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  • arXiv  (12)
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  • 1
    Description: In 1977, Young proposed a voting scheme that extends the Condorcet Principle based on the fewest possible number of voters whose removal yields a Condorcet winner. We prove that both the winner and the ranking problem for Young elections is complete for the class of problems solvable in polynomial time by parallel access to NP. Analogous results for Lewis Carroll's 1876 voting scheme were recently established by Hemaspaandra et al. In contrast, we prove that the winner and ranking problems in Fishburn's homogeneous variant of Carroll's voting scheme can be solved efficiently by linear programming. Comment: 10 pages
    Keywords: Computer Science - Computational Complexity ; F.1.3 ; F.2.2 ; J.4
    Source: Cornell University
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  • 2
    In: Jiang, Yuxiang; Oron, Tal Ronnen; Clark, Wyatt T. Bankapur, Asma R.; D’Andrea, Daniel; Lepore, Rosalba; Funk, Christopher S.; Kahanda, Indika; Verspoor, Karin M.; Ben-Hur, Asa; Koo, Da Chen Emily; Penfold-Brown, Duncan; Shasha, Dennis; Youngs, Noah; Bonneau, Richard; Lin, Alexandra; Sahraeian, Sayed M. E.; Martelli, Pier Luigi; Profiti, Giuseppe; Casadio, Rita; Cao, Renzhi; Zhong, Zhaolong; Cheng, Jianlin; Altenhoff, Adrian; Skunca, Nives; Dessimoz, Christophe; Dogan, Tunca; Hakala, Kai; Kaewphan, Suwisa; Mehryary, Farrokh; Salakoski, Tapio; Ginter, Filip; Fang, Hai; Smithers, Ben; Oates, Matt; Gough, Julian; Törönen, Petri; Koskinen, Patrik; Holm, Liisa; Chen, Ching-Tai; Hsu, Wen-Lian; Bryson, Kevin; Cozzetto, Domenico; Minneci, Federico; Jones, David T.; Chapman, Samuel; BKC, Dukka; Khan, Ishita K.; Kihara, Daisuke; Ofer, Dan; Rappoport, Nadav; Stern, Amos; Cibrian-Uhalte, Elena; Denny, Paul; Foulger, Rebecca E.; Hieta, Reija; Legge, Duncan; Lovering, Ruth C.; Magrane, Michele; Melidoni, Anna N.; Mutowo-Meullenet, Prudence; Pichler, Klemens; Shypitsyna, Aleksandra; Li, Biao; Zakeri, Pooya; ElShal, Sarah; Tranchevent, Léon-Charles; Das, Sayoni; Dawson, Natalie L.; Lee, David; Lees, Jonathan G.; Sillitoe, Ian; Bhat, Prajwal; Nepusz, Tamás; Romero, Alfonso E.; Sasidharan, Rajkumar; Yang, Haixuan; Paccanaro, Alberto; Gillis, Jesse; Sedeño-Cortés, Adriana E.; Pavlidis, Paul; Feng, Shou; Cejuela, Juan M.; Goldberg, Tatyana; Hamp, Tobias; Richter, Lothar; Salamov, Asaf; Gabaldon, Toni; Marcet-Houben, Marina; Supek, Fran; Gong, Qingtian; Ning, Wei; Zhou, Yuanpeng; Tian, Weidong; Falda, Marco; Fontana, Paolo; Lavezzo, Enrico; Toppo, Stefano; Ferrari, Carlo; Giollo, Manuel; Piovesan, Damiano; Tosatto, Silvio C.E.; del Pozo, Angela; Fernández, José M.; Maietta, Paolo; Valencia, Alfonso; Tress, Michael L.; Benso, Alfredo; Di Carlo, Stefano; Politano, Gianfranco; Savino, Alessandro; Rehman, Hafeez Ur; Re, Matteo; Mesiti, Marco; Valentini, Giorgio; Bargsten, Joachim W.; van Dijk, Aalt D. J.; Gemovic, Branislava; Glisic, Sanja; Perovic, Vladmir; Veljkovic, Veljko; Veljkovic, Nevena; Almeida-e-Silva, Danillo C.; Vencio, Ricardo Z. N.; Sharan, Malvika; Vogel, Jörg; Kansakar, Lakesh; Zhang, Shanshan; Vucetic, Slobodan; Wang, Zheng; Sternberg, Michael J. E.; Wass, Mark N.; Huntley, Rachael P.; Martin, Maria J.; O’Donovan, Claire; Robinson, Peter N.; Moreau, Yves; Tramontano, Anna; Babbitt, Patricia C.; Brenner, Steven E.; Linial, Michal; Orengo, Christine A.; Rost, Burkhard; Greene, Casey S.; Mooney, Sean D.; Friedberg, Iddo; Radivojac, Predrag (2016). An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology 17 ,
    Description: Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent.
    Keywords: Protein Function Prediction ; Disease Gene Prioritization ; Disintegrin ; Ontology ; Adam
    ISBN: 0003834282000
    ISSN: 1474-760X
    ISSN: 14747596
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  • 3
    Language: English
    In: Physical review letters, 15 July 2011, Vol.107(3), pp.032302
    Description: One of the most promising probes to study deconfined matter created in high energy nuclear collisions is the energy loss of (heavy) quarks. It has been shown in experiments at the Relativistic Heavy Ion Collider that even charm and bottom quarks, despite their high mass, experience a remarkable medium suppression in the quark gluon plasma. In this exploratory investigation we study the energy loss of heavy quarks in high multiplicity proton-proton collisions at LHC energies. Although the colliding systems are smaller than compared to those at the Relativistic Heavy Ion Collider (p+p vs Au+Au), the higher energy might lead to multiplicities comparable to Cu+Cu collisions at the Relativistic Heavy Ion Collider. The interaction of charm quarks with this environment gives rise to a non-negligible suppression of high momentum heavy quarks in elementary collisions.
    Keywords: High Energy Physics - Phenomenology ; High Energy Physics - Experiment ; Nuclear Theory;
    ISSN: 00319007
    E-ISSN: 1079-7114
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  • 4
    Language: English
    In: Physical Review C, 2013, Vol.87, p.064907
    Description: We study the dilepton production in heavy-ion collisions at energies of 1-2 AGeV as well as in proton induced pp, pn, pd and p+A reactions from 1 GeV up to 3.5 GeV. For the analysis we employ three different transport models - the microscopic off-shell Hadron-String-Dynamics (HSD) transport approach, the Isospin Quantum Molecular Dynamics (IQMD) approach as well as the Ultra-relativistic Quantum Molecular Dynamics (UrQMD) approach. We confirm the experimentally observed enhancement of the dilepton yield (normalized to the multiplicity of neutral pions $N_{\pi^0}$) in heavy-ion collisions with respect to that measured in $NN = (pp+pn)/2$ collisions. We identify two contributions to this enhancement: a) the $pN$ bremsstrahlung which scales with the number of collisions and not with the number of participants, i.e. pions; b) the dilepton emission from intermediate $\Delta$'s which are part of the reaction cycles $\Delta \to \pi N ; \pi N \to \Delta$ and $NN\to N\Delta; N\Delta \to NN$. With increasing system size more generations of intermediate $\Delta$'s are created. If such $\Delta$ decays into a pion, the pion can be reabsorbed, however, if it decays into a dilepton, the dilepton escapes from the system. Thus, experimentally one observes only one pion (from the last produced $\Delta$) whereas the dilepton yield accumulates the contributions from all $\Delta$'s of the cycle. We show as well that the Fermi motion enhances the production of pions and dileptons in the same way. Furthermore, employing the off-shell HSD approach, we explore the influence of in-medium effects like the modification of self-energies and spectral functions of the vector mesons due to their interactions with the hadronic environment.
    Keywords: Physics ; High Energy Physics - Phenomenology ; Physics ; Nuclear Experiment ; Physics ; Nuclear Theory ; Physics
    ISSN: 0556-2813
    E-ISSN: 1089-490X
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  • 5
    Language: English
    In: Physical Review C, 2010, Vol.82, p.014907
    Description: One of the fundamental objectives of experiments with ultrarelativistic heavy ions is to explore strongly interacting matter at high density and high temperature. In this investigation we study in particular the information which can be obtained by analyzing baryonic and mesonic resonances. The decay products of these resonances carry information on the resonances properties at the space time point of their decay. We especially investigate the percentage of reconstructable resonances as a function of density for heavy ion collisions in the energy range between $E_{lab}$ = 30 AGeV and $\sqrt{s}$ = 200 AGeV, the energy domain between the future FAIR facility and the present RHIC collider.
    Keywords: Physics ; High Energy Physics - Phenomenology ; Physics
    ISSN: 0556-2813
    E-ISSN: 1089-490X
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  • 6
    Language: English
    In: Journal of Physics G: Nuclear and Particle Physics, 2010, Vol.37, p.094046
    Description: One of the most fundamental questions in the field of relativistic heavy ion physics is how to reach and explore densities which are needed to cross the chiral and/or the deconfinement phase transition. In this analysis we investigate the information we can gather by analyzing baryonic and mesonic resonances on the hot and dense phase in such nuclear reactions. The decay products of these resonances carry information on the resonances properties at the space time point of their decay. We especially investigate the percentage of reconstructable resonances as a function of density for heavy ion collisions in the energy range between $E_{lab}$ = 30 AGeV and $\sqrt{s}$ = 200 AGeV, the energy domain between the future FAIR facility and the present RHIC collider.
    Keywords: Physics ; Nuclear Theory ; Physics
    ISSN: 09543899
    E-ISSN: 13616471
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  • 7
    Description: We study the impact of different Quark-Gluon Plasma expansion scenarios in heavy-ion collisions on spectra and elliptic flow of heavy quarks. For identical heavy-quark transport coefficients relativistic Langevin simulations with different expansion scenarios can lead to appreciable variations in the calculated suppression and elliptic flow of the heavy-quark spectra, by up to a factor of two. A cross comparison with two sets of transport coefficients supports these findings, illustrating the importance of realistic expansion models for quantitative evaluations of heavy-quark observables in heavy-ion collisions. It also turns out that differences in freeze-out prescriptions and Langevin realizations play a significant role in these variations. Light-quark observables are essential in reducing the uncertainties associated with the bulk-matter evolution, even though uncertainties due to the freeze-out prescription persist. Comment: submitted to Physical Review C
    Keywords: High Energy Physics - Phenomenology
    Source: Cornell University
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  • 8
    Description: In this contribution, we present some predictions for the production of D and B mesons in ultrarelativistic heavy ion collisions at RHIC and LHC energies and confront them with experimental results obtained so far by the STAR, PHENIX, ALICE and CMS collaborations. We next discuss some preliminary results obtained with an improved description of the medium based on EPOS initial conditions, and its possible implications on the nuclear modification factor and on the elliptic flow of heavy quarks. Comment: Proceedings from Sixth International Conference on Quarks and Nuclear Physics, April 16-20, 2012, Ecole Polytechnique, Palaiseau, Paris
    Keywords: High Energy Physics - Phenomenology ; Nuclear Experiment ; Nuclear Theory
    Source: Cornell University
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  • 9
    Language: English
    In: Classical and Quantum Gravity, 2007, Vol.24(2), pp.433-453
    Description: In this paper we describe applications of discrete differential forms in computational GR. In particular we consider the initial value problem in vacuum spacetimes that are spherically symmetric. The motivation to investigate this method is mainly its manifest coordinate independence. Three numerical schemes are introduced, the results of which are compared with the corresponding analytic solutions. The error of two schemes converges quadratically to zero. For one scheme the errors depend strongly on the initial data.
    Keywords: General Relativity And Quantum Cosmology;
    ISSN: 0264-9381
    E-ISSN: 1361-6382
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  • 10
    In: Class.Quant.Grav. 22 (2005) 1769-1793
    Description: The divergence of the constraint quantities is a major problem in computational gravity today. Apparently, there are two sources for constraint violations. The use of boundary conditions which are not compatible with the constraint equations inadvertently leads to 'constraint violating modes' propagating into the computational domain from the boundary. The other source for constraint violation is intrinsic. It is already present in the initial value problem, i.e. even when no boundary conditions have to be specified. Its origin is due to the instability of the constraint surface in the phase space of initial conditions for the time evolution equations. In this paper, we present a technique to study in detail how this instability depends on gauge parameters. We demonstrate this for the influence of the choice of the time foliation in context of the Weyl system. This system is the essential hyperbolic part in various formulations of the Einstein equations. Comment: 25 pages, 5 figures; v2: small additions, new reference, publication number, classification and keywords added, address fixed; v3: update to match journal version
    Keywords: General Relativity And Quantum Cosmology
    Source: Cornell University
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