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.

Massive stars exploding in a He-rich circumstellar medium - III. SN 2006jc: infrared echoes from new and old dust in the progenitor CSM

We present near- (NIR) and mid-infrared (MIR) photometric data of the Type Ibn supernova (SN) 2006jc obtained with the United Kingdom Infrared Telescope (UKIRT), the Gemini North Telescope and the Spitzer Space Telescope between days 86 and 493 post-explosion. We find that the IR behaviour of SN 2006jc can be explained as a combination of IR echoes from two manifestations of circumstellar material. The bulk of the NIR emission arises from an IR echo from newly condensed dust in a cool dense shell (CDs) produced by the interaction of the ejecta Outward shock with a dense shell of circumstellar material ejected by the progenitor in a luminous blue variable (LBV)-like outburst about two years prior to the SN explosion. The CDs dust mass reaches a modest 3.0 x 10(-4) M-circle dot by day 230. While dust condensation within a CDs formed behind the ejecta inward shock has been proposed before for one event (SN 1998S), SN 2006jc is the first one showing evidence for dust condensation in a CDs formed behind the ejecta outward shock in the circumstellar material. At later epochs, a substantial and growing contribution to the IR fluxes arises from an IR echo from pre-existing dust in the progenitor wind. The mass of the pre-existing circumstellar medium (CSM) dust is at least similar to 8 x 10(-3) M-circle dot. This paper therefore adds to the evidence that mass-loss from the progenitors of core-collapse SNe could be a major source of dust in the Universe. However, yet again, we see no direct evidence that the explosion of an SN produces anything other than a very modest amount of dust.

OXOIRON(IV) PORPHYRINS DERIVED FROM CHARGED IRON(III) TETRAARYLPORPHYRINS AND CHEMICAL OXIDANTS IN AQUEOUS AND METHANOLIC SOLUTIONS

The oxidation of six charged iron(III) tetraarylporphyrins with chemical oxidants has been investigated. In aqueous solution each can be converted by tert-butyl hydroperoxide or monopersulphate into its corresponding oxoiron(IV) porphyrin, whereas in methanol only the iron(III) tetra(N-methylpyridyl)porphyrins form detectable ferryl porphyrins at ambient temperatures. On standing, the iron species revert to the parent porphyrin with a small loss due to non-reversible oxidative destruction. That the oxidised porphyrin intermediates are oxoiron(IV) species has been determined using UV-VIS, resonance Raman, H1 NMR and EPR spectroscopy.

A 330-360 GHz spectral survey of G34.3+0.15 - III. The outer halo

We have undertaken a 330-360 GHz molecular line survey of the halo gas surrounding the hot core associated with G34.26+0.15. In contrast to our molecular line survey of the hot core itself, where 338 lines from at least 38 species were detected, only 18 lines from 9 species were detected in the halo. The lines are mainly single transitions of simple di atomic and triatomic molecules. Lower limits to their column densities have been evaluated by an LTE method. In the case of methanol, where four transitions were detected, the rotation temperature and column density have been evaluated by the rotation diagram technique. We have modified the previous depth-dependent chemical model developed in Paper II to calculate the column densities observed along a general line of sight drawn through the model cloud. The model is also extended to produce beam-averaged column densities for better comparison with those observed. We compare the model column densities with those observed and make recommendations for future depth-dependent chemical modelling of hot cores.

Molecular abundances in the magellanic clouds III. LIRS 36, a star-forming region in the Small Magellanic Cloud

Detections of CO, CS, SO, C2H, HCO+, HCN, HNC, H2CO, and C3H2 are reported from LIRS 36, a star-forming region in the Small Magellanic Cloud. (CO)-O-18, NO, CH3OH, and most notably CN have not been detected, while the rare isotopes (CO)-C-13 and, tentatively, (CS)-S-34 ar,seen. This is so far the most extensive molecular multiline study of an interstellar medium with a heavy element depletion exceeding a factor of four.

Early-type stars observed in the ESO UVES Paranal Observatory Project - III. Sub-parsec and AU-scale structure in the interstellar medium

UVES interstellar observations from the Paranal Observatory Project are presented for early-type stars located in the line of sight to the nearby open clusters IC 2391 (Omni Vel) and NGC 6475 (M7), with spectroscopic resolution R similar to 80 000 and signal-to-noise ratios in the Ti II (3383 angstrom), Ca II K, CH+ (4232 angstrom), Na I D and K I (7698 angstrom) lines of several hundred. The sightlines are a mixture of cluster and non-cluster objects. A total of 22 early-type stars (A and B type) are present in our sample towards IC 2391, with 21 towards NGC 6475/M7, and enable us to probe for differences in column density on scales from similar to 0.07 to 7.3 and similar to 0.05 to 4.9 pc in the respective clusters. Additionally, towards Praesepe the Na I D interstellar variation only is probed towards 13 sightlines and transverse scales of similar to 0.16-10.7 pc at R = 70 000. Towards IC 2391 variations are found in Ti II, Ca II K and Na I D column density in different sightlines of up to 0.7, 1.0 and 1.8 dex (excluding one star), respectively. This kind of variability correlates well with the Hipparcos parallax of the objects, and probes structure within the Local Bubble. For cluster-only objects the variations are 0.3, 0.3 and 0.5 dex, respectively. For the field of view towards NGC6475 the corresponding maximum variations are somewhat smaller, being 0.5, 0.3, 0.8 and 1.0 dex for Ti II, Ca II K, Na I and K I, respectively, for all objects and 0.4, 0.2, 0.6 and 0.7 dex for the cluster-only objects. These are uncorrelated with parallax, and again demonstrate that Ca II K tends to be more smoothly distributed than Na I D. A few likely cluster sightlines show evidence for CH+ and variations in this molecular species of a factor of 10 in equivalent width over sub-pc scales. Towards Praesepe variation in interstellar Na I D is small, being a maximum of only similar to 0.4 dex (including measurement errors), but with fewer sightlines studied. Overall, the scatter in the data is similar for the singly ionized species Ti II and Ca II, lending more support to the hypothesis that these two species sample similar parts of the interstellar medium (ISM). This also appears to be the case for the neutral species Na I D and K I in the one cluster studied. Finally, multiple-epoch observations from a variety of archive sources are used to search for astronomical unit (au) scale structure in the ISM towards 46 sightlines. There are tentative indications of structure on scales of tens to thousands of au for three sightlines. Future observations will confirm the veracity or otherwise of the time-variable components and others presented.

Energy levels, radiative rates and electron impact excitation rates for transitions in He-like Li II, Be III, B IV and C V

We report calculations for energy levels, radiative rates and electron impact excitation rates for transitions in He-like Li II, Be III, B IV and C V. grasp (general-purpose relativistic atomic structure package) is adopted for calculating energy levels and radiative rates. For determining the collision strengths and subsequently the excitation rates, the Dirac atomic R-matrix code (darc) is used. Oscillator strengths, radiative rates and line strengths are reported for all E1, E2, M1 and M2 transitions among the lowest 49 levels of each ion. Collision strengths have been averaged over a Maxwellian velocity distribution and the effective collision strengths so obtained are reported over a wide temperature range up to 10(6) K. Comparisons have been made with similar data obtained from the flexible atomic code (FAC) to highlight the importance of resonances, included in calculations from darc, in the determination of effective collision strengths. Discrepancies between the collision strengths from darc and fac, particularly for weak transitions and at low energies, have also been discussed. Additionally, lifetimes are also listed for all calculated levels of the above four ions.

Reactivity difference between protolytic forms of some macrocyclic chromium(III) complexes in ligand substitution and electron transfer processes

The review provides insight into the mechanism of ligand substitution and electron transfer (from chromium(III) to iron(III)) by comparison of the reactivity of some tetraazamacrocyclic chromium(III) complexes in the conjugate acid-base forms. Use of two geometrical isomers made possible to estimate the influence of geometry and protolytic reactions in trans and cis position towards the leaving group on the rate enhancement. Studies on the reaction rates in different media demonstrated the role played by outer sphere interactions in a monodentate ligand substitution. (C) 2009 Published by Elsevier B.V.

Kinetics and mechanism of a macrocyclic chromium(III) complex oxidation to chromium(IV) by hexacyanoferrate(III) in strongly alkaline media

Oxidation of the macrocyclic Cr(III) complex cis-[Cr(cycb)(OH)(2)](+), where cycb = rac-5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane, by an excess of the hexacyanoferrate( III) in basic solution, slowly produces Cr(V) species. These species, detected using e.p.r. spectroscopy, are stable under ambient conditions for many hours, and the hyperfine structure of the e.p.r. spectrum is consistent with the interaction of the d-electron with four equivalent nitrogen nuclei. Electro-spray ionization mass spectrometry suggests a concomitant oxidation of the macrocyclic ligand, in which double bonds and double bonded oxygen atoms have been introduced. By comparison basic chromate(III) solutions are oxidized rapidly to chromate(VI) by hexacyanoferrate(III) without any detectable generation of stable Cr(V) intermediates.

EFFECT OF ULTRASOUND ON THE KINETICS OF REDUCTION OF HEXACYANOFERRATE(III) BY THIOSULFATE IONS MEDIATED BY RUTHENIUM DIOXIDE HYDRATE

Ultrasound promotes the reduction of hexacyanoferrate(III) by thiosulfate ions mediated by RuO2 . xH(2)O under diffusion-controlled conditions. There is a strong correlation between the measured first-order rate constant and the absorbance of the dispersion, which, in turn, is closely related to the specific surface area of the catalyst. The enhancement in rate with ultrasonic irradiation appears to be largely associated with the dispersive action of the ultrasound on the aggregated particles of RuO2 . xH(2)O. The rate of reaction increases with increasing %duty cycle and ultrasonic intensity. The measured overall activation energies for the reaction with and without ultrasound, i.e. 18 +/- 1 and 20 +/- 1 kJ mol(-1), respectively, are very similar to those expected for a diffusion-controlled reaction. The homogeneous reaction is not promoted by ultrasound.

KINETICS OF REDUCTIVE DISSOLUTION OF SODIUM BISMUTHATE BY CE-III AND MN-II IONS

The kinetics of reductive dissolution of NaBiO3, by Mn-II and Ce-III ions are studied as a function of [Mn-II] or [Ce-III], [Bi-III], [H+] and temperature. They fit a simple inverse-cubic rate law and can be readily interpreted using a mechanism in which the rate-determining step is the reaction between an adsorbed reducing species (i.e. a Mn-II or Ce-III ion) and its associated surface site; protonation of the surface site promotes the rate of reaction. The rate of dissolution decreases with increasing initial concentration of Bi-III ions owing to competitive inhibition by the latter species. A kinetic model, based on this mechanism, is applied and provides a quantitative description of the observed kinetics.

KINETICS OF REDUCTION OF HEXACYANOFERRATE(III) BY THIOSULFATE IONS MEDIATED BY RUTHENIUM DIOXIDE HYDRATE

The kinetics of reduction of hexacyanoferrate(III) by excess thiosulfate, mediated by RuO2.xH2O, are investigated. At high concentrations of S2O32- (0.1 mol dm-3) the kinetics of Fe(CN)63- reduction are first order with respect to [Fe(CN)63-] and [RuO2.xH2O] and independent of [Fe(CN)64-], [S2O32-] and [S4O62-]. At relatively low concentrations Of S2O32- (0.01 mol dm-3) and in the presence of appreciable concentrations of Fe(CN)64- and S4O62- (0.01 mol dm-3) the kinetics depend directly upon [Fe(CN)63-] and [RuO2.xH2O] and inversely upon [Fe(CN)64-]. Both sets of kinetics can be rationalised using an electrochemical model of redox catalysts in which a reversible reduction reaction [Fe(CN)63- + e- --> Fe(CN)64-] is coupled to an irreversible oxidation reaction (s2O32- - e- --> 1/2S4O62-), by a dispersion of RuO2.xH2O microelectrodes. At high concentrations Of S2O32- this model predicts that the kinetics of Fe(CN)63- reduction are controlled by the rate of diffusion of the Fe(CN)63- ions to the RuO2.xH2O particles. The kinetics observed at low concentrations of S2O32- are predicted by the electrochemical model, assuming that the Tafel slope for the oxidation Of S2O32- to S4O62- on the RuO2.xH2O particles is 56.4 mV decade-1.