THIAMINE IN FISH AND ITS DEGRADATION DURING THERMAL PROCESSING OF SALTED-BOILED FISH

The existence of different forms of thiamine in the llesh of rainbow trout (Salmo gairdneri) and  their losses during thermal processing have been investigated

Synthesis, morphology and properties of segmented poly(ether ester amide)s comprising uniform glycine or β-alanine extended bisoxalamide hard segments

Segmented poly(ether ester amide)s comprising glycine or β-alanine extended bisoxalamide hard segments are highly phase separated thermoplastic elastomers with a broad temperature independent rubber plateau. These materials with molecular weights, Mn, exceeding 30 × 103 g mol−1 are conveniently prepared by polycondensation of preformed bisester–bisoxalamides and commercially available PTHF diols. FT-IR revealed strongly hydrogen bonded and highly ordered bisoxalamide hard segments with degrees of ordering between 73 and 99%. The morphology consists of fiber-like nano-crystals randomly dispersed in the soft polymer matrix. The micro-structural parameters of the copolymers were addressed by simultaneous small- and wide-angle X-ray scattering. It is shown that the crystals have strictly identical thickness, which is close to the contour length of the hard segment. The long dimension of the crystals is identified with the direction of the hydrogen bonds. The melting transitions of the hard segments are sharp, with temperatures up to 170 °C. The studied polymers have an elastic modulus in the range of 139–170 MPa, a stress at break in the range of 19–31 MPa combined with strains at break of higher than 800%. The segmented copolymer comprising the β-alanine based bisoxalamide hard segment with a spacer of 6 methylene groups has a melting transition of 141 °C which is higher than the melting transition of its glycine analogue of 119 °C. Likewise, the fracture stress increased from 22 to 31 MPa when the glycine ester group in the hard segment was replaced with β-alanine. The improved thermal and mechanical properties of the latter polymers is related to the crystal packing of the β-alanine based hard segments in the copolymer compared to the packing of the hard segments comprising glycine ester group

Averaging Robertson-Walker Cosmologies

The cosmological backreaction arises when one directly averages the Einstein equations to recover an effective Robertson-Walker cosmology, rather than assuming a background a priori. While usually discussed in the context of dark energy, strictly speaking any cosmological model should be recovered from such a procedure. We apply the Buchert averaging formalism to linear Robertson-Walker universes containing matter, radiation and dark energy and evaluate numerically the discrepancies between the assumed and the averaged behaviour, finding the largest deviations for an Einstein-de Sitter universe, increasing rapidly with Hubble rate to a 0.01% effect for h=0.701. For the LCDM concordance model, the backreaction is of the order of Omega_eff~4x10^-6, with those for dark energy models being within a factor of two or three. The impacts at recombination are of the order of 10^-8 and those in deep radiation domination asymptote to a constant value. While the effective equations of state of the backreactions in Einstein-de Sitter, concordance and quintessence models are generally dust-like, a backreaction with an equation of state w_eff<-1/3 can be found for strongly phantom models.Comment: 18 pages, 11 figures, ReVTeX. Updated to version accepted by JCA

Contribution de la culture des foraminifères benthiques à la calibration de proxies paléocéanographiques

Grâce aux connaissances acquises sur les conditions idéales de culture de différentes espèces de foraminifères benthiques, il est désormais possible de réaliser des calibrations de proxies paléocéanographiques en laboratoire. Plusieurs expériences ont déjà été réalisées : 1) Calibration du δ18O de foraminifères benthiques profonds (Barras et al., 2010) La culture de Bulimina marginata en conditions contrôlées à différentes températures (4 à 19°C) a permis de démontrer que l’effet de la température sur le δ18O de cette espèce est semblable à l’effet thermodynamique enregistré pour la calcite inorganique. Nous avons pu mettre en évidence également un effet ontogénétique non négligeable pour les études de reconstitutions paléoclimatiques. 2) Calibration du Mg/Ca de coquilles de Hyalinea balthica (Rosenthal et al., 2011) La calcification de nouvelles loges de H. balthica à différentes températures (8, 10 et 13°C) a permis de mesurer, à l’aide de l’ablation laser ICP-MS, un effet d’environ 12%/°C sur la concentration en Mg/Ca. Ces résultats confirment la calibration in situ réalisée pour cette espèce qui se trouve avoir une sensibilité 4 fois supérieure à celle des autres espèces benthiques profondes. 3) Effet de la salinité sur le δ18O, le Mg/Ca et le Sr/Ca d’une espèce côtière (Diz et al., 2012) La culture d’Ammonia tepida en conditions contrôlées à différentes salinités (29.8, 32.2, 35.5) n’a pas montré d’effet significatif de ce paramètre sur la composition isotopique et en éléments traces de la calcite. Par contre, ces expériences ont permis de mettre en évidence un effet de la taille des individus sur la composition en Sr/Ca et une forte variabilité des mesures de Mg/Ca entre les coquilles d’individus ayant calcifié dans les mêmes conditions. 4) Effet de la nourriture sur le δ13C d’espèces intertidales (Mojtahid et al., 2011) Des expériences menées en laboratoire sur des coquilles adultes de Hyanesina germanica et A. beccarii avec de la nourriture labélisée radioactivement (3H et 14C) ont montré que très peu de carbone ingéré est incorporé dans la coquille. Cependant, aucun des spécimens n’a formé de nouvelles loges pendant les expériences ce qui ne permet pas une conclusion définitive sur l’influence de la nourriture sur la signature isotopique de la calcite. Ceci ouvre les portes à d’autres expériences sur des juvéniles avec le même protocole qui s’est avéré très approprié. Ces études ont démontré l’utilité de réaliser des calibrations de proxies en laboratoire. Nous prévoyons de poursuivre ce travail en travaillant au développement de nouveaux proxies de paléo-oxygénation grâce au programme de recherche régional MADONA

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 7 TeV pp collisions with the ATLAS detector

A search for the direct production of charginos and neutralinos in final states with three electrons or muons and missing transverse momentum is presented. The analysis is based on 4.7 fb−1 of proton–proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in three signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric models and in simplified models, significantly extending previous results

Jet size dependence of single jet suppression in lead-lead collisions at sqrt(s(NN)) = 2.76 TeV with the ATLAS detector at the LHC

Measurements of inclusive jet suppression in heavy ion collisions at the LHC provide direct sensitivity to the physics of jet quenching. In a sample of lead-lead collisions at sqrt(s) = 2.76 TeV corresponding to an integrated luminosity of approximately 7 inverse microbarns, ATLAS has measured jets with a calorimeter over the pseudorapidity interval |eta| < 2.1 and over the transverse momentum range 38 < pT < 210 GeV. Jets were reconstructed using the anti-kt algorithm with values for the distance parameter that determines the nominal jet radius of R = 0.2, 0.3, 0.4 and 0.5. The centrality dependence of the jet yield is characterized by the jet "central-to-peripheral ratio," Rcp. Jet production is found to be suppressed by approximately a factor of two in the 10% most central collisions relative to peripheral collisions. Rcp varies smoothly with centrality as characterized by the number of participating nucleons. The observed suppression is only weakly dependent on jet radius and transverse momentum. These results provide the first direct measurement of inclusive jet suppression in heavy ion collisions and complement previous measurements of dijet transverse energy imbalance at the LHC.Comment: 15 pages plus author list (30 pages total), 8 figures, 2 tables, submitted to Physics Letters B. All figures including auxiliary figures are available at http://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/HION-2011-02

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy

The performance of the jet trigger for the ATLAS detector during 2011 data taking

The performance of the jet trigger for the ATLAS detector at the LHC during the 2011 data taking period is described. During 2011 the LHC provided proton–proton collisions with a centre-of-mass energy of 7 TeV and heavy ion collisions with a 2.76 TeV per nucleon–nucleon collision energy. The ATLAS trigger is a three level system designed to reduce the rate of events from the 40 MHz nominal maximum bunch crossing rate to the approximate 400 Hz which can be written to offline storage. The ATLAS jet trigger is the primary means for the online selection of events containing jets. Events are accepted by the trigger if they contain one or more jets above some transverse energy threshold. During 2011 data taking the jet trigger was fully efficient for jets with transverse energy above 25 GeV for triggers seeded randomly at Level 1. For triggers which require a jet to be identified at each of the three trigger levels, full efficiency is reached for offline jets with transverse energy above 60 GeV. Jets reconstructed in the final trigger level and corresponding to offline jets with transverse energy greater than 60 GeV, are reconstructed with a resolution in transverse energy with respect to offline jets, of better than 4 % in the central region and better than 2.5 % in the forward direction