Efficiency clustering for low-density microarrays and its application to QPCR

<p>Abstract</p> <p>Background</p> <p>Pathway-targeted or low-density arrays are used more and more frequently in biomedical research, particularly those arrays that are based on quantitative real-time PCR. Typical QPCR arrays contain 96-1024 primer pairs or probes, and they bring with it the promise of being able to reliably measure differences in target levels without the need to establish absolute standard curves for each and every target. To achieve reliable quantification all primer pairs or array probes must perform with the same efficiency.</p> <p><b>Results</b></p> <p>Our results indicate that QPCR primer-pairs differ significantly both in reliability and efficiency. They can only be used in an array format if the raw data (so called CT values for real-time QPCR) are transformed to take these differences into account. We developed a novel method to obtain efficiency-adjusted CT values. We introduce transformed confidence intervals as a novel measure to identify unreliable primers. We introduce a robust clustering algorithm to combine efficiencies of groups of probes, and our results indicate that using <it>n </it>< 10 cluster-based mean efficiencies is comparable to using individually determined efficiency adjustments for each primer pair (<it>N </it>= 96-1024).</p> <p><b>Conclusions</b></p> <p>Careful estimation of primer efficiency is necessary to avoid significant measurement inaccuracies. Transformed confidence intervals are a novel method to assess and interprete the reliability of an efficiency estimate in a high throughput format. Efficiency clustering as developed here serves as a compromise between the imprecision in assuming uniform efficiency, and the computational complexity and danger of over-fitting when using individually determined efficiencies.</p

BCL-2 family protein expression and platinum drug resistance in ovarian carcinoma

The expression of the BCL-2 family proteins, BCL-2, BAX, BCLXLand BAK have been determined in a panel of 12 human ovarian carcinoma cell lines encompassing a wide range in sensitivity to cisplatin. Whereas BAX, BCLXLand BAK levels did not correlate with sensitivity, there was a statistically significant inverse correlation (r = –0.81;P = 0.002) between growth inhibition by cisplatin and BCL-2 levels. In sublines possessing acquired resistance to various platinum-based drugs or across a panel of human ovarian carcinoma xenografts, there was no consistent pattern of BCL-2 expression. Two relatively sensitive lines (A2780 and CH1) have been stably transfected with bcl-2 and bclXLrespectively and two relatively resistant lines (A2780cisR and SKOV-3) stably transfected with bax. Overexpression of BCL-2 in A2780 cells led to resistance to cisplatin compared to the vector control when assayed at 48 h post-drug incubation but a significant increase in sensitivity at 96 h. Relative rates of apoptosis at 48- and 96-h post-cisplatin exposure mirrored the growth inhibition. There was no significant difference in sensitivity of the pair of lines by clonogenic assay. No significant changes in chemosensitivity to a variety of DNA-damaging or tubulin-interactive agents were observed in the remaining transfected lines. Taken together, these results suggest that, in human ovarian carcinoma cells, high BCL-2 levels (either naturally occurring or through gene transfection) confers a trend towards sensitivity not resistance to platinum drugs. © 2000 Cancer Research Campaig

The Critical Behaviour of the Spin-3/2 Blume-Capel Model in Two Dimensions

The phase diagram of the spin-3/2 Blume-Capel model in two dimensions is explored by conventional finite-size scaling, conformal invariance and Monte Carlo simulations. The model in its $\tau$-continuum Hamiltonian version is also considered and compared with others spin-3/2 quantum chains. Our results indicate that differently from the standard spin-1 Blume-Capel model there is no multicritical point along the order-disorder transition line. This is in qualitative agreement with mean field prediction but in disagreement with previous approximate renormalization group calculations. We also presented new results for the spin-1 Blume-Capel model.Comment: latex 18 pages, 4 figure

Electron attachment to valence-excited CO

The possibility of electron attachment to the valence $^{3}\Pi$ state of CO is examined using an {\it ab initio} bound-state multireference configuration interaction approach. The resulting resonance has $^{4}\Sigma^{-}$ symmetry; the higher vibrational levels of this resonance state coincide with, or are nearly coincident with, levels of the parent $a^{3}\Pi$ state. Collisional relaxation to the lowest vibrational levels in hot plasma situations might yield the possibility of a long-lived CO$^-$ state.Comment: Revtex file + postscript file for one figur

On isovector meson exchange currents in the Bethe-Salpeter approach

We investigate the nonrelativistic reduction of the Bethe-Salpeter amplitude for the deuteron electrodisintegration near threshold energies. To this end, two assumptions have been used in the calculations: 1) the static approximation and 2) the one iteration approximation. Within these assumptions it is possible to recover the nonrelativistic result including a systematic extension to relativistic corrections. We find that the so-called pair current term can be constructed from the $P$-wave contribution of the deuteron Bethe-Salpeter amplitude. The form factor that enters into the calculation of the pair current is constrained by the manifestly gauge independent matrix elements.Comment: 15 pages, incl. 3 figures, to be published Phys. Rev.

Developing an intervention to facilitate family communication about inherited genetic conditions, and training genetic counsellors in its delivery.

Many families experience difficulty in talking about an inherited genetic condition that affects one or more of them. There have now been a number of studies identifying the issues in detail, however few have developed interventions to assist families. The SPRinG collaborative have used the UK Medical Research Council's guidance on Developing and Evaluating Complex Interventions, to work with families and genetic counsellors (GCs) to co-design a psycho-educational intervention to facilitate family communication and promote better coping and adaptation to living with an inherited genetic condition for parents and their children (<18 years). The intervention is modelled on multi-family discussion groups (MFDGs) used in psychiatric settings. The MFDG was developed and tested over three phases. First focus groups with parents, young people, children and health professionals discussed whether MFDG was acceptable and proposed a suitable design. Using evidence and focus group data, the intervention and a training manual were developed and three GCs were trained in its delivery. Finally, a prototype MFDG was led by a family therapist and co-facilitated by the three GCs. Data analysis showed that families attending the focus groups and intervention thought MFDG highly beneficial, and the pilot sessions had a significant impact on their family' functioning. We also demonstrated that it is possible to train GCs to deliver the MFDG intervention. Further studies are now required to test the feasibility of undertaking a definitive randomised controlled trial to evaluate its effectiveness in improving family outcomes before implementing into genetic counselling practice.The National Institute of Health Research funded the study but any views expressed do not necessarily reflect those of the Authority. Funded by NIHR reference number: RP-DG-1211-10015

Enhancing Optical Up-Conversion Through Electrodynamic Coupling with Ancillary Chromophores

In lanthanide-based optical materials, control over the relevant operating characteristics–for example transmission wavelength, phase and quantum efficiency–is generally achieved through the modification of parameters such as dopant/host combination, chromophore concentration and lattice structure. An alternative avenue for the control of optical response is through the introduction of secondary, codoped chromophores. Here, such secondary centers act as mediators, commonly bridging the transfer of energy between primary absorbers of externally sourced optical input and other sites of frequency-converted emission. Utilizing theoretical models based on experimentally feasible, three-dimensional crystal lattice structures; a fully quantized theoretical framework provides insights into the locally modified mechanisms that can be implemented within such systems. This leads to a discussion of how such effects might be deployed to either enhance, or potentially diminish, the efficiency of frequency up-conversion

Nesting properties and anisotropy of the Fermi surface of LuNi2_{2}B2_{2}C

The rare earth nickel borocarbides, with the generic formula $R$Ni$_{2}$B$_{2}$C, have recently been shown to display a rich variety of phenomena. Most striking has been the competition between, and even coexistence of, antiferromagnetism and superconductivity. We have measured the Fermi surface (FS) of LuNi$_{2}$B$_{2}$C, and shown that it possesses nesting features capable of explaining some of the phenomena experimentally observed. In particular, it had previously been conjectured that a particular sheet of FS is responsible for the modulated magnetic structures manifest in some of the series. We report the first direct experimental observation of this sheet.Comment: 4 pages, 4 PS figure