Efficient labeling of french mammogram reports with MammoBERT.

Recent advances in deep learning and natural language processing (NLP) have broadened opportunities for automatic text processing in the medical field. However, the development of models for low-resource languages like French is challenged by limited datasets, often due to legal restrictions. Large-scale training of medical imaging models often requires extracting labels from radiology text reports.

Assessing the impact of transgenerational epigenetic variation on complex traits.

Loss or gain of DNA methylation can affect gene expression and is sometimes transmitted across generations. Such epigenetic alterations are thus a possible source of heritable phenotypic variation in the absence of DNA sequence change. However, attempts to assess the prevalence of stable epigenetic variation in natural and experimental populations and to quantify its impact on complex traits have been hampered by the confounding effects of DNA sequence polymorphisms.

Natural variation for sulfate content in Arabidopsis thaliana is highly controlled by APR2.

Most agronomic traits of importance, whether physiological (such as nutrient use efficiency) or developmental (such as flowering time), are controlled simultaneously by multiple genes and their interactions with the environment. Here, we show that variation in sulfate content between wild Arabidopsis thaliana accessions Bay-0 and Shahdara is controlled by a major quantitative trait locus that results in a strong interaction with nitrogen availability in the soil. Combining genetic and biochemical results and using a candidate gene approach, we have cloned the underlying gene, showing how a single-amino acid substitution in a key enzyme of the assimilatory sulfate reduction pathway, adenosine 5'-phosphosulfate reductase, is responsible for a decrease in enzyme activity, leading to sulfate accumulation in the plant.

Natural variation for carbohydrate content in Arabidopsis. Interaction with complex traits dissected by quantitative genetics.

Besides being a metabolic fuel, carbohydrates play important roles in plant growth and development, in stress responses, and as signal molecules. We exploited natural variation in Arabidopsis (Arabidopsis thaliana) to decipher the genetic architecture determining carbohydrate content. A quantitative trait locus (QTL) approach in the Bay-0 x Shahdara progeny grown in two contrasting nitrogen environments led to the identification of 39 QTLs for starch, glucose, fructose, and sucrose contents representing at least 14 distinct polymorphic loci.

Leaf yellowing and anthocyanin accumulation are two genetically independent strategies in response to nitrogen limitation in Arabidopsis thaliana.

For the first time in Arabidopsis thaliana, this work proposes the identification of quantitative trait loci (QTLs) associated with leaf senescence and stress response symptoms such as yellowing and anthocyanin-associated redness. When Arabidopsis plants were cultivated under low nitrogen conditions, we observed that both yellowing of the old leaves of the rosette and whole rosette redness were promoted. Leaf yellowing is a senescence symptom related to chlorophyll breakdown.

Analysis of C and N metabolisms and of C/N interactions using quantitative genetics.

Interaction between carbon (C) and nitrogen (N) metabolisms in plants is important to ensure efficient assimilation of these two major nutrients and thus to allow maximum growth and yield. Both pathways are well studied, but the regulatory elements and the processes are still mostly unknown. Quantitative genetics explore the natural variation of traits and offer an alternative approach to discover new genes and to unravel new interactions that would not have been detected by classical functional genomics.