Determining the Neutrino Mass Hierarchy with the Precision IceCube Next Generation Upgrade (PINGU)

In this thesis, the development of a fast effective simulation for the planned PINGU experiment at the geographic South Pole is described, which will make a precision measurement of the atmospheric neutrino flux at low GeV energies. In this flux, the effects of neutrino oscillations in the matter potential of the Earth are visible, which will be observed by PINGU with unprecedented precision. Using the aforementioned simulation, PINGU’s expected precision in determining the relevant neutrino oscillation parameters and the neutrino mass hierarchy is calculated, incorporating a variety of parameters covering systematic uncertainties in the experimental outcome. The analysis is done in the framework of the Fisher Matrix technique, whose application to a particle physics experiment is novel. It allows for a fast and stable evaluation of the multi-dimensional parameter space and an easy combination of different experiments

New Computational Tools for Sample Purification and Early-Stage Data Processing in High-Resolution Cryo-Electron Microscopy

Large macromolecular protein complexes play an important role in the quest of un- derstanding life at a molecular level. For this endeavor, the highly-resolved 3D structure of a large complex and its changes, which are called conformational dy- namics, are of high interest due to their close relation to biological function. A pop- ular method to gain access to this information is cryo-electron microscopy. Here, biological samples are vitrified in their native buffer conditions and then im- aged in a transmission electron microscope. The large amount of recorded noisy images, called micrographs, are then subjected to a series of sophisticated, compu- tationally expensive algorithmic steps that include particle extraction, averaging of similar particle images, angular assignment and 3D reconstruction. While a growing amount of 3D structures determined by cryo EM reach resolutions that allow atomic model building, a large share of structures never reach that level of possible biolog- ical detail. In this thesis, improvements to two of the problems that can limit the resolution of structures are presented: Sample quality and elimination of suboptimal micro- graphs. First, a new software for simulation of density gradient centrifugation ex- periments, which is a popular method for sample purification, is presented that can aid users in finding the right conditions to optimize their purification proto- cols through new algorithmic approaches. This can lead to purer and more stable samples that improve the recorded images. Then, a new software for live processing and machine learning based classification of TEM images whose quality is judged live by a user is introduced. This software, called the Micrograph Quality Checker, is part of the COW, which is a novel single particle cryo EM image processing framework that covers the whole data analysis workflow. Elimination of unwanted data and collection of metadata in parallel to image acquisition can reduce the data overhead, improve computational speed and can also lead to higher resolution in the obtained structures due to the self-referential image processing

The KOALA-study: study protocol for a comprehensive study of cognitive biases in adolescent anorexia nervosa patients compared to healthy and clinical controls

BACKGROUND Anorexia nervosa (AN) is characterized by dysfunctional cognitions including cognitive biases at various levels of information processing. However, less is known about the specificity of these biases, i.e., if they occur for eating-disorder-related information alone or also for non-eating-disorder-related emotional information in AN patients (content-specificity) and if they are unique to individuals with AN or are also shown by individuals with other mental disorders (disorder-specificity). METHODS The present study systematically assesses cognitive biases in 12-18-year-old female adolescents with AN on three levels of information processing (attention, interpretation, and memory) and with regard to two types of information content (eating-disorder-related, i.e., stimuli related to body weight and shape, and non-eating-disorder-related). To address not only content- but also disorder-specificity, adolescents with AN will be compared not only to a healthy control group but also to a clinical control group (adolescents with major depression or particular anxiety disorders). Cognitive biases are assessed within a single experimental paradigm based on the Scrambled Sentences Task. During the task eye movements are recorded in order to assess attention biases while interpretation biases are derived from the behavioural outcome. An incidental free recall test afterwards assesses memory biases. We expect adolescents with AN to show more pronounced negative cognitive biases on all three levels of information processing and for both types of content compared to healthy adolescents. In addition, we expect the specificity of biases to translate into differential results for the two types of content: AN patients are expected to show stronger biases for disorder-related stimuli but similar or less pronounced biases for non-disorder-related stimuli compared to the clinical control group. DISCUSSION This is the first study to comprehensively assess cognitive biases in adolescents with AN. It will have essential implications not only for cognitive-behavioural models of AN but also for subsequent studies aiming to modify cognitive biases in this population, thereby addressing important maintaining factors already at an early stage of the disorder

Family, friends, and feelings: the role of relationships to parents and peers and alexithymia in adolescents with anorexia nervosa

Background Anorexia nervosa (AN) is associated with impairments in socio-emotional functioning, including difficulties in interpersonal relationships as well as alexithymia (difficulties identifying and describing one’s emotions). Although the onset of the disorder is mostly in adolescence, a developmental period in which interpersonal relationships to parents as well as peers undergo major changes, only few studies have investigated the quality of interpersonal relationships in adolescent AN patients. Furthermore, the mechanisms linking poor relationship quality to eating disorder psychopathology are not yet clarified, albeit some research suggests that alexithymia might play a pivotal role. The aims of the present study were investigating the quality of interpersonal relationships to parents and peers in adolescents with AN compared to healthy adolescents as well as exploring the mediating role of alexithymia in the association between relationship quality and eating disorder symptoms. Methods Self-report questionnaires were used to assess relationship quality (Inventory of Parent and Peer Attachment) and alexithymia (Toronto Alexithymia Scale) in 12–18 year old female adolescents with AN (n = 35) in comparison to healthy adolescents (n = 40). Results Adolescents with AN reported lower relationship quality to both of their parents and to peers compared to healthy controls. Relationship quality scores were negatively correlated to alexithymia as well as eating disorder symptoms. Alexithymia fully meditated the association between eating disorder symptoms and relationship quality to parents and partially mediated the association between eating disorder symptoms and relationship quality to peers. Conclusion The results indicate difficulties in interpersonal relationships among adolescents with AN and emphasize the role of peer relationships for adolescents’ eating disorder psychopathology. Alexithymia seems to play an important role in explaining the link between quality of relationships and eating disorder psychopathology. Results suggest that treatment should not only focus on family relationships but also address relationships to peers as well as adolescents’ competence in identifying and dealing with their emotions

An exploratory study of bug-introducing changes: what happens when bugs are introduced in open source software?

Context: Many studies consider the relation between individual aspects and bug-introduction, e.g., software testing and code review. Due to the design of the studies the results are usually only about correlations as interactions or interventions are not considered. Objective: Within this study, we want to narrow this gap and provide a broad empirical view on aspects of software development and their relation to bug-introducing changes. Method: We consider the bugs, the type of work when the bug was introduced, aspects of the build process, code review, software tests, and any other discussion related to the bug that we can identify. We use a qualitative approach that first describes variables of the development process and then groups the variables based on their relations. From these groups, we can induce how their (pair-wise) interactions affect bug-introducing changes.Comment: Registered Report with Continuity Acceptance (CA) for submission to Empirical Software Engineering granted by RR-Committee of the MSR'2

Understanding issues related to personal data and data protection in open source projects on GitHub

Context: Data protection regulations such as the GDPR and the CCPA affect how software may handle the personal data of its users and how consent for handling of such data may be given. Prior literature focused on how this works in operation, but lacks a perspective of the impact on the software development process. Objective: Within our work, we will address this gap and explore how software development itself is impacted. We want to understand which data protection-related issues are reported, who reports them, and how developers react to such issues. Method: We will conduct an exploratory study based on issues that are reported with respect to data protection in open source software on GitHub. We will determine the roles of the actors involved, the status of such issues, and we use inductive coding to understand the data protection issues. We qualitatively analyze the issues as part of the inductive coding and further explore the reasoning for resolutions. We quantitatively analyze the relation between the roles, resolutions, and data protection issues to understand correlations.Comment: Registered Report with Continuity Acceptance (CA) for submission to Empirical Software Engineering granted by RR-Committee of the MSR'2

Diagnosing increased muscle activity and occlusal stress in temporo mandibular joint syndrome with Periotest

Bei 38 Patienten mit funktioneller Myoarthropathie und 25 Probanden einer Kontrollgruppe mit parodontal gesundem Gebiß wurden Periotestwerte bestimmt. Die Periotestmessungen wurden sowohl ohne Okklusalkontakt als auch in maximaler Interkuspidation durchgeführt. Der Vergleich der Patienten mit Myoarthropathie und der Probanden ohne Muskelbefund ergab signifikante Unterschiede auf dem 1 %.Niveau sowohl bei Periotestwerten ohne Okklusalkontakt als auch vor allem bei den Differenzen der Periotestwerte ohne Okklusalkontakt und der Periotestwerte in maximaler Interkuspidation. Dies betraf vor allem die Prämolaren und die ersten Molaren. Bei Probanden ohne Muskelbefund ergaben sich Periotestwertdifferenzen zwischen -2,0 und -3,4 (Vertrauensbereiche). Bei Patienten mit Muskelbefund waren die Periotestwerte mit -5,4 ... -7,9 ausgeprägter negativ. Punktbiserielle Korrelationskoeffizienten ergaben einen besonders ausgeprägten Zusammenhang zwischen Periotestwertdifferenzen und der Aktivität der aduktorischen Kaumuskulatur.Periotest measurements were carried out not in occlusal contact to the antagonist tooth and under maximum habitual occlusion in 38 patients with functional temporo mandibular joint syndrome and in a control group of 25 test subjects with periodontally sound dentition. A comparison between the patients with temporo mandibular joint syndrome and test subjects without muscle findings showed significant (1) variations both for Periotest measurements not in occlusal contact and particularly for Periotest value differences of the measurement carried out under maximum habitual occlusion and the measurement not in occlusal contact. This was especially true for the premolars and the first molars. In the test subjects without muscle findings, Periotest value differences were between -2.0 and -3.4 (confidence intervals). In patients with muscle findings, the Periotest value differences of -5.4 to -7.9 were greater. Point-biserial correlation coefficients showed a particularly pronounced correlation between Periotest value differences and sensitivity to pressure in the aductory masticatory muscles