Jets in GRBs: Tests and Predictions for the Structured Jet Model

The two leading interpretations of achromatic breaks that are observed in the light curves of GRBs afterglow are (i) the manifestation of the edge of a jet, which has a roughly uniform energy profile and a sharp edge and (ii) a line of sight effect in jets with a variable energy profile. The first scenario requires the inner engine to produce a jet with a different opening angle each explosion, while the latter requires a standard engine. The physical structure of the jet is a crucial factor in understanding GRB progenitors, and therefore discriminating the two jet scenarios is particularly relevant. In the structured jet case, specific predictions can be made for the distribution of observed break angles $\theta_{\rm break}$, while that distribution is arbitrary in the first scenario. We derive the theoretical distribution for the structured jet model. Specifically, we predict the most common angle to be about 0.12 rad, in rough agreement with the sample. If this agreement would hold as the sample size increases, it would strengthen the case for the standard jet hypothesis. We show that a prediction of this model is that the average viewing angle is an increasing function of the survey sensitivity, and in particular that a mission like {\em Swift} will find the typical viewing angle to be about 0.3 rad. The local event rate predicted by this model is $R_{\rm GRB}(z=0)\sim 0.5$ Gpc$^{-3}$ yr$^{-1}$.Comment: 14 pages, 3 figures; accepted to Ap

A Self-Similar Solution for the Propagation of a Relativistic Shock in an Exponential Atmosphere

We derive a fully relativistic, self-similar solution to describe the propagation of a shock along an exponentially decreasing atmosphere, in the limit of very large Lorentz factor. We solve the problem in planar symmetry and compute the acceleration of the shock in terms of the density gradient crossed during its evolution. We apply our solution to the acceleration of shocks within the atmosphere of a HyperNova, and show that velocities consistent with the requirements of GRB models can be achieved with exponential atmospheres spanning a wide density range.Comment: ApJL in pres

Probing the Mass Fraction of MACHOs in Extragalactic Halos

Current microlensing searches calibrate the mass fraction of the Milky Way halo which is in the form of Massive Compact Halo Objects (MACHOs). We show that surveys like the Sloan Digital Sky Survey (SDSS) can probe the same quantity in halos of distant galaxies. Microlensing of background quasars by MACHOs in intervening galaxies would distort the equivalent width distribution of the quasar emission lines by an amplitude that depends on the projected quasar-galaxy separation. For a statistical sample of detectable at the >2sigma level out to a quasar-galaxy impact parameter of several tens of kpc, as long as extragalactic halos are made of MACHOs. Detection of this signal would test whether the MACHO fraction inferred for the Milky-Way halo is typical of other galaxies.Comment: 12 pages, 2 figures, submitted to ApJ Letter

PIGSPro: prediction of immunoGlobulin structures v2

PIGSpro is a significant upgrade of the popular PIGS server for the prediction of the structure of immunoglobulins. The software has been completely rewritten in python following a similar pipeline as in the original method, but including, at various steps, relevant modifications found to improve its prediction accuracy, as demonstrated here. The steps of the pipeline include the selection of the appropriate framework for predicting the conserved regions of the molecule by homology; the target template alignment for this portion of the molecule; the selection of the main chain conformation of the hypervariable loops according to the canonical structure model, the prediction of the third loop of the heavy chain (H3) for which complete canonical structures are not available and the packing of the light and heavy chain if derived from different templates. Each of these steps has been improved including updated methods developed along the years. Last but not least, the user interface has been completely redesigned and an automatic monthly update of the underlying database has been implemented. The method is available as a web server at http://biocomputing.it/pigspro

Radio Foregrounds for the 21cm Tomography of the Neutral Intergalactic Medium at High Redshifts

Absorption or emission against the cosmic microwave background radiation (CMB) may be observed in the redshifted 21cm line if the spin temperature of the neutral intergalactic medium prior to reionization differs from the CMB temperature. This so-called 21cm tomography should reveal important information on the physical state of the intergalactic medium at high redshifts. The fluctuations in the redshifted 21 cm, due to gas density inhomogeneities at early times, should be observed at meter wavelengths by the next generation radio telescopes such as the proposed {\it Square Kilometer Array (SKA)}. Here we show that the extra-galactic radio sources provide a serious contamination to the brightness temperature fluctuations expected in the redshifted 21 cm emission from the IGM at high redshifts. Unless the radio source population cuts off at flux levels above the planned sensitivity of SKA, its clustering noise component will dominate the angular fluctuations in the 21 cm signal. The integrated foreground signal is smooth in frequency space and it should nonetheless be possible to identify the sharp spectral feature arising from the non-uniformities in the neutral hydrogen density during the epoch when the first UV sources reionize the intergalactic medium.Comment: 5 pages emulateapj with 1 figure, accepted to Ap

Multi view based imaging genetics analysis on Parkinson disease

Longitudinal studies integrating imaging and genetic data have recently become widespread among bioinformatics researchers. Combining such heterogeneous data allows a better understanding of complex diseases origins and causes. Through a multi-view based workflow proposal, we show the common steps and tools used in imaging genetics analysis, interpolating genotyping, neuroimaging and transcriptomic data. We describe the advantages of existing methods to analyze heterogeneous datasets, using Parkinson\u2019s Disease (PD) as a case study. Parkinson's disease is associated with both genetic and neuroimaging factors, however such imaging genetics associations are at an early investigation stage. Therefore it is desirable to have a free and open source workflow that integrates different analysis flows in order to recover potential genetic biomarkers in PD, as in other complex diseases

Synchrotron Emission from Hot Accretion Flows and the Cosmic Microwave Background Anisotropy

Current estimates of number counts of radio sources in the frequency range where the most sensitive Cosmic Microwave Background (CMB) experiments are carried out significantly under-represent sources with strongly inverted spectra. Hot accretion flows around supermassive black holes in the nuclei of nearby galaxies are expected to produce inverted radio spectra by thermal synchrotron emission. We calculate the temperature fluctuations and power spectra of these sources in the Planck Surveyor 30 GHz energy channel, where their emission is expected to peak. We find that their potential contribution is generally comparable to the instrumental noise, and approaches the CMB anisotropy level at small angular scales. Forthcoming CMB missions, which will provide a large statistical sample of inverted-spectra sources, will be crucial for determining the distribution of hot accretion flows in nearby quiescent galactic nuclei. Detection of these sources in different frequency channels will help constrain their spectral characteristics, hence their physical properties.Comment: 10 pages, 4 figures, accepted for publication in Ap

In Situ Real-Time Quantification of Microbial Communities: Applications to Cold and Dry Volcanic Habitats

We report field tests of an instrument using multi-wavelength excitation and detection of fluorescence capable of detection and discrimination of viable cells, non-viable cells (not metabolically active but not decomposed), and spores in extreme arid environments where low microbial abundances are expected. These new results are presented for cold and dry volcanic habitats worldwide, e.g., the arid core of the Atacama Desert, Mt. Kilimanjaro glacier and Kibo area, Pali Aike caldera, and the western US volcanic and desert soils in Utah, Idaho, Nevada, and California. Our results are comparable to previous studies reported in the literature for the same environments. We find these extreme environments there have a base level of ∼103 - 104 cells/g. This is the lower limit of detectable life on terrestrial soils, as we did not observe any quantities less than this, even though the described instrumentation is capable of such measurements. Samples from more conventional environments show much higher microbial cell densities, ca. 108 cells/g or higher, with this same instrument. This base level of microbial life is nearly equal in all the measurements from the extreme environments both hot and cold, and is likely controlled primarily by the sparse nutrients rather than temperature