By temple shrine and lotus pool

http://www.archive.org/details/bytempleshrine00robiuoft/

Litigation-Generated Science: Why Should We Care?

BACKGROUND: In a 1994 Ninth Circuit decision on the remand of Daubert v. Merrell Dow Pharmaceuticals, Inc., Judge Alex Kosinski wrote that science done for the purpose of litigation should be subject to more stringent standards of admissibility than other science. OBJECTIVES: We analyze this proposition by considering litigation-generated science as a subset of science involving conflict of interest. DISCUSSION: Judge Kosinski's formulation suggests there may be reasons to treat science involving conflict of interest differently but raises questions about whether litigation-generated science should be singled out. In particular we discuss the similar problems raised by strategically motivated science done in anticipation of possible future litigation or otherwise designed to benefit the sponsor and ask what special treatment, if any, should be given to science undertaken to support existing or potential future litigation. CONCLUSION: The problems with litigation-generated science are not special. On the contrary, they are very general and apply to much or most science that is relevant and reliable in the courtroom setting.

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.

BU Computer Science 1998 Proxy Trace: Release Notes

In a recent paper (Changes in Web Client Access Patterns: Characteristics and Caching Implications by Barford, Bestavros, Bradley, and Crovella) we performed a variety of analyses upon user traces collected in the Boston University Computer Science department in 1995 and 1998. A sanitized version of the 1995 trace has been publicly available for some time; the 1998 trace has now been sanitized, and is available from: http://www.cs.bu.edu/techreports/1999-011-usertrace-98.gz ftp://ftp.cs.bu.edu/techreports/1999-011-usertrace-98.gz This memo discusses the format of this public version of the log, and includes additional discussion of how the data was collected, how the log was sanitized, what this log is and is not useful for, and areas of potential future research interest.