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A model of the PI cycle reveals the regulating roles of lipid-binding proteins and pitfalls of using mosaic biological data
The phosphatidylinositol (PI) cycle is central to eukaryotic cell signaling. Its complexity, due to the number of reactions and lipid and inositol phosphate intermediates involved makes it difficult to analyze experimentally. Computational modelling approaches are seen as a way forward to elucidate complex biological regulatory mechanisms when this cannot be achieved solely through experimental approaches. Whilst mathematical modelling is well established in informing biological systems, many models are often informed by data sourced from multiple unrelated cell types (mosaic data) or from purified enzyme data. In this work, we develop a model of the PI cycle informed by experimental and omics data taken from a single cell type, namely platelets. We were able to make a number of predictions regarding the regulation of PI cycle enzymes, the importance of the number of receptors required for successful GPCR signaling and the importance of lipid- and protein-binding proteins in regulating second messenger outputs. We then consider how pathway behavior differs, when fully informed by data for HeLa cells and show that model predictions remain consistent. However, when informed by mosaic experimental data model predictions greatly vary illustrating the risks of using mosaic datasets from unrelated cell types
Dynamism in the solar core
Recent results of a mixed shell model heated asymmetrically by transient
increases in nuclear burning indicate the transient generation of small hot
spots inside the Sun somewhere between 0.1 and 0.2 solar radii. These hot
bubbles are followed by a nonlinear differential equation system with finite
amplitude non-homologous perturbations which is solved in a solar model. Our
results show the possibility of a direct connection between the dynamic
phenomena of the solar core and the atmospheric activity. Namely, an initial
heating about DQ_0 ~ 10^{31}-10^{37} ergs can be enough for a bubble to reach
the outer convective zone. Our calculations show that a hot bubble can arrive
into subphotospheric regions with DQ_final ~ 10^{28} - 10^{34} ergs with a high
speed, up to 10 km s-1, approaching the local sound speed. We point out that
the developing sonic boom transforms the shock front into accelerated particle
beam injected upwards into the top of loop carried out by the hot bubble above
its forefront traveling from the solar interior. As a result, a new perspective
arises to explain flare energetics. We show that the particle beams generated
by energetic deep-origin hot bubbles in the subphotospheric layers have masses,
energies, and chemical compositions in the observed range of solar
chromospheric and coronal flares. It is shown how the emergence of a hot bubble
into subphotospheric regions offers a natural mechanism that can generate both
the eruption leading to the flare and the observed coronal magnetic topology
for reconnection. We show a list of long-standing problems of solar physics
that our model explains. We present some predictions for observations, some of
which are planned to be realized in the near future.Comment: 44 pages, 20 figure
First measurement of the |t|-dependence of coherent J/ψ photonuclear production
The first measurement of the cross section for coherent J/ψ photoproduction as a function of |t|, the square of the momentum transferred between the incoming and outgoing target nucleus, is presented. The data were measured with the ALICE detector in ultra-peripheral Pb–Pb collisions at a centre-of-mass energy per nucleon pair sNN=5.02TeV with the J/ψ produced in the central rapidity region |y|<0.8, which corresponds to the small Bjorken-x range (0.3−1.4)×10−3.
The measured |t|-dependence is not described by computations based only on the Pb nuclear form factor, while the photonuclear cross section is better reproduced by models including shadowing according to the leading-twist approximation, or gluon-saturation effects from the impact-parameter dependent Balitsky–Kovchegov equation. These new results are therefore a valid tool to constrain the relevant model parameters and to investigate the transverse gluonic structure at very low Bjorken-x.publishedVersio
First measurement of coherent ρ0 photoproduction in ultra-peripheral Xe–Xe collisions at √sNN = 5.44 TeV
The first measurement of the coherent photoproduction of ρ0 vector mesons in ultra-peripheral Xe–Xe collisions at sNN=5.44 TeV is presented. This result, together with previous HERA γp data and γ–Pb measurements from ALICE, describes the atomic number (A) dependence of this process, which is particularly sensitive to nuclear shadowing effects and to the approach to the black-disc limit of QCD at a semi-hard scale. The cross section of the Xe+Xe→ρ0+Xe+Xe process, measured at midrapidity through the decay channel ρ0→π+π−, is found to be dσ/dy=131.5±5.6(stat.)−16.9+17.5(syst.) mb. The ratio of the continuum to resonant contributions for the production of pion pairs is also measured. In addition, the fraction of events accompanied by electromagnetic dissociation of either one or both colliding nuclei is reported. The dependence on A of cross section for the coherent ρ0 photoproduction at a centre-of-mass energy per nucleon of the γA system of WγA,n=65 GeV is found to be consistent with a power-law behaviour σ(γA→ρ0A)∝Aα with a slope α=0.96±0.02(syst.). This slope signals important shadowing effects, but it is still far from the behaviour expected in the black-disc limit.publishedVersio
Resolving the strange behavior of extraterrestrial potassium in the upper atmosphere
It has been known since the 1960s that the layers of Na and K atoms, which occur between 80 and 105 km in the Earth's atmosphere as a result of meteoric ablation, exhibit completely different seasonal behavior. In the extratropics Na varies annually, with a pronounced wintertime maximum and summertime minimum. However, K varies semiannually with a small summertime maximum and minima at the equinoxes. This contrasting behavior has never been satisfactorily explained. Here we use a combination of electronic structure and chemical kinetic rate theory to determine two key differences in the chemistries of K and Na. First, the neutralization of K+ ions is only favored at low temperatures during summer. Second, cycling between K and its major neutral reservoir KHCO3 is essentially temperature independent. A whole atmosphere model incorporating this new chemistry, together with a meteor input function, now correctly predicts the seasonal behavior of the K layer
Flow Dominance and Factorization of Transverse Momentum Correlations in Pb-Pb Collisions at the LHC
We present the first measurement of the two-particle transverse momentum differential correlation function, P2≡ ΔpTΔpT/ pT2, in Pb-Pb collisions at sNN=2.76 TeV. Results for P2 are reported as a function of the relative pseudorapidity (Δη) and azimuthal angle (Δφ) between two particles for different collision centralities. The Δφ dependence is found to be largely independent of Δη for |Δη|≥0.9. In the 5% most central Pb-Pb collisions, the two-particle transverse momentum correlation function exhibits a clear double-hump structure around Δφ=π (i.e., on the away side), which is not observed in number correlations in the same centrality range, and thus provides an indication of the dominance of triangular flow in this collision centrality. Fourier decompositions of P2, studied as a function of the collision centrality, show that correlations at |Δη|≥0.9 can be well reproduced by a flow ansatz based on the notion that measured transverse momentum correlations are strictly determined by the collective motion of the system
K*(892)(0) and phi(1020)meson production at high transverse momentum in pp and Pb-Pb collisions at root sNN=2.76 TeV
The production of K∗(892)0 and φ(1020) mesons in proton-proton (pp) and lead-lead (Pb-Pb) collisions
at √sNN = 2.76 TeV has been analyzed using a high luminosity data sample accumulated in 2011 with the
ALICE detector at the Large Hadron Collider (LHC). Transverse momentum (pT) spectra have been measured
for K∗(892)0 and φ(1020) mesons via their hadronic decay channels for pT up to 20 GeV/c. The measurements
in pp collisions have been compared to model calculations and used to determine the nuclear modification factor
and particle ratios. The K∗(892)0/K ratio exhibits significant reduction from pp to central Pb-Pb collisions,
consistent with the suppression of the K∗(892)0 yield at low pT due to rescattering of its decay products in
the hadronic phase. In central Pb-Pb collisions the pT dependent φ(1020)/π and K∗(892)0/π ratios show an
enhancement over pp collisions for pT ≈ 3 GeV/c, consistent with previous observations of strong radial flow.
At high pT, particle ratios in Pb-Pb collisions are similar to those measured in pp collisions. In central Pb-Pb
collisions, the production of K∗(892)0 and φ(1020) mesons is suppressed for pT > 8 GeV/c. This suppression is
similar to that of charged pions, kaons, and protons, indicating that the suppression does not depend on particle
mass or flavor in the light quark sector
A(c)(+) Production and Baryon-to-Meson Ratios in pp and p-Pb Collisions at root S-NN=5.02 TeV at the LHC
The prompt production of the charm baryon \u39bc+ and the \u39bc+/D0 production ratios were measured at midrapidity with the ALICE detector in pp and p-Pb collisions at sNN=5.02 TeV. These new measurements show a clear decrease of the \u39bc+/D0 ratio with increasing transverse momentum (pT) in both collision systems in the range 2<12 GeV/c, exhibiting similarities with the light-flavor baryon-to-meson ratios p/\u3c0 and \u39b/KS0. At low pT, predictions that include additional color-reconnection mechanisms beyond the leading-color approximation, assume the existence of additional higher-mass charm-baryon states, or include hadronization via coalescence can describe the data, while predictions driven by charm-quark fragmentation processes measured in e+e- and e-p collisions significantly underestimate the data. The results presented in this Letter provide significant evidence that the established assumption of universality (colliding-system independence) of parton-to-hadron fragmentation is not sufficient to describe charm-baryon production in hadronic collisions at LHC energies
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