Biomedical subjects

Gwendal Josse

Publications and source records attributed to Gwendal Josse.

4 recordsLinked to original sources

PubMed2025

NMFProfiler: a multi-omics integration method for samples stratified in groups.

MOTIVATION: The development of high-throughput sequencing enabled the massive production of "omics" data for various applications in biology. By analyzing simultaneously paired datasets collected on the same samples, integrative statistical approaches allow researchers to get a global picture of such systems and to highlight existing relationships between various molecular types and levels. Here, we introduce NMFProfiler, an integrative supervised NMF that accounts for the stratification of samples into groups of biological interest. RESULTS: NMFProfiler was shown to successfully extract signatures characterizing groups with performances comparable to or better than state-of-the-art approaches. In particular, NMFProfiler was used in a clinical study on atopic dermatitis (AD) and to analyze a multi-omic cancer dataset. In the first case, it successfully identified signatures combining known AD protein biomarkers and novel transcriptomic biomarkers. In addition, it was also able to extract signatures significantly associated to cancer survival. AVAILABILITY AND IMPLEMENTATION: NMFProfiler is released as a Python package, NMFProfiler (v0.3.0), available on PyPI.

Humans↗

PubMed2006

In-vivo imaging of skin under stress: potential of high-frequency (20 MHz) static 2-D elastography.

The aim of this study was to evaluate the potential of high-frequency static two-dimensional (2-D) elastography for in vivo exploration of the mechanical behavior of skin. Our device was based on the combination of a 20 MHz sonographer and a patented extensiometer device able to apply calibrated uniaxial stretching of the skin. We used a new algorithm to compute elastograms that improve elastographic signal-to-noise ratio (SNRe) without sacrificing resolution. Mechanical behavior was described according to the axial strain and lateral displacements induced in the tissue. The efficacy of the strain anpolyvinyl alcohol first evaluated in polyvinyl alcohol (PVA)-cryogel phantoms. Several in vivo experiments then were conducted, mainly with the multistretching averaging method, and demonstrated the potential of this technique in the evaluation of mechanical behavior of the dermis and the hypodermis under stress.

Compressive Strength↗

PubMed2006

Measurement of the mechanical properties of the skin using the suction test.

INTRODUCTION: The suction test is commonly used to study the mechanical properties of human skin in vivo. The unevenness of the stress fields complicates obtaining the intrinsic mechanical parameters of the skin in vivo because the values of the local stresses and deformations cannot be calculated directly from the displacements and forces applied by the test apparatus. In general, users only take into account the negative pressure applied and the elevation of the dome of skin drawn up in order to deduce the properties of the skin. This method has the major disadvantage of being dependent on the experimental conditions used: in particular, the size of the suction cup and the negative pressure applied. Here, we propose a full mechanical study of the test to provide rigorous results. We compare the frequently used geometric method (making the thin plate hypothesis), Timoshenko's method (which can take greater plate thicknesses into account) and finally various results obtained by the finite elements (FE) technique. METHODS: The suction test was modelled by FE with large displacements and large deformations both for orthotropic and isotropic plates. The results obtained in the elastic domain for various values of Young's modulus and of applied negative pressure were used as references and were compared with methods using analytical relationships. RESULTS: The geometric method generally used in the interpretation of suction tests gives results, which in certain configurations, are very different from those obtained by FE. The method of Timoshenko is suited to thick plates 'in contact' or embedded round the edge, the elevation of the dome and the tension and flexion stresss are analytically accessible through relationships involving four constants that are dependent on the limit conditions. Comparison with the FE results enabled the optimisation of the coefficients to adapt the relationships to the particular conditions of the suction trials. CONCLUSION: We showed the limits of the geometrical method and proposed a solution, which while remaining simple to use, gives results that are closer to reality both for the calculation of the modulus and for the determination of the state of the stresses obtained.

Biomechanical Phenomena↗

PubMed2005

Characterization of the mechanical properties of skin by inverse analysis combined with the indentation test.

This study proposes a new method to determine the mechanical properties of human skin by the use of the indentation test [Pailler-Mattei, 2004. Caractérisation mécanique et tribologique de la peau humaine in vivo, Ph.D. Thesis, ECL-no. 2004-31; Pailler-Mattei, Zahouani, 2004. Journal of Adhesion Science and Technology 18, 1739-1758]. The principle of the measurements consists in applying an in vivo compressive stress [Zhang et al., 1994. Proceedings of the Institution of Mechanical Engineers 208, 217-222; Bosboom et al., 2001. Journal of Biomechanics 34, 1365-1368; Oomens et al., 1984. Selected Proceedings of Meetings of European Society of Biomechanics, pp. 227-232; Oomens et al., 1987. Journal of Biomechanics 20(9), 877-885] on the skin tissue of an individual's forearm. These measurements show an increase in the normal contact force as a function of the indentation depth. The interpretation of such results usually requires a long and tedious phenomenological study. We propose a new method to determine the mechanical parameters which control the response of skin tissue. This method is threefold: experimental, numerical, and comparative. It consists combining experimental results with a numerical finite elements model in order to find out the required parameters. This process uses a scheme of extended Kalman filters (EKF) [Gu et al., 2003. Materials Science and Engineering A345, 223-233; Nakamura et al., 2000. Acta Mater 48, 4293-4306; Leustean and Rosu, 2003. Certifying Kalman filters. RIACS Technical Report 03.02, 27pp. http://gureni.cs.uiuc.edu/~grosu/download/luta + leo.pdf; Welch and Bishop, An introduction to Kalman filter, University of North Carolina at Chapel Hill, 16p. http://www.cs.unc.edu/~welch/kalman/]. The first results presented in this study correspond to a simplified numerical modeling of the global system. The skin is assumed to be a semi-infinite layer with an isotropic linear elastic mechanical behavior [Zhang et al., 1994. Proceedings of the Institution of Mechanical Engineers 208, 217-222] This analysis will be extended to more realistic models in further works.

Biomechanical Phenomena↗