Community detection based on "clumpiness" matrix in complex networks

The "clumpiness" matrix of a network is used to develop a method to identify its community structure. A "projection space" is constructed from the eigenvectors of the clumpiness matrix and a border line is defined using some kind of angular distance in this space. The community structure of the network is identified using this borderline and/or hierarchical clustering methods. The performance of our algorithm is tested on some computer-generated and real-world networks. The accuracy of the results is checked using normalized mutual information. The effect of community size heterogeneity on the accuracy of the method is also discussed.Comment: 18 pages and 13 figure

Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

Eukaryotic genomes are packaged into a 3-dimensional structure in the nucleus. Current methods for studying genome-wide structure are based on proximity ligation. However, this approach can fail to detect known structures, such as interactions with nuclear bodies, because these DNA regions can be too far apart to directly ligate. Accordingly, our overall understanding of genome organization remains incomplete. Here, we develop split-pool recognition of interactions by tag extension (SPRITE), a method that enables genome-wide detection of higher-order interactions within the nucleus. Using SPRITE, we recapitulate known structures identified by proximity ligation and identify additional interactions occurring across larger distances, including two hubs of inter-chromosomal interactions that are arranged around the nucleolus and nuclear speckles. We show that a substantial fraction of the genome exhibits preferential organization relative to these nuclear bodies. Our results generate a global model whereby nuclear bodies act as inter-chromosomal hubs that shape the overall packaging of DNA in the nucleus

Measurement of negatively charged pion spectra in inelastic p+p interactions at plabp_{lab} = 20, 31, 40, 80 and 158 GeV/c

We present experimental results on inclusive spectra and mean multiplicities of negatively charged pions produced in inelastic p+p interactions at incident projectile momenta of 20, 31, 40, 80 and 158 GeV/c ($\sqrt{s} =$ 6.3, 7.7, 8.8, 12.3 and 17.3 GeV, respectively). The measurements were performed using the large acceptance NA61/SHINE hadron spectrometer at the CERN Super Proton Synchrotron. Two-dimensional spectra are determined in terms of rapidity and transverse momentum. Their properties such as the width of rapidity distributions and the inverse slope parameter of transverse mass spectra are extracted and their collision energy dependences are presented. The results on inelastic p+p interactions are compared with the corresponding data on central Pb+Pb collisions measured by the NA49 experiment at the CERN SPS. The results presented in this paper are part of the NA61/SHINE ion program devoted to the study of the properties of the onset of deconfinement and search for the critical point of strongly interacting matter. They are required for interpretation of results on nucleus-nucleus and proton-nucleus collisions.Comment: Numerical results available at: https://edms.cern.ch/document/1314605 Updates in v3: Updated version, as accepted for publicatio

NA61/SHINE facility at the CERN SPS: beams and detector system

NA61/SHINE (SPS Heavy Ion and Neutrino Experiment) is a multi-purpose experimental facility to study hadron production in hadron-proton, hadron-nucleus and nucleus-nucleus collisions at the CERN Super Proton Synchrotron. It recorded the first physics data with hadron beams in 2009 and with ion beams (secondary 7Be beams) in 2011. NA61/SHINE has greatly profited from the long development of the CERN proton and ion sources and the accelerator chain as well as the H2 beamline of the CERN North Area. The latter has recently been modified to also serve as a fragment separator as needed to produce the Be beams for NA61/SHINE. Numerous components of the NA61/SHINE set-up were inherited from its predecessors, in particular, the last one, the NA49 experiment. Important new detectors and upgrades of the legacy equipment were introduced by the NA61/SHINE Collaboration. This paper describes the state of the NA61/SHINE facility - the beams and the detector system - before the CERN Long Shutdown I, which started in March 2013

Passive Mineral Carbonation of Mg-rich Mine Wastes by Atmospheric CO2

Mg-rich process tailings and waste rocks from mining operations can react spontaneously with atmospheric CO2 to form stable carbonate minerals by exothermic reactions. Over the last decade, we have conducted a number of laboratory and field experiments and surveys on both mine waste rocks and different types of mine tailings from Ni-Cu, chrysotile, and diamond mines. The experiments and surveys cover a wide range of time (103 to 108 s) and mass (1-108 g) scales. Mine waste rich in brucite or chrysotile enhances the mineral carbonation reactions. Water saturation, but more importantly, watering frequency, are highly important to optimize carbonation. Adjusting the chemical composition of the interstitial water to favour Mg dissolution and to prevent passivation of the reaction surfaces is crucial to ensure the progress of the carbonation reactions. Preservation of the permeability structure is also critical to facilitate water and CO2 migration in the rock wastes and tailings. In field experiments, CO2 supply controled by diffusion in the mining waste is slower than the reaction rate which limits the capture of atmospheric CO2. Industrial implementation of passive mineral carbonation of mine waste by atmospheric CO2 can be optimized using the above parameters

Molecules in bipolar proto-planetary nebulae

Two bipolar proto-planetary nebulae, IRAS16594-4656 and IRAS17150-3224, have been detected in various molecular lines, namely CO, ^{13}CO, HCN and CN, and remain undetected in several other species. CO(J=2-1) and CO(J=3-2) line profiles are compared to new spectra of similar PPN candidates, previously undetected in CO(J=2-1): CPD-53^{o}5736, IRAS17106-3046, IRAS17245-3951 and IRAS17441-2411. CO(J=2-1) maps of IRAS16594-4656 and IRAS17150-3224 show that both PPNe have little separation between blue, centre and red-shifted emission, and also that the CO(J=2-1) emission is of a similar size to the telescope beam. Fractional abundances of all detected molecules (except CO) are calculated using the results of CO line modelling and a simple photodissociation model. For those species not detected, upper limits are derived. Comparisons between these fractional abundances and those of other PPNe show that IRAS16594-4656 and IRAS17150-3224 are quite under-abundant when compared to molecule-rich sources like CRL618, CRL2688 and OH231.8+4.2. As a reason for this deficit, the difference in circumstellar envelope/torus density between the molecule-rich sources and the molecule-poor sources is proposed, and supported by a chemical model which follows the transition of a circumstellar envelope through the AGB phase and into the PPN phase of evolution. The model includes the effects of UV radiation, cosmic rays and also X-rays. Finally, the post-AGB ages of these two objects (200-400 yr) are estimated using CN/HCN and HCN/CO ratios and both ages are found to be in agreement with previous figures cited in the literature, IRAS17150-3224 being the younger of the two PPNe.Comment: Accepted by Astronomy & Astrophysics. 21 pages, 11 figure

Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

Eukaryotic genomes are packaged into a 3-dimensional structure in the nucleus. Current methods for studying genome-wide structure are based on proximity ligation. However, this approach can fail to detect known structures, such as interactions with nuclear bodies, because these DNA regions can be too far apart to directly ligate. Accordingly, our overall understanding of genome organization remains incomplete. Here, we develop split-pool recognition of interactions by tag extension (SPRITE), a method that enables genome-wide detection of higher-order interactions within the nucleus. Using SPRITE, we recapitulate known structures identified by proximity ligation and identify additional interactions occurring across larger distances, including two hubs of inter-chromosomal interactions that are arranged around the nucleolus and nuclear speckles. We show that a substantial fraction of the genome exhibits preferential organization relative to these nuclear bodies. Our results generate a global model whereby nuclear bodies act as inter-chromosomal hubs that shape the overall packaging of DNA in the nucleus