BioDiVinE: A Framework for Parallel Analysis of Biological Models

In this paper a novel tool BioDiVinEfor parallel analysis of biological models is presented. The tool allows analysis of biological models specified in terms of a set of chemical reactions. Chemical reactions are transformed into a system of multi-affine differential equations. BioDiVinE employs techniques for finite discrete abstraction of the continuous state space. At that level, parallel analysis algorithms based on model checking are provided. In the paper, the key tool features are described and their application is demonstrated by means of a case study

Small eigenvalues of the SU(3) Dirac operator on the lattice and in Random Matrix Theory

We have calculated complete spectra of the staggered Dirac operator on the lattice in quenched SU(3) gauge theory for \beta = 5.4 and various lattice sizes. The microscopic spectral density, the distribution of the smallest eigenvalue, and the two-point spectral correlation function are analyzed. We find the expected agreement of the lattice data with universal predictions of the chiral unitary ensemble of random matrix theory up to a certain energy scale, the Thouless energy. The deviations from the universal predictions are determined using the disconnected scalar susceptibility. We find that the Thouless energy scales with the lattice size as expected from theoretical arguments making use of the Gell-Mann--Oakes--Renner relation.Comment: REVTeX, 5 pages, 4 figure

Small eigenvalues of the staggered Dirac operator in the adjoint representation and Random Matrix Theory

The low-lying spectrum of the Dirac operator is predicted to be universal, within three classes, depending on symmetry properties specified according to random matrix theory. The three universal classes are the orthogonal, unitary and symplectic ensemble. Lattice gauge theory with staggered fermions has verified two of the cases so far, unitary and symplectic, with staggered fermions in the fundamental representation of SU(3) and SU(2). We verify the missing case here, namely orthogonal, with staggered fermions in the adjoint representation of SU(N_c), N_c=2, 3.Comment: 3 pages, revtex, 2 postscript figure

Links between traumatic brain injury and ballistic pressure waves originating in the thoracic cavity and extremities

Identifying patients at risk of traumatic brain injury (TBI) is important because research suggests prophylactic treatments to reduce risk of long-term sequelae. Blast pressure waves can cause TBI without penetrating wounds or blunt force trauma. Similarly, bullet impacts distant from the brain can produce pressure waves sufficient to cause mild to moderate TBI. The fluid percussion model of TBI shows that pressure impulses of 15-30 psi cause mild to moderate TBI in laboratory animals. In pigs and dogs, bullet impacts to the thigh produce pressure waves in the brain of 18-45 psi and measurable injury to neurons and neuroglia. Analyses of research in goats and epidemiological data from shooting events involving humans show high correlations (r > 0.9) between rapid incapacitation and pressure wave magnitude in the thoracic cavity. A case study has documented epilepsy resulting from a pressure wave without the bullet directly hitting the brain. Taken together, these results support the hypothesis that bullet impacts distant from the brain produce pressure waves that travel to the brain and can retain sufficient magnitude to induce brain injury. The link to long-term sequelae could be investigated via epidemiological studies of patients who were gunshot in the chest to determine whether they experience elevated rates of epilepsy and other neurological sequelae

Harnessing nuclear spin polarization fluctuations in a semiconductor nanowire

Soon after the first measurements of nuclear magnetic resonance (NMR) in a condensed matter system, Bloch predicted the presence of statistical fluctuations proportional to $1/\sqrt{N}$ in the polarization of an ensemble of $N$ spins. First observed by Sleator et al., so-called "spin noise" has recently emerged as a critical ingredient in nanometer-scale magnetic resonance imaging (nanoMRI). This prominence is a direct result of MRI resolution improving to better than 100 nm^3, a size-scale in which statistical spin fluctuations begin to dominate the polarization dynamics. We demonstrate a technique that creates spin order in nanometer-scale ensembles of nuclear spins by harnessing these fluctuations to produce polarizations both larger and narrower than the natural thermal distribution. We focus on ensembles containing ~10^6 phosphorus and hydrogen spins associated with single InP and GaP nanowires (NWs) and their hydrogen-containing adsorbate layers. We monitor, control, and capture fluctuations in the ensemble's spin polarization in real-time and store them for extended periods. This selective capture of large polarization fluctuations may provide a route for enhancing the weak magnetic signals produced by nanometer-scale volumes of nuclear spins. The scheme may also prove useful for initializing the nuclear hyperfine field of electron spin qubits in the solid-state.Comment: 18 pages, 5 figure

The role of substance P in secondary pathophysiology after traumatic brain injury

It has recently been shown that substance P (SP) plays a major role in the secondary injury process following traumatic brain injury (TBI), particularly with respect to neuroinflammation, increased blood-brain barrier (BBB) permeability, and edema formation. Edema formation is associated with the development of increased intracranial pressure (ICP) that has been widely associated with increased mortality and morbidity after neurotrauma. However, a pharmacological intervention to specifically reduce ICP is yet to be developed, with current interventions limited to osmotic therapy rather than addressing the cause of increased ICP. Given that previous publications have shown that SP, NK1 receptor antagonists reduce edema after TBI, more recent studies have examined whether these compounds might also reduce ICP and improve brain oxygenation after TBI. We discuss the results of these studies, which demonstrate that NK1 antagonists reduce posttraumatic ICP to near normal levels within 4 h of drug administration, as well as restoring brain oxygenation to near normal levels in the same time frame. The improvements in these parameters occurred in association with an improvement in BBB integrity to serum proteins, suggesting that SP-mediated increases in vascular permeability significantly contribute to the development of increased ICP after acute brain injury. NK1 antagonists may therefore provide a novel, mechanistically targeted approach to the management of increased ICP.Robert Vink, Levon Gabrielian and Emma Thornto

Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation (extended abstract)

In this paper, a novel computational technique for finite discrete approximation of continuous dynamical systems suitable for a significant class of biochemical dynamical systems is introduced. The method is parameterized in order to affect the imposed level of approximation provided that with increasing parameter value the approximation converges to the original continuous system. By employing this approximation technique, we present algorithms solving the reachability problem for biochemical dynamical systems. The presented method and algorithms are evaluated on several exemplary biological models and on a real case study.Comment: In Proceedings CompMod 2011, arXiv:1109.104

Subregional localization and characterization of Ly6aGFP-expressing hematopoietic cells in the mouse embryonic head

Hematopoietic cell generation in the midgestation mouse embryo occurs through the natural transdifferentiation of temporally and spatially restricted set of hemogenic endothelial cells. These cells take on hematopoietic fate in the aorta, vitelline and umbilical arteries and appear as hematopoietic cell clusters that emerge from the vascular wall. Gen

Driven coherent oscillations of a single electron spin in a quantum dot

The ability to control the quantum state of a single electron spin in a quantum dot is at the heart of recent developments towards a scalable spin-based quantum computer. In combination with the recently demonstrated exchange gate between two neighbouring spins, driven coherent single spin rotations would permit universal quantum operations. Here, we report the experimental realization of single electron spin rotations in a double quantum dot. First, we apply a continuous-wave oscillating magnetic field, generated on-chip, and observe electron spin resonance in spin-dependent transport measurements through the two dots. Next, we coherently control the quantum state of the electron spin by applying short bursts of the oscillating magnetic field and observe about eight oscillations of the spin state (so-called Rabi oscillations) during a microsecond burst. These results demonstrate the feasibility of operating single-electron spins in a quantum dot as quantum bits.Comment: Total 25 pages. 11 pages main text, 5 figures, 9 pages supplementary materia

Olmesartan Attenuates the Impairment of Endothelial Cells Induced by Oxidized Low Density Lipoprotein through Downregulating Expression of LOX-1

Oxidized low density lipoprotein (ox-LDL) and its receptor, lectin-Like ox-LDL receptor-1 (LOX-1), play important roles in the development of endothelial injuries. Olmesartan can protect endothelial cells from the impairment caused by various pathological stimulations. In the present study we investigated whether olmesartan decreased the impairment of endothelial cells induced by ox-LDL by exerting its effects on LOX-1 both in vitro and in vivo. Incubation of cultured endothelial cells of neonatal rats with ox-LDL for 24 h or infusion of ox-LDL in mice for 3 weeks led to the remarkable impairment of endothelial cells, including increased lactate dehydrogenase synthesis, phosphorylation of p38 mitogen-activated protein kinases (p38 MAPK) and expression of apoptotic genes such as B-cell leukemia/lymphoma 2 (Bcl-2)-associated X protein (Bax) and caspase-3. Simultaneously, the cell vitality and expression of Bcl-2 gene were greatly reduced. All these effects, however, were significantly suppressed by the treatment with olmesartan. Furthermore, ox-LDL promoted up-regulation of LOX-1 expression either in cultured endothelial cells or in the aortas of mice, which was reversed with the administration of olmesartan. Our data indicated that olmesartan may attenuate the impairment of endothelial cell via down-regulation of the increased LOX-1 expression induced by ox-LDL