Analyzing and Visualizing State Sequences in R with TraMineR

This article describes the many capabilities offered by the TraMineR toolbox for categorical sequence data. It focuses more specifically on the analysis and rendering of state sequences. Addressed features include the description of sets of sequences by means of transversal aggregated views, the computation of longitudinal characteristics of individual sequences and the measure of pairwise dissimilarities. Special emphasis is put on the multiple ways of visualizing sequences. The core element of the package is the state se- quence object in which we store the set of sequences together with attributes such as the alphabet, state labels and the color palette. The functions can then easily retrieve this information to ensure presentation homogeneity across all printed and graphical displays. The article also demonstrates how TraMineRâÂÂs outcomes give access to advanced analyses such as clustering and statistical modeling of sequence data.

Analyzing and Visualizing State Sequences in R with TraMineR

This article describes the many capabilities offered by the TraMineR toolbox for categorical sequence data. It focuses more specifically on the analysis and rendering of state sequences. Addressed features include the description of sets of sequences by means of transversal aggregated views, the computation of longitudinal characteristics of individual sequences and the measure of pairwise dissimilarities. Special emphasis is put on the multiple ways of visualizing sequences. The core element of the package is the state se- quence object in which we store the set of sequences together with attributes such as the alphabet, state labels and the color palette. The functions can then easily retrieve this information to ensure presentation homogeneity across all printed and graphical displays. The article also demonstrates how TraMineR’s outcomes give access to advanced analyses such as clustering and statistical modeling of sequence data

Intestinal Colonization of IL-2 Deficient Mice with Non-Colitogenic B. vulgatus Prevents DC Maturation and T-Cell Polarization

BACKGROUND: IL-2 deficient (IL-2(-/-)) mice mono-colonized with E. coli mpk develop colitis whereas IL-2(-/-)-mice mono-colonized with B. vulgatus mpk do not and are even protected from E. coli mpk induced colitis. METHODOLOGY/PRINCIPAL FINDINGS: We investigated if mono-colonization with E. coli mpk or B. vulgatus mpk differentially modulates distribution, activation and maturation of intestinal lamina propria (LP) dendritic cells (DC). LP DC in mice mono-colonized with protective B. vulgatus mpk or co-colonized with E. coli mpk/B. vulgatus mpk featured a semi-mature LP DC phenotype (CD40(lo)CD80(lo)MHC-II(hi)) whereas mono-colonization with colitogenic E. coli mpk induced LP DC activation and maturation prior to onset of colitis. Accordingly, chemokine receptor (CCR) 7 surface expression was more strikingly enhanced in mesenteric lymph node DC from E. coli mpk than B. vulgatus mpk mono- or co-colonized mice. Mature but not semi-mature LP DC promoted Th1 polarization. As B. vulgatus mpk promotes differentiation of semi-mature DC presumably by IL-6, mRNA and protein expression of IL-6 was investigated in LP DC. The data demonstrated that IL-6 mRNA and protein was increased in LP DC of B. vulgatus mpk as compared to E. coli mpk mono-colonized IL-2(-/-)-mice. The B. vulgatus mpk mediated suppression of CCR7 expression and DC migration was abolished in IL-6(-/-)-DC in vitro. CONCLUSIONS/SIGNIFICANCE: From this data we conclude that the B. vulgatus triggered IL-6 secretion by LP DC in absence of proinflammatory cytokines such as IL-12 or TNF-alpha induces a semi-mature LP DC phenotype, which might prevent T-cell activation and thereby the induction of colitis in IL-2(-/-)-mice. The data provide new evidence that IL-6 might act as an immune regulatory cytokine in the mucosa by targeting intestinal DC

Ridge subduction sparked reorganization of the Pacific plate-mantle system 60-50 million years ago

A reorganization centered on the Pacific plate occurred ~53–47 million years ago. A “top-down” plate tectonic mechanism, complete subduction of the Izanagi plate, as opposed to a “bottom-up” mantle flow mechanism, has been proposed as the main driver. Verification based on marine geophysical observations is impossible as most ocean crust recording this event has been subducted. Using a forward modeling approach, which assimilates surface plate velocities and shallow thermal structure of slabs into mantle flow models, we show that complete Izanagi plate subduction and margin-wide slab detachment induced a major change in sub-Pacific mantle flow, from dominantly southward before 60 Ma to north-northeastward after 50 Ma. Our results agree with onshore geology, mantle tomography, and the inferred motion of the Hawaiian hot spot and are consistent with a plate tectonic process driving the rapid plate-mantle reorganization in the Pacific hemisphere between 60 and 50 Ma. This reorganization is reflected in tectonic changes in the Pacific and surrounding ocean basins

Breakdown of superfluidity of an atom laser past an obstacle

The 1D flow of a continuous beam of Bose-Einstein condensed atoms in the presence of an obstacle is studied as a function of the beam velocity and of the type of perturbing potential (representing the interaction of the obstacle with the atoms of the beam). We identify the relevant regimes: stationary/time-dependent and superfluid/dissipative; the absence of drag is used as a criterion for superfluidity. There exists a critical velocity below which the flow is superfluid. For attractive obstacles, we show that this critical velocity can reach the value predicted by Landau's approach. For penetrable obstacles, it is shown that superfluidity is recovered at large beam velocity. Finally, enormous differences in drag occur when switching from repulsive to attractive potential.Comment: 15 pages, 6 figure

Fixed points and amenability in non-positive curvature

Consider a proper cocompact CAT(0) space X. We give a complete algebraic characterisation of amenable groups of isometries of X. For amenable discrete subgroups, an even narrower description is derived, implying Q-linearity in the torsion-free case. We establish Levi decompositions for stabilisers of points at infinity of X, generalising the case of linear algebraic groups to Is(X). A geometric counterpart of this sheds light on the refined bordification of X (\`a la Karpelevich) and leads to a converse to the Adams-Ballmann theorem. It is further deduced that unimodular cocompact groups cannot fix any point at infinity except in the Euclidean factor; this fact is needed for the study of CAT(0) lattices. Various fixed point results are derived as illustrations.Comment: 33 page

Oval Domes: History, Geometry and Mechanics

An oval dome may be defined as a dome whose plan or profile (or both) has an oval form. The word Aoval@ comes from the latin Aovum@, egg. Then, an oval dome has an egg-shaped geometry. The first buildings with oval plans were built without a predetermined form, just trying to close an space in the most economical form. Eventually, the geometry was defined by using arcs of circle with common tangents in the points of change of curvature. Later the oval acquired a more regular form with two axis of symmetry. Therefore, an “oval” may be defined as an egg-shaped form, doubly symmetric, constructed with arcs of circle; an oval needs a minimum of four centres, but it is possible also to build polycentric ovals. The above definition corresponds with the origin and the use of oval forms in building and may be applied without problem until, say, the XVIIIth century. Since then, the teaching of conics in the elementary courses of geometry made the cultivated people to define the oval as an approximation to the ellipse, an “imperfect ellipse”: an oval was, then, a curve formed with arcs of circles which tries to approximate to the ellipse of the same axes. As we shall see, the ellipse has very rarely been used in building. Finally, in modern geometrical textbooks an oval is defined as a smooth closed convex curve, a more general definition which embraces the two previous, but which is of no particular use in the study of the employment of oval forms in building. The present paper contains the following parts: 1) an outline the origin and application of the oval in historical architecture; 2) a discussion of the spatial geometry of oval domes, i. e., the different methods employed to trace them; 3) a brief exposition of the mechanics of oval arches and domes; and 4) a final discussion of the role of Geometry in oval arch and dome design

Predicting enhanced absorption of light gases in polyethylene using simplified PC-SAFT and SAFT-VR

International audienceAbsorption of light gases in polyethylene (PE) is studied using two versions of the Statistical Associating Fluid Theory (SAFT): SAFT for chain molecules with attractive potentials of variable range (VR) and simplified perturbed-chain (PC) SAFT. Emphasis is placed on the light gases typically present during ethylene polymerisation in the gas-phase reactor (GPR) process. The two approaches are validated using experimental binary-mixture data for gas absorbed in PE, and predictions are made for mixtures of more components. For most cases studied both SAFT versions perform equally well. For the case of ternary mixtures of two gases with PE, it is predicted that the less-volatile of the two gases acts to enhance the absorption of the more-volatile gas, while the more-volatile gas inhibits the absorption of the less-volatile gas. This general behaviour is also predicted in mixtures containing more gases, such as typical reactor mixtures. The magnitude of the effect may vary considerably, depending on the relative proximity of the gas-mixture saturation pressure to the reactor pressure; for example it is predicted that the absorption of ethylene may be approximately doubled if diluent gases, propane or nitrogen, are partially or completely replaced by less-volatile butane or pentane for a reactor pressure similar to 2 MPa. In the case of a co-polymerisation reaction, it is predicted that increases in absorption of both co-monomers may be obtained in roughly equal proportion. Our findings cast light on the so-called co-monomer effect, in which substantial increases in the rate of ethylene polymerisation are observed in the presence of hexene co-monomer, while suggesting that the effect is more general and not restricted to co-monomer. For example, similar rate increases may be expected in the presence of, e.g., pentane instead of hexene, but without the change in the branch structure of the produced polymer that is inevitable when the amount of co-monomer is increased