A higher-order entity formed by the flexible assembly of RAP1 with TRF2

Essonne committee of the Ligue contre le cancer M18756 M22897 Foundation ARC pour la Recherche sur le Cancer SFI20121205503International audienceTelomere integrity is essential to maintain genome stability, and telomeric dysfunctions are associated with cancer and aging pathologies. In human, the shelterin complex binds TTAGGG DNA repeats and provides capping to chromosome ends. Within shel-terin, RAP1 is recruited through its interaction with TRF2, and TRF2 is required for telomere protection through a network of nucleic acid and protein interactions. RAP1 is one of the most conserved shelterin proteins although one unresolved question is how its interaction may influence TRF2 properties and regulate its capacity to bind multiple proteins. Through a combination of biochemical, biophysical and structural approaches, we unveiled a unique mode of assembly between RAP1 and TRF2. The complete interaction scheme between the full-length proteins involves a complex biphasic interaction of RAP1 that directly affects the binding properties of the assembly. These results reveal how a non-DNA binding protein can influence the properties of a DNA-binding partner by mutual conformational adjustments

Visualization of medical concepts represented using word embeddings: a scoping review.

International audienceBackgroundAnalyzing the unstructured textual data contained in electronic health records (EHRs) has always been a challenging task. Word embedding methods have become an essential foundation for neural network-based approaches in natural language processing (NLP), to learn dense and low-dimensional word representations from large unlabeled corpora that capture the implicit semantics of words. Models like Word2Vec, GloVe or FastText have been broadly applied and reviewed in the bioinformatics and healthcare fields, most often to embed clinical notes or activity and diagnostic codes. Visualization of the learned embeddings has been used in a subset of these works, whether for exploratory or evaluation purposes. However, visualization practices tend to be heterogeneous, and lack overall guidelines.ObjectiveThis scoping review aims to describe the methods and strategies used to visualize medical concepts represented using word embedding methods. We aim to understand the objectives of the visualizations and their limits.MethodsThis scoping review summarizes different methods used to visualize word embeddings in healthcare. We followed the methodology proposed by Arksey and O’Malley (Int J Soc Res Methodol 8:19–32, 2005) and by Levac et al. (Implement Sci 5:69, 2010) to better analyze the data and provide a synthesis of the literature on the matter.ResultsWe first obtained 471 unique articles from a search conducted in PubMed, MedRxiv and arXiv databases. 30 of these were effectively reviewed, based on our inclusion and exclusion criteria. 23 articles were excluded in the full review stage, resulting in the analysis of 7 papers that fully correspond to our inclusion criteria. Included papers pursued a variety of objectives and used distinct methods to evaluate their embeddings and to visualize them. Visualization also served heterogeneous purposes, being alternatively used as a way to explore the embeddings, to evaluate them or to merely illustrate properties otherwise formally assessed.ConclusionsVisualization helps to explore embedding results (further dimensionality reduction, synthetic representation). However, it does not exhaust the information conveyed by the embeddings nor constitute a self-sustaining evaluation method of their pertinence

Elaboration, structure, microstructure and magnetic properties of soft Fe

The aim of the present work is to elaborate nanocrystalline soft Fe80Ni20 powders and to study the relationship between their magnetic behaviour and structural changes after different milling times. A series of Fe80Ni20 powders were elaborated by the mechanical alloying process for milling time ranging from 3 to 25 h. X-ray diffraction results showed that nickel dissolved in the iron lattice and formed a complete cubic centered (bcc) solid solution after 10 h of milling time. As the milling time increases from 0 to 25 h, the lattice parameter increases from 0.28610 nm for pure Fe to 0.28670 nm, the grain size decreases from 75 to 11 nm, while the mean level of strain increases from 0.09% to 0.5%. It is found that the saturation magnetization increases while the coercivity decreases when the milling time increases. The increase of saturation magnetization and decrease of coercivity are attributed to the decrease of the grain size with milling time. We have shown that nanocrystalline Fe80Ni20 powders exhibit a soft magnetic behaviour

Microstructure investigation and magnetic study of permalloy thin films grown by thermal evaporation

We study the effect of thickness on the structural and magnetic properties of permalloy thin films, evaporated on glass substrate. The films thicknesses range from 16 to 90 nm. From X-ray diffraction spectra analysis, we show that the thinner films present a ‹1,1,1› preferred orientation. However, the thicker films exhibit a random orientation. The grains size increases and the lattice parameter decreases with increasing thickness. The magnetic force microscopy observations display cross-tie walls features only for the two thicker films (60 and 90 nm thick films). The magnetic microstructure, carried out by Kerr microscopy technique, shows the presence of magnetic domains changing with the direction of applied magnetic field. The coercive field, Hc, was found to decrease from 6.5 for 16 to 1.75 Oe for 90 nm. All these results will be discussed and correlated

Laser-Induced Breakdown Spectroscopy for Determination of Spectral Fundamental Parameters

In this review, we report and critically discuss the application of LIBS for the determination of plasma-emission fundamental parameters, such as transition probabilities, oscillator strengths, Stark broadening and shifts, of the emission lines in the spectrum. The knowledge of these parameters is of paramount importance for plasma diagnostics or for quantitative analysis using calibration-free LIBS methods. In the first part, the theoretical basis of the analysis is laid down; in the second part, the main experimental and analytical approaches for the determination by LIBS of the spectral line spectroscopic parameters are presented. In the conclusion, the future perspectives of this kind of analysis are discussed

A higher-order entity formed by the flexible assembly of RAP1 with TRF2.

Telomere integrity is essential to maintain genome stability, and telomeric dysfunctions are associated with cancer and aging pathologies. In human, the shelterin complex binds TTAGGG DNA repeats and provides capping to chromosome ends. Within shelterin, RAP1 is recruited through its interaction with TRF2, and TRF2 is required for telomere protection through a network of nucleic acid and protein interactions. RAP1 is one of the most conserved shelterin proteins although one unresolved question is how its interaction may influence TRF2 properties and regulate its capacity to bind multiple proteins. Through a combination of biochemical, biophysical and structural approaches, we unveiled a unique mode of assembly between RAP1 and TRF2. The complete interaction scheme between the full-length proteins involves a complex biphasic interaction of RAP1 that directly affects the binding properties of the assembly. These results reveal how a non-DNA binding protein can influence the properties of a DNA-binding partner by mutual conformational adjustments