A unified framework for unraveling the functional interaction structure of a biomolecular network based on stimulus-response experimental data

Cho, K.H.,Choo, S.M.,Wellstead, P.,Wolkenhauer, O. North-Holland Pub ; Elsevier Science Ltd 2005 FEBS letters Vol.579 No.20

We propose a unified framework for the identification of functional interaction structures of biomolecular networks in a way that leads to a new experimental design procedure. In developing our approach, we have built upon previous work. Thus we begin by pointing out some of the restrictions associated with existing structure identification methods and point out how these restrictions may be eased. In particular, existing methods use specific forms of experimental algebraic equations with which to identify the functional interaction structure of a biomolecular network. In our work, we employ an extended form of these experimental algebraic equations which, while retaining their merits, also overcome some of their disadvantages. Experimental data are required in order to estimate the coefficients of the experimental algebraic equation set associated with the structure identification task. However, experimentalists are rarely provided with guidance on which parameters to perturb, and to what extent, to perturb them. When a model of network dynamics is required then there is also the vexed question of sample rate and sample time selection to be resolved. Supplying some answers to these questions is the main motivation of this paper. The approach is based on stationary and/or temporal data obtained from parameter perturbations, and unifies the previous approaches of Kholodenko et al. (PNAS 99 (2002) 12841-12846) and Sontag et al. (Bioinformatics 20 (2004) 1877-1886). By way of demonstration, we apply our unified approach to a network model which cannot be properly identified by existing methods. Finally, we propose an experiment design methodology, which is not limited by the amount of parameter perturbations, and illustrate its use with an in numero example.

Measurement of electrons from beauty hadron decays in pp collisions at s=7 TeV

ALICE Collaboration,Abelev, B.,Adam, J.,Adamova, D.,Adare, A.M.,Aggarwal, M.M.,Aglieri Rinella, G.,Agocs, A.G.,Agostinelli, A.,Aguilar Salazar, S.,Ahammed, Z.,Ahmad, N.,Ahmad Masoodi, A.,Ahn, S.A.,Ahn North-Holland Pub. Co 2013 Physics letters: B Vol.721 No.1

The production cross section of electrons from semileptonic decays of beauty hadrons was measured at mid-rapidity (|y|<0.8) in the transverse momentum range 1<p<SUB>T</SUB><8 GeV/c with the ALICE experiment at the CERN LHC in pp collisions at a center of mass energy s=7 TeV using an integrated luminosity of 2.2 nb<SUP>-1</SUP>. Electrons from beauty hadron decays were selected based on the displacement of the decay vertex from the collision vertex. A perturbative QCD calculation agrees with the measurement within uncertainties. The data were extrapolated to the full phase space to determine the total cross section for the production of beauty quark-antiquark pairs.

Charge correlations using the balance function in Pb-Pb collisions at s_NN=2.76 TeV

North-Holland Pub. Co 2013 Physics letters: B Vol.723 No.4

In high-energy heavy-ion collisions, the correlations between the emitted particles can be used as a probe to gain insight into the charge creation mechanisms. In this Letter, we report the first results of such studies using the electric charge balance function in the relative pseudorapidity (Δη) and azimuthal angle (Δφ) in Pb-Pb collisions at s<SUB>NN</SUB>=2.76 TeV with the ALICE detector at the Large Hadron Collider. The width of the balance function decreases with growing centrality (i.e. for more central collisions) in both projections. This centrality dependence is not reproduced by HIJING, while AMPT, a model which incorporates strings and parton rescattering, exhibits qualitative agreement with the measured correlations in Δφ but fails to describe the correlations in Δη. A thermal blast-wave model incorporating local charge conservation and tuned to describe the p<SUB>T</SUB> spectra and v<SUB>2</SUB> measurements reported by ALICE, is used to fit the centrality dependence of the width of the balance function and to extract the average separation of balancing charges at freeze-out. The comparison of our results with measurements at lower energies reveals an ordering with s<SUB>NN</SUB>: the balance functions become narrower with increasing energy for all centralities. This is consistent with the effect of larger radial flow at the LHC energies but also with the late stage creation scenario of balancing charges. However, the relative decrease of the balance function widths in Δη and Δφ with centrality from the highest SPS to the LHC energy exhibits only small differences. This observation cannot be interpreted solely within the framework where the majority of the charge is produced at a later stage in the evolution of the heavy-ion collision.

Centrality dependence of the pseudorapidity density distribution for charged particles in Pb-Pb collisions at s_NN=2.76 TeV

North-Holland Pub. Co 2013 Physics letters: B Vol.726 No.4

We present the first wide-range measurement of the charged-particle pseudorapidity density distribution, for different centralities (the 0-5%, 5-10%, 10-20%, and 20-30% most central events) in Pb-Pb collisions at s<SUB>NN</SUB>=2.76 TeV at the LHC. The measurement is performed using the full coverage of the ALICE detectors, -5.0<η<5.5, and employing a special analysis technique based on collisions arising from LHC 'satellite' bunches. We present the pseudorapidity density as a function of the number of participating nucleons as well as an extrapolation to the total number of produced charged particles (N<SUB>ch</SUB>=17165+/-772 for the 0-5% most central collisions). From the measured dN<SUB>ch</SUB>/dη distribution we derive the rapidity density distribution, dN<SUB>ch</SUB>/dy, under simple assumptions. The rapidity density distribution is found to be significantly wider than the predictions of the Landau model. We assess the validity of longitudinal scaling by comparing to lower energy results from RHIC. Finally the mechanisms of the underlying particle production are discussed based on a comparison with various theoretical models.

In-medium modified π-ρ-ω mesonic Lagrangian and properties of nuclear matter

Jung, J.H.,Yakhshiev, U.T.,Kim, H.-Ch. North-Holland Pub. Co 2013 Physics letters: B Vol.723 No.4

We investigate the bulk properties of symmetric nuclear matter within the framework of an in-medium modified chiral solitonic model with π, ρ and ω mesons. We consider the modification of meson degrees of freedom in nuclear matter, based on phenomenology of pion-nucleus scattering and the empirical nuclear mass formula. We discuss the results of the density dependence of the volume term in the mass formula and the incompressibility of symmetric nuclear matter, comparing them with relativistic mean-field models. The mass dropping of the ρ meson in nuclear matter is also obtained and discussed.

J/ψ production at high transverse momenta in p+p and Au + Au collisions at s_NN=200 GeV

North-Holland Pub. Co 2013 Physics letters: B Vol.722 No.1

We report J/ψ spectra for transverse momenta p<SUB>T</SUB>>5 GeV/c at mid-rapidity in p+p and Au+Au collisions at s<SUB>NN</SUB>=200 GeV. The inclusive J/ψ spectrum and the extracted B-hadron feed-down are compared to models incorporating different production mechanisms. We observe significant suppression of the J/ψ yields for p<SUB>T</SUB>>5 GeV/c in 0-30% central Au+Au collisions relative to the p+p yield scaled by the number of binary nucleon-nucleon collisions in Au+Au collisions. In 30-60% mid-central collisions, no such suppression is observed. The level of suppression is consistently less than that of high-p<SUB>T</SUB>π<SUP>+/-</SUP> and low-p<SUB>T</SUB>J/ψ at RHIC and high-p<SUB>T</SUB>J/ψ at the LHC.

U(1)_B'1+B'2-2L'1 mediation for the natural SUSY and the anomalous muon g-2

Huh, J.H.,Kyae, B. North-Holland Pub. Co 2013 Physics letters: B Vol.726 No.4

We propose a U(1)<SUP>'</SUP> mediated supersymmetry (SUSY) breaking, in which U(1)<SUP>'</SUP> is identified with U(1)<SUB>B'1+B'2-2L'1</SUB>. The U(1)<SUB>B'1+B'2-2L'1</SUB> gauge symmetry, which is anomaly-free with the field contents of the minimal supersymmetric standard model, assigns +/-1/3 charges to the first and second generations of the quarks, and @?2 to the first generation of the leptons. As a result, the first two generations of squarks acquire masses of about 7 TeV, and the first generation of the sleptons do those of 40 TeV, respectively, in the presence of one or three pairs of extra vector-like matter {5,5@?}. Non-observation on extra colored particles below 1 TeV at the large hadron collider, and also the flavor violations such as μ<SUP>-</SUP>→e<SUP>-</SUP>γ are explained. By virtue of such a gauge symmetry, proton stability can be protected. The other squarks and sleptons as well as the gauginos can obtain masses of order 10<SUP>2-3</SUP> GeV through the conventional gravity or gauge mediated SUSY breaking mechanism. The relative light smuon/sneutrino and the neutralino/chargino could be responsible for the (g-2)<SUB>μ</SUB> deviated from the standard model prediction. The stop mass of ~500 GeV relieves the fine-tuning problem in the Higgs sector. Two-loop effects by the relatively heavy sfermions can protect the smallness of the stop mass from the radiative correction by the heavy gluino (@?1 TeV). Extra vector-like matter can enhance the radiative corrections to the Higgs mass up to 126 GeV, and induce the desired mixing among the chiral fermions after U(1)<SUB>B'1+B'2-2L'1</SUB> breaking.

Dark matter asymmetry in supersymmetric Dirac leptogenesis

Choi, K.Y.,Chun, E.J.,Shin, C.S. North-Holland Pub. Co 2013 Physics letters: B Vol.723 No.1

We discuss asymmetric or symmetric dark matter candidate in the supersymmetric Dirac leptogenesis scenario. By introducing a singlet superfield coupling to right-handed neutrinos, the overabundance problem of dark matter can be evaded and various possibilities for dark matter candidate arise. If the singlino is the lightest supersymmetric particle (LSP), it becomes naturally asymmetric dark matter. On the other hand, the right-handed sneutrino is a symmetric dark matter candidate whose relic density can be determined by the usual thermal freeze-out process. The conventional neutralino or gravitino LSP can be also a dark matter candidate as its non-thermal production from the right-handed sneutrino can be controlled appropriately. In our scenario, the late-decay of heavy supersymmetric particles mainly produces the right-handed sneutrino and neutrino which is harmless to the standard prediction of the Big-Bang Nucleosynthesis.

Long-range angular correlations on the near and away side in p-Pb collisions at s_NN=5.02 TeV

ALICE Collaboration,Abelev, B.,Adam, J.,Adamova, D.,Adare, A.M.,Aggarwal, M.,Aglieri Rinella, G.,Agnello, M.,Agocs, A.G.,Agostinelli, A.,Ahammed, Z.,Ahmad, N.,Ahmad, A.,Ahn, S.A.,Ahn, S.U.,Ajaz, M.,Ak North-Holland Pub. Co 2013 Physics letters: B Vol.719 No.1

Angular correlations between charged trigger and associated particles are measured by the ALICE detector in p-Pb collisions at a nucleon-nucleon centre-of-mass energy of 5.02 TeV for transverse momentum ranges within 0.5<p<SUB>T,assoc</SUB><p<SUB>T,trig</SUB><4 GeV/c. The correlations are measured over two units of pseudorapidity and full azimuthal angle in different intervals of event multiplicity, and expressed as associated yield per trigger particle. Two long-range ridge-like structures, one on the near side and one on the away side, are observed when the per-trigger yield obtained in low-multiplicity events is subtracted from the one in high-multiplicity events. The excess on the near-side is qualitatively similar to that recently reported by the CMS Collaboration, while the excess on the away-side is reported for the first time. The two-ridge structure projected onto azimuthal angle is quantified with the second and third Fourier coefficients as well as by near-side and away-side yields and widths. The yields on the near side and on the away side are equal within the uncertainties for all studied event multiplicity and p<SUB>T</SUB> bins, and the widths show no significant evolution with event multiplicity or p<SUB>T</SUB>. These findings suggest that the near-side ridge is accompanied by an essentially identical away-side ridge.

Search for a Higgs boson decaying into a Z and a photon in pp collisions at s=7 and 8 TeV

North-Holland Pub. Co 2013 Physics letters: B Vol.726 No.4

A search for a Higgs boson decaying into a Z boson and a photon is described. The analysis is performed using proton-proton collision datasets recorded by the CMS detector at the LHC. Events were collected at center-of-mass energies of 7 TeV and 8 TeV, corresponding to integrated luminosities of 5.0 fb<SUP>-1</SUP> and 19.6 fb<SUP>-1</SUP>, respectively. The selected events are required to have opposite-sign electron or muon pairs. No excess above standard model predictions has been found in the 120-160 GeV mass range and the first limits on the Higgs boson production cross section times the H→Zγ branching fraction at the LHC have been derived. The observed at 95% confidence level limits are between about 4 and 25 times the standard model cross section times the branching fraction. For a standard model Higgs boson mass of 125 GeV the expected limit at the 95% confidence level is 10 and the observed limit is 9.5. Models predicting the Higgs boson production cross section times the H→Zγ branching fraction to be larger than one order of magnitude of the standard model prediction are excluded for most of the 125-157 GeV mass range.