The Three-Dimensional Structure of Cassiopeia A

We used the Spitzer Space Telescope's Infrared Spectrograph to map nearly the entire extent of Cassiopeia A between 5-40 micron. Using infrared and Chandra X-ray Doppler velocity measurements, along with the locations of optical ejecta beyond the forward shock, we constructed a 3-D model of the remnant. The structure of Cas A can be characterized into a spherical component, a tilted thick disk, and multiple ejecta jets/pistons and optical fast-moving knots all populating the thick disk plane. The Bright Ring in Cas A identifies the intersection between the thick plane/pistons and a roughly spherical reverse shock. The ejecta pistons indicate a radial velocity gradient in the explosion. Some ejecta pistons are bipolar with oppositely-directed flows about the expansion center while some ejecta pistons show no such symmetry. Some ejecta pistons appear to maintain the integrity of the nuclear burning layers while others appear to have punched through the outer layers. The ejecta pistons indicate a radial velocity gradient in the explosion. In 3-D, the Fe jet in the southeast occupies a "hole" in the Si-group emission and does not represent "overturning", as previously thought. Although interaction with the circumstellar medium affects the detailed appearance of the remnant and may affect the visibility of the southeast Fe jet, the bulk of the symmetries and asymmetries in Cas A are intrinsic to the explosion.Comment: Accepted to ApJ. 54 pages, 21 figures. For high resolution figures and associated mpeg movie and 3D PDF files, see http://homepages.spa.umn.edu/~tdelaney/pape

On the Expansion Rate, Age, and Distance of the Supernova Remnant G266.2-1.2 (Vela Jr.)

An analysis of Chandra ACIS data for two relatively bright and narrow portions of the northwestern rim of G266.2-1.2 (a.k.a. RX J0852.0-4622 or Vela Jr.) reveal evidence of a radial displacement of 2.40 +/- 0.56 arcsec between 2003 and 2008. The corresponding expansion rate (0.42 +/- 0.10 arcsec/yr or 13.6 +/- 4.2%/kyr) is about half the rate reported for an analysis of XMM-Newton data from a similar, but not identical, portion of the rim over a similar, but not identical, time interval (0.84 +/- 0.23 arcsec/yr, Katsuda et al. 2008a). If the Chandra rate is representative of the remnant as a whole, then the results of a hydrodynamic analysis suggest that G266.2-1.2 is between 2.4 and 5.1 kyr old if it is expanding into a uniform ambient medium (whether or not it was produced by a Type Ia or Type II event). If the remnant is expanding into the material shed by a steady stellar wind, then the age could be as much as 50% higher. The Chandra expansion rate and a requirement that the shock speed be greater than or equal to 1000 km/s yields a lower limit on the distance of 0.5 kpc. An analysis of previously-published distance estimates and constraints suggests G266.2-1.2 is no further than 1.0 kpc. This range of distances is consistent with the distance to the nearer of two groups of material in the Vela Molecular Ridge (0.7 +/- 0.2 kpc, Liseau et al. 1992) and to the Vel OB1 association (0.8 kpc, Eggen 1982).Comment: 30 pages, 7 figure

Sequence biases in large scale gene expression profiling data

We present the results of a simple, statistical assay that measures the G+C content sensitivity bias of gene expression experiments without the requirement of a duplicate experiment. We analyse five gene expression profiling methods: Affymetrix GeneChip, Long Serial Analysis of Gene Expression (LongSAGE), LongSAGELite, ‘Classic’ Massively Parallel Signature Sequencing (MPSS) and ‘Signature’ MPSS. We demonstrate the methods have systematic and random errors leading to a different G+C content sensitivity. The relationship between this experimental error and the G+C content of the probe set or tag that identifies each gene influences whether the gene is detected and, if detected, the level of gene expression measured. LongSAGE has the least bias, while Signature MPSS shows a strong bias to G+C rich tags and Affymetrix data show different bias depending on the data processing method (MAS 5.0, RMA or GC-RMA). The bias in the Affymetrix data primarily impacts genes expressed at lower levels. Despite the larger sampling of the MPSS library, SAGE identifies significantly more genes (60% more RefSeq genes in a single comparison)

Closed Strings with Low Harmonics and Kinks

Low-harmonic formulas for closed relativistic strings are given. General parametrizations are presented for the addition of second- and third-harmonic waves to the fundamental wave. The method of determination of the parametrizations is based upon a product representation found for the finite Fourier series of string motion in which the constraints are automatically satisfied. The construction of strings with kinks is discussed, including examples. A procedure is laid out for the representation of kinks that arise from self-intersection, and subsequent intercommutation, for harmonically parametrized cosmic strings.Comment: 39, CWRUTH-93-

Cosmic ray diffusion near the Bohm limit in the Cassiopeia A supernova remnant

Supernova remnants (SNRs) are believed to be the primary location of the acceleration of Galactic cosmic rays, via diffusive shock (Fermi) acceleration. Despite considerable theoretical work the precise details are still unknown, in part because of the difficulty in directly observing nucleons that are accelerated to TeV energies in, and affect the structure of, the SNR shocks. However, for the last ten years, X-ray observatories ASCA, and more recently Chandra, XMM-Newton, and Suzaku have made it possible to image the synchrotron emission at keV energies produced by cosmic-ray electrons accelerated in the SNR shocks. In this article, we describe a spatially-resolved spectroscopic analysis of Chandra observations of the Galactic SNR Cassiopeia A to map the cutoff frequencies of electrons accelerated in the forward shock. We set upper limits on the electron diffusion coefficient and find locations where particles appear to be accelerated nearly as fast as theoretically possible (the Bohm limit).Comment: 18 pages, 5 figures. Accepted for publication in Nature Physics (DOI below), final version available week of August 28, 2006 at http://www.nature.com/nphy

Dust and the type II-Plateau supernova 2004dj

We present mid-infrared (MIR) spectroscopy of a Type II-plateau supernova, SN 2004dj, obtained with the Spitzer Space Telescope, spanning 106--1393 d after explosion. MIR photometry plus optical/near-IR observations are also reported. An early-time MIR excess is attributed to emission from non-silicate dust formed within a cool dense shell (CDS). Most of the CDS dust condensed between 50 d and 165 d, reaching a mass of 0.3 x 10^{-5} Msun. Throughout the observations much of the longer wavelength (>10 microns) part of the continuum is explained as an IR echo from interstellar dust. The MIR excess strengthened at later times. We show that this was due to thermal emission from warm, non-silicate dust formed in the ejecta. Using optical/near-IR line-profiles and the MIR continua, we show that the dust was distributed as a disk whose radius appeared to be slowly shrinking. The disk radius may correspond to a grain destruction zone caused by a reverse shock which also heated the dust. The dust-disk lay nearly face-on, had high opacities in the optical/near-IR regions, but remained optically thin in the MIR over much of the period studied. Assuming a uniform dust density, the ejecta dust mass by 996 d was 0.5 +/- 0.1) x 10^{-4} Msun, and exceeded 10^{-4}Msun by 1393 d. For a dust density rising toward the center the limit is higher. Nevertheless, this study suggests that the amount of freshly-synthesized dust in the SN 2004dj ejecta is consistent with that found from previous studies, and adds further weight to the claim that such events could not have been major contributors to the cosmic dust budget.Comment: ApJ in press; minor changes c.f. v

Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach

BACKGROUND: High throughput sequencing-by-synthesis is an emerging technology that allows the rapid production of millions of bases of data. Although the sequence reads are short, they can readily be used for re-sequencing. By re-sequencing the mRNA products of a cell, one may rapidly discover polymorphisms and splice variants particular to that cell. RESULTS: We present the utility of massively parallel sequencing by synthesis for profiling the transcriptome of a human prostate cancer cell-line, LNCaP, that has been treated with the synthetic androgen, R1881. Through the generation of approximately 20 megabases (MB) of EST data, we detect transcription from over 10,000 gene loci, 25 previously undescribed alternative splicing events involving known exons, and over 1,500 high quality single nucleotide discrepancies with the reference human sequence. Further, we map nearly 10,000 ESTs to positions on the genome where no transcription is currently predicted to occur. We also characterize various obstacles with using sequencing by synthesis for transcriptome analysis and propose solutions to these problems. CONCLUSION: The use of high-throughput sequencing-by-synthesis methods for transcript profiling allows the specific and sensitive detection of many of a cell's transcripts, and also allows the discovery of high quality base discrepancies, and alternative splice variants. Thus, this technology may provide an effective means of understanding various disease states, discovering novel targets for disease treatment, and discovery of novel transcripts

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA binding domain sequencing (MBD-seq). We applied all four methods to biological replicates of human embryonic stem cells to assess their genome-wide CpG coverage, resolution, cost, concordance and the influence of CpG density and genomic context. The methylation levels assessed by the two bisulfite methods were concordant (their difference did not exceed a given threshold) for 82% for CpGs and 99% of the non-CpG cytosines. Using binary methylation calls, the two enrichment methods were 99% concordant and regions assessed by all four methods were 97% concordant. We combined MeDIP-seq with methylation-sensitive restriction enzyme (MRE-seq) sequencing for comprehensive methylome coverage at lower cost. This, along with RNA-seq and ChIP-seq of the ES cells enabled us to detect regions with allele-specific epigenetic states, identifying most known imprinted regions and new loci with monoallelic epigenetic marks and monoallelic expression

Galactic and Extragalactic Samples of Supernova Remnants: How They Are Identified and What They Tell Us

Supernova remnants (SNRs) arise from the interaction between the ejecta of a supernova (SN) explosion and the surrounding circumstellar and interstellar medium. Some SNRs, mostly nearby SNRs, can be studied in great detail. However, to understand SNRs as a whole, large samples of SNRs must be assembled and studied. Here, we describe the radio, optical, and X-ray techniques which have been used to identify and characterize almost 300 Galactic SNRs and more than 1200 extragalactic SNRs. We then discuss which types of SNRs are being found and which are not. We examine the degree to which the luminosity functions, surface-brightness distributions and multi-wavelength comparisons of the samples can be interpreted to determine the class properties of SNRs and describe efforts to establish the type of SN explosion associated with a SNR. We conclude that in order to better understand the class properties of SNRs, it is more important to study (and obtain additional data on) the SNRs in galaxies with extant samples at multiple wavelength bands than it is to obtain samples of SNRs in other galaxiesComment: Final 2016 draft of a chapter in "Handbook of Supernovae" edited by Athem W. Alsabti and Paul Murdin. Final version available at https://doi.org/10.1007/978-3-319-20794-0_90-