Cassis: detection of genomic rearrangement breakpoints

Summary: Genomes undergo large structural changes that alter their organization. The chromosomal regions affected by these rearrangements are called breakpoints, while those which have not been rearranged are called synteny blocks. Lemaitre et al. presented a new method to precisely delimit rearrangement breakpoints in a genome by comparison with the genome of a related species. Receiving as input a list of one2one orthologous genes found in the genomes of two species, the method builds a set of reliable and non-overlapping synteny blocks and refines the regions that are not contained into them. Through the alignment of each breakpoint sequence against its specific orthologous sequences in the other species, we can look for weak similarities inside the breakpoint, thus extending the synteny blocks and narrowing the breakpoints. The identification of the narrowed breakpoints relies on a segmentation algorithm and is statistically assessed. Here, we present the package Cassis that implements this method of precise detection of genomic rearrangement breakpoints

Interpretations of the Accelerating Universe

It is generally argued that the present cosmological observations support the accelerating models of the universe, as driven by the cosmological constant or `dark energy'. We argue here that an alternative model of the universe is possible which explains the current observations of the universe. We demonstrate this with a reinterpretation of the magnitude-redshift relation for Type Ia supernovae, since this was the test that gave a spurt to the current trend in favour of the cosmological constant.Comment: 12 pages including 2 figures, minor revision, references added, a paragraph on the interpretation of the CMB anisotropy in the QSSC added in conclusion, general results unchanged. To appear in the October 2002 issue of the "Publications of the Astronmical Society of the Pacific

Bistability of the Nuclear Polarisation created through optical pumping in InGaAs Quantum Dots

We show that optical pumping of electron spins in individual InGaAs quantum dots leads to strong nuclear polarisation that we measure via the Overhauser shift (OHS) in magneto-photoluminescence experiments between 0 and 4T. We find a strongly non-monotonous dependence of the OHS on the applied magnetic field, with a maximum nuclear polarisation of 40% for intermediate magnetic fields. We observe that the OHS is larger for nuclear fields anti-parallel to the external field than in the parallel configuration. A bistability in the dependence of the OHS on the spin polarization of the optically injected electrons is found. All our findings are qualitatively understood with a model based on a simple perturbative approach.Comment: Phys Rev B (in press

Topological acoustics in coupled nanocavity arrays

The Su-Schrieffer-Heeger (SSH) model is likely the simplest one-dimensional concept to study non-trivial topological phases and topological excitations. Originally developed to explain the electric conductivity of polyacetylene, it has become a platform for the study of topological effects in electronics, photonics and ultra-cold atomic systems. Here, we propose an experimentally feasible implementation of the SSH model based on coupled one-dimensional acoustic nanoresonators working in the GHz-THz range. In this simulator it is possible to implement different signs in the nearest neighbor interaction terms, showing full tunability of all parameters in the SSH model. Based on this concept we construct topological transition points generating nanophononic edge and interface states and propose an easy scheme to experimentally probe their spatial complex amplitude distribution directly by well-established optical pump-probe techniques.Comment: 10 pages, 4 figure

Particulate barium tracing of significant mesopelagic carbon remineralisation in the North Atlantic

The remineralisation of sinking particles by prokaryotic heterotrophic activity is important for controlling oceanic carbon sequestration. Here, we report mesopelagic particulate organic carbon (POC) remineralisation fluxes in the North Atlantic along the GEOTRACES-GA01 section (GEOVIDE cruise; May-June 2014) using the particulate biogenic barium (excess barium; Baxs/ proxy. Important mesopelagic (100-1000 m) Baxs differences were observed along the transect depending on the intensity of past blooms, the phytoplankton community structure, and the physical forcing, including downwelling. The subpolar province was characterized by the highest mesopelagic Baxs content (up to 727 pmol L-1/, which was attributed to an intense bloom averaging 6 mg chl a m-3 between January and June 2014 and by an intense 1500m deep convection in the central Labrador Sea during the winter preceding the sampling. This downwelling could have promoted a deepening of the prokaryotic heterotrophic activity, increasing the Baxs content. In comparison, the temperate province, characterized by the lowest Baxs content (391 pmol L-1/, was sampled during the bloom period and phytoplankton appear to be dominated by small and calcifying species, such as coccolithophorids. The Baxs content, related to oxygen consumption, was converted into a remineralisation flux using an updated relationship, proposed for the first time in the North Atlantic. The estimated fluxes were of the same order of magnitude as other fluxes obtained using independent methods (moored sediment traps, incubations) in the North Atlantic. Interestingly, in the subpolar and subtropical provinces, mesopelagic POC remineralisation fluxes (up to 13 and 4.6 mmol Cm-2 d-1, respectively) were equalling and occasionally even exceeding upper-ocean POC export fluxes, deduced using the 234Th method. These results highlight the important impact of the mesopelagic remineralisation on the biological carbon pump of the studied area with a near-zero, deep (> 1000 m) carbon sequestration efficiency in spring 2014

Optimization of interface layers in the design of ceramic fiber reinforced metal matrix composites

The potential of using an interface layer to reduce thermal stresses in the matrix of composites with a mismatch in coefficients of thermal expansion (CTE) of fiber and matrix was investigated. It was found that the performance of the layer can be defined by the product of the CTE and the thickness, and that a compensating layer with a sufficiently high CTE can reduce the thermal stresses in the matrix significantly. A practical procedure offering a window of candidate layer materials is proposed