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Search Results: 1 - 10 of 87770 matches for " I. Supek "
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Light response of pure CsI calorimeter crystals painted with wavelength-shifting lacquer
E. Frlez,Ch. Broennimann,B. Krause,D. Pocanic,D. Renker,S. Ritt,P. L. Slocum,I. Supek,H. P. Wirtz
Physics , 2000, DOI: 10.1016/S0168-9002(00)01045-7
Abstract: We have measured scintillation properties of pure CsI crystals used in the shower calorimeter built for a precise determination of the pi+ -> pi0 e+ nu decay rate at the Paul Scherrer Institute (PSI). All 240 individual crystals painted with a special wavelength-shifting solution were examined in a custom-build detection apparatus (RASTA=radioactive source tomography apparatus) that uses a 137Cs radioactive gamma source, cosmic muons and a light emitting diode as complementary probes of the scintillator light response. We have extracted the total light output, axial light collection nonuniformities and timing responses of the individual CsI crystals. These results predict improved performance of the 3 pi sr PIBETA calorimeter due to the painted lateral surfaces of 240 CsI crystals. The wavelength-shifting paint treatment did not affect appreciably the total light output and timing resolution of our crystal sample. The predicted energy resolution for positrons and photons in the energy range of 10-100 MeV was nevertheless improved due to the more favorable axial light collection probability variation. We have compared simulated calorimeter ADC spectra due to 70 MeV positrons and photons with a Monte Carlo calculation of an ideal detector light response.
Correction: Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity
Fran Supek, Kristian Vlahovi?ek
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-463
Abstract: The text referring to equation (1) states the value should be computed as the G-test statistic, which equals to 2*sum(O*ln(O/E)); therefore, the accompanying text is correct.The text "a constant of 0.5 is added to the correction factor C" in the paragraph following equation (4), should state: "a constant of 0.5 is subtracted from the correction factor C".The error in the formulae does not affect the results in the paper regarding performance of MILC, MELP and other codon distance measures as all calculations were performed using a correct implementation of MILC in the INCA software [2].
Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity
Fran Supek, Kristian Vlahovi?ek
BMC Bioinformatics , 2005, DOI: 10.1186/1471-2105-6-182
Abstract: We compared the performance of several commonly used measures and a novel method we introduce in this paper – Measure Independent of Length and Composition (MILC). Large, randomly generated sequence sets were used to test for dependence on (i) sequence length, (ii) overall amount of codon bias and (iii) codon bias discrepancy in the sequences. A derivative of the method, named MELP (MILC-based Expression Level Predictor) can be used to quantitatively predict gene expression levels from genomic data. It was compared to other similar predictors by examining their correlation with actual, experimentally obtained mRNA or protein abundances.We have established that MILC is a generally applicable measure, being resistant to changes in gene length and overall nucleotide composition, and introducing little noise into measurements. Other methods, however, may also be appropriate in certain applications. Our efforts to quantitatively predict gene expression levels in several prokaryotes and unicellular eukaryotes met with varying levels of success, depending on the experimental dataset and predictor used. Out of all methods, MELP and Rainer Merkl's GCB method had the most consistent behaviour. A 'reference set' containing known ribosomal protein genes appears to be a valid starting point for a codon usage-based expressivity prediction.As the numbers of sequenced genes grew, it became evident that synonymous codons are not used equally [1-3]. Codon frequencies were found to vary on 3 levels: between genomes, between genes in the same genome, and within a single gene [4]. Many factors have been shown to influence codon usage patterns, the most important being: (i) overall nucleotide composition of the genome, reflecting mutational biases; (ii) selective forces acting on highly expressed genes to improve efficiency of translation [5]; and (iii) horizontal gene transfer, with transferred genes retaining the codon frequencies of their former host [6]. Connections have also been de
Ratios of Elastic Scattering of Pions from 3H and 3He
W. J. Briscoe,B. L. Berman,R. W. C. Carter,K. S. Dhuga,S. K. Matthews,N-J. Nicholas,S. J. Greene,B. M. K. Nefkens,J. W. Price,L. D. Isenhower,M. E. Sadler,I. Slaus,I. Supek
Physics , 2002, DOI: 10.1103/PhysRevC.66.054006
Abstract: We have measured the elastic-scattering ratios of normalized yields for charged pions from 3H and 3He in the backward hemisphere. At 180 MeV, we completed the angular distribution begun with our earlier measurements, adding six data points in the angular range of 119 deg to 169 deg in the pi-nucleus center of mass. We also measured an excitation function with data points at 142, 180, 220, and 256 MeV incident pion energy at the largest achievable angle for each energy between 160 deg and 170 deg in the pi-nucleus center of mass. This excitation function corresponds to the energies of our forward-hemisphere studies. The data, taken as a whole, show an apparent role reversal of the two charge-symmetric ratios r1 and r2 in the backward hemisphere. Also, for data > 100 deg we observe a strong dependence on the four-momentum transfer squared (-t) for all of the ratios regardless of pion energy or scattering angle, and we find that the superratio R data match very well with calculations based on the forward-hemisphere data that predicts the value of the difference between the even-nucleon radii of 3H and 3He. Comparisons are also made with recent calculations incorporating different wave functions and double scattering models.
Nucleoid-Associated Proteins Affect Mutation Dynamics in E. coli in a Growth Phase-Specific Manner
Tobias Warnecke ,Fran Supek,Ben Lehner
PLOS Computational Biology , 2012, DOI: 10.1371/journal.pcbi.1002846
Abstract: The binding of proteins can shield DNA from mutagenic processes but also interfere with efficient repair. How the presence of DNA-binding proteins shapes intra-genomic differences in mutability and, ultimately, sequence variation in natural populations, however, remains poorly understood. In this study, we examine sequence evolution in Escherichia coli in relation to the binding of four abundant nucleoid-associated proteins: Fis, H-NS, IhfA, and IhfB. We find that, for a subset of mutations, protein occupancy is associated with both increased and decreased mutability in the underlying sequence depending on when the protein is bound during the bacterial growth cycle. On average, protein-bound DNA exhibits reduced mutability compared to protein-free DNA. However, this net protective effect is weak and can be abolished or even reversed during stages of colony growth where binding coincides – and hence likely interferes with – DNA repair activity. We suggest that the four nucleoid-associated proteins analyzed here have played a minor but significant role in patterning extant sequence variation in E. coli.
Cosmic muon tomography of pure cesium iodide calorimeter crystals
E. Frlez,I. Supek,K. A. Assamagan,Ch. Br"onnimann,Th. Fl"ugel,B. Krause,D. W. Lawrence,D. Mzavia,D. Pocanic,D. Renker,S. Ritt,P. L. Slocum,N. Soic
Physics , 1999, DOI: 10.1016/S0168-9002(99)00886-4
Abstract: Scintillation properties of pure CsI crystals used in the shower calorimeter being built for precise determination of the pi+ -> pi0 e+ nu decay rate are reported. Seventy-four individual crystals, polished and wrapped in Teflon foil, were examined in a multiwire drift chamber system specially designed for transmission cosmic muon tomography. Critical elements of the apparatus and reconstruction algorithms enabling measurement of spatial detector optical nonuniformities are described. Results are compared with a Monte Carlo simulation of the light response of an ideal detector. The deduced optical nonuniformity contributions to the FWHM energy resolution of the PIBETA CsI calorimeter for the pi+ -> e+ nu 69.8 MeV positrons and the monoenergetic 70.8 MeV photons were 2.7% and 3.7%, respectively. The upper limit of optical nonuniformity correction to the 69.8 MeV positron low-energy tail between 5 MeV and 55 MeV was +0.2%, as opposed to the +0.3% tail contribution for the photon of the equivalent total energy. Imposing the 5 MeV calorimeter veto cut to suppress the electromagnetic losses, GEANT-evaluated positron and photon lineshape tail fractions summed over all above-threshold ADCs were found to be 2.36+-0.05(stat)+-0.20(sys)% and 4.68+-0.07(stat)+-0.20(sys)%, respectively.
Measurement of $K^- p$ radiative capture to $γΛ$ and $γ Σ^0$ for $p_{K^-}$ between 514 and 750 MeV/$c$
S. Prakhov,P. Vancraeyveld,N. Phaisangittisakul,B. M. K. Nefkens,V. Bekrenev,W. J. Briscoe,L. De Cruz,D. Isenhower,N. Knecht,A. Koulbardis,N. Kozlenko,S. Kruglov,G. Lolos,I. Lopatin,A. Maru?i,S. McDonald,Z. Papandreou,D. Peaslee,J. W. Price,J. Ryckebusch,M. Sadler,A. Shafi,A. Starostin,H. M. Staudenmaier,I. I. Strakovsky,I. Supek,T. Van Cauteren
Physics , 2009, DOI: 10.1103/PhysRevC.82.015201
Abstract: Differential cross sections for $K^-$ radiative capture in flight on the proton, leading to the $\gamma\Lambda$ and $\gamma\Sigma^0$ final states, have been measured at eight $K^-$ momenta between 514 and 750 MeV/$c$. The data were obtained with the Crystal Ball multiphoton spectrometer installed at the separated $K/\pi$ beam line C6 of the BNL Alternating Gradient Synchrotron. The results substantially improve the existing experimental data available for studying radiative decays of excited hyperon states. An exploratory theoretical analysis is performed within the Regge-plus-resonance approach. According to this analysis, the $\gamma\Sigma^0$ final state is dominated by hyperonresonance exchange and hints at an important role for a resonance in the mass region of 1700 MeV. In the $\gamma\Lambda$ final state, on the other hand, the resonant contributions account for only half the strength, and the data suggest the importance of a resonance in the mass region of 1550 MeV.
Measurement of $π^0 Λ$, $\bar{K}^0 n$, and $π^0 Σ^0$ production in $K^- p$ interactions for $p_{K^-}$ between 514 and 750 MeV/$c$
S. Prakhov,B. M. K. Nefkens,V. Bekrenev,W. J. Briscoe,N. Knecht,A. Koulbardis,N. Kozlenko,S. Kruglov,G. Lolos,I. Lopatin,A. Maru?i,S. McDonald,D. Peaslee,N. Phaisangittisakul,J. W. Price,A. Shafi,A. Starostin,H. M. Staudenmaier,I. I. Strakovsky,I. Supek
Physics , 2008, DOI: 10.1103/PhysRevC.80.025204
Abstract: Differential cross sections and hyperon polarizations have been measured for $\bar{K}^0 n$, $\pi^0 \Lambda$, and $\pi^0 \Sigma^0$ production in $K^- p$ interactions at eight $K^-$ momenta between 514 and 750 MeV/$c$. The experiment detected the multiphoton final states with the Crystal Ball spectrometer using a $K^-$ beam from the Alternating Gradient Synchrotron of BNL. The results provide significantly greater precision than the existing data, allowing a detailed reexamination of the excited hyperon states in our energy range.
REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms
Fran Supek, Matko Bo?njak, Nives ?kunca, Tomislav ?muc
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0021800
Abstract: Outcomes of high-throughput biological experiments are typically interpreted by statistical testing for enriched gene functional categories defined by the Gene Ontology (GO). The resulting lists of GO terms may be large and highly redundant, and thus difficult to interpret. REVIGO is a Web server that summarizes long, unintelligible lists of GO terms by finding a representative subset of the terms using a simple clustering algorithm that relies on semantic similarity measures. Furthermore, REVIGO visualizes this non-redundant GO term set in multiple ways to assist in interpretation: multidimensional scaling and graph-based visualizations accurately render the subdivisions and the semantic relationships in the data, while treemaps and tag clouds are also offered as alternative views. REVIGO is freely available at http://revigo.irb.hr/.
New Precise Measurement of the Pion Weak Form Factors in the Pi+ -> e+ nu gamma Decay
M. Bychkov,D. Po?ani?,B. A. VanDevender,V. A. Baranov,W. Bertl,Yu. M. Bystritsky,E. Frle?,V. A. Kalinnikov,N. V. Khomutov,A. S. Korenchenko,S. M. Korenchenko,M. Korolija,T. Kozlowski,N. P. Kravchuk,N. A. Kuchinsky,W. Li,D. Mekterovi?,D. Mzhavia,S. Ritt,P. Robmann,O. A. Rondon-Aramayo,A. M. Rozhdestvensky,T. Sakhelashvili,S. Scheu,U. Straumann,I. Supek,Z. Tsamalaidze,A. van der Schaaf,E. P. Velicheva,V. P. Volnykh,Y. Wang,H. -P. Wirtz
Physics , 2008, DOI: 10.1103/PhysRevLett.103.051802
Abstract: We have measured the $\pi^+\to {\rm e}^+\nu\gamma$ branching ratio over a wide region of phase space, based on a total of 65,460 events acquired using the PIBETA detector. Minimum-$\chi^2$ fits to the measured $(E_{e^+},E_\gamma)$ energy distributions result in the weak form factor value of $F_A=0.0119(1)$ with a fixed value of $F_V=0.0259$. An unconstrained fit yields $F_V=0.0258(17)$ and $F_A=0.0117(17)$. In addition, we have measured $a=0.10(6)$ for the dependence of $F_V$ on $q^2$, the ${\rm e}^{+}\nu$ pair invariant mass squared, parametrized as $F_V(q^2)=F_V(0)(1+a\cdot q^2)$. The branching ratio for the kinematic region $E_\gamma > 10 $MeV and $\theta_{{\rm e^+}\gamma} > 40^\circ $ is measured to be $B^{\rm exp}=73.86(54) \times 10^{-8}$. Earlier deviations we reported in the high-$E_\gamma$/low-$E_{{\rm e}^+}$ kinematic region are resolved, and we find full compatibility with CVC and standard $V$$-$$A$ calculations without a tensor term. We also derive new values for the pion polarizability, $\alpha_E = \rm 2.78(10) \times 10^{-4} fm^3$, and neutral pion lifetime, $\tau_{\pi 0} = (8.5 \pm 1.1) \times 10^{-17} $s.
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