A Conceptual Model of Exploration Wayfinding: An Integrated Theoretical Framework and Computational Methodology

This thesis is an attempt to integrate contending cognitive approaches to modeling wayfinding behavior. The primary goal is to create a plausible model for exploration tasks within indoor environments. This conceptual model can be extended for practical applications in the design, planning, and Social sciences. Using empirical evidence a cognitive schema is designed that accounts for perceptual and behavioral preferences in pedestrian navigation. Using this created schema, as a guiding framework, the use of network analysis and space syntax act as a computational methods to simulate human exploration wayfinding in unfamiliar indoor environments. The conceptual model provided is then implemented in two ways. First of which is by updating an existing agent-based modeling software directly. The second means of deploying the model is using a spatial interaction model that distributed visual attraction and movement permeability across a graph-representation of building floor plans

\u3ci\u3eDrosophila\u3c/i\u3e Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu