Graph theoretic analysis of protein interaction networks of eukaryotes

Thanks to recent progress in high-throughput experimental techniques, the datasets of large-scale protein interactions of prototypical multicellular species, the nematode worm Caenorhabditis elegans and the fruit fly Drosophila melanogaster, have been assayed. The datasets are obtained mainly by using the yeast hybrid method, which contains false-positive and false-negative simultaneously. Accordingly, while it is desirable to test such datasets through further wet experiments, here we invoke recent developed network theory to test such high throughput datasets in a simple way. Based on the fact that the key biological processes indispensable to maintaining life are universal across eukaryotic species, and the comparison of structural properties of the protein interaction networks (PINs) of the two species with those of the yeast PIN, we find that while the worm and the yeast PIN datasets exhibit similar structural properties, the current fly dataset, though most comprehensively screened ever, does not reflect generic structural properties correctly as it is. The modularity is suppressed and the connectivity correlation is lacking. Addition of interlogs to the current fly dataset increases the modularity and enhances the occurrence of triangular motifs as well. The connectivity correlation function of the fly, however, remains distinct under such interlogs addition, for which we present a possible scenario through an in silico modeling.Comment: 7 pages, 6 figures, 2 table

New antineutrino energy spectra predictions from the summation of beta decay branches of the fission products

In this paper, we study the impact of the inclusion of the recently measured beta decay properties of the $^{102;104;105;106;107}$Tc, $^{105}$Mo, and $^{101}$Nb nuclei in an updated calculation of the antineutrino energy spectra of the four fissible isotopes $^{235, 238}$U, and $^{239,241}$Pu. These actinides are the main contributors to the fission processes in Pressurized Water Reactors. The beta feeding probabilities of the above-mentioned Tc, Mo and Nb isotopes have been found to play a major role in the $\gamma$ component of the decay heat of $^{239}$Pu, solving a large part of the $\gamma$ discrepancy in the 4 to 3000\,s range. They have been measured using the Total Absorption Technique (TAS), avoiding the Pandemonium effect. The calculations are performed using the information available nowadays in the nuclear databases, summing all the contributions of the beta decay branches of the fission products. Our results provide a new prediction of the antineutrino energy spectra of $^{235}$U, $^{239,241}$Pu and in particular of $^{238}$U for which no measurement has been published yet. We conclude that new TAS measurements are mandatory to improve the reliability of the predicted spectra.Comment: 10 pages, 2 figure

Large-scale inference and graph theoretical analysis of gene-regulatory networks in B. stubtilis

We present the methods and results of a two-stage modeling process that generates candidate gene-regulatory networks of the bacterium B. subtilis from experimentally obtained, yet mathematically underdetermined microchip array data. By employing a computational, linear correlative procedure to generate these networks, and by analyzing the networks from a graph theoretical perspective, we are able to verify the biological viability of our inferred networks, and we demonstrate that our networks' graph theoretical properties are remarkably similar to those of other biological systems. In addition, by comparing our inferred networks to those of a previous, noisier implementation of the linear inference process [17], we are able to identify trends in graph theoretical behavior that occur both in our networks as well as in their perturbed counterparts. These commonalities in behavior at multiple levels of complexity allow us to ascertain the level of complexity to which our process is robust to noise.Comment: 22 pages, 4 figures, accepted for publication in Physica A (2006

Development of a quality assurance process for the SoLid experiment

The SoLid experiment has been designed to search for an oscillation pattern induced by a light sterile neutrino state, utilising the BR2 reactor of SCK circle CEN, in Belgium. The detector leverages a new hybrid technology, utilising two distinct scintillators in a cubic array, creating a highly segmented detector volume. A combination of 5 cm cubic polyvinyltoluene cells, with (LiF)-Li-6:ZnS(Ag) sheets on two faces of each cube, facilitate reconstruction of the neutrino signals. Whilst the high granularity provides a powerful toolset to discriminate backgrounds; by itself the segmentation also represents a challenge in terms of homogeneity and calibration, for a consistent detector response. The search for this light sterile neutrino implies a sensitivity to distortions of around O(10)% in the energy spectrum of reactor (v) over bare. Hence, a very good neutron detection efficiency, light yield and homogeneous detector response are critical for data validation. The minimal requirements for the SoLid physics program are a light yield and a neutron detection efficiency larger than 40 PA/MeV/cube and 50% respectively. In order to guarantee these minimal requirements, the collaboration developed a rigorous quality assurance process for all 12800 cubic cells of the detector. To carry out the quality assurance process, an automated calibration system called CALIPSO was designed and constructed. CALIPSO provides precise, automatic placement of radioactive sources in front of each cube of a given detector plane (16 x 16 cubes). A combination of Na-22, Cf-252 and AmBe gamma and neutron sources were used by CALIPSO during the quality assurance process. Initially, the scanning identified defective components allowing for repair during initial construction of the SoLid detector. Secondly, a full analysis of the calibration data revealed initial estimations for the light yield of over 60 PA/MeV and neutron reconstruction efficiency of 68%, validating the SoLid physics requirements

Online Monitoring of the Osiris Reactor with the Nucifer Neutrino Detector

Originally designed as a new nuclear reactor monitoring device, the Nucifer detector has successfully detected its first neutrinos. We provide the second shortest baseline measurement of the reactor neutrino flux. The detection of electron antineutrinos emitted in the decay chains of the fission products, combined with reactor core simulations, provides an new tool to assess both the thermal power and the fissile content of the whole nuclear core and could be used by the Inter- national Agency for Atomic Energy (IAEA) to enhance the Safeguards of civil nuclear reactors. Deployed at only 7.2m away from the compact Osiris research reactor core (70MW) operating at the Saclay research centre of the French Alternative Energies and Atomic Energy Commission (CEA), the experiment also exhibits a well-suited configuration to search for a new short baseline oscillation. We report the first results of the Nucifer experiment, describing the performances of the 0.85m3 detector remotely operating at a shallow depth equivalent to 12m of water and under intense background radiation conditions. Based on 145 (106) days of data with reactor ON (OFF), leading to the detection of an estimated 40760 electron antineutrinos, the mean number of detected antineutrinos is 281 +- 7(stat) +- 18(syst) electron antineutrinos/day, in agreement with the prediction 277(23) electron antineutrinos/day. Due the the large background no conclusive results on the existence of light sterile neutrinos could be derived, however. As a first societal application we quantify how antineutrinos could be used for the Plutonium Management and Disposition Agreement.Comment: 22 pages, 16 figures - Version

Experimental evidence for subshell closure in 8^{8}He and indication of a resonant state in 7^{7}He below 1 MeV

NESTERThe spectroscopy of the unstable $^{8}$He and unbound $^{7}$He nuclei is investigated via the p($^{8}$He, d) transfer reaction with a 15.7A MeV $^{8}$He beam from the SPIRAL facility. The emitted deuterons were detected by the telescope array MUST. The results are analyzed within the coupled-channels Born approximation framework, and a spectroscopic factor $C^2$S=4.4±1.3 for neutron pickup to the $^{7}$He_g.s.$is deduced. This value is consistent with a full p3/2 subshell for$^{8}$He. Tentative evidence for the first excited state of$^{7}$He is found at$E^*$=0.9±0.5 MeV (width$\Gamma$=1.0±0.9 MeV). The second one is observed at a position compatible with previous measurements,$E^*$=2.9±0.1 MeV. Both are in agreement with previous separate measurements. The reproduction of the first excited state below 1 MeV would be a challenge for the most sophisticated nuclear theories

MAYA: An active-target detector for binary reactions with exotic beams

International audienceWith recent improvements in the production of radioactive beams in facilities such as SPIRAL at GANIL, a larger area of the nuclear chart is now accessible for experimentation. For these usually low-intensity and low-energy secondary beams, we have developed the new MAYA detector based on the active-target concept. This device allows to use a relatively thick target without loss of resolution by using the detection gas as target material. Dedicated 3D tracking, particle identification, energy loss and range measurements allow complete kinematic reconstruction of reactions taking place inside MAYA

Search for a long lived component in the reaction U+U near the Coulomb barrier

Expérience GANILInternational audienceWe performed an experiment to search for a signature of a long living component in the collision of $^{238}$U + $^{238}$U between 6.09 and 7.35A MeV. The experiment was performed at GANIL using the spectrometer VAMOS, tuned for observing reactions with kinematics similar to fusion-fission events. Theoretical calculations indicate that if a long living component would exist for this reaction, the most probable fission channel of such a giant system would be via the emissionof quasi-lead nuclei. We detected events of such a category in the focal plane of VAMOS. These events present an excitation function growing as a function of the bombarding energy

Toward automatic comparison of visualization techniques: Application to graph visualization

Many end-user evaluations of data visualization techniques have been run during the last decades. Their results are cornerstones to build efficient visualization systems. However, designing such an evaluation is always complex and time-consuming and may end in a lack of statistical evidence and reproducibility. We believe that modern and efficient computer vision techniques, such as deep convolutional neural networks (CNNs), may help visualization researchers to build and/or adjust their evaluation hypothesis. The basis of our idea is to train machine learning models on several visualization techniques to solve a specific task. Our assumption is that it is possible to compare the efficiency of visualization techniques based on the performance of their corresponding model. As current machine learning models are not able to strictly reflect human capabilities, including their imperfections, such results should be interpreted with caution. However, we think that using machine learning-based pre-evaluation, as a pre-process of standard user evaluations, should help researchers to perform a more exhaustive study of their design space. Thus, it should improve their final user evaluation by providing it better test cases. In this paper, we present the results of two experiments we have conducted to assess how correlated the performance of users and computer vision techniques can be. That study compares two mainstream graph visualization techniques: node-link (\NL) and adjacency-matrix (\MD) diagrams. Using two well-known deep convolutional neural networks, we partially reproduced user evaluations from Ghoniem \textit{et al.} and from Okoe \textit{et al.}. These experiments showed that some user evaluation results can be reproduced automatically.Comment: 35 pages, 6 figures, 4 table