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

Le problème de Molyneux de Locke à Diderot

Les réponses positives et négatives apportées au célèbre problème soumis par W. Molyneux à J. Locke sont interdépendantes. Cette intervention vise à montrer comment les objections que Condillac adresse à la réponse de Locke d’une part, l’interprétation que Berkeley donne de cette même réponse d’autre part, masquent les données réelles du problème dans l’Essai de Locke. Paradoxalement c’est Diderot qui, dans la Lettre sur les aveugles, les retrouve et les réactualise, par la force de sa propre analyse, tout en contribuant à son tour à déformer les arguments apportés en faveur d’une réponse négative.Molyneux’s Query from Locke to DiderotThe positive and negative replies to Molyneux’s famous question to Locke are interdependent. This article tries to show how Condillac’s objections to Locke’s reply, on the one hand, and Berkeley’s interpretation of the same reply, on the other, make the real issues at stake in Locke’s Essay. Surprisingly, it was Diderot, in the Letter on the Blind, who rediscovered these issues and brought them up to date, while at the same time helping to deform once more the arguments in favour of a negative reply

Voltaire et l’optimisme leibnizien

Voltaire découvre d’abord une défense de l’optimisme dans l’Essai sur l’homme d’Alexander Pope et c’est cet ouvrage qui est au centre du Poème sur le désastre de Lisbonne. Mais l’optimisme de Pope, pour qui le mal est apparent, est très éloigné de celui de Leibniz pour qui le mal est réel. Or Voltaire possède une connaissance précise de la philosophie de Leibniz, dont certains aspects lui semblent « extraordinaires » et qui lui semble conduire au fatalisme. C’est surtout la méthode qu’il condamne : elle vise trop haut. Dans Candide, c’est l’optimisme leibnizien qui est visé. Le conte le soumet à une épreuve expérimentale en faisant passer les personnages d’un monde à l’autre. C’est donc le concept leibnizien de « monde possible » qui fournit le cadre de l’expérience. Il résulte de ce test que l’optimisme n’est ni prouvable ni falsifiable par les faits, ce qui suffit à le discréditer.Voltaire first discovers the defence of optimism in the Essay on Man by Alexander Pope, the work that we can find at the very centre of the Poem on the Lisbon Disaster. But Pope’s optimism, for whom evil is apparent, is far away from that of Leibniz’s for whom evil is real. Yet, Voltaire has a precise knowledge of Leibniz’s philosophy, and considers some aspects of it as “extraordinary” that seem to lead to fatalism. He condemns the method in particular: it aims too high. In Candide, it is the Leibnizian optimism that is targeted. In the tale the hero undergoes an experimental test that passes the characters from one world to another. So it is the concept of Leibniz’s “possible world” that provides the framework for the experiment. The result of the test is that optimism is neither provable nor falsifiable by facts, which is enough to discredit it.Voltaire descobriu pela primeira vez uma defesa do optimismo no Ensaio sobre o Homem de Alexander Pope, e é esta obra que está no centro do Poema sobre o Desastre de Lisboa. Mas o optimismo de Pope, para quem o mal é aparente, está muito longe do de Leibniz, para quem o mal é real. Voltaire tem um conhecimento preciso da filosofia de Leibniz, e alguns aspectos lhe parecem 'extraordinários' e parecem levar ao fatalismo. O que ele condena é sobretudo o método: visa demasiado alto. Em Cândido, o que é visado é o optimismo Leibniziano. O conto põe-no à prova experimental ao mover as personagens de um mundo para outro. O conceito Leibniziano do "mundo possível" fornece assim o enquadramento para a experiência. O resultado deste teste é que o optimismo não é provável nem falsificável por factos, o que é suficiente para o desacreditar

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

A high sensitivity ultra-low temperature RF conductance and noise measurement setup

We report on the realization of a high sensitivity RF noise measurement scheme to study small current fluctuations of mesoscopic systems at milliKelvin temperatures. The setup relies on the combination of an interferometric ampli- fication scheme and a quarter-wave impedance transformer, allowing the mea- surement of noise power spectral densities with GHz bandwith up to five orders of magnitude below the amplifier noise floor. We simultaneously measure the high frequency conductance of the sample by derivating a portion of the signal to a microwave homodyne detection. We describe the principle of the setup, as well as its implementation and calibration. Finally, we show that our setup allows to fully characterize a subnanosecond on-demand single electron source. More generally, its sensitivity and bandwith make it suitable for applications manipulating single charges at GHz frequencies.Comment: The following article has been submitted to Review of Scientific Instrument

Melt segregation and depletion during ascent of buoyant diapirs in subduction zones

Author Posting. © American Geophysical Union, 2020. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research-Solid Earth 125(2), (2020): e2019JB018203, doi:10.1029/2019JB018203.Cold, low‐density diapirs arising from hydrated mantle and/or subducted sediments on the top of subducting slabs have been invoked to transport key chemical signatures to the source region of arc magmas. However, to date there have been few quantitative models to constrain melting in such diapirs. Here we use a two‐phase Darcy‐Stokes‐energy model to investigate thermal evolution, melting, and depletion in a buoyant sediment diapir ascending through the mantle wedge. Using a simplified 2‐D circular geometry, we investigate diapir evolution in three scenarios with increasing complexity. In the first two scenarios we consider instantaneous heating of a diapir by thermal diffusion with and without the effect of the latent heat of melting. Then, these simplified calculations are compared to numerical simulations that include melting, melt segregation, and the influence of depletion on the sediment solidus along pressure‐temperature‐time (P ‐T ‐t ) paths appropriate for ascent through the mantle wedge. The high boundary temperature induces a rim of high porosity, into which new melts are focused and then migrate upward. The rim thus acts like an annulus melt channel, while the effect of depletion buffers additional melt production. Solid matrix flow combined with recrystallization of melt pooled near the top of the diapir can result in large gradients in depletion across the diapir. These large depletion gradients can either be preserved if the diapir leaks melt during ascent, or rehomogenized in a sealed diapir. Overall our numerical simulations predict less melt production than the simplified thermal diffusion calculations. Specifically, we show that diapirs whose ascent paths favor melting beneath the volcanic arc will undergo no more than ~40–50% total melting.We thank careful reviews by Juliane Dannberg, Harro Schmeling, and Bernhard steinberger. This work is supported by NSF‐1316333 (MB & NZ), NSF‐1551023 (MB), NSF‐1316310 (CK), and by China's Thousand Talents Plan (2015) and NSFC‐41674098 funding to NZ. The public data repository of Deal.ii (www.dealii.org) is thanked for distributing the software and examples that are used in this study. Computational work was conducted in High‐performance Computing Platform of Peking University, Kenny cluster of WHOI, and Pawsey Supercomputing Centre of Western Australia. We thank Timo Heister and Juliane Dannberg for deal.II technical assistance. The data of mantle wedge thermal structure and diapir trajectories, and the source code to compute the model results are available in the Mendeley data (http://dx.doi.org/10.17632/73n8zkc68s.1).2020-07-3

vHOG, a multispecies vertebrate ontology of homologous organs groups

Motivation: Most anatomical ontologies are species-specific, whereas a framework for comparative studies is needed. We describe the vertebrate Homologous Organs Groups ontology, vHOG, used to compare expression patterns between species. Results: vHOG is a multispecies anatomical ontology for the vertebrate lineage. It is based on the HOGs used in the Bgee database of gene expression evolution. vHOG version 1.4 includes 1184 terms, follows OBO principles and is based on the Common Anatomy Reference Ontology (CARO). vHOG only describes structures with historical homology relations between model vertebrate species. The mapping to species-specific anatomical ontologies is provided as a separate file, so that no homology hypothesis is stated within the ontology itself. Each mapping has been manually reviewed, and we provide support codes and references when available. Availability and implementation: vHOG is available from the Bgee download site (http://bgee.unil.ch/), as well as from the OBO Foundry and the NCBO Bioportal websites. Contact: [email protected]; [email protected]

Tracking selenium in the Chalk aquifer of northern France: Sr isotope constraints

International audienceGroundwater at the southern and eastern edges of France's Paris Basin has a selenium content that at times exceeds the European Framework Directive's drinking-water limit value of 10 µg/L. To better understand the dynamics of the Chalk groundwater being tapped to supply the city of Lille and the Se origins, we used a combination of geochemical and isotopic tools. Strontium isotopes, coupled with Ca/Sr, Mg/Sr and Se/Sr ratios, were used to identify the main groundwater bodies and their mixings, with the Mg/Sr ratio constraining a ternary system. Groundwater in the agricultural aquifer-recharge zone represents a first end-member and displays the youngest water ages of the catchment along with the highest strontium isotopic signature (0.7084) and low Se contents. Anaerobic groundwater constitutes a second major end-member affected by water-rock interactions over a long residence time, with the lowest strontium isotopic signature (0.7079) and the lowest Se content, its low SF6 content confirming the contribution of old water. Se-rich groundwater containing up to 30 µg/L of Se represents a third major end-member, with an intermediate Sr isotopic ratio, and is mainly constrained by the clayey Se-rich formation overlying the Chalk aquifer. The spatial and temporal Se variability in the groundwater is clearly linked to the presence of this formation identified as Tertiary and also to the hydrological conditions; saturation of the Se-rich clays by oxygenated groundwater enhances Se mobility and also Sr adsorption onto the clays. This multi-tool study including Sr isotopes successfully identified the Se origins in the aquifer and has led to a better understanding of the regional mixing and processes affecting the Chalk groundwater