956 research outputs found
Manipulating Protein Conformations By Single-molecule Afm-fret Nanoscopy
Combining atomic force microscopy and fluorescence resonance energy transfer spectroscopy (AFM-FRET), we have developed a single-molecule AFM-FRET nanoscopy approach capable of effectively pinpointing and mechanically manipulating a targeted dye-labeled single protein in a large sampling area and simultaneously monitoring the conformational changes of the targeted protein by recording single-molecule FRET time trajectories. We have further demonstrated an application of using this nanoscopy on manipulation of single-molecule protein conformation and simultaneous single-molecule FRET measurement of a Cy3-Cy5-labeled kinase enzyme, HPPK (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase). By analyzing time-resolved FRET trajectories and correlated AFM force pulling curves of the targeted single-molecule enzyme, we are able to observe the protein conformational changes of a specific coordination by AFM mechanic force pulling
Meta-analysis of several gene lists for distinct types of cancer: A simple way to reveal common prognostic markers
BACKGROUND: Although prognostic biomarkers specific for particular cancers have been discovered, microarray analysis of gene expression profiles, supported by integrative analysis algorithms, helps to identify common factors in molecular oncology. Similarities of Ordered Gene Lists (SOGL) is a recently proposed approach to meta-analysis suitable for identifying features shared by two data sets. Here we extend the idea of SOGL to the detection of significant prognostic marker genes from microarrays of multiple data sets. Three data sets for leukemia and the other six for different solid tumors are used to demonstrate our method, using established statistical techniques. RESULTS: We describe a set of significantly similar ordered gene lists, representing outcome comparisons for distinct types of cancer. This kind of similarity could improve the diagnostic accuracies of individual studies when SOGL is incorporated into the support vector machine algorithm. In particular, we investigate the similarities among three ordered gene lists pertaining to mesothelioma survival, prostate recurrence and glioma survival. The similarity-driving genes are related to the outcomes of patients with lung cancer with a hazard ratio of 4.47 (p = 0.035). Many of these genes are involved in breakdown of EMC proteins regulating angiogenesis, and may be used for further research on prognostic markers and molecular targets of gene therapy for cancers. CONCLUSION: The proposed method and its application show the potential of such meta-analyses in clinical studies of gene expression profiles
All-sky LIGO Search for Periodic Gravitational Waves in the Early S5 Data
We report on an all-sky search with the LIGO detectors for periodic
gravitational waves in the frequency range 50--1100 Hz and with the frequency's
time derivative in the range -5.0E-9 Hz/s to zero. Data from the first eight
months of the fifth LIGO science run (S5) have been used in this search, which
is based on a semi-coherent method (PowerFlux) of summing strain power.
Observing no evidence of periodic gravitational radiation, we report 95%
confidence-level upper limits on radiation emitted by any unknown isolated
rotating neutron stars within the search range. Strain limits below 1.E-24 are
obtained over a 200-Hz band, and the sensitivity improvement over previous
searches increases the spatial volume sampled by an average factor of about 100
over the entire search band. For a neutron star with nominal equatorial
ellipticity of 1.0E-6, the search is sensitive to distances as great as 500
pc--a range that could encompass many undiscovered neutron stars, albeit only a
tiny fraction of which would likely be rotating fast enough to be accessible to
LIGO. This ellipticity is at the upper range thought to be sustainable by
conventional neutron stars and well below the maximum sustainable by a strange
quark star.Comment: 6 pages, 1 figur
Gravitational Waves From Known Pulsars: Results From The Initial Detector Era
We present the results of searches for gravitational waves from a large selection of pulsars using data from the most recent science runs (S6, VSR2 and VSR4) of the initial generation of interferometric gravitational wave detectors LIGO (Laser Interferometric Gravitational-wave Observatory) and Virgo. We do not see evidence for gravitational wave emission from any of the targeted sources but produce upper limits on the emission amplitude. We highlight the results from seven young pulsars with large spin-down luminosities. We reach within a factor of five of the canonical spin-down limit for all seven of these, whilst for the Crab and Vela pulsars we further surpass their spin-down limits. We present new or updated limits for 172 other pulsars (including both young and millisecond pulsars). Now that the detectors are undergoing major upgrades, and, for completeness, we bring together all of the most up-to-date results from all pulsars searched for during the operations of the first-generation LIGO, Virgo and GEO600 detectors. This gives a total of 195 pulsars including the most recent results described in this paper.United States National Science FoundationScience and Technology Facilities Council of the United KingdomMax-Planck-SocietyState of Niedersachsen/GermanyAustralian Research CouncilInternational Science Linkages program of the Commonwealth of AustraliaCouncil of Scientific and Industrial Research of IndiaIstituto Nazionale di Fisica Nucleare of ItalySpanish Ministerio de Economia y CompetitividadConselleria d'Economia Hisenda i Innovacio of the Govern de les Illes BalearsNetherlands Organisation for Scientific ResearchPolish Ministry of Science and Higher EducationFOCUS Programme of Foundation for Polish ScienceRoyal SocietyScottish Funding CouncilScottish Universities Physics AllianceNational Aeronautics and Space AdministrationOTKA of HungaryLyon Institute of Origins (LIO)National Research Foundation of KoreaIndustry CanadaProvince of Ontario through the Ministry of Economic Development and InnovationNational Science and Engineering Research Council CanadaCarnegie TrustLeverhulme TrustDavid and Lucile Packard FoundationResearch CorporationAlfred P. Sloan FoundationAstronom
First LIGO search for gravitational wave bursts from cosmic (super)strings
We report on a matched-filter search for gravitational wave bursts from
cosmic string cusps using LIGO data from the fourth science run (S4) which took
place in February and March 2005. No gravitational waves were detected in 14.9
days of data from times when all three LIGO detectors were operating. We
interpret the result in terms of a frequentist upper limit on the rate of
gravitational wave bursts and use the limits on the rate to constrain the
parameter space (string tension, reconnection probability, and loop sizes) of
cosmic string models.Comment: 11 pages, 3 figures. Replaced with version submitted to PR
Stacked Search for Gravitational Waves from the 2006 SGR 1900+14 Storm
We present the results of a LIGO search for short-duration gravitational
waves (GWs) associated with the 2006 March 29 SGR 1900+14 storm. A new search
method is used, "stacking'' the GW data around the times of individual
soft-gamma bursts in the storm to enhance sensitivity for models in which
multiple bursts are accompanied by GW emission. We assume that variation in the
time difference between burst electromagnetic emission and potential burst GW
emission is small relative to the GW signal duration, and we time-align GW
excess power time-frequency tilings containing individual burst triggers to
their corresponding electromagnetic emissions. We use two GW emission models in
our search: a fluence-weighted model and a flat (unweighted) model for the most
electromagnetically energetic bursts. We find no evidence of GWs associated
with either model. Model-dependent GW strain, isotropic GW emission energy
E_GW, and \gamma = E_GW / E_EM upper limits are estimated using a variety of
assumed waveforms. The stacking method allows us to set the most stringent
model-dependent limits on transient GW strain published to date. We find E_GW
upper limit estimates (at a nominal distance of 10 kpc) of between 2x10^45 erg
and 6x10^50 erg depending on waveform type. These limits are an order of
magnitude lower than upper limits published previously for this storm and
overlap with the range of electromagnetic energies emitted in SGR giant flares.Comment: 7 pages, 3 figure
Search for gravitational waves associated with the InterPlanetary Network short gamma ray bursts
We outline the scientific motivation behind a search for gravitational waves
associated with short gamma ray bursts detected by the InterPlanetary Network
(IPN) during LIGO's fifth science run and Virgo's first science run. The IPN
localisation of short gamma ray bursts is limited to extended error boxes of
different shapes and sizes and a search on these error boxes poses a series of
challenges for data analysis. We will discuss these challenges and outline the
methods to optimise the search over these error boxes.Comment: Methods paper; Proceedings for Eduardo Amaldi 9 Conference on
Gravitational Waves, July 2011, Cardiff, U
Swift follow-up observations of candidate gravitational-wave transient events
We present the first multi-wavelength follow-up observations of two candidate
gravitational-wave (GW) transient events recorded by LIGO and Virgo in their
2009-2010 science run. The events were selected with low latency by the network
of GW detectors and their candidate sky locations were observed by the Swift
observatory. Image transient detection was used to analyze the collected
electromagnetic data, which were found to be consistent with background.
Off-line analysis of the GW data alone has also established that the selected
GW events show no evidence of an astrophysical origin; one of them is
consistent with background and the other one was a test, part of a "blind
injection challenge". With this work we demonstrate the feasibility of rapid
follow-ups of GW transients and establish the sensitivity improvement joint
electromagnetic and GW observations could bring. This is a first step toward an
electromagnetic follow-up program in the regime of routine detections with the
advanced GW instruments expected within this decade. In that regime
multi-wavelength observations will play a significant role in completing the
astrophysical identification of GW sources. We present the methods and results
from this first combined analysis and discuss its implications in terms of
sensitivity for the present and future instruments.Comment: Submitted for publication 2012 May 25, accepted 2012 October 25,
published 2012 November 21, in ApJS, 203, 28 (
http://stacks.iop.org/0067-0049/203/28 ); 14 pages, 3 figures, 6 tables;
LIGO-P1100038; Science summary at
http://www.ligo.org/science/Publication-S6LVSwift/index.php ; Public access
area to figures, tables at
https://dcc.ligo.org/cgi-bin/DocDB/ShowDocument?docid=p110003
Implementation and testing of the first prompt search for gravitational wave transients with electromagnetic counterparts
Aims. A transient astrophysical event observed in both gravitational wave
(GW) and electromagnetic (EM) channels would yield rich scientific rewards. A
first program initiating EM follow-ups to possible transient GW events has been
developed and exercised by the LIGO and Virgo community in association with
several partners. In this paper, we describe and evaluate the methods used to
promptly identify and localize GW event candidates and to request images of
targeted sky locations.
Methods. During two observing periods (Dec 17 2009 to Jan 8 2010 and Sep 2 to
Oct 20 2010), a low-latency analysis pipeline was used to identify GW event
candidates and to reconstruct maps of possible sky locations. A catalog of
nearby galaxies and Milky Way globular clusters was used to select the most
promising sky positions to be imaged, and this directional information was
delivered to EM observatories with time lags of about thirty minutes. A Monte
Carlo simulation has been used to evaluate the low-latency GW pipeline's
ability to reconstruct source positions correctly.
Results. For signals near the detection threshold, our low-latency algorithms
often localized simulated GW burst signals to tens of square degrees, while
neutron star/neutron star inspirals and neutron star/black hole inspirals were
localized to a few hundred square degrees. Localization precision improves for
moderately stronger signals. The correct sky location of signals well above
threshold and originating from nearby galaxies may be observed with ~50% or
better probability with a few pointings of wide-field telescopes.Comment: 17 pages. This version (v2) includes two tables and 1 section not
included in v1. Accepted for publication in Astronomy & Astrophysic
A First Search for coincident Gravitational Waves and High Energy Neutrinos using LIGO, Virgo and ANTARES data from 2007
We present the results of the first search for gravitational wave bursts
associated with high energy neutrinos. Together, these messengers could reveal
new, hidden sources that are not observed by conventional photon astronomy,
particularly at high energy. Our search uses neutrinos detected by the
underwater neutrino telescope ANTARES in its 5 line configuration during the
period January - September 2007, which coincided with the fifth and first
science runs of LIGO and Virgo, respectively. The LIGO-Virgo data were analysed
for candidate gravitational-wave signals coincident in time and direction with
the neutrino events. No significant coincident events were observed. We place
limits on the density of joint high energy neutrino - gravitational wave
emission events in the local universe, and compare them with densities of
merger and core-collapse events.Comment: 19 pages, 8 figures, science summary page at
http://www.ligo.org/science/Publication-S5LV_ANTARES/index.php. Public access
area to figures, tables at
https://dcc.ligo.org/cgi-bin/DocDB/ShowDocument?docid=p120000
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