4,449 research outputs found
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.
Data visualization is an essential component of genomic data analysis. However, the size and diversity of the data sets produced by today's sequencing and array-based profiling methods present major challenges to visualization tools. The Integrative Genomics Viewer (IGV) is a high-performance viewer that efficiently handles large heterogeneous data sets, while providing a smooth and intuitive user experience at all levels of genome resolution. A key characteristic of IGV is its focus on the integrative nature of genomic studies, with support for both array-based and next-generation sequencing data, and the integration of clinical and phenotypic data. Although IGV is often used to view genomic data from public sources, its primary emphasis is to support researchers who wish to visualize and explore their own data sets or those from colleagues. To that end, IGV supports flexible loading of local and remote data sets, and is optimized to provide high-performance data visualization and exploration on standard desktop systems. IGV is freely available for download from http://www.broadinstitute.org/igv, under a GNU LGPL open-source license
The WDR11 complex facilitates the tethering of AP-1-derived vesicles.
Vesicluar transport of proteins from endosomes to the trans-Golgi network (TGN) is an essential cellular pathway, but much of its machinery is still unknown. A screen for genes involved in endosome-to-TGN trafficking produced two hits, the adaptor protein-1 (AP-1 complex), which facilitates vesicle budding, and WDR11. Here we demonstrate that WDR11 forms a stable complex with two other proteins, which localises to the TGN region and does not appear to be associated with AP-1, suggesting it may act downstream from budding. In a vesicle tethering assay, capture of vesicles by golgin-245 was substantially reduced in WDR11-knockout cells. Moreover, structured illumination microscopy and relocation assays indicate that the WDR11 complex is initially recruited onto vesicles rather than the TGN, where it may in turn recruit the golgin binding partner TBC1D23. We propose that the complex acts together with TBC1D23 to facilitate the golgin-mediated capture of vesicles that were generated using AP-1
GBM heterogeneity as a function of variable epidermal growth factor receptor variant III activity.
Abnormal activation of the epidermal growth factor receptor (EGFR) due to a deletion of exons 2-7 of EGFR (EGFRvIII) is a common alteration in glioblastoma (GBM). While this alteration can drive gliomagenesis, tumors harboring EGFRvIII are heterogeneous. To investigate the role for EGFRvIII activation in tumor phenotype we used a neural progenitor cell-based murine model of GBM driven by EGFR signaling and generated tumor progenitor cells with high and low EGFRvIII activation, pEGFRHi and pEGFRLo. In vivo, ex vivo, and in vitro studies suggested a direct association between EGFRvIII activity and increased tumor cell proliferation, decreased tumor cell adhesion to the extracellular matrix, and altered progenitor cell phenotype. Time-lapse confocal imaging of tumor cells in brain slice cultures demonstrated blood vessel co-option by tumor cells and highlighted differences in invasive pattern. Inhibition of EGFR signaling in pEGFRHi promoted cell differentiation and increased cell-matrix adhesion. Conversely, increased EGFRvIII activation in pEGFRLo reduced cell-matrix adhesion. Our study using a murine model for GBM driven by a single genetic driver, suggests differences in EGFR activation contribute to tumor heterogeneity and aggressiveness
Resolved Mid-IR Emission in the Narrow Line Region of NGC 4151
We present subarcsecond resolution mid infrared images of NGC 4151 at 10.8
micron and 18.2 micron. These images were taken with the University of Florida
mid-IR camera/spectrometer OSCIR at the Gemini North 8-m telescope. We resolve
emission at both 10.8 micron and 18.2 micron extending ~ 3.5" across at a P.A.
of ~ 60 degrees. This coincides with the the narrow line region of NGC 4151 as
observed in [OIII] by the Hubble Space Telescope. The most likely explanation
for this extended mid-IR emission is dust in the narrow line region heated by a
central engine. We find no extended emission associated with the proposed torus
and place an upper limit on its mid-IR size of less than or equal to ~ 35 pc.Comment: accepted for publication in the Astrophysical Journal, 19 pages
including 5 figure
Closing the shell: Gas-phase solvation of halides by 1,3-butadiene
Gas-phase solvation of halides by 1,3-butadiene has been studied via a combination of photoelectron spectroscopy and density functional theory. Photoelectron spectra for X−⋯(C4H6)n (X=Cl, Br, I where n=1-3, 1–3 and 1–7 respectively) are presented. For all complexes, the calculated structures indicate that butadiene is bound in a bidentate fashion through hydrogen-bonding, with the chloride complex showing the greatest degree of stabilisation of the internal C−C rotation of cis-butadiene. In both Cl− and Br− complexes, the first solvation shell is shown to be at least n = 4 from the vertical detachment energies (VDEs), however for I−, increases in the VDE may suggest a metastable, partially filled, first solvation shell for n = 4 and a complete shell at n = 6. These results have implications for gas-phase clustering in atmospheric and extraterrestrial environments
The ``Outside-In'' Outburst of HT Cassiopeiae
We present results from photometric observations of the dwarf nova system HT
Cas during the eruption of November 1995. The data include the first
two--colour observations of an eclipse on the rise to outburst. They show that
during the rise to outburst the disc deviates significantly from steady state
models, but the inclusion of an inner-disc truncation radius of about 4
and a ``flared'' disc of semi-opening angle of produces
acceptable fits. The disc is found to have expanded at the start of the
outburst to about , as compared to quiescent measurements. The
accretion disc then gradually decreases in radius reaching during
the last stages of the eruption. Quiescent eclipses were also observed prior to
and after the eruption and a revised ephemeris is calculated.Comment: 9 pages, 11 figures, to appear in MNRA
Williams Syndrome and Neonatal Cardiac Surgery for Congenital Single Ventricle
Williams syndrome (WS) is an arteriopathic derangement associated with supravalvular aortic stenosis and branch pulmonary stenosis. We describe double-outlet right ventricle with mitral atresia and aortic arch hypoplasia in an infant with WS. This case demonstrates the difficulty in managing patients with WS with complex cardiac defects. To our knowledge, this is the first reported single-ventricle physiology in a patient with WS. (Level of Difficulty: Advanced.)
Structure formation by cosmic strings with a cosmological constant
Final published version.Comment: 4 Page
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