NIRCam: Development and Testing of the JWST Near-Infrared Camera

The Near Infrared Camera (NIRCam) is one of the four science instruments of the James Webb Space Telescope (JWST). Its high sensitivity, high spatial resolution images over the 0.6 - 5 microns wavelength region will be essential for making significant findings in many science areas as well as for aligning the JWST primary mirror segments and telescope. The NIRCam engineering test unit was recently assembled and has undergone successful cryogenic testing. The NIRCam collimator and camera optics and their mountings are also progressing, with a brass-board system demonstrating relatively low wavefront error across a wide field of view. The flight model?s long-wavelength Si grisms have been fabricated, and its coronagraph masks are now being made. Both the short (0.6 - 2.3 microns) and long (2.4 - 5.0 microns) wavelength flight detectors show good performance and are undergoing final assembly and testing. The flight model subsystems should all be completed later this year through early 2011, and NIRCam will be cryogenically tested in the first half of 2011 before delivery to the JWST integrated science instrument module (ISIM)

The X-ray Emissions from the M87 Jet: Diagnostics and Physical Interpretation

We reanalyze the deep Chandra observations of the M87 jet, first examined by Wilson & Yang (2002). By employing an analysis chain that includes image deconvolution, knots HST-1 and I are fully separated from adjacent emission. We find slight but significant variations in the spectral shape, with values of $\alpha_x$ ranging from $\sim 1.2-1.6$. We use VLA radio observations, as well as HST imaging and polarimetry data, to examine the jet's broad-band spectrum and inquire as to the nature of particle acceleration in the jet. As shown in previous papers, a simple continuous injection model for synchrotron-emitting knots, in which both the filling factor, $f_{acc}$, of regions within which particles are accelerated and the energy spectrum of the injected particles are constant, cannot account for the X-ray flux or spectrum. Instead, we propose that $f_{acc}$ is a function of position and energy and find that in the inner jet, $f_{acc} \propto E_\gamma^{-0.4 \pm 0.2} \propto E_e^{-0.2 \pm 0.1}$, and in knots A and B, $f_{acc} \propto E_\gamma^{-0.7 \pm 0.2} \propto E_e^{-0.35 \pm 0.1}$, where $E_\gamma$ is the emitted photon energy and and $E_e$ is the emitting electron energy. In this model, the index $p$ of the injected electron energy spectrum ($n(E_{e}) \propto E_{e}^{-p}$) is $p=2.2$ at all locations in the jet, as predicted by models of cosmic ray acceleration by ultrarelativistic shocks. There is a strong correlation between the peaks of X-ray emission and minima of optical percentage polarization, i.e., regions where the jet magnetic field is not ordered. We suggest that the X-ray peaks coincide with shock waves which accelerate the X-ray emitting electrons and cause changes in the direction of the magnetic field; the polarization is thus small because of beam averaging.Comment: Accepted for publication in ApJ; 21 pages, 9 figures, 2 tables; abstract shortened for astro-ph; Figures 1, 7 and 8 at reduced resolutio

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

Detection of somatic point substitutions is a key step in characterizing the cancer genome. Mutations in cancer are rare (0.1–100/Mb) and often occur only in a subset of the sequenced cells, either due to contamination by normal cells or due to tumor heterogeneity. Consequently, mutation calling methods need to be both specific, avoiding false positives, and sensitive to detect clonal and sub-clonal mutations. The decreased sensitivity of existing methods for low allelic fraction mutations highlights the pressing need for improved and systematically evaluated mutation detection methods. Here we present MuTect, a method based on a Bayesian classifier designed to detect somatic mutations with very low allele-fractions, requiring only a few supporting reads, followed by a set of carefully tuned filters that ensure high specificity. We also describe novel benchmarking approaches, which use real sequencing data to evaluate the sensitivity and specificity as a function of sequencing depth, base quality and allelic fraction. Compared with other methods, MuTect has higher sensitivity with similar specificity, especially for mutations with allelic fractions as low as 0.1 and below, making MuTect particularly useful for studying cancer subclones and their evolution in standard exome and genome sequencing data

The Optical-Near-IR Spectrum of the M87 Jet From HST Observations

We present 1998 HST observations of M87 which yield the first single-epoch optical and radio-optical spectral index images of the jet at $0.15''$ resolution. We find $\approx 0.67$, comparable to previous measurements, and $\approx 0.9$ ($F_\nu \propto \nu^{-\alpha}$), slightly flatter than previous workers. Reasons for this discrepancy are discussed. These observations reveal a large variety of spectral slopes. Bright knots exhibit flatter spectra than interknot regions. The flattest spectra ($\alpha_o \sim 0.5-0.6$; comparable to or flatter than $\alpha_{ro}$) are found in two inner jet knots (D-East and HST-1) which contain the fastest superluminal components. In knots A, B and C, $\alpha_o$ and $\alpha_{ro}$ are essentially anti-correlated. Near the flux maxima of knots HST-1 and F, changes in $\alpha_{ro}$ lag changes in $\alpha_o$, but in knots D and E, the opposite relationship is observed. This is further evidence that radio and optical emissions in the M87 jet come from substantially different physical regions. The delays observed in the inner jet are consistent with localized particle acceleration, with $t_{acc} << t_{cool}$ for optically emitting electrons in knots HST-1 and F, and $t_{acc} \sim t_{cool}$ for optically emitting electrons in knots D and E. Synchrotron models yield \nu_B \gsim 10^{16} Hz for knots D, A and B, and somewhat lower values, $\nu_B \sim 10^{15}- 10^{16}$ Hz, in other regions. If X-ray emissions from knots A, B and D are co-spatial with optical and radio emission, we can strongly rule out the ``continuous injection'' model. Because of the short lifetimes of X-ray synchrotron emitting particles, the X-ray emission likely fills volumes much smaller than the optical emission regions.Comment: Text 17 pages, 3 Tables, 11 figures, accepted by Ap

Physics-Based Modeling of Meteor Entry and Breakup

A new research effort at NASA Ames Research Center has been initiated in Planetary Defense, which integrates the disciplines of planetary science, atmospheric entry physics, and physics-based risk assessment. This paper describes work within the new program and is focused on meteor entry and breakup. Over the last six decades significant effort was expended in the US and in Europe to understand meteor entry including ablation, fragmentation and airburst (if any) for various types of meteors ranging from stony to iron spectral types. These efforts have produced primarily empirical mathematical models based on observations. Weaknesses of these models, apart from their empiricism, are reliance on idealized shapes (spheres, cylinders, etc.) and simplified models for thermal response of meteoritic materials to aerodynamic and radiative heating. Furthermore, the fragmentation and energy release of meteors (airburst) is poorly understood. On the other hand, flight of human-made atmospheric entry capsules is well understood. The capsules and their requisite heatshields are designed and margined to survive entry. However, the highest speed Earth entry for capsules is less than 13 km/s (Stardust). Furthermore, Earth entry capsules have never exceeded diameters of 5 m, nor have their peak aerothermal environments exceeded 0.3 atm and 1 kW/cm2. The aims of the current work are: (i) to define the aerothermal environments for objects with entry velocities from 13 to greater than 20 km/s; (ii) to explore various hypotheses of fragmentation and airburst of stony meteors in the near term; (iii) to explore the possibility of performing relevant ground-based tests to verify candidate hypotheses; and (iv) to quantify the energy released in airbursts. The results of the new simulations will be used to anchor said risk assessment analyses. With these aims in mind, state-of-the-art entry capsule design tools are being extended for meteor entries. We describe: (i) applications of current simulation tools to spherical geometries of diameters ranging from 1 to 100 m for an entry velocity of 20 km/s and stagnation pressures ranging from 1 to 100 atm; (ii) the influence of shape and departure of heating environment predictions from those for a simple spherical geometry; (iii) assessment of thermal response models for silica subject to intense radiation; and (iv) results for porosity-driven gross fragmentation of meteors, idealized as a collection of smaller objects. Lessons learned from these simulations will be used to help understand the Chelyabinsk meteor entry up to its first point of fragmentation

A high-resolution map of human evolutionary constraint using 29 mammals.

The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease