Progressive HIV infection in the presence of a raised CD4+ count: HIV/HTLV-1 co-infection

There are a number of pathophysiological causes for a normal or raised CD4 count in the context of progressive HIV infection. These include various co-infections, previous splenectomy, and lymphoproliferative disorders. Such circumstances can both confound HIV diagnosis and delay initiation of chemoprophylaxis and highly active antiretroviral therapy (HAART). We describe the case of a patient co-infected with HIV and human T-cell lymphotropic virus type 1 (HTLV-1) who, prior to HAART initiation, was found to have progressive immune deficiency associated with a raised CD4 count

solveME: fast and reliable solution of nonlinear ME models.

BackgroundGenome-scale models of metabolism and macromolecular expression (ME) significantly expand the scope and predictive capabilities of constraint-based modeling. ME models present considerable computational challenges: they are much (>30 times) larger than corresponding metabolic reconstructions (M models), are multiscale, and growth maximization is a nonlinear programming (NLP) problem, mainly due to macromolecule dilution constraints.ResultsHere, we address these computational challenges. We develop a fast and numerically reliable solution method for growth maximization in ME models using a quad-precision NLP solver (Quad MINOS). Our method was up to 45 % faster than binary search for six significant digits in growth rate. We also develop a fast, quad-precision flux variability analysis that is accelerated (up to 60× speedup) via solver warm-starts. Finally, we employ the tools developed to investigate growth-coupled succinate overproduction, accounting for proteome constraints.ConclusionsJust as genome-scale metabolic reconstructions have become an invaluable tool for computational and systems biologists, we anticipate that these fast and numerically reliable ME solution methods will accelerate the wide-spread adoption of ME models for researchers in these fields

Spin-to-Orbital Angular Momentum Conversion and Spin-Polarization Filtering in Electron Beams

We propose the design of a space-variant Wien filter for electron beams that induces a spin half-turn and converts the corresponding spin angular momentum variation into orbital angular momentum of the beam itself by exploiting a geometrical phase arising in the spin manipulation. When applied to a spatially coherent input spin-polarized electron beam, such a device can generate an electron vortex beam, carrying orbital angular momentum. When applied to an unpolarized input beam, the proposed device, in combination with a suitable diffraction element, can act as a very effective spin-polarization filter. The same approach can also be applied to neutron or atom beams.Comment: 9 pages, 5 figure

Semiclassical Strings Probing NS5 Brane Wrapped on S^5

We study little string theory on R^1 x S^5, defined by a theory which lives on type IIA N NS5 branes wrapped on S^5, using its supergravity dual. In particular we study semiclassical rotating closed strings in this background. We also consider Penrose limit of this background that leads to a plane wave on which string theory is exactly solvable.Comment: 14 pages, Latex, v2: typos corrected, Refs. added, v3: typos correcte

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization. First, users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users can draw pathways in a semi-automated way. Second, users can visualize data related to genes or proteins on the associated reactions and pathways, using rules that define which enzymes catalyze each reaction. Thus, users can identify trends in common genomic data types (e.g. RNA-Seq, proteomics, ChIP)--in conjunction with metabolite- and reaction-oriented data types (e.g. metabolomics, fluxomics). Third, Escher harnesses the strengths of web technologies (SVG, D3, developer tools) so that visualizations can be rapidly adapted, extended, shared, and embedded. This paper provides examples of each of these features and explains how the development approach used for Escher can be used to guide the development of future visualization tools