HER2 mRNA transcript quantitation in breast cancer.

Purpose: The human epidermal growth factor receptor 2 (HER2) status in breast cancer is important for prognostic prediction and the determination of optimal treatment. Current methods rely on protein expression, as determined by immunohistochemistry (IHC), as well as gene amplification as determined by in situ hybridisation (ISH). We explored whether quantitative droplet digital PCR (ddPCR) can be used for the detection and absolute quantitation of HER2 mRNA.

Developments in the immunophenotypic analysis of haematological malignancies.

Immunophenotyping is the method by which antibodies are used to detect cellular antigens in clinical samples. Although the major role is in the diagnosis and classification of haematological malignancies, applications have expanded over the past decade. Immunophenotyping is now used extensively for disease staging and monitoring, to detect surrogate markers of genetic aberrations, to identify potential immuno-therapeutic targets and to aid prognostic prediction.

Geometry optimization of molecular clusters and complexes using scaled internal coordinates.

Scaled internal coordinates are introduced for use in the geometry optimization of systems composed of multiple fragments, such as solvated molecules, clusters, and biomolecular complexes. The new coordinates are related to bond lengths, bond angles and torsion angles by geometry-dependent scaling factors. The scaling factors serve to expedite the optimization of complexes containing outlying fragments, without hindering the optimization of the intramolecular degrees of freedom.

Technique for incorporating the density functional Hessian into the geometry optimization of biomolecules, solvated molecules, and large floppy molecules.

Traditional geometry optimization methods require the gradient of the potential surface, together with a Hessian which is often approximated. Approximation of the Hessian causes difficulties for large, floppy molecules, increasing the number of steps required to reach the minimum. In this article, the costly evaluation of the exact Hessian is avoided by expanding the density functional to second order in both the nuclear and electronic variables, and then searching for the minimum of the quadratic functional.