Invariant scaling relationship between functional dissimilarity and co-occurrence in fish assemblages of the Patos Lagoon estuary (Brazil): environmental filtering consistently overshadows competitive exclusion

Determining how assembly rules (e.g. limiting similarity, environmental filtering and neutrality) shape community structure along environmental gradients and across spatial scales is still controversial. The study of functional relationships between coexisting species may help to disentangle among these assembly rules. Here, we compared pairwise functional dissimilarities between fish species to their corresponding pairwise co-occurrences. Fish assemblages (n = 835) were sampled monthly in Patos-Mirim system (Brazil) using both bottom trawling and beach seining. Species occurrences were recorded and functional traits related to locomotion and food acquisition were measured on several individuals from each species. The region studied was divided in two areas corresponding to each side of a floodgate located in São Gonçalo Channel: a freshwater channel up the floodgate and, down the floodgate, the Patos Lagoon estuary. The relationship between functional dissimilarity and co-occurrence between species pairs was assessed using quantile regressions for each month and at different spatial scales. Overall, quantile regression coefficients between functional dissimilarities (either based on locomotion types or feeding habits) and co-occurrence values were negative, suggesting that co-occurrence increases with functional redundancy regardless of spatial scale. Our results support the assumption that environmental filters have more influence than biotic interactions on the structure of fish assemblages even locally

In lab and in situ assessment of pesticide effects on aquatic organisms: key role of groundwater monitoring of Ariège alluvial plain (France).

International audiencePesticides emitted into the environment may contribute to complex mixtures including the parent molecules, degradates in association with other pollutants. It is of paramount importance to implement suitable monitoring procedures to assess the fate of pesticides, their transfer to groundwater and the effects of water quality on aquatic and terrestrial organisms. The alluvial domain of the Ariège River (about 538 km2) is an unconfined aquifer, the thin thickness of vadose zone making it vulnerable to contamination. The aquifer is in direct hydraulic connection with rivers Ariège and Hers Vif and feeds them during much of the year. As a result, the quality of surface water is highly influenced by groundwater quality. Due to intensive agriculture in this area, related to corn cultivation in particular, groundwater quality is affected by pesticides and some of their metabolites. Monthly monitoring of water quality at 16 water points in the plain was initiated in March 2009 and is still on-going. It includes some 50 organic molecules, major ions such as nitrate and other nonconservative parameters (pH, temperature, redox potential). A strong spatial variability of the contamination was demonstrated, with predominance of degradation products over parent molecules in some locations, and also showed a strong temporal variability. Besides aiming at a better understanding of the pesticides' fate, our study also addresses the effects of altered water quality on various aquatic organisms. Laboratory ecotoxicological tests calibrated with realistic environmental concentrations found in the aquifer and accounting for proportion of the different molecules were performed. In parallel, investigations of in situ exposures were better controlled. Spatial and temporal distribution of the microbial diversity in groundwater is followed to evaluate its relevance as bioindicators. Macro-organisms restricted to groundwater (hypogean organisms such as isopods or amphipods) are investigated in situ at the scale of species, populations and communities while acute and chronic toxicities are determined in laboratory. First results on amphibians, also studied, showed that the contamination of surface water affects populations (richness) in the environment while in most cases no toxicity has been demonstrated in Xenopus larvae. To our knowledge this project may be the first investigation of the effects of pesticides on these three types of organisms using both lab and aquifer studies

How to Improve Cancer Patients ENrollment in Clinical Trials From rEal-Life Databases Using the Observational Medical Outcomes Partnership Oncology Extension: Results of the PENELOPE Initiative in Urologic Cancers

International audiencePURPOSE To compare the computability of Observational Medical Outcomes Partnership (OMOP)–based queries related to prescreening of patients using two versions of the OMOP common data model (CDM; v5.3 and v5.4) and to assess the performance of the Greater Paris University Hospital (APHP) prescreening tool.MATERIALS AND METHODS We identified the prescreening information items being relevant for prescreening of patients with cancer. We randomly selected 15 academic and industry-sponsored urology phase I-IV clinical trials (CTs) launched at APHP between 2016 and 2021. The computability of the related prescreening criteria (PC) was defined by their translation rate in OMOP-compliant queries and by their execution rate on the APHP clinical data warehouse (CDW) containing data of 205,977 patients with cancer. The overall performance of the prescreening tool was assessed by the rate of true- and false-positive cases of three randomly selected CTs.RESULTS We defined a list of 15 minimal information items being relevant for patients' prescreening. We identified 83 PC of the 534 eligibility criteria from the 15 CTs. We translated 33 and 62 PC in queries on the basis of OMOP CDM v5.3 and v5.4, respectively (translation rates of 40% and 75%, respectively). Of the 33 PC translated in the v5.3 of the OMOP CDM, 19 could be executed on the APHP CDW (execution rate of 58%). Of 83 PC, the computability rate on the APHP CDW reached 23%. On the basis of three CTs, we identified 17, 32, and 63 patients as being potentially eligible for inclusion in those CTs, resulting in positive predictive values of 53%, 41%, and 21%, respectively. CONCLUSION We showed that PC could be formalized according to the OMOP CDM and that the oncology extension increased their translation rate through better representation of cancer natural history

AP-HP Health Data Space (AHDS) to the Test of the Covid-19 Pandemic

Sharing observational and interventional health data within a common data space enables university hospitals to leverage such data for biomedical discovery and moving towards a learning health system. Objective: To describe the AP-HP Health Data Space (AHDS) and the IT services supporting piloting, research, innovation and patient care. Methods: Built on three pillars – governance and ethics, technology and valorization – the AHDS and its major component, the Clinical Data Warehouse (CDW) have been developed since 2015. Results: The AP-HP CDW has been made available at scale to AP-HP both healthcare professionals and public or private partners in January 2017. Supported by an institutional secured and high-performance cloud and an ecosystem of tools, mostly open source, the AHDS integrates a large amount of massive healthcare data collected during care and research activities. As of December 2021, the AHDS operates the electronic data capture for almost +840 clinical trials sponsored by AP-HP, the CDW is enabling the processing of health data from more than 11 million patients and generated +200 secondary data marts from IRB authorized research projects. During the Covid-19 pandemic, AHDS has had to evolve quickly to support administrative professionals and caregivers heavily involved in the reorganization of both patient care and biomedical research. Conclusion: The AP-HP Data Space is a key facilitator for data-driven evidence generation and making the health system more efficient and personalized

Interposição jejunal após gastrectomia total radical por adenocarcinoma gástrico

Realizamos um estudo retrospectivo do tratamento cirúrgico do adenocarcinoma gástrico por uma gastrectomia total radical, com reconstrução do trânsito esofagoduodenal pela interposição de uma alça jejunal pediculada. Revisão de trabalhos nacionais e estrangeiros relacionados ao tratamento do adenocarcinoma gástrico pela gastrectomia total radical. De acordo com a operabilidade relacionada ao paciente e à ressecabilidade, à lesão primária e sua evolução, 126 pacientes foram submetidos à interposição de um segmento de alça jejunal após gastrectomia total radical. Ressecção oncológica total do estômago e sistematizada reconstrução técnica do reservatório gástrico e do trânsito esofagoduodenal. Nossos casos evoluíram de maneira satisfatória, não fugindo daqueles estudados na literatura. Ênfase especial foi dada ao procedimento técnico, mais anatômico e muito mais funcional, restituindo ao operado um neoestômago e um trânsito esôfago-intestinal através do duodeno. A interposição de uma alça jejunal pediculada entre o esôfago terminal e a segunda porção do duodeno age como neo-reservatório gástrico. Evita o refluxo esofágico e direciona o bolo alimentar para o delgado através do duodeno, trânsito anatômico e funcional capaz de proporcionar melhor qualidade de vida ao gastrectomizado total