685 research outputs found
Computation of protein geometry and its applications: Packing and function prediction
This chapter discusses geometric models of biomolecules and geometric
constructs, including the union of ball model, the weigthed Voronoi diagram,
the weighted Delaunay triangulation, and the alpha shapes. These geometric
constructs enable fast and analytical computaton of shapes of biomoleculres
(including features such as voids and pockets) and metric properties (such as
area and volume). The algorithms of Delaunay triangulation, computation of
voids and pockets, as well volume/area computation are also described. In
addition, applications in packing analysis of protein structures and protein
function prediction are also discussed.Comment: 32 pages, 9 figure
Functional maturation of isolated neural progenitor cells from the adult rat hippocampus
Although neural progenitor cells (NPCs) may provide a source of new neurons to alleviate neural trauma, little is known about their electrical properties as they differentiate. We have previously shown that single NPCs from the adult rat hippocampus can be cloned in the presence of heparan sulphate chains purified from the hippocampus, and that these cells can be pushed into a proliferative phenotype with the mitogen FGF2 [Chipperfield, H., Bedi, K.S., Cool, S.M. & Nurcombe, V. (2002) Int. J. Dev. Biol., 46, 661-670]. In this study, the active and passive electrical properties of both undifferentiated and differentiated adult hippocampal NPCs, from 0 to 12 days in vitro as single-cell preparations, were investigated. Sparsely plated, undifferentiated NPCs had a resting membrane potential of approximate to -90 mV and were electrically inexcitable. In > 70%, ATP and benzoylbenzoyl-ATP evoked an inward current and membrane depolarization, whereas acetylcholine, noradrenaline, glutamate and GABA had no detectable effect. In Fura-2-loaded undifferentiated NPCs, ATP and benzoylbenzoyl-ATP evoked a transient increase in the intracellular free Ca2+ concentration, which was dependent on extracellular Ca2+ and was inhibited reversibly by pyridoxalphosphate-6-azophenyl-2'-4'-disulphonic acid (PPADS), a P2 receptor antagonist. After differentiation, NPC-derived neurons became electrically excitable, expressing voltage-dependent TTX-sensitive Na+ channels, low- and high-voltage-activated Ca2+ channels and delayed-rectifier K+ channels. Differentiated cells also possessed functional glutamate, GABA, glycine and purinergic (P2X) receptors. Appearance of voltage-dependent and ligand-gated ion channels appears to be an important early step in the differentiation of NPCs
Quasars and their host galaxies
This review attempts to describe developments in the fields of quasar and
quasar host galaxies in the past five. In this time period, the Sloan and 2dF
quasar surveys have added several tens of thousands of quasars, with Sloan
quasars being found to z>6. Obscured, or partially obscured quasars have begun
to be found in significant numbers. Black hole mass estimates for quasars, and
our confidence in them, have improved significantly, allowing a start on
relating quasar properties such as radio jet power to fundamental parameters of
the quasar such as black hole mass and accretion rate. Quasar host galaxy
studies have allowed us to find and characterize the host galaxies of quasars
to z>2. Despite these developments, many questions remain unresolved, in
particular the origin of the close relationship between black hole mass and
galaxy bulge mass/velocity dispersion seen in local galaxies.Comment: Review article, to appear in Astrophysics Update
Using the Wigner-Ibach Surmise to Analyze Terrace-Width Distributions: History, User's Guide, and Advances
A history is given of the applications of the simple expression generalized
from the surmise by Wigner and also by Ibach to extract the strength of the
interaction between steps on a vicinal surface, via the terrace width
distribution (TWD). A concise guide for use with experiments and a summary of
some recent extensions are provided.Comment: 11 pages, 4 figures, reformatted (with revtex) version of refereed
paper for special issue of Applied Physics A entitled "From Surface Science
to Device Physics", in honor of the retirements of Prof. H. Ibach and Prof.
H. L\"ut
Excited Baryons in Lattice QCD
We present first results for the masses of positive and negative parity
excited baryons calculated in lattice QCD using an O(a^2)-improved gluon action
and a fat-link irrelevant clover (FLIC) fermion action in which only the
irrelevant operators are constructed with APE-smeared links. The results are in
agreement with earlier calculations of N^* resonances using improved actions
and exhibit a clear mass splitting between the nucleon and its chiral partner.
An correlation matrix analysis reveals two low-lying J^P=(1/2)^- states with a
small mass splitting. The study of different Lambda interpolating fields
suggests a similar splitting between the lowest two Lambda1/2^- octet states.
However, the empirical mass suppression of the Lambda^*(1405) is not evident in
these quenched QCD simulations, suggesting a potentially important role for the
meson cloud of the Lambda^*(1405) and/or a need for more exotic interpolating
fields.Comment: Correlation matrix analysis performed. Increased to 400
configurations. 22 pages, 13 figures, 15 table
Observing Supermassive Black Holes across cosmic time: from phenomenology to physics
In the last decade, a combination of high sensitivity, high spatial
resolution observations and of coordinated multi-wavelength surveys has
revolutionized our view of extra-galactic black hole (BH) astrophysics. We now
know that supermassive black holes reside in the nuclei of almost every galaxy,
grow over cosmological times by accreting matter, interact and merge with each
other, and in the process liberate enormous amounts of energy that influence
dramatically the evolution of the surrounding gas and stars, providing a
powerful self-regulatory mechanism for galaxy formation. The different
energetic phenomena associated to growing black holes and Active Galactic
Nuclei (AGN), their cosmological evolution and the observational techniques
used to unveil them, are the subject of this chapter. In particular, I will
focus my attention on the connection between the theory of high-energy
astrophysical processes giving rise to the observed emission in AGN, the
observable imprints they leave at different wavelengths, and the methods used
to uncover them in a statistically robust way. I will show how such a combined
effort of theorists and observers have led us to unveil most of the SMBH growth
over a large fraction of the age of the Universe, but that nagging
uncertainties remain, preventing us from fully understating the exact role of
black holes in the complex process of galaxy and large-scale structure
formation, assembly and evolution.Comment: 46 pages, 21 figures. This review article appears as a chapter in the
book: "Astrophysical Black Holes", Haardt, F., Gorini, V., Moschella, U and
Treves A. (Eds), 2015, Springer International Publishing AG, Cha
An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics
For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types
Search for displaced vertices arising from decays of new heavy particles in 7 TeV pp collisions at ATLAS
We present the results of a search for new, heavy particles that decay at a
significant distance from their production point into a final state containing
charged hadrons in association with a high-momentum muon. The search is
conducted in a pp-collision data sample with a center-of-mass energy of 7 TeV
and an integrated luminosity of 33 pb^-1 collected in 2010 by the ATLAS
detector operating at the Large Hadron Collider. Production of such particles
is expected in various scenarios of physics beyond the standard model. We
observe no signal and place limits on the production cross-section of
supersymmetric particles in an R-parity-violating scenario as a function of the
neutralino lifetime. Limits are presented for different squark and neutralino
masses, enabling extension of the limits to a variety of other models.Comment: 8 pages plus author list (20 pages total), 8 figures, 1 table, final
version to appear in Physics Letters
Measurement of the polarisation of W bosons produced with large transverse momentum in pp collisions at sqrt(s) = 7 TeV with the ATLAS experiment
This paper describes an analysis of the angular distribution of W->enu and
W->munu decays, using data from pp collisions at sqrt(s) = 7 TeV recorded with
the ATLAS detector at the LHC in 2010, corresponding to an integrated
luminosity of about 35 pb^-1. Using the decay lepton transverse momentum and
the missing transverse energy, the W decay angular distribution projected onto
the transverse plane is obtained and analysed in terms of helicity fractions
f0, fL and fR over two ranges of W transverse momentum (ptw): 35 < ptw < 50 GeV
and ptw > 50 GeV. Good agreement is found with theoretical predictions. For ptw
> 50 GeV, the values of f0 and fL-fR, averaged over charge and lepton flavour,
are measured to be : f0 = 0.127 +/- 0.030 +/- 0.108 and fL-fR = 0.252 +/- 0.017
+/- 0.030, where the first uncertainties are statistical, and the second
include all systematic effects.Comment: 19 pages plus author list (34 pages total), 9 figures, 11 tables,
revised author list, matches European Journal of Physics C versio
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