Tissue biomarker development in a multicentre trial context: a feasibility study on the PETACC3 stage II and III colon cancer adjuvant treatment trial.

Purpose: We evaluated the feasibility of biomarker development in the context of multicenter clinical trials.

Experimental Design: Formalin-fixed, paraffin-embedded (FFPE) tissue samples were collected from a prospective adjuvant colon cancer trial (PETACC3). DNA was isolated from tumor as well as normal tissue and used for analysis of microsatellite instability, KRAS and BRAF genotyping, UGT1A1 genotyping, and loss of heterozygosity of 18 q loci. Immunohistochemistry was used to test expression of TERT, SMAD4, p53, and TYMS. Messenger RNA was retrieved and tested for use in expression profiling experiments.

Results: Of the 3,278 patients entered in the study, FFPE blocks were obtained from 1,564 patients coming from 368 different centers in 31 countries. In over 95% of the samples, genomic DNA tests yielded a reliable result. Of the immmunohistochemical tests, p53 and SMAD4 staining did best with reliable results in over 85% of the cases. TERT was the most problematic test with 46% of failures, mostly due to insufficient tissue processing quality. Good quality mRNA was obtained, usable in expression profiling experiments.

Conclusions: Prospective clinical trials can be used as framework for biomarker development using routinely processed FFPE tissues. Our results support the notion that as a rule, translational studies based on FFPE should be included in prospective clinical trials.

Fitness reduction and potential extinction of wild populations of Atlantic salmon, Salmo salar, as a result of interactions with escaped farm salmon.

The high level of escapes from Atlantic salmon farms, up to two million fishes per year in the North Atlantic, has raised concern about the potential impact on wild populations. We report on a twogeneration experiment examining the estimated lifetime successes, relative to wild natives, of farm, F1 and F2 hybrids and BC1 backcrosses to wild and farm salmon. Offspring of farm and hybrids (i.e. all F1 , F2 and BC1 groups) showed reduced survival compared with wild salmon but grew faster as juveniles and displaced wild parr, which as a group were significantly smaller. Where suitable habitat for these emigrant parr is absent, this competition would result in reduced wild smolt production. In the experimental conditions, where emigrants survived downstream, the relative estimated lifetime success ranged from 2% (farm) to 89% (BC1 wild) of that of wild salmon, indicating additive genetic variation for survival . Wild salmon primarily returned to fresh water after one sea winter (1SW) but farm and hybrids produced proportionately more 2SW salmon. However, lower overall survival means that this would result in reduced recruitment despite increased 2SW fecundity. We thus demonstrate that interaction of farm with wild salmon results in lowered fitness, with repeated escapes causing cumulative fitness depression and potentially an extinction vortex in vulnerable populations.

A reliable externally fixated murine femoral fracture model that accounts for variation in movement between animals.

Fifty-two CFLP mice had an open femoral diaphyseal osteotomy held in compression by a four-pin external fixator. The movement of 34 of the mice in their cages was quantified before and after operation, until sacrifice at 4, 8, 16 or 24 days. Thirty-three specimens underwent histomorphometric analysis and 19 specimens underwent torsional stiffness measurement. The expected combination of intramembranous and endochondral bone formation was observed, and the model was shown to be reliable in that variation in the histological parameters of healing was small between animals at the same time point, compared to the variation between time-points. There was surprisingly large individual variation in the amount of animal movement about the cage, which correlated with both histomorphometric and mechanical measures of healing. Animals that moved more had larger external calluses containing more cartilage and demonstrated lower torsional stiffness at the same time point. Assuming that movement of the whole animal predicts, at least to some extent, movement at the fracture site, this correlation is what would be expected in a model that involves similar processes to those in human fracture healing. Models such as this, employed to determine the effect of experimental interventions, will yield more information if the natural variation in animal motion is measured and included in the analysis.

Depressed mood and dietary fish intake: Direct relationship or indirect relationship as a result of diet and lifestyle?

Previous studies have suggested an association between depressed mood and the dietary intake of fish. In all cases, however, dietary fish intake has been considered at the exclusion of all other aspects of the diet. This analysis investigates associations between depressed mood and dietary fish intake, while also concurrently investigating intake of a number of other dietary components. The analysis is conducted on data from 10,602 men from Northern Ireland and France screened for inclusion into the PRIME cohort study. Depressed mood was assessed using a self-report questionnaire based on the Welsh Pure Depression sub-scale of the Minnesota Multiphasic Personality Inventory, diet was assessed using a Food Frequency Questionnaire, and limited demographics were also measured. Using regression, depressed mood is initially inversely associated with dietary fish intake. On inclusion of all other dietary variables, the strength of this relationship reduces but remains, and significant associations with a number of other foods are also found. On additional inclusion of all demographic variables, the strength of the above relationships again reduces, and associations with various measures of socio-economic status and education are also significant. These findings suggest that depressed mood is associated with fish intake both directly, and indirectly as part of a diet that is associated with depression and as part of a lifestyle that is associated with depression. Additional support for these conclusions is also provided in the pattern of associations between depressed mood and diet in the two countries. The relative contributions of fish intake to depressed mood both directly and indirectly are yet to be determined. However, while diet is not measured and until lifestyle can be adequately measured, the potential roles of diet and lifestyle in the association between depressed mood and dietary fish intake should not be ignored.

High levels of genetic structuring as a result of population fragmentation in the tropical tree species Caesalpinia echinata Lam.

We have investigated levels of genetic diversity within and among seven remnant populations of Caesalpinia echinata Lam., an endangered species found as fragmented populations in three major areas around the coastal regions of Brazil. Using amplified fragment length polymorphism (AFLP) genetic markers, we detected levels of within-population genetic diversity ranging from 0.092 to 0.163, with the lowest values generally being found in the smallest populations. Estimates of between-population genetic differentiation were strongly correlated with geographical distance ( r = 0.884, p <0.001), which, along with a neighbour-joining phylogenetic analysis, strongly suggested high levels of genetic isolation by distance. Over half (62%) of the total genetic diversity was partitioned between populations, further highlighting the genetic distinctness of individual populations. Taken together, these results suggest that fragmentation has led to an increase in population differentiation between fragments of C. echinata. These formations will be of great value in the development of conservation plans for species exhibiting high levels of genetic differentiation due to fragmentation, such as indication of conservation unit size, which populations should be chosen as priority in conservation plans and which samples should be introduced in areas with a low number of individuals of brazilwood.

Is the flow tube reactor with NO2 titration a reliable absolute source for atomic hydrogen?

The H+NO2 titration scheme for the determination of atomic hydrogen densities within a microwave excited flow tube reactor has been investigated by laser-induced fluorescence spectroscopy in the vacuum UV. Absolute hydrogen densities are determined on the basis of calibration by Rayleigh scattering from argon. The measurement is performed at a gas mixture containing 0.5% of D2 added to the main gas H2. The ground state density of the hydrogen atoms generated in the flow tube reactor was inferred from the fluorescence radiation of the spectrally shifted optically thin D-Lyman-a transition.

The rotational broadening of V395 Carinae. Implications on the compact object's mass

Context: The masses previously obtained for the X-ray binary 2S 0921-630 inferred a compact object that was either a high-mass neutron star or low-mass black-hole, but used a previously published value for the rotational broadening (v sin i) with large uncertainties. Aims: We aim to determine an accurate mass for the compact object through an improved measurement of the secondary star's projected equatorial rotational velocity. Methods: We have used UVES echelle spectroscopy to determine the v sin i of the secondary star (V395 Car) in the low-mass X-ray binary 2S 0921-630 by comparison to an artificially broadened spectral-type template star. In addition, we have also measured v sin i from a single high signal-to-noise ratio absorption line profile calculated using the method of Least-Squares Deconvolution (LSD). Results: We determine v sin i to lie between 31.3±0.5 km s-1 to 34.7±0.5 km s-1 (assuming zero and continuum limb darkening, respectively) in disagreement with previous results based on intermediate resolution spectroscopy obtained with the 3.6 m NTT. Using our revised v sin i value in combination with the secondary star's radial velocity gives a binary mass ratio of 0.281±0.034. Furthermore, assuming a binary inclination angle of 75° gives a compact object mass of 1.37±0.13 M_?. Conclusions: We find that using relatively low-resolution spectroscopy can result in systemic uncertainties in the measured v sin i values obtained using standard methods. We suggest the use of LSD as a secondary, reliable check of the results as LSD allows one to directly discern the shape of the absorption line profile. In the light of the new v sin i measurement, we have revised down the compact object's mass, such that it is now compatible with a canonical neutron star mass.

Roche tomography of cataclysmic variables - I. Artefacts and techniques

Roche tomography is a technique used for imaging the Roche-lobe-filling secondary stars in cataclysmic variables (CVs). In order to interpret Roche tomograms correctly, one must determine whether features in the reconstruction are real, or the result of statistical or systematic errors. We explore the effects of systematic errors using reconstructions of simulated data sets, and show that systematic errors result in characteristic distortions of the final reconstructions that can be identified and corrected. In addition, we present a new method of estimating statistical errors on tomographic reconstructions using a Monte Carlo bootstrapping algorithm, and show this method to be much more reliable than Monte Carlo methods which 'jiggle' the data points in accordance with the size of their error bars.

Deuterium in the Galactic Centre as a result of recent infall of low-metallicity gas

The Galactic Centre is the most active and heavily processed region of the Milky Way, so it can be used as a stringent test for the abundance of deuterium (a sensitive indicator of conditions in the first 1,000 seconds in the life of the Universe). As deuterium is destroyed in stellar interiors, chemical evolution models 1 predict that its Galactic Centre abundance relative to hydrogen is D/H = 5 x 10(-12), unless there is a continuous source of deuterium from relatively primordial (low-metallicity) gas. Here we report the detection of deuterium (in the molecule DCN) in a molecular cloud only 10 parsecs from the Galactic Centre. Our data, when combined with a model of molecular abundances, indicate that D/H = (1.7 +/- 0.3) x 10(-6), five orders of magnitude larger than the predictions of evolutionary models with no continuous source of deuterium. The most probable explanation is recent infall of relatively unprocessed metal-poor gas into the Galactic Centre (at the rate inferred by Wakker(2)). Our measured D/H is nine times less than the local interstellar value, and the lowest D/H observed in the Galaxy. We conclude that the observed Galactic Centre deuterium is cosmological, with an abundance reduced by stellar processing and mixing, and that there is no significant Galactic source of deuterium.