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With the advent of highthroughput sequencing (HTS), profiling immunoglobulin (IG) repertoires has become an essential part of immunological research. The dissection of IG repertoires promises to transform our understanding of the adaptive immune system dynamics. Advances in sequencing technology now also allow the use of the Ion Torrent Personal Genome Machine (PGM) to cover the full length of IG mRNA transcripts. The applications of this benchtop scale HTS platform range from identification of new therapeutic antibodies to the deconvolution of malignant B cell tumors. In the context of this thesis, the usability of the PGM is assessed to investigate the IG heavy chain (IGH) repertoires of animal models. First, an innovate bioinformatics approach is presented to identify antigendriven IGH sequences from bulk sequenced bone marrow samples of transgenic humanized rats, expressing a human IG repertoire (OmniRatTM). We show, that these rats mount a convergent IGH CDR3 response towards measles virus hemagglutinin protein and tetanus toxoid, with high similarity to human counterparts. In the future, databases could contain all IGH CDR3 sequences with known specificity to mine IG repertoire datasets for past antigen exposures, ultimately reconstructing the immunological history of an individual. Second, a unique molecular identifier (UID) based HTS approach and network property analysis is used to characterize the CLLlike CD5+ B cell expansion of A20BKO mice overexpressing a natural short splice variant of the CYLD gene (A20BKOsCYLDBOE). We could determine, that in these mice, overexpression of sCYLD leads to unmutated subvariant of CLL (UCLL). Furthermore, we found that this short splice variant is also seen in human CLL patients highlighting it as important target for future investigations. Third, the UID based HTS approach is improved by adapting it to the PGM sequencing technology and applying a custommade data processing pipeline including the ImMunoGeneTics (IMGT) database error detection. Like this, we were able to obtain correct IGH sequences with over 99.5% confidence and correct CDR3 sequences with over 99.9% confidence. Taken together, the results, protocols and sample processing strategies described in this thesis will improve the usability of animal models and the Ion Torrent PGM HTS platform in the field if IG repertoire research.
Academic self-concept (ASC) is comprised of individual perceptions of one- own academic ability. In a cross-sectional quasi-representative sample of 3,779 German elementary school children in grades 1 to 4, we investigated (a) the structure of ASC, (b) ASC profile formation, an aspect of differentiation that is reflected in lower correlations between domain-specific ASCs with increasing grade level, (c) the impact of (internal) dimensional comparisons of one- own ability in different school subjects for profile formation of ASC, and (d) the role played by differences in school grades between subjects for these dimensional comparisons. The nested Marsh/Shavelson model, with general ASC at the apex and math, writing, and reading ASC as specific factors nested under general ASC fitted the data at all grade levels. A first-order factor model with math, writing, reading, and general ASCs as correlated factors provided a good fit, too. ASC profile formation became apparent during the first two to three years of school. Dimensional comparisons across subjects contributed to ASC profile formation. School grades enhanced these comparisons, especially when achievement profiles were uneven. In part, findings depended on the assumed structural model of ASCs. Implications for further research are discussed with special regard to factors influencing and moderating dimensional comparisons.
Background: We evaluated depression and social isolation assessed at time of waitlisting as predictors of survival in heart transplant (HTx) recipients. Methods and Results: Between 2005 and 2006, 318 adult HTx candidates were enrolled in the Waiting for a New Heart Study, and 164 received transplantation. Patients were followed until February 2013. Psychosocial characteristics were assessed by questionnaires. Eurotransplant provided medical data at waitlisting, transplantation dates, and donor characteristics; hospitals reported medical data at HTx and date of death after HTx. During a median followâ€up of 70 months (<1"93 months postâ€HTx), 56 (38%) of 148 transplanted patients with complete data died. Depression scores were unrelated to social isolation, and neither correlated with disease severity. Higher depression scores increased the risk of dying (hazard ratio=1.07, 95% confidence interval, 1.01, 1.15, P=0.032), which was moderated by social isolation scores (significant interaction term; hazard ratio = 0.985, 95% confidence interval, 0.973, 0.998; P=0.022). These findings were maintained in multivariate models controlling for covariates (P values 0.020"0.039). Actuarial 1â€year/5â€year survival was best for patients with low depression who were not socially isolated at waitlisting (86% after 1 year, 79% after 5 years). Survival of those who were either depressed, or socially isolated or both, was lower, especially 5 years posttransplant (56%, 60%, and 62%, respectively). Conclusions: Low depression in conjunction with social integration at time of waitlisting is related to enhanced chances for survival after HTx. Both factors should be considered for inclusion in standardized assessments and interventions for HTx candidates. We evaluated depression and social isolation assessed at time of waitlisting as predictors of survival in heart transplant (HTx) recipients.\r\n\r\nMethods and Results: Between 2005 and 2006, 318 adult HTx candidates were enrolled in the Waiting for a New Heart Study, and 164 received transplantation. Patients were followed until February 2013. Psychosocial characteristics were assessed by questionnaires. Eurotransplant provided medical data at waitlisting, transplantation dates, and donor characteristics; hospitals reported medical data at HTx and date of death after HTx. During a median followâ€up of 70 months (<1"93 months postâ€HTx), 56 (38%) of 148 transplanted patients with complete data died. Depression scores were unrelated to social isolation, and neither correlated with disease severity. Higher depression scores increased the risk of dying (hazard ratio=1.07, 95% confidence interval, 1.01, 1.15, P=0.032), which was moderated by social isolation scores (significant interaction term; hazard ratio = 0.985, 95% confidence interval, 0.973, 0.998; P=0.022). These findings were maintained in multivariate models controlling for covariates (P values 0.020"0.039). Actuarial 1â€year/5â€year survival was best for patients with low depression who were not socially isolated at waitlisting (86% after 1 year, 79% after 5 years). Survival of those who were either depressed, or socially isolated or both, was lower, especially 5 years posttransplant (56%, 60%, and 62%, respectively).
Numerous RCTs demonstrate that cognitive behavioral therapy (CBT) for depression is effective. However, these findings are not necessarily representative of CBT under routine care conditions. Routine care studies are not usually subjected to comparable standardizations, e.g. often therapists may not follow treatment manuals and patients are less homogeneous with regard to their diagnoses and sociodemographic variables. Results on the transferability of findings from clinical trials to routine care are sparse and point in different directions. As RCT samples are selective due to a stringent application of inclusion/exclusion criteria, comparisons between routine care and clinical trials must be based on a consistent analytic strategy. The present work demonstrates the merits of propensity score matching (PSM), which offers solutions to reduce bias by balancing two samples based on a range of pretreatment differences. The objective of this dissertation is the investigation of the transferability of findings from RCTs to routine care settings.
GIS – what can and what can’t it say about social relations in adaptation to urban flood risk?
(2017)
Urban flooding cannot be avoided entirely and in all areas, particularly in coastal cities. Therefore adaptation to the growing risk is necessary. Geographical Information Systems (GIS) based knowledge on risk informs location-based approach to adaptation to climate risk. It allows managing city- wide coordination of adaptation measures, reducing adverse impacts of local strategies on neighbouring areas to the minimum. Quantitative assessments dominate GIS applications in flood risk management, for instance to demonstrate the distribution of people and assets in a flood prone area. Qualitative, participatory approaches to GIS are on the rise but have not been applied in the context of flooding yet. The overarching research question of this working paper is: what can GIS, and what can it not say about relationships / social relations in adaptation to urban flood risk? The use of GIS in risk mapping has exposed environmental injustices. Applications of GIS further allow model- ling future flood risk in function of demographic and land use changes, and combining it with decision support systems (DSS). While such GIS applications provide invaluable information for urban planners steering adaptation they however fall short on revealing the social relations that shape individual and household adaptation decisions. The relevance of networked social relations in adaptation to flood risk has been demonstrated in case studies, and extensively in the literature on organizational learning and adaptation to change. The purpose of this literature review is to identify the type of social relations that shape adaptive capacities towards urban flood risk which can- not be identified in a conventional GIS application.
Dysfunctional eating behavior is a major risk factor for developing all sorts of eating disorders. Food craving is a concept that may help to understand better why and how these and other eating disorders become chronic conditions through non homeastatically-driven mechanisms. As obesity affects people worldwide, cultural differences must be acknowledged to apply proper therapeutic strategies. In this work, we adapted the Food Craving Inventory (FCI) to the German population. We performed a factor analysis of an adaptation of the original FCI in a sample of 326 men and women. We could replicate the factor structure of the FCI on a German population.rnThe factor extraction procedure produced a factor solution that reproduces the fourfactors described in the original inventory, the FCI. Our instrument presents high internal consistency, as well as a significant correlation with measures of convergent and discriminant validity. The FCI-Deutsch (FCI-DE) is a valid instrument to assess craving for particular foods in Germany, and it could, therefore, prove useful in the clinical and research practice in the field of obesity and eating behaviors.
Interaction between the Hypothalamic-Pituitary-Adrenal Axis and the Circadian Clock System in Humans
(2017)
Rotation of the Earth creates day and night cycles of 24 h. The endogenous circadian clocks sense these light/dark rhythms and the master pacemaker situated in the suprachiasmatic nucleus of the hypothalamus entrains the physical activities according to this information. The circadian machinery is built from the transcriptional/translational feedback loops generating the oscillations in all nucleated cells of the body. In addition, unexpected environmental changes, called stressors, also challenge living systems. A response to these stimuli is provided immediately via the autonomic-nervous system and slowly via the hypothalamus"pituitary"adrenal (HPA) axis. When the HPA axis is activated, circulating glucocorticoids are elevated and regulate organ activities in order to maintain survival of the organism. Both the clock and the stress systems are essential for continuity and interact with each other to keep internal homeostasis. The physiological interactions between the HPA axis and the circadian clock system are mainly addressed in animal studies, which focus on the effects of stress and circadian disturbances on cardiovascular, psychiatric and metabolic disorders. Although these studies give opportunity to test in whole body, apply unwelcome techniques, control and manipulate the parameters at the high level, generalization of the results to humans is still a debate. On the other hand, studies established with cell lines cannot really reflect the conditions occurring in a living organism. Thus, human studies are absolutely necessary to investigate mechanisms involved in stress and circadian responses. The studies presented in this thesis were intended to determine the effects of cortisol as an end-product of the HPA axis on PERIOD (PER1, PER2 and PER3) transcripts as circadian clock genes in healthy humans. The expression levels of PERIOD genes were measured under baseline conditions and after stress in whole blood. The results demonstrated here have given better understanding of transcriptional programming regulated by pulsatile cortisol at standard conditions and short-term effects of cortisol increase on circadian clocks after acute stress. These findings also draw attention to inter-individual variations in stress response as well as non-circadian functions of PERIOD genes in the periphery, which need to be examined in details in the future.
Long-Term Memory Updating: The Reset-of-Encoding Hypothesis in List-Method Directed Forgetting
(2017)
People- memory for new information can be enhanced by cuing them to forget older information, as is shown in list-method directed forgetting (LMDF). In this task, people are cued to forget a previously studied list of items (list 1) and to learn a new list of items (list 2) instead. Such cuing typically enhances memory for the list 2 items and reduces memory for the list 1 items, which reflects effective long-term memory updating. This review focuses on the reset-of-encoding (ROE) hypothesis as a theoretical explanation of the list 2 enhancement effect in LMDF. The ROE hypothesis is based on the finding that encoding efficacy typically decreases with number of encoded items and assumes that providing a forget cue after study of some items (e.g., list 1) resets the encoding process and makes encoding of subsequent items (e.g., early list 2 items) as effective as encoding of previously studied (e.g., early list 1) items. The review provides an overview of current evidence for the ROE hypothesis. The evidence arose from recent behavioral, neuroscientific, and modeling studies that examined LMDF on both an item and a list level basis. The findings support the view that ROE plays a critical role for the list 2 enhancement effect in LMDF. Alternative explanations of the effect and the generalizability of ROE to other experimental tasks are discussed.
Background: Psychotherapy is successful for the majority of patients , but not for every patient. Hence, further knowledge is needed on how treatments should be adapted for those who do not profit or deteriorate. In the last years prediction tools as well as feedback interventions were part of a trend to more personalized approaches in psychotherapy. Research on psychometric prediction and feedback into ongoing treatment has the potential to enhance treatment outcomes, especially for patients with an increased risk of treatment failure or drop-out.rnMethods/design: The research project investigates in a randomized controlled trial the effectiveness as well as moderating and mediating factors of psychometric feedback to therapists. In the intended study a total of 423 patients, who applied for a cognitive-behavioral therapy at the psychotherapy clinic of the University Trier and suffer from a depressive and/or an anxietyrndisorder (SCID interviews), will be included. The patients will be randomly assigned either to one therapist as well as to one of two intervention groups (CG, IG2). An additional intervention group (IG1) will be generated from an existing archival data set via propensity score matching. Patients of the control group (CG; n = 85) will be monitored concerning psychological impairment but therapists will not be provided with any feedback about the patients assessments. In both intervention groups (IG1: n = 169; IG2: n = 169) the therapists are provided with feedback about the patients self-evaluation in a computerized feedback portal. Therapists of the IG2 will additionally be provided with clinical support tools, which will be developed in thisrnproject, on the basis of existing systems. Therapists will also be provided with a personalized treatment recommendation based on similar patients (Nearest Neighbors) at the beginning of treatment. Besides the general effectiveness of feedback and the clinical support tools for negatively developing patients, further mediating and moderating variables on this feedback effectrnshould be examined: treatment length, frequency of feedback use, therapist effects, therapist- experience, attitude towards feedback as well as congruence of therapist-andpatient- evaluation concerning the progress. Additional procedures will be implemented to assess treatment adherence as well as the reliability of diagnosis and to include it into the analyses.rnDiscussion: The current trial tests a comprehensive feedback system which combines precision mental health predictions with routine outcome monitoring and feedback tools in routine outpatient psychotherapy. It also adds to previous feedback research a stricter design by investigating another repeated measurement CG as well as a stricter control of treatment integrity. It also includes a structured clinical interview (SCID) and controls for comorbidity (within depression and anxiety). This study also investigates moderators (attitudes towards, use of the feedback system, diagnoses) and mediators (therapists" awareness of negative change and treatment length) in one study.
The search for relevant determinants of knowledge acquisition has a long tradition in educational research, with systematic analyses having started over a century ago. To date, a variety of relevant environmental and learner-related characteristics have been identified, providing a wide body of empirical evidence. However, there are still some gaps in the literature, which are highlighted in the current dissertation. The dissertation includes two meta-analyses summarizing the evidence on the effectiveness of electrical brain stimulation and the effects of prior knowledge on later learning outcomes and one empirical study employing latent profile transition analysis to investigate the changes in conceptual knowledge over time. The results from the three studies demonstrate how learning outcomes can be advanced by input from the environment and that they are highly related to the students" level of prior knowledge. It is concluded that the effects of environmental and learner-related variables impact both the biological and cognitive processes underlying knowledge acquisition. Based on the findings from the three studies, methodological and practical implications are provided, followed by an outline of four recommendations for future research on knowledge acquisition.