JGU-Hochschulschriften

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  • ItemDissertationOpen Access
  • ItemDissertationOpen Access
    Novel bioinformatic tools and methods to study Next Generation Sequencing data with a focus on DNA repair and genome stability
    (2024) Sayols Puig, Sergi; Andrade-Navarro, Miguel; Beli, Petra
    Next Generation Sequencing is a widely used technology that enables precise identification and quantification of nucleic acids. Advanced sequencing-based experimental protocols have enabled the investigation of their modifications, organization, interaction, and regulation, among others. This thesis introduces three novel methodologies implemented as software packages for facilitating the comprehensive analysis, visualization and interpretation of *omics* sequencing data. In *Chapter 1* we describe the problem of PCR clonal artefacts in RNA-seq and enrichment-based assays, such as ChIP-seq. We present the tool *dupRadar*, a novel method to tell apart those PCR artifacts from normal read duplication due to natural over-sequencing of highly expressed genes or enriched loci. We apply our method to detect over-sequenced libraries of limited complexity in cases of little input material in a synthetic dataset and also in public datasets of bulk RNA-seq and single-cell RNA-seq. We found that datasets generated from lower input material exhibit limited library complexity, leading to increased duplication rates even among lowly expressed genes. Finally, we run differential expression analysis to demonstrate that even low levels of PCR artifacts can have an influence on downstream analysis and data interpretation. *Chapter 2* introduces *rrvgo*, a novel tool for interpreting large lists of Gene Ontology terms. The package gives access to several semantic similarity methods; here, I apply the *Relevance* method to GO terms significantly enriched in the publicly available gene expression data from the breast cancer study published by Schmidt et al. in 2008, comparing grade III to grade I breast cancer patients. This approach identifies clusters of potentially redundant terms with high correlation of information content within the set of GO terms. We further demonstrate the utility of rrvgo's visualizations, which facilitate the detection and refinement of a non-redundant set of GO terms for more focused biological interpretation. *Chapter 3* introduces *BreakTag*, an innovative approach for genome-wide identification and quantification of DNA double-strand breaks and their structural characteristics at single nucleotide resolution using high-throughput sequencing. Additionally, we developed *breakinspectoR*, a bioinformatics pipeline designed to detect, quantify and study the end structure of Cas9-induced DSBs in BreakTag data. Using BreakTag, we analyzed cleavage patterns by SpCas9 across three genome-wide CRISPR libraries, comprising 3,500 distinct single-guide RNAs, and identified over 150,000 on- and off-target cleavage sites. Analysis of DSB break ends revealed that approximately 35% of the identified breaks exhibit staggered ends. A machine learning model trained using target site sequence composition and DSB end structure data revealed that protospacer sequence significantly influences Cas9 incision patterns. Furthermore, by examining matched datasets of Cas9 cleavage sites and subsequent repair outcomes, we found a link between staggered breaks and single-nucleotide insertions. In conclusion, these findings demonstrate that the structure of Cas9 DSB ends is sequence-dependent, suggesting that guide RNAs can be strategically designed to produce precise, predictable repair outcomes. This approach may provide new opportunities for correcting diseases caused by single-nucleotide deletions. Overall during my PhD, in collaboration with wet-lab researchers, I have developed novel tools and methods to a broad range of applications of *omics* sequencing data, with special focus on the study of DNA repair and genome stability.
  • ItemDissertationOpen Access
    Laser system for precision spectroscopy of the ground state hyperfine splitting in muonic hydrogen
    (2025) Rajamohanan, Siddharth; Pohl, Randolf
    This thesis describes the laser system for the spectroscopy of the 1S HFS (1SF=1 1/2 -1SF=01/2 ) in muonic hydrogen (μH), pursued by the CREMA collaboration with its current experiment HyperMu. Muonic hydrogen is an atomic system formed by a muon (μ−), a negatively charged unstable lepton with a lifetime of ∼2.2 μs, and a proton (p), much like the hydrogen atom (eH). As the muon is ∼ 207 times more massive than the electron, the wavefunction of the muon has a larger overlap with that of the nucleus, making its bound-state energy levels characteristically perturbed by nuclear structure effects. A measurement of the 1S HFS to about 1ppm in μH allows the determination of the nuclear structure contribution to about 200 ppm. In a second step from this contribution, the Zemach radius and the polarizability contribution can be deduced, assuming polarizability from theory or the Zemach radius from ep scattering of eH. The experiment is to be conducted at the Paul Scherrer Institute (PSI), Switzerland, where a high-intensity continuous muon beam is available. The muons from the ΠE5 beamline are stopped within a H2 target (22K temperature, 0.5 bar pressure) to form μH. After thermalization, these atoms are excited by the laser pulses that undergo multiple reflections in a toroidal enhancement cell, placed in the H2 target, to increase the 1SF=0 1/2 - 1SF=1 1/2 transition probability. The lifetime of the 1SF=1 1/2 state is longer than that of the muons, which makes the fluorescence from the deexcitation not a viable indicator of laser excitation. An indirect detection scheme is designed based on diffusion of μH through the H2 and the production of X-rays at its arrival at the target walls. The laser-excited μH undergoing a collision with H2 molecules acquires a kinetic energy of 0.1 eV and diffuses efficiently to the target walls coated with gold. The transfer of μ− from the μH to the Au atom creates μAu in an excited state. The deexcitation of μAu generates characteristic X-rays that are detected by X-ray detectors to indicate laser excitation. The resonance curve of the HFS transition is obtained by plotting the number of μAu events versus the frequency of the laser. Simulations indicate that the laser pulses for the spectroscopy must have an energy of 3 mJ with 100MHz frequency bandwidth at the predicted transition wavelength of 6.8 μm. Moreover, as the muons arrive stochastically within the target, the laser system must be stochastically triggerable with an average repetition rate of >100 s−1. The muon lifetime constrains the maximum pulse build-up time to be ∼1 μs. Generating such high-energy pulses in the mid-infrared in such a short time and with adequate frequency control is technologically challenging. We pursue a two-stage design that begins with the generation of NIR 1030nm pulses, followed by a second stage that downconverts the 1030nm pulses into the required 6.8μm pulses via nonlinear difference frequency generation (DFG). Pulses of 1030nm of 50 ns duration and energy 30 mJ are generated in a thin-disk oscillator by the method of cavity dumping within <1 μs. These pulses are amplified to the energy of 300 mJ by a thin-disk multipass amplifier (TDA). These 1030nm pulses are used for pumping two optical parametric oscillators (OPO) operating at 2.1μm and 3.1μm wavelengths. The 2.1 μm-OPO converts the 1030nm pulse into pulses of wavelength 2.1μm and 1.9μm while the 3.1 μm-OPO converts the 1030nm pulse into pulses of wavelength 3.1μm and 1.5 μm. In a similar process, the 2.1μm and 3.1μm pulses are amplified by 1030nm pulses to energies of 25 mJ and 3 mJ, respectively, in their respective optical parametric amplifiers. The 6.8μm pulses are eventually obtained by difference frequency generation of the 2.1μm pulse and the 3.1μm pulse. The TDO and the two OPOs are injection-seeded and Pound-Drever-Hall (PDH) stabilized to ensure single-frequency operation. While the wavelength of the 1030nm and 2.1μm pulses are fixed, the wavelength of the 3.1μm pulses can be varied by changing the frequency of the seed-laser. This allows the 6.8μm pulses to be scanned across the search range of 6798nm - 6785nm of the 1S HFS in μH. This thesis deals with the development of the 2.1 μm-OPO, the 2.1 μm-OPA, the 6.8 μm- DFG stage and the frequency calibration of the 6.8μm pulses. Chapter 1 of the thesis elaborates on the motivation of the experiment along with a summary of the theoretical efforts parallel to the experiment. Details of the experimental scheme are given, focusing on the aspects that constrain the requirements of the laser system. Chapter 2 of the thesis discusses the layout of the laser system under development, designed to satisfy these requirements. A brief review of laser physics and nonlinear optics, as well as the current status of the laser system, is provided. Chapter 3 compiles the results on the 2.1μm-OPO and the implications on its variablefinesse cavity layout. The effect of injection-seeding and PDH stabilization of the cavity on the energy and stability is studied. Generation of 2.1μm pulses of energy 1 mJ of average beam qualityM2 ∼ 1.12 with 5 mJ of input 1030nm pulse energy is demonstrated. Chapter 4 describes the amplification of the 2.1μm pulses of 1 mJ energy by the 2.1 μm- OPA to ∼5 mJ while providing a beam with average M2 of 1.56, for input 1030nm pulse energy of 25 mJ from the TDO. Preliminary tests of the 2.1 μm-OPA with 1030nm pulses of energy 95 mJ are shown to amplify the 2.1μm pulses to 22 mJ. Chapter 5 focuses on the 6.8 μm-DFG stage that converts the 2.1μm pulses into 6.8μm pulses. 300 μJ of 6.8μm is generated from 6 mJ of 2.1μm and 300 μJ of 3.1 μm-seed pulses. The dependence of the nonlinear process on the orientation and temperature of the crystal, as well as the frequency of the 6.8μm beam, is studied for optimum frequency and energy control during the μH spectroscopy campaign. Chapter 6 reports on the frequency calibration of the 6.8μm pulses. By absorption spectroscopy in a H2O vapour cell, three resonances of H2O are studied for various pressures between the range 0.1 mbar and 7 mbar. From a fit to the measured transition, the centroid position and linewidth of the transitions are obtained. The obtained centroid positions were all systematically deviating by 50MHz from the HITRAN value, indicating the need to recheck the frequency calibration. From the linewidth, the upper limit of the laser bandwidth was determined to be 110 MHz. This fulfils the minimum requirement for the spectroscopy in μH. In this thesis, we have demonstrated for the first time our ability to produce 6.8μm pulses with the necessary frequency control. Energy scaling of the laser system will be needed to reach 3 mJ energy at the 6.8μm wavelength, but the observed efficiency is promising.
  • ItemDissertationOpen Access
    The role of plasma cell-free DNA as predictor of clinical outcome in heart failure – Results from the MyoVasc study
    (2025) Hankeln, Tim Jeremy; Wild, Philipp; Simon, Perikles
    Heart failure (HF) represents a major cause of mortality with a prevalence of 1-2% in the adult population in developed countries. As populations age, the role of HF is expected to grow. This comes with a steep increase in healthcare costs, placing a substantial burden on society. Identifying HF risk patients earlier, possibly even before symptoms manifest, becomes crucial to initiate interventions promptly, such as lifestyle adjustments or medication. In preventive medicine, the identification of suitable biomarkers plays a key role, as they allow an objective and early disease detection. Cell-free DNA (cfDNA) is a widely used diagnostic biomarker in clinical fields like oncology or transplantation medicine. In clinical cardiology, however, cfDNA analytics does not yet play a major role. Only a handful of rather small-scale studies have so far investigated the potential of cfDNA diagnostics in HF patients, indicating that cfDNA could be an independent risk factor for cardiovascular disease and overall mortality. The aim of the present study was therefore to evaluate the potential of cfDNA in HF diagnostics in a large cohort of subjects and to compare its predictive power to the currently most often used biomarker, NT-proBNP. To achieve this, a reliable, reproduceable, and quick high throughput cfDNA quantification method needed to be implemented. The existing manual, time- and labour-consuming qPCR assay was automated by testing and establishing an INTEGRA pipetting robot and tuning its workflow to the special needs of high-viscosity plasma samples. The assay was adjusted to reliably produce the same test results as with the already published qPCR assay established by Neuberger et al. (183). This way a consistent measuring of the study samples was ensured. cfDNA levels were then quantified in 3109 EDTA plasma samples from the prospective MyoVasc study (NCT04064450). Two qPCR assays of different amplicon lengths (cfDNA90 bp/ cfDNA222 bp), both targeting a repetitive LINE1 element, were used for cfDNA quantification and to calculate the cfDNA integrity index, which indicates the fragmentation level of the cfDNA. Competing risk models were applied to investigate the associations of cfDNA with worsening of HF, and Cox proportional hazard regression analyses were used to assess the endpoints of cardiac death and all-cause death. C-statistics were calculated and compared for each model. The participants were classified as 0 (healthy) or HF stages A (at risk for HF) to D (advanced HF) according to the current Universal Definition of Heart Failure. Analyses were adjusted for age, sex, cardiovascular risk factors (CVRFs) and medication (models 1-3) and additionally for NT-proBNP (model 4). Outcome data were presented as cumulative incidence plots for cfDNA90bp and 222bp levels and for the integrity index. The cohort included 3109 study participants with an age between 34 to 85 years and 35.7% females. cfDNA concentration was lowest in stage 0/A subjects (n=534) with 10.99 (8.70/13.93) ng/ml (median (Q1/Q3)). Stage B (pre-HF) (n=923) or stage C/D subjects (n=1652) showed elevated cfDNA90bp concentrations with 13.37 (10.35/18.11) or 17.11 (12.56/22.80) ng/ml, respectively. Cox proportional hazard regression analyses indicated that the concentration of cfDNA90bp is a relevant prognostic marker for all-cause death, adjusted for age, sex, CVRFs and medication (HR = 1.312 [1.205-1.430], p < 0.0001). After additional adjustment for NT-proBNP, the effect estimates were lower, but still statistically significant (HR = 1.173 [1.073-1.282], p = 0.00046). Regarding the endpoints worsening of HF and cardiac death, the effect estimates were no longer significant after adjustment for NT-proBNP. A C- index comparison showed the same tendency, with a significant added value of testing cfDNA additionally to NT-proBNP only when looking at all-cause death (C = 0.807 vs. C = 0.805; p = 0.050). However, cumulative incidence plots for dichotomised values of NT-proBNP and cfDNA showed the highest incidence rates for all three outcomes in patients with elevations in both biomarkers, significantly higher than in patients with elevations of NT-pro BNP alone. The present results indicate that cfDNA is a risk factor, which independently of NT-proBNP contributes to the prediction of overall mortality (all-cause death) in the study cohort. cfDNA also appears to possess additional information value to NT-proBNP for predicting worsening of HF and cardiac death.
  • ItemDissertationOpen Access
    Molekulare Untersuchungen onkologisch relevanter Biomarker als Baustein für die personalisierte Medizin
    (2025) Leunov, Alena
    Molekulare Untersuchungen onkologisch-relevanter Biomarker sind entscheidend für die personalisierte Medizin, da sie die Diagnose von Krebserkrankungen präzisieren und die Entwicklung zielgerichteter Therapien ermöglichen können. Durch die grundlagenwissenschaftliche Analyse von Tumor-assoziierten Strukturen können individuelle Tumoreigenschaften identifiziert und somit maßgeschneiderte Behandlungsstrategien entwickelt werden. Die Threonin Aspartase 1 (Taspase1) wurde in diesem Zusammenhang als onkologisch-relevante Protease mit Biomarker-Potential für verschiedene Tumorentitäten charakterisiert. Taspase1 spielt eine entscheidende Rolle bei der Aktivierung von Mixed Lineage Leukemia (MLL)-Fusionsproteinen und demzufolge bei der Entstehung aggressiver Leukämien. Darüber hinaus wurde eine funktionelle Überexpression von Taspase1 bei einer Reihe von soliden Tumoren, wie auch den Kopf-Hals-Tumoren (head and neck squamous cell carcinoma, HNSCC) gezeigt. Die Erforschung neuartiger Biomarker ist insbesondere auch für HNSCC notwendig, da HNSCC-Patienten durch Metastasierung und Rezidive eine äußerst schlechte Prognose aufweisen. Hier kann Taspase1 nicht nur als prognostischer Biomarker, sondern auch als mögliches therapeutisches Zielprotein dienen. Zur detaillierten Charakterisierung der onkologischen Aktivität von Taspase1 wurde im Rahmen dieser Arbeit ein besonderer Fokus auf Protein-Interaktionen und subzellulären Transportmechanismen gelegt, welche entscheidend an der Regulation ihrer proteolytischen Aktivität und somit ihrer onkogenen Wirkung beteiligt sind. Einer der wichtigsten und zugleich onkologisch-relevanten Interaktionspartner von Taspase1, welcher der Protease den Zugang zum Nukleus und insbesondere zum Nukleolus ermöglicht, ist Nucleophosmin1 (NPM1). Da eine Hemmung der spezifischen Taspase1-NPM1-Interaktion einen innovativen Ansatz zur Taspase1-Hemmung darstellt, wurde zunächst die Interaktionsdomäne beider Proteine identifiziert. Die hierfür generierte Deletions- und Lokalisationsmutanten von NPM1 wiesen auf eine funktionell bedeutsame Region im N-Terminus von NPM1 hin. Veränderungen im Bereich von ±100 Aminosäuren im N-Terminus beeinträchtigen die nukleoläre Lokalisation der NPM1-Mutanten. Die Aktivität von NPM1 wird zudem durch die Oligomerisationsdomäne gesteuert, wie Untersuchungen mit NPM1-knockdown-Zellen und Mutanten ohne Oligomerisationsdomäne belegen. Darüber hinaus wird die Interaktion von NPM1 mit Taspase1 hauptsächlich durch die N-terminale Oligomerisations-/Chaperondomäne gesteuert, wobei die C-terminale Region (aa187-260) ebenfalls eine wichtige Rolle spielt. Um die NPM1-Taspase1-Interaktion im Detail zu verstehen, wurden weitere Untersuchungen mit Hilfe von chimären Proteinen aus humaner und Drosophila Taspase1 (dTasp) durchgeführt. Im Gegensatz zur humanen Taspase1, zeigt die homologe Protease aus Drosophila keine Interaktion mit NPM1. Die proteolytisch aktive Taspase1 besteht aus zwei Untereinheiten, der α- und β- Untereinheit, welche in den hergestellten chimären Varianten aus unterschiedlichen Spezies stammen (α-hTasp/β-dTasp und α-dTasp/β-hTasp). Beide Taspase1-Chimären zeigten keine Interaktion mit endogenem NPM1. Lokalisationsstudien und Messung der proteolytischen Aktivität der chimären Proteasen verdeutlichten, dass die subzelluläre Taspase1-Lokalisation von der α-Untereinheit abhängt, während die proteolytische Aktivität von der β-Untereinheit gesteuert wird. Interessanterweise zeigen Zellen, welche NPM1-Mutanten in Kombination mit Taspase1 exprimieren, eine erhöhte Viabilität, was auf eine unterstützende Wirkung von Taspase1 auf NPM1 hinweist. Des Weiteren führte eine Taspase1-Überexpression zur gesteigerten Empfindlichkeit von HNSCC-Zellen gegenüber der chemotherapeutischen Behandlung mit Cisplatin. Eine kombinierte Chemo- und Strahlentherapie erwies sich als besonders effektiv, wobei höhere Cisplatin-Dosen einen synergistischen Effekt mit der Bestrahlung aufweisen. Neben der molekularen Untersuchung der Taspase1-NPM1-Interaktion, wurden zudem neuartige Möglichkeiten zur Etablierung von zirkulierenden Biomarkern für die Tumor-Diagnostik erforscht. Um einerseits die Behandlungsoption der Patienten zu optimieren und auf das Niveau einer personalisierten Therapie zu bringen, und andererseits eine frühere Diagnose der Erkrankung stellen zu können, wurden die im Rahmen von „liquid biopsy“ zirkulierende Tumorzellen im Blut von HNSCC-Patienten untersucht. Verschiedene Detektionssysteme und Kulturmethoden zur Isolierung und Identifikation dieser Zellen wurden optimiert. Kleine extrazelluläre Vesikel, sogenannte Exosomen, erwiesen sich als potenzielle Biomarker für die Frühdiagnostik. Experimente zur Isolierung und Untersuchung ihrer Interaktion mit anderen Zellen und Partikeln, sowie die zelluläre Aufnahme von Exosomen durch Makrophagen lieferten neue Einblicke in die Transportmechanismen innerhalb von Zellen. Diese Erkenntnisse legen nahe, dass Exosomen als diagnostische Biomarker, therapeutische Zielstrukturen oder Nanosysteme zur Medikamentenverabreichung genutzt werden könnten. Zusammenfassend konnten im Rahmen dieser Arbeit wichtige Erkenntnisse gewonnen werden, welche neben ihrer grundlagenwissenschaftlichen Relevanz zudem das Potential haben, zukünftige Strategien der Krebs-Diagnostik und -Therapie zu beeinflussen.
  • ItemDissertationOpen Access
    Molekulare Konsequenzen der Methionin-Restriktion
    (2025) Abrosimov, Roman
  • ItemDissertationOpen Access
    Between commodification and autonomy. The impact of audience analytics on editorial production processes and implications for media organizations and society
    (2025) Riemann, Robin Lukas; von Rimscha, Bjørn; Schupp, Katja
    This dissertation explores commodification tendencies in journalism through the lens of audience analytics use. Its aim is to provide a detailed understanding of these data-driven evaluation practices and their impact on editorial routines, journalistic role conceptions, and strategic media management. Drawing on five interlinked sub-projects that employ multiple theoretical and methodological approaches, it examines how audience analytics are used, what drives their adoption, and what implications they hold across various levels of journalistic production, from individual attitudes to organizational legitimacy practices. The findings indicate that while audience analytics are widely integrated into newsroom workflows, their influence remains context-dependent. Market orientation emerges as a dominant but often unreflected paradigm, often subtly shaping editorial priorities. At the same time, traditional journalistic values and professional autonomy persist, coexisting in hybrid role configurations. Audience analytics also contribute to the emergence of an audit culture, enabling new forms of managerial control and strategic legitimation both internally and externally. The dissertation highlights reflection as a critical yet underutilized counterbalance to the instrumental use of performance metrics. It proposes proprietary, value-based measurement systems as a promising but challenging alternative to commercially defined success criteria. Rather than rejecting quantification outright, the dissertation argues for a more deliberate integration of normative, democratic considerations into the evaluation of journalistic performance. In sum, the work advocates for a heightened awareness among journalists, media managers, and policymakers of the normative foundations of journalism as a democratic institution. Commodification is not inherently problematic—but becomes so when it silently reshapes professional practices without critical reflection. Measuring the quality of journalism should not be reduced to audience metrics alone; instead, it must account for the broader societal role journalism plays in informing the public and strengthening democracy.
  • ItemDissertationOpen Access
  • ItemDissertationOpen Access
    Human models for White Sutton syndrome: POGZ mutations change the transcriptome and induce defects in neural progenitor cell biology
    (2025) Soliman, Azza; Winter, Jennifer; Hankeln, Thomas
    Intellectual disability (ID) and autism spectrum disorders (ASD) are complex neurodevelopmental conditions with high genetic heterogeneity. Studies indicate that 10%-40% of individuals with ID also have ASD, suggesting shared molecular mechanisms between these disorders. Recent next-generation sequencing studies have highlighted a significant role of de novo mutations in ASD, particularly those with large effects. Among these, POGZ (Pogo Transposable Element with zinc finger “ZNF” domain) has emerged as a frequently mutated gene with potential loss-of-function effects in ASD patients. However, the underlying molecular mechanisms and the pathogenic impact of POGZ mutations are not fully understood. POGZ encodes a protein that is mainly binds to heterochromatin protein 1α and contributes to gene regulatory functions. Functionally, POGZ is critical for kinetochore assembly, sister chromatid cohesion, and mitotic chromosome segregation. POGZ deficiency can lead to premature mitotic exit, polyploidy, and potential cell death or genomic instability, which may disrupt neural development and brain function. POGZ thought to act as a transcriptional regulator, potentially influencing molecular networks that are critical for neuronal function. This PhD study investigated the cellular and molecular mechanisms by which POGZ mutations contribute to neurodevelopmental disorders (NDDs) using human induced pluripotent stem cells (iPSCs) derived from patient and CRISPR/Cas9-mediated gene editing to introduce heterozygous POGZ mutations. These mutant iPSCs were differentiated into neural progenitor cells (NPCs) and neurons under both two-dimensional (2D) and three-dimensional (3D) culture conditions to analyze the effects of POGZ mutations on neural development. Key findings of the study indicated that frameshift mutations in the N-terminus or the HP1-binding zinc finger-like (HPZ) domain of POGZ led to decreased POGZ protein expression without disrupting its nuclear localization. Using 3D neurospheres and brain organoids, it was found that POGZ-deficient cells exhibited impaired self-renewal of NPCs, alongside enhanced differentiation and increased neuronal migration. Additionally, analysis of the transcriptome via RNA sequencing revealed widespread changes in gene expression in NPCs carrying POGZ mutations. These alterations were significantly enriched for genes involved in mitotic chromatid segregation, DNA repair, nonsense-mediated decay, and alternative splicing. Notably, the data revealed a transcriptomic signature characterized by the elevated expression of neuron-specific genes, suggesting an "accelerated differentiation" phenotype in mutant NPCs, mirroring the behavior observed in the 3D neurosphere models. Furthermore, CUT&Tag sequencing was employed to identify direct targets of POGZ, providing evidence that POGZ directly regulated genes linked to synaptic function, chromosome segregation, and Wnt signaling. The overrepresentation of autism-associated risk genes among POGZ-regulated targets further suggested a potential link between POGZ dysfunction and the etiology of NDDs, including ASD. This analysis emphasized the critical role of POGZ in regulating neural development at both the cellular and molecular levels. Understanding how POGZ mutations drive alterations in NPC behavior and gene regulation, is crucial for developing targeted therapeutic strategies for conditions associated with POGZ dysfunction. Ultimately, this study aimed to bridge the gap between genetic findings and pathophysiological mechanisms in NDDs, providing deeper insights into the developmental disruptions caused by POGZ mutations.
  • ItemDissertationOpen Access
  • ItemDissertationOpen Access
    Precise muon momentum calibration and Z mass measurement with the ATLAS experiment, using pp collisions at √s =13 TeV
    (2024) Fakoudis, Dionysios; Tapprogge, Stefan
    Standard Model is the foundation of modern particle physics. Precise measurements are in the center of major studies. The Higgs boson discovery probes for further Electro-Weak measurements, to test the consistency of the model. ATLAS is a multi-purpose detector and one of the experiments at the CERN LHC. With a dedicated tracking and magnetic system, the experiment achieves high precision measurements of the muon momentum at the final state. In that context, the Z mass measurement in ATLAS is part of these efforts. The Z boson mass has been measured with excellent accuracy in the LEP experiment at CERN, without delving into reconstruction systematic uncertainties. In ATLAS, the measurement involves the reconstruction of final muon objects introducing corresponding biases. The comparison between the two measurements is of high scientific interest and a test for ATLAS capabilities. The thesis investigates muon momentum calibration in the ATLAS experiment, with pp collisions, at center of mass energy $\sqrt{s}=13$ TeV. ATLAS uses "standard candles" resonances for the calibration, $\Jpsi$ meson and Z boson. By comparing di-muon mass spectrum in simulation and data, for the two resonances, the calibration is derived. The calibration in this thesis is in the context of official ATLAS recommendations but also for Z mass measurement primarily, but also other Electro-Weak measurements, such as the W mass measurement. The work focuses on calibration challenges using official ATLAS tools, with results divided into two main sections. The first section addresses calibration work performed for the ATLAS experiment. Specifically, the relative momentum resolution of muons in ATLAS is investigated for the Inner Detector (ID), the Muon Spectrometer (MS), and the Combined (CB) tracks. From these studies, maps of the muon relative momentum uncertainty are generated for both simulation and data. These maps reveal systematic deficiencies in the detector subsystems and mis-modelings in the simulations. The maps are then integrated into the official ATLAS calibration framework to assess their potential for improving calibration precision, with a comparison of results both with and without this additional information. Lastly, the process and outcomes of deriving the official ATLAS calibration recommendations are presented. These recommendations are developed separately for the ID, MS, and CB tracks. The second part of this thesis focuses on calibration in the context a the Z mass measurement, including a detailed analysis of a Z mass measurement with the applied calibration. The calibration process is altered so it does not include the Z boson resonance. Calibration corrections are derived with the $\Jpsi$ meson. Using official ATLAS tools, the calibration is compared for Prompt and Non-Prompt $J/\psi$ mesons. Kinematic distributions for both types are analyzed, and the differences between their calibrations are discussed. The calibration parameters are derived as a function of detector pseudorapidity and muon transverse momentum. Lastly, an assessment of the calibration uncertainties on the Z boson mass is extracted using a likelihood fit, with the di-muon channel.
  • ItemDissertationOpen Access
    Traumatische Wirbelsäulenfrakturen bei Mehrfachverletzten: eine Vergleichsstudie zwischen alleiniger dorsaler Stabilisierung und kombinierter dorsoventraler Versorgung
    (2025) Mulhem, Ali; Kantelhardt, Sven Rainer
    Ziel: Der optimale Ansatz für die chirurgische Behandlung schwerer traumatischer Wirbelsäulenfrakturen bei Patienten mit Polytrauma ist umstritten. Diese Studie vergleicht die alleinige dorsale Stabilisierung (Gruppe I) mit dem kombinierten dorsoventralen Ansatz (dorsale Stabilisierung + Wirbelkörperersatz Gruppe II). Analysiert wurden bildmorphologische Ergebnisse, einschließlich des sagittalen Index (SI) und des Loss of Vertebral Height (LVH), sowie klinischer Ergebnisse wie Schmerzen, neurologischer Status und postoperativen Komplikationen. Methoden: In dieser retrospektiven, monozentrischen Studie wurden alle Patienten mit Polytrauma und diagnostizierten Wirbelsäulenfrakturen (BW1 bis LW5), die sich zwischen dem 1. Januar 2015 und dem 30. September 2024 einer chirurgischen Stabilisierung unterzogen, einbezogen. Die Patientenakten und die Bildgebungen wurden analysiert, wobei Sagittal Index (SI), Loss of Vertebral Height (LVH), Schmerz gemäß Visuelle Analog Skala (VAS) und neurologischer Status zu Studienbeginn, nach jedem chirurgischen Eingriff und beim Follow-up erfasst wurden. Lineare gemischte Regressionsmodelle, angepasst an die Ausgangswerte, verglichen SI, LVH und Schmerzen, während ein Proportional Odds Ratio-Modell für den Vergleich des neurologischen Status zwischen den beiden Gruppen verwendet wurde. Ergebnisse: Insgesamt wurden 77 Patienten (47 Männer) eingeschlossen, davon 31 in Gruppe I und 46 in Gruppe II. Die demografischen Merkmale wie Alter, Geschlecht, Verletzungsursache, initiales Hämoglobin und Begleitverletzungen waren zwischen den Gruppen vergleichbar. Das mediane Follow-up betrug 16 Monaten in Gruppe I und 19 Monaten in Gruppe II. Die meisten Frakturen lagen im thorakolumbalen Übergangsbereich (BW12 und LW1), und laut AO-Klassifikation handelte es sich größtenteils um Kompressionsfrakturen (A3 oder 4, mit 12 und 10 in Gruppe I sowie 11 und 28 in Gruppe II). Das Regressionsmodell zeigte eine überlegene sagittale Ausrichtung in Gruppe II mit einer mittleren Differenz für den SI von -4,24 (95 % CI -7,13 bis -1,36; p-Wert = 0,004) und eine verbesserte Wiederherstellung der Wirbelkörperhöhe mit einer mittleren Differenz für LVH von 0,11 im kombinierten Ansatz (95 % CI 0,02 bis 0,20; p-Wert = 0,02). In Bezug auf die Schmerzreduktion beim Follow-up zeigte der kombinierte Ansatz bessere Ergebnisse mit einer mittleren Differenz von -1,55 (95 % CI -3,05 bis -0,05; p-Wert = 0,047). Das Proportional-Odds-Modell bezüglich des neurologischen Status zeigte in der kombinierten Gruppe bessere Ergebnisse mit einem Proportional-Odds-Ratio (POR) von 5,12 (95 % CI 1,51 bis 23,77; p-Wert = 0,022). Postoperative Komplikationen traten in beiden Gruppen bei jeweils sieben Patienten auf. Schlussfolgerung: Die kombinierte dorsoventrale Stabilisierung bei Wirbelsäulenfrakturen verbessert die Stellung der Wirbelsäule durch eine bessere sagittale Ausrichtung und eine erhöhte Wirbelkörperhöhe. Dies traf insbesondere auf das letzte follow-up zu, da nach initialer Versorgung ein deutlich geringerer Korrekturverlaust auftrat. Damit gingen im Vergleich zur alleinigen dorsalen Stabilisierung bessere klinische Ergebnisse einher, einschließlich Schmerzlinderung und neurologischem Status. Bezüglich Komplikationen gab es zwischen den beiden Gruppen keine signifikanten Unterschiede.
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    Detection and estimation limits of single electron cyclotron radiation with phased array antennas
    (2024) Thomas, Florian; Schömer, Elmar; Böser, Sebastian
    CRES is a new technique for energy spectroscopy of charged particles with sub-eV resolution. With CRES, particle energies are determined by measuring the frequency of the emitted cyclotron radiation in a magnetic field, which can be detected by an array of radio antennas and converted into digital voltages. Experiments that require large volumes of source material for gathering sufficient statistics may potentially need hundreds to thousands of these antennas, which can generate hundreds of gigabytes of raw data per second. This necessitates efficient data analysis and reduction solutions. In this thesis, algorithms for detection and parameter estimation of these signals within detector noise are discussed. The focus is on the development and efficiency analysis of optimal solutions assuming unlimited computing resources, specifically through matched filtering and maximum likelihood estimation. These optimal solutions are critical because their limits on detection efficiency and energy resolution are key factors in both sensitivity estimation and the optimization of experimental designs. To support this work, a new simulation tool was developed, achieving a 500 times speedup compared to the baseline simulation software through advancements in the physical modeling of CRES signals. This simulation tool was utilized, alongside the implementation of the optimal solutions, to evaluate the detection efficiency and energy resolution of an idealized example setup for a neutrino mass measurement with tritium β-decay electron spectroscopy in the Project 8 experiment. This represents the first time a study of the theoretical limits of a concrete experimental design based on a large antenna array could be conducted, made possible by the improved simulation run time. An initial assessment suggests that the results are consistent with the requirements for achieving the project goal of being sensitive to neutrino masses with mβ > 0.04 eV.
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    Evaluation der Entwicklung heterotoper Ossifikationen durch Bone Sialoprotein (BSP) im Muskel-Pouch-Modell der Ratte
    (2025) Schardt-Knauf, Bianca
    Die demografische Alterung stellt das Gesundheitssystem vor erhebliche gesellschaftliche Herausforderungen, die bereits heute sowohl im ambulanten als auch im stationären Sektor deutlich sichtbar sind. Neben der tertiären Prävention ist insbesondere die Förderung von Autonomie, sozialer Teilhabe sowie die Lebensqualität im höheren Alter von entscheidender Bedeutung. Bei erhöhtem Sturzrisiko und geringerer Knochendichte sind Knochenersatzmaterialien zukünftig unabdingbar. Das Bone Morphogenic Protein ist in vielen menschlichen Geweben präsent und wird bereits klinisch für seine osteoinduktiven und -regulativen Eigenschaften genutzt [6, 7]. Das Bone-Sialoprotein, ein Mitglied der small integrin-binding ligand N-linked glycoproteins, ist eine wesentliche Komponente der extrazellulären Knochenmatrix. Im Rahmen experimenteller Untersuchungen wurden sowohl in vitro als auch in vivo mehrfach potenzielle Einflüsse des BSP auf den Knochenstoffwechsel nachgewiesen [5;112;120-127;229]. Im Rahmen dieser Dissertation wurde die osteoinduktive Eigenschaft des BSP der SIBLING-Familie anhand des Muskel-Pouch-Modells an 51 männlichen Wistar-Ratten im Alter von sechs Wochen untersucht. Ziel war es, die potenzielle Knochenbildung durch BSP mittels Kollagen-Typ-1-Scaffolds zu evaluieren. Hierzu wurden zwei unterschiedliche Konzentrationen des BSP untersucht. Das BMP diente als Positivkontrolle, da es in zahlreichen früheren Studien osteoinduktive Eigenschaften gezeigt hat [231-233]. Die Auswertung wurde durch regelmäßige Röntgenkontrollen über einen Zeitraum von sechs bis acht Wochen durchgeführt. In der ersten Versuchsreihe wurden insgesamt 70 Scaffolds an 35 Versuchstieren untersucht. Die Implantation erfolgte in die distale Oberschenkelmuskulatur streckseitig an beiden unteren Extremitäten. In 60 % der implantierten Scaffolds im Behandlungsarm der BSPld wurden HO-Formationen mit einer durchschnittlichen Größe von 0,60 mm +/- 0,70 mm festgestellt. Diese waren im Vergleich zur Negativkontrolle (p = 0,04) sowie zur BSPhd-Gruppe (p < 0,05) insgesamt größer. Die ektopen Verknöcherungen der Positivkontrolle hatten eine durchschnittliche Größe von 3,19 mm +/- 1,24 mm. Im Vergleich zu den anderen Behandlungsarmen des Experiments waren diese signifikant größer (BSPld p < 0,05; BSPhd p < 0,05; Negativkontrolle p < 0,05). An Tag 14 war das maximale Größenwachstum der einzelnen heterotopen Ossifikationen sichtbar. Die Verknöcherungen nahmen im weiteren Verlauf ab und waren teilweise nicht mehr nachweisbar. Einige der HO blieben jedoch über Wochen hinweg in ihrer Größe konstant bis zum Zeitpunkt der Euthanasie der Versuchstiere. Unterschiede innerhalb der Versuchsgruppen könnten auf unterschiedliche Bindungskapazitäten der RGD-Sequenzen sowie der möglichen Zielzellen (z.B. Osteoblasten, Fibroblasten, mesenchymale Zellen) zurückzuführen sein. In der zweiten Versuchsreihe wurden insgesamt 12 Ratten mit je 4 Scaffolds operiert. Die Implantation der Kollagenschwämme erfolgte in die proximale Oberschenkel- und Unterschenkelmuskulatur beidseits. Nach drei Wochen zeigten weder konventionelle Radiologie noch µCT-Aufnahmen Hinweise auf ektope Ossifikationen in beiden BSP-Gruppen, sodass die Tiere nach 21 Tagen abgesetzt wurden. Die Ossifikationsrate für BSP lag bei 0 %. Die Lokalisation der Scaffolds war besonders für das niedrig dosierte BSP wichtig. Es gab einen signifikanten Unterschied in der Anzahl ektoper Verknöcherungen durch BSPld zwischen den zwei Versuchsreihen (p < 0,01). Heterotope Ossifikationen traten nur in der ersten Versuchsreihe im distalen Bereich des Musculus vastus lateralis auf. Diese Studie zeigt, dass BSP osteoinduktive Eigenschaften besitzt. Weitere Forschung könnte sich auf die optimale BSP-Konzentration sowie Platzierung der Knochengerüste konzentrieren. Zusätzlich sind histologische und immunhistochemische Untersuchungen erforderlich, um die knochenbildende Funktion des BSP weiter zu bewerten und mögliche Interaktionen sowie Prozesse auf Zellebene zu identifizieren. Auf Basis der derzeitigen Datenlage ist es möglich, dass BSP zukünftig im Rahmen therapeutischer Ansätze klinisch relevant wird.
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    Einfluss von körperlicher Aktivität auf Lebensqualität, Fatigue, Sarkopenie und Mortalität bei Patienten mit gastrointestinalen Tumoren
    (2025) Schulz, Mark Vincent; Möhler, Markus
    Die vorliegende Arbeit untersucht die Rolle körperlicher Aktivität auf Lebensqualität, Fatigue, Sarkopenie/Kachexie und Mortalität bei Patienten mit gastrointestinalen Tumoren. Eine systematische Literaturrecherche ergab 49 Studien, die in die Analyse miteinflossen. Diese Studien umfassen randomisiert-kontrollierte Studien (RCTs), Reviews und Meta-Analysen. Die Interventionen, teils kombiniert mit Ernährungs- und psychologischer Beratung, fanden in verschiedenen Therapiephasen statt. Die Ergebnisse zeigen, dass körperliche Aktivität, bei ausreichender Dauer und Intensität (150–300 Minuten/Woche), die Lebensqualität und Fatigue verbessert, vor allem bei Ösophagus-, Pankreas- und Kolonkarzinomen. Frühzeitige, multimodale Programme mit Ausdauer- und Krafttraining wirken präventiv gegen Sarkopenie/ Kachexie und senken das postoperative Komplikationsrisiko sowie die krebsspezifische Mortalität. Weitere Studien sind erforderlich, um spezifischere Empfehlungen für alle Tumorarten zu geben.
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