Diffusive spatio-temporal noise in a first-passage time model for intracellular calcium release

The intracellular release of calcium from the endoplasmic reticulum is controlled by ion channels. The resulting calcium signals exhibit a rich spatio-temporal signature, which originates at least partly from microscopic fluctuations. While stochasticity in the gating transition of ion channels has been incorporated into many models, the distribution of calcium is usually described by deterministic reaction-diffusion equations. Here we test the validity of the latter modeling approach by using two different models to calculate the frequency of localized calcium signals (calcium puffs) from clustered IP3 receptor channels. The complexity of the full calcium system is here limited to the basic opening mechanism of the ion channels and, in the mathematical reduction simplifies to the calculation of a first passage time. Two models are then studied: (i) a hybrid model, where channel gating is treated stochastically, while calcium concentration is deterministic and (ii) a fully stochastic model with noisy channel gating and Brownian calcium ion motion. The second model utilises the recently developed two-regime method [M. B. Flegg, S. J. Chapman, and R. Erban, “The two-regime method for optimizing stochastic reaction-diffusion simulations,” J. R. Soc., Interface9, 859–868 (Year: 2012)]10.1098/rsif.2011.0574 in order to simulate a large domain with precision required only near the Ca2+ absorbing channels. The expected time for a first channel opening that results in a calcium puff event is calculated. It is found that for a large diffusion constant, predictions of the interpuff time are significantly overestimated using the model (i) with a deterministic non-spatial calcium variable. It is thus demonstrated that the presence of diffusive noise in local concentrations of intracellular Ca2+ ions can substantially influence the occurrence of calcium signals. The presented approach and results may also be relevant for other cell-physiological first-passage time problems with small ligand concentration and high cooperativity

BILIPROTEINS FROM THE BUTTERFLY Pieris brassicae STUDIED BY TIME-RESOLVED FLUORESCENCE AND COHERENT ANTI-STOKES RAMAN SPECTROSCOPY

The fluorescence decay time of the biliverdin IX7 chromophore present in biliproteins isolated from Pieris brassicae is determined to be 44 ± 3 ps. This value suggests a cyclic helical chromophore structure. The vibrational frequencies determined by CARS-spectroscopy are compared with those of model compounds. The data confirm that the chromophore in the protein-bound state adopts a cyclic-helical, flexible conformation

EEG-Based Asynchronous BCI Controls Functional Electrical Stimulation in a Tetraplegic Patient

The present study reports on the use of an EEG-based asynchronous (uncued, user-driven) brain-computer interface (BCI) for the control of functional electrical stimulation (FES). By the application of FES, noninvasive restoration of hand grasp function in a tetraplegic patient was achieved. The patient was able to induce bursts of beta oscillations by imagination of foot movement. These beta oscillations were recorded in a one EEG-channel configuration, bandpass filtered and squared. When this beta activity exceeded a predefined threshold, a trigger for the FES was generated. Whenever the trigger was detected, a subsequent switching of a grasp sequence composed of 4 phases occurred. The patient was able to grasp a glass with the paralyzed hand completely on his own without additional help or other technical aids

Matched filters for coalescing binaries detection on massively parallel computers

We discuss some computational problems associated to matched filtering of experimental signals from gravitational wave interferometric detectors in a parallel-processing environment. We then specialize our discussion to the use of the APEmille and apeNEXT processors for this task. Finally, we accurately estimate the performance of an APEmille system on a computational load appropriate for the LIGO and VIRGO experiments, and extrapolate our results to apeNEXT.Comment: 19 pages, 6 figure

The Accretion Rates and Spectral Energy Distributions of BL Lacertae Objects

We investigate the relationship between accretion rates and the spectral energy distributions (SEDs) of BL Lac objects, using a sample of objects for which published information on the host galaxies, emission-line luminosities, and peak frequencies and luminosities of their SEDs are available. The sample is composed of 43 BL Lac objects which have a relatively continuous distribution of peak frequencies. Under the assumption that the observed emission lines are photoionized by the central accretion disk, we use the line luminosities to estimate the accretion luminosities and hence accretion rates. We find that low frequency-peaked BL Lac objects (LBLs) span a wide range of accretion rates, whereas high frequency-peaked BL Lac objects (HBLs) cover a more restricted range of lower values. There appears to be a continuous distribution of accretion rates between the two subclasses of BL Lac objects. We find that the peak frequency of the SED, \pknu, correlates with the accretion rate, approximately with the form \pknu\propto \Lambda^{-3} in HBLs and \pknu \propto \Lambda^{-0.25} in LBLs, where $\Lambda \equiv L_{\rm lines}/c^2$. The peak luminosity of the SED is also correlated with $\Lambda$. These results suggest that the accretion rate influences the shape of the SED in BL Lac objects. They also support models which couple the jet and the accretion disk. We present a physical scenario to account for the empirical trends.Comment: 6 pages in emulateapj.sty, 3 figures 1 table. The Astrophysical Journal (in press

The inverse cascade and nonlinear alpha-effect in simulations of isotropic helical hydromagnetic turbulence

A numerical model of isotropic homogeneous turbulence with helical forcing is investigated. The resulting flow, which is essentially the prototype of the alpha^2 dynamo of mean-field dynamo theory, produces strong dynamo action with an additional large scale field on the scale of the box (at wavenumber k=1; forcing is at k=5). This large scale field is nearly force-free and exceeds the equipartition value. As the magnetic Reynolds number R_m increases, the saturation field strength and the growth rate of the dynamo increase. However, the time it takes to built up the large scale field from equipartition to its final super-equipartition value increases with magnetic Reynolds number. The large scale field generation can be identified as being due to nonlocal interactions originating from the forcing scale, which is characteristic of the alpha-effect. Both alpha and turbulent magnetic diffusivity eta_t are determined simultaneously using numerical experiments where the mean-field is modified artificially. Both quantities are quenched in a R_m-dependent fashion. The evolution of the energy of the mean field matches that predicted by an alpha^2 dynamo model with similar alpha and eta_t quenchings. For this model an analytic solution is given which matches the results of the simulations. The simulations are numerically robust in that the shape of the spectrum at large scales is unchanged when changing the resolution from 30^3 to 120^3 meshpoints, or when increasing the magnetic Prandtl number (viscosity/magnetic diffusivity) from 1 to 100. Increasing the forcing wavenumber to 30 (i.e. increasing the scale separation) makes the inverse cascade effect more pronounced, although it remains otherwise qualitatively unchanged.Comment: 21 pages, 26 figures, ApJ (accepted

Resistance of a domain wall in the quasiclassical approach

Starting from a simple microscopic model, we have derived a kinetic equation for the matrix distribution function. We employed this equation to calculate the conductance $G$ in a mesoscopic F'/F/F' structure with a domain wall (DW). In the limit of a small exchange energy $J$ and an abrupt DW, the conductance of the structure is equal to $G_{2d}=4\sigma_{\uparrow}\sigma_{\downarrow }/(\sigma_{\uparrow}+\sigma_{\downarrow})L$. Assuming that the scattering times for electrons with up and down spins are close to each other we show that the account for a finite width of the DW leads to an increase in this conductance. We have also calculated the spatial distribution of the electric field in the F wire. In the opposite limit of large $J$ (adiabatic variation of the magnetization in the DW) the conductance coincides in the main approximation with the conductance of a single domain structure $G_{1d}=(\sigma_{\uparrow}+\sigma_{\downarrow})/L$. The account for rotation of the magnetization in the DW leads to a negative correction to this conductance. Our results differ from the results in papers published earlier.Comment: 11 pages; replaced with revised versio

Magnetic field generation in fully convective rotating spheres

Magnetohydrodynamic simulations of fully convective, rotating spheres with volume heating near the center and cooling at the surface are presented. The dynamo-generated magnetic field saturates at equipartition field strength near the surface. In the interior, the field is dominated by small-scale structures, but outside the sphere by the global scale. Azimuthal averages of the field reveal a large-scale field of smaller amplitude also inside the star. The internal angular velocity shows some tendency to be constant along cylinders and is ``anti-solar'' (fastest at the poles and slowest at the equator).Comment: 12 pages, 11 figures, 2 tables, to appear in the 10 Feb issue of Ap

A review of image processing methods for fetal head and brain analysis in ultrasound images

Background and objective: Examination of head shape and brain during the fetal period is paramount to evaluate head growth, predict neurodevelopment, and to diagnose fetal abnormalities. Prenatal ultrasound is the most used imaging modality to perform this evaluation. However, manual interpretation of these images is challenging and thus, image processing methods to aid this task have been proposed in the literature. This article aims to present a review of these state-of-the-art methods. Methods: In this work, it is intended to analyze and categorize the different image processing methods to evaluate fetal head and brain in ultrasound imaging. For that, a total of 109 articles published since 2010 were analyzed. Different applications are covered in this review, namely analysis of head shape and inner structures of the brain, standard clinical planes identification, fetal development analysis, and methods for image processing enhancement. Results: For each application, the reviewed techniques are categorized according to their theoretical approach, and the more suitable image processing methods to accurately analyze the head and brain are identified. Furthermore, future research needs are discussed. Finally, topics whose research is lacking in the literature are outlined, along with new fields of applications. Conclusions: A multitude of image processing methods has been proposed for fetal head and brain analysis. Summarily, techniques from different categories showed their potential to improve clinical practice. Nevertheless, further research must be conducted to potentiate the current methods, especially for 3D imaging analysis and acquisition and for abnormality detection. (c) 2022 Elsevier B.V. All rights reserved.FCT - Fundação para a Ciência e a Tecnologia(UIDB/00319/2020)This work was funded by projects “NORTE-01–0145-FEDER- 0 0 0 059 , NORTE-01-0145-FEDER-024300 and “NORTE-01–0145- FEDER-0 0 0 045 , supported by Northern Portugal Regional Opera- tional Programme (Norte2020), under the Portugal 2020 Partner- ship Agreement, through the European Regional Development Fund (FEDER). It was also funded by national funds, through the FCT – Fundação para a Ciência e Tecnologia within the R&D Units Project Scope: UIDB/00319/2020 and by FCT and FCT/MCTES in the scope of the projects UIDB/05549/2020 and UIDP/05549/2020 . The authors also acknowledge support from FCT and the Euro- pean Social Found, through Programa Operacional Capital Humano (POCH), in the scope of the PhD grant SFRH/BD/136670/2018 and SFRH/BD/136721/2018