History of the Catholic missions among the Indian tribes of the United States, 1529-1854 / by John Gilmary Shea.

http://www.archive.org/details/historyofcatholi00sheaiala

Exponential sensitivity of noise-driven switching in genetic networks

Cells are known to utilize biochemical noise to probabilistically switch between distinct gene expression states. We demonstrate that such noise-driven switching is dominated by tails of probability distributions and is therefore exponentially sensitive to changes in physiological parameters such as transcription and translation rates. However, provided mRNA lifetimes are short, switching can still be accurately simulated using protein-only models of gene expression. Exponential sensitivity limits the robustness of noise-driven switching, suggesting cells may use other mechanisms in order to switch reliably.

AIDA-Based Distributed File System

This paper describes a prototype implementation of a Distributed File System (DFS) based on the Adaptive Information Dispersal Algorithm (AIDA). Using AIDA, a file block is encoded and dispersed into smaller blocks stored on a number of DFS nodes distributed over a network. The implementation devises file creation, read, and write operations. In particular, when reading a file, the DFS accepts an optional timing constraint, which it uses to determine the level of redundancy needed for the read operation. The tighter the timing constraint, the more nodes in the DFS are queried for encoded blocks. Write operations update all blocks in all DFS nodes--with future implementations possibly including the use of read and write quorums. This work was conducted under the supervision of Professor Azer Bestavros (best@cs.bu.edu) in the Computer Science Department as part of Mohammad Makarechian's Master's project.

Integrated Chest Image Analysis System "BU-MIA"

We introduce "BU-MIA," a Medical Image Analysis system that integrates various advanced chest image analysis methods for detection, estimation, segmentation, and registration. BU-MIA evaluates repeated computed tomography (CT) scans of the same patient to facilitate identification and evaluation of pulmonary nodules for interval growth. It provides a user-friendly graphical user interface with a number of interaction tools for development, evaluation, and validation of chest image analysis methods. The structures that BU-MIA processes include the thorax, lungs, and trachea, pulmonary structures, such as lobes, fissures, nodules, and vessels, and bones, such as sternum, vertebrae, and ribs.

Visible Volume: a Robust Measure for Protein Structure Characterization

We propose a new characterization of protein structure based on the natural tetrahedral geometry of the β carbon and a new geometric measure of structural similarity, called visible volume. In our model, the side-chains are replaced by an ideal tetrahedron, the orientation of which is fixed with respect to the backbone and corresponds to the preferred rotamer directions. Visible volume is a measure of the non-occluded empty space surrounding each residue position after the side-chains have been removed. It is a robust, parameter-free, locally-computed quantity that accounts for many of the spatial constraints that are of relevance to the corresponding position in the native structure. When computing visible volume, we ignore the nature of both the residue observed at each site and the ones surrounding it. We focus instead on the space that, together, these residues could occupy. By doing so, we are able to quantify a new kind of invariance beyond the apparent variations in protein families, namely, the conservation of the physical space available at structurally equivalent positions for side-chain packing. Corresponding positions in native structures are likely to be of interest in protein structure prediction, protein design, and homology modeling. Visible volume is related to the degree of exposure of a residue position and to the actual rotamers in native proteins. In this article, we discuss the properties of this new measure, namely, its robustness with respect to both crystallographic uncertainties and naturally occurring variations in atomic coordinates, and the remarkable fact that it is essentially independent of the choice of the parameters used in calculating it. We also show how visible volume can be used to align protein structures, to identify structurally equivalent positions that are conserved in a family of proteins, and to single out positions in a protein that are likely to be of biological interest. These properties qualify visible volume as a powerful tool in a variety of applications, from the detailed analysis of protein structure to homology modeling, protein structural alignment, and the definition of better scoring functions for threading purposes.