291 research outputs found
GPU-based Augmented Trajectory Propagation: Orbital Regularization Interface and NVIDIA CUDA Tensor Core Performance
UV Light Shower Simulator for Fluorescence and Cerenkov Radiation Studies
All experiments observing showers light use telescopes equipped with
pixellised photodetectors. Monte-Carlo (MC) simulations of the apparatus
operation in various situations (background light, shower energy, proximity of
tracks...) are mandatory, but never enter into detector details like pulse
shape, dead-time, or charge space effects which are finally responsible for the
data quality. An apparatus where each pixel receives light from individual 370
nm UV LEDs through silica fibers is being built. The LEDs receive voltage
through DACs, which get their input (which pixel, at what time, which
amplitude) from a shower plus noise generator code. The typical time constant
of a shower being one s (300 m for light), the pulses are one s wide.
This is rather long compared to the intrinsic time constant (around 10 ns) of
the light detectors, hence, these see "constant light" changing every s.
This is where important loading effects which are not included in MC code can
be observed. The fibers illuminate the pixels through a diffuser, and each
fiber illuminates only one pixel. The number of equipped pixels is such that it
englobes a full shower (much less than the full focal surface). Finally, this
equipment can be used also to calibrate the pixels
Quality measures for protein alignment benchmarks
Multiple protein sequence alignment methods are central to many applications in molecular biology. These methods are typically assessed on benchmark datasets including BALIBASE, OXBENCH, PREFAB and SABMARK, which are important to biologists in making informed choices between programs. In this article, annotations of domain homology and secondary structure are used to define new measures of alignment quality and are used to make the first systematic, independent evaluation of these benchmarks. These measures indicate sensitivity and specificity while avoiding the ambiguous residue correspondences and arbitrary distance cutoffs inherent to structural superpositions. Alignments by selected methods that indicate high-confidence columns (ALIGN-M, DIALIGN-T, FSA and MUSCLE) are also assessed. Fold space coverage and effective benchmark database sizes are estimated by reference to domain annotations, and significant redundancy is found in all benchmarks except SABMARK. Questionable alignments are found in all benchmarks, especially in BALIBASE where 87% of sequences have unknown structure, 20% of columns contain different folds according to SUPERFAMILY and 30% of ‘core block’ columns have conflicting secondary structure according to DSSP. A careful analysis of current protein multiple alignment benchmarks calls into question their ability to determine reliable algorithm rankings
APC/CCdh1-Mediated Degradation of the F-Box Protein NIPA Is Regulated by Its Association with Skp1
NIPA (Nuclear Interaction Partner of Alk kinase) is an F-box like protein
that targets nuclear Cyclin B1 for degradation. Integrity and therefore activity
of the SCFNIPA E3 ligase is regulated by cell-cycle-dependent phosphorylation
of NIPA, restricting substrate ubiquitination to interphase. Here we show
that phosphorylated NIPA is degraded in late mitosis in an APC/CCdh1-dependent
manner. Binding of the unphosphorylated form of NIPA to Skp1 interferes with
binding to the APC/C-adaptor protein Cdh1 and therefore protects unphosphorylated
NIPA from degradation in interphase. Our data thus define a novel mode of
regulating APC/C-mediated ubiquitination
Colour categories are reflected in sensory stages of colour perception when stimulus issues are resolved
Debate exists about the time course of the effect of colour categories on visual processing. We investigated the effect of colour categories for two groups who differed in whether they categorised a blue-green boundary colour as the same- or different-category to a reliably-named blue colour and a reliably-named green colour. Colour differences were equated in just-noticeable differences to be equally discriminable. We analysed event-related potentials for these colours elicited on a passive visual oddball task and investigated the time course of categorical effects on colour processing. Support for category effects was found 100 ms after stimulus onset, and over frontal sites around 250 ms, suggesting that colour naming affects both early sensory and later stages of chromatic processing
MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts
<p>Abstract</p> <p>Background</p> <p>Multiple Sequence Alignment (MSA) is a basic tool for bioinformatics research and analysis. It has been used essentially in almost all bioinformatics tasks such as protein structure modeling, gene and protein function prediction, DNA motif recognition, and phylogenetic analysis. Therefore, improving the accuracy of multiple sequence alignment is important for advancing many bioinformatics fields.</p> <p>Results</p> <p>We designed and developed a new method, MSACompro, to synergistically incorporate predicted secondary structure, relative solvent accessibility, and residue-residue contact information into the currently most accurate posterior probability-based MSA methods to improve the accuracy of multiple sequence alignments. The method is different from the multiple sequence alignment methods (e.g. 3D-Coffee) that use the tertiary structure information of some sequences since the structural information of our method is fully predicted from sequences. To the best of our knowledge, applying predicted relative solvent accessibility and contact map to multiple sequence alignment is novel. The rigorous benchmarking of our method to the standard benchmarks (i.e. BAliBASE, SABmark and OXBENCH) clearly demonstrated that incorporating predicted protein structural information improves the multiple sequence alignment accuracy over the leading multiple protein sequence alignment tools without using this information, such as MSAProbs, ProbCons, Probalign, T-coffee, MAFFT and MUSCLE. And the performance of the method is comparable to the state-of-the-art method PROMALS of using structural features and additional homologous sequences by slightly lower scores.</p> <p>Conclusion</p> <p>MSACompro is an efficient and reliable multiple protein sequence alignment tool that can effectively incorporate predicted protein structural information into multiple sequence alignment. The software is available at <url>http://sysbio.rnet.missouri.edu/multicom_toolbox/</url>.</p
Letter of intent for KM3NeT 2.0
The main objectives of the KM3NeT Collaboration are
(
i
)
the discovery and
subsequent observation of high-energy neutrino sources in the Universe and
(
ii
)
the determination of the mass hierarchy of neutrinos. These objectives are
strongly motivated by two recent important discoveries, namely:
(
1
)
the high-
energy astrophysical neutrino signal reported by IceCube and
(
2
)
the sizable
contribution of electron neutrinos to the third neutrino mass eigenstate as
reported by Daya Bay, Reno and others. To meet these objectives, the
KM3NeT Collaboration plans to build a new Research Infrastructure con-
sisting of a network of deep-sea neutrino telescopes in the Mediterranean Sea.
A phased and distributed implementation is pursued which maximises the
access to regional funds, the availability of human resources and the syner-
gistic opportunities for the Earth and sea sciences community. Three suitable
deep-sea sites are selected, namely off-shore Toulon
(
France
)
, Capo Passero
(
Sicily, Italy
)
and Pylos
(
Peloponnese, Greece
)
. The infrastructure will consist
of three so-called building blocks. A building block comprises 115 strings,
each string comprises 18 optical modules and each optical module comprises
31 photo-multiplier tubes. Each building block thus constitutes a three-
dimensional array of photo sensors that can be used to detect the Cherenkov
light produced by relativistic particles emerging from neutrino interactions.
Two building blocks will be sparsely con
fi
gured to fully explore the IceCube
signal with similar instrumented volume, different methodology, improved
resolution and complementary
fi
eld of view, including the galactic plane. One
building block will be densely con
fi
gured to precisely measure atmospheric
neutrino oscillations.
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As representações quanto ao lugar dos saberes na educação histórica, manifestadas durante o debate em torno do novo currículo de História no Quebec (2006-2010)
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