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Tumour hypoxia plays a pivotal role in cancer therapy for most therapeutic approaches from radiotherapy to immunotherapy. The detailed and accurate knowledge of the oxygen distribution in a tumour is necessary in order to determine the right treatment strategy. Still, due to the limited spatial and temporal resolution of imaging methods as well as lacking fundamental understanding of internal oxygenation dynamics in tumours, the precise oxygen distribution map is rarely available for treatment planing. We employ an agent-based in silico tumour spheroid model in order to study the complex, localized and fast oxygen dynamics in tumour micro-regions which are induced by radiotherapy. A lattice-free, 3D, agent-based approach for cell representation is coupled with a high-resolution diffusion solver that includes a tissue density-dependent diffusion coefficient. This allows us to assess the space- and time-resolved reoxygenation response of a small subvolume of tumour tissue in response to radiotherapy. In response to irradiation the tumour nodule exhibits characteristic reoxygenation and re-depletion dynamics which we resolve with high spatio-temporal resolution. The reoxygenation follows specific timings, which should be respected in treatment in order to maximise the use of the oxygen enhancement effects. Oxygen dynamics within the tumour create windows of opportunity for the use of adjuvant chemotherapeutica and hypoxia-activated drugs. Overall, we show that by using modelling it is possible to follow the oxygenation dynamics beyond common resolution limits and predict beneficial strategies for therapy and in vitro verification. Models of cell cycle and oxygen dynamics in tumours should in the future be combined with imaging techniques, to allow for a systematic experimental study of possible improved schedules and to ultimately extend the reach of oxygenation monitoring available in clinical treatment.
The physics goal of the strong interaction program of the NA61/SHINE experiment at the CERN Super Proton Synchrotron (SPS) is to study the phase diagram of hadronic matter by a scan of particle production in collisions of nuclei with various sizes at a set of energies covering the SPS energy range. This paper presents differential inclusive spectra of transverse momentum, transverse mass and rapidity of π− mesons produced in central 40Ar+45Sc collisions at beam momenta of 13A, 19A, 30A, 40A, 75A and 150A Ge V /c. Energy and system size dependence of parameters of these distributions – mean transverse mass, the inverse slope parameter of transverse mass spectra, width of the rapidity distribution and mean multiplicity – are presented and discussed. Furthermore, the dependence of the ratio of the mean number of produced pions to the mean number of wounded nucleons on the collision energy was derived. The results are compared to predictions of several models.
We suggest a new method to compute the spectrum and wave functions of excited states. We construct a stochastic basis of Bargmann link states, drawn from a physical probability density distribution and compute transition amplitudes between stochastic basis states. From such transition matrix we extract wave functions and the energy spectrum. We apply this method toU(1)2+1 lattice gauge theory. As a test we compute the energy spectrum, wave functions and thermodynamical functions of the electric Hamiltonian and compare it with analytical results. We find excellent agreement. We observe scaling of energies and wave functions in the variable of time. We also present first results on a small lattice for the full Hamiltonian including the magnetic term.
Spherical harmonics coeffcients for ligand-based virtual screening of cyclooxygenase inhibitors
(2011)
Background: Molecular descriptors are essential for many applications in computational chemistry, such as ligand-based similarity searching. Spherical harmonics have previously been suggested as comprehensive descriptors of molecular structure and properties. We investigate a spherical harmonics descriptor for shape-based virtual screening. Methodology/Principal Findings: We introduce and validate a partially rotation-invariant three-dimensional molecular shape descriptor based on the norm of spherical harmonics expansion coefficients. Using this molecular representation, we parameterize molecular surfaces, i.e., isosurfaces of spatial molecular property distributions. We validate the shape descriptor in a comprehensive retrospective virtual screening experiment. In a prospective study, we virtually screen a large compound library for cyclooxygenase inhibitors, using a self-organizing map as a pre-filter and the shape descriptor for candidate prioritization. Conclusions/Significance: 12 compounds were tested in vitro for direct enzyme inhibition and in a whole blood assay. Active compounds containing a triazole scaffold were identified as direct cyclooxygenase-1 inhibitors. This outcome corroborates the usefulness of spherical harmonics for representation of molecular shape in virtual screening of large compound collections. The combination of pharmacophore and shape-based filtering of screening candidates proved to be a straightforward approach to finding novel bioactive chemotypes with minimal experimental effort.
In self-organized critical (SOC) systems avalanche size distributions follow power-laws. Power-laws have also been observed for neural activity, and so it has been proposed that SOC underlies brain organization as well. Surprisingly, for spiking activity in vivo, evidence for SOC is still lacking. Therefore, we analyzed highly parallel spike recordings from awake rats and monkeys, anesthetized cats, and also local field potentials from humans. We compared these to spiking activity from two established critical models: the Bak-Tang-Wiesenfeld model, and a stochastic branching model. We found fundamental differences between the neural and the model activity. These differences could be overcome for both models through a combination of three modifications: (1) subsampling, (2) increasing the input to the model (this way eliminating the separation of time scales, which is fundamental to SOC and its avalanche definition), and (3) making the model slightly sub-critical. The match between the neural activity and the modified models held not only for the classical avalanche size distributions and estimated branching parameters, but also for two novel measures (mean avalanche size, and frequency of single spikes), and for the dependence of all these measures on the temporal bin size. Our results suggest that neural activity in vivo shows a mélange of avalanches, and not temporally separated ones, and that their global activity propagation can be approximated by the principle that one spike on average triggers a little less than one spike in the next step. This implies that neural activity does not reflect a SOC state but a slightly sub-critical regime without a separation of time scales. Potential advantages of this regime may be faster information processing, and a safety margin from super-criticality, which has been linked to epilepsy.
Cortical neurons are typically driven by several thousand synapses. The precise spatiotemporal pattern formed by these inputs can modulate the response of a post-synaptic cell. In this work, we explore how the temporal structure of pre-synaptic inhibitory and excitatory inputs impact the post-synaptic firing of a conductance-based integrate and fire neuron. Both the excitatory and inhibitory input was modeled by renewal gamma processes with varying shape factors for modeling regular and temporally random Poisson activity. We demonstrate that the temporal structure of mutually independent inputs affects the post-synaptic firing, while the strength of the effect depends on the firing rates of both the excitatory and inhibitory inputs. In a second step, we explore the effect of temporal structure of mutually independent inputs on a simple version of Hebbian learning, i.e., hard bound spike-timing-dependent plasticity. We explore both the equilibrium weight distribution and the speed of the transient weight dynamics for different mutually independent gamma processes. We find that both the equilibrium distribution of the synaptic weights and the speed of synaptic changes are modulated by the temporal structure of the input. Finally, we highlight that the sensitivity of both the post-synaptic firing as well as the spike-timing-dependent plasticity on the auto-structure of the input of a neuron could be used to modulate the learning rate of synaptic modification.
This thesis is dedicated to the study of fluctuation and correlation observables of hadronic equilibrium systems. The statistical hadronization model of high energy physics, in its ideal, i.e. non-interacting, gas approximation will be investigated in different ensemble formulations. The hypothesis of thermal and chemical equilibrium in high energy interaction will be tested against qualitative and quantitative predictions.
Spike count correlations (SCCs) are ubiquitous in sensory cortices, are characterized by rich structure and arise from structured internal interactions. Yet, most theories of visual perception focus exclusively on the mean responses of individual neurons. Here, we argue that feedback interactions in primary visual cortex (V1) establish the context in which individual neurons process complex stimuli and that changes in visual context give rise to stimulus-dependent SCCs. Measuring V1 population responses to natural scenes in behaving macaques, we show that the fine structure of SCCs is stimulus-specific and variations in response correlations across-stimuli are independent of variations in response means. Moreover, we demonstrate that stimulus-specificity of SCCs in V1 can be directly manipulated by controlling the high-order structure of synthetic stimuli. We propose that stimulus-specificity of SCCs is a natural consequence of hierarchical inference where inferences on the presence of high-level image features modulate inferences on the presence of low-level features.
When a visual stimulus is repeated, average neuronal responses typically decrease, yet they might maintain or even increase their impact through increased synchronization. Previous work has found that many repetitions of a grating lead to increasing gamma-band synchronization. Here, we show in awake macaque area V1 that both repetition-related reductions in firing rate and increases in gamma are specific to the repeated stimulus. These effects show some persistence on the timescale of minutes. Gamma increases are specific to the presented stimulus location. Further, repetition effects on gamma and on firing rates generalize to images of natural objects. These findings support the notion that gamma-band synchronization subserves the adaptive processing of repeated stimulus encounters.
When a visual stimulus is repeated, average neuronal responses typically decrease, yet they might maintain or even increase their impact through increased synchronization. Previous work has found that many repetitions of a grating lead to increasing gamma-band synchronization. Here we show in awake macaque area V1 that both, repetition-related reductions in firing rate and increases in gamma are specific to the repeated stimulus. These effects showed some persistence on the timescale of minutes. Further, gamma increases were specific to the presented stimulus location. Importantly, repetition effects on gamma and on firing rates generalized to natural images. These findings suggest that gamma-band synchronization subserves the adaptive processing of repeated stimulus encounters, both for generating efficient stimulus responses and possibly for memory formation.
The present status in the field of strange mesons in nuclei and neutron stars is reviewed. In particular, the K̅N interaction, that is governed by the presence of the Λ(1405), is analyzed and the formation of the K̅NN bound state is discussed. Moreover, the properties of K̅ in dense nuclear matter are studied, in connection with strangeness production in nuclear collisions and kaon condensation in neutron stars.
The results of the microscopic transport calculations of -nucleus interactions within a GiBUU model are presented. The dominating mechanism of hyperon production is the strangeness exchange processes → γπ and → ΞK. The calculated rapidity spectra of Ξ hyperons are significantly shifted to forward rapidities with respect to the spectra of S = −1 hyperons. We argue that this shift should be a sensitive test for the possible exotic mechanisms of -nucleus annihilation. The production of the double Λ-hypernuclei by Ξ− interaction with a secondary target is calculated.
Simulating Many Accelerated Strongly-interacting Hadrons (SMASH) is a new hadronic transport approach designed to describe the non-equilibrium evolution of heavy-ion collisions. The production of strange particles in such systems is enhanced compared to elementary reactions (Blume and Markert 2011), providing an interesting signal to study. Two different strangeness production mechanisms are discussed: one based on resonances and another using forced canonical thermalization. Comparisons to experimental data from elementary collisions are shown.
We report multi-differential measurements of strange hadron production ranging from mid- to target-rapidity in Au+Au collisions at a center-of-momentum energy per nucleon pair of sNN−−−√=3 GeV with the STAR experiment at RHIC. K0S meson and Λ hyperon yields are measured via their weak decay channels. Collision centrality and rapidity dependences of the transverse momentum spectra and particle ratios are presented. Particle mass and centrality dependence of the average transverse momenta of Λ and K0S are compared with other strange particles, providing evidence of the development of hadronic rescattering in such collisions. The 4π yields of each of these strange hadrons show a consistent centrality dependence. Discussions on radial flow, the strange hadron production mechanism, and properties of the medium created in such collisions are presented together with results from hadronic transport and thermal model calculations.
We study the equilibrium properties of strongly-interacting infinite parton-hadron matter, characterized by the transport coefficients such as shear and bulk viscosity and electric conductivity, and the non-equilibrium dynamics of heavy-ion collisions within the Parton-Hadron-String Dynamics (PHSD) transport approach, which incorporates explicit partonic degrees of freedom in terms of strongly interacting quasiparticles (quarks and gluons) in line with an equation of state from lattice QCD as well as the dynamical hadronization and hadronic collision dynamics in the final reaction phase. We discuss in particular the possible origin for the strong elliptic flow v2 of direct photons observed at RHIC energies.
Human Transformer2-beta (hTra2-beta) is an important member of the serine/arginine-rich protein family, and contains one RNA recognition motif (RRM). It controls the alternative splicing of several pre-mRNAs, including those of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Accordingly, the RRM of hTra2-beta specifically binds to two types of RNA sequences [the CAA and (GAA)2 sequences]. We determined the solution structure of the hTra2-beta RRM (spanning residues Asn110–Thr201), which not only has a canonical RRM fold, but also an unusual alignment of the aromatic amino acids on the beta-sheet surface. We then solved the complex structure of the hTra2-beta RRM with the (GAA)2 sequence, and found that the AGAA tetra-nucleotide was specifically recognized through hydrogen-bond formation with several amino acids on the N- and C-terminal extensions, as well as stacking interactions mediated by the unusually aligned aromatic rings on the beta-sheet surface. Further NMR experiments revealed that the hTra2-beta RRM recognizes the CAA sequence when it is integrated in the stem-loop structure. This study indicates that the hTra2-beta RRM recognizes two types of RNA sequences in different RNA binding modes.
As microscopic transport models usually have difficulties to deal with in-medium effects in heavy-ion collisions, we present an alternative approach that uses coarse-grained output from transport calculations with the UrQMD model to determine thermal dilepton emission rates. A four-dimensional space-time grid is set up to extract local baryon and energy densities, respectively temperature and baryon chemical potential. The lepton pair emission is then calculated for each cell of the grid using thermal equilibrium rates. In the current investigation we inlcude the medium-modified r spectral function by Eletsky et al., as well as contributions from the QGP and four-pion interactions for high collision energies. First dielectron invariant mass spectra for Au+Au collisions at 1.25 AGeV and for dimuons from In+In at 158 AGeV are shown. At 1.25 AGeV a clear enhancement of the total dilepton yield as compared to a pure transport result is observed. In the latter case, we compare our outcome with the NA60 dimuon excess data. Here a good agreement is achieved, but the yield in the low-mass tail is underestimated. In general the results show that the coarse-graining approach gives reasonable results and can cover a broad collision-energy range.
The inclusive J/ψ production in Pb–Pb collisions at the center-of-mass energy per nucleon pair sNN−−−√ = 5.02 TeV, measured with the ALICE detector at the CERN LHC, is reported. The J/ψ meson is reconstructed via the dimuon decay channel at forward rapidity (2.5 < y < 4) down to zero transverse momentum. The suppression of the J/ψ yield in Pb–Pb collisions with respect to binary-scaled pp collisions is quantified by the nuclear modification factor (RAA). The RAA at sNN−−−√ = 5.02 TeV is presented and compared with previous measurements at sNN−−−√ = 2.76 TeV as a function of the centrality of the collision, and of the J/ψ transverse momentum and rapidity. The inclusive J/ψ RAA shows a suppression increasing toward higher transverse momentum, with a steeper dependence for central collisions. The modification of the J/ψ average transverse momentum and average squared transverse momentum is also studied. Comparisons with the results of models based on a transport equation and on statistical hadronization are carried out.
The inclusive J/ψ production in Pb-Pb collisions at the center-of-mass energy per nucleon pair sNN−−−√ = 5.02 TeV, measured with the ALICE detector at the CERN LHC, is reported. The J/ψ meson is reconstructed via the dimuon decay channel at forward rapidity (2.5<y<4) down to zero transverse momentum. The suppression of the J/ψ yield in Pb-Pb collisions with respect to binary-scaled pp collisions is quantified by the nuclear modification factor (RAA). The RAA at sNN−−−√ = 5.02 TeV is presented and compared with previous measurements at sNN−−−√ = 2.76 TeV as a function of the centrality of the collision, and of the J/ψ transverse momentum and rapidity. The inclusive J/ψ RAA shows a suppression increasing toward higher pT, with a steeper dependence for central collisions. The modification of the J/ψ average pT and p2T is also studied. Comparisons with the results of models based on a transport equation and on statistical hadronization are also carried out.