Findings of the WMT 2020 Biomedical Translation Shared Task: Basque, Italian and Russian as New Additional Languages

Machine translation of scientific abstracts and terminologies has the potential to support health professionals and biomedical researchers in some of their activities. In the fifth edition of the WMT Biomedical Task, we addressed a total of eight language pairs. Five language pairs were previously addressed in past editions of the shared task, namely, English/German, English/French, English/Spanish, English/Portuguese, and English/Chinese. Three additional languages pairs were also introduced this year: English/Russian, English/Italian, and English/Basque. The task addressed the evaluation of both scientific abstracts (all language pairs) and terminologies (English/Basque only). We received submissions from a total of 20 teams. For recurring language pairs, we observed an improvement in the translations in terms of automatic scores and qualitative evaluations, compared to previous years

Evidence of the association of BIN1 and PICALM with the AD risk in contrasting European populations

Recent genome-wide association studies have identified five loci (BIN1, CLU, CR1, EXOC3L2 and PICALM) as genetic determinants of Alzheimer’s disease (AD). We attempted to confirm the association between these genes and the AD risk in three contrasting European populations (from Finland, Italy and Spain). Since CLU and CR1 had already been analyzed in these populations, we restricted our investigation to BIN1, EXO2CL3 and PICALM. In a total of 2,816 AD cases and 2,706 controls, we unambiguously replicated the association of rs744373 (for BIN1) and rs541458 (for PICALM) polymorphisms with the AD risk (OR=1.26, 95% CI [1.15-1.38], p=2.9x10-7, and OR=0.80, 95% CI [0.74-0.88], p=4.6x10-7, respectively). In a meta-analysis, rs597668 (EXOC3L2) was also associated with the AD risk, albeit to a lesser extent (OR=1.19, 95% CI [1.06-1.32], p=2.0x10-3). However, this signal did not appear to be independent of APOE. In conclusion, we confirmed that BIN1 and PICALM are genetic determinants of AD, whereas the potential involvement of EXOC3L2 requires further investigation

Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease

We sought to identify new susceptibility loci for Alzheimer's disease through a staged association study (GERAD+) and by testing suggestive loci reported by the Alzheimer's Disease Genetic Consortium (ADGC) in a companion paper. We undertook a combined analysis of four genome-wide association datasets (stage 1) and identified ten newly associated variants with P ≤ 1 × 10−5. We tested these variants for association in an independent sample (stage 2). Three SNPs at two loci replicated and showed evidence for association in a further sample (stage 3). Meta-analyses of all data provided compelling evidence that ABCA7 (rs3764650, meta P = 4.5 × 10−17; including ADGC data, meta P = 5.0 × 10−21) and the MS4A gene cluster (rs610932, meta P = 1.8 × 10−14; including ADGC data, meta P = 1.2 × 10−16) are new Alzheimer's disease susceptibility loci. We also found independent evidence for association for three loci reported by the ADGC, which, when combined, showed genome-wide significance: CD2AP (GERAD+, P = 8.0 × 10−4; including ADGC data, meta P = 8.6 × 10−9), CD33 (GERAD+, P = 2.2 × 10−4; including ADGC data, meta P = 1.6 × 10−9) and EPHA1 (GERAD+, P = 3.4 × 10−4; including ADGC data, meta P = 6.0 × 10−10)

Contacts et acculturations en Méditerranée occidentale

La question des contacts entre les différents peuples qui bordent les rives de la Méditerranée nord occidentale est l’un des sujets phares de la recherche archéologique de ces trente dernières années. Que l’on parle d’époque archaïque et classique ou de Protohistoire et d’âge du Fer, les échanges et les processus d’acculturation de ces peuples qui entrèrent alors en contact les uns avec les autres : Grecs, Celtes, Phéniciens, Ibères, Ligures, Étrusques, ont retenu l’attention des chercheurs travaillant sur l’expansion grecque dans ces régions, sur les trafics commerciaux, sur les échanges culturels. L’œuvre de Michel Bats (Directeur de recherche honoraire du CNRS) traverse toutes ces thématiques : la présence des Phocéens et des Étrusques dans le bassin occidental de la Méditerranée, l’acculturation et les identités ethno-culturelles, les recherches sur la céramique et ses usages dans une perspective anthropologique, l’appropriation de l’écriture par les sociétés protohistoriques. Ses collègues et amis, en organisant ce colloque et en participant à ces actes, entendent lui témoigner leur amitié et leur dette intellectuelle. Ce volume réunit des articles des meilleurs spécialistes, actuels de la question - des chercheurs de toute la Méditerranée - autour des quatre grands thèmes que nous venons d’évoquer afin tout à la fois de dresser un bilan et de définir de nouvelles perspectives. Cet ouvrage présente donc aussi bien des synthèses - sur la présence grecque en Espagne, sur l’origine de l’écriture, sur les pratiques funéraires, sur les identités culturelles et ethniques - que des découvertes récentes concernant la thématique des contacts et de l’acculturation en Méditerranée nord occidentale : l’agglomération du Premier âge du Fer de La Cougourlude (Lattes, Hérault) fouillée durant l’été 2010 ; le sanctuaire hellénistique de Cumes et les fouilles récentes de Fratte en Italie ; les ateliers de potiers de Rosas en Espagne ; les dernières découvertes d’Olbia de Provence

SociaI interactions within a synthetic microbial community

A key question in ecology and evolution is how species interact and what make a species help or harm another. Disentangling social interactions is extremely challenging without a thorough understanding of simpler systems. Here, we studied a semi-natural bacterial community composed of 4 species: Agrobacterium tumefaciens, Comamonas testosteroni, Microbacterium saperdae and Ochrobactrum anthropi. Together, these four species can degrade Metal Working Fluids (MWF), a toxic industrial product. By firstly analyzing the ecological interactions in these fluids, we found that facilitation dominated the bacterial community. However, the sign of interactions depended on the environment: in line with the Stress Gradient hypothesis, positive interactions were most common in the harsh MWF environment, but the four species competed when we made the environment more benign. To track how the positive interactions in the MWF community evolve over time, we next performed experimental evolution where we transferred the community into fresh culture weekly for 44 weeks. The co-evolved community was still dominated by facilitation and there was no evidence for inter-species competition, except when each species evolved alone. A. tumefaciens became autonomous and interacted more neutrally with co-evolved C. testosteroni, which initially supported its survival. Instead, M. saperdae and O. anthropi, that initially relied fully on others to survive continued to do so. Genetic analyses showed that, as one would expect according to the Black Queen hypothesis, co-evolving species lost more genetic material than when evolving alone, and species that still relied on others to grow lost even more. Since bacterial interactions differed between environmental conditions and over time, we then asked what interactions make a bacterial community more resistant to invasion. The growth of new bacterial isolates was promoted when they invaded the ancestral community in the harsh MWF environment. Instead, it was inhibited if they could grow alone in the more benign environment or when inoculated into the evolved community. Our work suggests that, although many environments can be difficult to colonize, species that arrive first may improve the environment and facilitate the survival and growth of others. However, late arriving species may be hindered when colonizing a previously co-evolved community. In line with the Community Monopolization hypothesis, this is presumably because community members have adapted to each other and occupied all available niches. Our work shows that interactions are context-dependent, a pattern that may be general to many microbial populations. -- Une des questions clef en écologie et évolution est de comprendre ce qui fait qu’une espèce peut aider ou nuire à la croissance d’une autre. Pour comprendre ces dynamiques, nous avons étudié une communauté bactérienne semi-naturelle composée de 4 espèces : Agrobacterium tumefaciens, Comamonas testosteroni, Microbacterium saperdae et Ochrobactrum anthropi. Celles-ci peuvent dégrader le Metal Working Fluid (MWF), un produit industriel toxique. En analysant les interactions écologiques, nous avons constaté que les quatre espèces inter- agissent positivement entre elles dans le MWF. Nous avons découvert que le type d’interaction dépend de l’environnement. Conformément à la Stress Gradient Hypothesis, les interactions positives étaient plus fréquentes dans un environnement toxique. En revanche, les espèces étaient en compétition dans un environnement moins toxique. Ensuite, nous avons effectué une experience afin de suivre l’évolution des interactions positives de la communauté dans le MWF. Chaque semaine, pendant 44 semaines, nous avons transféré la communauté dans une nouvelle culture. La communauté évoluée était dominée par les interactions positives. Nous n’avons trouvé aucune preuve de compétition inter-espèces, sauf lorsque chaque espèce évoluait seule. A. tumefaciens est devenue autonome et a interagi de manière plus neutre avec C. testosteroni, qui, initialement, soutenait sa survie. A contrario, M. saperdae et O. anthropi, qui au départ dépendaient des autres pour survivre, ont continué de le faire. Les analyses génétiques ont montré que, comme on pouvait s’y attendre selon la Black Queen hypothesis, les espèces co-évoluées ont perdu plus de matériel génétique que celles évoluant seules. En outre, les espèces dépendant des autres avaient perdu encore plus de matériel génétique. Étant donné la différence des interactions bactériennes entre les conditions environnementales et l’expérience évolutive, nous nous sommes demandés quelles interactions rendaient une communauté bactérienne plus résistante à l’invasion. La croissance des espèces invasives était favorisée lorsqu’elles envahissaient la communauté ancestrale dans le MWF. En revanche, la croissance était inhibée si l’envahisseur pouvait pousser seul dans un environnement moins toxique ou s’il était inoculé dans la communauté évoluée. Nos résultats suggèrent que, malgré la difficulté à coloniser de nombreux environnements, les espèces qui arrivent en premier peuvent l’améliorer et faciliter la survie des autres. Conformément à la Community Monopoli- zation hypothesis, les espèces invasives auront plus de difficulté à envahir une communauté qui a eu assez de temps pour s’adapter. Nous suggérons que la manière d’interagir dépend du contexte et que notre modèle peut être généralisé à d’autres populations microbiennes

Microbial invasion of a toxic medium is facilitated by a resident community but inhibited as the community co-evolves

Predicting whether microbial invaders will colonize an environment is critical for managing natural and engineered ecosystems, and controlling infectious disease. Invaders often face competition by resident microbes. But how invasions play out in communities dominated by facilitative interactions is less clear. We previously showed that growth medium toxicity can promote facilitation between four bacterial species, as species that cannot grow alone rely on others to survive. Following the same logic, here we allowed other bacterial species to invade the four-species community and found that invaders could more easily colonize a toxic medium when the community was present. In a more benign environment instead, invasive species that could survive alone colonized more successfully when the residents were absent. Next, we asked whether early colonists could exclude future ones through a priority effect, by inoculating the invaders into the resident community only after its members had co-evolved for 44 weeks. Compared to the ancestral community, the co-evolved resident community was more competitive toward invaders and less affected by them. Our experiments show how communities may assemble by facilitating one another in harsh, sterile environments, but that arriving after community members have co-evolved can limit invasion success.ISSN:1751-7362ISSN:1751-737