Neural Networks beyond explainability: Selective inference for sequence motifs

Over the past decade, neural networks have been successful at making predictions from biological sequences, especially in the context of regulatory genomics. As in other fields of deep learning, tools have been devised to extract features such as sequence motifs that can explain the predictions made by a trained network. Here we intend to go beyond explainable machine learning and introduce SEISM, a selective inference procedure to test the association between these extracted features and the predicted phenotype. In particular, we discuss how training a one-layer convolutional network is formally equivalent to selecting motifs maximizing some association score. We adapt existing sampling-based selective inference procedures by quantizing this selection over an infinite set to a large but finite grid. Finally, we show that sampling under a specific choice of parameters is sufficient to characterize the composite null hypothesis typically used for selective inference-a result that goes well beyond our particular framework. We illustrate the behavior of our method in terms of calibration, power and speed and discuss its power/speed trade-off with a simpler data-split strategy. SEISM paves the way to an easier analysis of neural networks used in regulatory genomics, and to more powerful methods for genome wide association studies (GWAS)

Iongel Soft Solid Electrolytes Based on [DEME][TFSI] Ionic Liquid for Low Polarization Lithium-O-2 Batteries

Lithium-air/O-2 batteries are a promising battery technology for automotive applications due to their high energy density. However, many challenges need to be solved, particularly the high reactivity of the electrolyte with oxygen superoxide radicals and its low cyclability. In this work, we present a simple and fast way to prepare polymer-based iongel soft solid electrolytes. Thermally and mechanically stable iongels are prepared by fast UV-photopolymerisation exhibiting a high ionic conductivity (similar to 1.2 x 10(-3) S cm(-1) at 25 degrees C). When used as solid electrolytes in lithium symmetrical cells, they can withstand a critical current density of 0.5 mA cm(-2). Performance in Li-O-2 cells showed capacities as large as 3.3 mAh cm(-2), and cycling capability of 25 cycles, exceeding results on liquid-counterpart cells.European Commission's funded Marie Skłodowska-Curie. Grant Number: 76582

from TEI Lex-0 to Ontolex-Lemon

UIDB/03213/2020 UIDP/03213/2020This paper describes ongoing work in the modelling of usage information in the context of the MORDigital project. The latter is based on the encoding and publication as linked data of Diccionario da Lingua Portugueza, a Portuguese legacy dictionary authored by António de Morais Silva, whose first edition was published in 1789. In this paper, we will focus on the modelling of domain labels in Ontolex-Lemon, based on a previous encoding of the dictionary’s entries in TEI Lex-0. This approach should be reusable for other projects involving the linked data publication of legacy dictionaries.publishersversionpublishe

Matériaux d'électrode positive à base de phosphates pour accumulateurs Li-ion et phénomènes aux interfaces (apport de la spectroscopie photoélectronique à rayonnement X (XPS))

Ce travail de thèse est centré sur l étude de matériaux LiMPO4 (M=Fe, Mn, Co) et de leur évolution en cyclage (processus rédox et interfaces électrode / électrolyte) dans des accumulateurs Li-ion. Il a été mené essentiellement sur la base d analyses en spectroscopie photoélectronique à rayonnement X (XPS) couplées à des tests électrochimiques. Une oxydation de surface du phosphate LiFePO4 a été mise en évidence lors d une exposition à l air de ce matériau avec la formation d impuretés de surface type Fe2O3. Au plan structure électronique, l analyse des bandes de valence des matériaux LiMPO4 (M=Fe, Mn, Co) a notamment permis, pour LiFePO4, la visualisation de l électron spin down du niveau Fe 3d amenant la première preuve expérimentale de la configuration électronique particulière (3d )5(3d )1 de Fe2+dans ce matériau. Ce travail a également contribué à mieux comprendre l influence de la température de fonctionnement ainsi que de la nature de l électrode négative sur les mécanismes de vieillissement des accumulateurs Li-ion. Pour les accumulateurs LiFePO4 // Graphite, la comparaison d interfaces solide/électrolyte distribuées spatialement a montré que le vieillissement se caractérisant par la perte de lithium actif pouvait être mis en parallèle avec une hétérogénéité de fonctionnement de l électrode positive. Enfin, l extension des travaux aux matériaux prometteurs d électrode positive Li(FeMn)PO4 a révélé que le potentiel de travail de fin de charge plus élevé pour le phosphate mixte, comparativement à LiFePO4, résultait dans une réactivité accrue vis-à-vis de l électrolyte dont les conséquences ont été analysées.This thesis is focused on the study of LiMPO4 (M = Fe, Mn, Co) materials and on their evolution upon cycling (redox process end electrodes / electrolyte interfaces) in lithium ion cells. It is based on X-Ray Photoelectron Spectroscopy (XPS) analyses coupled with electrochemical tests. During air exposure, a surface oxidation of phosphate LiFePO4 was observed that lead to the formation of surface impurities such as Fe2O3. Concerning electronic structure, the analysis of LiMPO4 (M=Fe, Mn, Co) materials valence spectra allowed for LiFePO4 the visualization of spin down Fe 3d electron which is the first experimental proof of the particular electronic configuration (3d )5(3d )1 of Fe2+ in this material. This work also allowed a better understanding of the effect of the working temperature as well as the nature of the negative electrode on Li-ion cells ageing mechanisms. For LiFePO4 // Graphite cell, the comparison of spatially distributed solid/electrolyte interfaces showed that ageing mechanisms, characterized by a loss of active lithium, could be associated with a heterogeneity of working of the positive electrode. In addition, the extension of these studies on new promising Li(FeMn)PO4 materials for positive electrode showed that higher working potential of mixed phosphate material compared to LiFePO4 material leads to a higher electrolyte reactivity which consequences were analysed.PAU-BU Sciences (644452103) / SudocSudocFranceF

Las protestas son el temor a los gobiernos colombiano y chileno en los años 2020 a 2021

Colombia y Chile han sido países que siempre se han encontrado inmersos en la violencia, en gobiernos corruptos y en las muertes de personas inocentes que se manifiestan con la esperanza de que el Estado las escuche y garantice sus derechos equitativamente. Teniendo en cuenta ello, se decidió realizar este artículo de investigación de carácter científico y tecnológico sobre el derecho a la protesta en los gobiernos en mención, con el propósito de exponer las causas, circunstancias y efectos sociopolíticos que sufren dichos países, considerando los motivos de las protestas que tuvieron lugar durante el período de los años 2020-2021, y se llevó a cabo una comparación con el objeto de identificar las similitudes y diferencias en los contextos de estos gobiernos; así mismo, se determinaron los derechos fundamentales y humanos que fueron vulnerados a la población y a los individuos pertenecientes a la fuerza pública en el lapso de las protestas. Por último, se hizo un análisis desde la perspectiva maquiavélica, misma que ha sido aplicada por los Estados anteriormente indicados con respecto a los mecanismos implementados como respuesta a las manifestaciones, tal como el uso gradual de la fuerza. Ahora bien, se recibió una respuesta violenta y quebrantadora por parte de los gobiernos objeto de estudio, la cual afecta directamente los derechos fundamentales, evidenciándose cierta incongruencia con lo propuesto por el autor Maquiavelo en cuanto a contemplar las protestas como medios idóneos para poder conocer las inconformidades que presenta el pueblo, a fin de poder fortalecer el gobierno

Single-ion polymer/LLZO hybrid electrolytes with high lithium conductivity

Hybrid solid electrolytes which combine the properties of inorganic and polymeric ion conductors are being investigated for lithium batteries which use lithium metal anodes. The number of inorganic/polymer compositions and their synergy in ion-conducting properties are limited by the hybrid fabrication method and the limited compatibility between both types of materials. Here we report a hybrid solid electrolyte formed by a poly(ethylene glycol) type single-ion polymer network and ceramic garnet-type nanoparticles of Li7−3XAlXLa3Zr2O12 (LLZO) with very high lithium conductivity. The combination of a lithium-single ion polymer matrix with LLZO inorganic particles results in flexible free-standing films by using a fast UV-photopolymerization process with facile control of its composition. This methodology showed excellent dispersion of the LLZO nanoparticles within the gel polymer network with up to 50 wt% ceramic content, as shown in the enviromental ESEM images. These hybrid electrolytes have high ionic conductivity values (1.4 × 10−4 S cm−1 at 25 °C) and high lithium transference number as compared to previous hybrid electrolytes. The effect of LLZO nanoparticle content on the lithium transport was investigated in detail using solid-state nuclear magnetic resonance spectroscopy (NMR). Finally, determination of the critical current density (CCD) before lithium dendrites are initiated has been carried out on both pristine and hybrid electrolytes, so as to assess their potential as solid electrolytes for lithium metal batteries.This work was supported by the European Commission’s funded Marie Sklodowska-Curie project POLYTE-EID (Project No. 765828). L.P. has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska–Curie grant agreement No 797295

ViralZone: recent updates to the virus knowledge resource

ViralZone (http://viralzone.expasy.org) is a knowledge repository that allows users to learn about viruses including their virion structure, replication cycle and host-virus interactions. The information is divided into viral fact sheets that describe virion shape, molecular biology and epidemiology for each viral genus, with links to the corresponding annotated proteomes of UniProtKB. Each viral genus page contains detailed illustrations, text and PubMed references. This new update provides a linked view of viral molecular biology through 133 new viral ontology pages that describe common steps of viral replication cycles shared by several viral genera. This viral cell-cycle ontology is also represented in UniProtKB in the form of annotated keywords. In this way, users can navigate from the description of a replication-cycle event, to the viral genus concerned, and the associated UniProtKB protein record

Parametric field modeling for the LHC main magnets in operating conditions

The first beam injections and current ramps in the LHC will require a prediction of the settings of the magnet current as well as the main correctors. For this reason we are developing a parametric model of the magnetic field generated by the LHC magnets that will provide the field dependence on current, ramp-rate, time, and history. The model of the field is fitted on magnetic field measurements performed during the acceptance tests of the magnets before their installation in the machine. In this paper we summarize the different steps necessary to select the relevant data and identify the parameters: the data extraction, the filtering and the validation of the measurements, and the fitting procedure that is used to obtain the parameters from the experimental results. The main result reported is a summary of the value of the parameters obtained with the above procedure, and describing the behavior of the magnetic field in the LHC main dipoles and quadrupoles.peer-reviewe

Chitosan as an antioxidant alternative to sulphites in oenology: EPR investigation of inhibitory mechanisms

The efficacy against oxidative degradation in model and sulphite-free white wines of two commercial, insoluble chitosans (one being approved for winemaking) were investigated by electron paramagnetic resonance (EPR). Both compounds at various doses significantly inhibited the formation of \u3b1-(4-pyridyl-1-oxide)-N-t-butylnitrone (4-POBN)-1-hydroxyethyl adducts under normal wine storage conditions. Pre-incubation with 2 g/L chitosan followed by filtration had a better effect than adding 50 mg/L sulphur dioxide to the experimental Chardonnay wine on the release of 4-POBN adducts after 6 days of incubation with 100 \u3bcM iron(II). In a relevant photooxidative system acetaldehyde formation was significantly reduced after 6 days of incubation. Parallel EPR tests were performed to assess the importance of metal chelation (iron and copper) versus direct scavenging of hydroxyl radicals on the effect of chitosan. The present data support the potentiality of using biocompatible chitosan as a healthier complement and/or alternative to sulphur dioxide against white wine oxidative spoilage