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  1. Abstract Background Cancer progression reconstruction is an important development stemming from the phylogenetics field. In this context, the reconstruction of the phylogeny representing the evolutionary history presents some peculiar aspects that depend on the technology used to obtain the data to analyze: Single Cell DNA Sequencing data have great specificity, but are affected by moderate false negative and missing value rates. Moreover, there has been some recent evidence of back mutations in cancer: this phenomenon is currently widely ignored. Results We present a new tool, , that reconstructs a tumor phylogeny from Single Cell Sequencing data, allowing each mutation tomore »be lost at most a fixed number of times. The General Parsimony Phylogeny from Single cell () tool is open source and available at https://github.com/AlgoLab/gpps . Conclusions provides new insights to the analysis of intra-tumor heterogeneity by proposing a new progression model to the field of cancer phylogeny reconstruction on Single Cell data.« less
  2. Abstract

    Results are presented from two dye release experiments conducted in the seasonal thermocline of the Sargasso Sea, one in a region of low horizontal strain rate (~10−6 s−1), the second in a region of intermediate horizontal strain rate (~10−5 s−1). Both experiments lasted ~6 days, covering spatial scales of 1–10 and 1–50 km for the low and intermediate strain rate regimes, respectively. Diapycnal diffusivities estimated from the two experiments were κz = (2–5) × 10−6 m2 s−1, while isopycnal diffusivities were κH = (0.2–3) m2 s−1, with the range in κH being less a reflection of site-to-site variability, andmore »more due to uncertainties in the background strain rate acting on the patch combined with uncertain time dependence. The Site I (low strain) experiment exhibited minimal stretching, elongating to approximately 10 km over 6 days while maintaining a width of ~5 km, and with a notable vertical tilt in the meridional direction. By contrast, the Site II (intermediate strain) experiment exhibited significant stretching, elongating to more than 50 km in length and advecting more than 150 km while still maintaining a width of order 3–5 km. Early surveys from both experiments showed patchy distributions indicative of small-scale stirring at scales of order a few hundred meters. Later surveys show relatively smooth, coherent distributions with only occasional patchiness, suggestive of a diffusive rather than stirring process at the scales of the now larger patches. Together the two experiments provide important clues as to the rates and underlying processes driving diapycnal and isopycnal mixing at these scales.

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  3. Abstract Quantum chromodynamics, the theory of the strong force, describes interactions of coloured quarks and gluons and the formation of hadronic matter. Conventional hadronic matter consists of baryons and mesons made of three quarks and quark-antiquark pairs, respectively. Particles with an alternative quark content are known as exotic states. Here a study is reported of an exotic narrow state in the D 0 D 0 π + mass spectrum just below the D *+ D 0 mass threshold produced in proton-proton collisions collected with the LHCb detector at the Large Hadron Collider. The state is consistent with the ground isoscalarmore »$${{{{{{\rm{T}}}}}}}_{{{{{{\rm{c}}}}}}{{{{{\rm{c}}}}}}}^{+}$$ T c c + tetraquark with a quark content of $${{{{{\rm{c}}}}}}{{{{{\rm{c}}}}}}\overline{{{{{{\rm{u}}}}}}}\overline{{{{{{\rm{d}}}}}}}$$ c c u ¯ d ¯ and spin-parity quantum numbers J P  = 1 + . Study of the DD mass spectra disfavours interpretation of the resonance as the isovector state. The decay structure via intermediate off-shell D *+ mesons is consistent with the observed D 0 π + mass distribution. To analyse the mass of the resonance and its coupling to the D * D system, a dedicated model is developed under the assumption of an isoscalar axial-vector $${{{{{{\rm{T}}}}}}}_{{{{{{\rm{c}}}}}}{{{{{\rm{c}}}}}}}^{+}$$ T c c + state decaying to the D * D channel. Using this model, resonance parameters including the pole position, scattering length, effective range and compositeness are determined to reveal important information about the nature of the $${{{{{{\rm{T}}}}}}}_{{{{{{\rm{c}}}}}}{{{{{\rm{c}}}}}}}^{+}$$ T c c + state. In addition, an unexpected dependence of the production rate on track multiplicity is observed.« less
    Free, publicly-accessible full text available December 1, 2023
  4. Abstract Conventional, hadronic matter consists of baryons and mesons made of three quarks and a quark–antiquark pair, respectively 1,2 . Here, we report the observation of a hadronic state containing four quarks in the Large Hadron Collider beauty experiment. This so-called tetraquark contains two charm quarks, a $$\overline{{{{{u}}}}}$$ u ¯ and a $$\overline{{{{{d}}}}}$$ d ¯ quark. This exotic state has a mass of approximately 3,875 MeV and manifests as a narrow peak in the mass spectrum of D 0 D 0 π + mesons just below the D *+ D 0 mass threshold. The near-threshold mass together with the narrow widthmore »reveals the resonance nature of the state.« less
    Free, publicly-accessible full text available July 1, 2023
  5. A bstract A precision measurement of the Z boson production cross-section at $$ \sqrt{\mathrm{s}} $$ s = 13 TeV in the forward region is presented, using pp collision data collected by the LHCb detector, corresponding to an integrated luminosity of 5.1 fb − 1 . The production cross-section is measured using Z → μ + μ − events within the fiducial region defined as pseudorapidity 2 . 0 < η < 4 . 5 and transverse momentum p T > 20 GeV /c for both muons and dimuon invariant mass 60 < M μμ < 120 GeV /c 2 .more »The integrated cross-section is determined to be $$ \sigma \left(Z\to {\mu}^{+}{\mu}^{-}\right)=196.4\pm 0.2\pm 1.6\pm 3.9\ \mathrm{pb}, $$ σ Z → μ + μ − = 196.4 ± 0.2 ± 1.6 ± 3.9 pb , where the first uncertainty is statistical, the second is systematic, and the third is due to the luminosity determination. The measured results are in agreement with theoretical predictions within uncertainties.« less
    Free, publicly-accessible full text available July 1, 2023
  6. A bstract Coherent production of J/ψ mesons is studied in ultraperipheral lead-lead collisions at a nucleon-nucleon centre-of-mass energy of 5 TeV, using a data sample collected by the LHCb experiment corresponding to an integrated luminosity of about 10 μb −1 . The J/ψ mesons are reconstructed in the dimuon final state and are required to have transverse momentum below 1 GeV. The cross-section within the rapidity range of 2 . 0 < y < 4 . 5 is measured to be 4 . 45 ± 0 . 24 ± 0 . 18 ± 0 . 58 mb, where the firstmore »uncertainty is statistical, the second systematic and the third originates from the luminosity determination. The cross-section is also measured in J/ψ rapidity intervals. The results are compared to predictions from phenomenological models.« less
    Free, publicly-accessible full text available July 1, 2023
  7. Free, publicly-accessible full text available June 1, 2023
  8. Abstract The centrality of heavy-ion collisions is directly related to the created medium in these interactions. A procedure to determine the centrality of collisions with the LHCb detector is implemented for lead-lead collisions at √ s NN = 5 TeV and lead-neon fixed-target collisions at √ s NN = 69 GeV. The energy deposits in the electromagnetic calorimeter are used to determine and define the centrality classes. The correspondence between the number of participants and the centrality for the lead-lead collisions is in good agreement with the correspondence found in other experiments, and the centrality measurements for the lead-neon collisionsmore »presented here are performed for the first time in fixed-target collisions at the LHC.« less
    Free, publicly-accessible full text available May 1, 2023
  9. Free, publicly-accessible full text available May 1, 2023