Generating Homology Relationships by Alignment of Anatomical Ontologies

The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we aim to establish homology relations between ontologies describing different species. We present a new algorithm, and its implementation in the software Homolonto, to create new relationships between anatomical ontologies, based on the homology concept. These relationships and the Homolonto software are available at "http://bgee.unil.ch/.":http://bgee.unil.ch

The star cluster survivability after gas expulsion is independent of the impact of the Galactic tidal field

We study the impact of the tidal field on the survivability of star clusters following instantaneous gas expulsion. Our model clusters are formed with a centrally-peaked star-formation efficiency profile as a result of star-formation taking place with a constant efficiency per free-fall time. We define the impact of the tidal field as the ratio of the cluster half-mass radius to its Jacobi radius immediately after gas expulsion, $\lambda = r_{h}/R_{J}$. We vary $\lambda$ by varying either the Galactocentric distance, or the size (hence volume density) of star clusters. We propose a new method to measure the violent relaxation duration, in which we compare the total mass-loss rate of star clusters with their stellar evolutionary mass-loss rate. That way, we can robustly estimate the bound mass fraction of our model clusters at the end of violent relaxation. The duration of violent relaxation correlates linearly with the Jacobi radius, when considering identical clusters at different Galactocentric distances. In contrast, it is nearly constant for the solar neighbourhood clusters, slightly decreasing with $\lambda$. The violent relaxation does not last longer than 50 Myr in our simulations. Identical model clusters placed at different Galactocentric distances have the same final bound fraction, despite experiencing different impacts of the tidal field. The solar neighbourhood clusters with different densities experience only limited variations of their final bound fraction. In general, we conclude that the cluster survivability after instantaneous gas expulsion, as measured by their bound mass fraction at the end of violent relaxation, $F_{bound}$, is independent of the impact of the tidal field, $\lambda$.Comment: accepted for publication in MNRAS, 8 pages, 5 figures,3 table

Root selection methods in flood analysis

International audienceIn the 1970s, de Laine developed a root-matching procedure for estimating unit hydrograph ordinates from estimates of the fast component of the total runoff from multiple storms. Later, Turner produced a root selection method which required only data from one storm event and was based on recognising a pattern typical of unit hydrograph roots. Both methods required direct runoff data, i.e. prior separation of the slow response. This paper introduces a further refinement, called root separation, which allows the estimation of both the unit hydrograph ordinates and the effective precipitation from the full discharge hydrograph. It is based on recognising and separating the quicker component of the response from the much slower components due to interflow and/or baseflow. The method analyses the z-transform roots of carefully selected segments of the full hydrograph. The root patterns of these separate segments tend to be dominated by either the fast response or the slow response. This paper shows how their respective time-scales can be distinguished with an accuracy sufficient for practical purposes. As an illustration, theoretical equations are derived for a conceptual rainfall-runoff system with the input split between fast and slow reservoirs in parallel. These are solved analytically to identify the reservoir constants and the input splitting parameter. The proposed method, called "root separation", avoids the subjective selection of rainfall roots in the Turner method as well as the subjective matching of roots in the original de Laine method. Keywords: unit hydrograph,identification methods, z-transform, polynomial roots, root separation, fast andslow response, Nash cascade</p

Trophic ecology of the seagrass-inhabiting footballer demoiselle <i>Chrysiptera annulata</i> (Peters, 1855); comparison with three other reef-associated damselfishes

Many damselfishes (Pomacentridae) are herbivorous or omnivorous with an important contribution from different kinds of algae in their diet. They display different levels of territoriality and farming behavior, from almost non territorial to monoculture farmers. In addition, a few species inhabit seagrass meadows but, presently, none can be considered as seagrass-eating specialists. The footballer demoiselle, Chrysiptera annulata, is found in the seagrass meadows on the reef flat of the Great Reef of Toliara (Madagascar, Mozambique Channel). In the light of this unusual habitat for a pomacentrid, this study aimed to answer three questions: 1) What is the diet of C. annulata? 2) Do the resources supporting this diet include seagrass? 3) Does its trophic niche overlap those of other sympatric damselfishes (Pomacentrus trilineatus, Chrysiptera unimaculata and Plectroglyphidodon lacrymatus) living in close association with macrophytes or eating algae? Stomach content examination and stable isotope analysis showed that the footballer demoiselle is not a seagrass consumer but is an omnivorous/herbivorous species heavily relying on algal resources and small invertebrates. SIAR, a stable isotope mixing model, indicated it assimilated large amounts of turf algae, and various benthic or planktonic invertebrates in lower proportions. SIBER metrics revealed that the isotopic niche of the footballer demoiselle partly overlaps that of its congener, C. unimaculata, but not those of P. trilineatusand P. lacrymatus. Trophic strategies of C. annulata differed both from farming species such as P. lacrymatus and from less territorial herbivores such as P. trilineatus. Its seagrass meadow habitat on the Great Reef of Toliara allows the conquest of an unusual habitat for damselfishes and could limit competition with C. unimaculata, a species displaying the same territorial behavior and the same isotopic niche but living on the reef itself

Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy

Motivation: The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we need to establish relations between ontologies describing different species. Results: We present a new algorithm, and its implementation in the software Homolonto, to create new relationships between anatomical ontologies, based on the homology concept. Homolonto uses a supervised ontology alignment approach. Several alignments can be merged, forming homology groups. We also present an algorithm to generate relationships between these homology groups. This has been used to build a multi-species ontology, for the database of gene expression evolution Bgee. Availability: download section of the Bgee website http://bgee.unil.ch/ Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

Call properties and morphology of the sound-producing organ in <i>Ophidion rochei</i> (Ophidiidae)

The anatomical structures of the sound-producing organ in Ophidion rochei males present an important panel of highly derived characters: three pairs of putatively slow sonic muscles; a neural arch that pivots; a rocker bone at the front pole of the swimbladder; a stretchable swimbladder fenestra; a swimbladder plate; and an internal cone that terminates in a pair of membranes in the caudal swimbladder. Male courtship calls are produced nocturnally and consist of trains of 10 to 40 pulses that increase in amplitude and decrease in rate before exhibiting alternating periods of ca. 84 and 111 ms. Each pulse includes an unusual waveform with two parts. Pulse part 1 is a single cycle followed by a longer duration pulse part that exhibits gradual damping. Sounds and morphology suggest two hypotheses on the sound-producing mechanism. The ‘pulley’ hypothesis would require an alternate contraction of the ventral and dorsal muscles to form the two parts of each pulse. The ‘bow’ hypothesis involves a release mechanism with the sustained contraction of the dorsal muscle during all of the call, and the rapid contraction/relaxation of the ventral muscle to form each pulse

Electron quantum optics : partitioning electrons one by one

We have realized a quantum optics like Hanbury Brown and Twiss (HBT) experiment by partitioning, on an electronic beam-splitter, single elementary electronic excitations produced one by one by an on-demand emitter. We show that the measurement of the output currents correlations in the HBT geometry provides a direct counting, at the single charge level, of the elementary excitations (electron/hole pairs) generated by the emitter at each cycle. We observe the antibunching of low energy excitations emitted by the source with thermal excitations of the Fermi sea already present in the input leads of the splitter, which suppresses their contribution to the partition noise. This effect is used to probe the energy distribution of the emitted wave-packets.Comment: 5 pages, 4 figure