274 research outputs found
Profiling lung adenocarcinoma by liquid biopsy: can one size fit all?
BACKGROUND: Cancer is first and foremost a disease of the genome. Specific genetic signatures within a tumour are prognostic of disease outcome, reflect subclonal architecture and intratumour heterogeneity, inform treatment choices and predict the emergence of resistance to targeted therapies. Minimally invasive liquid biopsies can give temporal resolution to a tumour's genetic profile and allow the monitoring of treatment response through levels of circulating tumour DNA (ctDNA). However, the detection of ctDNA in repeated liquid biopsies is currently limited by economic and time constraints associated with targeted sequencing. METHODS: Here we bioinformatically profile the mutational and copy number spectrum of The Cancer Genome Network's lung adenocarcinoma dataset to uncover recurrently mutated genomic loci. RESULTS: We build a panel of 400 hotspot mutations and show that the coverage extends to more than 80% of the dataset at a median depth of 8 mutations per patient. Additionally, we uncover several novel single-nucleotide variants present in more than 5% of patients, often in genes not commonly associated with lung adenocarcinoma. CONCLUSION: With further optimisation, this hotspot panel could allow molecular diagnostics laboratories to build curated primer banks for 'off-the-shelf' monitoring of ctDNA by droplet-based digital PCR or similar techniques, in a time- and cost-effective manner
Object-oriented Programming Laws for Annotated Java Programs
Object-oriented programming laws have been proposed in the context of
languages that are not combined with a behavioral interface specification
language (BISL). The strong dependence between source-code and interface
specifications may cause a number of difficulties when transforming programs.
In this paper we introduce a set of programming laws for object-oriented
languages like Java combined with the Java Modeling Language (JML). The set of
laws deals with object-oriented features taking into account their
specifications. Some laws deal only with features of the specification
language. These laws constitute a set of small transformations for the
development of more elaborate ones like refactorings
Abundance of Delta Resonances in 58Ni+58Ni Collisions between 1 and 2 AGeV
Charged pion spectra measured in 58Ni-58Ni collisions at 1.06, 1.45 and 1.93
AGeV are interpreted in terms of a thermal model including the decay of Delta
resonances. The transverse momentum spectra of pions are well reproduced by
adding the pions originating from the Delta-resonance decay to the component of
thermal pions, deduced from the high transverse momentum part of the pion
spectra. About 10 and 18% of the nucleons are excited to Delta states at
freeze-out for beam energies of 1 and 2 AGeV, respectively.Comment: 14 pages, LaTeX with 3 included figures; submitted to Physics Letters
Strange meson production in Al+Al collisions at 1.9A GeV
The production of K, K and (1020) mesons is studied in Al+Al
collisions at a beam energy of 1.9A GeV which is close or below the production
threshold in NN reactions. Inverse slopes, anisotropy parameters, and total
emission yields of K mesons are obtained. A comparison of the ratio of
kinetic energy distributions of K and K mesons to the HSD transport
model calculations suggests that the inclusion of the in-medium modifications
of kaon properties is necessary to reproduce the ratio. The inverse slope and
total yield of mesons are deduced. The contribution to K production
from meson decays is found to be [17 3 (stat) (syst)]
%. The results are in line with previous K and data obtained for
different colliding systems at similar incident beam energies.Comment: 16 pages, 11 figure
Centrality dependence of subthreshold meson production in Ni+Ni collisions at 1.9A GeV
We analysed the meson production in central Ni+Ni collisions at the
beam kinetic energy of 1.93A GeV with the FOPI spectrometer and found the
production probability per event of . This new data point allows for the first time
to inspect the centrality dependence of the subthreshold meson
production in heavy-ion collisions. The rise of meson multiplicity per
event with mean number of participants can be parameterized by the power
function with exponent . The ratio of to
production yields seems not to depend within the experimental
uncertainties on the collision centrality, and the average of measured values
was found to be .Comment: 9 pages, 5 figure
Stopping and Radial Flow in Central 58Ni + 58Ni Collisions between 1 and 2 AGeV
The production of charged pions, protons and deuterons has been studied in
central collisions of 58Ni on 58Ni at incident beam energies of 1.06, 1.45 and
1.93 AGeV. The dependence of transverse-momentum and rapidity spectra on the
beam energy and on the centrality of the collison is presented. It is shown
that the scaling of the mean rapidity shift of protons established for AGS and
SPS energies is valid down to 1 AGeV. The degree of nuclear stopping is
discussed; the IQMD transport model reproduces the measured proton rapidity
spectra for the most central events reasonably well, but does not show any
sensitivity between the soft and the hard equation of state (EoS). A radial
flow analysis, using the midrapidity transverse-momentum spectra, delivers
freeze-out temperatures T and radial flow velocities beta_r which increase with
beam energy up to 2 AGeV; in comparison to existing data of Au on Au over a
large range of energies only beta_r shows a system size dependence
Isospin dependence of relative yields of and mesons at 1.528 AGeV
Results on and meson production in Ru +
Ru and Zr + Zr collisions at a beam kinetic
energy of 1.528 GeV, measured with the FOPI detector at GSI-Darmstadt, are
investigated as a possible probe of isospin effects in high density nuclear
matter. The measured double ratio ()/() is
compared to the predictions of a thermal model and a Relativistic Mean Field
transport model using two different collision scenarios and under different
assumptions on the stiffness of the symmetry energy. We find a good agreement
with the thermal model prediction and the assumption of a soft symmetry energy
for infinite nuclear matter while more realistic transport simulations of the
collisions show a similar agreement with the data but also exhibit a reduced
sensitivity to the symmetry term.Comment: 5 pages, 3 figures. accepted for publication in Phys. Rev.
Two-proton small-angle correlations in central heavy-ion collisions: a beam-energy and system-size dependent study
Small-angle correlations of pairs of protons emitted in central collisions of
Ca + Ca, Ru + Ru and Au + Au at beam energies from 400 to 1500 MeV per nucleon
are investigated with the FOPI detector system at SIS/GSI Darmstadt.
Dependences on system size and beam energy are presented which extend the
experimental data basis of pp correlations in the SIS energy range
substantially. The size of the proton-emitting source is estimated by comparing
the experimental data with the output of a final-state interaction model which
utilizes either static Gaussian sources or the one-body phase-space
distribution of protons provided by the BUU transport approach. The trends in
the experimental data, i.e. system-size and beam energy dependences, are well
reproduced by this hybrid model. However, the pp correlation function is found
rather insensitive to the stiffness of the equation of state entering the
transport model calculations.Comment: 9 pages, 8 figures, accepted at Eur. Phys. Journ.
Measurement of and mesons in Al+Al collisions at 1.9 GeV
New measurement of sub-threshold and production is
presented. The experimental data complete the measurement of strange particles
produced in Al+Al collisions at 1.9 GeV measured with the FOPI detector at
SIS/GSI. The / yield ratio is found to be and is in good agreement with the
UrQMD model prediction. These measurements provide information on in-medium
cross section of - fusion which is the dominant process on
sub-threshold production.Comment: 5 pages, 4 figures, accepted for publication in Phys. Rev.
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