991 research outputs found
Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'
We combined large-scale mRNA expression analysis and gene mapping to identify genes and loci that control hematopoietic stem cell (HSC) function. We measured mRNA expression levels in purified HSCs isolated from a panel of densely genotyped recombinant inbred mouse strains. We mapped quantitative trait loci (QTLs) associated with variation in expression of thousands of transcripts. By comparing the physical transcript position with the location of the controlling QTL, we identified polymorphic cis-acting stem cell genes. We also identified multiple trans-acting control loci that modify expression of large numbers of genes. These groups of coregulated transcripts identify pathways that specify variation in stem cells. We illustrate this concept with the identification of candidate genes involved with HSC turnover. We compared expression QTLs in HSCs and brain from the same mice and identified both shared and tissue-specific QTLs. Our data are accessible through WebQTL, a web-based interface that allows custom genetic linkage analysis and identification of coregulated transcripts.
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Is there an association between ACTN3 R577X polymorphism and muscle power phenotypes in young, non-athletic adults?
We investigated the association between ACTN3 R577X polymorphism and jumping (vertical squat and counter-movement jump tests) and sprint ability (30 m dash) in non-athletic, healthy young adults [N=284 (217 male), mean (SD) age: 21 (2) years]. We analyzed the differences in the study phenotypes among ACTN3 R577X genotypes by one-way analysis of covariance before and after adjusting for sex, age, weight and height (confounders). We also compared the genotype and allele frequencies between those with the best and worst results in the aforementioned tests (≥90th vs 0.05). In summary, α-actinin-3 deficiency does not negatively influence the ability to generate explosive leg muscle power in a young non-athletic population
Reconstruction of the gravitational wave signal during the Virgo science runs and independent validation with a photon calibrator
The Virgo detector is a kilometer-scale interferometer for gravitational wave
detection located near Pisa (Italy). About 13 months of data were accumulated
during four science runs (VSR1, VSR2, VSR3 and VSR4) between May 2007 and
September 2011, with increasing sensitivity.
In this paper, the method used to reconstruct, in the range 10 Hz-10 kHz, the
gravitational wave strain time series from the detector signals is
described. The standard consistency checks of the reconstruction are discussed
and used to estimate the systematic uncertainties of the signal as a
function of frequency. Finally, an independent setup, the photon calibrator, is
described and used to validate the reconstructed signal and the
associated uncertainties.
The uncertainties of the time series are estimated to be 8% in
amplitude. The uncertainty of the phase of is 50 mrad at 10 Hz with a
frequency dependence following a delay of 8 s at high frequency. A bias
lower than and depending on the sky direction of the GW is
also present.Comment: 35 pages, 16 figures. Accepted by CQ
Virgo calibration and reconstruction of the gravitational wave strain during VSR1
Virgo is a kilometer-length interferometer for gravitational waves detection
located near Pisa. Its first science run, VSR1, occured from May to October
2007. The aims of the calibration are to measure the detector sensitivity and
to reconstruct the time series of the gravitational wave strain h(t). The
absolute length calibration is based on an original non-linear reconstruction
of the differential arm length variations in free swinging Michelson
configurations. It uses the laser wavelength as length standard. This method is
used to calibrate the frequency dependent response of the Virgo mirror
actuators and derive the detector in-loop response and sensitivity within ~5%.
The principle of the strain reconstruction is highlighted and the h(t)
systematic errors are estimated. A photon calibrator is used to check the sign
of h(t). The reconstructed h(t) during VSR1 is valid from 10 Hz up to 10 kHz
with systematic errors estimated to 6% in amplitude. The phase error is
estimated to be 70 mrad below 1.9 kHz and 6 micro-seconds above.Comment: 8 pages, 8 figures, proceedings of Amaldi 8 conference, to be
published in Journal of Physics Conference Series (JPCS). Second release:
correct typo
Calibration and sensitivity of the Virgo detector during its second science run
The Virgo detector is a kilometer-length interferometer for gravitational
wave detection located near Pisa (Italy). During its second science run (VSR2)
in 2009, six months of data were accumulated with a sensitivity close to its
design. In this paper, the methods used to determine the parameters for
sensitivity estimation and gravitational wave reconstruction are described. The
main quantities to be calibrated are the frequency response of the mirror
actuation and the sensing of the output power. Focus is also put on their
absolute timing. The monitoring of the calibration data as well as the
parameter estimation with independent techniques are discussed to provide an
estimation of the calibration uncertainties. Finally, the estimation of the
Virgo sensitivity in the frequency-domain is described and typical
sensitivities measured during VSR2 are shown.Comment: 30 pages, 23 figures, 1 table. Published in Classical and Quantum
Gravity (CQG), Corrigendum include
The variable finesse locking technique
Virgo is a power recycled Michelson interferometer, with 3 km long Fabry-Perot cavities in the arms. The locking of the interferometer has been obtained with an original lock acquisition technique. The main idea is to lock the instrument away from its working point. Lock is obtained by misaligning the power recycling mirror and detuning the Michelson from the dark fringe. In this way, a good fraction of light escapes through the antisymmetric port and the power build-up inside the recycling cavity is extremely low. The benefit is that all the degrees of freedom are controlled when they are almost decoupled, and the linewidth of the recycling cavity is large. The interferometer is then adiabatically brought on to the dark fringe. This technique is referred to as variable finesse, since the recycling cavity is considered as a variable finesse Fabry-Perot. This technique has been widely tested and allows us to reach the dark fringe in few minutes, in an essentially deterministic way
A Cross-correlation method to search for gravitational wave bursts with AURIGA and Virgo
We present a method to search for transient GWs using a network of detectors
with different spectral and directional sensitivities: the interferometer Virgo
and the bar detector AURIGA. The data analysis method is based on the
measurements of the correlated energy in the network by means of a weighted
cross-correlation. To limit the computational load, this coherent analysis step
is performed around time-frequency coincident triggers selected by an excess
power event trigger generator tuned at low thresholds. The final selection of
GW candidates is performed by a combined cut on the correlated energy and on
the significance as measured by the event trigger generator. The method has
been tested on one day of data of AURIGA and Virgo during September 2005. The
outcomes are compared to the results of a stand-alone time-frequency
coincidence search. We discuss the advantages and the limits of this approach,
in view of a possible future joint search between AURIGA and one
interferometric detector.Comment: 11 pages, 6 figures, submitted to CQG special issue for Amaldi 7
Proceeding
Improved functional prediction of proteins by learning kernel combinations in multilabel settings
Background
We develop a probabilistic model for combining kernel matrices to predict the function of proteins. It extends previous approaches in that it can handle multiple labels which naturally appear in the context of protein function.
Results
Explicit modeling of multilabels significantly improves the capability of learning protein function from multiple kernels. The performance and the interpretability of the inference model are further improved by simultaneously predicting the subcellular localization of proteins and by combining pairwise classifiers to consistent class membership estimates.
Conclusion
For the purpose of functional prediction of proteins, multilabels provide valuable information that should be included adequately in the training process of classifiers. Learning of functional categories gains from co-prediction of subcellular localization. Pairwise separation rules allow very detailed insights into the relevance of different measurements like sequence, structure, interaction data, or expression data. A preliminary version of the software can be downloaded from http://www.inf.ethz.ch/personal/vroth/KernelHMM/.ISSN:1471-210
Search for Gravitational Wave Bursts from Six Magnetars
Soft gamma repeaters (SGRs) and anomalous X-ray pulsars (AXPs) are thought to be magnetars: neutron stars powered by extreme magnetic fields. These rare objects are characterized by repeated and sometimes spectacular gamma-ray bursts. The burst mechanism might involve crustal fractures and excitation of non-radial modes which would emit gravitational waves (GWs). We present the results of a search for GW bursts from six galactic magnetars that is sensitive to neutron star f-modes, thought to be the most efficient GW emitting oscillatory modes in compact stars. One of them, SGR 0501+4516, is likely similar to 1 kpc from Earth, an order of magnitude closer than magnetars targeted in previous GW searches. A second, AXP 1E 1547.0-5408, gave a burst with an estimated isotropic energy >10(44) erg which is comparable to the giant flares. We find no evidence of GWs associated with a sample of 1279 electromagnetic triggers from six magnetars occurring between 2006 November and 2009 June, in GW data from the LIGO, Virgo, and GEO600 detectors. Our lowest model-dependent GW emission energy upper limits for band-and time-limited white noise bursts in the detector sensitive band, and for f-mode ringdowns (at 1090 Hz), are 3.0 x 10(44)d(1)(2) erg and 1.4 x 10(47)d(1)(2) erg, respectively, where d(1) = d(0501)/1 kpc and d(0501) is the distance to SGR 0501+4516. These limits on GW emission from f-modes are an order of magnitude lower than any previous, and approach the range of electromagnetic energies seen in SGR giant flares for the first time.United States National Science FoundationScience and Technology Facilities Council of the United KingdomMax-Planck-SocietyState of Niedersachsen/GermanyItalian Istituto Nazionale di Fisica NucleareFrench Centre National de la Recherche ScientifiqueAustralian Research CouncilCouncil of Scientific and Industrial Research of IndiaIstituto Nazionale di Fisica Nucleare of ItalySpanish Ministerio de Educacion y CienciaConselleria d'Economia Hisenda i Innovacio of the Govern de les Illes BalearsFoundation for Fundamental Research on Matter supported by the Netherlands Organisation for Scientific ResearchPolish Ministry of Science and Higher EducationFoundation for Polish ScienceRoyal SocietyScottish Funding CouncilScottish Universities Physics AllianceNational Aeronautics and Space Administration NNH07ZDA001-GLASTCarnegie TrustLeverhulme TrustDavid and Lucile Packard FoundationResearch CorporationAlfred P. Sloan FoundationRussian Space AgencyRFBR 09-02-00166aIPN JPL Y503559 (Odyssey), NASA NNG06GH00G, NASA NNX07AM42G, NASA NNX08AC89G (INTEGRAL), NASA NNG06GI896, NASA NNX07AJ65G, NASA NNX08AN23G (Swift), NASA NNX07AR71G (MESSENGER), NASA NNX06AI36G, NASA NNX08AB84G, NASA NNX08AZ85G (Suzaku), NASA NNX09AU03G (Fermi)Astronom
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