A pseudo-spectral method for the simulation of poro-elastic seismic wave propagation in 2D polar coordinates using domain decomposition

We present a novel numerical approach for the comprehensive, flexible, and accurate simulation of poro-elastic wave propagation in 2D polar coordinates. An important application of this method and its extensions will be the modeling of complex seismic wave phenomena in fluid-filled boreholes, which represents a major, and as of yet largely unresolved, computational problem in exploration geophysics. In view of this, we consider a numerical mesh, which can be arbitrarily heterogeneous, consisting of two or more concentric rings representing the fluid in the center and the surrounding porous medium. The spatial discretization is based on a Chebyshev expansion in the radial direction and a Fourier expansion in the azimuthal direction and a Runge-Kutta integration scheme for the time evolution. A domain decomposition method is used to match the fluid-solid boundary conditions based on the method of characteristics. This multi-domain approach allows for significant reductions of the number of grid points in the azimuthal direction for the inner grid domain and thus for corresponding increases of the time step and enhancements of computational efficiency. The viability and accuracy of the proposed method has been rigorously tested and verified through comparisons with analytical solutions as well as with the results obtained with a corresponding, previously published, and independently bench-marked solution for 2D Cartesian coordinates. Finally, the proposed numerical solution also satisfies the reciprocity theorem, which indicates that the inherent singularity associated with the origin of the polar coordinate system is adequately handled.

Neuronal Thy-1 induces astrocyte adhesion by engaging syndecan-4 in a cooperative interaction with alphavbeta3 integrin that activates PKCalpha and RhoA.

Clustering of alphavbeta3 integrin after interaction with the RGD-like integrin-binding sequence present in neuronal Thy-1 triggers formation of focal adhesions and stress fibers in astrocytes via RhoA activation. A putative heparin-binding domain is present in Thy-1, raising the possibility that this membrane protein stimulates astrocyte adhesion via engagement of an integrin and the proteoglycan syndecan-4. Indeed, heparin, heparitinase treatment and mutation of the Thy-1 heparin-binding site each inhibited Thy-1-induced RhoA activation, as well as formation of focal adhesions and stress fibers in DI TNC(1) astrocytes. These responses required both syndecan-4 binding and signaling, as evidenced by silencing syndecan-4 expression and by overexpressing a syndecan-4 mutant lacking the intracellular domain, respectively. Furthermore, lack of RhoA activation and astrocyte responses in the presence of a PKC inhibitor or a dominant-negative form of PKCalpha implicated PKCalpha and RhoA activation in these events. Therefore, combined interaction of the astrocyte alphavbeta3-integrin-syndecan-4 receptor pair with Thy-1, promotes adhesion to the underlying matrix via PKCalpha- and RhoA-dependent pathways. Importantly, signaling events triggered by such receptor cooperation are shown here to be the consequence of cell-cell rather than cell-matrix interactions. These observations are likely to be of widespread biological relevance because Thy-1-integrin binding is reportedly relevant to melanoma invasion, monocyte transmigration through endothelial cells and host defense mechanisms.

Twitch and M-wave potentiation induced by intermittent maximal voluntary quadriceps contractions: Differences between direct quadriceps and femoral nerve stimulation.

Introduction: To investigate differences in twitch and M-wave potentiation in the quadriceps femoris when electrical stimulation is applied over the quadriceps muscle belly versus the femoral nerve trunk. Methods: M-waves and mechanical twitches were evoked using direct quadriceps muscle and femoral nerve stimulation between 48 successive isometric maximal voluntary contractions (MVC) from 10 young, healthy subjects. Potentiation was investigated by analyzing the changes in M-wave amplitude recorded from the vastus medialis (VM) and vastus lateralis (VL) muscles and in quadriceps peak twitch force. Results: Potentiation of twitch, VM M-wave, and VL M-wave were greater for femoral nerve than for direct quadriceps stimulation (P<0.05). Despite a 50% decrease in MVC force, the amplitude of the M-waves increased significantly during exercise. Conclusions: In addition to enhanced electrogenic Na(+) -K(+) pumping, other factors (such as synchronization in activation of muscle fibers and muscle architectural properties) might significantly influence the magnitude of M-wave enlargement. © 2013 Wiley Periodicals, Inc.

Interaction between tobacco and alcohol use and the risk of head and neck cancer: pooled analysis in the International Head and Neck Cancer Epidemiology Consortium.

BACKGROUND: The magnitude of risk conferred by the interaction between tobacco and alcohol use on the risk of head and neck cancers is not clear because studies have used various methods to quantify the excess head and neck cancer burden. METHODS: We analyzed individual-level pooled data from 17 European and American case-control studies (11,221 cases and 16,168 controls) participating in the International Head and Neck Cancer Epidemiology consortium. We estimated the multiplicative interaction parameter (psi) and population attributable risks (PAR). RESULTS: A greater than multiplicative joint effect between ever tobacco and alcohol use was observed for head and neck cancer risk (psi = 2.15; 95% confidence interval, 1.53-3.04). The PAR for tobacco or alcohol was 72% (95% confidence interval, 61-79%) for head and neck cancer, of which 4% was due to alcohol alone, 33% was due to tobacco alone, and 35% was due to tobacco and alcohol combined. The total PAR differed by subsite (64% for oral cavity cancer, 72% for pharyngeal cancer, 89% for laryngeal cancer), by sex (74% for men, 57% for women), by age (33% for cases <45 years, 73% for cases >60 years), and by region (84% in Europe, 51% in North America, 83% in Latin America). CONCLUSIONS: Our results confirm that the joint effect between tobacco and alcohol use is greater than multiplicative on head and neck cancer risk. However, a substantial proportion of head and neck cancers cannot be attributed to tobacco or alcohol use, particularly for oral cavity cancer and for head and neck cancer among women and among young-onset cases.

Quantitative comparison of simulations of seismic wave propagation in heterogeneous poro-elastic media involving fluid-solid interfaces and in equivalent visco-elastic solids

There is increasing evidence to suggest that the presence of mesoscopic heterogeneities constitutes the predominant attenuation mechanism at seismic frequencies. As a consequence, centimeter-scale perturbations of the subsurface physical properties should be taken into account for seismic modeling whenever detailed and accurate responses of the target structures are desired. This is, however, computationally prohibitive since extremely small grid spacings would be necessary. A convenient way to circumvent this problem is to use an upscaling procedure to replace the heterogeneous porous media by equivalent visco-elastic solids. In this work, we solve Biot's equations of motion to perform numerical simulations of seismic wave propagation through porous media containing mesoscopic heterogeneities. We then use an upscaling procedure to replace the heterogeneous poro-elastic regions by homogeneous equivalent visco-elastic solids and repeat the simulations using visco-elastic equations of motion. We find that, despite the equivalent attenuation behavior of the heterogeneous poro-elastic medium and the equivalent visco-elastic solid, the seismograms may differ due to diverging boundary conditions at fluid-solid interfaces, where there exist additional options for the poro-elastic case. In particular, we observe that the seismograms agree for closed-pore boundary conditions, but differ significantly for open-pore boundary conditions. This is an interesting result, which has potentially important implications for wave-equation-based algorithms in exploration geophysics involving fluid-solid interfaces, such as, for example, wave field decomposition.

Interaction of alpha-melanotropin with central dopamine systems: role of hormonal state and molecular structure

The tubero-infundibular and nigrostriatal DA neurone systems of rats respond to systemic (i.p.) injection of alpha-MSH (2-100 microgram/kg). The response of the tubero-infundibular (arcuate) DA neurones, an increase in cellular fluorescence intensity which can be interpreted as a sign of increased neuronal activity, is essentially the same in males, estrogen-progesterone-pretreated ovariectomized females and hypophysectomized males, whereas the type of response elicited by alpha-MSH in the nigral DA neurones depends upon the hormonal state of the animal. Differences between the two DA neurone groups exist also with regard to the effects of peptide fragments containing the two active sites of the alpha-MSH molecule. Results of lesion experiments in the lower brainstem (area postrema) and of blockade of muscarinic mechanisms by atropine further point to differences in the mechanisms underlying the peptide effects on the two neurone systems. The reaction of the tubero-infundibular DA system (which controls the pars intermedia of the pituitary) can be considered to reflect the activation of a feedback mechanism on MSH secretion, while the functional counterpart of the changes observed in the nigral system remains unknown at the present time.

Développement de la communication intentionnelle gestuelle à partir des usages culturels des objets dans l'interaction triadique enfant-objet-adulte

Pour que deux protagonistes parviennent à communiquer, ils doivent non seulement partager les signes verbaux et/ou non verbaux qu'ils utilisent, mais ils doivent également parvenir à accéder à l'intention communicative de chacun. Ce dernier aspect de la communication a été intimement lié aux significations et aux connaissances que les protagonistes partagent (angl. common ground). Malgré le fait que l'importance des significations partagées ait été soulignée dans la littérature concernant la communication entre adultes, cet aspect n'a pas été étudié en ce qui concerne le développement précoce de la communication. Dans le présent travail, nous suggérons d'investiguer le lien entre les significations partagées entre le jeune enfant et l'adulte et la capacité de l'enfant à communiquer de manière intentionnelle via des gestes. En nous appuyant sur l'approche de la Pragmatique de l'Objet (Moro & Rodríguez, 2005), nous suggérons que les connaissances concernant l'usage culturel de l'objet que construit progressivement l'enfant représentent un type de significations que l'enfant partage avec autrui. 12 dyades mère-enfant ont été enregistrées à l'aide d'une caméra lors d'interactions avec quatre objets. Les observations ont eu lieu au domicile des familles et ont été conduites chaque deuxième mois lorsque les enfants ont été âgés de 8 à 16 mois (groupe 1) et de 16 à 24 mois (groupe 2). Les observations ont été codées pour le niveau de maîtrise de l'usage culturel par l'enfant ainsi que pour la production de gestes par l'enfant et par l'adulte. Nous avons trouvé que plus l'enfant maîtrise les usages culturels des objets, plus il produit de gestes, et plus ces gestes remplissent une fonction communicative explicite. Concernant les gestes de l'adulte, les résultats dévoilent que plus l'enfant maîtrise les usages conventionnels des objets, plus l'adulte adresse des gestes communicatifs à l'enfant, plus ses gestes sont produits de manière complexe et plus l'intention des gestes communicatifs de l'adulte est complexe. Pris ensemble, ces résultats suggèrent que le partage de significations sur l'usage culturel des objets représente un type de connaissances communes qui permettent au bébé et à ses protagonistes de communiquer.

Interaction between widening of diameter of abdominal aorta and cardiovascular risk factors and atherosclerosis burden.

The aim of this study was to investigate influence of traditional cardiovascular risk factors (CVRF) and subclinical atherosclerosis (ATS) burden on early stages of abdominal aortic diameter (AAD) widening among adults. 2,052 consecutive patients (P) (39 % women), mean age 52 ± 13 years, were prospectively screened for CVRF, ATS, and AAD. B-mode ultrasound was used to evaluate the largest AAD and to detect carotid and femoral atherosclerotic plaques. Mean AAD was 15.2 ± 2.8 mm. Atherosclerotic plaques were detected in 71 % of patients. Significant univariate correlation between AAD, traditional CVRF, and ABS was found. However, multiple regression analysis showed that only seven of them were significantly and weakly correlated with AAD (R² = 0.27, p < 0.001). On the other hand, a multivariate logistic analysis was used to evaluate CVRF impact on enlarged AAD ≥25 mm (EAAD) as compared to those with AAD <25 mm. These factors did not account for more than 30 % of interaction (R² = 0.30, p = 0.001). Furthermore, despite a large proportion of patients with high number of CVRF, and subclinical ATS, rate of patients with AAD ≥25 mm was low (1 %) and scattered regardless their CHD risk score or ATS burden. In conclusion, these results suggest that although some traditional CVRF and presence of ATS are associated with early stages of EAAD, other determinants still need to be identified for a better understanding of abdominal aortic aneurysm pathogenesis.

Shaping the interaction landscape of bioactive molecules.

MOTIVATION: Most bioactive molecules perform their action by interacting with proteins or other macromolecules. However, for a significant fraction of them, the primary target remains unknown. In addition, the majority of bioactive molecules have more than one target, many of which are poorly characterized. Computational predictions of bioactive molecule targets based on similarity with known ligands are powerful to narrow down the number of potential targets and to rationalize side effects of known molecules. RESULTS: Using a reference set of 224 412 molecules active on 1700 human proteins, we show that accurate target prediction can be achieved by combining different measures of chemical similarity based on both chemical structure and molecular shape. Our results indicate that the combined approach is especially efficient when no ligand with the same scaffold or from the same chemical series has yet been discovered. We also observe that different combinations of similarity measures are optimal for different molecular properties, such as the number of heavy atoms. This further highlights the importance of considering different classes of similarity measures between new molecules and known ligands to accurately predict their targets. CONTACT: olivier.michielin@unil.ch or vincent.zoete@unil.ch SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Efficient T cell activation requires an optimal dwell-time of interaction between the TCR and the pMHC complex.

Cytotoxic T cell (CTL) activation by antigen requires the specific detection of peptide-major histocompatibility class I (pMHC) molecules on the target-cell surface by the T cell receptor (TCR). We examined the effect of mutations in the antigen-binding site of a Kb-restricted TCR on T cell activation, antigen binding and dissociation from antigen.These parameters were also examined for variants derived from a Kd-restricted peptide that was recognized by a CTL clone. Using these two independent systems, we show that T cell activation can be impaired by mutations that either decrease or increase the binding half-life of the TCR-pMHC interaction. Our data indicate that efficient T cell activation occurs within an optimal dwell-time range of TCR-pMHC interaction. This restricted dwell-time range is consistent with the exclusion of either extremely low or high affinity T cells from the expanded population during immune responses.

A Role for cis Interaction between the Inhibitory Ly49A receptor and MHC class I for natural killer cell education.

Natural killer (NK) cells show enhanced functional competence when they express inhibitory receptors specific for inherited major histocompatibility complex class I (MHC-I) molecules. Current models imply that NK cell education requires an interaction of inhibitory receptors with MHC-I expressed on other cells. However, the inhibitory Ly49A receptor can also bind MHC-I ligand on the NK cell itself (in cis). Here we describe a Ly49A variant, which can engage MHC-I expressed on other cells but not in cis. Even though this variant inhibited NK cell effector function, it failed to educate NK cells. The association with MHC-I in cis sequestered wild-type Ly49A, and this was found to relieve NK cells from a suppressive effect of unengaged Ly49A. These data explain how inhibitory MHC-I receptors can facilitate NK cell activation. They dissociate classical inhibitory from educating functions of Ly49A and suggest that cis interaction of Ly49A is necessary for NK cell education.