Assembling networks of microbial genomes using linear programming

<p>Abstract</p> <p>Background</p> <p>Microbial genomes exhibit complex sets of genetic affinities due to lateral genetic transfer. Assessing the relative contributions of parent-to-offspring inheritance and gene sharing is a vital step in understanding the evolutionary origins and modern-day function of an organism, but recovering and showing these relationships is a challenging problem.</p> <p>Results</p> <p>We have developed a new approach that uses linear programming to find between-genome relationships, by treating tables of genetic affinities (here, represented by transformed BLAST e-values) as an optimization problem. Validation trials on simulated data demonstrate the effectiveness of the approach in recovering and representing vertical and lateral relationships among genomes. Application of the technique to a set comprising <it>Aquifex aeolicus </it>and 75 other thermophiles showed an important role for large genomes as 'hubs' in the gene sharing network, and suggested that genes are preferentially shared between organisms with similar optimal growth temperatures. We were also able to discover distinct and common genetic contributors to each sequenced representative of genus <it>Pseudomonas</it>.</p> <p>Conclusions</p> <p>The linear programming approach we have developed can serve as an effective inference tool in its own right, and can be an efficient first step in a more-intensive phylogenomic analysis.</p

Dual-Career Relocation Benefits: A Study of Executive Search Firms

C. Richard Scott is an Assistant Professor of Management in the Department of Management at Radford University. Robert W. Holloway is a Technical Writer for Hercules, lnc. (Aerospace Division), Radford, Virginia

Reaganism and the Poor Family: Life on AFDC after the Budget Cuts

Recent changes in federal and state welfare policies have had negative consequences for public welfare recipients. This paper summarizes a study which focused on the impact of these policy changes on the AFDC population in the most populous region of Oregon. Of particular importance are the changes in income levels, employment, and social service utilization of recipients. Personal reactions of recipients are also reviewed, as are expectations for the future. The differential economic impact of the policy changes on various categories of recipients is stressed

Delivering a collaborative monitoring program with industry to manage and facilitate trade

The current project represents national resistance monitoring for a period of 12 months with the purpose of transitioning this important program to a long term, self-sustainable model and establishing an enduring legacy. The findings from this research are addendum to the previously submitted final report for project PBCRC3035. While new data on resistance spread and frequency for the period 2015-16 are presented here, the methodology remains the same and the response from the end-user advocate is quite similar to the previous one. The following are the highlights from the 2015-16 season. The project has been proven to be a highly successful program as the outputs from this form the basis for development and deployment of major pest and resistance management strategies

Statistics of an Unstable Barotropic Jet from a Cumulant Expansion

Low-order equal-time statistics of a barotropic flow on a rotating sphere are investigated. The flow is driven by linear relaxation toward an unstable zonal jet. For relatively short relaxation times, the flow is dominated by critical-layer waves. For sufficiently long relaxation times, the flow is turbulent. Statistics obtained from a second-order cumulant expansion are compared to those accumulated in direct numerical simulations, revealing the strengths and limitations of the expansion for different relaxation times.Comment: 23 pages, 8 figures. Version to appear in J. Atmos. Sc

Cloud trails past Bermuda: a five-year climatology from 2012-2016

Cloud trails are primarily thermally forced bands of cloud that extend down-wind of small islands. A novel algorithm to classify conventional geostationary visible-channel satellite images as Cloud Trail (CT), Non-Trail (NT), or Obscured (OB) is defined. The algorithm is then applied to the warm season months of five years at Bermuda comprising 16,400 images. Bermuda’s low elevation and location make this island ideal for isolating the role of the island thermal contrast on CT formation. CT are found to occur at Bermuda with an annual cycle, peaking in July, and a diurnal cycle that peaks in mid-afternoon. Composites of radiosonde observations and ERA-interim data suggest that a warm and humid low-level environment is conducive for CT development. From a Lagrangian perspective, wind direction modulates CT formation by maximizing low-level heating on local scales when winds are parallel to the long axis of the island. On larger scales, low-level wind direction also controls low-level humidity through advection

Cutaneous Angiosarcoma of the Scalp: A Case Report of Sustained Complete Response Following Liposomal Doxorubicin and Radiation Therapy

Cutaneous angiosarcomas of the head and neck are aggressive cancers with a mean overall survival of 30 months. We add to the literature a case report of a 65-year-old man with a large, >10 cm, unresectable, angiosarcoma of the scalp who was treated with two cycles of liposomal doxorubicin (Caelyx®) followed by electron beam radiation therapy (30 Gy in 10 fractions over 2 weeks) who has sustained a complete response with a 4-year follow-up. The dose and fractionation of the radiation therapy in this case was palliative and was not expected to give lasting local control of this lesion. It is therefore possible that either the genetic profile of the tumour conferred radiosensitivity or that the radiation therapy induced a recall phenomenon of the liposomal doxorubicin