An Efficient Algorithm for Clustering of Large-Scale Mass Spectrometry Data

High-throughput spectrometers are capable of producing data sets containing thousands of spectra for a single biological sample. These data sets contain a substantial amount of redundancy from peptides that may get selected multiple times in a LC-MS/MS experiment. In this paper, we present an efficient algorithm, CAMS (Clustering Algorithm for Mass Spectra) for clustering mass spectrometry data which increases both the sensitivity and confidence of spectral assignment. CAMS utilizes a novel metric, called F-set, that allows accurate identification of the spectra that are similar. A graph theoretic framework is defined that allows the use of F-set metric efficiently for accurate cluster identifications. The accuracy of the algorithm is tested on real HCD and CID data sets with varying amounts of peptides. Our experiments show that the proposed algorithm is able to cluster spectra with very high accuracy in a reasonable amount of time for large spectral data sets. Thus, the algorithm is able to decrease the computational time by compressing the data sets while increasing the throughput of the data by interpreting low S/N spectra.Comment: 4 pages, 4 figures, Bioinformatics and Biomedicine (BIBM), 2012 IEEE International Conference o

The East Chacon Project Project: 11,000 Years of Prehistory Along the Upper Nueces River, Southern Texas

During 1981 and 1982, the Center for Archaeological Research, The University of Texas at San Antonio, conducted a cultural resources assessment of ca. 30,000 acres leased to the Carter Mining Company in Uvalde and Zavala Counties, Texas. Known as the East Chacon project, the survey was undertaken to identify and assess the cultural resources of the locality prior to potential modification or destruction due to proposed mining operations. Archaeological and historical sites (149) were identified and recorded that represent a span of human activities from approximately 11,000 B.P. to the Historic period. A detailed description of these site locations, interpretations of their cultural environmental contexts, and determinations of potential eligibility to the National Register of Historic Places are presented in this report

Campus Bridging Birds-of-a-Feather Session at TeraGrid 2011 Conference

Richard Knepper attended the TeraGrid 2011 conference in Salt Lake City, Utah, and together with representatives from the TeraGrid Campus Champions program conducted a Birds of a Feather session discussing the XSEDE Campus Bridging initiative and the Campus Champions program. The attendees discussed the Campus Bridging and Campus Champions plans for XSEDE.This research was supported in part by the National Science Foundation through XSEDE resources provided by the XSEDE Campus Bridging program. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the NSF. More information is available at: http://xsede.org

On the completeness of ensembles of motion planners for decentralized planning

We provide a set of sufficient conditions to establish the completeness of an ensemble of motion planners-that is, a set of loosely-coupled motion planners that produce a unified result. The planners are assumed to divide the total planning problem across some parameter space(s), such as task space, state space, action space, or time. Robotic applications have employed ensembles of planners for decades, although the concept has not been formally unified or analyzed until now. We focus on applications in multi-robot navigation and collision avoidance. We show that individual resolutionor probabilistically-complete planners that meet certain communication criteria constitute a (respectively, resolution- or probabilistically-) complete ensemble of planners. This ensemble of planners, in turn, guarantees that the robots are free of deadlock, livelock, and starvation.Boeing Compan

Pathways of urea transport in the mammalian kidney

Urea is the chief end product of nitrogen metabolism in mammals. Most of the urea produced is excreted by the kidneys. Excretion of a large fraction of the urea filtered by the glomerulus is required to keep pace with the rate of hepatic urea production. Consequently, the maintenance of nitrogen balance depends on a sustained high rate of renal urea excretion. One factor that might challenge the ability of the kidney to maintain a high rate of urea excretion is the need to limit water excretion. Theoretically, an increase in water absorption along the nephron would be expected to increase luminal urea concentration and consequently increase the driving force for passive urea reabsorption. Indeed, as demonstrated originally by Shannon [1] and confirmed in many subsequent studies, the rate of urea excretion decreases when water excretion decreases. However, the decline in urea excretion is relatively modest, even when the rate of water excretion is very low. In Shannon's studies in dogs [1], when water diuresis was established (water excretion 5–10 percent of filtered load), urea excretion was about 60 percent of the filtered load. During antidiuresis, when water excretion was reduced by 95% or more (to less than 0.5 percent of the glomerular filtration rate), urea excretion fell only by 25 to 30% (to 40 to 45 percent of the filtered load)

Workshop Report: Campus Bridging: Reducing Obstacles on the Path to Big Answers 2015

For the researcher whose experiments require large-scale cyberinfrastructure, there exists significant challenges to successful completion. These challenges are broad and go far beyond the simple issue that there are not enough large-scale resources available; these solvable issues range from a lack of documentation written for a non-technical audience to a need for greater consistency with regard to system configuration and consistent software configuration and availability on the large-scale resources at national tier supercomputing centers, with a number of other challenges existing alongside the ones mentioned here. Campus Bridging is a relatively young discipline that aims to mitigate these issues for the academic end-user, for whom the entire process can feel like a path comprised entirely of obstacles. The solutions to these problems must by necessity include multiple approaches, with focus not only on the end user but on the system administrators responsible for supporting these resources as well as the systems themselves. These system resources include not only those at the supercomputing centers but also those that exist at the campus or departmental level and even on the personal computing devices the researcher uses to complete his or her work. This workshop report compiles the results of a half-day workshop, held in conjunction with IEEE Cluster 2015 in Chicago, IL.NSF XSED