Du nom place aux verbes déplacer et replacer : quelques questions de legs et d’appropriations sémantiques

Dans leurs emplois spatiaux concrets les deux verbes replacer et déplacer illustrent deux modes d’exploitation différents du sens du nom d’espace place qui entre dans leur structure. Replacer est un verbe de déplacement qui utilise et respecte au plus près les spécificités sémantiques du nom en question, notamment sa vocation à la localisation substantielle. En effet, replacer X désigne un procès à polarité aspectuelle / locative finale qui consiste globalement à faire changer une substance X de place. Pour le verbe déplacer, si le changement de localisation concerne bien des substances, il n’est en revanche nullement restreint à un changement de localisation de type place (il peut s’agir aussi bien d’un changement de lieu ou d’emplacement), pas plus qu’il n’est restreint à une polarité aspectuelle ou locative particulière. Ce travail examine ce qui dans la structure sémantique de ces deux verbes permet d’expliquer ces différences de comportement.In their concrete spatial uses, the French verbs replacer “replace, put back” and déplacer “displace, move away” illustrate two different instanciations of the name place, on which they are based. Replacer is a verb of motion, which closely follows the semantic specificity of the name in question, namely its tendency to ‘substantially localize’. For instance, replacer X stands for a process with a final aspectual and locative polarity, which amounts to describing a change of place for the substance X. For the verb déplacer, the change of location also affects a substance, but it does not have to be a change of place in a restrictive sense, and neither is it linked to a specific aspectual or locative polarity. The aim of this study is to find an explanation for the differences in semantic behavior between these two verbs

EpIG‐DB: A database of vascular epiphyte assemblages in the Neotropics

Vascular epiphytes are a diverse and conspicuous component of biodiversity in tropical and subtropical forests. Yet, the patterns and drivers of epiphyte assemblages are poorly studied in comparison with soil‐rooted plants. Current knowledge about diversity patterns of epiphytes mainly stems from local studies or floristic inventories, but this information has not yet been integrated to allow a better understanding of large‐scale distribution patterns. EpIG‐DB, the first database on epiphyte assemblages at the continental scale, resulted from an exhaustive compilation of published and unpublished inventory data from the Neotropics. The current version of EpIG‐DB consists of 463,196 individual epiphytes from 3,005 species, which were collected from a total of 18,148 relevés (host trees and ‘understory’ plots). EpIG‐DB reports the occurrence of ‘true’ epiphytes, hemiepiphytes and nomadic vines, including information on their cover, abundance, frequency and biomass. Most records (97%) correspond to sampled host trees, 76% of them aggregated in forest plots. The data is stored in a TURBOVEG database using the most up‐to‐date checklist of vascular epiphytes. A total of 18 additional fields were created for the standardization of associated data commonly used in epiphyte ecology (e.g. by considering different sampling methods). EpIG‐DB currently covers six major biomes across the whole latitudinal range of epiphytes in the Neotropics but welcomes data globally. This novel database provides, for the first time, unique biodiversity data on epiphytes for the Neotropics and unified guidelines for future collection of epiphyte data. EpIG‐DB will allow exploration of new ways to study the community ecology and biogeography of vascular epiphytes

Genome-wide identification and phenotypic characterization of seizure-associated copy number variations in 741,075 individuals

Copy number variants (CNV) are established risk factors for neurodevelopmental disorders with seizures or epilepsy. With the hypothesis that seizure disorders share genetic risk factors, we pooled CNV data from 10,590 individuals with seizure disorders, 16,109 individuals with clinically validated epilepsy, and 492,324 population controls and identified 25 genome-wide significant loci, 22 of which are novel for seizure disorders, such as deletions at 1p36.33, 1q44, 2p21-p16.3, 3q29, 8p23.3-p23.2, 9p24.3, 10q26.3, 15q11.2, 15q12-q13.1, 16p12.2, 17q21.31, duplications at 2q13, 9q34.3, 16p13.3, 17q12, 19p13.3, 20q13.33, and reciprocal CNVs at 16p11.2, and 22q11.21. Using genetic data from additional 248,751 individuals with 23 neuropsychiatric phenotypes, we explored the pleiotropy of these 25 loci. Finally, in a subset of individuals with epilepsy and detailed clinical data available, we performed phenome-wide association analyses between individual CNVs and clinical annotations categorized through the Human Phenotype Ontology (HPO). For six CNVs, we identified 19 significant associations with specific HPO terms and generated, for all CNVs, phenotype signatures across 17 clinical categories relevant for epileptologists. This is the most comprehensive investigation of CNVs in epilepsy and related seizure disorders, with potential implications for clinical practice

GWAS meta-analysis of over 29,000 people with epilepsy identifies 26 risk loci and subtype-specific genetic architecture

Epilepsy is a highly heritable disorder affecting over 50 million people worldwide, of which about one-third are resistant to current treatments. Here we report a multi-ancestry genome-wide association study including 29,944 cases, stratified into three broad categories and seven subtypes of epilepsy, and 52,538 controls. We identify 26 genome-wide significant loci, 19 of which are specific to genetic generalized epilepsy (GGE). We implicate 29 likely causal genes underlying these 26 loci. SNP-based heritability analyses show that common variants explain between 39.6% and 90% of genetic risk for GGE and its subtypes. Subtype analysis revealed markedly different genetic architectures between focal and generalized epilepsies. Gene-set analyses of GGE signals implicate synaptic processes in both excitatory and inhibitory neurons in the brain. Prioritized candidate genes overlap with monogenic epilepsy genes and with targets of current antiseizure medications. Finally, we leverage our results to identify alternate drugs with predicted efficacy if repurposed for epilepsy treatment

ATLANTIC EPIPHYTES: a data set of vascular and non-vascular epiphyte plants and lichens from the Atlantic Forest

Epiphytes are hyper-diverse and one of the frequently undervalued life forms in plant surveys and biodiversity inventories. Epiphytes of the Atlantic Forest, one of the most endangered ecosystems in the world, have high endemism and radiated recently in the Pliocene. We aimed to (1) compile an extensive Atlantic Forest data set on vascular, non-vascular plants (including hemiepiphytes), and lichen epiphyte species occurrence and abundance; (2) describe the epiphyte distribution in the Atlantic Forest, in order to indicate future sampling efforts. Our work presents the first epiphyte data set with information on abundance and occurrence of epiphyte phorophyte species. All data compiled here come from three main sources provided by the authors: published sources (comprising peer-reviewed articles, books, and theses), unpublished data, and herbarium data. We compiled a data set composed of 2,095 species, from 89,270 holo/hemiepiphyte records, in the Atlantic Forest of Brazil, Argentina, Paraguay, and Uruguay, recorded from 1824 to early 2018. Most of the records were from qualitative data (occurrence only, 88%), well distributed throughout the Atlantic Forest. For quantitative records, the most common sampling method was individual trees (71%), followed by plot sampling (19%), and transect sampling (10%). Angiosperms (81%) were the most frequently registered group, and Bromeliaceae and Orchidaceae were the families with the greatest number of records (27,272 and 21,945, respectively). Ferns and Lycophytes presented fewer records than Angiosperms, and Polypodiaceae were the most recorded family, and more concentrated in the Southern and Southeastern regions. Data on non-vascular plants and lichens were scarce, with a few disjunct records concentrated in the Northeastern region of the Atlantic Forest. For all non-vascular plant records, Lejeuneaceae, a family of liverworts, was the most recorded family. We hope that our effort to organize scattered epiphyte data help advance the knowledge of epiphyte ecology, as well as our understanding of macroecological and biogeographical patterns in the Atlantic Forest. No copyright restrictions are associated with the data set. Please cite this Ecology Data Paper if the data are used in publication and teaching events. © 2019 The Authors. Ecology © 2019 The Ecological Society of Americ

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Du statut des séquences non dénominatives construites par dérivation

International audienceFrancine Gerhard-Krait revisite le statut des séquences non dénominatives construites par dérivation, c’est-à-dire des désignations occasionnelles dont elle précise les propriétés sémantiques et référentielles. Après quelques précisions théoriques et méthodologiques, elle évoque les difficultés à vérifier le statut dénominatif des séquences construites (SC) non lemmatisées dans les grands dictionnaires et pointe ce qui brouille la frontière entre séquences construites sémantiquement codées et non codées. Elle montrer ensuite ce qui peut rapprocher les SC non lexicalement codées d’une « désignation occasionnelle ». Quelques prolongements sur la possible confusion entre motivation sémantique des SC et sens lexical permettront de conclure

Du statut des séquences non dénominatives construites par dérivation

International audienceFrancine Gerhard-Krait revisite le statut des séquences non dénominatives construites par dérivation, c’est-à-dire des désignations occasionnelles dont elle précise les propriétés sémantiques et référentielles. Après quelques précisions théoriques et méthodologiques, elle évoque les difficultés à vérifier le statut dénominatif des séquences construites (SC) non lemmatisées dans les grands dictionnaires et pointe ce qui brouille la frontière entre séquences construites sémantiquement codées et non codées. Elle montrer ensuite ce qui peut rapprocher les SC non lexicalement codées d’une « désignation occasionnelle ». Quelques prolongements sur la possible confusion entre motivation sémantique des SC et sens lexical permettront de conclure

Du nom place aux verbes déplacer et replacer : quelques questions de legs et d’appropriations sémantiques

In their concrete spatial uses, the French verbs replacer “replace, put back” and déplacer “displace, move away” illustrate two different instanciations of the name place, on which they are based. Replacer is a verb of motion, which closely follows the semantic specificity of the name in question, namely its tendency to ‘substantially localize’. For instance, replacer X stands for a process with a final aspectual and locative polarity, which amounts to describing a change of place for the substance X. For the verb déplacer, the change of location also affects a substance, but it does not have to be a change of place in a restrictive sense, and neither is it linked to a specific aspectual or locative polarity. The aim of this study is to find an explanation for the differences in semantic behavior between these two verbs