Gene Set Enrichment and Projection: A Computational Tool for Knowledge Discovery in Transcriptomes

Explaining the mechanism behind a genetic disease involves two phases, collecting and analyzing data associated to the disease, then interpreting those data in the context of biological systems. The objective of this dissertation was to develop a method of integrating complementary datasets surrounding any single biological process, with the goal of presenting the response to a signal in terms of a set of downstream biological effects. This dissertation specifically tests the hypothesis that computational projection methods overlaid with domain expertise can direct research towards relevant systems-level signals underlying complex genetic disease. To this end, I developed a software algorithm named Geneset Enrichment and Projection Displays (GSEPD) that can visualize multidimensional genetic expression to identify the biologically relevant gene sets that are altered in response to a biological process. This dissertation highlights a problem of data interpretation facing the medical research community, and shows how computational sciences can help. By bringing annotation and expression datasets together, a new analytical and software method was produced that helps unravel complicated experimental and biological data. The dissertation shows four coauthored studies where the experts in their field have desired to annotate functional significance to a gene-centric experiment. Using GSEPD to show inherently high dimensional data as a simple colored graph, a subspace vector projection directly calculated how each sample behaves like test conditions. The end-user medical researcher understands their data as a series of somewhat-independent subsystems, and GSEPD provides a dimensionality reduction for high throughput experiments of limited sample size. Gene Ontology analyses are accessible on a sample-to-sample level, and this work highlights not just the expected biological systems, but many annotated results available in vast online databases

A finder and representation system for knowledge carriers based on granular computing

In one of his publications Aristotle states ”All human beings by their nature desire to know” [Kraut 1991]. This desire is initiated the day we are born and accompanies us for the rest of our life. While at a young age our parents serve as one of the principle sources for knowledge, this changes over the course of time. Technological advances and particularly the introduction of the Internet, have given us new possibilities to share and access knowledge from almost anywhere at any given time. Being able to access and share large collections of written down knowledge is only one part of the equation. Just as important is the internalization of it, which in many cases can prove to be difficult to accomplish. Hence, being able to request assistance from someone who holds the necessary knowledge is of great importance, as it can positively stimulate the internalization procedure. However, digitalization does not only provide a larger pool of knowledge sources to choose from but also more people that can be potentially activated, in a bid to receive personalized assistance with a given problem statement or question. While this is beneficial, it imposes the issue that it is hard to keep track of who knows what. For this task so-called Expert Finder Systems have been introduced, which are designed to identify and suggest the most suited candidates to provide assistance. Throughout this Ph.D. thesis a novel type of Expert Finder System will be introduced that is capable of capturing the knowledge users within a community hold, from explicit and implicit data sources. This is accomplished with the use of granular computing, natural language processing and a set of metrics that have been introduced to measure and compare the suitability of candidates. Furthermore, are the knowledge requirements of a problem statement or question being assessed, in order to ensure that only the most suited candidates are being recommended to provide assistance

Deconstructing Events: The Neural Bases for Space, Time, and Causality

Space, time, and causality provide a natural structure for organizing our experience. These abstract categories allow us to think relationally in the most basic sense; understanding simple events requires one to represent the spatial relations among objects, the relative durations of actions or movements, and the links between causes and effects. The present fMRI study investigates the extent to which the brain distinguishes between these fundamental conceptual domains. Participants performed a 1-back task with three conditions of interest (space, time, and causality). Each condition required comparing relations between events in a simple verbal narrative. Depending on the condition, participants were instructed to either attend to the spatial, temporal, or causal characteristics of events, but between participants each particular event relation appeared in all three conditions. Contrasts compared neural activity during each condition against the remaining two and revealed how thinking about events is deconstructed neurally. Space trials recruited neural areas traditionally associated with visuospatial processing, primarily bilateral frontal and occipitoparietal networks. Causality trials activated areas previously found to underlie causal thinking and thematic role assignment, such as left medial frontal and left middle temporal gyri, respectively. Causality trials also produced activations in SMA, caudate, and cerebellum; cortical and subcortical regions associated with the perception of time at different timescales. The time contrast, however, produced no significant effects. This pattern, indicating negative results for time trials but positive effects for causality trials in areas important for time perception, motivated additional overlap analyses to further probe relations between domains. The results of these analyses suggest a closer correspondence between time and causality than between time and space

Aggregated search: a new information retrieval paradigm

International audienceTraditional search engines return ranked lists of search results. It is up to the user to scroll this list, scan within different documents and assemble information that fulfill his/her information need. Aggregated search represents a new class of approaches where the information is not only retrieved but also assembled. This is the current evolution in Web search, where diverse content (images, videos, ...) and relational content (similar entities, features) are included in search results. In this survey, we propose a simple analysis framework for aggregated search and an overview of existing work. We start with related work in related domains such as federated search, natural language generation and question answering. Then we focus on more recent trends namely cross vertical aggregated search and relational aggregated search which are already present in current Web search

A New Grammar of Images: Werner Herzog and the Contemporary Philosophy of Cinema

In his central mission of working on “a new grammar of images,” the German film director Werner Herzog presents a challenge to the philosophy of cinema. Pairing Herzog’s work with Deleuzian film theory, I argue against the prevalent secondary literature that Herzog’s oeuvre engages with an anti-romantic and non-ironic material philosophy in order to provide ethical challenges to a contemporary, connected world. Specifically focusing on spatiotemporal formations derived from empirical science, I demonstrate that Herzog’s approach to cinema utilizes a four-tiered semiotic that is at its core not merely a film theory, but rather an entire material philosophy of nature with profound ethical and political implications

Discovering novel mechanisms of human cortical development & disease using in vivo mouse model and in vitro human-derived cerebral organoids

This thesis combines three research studies with the common interest of identifying novel mechanisms underlying human cortical development. This aim is pursued from different angles, always basing the investigations on human induced pluripotent stem cell-derived 2D and 3D in vitro model systems that are partly combined with in vivo studies in the developing mouse cortex. Namely, in the pieces of work combined here, we 1) bring to light a neurodevelopmental role of a gene already implicated in adult nervous system function, 2) discover a novel mechanism that fine-tunes human neurogenesis, and 3) identify a novel gene whose mutations lead to a malformation of cortical development. The entirety of this work thus adds several aspects to the existing knowledge. In the first study, we identified a neurodevelopmental function of a gene mutated in patients with the progressive gait disorder hereditary spastic paraplegia (HSP). In this group of inherited neurodegenerative diseases, mutations in lipid, mitochondrial, cytoskeletal or transport proteins lead to degeneration of primary motor neurons, which, due to the length of their axons, are particularly sensitive to disruption of these processes. Here, were generated cerebral organoids (COs) derived from HSP patients with mutations in SPG11 coding for spatacsin. Previous work had shown impaired proliferation of SPG11 patient-derived neural progenitor cells (NPCs). We found a proliferation defect also in CO NPCs, leading to a thinner progenitor zone and premature neurogenesis due to increased asymmetric progenitor divisions, along with smaller size of patient-derived COs. Molecularly, we found a decrease in deactivated GSK3β and increase in P-βcatenin at the basis of the observed proliferation/neurogenesis imbalance. We thus confirmed the neurodevelopmental role of SPG11 that had previously been suggested from 2D human in vitro findings. Both the observed reduction in proliferating progenitors and in organoid size were rescued through inhibition of GSK3β, with the Food and Drug Administration (FDA) approved compound tideglusib only affecting patient COs. These rescue experiments thus stressed the opportunity that COs represent for drug testing and translation of findings to precision medicine. In the second study, we investigated the role of a novel posttranslational modification (PTM) termed AMPylation in neurogenesis. Using a novel probe for the detection of AMPylated proteins and a combination of mass spectrometry-based proteomics, immunohistochemistry, and acute interference with the expression of the AMPylating enzyme, we made several interesting findings: AMPylation takes place on a cell type-specific set of proteins, is responsive to the predominant environmental condition, and both AMPylator and targets localize to cell type-specific intracellular localizations. During the process of neuronal differentiation, the set of AMPylated proteins is completely remodeled, with a very high number of unique targets in neurons. These include metabolic enzymes as in all analyzed cell types and, additionally and specifically, cytoskeletal and motor proteins. Cytoskeletal and motor proteins in neural progenitors and neurons are known to be differentially modified by several PTMs whose correct establishment is highly important during neurodevelopment; AMPylation may thus be an additional one. To assess the role of AMPylation in neurodevelopment, we manipulated the expression of the AMPylating enzyme FICD in COs. Downregulation kept cells in a proliferating progenitor state, whereas overexpression increased neurogenesis. We thus suggest AMPylation as a novel PTM fine-tuning neurogenesis. The third study focused on the identification of new mechanisms underlying cortical malformations, aiming at a better understanding of how the human brain develops. In patients with periventricular heterotopia (PH), a neuronal migration disorder in which a subset of neurons fail to migrate to the developing cortical plate and instead form nodules of grey matter lining the lateral ventricles as their site of production, biallelic mutations in endothelin converting enzyme 2 (ECE2) were identified as candidate causative. Combining in vitro and in vivo models, we found a role for ECE2 in neuronal migration and cortical development. In the absence of ECE2, several processes of general importance to proper neuronal migration were disrupted. Namely, changes in progenitor cell polarity and morphology and in apical adherens junctions led to their delamination, restricting their use as a scaffold for neuronal migration. This resulted in ectopic neurons reminiscent of nodules in PH. Besides a deregulation of cytoskeletal, polarity, and apical adhesion proteins, extracellular matrix (ECM) proteins were reduced in absence of ECE2, suggesting its role in ECM production and underlining the necessity of ECM components for proper neuronal migration during cortical development. Moreover, we detected differential phosphorylation of several cytoskeletal, motor and adhesion proteins in the absence of ECE2, which is functionally in line with the former findings and suggests an additional involvement of ECE2 in the regulation of PTMs. Altogether, the studies presented here underline the heterogeneity and complexity of pathways and mechanisms that contribute to human cortical development and its disorders, converging on the regulation of cytoskeleton and transport within the involved cells and of the ECM on their outside

Student learning and cognition in cooperative small groups : towards a fourth metaphor of human learning

Research into the benefits of cooperative learning has focussed most attention onto a social psychological perspective with the result that the putative cognitive benefits of these strategies have not been thoroughly researched and clearly delineated. One consequence of this research focus has been that cooperative learning strategies are not always adopted by teachers and included permanently into their regular classroom practice, thereby possibly denying some students the potential for cognitive gain. This study was conceived originally as an investigation into the claimed cognitive benefits of small-group cooperative learning from a cognitive perspective but the investigation of the cooperative learning literature also led to an investigation of the general learning literature base. Recent research suggested that human learning might not have been described adequately by the earlier perspectives. Some authors contended that a fourth metaphor of human learning may be emerging from the socio-cultural perspectives. Investigating how students learn in cooperative situations was seen as a potential vehicle for the wider investigation of a fourth metaphor. It was against this background that the present study was undertaken. Learning was not seen in terms of a dichotomy between the main cognitivist and socially based perspectives so a pluralist approach was adopted in this study in an attempt to reconcile some of the differences between the main perspectives. Process-product research has been criticised for providing a narrow view of the classroom lives of students. Additionally, critics of laboratory-based research have argued for research to regain its connection with real classroom settings. Given the contentions of several authors, this study was conceived as non-positivist, naturalistic and pluralist within the post-modernist era. Five groups of students at two schools were recruited for this qualitative case study. The students\u27 learning from five purpose-designed lessons was tracked through their transcribed discussions and their recall in learning journals . Journal data were collected as much as twelve months after the last lesson was completed, enabling the longitudinal tracking of student learning. A major finding of the research was the strong mediational effects on student learning of the classroom context and the group within the classroom. The nature of student talk also impacted strongly upon student learning. Evidence was found of both individual and social construction of knowledge. Knowledge sometimes seemed to appear initially as a group construct but was later modified significantly by the students\u27 individual minds. Although all knowledge originated in socio-cultural contexts, usually through the ultimate human social semiotic of language, the final form of the knowledge appeared highly individual and idiosyncratic. The idiosyncratic nature of the students\u27 learning led the researcher to posit that knowledge resided in the individual neural structures of the brain. This mind-as-brain proposition was advanced as a contribution towards a fourth metaphor of human learning. The findings suggested several implications for teachers about the recommended procedures for small-group cooperative learning. Implications for research included further neuroscience investigations into human learning because of the potential for this kind of research to inform practice