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*-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments.
BackgroundOver the past few years the variety of experimental designs and protocols for sequencing experiments increased greatly. To ensure the wide usability of the produced data beyond an individual project, rich and systematic annotation of the underlying experiments is crucial.FindingsWe first developed an annotation structure that captures the overall experimental design as well as the relevant details of the steps from the biological sample to the library preparation, the sequencing procedure, and the sequencing and processed files. Through various design features, such as controlled vocabularies and different field requirements, we ensured a high annotation quality, comparability, and ease of annotation. The structure can be easily adapted to a large variety of species. We then implemented the annotation strategy in a user-hosted web platform with data import, query, and export functionality.ConclusionsWe present here an annotation structure and user-hosted platform for sequencing experiment data, suitable for lab-internal documentation, collaborations, and large-scale annotation efforts
MesonNet 2013 International Workshop. Mini-proceedings
The mini-proceedings of the MesonNet 2013 International Workshop held in
Prague from June 17th to 19th, 2013, are presented. MesonNet is a research
network within EU HadronPhysics3 project (1/2012 -- 12/2014). The web page of
the conference, which contains all talks, can be found at
http://ipnp.mff.cuni.cz/mesonnet13Comment: 106 pages, 53 contributions. Mini-proceedings of the MesonNet 2013
International Workshop. Editors: K. Kampf, A. Kupsc, and P. Masjua
Surface Nano-structured Coating for Improved Performance of Axial Piston Pumps
The work starts from the consideration that most of the power losses in a hydraulic pump is due to frictional losses made by the relative motion between moving parts. This fact is particularly true at low operating velocities, when the hydraulic lift effect must be able to maintain a minimum clearance in meatus to limit the volumetric losses. The potential of structured coatings at nanoscale, with super-hydrophobic and oleophobic characteristics, has never been exploited before in an industrial application. The work studies the potential application of nano-coating on piston slippers surface in a real industrial case. The aim is to develop a new industrial solution to increase the energetic efficiency of hydraulic pump used in earthmoving machines. The proposed solution is investigated using a dedicated test bench, designed to reproduce real working conditions of the pump. The results showa reduction of friction coefficient while changing working pressure and rotation velocity
ACBAR: The Arcminute Cosmology Bolometer Array Receiver
We describe the Arcminute Cosmology Bolometer Array Receiver (ACBAR); a
multifrequency millimeter-wave receiver designed for observations of the Cosmic
Microwave Background (CMB) and the Sunyaev-Zel'dovich effect in clusters of
galaxies. The ACBAR focal plane consists of a 16-pixel, background-limited, 240
mK bolometer array that can be configured to observe simultaneously at 150,
220, 280, and 350 GHz. With 4-5' FWHM Gaussian beam sizes and a 3 degree
azimuth chop, ACBAR is sensitive to a wide range of angular scales. ACBAR was
installed on the 2 m Viper telescope at the South Pole in January 2001. We
describe the design of the instrument and its performance during the 2001 and
2002 observing seasons.Comment: 59 pages, 16 figures -- updated to reflect version published in ApJ
High resolution CMB power spectrum from the complete ACBAR data set
In this paper, we present results from the complete set of cosmic microwave
background (CMB) radiation temperature anisotropy observations made with the
Arcminute Cosmology Bolometer Array Receiver (ACBAR) operating at 150 GHz. We
include new data from the final 2005 observing season, expanding the number of
detector-hours by 210% and the sky coverage by 490% over that used for the
previous ACBAR release. As a result, the band-power uncertainties have been
reduced by more than a factor of two on angular scales encompassing the third
to fifth acoustic peaks as well as the damping tail of the CMB power spectrum.
The calibration uncertainty has been reduced from 6% to 2.1% in temperature
through a direct comparison of the CMB anisotropy measured by ACBAR with that
of the dipole-calibrated WMAP5 experiment. The measured power spectrum is
consistent with a spatially flat, LambdaCDM cosmological model. We include the
effects of weak lensing in the power spectrum model computations and find that
this significantly improves the fits of the models to the combined ACBAR+WMAP5
power spectrum. The preferred strength of the lensing is consistent with
theoretical expectations. On fine angular scales, there is weak evidence (1.1
sigma) for excess power above the level expected from primary anisotropies. We
expect any excess power to be dominated by the combination of emission from
dusty protogalaxies and the Sunyaev-Zel'dovich effect (SZE). However, the
excess observed by ACBAR is significantly smaller than the excess power at ell
> 2000 reported by the CBI experiment operating at 30 GHz. Therefore, while it
is unlikely that the CBI excess has a primordial origin; the combined ACBAR and
CBI results are consistent with the source of the CBI excess being either the
SZE or radio source contamination.Comment: Submitted to ApJ; Changed to apply a WMAP5-based calibration. The
cosmological parameter estimation has been updated to include WMAP
Improved Measurements of the CMB Power Spectrum with ACBAR
We report improved measurements of temperature anisotropies in the cosmic microwave background (CMB) radiation made with the Arcminute Cosmology Bolometer Array Receiver (ACBAR). In this paper, we use a new analysis technique and include 30% more data from the 2001 and 2002 observing seasons than the first release to derive a new set of band-power measurements with significantly smaller uncertainties. The planet-based calibration used previously has been replaced by comparing the flux of RCW38 as measured by ACBAR and BOOMERANG to transfer the WMAP-based BOOMERANG calibration to ACBAR. The resulting power spectrum is consistent with the theoretical predictions for a spatially flat, dark energy dominated LCDM cosmology including the effects of gravitational lensing. Despite the exponential damping on small angular scales, the primary CMB fluctuations are detected with a signal-to-noise ratio of greater than 4 up to multipoles of l=2000. This increase in the precision of the fine-scale CMB power spectrum leads to only a modest decrease in the uncertainties on the parameters of the standard cosmological model. At high angular resolution, secondary anisotropies are predicted to be a significant contribution to the measured anisotropy. A joint analysis of the ACBAR results at 150 GHz and the CBI results at 30 GHz in the multipole range 2000 < l < 3000 shows that the power, reported by CBI in excess of the predicted primary anisotropy, has a frequency spectrum consistent with the thermal Sunyaev-Zel'dovich effect and inconsistent with primary CMB. The results reported here are derived from a subset of the total ACBAR data set; the final ACBAR power spectrum at 150 GHz will include 3.7 times more effective integration time and 6.5 times more sky coverage than is used here
γ-ray decay from neutron-bound and unbound states in Mo 95 and a novel technique for spin determination
The emission of γ rays from neutron-bound and neutron-unbound states in Mo95, populated in the Mo94(d,p) reaction, has been investigated. Charged particles and γ radiation were detected with arrays of annular silicon and Clover-type high-purity Germanium detectors, respectively. Utilizing p-γ and p-γ-γ coincidences, the Mo95 level scheme was greatly enhanced with 102 new transitions and 43 new states. It agrees well with shell model calculations for excitation energies below ≈2 MeV. From p-γ coincidence data, a new method for the determination of spins of discrete levels is proposed. The method exploits the suppression of high-angular momentum neutron emission from levels with high spins populated in the (d,p) reaction above the neutron separation energy. Spins for almost all Mo95 levels below 2 MeV (and for a few levels above) have been determined with this method
How to employ B ¯ d 0 → J / ψ π η , K ¯ K {\overline{B}}_d^0\to J/\psi \left(\uppi \eta, \overline{K}K\right) decays to extract information on πη scattering
Functional Diversity and Structural Disorder in the Human Ubiquitination Pathway
The ubiquitin-proteasome system plays a central role in cellular regulation and protein quality control (PQC). The system is built as a pyramid of increasing complexity, with two E1 (ubiquitin activating), few dozen E2 (ubiquitin conjugating) and several hundred E3 (ubiquitin ligase) enzymes. By collecting and analyzing E3 sequences from the KEGG BRITE database and literature, we assembled a coherent dataset of 563 human E3s and analyzed their various physical features. We found an increase in structural disorder of the system with multiple disorder predictors (IUPred - E1: 5.97%, E2: 17.74%, E3: 20.03%). E3s that can bind E2 and substrate simultaneously (single subunit E3, ssE3) have significantly higher disorder (22.98%) than E3s in which E2 binding (multi RING-finger, mRF, 0.62%), scaffolding (6.01%) and substrate binding (adaptor/substrate recognition subunits, 17.33%) functions are separated. In ssE3s, the disorder was localized in the substrate/adaptor binding domains, whereas the E2-binding RING/HECT-domains were structured. To demonstrate the involvement of disorder in E3 function, we applied normal modes and molecular dynamics analyses to show how a disordered and highly flexible linker in human CBL (an E3 that acts as a regulator of several tyrosine kinase-mediated signalling pathways) facilitates long-range conformational changes bringing substrate and E2-binding domains towards each other and thus assisting in ubiquitin transfer. E3s with multiple interaction partners (as evidenced by data in STRING) also possess elevated levels of disorder (hubs, 22.90% vs. non-hubs, 18.36%). Furthermore, a search in PDB uncovered 21 distinct human E3 interactions, in 7 of which the disordered region of E3s undergoes induced folding (or mutual induced folding) in the presence of the partner. In conclusion, our data highlights the primary role of structural disorder in the functions of E3 ligases that manifests itself in the substrate/adaptor binding functions as well as the mechanism of ubiquitin transfer by long-range conformational transitions. © 2013 Bhowmick et al
Kinome rewiring reveals AURKA limits PI3K-pathway inhibitor efficacy in breast cancer.
Dysregulation of the PI3K-AKT-mTOR signaling network is a prominent feature of breast cancers. However, clinical responses to drugs targeting this pathway have been modest, possibly because of dynamic changes in cellular signaling that drive resistance and limit drug efficacy. Using a quantitative chemoproteomics approach, we mapped kinome dynamics in response to inhibitors of this pathway and identified signaling changes that correlate with drug sensitivity. Maintenance of AURKA after drug treatment was associated with resistance in breast cancer models. Incomplete inhibition of AURKA was a common source of therapy failure, and combinations of PI3K, AKT or mTOR inhibitors with the AURKA inhibitor MLN8237 were highly synergistic and durably suppressed mTOR signaling, resulting in apoptosis and tumor regression in vivo. This signaling map identifies survival factors whose presence limits the efficacy of targeted therapies and reveals new drug combinations that may unlock the full potential of PI3K-AKT-mTOR pathway inhibitors in breast cancer
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