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Machine learning based screening of potential paper mill publications in cancer research: methodological and cross sectional study
No full textInternational audienceAbstract Objectives To train and validate a machine learning model to distinguish paper mill publications from genuine cancer research articles, and to screen the cancer research literature to assess the prevalence of papers that have textual similarities to paper mill papers. Design Methodological and cross sectional study applying a BERT (bidirectional encoder representations from transformers) based, text classification model to article titles and abstracts. Setting Retracted paper mill publications listed in the Retraction Watch database were used for model training. The cancer research corpus was screened by the model using the PubMed database restricted to original cancer research articles published between 1999 and 2024. Population The model was trained on 2202 retracted paper mill papers and validated on independent data collected by image integrity experts. 2.6 million cancer research papers were screened. Main outcome measures Classification performance of the model. Prevalence of papers flagged as similar to retracted paper mill publications with 95% confidence intervals and their distribution over time, by country, publisher, cancer type, research area, and within high impact journals (top 10%). Results The model achieved an accuracy of 0.91. When applied to the cancer research literature, it flagged 261 245 of 2 647 471 papers (9.87%, 95% confidence interval 9.83 to 9.90) and revealed a large increase in flagged papers from 1999 to 2024, both across the entire corpus and in the top 10% of journals by impact factor. More than 170 000 papers affiliated with Chinese institutions were flagged, accounting for 36% of Chinese cancer research articles. Most publishers had published substantial numbers of flagged papers. Flagged papers were overrepresented in fundamental research and in gastric, bone, and liver cancer. Conclusions Paper mills are a large and growing problem in the cancer literature and are not restricted to low impact journals. Collective awareness and action will be crucial to address the problem of paper mill publications
How to organise a scientific competition to benchmark methods and algorithms in computational biology?
No full textScientific competitions have driven methodological innovation in artificial intelligence and machine learning, yet remain underutilized in computational biology. This paper provides a comprehensive guide for organizing scientific competitions in bioinformatics, based on our experience with HADACA3, a data challenge focused on deconvolution algorithms for predicting cellular composition in cancer, from multi-omics data. We detail the complete organizational workflow from preparation to execution to postanalysis, offering practical strategies and lessons learned. Beyond advancing multiomics deconvolution methods, HADACA3 demonstrated how expert-guided competitions foster methodological development, scientific exploration, and collaborative networking. By sharing our organizational framework, we aim to democratize scientific competitions as a fundamental methodology for developing and benchmarking computational methods in life sciences.</div
Designing and evaluating livestock farming systems that promote biodiversity: example of a student project
No full textThis issu follows on from the Carrefour de l'innovation agronomique, forum dedicated to Grazing livestock : the contribution of biodiversity, from soils to landscapes event that took place on 12 December 2024 at the Institut Agro in Rennes, France. It provide an update on knowledge and feedback showing the trajectories of agroecological livestock farms that make the most of wild and domestic biodiversity and the interactions between them. The development of agroecological practices is necessary to adapt agri-food systems to climate change and its impacts, and to mitigate their environmental impact. Biodiversity has been identified as a key factor in the sustainability of farming systems in their environmental ecosystems, combining the genetic diversity of domestic species with that of wild species. This Agronomic Innovation Forum will present results on domestic biodiversity in herbivore farming and the environmental biodiversity impacted and mobilised, from the scale of soils to that of landscapes.International audienceThe article presents a project carried out at Institut Agro Rennes Angers for agronomy engineering students and second-year master's students specialising in animal production. The 24-hour pedagogical framework aimed at designing resilient and acceptable livestock systems that promote biodiversity. The objective was to develop skills in systemic analysis and multi-criteria assessment through collaborative work. The students used LEGO® to model livestock systems and evaluate transformation scenarios for a mixed farming operation in the Rennes region. Two scenarios were proposed and assessed using a grid created by the students. The results show that the scenarios strengthen the connection between society and biodiversity. Feedback from teachers highlights the importance of project-based learning and the need to adapt teaching to students' profiles
Transgenerational response to the ingestion of an endocrine disruptor: phenotypic, genetic, and epigenetic analyses in quail
No full textInternational audienceEpigenetic mechanisms such as DNA methylation can mediate the effect of the environment on an individual's phenotypes. While parental environments have also been shown to affect offspring phenotypes in several livestock species, evidence for transgenerational inheritance of environmentally induced epigenetic marks remains debated.This study aimed to assess the potential transgenerational inheritance of an environmental effect via epigenetic modifications in Japanese quails (Coturnix japonica). We investigated whether an initial dietary exposure to genistein - a natural phytoestrogen found in soybeans - could induce lasting phenotypic and epigenetic changes in subsequent generations.To disentangle genetic from epigenetic effects, we designed a balanced “mirror-crossing” scheme based on 20 founder families. In each family, two sisters were mated to the same male: one received a 30-day genistein supplementation (epi+ line), while the other was kept as a control, without genistein (epi– line). Their offspring were mated within each 'epiline' for three generations (G0–G2), ensuring a balanced representation of each genetic background in both epilines. Phenotypic data (body and tissue weights, egg production, and behavioral traits) were collected across all generations. DNA methylation profiles and genotypes were obtained from Reduced Representation Bisulfite Sequencing of 1,344 individual blood samples using BISCUIT, which allows jointly methylation and SNP calling. Differential methylation analysis was performed using the DSS package. Methylation heritability and methylation QTLs (metQTLs) were assessed with GCTA.Significant differences between epilines were detected for body weight. Epi+ females were consistently heavier than epi– controls at all ages, with the difference increasing across generations (up to +14 g in G2). A similar, though delayed, pattern was observed in males, becoming significant in G2 (+9 g at slaughter). Other traits, including reproduction and behavior, were not significantly affected. The proportion of phenotypic variance explained by the epiline increased over generations, suggesting either a genetic drift or non-genetic inherited effects.Methylation calling yielded 448,673 CpG sites in 1,267 individuals (mean coverage 34×). Among 111,168 variable CpGs (SD > 0.05), 22 and 72 were differentially methylated between epilines in G1 and G2, respectively, while no significant differences were detected in G0. A large number of CpGs showed significant sex × epiline interactions. The mean methylation heritability (h² = 0.24) supported moderate genetic control of methylation levels, with a high variability between CpGs.Ongoing analyses will contribute to a better understanding of the molecular mechanisms and biological significance of non-genetic inheritance in avian models.This project is funded by the European Union’s Horizon 2020 program GEroNIMO N°101000236, part of EuroFAANG (https://eurofaang.eu)
A Modern Guide to the Social and Solidarity Economy
No full textInternational audienceThis Modern Guide presents a comprehensive synthesis of contemporary knowledge on the social and solidarity economy (SSE). It provides an overview of the conceptual, historical, organizational, and developmental dimensions of the SSE, exploring current issues through the lenses of public policy, governance, finance, and legislation
Bénéfices des aliments fermentés, de l’empirisme aux démonstrations scientifiques : l’apport de Ferments du Futur
No full textInternational audienceFermentation has held a central place in human nutrition for millennia, both for the preservation of perishable goods and for their transformation. Fermented foods indeed have unique sensory properties, in addition to health benefits that are increasingly well-documented. Furthermore, fermentation contributes to the sustainability of our food systems. As we move towards more natural, healthy and sustainable diets, fermentation represents a key technology for transforming agri-food systems. The Ferments du Futur (FdF) initiative, led by INRAE and ANIA with the support of France 2030, aims to develop new ferments, to improve fermentation processes and to create high added-value fermented foods, drawing on biotechnologies, data science and public–private collaborations. This article outlines the major benefits associated with fermentation: food safety, sensory properties, nutrition and health and environmental impact, while highlighting the concrete solutions that FdF will provide, through its projects and technological platforms.La fermentation occupe une place centrale dans l’alimentation humaine depuis des millénaires, pour la conservation des denrées périssables mais aussi pour leur transformation. Les aliments fermentés ont en effet des propriétés sensorielles uniques, auxquelles s’ajoute un bénéfice santé de mieux en mieux documenté. La fermentation contribue par ailleurs à la durabilité de nos systèmes alimentaires. Dans un contexte de transition vers une alimentation plus naturelle, plus saine et plus durable, la fermentation émerge comme une solution innovante pour transformer les systèmes agroalimentaires. L’initiative Ferments du Futur (FdF), portée par INRAE et l’ANIA dans le cadre de France 2030, vise à développer de nouveaux ferments, améliorer les procédés de fermentation et créer des aliments fermentés à haute valeur ajoutée, en s’appuyant sur les biotechnologies, les sciences des données et un dialogue poussé entre acteurs publics et privés. Cet article présente les grands enjeux associés à la fermentation : sécurité des aliments, propriétés sensorielles, nutrition et santé, impact environnemental, tout en illustrant les solutions concrètes qu’apportera FdF, notamment via ses projets et plateformes technologiques
Functional performance of constructed technosols as a soil management solution for urban green infrastructure
No full textInternational audienceUrban green infrastructure (UGI) requires functional soils, yet sourcing fertile topsoil and natural aggregates cancreate environmental trade-offs. This study evaluated the performance of waste-derived constructed Technosols for UGI using an 18-month mesocosm experiment under semi-arid urban conditions. Four Technosol mixtures were assembled from locally available waste streams, including excavated subsoil (ExS), crushed concrete (CC),green-waste compost (GWC), together with a sand gravel control. Mesocosms were planted with Lavandula angustifolia and subjected to two irrigation regimes (6 vs 12 mm wk− 1 ). Physical, chemical, and biological soil indicators were measured and integrated into function-based performance scores. The ExS-rich loamy sand Technosol (TE; 35% ExS, 35% CC) improved key soil properties relative to the sand-gravel control. Bulk density by 0.18 g cm− 3 , while microporosity (22.7 vs 8.4%) and plant-available water increased by 6.3%. Near-saturated hydraulic conductivity remained high (11 cm h− 1 ) relative to the sand gravel control. TE also increased cation exchange capacity (29.4 vs 12.2 meq 100 g− ) and soil organic carbon (31.2 vs 19.2 g kg− 1 ). Across mixtures, the higher irrigation regime increased shoot biomass by 26% and root biomass by 39%. Functional performance scores were higher in ExS-rich mixtures for nutrient provision, nutrient cycling, water regulation and carbon storage. These results show that replacing coarse mineral fractions with locally available excavated subsoil combined with recycled mineral materials and green-waste compost can rapidly develop key soil quality attributes in Technosols. Waste-derived Technosols therefore represent a promising strategy to design functional soils for semi-arid urban green infrastructure. Long-term field validation across vegetation types is needed to refine design thresholds and evaluate large-scale deployment
Trajectoires professionnelles et personnelles des éleveurs qui s’installent avec un BAC+5
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Brassinosteroids at the Crossroads of Crop Architecture and Nitrogen Efficiency: Engineering Smart Ideotypes for the Next Green Revolution
No full textInternational audienceABSTRACT Brassinosteroids (BRs), a class of essential plant steroid hormones, have emerged as central regulators in optimizing crop architecture, yield potential, and nutrient use efficiency (NUE). Through crosstalk with gibberellin (GA), auxin (IAA), strigolactone (SL), and nitrogen (N) signaling pathways, BRs coordinate cell elongation, tillering, and nutrient assimilation to optimize growth‐resource balance. Allelic variations affecting BR biosynthesis or perception often generate compact, erect‐leaf plant types suited for dense planting and enhanced lodging resistance—key traits for high‐yield ideotypes. This review outlines BR signaling networks and crosstalk with GA, IAA, SL, and N pathways in cereals. Two principal regulatory hubs are emphasized: the Zinc Finger protein (ZnF)–BRASSINOSTEROID INSENSITIVE1 KINASE INHIBITOR1 (BKI1)–BRASSINOSTEROID INSENSITIVE1 (BRI1) receptor module, which fine‐tunes BR perception and determines architectural traits, and the GLYCOGEN SYNTHASE KINASE 2 (GSK2)–BRASSINAZOLE‐RESISTANT1 (BZR1)–DWARF AND LOW‐TILLERING (DLT)–SMALL ORGAN SIZE1 (SMOS1)–GROWTH‐REGULATING FACTOR4 (GRF4)–DELLA regulatory module, which integrates BR signaling with GA responsiveness and nitrogen metabolism. Moreover, deletion of the “ r‐e‐z ” haploblock, encompassing Rht‐B1b , EamA‐B , and ZnF‐B , elicits a semi‐dwarf phenotype with 6.48%–15.25% yield increases. These interconnected networks establish a molecular framework for engineering BR‐driven cereal ideotypes. Future breeding could improve resource efficiency by fine‐tuning BR activity in shoots for compact growth and promoting it in roots for enhanced nutrient uptake. Integrating genomics and precision gene editing will enable fine‐tuning of BR signaling intensity and its crosstalk with other hormonal and nutrient pathways. By prioritizing growth optimization over mere growth maximization, BR‐based strategies offer a sustainable path toward high‐yield, nitrogen‐efficient cereal production
Genetic architecture of backfat thickness in laying hens: implications for extended egg production
No full textInternational audienceTo extend the egg production period of laying hens, it is important to understand the energy trade-offs during the late laying period (after 80 weeks of age) to avoid decreasing egg production or compromising health through inadequate body reserves. Although egg production is routinely recorded, fatness is not. In this study, we were interested in backfat thickness as a new selection criterion for fatness in laying hens, analyzing its genetic architecture and relationships with energy-related traits. Data were collected from a commercial pure line of Rhode Island Red layers. Hens were phenotyped at 90 weeks of age for backfat thickness by ultrasound, feed intake, body weight, abdominal fat pad weight and liver weight, and throughout the period (70–90 weeks) for total egg mass laid. Hens were genotyped on a 60k SNP chip. Genetic parameters were estimated using a multivariate animal model. Segregation analysis was used to detect major gene influencing backfat thickness, and a genome-wide association study was performed.Backfat thickness was highly heritable (h2 = 0.47) and showed a moderate positive genetic correlation with abdominal fat pad weight and with body weight. It showed moderately negative genetic correlation with total egg mass and a very weak positive genetic correlation with feed intake. Feed intake and total egg mass had a moderate positive genetic correlation. A major gene influencing backfat thickness was detected. A QTL was localized on chromosome 9.Backfat thickness showed potential as a selection criterion to maintain fatness in laying hens for extending the laying period. Using body weight as a selection criterion to manage fatness is probably not optimal because its genetic correlation with fatness was only moderate. In addition, the trade-off between egg production and backfat thickness may be a limiting factor for extending the laying cycle. Inclusion of backfat thickness at 90 weeks in the selection index also requires estimation of genetic correlations with all other criteria, including those at early stages of production. In addition, the effect of the identifed major gene on backfat thickness and other traits must be detailed before inclusion of this new trait in breeding programs