CiteULike: Author Bixby

Solving a Truck Dispatching Scheduling Problem Using Branch-And-Cut

Robert Bixby — 2008-07-10T01:40:35-00:00

Oper. Res., Vol. 46, No. 3. (March 1998), pp. 355-367.

EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries

Robin Smith — 2008-04-11T06:36:45-00:00

BMC Bioinformatics, Vol. 9 (10 April 2008), 186.

The projections from striate cortex (V1) to areas V2 and V3 in the macaque monkey: asymmetries, areal boundaries, and patchy connections.

DC Van Essen — 2008-05-14T14:46:52-00:00

The Journal of comparative neurology, Vol. 244, No. 4. (22 February 1986), pp. 451-480.

The organization of projections from V1 to areas V2 and V3 in the macaque monkey was studied with a combination of anatomical techniques, including lesions and tracer injections made in different portions of V1 and V2 in 20 experimental hemispheres. Our results indicate that dorsal V1 (representing the inferior contralateral visual quadrant) consistently projects in topographically organized fashion to V3 in the lunate and parietooccipital sulci as well as to the middle temporal area (MT) and dorsal V2. In contrast, ventral V1 (representing the superior contralateral quadrant) projects only to MT and ventral V2. A corresponding dorsoventral asymmetry in myeloarchitecture supports the idea that V3 is an area that is restricted to dorsal extrastriate cortex and lacks a complete representation of the visual field. The average surface area of myeloarchitectonically identified V3 was 89 mm2. Additional information was obtained concerning the laminar distribution of connections from V1 to V2 and V3, the patchiness of these projections, and the consistency of projections to other extrastriate areas, including V4 and V3A.

Solving Real-World Linear Programs: A Decade and More of Progress

Robert Bixby — 2006-08-03T22:53:57-00:00

Oper. Res., Vol. 50, No. 1. (January 2002), pp. 3-15.

This paper is an invited contribution to the 50th anniversary issue of the journal Operations Research, published by the Institute of Operations Research and Management Science (INFORMS). It describes one person's perspective on the development of computational tools for linear programming. The paper begins with a short personal history, followed by historical remarks covering the some 40 years of linear-programming developments that predate my own involvement in this subject. It concludes with a more detailed look at the evolution of computational linear programming since 1987.

Simian Immunodeficiency Virus Engrafted with Human Immunodeficiency Virus Type 1 (HIV-1)-Specific Epitopes: Replication, Neutralization, and Survey of HIV-1-Positive Plasma.

E Yuste — 2006-03-02T20:23:03-00:00

J Virol, Vol. 80, No. 6. (March 2006), pp. 3030-3041.

To date, only a small number of anti-human immunodeficiency virus type 1 (HIV-1) monoclonal antibodies (MAbs) with relatively broad neutralizing activity have been isolated from infected individuals. Adequate techniques for defining how frequently antibodies of these specificities arise in HIV-infected people have been lacking, although it is generally assumed that such antibodies are rare. In order to create an epitope-specific neutralization assay, we introduced well-characterized HIV-1 epitopes into the heterologous context of simian immunodeficiency virus (SIV). Specifically, epitope recognition sequences for the 2F5, 4E10, and 447-52D anti-HIV-1 neutralizing monoclonal antibodies were introduced into the corresponding regions of SIVmac239 by site-directed mutagenesis. Variants with 2F5 or 4E10 recognition sequences in gp41 retained replication competence and were used for neutralization assays. The parental SIVmac239 and the neutralization-sensitive SIVmac316 were not neutralized by the 2F5 and 4E10 MAbs, nor were they neutralized significantly by any of the 96 HIV-1-positive human plasma samples that were tested. The SIV239-2F5 and SIV239-4E10 variants were specifically neutralized by the 2F5 and 4E10 MAbs, respectively, at concentrations within the range of what has been reported previously for HIV-1 primary isolates (J. M. Binley et al., J. Virol. 78:13232-13252, 2004). The SIV239-2F5 and SIV239-4E10 epitope-engrafted variants were used as biological screens for the presence of neutralizing activity of these specificities. None of the 92 HIV-1-positive human plasma samples that were tested exhibited significant neutralization of SIV239-2F5. One plasma sample exhibited >90% neutralization of SIV239-4E10, but this activity was not competed by a 4E10 target peptide and was not present in concentrated immunoglobulin G (IgG) or IgA fractions. We thus confirm by direct analysis that neutralizing activities of the 2F5 and 4E10 specificities are either rare among HIV-1-positive individuals or, if present, represent only a very small fraction of the total neutralizing activity in any given plasma sample. We further conclude that the structures of gp41 from SIVmac239 and HIV-1 are sufficiently similar such that epitopes engrafted into SIVmac239 can be readily recognized by the cognate anti-HIV-1 monoclonal antibodies.

The diversity and evolutionary relationships of the pregnancy-associated glycoproteins, an aspartic proteinase subfamily consisting of many trophoblast-expressed genes.

S Xie — 2006-03-01T05:26:47-00:00

Proc Natl Acad Sci U S A, Vol. 94, No. 24. (25 November 1997), pp. 12809-12816.

The pregnancy-associated glycoproteins (PAGs) are structurally related to the pepsins, thought to be restricted to the hooved (ungulate) mammals and characterized by being expressed specifically in the outer epithelial cell layer (chorion/trophectoderm) of the placenta. At least some PAGs are catalytically inactive as proteinases, although each appears to possess a cleft capable of binding peptides. By cloning expressed genes from ovine and bovine placental cDNA libraries, by Southern genomic blotting, by screening genomic libraries, and by using PCR to amplify portions of PAG genes from genomic DNA, we estimate that cattle, sheep, and most probably all ruminant Artiodactyla possess many, possibly 100 or more, PAG genes, many of which are placentally expressed. The PAGs are highly diverse in sequence, with regions of hypervariability confined largely to surface-exposed loops. Nonsynonymous (replacement) mutations in the regions of the genes coding for these hypervariable loop segments have accumulated at a higher rate than synonymous (silent) mutations. Construction of distance phylograms, based on comparisons of PAG and related aspartic proteinase amino acid sequences, suggests that much diversification of the PAG genes occurred after the divergence of the Artiodactyla and Perissodactyla, but that at least one gene is represented outside the hooved species. The results also suggest that positive selection of duplicated genes has acted to provide considerable functional diversity among the PAGs, whose presence at the interface between the placenta and endometrium and in the maternal circulation indicates involvement in fetal-maternal interactions.