Fast and low cost analysis of dioxin and dioxin-like compounds in marine matrices: final report

0info:eu-repo/semantics/publishe

A vision transformer-based framework for knowledge transfer from multi-modal to mono-modal lymphoma subtyping models

Determining lymphoma subtypes is a crucial step for better patients treatment targeting to potentially increase their survival chances. In this context, the existing gold standard diagnosis method, which is based on gene expression technology, is highly expensive and time-consuming making difficult its accessibility. Although alternative diagnosis methods based on IHC (immunohistochemistry) technologies exist (recommended by the WHO), they still suffer from similar limitations and are less accurate. WSI (Whole Slide Image) analysis by deep learning models showed promising new directions for cancer diagnosis that would be cheaper and faster than existing alternative methods. In this work, we propose a vision transformer-based framework for distinguishing DLBCL (Diffuse Large B-Cell Lymphoma) cancer subtypes from high-resolution WSIs. To this end, we propose a multi-modal architecture to train a classifier model from various WSI modalities. We then exploit this model through a knowledge distillation mechanism for efficiently driving the learning of a mono-modal classifier. Our experimental study conducted on a dataset of 157 patients shows the promising performance of our mono-modal classification model, outperforming six recent methods from the state-of-the-art dedicated for cancer classification. Moreover, the power-law curve, estimated on our experimental data, shows that our classification model requires a reasonable number of additional patients for its training to potentially reach identical diagnosis accuracy as IHC technologies

SHREC2020 track:Multi-domain protein shape retrieval challenge

Proteins are natural modular objects usually composed of several domains, each domain bearing a specific function that is mediated through its surface, which is accessible to vicinal molecules. This draws attention to an understudied characteristic of protein structures: surface, that is mostly unexploited by protein structure comparison methods. In the present work, we evaluated the performance of six shape comparison methods, among which three are based on machine learning, to distinguish between 588 multi-domain proteins and to recreate the evolutionary relationships at the proteinand species levels of the SCOPe database. The six groups that participated in the challenge submitted a total of 15 sets of results. We observed that the performance of all the methods significantly decreases at the species level, suggesting that shape-only protein comparison is challenging for closely related proteins. Even if the dataset is limited in size (only 588 proteins are considered whereas more than 160,000 protein structures are experimentally solved), we think that this work provides useful insights into the current shape comparison methods performance, and highlights possible limitations to large-scale applications due to the computational cost

Surface-based protein domains retrieval methods from a SHREC2021 challenge

publication dans une revue suite à la communication hal-03467479 (SHREC 2021: surface-based protein domains retrieval)International audienceProteins are essential to nearly all cellular mechanism and the effectors of the cells activities. As such, they often interact through their surface with other proteins or other cellular ligands such as ions or organic molecules. The evolution generates plenty of different proteins, with unique abilities, but also proteins with related functions hence similar 3D surface properties (shape, physico-chemical properties, …). The protein surfaces are therefore of primary importance for their activity. In the present work, we assess the ability of different methods to detect such similarities based on the geometry of the protein surfaces (described as 3D meshes), using either their shape only, or their shape and the electrostatic potential (a biologically relevant property of proteins surface). Five different groups participated in this contest using the shape-only dataset, and one group extended its pre-existing method to handle the electrostatic potential. Our comparative study reveals both the ability of the methods to detect related proteins and their difficulties to distinguish between highly related proteins. Our study allows also to analyze the putative influence of electrostatic information in addition to the one of protein shapes alone. Finally, the discussion permits to expose the results with respect to ones obtained in the previous contests for the extended method. The source codes of each presented method have been made available online

The Role of Molecular Biology in the Biomonitoring of Human Exposure to Chemicals

Exposure to different substances in an occupational environment is of utmost concern to global agencies such as the World Health Organization and the International Labour Organization. Interest in improving work health conditions, particularly of those employees exposed to noxious chemicals, has increased considerably and has stimulated the search for new, more specific and selective tests. Recently, the field of molecular biology has been indicated as an alternative technique for monitoring personnel while evaluating work-related pathologies. Originally, occupational exposure to environmental toxicants was assessed using biochemical techniques to determine the presence of higher concentrations of toxic compounds in blood, urine, or other fluids or tissues; results were used to evaluate potential health risk. However, this approach only estimates the presence of a noxious chemical and its effects, but does not prevent or diminish the risk. Molecular biology methods have become very useful in occupational medicine to provide more accurate and opportune diagnostics. In this review, we discuss the role of the following common techniques: (1) Use of cell cultures; (2) evaluation of gene expression; (3) the “omic” sciences (genomics, transcriptomics, proteomics and metabolomics) and (4) bioinformatics. We suggest that molecular biology has many applications in occupational health where the data can be applied to general environmental conditions

AhR transcriptional activity in serum of Inuits across Greenlandic districts

<p>Abstract</p> <p>Background</p> <p>Human exposure to lipophilic persistent organic pollutants (POPs) including polychlorinated dibenzo-<it>p</it>-dioxins/furans (PCDDs/PCDFs), polychlorinated biphenyls (PCBs) and organochlorine pesticide is ubiquitous. The individual is exposed to a complex mixture of POPs being life-long beginning during critical developmental windows. Exposure to POPs elicits a number of species- and tissue-specific toxic responses, many of which involve the aryl hydrocarbon receptor (AhR). The aim of this study was to compare the actual level of integrated AhR transcriptional activity in the lipophilic serum fraction containing the actual POP mixture among Inuits from different districts in Greenland, and to evaluate whether the AhR transactivity is correlated to the bio-accumulated POPs and/or lifestyle factors.</p> <p>Methods</p> <p>The study included 357 serum samples from the Greenlandic districts: Nuuk and Sisimiut (South West Coast), Qaanaaq (North Coast) and Tasiilaq (East Coast). The bio-accumulated serum POPs were extracted by ethanol: hexane and clean-up on Florisil columns. Effects of the serum extract on the AhR transactivity was determined using the Hepa 1.12cR mouse hepatoma cell line carrying an AhR-luciferase reporter gene, and the data was evaluated for possible association to the serum levels of 14 PCB congeners, 10 organochlorine pesticide residues and/or lifestyle factors.</p> <p>Results</p> <p>In total 85% of the Inuit samples elicited agonistic AhR transactivity in a district dependent pattern. The median level of the AhR-TCDD equivalent (AhR-TEQ) of the separate genders was similar in the different districts. For the combined data the order of the median AhR-TEQ was Tasiilaq > Nuuk ≥ Sisimiut > Qaanaaq possibly being related to the different composition of POPs. In overall, the AhR transactivity was inversely correlated to the levels of sum POPs, age and/or intake of marine food.</p> <p>Conclusion</p> <p>i) We observed that the proportion of dioxin like (DL) compounds in the POP mixture was the dominating factor affecting the level of serum AhR transcriptional activity even at very high level of non DL-PCBs; ii) The inverse association between the integrated serum AhR transactivity and sum of POPs might be explained by the higher level of compounds antagonizing the AhR function probably due to selective POP bioaccumulation in the food chain.</p

« J’ai soif » l’accomplissement de l’Écriture en Jn 19, 28

L’article retrace l’histoire de l’interprétation par les exégètes contemporains de la parole du Christ « J’ai soif », associée en Jn 19, 28 à la mention de « l’accomplissement de l’Écriture ». En analysant la structure syntaxique du verset et son lexique, son insertion dans le chapitre 19 et plus largement dans la christologie johannique, l’auteur met en évidence le sens plénier de l’affirmation, que les traductions disponibles ont parfois tendance à restreindre.The article retraces the history of contemporary interpretations of Christ’s words « I am thirsty », associated in John 19, 28 to the mention of « the accomplishment of the Scripture ». In analysing the syntactical structure of the verse and its lexicon, its insertion in chapter 19 and more broadly in Johannine christology, the author shows the full meaning of the affirmation, which available translations sometimes tend to restrict

Pour un positionnement à la carte: Un exemple automobile

International audienceL'auteur présente une démarche mise en œuvre pour l'élaboration d'un positionnement pertinent, à travers un exemple emprunté à l'automobile. Cette démarche aboutit à l'identification d'un «polygone de crédibilité» indiquant clairement la direction dans laquelle il est souhaitable d'infléchir le positionnement. Un exemple concret illustre la pertinence de la méthode