Theory of photospheric emission from relativistic outflows

In this paper we reexamine the optical depth of ultrarelativistic spherically symmetric outflows and reevaluate the photospheric radius for each model during both the acceleration and coasting phases. It is shown that for both the wind and the shell models there are two asymptotic solutions for the optical depth during the coasting phase of the outflow. In particular we show that quite counterintuitively a geometrically thin shell may appear as a thick wind for photons propagating inside it. For this reason we introduce notions of photon thick and photon thin outflows, which appear more general and better physically motivated with respect to winds and shells. Photosphere of relativistic outflow is a dynamic surface. We study its geometry and find that the photosphere of photon thin outflow has always a convex shape, while in the photon thick one it is initially convex (there is always a photon thin layer in any outflow) and then it becomes concave asymptotically approaching the photosphere of an infinitely long wind. We find that both instantaneous and time integrated observed spectra are very close to the thermal one for photon thick outflows, in line with existing studies. It is our main finding that the photospheric emission from the photon thin outflow produces non thermal time integrated spectra, which may be described by the Band function well known in the GRB literature. We find that energetic GRBs should produce photon thin outflows with photospheric emission lasting less than one second for the total energy $E_0\leq10^{54}$ erg and baryonic loading parameter $B\leq10^{-2}$. It means that only time integrated spectra may be observed from such GRBs.Comment: Revision of the previous version, new effect is discussed. Conclusions remain unchange

Trick or treat: the effect of placebo on the power of pharmacogenetic association studies

The genetic mapping of drug-response traits is often characterised by a poor signal-to-noise ratio that is placebo related and which distinguishes pharmacogenetic association studies from classical case-control studies for disease susceptibility. The goal of this study was to evaluate the statistical power of candidate gene association studies under different pharmacogenetic scenarios, with special emphasis on the placebo effect. Genotype/phenotype data were simulated, mimicking samples from clinical trials, and response to the drug was modelled as a binary trait. Association was evaluated by a logistic regression model. Statistical power was estimated as a function of the number of single nucleotide polymorphisms (SNPs) genotyped, the frequency of the placebo 'response', the genotype relative risk (GRR) of the response polymorphism, the strategy for selecting SNPs for genotyping, the number of individuals in the trial and the ratio of placebo-treated to drug-treated patients. We show that: (i) the placebo 'response' strongly affects the statistical power of association studies--even a highly penetrant drug-response allele requires at least a 500-patient trial in order to reach 80 per cent power, several-fold more than the value estimated by standard tools that are not calibrated to pharmacogenetics; (ii) the power of a pharmacogenetic association study depends primarily on the penetrance of the response genotype and, when this penetrance is fixed, power decreases for larger placebo effects; (iii) power is dramatically increased when adding markers; (iv) an optimal study design includes a similar number of placebo- and drug-treated patients; and (v) in this setting, straightforward haplotype analysis does not seem to have an advantage over single marker analysis

Constraining Sources of Ultra High Energy Cosmic Rays Using High Energy Observations with the Fermi Satellite

We analyze the conditions that enable acceleration of particles to ultra-high energies, ~10^{20} eV (UHECRs). We show that broad band photon data recently provided by WMAP, ISOCAM, Swift and Fermi satellites, yield constraints on the ability of active galactic nuclei (AGN) to produce UHECRs. The high energy (MeV - GeV) photons are produced by Compton scattering of the emitted low energy photons and the cosmic microwave background or extra-galactic background light. The ratio of the luminosities at high and low photon energies can therefore be used as a probe of the physical conditions in the acceleration site. We find that existing data excludes core regions of nearby radio-loud AGN as possible acceleration sites of UHECR protons. However, we show that giant radio lobes are not excluded. We apply our method to Cen A, and show that acceleration of protons to ~10^{20} eV can only occur at distances >~ 100 kpc from the core.Comment: Extended discussion on former results; Accepted for publication in JCA

Evolution of Global Relativistic Jets: Collimations and Expansion with kKHI and the Weibel Instability

One of the key open questions in the study of relativistic jets is their interaction with the environment. Here, we study the initial evolution of both electron-proton and electron-positron relativistic jets, focusing on their lateral interaction with the ambient plasma. We trace the generation and evolution of the toroidal magnetic field generated by both kinetic Kelvin-Helmholtz (kKH) and Mushroom instabilities (MI). This magnetic field collimates the jet. We show that in electron-proton jet, electrons are perpendicularly accelerated with jet collimation. The magnetic polarity switches from the clockwise to anti-clockwise in the middle of jet, as the instabilities weaken. For the electron-positron jet, we find strong mixture of electron-positron with the ambient plasma, that results in the creation of a bow shock. Merger of magnetic field current filaments generate density bumps which initiate a forward shock. The strong mixing between jet and ambient particles prevents full development of the jet on the studied scale. Our results therefore provide a direct evidence for both jet collimation and particle acceleration in the created bow shock. Differences in the magnetic field structures generated by electron-proton and electron-positron jets may contribute to observable differences in the polarized properties of emission by electrons.Comment: 25 pages, 12 figures, ApJ, accepte

Gamma Ray Bursts: recent results and connections to very high energy Cosmic Rays and Neutrinos

Gamma-ray bursts are the most concentrated explosions in the Universe. They have been detected electromagnetically at energies up to tens of GeV, and it is suspected that they could be active at least up to TeV energies. It is also speculated that they could emit cosmic rays and neutrinos at energies reaching up to the $10^{18}-10^{20}$ eV range. Here we review the recent developments in the photon phenomenology in the light of \swift and \fermi satellite observations, as well as recent IceCube upper limits on their neutrino luminosity. We discuss some of the theoretical models developed to explain these observations and their possible contribution to a very high energy cosmic ray and neutrino background.Comment: 12 pages, 7 figures. Text of a plenary lecture at the PASCOS 12 conference, Merida, Yucatan, Mexico, June 2012; to appear in J.Phys. (Conf. Series

The Gamma Ray Burst section of the White Paper on the Status and Future of Very High Energy Gamma Ray Astronomy: A Brief Preliminary Report

Original paper can be found at: http://proceedings.aip.org/proceedings/ Copyright American Institute of Physics DOI: 10.1063/1.2943545otherPeer reviewe

A classification-based framework for predicting and analyzing gene regulatory response

BACKGROUND: We have recently introduced a predictive framework for studying gene transcriptional regulation in simpler organisms using a novel supervised learning algorithm called GeneClass. GeneClass is motivated by the hypothesis that in model organisms such as Saccharomyces cerevisiae, we can learn a decision rule for predicting whether a gene is up- or down-regulated in a particular microarray experiment based on the presence of binding site subsequences ("motifs") in the gene's regulatory region and the expression levels of regulators such as transcription factors in the experiment ("parents"). GeneClass formulates the learning task as a classification problem — predicting +1 and -1 labels corresponding to up- and down-regulation beyond the levels of biological and measurement noise in microarray measurements. Using the Adaboost algorithm, GeneClass learns a prediction function in the form of an alternating decision tree, a margin-based generalization of a decision tree. METHODS: In the current work, we introduce a new, robust version of the GeneClass algorithm that increases stability and computational efficiency, yielding a more scalable and reliable predictive model. The improved stability of the prediction tree enables us to introduce a detailed post-processing framework for biological interpretation, including individual and group target gene analysis to reveal condition-specific regulation programs and to suggest signaling pathways. Robust GeneClass uses a novel stabilized variant of boosting that allows a set of correlated features, rather than single features, to be included at nodes of the tree; in this way, biologically important features that are correlated with the single best feature are retained rather than decorrelated and lost in the next round of boosting. Other computational developments include fast matrix computation of the loss function for all features, allowing scalability to large datasets, and the use of abstaining weak rules, which results in a more shallow and interpretable tree. We also show how to incorporate genome-wide protein-DNA binding data from ChIP chip experiments into the GeneClass algorithm, and we use an improved noise model for gene expression data. RESULTS: Using the improved scalability of Robust GeneClass, we present larger scale experiments on a yeast environmental stress dataset, training and testing on all genes and using a comprehensive set of potential regulators. We demonstrate the improved stability of the features in the learned prediction tree, and we show the utility of the post-processing framework by analyzing two groups of genes in yeast — the protein chaperones and a set of putative targets of the Nrg1 and Nrg2 transcription factors — and suggesting novel hypotheses about their transcriptional and post-transcriptional regulation. Detailed results and Robust GeneClass source code is available for download from

Discovery of Sexual Dimorphisms in Metabolic and Genetic Biomarkers

Metabolomic profiling and the integration of whole-genome genetic association data has proven to be a powerful tool to comprehensively explore gene regulatory networks and to investigate the effects of genetic variation at the molecular level. Serum metabolite concentrations allow a direct readout of biological processes, and association of specific metabolomic signatures with complex diseases such as Alzheimer's disease and cardiovascular and metabolic disorders has been shown. There are well-known correlations between sex and the incidence, prevalence, age of onset, symptoms, and severity of a disease, as well as the reaction to drugs. However, most of the studies published so far did not consider the role of sexual dimorphism and did not analyse their data stratified by gender. This study investigated sex-specific differences of serum metabolite concentrations and their underlying genetic determination. For discovery and replication we used more than 3,300 independent individuals from KORA F3 and F4 with metabolite measurements of 131 metabolites, including amino acids, phosphatidylcholines, sphingomyelins, acylcarnitines, and C6-sugars. A linear regression approach revealed significant concentration differences between males and females for 102 out of 131 metabolites (p-values<3.8 x 10(-4); Bonferroni-corrected threshold). Sex-specific genome-wide association studies (GWAS) showed genome-wide significant differences in beta-estimates for SNPs in the CPS1 locus (carbamoyl-phosphate synthase 1, significance level: p<3.8 x 10(-10); Bonferroni-corrected threshold) for glycine. We showed that the metabolite profiles of males and females are significantly different and, furthermore, that specific genetic variants in metabolism-related genes depict sexual dimorphism. Our study provides new important insights into sex-specific differences of cell regulatory processes and underscores that studies should consider sex-specific effects in design and interpretation

GRB Fireball Physics: Prompt and Early Emission

We review the fireball shock model of gamma-ray burst prompt and early afterglow emission in light of rapid follow-up measurements made and enabled by the multi-wavelength Swift satellite. These observations are leading to a reappraisal and expansion of the previous standard view of the GRB and its fireball. New information on the behavior of the burst and afterglow on minutes to hour timescales has led, among other results, to the discovery and follow-up of short GRB afterglows, the opening up of the z>6 redshift range, and the first prompt multi-wavelength observations of a long GRB-supernova. We discuss the salient observational results and some associated theoretical issues.Comment: 23 pages. Published in the New Journal of Physics Focus Issue, "Focus on Gamma-Ray Bursts in the Swift Era" (Eds. D. H. Hartmann, C. D. Dermer & J. Greiner). V2: Minor change