Formation trinationale Franco-Suisse-Allemande « Information Communication Systems » à l’Université de Haute Alsace

La formation trinationale « Information Communication Systems » a pour objectif la formation de Licence (Bachelor) dans le domaine des sciences pour l’ingénieur en électronique, automatique et informatique industrielle. Ce parcours est réalisé entre les trois partenaires de la Fachhochschule Nordwestschweiz en Suisse, la Hochschule de Furtwangen en Allemagne et l’Université de Haute Alsace à Mulhouse. Les étudiants provenant des baccalauréats scientifiques S ou STI, s’inscrivent dans ce cursus sur 3 années dont deux effectuées dans les universités partenaires et obtiennent les diplômes des trois pays. Le diplôme est validé lors du septième semestre par un stage de fin d’études dans une entreprise du domaine. La formation ICS fait partie d’un ensemble de formations transfrontalières proposées par l’Université de Haute Alsace. Son modèle de fonctionnement proche du LMD, fourni une souplesse de fonctionnement et permet son adaptation à d’autres domaines pour un coût de fonctionnement réduit

Detection and Automated Scoring of Dicentric Chromosomes in Nonstimulated Lymphocyte Prematurely Condensed Chromosomes After Telomere and Centromere Staining

PurposeTo combine telomere and centromere (TC) staining of premature chromosome condensation (PCC) fusions to identify dicentrics, centric rings, and acentric chromosomes, making possible the realization of a dose–response curve and automation of the process.Methods and MaterialsBlood samples from healthy donors were exposed to 60Co irradiation at varying doses up to 8 Gy, followed by a repair period of 8 hours. Premature chromosome condensation fusions were carried out, and TC staining using peptide nucleic acid probes was performed. Chromosomal aberration (CA) scoring was carried out manually and automatically using PCC-TCScore software, developed in our laboratory.ResultsWe successfully optimized the hybridization conditions and image capture parameters, to increase the sensitivity and effectiveness of CA scoring. Dicentrics, centric rings, and acentric chromosomes were rapidly and accurately detected, leading to a linear-quadratic dose–response curve by manual scoring at up to 8 Gy. Using PCC-TCScore software for automatic scoring, we were able to detect 95% of dicentrics and centric rings.ConclusionThe introduction of TC staining to the PCC fusion technique has made possible the rapid scoring of unstable CAs, including dicentrics, with a level of accuracy and ease not previously possible. This new approach can be used for biological dosimetry in radiation emergency medicine, where the rapid and accurate detection of dicentrics is a high priority using automated scoring. Because there is no culture time, this new approach can also be used for the follow-up of patients treated by genotoxic therapy, creating the possibility to perform the estimation of induced chromosomal aberrations immediately after the blood draw

POINT-SPREAD FUNCTION MODEL FOR FLUORESCENCE MACROSCOPY IMAGING

International audienceIn this paper, we model the point-spread function (PSF) of a fluo- rescence MACROscope with a field aberration. The MACROscope is an imaging arrangement that is designed to directly study small and large specimen preparations without physically sectioning them. However, due to the different optical components of the MACRO- scope, it cannot achieve the condition of lateral spatial invariance for all magnifications. For example, under low zoom settings, this field aberration becomes prominent, the PSF varies in the lateral field, and is proportional to the distance from the center of the field. On the other hand, for larger zooms, these aberrations become gradually ab- sent. A computational approach to correct this aberration often relies on an accurate knowledge of the PSF. The PSF can be defined either theoretically using a scalar diffraction model or empirically by ac- quiring a three-dimensional image of a fluorescent bead that approx- imates a point source. The experimental PSF is difficult to obtain and can change with slight deviations from the physical conditions. In this paper, we model the PSF using the scalar diffraction approach, and the pupil function is modeled by chopping it. By comparing our modeled PSF with an experimentally obtained PSF, we validate our hypothesis that the spatial variance is caused by two limiting optical apertures brought together on different conjugate planes

Validation of image processing tools for 3-D fluorescence microscopy

International audience3-D optical fluorescent microscopy becomes nowadays an efficient tool for volumic investigation of living biological samples. Using optical sectioning technique, a stack of 2-D images is obtained. However, due to the nature of the system optical transfer function and non-optimal experimental conditions, acquired raw data usually suffer from some distortions. In order to carry out biological analysis, raw data have to be restored by deconvolution. The system identification by the point-spread function is useful to obtain the knowledge of the actual system and experimental parameters, which is necessary to restore raw data. It is furthermore helpful to precise the experimental protocol. In order to facilitate the use of image processing techniques, a multi-platform-compatible software package called VIEW3D has been developed. It integrates a set of tools for the analysis of fluorescence images from 3-D wide-field or confocal microscopy. A number of regularisation parameters for data restoration are determined automatically. Common geometrical measurements and morphological descriptors of fluorescent sites are also implemented to facilitate the characterisation of biological samples. An example of this method concerning cytogenetics is presented

The Transition between Telomerase and ALT Mechanisms in Hodgkin Lymphoma and Its Predictive Value in Clinical Outcomes

International audienceBackground: We analyzed telomere maintenance mechanisms (TMMs) in lymph node samples from HL patients treated with standard therapy. The TMMs correlated with clinical outcomes of patients. Materials and Methods: Lymph node biopsies obtained from 38 HL patients and 24 patients with lymphadenitis were included in this study. Seven HL cell lines were used as in vitro models. Telomerase activity (TA) was assessed by TRAP assay and verified through hTERT immunofluorescence expression; alternative telomere lengthening (ALT) was also assessed, along with EBV status. Results: Both TA and ALT mechanisms were present in HL lymph nodes. Our findings were reproduced in HL cell lines. The highest levels of TA were expressed in CD30−/CD15− cells. Small cells were identified with ALT and TA. Hodgkin and Reed Sternberg cells contained high levels of PML bodies, but had very low hTERT expression. There was a significant correlation between overall survival (p < 10−3), event-free survival (p < 10−4), and freedom from progression (p < 10−3) and the presence of an ALT profile in lymph nodes of EBV+ patients. Conclusion: The presence of both types of TMMs in HL lymph nodes and in HL cell lines has not previously been reported. TMMs correlate with the treatment outcome of EBV+ HL patients

Collection of substantial amount of fine and ultrafine particles during the combustion of miscanthus and forest residues in small and medium scale boilers for morphological and chemical characterizations

Renewable energies are destined to play a very important role in the future world energy balance. Among these energies, biomass production and utilization is growing considerably since it offers the possibility to provide partial substitution of fossil fuels. If health impacts of fine particles (PM2.5) from diesel combustion are well documented (Gangwar et al., 2012), those from biomass combustion need substantial information and improvements. Size fractionations of PM2.5 have to be performed in order to both determine morphological and chemical characteristics, these properties being essential for biological effects. Particulate matter was sampled during combustion of miscanthus and forest residues in medium and small scale biomass boilers (400 kW from Köb Pyrot and 40 kW from REKA). Fly ashes from medium scale boiler were sampled with a cyclone device and their granulometry was studied with both optical microscope and Malvern laser granulometer. PM2.5 (sized in the range of 0.4 μm to 2.07 μm) from low scale boiler were sampled using a DEKATI DGI impactor modified for substantial PM collection. A quick overview of setup modifications for manual impactor will be developed. Particles were observed using fluorescence microscopy. A semi-quantitative method to compare fly ashes fluorescence was developped using ImageJ (Schneider et al., 2012). Speciation of organic compounds Polycyclic Aromatic Hydrocarbon (PAH) and Humic Like Substances (HULIS) was determined on PM2.5 and fly ashes. A correlation between observed fluorescence and concentration was attempted

Instrumentation associee a l'etude de l'agregation des plaquettes sanguines in vitro: changement de forme et taille des agregats

SIGLEAvailable from INIST (FR), Document Supply Service, under shelf-number : T 82571 / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc

Segmentation et classification des signaux non-stationnaires (application au traitement des sons cardiaque et à l'aide au diagnostic)

Cette thèse dans le domaine du traitement des signaux non-stationnaires, appliqué aux bruits du cœur mesurés avec un stéthoscope numérique, vise à concevoir un outil automatisé et intelligent , permettant aux médecins de disposer d une source d information supplémentaire à celle du stéthoscope traditionnel. Une première étape dans l analyse des signaux du cœur, consiste à localiser le premier et le deuxième son cardiaque (S1 et S2) afin de le segmenter en quatre parties : S1, systole, S2 et diastole. Plusieurs méthodes de localisation des sons cardiaques existent déjà dans la littérature. Une étude comparative entre les méthodes les plus pertinentes est réalisée et deux nouvelles méthodes basées sur la transformation temps-fréquence de Stockwell sont proposées. La première méthode, nommée SRBF, utilise des descripteurs issus du domaine temps-fréquence comme vecteur d entré au réseau de neurones RBF qui génère l enveloppe d amplitude du signal cardiaque, la deuxième méthode, nommée SSE, calcule l énergie de Shannon du spectre local obtenu par la transformée en S. Ensuite, une phase de détection des extrémités (onset, ending) est nécessaire. Une méthode d extraction des signaux S1 et S2, basée sur la transformée en S optimisée, est discutée et comparée avec les différentes approches qui existent dans la littérature. Concernant la classification des signaux cardiaques, les méthodes décrites dans la littérature pour classifier S1 et S2, se basent sur des critères temporels (durée de systole et diastole) qui ne seront plus valables dans plusieurs cas pathologiques comme par exemple la tachycardie sévère. Un nouveau descripteur issu du domaine temps-fréquence est évalué et validé pour discriminer S1 de S2. Ensuite, une nouvelle méthode de génération des attributs, basée sur la décomposition modale empirique (EMD) est proposée.Des descripteurs non-linéaires sont également testés, dans le but de classifier des sons cardiaques normaux et sons pathologiques en présence des souffles systoliques. Des outils de traitement et de reconnaissance des signaux non-stationnaires basés sur des caractéristiques morphologique, temps-fréquences et non linéaire du signal, ont été explorés au cours de ce projet de thèse afin de proposer un module d aide au diagnostic, qui ne nécessite pas d information à priori sur le sujet traité, robuste vis à vis du bruit et applicable dans des conditions cliniques.This thesis in the field of biomedical signal processing, applied to the heart sounds, aims to develop an automated and intelligent module, allowing medical doctors to have an additional source of information than the traditional stethoscope. A first step in the analysis of heart sounds is the segmentation process. The heart sounds segmentation process segments the PCG (PhonoCardioGram) signal into four parts: S1 (first heart sound), systole, S2 (second heart sound) and diastole. It can be considered one of the most important phases in the auto-analysis of PCG signals. The proposed segmentation module in this thesis can be divided into three main blocks: localization of heart sounds, boundaries detection of the localized heart sounds and classification block to distinguish between S1and S2. Several methods of heart sound localization exist in the literature. A comparative study between the most relevant methods is performed and two new localization methods of heart sounds are proposed in this study. Both of them are based on the S-transform, the first method uses Radial Basis Functions (RBF) neural network to extract the envelope of the heart sound signal after a feature extraction process that operates on the S-matrix. The second method named SSE calculates the Shannon Energy of the local spectrum calculated by the S-transform for each sample of the heart sound signal. The second block contains a novel approach for the boundaries detection of S1 and S2 (onset & ending). The energy concentrations of the S-transform of localized sounds are optimized by using a window width optimization algorithm. Then the SSE envelope is recalculated and a local adaptive threshold is applied to refine the estimated boundaries. For the classification block, most of the existing methods in the literature use the systole and diastole duration (systole regularity) as a criterion to discriminate between S1 and S2. These methods do not perform well for all types of heart sounds, especially in the presence of high heart rate or in the presence of arrhythmic pathologies. To deal with this problem, two feature extraction methods based on Singular Value Decomposition (SVD) technique are examined. The first method uses the S-Transform and the second method uses the Intrinsic Mode Functions (IMF) calculated by the Empirical Mode Decomposition (EMD) technique. The features are applied to a KNN classifier to estimate the performance of each feature extraction method. Nonlinear features are also tested in order to classify the normal and pathological heart sounds in the presence of systolic murmurs. Processing and recognition signal processing tools based on morphological, time-frequency and nonlinear signal features, were explored in this thesis in order to propose an auto-diagnosis module, robust against noise and applicable in clinical conditions.MULHOUSE-SCD Sciences (682242102) / SudocSudocFranceF