Images inside a reflecting spherical surface with possible application in astronomy

This report studies an algebraic equation whose solution gives the image system of a source of light as seen by an observer inside a reflecting spherical surface. The equation is looked at numerically using GeoGebra. Under the hypothesis that our galaxy is enveloped by a reflecting interface this becomes a possible model for many mysterious extra galactic observations.

Modeling kinect sensor noise for improved 3D reconstruction and tracking

We contribute an empirically derived noise model for the Kinect sensor. We systematically measure both lateral and axial noise distributions, as a function of both distance and angle of the Kinect to an observed surface. The derived noise model can be used to filter Kinect depth maps for a variety of applications. Our second contribution applies our derived noise model to the KinectFusion system to extend filtering, volumetric fusion, and pose estimation within the pipeline. Qualitative results show our method allows reconstruction of finer details and the ability to reconstruct smaller objects and thinner surfaces. Quantitative results also show our method improves pose estimation accuracy. © 2012 IEEE.

Response of segmented bored transit tunnels to surface blast

Increasing threat of terrorism highlights the importance of enhancing the resilience of underground tunnels to all hazards. This paper develops, applies and compares the Arbitrary Lagrangian Eulerian (ALE) and Smooth Particle Hydrodynamics (SPH) techniques to treat the response of buried tunnels to surface explosions. The results and outcomes of the two techniques were compared, along with results from existing test data. The comparison shows that the ALE technique is a better method for describing the tunnel response for above ground explosion with regards to modeling accuracy and computational efficiency. The ALE technique was then applied to treat the blast response of different types of segmented bored tunnels buried in dry sand. Results indicate that the most used modern ring type segmented tunnels were more flexible for in-plane response, however, they suffered permanent drifts between the rings. Hexagonal segmented tunnels responded with negligible drifts in the longitudinal direction, but the magnitudes of in-plane drifts were large and hence hazardous for the tunnel. Interlocking segmented tunnels suffered from permanent drifts in both the longitudinal and transverse directions. Multi-surface radial joints in both the hexagonal and interlocking segments affected the flexibility of the tunnel in the transverse direction. The findings offer significant new information in the behavior of segmented bored tunnels to guide their future implementation in civil engineering applications.

Quantitative genetic modeling of lateral ventricular shape and volume using multi-atlas fluid image alignment in twins

Despite substantial progress in measuring the 3D profile of anatomical variations in the human brain, their genetic and environmental causes remain enigmatic. We developed an automated system to identify and map genetic and environmental effects on brain structure in large brain MRI databases . We applied our multi-template segmentation approach ("Multi-Atlas Fluid Image Alignment") to fluidly propagate hand-labeled parameterized surface meshes into 116 scans of twins (60 identical, 56 fraternal), labeling the lateral ventricles. Mesh surfaces were averaged within subjects to minimize segmentation error. We fitted quantitative genetic models at each of 30,000 surface points to measure the proportion of shape variance attributable to (1) genetic differences among subjects, (2) environmental influences unique to each individual, and (3) shared environmental effects. Surface-based statistical maps revealed 3D heritability patterns, and their significance, with and without adjustments for global brain scale. These maps visualized detailed profiles of environmental versus genetic influences on the brain, extending genetic models to spatially detailed, automatically computed, 3D maps.

Conformational epitopes on the diabetes autoantigen GAD65 identified by peptide phage display and molecular modeling

The major diabetes autoantigen, glutamic acid decarboxylase (GAD65), contains a region of sequence similarity, including six identical residues PEVKEK, to the P2C protein of coxsackie B virus, suggesting that cross-reactivity between coxsackie B virus and GAD65 can initiate autoimmune diabetes. We used the human islet cell mAbs MICA3 and MICA4 to identify the Ab epitopes of GAD65 by screening phage-displayed random peptide libraries. The identified peptide sequences could be mapped to a homology model of the pyridoxal phosphate (PLP) binding domain of GAD65. For MICA3, a surface loop containing the sequence PEVKEK and two adjacent exposed helixes were identified in the PLP binding domain as well as a region of the C terminus of GAD65 that has previously been identified as critical for MICA3 binding. To confirm that the loop containing tile PEVKEK sequence contributes to the MICA3 epitope, this loop was deleted by mutagenesis. This reduced binding of MICA3 by 70%. Peptide sequences selected using MICA4 were rich in basic or hydroxyl-containing amino acids, and the surface of the GAD65 PLP-binding domain surrounding Lys358, which is known to be critical for MICA4 binding, was likewise rich in these amino acids. Also, the two phage most reactive width MICA4 encoded the motif VALxG, and the reverse of this sequence, LAV, was located in this same region. Thus, we have defined the MICA3 and MICA4 epitopes on GAD65 using the combination of phage display, molecular modeling, and mutagenesis and have provided compelling evidence for the involvement of the PEVKEK loop in the MICA3 epitope.

Modeling approaches for pesticide exposure assessment in rice paddies

Pesticide use in paddy rice production may contribute to adverse ecological effects in surface waters. Risk assessments conducted for regulatory purposes depend on the use of simulation models to determine predicted environment concentrations (PEC) of pesticides. Often tiered approaches are used, in which assessments at lower tiers are based on relatively simple models with conservative scenarios, while those at higher tiers have more realistic representations of physical and biochemical processes. This chapter reviews models commonly used for predicting the environmental fate of pesticides in rice paddies. Theoretical considerations, unique features, and applications are discussed. This review is expected to provide information to guide model selection for pesticide registration, regulation, and mitigation in rice production areas.

Molecular modeling of Bt Cry1Ac (DI–DII)–ASAL (Allium sativum lectin)–fusion protein and its interaction with aminopeptidase N (APN) receptor of Manduca sexta

Genetic engineering of Bacillus thuringiensis (Bt) Cry proteins has resulted in the synthesis of various novel toxin proteins with enhanced insecticidal activity and specificity towards different insect pests. In this study, a fusion protein consisting of the DI–DII domains of Cry1Ac and garlic lectin (ASAL) has been designed in silico by replacing the DIII domain of Cry1Ac with ASAL. The binding interface between the DI–DII domains of Cry1Ac and lectin has been identified using protein–protein docking studies. Free energy of binding calculations and interaction profiles between the Cry1Ac and lectin domains confirmed the stability of fusion protein. A total of 18 hydrogen bonds was observed in the DI–DII–lectin fusion protein compared to 11 hydrogen bonds in the Cry1Ac (DI–DII–DIII) protein. Molecular mechanics/Poisson–Boltzmann (generalized-Born) surface area [MM/PB (GB) SA] methods were used for predicting free energy of interactions of the fusion proteins. Protein–protein docking studies based on the number of hydrogen bonds, hydrophobic interactions, aromatic–aromatic, aromatic–sulphur, cation–pi interactions and binding energy of Cry1Ac/fusion proteins with the aminopeptidase N (APN) of Manduca sexta rationalised the higher binding affinity of the fusion protein with the APN receptor compared to that of the Cry1Ac–APN complex, as predicted by ZDOCK, Rosetta and ClusPro analysis. The molecular binding interface between the fusion protein and the APN receptor is well packed, analogously to that of the Cry1Ac–APN complex. These findings offer scope for the design and development of customized fusion molecules for improved pest management in crop plants.