Testing the distance duality relation with present and future data

The assumptions that "light propagates along null geodesics of the spacetime metric" and "the number of photons is conserved along the light path" lead to the distance duality relation (DDR), $\eta = D_L(z) (1 + z)^{-2}/D_A(z) = 1$, with $D_L(z)$ and $D_A(z)$ the luminosity and angular diameter distances to a source at redshift $z$. In order to test the DDR, we follow the usual strategy comparing the angular diameter distances of a set of clusters, inferred from X - ray and radio data, with the luminosity distance at the same cluster redshift using the local regression technique to estimate $D_L(z)$ from Type Ia Supernovae (SNeIa) Hubble diagram. In order to both strengthen the constraints on the DDR and get rid of the systematics related to the unknown cluster geometry, we also investigate the possibility to use Baryon Acoustic Oscillations (BAO) to infer $D_A(z)$ from future BAO surveys. As a test case, we consider the proposed Euclid mission investigating the precision can be afforded on $\eta(z)$ from the expected SNeIa and BAO data. We find that the combination of BAO and the local regression coupled allows to reduce the errors on $\eta_a = d\eta/dz|_{z = 0}$ by a factor two if one $\eta_0 = \eta(z = 0) = 1$ is forced and future data are used. On the other hand, although the statistical error on $\eta_0$ is not significantly reduced, the constraints on this quantity will be nevertheless ameliorated thanks to the reduce impact of systematics.Comment: 10 pages, 1 figure, 1 table, accepted for publication on Physical Review

SN 2009ip at late times - an interacting transient at+2 years

We present photometric and spectroscopic observations of the interacting transient SN 2009ip taken during the 2013 and 2014 observing seasons. We characterize the photometric evolution as a steady and smooth decline in all bands, with a decline rate that is slower than expected for a solely Co-56-powered supernova at late phases. No further outbursts or eruptions were seen over a two year period from 2012 December until 2014 December. SN 2009ip remains brighter than its historic minimum from pre-discovery images. Spectroscopically, SN 2009ip continues to be dominated by strong, narrow (less than or similar to 2000 km s(-1)) emission lines of H, He, Ca, and Fe. While we make tenuous detections of [Fe II] lambda 7155 and [O I] lambda lambda 6300, 6364 lines at the end of 2013 June and the start of 2013 October, respectively, we see no strong broad nebular emission lines that could point to a core-collapse origin. In general, the lines appear relatively symmetric, with the exception of our final spectrum in 2014 May, when we observe the appearance of a redshifted shoulder of emission at +550 km s(-1). The lines are not blueshifted, and we see no significant near-or mid-infrared excess. From the spectroscopic and photometric evolution of SN 2009ip until 820 d after the start of the 2012a event, we still see no conclusive evidence for core-collapse, although whether any such signs could be masked by ongoing interaction is unclear

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Studying early Gamma Ray Burst stages with MAGIC and REM telescopes

I Gamma Ray Burst (GRB) sono fenomeni complessi la cui origine ed i cui meccanismi fisici sono ancora oggetto di dibattito scientifico. Osservazioni multifrequenza dell’afterglow dei Gamma Ray Burst possono essere utilizzate per porre dei vincoli ai parametri fisici fondamentali dell’esplosione. Uno dei maggiori aspetti del successo nella ricerca dei GRB ´e dato dalla rapidit´a con cui il telescopio ´e in grado di puntare la regione del GRB. Lo scopo del mio lavoro ´e stato quello di studiare le prime fasi dei Gamma Ray Burst a differenti lunghezze d’onda per capirne meglio le propriet´a fisiche, anche in vista delle prospettive future nella rivelazione di fotoni ad alta energia dai GRB offerte dalla nuova generazione di strumenti. Al fine di studiare l’emissione ad alta energia e nelle bande infrarosse ho utilizzato dati collezionati dai telescopi terrestri MAGIC (per le alte energie) e REM (nelle banda infrarosse). Entrambi questi strumenti sono stati costruiti con l’intento di permettere un rapido riposizionamento (nell’ ordine delle decine di secondi) nel caso di un GRB. Grazie al progetto di questa tesi il primo catalogo dei GRB rivelati da REM sar´a presto disponibile. Il catalogo conterr´a dettagliate informazioni sulle posizioni, sulle propriet´a temporali e fotometriche di tutti gli oggetti. Utilizzando le propriet´a delle curve di luce nelle bande infrarosse, ottenute attraverso un’analisi di fitting dei burst con un’estesa copertura temporale, ho posto dei limiti su alcuni parametri fondamentali della fireball che possono essere utilizzati per discriminare tra diversi meccanismi al lavoro nei GRB. In particolare ho studiato in dettaglio il meccanismo di emissione da Synchrotron Self Compton (SSC) concludendo che grazie ai nuovi strumenti, in particolare con MAGIC ed i suoi recenti miglioramenti tecnologici, la rivelazione di fotoni emessi per SSC ´e possibile nel caso di un burst sufficientemente energetico ed a basso redshift. Nella prima parte di questa tesi, dopo un’introduzione sui Gamma Ray Burst (capitolo 1), introdurr´o il telescopio MAGIC (capitolo 2) e presenter´o due burst interessanti seguiti da MAGIC per i quali ho studiato l’emissione gamma nel GeV nel contesto del meccanismo di Synchrotron Self Compton: GRB 080430 e GRB 090102 (capitolo 3). La seconda parte ´e dedicata all’osservazione dei Gamma Ray Burst nelle bande infrarosse effettuata con il telescopio REM (capitolo 4). Per la prima volta sono stati analizzati tutti i GRB osservati da REM dall’inizio delle operazioni fino alla fine del 2009 (capitolo 5). Per alcuni burst ben campionati ´e stato possibile stimare l’epoca del picco dell’afterglow e quindi determinare il fattore di Lorentz ed il parametro e della fireball. Questi parametri sono stati utilizzati per ottenere una stima precisa del flusso atteso alle alte energie dal meccanismo di SSC. Infine queste previsioni teoriche sono state confrontate con i risultati di MAGIC.Gamma-ray bursts (GRBs) are an enigmatic phenomenon whose physics and origins are still to be fully understood. Broadband observations of gamma-ray burst afterglows can in principle be used to constrain fundamental physical parameters of the explosion. One major aspect of successful GRB research is how fast the telescope can point the GRB region. The aim of my work was to investigate the early phases of GRB phenomenon at different wavelenghts to better understand their physical properties, also in view of the future perspectives offered by the new instruments in detecting the high energy photons from GRBs. In order to investigate high energy and infrared emission from GRBs I used data collected by the ground-based MAGIC Telescopes (at the high energies) and the REM telescope (in the near infrared band). Both instruments have been built in order to allow a rapid repositioning (tens of seconds). Thanks to the project of this thesis the first REM gamma -ray burst afterglow catalog will be avaiable soon. The catalogue will contain detailed burst positional, temporal and photometric information. Moreover, using the observed infrared properties obtained by the fitting analysis of those burst with an extended time-coverage, I put some constrains on fundamental fireball parameters that can be used to discriminate between different mechanism at work in GRBs. In particular I investigated the Synchrotron Self Compton (SSC) emission mechanism leading to the conclusion that thanks to the new incoming instruments, in particular with MAGIC and its new hardware upgrade, the detection of SSC emission from an energetic and low redshift burst is possible. In the first part of this thesis, after an introduction about the GRB phenomenon (chapter 1), I will introduce the MAGIC telescope (chapter 2) and I will present two interesting burst followed up by MAGIC for which I explored the GeV gamma-ray emission in the context of Synchrotron Self Compton mechanism (SSC): GRB 080430 and GRB 090102 (chapter 3). The second part is dedicated to infrared observations of GRBs performed by REM telescope (chapter 4). For the first time all the GRBs observed by REM, since the beginning of its operations up to the end of 2009, are analyzed (chapter 5). For some well sampled burst it was possible to evaluate the epoch of the afterglow peaks and thereby constrain the Lorentz factor and the e fireball parameters. These parameters obtained were used to derive meaningful prediction for the expected SSC flux at higher energy. Finally those predictions were compared with the MAGIC results

GRB 090426: the farthest short gamma-ray burst?

International audienceAims: With an observed and rest-frame duration o

Sex differences in oncogenic mutational processes

Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Peer reviewe

Sex differences in oncogenic mutational processes

Funder: Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology); doi: https://doi.org/10.13039/501100002790Funder: Genome Canada (Génome Canada); doi: https://doi.org/10.13039/100008762Funder: Canada Foundation for Innovation (Fondation canadienne pour l'innovation); doi: https://doi.org/10.13039/501100000196Funder: Terry Fox Research Institute (Institut de Recherche Terry Fox); doi: https://doi.org/10.13039/501100004376Abstract: Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts