Direct Approach or Detour: A Comparative Model of Inhibition and Neural Ensemble Size in Behavior Selection

Organisms must cope with different risk/reward landscapes in their ecological niche. Hence, species have evolved behavior and cognitive processes to optimally balance approach and avoidance. Navigation through space, including taking detours, appears also to be an essential element of consciousness. Such processes allow organisms to negotiate predation risk and natural geometry that obstruct foraging. One aspect of this is the ability to inhibit a direct approach toward a reward. Using an adaptation of the well-known detour paradigm in comparative psychology, but in a virtual world, we simulate how different neural configurations of inhibitive processes can yield behavior that approximates characteristics of different species. Results from simulations may help elucidate how evolutionary adaptation can shape inhibitive processing in particular and behavioral selection in general. More specifically, results indicate that both the level of inhibition that an organism can exert and the size of neural populations dedicated to inhibition contribute to successful detour navigation. According to our results, both factors help to facilitate detour behavior, but the latter (i.e., larger neural populations) appears to specifically reduce behavioral variation.

Extrusioncutter : a novel system for generating interactive context-preserving cutaways of anatomical surface meshes

This thesis presents ExtrusionCutter - a novel 3D visualization tool that enables users to create complex, context-preserving cutaways of anatomical surface meshes. To accomplish this, a "paint-roller" interaction metaphor has been developed that allows users to extrude an editable cutting mesh along the natural geometry of an occluding surface. This virtual analogy of a familiar real-world action not only facilitates the removal of occluding surfaces, but also creates a user-defined region parameterization which makes it possible to also generate an effective contextual outline view of the removed material. This thesis will demonstrate how the paint roller interaction metaphor has been implemented to facilitate the creation of multiple editable cutaway types on 3D anatomical surface meshes. Additionally, it will show that the resulting cutaway views are capable of exposing occluded parts while still maintaining their context in the visualization.

Extrusioncutter : a novel system for generating interactive context-preserving cutaways of anatomical surface meshes

This thesis presents ExtrusionCutter - a novel 3D visualization tool that enables users to create complex, context-preserving cutaways of anatomical surface meshes. To accomplish this, a "paint-roller" interaction metaphor has been developed that allows users to extrude an editable cutting mesh along the natural geometry of an occluding surface. This virtual analogy of a familiar real-world action not only facilitates the removal of occluding surfaces, but also creates a user-defined region parameterization which makes it possible to also generate an effective contextual outline view of the removed material. This thesis will demonstrate how the paint roller interaction metaphor has been implemented to facilitate the creation of multiple editable cutaway types on 3D anatomical surface meshes. Additionally, it will show that the resulting cutaway views are capable of exposing occluded parts while still maintaining their context in the visualization.

On comprehensive analysis of root canal shaping ability of three endodontic files of different kinematics

Infection of the tooth’s root canal requires what is called root canal treatment (RTC). The most important part of endodontic treatment is to shape the root canal and remove its infected portion using endodontic files of various protocols, kinematics and designs that suit the particular geometry. Cleaning and Shaping the canal efficiently remove the root canal bacterial biofilms or tissue remnants while keeping its natural geometry. The result is determined by shaping the ability of the relevant endodontic file. In the available literature, no norm has been established for the measurement of various endodontic files’ ability to do effective shaping. We present in this study a method to analyse and measure the shaping ability of endodontic files of three different kinematics.

RGB Colors and Ecological Optics

Object color space is highly structured due to optical constraints (radiant power non-negative, reflectance factors between zero and unity) and ecological context (daylight illuminant). In this setting trichromacy induces a natural geometry through a unique spectral tripartition. Different from null-context colorimetry, one gains two desirable relations: The colorimetric coordinates are coarse-grained spectral reflectance factors and there is a direct link to color experiences, since RGB–coordinates provide ostensive definitions. The framework allows one to deal with subtractive color mixture, source variation, effects of metamerism and relations between scenes and image data in a unified, structured manner. In ecological contexts, colors are effectively object properties. The formal framework is linear algebra and convex geometry. Applications in human biology, computer graphics, design, etc., are immediate.

On the Reaction of 2,5-Dihydroxy-[1,4]-benzoquinone with Diamines – Strain-induced Reactivity Effects

: The regioselectivity of the reaction of 2,5-dihydroxy-[1,4]-benzoquinone (DHBQ) with diamines could not be explained satisfactorily so far. In general, the reaction products can be derived from the tautomeric ortho-quinoid structure of a hypothetical 4,5-dihydroxy-[1,2]-benzoquinone. However, both aromatic and aliphatic 1,2-diamines form in some cases phenazines, formally by diimine formation on the quinoid carbonyl groups, and in other cases the corresponding 1,2- diamino-[1,2]-benzoquinones, by nucleophilic substitution of the OH groups, the regioselectivity apparently not following any discernible pattern. The reactivity was now explained by an adapted theory of strain-induced bond localization (SIBL). Here, the preservation of the "natural" geometry of the two quinoid C–C double bonds (C3=C4 and C5=C6) as well as the N–N distance of the co-reacting diamine are crucial. A decrease of the annulation angle sum (N–C4–C5 + C4–C5–N) is tolerated well and the 4,5-diamino-ortho-quinones, having relatively short N–N spacings are formed. An increase in the angular sum is energetically unfavorable, so that diamines with a larger N–N distance afford the corresponding ortho-quinone imines. Thus, for the reaction of DHBQ with diamines, exact predictions of the regioselectivity, and the resulting product structure, can be made on the basis of simple computations of bond spacings and product geometries.

Plato’s cube and the natural geometry of fragmentation

Plato envisioned Earth’s building blocks as cubes, a shape rarely found in nature. The solar system is littered, however, with distorted polyhedra—shards of rock and ice produced by ubiquitous fragmentation. We apply the theory of convex mosaics to show that the average geometry of natural two-dimensional (2D) fragments, from mud cracks to Earth’s tectonic plates, has two attractors: “Platonic” quadrangles and “Voronoi” hexagons. In three dimensions (3D), the Platonic attractor is dominant: Remarkably, the average shape of natural rock fragments is cuboid. When viewed through the lens of convex mosaics, natural fragments are indeed geometric shadows of Plato’s forms. Simulations show that generic binary breakup drives all mosaics toward the Platonic attractor, explaining the ubiquity of cuboid averages. Deviations from binary fracture produce more exotic patterns that are genetically linked to the formative stress field. We compute the universal pattern generator establishing this link, for 2D and 3D fragmentation.

Material Selection Based on Finite Element Method in Customized Iliac Implant

Osteosarcoma, as the most frequent bone tumor cases, can be found in the pelvis bone. Within the pelvis, the ilium is the most common location for osteosarcoma, followed by the acetabulum and then the ischium. Surgery of pelvis is difficult and the reconstruction is complicated mainly due to the geometry complexity and also the weight support function of the pelvis. Endoprosthesis of the ilium is therefore designed to increase the quality of life of the patient. In this study, the iliac implant is designed based on the natural geometry of the ilium, and the size is modified to fit the morphometry of the Eastern Asian. A finite element method (FEM) is proposed as a basic study in material selection. Titanium and its alloy (Ti-6Al-4V) are studied as the potential candidate for the proposed implant while the finite analysis of the bone was also included. As a preliminary study, in this FEM, only the static load is given, each material is assumed to be isotropic and the contacts were considered bonded. FEM in this study is expected to give a better understanding of the stress distribution, and to optimize the selection of materials.

The geometric influence on the Cys2His2 zinc finger domain and functional plasticity

The Cys2His2 zinc finger is the most common DNA-binding domain expanding in metazoans since the fungi human split. A proposed catalyst for this expansion is an arms race to silence transposable elements yet it remains poorly understood how this domain is able to evolve the required specificities. Likewise, models of its DNA binding specificity remain error prone due to a lack of understanding of how adjacent fingers influence each other's binding specificity. Here, we use a synthetic approach to exhaustively investigate binding geometry, one of the dominant influences on adjacent finger function. By screening over 28 billion protein–DNA interactions in various geometric contexts we find the plasticity of the most common natural geometry enables more functional amino acid combinations across all targets. Further, residues that define this geometry are enriched in genomes where zinc fingers are prevalent and specificity transitions would be limited in alternative geometries. Finally, these results demonstrate an exhaustive synthetic screen can produce an accurate model of domain function while providing mechanistic insight that may have assisted in the domains expansion.