Identification, alignement, et traductions des adjectifs relationnels en corpus comparables

National audienceRÉSUMÉ Dans cet article, nous extrayons des adjectifs relationnels français et nous les alignons automatiquement avec les noms dont ils sont dérivés en utilisant un corpus monolingue. Les alignements adjectif-nom seront ensuite utilisés dans la traduction compositionelle des termes complexes de la forme [N AdjR] à partir d'un corpus comparable français-anglais. Un nouveau terme [N N ï¿¿ ] (ex. cancer du poumon) sera obtenu en remplaçant l'adjectif relationnel Ad jR (ex. pulmonaire) dans [N AdjR] (ex. cancer pulmonaire) par le nom N ï¿¿ (ex. poumon) avec lequel il est aligné. Si aucune traduction n'est proposée pour [N AdjR], nous considérons que ses traduction(s) sont équivalentes à celle(s) de sa paraphrase [N N ï¿¿ ]. Nous expérimentons avec un corpus comparable dans le domaine de cancer du sein, et nous obtenons des alignements adjectif-nom qui aident à traduire des termes complexes de la forme [N AdjR] vers l'anglais avec une précision de 86 %. ABSTRACT Identification, Alignment, and Tranlsation of Relational Adjectives from Comparable Corpora In this paper, we extract French relational adjectives and automatically align them with the nouns they are derived from by using a monolingual corpus. The obtained adjective-noun alignments are then used in the compositional translation of compound nouns of the form [N ADJR] with a French-English comparable corpora. A new term [N N ï¿¿ ] (eg, cancer du poumon) is obtained by replacing the relational adjective Ad jR (eg, pulmonaire) in [N AdjR] (eg, cancer pulmonaire) by its corresponding N ï¿¿ (eg, poumon). If no translation(s) are obtained for [N AdjR], we consider the one(s) obtained for its paraphrase [N N ï¿¿ ]. We experiment with a comparable corpora in the field of breast cancer, and we get adjective-noun alignments that help in translating French compound nouns of the form [N AdjR] to English with a precision of 86%

Différentes interprétations d'un modèle de RI à base d'inclusion graduelle

National audienceRécemment, un modèle théorique de RI à base d'inclusion graduelle a été proposé (Bosc et al., 2008b). Dans ce modèle, dérivé de la division de relations floues, l'inclusion gra- duelle d'une requête dans un document est modélisée par une implication floue. Dans des tra- vaux précédents, nous avons montré que ce modèle pouvait être interprété comme un modèle vectoriel sous certaines conditions. Dans cet article, nous proposons d'explorer d'autres inter- prétations possibles offertes par la modélisation à base d'inclusion graduelle. Nous montrons notamment qu'il est possible d'interpréter notre système flou comme un système de RI à base de modèles de langues, et nous revenons sur les liens entre le modèle flou et les modèles logiques de RI. Plus généralement, nous essayons de clarifier les liens existants entre ces différents mo- dèles, vus sous l'angle de notre SRI flou. RÉSUMÉ. Recently, a theoretical fuzzy IR system, based on gradual inclusion measures, has been proposed (Bosc et al., 2008b). In this model, derived from the division of fuzzy relations, the gradual inclusion of a query in a document is modeled by a fuzzy implication. In previous papers, we have shown that, under some assumptions, this model can be seen as a Vector Space Model. This paper also studies other itnerpretations of our fuzzy IR models based on gradual inclusions. It is shown that the fuzzy models can be interpreted as language models for IR. The links with logical models to IR are also recalled. More generaly, this paper discusses the links between these models, shown from the angle of our fuzzy models

Prevalence of Bourbon and Heartland viruses in field collected ticks at an environmental field station in St. Louis County, Missouri, USA

Heartland and Bourbon viruses are pathogenic tick-borne viruses putatively transmitted by Amblyomma americanum, an abundant tick species in Missouri. To assess the prevalence of these viruses in ticks, we collected 2778 ticks from eight sampling sites at Tyson Research Center, an environmental field station within St. Louis County and close to the City of St. Louis, from May - July in 2019 and 2021. Ticks were pooled according to life stage and sex, grouped by year and sampling site to create 355 pools and screened by RT-qPCR for Bourbon and Heartland viruses. Overall, 14 (3.9%) and 27 (7.6%) of the pools were positive for Bourbon virus and Heartland virus respectively. In 2019, 11 and 23 pools were positive for Bourbon and Heartland viruses respectively. These positives pools were of males, females and nymphs. In 2021, there were 4 virus positive pools out of which 3 were positive for both viruses and were comprised of females and nymphs. Five out of the 8 sampling sites were positive for at least one virus. This included a site that was positive for both viruses in both years. Detection of these viruses in an area close to a relatively large metropolis presents a greater public health threat than previously thought

6-Thioguanine blocks SARS-CoV-2 replication by inhibition of PLpro

The emergence of SARS-CoV-2 has led to a global health crisis that, in addition to vaccines and immunomodulatory therapies, calls for the identification of antiviral therapeutics. The papain-like protease (PLpro) activity of nsp3 is an attractive drug target as it is essential for viral polyprotein cleavage and for deconjugation of ISG15, an antiviral ubiquitin-like protein. We show here that 6-Thioguanine (6-TG), an orally available and widely available generic drug, inhibits SARS-CoV-2 replication in Vero-E6 cells with an EC50 of approximately 2 μM. 6-TG also inhibited PLpro-catalyzed polyprotein cleavage and de-ISGylation in cells and inhibited proteolytic activity of the purified PLpro domai

A simplified quantitative real-time PCR assay for monitoring SARS-CoV-2 growth in cell culture

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected millions within just a few months, causing severe respiratory disease and mortality. Assays to monitor SARS-CoV-2 growt

A single intranasal or intramuscular immunization with chimpanzee adenovirus-vectored SARS-CoV-2 vaccine protects against pneumonia in hamsters

The development of an effective vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of coronavirus disease 2019 (COVID-19), is a global priority. Here, we compare the protective capacity of intranasal and intramuscular delivery of a chimpanzee adenovirus-vectored vaccine encoding a prefusion stabilized spike protein (chimpanzee adenovirus [ChAd]-SARS-CoV-2-S) in Golden Syrian hamsters. Although immunization with ChAd-SARS-CoV-2-S induces robust spike-protein-specific antibodies capable of neutralizing the virus, antibody levels in serum are higher in hamsters vaccinated by an intranasal compared to intramuscular route. Accordingly, against challenge with SARS-CoV-2, ChAd-SARS-CoV-2-S-immunized hamsters are protected against less weight loss and have reduced viral infection in nasal swabs and lungs, and reduced pathology and inflammatory gene expression in the lungs, compared to ChAd-control immunized hamsters. Intranasal immunization with ChAd-SARS-CoV-2-S provides superior protection against SARS-CoV-2 infection and inflammation in the upper respiratory tract. These findings support intranasal administration of the ChAd-SARS-CoV-2-S candidate vaccine to prevent SARS-CoV-2 infection, disease, and possibly transmission

JIB-04 has broad-spectrum antiviral activity and inhibits SARS-CoV-2 replication and coronavirus pathogenesis

Pathogenic coronaviruses are a major threat to global public health. Here, using a recombinant reporter virus-based compound screening approach, we identified small-molecule inhibitors that potently block the replication of severe acute respiratory syndrome virus 2 (SARS-CoV-2). Among them, JIB-04 inhibited SARS-CoV-2 replication in Vero E6 cells with a 50% effective concentration of 695 nM, with a specificity index of greater than 1,000. JIB-04 showe

Advances in Xmipp for cryo-electron microscopy: from Xmipp to Scipion

Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and electron tomography, designed and managed by the Biocomputing Unit of the Spanish National Center for Biotechnology, although with contributions from many other developers over the world. During its 25 years of existence, Xmipp underwent multiple changes and updates. While there were many publications related to new programs and functionality added to Xmipp, there is no single publication on the Xmipp as a package since 2013. In this article, we give an overview of the changes and new work since 2013, describe technologies and techniques used during the development, and take a peek at the future of the package

Développement de méthodes d'analyse d'images pour les études in vitro et in situ de la variabilité conformationnelle des complexes biomoléculaires par cryo-tomographie électronique : cas d'études de la structure et de la dynamique des nucléosomes

Cryogenic electron tomography (cryo-ET) allows visualizing biomolecular complexes in situ. 3D data of biomolecules produced using cryo-ET are noisy, suffer from spacial anisotropies, and are difficult to analyze individually. Biomolecules are flexible, and analyzing their conformational variability is necessary to understand their functional mechanisms. Standard cryo-ET data processing methods average multiple copies of individual biomolecules to obtain structures at higher resolutions and consider that biomolecular conformational variability is discrete rather than continuous using the classification. This thesis presents the first two cryo-ET data processing methods for analyzing biomolecular continuous conformational variability, HEMNMA-3D and TomoFlow. HEMNMA-3D analyzes experimental data with the motion directions simulated by Normal Mode Analysis and allows the discovery of a large range of biomolecular motions. TomoFlow extracts motions from the data using the computer vision technique of Optical Flow. I show the potential of these two methods on experimental cryo-ET data of nucleosome conformational variability in cells. The two methods show coherent results, shedding light on the conformational variability of nucleosomes in cells.La tomographie électronique cryogénique (cryo-TE) permet de visualiser des complexes biomoléculaires in situ. Les données 3D de biomolécules produites à l'aide de cryo-ET sont bruitées, souffrent d'anisotropies spatiales et sont difficiles à analyser individuellement. Les biomolécules sont flexibles et l'analyse de leur variabilité conformationnelle est nécessaire pour comprendre leurs mécanismes fonctionnels. Les méthodes standards de traitement de données de cryo-ET moyennent plusieurs copies de biomolécules individuelles pour obtenir des structures à des résolutions plus élevées et considèrent que la variabilité conformationnelle biomoléculaire est discrète plutôt que continue en utilisant la classification. Cette thèse présente les deux premières méthodes de traitement de données cryo-ET pour l'analyse de la variabilité conformationnelle continue biomoléculaire, HEMNMA-3D et TomoFlow. HEMNMA-3D analyse des données expérimentales avec les directions de mouvement simulées par l'Analyse de Modes Normaux et permet la découverte d'une large gamme de mouvements biomoléculaires. TomoFlow extrait des mouvements à partir des données en utilisant la technique de vision par ordinateur de Flux Optique. Je montre le potentiel de ces deux méthodes sur des données cryo-ET expérimentales de variabilité conformationnelle des nucléosomes dans les cellules. Les deux méthodes montrent des résultats cohérents, faisant la lumière sur la variabilité conformationnelle des nucléosomes dans les cellules