We report the discovery of a giant Ly{alpha} emitter (LAE) with a Spitzer/IRAC counterpart near the reionization epoch at z = 6.595. The giant LAE is found from the extensive 1 deg{sup 2} Subaru narrow-band survey for z = 6.6 LAEs in the Subaru/XMM-Newton Deep Survey (SXDS) field, and subsequently identified by deep spectroscopy of Keck/DEIMOS and Magellan/IMACS. Among our 207 LAE candidates, this LAE is not only the brightest narrow-band object with L(Ly{alpha}) = 3.9 {+-} 0.2 x 10{sup 43} erg s{sup -1} in our survey volume of 10{sup 6} Mpc{sup 3}, but also a spatially extended Ly{alpha} nebula with the largest isophotal area whose major axis is at least {approx_equal} 3-inches. This object is more likely to be a large Ly{alpha} nebula with a size of {approx}> 17-kpc than to be a strongly-lensed galaxy by a foreground object. Our Keck spectrum with medium-high spectral and spatial resolutions suggests that the velocity width is v{sub FWHM} = 251 {+-} 21 km s{sup -1}, and that the line-center velocity changes by {approx_equal} 60 km s{sup -1} in a 10-kpc range. The stellar mass and star-formation rate are estimated to be 0.9-5.0 x 10{sup 10}M{sub {circle_dot}} and > 34 M{sub {circle_dot}}yr{sup …

The connection between macro-particle shape functions and non-physical phase-space"heating" in the particle-in-cell (PIC) algorithm is examined. The development of fine-scale phasespace structures starting from a cold initial condition is shown to be related to spatial correlations in the interpolated fields used in the Lorentz force. It is shown that the plasma evolution via the PIC algorithm from a cold initial condition leads to a state that is not consistent with that of a thermal plasma.

As random shotgun metagenomic projects proliferate and become the dominant source of publicly available sequence data, procedures for best practices in their execution and analysis become increasingly important. Based on our experience at the Joint Genome Institute, we describe step-by-step the chain of decisions accompanying a metagenomic project from the viewpoint of a bioinformatician. We guide the reader through a standard workflow for a metagenomic project beginning with pre-sequencing considerations such as community composition and sequence data type that will greatly influence downstream analyses. We proceed with recommendations for sampling and data generation including sample and metadata collection, community profiling, construction of shotgun libraries and sequencing strategies. We then discuss the application of generic sequence processing steps (read preprocessing, assembly, and gene prediction and annotation) to metagenomic datasets by contrast to genome projects. Different types of data analyses particular to metagenomes are then presented including binning, dominant population analysis and gene-centric analysis. Finally data management systems and issues are presented and discussed. We hope that this review will assist bioinformaticians and biologists in making better-informed decisions on their journey during a metagenomic project.

The 2008 Columbia River Estuary Conference was held at the Liberty Theater in Astoria, Oregon, on April 19-20. The conference theme was ecosystem restoration. The purpose of the conference was to exchange data and information among researchers, policy-makers, and the public, i.e., interrelate science with management. Conference organizers invited presentations synthesizing material on Restoration Planning and Implementation (Session 1), Research to Reduce Restoration Uncertainties (Session 2), Wetlands and Flood Management (Session 3), Action Effectiveness Monitoring (Session 4), and Management Perspectives (Session 5). A series of three plenary talks opened the conference. Facilitated speaker and audience discussion periods were held at the end of each session. Contributed posters conveyed additional data and information. These proceedings include abstracts and notes documenting questions from the audience and clarifying answers from the presenter for each talk. The proceedings also document key points from the discussion periods at the end of each session. The conference program is outlined in the agenda section. Speaker biographies are presented in Appendix A. Poster titles and authors are listed in Appendix B. A list of conference attendees is contained in Appendix C.