Superconducting Films for Absorber-Coupled MKID Detectors for Sub-Millimeter and Far-Infrared Astronomy

We describe measurements of the properties, at dc, gigahertz, and terahertz frequencies, of thin (10 nm) aluminum films with 10 ohm/{rm square}$ normal state sheet resistance. Such films can be applied to construct microwave kinetic inductance detector arrays for submillimeter and far-infrared astronomical applications in which incident power excites quasiparticles directly in a superconducting resonator that is configured to present a matched-impedance to the high frequency radiation being detected. For films 10 nm thick, we report normal state sheet resistance, resistance-temperature curves for the superconducting transition, quality factor and kinetic inductance fraction for microwave resonators made from patterned films, and terahertz measurements of sheet impedance measured with a Fourier Transform Spectrometer. We compare properties with similar resonators made from niobium 600 nm thick

ViCTree: an automated framework for taxonomic classification from protein sequences

Motivation: The increasing rate of submission of genetic sequences into public databases is providing a growing resource for classifying the organisms that these sequences represent. To aid viral classification, we have developed ViCTree, which automatically integrates the relevant sets of sequences in NCBI GenBank and transforms them into an interactive maximum likelihood phylogenetic tree that can be updated automatically. ViCTree incorporates ViCTreeView, which is a JavaScript-based visualisation tool that enables the tree to be explored interactively in the context of pairwise distance data. Results: To demonstrate utility, ViCTree was applied to subfamily Densovirinae of family Parvoviridae. This led to the identification of six new species of insect virus. Availability: ViCTree is open-source and can be run on any Linux- or Unix-based computer or cluster. A tutorial, the documentation and the source code are available under a GPL3 license, and can be accessed at http://bioinformatics.cvr.ac.uk/victree_web/

Mouse cytomegalovirus-experienced ILC1s acquire a memory response dependent on the viral glycoprotein m12.

Innate lymphoid cells (ILCs) are tissue-resident sentinels that are essential for early host protection from pathogens at initial sites of infection. However, whether pathogen-derived antigens directly modulate the responses of tissue-resident ILCs has remained unclear. In the present study, it was found that liver-resident type 1 ILCs (ILC1s) expanded locally and persisted after the resolution of infection with mouse cytomegalovirus (MCMV). ILC1s acquired stable transcriptional, epigenetic and phenotypic changes a month after the resolution of MCMV infection, and showed an enhanced protective effector response to secondary challenge with MCMV consistent with a memory lymphocyte response. Memory ILC1 responses were dependent on the MCMV-encoded glycoprotein m12, and were independent of bystander activation by proinflammatory cytokines after heterologous infection. Thus, liver ILC1s acquire adaptive features in an MCMV-specific manner

Spitzer, Near-Infrared, and Submillimeter Imaging of the Relatively Sparse Young Cluster, Lynds 988e

We present {\it Spitzer} images of the relatively sparse, low luminosity young cluster L988e, as well as complementary near-infrared (NIR) and submillimeter images of the region. The cluster is asymmetric, with the western region of the cluster embedded within the molecular cloud, and the slightly less dense eastern region to the east of, and on the edge of, the molecular cloud. With these data, as well as with extant H$\alpha$ data of stars primarily found in the eastern region of the cluster, and a molecular $^{13}$CO gas emission map of the entire region, we investigate the distribution of forming young stars with respect to the cloud material, concentrating particularly on the differences and similarities between the exposed and embedded regions of the cluster. We also compare star formation in this region to that in denser, more luminous and more massive clusters already investigated in our comprehensive multi-wavelength study of young clusters within 1 kpc of the Sun.Comment: 21 pages, 6 tables, 13 figures. Full resolution figures at: http://astro.pas.rochester.edu/~tom/Preprints/L988e.pd

Phenotypic consequences of somatic mutations in the ataxia-telangiectasia mutated gene in non-small cell lung cancer

Mutations in the Ataxia-telangiectasia mutated (ATM) gene are frequently found in human cancers, including non-small cell lung cancer (NSCLC). Loss of ATM function confers sensitivity to ionising radiation (IR) and topoisomerase inhibitors and may thus define a subset of cancer patients that could get increased benefit from these therapies. In this study, we evaluated the phenotypic consequences of ATM missense changes reported in seven NSCLC cell lines with regard to radiosensitivity and functionality of ATM signalling. Our data demonstrate that only 2/7 NSCLC cell lines (H1395 and H23) harbouring ATM missense mutations show a functional impairment of ATM signalling following IR-exposure. In these two cell lines, the missense mutations caused a significant reduction in ATM protein levels, impairment of ATM signalling and marked radiosensitivity. Of note, only cell lines with homozygous mutations in the ATM gene showed significant impairment of ATM function. Based on these observations, we developed an immunohistochemistry-based assay to identify patients with loss or reduction of ATM protein expression in a clinical setting. In a set of 137 NSCLC and 154 colorectal cancer specimens we identified tumoral loss of ATM protein expression in 9.5% and 3.9% of cases, respectively, demonstrating the potential utility of this method

Active and Passive Radiative Transfer Simulations for GPM-Related Field Campaigns

Using a three-dimensional radiative transfer model combined with cloud-resolving model output, we simulate active and passive sensor observations of clouds and precipitaiton. This combination of tools allows us to diagnose the contributions of various hydrometeor types. Radar multiple scattering is most closely associated with the presence of graupel. At Wband, massive amounts multiple scattering in deep convection can decorrelate the reflectivity profile from the vertical structure, but for less intense events, multiple scattering could be a useful indicator of riming. For passive sensors, polarization differences at 166 GHz indicate the presence of horizontally aligned frozen particles with pronounced aspect ratios, while high concentrations of more isotropic aggregates and graupel dampen the polarization difference while also contributing to the lowest brightness temperature depressions. The insights into remote sensing measurements will facilitate the development of improved algorithms and advanced sensors

SOFIA/FORCAST and Spitzer/IRAC Imaging of the Ultra Compact H II Region W3(OH) and Associated Protostars in W3

We present infrared observations of the ultra-compact H II region W3(OH) made by the FORCAST instrument aboard SOFIA and by Spitzer/IRAC. We contribute new wavelength data to the spectral energy distribution, which constrains the optical depth, grain size distribution, and temperature gradient of the dusty shell surrounding the H II region. We model the dust component as a spherical shell containing an inner cavity with radius ~ 600 AU, irradiated by a central star of type O9 and temperature ~ 31,000 K. The total luminosity of this system is 71,000 L_solar. An observed excess of 2.2 - 4.5 microns emission in the SED can be explained by our viewing a cavity opening or clumpiness in the shell structure whereby radiation from the warm interior of the shell can escape. We claim to detect the nearby water maser source W3 (H2O) at 31.4 and 37.1 microns using beam deconvolution of the FORCAST images. We constrain the flux densities of this object at 19.7 - 37.1 microns. Additionally, we present in situ observations of four young stellar and protostellar objects in the SOFIA field, presumably associated with the W3 molecular cloud. Results from the model SED fitting tool of Robitaille et al. (2006, 2007} suggest that two objects (2MASS J02270352+6152357 and 2MASS J02270824+6152281) are intermediate-luminosity (~ 236 - 432 L_solar) protostars; one object (2MASS J02270887+6152344) is either a high-mass protostar with luminosity 3000 L_solar or a less massive young star with a substantial circumstellar disk but depleted envelope; and one object (2MASS J02270743+6152281) is an intermediate-luminosity (~ 768 L_solar) protostar nearing the end of its envelope accretion phase or a young star surrounded by a circumstellar disk with no appreciable circumstellar envelope.Comment: 12 pages, 8 figures, 2 tables, accepted by Ap

Regulation of the Epstein-Barr virus DNA polymerase gene.

The gene (pol) encoding the Epstein-Barr virus (EBV) DNA polymerase is a member of the "early" class of viral genes which are expressed shortly after activation of latent virus infection. First, mRNA from the EBV-producing cell line, B95-8, treated with 12-O-tetradecanoylphorbol-13-acetate and sodium butyrate to induce lytic replication and expression of this gene was analyzed. Northern (RNA) analysis revealed a message of 3.7 kb found only in induced cells. 5' mapping of pol mRNA by S1 nuclease and primer extension analyses indicates that transcription initiates at tightly clustered sites within a G + C-rich region 126 bp upstream of the open reading frame. The same initiation region was identified in two other EBV-infected cell lines, P3HR1 and Raji, after induction. Second, a 1.29-kb genomic fragment containing this region, when cloned upstream of the chloramphenicol acetyltransferase reporter gene, demonstrated promoter activity in lymphoid cells cotransfected with pEBV-RZ, a genomic expression construct that includes genes for the EBV immediate-early transactivator proteins, BZLF-1 and BRLF-1. Within the upstream 1.29-kb sequence, two regions of 140 bp and 101 bp appear to be needed for promoter activity. These results demonstrate that unlike most EBV genes studied thus far, the pol gene contains multiple transcriptional start sites. The upstream regulatory region of the promoter for the pol gene does not contain canonical promoter elements such as TATA and CAAT boxes and, furthermore, is not constitutively active but requires transactivation by two or more viral proteins

Genetic Interactions between Doublecortin and Doublecortin-like Kinase in Neuronal Migration and Axon Outgrowth

SummaryAlthough mutations in the human doublecortin gene (DCX) cause profound defects in cortical neuronal migration, a genetic deletion of Dcx in mice produces a milder defect. A second locus, doublecortin-like kinase (Dclk), encodes a protein with similar “doublecortin domains” and microtubule stabilization properties that may compensate for Dcx. Here, we generate a mouse with a Dclk mutation that causes no obvious migrational abnormalities but show that mice mutant for both Dcx and Dclk demonstrate perinatal lethality, disorganized neocortical layering, and profound hippocampal cytoarchitectural disorganization. Surprisingly, Dcx−/y;Dclk−/− mutants have widespread axonal defects, affecting the corpus callosum, anterior commissure, subcortical fiber tracts, and internal capsule. Dcx/Dclk-deficient dissociated neurons show abnormal axon outgrowth and dendritic structure, with defects in axonal transport of synaptic vesicle proteins. Dcx and Dclk may directly or indirectly regulate microtubule-based vesicle transport, a process critical to both neuronal migration and axon outgrowth