1,187 research outputs found
The Family Name as Socio-Cultural Feature and Genetic Metaphor: From Concepts to Methods
A recent workshop entitled The Family Name as Socio-Cultural Feature and Genetic Metaphor: From Concepts to Methods was held in Paris in December 2010, sponsored by the French National Centre for Scientific Research (CNRS) and by the journal Human Biology. This workshop was intended to foster a debate on questions related to the family names and to compare different multidisciplinary approaches involving geneticists, historians, geographers, sociologists and social anthropologists. This collective paper presents a collection of selected communications
Speeding up the Consensus Clustering methodology for microarray data analysis
<p>Abstract</p> <p>Background</p> <p>The inference of the number of clusters in a dataset, a fundamental problem in Statistics, Data Analysis and Classification, is usually addressed via internal validation measures. The stated problem is quite difficult, in particular for microarrays, since the inferred prediction must be sensible enough to capture the inherent biological structure in a dataset, e.g., functionally related genes. Despite the rich literature present in that area, the identification of an internal validation measure that is both fast and precise has proved to be elusive. In order to partially fill this gap, we propose a speed-up of <monospace>Consensus</monospace> (Consensus Clustering), a methodology whose purpose is the provision of a prediction of the number of clusters in a dataset, together with a dissimilarity matrix (the consensus matrix) that can be used by clustering algorithms. As detailed in the remainder of the paper, <monospace>Consensus</monospace> is a natural candidate for a speed-up.</p> <p>Results</p> <p>Since the time-precision performance of <monospace>Consensus</monospace> depends on two parameters, our first task is to show that a simple adjustment of the parameters is not enough to obtain a good precision-time trade-off. Our second task is to provide a fast approximation algorithm for <monospace>Consensus</monospace>. That is, the closely related algorithm <monospace>FC</monospace> (Fast Consensus) that would have the same precision as <monospace>Consensus</monospace> with a substantially better time performance. The performance of <monospace>FC</monospace> has been assessed via extensive experiments on twelve benchmark datasets that summarize key features of microarray applications, such as cancer studies, gene expression with up and down patterns, and a full spectrum of dimensionality up to over a thousand. Based on their outcome, compared with previous benchmarking results available in the literature, <monospace>FC</monospace> turns out to be among the fastest internal validation methods, while retaining the same outstanding precision of <monospace>Consensus</monospace>. Moreover, it also provides a consensus matrix that can be used as a dissimilarity matrix, guaranteeing the same performance as the corresponding matrix produced by <monospace>Consensus</monospace>. We have also experimented with the use of <monospace>Consensus</monospace> and <monospace>FC</monospace> in conjunction with <monospace>NMF</monospace> (Nonnegative Matrix Factorization), in order to identify the correct number of clusters in a dataset. Although <monospace>NMF</monospace> is an increasingly popular technique for biological data mining, our results are somewhat disappointing and complement quite well the state of the art about <monospace>NMF</monospace>, shedding further light on its merits and limitations.</p> <p>Conclusions</p> <p>In summary, <monospace>FC</monospace> with a parameter setting that makes it robust with respect to small and medium-sized datasets, i.e, number of items to cluster in the hundreds and number of conditions up to a thousand, seems to be the internal validation measure of choice. Moreover, the technique we have developed here can be used in other contexts, in particular for the speed-up of stability-based validation measures.</p
The pharmacological regulation of cellular mitophagy
Small molecules are pharmacological tools of considerable value for dissecting complex biological processes and identifying potential therapeutic interventions. Recently, the cellular quality-control process of mitophagy has attracted considerable research interest; however, the limited availability of suitable chemical probes has restricted our understanding of the molecular mechanisms involved. Current approaches to initiate mitophagy include acute dissipation of the mitochondrial membrane potential (ΔΨm) by mitochondrial uncouplers (for example, FCCP/CCCP) and the use of antimycin A and oligomycin to impair respiration. Both approaches impair mitochondrial homeostasis and therefore limit the scope for dissection of subtle, bioenergy-related regulatory phenomena. Recently, novel mitophagy activators acting independently of the respiration collapse have been reported, offering new opportunities to understand the process and potential for therapeutic exploitation. We have summarized the current status of mitophagy modulators and analyzed the available chemical tools, commenting on their advantages, limitations and current applications
Measurement and Interpretation of Fermion-Pair Production at LEP energies above the Z Resonance
This paper presents DELPHI measurements and interpretations of
cross-sections, forward-backward asymmetries, and angular distributions, for
the e+e- -> ffbar process for centre-of-mass energies above the Z resonance,
from sqrt(s) ~ 130 - 207 GeV at the LEP collider. The measurements are
consistent with the predictions of the Standard Model and are used to study a
variety of models including the S-Matrix ansatz for e+e- -> ffbar scattering
and several models which include physics beyond the Standard Model: the
exchange of Z' bosons, contact interactions between fermions, the exchange of
gravitons in large extra dimensions and the exchange of sneutrino in R-parity
violating supersymmetry.Comment: 79 pages, 16 figures, Accepted by Eur. Phys. J.
A Determination of the Centre-of-Mass Energy at LEP2 using Radiative 2-fermion Events
Using e+e- -> mu+mu-(gamma) and e+e- -> qqbar(gamma) events radiative to the
Z pole, DELPHI has determined the centre-of-mass energy, sqrt{s}, using energy
and momentum constraint methods. The results are expressed as deviations from
the nominal LEP centre-of-mass energy, measured using other techniques. The
results are found to be compatible with the LEP Energy Working Group estimates
for a combination of the 1997 to 2000 data sets.Comment: 20 pages, 6 figures, Accepted by Eur. Phys. J.
Study of Inclusive J/psi Production in Two-Photon Collisions at LEP II with the DELPHI Detector
Inclusive J/psi production in photon-photon collisions has been observed at
LEP II beam energies. A clear signal from the reaction gamma gamma -> J/psi+X
is seen. The number of observed N(J/psi -> mu+mu-) events is 36 +/- 7 for an
integrated luminosity of 617 pb^{-1}, yielding a cross-section of
sigma(J/psi+X) = 45 +/- 9 (stat) +/- 17 (syst) pb. Based on a study of the
event shapes of different types of gamma gamma processes in the PYTHIA program,
we conclude that (74 +/- 22)% of the observed J/psi events are due to
`resolved' photons, the dominant contribution of which is most probably due to
the gluon content of the photon.Comment: 13 pages, 8 figures, Accepted by Phys. Lett.
Study of Tau-pair Production in Photon-Photon Collisions at LEP and Limits on the Anomalous Electromagnetic Moments of the Tau Lepton
Tau-pair production in the process e+e- -> e+e-tau+tau- was studied using
data collected by the DELPHI experiment at LEP2 during the years 1997 - 2000.
The corresponding integrated luminosity is 650 pb^{-1}. The values of the
cross-section obtained are found to be in agreement with QED predictions.
Limits on the anomalous magnetic and electric dipole moments of the tau lepton
are deduced.Comment: 20 pages, 9 figures, Accepted by Eur. Phys. J.
A Measurement of the Tau Hadronic Branching Ratios
The exclusive and semi-exclusive branching ratios of the tau lepton hadronic
decay modes (h- v_t, h- pi0 v_t, h- pi0 pi0 v_t, h- \geq 2pi0 v_t, h- \geq 3pi0
v_t, 2h- h+ v_t, 2h- h+ pi0 v_t, 2h- h+ \geq 2pi0 v_t, 3h- 2h+ v_t and 3h- 2h+
\geq 1pi0 v_t) were measured with data from the DELPHI detector at LEP.Comment: 53 pages, 18 figures, Accepted by Eur. Phys. J.
Study of Leading Hadrons in Gluon and Quark Fragmentation
The study of quark jets in e+e- reactions at LEP has demonstrated that the
hadronisation process is reproduced well by the Lund string model. However, our
understanding of gluon fragmentation is less complete. In this study enriched
quark and gluon jet samples of different purities are selected in three-jet
events from hadronic decays of the Z collected by the DELPHI experiment in the
LEP runs during 1994 and 1995. The leading systems of the two kinds of jets are
defined by requiring a rapidity gap and their sum of charges is studied. An
excess of leading systems with total charge zero is found for gluon jets in all
cases, when compared to Monte Carlo Simulations with JETSET (with and without
Bose-Einstein correlations included) and ARIADNE. The corresponding leading
systems of quark jets do not exhibit such an excess. The influence of the gap
size and of the gluon purity on the effect is studied and a concentration of
the excess of neutral leading systems at low invariant masses (<~ 2 GeV/c^2) is
observed, indicating that gluon jets might have an additional hitherto
undetected fragmentation mode via a two-gluon system. This could be an
indication of a possible production of gluonic states as predicted by QCD.Comment: 19 pages, 6 figures, Accepted by Phys. Lett.
Evidence for an Excess of Soft Photons in Hadronic Decays of Z^0
Soft photons inside hadronic jets converted in front of the DELPHI main
tracker (TPC) in events of qqbar disintegrations of the Z^0 were studied in the
kinematic range 0.2 < E_gamma < 1 GeV and transverse momentum with respect to
the closest jet direction p_T < 80 MeV/c. A clear excess of photons in the
experimental data as compared to the Monte Carlo predictions is observed. This
excess (uncorrected for the photon detection efficiency) is (1.17 +/- 0.06 +/-
0.27) x 10^{-3} gamma/jet in the specified kinematic region, while the expected
level of the inner hadronic bremsstrahlung (which is not included in the Monte
Carlo) is (0.340 +/- 0.001 +/- 0.038) x 10^{-3} gamma/jet. The ratio of the
excess to the predicted bremsstrahlung rate is then (3.4 +/- 0.2 +/- 0.8),
which is similar in strength to the anomalous soft photon signal observed in
fixed target experiments with hadronic beams.Comment: 37 pages, 9 figures, Accepted by Eur. Phys. J.
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