Background: Prompt laboratory diagnosis of Herpes simplex virus (HSV) infection facilitates patient management and possible initiation of antiviral therapy. In our laboratory, which receives various specimen types for detection of HSV, we use enzyme immunoassay (EIA) for rapid detection and culture of this virus. The culture of HSV has traditionally been accepted as the diagnostic 'gold standard'. In this study, we compared the use of real time PCR (LightCycler) for amplification, detection and subtyping of specific DNA with our in-house developed rapid and culture tests for HSV.

We introduce the Cox homotopy algorithm for solving a sparse system of polynomial equations on a compact toric variety X Σ . The algorithm lends its name from a construction, described by Cox, of X Σ as a GIT quotient X Σ = (C k \ Z) G of a quasi-affine variety by the action of a reductive group. Our algorithm tracks paths in the total coordinate space C k of X Σ and can be seen as a homogeneous version of the standard polyhedral homotopy, which works on the dense torus of X Σ . It furthermore generalizes the commonly used path tracking algorithms in (multi)projective spaces in that it tracks a set of homogeneous coordinates contained in the G-orbit corresponding to each solution. The Cox homotopy combines the advantages of polyhedral homotopies and (multi)homogeneous homotopies, tracking only mixed volume many solutions and providing an elegant way to deal with solutions on or near the special divisors of X Σ . In addition, the strategy may help to understand the deficiency of the root count for certain families of systems with respect to the BKK bound.

We present numerical homotopy continuation algorithms for solving systems of equations on a variety in the presence of a finite Khovanskii basis. These take advantage of Anderson's flat degeneration to a toric variety. When Anderson's degeneration embeds into projective space, our algorithm is a special case of a general toric two-step homotopy algorithm. When Anderson's degeneration is embedded in a weighted projective space, we explain how to lift to a projective space and construct an appropriate modification of the toric homotopy. Our algorithms are illustrated on several examples using Macaulay2.

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We present numerical homotopy continuation algorithms for solving systems of equations on a variety in the presence of a finite Khovanskii basis. These homotopies take advantage of Anderson’s flat degeneration to a toric variety. When Anderson’s degeneration embeds into projective space, our algorithm is a special case of a general toric two-step homotopy algorithm. When Anderson’s degeneration is embedded in a weighted projective space, we explain how to lift to a projective space and construct an appropriate modification of the toric homotopy. Our algorithms are illustrated on several examples using Macaulay2.