cue. In contrast, experienced ants (foragers) use celestial compass cues for path integration during food search. If the panorama at the nest entrance is changed, foragers perform re-learning walks prior to heading out on new foraging excursions. Here, we show that initial learning walks and re-learning walks are structurally different. During re-learning walks, foragers circle around the nest entrance before leaving the nest area to search for food. During pirouettes, they do not gaze back to the nest entrance. In addition, foragers do not use the magnetic field as a compass cue to align their gaze directions during re-learning walk pirouettes. Nevertheless, magnetic alterations during re-learning walks under manipulated panoramic conditions induce changes in nest-directed views indicating that foragers are still magnetosensitive in a cue conflict situation.
Objectives
Vessel wall enhancement (VWE) may be commonly seen on MRI images of asymptomatic subjects. This study aimed to characterize the VWE of the proximal internal carotid (ICA) and vertebral arteries (VA) in a non-vasculitic elderly patient cohort.
Methods
Cranial MRI scans at 3 Tesla were performed in 43 patients (aged ≥ 50 years) with known malignancy for exclusion of cerebral metastases. For vessel wall imaging (VWI), a high-resolution compressed-sensing black-blood 3D T1-weighted fast (turbo) spin echo sequence (T1 CS-SPACE prototype) was applied post gadolinium with an isotropic resolution of 0.55 mm. Bilateral proximal intradural ICA and VA segments were evaluated for presence, morphology, and longitudinal extension of VWE.
Results
Concentric VWE of the proximal intradural ICA was found in 13 (30%) patients, and of the proximal intradural VA in 39 (91%) patients. Mean longitudinal extension of VWE after dural entry was 13 mm in the VA and 2 mm in the ICA. In 14 of 39 patients (36%) with proximal intradural VWE, morphology of VWE was suggestive of the mere presence of vasa vasorum. In 25 patients (64 %), morphology indicated atherosclerotic lesions in addition to vasa vasorum.
Conclusions
Vasa vasorum may account for concentric VWE within the proximal 2 mm of the ICA and 13 mm of the VA after dural entry in elderly subjects. Concentric VWE in these locations should not be confused with large artery vasculitis. Distal to these segments, VWE may be more likely related to pathologic conditions such as vasculitis.
X-ray dark-field imaging allows to resolve the conflict between the demand for centimeter scaled fields of view and the spatial resolution required for the characterization of fibrous materials structured on the micrometer scale. It draws on the ability of X-ray Talbot interferometers to provide full field images of a sample's ultra small angle scattering properties, bridging a gap of multiple orders of magnitude between the imaging resolution and the contrasted structure scale. The correspondence between shape anisotropy and oriented scattering thereby allows to infer orientations within a sample's microstructure below the imaging resolution. First demonstrations have shown the general feasibility of doing so in a tomographic fashion, based on various heuristic signal models and reconstruction approaches. Here, both a verified model of the signal anisotropy and a reconstruction technique practicable for general imaging geometries and large tensor valued volumes is developed based on in-depth reviews of dark-field imaging and tomographic reconstruction techniques.
To this end, a wide interdisciplinary field of imaging and reconstruction methodologies is revisited. To begin with, a novel introduction to the mathematical description of perspective projections provides essential insights into the relations between the tangible real space properties of cone beam imaging geometries and their technically relevant description in terms of homogeneous coordinates and projection matrices. Based on these fundamentals, a novel auto-calibration approach is developed, facilitating the practical determination of perspective imaging geometries with minimal experimental constraints. A corresponding generalized formulation of the widely employed Feldkamp algorithm is given, allowing fast and flexible volume reconstructions from arbitrary tomographic imaging geometries. Iterative reconstruction techniques are likewise introduced for general projection geometries, with a particular focus on the efficient evaluation of the forward problem associated with tomographic imaging. A highly performant 3D generalization of Joseph's classic linearly interpolating ray casting algorithm is developed to this end and compared to typical alternatives. With regard to the anisotropic imaging modality required for tensor tomography, X-ray dark-field contrast is extensively reviewed. Previous literature is brought into a joint context and nomenclature and supplemented by original work completing a consistent picture of the theory of dark-field origination. Key results are explicitly validated by experimental data with a special focus on tomography as well as the properties of anisotropic fibrous scatterers. In order to address the pronounced susceptibility of interferometric images to subtle mechanical imprecisions, an efficient optimization based evaluation strategy for the raw data provided by Talbot interferometers is developed. Finally, the fitness of linear tensor models with respect to the derived anisotropy properties of dark-field contrast is evaluated, and an iterative scheme for the reconstruction of tensor valued volumes from projection images is proposed. The derived methods are efficiently implemented and applied to fiber reinforced plastic samples, imaged at the ID19 imaging beamline of the European Synchrotron Radiation Facility. The results represent unprecedented demonstrations of X-ray dark-field tensor tomography at a field of view of 3-4cm, revealing local fiber orientations of both complex shaped and low-contrast samples at a spatial resolution of 0.1mm in 3D. The results are confirmed by an independent micro CT based fiber analysis.
Dual RNA-seq captures both host and pathogen transcriptomes at the site of infection, facilitating an exploration of processes that play an essential role in pathogenesis and the host defense. This work presents an application of this technique to explore processes occurring during the infection of the human endothelial cells with two clinical isolates of Orientia tsutsugamushi (Ot) — the causative agent of scrub typhus. Combining comparative genomics, transcriptomics, and proteomics, we investigated the transcriptional architecture of Ot and identified non-coding RNAs, operon structures, and widespread antisense transcription, that may have a role in regulation of repetitive genes that are abundant in the Ot genome. In addition, the comparative analysis of bacterial and eukaryotic transcriptomes allowed us to investigate factors that drive the difference in virulence between Karp and UT176 and the host response to these two Ot strains.
The host and pathogen transcriptional profiles in each dual RNA-seq study are obtained in‑silico by adopting tools developed for RNA-seq data analysis. The Dualrnaseq pipeline presented in the second part of this work is the first publicly available, highly reproducible, scalable, and user‑friendly workflow developed for processing dual RNA‑seq data of any eukaryotic and bacterial organisms with a reference genome and annotation. It provides three mapping and quantification strategies: (i) alignment-based mapping of reads onto the chimeric genome with STAR followed by counting of uniquely mapped reads with HTSeq; (ii) a fast transcriptome quantification method handling multi‑mapped reads (Salmon with Selective Alignment); (iii) and Salmon alignment-based mode which uses a STAR‑derived alignment combined with Salmon quantification. Performing an initial benchmark analysis of the employed methods we provided recommendations ensuring accurate estimation of host and pathogen transcript expression.
Aim
Recent advancements in PET technology have brought with it significant improvements in PET performance and image quality. In particular, the extension of the axial field of view of PET systems, and the introduction of semiconductor technology into the PET detector, initially for PET/MR, and more recently available long-field-of-view PET/CT systems (≥ 25 cm) have brought a step change improvement in the sensitivity of PET scanners. Given the requirement to limit paediatric doses, this increase in sensitivity is extremely welcome for the imaging of children and young people. This is even more relevant with PET/MR, where the lack of CT exposures brings further dose reduction benefits to this population. In this short article, we give some details around the benefits around new PET technology including PET/MR and its implications on the EANM paediatric dosage card.
Material and methods
Reflecting on EANM adult guidance on injected activities, and making reference to bed overlap and the concept of MBq.min bed\(^{-1}\) kg\(^{-1}\), we use published data on image quality from PET/MR systems to update the paediatric dosage card for PET/MR and extended axial field of view (≥ 25 cm) PET/CT systems. However, this communication does not cover the expansion of paediatric dosing for the half-body and total-body scanners that have recently come to market.
Results
In analogy to the existing EANM dosage card, new parameters for the EANM paediatric dosage card were developed (class B, baseline value: 10.7 MBq, minimum recommended activity 10 MBq). The recommended administered activities for the systems considered in this communication range from 11 MBq [\(^{18}\)F]FDG for a child with a weight of 3 kg to 149 MBq [\(^{18}\)F]FDG for a paediatric patient weight of 68 kg, assuming a scan of 3 min per bed position. The mean effective dose over all ages (1 year and older) is 2.85 mSv.
Conclusion
With this, recommendations for paediatric dosing are given for systems that have not been considered previously.
Breast cancer etiology is associated with both proliferation and DNA damage induced by estrogens. Breast cancer risk factors (BCRF) such as body mass index (BMI), smoking, and intake of estrogen-active drugs were recently shown to influence intratissue estrogen levels. Thus, the aim of the present study was to investigate the influence of BCRF on estrogen-induced proliferation and DNA damage in 41 well-characterized breast glandular tissues derived from women without breast cancer. Influence of intramammary estrogen levels and BCRF on estrogen receptor (ESR) activation, ESR-related proliferation (indicated by levels of marker transcripts), oxidative stress (indicated by levels of GCLC transcript and oxidative derivatives of cholesterol), and levels of transcripts encoding enzymes involved in estrogen biotransformation was identified by multiple linear regression models. Metabolic fluxes to adducts of estrogens with DNA (E-DNA) were assessed by a metabolic network model (MNM) which was validated by comparison of calculated fluxes with data on methoxylated and glucuronidated estrogens determined by GC- and UHPLC-MS/MS. Intratissue estrogen levels significantly influenced ESR activation and fluxes to E-DNA within the MNM. Likewise, all BCRF directly and/or indirectly influenced ESR activation, proliferation, and key flux constraints influencing E-DNA (i.e., levels of estrogens, CYP1B1, SULT1A1, SULT1A2, and GSTP1). However, no unambiguous total effect of BCRF on proliferation became apparent. Furthermore, BMI was the only BCRF to indeed influence fluxes to E-DNA (via congruent adverse influence on levels of estrogens, CYP1B1 and SULT1A2).
With accelerating global climate change, the Antarctic Ice Sheet is exposed to increasing ice dynamic change. During 1992 and 2017, Antarctica contributed ~7.6 mm to global sea-level-rise mainly due to ocean thermal forcing along West Antarctica and atmospheric warming along the Antarctic Peninsula (API). Together, these processes caused the progressive retreat of glaciers and ice shelves and weakened their efficient buttressing force causing widespread ice flow accelerations. Holding ~91% of the global ice mass and 57.3 m of sea-level-equivalent, the Antarctic Ice Sheet is by far the largest potential contributor to future sea-level-rise.
Despite the improved understanding of Antarctic ice dynamics, the future of Antarctica remains difficult to predict with its contribution to global sea-level-rise representing the largest uncertainty in current projections. Given that recent studies point towards atmospheric warming and melt intensification to become a dominant driver for future Antarctic ice mass loss, the monitoring of supraglacial lakes and their impacts on ice dynamics is of utmost importance. In this regard, recent progress in Earth Observation provides an abundance of high-resolution optical and Synthetic Aperture Radar (SAR) satellite data at unprecedented spatial and temporal coverage and greatly supports the monitoring of the Antarctic continent where ground-based mapping efforts are difficult to perform. As an automated mapping technique for supraglacial lake extent delineation in optical and SAR satellite imagery as well as a pan-Antarctic inventory of Antarctic supraglacial lakes at high spatial and temporal resolution is entirely missing, this thesis aims to advance the understanding of Antarctic surface hydrology through exploitation of spaceborne remote sensing.
In particular, a detailed literature review on spaceborne remote sensing of Antarctic supraglacial lakes identified several research gaps including the lack of (1) an automated mapping technique for optical or SAR satellite data that is transferable in space and time, (2) high-resolution supraglacial lake extent mappings at intra-annual and inter-annual temporal resolution and (3) large-scale mapping efforts across the entire Antarctic continent. In addition, past method developments were found to be restricted to purely visual, manual or semi-automated mapping techniques hindering their application to multi-temporal satellite imagery at large-scale. In this context, the development of automated mapping techniques was mainly limited by sensor-specific characteristics including the similar appearance of supraglacial lakes and other ice sheet surface features in optical or SAR data, the varying temporal signature of supraglacial lakes throughout the year as well as effects such as speckle noise and wind roughening in SAR data or cloud coverage in optical data. To overcome these limitations, this thesis exploits methods from artificial intelligence and big data processing for development of an automated processing chain for supraglacial lake extent delineation in Sentinel-1 SAR and optical Sentinel-2 satellite imagery. The combination of both sensor types enabled to capture both surface and subsurface lakes as well as to acquire data during cloud cover or wind roughening of lakes. For Sentinel-1, a deep convolutional neural network based on residual U-Net was trained on the basis of 21,200 labeled Sentinel-1 SAR image patches covering 13 Antarctic regions. Similarly, optical Sentinel-2 data were collected over 14 Antarctic regions and used for training of a Random Forest classifier. Optical and SAR classification products were combined through decision-level fusion at bi-weekly temporal scale and unprecedented 10 m spatial resolution. Finally, the method was implemented as part of DLR’s High-Performance Computing infrastructure allowing for an automated processing of large amounts of data including all required pre- and postprocessing steps. The results of an accuracy assessment over independent test scenes highlighted the functionality of the classifiers returning accuracies of 93% and 95% for supraglacial lakes in Sentinel-1 and Sentinel-2 satellite imagery, respectively.
Exploiting the full archive of Sentinel-1 and Sentinel-2, the developed framework for the first time enabled the monitoring of seasonal characteristics of Antarctic supraglacial lakes over six major ice shelves in 2015-2021. In particular, the results for API ice shelves revealed low lake coverage during 2015-2018 and particularly high lake coverage during the 2019-2020 and 2020-2021 melting seasons. On the contrary, East Antarctic ice shelves were characterized by high lake coverage during 2016-2019 and
extremely low lake coverage during the 2020-2021 melting season. Over all six investigated ice shelves, the development of drainage systems was revealed highlighting an increased risk for ice shelf instability. Through statistical correlation analysis with climate data at varying time lags as well as annual data on Southern Hemisphere atmospheric modes, environmental drivers for meltwater ponding were revealed. In addition, the influence of the local glaciological setting was investigated through computation of annual recurrence times of lakes. Over both ice sheet regions, the complex interplay between local, regional and large-scale environmental drivers was found to control supraglacial lake formation despite local to regional discrepancies, as revealed through pixel-based correlation analysis. Local control factors included the ice surface topography, the ice shelf geometry, the presence of low-albedo features as well as a reduced firn air content and were found to exert strong control on lake distribution. On the other hand, regional controls on lake evolution were revealed to be the amount of incoming solar radiation, air temperature and wind occurrence. While foehn winds were found to dictate lake evolution over the API, katabatic winds influenced lake ponding in East Antarctica. Furthermore, the regional near-surface climate was shown to be driven by large-scale atmospheric modes and teleconnections with the tropics. Overall, the results highlight that similar driving factors control supraglacial lake formation on the API and EAIS pointing towards their transferability to other Antarctic regions.
Immune-mediated polyneuropathies like chronic inflammatory demyelinating polyradiculoneuropathy or Guillain-Barré syndrome are rare diseases of the peripheral nervous system. A subgroup of patients harbors autoantibodies against nodal or paranodal antigens, associated with a distinct phenotype and treatment response. In a part of patients with pathologic paranodal or nodal immunoreactivity the autoantigens remain difficult or impossible to determine owing to limitations of the used detection approach - usually ELISAs (enzyme-linked-immunosorbent-assays) - and incomplete knowledge of the possible autoantigens. Due to their high-throughput, low sample consumption and high sensitivity as well as the possibility to display many putative nodal and paranodal autoantigens simultaneously, peptide microarray-based approaches are prime candidates for the discovery of novel autoantigens, point-of-care diagnostics and, in addition, monitoring of pathologic autoimmune response. Current applications of peptide microarrays are however limited by high false-positive rates and the associated need for detailed follow-up studies and validation. Here, robust peptide microarray-based detection of antibodies and the efficient validation of binding signals by on-chip neutralization is demonstrated. First, autoantigens were displayed as overlapping peptide libraries in microarray format. Copies of the biochips were used for the fine mapping of antibody epitopes. Next, binding signals were validated by antibody neutralization in solution. Since neutralizing peptides are obtained in the process of microarray fabrications, neither throughput nor costs are significantly altered. Similar in-situ validation approaches could contribute to future autoantibody characterization and detection methods as well as to therapeutic research. Areas of application could be expanded to any autoimmune-mediated neurological disease as a long-term vision.
The area northeast of Sudbury, Ontario, is known for one of the largest unexplained geophysical anomalies on the Canadian Shield, the 1,200 km2 Temagami Anomaly. The geological cause of this regional magnetic, conductive and gravity feature has previously been modelled to be a mafic-ultramafic body at relatively great depth (2–15 km) of unknown age and origin, which may or may not be related to the meteorite impact-generated Sudbury Igneous Complex in its immediate vicinity. However, with a profound lack of outcrops and drill holes, the geological cause of the anomaly remains elusive, a genetic link to the 1.85 Ga Sudbury impact event purely speculative.
In search for any potential surface expression of the deep-seated cause of the Temagami Anomaly, this study provides a first, yet comprehensive petrological and geochemical assessment of exotic igneous dykes recently discovered in outcrops above, and drill cores into, the Temagami Anomaly. Based on cross-cutting field relations, petrographic studies, lithogeochemistry, whole-rock Nd-Sr-Pb isotope systematics, and U-Pb geochronology, it was possible to identify, and distinguish between, at least six different groups of igneous dykes: (i) Calc-alkaline quartz diorite dykes related to the 1.85 Ga Sudbury Igneous Complex (locally termed Offset Dykes); (ii) tholeiitic quartz diabase of the regional 2.22 Ga Nipissing Suite/Senneterre Dyke Swarm; (iii) calc-alkaline quartz diabase of the regional 2.17 Ga Biscotasing Dyke Swarm; (iv) alkaline ultrabasic dykes correlated with the 1.88–1.86 Ga Circum-Superior Large Igneous Province (LIP); and (v) aplitic dykes as well as (vi) a hornblende syenite, the latter two of more ambiguous age and stratigraphic position.
The findings presented in this study – the discovery of three new Offset Dykes in particular – offer some unexpected insights into the geology and economic potential of one of the least explored areas of the world-class Sudbury Mining Camp as well as into the nature and distribution of both allochthonous and autochthonous impactites within one of the oldest and largest impact structures known on Earth. Not only do the geometric patterns of dyke (and breccia) distribution reaffirm previous notions of the existence of discrete ring structures in the sense of a ~200-km multi-ring basin, but they provide critical constraints as to the pre-erosional thickness and extent of the impact melt sheet, thus helping to identity new areas for Ni-Cu-PGE exploration. Furthermore, this study provides important insights into the pre-impact stratigraphy and the magmatic evolution of the region in general, which reveals to be much more complex, compositionally divers, and protracted than initially assumed. Of note is the discovery of rocks related to the 2.17 Ga Biscotasing and the 1.88–1.86 Ga Circum-Superior magmatic events, as these were not previously known to occur on the southeast margin of the Superior Craton. Shortly predating the Sudbury impact and being contemporaneous with ore-forming events at Thompson (Manitoba) and Raglan (Cape Smith), these magmatic rocks could provide the missing link between unusual mafic, pre-enriched, crustal target rocks, and the unique metal endowment of the Sudbury Impact Structure.
The actual geological cause of the Temagami Anomaly remains open to debate and requires the downward extension of existing bore holes as well as more detailed geophysical investigations. The hypothesis of a genetic relationship between Sudbury impact event and Temagami Anomaly is neither borne out by any evidence nor particularly realistic, even in case of an oblique impact, and should thus be abandoned. It is instead proposed, based on circumstantial evidence, that the anomaly might be explained by an ultramafic complex of the 1.88–1.86 Ga Circum-Superior LIP.
This thesis describes novel concepts for the measurement of the static and dynamic properties of the electronic structure of molecules and nanocrystals in the liquid phase by means of coherent fluorescence-detected spectroscopy in two and three frequency dimensions. These concepts are based on the systematic variation ("phase cycling") of a sequence of multiple time-delayed femtosecond excitation pulses in order to decode a multitude of novel nonlinear signals from the resulting phase-dependent fluorescence signal. These signals represent any permutation of correlations between zero-, one-, two-, and three-quantum coherences. To this end, two new phase-cycling schemes have been developed which can simultaneously resolve and discriminate several nonlinear signals of sixth order, including those of the fourth order of nonlinearity.
By means of the sixth-order signals recorded in this work, static properties of highly excited electronic states in molecules such as their energies, transition dipole moments, and relative displacement of electronic potential surfaces, as well as dynamic properties in terms of their relaxation kinetics, can be ascertained. Furthermore, it was shown that these signals are suitable for the characterization of exciton-exciton correlations in colloidal quantum dots and for the measurement of ultrafast exciton-exciton annihilation in molecular aggregates.
The experiments performed in this thesis mark an important step towards the complete characterization of the nonlinear response of quantum systems. In view of this, the concept of fluorescence-detected multiple-quantum coherence multidimensional spectroscopy introduced here offers a unified, systematic approach.
In virtue of the technical advantages such as the use of a single excitation beam and the absence of nonresonant contributions, the measurement protocols developed here can be directly transferred to other incoherent observables and to sample systems in other states of matter. Furthermore, the approaches presented here can be systematically extended to higher frequency dimensions and higher orders of nonlinearity.
The present work focusses on the borylation of aryl halides. The first chapter presents a detailed review about previously reported nickel-catalyzed borylation reactions. The second chapter of the thesis describes, the borylation reaction of C–Cl bonds in aryl chlorides mediated by an NHC-stabilized nickel catalyst. The cyclohexyl substituted NHC Cy2Im was used to synthesize novel Cy2Im-stabilized nickel complexes [Ni2(Cy2Im)4(μ-(η2:η2)-COD)] 1, [Ni(Cy2Im)2(η2-C2H4)] 2, and [Ni(Cy2Im)2(η2-COE)] 3. An optimized procedure was developed using 5 mol% of the Ni-catalyst, 1.5 equivalents of the boron reagent B2pin2, and 1.5 equivalents of NaOAc as the base in methylcyclohexane at 100 °C. With these optimized conditions, it was shown that a variety of aryl chlorides, containing either electron-withdrawing or -donating groups, were converted to the corresponding aryl boronic esters in yields up to 99% (88% isolated) yield. Mechanistic investigations revealed that the C–Cl oxidative addition product [Ni(Cy2Im)2(Cl)(4-F3C-C6H4)] 11, which has been synthesized and isolated separately, also catalyzes the reaction. Thus, rapid oxidative addition of the C–Cl bond of the aryl chloride to [Ni2(Cy2Im)4(μ-(η2:η2)-COD)] 1 to yield trans-[Ni(Cy2Im)2(Cl)(Ar)] represents the first step in the catalytic cycle. The rate limiting step in this catalytic cycle is the transmetalation of boron to nickel forming trans-[Ni(Cy2Im)2(Bpin)(Ar)], which was not possible to isolate. The boryl transfer reagent is assumed to be the anionic adduct Na[B2pin2(OAc)]. A final reductive elimination step gives the desired borylated product Ar–Bpin and regenerates [Ni(Cy2Im)2].
In the next chapter the first effective C–Cl bond borylation of aryl chlorides using NHC-stabilized Cu(I)-complexes of the type [Cu(NHC)(Cl)] was developed. The known complexes [Cu(iPr2Im)(Cl)] 15, [Cu(Me2ImMe)(Cl)] 16, and [Cu(Cy2Im)(Cl)] 17, bearing the small alkyl substituted NHCs, were synthesized in good yields by the reaction of copper(I) chloride with the corresponding free NHC at low temperature (-78 °C) in THF. A range of catalysts, bases, solvents, and boron sources were screened to determine the scope and limitations of this reaction. [Cu(Cy2Im)(Cl)] 17 revealed a significantly higher catalytic activity than [Cu(iPr2Im)(Cl)] 15. KOtBu turned out to be the only efficient base for this borylation reaction. Besides methylcyclohexane, toluene was the only solvent that gave the borylated product in moderate yields of 53%. It was shown that a variety of electron-rich and electron-poor aryl chlorides can be converted to the corresponding aryl boronic esters in isolated yields of up to 80%. A mechanism was proposed, in which a Cu-boryl complex [Cu(L)(Bpin)] is formed in the initial step. This is followed by C–B bond formation via σ-bond metathesis with the aryl chloride forming the aryl boronic ester and [Cu(L)(Cl)]. The latter reacts with KOtBu to give [Cu(L)(OtBu)], which regenerates the copper boryl complex by reaction with B2pin2.
Chapter 4 describes studies directed towards the transition metal-free borylation of aryl halides using Lewis base adducts of diborane(4) compounds. A variety of novel pyridine and NHC adducts of boron compounds were synthesized. Adducts of the type pyridine·B2cat2 18-19 and NHC·B2(OR)4 20-23 were examined for their ability to transfer a boryl moiety to an aryl iodide. However, only Me2ImMe∙B2pin2 20 was found to be effective. The stoichiometric reaction of 20 with different substituted aryl iodides and bromides in benzene, at elevated temperatures, gave the desired aryl boronic esters in good yields. Interestingly, depending on the reaction temperature, C–C coupling between the aryl halide and the solvent (benzene), was detected leading to a side product which, together with observed hydrodehalogenation of the aryl halide, provided indications that the reaction might be radical in nature.
When the boryl transfer reaction based on Me2ImMe∙B2pin2 20 was followed by EPR spectroscopy, a signal (though very weak and ill-defined) was detected, which is suggestive of a mechanism involving a boron-based radical. In addition, the boronium cation [(Me2ImMe)2∙Bpin]+ 37 with iodide as the counterion was isolated from the reaction residue, indicating the fate of the second boryl moiety. A preliminary mechanism for the boryl transfer from 20 to aryl iodides was proposed, which involves an NHC–Bpin˙ radical as the key intermediate. Me2ImMe–Bpin˙ is formed by homolytic B–B bond cleavage of the bis-NHC adduct (Me2ImMe)2∙B2pin2, which is formed in situ in small amounts under the reaction conditions. Me2ImMe–Bpin˙ reacts with the aryl iodide to give the aryl boronic ester with recovery of aromaticity. In the same step, from the second equivalent of NHC–Bpin˙, an NHC-stabilized iodo-Bpin adduct is formed as an intermediate, which is further coordinated by another NHC, yielding [(Me2ImMe)2∙Bpin]+I- 37.
Motivated by the great potential offered by the combination of additive manufacturing technology and hydrogels, especially in the field of tissue engineering and regenerative medicine, a series of novel hybrid hydrogel inks were developed based on the recently described thermogelling poly(2-oxazoline)s-block-poly(2-oxazine)s diblock copolymers, which may help to expand the platform of available hydrogel inks for this transformative 3D printing technology (Fig. 5.1).
In the present thesis, the first reported thermogelling polymer solely consisting of POx and POzi, i.e., the diblock copolymer PMeOx-b-PnPrOzi comprising a hydrophilic block (PMeOx) and a thermoresponsive block (PnPrOzi), was selected and used as a proof-of-concept for the preparation of three novel hybrid hydrogels. Therefore, three batches of the diblock copolymers with a DP of 100 were synthesized for the study of three different hybrid hydrogels with a special focus on their suitability as (bio)inks for extrusion-based 3D printing. The PMeOx-b-PnPrOzi diblock copolymer solution shows a temperature induced reversible gelation behavior above a critical polymer concentration of 20 wt%, as described for the Pluronic F127 solution but with a unique gelation mechanism, working through the formation of a bicontinuous sponge-like structure from the physically crosslinked vesicles. Specially, its intrinsic shear thinning behavior and excellent recovery property with a certain yield point make it a promising ink candidate for extrusion-based printing technology.
Increasing the polymer concentration is the most traditional approach to improve the printability of an ink material, and serve as the major strategy available to improve the printability of PMeOx-b-PnPrOzi systems prior to this work. From the analysis of rheological properties related to printability, it came a conclusion that increasing the copolymer concentration does improve the hydrogel strength and thus the printability. However, such improvement is very limited and usually leads to other problems such as more viscous systems and stringent requirements on the printers, which are not ideal for the printing process and applications especially in the cell-embedded biofabrication field.
POx-b-POzi/clay Hybrid Hydrogel
An alternative method proposed to improve the printability of this thermoresponsive hydrogel ink is through nanoclay (Laponite XLG) addition, i.e., the first hybrid hydrogel system of PMeOx-b-PnPrOzi/clay (also named shortly as POx-b-POzi/clay) in this thesis. To optimize the viscoelastic properties of the ink material, Laponite XLG acted as a reinforcement additive and a physically crosslinker was blended with the copolymers. Compared with the pristine copolymer solution of PMeOx-b-PnPrOzi, the hybrid PMeOx-b-PnPrOzi/clay solution well retained the temperature induced gelation performance of the copolymers.
The obtained hybrid hydrogels exhibited a rapid in situ reversible thermogelation at a physiological relevant Tgel of around 15 ℃ and a rapid recovery of viscoelastic properties within a few seconds. More importantly, with the addition of only a small amount of 1.2 wt% clay, it exhibited obviously enhanced shear thinning character (n = 0.02), yield stress (240 Pa) and mechanical strength (storage modulus over 5 kPa). With this novel hybrid hydrogel, real three-dimensional constructs with multiple layers and various geometries are generation with greatly enhanced shape fidelity and resolution. In this context, the thermogelling properties of the hybrid hydrogels over a copolymer concentration range of 10-20 wt% and a clay concentration of 0-4 wt% were systematically investigated, and from which a printable window was obtained from the laboratory as a reference.
In fact, the printing performance of an ink is not only determined by the intrinsic physicochemical properties of the material, but is also influenced by the external printing environments as well as the printer parameter settings. All the printing experiments in this study were conducted under a relatively optimized conditions obtained from preliminary experiments. In future work, the relationship between material rheology properties, printer parameters and printing performance could be systematically explored. Such a fundamental study will help to develop models that allows the prediction and comparison of printing results from different researches based on the parameters available through rheology, which is very beneficial for further development of more advanced ink systems.
Although the printability has been significantly improved by the addition of nanoclay Laponite XLG, the hybrid hydrogels and their printed constructs still suffer from some major limitations. For example, these materials are still thermoresponsive, which will cause the printed constructs to collapse when the environment temperature changes below their Tgel. In addition, the formed hydrogel constructs are mechanical too weak for load-bearing applications, and the allowed incubation time is very limited during media exchange/addition as it will lead to dissolution of the hydrogels due to dilution effects. Therefore, it is essential to establish a second (chemical or physical) crosslinking mechanism that allows further solidification of the gels after printing. It should be kept in mind that the second crosslinking step will eliminate the thermoresponsive behavior of the gels and thus the possibility of cell recovery. In this case, besides through the traditional approach of copolymer modification to realize further crosslinking, like one of the well-known post-polymerization modification approach Diels-Alder reaction,[430] designing of interpenetrating networks (IPN) hydrogels serves as one of the major strategy for advanced (bio)ink preparation.[311] Therefore, the second hybrid hydrogel system of PMeOx-b-PnPrOzi/PDMAA/clay (also named shortly as POx-b-POzi/PDMAA/clay) was developed in this thesis, which is a 3D printable and highly stretchable ternary organic-inorganic IPN hydrogel.
POx-b-POzi/PDMAA/clay Hybrid Hydrogel
The nanocomposite IPN hydrogel combines a thermoresponsive hydrogel with clay described above and in situ polymerized poly(N, N-dimethylacrylamide). Before in situ polymerization, the thermoresponsive hydrogel precursors exhibited thermogelling behavior (Tgel ~ 25 ℃, G' ~ 6 kPa) and shear thinning properties, making the system well-suited for extrusion-based 3D printing. After chemical curing of the 3D-printed constructs by free radical polymerization, the resulting IPN hydrogels show excellent mechanical strength with a high stretchability to a tensile strain at break exceeding 550%. The hybrid hydrogel can sustain a high stretching deformation and recover quickly due to the energy dissipation from the non-covalent interactions. With this hybrid hydrogel, integrating with the advanced 3D-printing technique, various 3D constructs can be printed and cured successfully with high shape fidelity and geometric accuracy.
In this context, we also investigated the possibility of acrylic acid (AA) and 2-hydroxyethylmethacrylate (HEMA) as alternative hydrogel precursors. However, the addition of these two monomers affected the thermogelation of POx-b-POzi in an unfavorable manner, as these monomers competed more effectively with water molecules, preventing the hydration of nPrOzi block at lower temperatures and therefore, the liquefaction of the gels. Furthermore, the influence of the printing process and direction on the mechanical properties of the hydrogel was investigated and compared with the corresponding bulk materials obtained from a mold. No significant effects from the additive manufacturing process were observed due to a homogeneously adhesion and merging between sequentially deposited layers. In the future, further studies on the specific performance differences among hydrogels fabricated at different printing directions/speeds would be of great interest to the community, as this allows for a more accurately control and better predict of the printed structures.
This newly developed hybrid IPN hydrogel is expected to expand the material toolbox available for hydrogel-based 3D printing, and may be interesting for a wide range of applications including tissue engineering, drug delivery, soft robotics, and additive manufacturing in general. However, in this case, the low toxicity from the monomer DMAA and other small molecules residuals in the polymerized hydrogels made this hybrid hydrogel not ideal for bioprinting in the field of biofabrication. For this problem, cyto-/biocompatible monomers such as polyethylene glycol diacrylate (PEGDA) can be used as an alternative, while the overall properties of the hydrogels including mechanical properties should be re-evaluated accordingly. Moreover, the swelling behavior of the hydrogels should also be taken into account, as it may most likely affect the mechanical strength and geometry size of the printed scaffold, but is often be overlooked after printing. For example, regarding the specific hybrid hydrogel POx-b-POzi/PDMAA/clay in this work, an equilibrium swelling ratio of 1100% was determined. The printed hydrogel cuboid experienced a volume increasing over 6-fold after equilibrium swelling in water, and became mechanical fragile due to the formation of a swollen hydrogel network absorbing large amount of water.
POx-b-POzi/Alg/clay Hybrid Hydrogel
In the final part of this dissertation, to enable the cell-loaded bioprinting and long-term cell culture, the third hybrid hydrogel system POx-b-POzi/Alg/clay was introduced by replacing the monomer DMAA to the natural polysaccharides alginate. Initially, detailed rheological characterization and mechanical tests were performed to evaluate their printability and mechanically properties. Subsequently, some simple patterns were printed with the optimized hydrogel precursor solutions for the preliminary filament fusion and collapse test before proceeding to more complex printings. The fibers showed a sufficient stability which allows the creation of large structures with a height of a few centimeters and a suspended filament up to centimeter. Accordingly, various 3D constructs including suspended filaments were printed successfully with high stackability and shape fidelity. The structure after extrusion was physical crosslinked easily by soaking in CaCl2 solution and, thereafter exhibited a good mechanical flexibility and long-term stability. Interestingly, the mechanical strength and geometry size of the generated scaffolds were well maintained over a culture period of weeks in water, which is of great importance for clinical applications. In addition, the post-printing ionic crosslinking of alginate could also be realized by other di/trivalent cations such as Fe3+ and Tb3+.
Subsequently, the cell-laden printing with this hybrid hydrogel and post-printing crosslinking by Ca2+ ions highlighting its feasibility for 3D bioprinting. WST-1 assay of fibroblast suggested no-dose dependent cytocompatibility of the hydrogel precursor solution. The cell distribution was uniform throughout the printed construct, and proliferated with high cell viability during the 21 days culture. The presented hybrid approach, utilizing the beneficial properties of the POx-b-POzi base material, could be interesting for a wide range of bioprinting applications and potentially enabling also other biological bioinks such as collagen, hyaluronic acid, decellularized extracellular matrix or cellulose based bioinks. Although the results look promising and the developed hydrogel is an important bioink candidate, the long-term in vitro cell studies with different cell lines and clinical model establishment are still under investigation, which remains a long road but is of great importance before realizing real clinical application.
Last but not least, the improvement to the printability of thermogelling POx/POzi-based copolymers by the clay Laponite XLG was also demonstrated in another thermogelling copolymer PEtOx-b-PnPrOzi. This suggests that the addition of clay may be a general strategy to improve the printability of such polymers. Despite these advances in this work which significantly extended the (bio)material platform of additive manufacturing technology, the competition is still fierce and more work should be done in the further to reveal the potential and limitations of this kind of new and promising candidate (bio)ink materials. It is also highly expected for further creative works based on the thermogelling POx/POzi polymers, such as crosslinking in Ca2+ solution containing monomer acrylamide to prepare printable and mechanically tough hydrogels, research on POx-based support bath material, and print of clinically more relevant sophisticated structures such as 3D microvascular networks omnidirectionally.
Deoxyribozymes are artificially evolved DNA molecules with catalytic abilities. RNA-cleaving deoxyribozymes have been recognized as an efficient tool for detection of modifications in target RNAs and provide an alternative to traditional and modern methods for detection of ribose or nucleobase methylation. However, there are only few examples of DNA enzymes that specifically reveal the presence of a certain type of modification, including N6-methyladenosine, and the knowledge about how DNA enzymes recognize modified RNAs is still extremely limited. Therefore, DNA enzymes cannot be easily engineered for the analysis of desired RNA modifications, but are instead identified by in vitro selection from random DNA libraries using synthetic modified RNA substrates. This protocol describes a general in vitro selection stagtegy to evolve new RNA-cleaving DNA enzymes that can efficiently differentiate modified RNA substrates from their unmodified counterpart.
Estrogens, namely 17β-estradiol (E2) and estrone (E1) are considered to play an important role in the initiation and promotion of breast cancer (summarized in Raftogianis et al., 2000), a malignancy responsible for around 500,000 deaths per year (summarized in Ghislain et al., 2016). Two major mechanisms have been postulated to explain the carcinogenic effects of estrogens: (1) the estrogen receptor-mediated stimulation of breast cell proliferation with a concomitant enhanced rate of mutations and (2) the metabolism of hydroxylated estrogens to quinone derivatives which can react with the DNA (Russo and Russo, 2006, summarized in Yager and Davidson, 2006). Nevertheless, as a detoxifying mechanism, E1, E2, and their hydroxylated and methoxylated metabolites are reversibly conjugated into sulfates and glucuronides devoid of biological activity (summarized in Guillemette et al., 2004). Yet, despite the key detoxifying function of these conjugates, the study of their circulating levels face some significant problems: (1) analysis by techniques such as radioimmunoassay lack specificity and accuracy and requires enzymatic/chemical hydrolysis before analysis, being unable to differentiate between sulfates and glucuronides (summarized in Stanczyk et al., 2007, summarized in Wang et al., 2016), (2) very little knowledge in healthy women, which has been identified as a barrier to advance in breast cancer research (summarized in Liu, 2000), and (3) far fewer studies in pre- than in postmenopausal women (summarized in Samavat and Kurzer, 2015). Therefore, to get more insights into the research of breast cancer etiology and prevention, the analysis of circulating levels of estrogens (including metabolites and conjugates) in women without breast cancer through reliable analytical techniques, is required.
The objective of this thesis was the synthesis and characterisation of two linear multifunctional PEG-alternatives for bioconjugation and hydrogel formation: i) Hydrophilic acrylate based copolymers containing peptide binding units and ii) hydrophilic polyether based copolymers containing different functional groups for a physical crosslinking.
In section 3.1 the successful synthesis of water soluble and linear acrylate based polymers containing oligo(ethylene glycol) methyl ether acrylate with either linear thioester functional 2-hydroxyethyl acrylate, thiolactone acrylamide, or vinyl azlactone via the living radical polymerisation technique Reversible Addition Fragmentation Chain Transfer (RAFT) and via free-radical polymerisation is described. The obtained polymers were characterized via GPC, 1H NMR, IR and RAMAN spectroscopy.
The RAFT end group was found to be difficult to remove from these short polymer chains and accordingly underwent the undesired side reaction aminolysis with the peptide during the conjugation studies. Besides that, polymers without RAFT end groups did not show any binding of the peptide at the thioester groups, which can be improved in future by using higher reactant concentrations and higher amount of binding units at the polymer. Polymers containing the highly reactive azlactone group showed a peptide binding of 19 %, but unfortunately this function also underwent spontaneous hydrolysis before the peptide could even be bound. In all cases, oligo(ethylene glycol) methyl ether acrylate was used with a relatively high molecular weight (Mn = 480 Da) was used, which eventually was efficiently shielding the introduced binding units from the added peptide. In future, a shorter monomer with Mn = 300 Da or less or hydrophilic N,N’-dialkyl acrylamide based polymers with less steric hindrance could be used to improve this bioconjugation system. Additionally, the amount of monomers containing peptide binding units in the polymer can be increased and have an additional spacer to achieve higher loading efficiency.
The water soluble, linear and short polyether based polymers, so called polyglycidols, were successfully synthesized and modified as described in section 3.2. The obtained polymers were characterized using GPC, 1H NMR, 31P{1H} NMR, IR, and RAMAN spectroscopy. The allyl groups which were present up to 20 % were used for radical induced thiol-ene chemistry for the introduction of functional groups intended for the formation of the physically crosslinking hydrogels. For the positively charged polymers, first a chloride group had to be introduced for the subsequent nucleophilic substitution with the imidazolium compound. There, degrees of modifications were found in the range 40-97 % due to the repulsion forces of the charges, decreased concentration of active chloride groups, and limiting solution concentrations of the polymer for this reaction. For the negatively charged polymers, first a protected phosphonamide moiety was introduced with a deprotection step afterwards showing 100 % conversion for all reactions. Preliminary hydrogel tests did not show a formation of a three-dimensional network of the polymer chains which was attributed to the short backbone length of the used polymers, but the gained knowledge about the synthetic routes for the modification of the polymer was successfully transferred to longer linear polyglycidols. The same applies to the introduction of electron rich and electron poor compounds showing π-π stacking interactions by UV-vis spectroscopy.
Finally, long linear polyglycidyl ethers were synthesised successfully up to molecular weights of Mn ~ 30 kDa in section 3.3, which was also proven by GPC, 1H NMR, IR and RAMAN spectroscopy. This applies to the homopolymerisation of ethoxyethyl glycidyl ether, allyl glycidyl ether and their copolymerisation with an amount of the allyl compound ~ 10 %. Attempts for higher molecular weights up to 100 kDa showed an uncontrolled polymerisation behaviour and eventually can be improved in future by choosing a lower initiation temperature. Also, the allyl side groups were modified via radical induced thiol-ene chemistry to obtain positively charged functionalities via imidazolium moieties (85 %) and negatively charged functionalities via phosphonamide moieties (100 %) with quantitative degree of modifications. Hydrogel tests have still shown a remaining solution by using long linear polyglycidols carrying negative charges with long/short linear polyglycidols carrying positive charges. The addition of calcium chloride led to a precipitate of the polymer instead of a three-dimensional network formation representing a too high concentration of ions and therefore shielding water molecules with prevention from dissolving the polymer. These systems can be improved by tuning the polymers structure like longer polymer chains, longer spacer between polymer backbone and charge, and higher amount of functional groups.
The objective of the thesis was partly reached containing detailed investigated synthetic routes for the design and characterisation of functional polymers which could be used in future with improvements for bioconjugation and hydrogel formation tests.
Within my PhD project I gained several novel insights into the poorly investigated
symbiotic world of fungus farming ambrosia beetles and their bark beetle ancestors,
where I especially focused on physiological interactions and capabilities of
associated fungal symbionts. Here, (i) I could confirm the association of mutualistic
Phialophoropsis fungi with the ambrosia beetle genus Trypodendron and found hints
for a possible new Phialophoropsis species in T. signatum and T. domesticum.
Moreover, I could show that mutualistic fungi of Trypodendron ambrosia beetles are
able to decompose major woody polysaccharides such as cellulose and xylan.
Additionally, (ii) I provided the first images using micro-computed tomography (µCT)
of the formerly unknown structure of the mycetangium of Trypodendron leave. (iii) I
could confirm a general tolerance towards ethanol in mutualistic ambrosia beetle
fungi, while antagonistic fungi as well as most examined fungal bark beetle
associates (e.g. possibly tree-defense detoxifying species) were highly sensitive to
even low concentrations of ethanol. Further, (iv) I found that natural galleries of
ambrosia beetles are highly enriched with several biologically important elements
(such as N, P, S, K, Mg) compared to the surrounding woody tissue and suggest that
mutualistic fungi are translocating and concentrating elements from the immediate
surrounding xylem to the beetles galleries. Furthermore, (v) I could show that various
fungi associated with bark and ambrosia beetles (mutualists, possibly beneficial
symbionts) are emitting several volatile organic compounds mostly within aliphatic
and aromatic alcohols and esters, while non-mutualistic and free living species were
generally emitting a lower number and amount of volatiles. Finally, especially bark
and ambrosia beetle fungi were found to incorporate several amino acids, from which
some are especially important for the production of certain volatile organic
compounds. Amino acid content also indicated a higher nutritional value for certain
species. Here, I propose that especially volatile organic compounds are widespread
key players in maintaining various symbioses between fungi and beetles, as already
proven by a recent study on the bark beetle Ips typographus (as well as for some
other bark beetle-fungus symbioses, see summary in Kandasamy et al. 2016) and
also suggested for ambrosia beetles.
This thesis is about composite-based structural equation modeling. Structural equation modeling in general can be used to model both theoretical concepts and their relations to one another. In traditional factor-based structural equation modeling, these theoretical concepts are modeled as common factors, i.e., as latent variables which explain the covariance structure of their observed variables. In contrast, in composite-based structural equation modeling, the theoretical concepts can be modeled both as common factors and as composites, i.e., as linear combinations of observed variables that convey all the information between their observed variables and all other variables in the model. This thesis presents some methodological advancements in the field of composite-based structural equation modeling. In all, this thesis is made up of seven chapters. Chapter 1 provides an overview of the underlying model, as well as explicating the meaning of the term composite-based structural equation modeling. Chapter 2 gives guidelines on how to perform Monte Carlo simulations in the statistic software R using the package “cSEM” with various estimators in the context of composite-based structural equation modeling. These guidelines are illustrated by an example simulation study that investigates the finite sample behavior of partial least squares path modeling (PLS-PM) and consistent partial least squares (PLSc) estimates, particularly regarding the consequences of sample correlations between measurement errors on statistical inference. The third Chapter presents estimators of composite-based structural equation modeling that are robust in responding to outlier distortion. For this purpose, estimators of composite-based structural equation modeling, PLS-PM and PLSc, are adapted. Unlike the original estimators, these adjustments can avoid distortion that could arise from random outliers in samples, as is demonstrated through a simulation study. Chapter 4 presents an approach to performing predictions based on models estimated with ordinal partial least squares and ordinal consistent partial least squares. Here, the observed variables lie on an ordinal categorical scale which is explicitly taken into account in both estimation and prediction. The prediction performance is evaluated by means of a simulation study. In addition, the chapter gives guidelines on how to perform such predictions using the R package “cSEM”. This is demonstrated by means of an empirical example. Chapter 5 introduces confirmatory composite analysis (CCA) for research in “Human Development”. Using CCA, composite models can be estimated and assessed. This chapter uses the Henseler-Ogasawara specification for composite models, allowing, for example, the maximum likelihood method to be used for parameter estimation. Since the maximum likelihood estimator based on the Henseler-Ogasawara specification has limitations, Chapter 6 presents another specification of the composite model by means of which composite models can be estimated with the maximum likelihood method. The results of this maximum likelihood estimator are compared with those of PLS-PM, thus showing that this maximum likelihood estimator gives valid results even in finite samples. The last chapter, Chapter 7, gives an overview of the development and different strands of composite-based structural equation modeling. Additionally, here I examine the contribution the previous chapters make to the wider distribution of composite-based structural equation modeling.
Anthropogenic activities are causing air pollution. Amongst air pollutants, tropospheric ozone is a major threat to human health and ecosystem functioning. In this dissertation, I present three studies that aimed at increasing our knowledge on how plant exposure to ozone affects its reproduction and its interactions with insect herbivores and pollinators.
For this purpose, a new fumigation system was built and placed in a greenhouse. The annual plant Sinapis arvensis (wild mustard) was used as the model plant.
Plants were exposed to either 0 ppb (control) or 120 ppb of ozone, for variable amounts of time and at different points of their life cycle. After fumigation, plants were exposed to herbivores or pollinators in the greenhouse, or to both groups of insects in the field.
My research shows that ozone affected reproductive performance differently, depending on the timing of exposure: plants exposed at earlier ages had their reproductive fitness increased, while plants exposed later in their life cycle showed a tendency for reduced reproductive fitness. Plant phenology was a key factor influencing reproductive fitness: ozone accelerated flowering and increased the number of flowers produced by plants exposed at early ages, while plants exposed to ozone at later ages tended to have fewer flowers. On the other hand, the ozone-mediated changes in plant-insect interactions had little impact on plant reproductive success.
The strongest effect of ozone on plant-pollinator interactions was the change in the number of flower visits received per plant, which was strongly linked to the number of open flowers. This means that, as a rule, exposure of plants to ozone early in the life cycle resulted in a higher number of pollinator visits, while exposure later in the life cycle resulted in fewer flower visits by potential pollinators. An exception was observed: the higher number of visits performed by large syrphid flies to young ozone-exposed plants than to the respective control plants went beyond the increase in the number of open flowers in those plants. Also, honeybees spent more time per flower in plants exposed to ozone than on control plants, while other pollinators spent similar amounts of time in control and ozone-exposed plants. This guild-dependent preference for ozone-exposed plants may be due to species-specific preferences related to changes in the quality and quantity of floral rewards.
In the field, ozone-exposed plants showed only a tendency for increased colonization by sucking herbivores and slightly more damage by chewing herbivores than control plants. On the other hand, in the greenhouse experiment, Pieris brassicae butterflies preferred control plants over ozone-exposed plants as oviposition sites. Eggs laid on ozone-exposed plants took longer to hatch, but the chances of survival were higher. Caterpillars performed better in control plants than in ozone-exposed plants, particularly when the temperature was high.
Most of the described effects were dependent on the duration and timing of the ozone exposure and the observed temperature, with the strongest effects being observed for longer exposures and higher temperatures. Furthermore, the timing of exposure altered the direction of the effects.
The expected climate change provides ideal conditions for further increases in tropospheric ozone concentrations, therefore for stronger effects on plants and plant-insect interactions. Acceleration of flowering caused by plant exposure to ozone may put plant-pollinator interactions at risk by promoting desynchronization between plant and pollinator activities. Reduced performance of caterpillars feeding on ozone-exposed plants may weaken herbivore populations. On the other hand, the increased plant reproduction that results from exposing young plants to ozone may be a source of good news in the field of horticulture, when similar results would be achieved in high-value crops. However, plant response to ozone is highly species-specific. In fact, Sinapis arvensis is considered a weed and the advantage conferred by ozone exposure may increase its competitiveness, with negative consequences for crops or plant communities in general. Overall, plant exposure to ozone might constitute a threat for the balance of natural and agro-ecosystems.
Global Existence and Uniqueness Results for Nematic Liquid Crystal and Magnetoviscoelastic Flows
(2022)
Liquid crystals and polymeric fluids are found in many technical applications with liquid crystal displays probably being the most prominent one. Ferromagnetic materials are well established in industrial and everyday use, e.g. as magnets in generators, transformers and hard drive disks. Among ferromagnetic materials, we find a subclass which undergoes deformations if an external magnetic field is applied. This effect is exploited in actuators, magnetoelastic sensors, and new fluid materials have been produced which retain their induced magnetization during the flow.
A central issue consists of a proper modelling for those materials. Several models exist regarding liquid crystals and liquid crystal flows, but up to now, none of them has provided a full insight into all observed effects. On materials encompassing magnetic, elastic and perhaps even fluid dynamic effects, the mathematical literature seems sparse in terms of models. To some extent, one can unify the modeling of nematic liquid crystals and magnetoviscoelastic materials employing a so-called energetic variational approach.
Using the least action principle from theoretical physics, the actual task reduces to finding appropriate energies describing the observed behavior. The procedure leads to systems of evolutionary partial differential equations, which are analyzed in this work.
From the mathematical point of view, fundamental questions on existence, uniqueness and stability of solutions remain unsolved. Concerning the Ericksen-Leslie system modelling nematic liquid crystal flows, an approximation to this model is given by the so-called Ginzburg-Landau approximation. Solutions to the latter are intended to approximately represent solutions to the Ericksen-Leslie system. Indeed, we verify this presumption in two spatial dimensions. More precisely, it is shown that weak solutions of the Ginzburg-Landau approximation converge to solutions of the Ericksen-Leslie system in the energy space for all positive times of evolution. In order to do so, theory for the Euler equations invented by DiPerna and Majda on weak compactness and concentration measures is used.
The second part of the work deals with a system of partial differential equations modelling magnetoviscoelastic fluids. We provide a well-posedness result in two spatial dimensions for large energies and large times. Along the verification of that conclusion, existing theory on the Ericksen-Leslie system and the harmonic map flow is deployed and suitably extended.
Recent studies have hinted to an involvement of epithelial to mesenchymal transition, a mechanism often associated with metastasis in epithelial cancers, in adrenocortical carcinoma. In addition, the knowledge about the FGF/FGFR pathway in pathogenesis of the adrenal gland, a pathway often associated with the epithelial to mesenchymal transition, is sparse and fragmented.
We assessed, in a large number of normal, benign and malignant adrenocortical tissues (a total of 181 different samples), the expression of canonical and novel epithelial and mesenchymal markers and compared it with their expression in typical epithelial and mesenchymal tissues. In addition, we also quantified the expression of most members of the FGF/FGFR pathway in adrenocortical tissues and compared it against well-studied epithelial and mesenchymal tissues as well as between malignant and not malignant adrenocortical tissues, in order to assess the possible connection to epithelial to mesenchymal transition and find possible drug targets. Surprisingly, both normal and neoplastic adrenocortical tissues lacked expression of epithelial markers (e.g. E-Cadhering or EpCAM) but strongly expressed mesenchymal markers (e.g. N-Cadherin or SLUG), suggesting a higher similarity of adrenocortical tissues to mesenchymal compared to epithelial tissues, reminiscent of the adrenocortical origin from the intermediate mesoderm. Despite their ubiquitous expression in all adrenocortical tissues, mesenchymal markers had a variable expression in adrenocortical carcinoma, associating either directly or inversely with different clinical markers of tumor aggressiveness. Lymph node infiltration was associated with high expression of SLUG (p = 0.04), and at the same time low expression of N-cadherin (p = 0.001), and the same pattern was observed for venous infiltration of tumoral tissue, Weiss score of tumor malignancy or Ki67 proliferation marker. In malignant compared to benign adrenal tumors, we found significant differences in the expression of 16 out of the 94 studied FGF receptor pathway related genes. Genes involved in tissue differentiation and metastatic spread through epithelial to mesenchymal transition were most strongly altered. The therapeutically targetable FGF receptors 1 and 4 were upregulated 4.6- and 6-fold, respectively, in malignant compared to benign adrenocortical tumors, which was confirmed by using two different quantification methods in both frozen and paraffin embedded tissue material. High expression of FGFR1 and 4 was significantly associated with worse patient prognosis (High FGFR1 expression was associated with a shorter overall patient survival of 84 vs 148 months (HR=1.8, 95% CI: 1.01-3.25) as well as a shorter resection free survival of 25 vs 75 months ((HR=2.93, 95% CI: 1.25-6.84), while high FGFR4 was associated with a much shorter overall survival of 50 vs 155 months (HR=2.44, 95% CI: 1.41-4.22).
In conclusion, epithelial to mesenchymal transition does not seem to play a role in adrenocortical carcinoma tumor progression, and the FGF/FGFR pathway, even if it is probably not related to EMT, is nonetheless associated with tumor aggressiveness. Furthermore, quantification of FGF receptors may enable a stratification of adrenocortical carcinoma for the use of FGFR inhibitors in future clinical trials.
Novel deep learning (DL) architectures, better data availability, and a significant increase in computing power have enabled scientists to solve problems that were considered unassailable for many years. A case in point is the “protein folding problem“, a 50-year-old grand challenge in biology that was recently solved by the DL-system AlphaFold. Other examples comprise the development of large DL-based language models that, for instance, generate newspaper articles that hardly differ from those written by humans. However, developing unbiased, reliable, and accurate DL models for various practical applications remains a major challenge - and many promising DL projects get stuck in the piloting stage, never to be completed. In light of these observations, this thesis investigates the practical challenges encountered throughout the life cycle of DL projects and proposes solutions to develop and deploy rigorous DL models.
The first part of the thesis is concerned with prototyping DL solutions in different domains. First, we conceptualize guidelines for applied image recognition and showcase their application in a biomedical research project. Next, we illustrate the bottom-up development of a DL backend for an augmented intelligence system in the manufacturing sector. We then turn to the fashion domain and present an artificial curation system for individual fashion outfit recommendations that leverages DL techniques and unstructured data from social media and fashion blogs. After that, we showcase how DL solutions can assist fashion designers in the creative process. Finally, we present our award-winning DL solution for the segmentation of glomeruli in human kidney tissue images that was developed for the Kaggle data science competition HuBMAP - Hacking the Kidney.
The second part continues the development path of the biomedical research project beyond the prototyping stage. Using data from five laboratories, we show that ground truth estimation from multiple human annotators and training of DL model ensembles help to establish objectivity, reliability, and validity in DL-based bioimage analyses.
In the third part, we present deepflash2, a DL solution that addresses the typical challenges encountered during training, evaluation, and application of DL models in bioimaging. The tool facilitates the objective and reliable segmentation of ambiguous bioimages through multi-expert annotations and integrated quality assurance. It is embedded in an easy-to-use graphical user interface and offers best-in-class predictive performance for semantic and instance segmentation under economical usage of computational resources.
Today’s cloud data centers consume an enormous amount of energy, and energy consumption will rise in the future. An estimate from 2012 found that data centers consume about 30 billion watts of power, resulting in about 263TWh of energy usage per year. The energy consumption will rise to 1929TWh until 2030. This projected rise in energy demand is fueled by a growing number of services deployed in the cloud. 50% of enterprise workloads have been migrated to the cloud in the last decade so far. Additionally, an increasing number of devices are using the cloud to provide functionalities and enable data centers to grow. Estimates say more than 75 billion IoT devices will be in use by 2025.
The growing energy demand also increases the amount of CO2 emissions. Assuming a CO2-intensity of 200g CO2 per kWh will get us close to 227 billion tons of CO2. This emission is more than the emissions of all energy-producing power plants in Germany in 2020.
However, data centers consume energy because they respond to service requests that are fulfilled through computing resources. Hence, it is not the users and devices that consume the energy in the data center but the software that controls the hardware. While the hardware is physically consuming energy, it is not always responsible for wasting energy. The software itself plays a vital role in reducing the energy consumption and CO2 emissions of data centers. The scenario of our thesis is, therefore, focused on software development.
Nevertheless, we must first show developers that software contributes to energy consumption by providing evidence of its influence. The second step is to provide methods to assess an application’s power consumption during different phases of the development process and to allow modern DevOps and agile development methods. We, therefore, need to have an automatic selection of system-level energy-consumption models that can accommodate rapid changes in the source code and application-level models allowing developers to locate power-consuming software parts for constant improvements. Afterward, we need emulation to assess the energy efficiency before the actual deployment.
The epithelial layer of the gastrointestinal (GI) tract provides a barrier between the environment and the body. Dysfunction of the epithelium, including changes of the innate immune response facilitated by pattern recognition receptors (PRRs), plays a major role in the development of GI disorders. However, the organization of innate immune sensing, the expression and activity of PRRs and the factors contri¬buting to such possible organization along the GI tract are unclear. In recent years, stem cell-derived organoids gained increasing attention as promising tissue models. Here, a biobank of human and murine organoids comprising three lines from each GI segment; corpus, pylorus, duodenum, jejunum, ileum, colon was generated. RNA sequencing of 42 lines confirmed the preservation of tissue identity and revealed an extensive organization of innate immune signaling components along the cephalocaudal axis, giving each segment a specific innate immune profile. Comple-menting the region-specific expression analysis, several PRRs in human and murine organoids showed region- and species-specific function. To investigate the factors contributing to the patterning of innate immunity in the GI tract, the impact of microbial components was analyzed using murine embryo-derived, never colonized gastric and proximal intestinal organoids. Transcriptional profiling of embryo-derived organoids showed that while expression of some PRRs may depend on environmental cues as expected, an unexpectedly large part of segment-specific expression of PRR signaling components is independent of prior contact with microbial products. Further, analysis of published RNA-seq data as well as in vitro experiments using directed differentiation of organoids into specific cell types showed that expression of innate immune gene also depended on cellular differentiation along the crypt-villus axis. This underlined the importance of cellular differentiation rather than contact to microbial compounds for expression of PRRs. Lastly, analysis of published datasets of RNA-seq and ATAC-seq after knockout of the intestinal transcription factor Cdx2 demonstrated that Cdx2 is likely important for the expression of Nlrp6 and Naip1 in the murine intestine. Future experiments have to support these preliminary findings. Taken together, the expression of a large part of epithelial innate immunity is develop¬mentally defined and conserved in tissue-resident stem cells. The identification of mechanisms governing expression of genes related to immunity will provide further insights into the mechanisms that play a role in the progress of inflammatory diseases.
Post-error slowing is one of the most widely employed measures to study cognitive and behavioral consequences of error commission. Several methods have been proposed to quantify the post-error slowing effect, and we discuss two main methods: The traditional method of comparing response times in correct post-error trials to response times of correct trials that follow another correct trial, and a more recent proposal of comparing response times in correct post-error trials to the corresponding correct pre-error trials. Based on thorough re-analyses of two datasets, we argue that the latter method provides an inflated estimate by also capturing the (partially) independent effect of pre-error speeding. We propose two solutions for improving the assessment of human error processing, both of which highlight the importance of distinguishing between initial pre-error speeding and later post-error slowing.
Human attention is strongly attracted by direct gaze and sudden onset motion. The sudden direct-gaze effect refers to the processing advantage for targets appearing on peripheral faces that suddenly establish eye contact. Here, we investigate the necessity of social information for attention capture by (sudden onset) ostensive cues. Six experiments involving 204 participants applied (1) naturalistic faces, (2) arrows, (3) schematic eyes, (4) naturalistic eyes, or schematic facial configurations (5) without or (6) with head turn to an attention-capture paradigm. Trials started with two stimuli oriented towards the observer and two stimuli pointing into the periphery. Simultaneous to target presentation, one direct stimulus changed to averted and one averted stimulus changed to direct, yielding a 2 × 2 factorial design with direction and motion cues being absent or present. We replicated the (sudden) direct-gaze effect for photographic faces, but found no corresponding effects in Experiments 2-6. Hence, a holistic and socially meaningful facial context seems vital for attention capture by direct gaze. STATEMENT OF SIGNIFICANCE: The present study highlights the significance of context information for social attention. Our findings demonstrate that the direct-gaze effect, that is, the prioritization of direct gaze over averted gaze, critically relies on the presentation of a meaningful holistic and naturalistic facial context. This pattern of results is evidence in favor of early effects of surrounding social information on attention capture by direct gaze.
We present a technique for computing multi-branch-point covers with prescribed ramification and demonstrate the applicability of our method in relatively large degrees by computing several families of polynomials with symplectic and linear Galois groups.
As a first application, we present polynomials over \(\mathbb{Q}(\alpha,t)\) for the primitive rank-3 groups \(PSp_4(3)\) and \(PSp_4(3).C_2\) of degree 27 and for the 2-transitive group \(PSp_6(2)\) in its actions on 28 and 36 points, respectively. Moreover, the degree-28 polynomial for \(PSp_6(2)\) admits infinitely many totally real specializations.
Next, we present the first (to the best of our knowledge) explicit polynomials for the 2-transitive linear groups \(PSL_4(3)\) and \(PGL_4(3)\) of degree 40, and the imprimitive group \(Aut(PGL_4(3))\) of degree 80.
Additionally, we negatively answer a question by König whether there exists a degree-63 rational function with rational coefficients and monodromy group \(PSL_6(2)\) ramified over at least four points. This is achieved due to the explicit computation of the corresponding hyperelliptic genus-3 Hurwitz curve parameterizing this family, followed by a search for rational points on it. As a byproduct of our calculations we obtain the first explicit \(Aut(PSL_6(2))\)-realizations over \(\mathbb{Q}(t)\).
At last, we present a technique by Elkies for bounding the transitivity degree of Galois groups. This provides an alternative way to verify the Galois groups from the previous chapters and also yields a proof that the monodromy group of a degree-276 cover computed by Monien is isomorphic to the sporadic 2-transitive Conway group \(Co_3\).
Photoelectron spectroscopy proves as a versatile tool for investigating various aspects of the electronic structure in strongly correlated electron systems. Influencing the manifestation of strong correlation in Ce-based surface alloys is the main task of this work. It is shown, that the manifestation of the Kondo ground state is influenced by a multitude of parameters such as the choice of the metal binding partner in binary Ce compounds, the surface alloy layer thickness and accompanying variations in the lattice structure as well as the interfaces to substrate or vacuum. Gaining access to these parameters allows to directly influence essential state variables, such as the f level occupancy nf or the Kondo temperature TK.
The center of this work are the intermetallic thin films of CePt5/Pt(111) and CeAgx/Ag(111). By utilizing different excitation energies, photoemission spectroscopy provides access to characteristic features of Kondo physics in the valence band, such as the Kondo resonance and its spin-orbit partner at the Fermi level, as well as the multiplet structure of the Ce 3d core levels. In this work both approaches are applied to CePt5/Pt(111) to determine nf and TK for a variety of surface alloy layer thicknesses. A temperature dependent study of the Ce 3d core levels allows to determine the systems TK for the different layer thicknesses. This leads to TK ≈200–270K in the thin layer thickness regime and TK >280K for larger layer thicknesses. These results are confirmed by fitting the Ce 3d multiplet based on the Gunnarsson-Schönhammer formalism for core level spectroscopy and additionally by valence band photoemission spectra of the respective Kondo resonances. The influence of varying layer thickness on the manifestation of strong correlation is subsequently studied for the surface alloy CeAgx/Ag(111). Furthermore, the heavy element Bi is added, to investigate the effects of strong spin-orbit coupling on the electronic structure of the surface alloy.
A multitude of human tissues, such as bones, tendons, or muscles, are characterized by a hierarchical and highly ordered structure. In many cases, the loss of these tissues requires reconstruction using biocompatible replacement materials. In the field of bone replacement, the pore structure of the material has a crucial influence. Anisotropic porosity would have the advantage of facilitating the ingrowth of cells and newly formed blood vessels as well as the transport of nutrients.
In this thesis, scaffolds with a highly ordered and anisotropic pore structure were fabricated using unidirectional freezing.
Systematic investigations were carried out on biopolymer solutions (alginate and chitosan) to gain a deeper understanding of the freeze-structuring process. The knowledge gained was then applied to the development of anisotropically structured bone substitute materials. Here, the previously existing material platform for anisotropically structured calcium phosphates was extended to low-temperature phases such as calcium deficient hydroxyapatite (CDHA) or the secondary phosphates monetite and brushite.
After the implantation of a biomaterial, the inevitably triggered initial immune response plays a key role in the success of a graft, with immune cells such as neutrophils or macrophages being of particular importance. In this thesis, the influence of anisotropically structured alpha-TCP and CDHA scaffolds as well as their unstructured references on human monocytes/macrophages was investigated. Macrophages produced extracellular traps (ETs) due to mineral nanoparticles formed by the binding of phosphate and calcium ions to human platelet lysate. In particular, incubation of alpha-TCP samples in lysate containing cell culture medium resulted in pronounced particle formation and enhanced release of ETs.
Impact of cardiovascular risk factors on myocardial work-insights from the STAAB cohort study
(2022)
Myocardial work is a new echocardiography-based diagnostic tool, which allows to quantify left ventricular performance based on pressure-strain loops, and has been validated against invasively derived pressure-volume measurements. Myocardial work is described by its components (global constructive work [GCW], global wasted work [GWW]) and indices (global work index [GWI], global work efficiency [GWE]). Applying this innovative concept, we characterized the prevalence and severity of subclinical left ventricular compromise in the general population and estimated its association with cardiovascular (CV) risk factors. Within the Characteristics and Course of Heart Failure STAges A/B and Determinants of Progression (STAAB) cohort study we comprehensively phenotyped a representative sample of the population of Würzburg, Germany, aged 30-79 years. Indices of myocardial work were determined in 1929 individuals (49.3% female, mean age 54 ± 12 years). In multivariable analysis, hypertension was associated with a mild increase in GCW, but a profound increase in GWW, resulting in higher GWI and lower GWE. All other CV risk factors were associated with lower GCW and GWI, but not with GWW. The association of hypertension and obesity with GWI was stronger in women. We conclude that traditional CV risk factors impact selectively and gender-specifically on left ventricular myocardial performance, independent of systolic blood pressure. Quantifying active systolic and diastolic compromise by derivation of myocardial work advances our understanding of pathophysiological processes in health and cardiac disease.