GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts

Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation will allow better data mining of genomes, and more secure planning and design of experiments. The purpose of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for Arabidopsis nuclear genes and gene products, and to enter them into an added-value database. This re-annotation project is being performed exhaustively on every member of each gene family. Performing a family-wide annotation makes the task easier and more efficient than a gene-by-gene approach since many features obtained for one gene can be extrapolated to some or all the other genes of a family. A complete annotation procedure based on the most efficient prediction tools available is being used by 16 partner laboratories, each contributing annotated families from its field of expertise. A database, named GeneFarm, and an associated user-friendly interface to query the annotations have been developed. More than 3000 genes distributed over 300 families have been annotated and are available at http://genoplante-info.infobiogen.fr/Genefarm/. Furthermore, collaboration with the Swiss Institute of Bioinformatics is underway to integrate the GeneFarm data into the protein knowledgebase Swiss-Pro

GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts

Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation will allow better data mining of genomes, and more secure planning and design of experiments. The purpose of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for Arabidopsis nuclear genes and gene products, and to enter them into an added-value database. This re-annotation project is being performed exhaustively on every member of each gene family. Performing a family-wide annotation makes the task easier and more efficient than a gene-by-gene approach since many features obtained for one gene can be extrapolated to some or all the other genes of a family. A complete annotation procedure based on the most efficient prediction tools available is being used by 16 partner laboratories, each contributing annotated families from its field of expertise. A database, named GeneFarm, and an associated user-friendly interface to query the annotations have been developed. More than 3000 genes distributed over 300 families have been annotated and are available at http://genoplante-info.infobiogen.fr/Genefarm/. Furthermore, collaboration with the Swiss Institute of Bioinformatics is underway to integrate the GeneFarm data into the protein knowledgebase Swiss-Prot

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

Scata-d’Ampugnani (Haute-Corse). Castellu di Lumitu

Mentionné dans diverses sources écrites médiévales, le site castral de Lumitu est bien connu de la population locale mais aussi des historiens et des archéologues insulaires. Le chroniqueur Giovanni della Grossa (1388-1464) l’évoque à plusieurs reprises et rappelle que le premier occupant du lieu s’appelait Guglielmo Cortinco, ancien fonctionnaire de l’administration comtale d’Arrigo Bel Messer. Après l’assassinat de ce dernier et le début de l’anarchie seigneuriale, il se fortifia sur cette ..

I. Psychologie générale

Andrieux C., Bloch Vincent, Bresson F., Ehrlich Stéphane, Florès César, Fraisse P, Oléron Geneviève, Orsini F., Vurpillot Eliane. I. Psychologie générale. In: L'année psychologique. 1956 vol. 56, n°2. pp. 597-610

I. Psychologie générale : Par F. Bresson, R. Chocholle, S. Ehrlich, C. Florès, P. Jampolsky, P. Oléron, F. Orsini, R. Perron, E. Vurpillot

Bresson F., Chocholle R., Ehrlich Stéphane, Florès César, Jampolsky P., Oléron Pierre, Orsini F., Perron R., Vurpillot Eliane. I. Psychologie générale : Par F. Bresson, R. Chocholle, S. Ehrlich, C. Florès, P. Jampolsky, P. Oléron, F. Orsini, R. Perron, E. Vurpillot. In: L'année psychologique. 1957 vol. 57, n°1. pp. 283-293

I. Psychologie générale

Andrieux C., Bloch Vincent, Bresson F., Ehrlich Stéphane, Florès César, Fraisse P, Oléron Geneviève, Orsini F., Vurpillot Eliane. I. Psychologie générale. In: L'année psychologique. 1956 vol. 56, n°2. pp. 597-610

I. Psychologie générale : Par F. Bresson, R. Chocholle, S. Ehrlich, C. Florès, P. Jampolsky, P. Oléron, F. Orsini, R. Perron, E. Vurpillot

Bresson F., Chocholle R., Ehrlich Stéphane, Florès César, Jampolsky P., Oléron Pierre, Orsini F., Perron R., Vurpillot Eliane. I. Psychologie générale : Par F. Bresson, R. Chocholle, S. Ehrlich, C. Florès, P. Jampolsky, P. Oléron, F. Orsini, R. Perron, E. Vurpillot. In: L'année psychologique. 1957 vol. 57, n°1. pp. 283-293

Clinical Outcome Predictive Value of Procalcitonin in Patients Suspected with Infection in the Emergency Department

Procalcitonin (PCT) may be useful for early risk stratification in the emergency department (ED), but the transposition of published data to routine emergency practice is sometimes limited. An observational retrospective study was conducted in the adult ED of the Reims University Hospital (France). Over one year, 852 patients suspected of infection were included, of mean age 61.7 years (SD: 22.6), and 624 (73.2%) were hospitalized following ED visit. Overall, 82 (9.6%) patients died during their hospitalization with an odds ratio (OR) of 5.10 (95% CI: 2.19–11.87) for PCT ≥ 0.5, in multivariate logistic regression analyses. Moreover, 78 (9.2%) patients were admitted to an ICU, 74 (8.7%) had attributable bacteremia, and 56 (6.6%) evolved toward septic shock with an OR of 4.37 (2.08–9.16), 6.38 (2.67–15.24), and 6.38 (2.41–16.86), respectively, for PCT ≥ 0.5. The highest discriminatory values were found for patients with age <65 years, but PCT lost its discrimination power for in-hospital mortality in patients with a bronchopulmonary infection site or a temperature ≥37.8°C and for ICU admission in patients with severe clinical presentations. PCT could be helpful in risk stratification, but several limitations must be considered, including being sometimes outperformed by a simple clinical examination

Lack of admission biomarkers' clinical utility in outcomes prediction in patients suspected with infection in the emergency department

International audienceIntroduction: Initial procalcitonin (PCT) levels may fail in mortality and septic shock prediction and raise cost-effectiveness issues. Since measurement of lactate, C-reactive protein (CRP), white blood cells and neutrophils is common in the emergency department (ED), we compared prediction abilities of these biomarkers to PCT.Methods: From January 1st to December 31st, 2018, an observational, single center, retrospective study was conducted in the adult ED of the Reims University Hospital (France). Endpoints were bacteremia, septic shock, and in-hospital mortality, related to the same ED visit.Results: Over one year, 459 patients suspected with infection were included, of mean age 60.4 years (SD: 22.0), with 50.8% male, and 364 (79.3%) were hospitalized following ED visit. Overall, 45 (9.8%) patients had a bacteremia, 39 (8.5%) a septic shock and 54 (11.8%) died during their hospitalization. PCT and CRP showed the best discrimination for bacteremia, with an area under curve (AUC) of 0.68 for PCT and 0.65 for CRP. PCT and lactate showed similar good discriminative power for septic shock, with an AUC of 0.78 for both, and poor discrimination for in-hospital mortality, with an AUC of 0.62 for PCT and 0.69 for lactate. Systolic blood pressure and pulse oximetry showed similar discrimination for septic shock as PCT or lactate, while they showed higher discrimination for in-hospital mortality than PCT.Conclusion: Usual admission biomarkers lack clinical utility in predicting septic shock or in-hospital mortality. CRP and PCT are poorly efficient in predicting bacteremia