Oscillations in the expression of a self-repressed gene induced by a slow transcriptional dynamics

We revisit the dynamics of a gene repressed by its own protein in the case where the transcription rate does not adapt instantaneously to protein concentration but is a dynamical variable. We derive analytical criteria for the appearance of sustained oscillations and find that they require degradation mechanisms much less nonlinear than for infinitely fast regulation. Deterministic predictions are also compared with stochastic simulations of this minimal genetic oscillator

Oscillations in the expression of a self-repressed gene induced by a slow transcriptional dynamics

We revisit the dynamics of a gene repressed by its own protein in the case where the transcription rate does not adapt instantaneously to protein concentration but is a dynamical variable. We derive analytical criteria for the appearance of sustained oscillations and find that they require degradation mechanisms much less nonlinear than for infinitely fast regulation. Deterministic predictions are also compared with stochastic simulations of this minimal genetic oscillator

Susceptibility gradient quantization by MRI signal response mapping (SIRMA) to dephaser

Purpose: Susceptibility effects are a very efficient source of contrast in magnetic resonance imaging. However, detection is hampered by the fact the induced contrast is negative. In this work, the SIgnal Response MApping (SIRMA) to dephaser method is proposed to map susceptibility gradient to improve visualization. Methods: In conventional gradient echo acquisitions, the echo formation of susceptibility affected spins is shifted in k -space, the shift being proportional to the susceptibility gradient. Susceptibility gradients map can be produced by measuring this induced shifts. The SIRMA method measures these shifts from a series of dephased images collected with additional incremental dephasers. These additional dephasers correspond either to a slice refocusing gradient offset or to a reconstruction window off-centering. The signal intensity profile as a function of the additional dephaser was determined on a pixel-by-pixel basis from the ensemble of dephased images. Susceptibility affected voxels presented a signal response profile maximum shifted compared to nonaffected voxels ones. Shift magnitude and sign were measured for each pixel to determine susceptibility gradients and produce a susceptibility gradient map. Results: In vitro experiments demonstrated the ability of the method to map gradient inhomogeneities induced by a cylinder. Quantization accuracy was evaluated comparing SIRMA images and simulations performed on the well-characterized air filled cylinder model. Performances of the SIRMA method, evaluated in vitro on cylinders filled with various superparamagnetic iron oxide SPIO concentrations, showed limited influence of acquisition parameters. Robustness of the method was then assessed in vivo after an infusion of SPIO-loaded nanocapsules into the rat brain using a convection-enhanced drug delivery approach. The region of massive susceptibility gradient induced by the SPIO-loaded nanocapsules was clearly delineated on SIRMA maps and images were compared to T 2 weighted images, Susceptibility Gradient Map (SGM), and histological Perl\u27s staining slice. The potential for quantitative evaluation of SPIO distribution volume was demonstrated. Conclusions: The proposed method is a promising technique for a wide range of applications especially in molecular or cellular imaging with respect to its quantitative nature and its computational simplicity

The flow of plasma in the solar terrestrial environment

The overall goal of our NASA Theory Program was to study the coupling, time delays, and feedback mechanisms between the various regions of the solar-terrestrial system in a self-consistent, quantitative manner. To accomplish this goal, it will eventually be necessary to have time-dependent macroscopic models of the different regions of the solar-terrestrial system and we are continually working toward this goal. However, with the funding from this NASA program, we concentrated on the near-earth plasma environment, including the ionosphere, the plasmasphere, and the polar wind. In this area, we developed unique global models that allowed us to study the coupling between the different regions. These results are highlighted in the next section. Another important aspect of our NASA Theory Program concerned the effect that localized 'structure' had on the macroscopic flow in the ionosphere, plasmasphere, thermosphere, and polar wind. The localized structure can be created by structured magnetospheric inputs (i.e., structured plasma convection, particle precipitation or Birkland current patterns) or time variations in these input due to storms and substorms. Also, some of the plasma flows that we predicted with our macroscopic models could be unstable, and another one of our goals was to examine the stability of our predicted flows. Because time-dependent, three-dimensional numerical models of the solar-terrestrial environment generally require extensive computer resources, they are usually based on relatively simple mathematical formulations (i.e., simple MHD or hydrodynamic formulations). Therefore, another goal of our NASA Theory Program was to study the conditions under which various mathematical formulations can be applied to specific solar-terrestrial regions. This could involve a detailed comparison of kinetic, semi-kinetic, and hydrodynamic predictions for a given polar wind scenario or it could involve the comparison of a small-scale particle-in-cell (PIC) simulation of a plasma expansion event with a similar macroscopic expansion event. The different mathematical formulations have different strengths and weaknesses and a careful comparison of model predictions for similar geophysical situations provides insight into when the various models can be used with confidence

SUMER: Solar Ultraviolet Measurements of Emitted Radiation

The SUMER (solar ultraviolet measurements of emitted radiation) experiment is described. It will study flows, turbulent motions, waves, temperatures and densities of the plasma in the upper atmosphere of the Sun. Structures and events associated with solar magnetic activity will be observed on various spatial and temporal scales. This will contribute to the understanding of coronal heating processes and the solar wind expansion. The instrument will take images of the Sun in EUV (extreme ultra violet) light with high resolution in space, wavelength and time. The spatial resolution and spectral resolving power of the instrument are described. Spectral shifts can be determined with subpixel accuracy. The wavelength range extends from 500 to 1600 angstroms. The integration time can be as short as one second. Line profiles, shifts and broadenings are studied. Ratios of temperature and density sensitive EUV emission lines are established

Generalized Forward-Backward Splitting

This paper introduces the generalized forward-backward splitting algorithm for minimizing convex functions of the form $F + \sum_{i=1}^n G_i$, where $F$ has a Lipschitz-continuous gradient and the $G_i$'s are simple in the sense that their Moreau proximity operators are easy to compute. While the forward-backward algorithm cannot deal with more than $n = 1$ non-smooth function, our method generalizes it to the case of arbitrary $n$. Our method makes an explicit use of the regularity of $F$ in the forward step, and the proximity operators of the $G_i$'s are applied in parallel in the backward step. This allows the generalized forward backward to efficiently address an important class of convex problems. We prove its convergence in infinite dimension, and its robustness to errors on the computation of the proximity operators and of the gradient of $F$. Examples on inverse problems in imaging demonstrate the advantage of the proposed methods in comparison to other splitting algorithms.Comment: 24 pages, 4 figure

Volumetric assessment of myocardial viability in rats using 3D double contrast enhanced T1 and T2-weighted MRI

OBJECTIVE: Volumetric evaluation of the myocardial viability post-infarction in rats using 3D in vivo MR imaging at 7 T using injection of an extracellular paramagnetic contrast agent and intravascular superparamagnetic iron oxide nanoparticles in the same imaging session. MATERIALS AND METHODS: Five hours after induction of permanent myocardial infarction in rats (n=6), 3D in vivo T1- and T2-weighted MR Imaging was performed prior to and after Gd-DOTA injection (0.2 mmol/kg) and prior to and after nanoparticle injection (5 mg Fe/kg) to assess infarct size and myocardial viability. RESULTS: 3D MR Imaging using a successive contrast agent injection showed a difference of infarct size after Gd-DOTA injection on T1-weighted images compared to the one measured on T2-weighted images after Gd-DOTA and nanoparticle injection. CONCLUSION: The use of 3D T1- and T2-weighted MR Imaging using a double contrast agents protocol made possible the accurate characterization of myocardial infarction volume and allowed the detection of myocardial viability post-infarction in rats

Temperature dependent characterization of optical fibres for distributed temperature sensing in hot geothermal wells

This study was performed in order to select a proper fibre for the application of a distributed temperature sensing system within a hot geothermal well in Iceland. Commercially available high temperature graded index fibres have been tested under in-situ temperature conditions. Experiments have been performed with four different polyimide coated fibres, a fibre with an aluminum coating and a fibre with a gold coating. To select a fibre, the relationship between attenuation, temperature, and time has been analyzed together with SEM micrographs. On the basis of these experiments, polyimide fibres have been chosen for utilisation. Further tests in ambient and inert atmosphere have been conducted with two polyimide coated fibres to set an operating temperature limit for these fibres. SEM micrographs, together with coating colour changes have been used to characterize the high temperature performance of the fibres. A novel cable design has been developed, a deployment strategy has been worked out and a suitable well for deployment has been selected.Comment: PACS: 42.81.Pa, 93.85.Fg, 47.80.Fg, 91.35.Dc, 07.20.Dt, 07.60.V

Magnetic properties of Gd_xY_{1-x}Fe_2Zn_{20}: dilute, large, S\textbf {S} moments in a nearly ferromagnetic Fermi liquid

Single crystals of the dilute, rare earth bearing, pseudo-ternary series, Gd_xY_{1-x}Fe_2Zn_{20} were grown out of Zn-rich solution. Measurements of magnetization, resistivity and heat capacity on Gd_xY_{1-x}Fe_2Zn_{20} samples reveal ferromagnetic order of Gd^{3+} local moments across virtually the whole series ($x \geq 0.02$). The magnetic properties of this series, including the ferromagnetic ordering, the reduced saturated moments at base temperature, the deviation of the susceptibilities from Curie-Weiss law and the anomalies in the resistivity, are understood within the frame work of dilute, $\textbf {S}$ moments (Gd^{3+}) embedded in a nearly ferromagnetic Fermi liquid (YFe_2Zn_{20}). The s-d model is employed to further explain the variation of $T_{\mathrm{C}}$ with x as well as the temperature dependences of of the susceptibilities