Solving mixed sparse-dense linear least-squares problems by preconditioned iterative methods

The efficient solution of large linear least-squares problems in which the system matrix A contains rows with very different densities is challenging. Previous work has focused on direct methods for problems in which A has a few relatively dense rows. These rows are initially ignored, a factorization of the sparse part is computed using a sparse direct solver, and then the solution is updated to take account of the omitted dense rows. In some practical applications the number of dense rows can be significant and for very large problems, using a direct solver may not be feasible. We propose processing rows that are identified as dense separately within a conjugate gradient method using an incomplete factorization preconditioner combined with the factorization of a dense matrix of size equal to the number of dense rows. Numerical experiments on large-scale problems from real applications are used to illustrate the effectiveness of our approach. The results demonstrate that we can efficiently solve problems that could not be solved by a preconditioned conjugate gradient method without exploiting the dense rows

Draft Genome Sequence of the Redox-Active Enteric Bacterium Citrobacter portucalensis Strain MBL

We grew a soil enrichment culture to identify organisms that anaerobically oxidize phenazine-1-carboxylic acid. A strain of Citrobacter portucalensis was isolated from this enrichment and sequenced by both Illumina and PacBio technologies. It has a genome with a length of 5.3 Mb, a G+C content of 51.8%, and at least one plasmid

Draft Genome Sequence of the Redox-Active Enteric Bacterium Citrobacter portucalensis Strain MBL

We grew a soil enrichment culture to identify organisms that anaerobically oxidize phenazine-1-carboxylic acid. A strain of Citrobacter portucalensis was isolated from this enrichment and sequenced by both Illumina and PacBio technologies. It has a genome with a length of 5.3 Mb, a G+C content of 51.8%, and at least one plasmid

The Colorful World of Extracellular Electron Shuttles

Descriptions of the changeable, striking colors associated with secreted natural products date back well over a century. These molecules can serve as extracellular electron shuttles (EESs) that permit microbes to access substrates at a distance. In this review, we argue that the colorful world of EESs has been too long neglected. Rather than simply serving as a diagnostic attribute of a particular microbial strain, redox-active natural products likely play fundamental, underappreciated roles in the biology of their producers, particularly those that inhabit biofilms. Here, we describe the chemical diversity and potential distribution of EES producers and users, discuss the costs associated with their biosynthesis, and critically evaluate strategies for their economical usage. We hope this review will inspire efforts to identify and explore the importance of EES cycling by a wide range of microorganisms so that their contributions to shaping microbial communities can be better assessed and exploited

The simplest demonstrations of quantum nonlocality

We investigate the complexity cost of demonstrating the key types of nonclassical correlations-Bell inequality violation, Einstein, Podolsky, Rosen (EPR)-steering, and entanglement-with independent agents, theoretically and in a photonic experiment. We show that the complexity cost exhibits a hierarchy among these three tasks, mirroring the recently discovered hierarchy for how robust they are to noise. For Bell inequality violations, the simplest test is the well-known Clauser-Horne-Shimony-Holt test, but for EPR-steering and entanglement the tests that involve the fewest number of detection patterns require nonprojective measurements. The simplest EPR-steering test requires a choice of projective measurement for one agent and a single nonprojective measurement for the other, while the simplest entanglement test uses just a single nonprojective measurement for each agent. In both of these cases, we derive our inequalities using the concept of circular two-designs. This leads to the interesting feature that in our photonic demonstrations, the correlation of interest is independent of the angle between the linear polarizers used by the two parties, which thus require no alignment

Extracellular DNA Promotes Efficient Extracellular Electron Transfer by Pyocyanin in Pseudomonas aeruginosa Biofilms

Redox cycling of extracellular electron shuttles can enable the metabolic activity of subpopulations within multicellular bacterial biofilms that lack direct access to electron acceptors or donors. How these shuttles catalyze extracellular electron transfer (EET) within biofilms without being lost to the environment has been a long-standing question. Here, we show that phenazines mediate efficient EET through interactions with extracellular DNA (eDNA) in Pseudomonas aeruginosa biofilms. Retention of pyocyanin (PYO) and phenazine carboxamide in the biofilm matrix is facilitated by eDNA binding. In vitro, different phenazines can exchange electrons in the presence or absence of DNA and can participate directly in redox reactions through DNA. In vivo, biofilm eDNA can also support rapid electron transfer between redox active intercalators. Together, these results establish that PYO:eDNA interactions support an efficient redox cycle with rapid EET that is faster than the rate of PYO loss from the biofilm

The Canada-UK Deep Submillimetre Survey: The Survey of the 14-hour field

We have used SCUBA to survey an area of 50 square arcmin, detecting 19 sources down to a 3sigma sensitivity limit of 3.5 mJy at 850 microns. We have used Monte-Carlo simulations to assess the effect of source confusion and noise on the SCUBA fluxes and positions, finding that the fluxes of sources in the SCUBA surveys are significantly biased upwards and that the fraction of the 850 micron background that has been resolved by SCUBA has been overestimated. The radio/submillmetre flux ratios imply that the dust in these galaxies is being heated by young stars rather than AGN. We have used simple evolution models based on our parallel SCUBA survey of the local universe to address the major questions about the SCUBA sources: (1) what fraction of the star formation at high redshift is hidden by dust? (2) Does the submillimetre luminosity density reach a maximum at some redshift? (3) If the SCUBA sources are proto-ellipticals, when exactly did ellipticals form? However, we show that the observations are not yet good enough for definitive answers to these questions. There are, for example, acceptable models in which 10 times as much high-redshift star formation is hidden by dust as is seen at optical wavelengths, but also acceptable ones in which the amount of hidden star formation is less than that seen optically. There are acceptable models in which very little star formation occurred before a redshift of three (as might be expected in models of hierarchical galaxy formation), but also ones in which 30% of the stars have formed by this redshift. The key to answering these questions are measurements of the dust temperatures and redshifts of the SCUBA sources.Comment: 41 pages (latex), 17 postscript figures, to appear in the November issue of the Astronomical Journa

Bostonia: The Boston University Alumni Magazine. Volume 32

Founded in 1900, Bostonia magazine is Boston University's main alumni publication, which covers alumni and student life, as well as university activities, events, and programs

The local FIR Galaxy Colour-Luminosity distribution: A reference for BLAST, and Herschel/SPIRE sub-mm surveys

We measure the local galaxy far-infrared (FIR) 60-to-100 um colour-luminosity distribution using an all-sky IRAS survey. This distribution is an important reference for the next generation of FIR--submillimetre surveys that have and will conduct deep extra-galactic surveys at 250--500 um. With the peak in dust-obscured star-forming activity leading to present-day giant ellipticals now believed to occur in sub-mm galaxies near z~2.5, these new FIR--submillimetre surveys will directly sample the SEDs of these distant objects at rest-frame FIR wavelengths similar to those at which local galaxies were observed by IRAS. We have taken care to correct for temperature bias and evolution effects in our IRAS 60 um-selected sample. We verify that our colour-luminosity distribution is consistent with measurements of the local FIR luminosity function, before applying it to the higher-redshift Universe. We compare our colour-luminosity correlation with recent dust-temperature measurements of sub-mm galaxies and find evidence for pure luminosity evolution of the form (1+z)^3. This distribution will be useful for the development of evolutionary models for BLAST and SPIRE surveys as it provides a statistical distribution of rest-frame dust temperatures for galaxies as a function of luminosity.Comment: 12 pages, 7 figures. MNRAS in press. This revision matches final published version. Fixes typos in footnote 1 and equation 8. Minor modifications to text and references. Final results unchange