Tuesday, 14 July 2020

Publications

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For updated lists of publications, cf. ULB Institutional Repository


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2021

Conferences

A. Schenkel, H. Guillaume, O. Debeir,
3D scanner colorization taking into account lighting problems (shadows, overexposures, lighting changes, and lack of light)
Proceedings of the 24th International Conference on Cultural Heritage and New Technologies 2019 (CHNT024, 2019), Vienna, Austria, 2021
Bibtex
Bibtex : info:hdl:2013/296294
Note : Language of publication: en




2020

Conferences

A. Schenkel, R. Ercek, O. Debeir,
3D digitization of the Brussels City Hall and the medieval archangel Michael wind vane: architectural and archaeological exploitation
Proceedings of the 23th International Conference on Cultural Heritage and New Technologies 2018 (CHNT023, 2018), Vienna, Austria, 2020
Bibtex
Bibtex : info:hdl:2013/285626
Note : Language of publication: en
Abstract : In order to make the architectural and archaeological study, the roofs, the courtyard and the facades of the Brussels City Hall were digitized with a 3D scanner, coupled with photographic acquisitions. Various elements, such as the main portal tympanum and the archangel Michael, – an exceptionally preserved 5-metre-high medieval metal wind vane that adorned the top of the 96-metre-high tower –, were also digitized in high definition. Numerical surveys shows different colorimetric (variation of colorimetry related to the changes in natural lighting) and geometric defects (erroneous points related to the passages of persons and vehicles, flying points or noises inherent to the acquisition device). A specific and automatic processing pipeline has therefore been developed and applied to correct all this problems. Given the amount of data and operations for creating plans, a software has been developed to present the data as an enriched 2D representation. This is similar to orthophotos complemented by the possibility to navigate in the depth and to vary the rendering mode (color, intensity, orientation ...), to highlight elements (surfaces, edges ...) hardly visible in simple color mode of rendering. Its functionalities allowed the drawing of very precise elevations and to generate projection images in high definition of all buildings parts and also of the archangel statue. Indeed, this survey allowed to draw the entire statue to the real scale and in a completely proportioned way. Archeologists have been able to distinguish the main work components, and they better understand the articulations between its constitutive parts and the various transformations made to the metal statue over the centuries.



Y. Li, L. Zhang, Q. Wang, G. Lafruit,
MANet: Multi-scale aggregated network for light field depth estimation
ICASSP 2020, 2020
Bibtex
Bibtex : info:hdl:2013/300996
Note : Language of publication: fr



D. Bonatto, S. Fernandes Pinto Fachada, G. Lafruit,
RaViS: Real-time accelerated view synthesizer for immersive video 6DoF VR
IS&T Electronic Imaging 2020: The Engineering Reality of Virtual Reality Conference, 2020
Bibtex
Bibtex : info:hdl:2013/295062
Note : Language of publication: fr



S. Fachada, G. Lafruit,
Xslit cameras for free navigation with depth image-based rendering
SPIE Photonics Europe: Digital Optics for 3D Imaging and 3D Display, Palais de la Musique et des Congrès, Strasbourg, France, 2020
Bibtex
Bibtex : info:hdl:2013/298146
Note : Language of publication: fr




2019

Papers

X. Fan, N. Gaspard, B. Legros, F. Lucchetti, R. Ercek, A. Nonclercq,
Automated epileptic seizure detection based on break of excitation/inhibition balance.
Computers in biology and medicine, Vol. 107, pp. 30-38, 2019
Bibtex
Bibtex : info:hdl:2013/284863
Note : SCOPUS: ar.j
Abstract : Physiological models are attractive for seizure detection, as their parameters are related to physiological meanings. We propose an algorithm to early detect epileptic seizures based on automatic estimation of average synaptic gains (excitatory Ae, slow and fast inhibitory B and G) by combining clinical data with a neural mass model. Three indices (Ae/B, Ae/G and Ae/(B + G)), all related to excitation/inhibition balance, were calculated and used as cues to detect seizures. A simple thresholding method was employed. We evaluated the algorithm against the manual scoring of a human expert on intracranial EEG samples from 23 patients suffering from different types of epilepsy. Best performance was achieved using Ae/(B + G) as a cue, i.e. excitation/(slow + fast) inhibition, on temporal lobe epilepsy (TLE) patients. A leave-one-out cross-validation showed that the algorithm achieved 92.98\% sensitivity for TLE patients. The median false positive rate was 0.16 per hour, and median detection delay was 14.5 s. Of interest, the threshold values determined by a leave-one-out cross-validation did nearly not vary among TLE patients, suggesting a general excitation/inhibition balance baseline in TLE patients. The same approach could be used with other types of epilepsy by adapting the neural mass model to these types.



D. Jiang, K. Zhang, O. Debeir,
基于最优路径的多视场全天自主星图识别
Xitong gongcheng yu dianzi jishu, Vol. 41, 1, pp. 148-153, 2019
Bibtex
Bibtex : info:hdl:2013/287208
Note : SCOPUS: ar.j
Abstract : Based on optimal path features and multiple fields of view (FOVs), a star recognition algorithm is developed to improve the recognition rate of star sensors with low cost and small FOV under all-sky autonomous recognition pattern. First, observed star images in multiple FOVs are fused through identification between images. Second, randomly distributed ant colonies are set at the positions of all the stars in the neighborhood of the main star. Then an optimal traversal path combining all these stars is acquired by iteration. The geometrical features of the path are applied for matching with guide star catalogue. Compared with several existing methods, the proposed algorithm provides high recognition rate and robustness against position and magnitude noise.



G. Lafruit,
MPEG-I MIV: Lafruit est dans la VR
G Square, Vol. 33, pp. 9, 2019
Bibtex
Bibtex : info:hdl:2013/298138
Note : Language of publication: fr



F. Almasri, O. Debeir,
Multimodal Sensor Fusion in Single Thermal Image Super-Resolution
Lecture notes in computer science, Vol. 11367 LNCS, pp. 418-433, 2019
Bibtex
Bibtex : info:hdl:2013/291229
Note : SCOPUS: cp.k
Abstract : With the fast growth in the visual surveillance and security sectors, thermal infrared images have become increasingly necessary in a large variety of industrial applications. This is true even though IR sensors are still more expensive than their RGB counterpart having the same resolution. In this paper, we propose a deep learning solution to enhance the thermal image resolution. The following results are given: (I) Introduction of a multimodal, visual-thermal fusion model that addresses thermal image super-resolution, via integrating high-frequency information from the visual image. (II) Investigation of different network architecture schemes in the literature, their up-sampling methods, learning procedures, and their optimization functions by showing their beneficial contribution to the super-resolution problem. (III) A benchmark ULB17-VT dataset that contains thermal images and their visual images counterpart is presented. (IV) Presentation of a qualitative evaluation of a large test set with 58 samples and 22 raters which shows that our proposed model performs better against state-of-the-arts.



Y. Van Eycke, A. Foucart, C. Decaestecker,
Strategies to Reduce the Expert Supervision Required for Deep Learning-Based Segmentation of Histopathological Images
Frontiers in Medicine, Vol. 6, 2019
Bibtex
Bibtex : info:hdl:2013/296977
Note : SCOPUS: re.j
Abstract : The emergence of computational pathology comes with a demand to extract more and more information from each tissue sample. Such information extraction often requires the segmentation of numerous histological objects (e.g., cell nuclei, glands, etc.) in histological slide images, a task for which deep learning algorithms have demonstrated their effectiveness. However, these algorithms require many training examples to be efficient and robust. For this purpose, pathologists must manually segment hundreds or even thousands of objects in histological images, i.e., a long, tedious and potentially biased task. The present paper aims to review strategies that could help provide the very large number of annotated images needed to automate the segmentation of histological images using deep learning. This review identifies and describes four different approaches: the use of immunohistochemical markers as labels, realistic data augmentation, Generative Adversarial Networks (GAN), and transfer learning. In addition, we describe alternative learning strategies that can use imperfect annotations. Adding real data with high-quality annotations to the training set is a safe way to improve the performance of a well configured deep neural network. However, the present review provides new perspectives through the use of artificially generated data and/or imperfect annotations, in addition to transfer learning opportunities.



G. Lafruit, D. Bonatto, C. Tulvan, M. Preda, L. Yu,
Understanding MPEG-I Coding Standardization in Immersive VR/AR Applications
SMPTE motion imaging journal, Vol. 128, 10, pp. 33-39, 2019
Bibtex
Bibtex : info:hdl:2013/293627
Note : Language of publication: fr



M. Peerboccus, Y. Van Eycke, E. Gyssels, L. Verset, P. Lucchesi, J. Absil, S. Chao, C. Decaestecker, J. Van Laethem, T. Metens, M. Bali,
Volumetric-Based Analysis of In-Vivo and Ex-Vivo Quantitative MR Diffusion Parameters in Pancreatic Adenocarcinoma: Correlation with Pathologic Findings.
Japanese Journal of Gastroenterology and Hepatology, Vol. 1, 4, pp. 1-8, 2019
Bibtex
Bibtex : info:hdl:2013/291482
Note : Language of publication: en



Conferences

J. Rosenfeld, Y. De Smet, C. Decaestecker,
An Alternative to L1 K-Means Algorithm to Obtain Partially Ordered Clustering
Conference: MCDM XXV 2019(June 16-21, 2019: Istambul), 2019
Bibtex
Bibtex : info:hdl:2013/298612
Note : Language of publication: en



X. Fan, D. Bonatto, G. Lafruit,
Consistent Long Sequences Deep Faces
IEEE International Conference on 3D Immersion: IC3D, 2019
Bibtex
Bibtex : info:hdl:2013/294868
Note : Language of publication: fr



O. Debeir, C. Decaestecker,
Data augmentation for training deep regression for in vitro cell detection
Fifth International Conference on Advances in Biomedical Engineering (ICABME), pp. 1--3, Lebanon, 2019
Bibtex
Bibtex : info:hdl:2013/298616
Note : Language of publication: fr



O. Debeir, F. Almasri, C. Decaestecker,
Deep-shift phase contrast cell detection and tracking
IEEE International Symposium on Biomedical Imaging, Venise, Italy, 2019
Bibtex
Bibtex : info:hdl:2013/288134
Note : Language of publication: fr



G. Lafruit,
MPEG compression in dynamic point clouds and immersive video: V-PCC & MPEG-I Visual
Conference: Stereopsia(12 dec 2019), 2019
Bibtex
Bibtex : info:hdl:2013/297631
Note : Language of publication: fr



S. Rogge, D. Bonatto, J. Sancho, R. Salvador, E. Juarez, A. Munteanu, G. Lafruit,
MPEG-I Depth Estimation Reference Software
IEEE International Conference on 3D Immersion: IC3D, 2019
Bibtex
Bibtex : info:hdl:2013/294869
Note : Language of publication: fr



G. Lafruit,
Real-time View Synthesis for Virtual Reality and Light Field displays
Conference: (27-28 May 2019: INRIA, Rennes, France), 2019
Bibtex
Bibtex : info:hdl:2013/285876
Note : Language of publication: en



A. Foucart, O. Debeir, C. Decaestecker,
SNOW: Semi-Supervised, NOisy and/or Weak Data for Deep Learning in Digital Pathology
2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019), pp. 1869-1872, Venice, Italy, 2019
Bibtex
Bibtex : info:hdl:2013/286269
Note : Language of publication: en
Abstract : Digital pathology produces a lot of images. For machine learning applications, these images need to be annotated, which can be complex and time consuming. Therefore, outside of a few benchmark datasets, real-world applications often rely on data with scarce or unreliable annotations. Inthis paper, we quantitatively analyze how different types of perturbations influence the results of a typical deep learning algorithm by artificially weakening the annotations of a benchmark biomedical dataset. We use classical machine learning paradigms (semi-supervised, noisy and weak learning) adapted to deep learning to try to counteract those effects, and analyze the effectiveness of these methods in addressing different types of weakness.



Thesis

D. Van Assche,
New methodological perspectives on PROMETHEE methods
2019
Bibtex
Bibtex : info:hdl:2013/287858
Note : Doctorat en Sciences de l'ingénieur et technologie
Abstract : A few methodological contributions to the PROMETHEE method, essentially based on 3 articles:-FlowSort parameters elicitation based on categorization examples;-PROMETHEE is Not Quadratic: An O (qnlog (n)) Algorithm;-Lexicographic constrained multicriteria ordered clustering.



Technical report

G. Lafruit, S. Fernandes Pinto Fachada,
D-Houdini: Digital Holography Unleashed with Depth Images and Inter-Image Numerical Interpolation
2019
Bibtex
Bibtex : info:hdl:2013/288007
Note : Language of publication: fr



D. Bonatto, S. Fernandes Pinto Fachada, G. Lafruit,
RaViS: Real-time Accelerated VIew Synthesis: Depth Image-Based Rendering (DIBR)
2019
Bibtex
Bibtex : info:hdl:2013/291526
Note : Language of publication: fr



D. Bonatto, S. Fernandes Pinto Fachada, A. Schenkel, G. Lafruit,
RVS View Synthesis with view-coherent depth maps and DIBR
2019
Bibtex
Bibtex : info:hdl:2013/294240
Note : Language of publication: fr



Misc

L. Lebrun, B. Melendez Asensio, O. Blanchard, N. De Nève, S. De Clercq, C. Balsat, M. Riva, O. De Witte, D. Balériaux, J. Brotchi, M. Bruneau, C. Decaestecker, N. D'Haene, I. Salmon,
Morphological And Molecular Characterization Of Intramedullary Astrocytomas
Language of publication: en, 2019
Bibtex
Bibtex : info:hdl:2013/298617
Note : Language of publication: en



D. Bonatto, S. Fachada, G. Lafruit,
RVS kickstart: example test sequences and config files
Language of publication: fr, 2019
Bibtex
Bibtex : info:hdl:2013/296313
Note : Language of publication: fr




2018

Papers

T. Roumeguere, F. Legrand, E. El Rassy, M. Idrissi Kaitouni, S. Albisinni, A. Rousseau, M. Vanhaeverbeek, S. Rorive, C. Decaestecker, O. Debeir, K. Zouaoui Boudjeltia, F. Aoun,
A prospective clinical study of the implications of IL-8 in the diagnosis, aggressiveness and prognosis of prostate cancer.
Future science OA, Vol. 4, 2, pp. FSO266, 2018
Bibtex
Bibtex : info:hdl:2013/266399
Note : Language of publication: en
Abstract : We evaluated the relationship between IL-8 and prostate cancer (PCa) with emphasis on diagnosis, aggressiveness and prognosis.



S. Hahn, J. Absil, O. Debeir, T. Metens,
Assessment of cardiac-driven liver movements with filtered harmonic phase image representation, optical flow quantification, and motion amplification.
Magnetic resonance in medicine, 2018
Bibtex
Bibtex : info:hdl:2013/279156
Note : SCOPUS: ar.j
Abstract : To characterize cardiac-driven liver movements using a harmonic phase image representation (HARP) with an optical flow quantification and motion amplification method. The method was applied to define the cardiac trigger delay providing minimal signal losses in liver DWI images.



T. Gevaert, Y. Van Eycke, T. Vanden Broeck, H. Van Poppel, I. Salmon, S. Rorive, F. Claessens, D. De Ridder, C. Decaestecker, S. Joniau,
Comparing the expression profiles of steroid hormone receptors and stromal cell markers in prostate cancer at different Gleason scores.
Scientific reports, Vol. 8, 1, pp. 14326, 2018
Bibtex
Bibtex : info:hdl:2013/278834
Note : SCOPUS: ar.j
Abstract : The recent developments in anti-angiogenic and immunomodulatory drugs show that the tumour micro-environment (TME) becomes increasingly important in cancer research. Here we investigated the correlation between the Gleason score (GS) and the TME by comparing tissue expression profiles of steroid hormone receptors, cancer activated fibroblast (CAF) markers and vessel densities between different GS groups. Therefore, matched patient cohorts were composed for different GS (6-7-8). Tissue micro-arrays with 6 samples/patient were processed for immunohistochemistry. Stained slides were digitised, stroma and epithelium were selectively annotated, and all selected areas were quantitatively analysed for marker expression. The most striking findings were decreased stromal expression levels of several steroid hormone receptors, increased CAF-phenotypes and increased vessel densities in high GS prostate cancer compared to low GS prostate cancer and paired prostate non-tumour tissue. The present data reveal a complex correlation between prostate cancer differentiation and TME components and suggest that different GS can be associated with different possible actionable targets in the TME. The use of standardised digital image analysis tools generated robust and reproducible quantitative data, which is novel and more informative compared to the classic semi-quantitative and observer-dependent visual scoring of immunohistochemistry.



L. Tosco, A. Laenen, T. Gevaert, I. Salmon, C. Decaestecker, E. Davicioni, C. Buerki, F. Claessens, J. Swinnen, K. Goffin, R. Oyen, W. Everaerts, L. Moris, G. De Meerleer, K. Haustermans, S. Joniau, P.E.A.R.L. (ProstatE cAncer Research Leuven),
Neoadjuvant degarelix with or without apalutamide followed by radical prostatectomy for intermediate and high-risk prostate cancer: ARNEO, a randomized, double blind, placebo-controlled trial.
BMC cancer, Vol. 18, 1, pp. 354, 2018
Bibtex
Bibtex : info:hdl:2013/269190
Note : SCOPUS: ar.j
Abstract : Recent retrospective data suggest that neoadjuvant androgen deprivation therapy can improve the prognosis of high-risk prostate cancer (PCa) patients. Novel androgen receptor pathway inhibitors are nowadays available for treatment of metastatic PCa and these compounds are promising for early stage disease. Apalutamide is a pure androgen antagonist with a very high affinity with the androgen receptor. The combination of apalutamide with degarelix, an LHRH antagonist, could increase the efficacy compared to degarelix alone.



M. Fontaine, I. Vogel, Y. Van Eycke, A. Galuppo, Y. Ajouaou, C. Decaestecker, G. Kassiotis, M. Moser, O. Leo,
Regulatory T cells constrain the TCR repertoire of antigen-stimulated conventional CD4 T cells.
EMBO journal, Vol. 37, 3, pp. 398-412, 2018
Bibtex
Bibtex : info:hdl:2013/282779
Note : Language of publication: en
Abstract : To analyze the potential role of Tregs in controlling the TCR repertoire breadth to a non-self-antigen, a TCRβ transgenic mouse model (EF4.1) expressing a limited, yet polyclonal na{\"i}ve T-cell repertoire was used. The response of EF4.1 mice to an I-Ab-associated epitope of the F-MuLV envelope protein is dominated by clones expressing a Vα2 gene segment, thus allowing a comprehensive analysis of the TCRα repertoire in a relatively large cohort of mice. Control and Treg-depleted EF4.1 mice were immunized, and the extent of the Vα2-bearing, antigen-specific TCR repertoire was characterized by high-throughput sequencing and spectratyping analysis. In addition to increased clonal expansion and acquisition of effector functions, Treg depletion led to the expression of a more diverse TCR repertoire comprising several private clonotypes rarely observed in control mice or in the pre-immune repertoire. Injection of anti-CD86 antibodies in vivo led to a strong reduction in TCR diversity, suggesting that Tregs may influence TCR repertoire diversity by modulating costimulatory molecule availability. Collectively, these studies illustrate an additional mechanism whereby Tregs control the immune response to non-self-antigens.



Y. Li, G. Lafruit,
Robust disparity estimation on sparse sampled light field images
3DTV-Conference, Vol. 2017-June, pp. 1-4, 2018
Bibtex
Bibtex : info:hdl:2013/284235
Note : SCOPUS: cp.p
Abstract : The paper presents a robust approach to compute disparities on sparse sampled light field images based on Epipolar-Plane Image (EPI) analysis. The Relative Gradient is leveraged as a kernel density function to cope with radiometric changes in non-Lambertian scenes. To account for the sparse light field, a window-based filtering is introduced to handle the noisy and homogenous regions, decomposing the scene images into edge and non-edge regions. Separate score-volume filtering over these regions avoids boundary fattening effects common to stereo matching. Finally, a consistency measure detects unreliable pixels with false disparities, to which a disparity refinement is applied. Evaluation analysis is performed on the Disney light field dataset and the proposed method shows superior results over state-of-the-art.



B. Ceulemans, S. Lu, G. Lafruit, A. Munteanu,
Robust Multiview Synthesis For Wide-Baseline Camera Arrays
IEEE transactions on multimedia, 2018
Bibtex
Bibtex : info:hdl:2013/267425
Note : Language of publication: fr



C. Decaestecker, S. De Clercq, I. Salmon,
S100A4, a key factor in glioblastoma biology
Translational cancer research, Vol. 7(S1), pp. S71-S73, 2018
Bibtex
Bibtex : info:hdl:2013/269191
Note : Editorial



Y. Li, G. Lafruit,
Scalable light field disparity estimation with occlusion detection
Journal of WSCG, Vol. 26, 2, pp. 66-75, 2018
Bibtex
Bibtex : info:hdl:2013/278296
Note : SCOPUS: ar.j
Abstract : An occlusion-aware framework is proposed to robustly estimate the disparities of light field images. It is mainly realized by leveraging multiple edge cues to occlusion detection and then integrate it with local costs into an energy function. To check the performance, the quantitative and/or qualitative evaluations are performed on both synthetic and natural light field datasets. It demonstrates that the proposed framework is robust to the density and disparity range of the light field, advancing the state-of-the-art light field disparity estimation frameworks on aspect of accuracies.



Y. Van Eycke, C. Balsat, L. Verset, O. Debeir, I. Salmon, C. Decaestecker,
Segmentation of glandular epithelium in colorectal tumours to automatically compartmentalise IHC biomarker quantification: a deep learning approach
Medical image analysis, Vol. 49, pp. 35-45, 2018
Bibtex
Bibtex : info:hdl:2013/273557
Note : SCOPUS: ar.j
Abstract : In this paper, we propose a method for automatically annotating slide images from colorectal tissue samples. Our objective is to segment glandular epithelium in histological images from tissue slides submitted to different staining techniques, including usual haematoxylin-eosin (H&E) as well as immunohistochemistry (IHC). The proposed method makes use of Deep Learning and is based on a new convolutional network architecture. Our method achieves better performances than the state of the art on the H&E images of the GlaS challenge contest, whereas it uses only the haematoxylin colour channel extracted by colour deconvolution from the RGB images in order to extend its applicability to IHC. The network only needs to be fine-tuned on a small number of additional examples to be accurate on a new IHC dataset. Our approach also includes a new method of data augmentation to achieve good generalisation when working with different experimental conditions and different IHC markers. We show that our methodology enables to automate the compartmentalisation of the IHC biomarker analysis, results concurring highly with manual annotations.



X. Fan, N. Gaspard, B. Legros, F. Lucchetti, R. Ercek, A. Nonclercq,
Seizure evolution can be characterized as path through synaptic gain space of a neural mass model.
European journal of neuroscience, Vol. 48, 9, pp. 3097-3112, 2018
Bibtex
Bibtex : info:hdl:2013/278728
Note : SCOPUS: ar.j
Abstract : Physiologically based models could facilitate better understanding of mechanisms underlying epileptic seizures. In this paper, we attempt to reveal the dynamic evolution of intracranial EEG activity during epileptic seizures based on synaptic gain identification procedure of a neural mass model. The distribution of average excitatory, slow and fast inhibitory synaptic gain in the parameter space and their temporal evolution, i.e., the path through the model parameter space, were analyzed in thirty seizures from ten temporal lobe epileptic patients. Results showed that the synaptic gain values located roughly on a plane before seizure onset, dispersed during seizure and returned to the plane when seizure terminated. Cluster analysis was performed on seizure paths and demonstrated consistency in synaptic gain evolution across different seizures from the individual patient. Furthermore, two patient groups were identified, each one corresponding to a specific synaptic gain evolution in the parameter space during a seizure. Results were validated by a bootstrapping approach based on comparison with random paths. The differences in the path revealed variations in EEG dynamics for patients despite showing identical seizure onset pattern. Our approach may have the potential to classify the epileptic patients into subgroups based on different mechanisms revealed by subtle changes in synaptic gains and further enable more robust decisions regarding treatment strategy.



D. Jiang, K. Zhang, O. Debeir,
Star image recognition based on mutual star distribution
Journal of Systems Engineering and Electronics, Vol. 40, 1, pp. 127, 2018
Bibtex
Bibtex : info:hdl:2013/271226
Note : SCOPUS: ar.j
Abstract : A novel method is designed to divide the star image into polygons, in order to solve the problem of setting the grid size in the grid algorithm. Via the method, each star is located in a corresponding polygon. The geometric features of these polygons are extracted and applied for matching the feature patterns of the guidance star database and the observed star image. Simulations indicate that the novel method removes the possible phenomenon in the grid algorithm where more than one star are located in the same grid. The grid algorithm's disadvantage of recognition failure resulting from identifying incorrect close neighbor star for reference star can be overcome and the accuracy of star image recognition is greatly improved.



D. Jiang, K. Zhang, O. Debeir,
Star Recognition Based on Path Optimization in Star Sensor with Multiple Fields of View
Advances in Astronomy, Vol. 2018, pp. 1-8, 2018
Bibtex
Bibtex : info:hdl:2013/277316
Note : SCOPUS: ar.j
Abstract : Star sensors make use of astronomical information in stars to determine attitude for spacecrafts by star image recognition. For low-cost star sensors with small field of view, fusion of observed images from multiple fields of view is performed and a novel recognition algorithm based on path optimization by randomly distributed ant colony is proposed. According to pheromone intensity, the ant colony can autonomously figure out a close optimal path without starting or ending point, rather than certifying a starting point first. Feature patterns extracted from the optimal path in guiding template and observed image after fusion are compared to perform star recognition. By the proposed algorithm, starting point for path optimization has no influence on the extracted feature pattern. Thus the star recognition rate is improved due to the higher stability of the extracted pattern. Simulations indicate that the algorithm improves recognition accuracy and robustness against noise for sensors with multiple fields of view.



N. D'Haene, C. Koopmansch, Y. Van Eycke, F. Hulet, J. Allard, S. Bouri, S. Rorive, M. Remmelink, C. Decaestecker, C. Maris, I. Salmon,
The Prognostic Value of the Combination of Low VEGFR-1 and High VEGFR-2 Expression in Endothelial Cells of Colorectal Cancer.
International journal of molecular sciences, Vol. 19, 11, 2018
Bibtex
Bibtex : info:hdl:2013/278835
Note : SCOPUS: ar.j
Abstract : Research on tumor angiogenesis has mainly focused on the vascular endothelial growth factor (VEGF) family and on methods to block its actions. However, reports on VEGF receptor (VEGFR) expression in tumor-associated endothelial cells (ECs) are limited. Thus, we evaluated VEGF, VEGFR-1 and VEGFR-2 expression in ECs of colorectal cancer (CRC) using immunohistochemistry. VEGF, VEGFR-1 and -2 expression in ECs was quantitatively evaluated by digital image analysis in a retrospective series of 204 tumor tissue samples and related to clinical variables. The data show that the VEGF, VEGFR-1 and VEGFR-2 expression in ECs is heterogeneous. Multivariate analysis including a set of clinicopathological variables reveals that high EC VEGFR-1 expression is an independent prognostic factor for overall survival (OS). The combination of low VEGFR-1 and high VEGFR-2 expression in ECs outperforms models integrating VEGFR-1 and VEGFR-2 as separate markers. Indeed, this VEGFR-1\_VEGFR-2 combination is an independent negative prognostic factor for OS (p = 0.012) and metastasis-free survival (p = 0.007). In conclusion, this work illustrates the importance of studying the distribution of VEGF members in ECs of CRC. Interestingly, our preliminary data suggest that high VEGFR-1 and low VEGFR-2 expression in ECs appear to be involved in the progression of CRC, suggesting that targeting EC VEGFR-1 could offer novel opportunities for CRC treatment. However, a prospective validation study is needed.



L. Lebrun, D. Milowich, M. Le Mercier, J. Allard, Y. Van Eycke, T. Roumeguere, C. Decaestecker, I. Salmon, S. Rorive,
UCA1 overexpression is associated with less aggressive subtypes of bladder cancer.
Oncology Reports, Vol. 40, 5, pp. 2497-2506, 2018
Bibtex
Bibtex : info:hdl:2013/278833
Note : SCOPUS: ar.j
Abstract : Non‑coding RNAs (ncRNAs) have been shown to serve important roles in carcinogenesis via complex mechanisms, including transcriptional and post‑transcriptional regulation, and chromatin interactions. Urothelial carcinoma‑associated 1 (UCA1), a long ncRNA, was recently shown to have tumorigenic properties in urothelial bladder cancer (UBC), as demonstrated by enhanced proliferation, migration, invasion and therapy resistance of UBC cell lines in vitro. These in vitro findings suggested that UCA1 is associated with aggressive tumor behavior and could have prognostic implications in UBC. The aims of the present study were to therefore to investigate the statistical associations between UCA1 RNA expression and UBC pathological features, patient prognosis and p53 and Ki‑67 expression. Chromogenic in situ hybridization and immunohistochemistry were performed on UBC tissue microarrays to characterize UCA1 RNA, and p53 and Ki‑67 expression in 208 UBC cases, including 145 non‑muscle‑invasive and 63 muscle‑invasive cases. UCA1 was observed in the tumor cells of 166/208 (80\%) UBC cases tested. No expression was noted in normal stromal and endothelium cells. Patients with UBC that overexpressed UCA1 (35\%) had a significantly higher survival rate (P=0.006) compared with that in patients with UBC that did not overexpress UCA1. This prognostic factor was independent of tumor morphology, concomitant carcinoma in situ, tumor grade and tumor stage. In addition, the absence of UCA1 overexpression was significantly associated with a high Ki‑67 proliferative index (P=0.008) and a p53 'mutated' immunoprofile (strong nuclear expression or complete absence of staining; P=0.003). In conclusion, the present results identified UCA1 as potentially being a novel independent prognostic marker in UBC that was associated with a better patient prognosis and that could serve a pivotal role in bladder cancer carcinogenesis.



L. Jorissen, J. Boaz Jessie, K. Wakunami, K. Yamamoto, G. Lafruit, P. Bekaert,
View synthesis from sparse camera array for pop-out rendering on hologram displays
Proceedings of SPIE - The International Society for Optical Engineering, Vol. 10558, 2018
Bibtex
Bibtex : info:hdl:2013/278877
Note : SCOPUS: cp.p
Abstract : A hologram of a scene can be digitally created by using a large set of images of that scene. Since capturing such a large amount is infeasible to accomplish, one may use view synthesis approaches to reduce the number of cameras and generate the missing views. We propose a view interpolation algorithm that creates views inside the scene, based on a sparse set of camera images. This allows the objects to pop out of the holographic display. We show that our approach outperforms existing view synthesis approaches and show the applicability on holographic stereograms.



T. De Mil, Y. Tarelkin, S. Hahn, W. Hubau, V. Deklerck, O. Debeir, J. Van Acker, C. De Cannière, H. Beeckman, J. Van Den Bulcke,
Wood density profiles and their corresponding tissue fractions in tropical angiosperm trees
Forests, Vol. 9, 12, 2018
Bibtex
Bibtex : info:hdl:2013/283898
Note : SCOPUS: ar.j
Abstract : Wood density profiles reveal a tree's life strategy and growth. Density profiles are, however, rarely defined in terms of tissue fractions for wood of tropical angiosperm trees. Here, we aim at linking these fractions to corresponding density profiles of tropical trees from the Congo Basin. Cores of 8 tree species were scanned with X-ray Computed Tomography to calculate density profiles. Then, cores were sanded and the outermost 3 cm were used to semi-automatically measure vessel lumen, parenchyma and fibre fractions using theWeka segmentation tool in ImageJ. Fibre wall and lumen widths were measured using a newly developed semi-automated method. An assessment of density variation in function of growth ring boundary detection is done. A mixed regression model estimated the relative contribution of each trait to the density, with a species effect on slope and intercept of the regression. Position-dependent correlations were made between the fractions and the corresponding wood density profile. On average, density profile variation mostly reflects variations in fibre lumen and wall fractions, but these are species- and position-dependent: on some positions, parenchyma and vessels have a more pronounced effect on density. The model linking density to traits explains 92\% of the variation, with 65\% of the density profile variation attributed to the three measured traits. The remaining 27\% is explained by species as a random effect. There is a clear variation between trees and within trees that have implications for interpreting density profiles in angiosperm trees: the exact driving anatomical fraction behind every density value will depend on the position within the core. The underlying function of density will thus vary accordingly.



Conferences

T. Gevaert, Y. Van Eycke, D. De Ridder, I. Salmon, S. Rorive, F. Claessens, T. Vandenbroeck, H. Van Poppel, C. Decaestecker, S. Joniau,
A multivariate survival analysis of tumour micro-environment markers reveals an independent prognostic subgroup in matched prostate cancer cohorts
Conference: 33rd Annual EAU Congress(16-20 March 2018: Copenhagen, Denmark), 2018
Bibtex
Bibtex : info:hdl:2013/281972
Note : Language of publication: en



A. Foucart, O. Debeir, C. Decaestecker,
Artifact Identification in Digital Pathology from Weak and Noisy Supervision with Deep Residual Networks
Brussels, Belgium, 2018
Bibtex
Bibtex : info:hdl:2013/286814
Note : Language of publication: en



S. Fachada, D. Bonatto, A. Schenkel, G. Lafruit,
Depth Image-Based View Synthesis with Multiple Reference Views for Virtual Reality
3DTV-CON 2018, 2018
Bibtex
Bibtex : info:hdl:2013/270850
Note : Language of publication: fr



S. Fachada, D. Bonatto, A. Schenkel, G. Lafruit,
Free Navigation in Natural Scenery with DIBR: RVS and VSRS in MPEG-I standardization
IC3D, International Conference on 3D Immersion, 2018
Bibtex
Bibtex : info:hdl:2013/277817
Note : Language of publication: fr



G. Lafruit, A. Schenkel, C. Tulvan, M. Preda, L. Yu,
MPEG-I Coding performance in Immersive VR/AR applications
IBC 2018, International Broadcasting Convention: IET: Best of IBC 2018, 2018
Bibtex
Bibtex : info:hdl:2013/270851
Note : Language of publication: fr



F. Almasri, O. Debeir,
Multimodal Sensor Fusion In Single Thermal image Super-Resolution
14th Asian Conference on Computer Vision (ACCV) 2018, Perth, WA, Australia, 2018
Bibtex
Bibtex : info:hdl:2013/288193
Note : Language of publication: en
Abstract : With the fast growth in the visual surveillance and security sectors, thermal infrared images have become increasingly necessary ina large variety of industrial applications. This is true even though IR sensors are still more expensive than their RGB counterpart having the same resolution. In this paper, we propose a deep learning solution to enhance the thermal image resolution. The following results are given:(I) Introduction of a multimodal, visual-thermal fusion model that ad-dresses thermal image super-resolution, via integrating high-frequency information from the visual image.(II) Investigation of different net-work architecture schemes in the literature, their up-sampling methods, learning procedures, and their optimization functions by showing their beneficial contribution to the super-resolution problem.(III) A bench-mark ULB17-VT dataset that contains thermal images and their visual images counterpart is presented.(IV) Presentation of a qualitative evaluation of a large test set with 58 samples and 22 raters which shows that our proposed model performs better against state-of-the-arts.



A. Schenkel, D. Bonatto, S. Fachada, H. Guillaume, G. Lafruit,
Natural Scenes Datasets for Exploration in 6DoF Navigation
IC3D, International Conference on 3D Immersion, 2018
Bibtex
Bibtex : info:hdl:2013/277818
Note : Language of publication: fr



A. Schenkel, R. Ercek, O. Debeir,
Numérisation 3D de l’Hôtel de Ville de Bruxelles et de la statue du saint Michel : exploitation architecturale et archéologique
Studia Bruxellae, pp. 29-36, Bruxelles, 2018
Bibtex
Bibtex : info:hdl:2013/282906
Note : Language of publication: fr



F. Almasri, O. Debeir,
RGB Guided Thermal Super-Resolution Enhancement
4th International Conference on Cloud Computing Technologies and Applications (Cloudtech) 2018, 26-28 November 2018: Brussels, Belgium, 2018
Bibtex
Bibtex : info:hdl:2013/288194
Note : Language of publication: fr
Abstract : In visual surveillance and security problems, objects can occur in different conditions of illumination and occlusion, therefore thermal images have become a major tool in a large variety of applications. By the reason of their high cost compared to their visual (RGB) counterpart, thermal sensors are used in low-resolution and in low contrast which introduces the necessity to obtain a higher resolution version. In this work, we propose a deep learning model by which to enhance the thermal image resolution guided by RGB images using GAN based model. The results indicate an improvement in resolution enhancement using RGB guided thermal super-resolution models compared to the classical single thermal super-resolution approach.



Y. Li, G. Lafruit,
Scalable Light Field Disparity Estimation with Occlusion Detection
WSCG 2018, 26th International Conference on Computer Graphics, Visualization and Computer Vision 2018, 2018
Bibtex
Bibtex : info:hdl:2013/262695
Note : Language of publication: fr



Thesis

X. Fan,
Dynamics underlying epileptic seizures: insights from a neural mass model
2018
Bibtex
Bibtex : info:hdl:2013/279546
Note : Doctorat en Sciences de l'ingénieur et technologie
Abstract : In this work, we propose an approach that allows to explore the potential pathophysiological mechanisms (at neuronal population level) of ictogenesis by combining clinical intracranial electroencephalographic (iEEG) recordings with a neural mass model. IEEG recordings from temporal lobe epilepsy (TLE) patients around seizure onset were investigated. Physiologically meaningful parameters (average synaptic gains of the excitatory, slow and fast inhibitory population, Ae, B and G) were identified during interictal to ictal transition. We analyzed the temporal evolution of four ratios, i.e. Ae/G, Ae/B, Ae/(B + G), and B/G. The excitation/inhibition ratio increased around seizure onset and decreased before seizure offset, suggesting the disturbance and restoration of balance between excitation and inhibition around seizure onset and before seizure offset, respectively. Moreover, the slow inhibition may have an earlier effect on the breakdown of excitation/inhibition balance. Results confirm the decrease in excitation/inhibition ratio upon seizure termination in human temporal lobe epilepsy, as revealed by optogenetic approaches both in vivo in animal models and in vitro. We further explored the distribution of the average synaptic gains in parameter space and their temporal evolution, i.e. the path through the model parameter space, in TLE patients. Results showed that the synaptic gain values located roughly on a plane before seizure onset, dispersed during ictal and returned when the seizure terminated. Cluster analysis was performed on seizure paths and demonstrated consistency in synaptic gain evolution across different seizures from individual patients. Furthermore, two patient groups were identified, each one corresponding to a specific synaptic gain evolution in the parameter space during a seizure. Results were validated by a bootstrapping approach based on comparison with random paths. The differences in the path revealed variations in EEG dynamics for patients despite showing an identical seizure onset pattern. Our approach may have the potential to classify the epileptic patients into subgroups based on different mechanisms revealed by subtle changes in synaptic gains and further enable more robust decisions regarding treatment strategy. The increase of excitation/inhibition ratios, i.e. Ae/G, Ae/B and Ae/(B+G), around seizure onset makes them potential cues for seizure detection. We explored the feasibility of a model based seizure detection algorithm. A simple thresholding method was employed. We evaluated the algorithm against the manual scoring of a human expert on iEEG samples from patients suffering from different types of epilepsy. Results suggest that Ae/(B+G), i.e. excitation/(slow + fast inhibition) ratio, allowed the best performance and that the algorithm best suited TLE patients. Leave-one-out cross-validation showed that the algorithm achieved 94.74\% sensitivity for TLE patients. The median false positive rate was 0.16 per hour, and median detection delay was -1.0 s. Of interest, the values of the threshold determined by leave-one-out cross-validation for TLE patients were quite constant, suggesting a general excitation/inhibition balance baseline in background iEEG among TLE patients. Such a model-based seizure detection approach is of clinical interest and could also achieve good performance for other types of epilepsy provided that more appropriate model, i.e. better describe epileptic EEG waveforms for other types of epilepsy, is implemented. Altogether, this thesis contributes to the field of epilepsy research from two perspectives. Scientifically, it gives new insights into the mechanisms underlying interictal to ictal transition, and facilitates better understanding of epileptic seizures. Clinically, it provides a tool for reviewing EEG data in a more efficient and objective manner and offers an opportunity for on-demand therapeutic devices.



J. Randall,
Estimating productivity in habitat-forming seaweeds
2018
Bibtex
Bibtex : info:hdl:2013/271489
Note : Doctorat en Sciences de l'ingénieur et technologie
Abstract : Macroalgal beds provide the ecological foundations for most shallow reef ecosystems in temperate environments. With distinctive canopies primarily of brown laminarian algae (northern hemisphere), or laminarian or fucalean algae (southern hemisphere), in many areas these habitats are at risk from human activity. Overexploitation, pollution, and other effects of coastal activities have resulted in significant habitat loss in coastal ecosystems, and human-induced climate change is now seen as a major threat to ecosystem health in marine systems. Understanding the impact of climate change is particularly important for habitat-forming ecosystem engineers like kelps, as these species form the basis of hierarchically organised communities and play a fundamental role in determining community structure and ecological processes. South eastern Australia has experienced increases in marine temperatures at nearly four times the global average, and there is now evidence that, in some locations, macroalgae communities are retreating in a manner consistent with ocean warming. Successful management of marine systems requires understanding ecosystem processes, particularly the patterns and magnitude of production. Macroalgal communities often show relatively low resistance to disturbance, yet rapid recovery once disturbances are removed, hence they are generally highly dynamic in response to environmental perturbations. As a result, macroalgae are likely to play an increasingly important role in buffering the short term/dynamic effects of climate change on temperate reef communities.Knowledge of the productivity of seaweed-dominated temperate reef systems is largely a synthesis from studies conducted over small spatial scales utilising a variety of methods that generally measure different characteristics of both individual seaweeds and collectively. As a result of the diversity of measurement methods, estimates of gross primary productivity (GPP), production potential, and macroalgal biomass for temperate reefs are numerous and variable. This can lead to challenges for ecologists attempting to amalgamate research findings to facilitate long-term, broad-scale perspectives or compare short-term research between spatially separated communities. However, to date there has been relatively little research to compare measurement approaches and quantify differences in productivity estimates across the different techniques.The present research provides a unique investigation into some of the techniques and methodology involved in measuring primary productivity in marine systems, particularly kelp forests, using the macroalgae Ecklonia radiata, Phyllospora comosa and Macrocystis pyrifera as study species. The work is based on both field and laboratory exploration of productivity measurements and associated parameters. In situ measurements of primary productivity (diel oxygen modelling, benthic oxygen exchange chambers) or PSII electron transport (PAM fluorometry) are compared, and the possibility of using acoustics as a means of quantifying oxygen production at large scales is explored, as has already been applied in seagrass beds. This thesis also provides an in depth investigation of the effect of variability in sampling methodology with regards to interpretation of PAM fluorometry-derived parameters. Chapter 2 investigates the acoustic properties of Ecklonia radiata. The density, sound speed and resulting adabiatic compressibility of E. radiata tissue were investigated in the laboratory. Four methods were developed and trialled to determine the intrinsic sound speed of Ecklonia radiata tissue based on measurement of the time of flight of an ultrasonic pulse, while compressibility was calculated from density measurements. The results show that Ecklonia radiata sound speed and density are higher, and compressibility lower, than that of seawater. Properties varied according to size and tissue type and the variation likely reflected differences in cell type, packing and structure as well as the concentrations of alginates and other carbohydrates. These are important considerations for acoustic propagation and the results provide valuable inputs for future acoustic work. Chapter 3 focuses on the acoustic modelling of different scenarios of primary production in a shallow water rocky reef environment of Fortescue Bay (Canoe Bay), Tasmania, where E. radiata dominates the canopy. In February 2012, the environment was continuously probed by acoustic signal transmission and monitored by a comprehensive set of oceanographic sensors with the aim to assess the potential for acoustics to quantify excess oxygen production in bubble form. Ray-theory acoustic modelling results indicate that ecologically-significant void fractions of oxygen in the canopy layer from production would be clearly seen in diel variation of propagation features such as the energy decay rate of the medium impulse response. The model can then be used to invert empirical data for retrieving void fraction. However, comparative analysis of part of FORTES 12 data and model suggests that no large excess of bubbles was produced by photosynthesis under the present environmental conditions, in contrast to earlier observations made in seagrasses. As a result, the use of acoustics as a means of measuring primary productivity in kelp could not be further explored during the course of this research.Chapter 4 provides a unique comparison of the estimates of photosynthetic O2 production rates in an Ecklonia radiata dominated community using three different measurement methods: diel oxygen GPP models, benthic oxygen exchange chambers, and electron transport rate from PAM fluorometry which is usually interpreted as a measure of production potential. All three methods were run concurrently in situ in Fortescue Bay, Tasmania. The first diel oxygen model was fitted to in situ measures of dissolved oxygen (DO) in the environment and demonstrated a good fit, however, a consequence of this approach is that large variation in oxygen production was predicted at low PAR levels. A second model was created which utilised an explicit relationship between DO production and PAR, but it didn’t represent DO at the surface as well as the first model. Importantly, the two models indicate similar daily production rates of the seaweed bed (all species combined) that are ~ 2 times that predicted for the kelp alone based on incubations in the benthic chambers and scaling for the average size of adult kelp sporophytes and their population density. Oxygen evolution from incubation of sporophytes in benthic chambers and PAM fluorometry derived electron transport rates showed similar patterns, but the results indicate that the latter method may overestimate potential photosynthesis. The results suggest that diel oxygen modelling, benthic oxygen exchange chambers and PAM fluorescence can all provide good indications of productivity in shallow water marine environments. However, care must be taken in interpretation of results as each method differs in the type of productivity estimates it provides. As a direct measure of total seaweed production per unit area of reef, estimates from models based on empirical measures of environmental DO have much to recommend them.Chapter 5 details a final analysis investigating the effects of diurnal, seasonal and latitudinal variability in ambient light on PAM-derived parameters, as well as possible effects associated with depth, within- and between-alga variation in PSII performance, and latitudinal effects unrelated to the light climate. This research was based on field measurements undertaken in Tasmania, Western Australia and New South Wales, Australia in both summer and winter during 2012 and 2013, focussing on Ecklonia radiata, Macrocystis pyrifera and Phyllospora comosa. Photosynthetic characteristics of all species were highly dependent on the time of day, depth, latitude/region, season, and part of the thallus from which measurements were taken. Patterns dependent on time-of-day, depth and thalli placement varied with season and/or geographic region, and the nature of these patterns varied between species. It is clear from this work that efforts to standardise approaches to taking measurements of seaweeds using PAM fluorometry will be essential if measurements are to be compared meaningfully across studies.The key findings of this thesis are: (1) a first determination of the acoustic properties of E. radiata tissue which enable the development of scattering models to interpret scientific echosounder data collected in kelp beds; (2) a Gaussian beam/finite element beam code (Bellhop) with detailed environmental input and a huge number of beams can predict the acoustic character of a shallow water rocky reef and bubble layers with low-frequency effective sound speed; (3) the model allows prediction of the acoustic energy decay rates due to various scenarios of ecologically-relevant photosynthetic O2 production rates; (4) day vs night acoustic measurement and model data comparisons challenge void fraction predictions made from well established measurements and methods; (5) diel oxygen modelling, benthic oxygen exchange chambers and PAM fluorescence can all provide good indications of productivity, however, understanding the limitations of each method is essential when interpreting the results as the measurements they provide are not directly comparable; and (6) applying a consistent sampling methodology is a key consideration when planning research utilising PAM fluorometry as diurnal, seasonal, and latitudinal variability, as well as effects associated with depth and within- and between-alga variation in PSII performance will have significant impact on PAM-derived parameters. The results of this work give valuable insight into the advantages and disadvantages involved with several main techniques currently utilised to measure production of macroalgal/seagrass beds, and the challenges faced by ecologists attempting to interpret results and compare research between methods and across studies. Last but not least, this study provides important and relevant information on the potential use of acoustics as a future means of determining productivity of benthic habitat on large scales in marine environments. The work presented herein will assist in both development and interpretation of future study of productivity in marine systems.



Y. Van Eycke,
Image processing in digital pathology: an opportunity to improve the characterization of IHC staining through normalization, compartmentalization and colocalization
2018
Bibtex
Bibtex : info:hdl:2013/277642
Note : Doctorat en Sciences de l'ingénieur et technologie
Abstract : With the increasing amount of information needed for diagnosis and therapeutic decision-making, and new trends such as “personalized medicine”, pathologists are expressing an increasing demand for automated tools that perform their most recurrent tasks in their daily practice, as well as an increase in the complexity of the analyses requested in their research activities. With current advances in histopathology, oncology, and biology, the current questions require the analysis of protein expression - evidenced using immunohistochemical (IHC) staining - within specific histological structures or tissue components, or the analysis of the co-expression of several proteins in a large number of tissue samples. In this Ph.D. thesis, we developed innovative solutions to make these analyses available for pathologists. To achieve this objective, we have used recent “machine learning” and, in particular, “deep learning” methodologies. We addressed different problems such as image normalization, to solve the important problem of inter-batch variability of IHC staining, and the automatic segmentation of histological structures, to compartmentalize protein expression quantification. Finally, we adapted image registration techniques to Tissue MicroArray (TMA) slide images to enable large-scale analyses of IHC staining colocalization. While imagenormalization will improve study reproducibility, the tools developed for automated segmentation will drastically reduce time and expert resources required for some studies as well as errors and imprecision due to the human factor. Finally, the work on image registration can provide answers to complex questions that require studying the potential interaction between several proteins on numerous histological samples.




2017

G. Lafruit,
3D Imaging & 3D Virtual Reality
2017
Bibtex
Bibtex : info:hdl:2013/253830
Note : China, Imec Academy



Papers

D. Mouraux, E. Brassinne, S. Sobczak, A. Nonclercq, N. Warzée, P. Sizer, T. Tuna, B. Penelle,
3D augmented reality mirror visual feedback therapy applied to the treatment of persistent, unilateral upper extremity neuropathic pain: a preliminary study.
The Journal of manual & manipulative therapy, Vol. 25, 3, pp. 137-143, 2017
Bibtex
Bibtex : info:hdl:2013/276757
Note : SCOPUS: ar.j
Abstract : Objective: We assessed whether or not pain relief could be achieved with a new system that combines 3D augmented reality system (3DARS) and the principles of mirror visual feedback. Methods: Twenty-two patients between 18 and 75 years of age who suffered of chronic neuropathic pain. Each patient performed five 3DARS sessions treatment of 20 mins spread over a period of one week. The following pain parameters were assessed: (1) visual analogic scale after each treatment session (2) McGill pain scale and DN4 questionnaire were completed before the first session and 24 h after the last session. Results: The mean improvement of VAS per session was 29\% (p < 0.001). There was an immediate session effect demonstrating a systematic improvement in pain between the beginning and the end of each session. We noted that this pain reduction was partially preserved until the next session. If we compare the pain level at baseline and 24 h after the last session, there was a significant decrease (p < 0.001) of pain of 37\%. There was a significant decrease (p < 0.001) on the McGill Pain Questionnaire and DN4 questionnaire (p < 0.01). Conclusion: Our results indicate that 3DARS induced a significant pain decrease for patients who presented chronic neuropathic pain in a unilateral upper extremity. While further research is necessary before definitive conclusions can be drawn, clinicians could implement the approach as a preparatory adjunct for providing temporary pain relief aimed at enhancing chronic pain patients’ tolerance of manual therapy and exercise intervention. Level of Evidence: 4.



L. Verset, J. Tommelein, C. Decaestecker, E. De Vlieghere, M. Bracke, I. Salmon, O. De Wever, P. Demetter,
ADAM-17/FHL2 Colocalisation Suggests Interaction and Role of These Proteins in Colorectal Cancer
Tumor biology, Vol. 39, 3, 2017
Bibtex
Bibtex : info:hdl:2013/242103
Note : SCOPUS: ar.j
Abstract : FHL2 is a multifunctional scaffolding protein; its expression is associated with poor prognosis in colorectal cancer. ADAM-17 is a metalloprotease implicated in ectodomain shedding. FHL2 regulates ADAM-17 plasma membrane localisation, and FHL2 deficiency leads to decreased activity of ADAM-17 in mouse macrophages. Presence and relationship of the ADAM-17/FHL2 complex with colorectal cancer progression is unknown. We studied FHL2 and ADAM-17 expression in several colon cancer cell lines by immunocytochemistry and western blot. To highlight the interaction between both molecules, we used the Duolink® kit for proximity ligation assay on SW480 cells. We also performed proximity ligation assay on biopsies and surgical specimens of colorectal adenocarcinoma and on matched normal mucosa. Furthermore, biopsies of colorectal adenoma with matched normal mucosa were selected. For quantification, pictures of the malignant, adenomatous and normal tissues were taken. Proximity ligation assay signals were quantified. Mean numbers of proximity ligation assay signals and of proximity ligation assay signals/nucleus were calculated. All cell lines showed FHL2 immunoreactivity; strongest positivity was observed in SW480 cells. ADAM-17 was expressed in all cell lines. Proximity ligation assay signals were present in SW480 cells. Quantitative analysis revealed that the interaction between FHL2 and ADAM-17 is more frequent in malignant than in normal tissue (p = 0.005). The mean number of ADAM-17/FHL2 proximity ligation assay signals was higher in colorectal adenocarcinoma than in adenoma with low-grade dysplasia (p = 0.0004). FHL2 interacts with ADAM-17 in normal, dysplastic and malignant colon epithelial cells. Colocalisation of these proteins is more frequent in malignant than in normal and dysplastic cells, suggesting a role for ADAM-17/FHL2 complex in the development of colorectal cancer.



X. Fan, N. Gaspard, B. Legros, F. Lucchetti, R. Ercek, A. Nonclercq,
Dynamics underlying interictal to ictal transition in temporal lobe epilepsy: insights from a neural mass model.
European journal of neuroscience, 2017
Bibtex
Bibtex : info:hdl:2013/264603
Note : SCOPUS: ar.j
Abstract : We propose an approach that combines a neural mass model and clinical intracranial electroencephalographic (iEEG) recordings to explore the potential pathophysiological mechanisms (at the neuronal population level) of ictogenesis. Thirty iEEG recordings from 10 temporal lobe epilepsy (TLE) patients around seizure onset were investigated. Physiologically meaningful parameters [average excitatory (Ae ), slow (B), and fast (G) inhibitory synaptic gain] were identified during interictal to ictal transition. Four ratios (Ae /G, Ae /B, Ae /(B + G), and B/G) were derived from these parameters, and their evolution over time was analyzed. The excitation/inhibition ratio increased around seizure onset and decreased before seizure offset, indicating the impairment and re-emergence of excitation/inhibition balance around seizure onset and before seizure offset, respectively. Moreover, the slow inhibition may have an earlier effect on excitation/inhibition imbalance. We confirm the decrease in excitation/inhibition ratio upon seizure termination in human temporal lobe epilepsy, as revealed by optogenetic approaches both in vivo in animal models and in vitro. The increase in excitation/inhibition ratio around seizure occurrence could be an indicator to detect seizures.



V. Arcolia, S. Boutry, S. Laurent, S. Saussez, F. Journé, A. Wattier, E. Leteurtre, F. Renaud, H. Gabius, M. Remmelink, C. Decaestecker, A. Rodriguez,
Galectin-1 is a diagnostic marker involved in thyroid cancer progression
International journal of oncology, Vol. 51, 3, pp. 760-770, 2017
Bibtex
Bibtex : info:hdl:2013/259145
Note : SCOPUS: ar.j
Abstract : Fine-needle aspiration (FNA) is the most commonly used pre-operative technique for diagnosis of malignant thyroid tumor. However, many benign lesions, with indeterminate diagnosis following FNA, are referred to surgery. Based on multifunctionality of the endogenous galectin-1, we aimed to assess its status for early diagnosis of thyroid cancer. Immunohistochemistry for galectin-1 and -3 was performed on a clinical series of 69 cases of thyroid lesions. Galectin-1 expression was further examined in two additional tissue microarrays (TMA) composed of 66 follicular adenomas and 66 papillary carcinomas in comparison to galectin-3 and cytokeratin-19 (CK19). In addition, a knockdown of galectin-1 in papillary (TPC-1) and anaplastic (8505C) thyroid cancer cell lines was achieved by lentiviral transduction for in vitro experiments. A murine orthotopic thyroid cancer model was used to investigate tumor growth and metastatic ability. Immunohistochemical analyses of galectin-1 and -3 in the series of 69 cases of thyroid lesions revealed that galectin-1 was completely absent in the epithelial compartment of all benign thyroid lesions. Levels of both galectins significantly increased in the cytoplasmic compartment of malignant thyroid cells. Galectin-1 expression in the TMA yielded an excellent specificity (97\%), while galectin-3 and CK19 presented a higher sensitivity (>97\%) in discriminating benign from malignant thyroid lesions. In vitro experiments revealed that migration was negatively affected in TPC-1 galectin-1 knockdown (KD) cells, and that proliferation and invasion capacity of 8505C cells decreased after galectin-1 KD. Moreover, an orthotopic mouse model displayed a lower rate of tumor development with galectin-1 KD thyroid anaplastic cancer cells than in the control. Our findings support the introduction of galectin-1 as a reliable diagnostic marker for thyroid carcinomas. Its involvement in cell proliferation, migration, invasion and tumor growth also intimate functional involvement of galectin-1 in the progression of thyroid carcinoma, suggesting its potential as a therapeutic target.



Y. Van Eycke, J. Allard, I. Salmon, O. Debeir, C. Decaestecker,
Image processing in digital pathology: an opportunity to solve inter-batch variability of immunohistochemical staining
Scientific Reports, Vol. 7, 2017
Bibtex
Bibtex : info:hdl:2013/246463
Note : SCOPUS: ar.j
Abstract : Immunohistochemistry (IHC) is a widely used technique in pathology to evidence protein expression in tissue samples. However, this staining technique is known for presenting inter-batch variations. Whole slide imaging in digital pathology offers a possibility to overcome this problem by means of image normalisation techniques. In the present paper we propose a methodology to objectively evaluate the need of image normalisation and to identify the best way to perform it. This methodology uses tissue microarray (TMA) materials and statistical analyses to evidence the possible variations occurring at colour and intensity levels as well as to evaluate the efficiency of image normalisation methods in correcting them. We applied our methodology to test different methods of image normalisation based on blind colour deconvolution that we adapted for IHC staining. These tests were carried out for different IHC experiments on different tissue types and targeting different proteins with different subcellular localisations. Our methodology enabled us to establish and to validate inter-batch normalization transforms which correct the non-relevant IHC staining variations. The normalised image series were then processed to extract coherent quantitative features characterising the IHC staining patterns.



S. Le Bon, J. Lechien, M. Ennaji, C. Decaestecker, M. Horoi, S. Saussez,
Radiofrequence des cornets inferieurs versus turbinectomie partielle : Une evaluation des symptomes post-operatoires
Revue de laryngologie, d'otologie et de rhinologie, Vol. 138, 1, pp. 21-25, 2017
Bibtex
Bibtex : info:hdl:2013/276771
Note : SCOPUS: ar.j
Abstract : Introduction: The aim of this study is to compare the degree of patient's satisfaction after partial turbinectomy versus radiofrequency turbinate reduction in a context of nasal obstruction due to inferior turbinate hypertrophy with or without nasal septum deviation. Material and methods: A retrospective cohort study was conducted at the department of Otolaryngology and Head and Neck surgery of the Saint-Pierre Hospital, from January 1, 2007 to December 31, 2010. A total of 177 patients composed 2 groups: The patients of the first group were treated by partial turbinectomy (N= 120), and the patients of the second group underwent an inferior turbinate radiofrequency (N= 57). A phone questionnaire was used to assess patients' satisfaction after at least 6 months after, the treatment. Results: Patients of the both groups have a high score of satisfaction. No statistically significant difference was found between both groups regarding the improvement of symptoms and the level of global satisfaction. Conclusions: Radiofrequency seems to be an efficient alternative approach in the treatment of nasal congestion due to inferior turbinate hypertrophy. Long-term studies with larger samples and control group are necessary to corroborate our results.



L. Buisseret, C. Desmedt, S. Garaud, M. Fornili, X. Wang, G. Van den Eyden, A. de Wind, S. Duquenne, A. Boisson, C. Naveaux, F. Rothé, S. Rorive, C. Decaestecker, D. Larsimont, M. Piccart-Gebhart, E. Biganzoli, C. Sotiriou, K. Willard-Gallo,
Reliability of tumor-infiltrating lymphocyte and tertiary lymphoid structure assessment in human breast cancer.
Modern pathology, Vol. 30, 9, pp. 1204-1212, 2017
Bibtex
Bibtex : info:hdl:2013/253706
Note : SCOPUS: ar.j
Abstract : The presence of tumor-infiltrating lymphocytes (TIL), reflecting host immune activity, is frequently correlated with better clinical outcomes, particularly in HER2-positive and triple-negative breast cancer. Recent findings suggest that organization of immune infiltrates in tertiary lymphoid structures also has a beneficial effect on survival. This study investigated inter- and intra-observer variation in TIL assessment using conventional hematoxylin-eosin versus immunohistochemical staining to identify immune cells. Global, intratumoral, and stromal TIL, as well as tertiary lymphoid structures were scored independently by experienced pathologists on full-face tumor sections (n=124). The fidelity of scoring infiltrates in core biopsies compared to surgical specimens, and pathological assessment compared to quantitative digital analysis was also evaluated. The inter-observer concordance correlation coefficient was 0.80 for global, 0.72 for intratumoral, and 0.71 for stromal TIL, while the intra-observer concordance correlation coefficient was 0.90 for global, 0.77 for intratumoral, and 0.89 for stromal TIL using immunohistochemical stains. Correlations were lower with hematoxylin-eosin stains, particularly for intratumoral TIL, while global scores had the highest concordance correlation coefficients. Our study concluded that tertiary lymphoid structures are accurately and consistently scored using immunohistochemical but not hematoxylin-eosin stains. A strong association was observed between TIL in core biopsies and surgical samples (R(2)=0.74) but this did not extend to tertiary lymphoid structures (R(2)=0.26). TIL scored by pathologists and digital analysis were correlated but our analysis reveals a constant bias between these methods. These data challenge current criteria for TIL and tertiary lymphoid structure assessment in breast cancer and recommend that how pathologists evaluate immune infiltrates be reexamined for future studies.Modern Pathology advance online publication, 16 June 2017; doi:10.1038/modpathol.2017.43.



D. Jiang, K. Zhang, O. Debeir,
Star pattern recognition based on features invariant under rotation
Pattern recognition and image analysis, Vol. 27, 3, pp. 532-537, 2017
Bibtex
Bibtex : info:hdl:2013/259250
Note : SCOPUS: ar.j
Abstract : A star pattern recognition algorithm is proposed on the basis of features invariant under rotation. Guidance star identification via the algorithm is performed on star images captured by star sensor and simulated images. The results indicate that the proposed method presents better robustness against position and magnitude noise than conventional ones and eliminates rotation procedure and avoids the influence caused by grid size choice. The database feature storage for each pattern consists of simply four floating point numbers.



Conferences

D. Jiang, K. Zhang, O. Debeir,
A Graph Based Algorithm for Star Recognition
2017 IEEE 2nd Information Technology, Networking, Electronic and Automation Control Conference (ITNEC), pp. 159-162, 2017
Bibtex
Bibtex : info:hdl:2013/271219
Note : Language of publication: en



S. Hahn, G. Maxime, D. Damien, J. Absil, O. Debeir, T. Metens,
Analysis of abdominal movement with Phase Optical Flow: Application to Diffusion imaging.
ISMRM: Magnetic Resonance in Medicine, Hawai'i Convention Center 1801 Kalakaua Ave., Honolulu, HI 96815 USA, 2017
Bibtex
Bibtex : info:hdl:2013/263961
Note : Language of publication: fr



Y. Van Eycke, C. Balsat, L. Verset, I. Salmon, C. Decaestecker,
Automatic segmentation of glandular epithelium in colorectal tissue images using Deep Learning in order to compartmentalize IHC biomarker quantification
Conference: Digital pathology congress (4: 2017-11-30 -> 2017-12-01: Londres), 2017
Bibtex
Bibtex : info:hdl:2013/293231
Note : Language of publication: en
Abstract : Immunohistochemistry (IHC) is commonly employed for diagnostic and prognostic purposes in histopathology as well as for biomarker validation in clinical research. Whole slide scanning and image analysis tools now enable objective and quantitative evaluation of IHC biomarkers in a whole tissue slide or a specific region of interest delineated by a pathologist. Compartmentalizing the quantitative evaluation of IHC biomarkers in a specific histological structure is often required to provide more relevant and informative measurements for clinical research. For this purpose, pathologists have to annotate thousands of structures present in histological slide series, a long, tedious and potentially biased task that would greatly benefit from automation.We developed an algorithm for automatically annotating glandular epithelium in slide images from colorectal tissue samples submitted to different staining techniques, including haematoxylin-eosin (H&E) as well as IHC. Our approach combines Deep Learning and a new method of data augmentation. The algorithm implements a convolutional neural network, which was first trained and evaluated with regard to the state-of-the-art on H&E images provided by the international GLaS (Gland Segmentation in Colon Histology Images) challenge contest. To apply our method in the context of IHC staining, we created a second dataset by using tissue microarray slides submitted to IHC to evidence the expression of different antigens on colorectal tumour samples. An expert manually annotated the images to delineate the glandular epithelium. We then quantified the IHC staining in and/or out of the glandular epithelium delineated on the basis of the manual or automatic annotations.Our method achieves state-of-the-art performances in epithelium segmentation on the H&E images and provides accurate segmentation on the IHC images, whatever the targeted antigen. Compartmentalized IHC quantification showed high concordance between measurements carried out using either manual or automatic segmentation. In addition to be efficient in terms of epithelium segmentation, our algorithm is very fast and thus relevant for quantitative IHC analysis performed on large series of whole (tissue or TMA) slides, as generally required in clinical research.



S. Boukhris, D. Bonatto, G. Lafruit,
Low-cost plenoptic camera with off-the-shelf components
International Conference on 3D Immersion: Stereopsia, 2017
Bibtex
Bibtex : info:hdl:2013/258590
Note : Language of publication: fr



L. Bienfait, B. Doukoure, N. D'Haene, I. Salmon, C. Decaestecker, P. Demetter, L. Verset,
Mismatch repair deficient colorectal cancer: comparison of an Ivory Coast with a Belgian cohort.
Conference: Belgian Week Pathology 2017 (19-21/10/2017: Gent, Belgium.), 2017
Bibtex
Bibtex : info:hdl:2013/261719
Note : Language of publication: en



G. Lafruit,
MPEG-I immersive video and VR standards
International Professional Conference on 3D Immersion, PCON Stereopsia, 2017
Bibtex
Bibtex : info:hdl:2013/262699
Note : Language of publication: fr



Y. Li, G. Lafruit,
Robust Disparity Estimation on Sparse Sampled Light Field Images
Conference: 3DTV-CON (2017-06-07), 2017
Bibtex
Bibtex : info:hdl:2013/249102
Note : Language of publication: en



T. Gevaert, H. Van Poppel, F. Claessens, I. Salmon, S. Rorive, C. Decaestecker, Y. Van Eycke, D. De Ridder, S. Joniau,
Steroid hormone receptors are differently expressed in prostate cancer depending on Gleason grade and presence of disease recurrence
Conference: 32nd Annual EAU Congress(March 2017: London), 2017
Bibtex
Bibtex : info:hdl:2013/263027
Note : Language of publication: en



T. Gevaert, Y. Van Eycke, T. Vandenbroeck, D. De Ridder, H. Van Poppel, F. Claessens, S. Rorive, I. Salmon, C. Decaestecker, S. Joniau,
TMPRSS2-ERG differentiates towards low-grade prostate cancer but is not an independent predictor for clinical outcome
Conference: 29th European Congress of Pathology(September 2017: Amsterdam), 2017
Bibtex
Bibtex : info:hdl:2013/286752
Note : Language of publication: en



A. Hinds, D. Doyen, P. Carballeira, G. Lafruit,
Toward the realization of six degrees-of-freedom with compressed light fields
IEEE International Conference on Multimedia and Expo, 2017
Bibtex
Bibtex : info:hdl:2013/249103
Note : Language of publication: fr



Books chapters

O. Stankiewicz, G. Lafruit, M. Domanski,
Multiview Video: Acquisition, Processing, Compression and Virtual View Rendering
Academic Press, Vol. 6, pp. 3-74, 2017
Bibtex
Bibtex : info:hdl:2013/234213
Note : SCOPUS: ch.b
Abstract : This chapter presents an overview of the acquisition, processing, and rendering pipeline in a multiview video system, targeting the unique feature of rendering virtual views, not captured by the input camera feeds. This is called Virtual View Synthesis and supports Free Navigation similar to The Matrix bullet time effect that was popularized in the late 1990s. A substantial part of the chapter is devoted in explaining how to estimate the respective camera parameters and their relative positions in the system, as well as how to estimate/measure depth, which is an essential information in order to obtain smooth virtual view transitions with Depth Image-Based Rendering.



F. Pereira, E. A. B. da Silva, G. Lafruit,
Plenoptic Imaging: Representation and Processing
Vol. 6, 2017
Bibtex
Bibtex : info:hdl:2013/233191
Note : SCOPUS: ch.b
Abstract : Light and vision are two sides of a coin playing a major role in everyday human life. Over the years, visual related technologies, notably acquisition, representation, coding, transmission, storage, and display have evolved to offer an increasingly large set of functionalities, applications, and services. With the invasion of the digital paradigm, the speed of this evolution has only increased, still mostly based on the so-called (2D) frame-based model, consistently used from the acquisition to the display. More recently, new cameras and displays have been emerging exploiting richer representations of the scene light, notably acquiring, processing, and displaying not only light at certain positions but also light with certain directions. This emerging richer light representation models reopened the fundamental discussion of light representation, processing, and coding, many times made under the umbrella of the so-called plenoptic function. This chapter will review and discuss the basics and recent developments related to visual acquisition, representation, and display from a plenoptic function perspective, notably plenoptic imaging representation and processing with particular emphasis on coding and rendering.



Thesis

F. Bodranghien,
A novel brain-computer interface (BCI) to assist upper limb pointing movements
2017
Bibtex
Bibtex : info:hdl:2013/261534
Note : Doctorat en Sciences biomédicales et pharmaceutiques (Médecine)
Abstract : Human to computer interaction only using thoughts is no longer a science fiction topic and recent progress made in this field are astounding. This work shows the creation of a novel upper limb pointing movement performance quantification platform (eCAM test) and its validation on a group of healthy subjects. After that, it shows that functional electrical stimulation (FES) enhances these upper limbs movements performance. Furthermore, this work shows that anodal transcranial direct current stimulation (atDCS) of the cerebellum impacts brain rhythms as well as postural tremor on a patient. Also, the MRI data gathered during this work will allow to better understand the underlying mechanisms of tDCS. Following that, it has been shown that the frequency and complexity of a tapping task increase the postural tremor of the contralateral limb. The same effect has been witnessed for neuromuscular fatigue. All these advances allowed us to place the foundations of a multimodal brain computer interface (BCI) based on sensors fusion. A development phase is now required to create this interface and test it on healthy and sick subjects.



A. Schenkel,
Corrections géométriques et colorimétriques automatisées de modèles 3D de grande taille
2017
Bibtex
Bibtex : info:hdl:2013/243331
Note : Doctorat en Sciences de l'ingénieur et technologie
Abstract : L’utilisation de scanners 3D permet d’obtenir, en fin de chaîne de traitement, des modèles tridimensionnels de haute résolution d’objets ou de sites. Ces modèles combinent une représentation formée d’un très grand nombre de points, couplée avec des textures photographiques pour simuler au mieux la réalité. Ils peuvent servir de base à de futures recherches, au calcul de diverses informations, à des propositions de restitutions, comme illustration, ou encore à l’archivage.Pour pouvoir être manipulées et exploitées, il est nécessaire de corriger ces données. Différents traitements doivent ainsi être appliqués : la suppression des défauts dus au processus de digitalisation ou à l’environnement de numérisation, la mise en correspondance de balayages partiels, l’élimination des objets parasites ou encore l’homogénéisation de l’aspect des surfaces. Les méthodes actuelles ne permettent pas d’effectuer aisément ces traitements de manière rapide et performante. Elles requièrent de nombreuses interventions manuelles, souvent lourdes et fastidieuses.Cette thèse vise à définir une méthodologie et à fournir les algorithmes et les outils nécessaires au post-traitement de ces acquisitions tridimensionnelles de grande taille, de manière automatisée tout en tenant compte des volumes de données à manipuler. Une structure de données adaptée au problème est proposée ainsi qu’une base d’outils destinée au traitement de volumes importants de points, en considérant la mémoire nécessaire et le temps de calcul requis. Nous proposons sur cette base une chaîne de traitement pour gérer les erreurs géométriques, liées au processus de numérisation, ainsi que les problèmes de colorisation, liés à l’acquisition de photographies dans des conditions variables (éclairage non contrôlé). Nous pouvons identifier quatre types d’erreurs géométriques qui vont ainsi être traitées : le bruit de mesure, la présence de valeurs aberrantes, les trainées de points et les inconsistances dans le modèle. La colorisation se base sur l’utilisation de l’ensemble des photographies effectuées sur le terrain en tenant compte de la variabilité des conditions d’acquisition (éclairage naturel, présence d’ombres, risque de surexposition,. . .). La solution proposée est compatible avec un calcul en temps réel comparativement à la durée d’acquisition sur le terrain, permettant d’obtenir des informations pertinentes pour guider le travail de terrain.




2016

Papers

Matthias Dorfer, Tom Kazmar, Matej Smid, Sanchit Sing, Julia Kneiss, Simone Keller, Olivier Debeir, Birgit Luber, Julian Mattes,
Associating approximate paths and temporal sequences of noisy detections: Application to the recovery of spatio-temporal cancer cell trajectories
Medical Image Analysis, Vol. 27, pp. 72--83, Jan 2016
Bibtex
Bibtex : dorfer2016



G. Descamps, Y. Karaca, J. Lechien, N. Kindt, C. Decaestecker, M. Remmelink, D. Larsimont, G. Andry, S. Hassid, A. Rodriguez, M. Khalifé, F. Journé, S. Saussez,
Classical risk factors, but not HPV status, predict survival after chemoradiotherapy in advanced head and neck cancer patients
Journal of cancer research and clinical oncology, Vol. 142, 10, pp. 2185-2196, 2016
Bibtex
Bibtex : info:hdl:2013/237944
Note : SCOPUS: ar.j
Abstract : Purpose: Despite the advent of concomitant chemoradiotherapy (CCRT), the prognosis of advanced head and neck squamous cell carcinoma (HNSCC) patients remains particularly poor. Classically, HNSCC, especially oropharyngeal carcinomas, associated with human papillomavirus (HPV) exhibits better treatment outcomes than HNSCCs in non-infected patients, eliciting a call for the de-escalation of current therapies. To improve the management of HNSCC patients, we aimed to determine the impact of active HPV infection on patient response, recurrence and survival after CCRT in a population of heavy tobacco and alcohol consumers. Methods: Paraffin-embedded samples from 218 advanced HNSCC patients, mostly smokers and/or drinkers treated by CCRT, were tested for the presence of HPV DNA by surrogate type-specific E6/E7 qPCR and p16 immunohistochemistry. Associations between the response to CCRT and patient outcomes according to HPV status and clinical data were evaluated by Kaplan–Meier analysis and both univariate and multivariate Cox regression. Results: Type-specific E6/E7 PCR demonstrated HPV positivity in 20 \% of HNSCC. Regarding HPV status, we did not find any significant relation with response to therapy in terms of progression-free survival or overall survival. However, we observed a significantly worse prognosis for consumers of alcohol and tobacco compared to nondrinkers (p = 0.003) and non-smokers (p = 0.03). Survival analyses also revealed that the outcome is compromised in stage IV patients (p = 0.007) and, in particular, for oral cavity, hypopharynx and oropharynx carcinoma patients (p = 0.001). Conclusion: The risk of death from HNSCC significantly increases when patients are exposed to tobacco and alcohol during their therapy, regardless of HPV status.



B. Ceulemans, S. Lu, G. Lafruit, P. Schelkens, A. Munteanu,
Efficient MRF-based disocclusion inpainting in multiview video
Proceedings (IEEE International Conference on Multimedia and Expo), Vol. 2016-August, 2016
Bibtex
Bibtex : info:hdl:2013/240006
Note : SCOPUS: cp.p
Abstract : View synthesis using depth image-based rendering generates virtual viewpoints of a 3D scene based on texture and depth information from a set of available cameras. One of the core components in view synthesis is image inpainting which performs the reconstruction of areas that were occluded in the available cameras but are visible from the virtual viewpoint. Inpainting methods based on Markov random fields (MRFs) have been shown to be very effective in inpainting large areas in images. In this paper, we propose a novel MRF-based in-painting method for multiview video. The proposed method steers the MRF optimization towards completion from background to foreground and exploits the available depth information in order to avoid bleeding artifacts. The proposed approach allows for efficiently filling-in large disocclusion areas and greatly accelerates execution compared to traditional MRF-based inpainting techniques. The experimental results show that view synthesis based on the proposed inpainting method systematically improves performance over the state-of-the-art in multiview view synthesis. Average PSNR gains up to 1.88 dB compared to the MPEG View Synthesis Reference software were observed.



L. Jorissen, P. Goorts, G. Lafruit, P. Bekaert,
Multi-view wide baseline depth estimation robust to sparse input sampling
3DTV-Conference, Vol. 2016-August, 2016
Bibtex
Bibtex : info:hdl:2013/240007
Note : SCOPUS: cp.p
Abstract : In this paper, we propose a depth map estimation algorithm, based on Epipolar Plane Image (EPI) line extraction, that is able to correctly handle partially occluded objects in wide baseline camera setups. Furthermore, we introduce a descriptor matching technique to reduce the negative influence of inaccurate color correction and similarly textured objects on the depth maps. A visual comparison between an existing EPI-line extraction algorithm and our method is provided, showing that our method provides more accurate and consistent depth maps in most cases.



G. Lafruit, A. Munteanu, B. Ceulemans, P. Carballeira, S. Garc{\'i}a, M. Tanimoto, M. Domański, K. Wegner, T. Grajek, T. Senoh, J. Jung, P. Kov{\'a}cs, P. Goorts, L. Jorissen,
New visual coding exploration in MPEG: Super-multiview and free navigation in free viewpoint TV
IS and T International Symposium on Electronic Imaging Science and Technology, Vol. Part F129972, 2016
Bibtex
Bibtex : info:hdl:2013/268396
Note : SCOPUS: cp.p
Abstract : ISO/IEC MPEG and ITU-T VCEG have recently jointly issued a new multiview video compression standard, called 3D-HEVC, which reaches unpreceded compression performances for linear, dense camera arrangements. In view of supporting future high-quality, auto-stereoscopic 3D displays and Free Navigation virtual/augmented reality applications with sparse, arbitrarily arranged camera setups, innovative depth estimation and virtual view synthesis techniques with global optimizations over all camera views should be developed. Preliminary studies in response to the MPEG-FTV (Free viewpoint TV) Call for Evidence suggest these targets are within reach, with at least 6\% bitrate gains over 3D-HEVC technology.



Conferences

L. Verset, J. Tommelein, C. Decaestecker, I. Salmon, O. De Wever, P. Demetter,
ADAM-17/FHL2 Colocalisation Suggests Interaction and Role of These Proteins in Colorectal Cancer
Conference: Joint Meeting of the British Division of the International Academy of Pathology and the Pathological Society of Great Britain & Ireland(9th: 28 June – 1 July 2016: Nottingham), 2016
Bibtex
Bibtex : info:hdl:2013/242090
Note : Language of publication: en



S. Lu, G. Dauphin, G. Lafruit, A. Munteanu,
Color retargeting: interactive time-varying color image composition from time-lapse sequences
Computational Visual Media, 2016
Bibtex
Bibtex : info:hdl:2013/221762
Note : Language of publication: fr



Y. Li, G. Lafruit,
Convergent Multi-View Geometric Error Correction with Pseudo-Inverse Projection Homography
International Conference on 3D Imaging, 2016
Bibtex
Bibtex : info:hdl:2013/239245
Note : Language of publication: fr



B. Ceulemans, S. Lu, G. Lafruit, P. Schelkens, A. Munteanu,
Efficient MRF-based disocclusion inpainting in multiview video
IEEE International Conference on Multimedia and Expo (ICME) 2016, 2016
Bibtex
Bibtex : info:hdl:2013/233530
Note : Language of publication: fr



D. Bonatto, S. Rogge, A. Schenkel, R. Ercek, G. Lafruit,
Explorations for Real-Time Point Cloud Rendering of Natural Scenes in Virtual Reality
International Conference on 3D Imaging, 2016
Bibtex
Bibtex : info:hdl:2013/239092
Note : Language of publication: fr



M. Tanimoto, G. Lafruit, J. Jung,
Free Navigation and Immersive 3D: ICME 2016 Special Session
Conference: ICME 2016 - Special Session co-chair, 2016
Bibtex
Bibtex : info:hdl:2013/233529
Note : Language of publication: fr



Y. Van Eycke, J. Allard, M. Derock, I. Salmon, O. Debeir, C. Decaestecker,
Image normalization for quantitative immunohistochemistry in digital pathology
2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI), pp. 795 - 798, Prague, Czech Republic, 2016
Bibtex
Bibtex : info:hdl:2013/233019
Note : SCOPUS: cp.p
Abstract : We propose to adapt to immunohistochemistry (IHC) some methods proposed to normalize images from histological slices stained with hematoxylin-eosin (H&E). Our final aim is to provide a coherent quantitative characterization of IHC biomarkers across different IHC batches with possible staining variations. In contrast to H&E, IHC staining strongly varies with the tissue analyzed and the protein targeted, making image normalization challenging. To solve this problem, we added in each IHC batch a slice from a reference tissue microarray (TMA) and then digitalized it to establish an inter-batch normalization transform. A comparison of two methods adapted to the specificity of IHC-stained slides evidences some normalization requirements to make valid IHC biomarker quantification across different staining batches.



G. Lafruit,
Keynote 3DTV-CON: Next-generation virtual and augmented reality exploration and standardization
Conference: 3DTV-CON (3-6 July 2016), 2016
Bibtex
Bibtex : info:hdl:2013/233189
Note : Language of publication: fr
Abstract : The keynote presents developments over the past ten years in immersive media standards, as well as recent technological breakthroughs in next-generation virtual and augmented reality.For instance, ISO/IEC MPEG and ITU-T VCEG have recently issued the 3D-HEVC multiview video compression standard, which reaches unpreceded compression performances for coding the video streams captured with dense, linear camera arrangements. With the aim of supporting future, high-quality 3D light field displays and Free Navigation virtual/augmented reality applications with sparse, curvelinear camera setups, new coding and view synthesis rendering techniques should be developed.In view of the high challenges, MPEG and JPEG engage in defining a collaboration for developing these next-generation Virtual Reality standards, supporting 360 degree 3D video and virtual walkthrough applications with correct motion parallax and visual accomodation cues. Point Cloud and Light Field technologies are the select candidates to serve this purpose. Commonalities between these technologies will be presented, aiming at identifying the most promising exploration and standardization approaches.



T. Lenertz, G. Lafruit,
Modular parallelization framework for multi-stream video processing
pp. 1192-1196, 2016
Bibtex
Bibtex : info:hdl:2013/233528
Note : Language of publication: fr



L. Jorissen, P. Goorts, G. Lafruit, P. Bekaert,
Multi-view Wide Baseline Depth Estimation Robust to Sparse Input Sampling
3DTV-CON 2016, 2016
Bibtex
Bibtex : info:hdl:2013/230076
Note : Language of publication: en



G. Lafruit, M. Domanski, K. Wegner, T. Grajek, T. Senoh, J. Jung, P. Kov{\'a}cs, P. Goorts, L. Jorissen, A. Munteanu, B. Ceulemans, P. Carballeira, S. Garc{\'i}a, M. Tanimoto,
New visual coding exploration in MPEG: Super-MultiView and Free Navigation in Free viewpoint TV
pp. 1-9, 2016
Bibtex
Bibtex : info:hdl:2013/225216
Note : Language of publication: fr



L. Jorissen, P. Goorts, G. Lafruit, P. Bekaert,
Nonuniform Depth Distribution Selection with Discrete Fourier Transform
Siggraph 2016: 43rd international conference on Computer Graphics & Interactive Techniques, 2016
Bibtex
Bibtex : info:hdl:2013/230613
Note : Language of publication: fr



X. Fan, R. Ercek, N. Gaspard, X. De Tiege, L. Benjamin, A. Nonclercq, others,
Study of dynamics underlying epileptic seizure crisis based on a neural mass model.
Conference: 12th European Congress on Epileptology, ECE 2016(11-15 Sept., 2016: Prague, Czech Republic), 2016
Bibtex
Bibtex : info:hdl:2013/238283
Note : Language of publication: en



L. Lebrun, D. Milowich, M. Le Mercier, J. Allard, Y. Van Eycke, T. Roumeguere, C. Decaestecker, I. Salmon, S. Rorive,
UCA1 Overexpression is a New Independent Prognostic Marker in Bladder Cancer Associated with Increased Patient Survival
Conference: Joint Meeting of the British Division of the International Academy of Pathology and the Pathological Society of Great Britain & Ireland(9th: 28 June – 1 July 2016: Nottingham), 2016
Bibtex
Bibtex : info:hdl:2013/242095
Note : Language of publication: en



A. Trepant, N. D'Haene, J. Allard, Y. Van Eycke, C. Decaestecker, I. Salmon, P. Demetter,
Vascular Insulin-Like Growth Factor Receptor Type 2 (IGF2R) Expression is Upregulated in Malignant Tumours
Conference: Joint Meeting of the British Division of the International Academy of Pathology and the Pathological Society of Great Britain & Ireland(9th: 28 June – 1 July 2016: Nottingham), 2016
Bibtex
Bibtex : info:hdl:2013/242086
Note : Language of publication: en



Thesis

S. Pianigiani,
Which data sources may be used to efficiently generate subject-specific knee models to meet clinical questions?
2016
Bibtex
Bibtex : info:hdl:2013/229798
Note : Doctorat en Sciences de l'ingénieur et technologie
Abstract : Knee joint kinematics is the result of a complex roto-translation movementcharacteristic of the tibio-femoral (TF) and patello-femoral (PF) articulations.This movement depends on the shape of the femur, the tibial plateau andthe patella. Moreover, it depends also on the morphological and mechanicalproperties of the soft tissues of the knee joint. In fact, the knee is characterizedby an extrinsic stability due to the active constraints (muscles and tendons)and passive soft tissues (menisci, retinaculum and ligaments) that surround it.As a result, knee kinematics and kinetics are different in each human being, andsometimes, even in the same person, with the right knee behaving differentlycompared to the left one.The ideal total knee arthroplasty TKA, used to correct pathologies that couldaffect the knee joint, should enable the restoration of the patient’s functionalknee kinematics and kinetics, so that the patient does not normally notice theTKA implant.Nowadays, TKA surgery is a well-established procedure and surgeons maychoose from among the broad range of TKA solutions available on the marketto meet the patient’s request. Prostheses may differ because of shape, materials,and mechanical constraints of their components. Consequently, the restorationof the knee joint biomechanics is limited by the degrees of freedom guaranteedby the adopted design solution.Despite the success of TKAs, pain and limited motor skills are reportedto still affect the clinical outcomes and not all patients are shown to be happyafter a TKA.Current complaints regarding post-TKA surgery might be related to the absenceof a proven tool that enables predicting patient-specific outcomes based ondifferent TKA solutions and providing guidelines to surgeons. In fact, surgicalpre-planning is usually based on a patient’s evaluation that the clinician canmake also based on medical images, and clinical experience. Data reported inthe literature can help in guiding the surgeon to a final decision regarding thebest subject-specific solution.Numerical methods, able to simulate knee biomechanics for various configurations,can be fundamental for the development of the appropriate reliableand effective tools to support clinically-tailored responses to a question.In particular, they can be used for subject-specific analyses on the intact kneeand for supporting the surgical pre-planning phase by comparing the effect ofdifferent solutions.When developing a subject-specific knee model, different kinds of datainputsare needed, such as the knee shapes and alignment information, softtissuesbehavior and boundary conditions describing the investigated motortasks. Often, most of this requested data are unlikely to be available (e.g.subject-specific soft-tissues material properties). Consequently, it is a commonoperating procedure to integrate literature data with subject-specific informationin order to develop knee models for collecting personalized outputsthat could be used to address research and clinical questions.However, up to now, the resulting effect of different generalized sources, asa mix of subject-specific and literature data, still needs to be evaluated for itsimpact on personalized outputs concerning knee behaviour.Furthermore, clinical questions are often focused on specific requests thatpartially use features of more complex knee models that could require too muchtime to be efficiently incorporated into daily clinical evaluations.For these reasons, the principal aims of this research have been to assess,first, the impact of differently derived generalized sources on the developmentof an intact subject-specific knee model or after a TKA; second,to provide guidelines to identify efficient clinically-tailored data sourcesused in and for knee modeling.To accomplish these tasks, a numerical knee model of an intact knee wasdeveloped based on both subject-specific and literature data sources. Theinfluence of different approaches to deal with a subject’s information, such asthe reconstruction of the knee geometries from different imaging sources, hasiiibeen evaluated. Moreover, a sensitivity analysis was performed to understandthe potential changes on kinetics and kinematics outcomes due to differentlyderived literature inputs, such as models and the properties that characterizethe joint materials and ligaments description. The outputs collected after finiteelement analyses were analyzed and compared with already published experimentaloutcomes for the same analyzed specimen and replicated boundaryconditions.Additionally, the effects on knee joint contact forces and kinematics afterTKA surgery and due to the mis-alignment of implant components or misidentificationsof ligament insertions were evaluated in another sensitivityanalysis performed with a rigid body analysis for four different TKA designsimplanted in a subject-specific knee model. As for the intact knee model, theanalyzed configurations were compared against already published experimentaloutputs or literature data replicating similar boundary conditions.Moreover, several dedicated knee models were developed to address specificclinical questions, such as the lack of biomechanical explanations for certainbehaviours of TKA designs.Once compared to already published experimental or literature data, the resultsof the developed models agree.The main results from the numerical simulations performed show that, changingthe values of some of the parameters used as inputs, the knee model kinematicsis less influenced than the contact forces and stresses outputs.In particular, in developing an intact knee model, the main effecting parameteris the material properties selection for the knee cartilage layers. Among theconfigurations analyzed using subject-specific knee models with TKAs, theposition of the tibial component and the height of the patellar buttonare the most effecting inputs.Exploring the different chapters of this research thesis, several specific resultsare shown regarding each main step followed in developing a knee numericalmodel. For example, new approaches based on MRIs have been suggested andtested proving that they are suitable for collecting subject-specific informationregarding geometrical shapes and landmark definitions. Moreover, a newgraphical method was proposed resulting more effective and immediate thanconventional representations in reporting huge amount of data. In particular,the method is the favourite to show complex biomechanical analyses especiallyfor the clinical audience that replied to a survey. Furthermore, the differentmodels tailored to address specific clinical questions collected useful biomechanicalresults, to provide clinical advice or industrial guidelines, and can beconsidered as examples of what should be included in a knee model for similarscenarios.The results of this thesis offer several contributions. Generally, these findingscould provide useful guidelines for knee-model developers to achievea more balanced approach to subject-specific intact knee models based upongeneral sources in order to improve the understanding of personalized kneebiomechanics.To address a general comment to the title of this thesis, there is no singleanswer. In fact, the selection of data sources is case-dependent using, forexample, the subject’s or literature available data to describe material’s behavioror the boundary conditions of a specific motor task. Moreover, differentclinical questions can be addressed with different numerical approaches, e.g.,finite element analysis is necessary especially in the case that stress outputs arerequested, but can be too time-consuming for addressing complex sensitivityanalyses.Once the knee model developer has identified the necessary data sources andthe approaches to be implemented, the question-tailored knee models can thusbe used for several applications such as predicting subject-specific abnormalknee kinematics and kinetics for different TKA designs, polyethylene wear,patellofemoral dislocation and bone remodeling, choosing the best fitting TKAdesign for a specific patient, and developing a procedure to optimize TKAimplant designs.



Technical report

G. Lafruit, S. Quackenbush, S. Foessel, A. Hinds,
Technical report of the joint ad hoc group for digital representations of light/sound fields for immersive media applications
2016
Bibtex
Bibtex : info:hdl:2013/234211
Note : N72033/N16352



Misc

G. Lafruit,
Tout s’explique : la lumière
intervention sur RTL-TVI abordant le sujet des hologrammes, 2016
Bibtex
Bibtex : info:hdl:2013/253831
Note : intervention sur RTL-TVI abordant le sujet des hologrammes




2015

Papers

D. Tran, B. Jansen, R. Deklerck, O. Debeir,
An approach for combining multiple descriptors for image classification
Proceedings of SPIE - The International Society for Optical Engineering, Vol. 9445, 2015
Bibtex
Bibtex : info:hdl:2013/197790
Note : SCOPUS: cp.p
Abstract : Recently, efficient image descriptors have shown promise for image classification tasks. Moreover, methods based on the combination of multiple image features provide better performance compared to methods based on a single feature. This work presents a simple and efficient approach for combining multiple image descriptors. We first employ a Naive-Bayes Nearest-Neighbor scheme to evaluate four widely used descriptors. For all features, a Image-to-Classa distances are directly computed without descriptor quantization. Since distances measured by different metrics can be of different nature and they may not be on the same numerical scale, a normalization step is essential to transform these distances into a common domain prior to combining them. Our experiments conducted on a challenging database indicate that z-score normalization followed by a simple sum of distances fusion technique can significantly improve the performance compared to applications in which individual features are used. It was also observed that our experimental results on the Caltech 101 dataset outperform other previous results.



P. Masuzzo, L. Martens, . 2014 Cell Migration Workshop Participants, C. Ampe, K. Anderson, J. Barry, O. De Wever, O. Debeir, C. Decaestecker, H. Dolznig, P. Friedl, C. Gaggioli, B. Geiger, I. Goldberg, E. Horn, R. Horwitz, Z. Kam, S. Le Dévédec, D. Vignjevic, J. Moore, J. Olivo-Marin, E. Sahai, S. Sansone, V. Sanz-Moreno, S. Str{\"o}mblad, J. Swedlow, J. Textor, M. Van Troys, R. Zantl,
An open data ecosystem for cell migration research.
Trends in cell biology, Vol. 25, 2, pp. 55-58, 2015
Bibtex
Bibtex : info:hdl:2013/197899
Note : SCOPUS: no.j
Abstract : Cell migration research has recently become both a high content and a high throughput field thanks to technological, computational, and methodological advances. Simultaneously, however, urgent bioinformatics needs regarding data management, standardization, and dissemination have emerged. To address these concerns, we propose to establish an open data ecosystem for cell migration research.



M. Dorfer, T. Kazmar, M. v Sm'id, S. Sing, J. Kneissl, S. Keller, O. Debeir, B. Luber, J. Mattes,
Associating Approximate Paths and Temporal Sequences of Noisy Detections: Application to the Recovery of Spatio-temporal Cancer Cell Trajectories
Medical image analysis, 2015
Bibtex
Bibtex : info:hdl:2013/199279
Note : SCOPUS: ar.j
Abstract : In this paper we address the problem of recovering spatio-temporal trajectories of cancer cells in phase contrast video-microscopy where the user provides the paths on which the cells are moving. The paths are purely spatial, without temporal information. To recover the temporal information associated to a given path we propose an approach based on automatic cell detection and on a graph-based shortest path search. The nodes in the graph consist of the projections of the cell detections onto the geometrical cell path. The edges relate nodes which correspond to different frames of the sequence and potentially to the same cell and trajectory. In this directed graph we search for the shortest path and use it to define a temporal parametrization of the corresponding geometrical cell path. An evaluation based on 286 paths of 7 phase contrast microscopy videos shows that our algorithm allows to recover 92\% of trajectory points with respect to the associated ground truth. We compare our method with a state-of-the-art algorithm for semi-automated cell tracking in phase contrast microscopy which requires interactively placed starting points for the cells to track. The comparison shows that supporting geometrical paths in combination with our algorithm allow us to obtain more reliable cell trajectories.



S. Lu, G. Dauphin, G. Lafruit, A. Munteanu,
Color retargeting: Interactive time-varying color image composition from time-lapse sequences
Computational Visual Media, Vol. 1, 4, pp. 321-330, 2015
Bibtex
Bibtex : info:hdl:2013/278302
Note : SCOPUS: ar.j
Abstract : In this paper, we present an interactive static image composition approach, namely color retargeting, to flexibly represent time-varying color editing effect based on time-lapse video sequences. Instead of performing precise image matting or blending techniques, our approach treats the color composition as a pixel-level resampling problem. In order to both satisfy the user’s editing requirements and avoid visual artifacts, we construct a globally optimized interpolation field. This field defines from which input video frames the output pixels should be resampled. Our proposed resampling solution ensures that (i) the global color transition in the output image is as smooth as possible, (ii) the desired colors/objects specified by the user from different video frames are well preserved, and (iii) additional local color transition directions in the image space assigned by the user are also satisfied. Various examples have been shown to demonstrate that our efficient solution enables the user to easily create time-varying color image composition results.



D. Milowich, M. Le Mercier, N. De Nève, F. Sandras, T. Roumeguere, C. Decaestecker, I. Salmon, S. Rorive,
Diagnostic value of the UCA1 test for bladder cancer detection: a clinical study.
SpringerPlus, Vol. 4, pp. 349, 2015
Bibtex
Bibtex : info:hdl:2013/208027
Note : SCOPUS: ar.j
Abstract : To evaluate the efficiency of the UCA1 test as a diagnostic tool for the detection of bladder cancer.



K. Degraux, V. Cambareri, J. Laurent, B. Geelen, C. Blanch, G. Lafruit,
Generalized inpainting method for hyperspectral image acquisition
Proceedings - International Conference on Image Processing, Vol. 2015-December, pp. 315-319, 2015
Bibtex
Bibtex : info:hdl:2013/226606
Note : SCOPUS: cp.p
Abstract : A recently designed hyperspectral imaging device enables multiplexed acquisition of an entire data volume in a single snapshot thanks to monolithically-integrated spectral filters. Such an agile imaging technique comes at the cost of a reduced spatial resolution and the need for a demosaicing procedure on its interleaved data. In this work, we address both issues and propose an approach inspired by recent developments in compressed sensing and analysis sparse models. We formulate our superresolution and demosaicing task as a 3-D generalized inpainting problem. Interestingly, the target spatial resolution can be adjusted for mitigating the compression level of our sensing. The reconstruction procedure uses a fast greedy method called Pseudo-inverse IHT. We also show on simulations that a random arrangement of the spectral filters on the sensor is preferable to regular mosaic layout as it improves the quality of the reconstruction. The efficiency of our technique is demonstrated through numerical experiments on both synthetic and real data as acquired by the snapshot imager.



A. Trepant, C. Bouchart, S. Rorive, S. Sauvage, C. Decaestecker, P. Demetter, I. Salmon,
Identification of OLIG2 as the most specific glioblastoma stem cell marker starting from comparative analysis of data from similar DNA chip microarray platforms.
Tumor biology, Vol. 36, 3, pp. 1943-1953, 2015
Bibtex
Bibtex : info:hdl:2013/197897
Note : SCOPUS: ar.j
Abstract : Despite advances in surgical and adjuvant treatments, overall survival of glioblastoma (GBM) patients remains poor. The cancer stem cell concept suggests that a rare stem cell population, called glioma stem cells (GSCs), has high ability to self-renewal leading to recurrence in GBM. The identification of specific markers of GSCs would provide a powerful tool to detect and to characterise them in order to develop targeted therapies. We carried out a comparative analysis based on the identification of inter-study concordances to identify the genes that exhibit at best differential levels of expression between GSC-enriched cell cultures and differentiated tumour cell cultures from independent studies using DNA chip microarray technologies. We finally studied the protein expression of the marker we considered the most specific by immunohistochemistry and semi-quantitative analysis on a retrospective series of 18 GBMs. Of the selected studies, 32 genes were retained. Among them, eight genes were identified to be overexpressed in GSC-enriched cultures compared to differentiated tumour cell cultures. Finally, among the eight genes, oligodendrocyte lineage transcription factor 2 (OLIG2) was characterised by the most different expression level in the "GSC model" compared to the "differentiated tumour cells model". Our approach suggests that OLIG2 is the most specific GSC marker; additional investigations with careful considerations about methodology and strategies of validation are, however, mandatory.



C. Maris, N. D'Haene, A. Trepant, M. Le Mercier, S. Sauvage, J. Allard, S. Rorive, P. Demetter, C. Decaestecker, I. Salmon,
IGF-IR: a new prognostic biomarker for human glioblastoma.
British Journal of Cancer, Vol. 113, 5, pp. 729-737, 2015
Bibtex
Bibtex : info:hdl:2013/219347
Note : SCOPUS: ar.j
Abstract : Glioblastomas (GBMs) are the most common malignant primary brain tumours in adults and are refractory to conventional therapy, including surgical resection, radiotherapy and chemotherapy. The insulin-like growth factor (IGF) system is a complex network that includes ligands (IGFI and IGFII), receptors (IGF-IR and IGF-IIR) and high-affinity binding proteins (IGFBP-1 to IGFBP-6). Many studies have reported a role for the IGF system in the regulation of tumour cell biology. However, the role of this system remains unclear in GBMs.



L. Verset, J. Tommelein, X. Moles Lopez, C. Decaestecker, T. Boterberg, E. De Vlieghere, I. Salmon, M. Mareel, M. Bracke, O. De Wever, P. Demetter,
Impact of neoadjuvant therapy on cancer-associated fibroblasts in rectal cancer.
Radiotherapy and oncology, Vol. 116, 3, pp. 449-54, 2015
Bibtex
Bibtex : info:hdl:2013/200672
Note : SCOPUS: cp.j
Abstract : Cancer-associated fibroblasts (CAFs) are increasingly recognised as promoters of tumour progression. It is poorly investigated whether cancer management protocols, such as neoadjuvant radio(chemo)therapy, have an impact on CAFs and, by consequence, on tumour progression. This prompted us to study the impact of neoadjuvant radio(chemo)therapy on the α-SMA/epithelial area ratio in rectal cancer, and the impact of this ratio on recurrence-free survival.



L. De Smedt, J. Lemahieu, S. Palmans, O. Govaere, T. Tousseyn, E. van Cutsem, H. Prenen, S. Tejpar, M. Spaepen, G. Matthijs, C. Decaestecker, X. Moles Lopez, P. Demetter, I. Salmon, X. Sagaert,
Microsatellite instable vs stable colon carcinomas: analysis of tumour heterogeneity, inflammation and angiogenesis.
British Journal of Cancer, Vol. 113, 3, pp. 500-9, 2015
Bibtex
Bibtex : info:hdl:2013/205313
Note : SCOPUS: ar.j
Abstract : Microsatellite instability (MSI) accounts for 15\% of all colorectal tumours. Several specific clinicopathologicals (e.g., preference for the proximal colon over the distal colon, improved prognosis and altered response to chemotherapeutics) are described for this subset of tumours. This study aimed to analyse morphological, inflammatory and angiogenic features of MSI vs microsatellite stable (MSS) tumours.



T. Gevaert, X. Moles Lopez, X. Sagaert, L. Libbrecht, T. Roskams, S. Rorive, C. Decaestecker, I. Salmon, D. De Ridder,
Morphometric and quantitative immunohistochemical analysis of disease-related changes in the upper (suburothelial) lamina propria of the human bladder dome.
PloS one, Vol. 10, 5, pp. e0127020, 2015
Bibtex
Bibtex : info:hdl:2013/200671
Note : SCOPUS: ar.j
Abstract : The upper (suburothelial) lamina propria (ULP) is a distinct region in the human bladder with dense populations of interstitial cells (IC), fine vascular networks and variable development of muscularis mucosae (MM). It is more and more obvious that the ULP plays an important role in bladder physiology and bladder disease, and in the present study we have quantified changes in the cellular key players of the ULP in bladders from patients with carcinoma in situ (CIS), multiple sclerosis (MS) and bladder pain syndrome (BPS). Tissue samples for the different patient groups were obtained from radical cystectomy-specimens. Standardized immunohistochemistry with a panel of specific cell markers was used to characterise the ULP cellular structures, followed by digitalised morphometry and quantitative staining analysis. Alterations in the ULP area were most pronounced in MS bladders, but also present in BPS and CIS bladders. We observed an increased thickness and increased variability in thickness of the ULP IC area in MS and BPS bladders; a significantly increased development of MM in MS bladders; a changed organization of vascular plexuses in the lamina propria in most pathologic bladders and a changed phenotype of ULP IC: a significantly decreased expression of progesterone receptor in MS bladders and a trend towards decreased expression of alpha-smooth muscle actin in BPS bladders. We show here for the first time the presence of disease-specific changes in organisation and/or phenotype of the different key players of the ULP area in human bladder. The present findings further support the hypothesis that the ULP area is involved and altered in different bladder diseases.



M. Dumont, P. Goorts, S. Maesen, G. Lafruit, P. Bekaert,
Real-time edge-sensitive local stereo matching with iterative disparity refinement
Communications in computer and information science, Vol. 554, pp. 435-456, 2015
Bibtex
Bibtex : info:hdl:2013/226776
Note : SCOPUS: cp.k
Abstract : First, we present a novel cost aggregation method for stereo matching that uses two edge-sensitive shape-adaptive support windows per pixel region; one following the horizontal edges in the image, the other the vertical edges. Their combination defines the final aggregation window shape that closely follows all object edges and thereby achieves increased hypothesis confidence. Second, we present a novel iterative disparity refinement process and apply it to the initially estimated disparity map. The process consists of four rigorously defined and lightweight modules that can be iterated multiple times: a disparity cross check, bitwise fast voting, invalid disparity handling, and median filtering. We demonstrate that our iterative refinement has a large effect on the overall quality, resulting in smooth disparity maps with sharp object edges, especially around occluded areas. It can be applied to any stereo matching algorithm and tends to converge to a final solution. Finally, we perform a quantitative evaluation on various Middlebury datasets, showing an increase in quality of over several dB PSNR compared with their ground truth. Our whole disparity estimation algorithm supports efficient GPU implementation to facilitate scalability and real-time performance.



X. Moles Lopez, P. Barbot, Y. Van Eycke, L. Verset, A. Trepant, L. Larbanoix, I. Salmon, C. Decaestecker,
Registration of whole immunohistochemical slide images: an efficient way to characterize biomarker colocalization.
Journal of the American Medical Informatics Association, Vol. 22, 1, pp. 86-99, 2015
Bibtex
Bibtex : info:hdl:2013/177042
Note : JOURNAL ARTICLE
Abstract : Extracting accurate information from complex biological processes involved in diseases, such as cancers, requires the simultaneous targeting of multiple proteins and locating their respective expression in tissue samples. This information can be collected by imaging and registering adjacent sections from the same tissue sample and stained by immunohistochemistry (IHC). Registration accuracy should be on the scale of a few cells to enable protein colocalization to be assessed.



M. Gilson, G. Deliens, R. Leproult, A. Bodart, A. Nonclercq, R. Ercek, P. Peigneux,
REM-enriched naps are associated with memory consolidation for sad stories and enhance mood-related reactivity.
Brain sciences, Vol. 6, 1, 2015
Bibtex
Bibtex : info:hdl:2013/223113
Note : SCOPUS: ar.j
Abstract : Emerging evidence suggests that emotion and affect modulate the relation between sleep and cognition. In the present study, we investigated the role of rapid-eye movement (REM) sleep in mood regulation and memory consolidation for sad stories. In a counterbalanced design, participants (n = 24) listened to either a neutral or a sad story during two sessions, spaced one week apart. After listening to the story, half of the participants had a short (45 min) morning nap. The other half had a long (90 min) morning nap, richer in REM and N2 sleep. Story recall, mood evolution and changes in emotional response to the re-exposure to the story were assessed after the nap. Although recall performance was similar for sad and neutral stories irrespective of nap duration, sleep measures were correlated with recall performance in the sad story condition only. After the long nap, REM sleep density positively correlated with retrieval performance, while re-exposure to the sad story led to diminished mood and increased skin conductance levels. Our results suggest that REM sleep may not only be associated with the consolidation of intrinsically sad material, but also enhances mood reactivity, at least on the short term.



Conferences

S. Bolis, O. Debeir, J. Beeckman, P. Kockaert,
Amplified spontaneous emission injection into an optical fiber with the aid of a nematicon
Proceedings Symposium IEEE Photonics Society Benelux, 2015, Brussels, Belgium, Brussels, Belgium, 2015
Bibtex
Bibtex : info:hdl:2013/233182
Note : Language of publication: en
Abstract : Amplified Spontaneous Emission (ASE) has become popular for applications like spectroscopy, fiber sensors and imaging that require incoherent light. In our setup ASE is generated in a dye-doped nematic liquid crystal cell and it is then collected into an optical fiber to integrate into the device. We demonstrate that, generating a nematicon from the same fiber, the ASE collection efficiency is increased of almost one order of magnitude thanks to the wave-guiding action of the nematicon that induces the injection into the fiber. Moreover the collected emission is highly linearly polarized parallel to the direction of the liquid crystal director



X. Fan, R. Ercek, N. Gaspard, A. Nonclercq,
Analysis of a neural model that simulates epileptiform/background eeg activities
Conference: 14th Belgian Day on Biomedical Engineering, joint meeting with IEEE EMBS Benelux Chapter(26-27 Nov., 2015: Brussels, Belgium), 2015
Bibtex
Bibtex : info:hdl:2013/300172
Note : Language of publication: fr



Y. Van Eycke, O. Debeir, L. Verset, P. Demetter, I. Salmon, C. Decaestecker,
Automated Tissue Microarray Image Processing in Digital Pathology.
Proceedings of the Fifth joint WIC/IEEE SP Symposium on Information Theory and Signal Processing in the Benelux, Brussels, Belgium, 2015
Bibtex
Bibtex : info:hdl:2013/199489
Note : Language of publication: en



A. Schenkel, O. Debeir,
Comparison of Normalized Transfer Functions for Fast Blending-based Color Correction of Scans Acquired under Natural Conditions
Proceedings of the Digital Heritage International Congress 2015, pp. 4, Grenada, Spain, 2015
Bibtex
Bibtex : info:hdl:2013/246493
Note : Language of publication: en



K. Degraux, V. Cambareri, L. Jacques, B. Geelen, C. Blanch, G. Lafruit,
Generalized Inpainting Method for Hyperspectral Image Acquisition
IEEE International Conference on Image Processing, 2015
Bibtex
Bibtex : info:hdl:2013/199469
Note : Language of publication: na



Y. Van Eycke, O. Debeir, L. Verset, P. Demetter, I. Salmon, C. Decaestecker,
High-Throughput Analysis of Tissue-Based Biomarkers in Digital Pathology
EMBC'15 Proceedings (IEEE Engineering in Medicine and Biology Society), pp. 7732 - 7735, Milan, 2015
Bibtex
Bibtex : info:hdl:2013/205314
Note : Language of publication: en



L. Verset, J. Tommelein, X. Moles Lopez, C. Decaestecker, T. Boterberg, E. De Vlieghere, I. Salmon, M. Mareel, M. Bracke, O. De Wever, P. Demetter,
Impact of neoadjuvant therapy on cancer-associated fibroblast in rectal cancer
Conference: Joint Meeting of the British Division of the International Academy of Pathology and the Pathological Society of Great Britain & Ireland(8th: 23 – 25 June 2015: Dublin), 2015
Bibtex
Bibtex : info:hdl:2013/223057
Note : Language of publication: en



L. De Smedt, J. Lemahieu, S. Palmans, O. Govaere, T. Tousseyn, E. van Cutsem, H. Prenen, S. Tejpar, C. Decaestecker, X. Moles Lopez, P. Demetter, I. Salmon, X. Sagaert,
Microsatellite instability versus microsatellite stability in colon carcinoma: documentation of tumour heterogeneity and inflammation
Conference: Belgian Week of Gastroenterology(XXVIIth : February 2015: Brussels), 2015
Bibtex
Bibtex : info:hdl:2013/223062
Note : Language of publication: en



L. Jorissen, P. Goorts, S. Rogmans, G. Lafruit, P. Bekaert,
Multi-Camera Epipolar Plane Image feature detection for Robust View Synthesis
3DTV-CON Immersive and Interactive 3D Media Experience over Networks, 2015
Bibtex
Bibtex : info:hdl:2013/200057
Note : Language of publication: fr



A. Schenkel, O. Debeir,
Real-time Fullscale Model Colorization and Global Color Quality Evaluation for Rapid Scanning in Uncontrolled Environment
Proceedings of the 36th WIC Symposium on Information Theory in the Benelux and the 5th Joint WIC/IEEE Symposium on Information Theory and Signal Processing in the Benelux, pp. 20-25, May 06-07, 2015: Brussels, Belgium, 2015
Bibtex
Bibtex : info:hdl:2013/246503
Note : Language of publication: fr



A. Trepant, C. Maris, N. D'Haene, S. Sauvage, S. Rorive, C. Decaestecker, I. Salmon, P. Demetter,
Role of IGFIIR/Man-6-P in Glioblastoma angiogenesis
Conference: Joint Meeting of the British Division of the International Academy of Pathology and the Pathological Society of Great Britain & Ireland(8 th: 23 – 25 June 2015: Dublin), 2015
Bibtex
Bibtex : info:hdl:2013/223051
Note : Language of publication: en



N. D'Haene, C. Koopmansch, J. Allard, F. Hulet, X. Moles Lopez, Y. Van Eycke, C. Decaestecker, I. Salmon,
The prognostic value of the VEGFR-1 and -2 combinations in endothelial cells of colorectal cancer.
Conference: Belgian Week of Pathology 2015 (October 2015: Ghent, Belgium), 2015
Bibtex
Bibtex : info:hdl:2013/224048
Note : abstract P01 (p. 156)



Thesis

C. Mertens,
Analysis of vocal tremor in normophonic and dysphonic speakers
2015
Bibtex
Bibtex : info:hdl:2013/218423
Note : Doctorat en Sciences de l'ingénieur et technologie
Abstract : The study concerns the analysis of vocal cycle length perturbations in normophonic and dysphonic speakers.A method for tracking cycle lengths in voiced speech is proposed. The speech cycles are detected via the saliences of the speech signal samples, defined as the length of the temporal interval over which a sample is a maximum. The tracking of the cycle lengths is based on a dynamic programming algorithm that does not request that the signal is locally periodic and the average period length known a priori.The method is validated on a corpus of synthetic stimuli. The results show a good agreement between the extracted and the synthetic reference length time series. The method is able to track accurately low-frequency modulations and ast cycle-to-cycle perturbations of up to 10\% and 4\% respectively over the whole range of vocal frequencies. Robustness with regard to the background noise has lso been tested. The results indicate that the tracking is reliable for signal-to-noise ratios higher than 15dB.A method for analyzing the size of the cycle length perturbations as well as their frequency is proposed. The cycle length time series is decomposed into a sum of oscillating components by empirical mode decomposition the instantaneous envelopes and frequencies of which are obtained via AM-FM decomposition. Based on their average instantaneous frequencies, the empirical modes are then assigned to four categories (declination, physiological tremor, neurological tremor as well as cycle length jitter) and added within each. The within-category size of the cycle length perturbations is estimated via the standard deviation of the empirical mode sum divided by the average cycle length. The neurological tremor modulation frequency and bandwidth are obtained via the instantaneous frequencies and amplitudes of empirical modes in the neurological tremor category and summarized via a weighted instantaneous frequency probability density, compensating for the effects of mode mixing.The method is applied to two corpora of vowels comprising 123 and 74 control and 456 and 205 Parkinson speaker recordings respectively. The results indicate that the neurological tremor modulation depth is statistically significantly higher for female Parkinson speakers than for female control speakers. Neurological tremor frequency differs statistically significantly between male and female speakers and increases statistically significantly for the pooled Parkinson speakers compared to the pooled control speakers. Finally, the average vocal frequency increases for male Parkinson speakers and decreases for female Parkinson speakers, compared to the control speakers.



L. Boussemaere,
Investigating off-axis digital holographic microscopy with a source of partial spatial coherence as a real-time sensor for cell cultures
2015
Bibtex
Bibtex : info:hdl:2013/209086
Note : Doctorat en Sciences de l'ingénieur
Abstract : Bio-pharmaceutical industry is a vast growing market and recent recommendations of the Food and Drug Administration have put a large emphasis on the characterization of biological processes and models. As a consequence, there is a high incentive on developing modern sensors in order to more accurately monitor and control processes. In that way, Digital Holographic Microscopy (DHM) presents unique features thanks to the refocusing and quantitative phase contrast imaging capabilities. In this thesis we investigate the usage of DHM to monitor yeast cultures that are often used in both the bio-pharmaceutical and bread industries and lay the basis of a methodological framework for the study of in-line cell cultures in the context of process control. We begin with a description of Digital Holography and the microscopy setup used in the thesis as well as a detailed explanation of the image processing required to extract the holographic data and its implementation on GPU with some speed execution figures given for three popular programming paradigms. We then describe the flow setup used and infer the limitations on the dynamic range of the technique due to both Poisson statistics and overlapping phenomena. Finally, we describe an algorithm that extracts the cells position, count and morphological information such as the size, aspect ratio, circularity and refraction index. Some experimental results are presented for yeasts before drawing a general overview of the technology and its dependencies. We further end with some conclusions concerning the technology and a brief comparison with existing competitors.



Q. Ren,
Remote sensing of sediment characteristics from the noise field due to a moving ship
2015
Bibtex
Bibtex : info:hdl:2013/222087
Note : Doctorat en Sciences de l'ingénieur et technologie
Abstract : Qun-yan Ren received his Diploma in Electronic and Information Engineering, master degree in Underwater Acoustics Engineering both from Harbin Engineering University (HEU) in 2006 and 2009, respectively. Then he became a PhD student at the Environmental Hydroacoustics Laboratory, Ecole polytechnique de Bruxelles, Faculty of Applied Sciences, Universitie libre de Bruxelles (U.L.B.), Belgium, in co-tutelle with the National Key Laboratory of Underwater Acoustic Technology, HEU, China, under the co-supervision of Prof. Jean-Pierre Hermand and Prof. Piao Shengchun from U.L.B. and HEU, respectively. Since 2013, he became a full PhD student at the ULB. In Oct 2011, he obtained a four-year `Aspirantq\{\} grant from the Belgian National Fund for Scientific Research (F.R.S.-F.N.R.S.).




2014

Papers

P. Mainali, G. Lafruit, K. Tack, L. Gool, R. Lauwereins,
D-SIFER: Derivative-based Scale Invariant Image Feature Detector with Error Resilience
IEEE transactions on image processing, Vol. 23, 5, pp. 2380-2391, 2014
Bibtex
Bibtex : info:hdl:2013/186269
Note : Language of publication: en



A. Duray, T. De Maesschalck, C. Decaestecker, M. Remmelink, G. Chantrain, J. Neiveyans, M. Horoi, X. Leroy, H. Gabius, S. Saussez,
Galectin fingerprinting in naso-sinusal diseases.
Oncology Reports, Vol. 32, 1, pp. 23-32, 2014
Bibtex
Bibtex : info:hdl:2013/174705
Note : Journal Article
Abstract : Galectins, a family of endogenous lectins, are multifunctional effectors that act at various sites and can be used in immunohistochemical localization studies of diseased states. Since they form a potentially cooperative and antagonistic network, we tested the hypothesis that histopathological fingerprinting of galectins could refine the molecular understanding of naso-sinusal pathologies. Using non-cross-reactive antibodies against galectin-1, -3, -4, -7, -8 and -9, we characterized the galectin profiles in chronic rhinosinusitis, nasal polyposis, inverted papillomas and squamous cell carcinomas. The expression, signal location and quantitative parameters describing the percentage of positive cells and labeling intensity were assessed for various cases. We discovered that inverted papillomas showed a distinct galectin immunohistochemical profile. Indeed, epithelial overexpression of galectin-3 (p=0.0002), galectin-4 (p<10-6), galectin-7 (p<10-6) and galectin-9 (p<10-6) was observed in inverted papillomas compared to non-malignant diseases. Regarding carcinomas, we observed increased expression of galectin-9 (p<10-6) in epithelial cells compared to non-tumor pathologies. Our results suggest that galectin-3, -4, -7 and -9 could be involved in the biology of inverted papillomas. In addition, we observed that the expression of galectin in naso-sinusal diseases seems to be affected by tumor progression and not inflammatory or allergic phenomena.



N. D'Haene, C. Maris, S. Rorive, C. Decaestecker, M. Le Mercier, I. Salmon,
Galectins and neovascularization in central nervous system tumors.
Glycobiology, Vol. 24, 10, pp. 892-898, 2014
Bibtex
Bibtex : info:hdl:2013/175597
Note : Journal Article
Abstract : Despite advances in diagnosis and treatment, the overall outcomes for patients with brain tumors remain unpredictable. New prognostic markers are still needed to identify high-risk patients for whom the standard treatment has poor outcomes and would thus be well suited for more aggressive therapies. Neovascularization has long been implicated as a salient feature of glioma progression. In fact, high-grade gliomas are among the most vascular of all solid tumors, and vascular proliferation is a pathological hallmark of glioblastomas. Galectins are known to play important roles in cancer biology, including cancer cell migration, tumor immune escape or tumor angiogenesis. Moreover, galectins were reported to be involved in glioma progression. Given the key role of angiogenesis in brain tumors, the expression of galectins in tumor-associated endothelial cells (EC) and the implication of galectins in angiogenesis, the present review will focus on the expression of galectins in ECs of normal brain and brain tumors.



V. Arcolia, P. Paci, L. Dhont, G. Chantrain, N. Sirtaine, C. Decaestecker, M. Remmelink, A. Belayew, S. Saussez,
Helicase-like transcription factor: a new marker of well-differentiated thyroid cancers.
BMC cancer, Vol. 14, 1, pp. 492, 2014
Bibtex
Bibtex : info:hdl:2013/174707
Note : Journal Article
Abstract : The preoperative characterization of thyroid nodules is a challenge for the clinicians. Fine-needle aspiration (FNA) is the commonly used pre-operative technique for diagnosis of malignant thyroid tumor. However, many benign lesions, with indeterminate diagnosis following FNA, are referred to surgery. There is an urgent need to identify biomarkers that could be used with the FNA to distinguish benign thyroid nodules from malignant tumors. The purpose of the study is to examine the level of expression of the helicase-like transcription factor (HLTF) in relation to neoplastic progression of thyroid carcinomas.



J. Allard, X. Moles Lopez, K. Li, O. Blanchard, P. Barbot, S. Rorive, C. Decaestecker, R. Pochet, D. Bohl, A. Lepore, I. Salmon, C. Nicaise,
Immunohistochemical toolkit for tracking and quantifying xenotransplanted human stem cells.
Regenerative medicine, Vol. 9, 4, pp. 437-452, 2014
Bibtex
Bibtex : info:hdl:2013/174921
Note : Journal Article
Abstract : Biomarker-based tracking of human stem cells xenotransplanted into animal models is crucial for studying their fate in the field of cell therapy or tumor xenografting.



V. Richard, N. Kindt, C. Decaestecker, H. Gabius, G. Laurent, J. No{\"e}l, S. Saussez,
Involvement of macrophage migration inhibitory factor and its receptor (CD74) in human breast cancer.
Oncology Reports, Vol. 32, 2, pp. 523-529, 2014
Bibtex
Bibtex : info:hdl:2013/174706
Note : Journal Article
Abstract : Macrophage migration inhibitory factor (MIF) and its receptor CD74 appear to be involved in tumorigenesis. We evaluated, by immunohistochemical staining, the tissue expression and distribution of MIF and CD74 in serial sections of human invasive breast cancer tumor specimens. The serum MIF level was also determined in breast cancer patients. We showed a significant increase in serum MIF average levels in breast cancer patients compared to healthy individuals. MIF tissue expression, quantified by a modified Allred score, was strongly increased in carcinoma compared to tumor-free specimens, in the cancer cells and in the peritumoral stroma, with fibroblasts the most intensely stained. We did not find any significant correlation with histoprognostic factors, except for a significant inverse correlation between tumor size and MIF stromal positivity. CD74 staining was heterogeneous and significantly decreased in cancer cells but increased in the surrounding stroma, namely in lymphocytes, macrophages and vessel endothelium. There was no significant variation according to classical histoprognostic factors, except that CD74 stromal expression was significantly correlated with triple-negative receptor (TRN) status and the absence of estrogen receptors. In conclusion, our data support the concept of a functional role of MIF in human breast cancer. In addition to auto- and paracrine effects on cancer cells, MIF could contribute to shape the tumor microenvironment leading to immunomodulation and angiogenesis. Interfering with MIF effects in breast tumors in a therapeutic perspective remains an attractive but complex challenge. Level of co-expression of MIF and CD74 could be a surrogate marker for efficacy of anti-angiogenic drugs, particularly in TRN breast cancer tumor.



N. Komen, J. Slieker, P. Willemsen, G. Mannaerts, P. Pattyn, T. Karsten, H. de Wilt, E. van der Harst, W. Van Leeuwen, C. Decaestecker, H. Jeekel, J. Lange,
Polymerase chain reaction for Enterococcus faecalis in drain fluid: the first screening test for symptomatic colorectal anastomotic leakage. The Appeal-study: analysis of parameters predictive for evident anastomotic leakage.
International journal of colorectal disease, Vol. 29, 1, pp. 15-21, 2014
Bibtex
Bibtex : info:hdl:2013/157762
Note : Journal Article
Abstract : With current diagnostic methods, the majority of patients with symptomatic colorectal anastomotic leakage(CAL) is identified approximately 1 week after operation.The aim of this study is to determine whether real-time polymerase chain reaction (RT-PCR) for detection of Escherichia coli and Enterococcus faecalis on drain fluid can serve as a screening test for CAL in the early postoperative phase.



Conferences

D. Mouraux, B. Penelle, E. Brassinne, S. Sobczak, A. Nonclercq, T. Tuna, N. Warzée,
3D augmented reality mirror visual feedback applied to the treatment of persistent neuropathic pain in the upper extremity
Conference: XIXth FESSH and XIth EFSHT joint meeting(18-21 June, 2014: Paris, France), 2014
Bibtex
Bibtex : info:hdl:2013/300029
Note : Language of publication: en



D. Mouraux, B. Penelle, E. Brassinne, S. Sobczak, A. Nonclercq, T. Tuna, N. Warzée,
3D augmented reality mirror visual feedback applied to the treatment of persistent neuropathic pain in the upper extremity.
Conference: 1st Symposium on Serious Gaming Technology as Clinical Tool in Rehabilitation(17-18 Feb., 2014: Brussels, Belgium), 2014
Bibtex
Bibtex : info:hdl:2013/163270
Note : Language of publication: en



L. Jorissen, P. Goorts, B. Bex, N. Michiels, S. Rogmans, P. Bekaert, G. Lafruit,
A qualitative comparison of MPEG view synthesis and light field rendering
3DTV-CON, 2014
Bibtex
Bibtex : info:hdl:2013/186780
Note : Language of publication: en



L. Jorissen, P. Goorts, B. Bex, N. Michiels, S. Rogmans, P. Bekaert, G. Lafruit,
A Qualitative Comparison of MPEG View Synthesis and Light Field Rendering
3DTV-CON, 2014
Bibtex
Bibtex : info:hdl:2013/188480
Note : Language of publication: na



K. Degraux, V. Cambareri, B. Geelen, L. Jacques, G. Lafruit, G. Setti,
Hyperspectral Compressive Sensing
iTWIST'14: international – International Traveling Workshop on Interactions between Sparse models and Technology, 2014
Bibtex
Bibtex : info:hdl:2013/186781
Note : Language of publication: en



A. Trepant, C. Bouchart, S. Rorive, S. Sauvage, C. Decaestecker, P. Demetter, I. Salmon,
Identification of OLIG2 as most specific glioblastoma stem cell marker starting from comparative analysis of data from similar DNA chip microarray platforms
Conference: 19th World Congress on Advances in Oncology and 17th International Symposium on Molecular Medecine(October 9-11, 2014: Athens), 2014
Bibtex
Bibtex : info:hdl:2013/193429
Note : Language of publication: en



G. Lafruit,
Keynote IWCIM: Image-based 3D scene visualization and Free Viewpoint TV
International Workshop on Computational Intelligence for Multimedia understanding, 2014
Bibtex
Bibtex : info:hdl:2013/253845
Note : Language of publication: en



R. Stahl, G. Vanmeerbeeck, G. Lafruit, V. Reumers, R. Huys, A. Lambrechts, M. Yashiro, M. Takemoto, N. Nishishita, S. Kawamata, S. Gomi, K. Hatabayashi, Y. Oshima, S. Ozaki,
Lens-free digital in-line holographic imaging for wide field-of-view, high resolution and real-time monitoring of complex microscopic objects
Proc. SPIE BiOS, 2014
Bibtex
Bibtex : info:hdl:2013/186782
Note : Language of publication: en



B. Penelle, O. Debeir,
Multi-sensor data fusion for hand tracking using Kinect and leap motion
Laval Virtual VRIC’14, Laval, France, 2014
Bibtex
Bibtex : info:hdl:2013/163271
Note : Language of publication: en



Y. Van Eycke, X. Moles Lopez, J. Allard, M. Derock, S. Rorive, I. Salmon, C. Decaestecker,
Multiresolution registration of whole slide images to evidence and quantify virtual colocalization of tissue-based biomarkers
Conference: Digital Pathology Congress(4-5 December 2014: London), 2014
Bibtex
Bibtex : info:hdl:2013/193430
Note : Language of publication: en
Abstract : Extracting relevant information from actors involved in complex biological processes (such as cancers or treatment responses) requires to target different antigens simultaneously. Multichromogenic (brightfield) immunohistochemistry (IHC) suffers from limitations that notably prevent the analysis of proteins expressed in the same cellular compartment. We thus developed an alternative based on the analysis of adjacent, or serial, tissue sections on which different proteins were targeted by means of standard IHC. For this analysis, we developed a multiresolution method for registering serial slide images. This method uses the pyramidal and multimodal registration framework of the elastix software to optimize two parametric registrations. The first, low-resolution registration, is applied on the 1X equivalent magnification images (4,000 by 3,000 pixels). The result of this first step was then used to initialize high-resolution registrations independently performed on 20X equivalent fields of view. Our method shows accuracy levels compatible with biomarker colocalization characterization. Indeed, registration error on serial slides was evaluated to be at most between 20 µm and 80 µm, depending respectively of the presence or absence of histological structures in the tissue (e.g. in colonic tumor as compared to brain gliomas). In the latter situation, a sequential IHC technique applied on the same slide can be usefully employed. This “Sequential Immunoperoxidase Labeling and Erasing” (SIMPLE) method is based on cycles of staining/digitization/erasing, where after IHC staining and slide digitization, staining is erased through an antibody elution technique. We improved the original SIMPLE method and successfully utilized it to identify antigens expressed in the same cellular compartment of high-grade glioma samples. We tested our registration on the virtual slides so obtained and achieved very good results, i.e. about 5 µm of registration error. We then implemented a method to extract biomarker colocalization measurements taking the level of registration error into account and validated our complete procedure by comparison to colocalization information obtained by means of double staining (with different cell locations).



P. Goorts, S. Maesen, Y. Liu, M. Dumont, P. Bekaert, G. Lafruit,
Real-time Local Stereo Matching using Edge Sensitive Adaptive Windows
SIGMAP, 2014
Bibtex
Bibtex : info:hdl:2013/188479
Note : Language of publication: na



X. Moles Lopez, C. Maris, T. Chattaway, M. Remmelink, B. Weynand, S. Rorive, C. Decaestecker, I. Salmon,
SecundOS: A Belgian digital pathology initiative to implement an inter-university network for second opinions and collaboration between expert pathologists.
Conference: Digital Pathology Congress(4-5 December 2014: London), 2014
Bibtex
Bibtex : info:hdl:2013/193431
Note : Available at http://www.globalengage.co.uk/pathology/posters14.pdf (Abstract No 11)



P. Goorts, S. Maesen, Y. Liu, M. Dumont, P. Bekaert, G. Lafruit,
Self-Calibration of Large Scale Camera Networks
SIGMAP, 2014
Bibtex
Bibtex : info:hdl:2013/188478
Note : Language of publication: na



Books chapters

M. Dumont, P. Goorts, G. Lafruit,
Plane Sweeping in eye-gaze corrected, tele-immersive 3D video conferencing
Springer, pp. 135-161, 2014
Bibtex
Bibtex : info:hdl:2013/187055
Note : Language of publication: na



Moles Lopez, Xavier, Debeir, Olivier, Salmon, Isabelle, Decaestecker, Christine,
Whole slide imaging and analysis for biomarker evaluation in digital pathology
A. Méndez-Vilas (Ed.), Microscopy: advances in scientific research and education, Vol. 2, pp. 776-787, 2014
Bibtex
Bibtex : info:hdl:2013/175598
Note : Language of publication: na



Thesis

B. Mertens,
Bringing 3D and quantitative data in flexible endoscopy
2014
Bibtex
Bibtex : info:hdl:2013/209275
Note : Doctorat en Sciences de l'ingénieur
Abstract : In a near future, the computation power will be widely used in endoscopy rooms. It will enable the augmented reality already implemented in some surgery. Before reaching this, a preliminary step is the development of a 3D reconstruction endoscope. In addition to that, endoscopists suffer from a lack of quantitative data to evaluate dimensions and distances, notably for the polyp size measurement.<p>In this thesis, a contribution to more a robust 3D reconstruction endoscopic device is proposed. Structured light technique is used and implemented using a diffractive optical element. Two patterns are developed and compared: the first is based on the spatial-neighbourhood coding strategy, the second on the direct-coding strategy. The latter is implemented on a diffractive optical element and used in an endoscopic 3D reconstruction device. It is tested in several conditions and shows excellent quantitative results but the robustness against bad visual conditions (occlusions, liquids, specular reflection,...) must be improved. <p>Based on this technology, an endoscopic ruler is developed. It is dedicated to answer endoscopists lack of measurement system. The pattern is simplified to a single line to be more robust. Quantitative data show a sub-pixel accuracy and the device is robust in all tested cases. The system has then been validated with a gastroenterologist to measure polyps. Compared to literature in this field, this device performs better and is more accurate.



X. Moles Lopez,
Characterization and Colocalization of Tissue-Based Biomarker Expression by Quantitative Image Analysis: Development and Extraction of Novel Features
2014
Bibtex
Bibtex : info:hdl:2013/209330
Note : Doctorat en Sciences de l'ingénieur
Abstract : Proteins are the actual actors in the (normal or disrupted) physiological processes and immunohistochemistry (IHC) is a very efficient mean of visualizing and locating protein expression in tissue samples. By comparing pathologic and normal tissue, IHC is thus able to evidence protein expression alterations. This is the reason why IHC plays a grow- ing role to evidence tissue-based biomarkers in clinical pathology for diagnosing var- ious diseases and directing personalized therapy. Therefore, IHC biomarker evaluation significantly impacts the adequacy of the therapeutic choices for patients with serious pathologies, such as cancer. However, this evaluation may be time-consuming and dif- ficult to apply in practice due to the absence of precise positive cut-off values as well as staining (i.e. protein expression) heterogeneity intra- and inter-samples. Quantifying IHC staining patterns has thus become a crucial need in histopathology. For this task, automated image analysis has multiple advantages, such as avoiding the evidenced ef- fects of human subjectivity. The recent introduction of whole-slide scanners opened a wide range of possibilities for addressing challenging image analysis problems, includ- ing the identification of tissue-based biomarkers. Whole-slide scanners are devices that are able to image whole tissue slides at resolutions up to 0.1 micrometers per pixels, often referred to as virtual slides. In addition to quantification of IHC staining patterns, virtual slides are invaluable tools for the implementation of digital pathology work- flows. The present work aims to make several contributions towards this current digital shift in pathology. Our first contribution was to propose an automated virtual slide sharpness assessment tool. Although modern whole-slide scanner devices resolve most image standardization problems, focusing errors are still likely to be observed, requiring a sharpness assessment procedure. Our proposed tool will ensure that images provided to subsequent pathologist examination and image analysis are correctly focused. Virtual slides also enable the characterization of biomarker expression heterogeneity. Our sec- ond contribution was to propose a method to characterize the distribution of densely stained regions in the case of nuclear IHC biomarkers, with a focus on the identification of highly proliferative tumor regions by analyzing Ki67-stained tissue slides. Finally, as a third contribution, we propose an efficient mean to register virtual slides in order to characterize biomarker colocalization on adjacent tissue slides. This latter contribution opens new prospects for the analysis of more complex questions at the tissue level and for finely characterizing disease processes and/or treatment responses./Les protéines sont les véritables acteurs des processus physiologiques (normaux ou per- turbés) et l’immunohistochimie (IHC) est un moyen efficace pour visualiser et localiser leur expression au sein d’échantillons histologiques. En comparant des échantillons de tissus pathologiques et normaux, l’IHC permet de révéler des altérations dans des pro- fils d’expression protéique. C’est pourquoi l’IHC joue un rôle de plus en plus important pour mettre en évidence des biomarqueurs histologiques intervenant dans le diagnos- tic de diverses pathologies et dans le choix de thérapies personnalisées. L’évaluation de l’expression de biomarqueurs révélés par IHC a donc des répercussions importantes sur l’adéquation des choix thérapeutiques pour les patients souffrant de pathologies graves, comme le cancer. Cependant, cette évaluation peut être chronophage et difficile à appliquer en pratique, d’une part, à cause de l’hétérogénéité de l’expression protéique intra- et inter-échantillon, d’autre part, du fait de l’absence de critères de positivité bien définis. Il est donc devenu crucial de quantifier les profils d’expression de marquages IHC en histopathologie. A cette fin, l’analyse d’image automatisée possède de multiples avantages, comme celui d’éviter les effets de la subjectivité humaine, déjà démontrés par ailleurs. L’apparition récente des numériseurs de lames histologiques complètes, ou scanners de lames, a permis l’émergence d’un large éventail de possibilités pour traiter des problèmes d’analyse d’image difficiles menant à l’identification de biomar- queurs histologiques. Les scanners de lames sont des dispositifs capables de numériser des lames histologiques à une résolution pouvant atteindre 0,1 micromètre par pixel, expliquant la dénomination de "lames virtuelles" des images ainsi acquises. En plus de permettre la quantification des marquages IHC, les lames virtuelles sont des outils indis- pensables pour la mise en place d’un flux de travail numérique en pathologie. Le travail présenté ici vise à fournir plusieurs contributions au récent changement de cap vers une numérisation de la discipline médicale qu’est l’anatomie pathologique. Notre première contribution consiste en un outil permettant d’évaluer automatiquement la netteté des lames virtuelles. En effet, bien que les scanners de lames résolvent la plupart des pro- blèmes liés à la standardisation de l’acquisition, les erreurs de focus restent fréquentes, ce qui nécessite la mise en place d’une procédure de vérification de la netteté. L’outil que nous proposons assurera la netteté des images fournies à l’examen du pathologiste et à l’analyse d’image. Les lames virtuelles permettent aussi de caractériser l’hétérogénéité de l’expression de biomarqueurs. Ainsi, la deuxième contribution de ce travail repose sur une méthode permettant de caractériser la distribution de régions densément marquées par des biomarqueurs IHC nucléaires. Pour ce travail, nous nous sommes concentrés sur l’identification de régions tumorales présentant une forte activité proliférative en analysant des lames virtuelles révélant l’expression de la protéine Ki67. Finalement, la troisième contribution de ce travail fut de proposer un moyen efficace de recaler des lames virtuelles dans le but de caractériser la colocalisation de biomarqueurs IHC révé- lés sur des coupes de tissu adjacentes. Cette dernière contribution ouvre de nouvelles perspectives pour l’analyse de questions complexes au niveau histologique ainsi que la caractérisation fine de processus pathologiques et de réponses thérapeutiques.



K. Lidouh,
Integration of multi-criteria tools in geographical information systems
2014
Bibtex
Bibtex : info:hdl:2013/209356
Note : Doctorat en Sciences de l'ingénieur
Abstract : For a little over twenty years, researchers have worked on integrating multi-criteria aggregation procedures (MCAP) to GIS. Several notable contributions have brought this field to what it is today. After studying the course of MCDA-GIS integration through several works, we question the future of such an attempt. Indeed most works that aim for an integration do not survive long after their direct purpose has been fulfilled. We end up understanding through a critical review of the existing systems that technical integration means nothing if it is not visible to the user on an operational level.<p><p>We therefore propose several contributions to improve the usability of MCDA methods in a geographic context. One of our works consists in adapting the PROMETHEE-GAIA methodology to be used on maps for spatially referenced problems. To do so, we define symbols/glyphs that display select parts of the results obtained through the PROMETHEE and GAIA methods. This allows for the comparison of alternatives' profiles and characteristics based on their geographic location which wasn't possible before. This adaptation helps us combine multicriteria and geographic aspects in an entirely new way.<p>We also propose some extensions of the GAIA method to improve the quality of the results and reduce the risk of wrong interpretations to be made due to losses of data.



P. Goorts, G. Lafruit,
Real-time, Adaptive Plane Sweeping for Free Viewpoint Navigation in Soccer Scenes. Ingénieur
2014
Bibtex
Bibtex : info:hdl:2013/188496
Note : Language of publication: na



P. Mainali, G. Lafruit,
Robust Registration in Integrated Hyperspectral Imaging. Computer Engineering
2014
Bibtex
Bibtex : info:hdl:2013/188497
Note : Language of publication: na



B. Penelle,
Système de réalité virtuelle d'aide à la réalisation et à l'évaluation d'exercices physiques
2014
Bibtex
Bibtex : info:hdl:2013/209284
Note : Doctorat en Sciences de l'ingénieur
Abstract : Les travaux de recherche présentés dans cette thèse ont pour but de développer un système de réalité virtuelle d'aide à la réalisation et à l'évaluation d'exercices physiques. La notion d'exercice physique étant très large, nous avons pris le parti de cibler des exercices réalisés dans le cadre médical de traitements de rééducation fonctionnelle. Dans un premier temps, nous avons mis au point un socle technologique et algorithmique basé sur du matériel standard, peu co{\^u}teux, simple à installer et à utiliser. Il met en place les fondations nécessaires pour le développement d'applications de réalité virtuelle destinées à supporter et à superviser des exercices de rééducation, qu'ils soient réalisés dans un centre de rééducation, dans le cabinet d'un kinésithérapeute, ou à domicile. Sur base de ce socle, nous avons ensuite développé deux applications de rééducation ciblant des pathologies différentes. La première application est destinée aux patients atteints de douleurs neuropathiques telles que les douleurs fantômes (DF) chez les amputés ou le Syndrome Douloureux Régional Complexe (SDRC). Gr{\^a}ce à la réalité virtuelle, nous donnons l'illusion au patient qu'il peut à nouveau bouger son membre amputé ou pathologique, réduisant ainsi l'intensité des douleurs. La seconde application a pour but d'offrir au thérapeute et au patient un outil de quantification des mouvements réalisés dans le cadre d'exercices de rééducation motrice. Les mesures ainsi obtenues vont permettre d'aider le médecin à identifier et à objectiver le diagnostic d'une pathologie du mouvement, et, par la suite, vont permettre au kinésithérapeute d'en suivre l'évolution tout au long du traitement de rééducation. Pour chacune de ces applications, un algorithme spécifique de suivi de mouvements, basé sur le socle commun, est au cœur de la solution mise en œuvre.




2013

Papers

L. Twyffels, C. Wauquier, R. Soin, C. Decaestecker, C. Gueydan, V. Kruys,
A Masked PY-NLS in Drosophila TIS11 and Its Mammalian Homolog Tristetraprolin.
PloS one, Vol. 8, 8, pp. e71686, 2013
Bibtex
Bibtex : info:hdl:2013/150049
Note : Journal Article
Abstract : Many RNA-binding proteins (RBPs) dynamically shuttle between the nucleus and the cytoplasm, often exerting different functions in each compartment. Therefore, the nucleo-cytoplasmic distribution of RBPs has a strong impact on their activity. Here we describe the localization and the shuttling properties of the tandem zinc finger RBP dTIS11, which is the Drosophila homolog of mammalian TIS11 proteins. Drosophila and mammalian TIS11 proteins act as destabilizing factors in ARE-mediated decay. At equilibrium, dTIS11 is concentrated mainly in the cytoplasm. We show that dTIS11 is a nucleo-cytoplasmic shuttling protein whose nuclear export is mediated by the exportin CRM1 through the recognition of a nuclear export signal (NES) located in a different region comparatively to its mammalian homologs. We also identify a cryptic Transportin-dependent PY nuclear localization signal (PY-NLS) in the tandem zinc finger region of dTIS11 and show that it is conserved across the TIS11 protein family. This NLS partially overlaps the second zinc finger ZnF2. Importantly, mutations disrupting the capacity of the ZnF2 to coordinate a Zinc ion unmask dTIS11 and TTP NLS and promote nuclear import. All together, our results indicate that the nuclear export of TIS11 proteins is mediated by CRM1 through diverging NESs, while their nuclear import mechanism may rely on a highly conserved PY-NLS whose activity is negatively regulated by ZnF2 folding.



R. Marée, B. Stévens, L. Rollus, N. Rocks, X. Moles Lopez, I. Salmon, D. Cataldo, L. Wehenkel,
A rich internet application for remote visualization and collaborative annotation of digital slides in histology and cytology
Diagnostic Pathology, Vol. 8, Suppl 1, pp. S26, 2013
Bibtex
Bibtex : info:hdl:2013/176838
Note : Language of publication: en



X. Moles Lopez, E. D'Andrea, P. Barbot, A. Bridoux, S. Rorive, I. Salmon, O. Debeir, C. Decaestecker,
An Automated Blur Detection Method for Histological Whole Slide Imaging
PloS one, Vol. 8, 12, 2013
Bibtex
Bibtex : info:hdl:2013/152899
Note : SCOPUS: ar.j
Abstract : Whole slide scanners are novel devices that enable high-resolution imaging of an entire histological slide. Furthermore, the imaging is achieved in only a few minutes, which enables image rendering of large-scale studies involving multiple immunohistochemistry biomarkers. Although whole slide imaging has improved considerably, locally poor focusing causes blurred regions of the image. These artifacts may strongly affect the quality of subsequent analyses, making a slide review process mandatory. This tedious and time-consuming task requires the scanner operator to carefully assess the virtual slide and to manually select new focus points. We propose a statistical learning method that provides early image quality feedback and automatically identifies regions of the image that require additional focus points.



F. Cordelières, V. Petit, M. Kumasaka, O. Debeir, V. Letort, G. Stuart, L. Larue,
Automated Cell Tracking and Analysis in Phase-Contrast Videos (iTrack4U): Development of Java Software Based on Combined Mean-Shift Processes
PloS one, Vol. 8, 11, pp. 1-10, 2013
Bibtex
Bibtex : info:hdl:2013/152341
Note : SCOPUS: ar.j
Abstract : Cell migration is a key biological process with a role in both physiological and pathological conditions. Locomotion of cells during embryonic development is essential for their correct positioning in the organism; immune cells have to migrate and circulate in response to injury. Failure of cells to migrate or an inappropriate acquisition of migratory capacities can result in severe defects such as altered pigmentation, skull and limb abnormalities during development, and defective wound repair, immunosuppression or tumor dissemination. The ability to accurately analyze and quantify cell migration is important for our understanding of development, homeostasis and disease. In vitro cell tracking experiments, using primary or established cell cultures, are often used to study migration as cells can quickly and easily be genetically or chemically manipulated. Images of the cells are acquired at regular time intervals over several hours using microscopes equipped with CCD camera. The locations (x,y,t) of each cell on the recorded sequence of frames then need to be tracked. Manual computer-assisted tracking is the traditional method for analyzing the migratory behavior of cells. However, this processing is extremely tedious and time-consuming. Most existing tracking algorithms require experience in programming languages that are unfamiliar to most biologists. We therefore developed an automated cell tracking program, written in Java, which uses a mean-shift algorithm and ImageJ as a library. iTrack4U is a user-friendly software. Compared to manual tracking, it saves considerable amount of time to generate and analyze the variables characterizing cell migration, since they are automatically computed with iTrack4U. Another major interest of iTrack4U is the standardization and the lack of inter-experimenter differences. Finally, iTrack4U is adapted for phase contrast and fluorescent cells. © 2013 CORDELIERES et al.



N. D'Haene, C. Maris, S. Rorive, X. Moles Lopez, J. Rostang, C. Marchessoux, L. Pantanowitz, A. Parwani, I. Salmon,
Comparison study of five different display modalities for whole slide images in surgical pathology and cytopathology in Europe
Progress in biomedical optics and imaging, Vol. 8676, 2013
Bibtex
Bibtex : info:hdl:2013/148928
Note : SCOPUS: cp.p
Abstract : User experience with viewing images in pathology is crucial for accurate interpretation and diagnosis. With digital pathology, images are being read on a display system, and this poses new types of questions: such as what is the difference in terms of pixelation, refresh lag or obscured features compared to an optical microscope. Is there a resultant change in user performance in terms of speed of slide review, perception of adequacy and quality or in diagnostic confidence? A prior psychophysical study was carried out comparing various display modalities on whole slide imaging (WSI) in pathology at the University of Pittsburgh Medical Center (UPMC) in the USA. This prior study compared professional and non-professional grade display modalities and highlighted the importance of using a medical grade display to view pathological digital images. This study was duplicated in Europe at the Department of Pathology in Erasme Hospital (Université Libre de Bruxelles (ULB)) in an attempt to corroborate these findings. Digital WSI with corresponding glass slides of 58 cases including surgical pathology and cytopathology slides of varying difficulty were employed. Similar non-professional and professional grade display modalities were compared to an optical microscope (Olympus BX51). Displays ranged from a laptop (DELL Latitude D620), to a consumer grade display (DELL E248WFPb), to two professional grade monitors (Eizo CG245W and Barco MDCC-6130). Three pathologists were selected from the Department of Pathology in Erasme Hospital (ULB) in Belgium to view and interpret the pathological images on these different displays. The results show that non-professional grade displays (laptop and consumer) have inferior user experience compared to professional grade monitors and the optical microscope. © 2013 SPIE.



L. Verset, J. Tommelein, X. Moles Lopez, C. Decaestecker, M. Mareel, M. Bracke, I. Salmon, O. De Wever, P. Demetter,
Epithelial expression of FHL2 is negatively associated with metastasis-free and overall survival in colorectal cancer
British Journal of Cancer, Vol. 109, 1, pp. 114-120, 2013
Bibtex
Bibtex : info:hdl:2013/149047
Note : SCOPUS: ar.j
Abstract : Background:Four-and-a-half LIM domains protein 2 (FHL2) is a component of the focal adhesion structures and has been suggested to have a role in cancer progression. It has been shown to be overexpressed in the colorectal cancer (CRC).Methods:Here, we examined a possible prognostic value of FHL2 in CRC. Immunohistochemistry for FHL2 was performed on 296 CRCs without distant metastases at the time of surgery. Staining in the epithelial compartment was quantitatively evaluated using image analysis, and results were related to clinical variables. Antibody specificity was tested using small-interfering RNA transfection in hTERT-immortalised myofibroblasts.Results:Varying degrees of cytoplasmic FHL2 expression by neoplastic epithelial cells were detectable in all cases. Higher FHL2 expression in the epithelial compartment was an independent adverse prognostic factor. Multivariate Cox analysis shows that expression in the tumour invasion front (P<0.001) as well as in the centre of the tumour (P<0.001) was associated with metachronous metastases independently of the clinicopathological variables; expression in the tumour invasion front was also associated with overall survival independently of the clinicopathological variables (P<0.01).Conclusion:Higher FHL2 expression is involved in CRC progression and correlates with the development of metachronous metastases and overall survival, suggesting that FHL2 is an independent adverse prognostic indicator for CRC. © 2013 Cancer Research UK. All rights reserved.



M. Torres-Cisneros, G. Avina-Cervantes, E. Perez-Careta, F. Ambriz-Colin, V. Tinoco, O. Ibarra-Manzano, H. Plascencia-Mora, E. Aguilera-Gomez, M. Ibarra-Manzano, R. Guzman-Cabrera, O. Debeir, J. S{\'a}nchez-Mondrag{\'o}n,
Fast and accurate cell tracking by a novel optical-digital hybrid method
International journal of thermophysics, Vol. 34, 8-9, pp. 1435-1443, 2013
Bibtex
Bibtex : info:hdl:2013/183200
Note : SCOPUS: ar.j
Abstract : An innovative methodology to detect and track cells using microscope images enhanced by optical cross-correlation techniques is proposed in this paper. In order to increase the tracking sensibility, image pre-processing has been implemented as a morphological operator on the microscope image. Results show that the pre-processing process allows for additional frames of cell tracking, therefore increasing its robustness. The proposed methodology can be used in analyzing different problems such as mitosis, cell collisions, and cell overlapping, ultimately designed to identify and treat illnesses and malignancies. © Springer Science+Business Media New York 2013.



A. Duray, G. Descamps, C. Decaestecker, N. Sirtaine, A. Gilles, M. Khalifé, G. Chantrain, C. Depuydt, P. Delvenne, S. Saussez,
Human papillomavirus predicts the outcome following concomitant chemoradiotherapy in patients with head and neck squamous cell carcinomas.
Oncology Reports, Vol. 30, 1, pp. 371-376, 2013
Bibtex
Bibtex : info:hdl:2013/150048
Note : Journal Article
Abstract : We investigated the prevalence of human papillomavirus (HPV) in a clinical series of 72 patients with head and neck squamous cell carcinoma (HNSCC) using a retrospective and prospective study design. The majority of patients were smokers and/or drinkers and were treated with concomitant chemoradiotherapy (CCR). Furthermore, we assessed the impact of HPV positivity on the response to CCR. Paraffin-embedded samples from HNSCC patients (n=72) were evaluated for the presence of HPV DNA using both GP5+/GP6+ consensus PCR and type-specific E6/E7 PCR to detect HPV types 6, 11, 16, 18, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 67 and 68. The type-specific E6/E7 PCR demonstrated that 20 out of 69 HNSCC patients (29\%) presented with high-risk (HR) HPV types and that 5 of the 69 HNSCC patients (7\%) presented with low-risk (LR) HPV types. Using the GP5+/GP6+ PCR, we observed that the rate of response was statistically lower in the HPV+ group (P=0.02). Concerning patient outcomes in terms of recurrence and survival, we observed that the prognosis was poorer for HPV+ patients. We showed for the first time that patients with HPV+ HNSCC present with a worse prognosis after CCR. This observation highlights the need for prospective studies with large numbers of patients and a detailed history of tobacco and alcohol consumption before validating HPV as a marker of prognosis following CCR.



N. Kindt, J. Preillon, H. Kaltner, H. Gabius, D. Chevalier, A. Rodriguez, B. Johnson, V. Megalizzi, C. Decaestecker, G. Laurent, S. Saussez,
Macrophage migration inhibitory factor in head and neck squamous cell carcinoma: clinical and experimental studies.
Journal of cancer research and clinical oncology, Vol. 139, 5, pp. 727-737, 2013
Bibtex
Bibtex : info:hdl:2013/158182
Note : Journal Article
Abstract : The present in vivo/in vitro study was undertaken in order to evaluate the importance of macrophage migration inhibitory factor (MIF) in the progression of head and neck squamous cell carcinoma (HNSCC).



B. Mertens, B. De Leener, O. Debeir, C. Beumier, P. Lambert, A. Delchambre,
Robust Structured Light Pattern for Use with a Spatial Light Modulator in 3-D Endoscopy
International Journal of Optomechatronics, Vol. 7, 2, pp. 105-121, 2013
Bibtex
Bibtex : info:hdl:2013/143725
Note : SCOPUS: ar.j
Abstract : This article introduces a novel structured light pattern designed to be compatible with the spatial light modulator (SLM) projection. The proposed pattern is a De Bruijn-based sequence applied to a combination of continuous and dashed lines for the pattern. The sequence is coded in the period and duty cycles of the dashed lines. It provides 16 different lines which limits to two the required number of dashed lines needed for identification. The segmentation has been made easier by alternating continuous and dashed lines. As required by the use of SLMs, the sequence has been adapted by making it symmetric. It has been improved by guaranteeing a hamming distance equal to two for two successive dashed lines. The implementation on a virtual model has shown that a subpixel accuracy has been achieved. This pattern has been developped for 3-D endoscopy. © 2013 Copyright Taylor and Francis Group, LLC.



P. Mainali, G. Lafruit, Q. Yang, B. Geelen, L. Van Gool, R. Lauwereins,
SIFER: Scale-Invariant Feature Detector with Error Resilience
International journal of computer vision, Vol. 104, 2, pp. 172-197, 2013
Bibtex
Bibtex : info:hdl:2013/186270
Note : Language of publication: en



A. Nonclercq, C. Urbain, D. Verheulpen, C. Decaestecker, P. Van Bogaert, P. Peigneux,
Sleep spindle detection through amplitude-frequency normal modelling.
Journal of neuroscience methods, Vol. 214, 2, pp. 192-203, 2013
Bibtex
Bibtex : info:hdl:2013/139889
Note : Language of publication: en



N. D'Haene, S. Sauvage, C. Maris, I. Adanja, M. Le Mercier, C. Decaestecker, L. Baum, I. Salmon,
VEGFR1 and VEGFR2 Involvement in Extracellular Galectin-1- and Galectin-3-Induced Angiogenesis
PloS one, Vol. 8, 6, 2013
Bibtex
Bibtex : info:hdl:2013/148927
Note : SCOPUS: ar.j
Abstract : Aim:Accumulating evidence suggests that extracellular galectin-1 and galectin-3 promote angiogenesis. Increased expression of galectin-1 and/or galectin-3 has been reported to be associated with tumour progression. Thus, it is critical to identify their influence on angiogenesis.Methods:We examined the individual and combined effects of galectin-1 and galectin-3 on endothelial cell (EC) growth and tube formation using two EC lines, EA.hy926 and HUVEC. The activation of vascular endothelial growth factor receptors (VEGFR1 and VEGFR2) was determined by ELISA and Western blots. We evaluated the VEGFR1 and VEGFR2 levels in endosomes by proximity ligation assay.Results:We observed different responses to exogenous galectins depending on the EC line. An enhanced effect on EA.hy926 cell growth and tube formation was observed when both galectins were added together. Focusing on this enhanced effect, we observed that together galectins induced the phosphorylation of both VEGFR1 and VEGFR2, whereas galectin-1 and -3 alone induced VEGFR2 phosphorylation only. In the same way, the addition of a blocking VEGFR1 antibody completely abolished the increase in tube formation induced by the combined addition of both galectins. In contrast, the addition of a blocking VEGFR2 antibody only partially inhibited this effect. Finally, the addition of both galectins induced a decrease in the VEGFR1 and VEGFR2 endocytic pools, with a significantly enhanced effect on the VEGFR1 endocytic pool. These results suggest that the combined action of galectin-1 and galectin-3 has an enhanced effect on angiogenesis via VEGFR1 activation, which could be related to a decrease in receptor endocytosis. © 2013 D'Haene et al.



Conferences

A. Schenkel, N. Warzée, O. Debeir,
Fast Color Correction for Rapid Scanning in Uncontrolled Environment
Proceedings of the Digital Heritage International Congress 2013, pp. 413, Marseille, France, 2013
Bibtex
Bibtex : info:hdl:2013/153333
Note : Language of publication: en



X. Moles Lopez, P. Barbot, N. D'Haene, C. Maris, S. Rorive, I. Salmon, C. Decaestecker,
How Digital Image Analysis Applied to Immunohistochemistry Helps To Assess Biomarker Coexpression.
Conference: 102nd USCAP Annual Meeting, 2013
Bibtex
Bibtex : info:hdl:2013/193241
Note : Language of publication: na



B. Penelle, O. Debeir,
Human Motion Tracking for Rehabilitation using Depth Images and Particle Filter Optimization
ACM SIGGRAPH conference on Motion in Games 2013, pp. 1, Dublin, Ireland, 2013
Bibtex
Bibtex : info:hdl:2013/153314
Note : Language of publication: na



B. Penelle, O. Debeir,
Human motion tracking for rehabilitation using depth images and particle filter optimization
2nd International Conference on Advances in Biomedical Engineering (ICABME), pp. 211 - 214, Tripoli, Lebanon, 2013
Bibtex
Bibtex : info:hdl:2013/150968
Note : Language of publication: na



Q. Ren, O. Debeir, J. Hermand,
Hybrid method to extract striation features from ship noise spectrogram
OCEANS - Bergen, 2013 MTS/IEEE, 2013
Bibtex
Bibtex : info:hdl:2013/208288
Note : Language of publication: fr



L. Verset, J. Tommelein, X. Moles Lopez, C. Decaestecker, M. Mareel, M. Bracke, I. Salmon, O. De Wever, P. Demetter,
Investigation of a possible link between epithelial four-and-a-half LIM domains protein 2 expression and prognosis in colorectal cancer
Conference: 2013 Gastrointestinal Cancers Symposium, 2013
Bibtex
Bibtex : info:hdl:2013/193428
Note : Language of publication: en



N. D'Haene, F. Hulet, J. Allard, C. Maris, C. Decaestecker, I. Salmon,
VEGFR1: Target for Anti-Angiogenic Therapy? An Immunohistochemical Study Highlighting Heterogeneity of Tumor-Associated Endothelial Cells
Conference: the 102nd USCAP Annual Meeting(Baltimore), 2013
Bibtex
Bibtex : info:hdl:2013/193242
Note : Language of publication: na



Thesis

A. El Mallahi,
Automated 3D object analysis by digital holographic microscopy
2013
Bibtex
Bibtex : info:hdl:2013/209489
Note : Doctorat en Sciences de l'ingénieur
Abstract : The main objective of this thesis is the development of new processing techniques for digital holograms. The present work is part of the HoloFlow project that intends to integrate the DHM technology for the monitoring of water quality. Different tools for an automated analysis of digital holograms have been developed to detect, refocus and classify particles in continuous fluid flows. A detailed study of the refocusing criterion permits to determine its dependencies and to quantify its robustness. An automated detection procedure has been developed to determine automatically the 3D positions of organisms flowing in the experiment volume. Two detection techniques are proposed: a usual method based on a global threshold and a new robust and generic method based on propagation matrices, allowing to considerably increase the amount of detected organisms (up to 95 \%) and the reliability of the detection. To handle the case of aggregates of particles commonly encountered when working with large concentrations, a new separation procedure, based on a complete analysis of the evolution of the focus planes, has been proposed. This method allows the separation aggregates up to an overlapping area of around 80 \%. These processing tools have been used to classify organisms where the use of the full interferometric information of species enables high classifier performances to be reached (higher than 93 \%).



K. Siemes,
Establishing a sea bottom model by applying a multi-sensor acoustic remote sensing approach
2013
Bibtex
Bibtex : info:hdl:2013/209381
Note : Doctorat en Sciences de l'ingénieur
Abstract : Detailed information about the oceanic environment is essential for many applications in the field of marine geology, marine biology, coastal engineering, and marine operations. Especially, knowledge of the properties of the sediment body is often required. Acoustic remote sensing techniques have become highly attractive for classifying the sea bottom and for mapping the sediment properties, due to their high coverage capabilities and low costs compared to common sampling methods. In the last decades, a number of different acoustic devices and related techniques for analyzing their signals have evolved. Each sensor has its specific application due to limitations in the frequency range and resolution. In practice, often a single acoustic tool is chosen based on the current application, supported by other non-acoustic data where required. However, different acoustic remote sensing techniques can supplement each other, as shown in this thesis. Even more, a combination of complementary approaches can contribute to the proper understanding of sound propagation, which is essential when using sound for environmental classification purposes. This includes the knowledge of the relation between acoustics and sediment properties, the focus of this thesis. Providing a detailed three dimensional picture of the sea bottom sediments that allows for gaining maximum insight into this relation is aimed at.<p><p><p>Chapters 4 and 5 are adapted from published work, with permission:<p>DOI:10.1121/1.3569718 (link: http://asadl.org/jasa/resource/1/jasman/v129/i5/p2878\_s1) and<p>DOI:10.1109/JOE.2010.2066711 (link: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=5618582&queryText\%3Dsiemes)<p>In reference to IEEE copyrighted material which is used with permission in this thesis, the IEEE does not endorse any of the Université libre de Bruxelles' products or services.<p>



S. Rogmans, G. Lafruit,
Intelligent Visual Supercomputing on Hybrid Graphical Multiprocessor Environments. Computer Engineering
2013
Bibtex
Bibtex : info:hdl:2013/188498
Note : Language of publication: na



Q. Jossen,
Unsupervised learning procedure for nonintrusive appliance load monitoring
2013
Bibtex
Bibtex : info:hdl:2013/209369
Note : Doctorat en Sciences de l'ingénieur
Abstract : There is a continuously growing amount of appliances and energy dependent services in households. To date, efforts have mostly focused on energy efficiency, however behavior changes are required for a more sustainable energy consumption. People therefore need to understand their consumption habits to be able to adapt them. Appliance-specific feedback is probably the most efficient way to impact behaviors, since people need to ‘see’ where their electricity goes. Smart meters, currently being extensively rolled out in Europe and in the U.S., are good potential candidates to provide end-users with<p>energy advice. The required functionalities must however be rapidly defined if they are expected to be integrated in the future massive roll out.<p><p>Nonintrusive appliance load monitoring aims to derive appliance-specific information from the aggregate electricity consumption. While techniques have been developed since the 80’s, those mainly address the identification of previously learned appliances, from a database. Building such a database is an intrusive and tedious process which should be avoided. Whereas most recent efforts have focused on unsupervised techniques to disambiguate energy consumption into individual appliances, they usually rely on prior information about measured appliances such as the number of appliances, the number of states in each appliance as well as the power they consume in each state. This information should ideally be learned from the data. This topic will be addressed in the present research.<p><p>This work will present a framework for unsupervised learning for nonintrusive appliance<p>load monitoring. It aims to discover information about appliances of a household solely from its aggregate consumption data, with neither prior information nor user intervention. The learning process can be segmented into five tasks: the detection of on/off switching, the extraction of individual load signatures, the identification of<p>recurrent signatures, the discovery of two-state electrical devices and, finally, the elaboration<p>of appliance models. The first four steps will be addressed in this paper.<p><p>The suite of algorithms proposed in this work allows to discover the set of two-states electrical loads from their aggregated consumption. This, along with the evaluation<p>of their operating sequences, is a prerequisite to learn appliance models from the data. Results show that loads consuming power down to some dozens of watts can be learned from the data. This should encourage future researchers to consider such an unsupervised learning.



Misc

P. Mainali, G. Lafruit,
Feature Detection in Numeric Data
Language of publication: na, 2013
Bibtex
Bibtex : info:hdl:2013/188506
Note : Language of publication: na



O. Debeir,
la Réalité Augmentée: émission Utopia (RTBF-radio)
Language of publication: na, 2013
Bibtex
Bibtex : info:hdl:2013/160881
Note : Language of publication: na




2012

Papers

M. Le Mercier, D. Hastir, X. Moles Lopez, N. De Nève, C. Maris, A. Trepant, S. Rorive, C. Decaestecker, I. Salmon,
A simplified approach for the molecular classification of glioblastomas.
PloS one, Vol. 7, 9, 2012
Bibtex
Bibtex : info:hdl:2013/132976
Note : Journal Article
Abstract : Glioblastoma (GBM) is the most common malignant primary brain tumors in adults and exhibit striking aggressiveness. Although GBM constitute a single histological entity, they exhibit considerable variability in biological behavior, resulting in significant differences in terms of prognosis and response to treatment. In an attempt to better understand the biology of GBM, many groups have performed high-scale profiling studies based on gene or protein expression. These studies have revealed the existence of several GBM subtypes. Although there remains to be a clear consensus, two to four major subtypes have been identified. Interestingly, these different subtypes are associated with both differential prognoses and responses to therapy. In the present study, we investigated an alternative immunohistochemistry (IHC)-based approach to achieve a molecular classification for GBM. For this purpose, a cohort of 100 surgical GBM samples was retrospectively evaluated by immunohistochemical analysis of EGFR, PDGFRA and p53. The quantitative analysis of these immunostainings allowed us to identify the following two GBM subtypes: the "Classical-like" (CL) subtype, characterized by EGFR-positive and p53- and PDGFRA-negative staining and the "Proneural-like" (PNL) subtype, characterized by p53- and/or PDGFRA-positive staining. This classification represents an independent prognostic factor in terms of overall survival compared to age, extent of resection and adjuvant treatment, with a significantly longer survival associated with the PNL subtype. Moreover, these two GBM subtypes exhibited different responses to chemotherapy. The addition of temozolomide to conventional radiotherapy significantly improved the survival of patients belonging to the CL subtype, but it did not affect the survival of patients belonging to the PNL subtype. We have thus shown that it is possible to differentiate between different clinically relevant subtypes of GBM by using IHC-based profiling, a method that is advantageous in its ease of daily implementation and in large-scale clinical application.



M. Cammaerts Tricot, F. Morel, F. Martino, N. Warzée,
An easy, cheap computerized method to assess two-dimensional trajectory parameters
Belgian journal of zoology, Vol. 142, 2, pp. 147-153, 2012
Bibtex
Bibtex : info:hdl:2013/179439
Note : SCOPUS: ar.j



D. Tondeleir, A. Lambrechts, M. Mueller, V. Jonckheere, T. Doll, D. Vandamme, K. Bakkali, D. Waterschoot, M. Lemaistre, O. Debeir, C. Decaestecker, B. Hinz, A. Staes, E. Timmerman, N. Colaert, K. Gevaert, J. Vanderkerckove, C. Ampe,
Cells lacking β-actin are genetically reprogrammed and maintain conditional migratory capacity
Molecular & cellular proteomics, Vol. 11, 8, pp. 255-71, 2012
Bibtex
Bibtex : info:hdl:2013/113768
Note : SCOPUS: ar.j
Abstract : Vertebrate nonmuscle cells express two actin isoforms: cytoplasmic β- and γ-actin. Because of the presence and localized translation of β-actin at the leading edge, this isoform is generally accepted to specifically generate protrusive forces for cell migration. Recent evidence also implicates β-actin in gene regulation. Cell migration without β-actin has remained unstudied until recently and it is unclear whether other actin isoforms can compensate for this cytoplasmic function and/or for its nuclear role. Primary mouse embryonic fibroblasts lacking β-actin display compensatory expression of other actin isoforms. Consistent with this preservation of polymerization capacity, β-actin knockout cells have unchanged lamellipodial protrusion rates despite a severe migration defect. To solve this paradox we applied quantitative proteomics revealing a broad genetic reprogramming of β-actin knockout cells. This also explains why reintroducing β-actin in knockout cells does not restore the affected cell migration. Pathway analysis suggested increased Rho-ROCK signaling, consistent with observed phenotypic changes. We therefore developed and tested a model explaining the phenotypes in β-actin knockout cells based on increased Rho-ROCK signaling and increased TGFβ production resulting in increased adhesion and contractility in the knockout cells. Inhibiting ROCK or myosin restores migration of β-actin knockout cells indicating that other actins compensate for β-actin in this process. Consequently, isoactins act redundantly in providing propulsive forces for cell migration, but β-actin has a unique nuclear function, regulating expression on transcriptional and post-translational levels, thereby preventing myogenic differentiation. © 2012 by The American Society for Biochemistry and Molecular Biology, Inc.



M. Cnop, M. Igoillo Esteve, M. Rai, A. Begu, Y. Serroukh, C. Depondt, A. Musuaya, I. Marhfour, L. Ladrière, X. Moles Lopez, D. Lefkaditis, F. Moore, J. Brion, M. Cooper, A. Schapira, A. Clark, A. Koeppen, P. Marchetti, M. Pandolfo, D. Eizirik, F. Fery,
Central role and mechanisms of beta-cell dysfunction and death in Friedreich ataxia- associated diabetes
Annals of neurology, Vol. 72, pp. 971-982, 2012
Bibtex
Bibtex : info:hdl:2013/136306
Note : Language of publication: en
Abstract : Abstract Objective: Friedreich ataxia (FRDA) is an autosomal recessive neurodegenerative disease caused in almost all cases by homozygosity for a GAA trinucleotide repeat expansion in the frataxin gene. Frataxin is a mitochondrial protein involved in iron homeostasis. FRDA patients have a high prevalence of diabetes, the pathogenesis of which is not known. We aimed to evaluate the relative contribution of insulin resistance and β-cell failure and the pathogenic mechanisms involved in FRDA diabetes. Methods: Forty-one FRDA patients, 26 heterozygous carriers of a GAA expansion, and 53 controls underwent oral and intravenous glucose tolerance tests. β-Cell proportion was quantified in postmortem pancreas sections from 9 unrelated FRDA patients. Using an in vitro disease model, we studied how frataxin deficiency affects β-cell function and survival. Results: FRDA patients had increased abdominal fat and were insulin resistant. This was not compensated for by increased insulin secretion, resulting in a markedly reduced disposition index, indicative of pancreatic β-cell failure. Loss of glucose tolerance was driven by β-cell dysfunction, which correlated with abdominal fatness. In postmortem pancreas sections, pancreatic islets of FRDA patients had a lower β-cell content. RNA interference–mediated frataxin knockdown impaired glucose-stimulated insulin secretion and induced apoptosis in rat β cells and human islets. Frataxin deficiency sensitized β cells to oleate-induced and endoplasmic reticulum stress-induced apoptosis, which could be prevented by the incretins glucagon-like peptide-1 and glucose-dependent insulinotropic polypeptide. Interpretation: Pancreatic β-cell dysfunction is central to diabetes development in FRDA as a result of mitochondrial dysfunction and higher sensitivity to metabolic and endoplasmic reticulum stress-induced β-cell death. ANN NEUROL 2012;72:971–982



L. Ferdinande, C. Decaestecker, L. Verset, A. Mathieu, X. Moles Lopez, A. Negulescu, T. Van Maerken, I. Salmon, C. Cuvelier, P. Demetter,
Clinicopathological significance of indoleamine 2,3-dioxygenase 1 expression in colorectal cancer.
British Journal of Cancer, Vol. 106, 1, pp. 141-147, 2012
Bibtex
Bibtex : info:hdl:2013/106373
Note : JOURNAL ARTICLE
Abstract : Background:Indoleamine 2,3-dioxygenase 1 (IDO1) is a tryptophan-catabolising enzyme that induces immune tolerance by modulating T-cell responses. Carcinomas may create an immunosuppressive state via IDO1 expression. Here we examined a possible contribution of IDO1 on this phenomenon and investigated whether IDO1 has prognostic value in colorectal cancer (CRC).Methods:IDO1 expression was investigated by quantitative PCR and western blotting in three colon cancer cell lines, in basal state and after interferon (IFN)-γ stimulation. Semi-quantitative immunohistochemistry was used to evaluate IDO1 expression in 265 pT1-4N0-2Mx-staged CRCs. Results were related to clinical variables and correlated with amounts of CD3(+) and CD8(+) T lymphocytes, which were quantitatively evaluated using image analysis.Results:In vitro expression of IDO1 depended on IFN-γ stimulation. Higher IDO1 expression at the tumour invasion front was an independent adverse prognostic factor in pT1-4N1Mx-staged CRC. It was associated with overall survival (P=0.001) and with metachronous metastases (P=0.018). IDO1 expression was not associated with the presence of CD3(+) or CD8(+) T lymphocytes.Conclusion:Higher IDO1 expression at the tumour invasion front is involved in CRC progression and correlates with impaired clinical outcome, suggesting that IDO1 is an independent prognostic indicator for CRC.British Journal of Cancer advance online publication, 22 November 2011; doi:10.1038/bjc.2011.513 www.bjcancer.com.



X. Moles Lopez, O. Debeir, C. Maris, S. Rorive, I. Roland, M. Saerens, I. Salmon, C. Decaestecker,
Clustering methods applied in the detection of Ki67 hot-spots in whole tumor slide images: An efficient way to characterize heterogeneous tissue-based biomarkers.
Cytometry. Part A, Vol. 81, 9, pp. 765-775, 2012
Bibtex
Bibtex : info:hdl:2013/127791
Note : Journal Article
Abstract : Whole-slide scanners allow the digitization of an entire histological slide at very high resolution. This new acquisition technique opens a wide range of possibilities for addressing challenging image analysis problems, including the identification of tissue-based biomarkers. In this study, we use whole-slide scanner technology for imaging the proliferating activity patterns in tumor slides based on Ki67 immunohistochemistry. Faced with large images, pathologists require tools that can help them identify tumor regions that exhibit high proliferating activity, called "hot-spots" (HSs). Pathologists need tools that can quantitatively characterize these HS patterns. To respond to this clinical need, the present study investigates various clustering methods with the aim of identifying Ki67 HSs in whole tumor slide images. This task requires a method capable of identifying an unknown number of clusters, which may be highly variable in terms of shape, size, and density. We developed a hybrid clustering method, referred to as Seedlink. Compared to manual HS selections by three pathologists, we show that Seedlink provides an efficient way of detecting Ki67 HSs and improves the agreement among pathologists when identifying HSs. © 2012 International Society for Advancement of Cytometry.



K. Zhang, G. Lafruit, R. Lauwereins, V. Luc,
Constant time joint bilateral filtering using joint integral histograms
IEEE transactions on image processing, Vol. 21, 9, pp. 4309-4314, 2012
Bibtex
Bibtex : info:hdl:2013/186271
Note : Language of publication: en



G. Lafruit,
Des Belges préparent la télé 3D du futur
Le Vif l'Express, pp. 54-55, 2012
Bibtex
Bibtex : info:hdl:2013/188514
Note : interviewé par Laurent Hovine



I. Marhfour, X. Moles Lopez, D. Lefkaditis, I. Salmon, F. Allagnat, S. Richardson, N. Morgan, D. Eizirik,
Expression of endoplasmic reticulum stress markers in the islets of patients with type 1 diabetes.
Diabetologia, Vol. 55, 9, pp. 2417-2420, 2012
Bibtex
Bibtex : info:hdl:2013/135708
Note : Journal Article
Abstract : Endoplasmic reticulum (ER) stress may play a role in cytokine-mediated beta cell death in type 1 diabetes, but it remains controversial whether ER stress markers are present in islets from type 1 diabetic individuals. Therefore, we evaluated by immunostaining the expression of markers of the three main branches of the ER stress response in islets from 13 individuals with and 15 controls without type 1 diabetes (eight adults and seven children).



N. Kindt, J. Lechien, C. Decaestecker, A. Rodriguez, G. Chantrain, M. Remmelink, G. Laurent, H. Gabius, S. Saussez,
Expression of macrophage migration-inhibitory factor is correlated with progression in oral cavity carcinomas.
Anticancer research, Vol. 32, 10, pp. 4499-4505, 2012
Bibtex
Bibtex : info:hdl:2013/132977
Note : Journal Article
Abstract : We have previously reported that macrophage migration-inhibitory factor (MIF) is associated with an unfavorable prognosis in hypopharyngeal carcinoma. Here, we quantified MIF expression in oral cavity carcinomas and looked for possible correlations with clinical outcome.



A. Duray, G. Descamps, C. Decaestecker, M. Remmelink, N. Sirtaine, J. Lechien, P. Ernoux-Neufcoeur, N. Bletard, J. Somja, C. Depuydt, P. Delvenne, S. Saussez,
Human papillomavirus DNA strongly correlates with a poorer prognosis in oral cavity carcinoma.
The Laryngoscope, Vol. 122, 7, pp. 1558-1565, 2012
Bibtex
Bibtex : info:hdl:2013/127793
Note : Journal Article
Abstract : The prevalence of human papillomavirus (HPV) in a clinical series of 162 patients with oral squamous cell carcinoma (OSCC) was studied. Furthermore, we analyzed the correlation between the immunohistochemical expression of p16, p53, epidermal growth factor receptor (EGFR), and HPV status to predict survival in OSCC patients.



V. Megalizzi, M. Le Mercier, C. Decaestecker,
Sigma receptors and their ligands in cancer biology: overview and new perspectives for cancer therapy.
Medicinal research reviews, Vol. 32, 2, pp. 410-427, 2012
Bibtex
Bibtex : info:hdl:2013/68368
Note : JOURNAL ARTICLE
Abstract : A large number of drugs are known to bind with high affinity to sigma receptors (sigma-Rs) and have been used in the clinic to treat mental disorders for many years. However, recent publications highlighting sigma-R overexpression in many cancer tissues suggest potential applications for sigma-R ligands in cancer diagnosis and therapy. The present review focuses on the involvement of sigma-Rs in cancer biology and the potential therapeutic contributions of their pharmacologic ligands in oncology. After summarizing the current and general knowledge regarding sigma-Rs, we detail data reported in the particular context of oncology. We then investigate the potential and specific signal transduction pathways and mechanisms involved in the actions of sigma-R ligands in cancer biology. These processes include modulations of (1) the plasma membrane and lipid raft components, (2) intracellular calcium levels, (3) cytoskeletal protein functions, and (4) endoplasmic reticulum stress. Finally, we conclude by speculating on the roles of sigma-R overexpression and sigma-R ligands in cancer biology and offer perspectives on cancer therapy. (c) 2010 Wiley Periodicals, Inc. Med Res Rev.



Conferences

B. Penelle, D. Mouraux, E. Brassinne, A. Nonclercq, N. Warzée,
3D augmented reality applied to the treatment of neuropathic pain.
Proceedings of the 9th International Conference on Disability, Virtual Reality and Associated Technologies, ICDVRAT 2012, Laval, France, 2012
Bibtex
Bibtex : info:hdl:2013/126850
Note : Language of publication: en



P. Mainali, G. Lafruit, L. Shuyang, K. Tack, B. Masschelein, L. Van Gool, R. Lauwereins,
Image registration software data correction algorithm for a hyperspectral imager
Optical Systems Design, 2012
Bibtex
Bibtex : info:hdl:2013/186783
Note : Language of publication: en



R. Stahl, V. Rochus, X. Rottenberg, S. Cosemans, L. Haspeslagh, S. Severi, G. Van der Plas, G. Lafruit, S. Donnay,
Modular sub-wavelength diffractive light modulator for high-definition holographic displays
9th International Symposium on Display Holography, pp. 436-442, 2012
Bibtex
Bibtex : info:hdl:2013/186785
Note : Language of publication: en



A. Schenkel, N. Warzée,
Plans Extraction From Complex Buildings 3D Acquisitions
Proceedings of the 17th International Conference on Cultural Heritage and New Technologies 2012 (CHNT 17, 2012), Vienna, Austria, 2012
Bibtex
Bibtex : info:hdl:2013/153329
Note : Language of publication: en



B. Mertens, B. De Leener, O. Debeir, C. Beumier, P. Lambert, A. Delchambre, others,
Robust Structured Light Pattern for Use with a Hologram in 3D Endoscopy
Proceedings of the 2012 International Symposium on Optomechatronic Technologies (ISOT'12), Paris, 2012
Bibtex
Bibtex : info:hdl:2013/128683
Note : Language of publication: en
Abstract : This paper introduces a novel structured light pattern designed to be compatible with the hologram projection. Here is proposed to use a De Bruijn-based sequence and a combination of continuous and dashed lines for the pattern. Dashed lines are coded by a combination of their period and of their duty cycles. It provides 16 different lines which limits to two the required number of lines for identification. The segmentation has been made easier by inserting continuous lines between two dashed lines. As required by the use of holograms, the sequence has been adapted by making it symmetric. It has been improved by guaranteeing a hamming distance equal to two for contiguous lines. The implementation on a virtual model has shown that a subpixel accuracy has been achieved. The aim of this pattern is to be used in 3D endoscopy



B. Mertens, B. De Leener, O. Debeir, C. Beumier, P. Lambert, A. Delchambre,
Robust structured light pattern for use with a hologram in 3D endoscopy
IEEE International Symposium on Optomechatronic Technologies (ISOT), 2012, pp. 6, 2012
Bibtex
Bibtex : info:hdl:2013/143724
Note : Language of publication: na



K. Zhang, R. Lauwereins, G. Yi, H. Yeh, C. Liao, C. Lin, G. Lafruit, L. Van Gool,
Towards a real-time high-definition depth sensor with hardware-efficient stereo matching
Stereoscopic Displays and Applications XXIII, pp. 91-98, 2012
Bibtex
Bibtex : info:hdl:2013/186784
Note : Language of publication: en



B. Penelle, D. Mouraux, E. Brassine, A. Nonclercq, N. Warzée,
Treatment of neuropathic pain using a Kinect based augmented reality system
Conference: 11th Belgian Day on Biomedical Engineering, joint Meeting with IEEE EMBS Benelux Chapter(07 Dec., 2012: Brussels, Belgium), 2012
Bibtex
Bibtex : info:hdl:2013/300007
Note : Language of publication: en



A. Foucart, O. Debeir,
Unsupervised vehicle detection in traffic scene using distributed one class classifiers
International Symposium on signal, Image, Video and Communications, 6 June 2012, 2012
Bibtex
Bibtex : info:hdl:2013/146728
Note : Language of publication: na



Books chapters

L. Zhang, K. Zhang, J. Lu, T. Chang, G. Lafruit,
Low-Complexity Stereo Matching and Viewpoint Interpolation in Embedded Consumer Applications
IGI Global, pp. 307-332, 2012
Bibtex
Bibtex : info:hdl:2013/187303
Note : Language of publication: na



C. Liao, C. Lin, K. Zhang, G. Vanmeerbeeck, G. Yi, H. Yeh, F. Chang, Y. Tseng, T. Chang, G. Lafruit,
Stereo Matching and Viewpoint Synthesis 3D-HDTV chipset
Springer, pp. 69-106, 2012
Bibtex
Bibtex : info:hdl:2013/187154
Note : Language of publication: na



Thesis

I. Adanja,
Automated tracking of unmarked cells migrating in three-dimensional matrices
2012
Bibtex
Bibtex : info:hdl:2013/209703
Note : Doctorat en Sciences de l'ingénieur
Abstract : The goal of this thesis is the development of a tracking algorithm for populations of unmarked cancer cells that migrate in 3D in vitro gels. The tracking algorithm is intended to be a tool for analysing the motility of large population (i.e., hundreds) of cells in the context of the anti-migratory drug development and more specifically drug screening. In oncology, cancer cell migration plays pivotal roles in the spread of cancer cells from a primary tumor site to neighboring and secondary sites, i.e. the processes of tissue invasion and metastasis. Preventing such processes represents an important therapeutic approach to cancer treatment. Providing tools able to test potential anti-migratory drugs thus constitutes currently a real need in oncology therapy. The goal of drug screening in this context aims to rapidly and efficiently test the anti-migratory effects of many experimental conditions on cancer cell populations.<p>The focus in this thesis lies in two specific aspects that are important in anti-migratory drug screening: tracking cells inside an in vitro 3D environment and doing so using unmarked cells.



K. Zhang, G. Lafruit,
Efficient Multi-View Processing with Algorithm-Architecture Co-Exploration. Computer Engineering
2012
Bibtex
Bibtex : info:hdl:2013/188499
Note : Language of publication: na



A. Valero Masa,
High impedance fault detection method in multi-grounded distribution networks
2012
Bibtex
Bibtex : info:hdl:2013/209580
Note : Doctorat en Sciences de l'ingénieur
Abstract : High Impedance Faults (HIFs) are undetectable by conventional protection technology under certain<p>conditions. These faults occur when an energized conductor makes undesired contact with a<p>quasi-insulating object, such as a tree or a road. This contact restricts the level of the fault current to a very low value, from a few mA up to 75A. In solidly grounded distribution networks where the value of the residual current under normal conditions is considerable, overcurrent devices do not protect against HIFs. However, such a protection is essential for guaranteeing public security, because of the possibility of reaching the fallen conductor and the risk of fire.




2011

H. Yeh, G. Lafruit,
Hardware Components for Real-Time Stereo Matching: Acceleration of 3D HDTV with FPGAs Based Rendering. Computer Engineering
2011
Bibtex
Bibtex : info:hdl:2013/188483
Note : Language of publication: na



G. Yi, G. Lafruit,
High-Quality, Real-Time HD Video Stereo Matching on FPGA. Circuits and Systems
2011
Bibtex
Bibtex : info:hdl:2013/188484
Note : Language of publication: na



,
ISB 2011 Conference book
2011
Bibtex
Bibtex : info:hdl:2013/241964
Note : Language of publication: en



,
XXIIIrd congress of the International Society of Biomechanics - ISB2011 Conference book – Programme & Abstracts
2011
Bibtex
Bibtex : info:hdl:2013/109381
Note : 1 v. (256 p.)



,
XXIIIrd congress of the International Society of Biomechanics - ISB2011 Conference book – Programme & Abstracts
2011
Bibtex
Bibtex : info:hdl:2013/223240
Note : Language of publication: fr



Papers

I. Adanja, V. Megalizzi, O. Debeir, C. Decaestecker,
A New Method to Address Unmet Needs for Extracting Individual Cell Migration Features from a Large Number of Cells Embedded in 3D Volumes
PloS one, Vol. 6, 7, 2011
Bibtex
Bibtex : info:hdl:2013/94206
Note : SCOPUS: ar.j
Abstract : Background: In vitro cell observation has been widely used by biologists and pharmacologists for screening molecule-induced effects on cancer cells. Computer-assisted time-lapse microscopy enables automated live cell imaging in vitro, enabling cell behavior characterization through image analysis, in particular regarding cell migration. In this context, 3D cell assays in transparent matrix gels have been developed to provide more realistic in vitro 3D environments for monitoring cell migration (fundamentally different from cell motility behavior observed in 2D), which is related to the spread of cancer and metastases. Methodology/Principal Findings: In this paper we propose an improved automated tracking method that is designed to robustly and individually follow a large number of unlabeled cells observed under phase-contrast microscopy in 3D gels. The method automatically detects and tracks individual cells across a sequence of acquired volumes, using a template matching filtering method that in turn allows for robust detection and mean-shift tracking. The robustness of the method results from detecting and managing the cases where two cell (mean-shift) trackers converge to the same point. The resulting trajectories quantify cell migration through statistical analysis of 3D trajectory descriptors. We manually validated the method and observed efficient cell detection and a low tracking error rate (6\%). We also applied the method in a real biological experiment where the pro-migratory effects of hyaluronic acid (HA) were analyzed on brain cancer cells. Using collagen gels with increased HA proportions, we were able to evidence a dose-response effect on cell migration abilities. Conclusions/Significance: The developed method enables biomedical researchers to automatically and robustly quantify the pro- or anti-migratory effects of different experimental conditions on unlabeled cell cultures in a 3D environment. © 2011 Adanja et al.



M. Cammaerts Tricot, O. Debeir, R. Cammaerts,
Changes in Paramecium caudatum (Protozoa) near a switched-on GSM telephone
Electromagnetic Biology and Medicine, Vol. 30, 1, pp. 57-66, 2011
Bibtex
Bibtex : info:hdl:2013/86163
Note : SCOPUS: ar.j
Abstract : The protozoan Paramecium caudatum was examined under normal conditions versus aside a switched-on GSM telephone (900 MHz; 2 Watts). Exposed individuals moved more slowly and more sinuously than usual. Their physiology was affected: they became broader, their cytopharynx appeared broader, their pulse vesicles had difficult in expelling their content outside the cell, their cilia less efficiently moved, and trichocysts became more visible. All these effects might result from some bad functioning or damage of the cellular membrane. The first target of communication electromagnetic waves might thus be the cellular membrane. © Informa Healthcare USA, Inc.



P. Ernoux-Neufcoeur, M. Arafa, C. Decaestecker, A. Duray, M. Remmelink, X. Leroy, M. Herfs, J. Somja, C. Depuydt, P. Delvenne, S. Saussez,
Combined analysis of HPV DNA, p16, p21 and p53 to predict prognosis in patients with stage IV hypopharyngeal carcinoma.
Journal of cancer research and clinical oncology, Vol. 137, 1, pp. 173-181, 2011
Bibtex
Bibtex : info:hdl:2013/106372
Note : Journal Article
Abstract : We examined p16, p21 and p53 expression in combination with the presence of human papillomavirus (HPV) DNA as molecular markers to predict survival in patients with stage IV hypopharyngeal squamous cell carcinoma (HSCC).



T. Leloup, W. El Kazzi, N. Warzée, F. Schuind,
Développements originaux des techniques de navigation en traumatologie.
Revue médicale de Bruxelles, Vol. 32, 6 Suppl, pp. S23-S29, 2011
Bibtex
Bibtex : info:hdl:2013/133188
Note : English Abstract
Abstract : This article presents an original method for long objects modeling and two navigation applications in trauma surgery. Both concern long bone fracture treatment. Our modeling method requires only two x-ray views. The projection cones of the object are determined and their intersection is computed, providing an approached 30 model, which can be improved by adding a priori knowledge or other information. The first application concerns the control of diaphyseal fracture reduction treated by external fixation. Reference frames are fixed to the bone fragments and tracked by a 3D optical localizer, allowing the computation of their relative position. Approached 3D models of the fragments are displayed in real time according to the manipulation effected by the surgeon. The principal axes of the fragments, very useful for the fracture reduction, are also displayed. The alignment of the bone fragments is quantified by parameters provided in real time during the reduction. The second application concerns the distal locking of intra-medullary nails. A 3D model of the nail and its locking holes is built from two calibrated fluoroscopic views. The nail and the surgical tool are tracked thanks to reference frames fixed to each of them. A 3D view of these two elements is displayed in real time, guiding the surgeon in the difficult task of distal targeting. Experiments and results are presented for both applications. These techniques provide real 3D models to the surgeon during the operation, allowing precise guidance of the surgical gesture and considerable reduction of the irradiation to the patient and the surgical team.



A. Duray, G. Descamps, M. Arafa, C. Decaestecker, M. Remmelink, N. Sirtaine, P. Ernoux-Neufcoeur, E. Mutijima, J. Somja, C. Depuydt, P. Delvenne, S. Saussez,
High incidence of high-risk HPV in benign and malignant lesions of the larynx.
International journal of oncology, Vol. 39, 1, pp. 51-59, 2011
Bibtex
Bibtex : info:hdl:2013/97507
Note : Journal Article
Abstract : The aim of this study was to determine the prevalence of human papillomavirus (HPV) in patients with laryngeal benign lesions (LBLs) and laryngeal squamous cell carcinomas (LSCCs) using a sensitive E6/E7 type-specific PCR. Paraffin-embedded samples from LBL (n=39) and LSCC patients (n=67) were evaluated for the presence of HPV DNA by GP5+/GP6+ consensus PCR and E6/E7 type-specific PCR for HPV types 6, 11, 16, 18, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66 and 68. In LSCCs, immunohistochemical staining of p16, p53 and EGFR was also assessed. The E6/E7 type-specific PCR showed that 44 out of 59 LSCC patients (i.e., 75\%) had high-risk (hr) HPV types and that 27 out of 35 LBL patients (i.e., 77\%) had hrHPV types. HPV-16 viral load was significantly higher in LSCC than in LBL patients (p<10-6). The presence of hrHPV DNA did not correlate with the proportion of disease-free patients. Comparable levels of p16, p53 and EGFR expression were observed in the hrHPV+ tumor group (100\% p16+, 56\% p53+ and 97\% EGFR+) and in the HPV- or low-risk (lr) HPV+ tumor group (92\% p16+, 66\% p53+ and 100\% EGFR+). A very high prevalence of oncogenic HPV-16 was found in a series of benign and malignant laryngeal lesions. LSCC appears to be characterized by an active hrHPV infection. In LSCCs, the hrHPV+ subgroup had a similar prognosis (in terms of risk of recurrence) as the HPV- subgroup.



M. Remmelink, L. de Leval, C. Decaestecker, A. Duray, E. Crompot, N. Sirtaine, S. André, H. Kaltner, X. Leroy, H. Gabius, S. Saussez,
Quantitative immunohistochemical fingerprinting of adhesion/growth-regulatory galectins in salivary gland tumours: divergent profiles with diagnostic potential.
Histopathology, Vol. 58, 4, pp. 543-556, 2011
Bibtex
Bibtex : info:hdl:2013/97506
Note : Journal Article
Abstract : This study tests the hypothesis that histopathological fingerprinting of galectins, which are emerging multifunctional effectors in cell sociology, could refine the differential diagnosis of salivary tumours.



K. Zhang, J. Lu, Q. Yang, G. Lafruit, R. Lauwereins, L. Van Gool,
Real-Time and Accurate Stereo: A Scalable Approach with Bitwise Fast Voting on CUDA
IEEE transactions on circuits and systems for video technology, Vol. 21, 7, pp. 867-878, 2011
Bibtex
Bibtex : info:hdl:2013/186273
Note : Language of publication: en



P. Mainali, Q. Yang, G. Lafruit, L. Van Gool, R. Lauwereins,
Robust low complexity corner detector
IEEE transactions on circuits and systems for video technology, Vol. 21, 4, pp. 435-445, 2011
Bibtex
Bibtex : info:hdl:2013/186272
Note : Language of publication: en



Conferences

K. Zhang, J. Lu, G. Lafruit, R. Lauwereins, L. Van Gool,
A cross-based filter for fast edge-preserving smoothing
Real-Time Image and Video Processing, pp. 78710H-78710H, 2011
Bibtex
Bibtex : info:hdl:2013/186786
Note : Language of publication: en



B. Penelle, A. Schenkel, N. Warzée,
Geometrical 3D reconstruction using real-time RGB-D cameras
2011 International Conference on 3D Imaging (IC3D 2011), Liège, Belgium, 2011
Bibtex
Bibtex : info:hdl:2013/153323
Note : Language of publication: en



N. D'Haene, S. Sauvage, C. Maris, A. Trepant, M. Le Mercier, C. Decaestecker, I. Salmon,
Involvement of Vascular Endothelial Growth Factor Receptors in Endothelial Cell Response to Galectin-1 and Galectin-3
Conference: 6th Joint Meeting of the British Division of the International Academy of Pathology and the Pathological Society of Great Britain & Ireland(May 2011), 2011
Bibtex
Bibtex : info:hdl:2013/193240
Note : Language of publication: na



S. Van Sint Jan, V. Feipel, D. Aerenhouts, J. Baeyens, A. Carpentier, E. Cattrysse, J. Clarys, J. Duchateau, N. Guissard, T. Leloup, S. Provyn, M. Rooze, A. Scafoglieri, F. Schuind, P. Van Roy, N. Warzée,
Programme and Abstracts
ISB 2011 Conference book, 2011
Bibtex
Bibtex : info:hdl:2013/149808
Note : ISBN 9789090260198



G. Yi, H. Yeh, G. Vanmeerbeeck, C. Lin, C. Liao, G. Lafruit,
Real-time depth extraction and viewpoint interpolation on FPGA
5th ACM/IEEE International Conference on Distributed Smart Cameras, 2011
Bibtex
Bibtex : info:hdl:2013/186788
Note : Language of publication: en



L. Zhang, K. Zhang, T. Chang, G. Lafruit, G. Kuzmanov, D. Verkest,
Real-Time High-Definition Stereo Matching on FPGA
19th ACM/SIGDA International Symposium on Field-Programmable Gate Arrays - FPGA, 2011
Bibtex
Bibtex : info:hdl:2013/186787
Note : Language of publication: en



A. Schenkel, R. Ercek, B. Penelle, A. Hubrecht, T. Saroléa, N. Warzée,
Tridimensional laser scanning to retrieve engineering site drawings. The experience of the Brussels Park Bunker rehabilitation project.
2011 International Conference on 3D Imaging (IC3D 2011), Liège, Belgium, 2011
Bibtex
Bibtex : info:hdl:2013/148261
Note : Language of publication: na



A. Schenkel, P. Malarme, T. Leloup, D. Wikler, B. Penelle, N. Warzée,
XSMILS Player : Un outil pédagogique pour l'enseignement de la chirurgie, développé dans le cadre d'un projet académique
Conference: Colloque sur l’enseignement des technologies et des sciences de l'information et des systèmes (CETSIS 2011) (9ème: Oct 2011: Trois-Rivières, Canada), 2011
Bibtex
Bibtex : info:hdl:2013/153322
Note : Language of publication: fr
Abstract : Dans le cadre du projet de développement de salles d’opération numériques intégrées « integrated Digital Operating Theater » (iDOT), une application, permettant de visualiser de manière synchronisée plusieurs flux de données collectés pendant une opération chirurgicale, a été développée. Elle offre la possibilité de reconstruire la phase d’observation d’une chirurgie dans son ensemble et d’interagir aisément avec les données. Une telle application permet de dépasser les limites spatiales et temporelles liées à la présence en salle durant une opération, en offrant la possibilité de rejouer ses différentes étapes quand et o{\`u} l’on veut. Cela constitue donc un excellent outil pédagogique pour l’enseignement de la chirurgie en permettant aux étudiants d’accéder à l’ensemble des données peropératoires utilisées par le praticien et d’observer une opération sans devoir se trouver en salle pendant son déroulement.



Books chapters

X. Ji, J. Huang, M. Huang, G. Lafruit, F. Catthoor,
Scheduling and resource allocation for SVC streaming over OFDM downlink systems
InTech, pp. 223-242, 2011
Bibtex
Bibtex : info:hdl:2013/187385
Note : Language of publication: na



Thesis

L. Engels,
Acquisition en temps réel, identification et mise en correspondance de données 3D
2011
Bibtex
Bibtex : info:hdl:2013/209852
Note : Doctorat en Sciences de l'ingénieur
Abstract : Cette thèse décrit le développement et la mise en œuvre d'un système d'acquisition 3D ayant pour but la localisation temps réel en 3D et l'identification d'électrodes et des antennes utilisées lors d'un examen MEG/EEG. La seconde partie concerne la mise en correspondance de ces données avec les informations de la résonance magnétique.



P. Malarme,
Conception d'un système d'aide à la chirurgie sur base de la modélisation d'opérations, d'un recalage temporel des données et d'un recalage sémantique de métadonnées
2011
Bibtex
Bibtex : info:hdl:2013/209844
Note : Doctorat en Sciences de l'ingénieur
Abstract : Le but principal de cette thèse de doctorat est de concevoir un système de chirurgie assistée par la connaissance. Cette connaissance est extraite de l'information issue des données et du contexte capturés en salle d'opération. Ce contexte est défini à l'aide d'un modèle de processus opératoire (surgical workflow - SWf). L'assistance porte sur la capture des modèles, l'automatisation de t{\^a}ches ou encore la gestion des erreurs et des imprévus.<p><p>The main goal of this PhD thesis is to design a computer assisted surgery system based on surgical workflow (SWf) modeling, and intra-operative data and metadata acquired during the operation. For the SWf modeling, workflow-mining techniques will be developed based on dynamic learning and incremental inference. An ontology will be used to describe the various steps of the surgery and their attributes.



Miendjé Deyi, Véronique Yvette,
Contribution au management de l'infection à Helicobacter pylori en Belgique
2011
Bibtex
Bibtex : info:hdl:2013/209925
Note : Doctorat en Sciences biomédicales et pharmaceutiques
Abstract : Peu étudiée et méconnue, initialement décrite au début du XXe siècle, Helicobacter pylori fut redécouverte en 1982 par deux chercheurs australiens, JR Warren et BJ Marshall. Ils soutinrent que la plupart des ulcères gastro-duodénaux étaient causés par cette bactérie, et non par le stress ou la nourriture épicée, comme pensé auparavant. Cette découverte révolutionna le monde de la gastroentérologie et leur valut le prix Nobel de physiologie et de médecine 2005. Environ la moitié de la population mondiale est colonisée par H. pylori au niveau de l'estomac. Dans 10 à 20\% des cas, l'infection peut évoluer vers un ulcère gastro-duodénal et dans certains cas vers une transformation maligne. Cette infection se soigne classiquement à l'aide d'une trithérapie associant 2 antibiotiques à un inhibiteur de la pompe à protons pour neutraliser l'acidité gastrique.<p>Notre travail de recherche a consisté à analyser la proportion de patients infectés par H. pylori dans une cohorte de plus de 22.000 patients, issus de divers groupes ethniques, vivant en Belgique. Ces souches de H. pylori, isolées dans notre laboratoire, à partir des biopsies gastriques, ont aussi servi à une étude pour suivre l'évolution de la résistance aux antibiotiques ces 20 dernières années afin de proposer des améliorations de la prise en charge thérapeutique de l'infection à H. pylori en Belgique.



V. Megalizzi,
Involvement of sigma receptors and thri ligands in the biology of cancers
2011
Bibtex
Bibtex : info:hdl:2013/209906
Note : Doctorat en Sciences biomédicales et pharmaceutiques
Abstract : Parmi les tumeurs cérébrales primaires, les gliomes sont les tumeurs les plus fréquemment rencontrées. Les glioblastomes (GBM) représentent 60 à 70\% de ces tumeurs et malgré de récents progrès dans leur traitement, leur pronostic reste sombre. Les gliomes malins sont caractérisés par une prolifération cellulaire importante, un taux élevé de néo-angiogenèse et une migration diffuse des cellules tumorales gliales dans le parenchyme cérébral, ce qui rend impossible une résection chirurgicale complète. De plus, les cellules gliales tumorales migrantes opposent une résistance particulière aux traitements chimiothérapiques de type pro-apoptotique, causant une récidive quasi inévitable de ce type de tumeur. La compréhension des aspects moléculaires à la base de la prolifération, de la migration et de la chimiorésitance des cellules gliales tumorales est donc essentielle pour élaborer des approches ciblées capables d’entraver ces processus. La littérature mentionne plusieurs stratégies qui permettraient, en théorie, de court-circuiter la résistance à l’apoptose des cellules tumorales gliales migrantes. Il s’agirait entre autres :<p>- de réduire le taux d’activation des voies de signalisation contrôlées par PI3K /Akt /mTOR et NFkappaB, qui diminuerait le taux de croissance des gliomes malins, ainsi que le taux de migration des cellules tumorales isolées dans le parenchyme cérébral;<p>- de réduire le taux de migration des cellules tumorales gliales afin de restaurer un certain degré de sensibilité à des agents chimiothérapiques pro-apoptotiques;<p>- d’endiguer l’export des agents chimiothérapiques par les pompes à efflux surexprimées dans les gliomes <p>- d'induire d’autres processus de mort cellulaire que l’apoptose, car les cellules tumorales gliales migrantes sont plus sensibles à d’autres formes de mort cellulaire.<p>Ces besoins de nouvelles stratégies thérapeutiques ont motivé ce travail qui se focalisera sur le potentiel antitumoral des ligands du R-sigma1 dans les glioblastomes. Ainsi, nous montrerons que les ligands des Rs-sigma sont capables de produire certains des effets visés dans les stratégies ci-dessus, dont la réduction de la prolifération et de la migration des cellules cancéreuses avec une certaine potentialisation des chimiothérapies. Ces propriétés ouvrent de nouvelles perspectives en thérapie anticancéreuse pour cette famille de ligands, dont plusieurs membres sont déjà utilisés depuis de nombreuses années comme antipsychotique.



C. Cloquet,
Optimiser l'utilisation des données en reconstruction TEP: modélisation de résolution dans l'espace image et contribution à l'évaluation de la correction de mouvement
2011
Bibtex
Bibtex : info:hdl:2013/209887
Note : Doctorat en Sciences de l'ingénieur
Abstract : Cancers et maladies cardio-vasculaires sont responsables de plus de 40 \% des décès dans le monde. De nombreuses personnes souffrent par ailleurs quotidiennement de ces maladies. En réduire la fréquence dans le futur passe avant tout par une adaptation de notre mode de vie et une prévention accrue, éclairées par une connaissance plus approfondie des mécanismes de ces maladies. Il est également crucial d'améliorer les diagnostics et les traitements actuels afin de mieux prendre en charge les malades d'aujourd'hui et de demain.<p><p>Lorsque le tableau clinique présenté par un patient n'est pas clair, de nombreuses techniques d'imagerie médicale permettent d'affiner le diagnostic, de préciser le pronostic et de suivre l'évolution des maladies au cours du temps. Ces mêmes techniques sont également utilisées en recherche fondamentale pour faire progresser la connaissance du fonctionnement normal et pathologique du corps humain. Il s'agit par exemple de l'échographie, de l'imagerie par résonance magnétique, de la tomodensitométrie à rayons X ou encore de la tomographie par émission de positrons (TEP).<p><p>Certaines de ces techniques mettent en évidence le métabolisme de molécules, comme le glucose et certains acides aminés. C'est le cas de la tomographie par émission de positrons, dans laquelle une petite quantité de molécules marquées avec un élément radioactif est injectée au patient. Ces molécules se concentrent de préférence dans les endroits du corps humain o{\`u} elles sont utilisées. Instables, les noyaux radioactifs se désintègrent en émettant un anti-électron, encore appelé positron. Chaque positron s'annihile ensuite à proximité du lieu d'émission avec un électron du corps du patient, provoquant l'émission simultanée de deux photons de haute énergie dans deux directions opposées. Après avoir traversé les tissus, ces photons sont captés par un anneau de détecteurs entourant le patient. Sur base de l'ensemble des événements collectés, un algorithme de reconstruction produit enfin une image de la distribution du traceur radioactif.<p><p>La tomographie par émission de positrons permet notamment d'évaluer l'efficacité du traitement des tumeurs avant que la taille de celles-ci n'ait changé, ce qui permet d'aider à décider de poursuivre ou non le traitement en cours. En cardiologie, cette technique permet de quantifier la viabilité du muscle cardiaque après un infarctus et aide ainsi à évaluer la pertinence d'une intervention chirurgicale.<p><p>Plusieurs facteurs limitent la précision des images TEP. Parmi ceux-ci, on trouve l'effet de volume partiel et le mouvement du coeur.<p><p>L'effet de volume partiel mène à des images floues, de la même manière qu'un objectif d'appareil photo incorrectement mis au point produit des photographies floues. Deux possibilités s'offrent aux photographes pour éviter cela : soit améliorer la mise au point de leur objectif, soit retoucher les images après les avoir réalisées ; améliorer la mise au point de l'objectif peut s'effectuer dans l'espace des données (ajouter une lentille correctrice avant l'objectif) ou dans l'espace des images (ajouter une lentille correctrice après l'objectif).<p><p>Le mouvement cardiaque provoque également une perte de netteté des images, analogue à l'effet de flou sur une photographie d'une voiture de course réalisée avec un grand temps de pose. Classiquement, on peut augmenter la netteté d'une image en diminuant le temps de pose. Cependant, dans ce cas, moins de photons traversent l'objectif et l'image obtenue est plus bruitée.<p><p>On pourrait alors imaginer obtenir de meilleurs images en suivant la voiture au moyen de l'appareil photo. <p><p>De cette manière, la voiture serait à la fois nette et peu corrompue par du bruit, car beaucoup de photons pourraient être détectés.<p><p>En imagerie TEP, l'effet de volume partiel est d{\^u} à de nombreux facteurs dont le fait que le positron ne s'annihile pas exactement à l'endroit de son émission et que le détecteur frappé par un photon n'est pas toujours correctement identifié. La solution passe par une meilleure modélisation de la physique de l'acquisition au cours de la reconstruction, qui, en pratique est complexe et nécessite d'effectuer des approximations.<p><p>La perte de netteté due au mouvement du coeur est classiquement traitée en figeant le mouvement dans plusieurs images successives au cours d'un battement cardiaque. Cependant, une telle solution résulte en une diminution du nombre de photons, et donc en une augmentation du bruit dans les images. Tenir compte du mouvement de l'objet pendant la reconstruction TEP permettrait d'augmenter la netteté en gardant un bruit acceptable. On peut également penser à superposer différentes images recalées au moyen du mouvement.<p><p>Au cours de ce travail, nous avons étudié des méthodes qui tirent le meilleur parti possible des informations fournies par les événements détectés. Pour ce faire, nous avons choisi de baser nos reconstructions sur une liste d'événements contenant la position exacte des détecteurs et le temps exact d'arrivée des photons, au lieu de l'histogramme classiquement utilisé.<p><p>L'amélioration de résolution passe par la connaissance de l'image d'une source ponctuelle radioactive produite par la caméra.<p><p>{\`A} la suite d'autres travaux, nous avons mesuré cette image et nous l'avons modélisée, pour la première fois, au moyen d'une fonction spatialement variable, non-gaussienne et asymétrique. Nous avons ensuite intégré cette fonction dans un algorithme de reconstruction, dans l'espace image. C'est la seule possibilité pratique dans le cas d'acquisitions en mode liste. Nous avons ensuite comparé les résultats obtenus avec un traitement de l'image après la reconstruction.<p><p>Dans le cadre de la correction de mouvement cardiaque, nous avons opté pour l'étude de la reconstruction simultanée de l'image et du déplacement, sans autres informations externes que les données TEP et le signal d'un électrocardiogramme. Nous avons ensuite choisi d'étudier la qualité de ces estimateurs conjoints intensité-déplacement au moyen de leur variance. Nous avons étudié la variance minimale que peut atteindre un estimateur conjoint intensité-mouvement, sur base des données TEP uniquement, au moyen d'un outil appelé borne de Cramer-Rao. Dans ce cadre, nous avons étudié différentes manières existantes d'estimer la borne de Cramer-Rao et nous avons proposé une nouvelle méthode d'estimation de la borne de Cramer-Rao adaptée à des images de grande dimension. Nous avons enfin mis en évidence que la variance de l'algorithme classique OSEM était supérieure à celle prédite par la borne de Cramer-Rao. En ce qui concerne les estimateurs combinés intensité-déplacement, nous avons observé la diminution de la variance minimale possible sur les intensités lorsque le déplacement était paramétrisé sur des fonctions spatiales lisses.<p><p>Ce travail est organisé comme suit. Le chapitre théorique commence par brosser brièvement le contexte historique de la tomographie par émission de positrons. Nous avons souhaité insister sur le fait que l'évolution des idées n'est romantique et linéaire qu'à grande échelle. Nous abordons ensuite la description physique de l'acquisition TEP. Dans un deuxième chapitre, nous rappelons quelques éléments de la théorie de l'estimation et de l'approximation et nous traitons des problèmes inverses en général et de la reconstruction TEP en particulier.<p><p>La seconde partie aborde le problème du manque de netteté des images et la solution que nous avons choisi d'y apporter : une modélisation dans l'espace image de la réponse impulsionnelle de la caméra, en tenant compte de ses caractéristiques non gaussienne, asymétrique et spatialement variable. Nous présentons également le résultat de la comparaison avec une déconvolution post-reconstruction. Les résultats présentés dans ce chapitre ont fait l'objet d'une publication dans la revue Physics in Medicine and Biology.<p><p>Dans un troisième volet, nous abordons la correction de mouvement. Une premier chapitre brosse le contexte de la correction de mouvement en TEP et remet en perspective les différentes méthodes existantes, dans un cadre bayésien unificateur.<p><p>Un second chapitre aborde ensuite l'estimation de la qualité des images TEP et étudie en particulier la borne de Cramer-Rao.<p><p>Les résultats obtenus sont enfin résumés et replacés dans leur contexte dans une conclusion générale.<p>




2010

L. Zhang, G. Lafruit,
Design and Implementation of Real-Time High-Definition Stereo Matching SoC on FPGA. Computer Engineering
2010
Bibtex
Bibtex : info:hdl:2013/188485
Note : Language of publication: na



Papers

A. Pozdzik, A. Berton, H. Schmeiser, W. Missoum, C. Decaestecker, I. Salmon, J. Vanherweghem, J. Nortier,
Aristolochic acid nephropathy revisited: a place for innate and adaptive immunity?
Histopathology, Vol. 56, 4, pp. 449-463, 2010
Bibtex
Bibtex : info:hdl:2013/159377
Note : FLWIN
Abstract : Pozdzik A A, Berton A, Schmeiser H H, Missoum W, Decaestecker C, Salmon I J, Vanherweghem J-L & Nortier J L(2010) Histopathology56, 449–463Aristolochic acid nephropathy revisited: a place for innate and adaptive immunity?Aims:  The histological features of aristolochic acid nephropathy (AAN) consist of paucicellular interstitial fibrosis, severe tubular atrophy, and almost intact glomeruli with media lesions of interlobular arteries. As an early phase of interstitial inflammation preceded peritubular fibrosis in the rat model of AAN, the aim was to investigate the presence of inflammatory cells in human AAN.Methods and results:  Reports of confirmed cases and case series of AAN were reviewed in terms of interstitial inflammation and found to have very conflicting results. This prompted us to search for and characterize inflammatory cells within the native kidneys provided from four end-stage AAN patients. Prior aristolochic acid exposure was attested by the intrarenal presence of the typical aristolactam I-derived DNA adduct. Besides the tubulointerstitial lesions usually seen in the cortex, a massive infiltration of macrophages, T and B lymphocytes was detected by immunohistochemistry in the medullary rays and in the outer medullae with some extension to the upper cortical labyrinth.Conclusions:  In parallel with histological findings reported in the rat model, inflammatory cells are present preferentially in the interstitium of the medullary rays and of the outer medulllae in renal interstitium from human AAN cases, even in the terminal stages. Further studies must be undertaken to determine the respective roles of innate and adaptive immunity in the progression of AAN.



A. Pozdzik, A. Berton, H. Schmeiser, W. Missoum, C. Decaestecker, I. Salmon, J. Vanherweghem, J. Nortier,
Aristolochic acid nephropathy revisited: a place for innate and adaptive immunity?
Histopathology, Vol. 56, 4, pp. 449-463, 2010
Bibtex
Bibtex : info:hdl:2013/68372
Note : Journal Article
Abstract : AIMS: The histological features of aristolochic acid nephropathy (AAN) consist of paucicellular interstitial fibrosis, severe tubular atrophy, and almost intact glomeruli with media lesions of interlobular arteries. As an early phase of interstitial inflammation preceded peritubular fibrosis in the rat model of AAN, the aim was to investigate the presence of inflammatory cells in human AAN. METHODS AND RESULTS: Reports of confirmed cases and case series of AAN were reviewed in terms of interstitial inflammation and found to have very conflicting results. This prompted us to search for and characterize inflammatory cells within the native kidneys provided from four end-stage AAN patients. Prior aristolochic acid exposure was attested by the intrarenal presence of the typical aristolactam I-derived DNA adduct. Besides the tubulointerstitial lesions usually seen in the cortex, a massive infiltration of macrophages, T and B lymphocytes was detected by immunohistochemistry in the medullary rays and in the outer medullae with some extension to the upper cortical labyrinth. CONCLUSIONS: In parallel with histological findings reported in the rat model, inflammatory cells are present preferentially in the interstitium of the medullary rays and of the outer medulllae in renal interstitium from human AAN cases, even in the terminal stages. Further studies must be undertaken to determine the respective roles of innate and adaptive immunity in the progression of AAN.



I. Adanja, O. Debeir, V. Megalizzi, R. Kiss, N. Warzée, C. Decaestecker,
Automated tracking of unmarked cells migrating in three-dimensional matrices applied to anti-cancer drug screening.
Experimental cell research, Vol. 316, 2, pp. 181-193, 2010
Bibtex
Bibtex : info:hdl:2013/52535
Note : Journal Article
Abstract : In oncology, combating the spread of tumor cells is a clinical need which currently remains unsatisfied. Identifying anti-migratory compounds usually requires in vitro screening of a large number of molecules. Efficient and realistic (i.e., preferably 3D) in vitro tests are thus required in order to quantify the anti-migratory effects of anti-cancer drugs. To remain compatible with high-throughput screening, we focus on assays where unlabeled cells are migrating in 3D transparent gels and are observed under time-lapse 3D phase-contrast microscopy. In this context, we present a method for automatically tracking cells that combines a template matching preprocessing step with a mean-shift process. The preprocessing step consists in performing a correlation of a cell template with each observed volume in order to provide a phase-contrast artifact-free volume where the cells appear as correlation peaks surrounded by smooth gradients. This transformation enables the cells to be efficiently tracked by a mean-shift process. Robustness and efficiency of this approach are qualitatively and quantitatively shown in various experiments. Finally, we successfully applied our method to the quantitative characterization of the anti-migratory impact of cytochalasin-D on cancer cells. In conclusion, our method can efficiently be used for drug screening aiming to evidence drug-induced effects on cell migration in 3D transparent environments, such as matrix gels.



D. Unay, b. Gosselin, O. Kleynen, V. Leemans, M. Destain, O. Debeir,
Automatic grading of Bi-colored apples by multispectral machine vision
Computers and electronics in agriculture, Vol. 75, 1, pp. 204-212, 2010
Bibtex
Bibtex : info:hdl:2013/71281
Note : SCOPUS: ar.j
Abstract : In this paper we present a novel application work for grading of apple fruits by machine vision. Following precise segmentation of defects by minimal confusion with stem/calyx areas on multispectral images, statistical, textural and geometric features are extracted from the segmented area. Using these features, statistical and syntactical classifiers are trained for two- and multi-category grading of the fruits. Results showed that feature selection provided improved performance by retaining only the important features, and statistical classifiers outperformed their syntactical counterparts. Compared to the state-of-the-art, our two-category grading solution achieved better recognition rates (93.5\% overall accuracy). In this work we further provided a more realistic multi-category grading solution, where different classification architectures are evaluated. Our observations showed that the single-classifier architecture is computationally less demanding, while the cascaded one is more accurate. © 2010 Elsevier B.V.



C. Leignel, E. Hanson, E. Wolff, O. Caelen, G. Bontempi, O. Debeir, T. Leloup, N. Warzée, C. Simler, C. Beumier,
Detecting man-made structure changes to assist geographic data producers in planning their update strategy
The international archives of the photogrammetry, remote sensing and spatial information sciences, Vol. 38, pp. 26-33, 2010
Bibtex
Bibtex : info:hdl:2013/197829
Note : SCOPUS: cp.p
Abstract : Topographical data producers are currently confronted with the need for a faster updating method. Indeed, this need was assessed at the first stage of the ARMURS(∗) project by surveying several Belgian and international mapping agencies. The aim of the project is to build a demonstrator to assist data producers in planning the update of their topographic database more efficiently relying on remote sensing images, together with socio-economic and demographic data. At a regional scale, the man-made structure changes extracted by the ETATS module on a SPOT5 panchromatic image will be fused with a change analysis on socio-demographic data. At a local scale, as regards areas of predicted changes, the older databases are compared with recent very high-resolution satellite or aerial images in order to detect changes in man-made structures. Changes are detected by comparing an object-oriented classified VHR image to a simplified version of the old database. This object-oriented approach consists in a segmentation followed by a classification. Three segmentation methods (Watershed Assembly, Graph Cut, Mean Shift) were implemented and compared to the one of a commercial software (Definiens); indices were proposed to assess the quality of these segmentations. Features are selected either according to a visual interpretation formalised into an interpretation key, or by quantitative methods such as the forward Jeffries-Matusita distance or mutual information criteria (mRMR); selections are compared. By using a common framework (images, training set and validation set), existing classification methods available in Definiens and in R are compared. A final step of change detection gives us preliminary results.



L. Engels, X. De Tiege, M. Op De Beeck, N. Warzée,
Factors influencing the spatial precision of electromagnetic tracking systems used for MEG/EEG source imaging
Neurophysiologie clinique, Vol. 40, 1, pp. 19-25, 2010
Bibtex
Bibtex : info:hdl:2013/71570
Note : SCOPUS: ar.j
Abstract : OBJECTIVES: The purpose of this study is to determine the factors influencing the spatial precision and the replicability of electromagnetic trackers (EMT) for the localization of electrodes and natural landmarks on the patient's head. MATERIALS AND METHODS: The effects of seven conditions on the measurement of the EMT were investigated with a Polhemus Fastrack: distance, contact between two components of the EMT, presence of magnetic object, localization of landmarks and electrodes on a phantom and a human subject without and with movements. RESULTS: The EMT has a precision of 0.15mm+/-0.36mm for the measurements made on still objects in a non-magnetic environment. On a human subject, the mean variation of the nasion position is 1.6mm+/-1.46mm and 2.7mm+/-1.40mm for the tragus. The increase of the electrode measurement dispersions is significant between the phantom and the human subject with a mean variation of 2.39mm+/-1.26mm. In certain conditions, up to 15\% of the measurements may be considered as outliers. CONCLUSION: The precision significantly decreases for this application in the following cases: (1) physical contacts between the stylus/transmitter/receiver cables, (2) presence of magnetic objects in the surrounding of the EMT system, (3) skin and hair softness and (4) subject's head movements.



S. Saussez, L. de Leval, C. Decaestecker, N. Sirtaine, S. Cludts, A. Duray, D. Chevalier, S. André, H. Gabius, M. Remmelink, X. Leroy,
Galectin fingerprinting in Warthin's tumors: lectin-based approach to trace its origin?
Histology and histopathology, Vol. 25, 5, pp. 541-550, 2010
Bibtex
Bibtex : info:hdl:2013/68369
Note : Journal Article
Abstract : Warthin's tumor of the parotid gland is assumed to originate from the proliferation of epithelial inclusions within parotid lymph nodes. In that case, these cells are supposed to retain characteristics similar to common salivary gland ductal cells. Using immunohistochemical fingerprinting with four members of the family of adhesion/growth-regulatory galectins and comparison to intra- and interlobular ducts, marked similarities were noted for presence of galectins-3, -7 and -8. Notably, profiles of lectin binding, determined by applying human lectins as probes, were also similar when testing biotinylated galectins-3 and -8. Besides defining the galectin histochemical parameters in Warthin's tumors this study adds support to the hypothesis of heterotopia.



E. Balde, V. Megalizzi, M. Traoré, P. Cos, L. Maes, C. Decaestecker, L. Pieters, A. Balde,
In vitro antiprotozoal, antimicrobial and antitumor activity of Pavetta crassipes K. Schum leaf extracts.
Journal of ethnopharmacology, Vol. 130, 3, pp. 529-535, 2010
Bibtex
Bibtex : info:hdl:2013/68373
Note : Journal Article
Abstract : AIM OF THE STUDY: To study the potential benefit of the traditional medicinal plant Pavetta crassipes K. Schum (Rubiaceae), which is widely distributed throughout West Africa, the methanol and dichloromethane extracts were isolated from the plant leaves to determine if they exhibited antiprotozoal, antibacterial, antifungal or antitumor activity in vitro. MATERIALS AND METHODS: The methanol and dichloromethane extracts and their specific fractions were obtained using bioassay-guided fractionation and investigated for antiproliferative activity in vitro in microorganisms (Staphylococcus aureus, Escherichia coli and Candida albicans), protozoans (Trypanosoma cruzi, Trypanosoma brucei, Leishmania infantum and Plasmodium falciparum), and cancer (U373, PC3, MXT and A549) and normal cell lines (NHDF and MRC-5). RESULTS: Most of the alkaloid fractions investigated exhibited antiproliferative activity in all the cancer cell lines, microorganisms and protozoans studied. CONCLUSIONS: The benefit of Pavetta crassipes as a traditional medicinal remedy was confirmed using antiprotozoal and cytotoxicity assays in vitro. These analyses revealed that the components present in the alkaloid extract of Pavetta crassipes are responsible for its antiprotozoal and cytotoxic efficacy.



N. Wauthoz, P. Deleuze, J. Hecq, I. Roland, S. Saussez, I. Adanja, O. Debeir, C. Decaestecker, V. Mathieu, R. Kiss, K. Amighi,
In vivo assessment of temozolomide local delivery for lung cancer inhalation therapy.
European journal of pharmaceutical sciences, Vol. 39, pp. 402-411, 2010
Bibtex
Bibtex : info:hdl:2013/51846
Note : JOURNAL ARTICLE
Abstract : The aim of this study was to compare the efficacy of local drug delivery by inhalation to intravenous delivery in a B16F10 melanoma metastatic lung model. Temozolomide was formulated as a suspension, which was elaborated and evaluated in terms of particle size, shape and agglomeration. An endotracheal administration device was used to aerosolise the suspension. This mode of delivery was evaluated at different temozolomide concentrations and was optimized for the uniformity of delivered dose, the droplet size distribution and the distribution of droplets in vivo. Of the particles in the stabilised suspension, 79\% were compatible with the human respirable size range, and this formulation retained 100\% in vitro anticancer activity as compared to temozolomide alone in three distinct cancer cell lines. The pulmonary delivery device provided good reproducibility in terms of both the dose delivered and the droplet size distribution. Most of the lung tissues that were exposed to aerosol droplets contained the particles, as revealed by fluorescent microscopy techniques. The global in vivo antitumour activity of the inhaled temozolomide provided a median survival period similar to that for intravenous temozolomide delivery, and three out of 27 mice (11\%) survived with almost complete eradication of the lung tumours. The present study thus shows that inhalation of a simple liquid formulation is well tolerated and active against a very biologically aggressive mouse melanoma pulmonary pseudo-metastatic model. This inhalation delivery could be used to deliver other types of anticancer drugs.



S. Cludts, C. Decaestecker, B. Johnson, J. Lechien, X. Leroy, N. Kindt, H. Kaltner, S. André, H. Gabius, S. Saussez,
Increased expression of macrophage migration inhibitory factor during progression to hypopharyngeal squamous cell carcinoma.
Anticancer research, Vol. 30, 9, pp. 3313-3319, 2010
Bibtex
Bibtex : info:hdl:2013/68384
Note : Journal Article
Abstract : BACKGROUND/AIM: To examine the presence of macrophage migration inhibitory factor (MIF) quantitatively in relation to neoplastic progression of hypopharyngeal squamous cell carcinoma (HSCC). MATERIALS AND METHODS: The presence of MIF was analysed by quantitative immunohistochemistry in sections of 81 HSCCs, and compared to 15 specimens of tumour-free epithelia (TF\_E), 29 low-grade dysplasias (Low\_D) and 25 high-grade dysplasias (High\_D). In parallel, MIF expression was studied using Western blotting on a series of 19 fresh biopsies. RESULTS: A significant increase in MIF staining intensity (mean optical density) was observed in carcinoma samples compared to TF\_E (p<10(-6)), Low\_D (p=0.0006) or High\_D (p=0.0006). Immunohistochemical MIF positivity was significantly higher in HSCCs than in TF\_E (p=0.00001) or Low\_D (p=0.001). The percentage of MIF-immunopositive cells (labelling index) significantly decreased in parallel with an apparent loss of histological differentiation (p=0.003). CONCLUSION: This study identified the presence of MIF as a parameter that positively correlates with neoplastic progression of HSCC and cell differentiation status.



V. Mancilla, C. Decaestecker, C. Ligny, L. Matagne, P. Simon, I. Courtmans,
La surdité moyenne: {\'E}tiologie, évaluation linguistique et scolaire
Cahiers de l'audition, Vol. 23, 3, pp. 5-9, 2010
Bibtex
Bibtex : info:hdl:2013/200158
Note : SCOPUS: ar.j



B. Le Calve, M. Rynkowski, M. Le Mercier, C. Bruyère, C. Lonez, T. Gras, B. Haibe-Kains, G. Bontempi, C. Decaestecker, J. Ruysschaert, R. Kiss, F. Lefranc,
Long-term in vitro treatment of human glioblastoma cells with temozolomide increases resistance in vivo through up-regulation of GLUT transporter and aldo-keto reductase enzyme AKR1C expression.
Neoplasia (New York, N.Y.), Vol. 12, 9, pp. 727-739, 2010
Bibtex
Bibtex : info:hdl:2013/68382
Note : Journal Article
Abstract : Glioblastoma (GBM) is the most frequent malignant glioma. Treatment of GBM patients is multimodal with maximum surgical resection, followed by concurrent radiation and chemotherapy with the alkylating drug temozolomide (TMZ). The present study aims to identify genes implicated in the acquired resistance of two human GBM cells of astrocytic origin, T98G and U373, to TMZ. Resistance to TMZ was induced by culturing these cells in vitro for months with incremental TMZ concentrations up to 1 mM. Only partial resistance to TMZ has been achieved and was demonstrated in vivo in immunocompromised mice bearing orthotopic U373 and T98G xenografts. Our data show that long-term treatment of human astroglioma cells with TMZ induces increased expression of facilitative glucose transporter/solute carrier GLUT/SLC2A family members, mainly GLUT-3, and of the AKR1C family of proteins. The latter proteins are phase 1 drug-metabolizing enzymes involved in the maintenance of steroid homeostasis, prostaglandin metabolism, and metabolic activation of polycyclic aromatic hydrocarbons. GLUT-3 has been previously suggested to exert roles in GBM neovascularization processes, and TMZ was found to exert antiangiogenic effects in experimental gliomas. AKR1C1 was previously shown to be associated with oncogenic potential, with proproliferative effects similar to AKR1C3 in the latter case. Both AKR1C1 and AKR1C2 proteins are involved in cancer pro-proliferative cell chemoresistance. Selective targeting of GLUT-3 in GBM and/or AKR1C proteins (by means of jasmonates, for example) could thus delay the acquisition of resistance to TMZ of astroglioma cells in the context of prolonged treatment with this drug.



D. Lamoral-Theys, M. Le Mercier, B. Le Calve, M. Rynkowski, C. Bruyère, C. Decaestecker, B. Haibe-Kains, G. Bontempi, J. Dubois, F. Lefranc, R. Kiss,
Long-term temozolomide treatment induces marked amino metabolism modifications and an increase in TMZ sensitivity in Hs683 oligodendroglioma cells.
Neoplasia (New York, N.Y.), Vol. 12, 1, pp. 69-79, 2010
Bibtex
Bibtex : info:hdl:2013/51182
Note : Journal Article
Abstract : Gliomas account for more than 50\% of all primary brain tumors. The worst prognosis is associated with gliomas of astrocytic origin, whereas gliomas with an oligodendroglial origin offer higher sensitivity to chemotherapy, especially when oligodendroglioma cells display 1p19q deletions. Temozolomide (TMZ) provides therapeutic benefits and is commonly used with radiotherapy in highly malignant astrocytic tumors, including glioblastomas. The actual benefits of TMZ during long-term treatment in oligodendroglioma patients have not yet been clearly defined. In this study, we have investigated the effects of such a long-term TMZ treatment in the unique Hs683 oligodendroglioma model. We have observed increased TMZ sensitivity of Hs683 orthotopic tumors that were previously treated in vitro with months of progressive exposure to increasing TMZ concentrations before being xenografted into the brains of immunocompromised mice. Whole-genome and proteomic analyses have revealed that this increased TMZ sensitivity of Hs683 oligodendroglioma cells previously treated for long periods with TMZ can be explained, at least partly, by a TMZ-induced p38-dependant dormancy state, which in turn resulted in changes in amino acid metabolism balance, in growth delay, and in a decrease in Hs683 oligodendroglioma cell-invasive properties. Thus, long-term TMZ treatment seems beneficial in this Hs683 oligodendroglioma model, which revealed itself unable to develop resistance against TMZ.



D. Lamoral-Theys, C. Decaestecker, V. Mathieu, J. Dubois, A. Kornienko, R. Kiss, A. Evidente, L. Pottier,
Lycorine and its derivatives for anticancer drug design.
Mini-reviews in medical chemistry, Vol. 10, 1, pp. 41-50, 2010
Bibtex
Bibtex : info:hdl:2013/70175
Note : Journal Article
Abstract : Amaryllidaceae alkaloids are extensively studied for their biological activities in several pharmaceutical areas, including, for example, Alzheimer's disease for which galanthamine has already reached the market. Among this chemical family, lycorine displays very promising anti-tumor properties. This review first focuses on the chemical diversity of natural and synthetic analogues of lycorine and their metabolites, and then on mechanisms of action and biological targets through which lycorine and its derivatives display their anti-tumor activity. Our analysis of the structure-activity relationships of this family of compounds highlights the existence of various potential leads for the development of novel anticancer agents.



B. Geelen, A. Ferentinos, F. Catthoor, G. Lafruit, D. Verkest, R. Lauwereins, T. Stouraitis,
Modeling and exploiting spatial locality trade-offs in wavelet-based applications under varying resource requirements
ACM transactions on embedded computing systems, Vol. 9, 3, pp. 17-42, 2010
Bibtex
Bibtex : info:hdl:2013/186274
Note : Language of publication: en



V. Letort, S. Fouliard, G. Letort, I. Adanja, M. Kumazaka, O. Debeir, S. Gallagher, L. Larue, F. Xavier,
Quantitative Analysis of Melanocyte Migration in vitro Based on Automated Cell Tracking under Phase Contrast Microscopy Considering the Combined Influence of Cell Division and Cell-Matrix Interactions
Mathematical Modelling of Natural Phenomena, Vol. 5, 1, pp. 4-33, 2010
Bibtex
Bibtex : info:hdl:2013/52947
Note : SCOPUS: re.j
Abstract : The aim of this study was to describe and analyze the regulation and spatio-temporal dynamics of melanocyte migration in vitro and its coupling to cell division and interaction with the matrix. The melanocyte lineage is particularly interesting because it is involved in both embryonic development and oncogenesis/metastasis (melanoma). Biological experiments were performed on two melanocyte cell lines established from wild-type and β-catenin- transgenic mice (bcat*). The multi-functional β-catenin molecule is known to be able to regulate the transcription of various genes involved in cell proliferation and migration, particularly in the melanocyte lineage. We also investigated fibronectin, an extra-cellular matrix protein that binds integrins, thereby providing adhesion points for cells and encouraging migration. As the migration of individual cells were followed, automated methods were required for processing the large amount of data generated by the time-lapse video-microscopy. A model-based approach for automated cell tracking was evaluated on a sample by comparison with manual tracking. This method was found reliable in studying overall cell behaviour. Its application to all the observed sequences provided insight into the factors affecting melanocyte migration in vitro: melanocytes of mutated form of β-catenin showed higher division rates and no contact inhibition of growth was induced by the resulting increase in cell density. However, cell density limited the amplitude of cell displacements, although their motility was less affected. The high fibronectin concentration bound to substratum promoted cell migration and motility, the effect being more intense for wild-type cells than for cells with β-catenin over-expression. During the division process, cell migration speed increased rapidly then decreased slowly. Analyses of such data is expected to lead both to biological answers and to a framework for a better modeling processes in the future. © EDP Sciences, 2010.



S. Rorive, X. Moles Lopez, C. Maris, A. Trepant, S. Sauvage, N. Sadeghi-Meibodi, I. Roland, C. Decaestecker, I. Salmon,
TIMP-4 and CD63: new prognostic biomarkers in human astrocytomas.
Modern pathology, Vol. 23, 10, pp. 1418-1428, 2010
Bibtex
Bibtex : info:hdl:2013/68379
Note : Journal Article
Abstract : Based on the molecular profiling of astrocytomas, we previously identified a series of genes involved in astrocytoma invasion. Of these, tissue inhibitor of metalloproteinase-4 (TIMP-4) was found to be overexpressed in pilocytic astrocytomas relative to diffuse astrocytomas of any histological grade. Although some data suggest that TIMP-4 may be an anti-tumoral actor in astrocytomas, recent findings challenge this concept. The present study aims to investigate the diagnostic and prognostic values of TIMP-4 and its putative partner CD63 in human astrocytomas. Tissue microarray and image analysis were first carried out to quantitatively analyze the immunohistochemical expression of these proteins in 471 gliomas including 354 astrocytomas. Pathological semi-quantitative scores of both markers' expression were then established and correlated to astrocytoma diagnosis and patient prognosis. TIMP-4 and CD63 expressions were both overexpressed in astrocytomas compared with oligodendrogliomas (P<0.001) and in pilocytic astrocytomas compared with grade II diffuse astrocytomas (P<0.001). In glioblastomas, high TIMP-4/CD63 co-expression scores were identified as independent prognostic factors associated with progression and shorter survival. In conclusion, this work provides the first evidence of a TIMP-4/CD63 association in astrocytoma tumor cells. It identifies TIMP-4 and CD63 as markers of the astrocytic phenotype in patients with gliomas. In addition, this work highlights the contribution of high TIMP-4/CD63 co-expression to the adverse outcomes of patients with glioblastomas.



S. Rorive, N. D'Haene, C. Fossion, I. Delpierre, N. Abarguia, E. Avni, C. Decaestecker, I. Salmon,
Ultrasound-guided fine-needle aspiration of thyroid nodules: stratification of malignancy risk using follicular proliferation grading, clinical and ultrasonographic features.
European journal of endocrinology, Vol. 162, 6, pp. 1107-1115, 2010
Bibtex
Bibtex : info:hdl:2013/59300
Note : Journal Article
Abstract : OBJECTIVE: To evaluate the diagnostic value of fine-needle aspiration (FNA) cytology and the additive contribution brought by clinical and ultrasound (US) features. METHOD: Cytological and histological diagnoses were compared in a series of 924 patients who underwent US-guided FNA before surgery. We additionally developed a grading system for follicular proliferation (FP) FNA diagnosis, and investigated its impact on the malignancy risk as well as the additive contribution of clinical and US features by means of decision tree analysis. RESULTS: Excluding FP cases (n=395), our data demonstrated that strictly benign or malignant FNA diagnoses exhibit great concordance with benign or malignant histological diagnoses (97.8\% accuracy). Our grading system that was applied to the 395 FP cases revealed that grades 1, 2 and 3 were associated with a 7.7, 17.7 and 45.7\% incidence of malignancy respectively. Decision tree analysis resulted in a classification model which involved FP grade, patient's age, serum thyroglobulin level, nodule size and nodule uniqueness. This model identified a subgroup of patients with grade 1 FP nodules who were older than 50 years, and who had a higher risk of malignancy (17.9\%). In addition, high serum thyroglobulin levels were associated with a very high malignancy risk (75.0\%) for patients with grade 3 FP nodules. Finally, among grade 2 FP patients, unique and large nodules were associated with a high malignancy risk of 36.1\%. CONCLUSIONS: The integration of FP grade, clinical and US features allows the stratification of patients with FP cytology according to their risk of malignancy.



Conferences

G. Mariani, C. Couvreur, K. Zhang, L. Zhang, G. Lafruit,
An efficient run-time management methodology for stereo matching application
23th International Conference on Architecture of Computing Systems 2010 - ARCS - Workshop Proceedings, pp. 1-6, 2010
Bibtex
Bibtex : info:hdl:2013/186790
Note : Language of publication: en



C. Laugerotte, N. Warzée,
Computerised geometric analysis of a spire coming from a Gothic tabernacle
Proceedings of CAA 2004, 2010
Bibtex
Bibtex : info:hdl:2013/73549
Note : Language of publication: en



C. Leignel, O. Caelen, O. Debeir, E. Hanson, T. Leloup, C. Simler, C. Beumier, G. Bontempi, N. Warzée, E. Wolff,
Detecting man-made structure changes to assist geographic data producers in planning their update strategy, ISPRS
Core Spatial Databases – Updating, Maintenance and Services – from Theory to Practise, Haifa, Israel, 2010
Bibtex
Bibtex : info:hdl:2013/97450
Note : Language of publication: en



A. Anthony, M. Jaumain, B. Penelle, N. Warzée, P. Mathys, A. Nonclercq,
Electromyogram pattern recognition in neurophysiology and physiotherapy
Conference: 9th Belgian Day on Biomedical Engineering, joint meeting of the IEEE EMBS Benelux Chapter(26 Nov., 2010: Brussels, Belgium), 2010
Bibtex
Bibtex : info:hdl:2013/300013
Note : Language of publication: en



L. Ferdinande, A. Mathieu, C. Decaestecker, A. Negulescu, C. Cuvelier, I. Salmon, P. Demetter,
Indoleamine 2,3-dioxygenase expression is an independent prognostic factor in pT1-4N1Mx staged colorectal cancer
Conference: Gastrointestinal Cancers Symposium Rabat (January,2010), 2010
Bibtex
Bibtex : info:hdl:2013/59389
Note : Language of publication: en



K. Zhang, G. Lafruit, R. Lauwereins, L. Van Gool,
Joint integral histograms and its appalication in stereo matching
IEEE International Conference on Image Processing - ICIP, pp. 817-820, 2010
Bibtex
Bibtex : info:hdl:2013/186794
Note : Language of publication: en



X. Moles Lopez, O. Debeir, C. Maris, I. Roland, I. Salmon, C. Decaestecker,
Ki-67 hot-spots detection on glioblastoma tissue sections
Proc. of the 2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2010), pp. pp 149-152, Rotterdam, 2010
Bibtex
Bibtex : info:hdl:2013/70188
Note : Language of publication: en



P. Mainali, Q. Yang, G. Lafruit, R. Lauwereins, L. Van Gool,
LOCOCO: LOw COmplexity COrner detector
IEEE International Conference on Acoustics, pp. 810-813, 2010
Bibtex
Bibtex : info:hdl:2013/186789
Note : Language of publication: en



P. Mainali, Q. Yang, G. Lafruit, R. Lauwereins, L. Van Gool,
Robust low complexity feature tracking
IEEE International Conference on Image Processing - ICIP, pp. 829-832, 2010
Bibtex
Bibtex : info:hdl:2013/186792
Note : Language of publication: en



R. Phull, P. Mainali, Q. Yang, H. Sips, G. Lafruit,
Robust low complexity feature tracking using CUDA
IEEE Workshop on Signal Processing Systems - SIPS, pp. 362-367, 2010
Bibtex
Bibtex : info:hdl:2013/186795
Note : Language of publication: en



C. Simler, C. Beumier, C. Leignel, O. Debeir, E. Wolff,
The use of ORFEO toolbox in the context of map updating
IEEE International Geoscience And Remote Sensing Symposium, Honolulu,Hawa{\"i}, 2010
Bibtex
Bibtex : info:hdl:2013/97451
Note : Language of publication: en



Books chapters

A. Cauchie, A. Xhibitte, N. Warzée,
Back to the future: l'ULB reconstitue l’Expo en 3D
{\'E}ditions Racine, pp. 211-233, 2010
Bibtex
Bibtex : info:hdl:2013/71563
Note : Language of publication: fr



A. Chirila-Rus, G. Lafruit, B. Masschelein,
Scalability and Error Protection: Means for Error-resilient, Adaptable Image Transmission in heterogeneous environments
Kluwer Academic Publishers, pp. 203-227, 2010
Bibtex
Bibtex : info:hdl:2013/187425
Note : Language of publication: na



Technical report

C. Leignel, O. Caelen, O. Debeir, E. Hanson, T. Leloup, C. Simler, C. Beumier, G. Bontempi, N. Warzée, E. Wolff,
Automatic Recognition for Map Update by Remote Sensing, final report.
2010
Bibtex
Bibtex : info:hdl:2013/97614
Note : Language of publication: en




2009

Papers

I. Sol{\'i}s, M. Torres-Cisneros, G. Avina-Cervantes, O. Ibarra-Manzano, O. Debeir, S. Ledesma-Orozco, E. Perez-Careta, J. S{\'a}nchez-Mondragon,
2D cell tracking by FPGA-optical correlation method
Proceedings of SPIE - The International Society for Optical Engineering, Vol. 7386, 2009
Bibtex
Bibtex : info:hdl:2013/167315
Note : SCOPUS: cp.p
Abstract : Our work uses 1080 images sequence obtained from "in vitro" samples taken every 4 min from a microscope under phase contrast technique. These images are in JPEG format and are 500{\?x}700 pixels size with a compression rate of 3:1. We developed an algorithm and characterize it over several image operations against the tracking effectiveness and its robustness respect mitosis and cell shape change. Image equalization, dilation and erosion were the image processing procedures founded to provide best tracking results. Equalization procedure, for example, required a time delay of 5 sec for a size target of 60x90 pixels and 9 sec for size target of 89x100 pixels. This algorithm was implemented into a FPGA which controlled our optical correlator in order to performance all Fourier operations by optical method. Our results showed that the use of the optical correlator can reduce the time consuming in the image process until for 90\% which able us to track cells in vascular structure. © 2009 SPIE.



S. Saussez, C. Decaestecker, S. Cludts, P. Ernoux-Neufcoeur, D. Chevalier, Smetana Jr. Karel, S. André, X. Leroy, H. Gabius,
Adhesion/growth-regulatory tissue lectin galectin-1 in relation to angiogenesis/lymphocyte infiltration and prognostic relevance of stromal up-regulation in laryngeal carcinomas
Anticancer research, Vol. 29, 1, pp. 59-65, 2009
Bibtex
Bibtex : info:hdl:2013/111872
Note : SCOPUS: ar.j



A. Mathieu, B. Weynand, E. Verbeken, S. Da Silva, C. Decaestecker, I. Salmon, P. Demetter,
Comparison of four antibodies for immunohistochemical evaluation of epidermal growth factor receptor expression in non-small cell lung cancer.
Lung cancer, Vol. 1301, pp. 152-162, 2009
Bibtex
Bibtex : info:hdl:2013/53634
Note : JOURNAL ARTICLE
Abstract : Agents acting on signalling molecules of growth pathways have emerged as therapeutics for non-small cell lung cancer (NSCLC). Among them are inhibitors of the epidermal growth factor receptor (EGFR). To meet Belgian reimbursement criteria for erlotinib, patients must have an EGFR-positive tumour, defined as at least 10\% of cells showing membranous staining on immunohistochemistry. This study compares results obtained with the Dako pharmDx kit versus other anti-EGFR antibodies in 634 NSCLC. More than 80\% of patients qualify for erlotinib therapy using the Dako pharmDx kit or antibodies from Zymed or Novocastra; when NeoMarkers antibodies are used, less than 70\% will do. Although immunohistochemical stainings for EGFR can be performed on biopsies, surgical and cytological samples from primary and metastatic NSCLC, highest positivity rates were obtained in biopsies from primary tumours. In conclusion, immunohistochemistry for patient selection for erlotinib therapy needs standardization in order to avoid results influenced by technical issues.



L. Mundeleer, D. Wikler, T. Leloup, V. Lucidi, V. Donckier De Donceel, N. Warzée,
Computer assisted needle positioning for liver tumor radiofrequency ablation (RFA)
The international journal of medical robotics and computer assisted surgery, Vol. 5, 4, pp. 458-465, 2009
Bibtex
Bibtex : info:hdl:2013/71569
Note : FLWIN
Abstract : Background. The RFA procedures rely on a precise positioning of the radiofrequency electrode and the complete destruction of the tumour. This article presents new optimization techniques to improve such surgical procedures.Methods. A method to optimize the coverage of the tumour by successive RFA destructions and an in vitro procedure with simulated tumours have been developed.Results. The guidance system and optimization coverage have been tested on 3D simulation and by the surgeon in vitro on a heifer liver. In this context, the RFA electrode is optically tracked and guided.Conclusions. The optimization method provides needle placements that ensure a complete theoretical ablation of the tumour, and the guidance system helps the surgeon to reach each position of destruction. Copyright © 2009 John Wiley & Sons, Ltd.



L. Mundeleer, D. Wikler, T. Leloup, V. Lucidi, V. Donckier De Donceel, N. Warzée,
Computer-assisted needle positioning for liver tumour radiofrequency ablation (RFA)
The international journal of medical robotics and computer assisted surgery, Vol. 5, 4, pp. 458-464, 2009
Bibtex
Bibtex : info:hdl:2013/127058
Note : SCOPUS: ar.j



T. Leloup, W. El Kazzi, F. Schuind, N. Warzée,
Conception of a navigation system controlling diaphyseal fracture reduction treated with external fixation
The international journal of medical robotics and computer assisted surgery, Vol. 5, 1, pp. 99-109, 2009
Bibtex
Bibtex : info:hdl:2013/71567
Note : FLWIN
Abstract : Background. The reduction of long bone fractures treated with external fixation is usually performed with fluoroscopic images, which include several disadvantages: 2D information, distortions, and irradiation to the patient and the surgical team. This article presents a new navigation technique to control the reduction of such fractures while minimizing the irradiation.Methods. Optically tracked markers are fixed to pins inserted into the bone fragments. These last are modelled using two initial calibrated radiographs. The models can be improved with several types of anatomical data and are displayed in real time.Results. This navigation system was tested on dry bones and an anatomical specimen leg.Conclusions. This new technique allows the visualization of the fracture in real time and from any viewpoint during the reduction. Irradiation is minimized using only two X-ray images. Copyright © 2009 John Wiley & Sons, Ltd.



K. Zhang, J. Lu, G. Lafruit,
Cross-based local stereo matching using orthogonal integral images
IEEE transactions on circuits and systems for video technology, Vol. 19, 7, pp. 1073-1079, 2009
Bibtex
Bibtex : info:hdl:2013/186276
Note : Language of publication: en



B. Geelen, A. Ferentinos, F. Catthoor, S. Toulatos, G. Lafruit, T. Stouraitis, R. Lauwereins, D. Verkest,
Exploiting varying resource requirements in wavelet-based applications in dynamic execution environments
Journal of Signal Processing Systems, Vol. 56, 2-3, pp. 125-139, 2009
Bibtex
Bibtex : info:hdl:2013/186279
Note : Language of publication: en



Q. Houben, J. Czyz, J. Tocino Diaz, O. Debeir, N. Warzée,
Feature-based stereo vision using smart cameras for traffic surveillance
Lecture notes in computer science, Vol. 5815 LNCS, pp. 144-153, 2009
Bibtex
Bibtex : info:hdl:2013/70566
Note : SCOPUS: cp.k



M. Le Mercier, S. Fortin, V. Mathieu, I. Roland, S. Spiegl-Kreinecker, B. Haibe-Kains, G. Bontempi, C. Decaestecker, W. Berger, F. Lefranc, R. Kiss,
Galectin 1 proangiogenic and promigratory effects in the Hs683 oligodendroglioma model are partly mediated through the control of BEX2 expression.
Neoplasia (New York, N.Y.), Vol. 11, 5, pp. 485-496, 2009
Bibtex
Bibtex : info:hdl:2013/51190
Note : Journal Article
Abstract : We have previously reported that galectin 1 (Gal-1) plays important biological roles in astroglial as well as in oligodendroglial cancer cells. As an oligodendroglioma model, we make use of the Hs683 cell line that has been previously extensively characterized at cell biology, molecular biology, and genetic levels. Galectin 1 has been shown to be involved in Hs683 oligodendroglioma chemoresistance, neoangiogenesis, and migration. Down-regulating Gal-1 expression in Hs683 cells through targeted small interfering RNA provokes a marked decrease in the expression of the brain-expressed X-linked gene: BEX2. Accordingly, the potential role of BEX2 in Hs683 oligodendroglioma cell biology has been investigated. The data presented here reveal that decreasing BEX2 expression in Hs683 cells increases the survival of Hs683 orthotopic xenograft-bearing mice. Furthermore, this decrease in BEX2 expression impairs vasculogenic mimicry channel formation in vitro and angiogenesis in vivo, and modulates glioma cell adhesion and invasive features through the modification of several genes previously reported to play a role in cancer cell migration, including MAP2, plexin C1, SWAP70, and integrin beta(6). We thus conclude that BEX2 is implicated in oligodendroglioma biology.



S. Cludts, C. Decaestecker, V. Mahillon, D. Chevalier, H. Kaltner, S. André, M. Remmelink, X. Leroy, H. Gabius, S. Saussez,
Galectin-8 up-regulation during hypopharyngeal and laryngeal tumor progression and comparison with galectin-1, -3 and -7.
Anticancer research, Vol. 29, 12, pp. 4933-4940, 2009
Bibtex
Bibtex : info:hdl:2013/75903
Note : Comparative Study
Abstract : To define specific staining patterns for the adhesion/growth-regulatory lectin tandem-repeat-type galectin-8 in hypopharyngeal and laryngeal tumor progression and relate these parameters to galectins 1, 3 and 7 in the quest to explore the galectin network.



L. Yen, F. Fouss, C. Decaestecker, P. Francq, M. Saerens,
Graph nodes clustering with the sigmoid commute-time kernel: a comparative study
Data & knowledge engineering, Vol. 68, 3, pp. 338-361, 2009
Bibtex
Bibtex : info:hdl:2013/68825
Note : Language of publication: en



R. Marechal, P. Demetter, N. Nagy, A. Berton, C. Decaestecker, M. Polus, J. Closset, J. Devière, I. Salmon, J. Van Laethem,
High expression of CXCR4 may predict poor survival in resected pancreatic adenocarcinoma.
British Journal of Cancer, Vol. 100, 9, pp. 1444-1451, 2009
Bibtex
Bibtex : info:hdl:2013/51024
Note : Journal Article
Abstract : Chemokines and their receptors are involved in tumourigenicity and clinicopathological significance of chemokines receptor expression in pancreatic adenocarcinoma (PA) is not fully understood. This study was conducted to determine patients' outcome according to the expressions of CXCR4, CXCR7 and HIF-1alpha after resection of PA. Immunohistochemistry for CXCR4, CXCR7 and HIF-1alpha expressions as well as cell proliferative index (Ki-67) was conducted in 71 resected (R0) PA and their 48 related lymph nodes (LN) using tissue microarray. CXCR4 and CXCR7 expressions were positively correlated to HIF-1alpha suggesting a potential role of HIF-1alpha in CXCR4 and CXCR7 transcription activation. Patients with CXCR4(high) tumour expression had shorter OS than those with low expression (median survival: 9.7 vs 43.2 months, P=0.0006), a higher risk of LN metastases and liver recurrence. In multivariate analysis, high CXCR4 expression, LN metastases and poorly differentiated tumour are independent negative prognosis factors. In a combining analysis, patients with CXCR4(low)/CXCR7(low) tumour had a significantly shorter DFS and OS than patients with a CXCR7(high)/CXCR4(high) tumour. CXCR4 in resected PA may represent a valuable prognostic factor as well as an attractive target for therapeutic purpose.



S. Saussez, S. Cludts, A. Capouillez, G. Mortuaire, K. Smetana, H. Kaltner, S. André, X. Leroy, H. Gabius, C. Decaestecker,
Identification of matrix metalloproteinase-9 as an independent prognostic marker in laryngeal and hypopharyngeal cancer with opposite correlations to adhesion/growth-regulatory galectins-1 and -7.
International journal of oncology, Vol. 34, 2, pp. 433-439, 2009
Bibtex
Bibtex : info:hdl:2013/75906
Note : Journal Article
Abstract : The enzymatic activity of matrix metalloproteinase-9 (MMP-9) suggests that its presence in hypopharyngeal and laryngeal squamous cell carcinomas (HSCCs, LSCCs) could have prognostic value. We tested this hypothesis by quantitative morphometric analysis of immunohistochemical staining in histological sections of 73 stage IV HSCCs and 45 LSCCs (30 cases of stage I/II, 15 cases of stage IV). As compared to tumour-free epithelium an increase for the labelling index in LSCCs reached statistical significance (p=0.04). Specimens of Reinke's edema were strongly higher in this parameter compared to tumour-free tissue area (p=0.000001), underscoring an association between the level of MMP-9 expression and inflammation. Focusing on patients' recurrence status we identified thresholds for the labelling index of 10\% for HSCCs and 18\% for LSCCs, both indicating rapid recurrence and dismal prognosis unless surpassed. When relating data for MMP-9 to those for three adhesion/growth-regulatory galectins, a positive correlation with galectin-7 expression was detected in LSCCs. This finding suggests a possible potential role of this endogenous lectin as inducer of MMP-9 gene expression in situ. Of note, galectin-1 expression was negatively correlated with MMP-9 and that of galectin-3, a substrate of MMP-9, not related. In conclusion our study delineated a prognostic role of MMP-9 immunodetection in high-stage HSCCs and in LSCCs when separating patients by a distinct threshold for the labelling index. Moreover, it indicated associations between MMP-9 and multifunctional galectins-1 and -7 in situ.



F. Lefranc, S. Sauvage, G. Van Goietsenoven, V. Megalizzi, D. Lamoral-Theys, O. Debeir, S. Spiegl-Kreinecker, W. Berger, V. Mathieu, C. Decaestecker, R. Kiss,
Narciclasine, a plant growth modulator, activates Rho and stress fibers in glioblastoma cells.
Molecular cancer therapeutics, Vol. 8, 7, pp. 1739-1750, 2009
Bibtex
Bibtex : info:hdl:2013/51193
Note : Journal Article
Abstract : Cell motility and resistance to apoptosis characterize glioblastoma multiforme growth and malignancy. Narciclasine, a plant growth modulator, could represent a powerful new weapon targeting the Achilles' heel of glioblastoma multiforme and may offer the potential to better combat these devastating malignancies. The in vitro effects of narciclasine on cell proliferation, morphology, actin cytoskeleton organization, and the Rho/Rho kinase/LIM kinase/cofilin pathway and its antitumor activity in vivo have been determined in models of human glioblastoma multiforme. Narciclasine impairs glioblastoma multiforme growth by markedly decreasing mitotic rates without inducing apoptosis. The compound also modulates the Rho/Rho kinase/LIM kinase/cofilin signaling pathway, greatly increasing GTPase RhoA activity as well as inducing actin stress fiber formation in a RhoA-dependent manner. Lastly, the treatment of human glioblastoma multiforme orthotopic xenograft- bearing mice with nontoxic doses of narciclasine significantly increased their survival. Narciclasine antitumor effects were of the same magnitude as those of temozolomide, the drug associated with the highest therapeutic benefits in treating glioblastoma multiforme patients. Our results show for the first time that narciclasine, a plant growth modulator, activates Rho and stress fibers in glioblastoma multiforme cells and significantly increases the survival of human glioblastoma multiforme preclinical models. This statement is made despite the recognition that to date, irrespective of treatment, no single glioblastoma multiforme patient has been cured.



S. Rogmans, J. Lu, P. Bekaert, G. Lafruit,
Real-time stereo-based view synthesis algorithms: a unified framework and evaluation on commodity GPUs
Signal processing. Image communication, Vol. 24, 1-2, pp. 49-64, 2009
Bibtex
Bibtex : info:hdl:2013/186280
Note : Language of publication: en



C. Decaestecker, X. Moles Lopez, N. D'Haene, I. Roland, S. Guendouz, C. Duponchelle, A. Berton, O. Debeir, I. Salmon,
Requirements for the valid quantification of immunostains on tissue microarray materials using image analysis.
Proteomics, Vol. 9, 19, pp. 4478-4494, 2009
Bibtex
Bibtex : info:hdl:2013/52938
Note : Journal Article
Abstract : Antibody-based proteomics applied to tissue microarray (TMA) technology provides a very efficient means of visualizing and locating antigen expression in large collections of normal and pathological tissue samples. To characterize antigen expression on TMAs, the use of image analysis methods avoids the effects of human subjectivity evidenced in manual microscopical analysis. Thus, these methods have the potential to significantly enhance both precision and reproducibility. Although some commercial systems include tools for the quantitative evaluation of immunohistochemistry-stained images, there exists no clear agreement on best practices to allow for correct and reproducible quantification results. Our study focuses on practical aspects regarding (i) image acquisition (ii) segmentation of staining and counterstaining areas and (iii) extraction of quantitative features. We illustrate our findings using a commercial system to quantify different immunohistochemistry markers targeting proteins with different expression patterns (cytoplasmic, nuclear or membranous) in colon cancer or brain tumor TMAs. Our investigations led us to identify several steps that we consider essential for standardizing computer-assisted immunostaining quantification experiments. In addition, we propose a data normalization process based on reference materials to be able to compare measurements between studies involving different TMAs. In conclusion, we recommend certain critical prerequisites that commercial or in-house systems should satisfy in order to permit valid immunostaining quantification.



X. Ji, J. Huang, M. Chiang, G. Lafruit, F. Catthoor,
Scheduling and resource allocation for SVC streaming over OFDM downlink systems
IEEE transactions on circuits and systems for video technology, Vol. 19, 10, pp. 1549-1555, 2009
Bibtex
Bibtex : info:hdl:2013/186278
Note : Language of publication: en



V. Megalizzi, C. Decaestecker, O. Debeir, S. Spiegl-Kreinecker, W. Berger, F. Lefranc, R. Kast, R. Kiss,
Screening of anti-glioma effects induced by sigma-1 receptor ligands: potential new use for old anti-psychiatric medicines.
European journal of cancer, Vol. 45, 16, pp. 2893-2905, 2009
Bibtex
Bibtex : info:hdl:2013/51188
Note : Journal Article
Abstract : The prognosis of glioblastoma (GBM) remains poor. Diffuse invasion of distant brain tissue by migrating cells from the primary tumour mass has already occurred at time of diagnosis. Anti-cancer effects of a selective sigma-1 agonist, 4-(N-benzylpiperidin-4-yl)-4-iodobenzamide (4-IBP), in glioblastoma were shown previously, leading to the present work where the effects on glioblastoma cells of 17 agonists or antagonists of sigma-1 receptors were studied, including currently marketed drugs fluvoxamine, dextromethorphan, donepezil, memantine and haloperidol. We first showed that established GBM cell lines, primary cultures and surgical specimens express sigma-1 receptors. In vitro analyses then focused on anti-proliferation and anti-migratory effects on human glioblastoma cell lines using quantitative videomicroscopy analyses. These cell monitoring assays revealed specific impacts on the mitotic cell process. Using an aggressive glioma model orthotopically grafted into the brains of immunocompromised mice, we showed that combining donepezil and temozolomide gave additive benefit in terms of long survivors as compared to temozolomide or donepezil alone. Clinical study is planned if further rodent dose-ranging studies of donepezil with temozolomide continue to show evidence of benefit in this model.



B. Geelen, A. Ferentinos, F. Catthoor, G. Lafruit, D. Verkest, R. Lauwereins, T. Stouraitis,
Spatial locality exploitation for runtime reordering of JPEG2000 wavelet data layouts
ACM transactions on design automation of electronic systems, Vol. 15, 1, 2009
Bibtex
Bibtex : info:hdl:2013/186275
Note : Language of publication: en



J. Lu, S. Rogmans, G. Lafruit, F. Catthoor,
Stream-centric stereo matching and view synthesis: a high-speed approach on GPUs
IEEE transactions on circuits and systems for video technology, Vol. 19, 11, pp. 1598-1611, 2009
Bibtex
Bibtex : info:hdl:2013/186277
Note : Language of publication: en



P. Malarme, D. Wikler, N. Warzée,
Synchronization of surgical data in a distributed computer system
International Journal of Computer Assisted Radiology and Surgery, Vol. 4, suppl. 1, pp. 145-149, 2009
Bibtex
Bibtex : info:hdl:2013/71568
Note : Language of publication: en



A. Capouillez, G. Debauve, C. Decaestecker, O. Filleul, D. Chevalier, G. Mortuaire, F. Coppée, X. Leroy, A. Belayew, S. Saussez,
The helicase-like transcription factor is a strong predictor of recurrence in hypopharyngeal but not in laryngeal squamous cell carcinomas.
Histopathology, Vol. 55, 1, pp. 77-90, 2009
Bibtex
Bibtex : info:hdl:2013/75904
Note : Comparative Study
Abstract : To examine the immunohistochemical expression of helicase-like transcription factor (HLTF) in relation to the prognosis of hypopharyngeal (HSCCs) and laryngeal (LSCCs) squamous cell carcinomas, and to characterize the HLTF protein variants expressed in biopsy specimens of head and neck squamous cell carcinoma (HNSCC) as well as the HeLa cell line.



S. Leyman, M. Sidani, L. Ritsma, D. Waterschoot, R. Eddy, D. Dewitte, O. Debeir, C. Decaestecker, J. Vandekerckhove, J. van Rheenen, C. Ampe, J. Condeelis, M. Van Troys,
Unbalancing the phosphatidylinositol-4,5-bisphosphate-cofilin interaction impairs cell steering.
Molecular biology of the cell, Vol. 20, 21, pp. 4509-4523, 2009
Bibtex
Bibtex : info:hdl:2013/52937
Note : Journal Article
Abstract : Cofilin is a key player in actin dynamics during cell migration. Its activity is regulated by (de)phosphorylation, pH, and binding to phosphatidylinositol-4,5-bisphosphate [PI(4,5)P(2)]. Here, we here use a human cofilin-1 (D122K) mutant with increased binding affinity for PI(4,5)P(2) and slower release from the plasma membrane to study the role of the PI(4,5)P(2)-cofilin interaction in migrating cells. In fibroblasts in a background of endogenous cofilin, D122K cofilin expression negatively affects cell turning frequency. In carcinoma cells with down-regulated endogenous cofilin, D122K cofilin neither rescues the drastic morphological defects nor restores the effects in cell turning capacity, unlike what has been reported for wild-type cofilin. In cofilin knockdown cells, D122K cofilin expression promotes outgrowth of an existing lamellipod in response to epidermal growth factor (EGF) but does not result in initiation of new lamellipodia. This indicates that, next to phospho- and pH regulation, the normal release kinetics of cofilin from PI(4,5)P(2) is crucial as a local activation switch for lamellipodia initiation and as a signal for migrating cells to change direction in response to external stimuli. Our results demonstrate that the PI(4,5)P(2) regulatory mechanism, that is governed by EGF-dependent phospholipase C activation, is a determinant for the spatial and temporal control of cofilin activation required for lamellipodia initiation.



Conferences

R. Ercek, D. Viviers, N. Warzée,
3D Reconstruction and Digitalization of an
archaeological site, Itanos, Crete
International Meeting on Archaeology and Graphic
Informatics, Proceedings of ARQUEOLOGICA 2.0, pp. 289-293, 2009
Bibtex
Bibtex : info:hdl:2013/60800
Note : Language of publication: en



J. Tocino Diaz, Q. Houben, J. Czyz, O. Debeir, N. Warzée,
A camera auto-calibration algorithm for realtime road traffic analysis
VISAPP 2009 : International Conference on Computer Vision Theory and Applications, Lisboa, Portugal, 2009
Bibtex
Bibtex : info:hdl:2013/53005
Note : Language of publication: en



S. Rogmans, P. Bekaert, G. Lafruit,
A high-level kernel transformation rule set for efficient caching on graphics hardware
International Conference on Signal Processing and Multimedia Applications - SIGMAP, 2009
Bibtex
Bibtex : info:hdl:2013/186802
Note : Language of publication: en



Q. Houben, J. Tocino Diaz, N. Warzée, O. Debeir, J. Czyz,
A multi-features stereo vision system for road traffic analysis
VISAPP 2009 : International Conference on Computer Vision Theory and Applications, Lisboa, Portugal, 2009
Bibtex
Bibtex : info:hdl:2013/53008
Note : Language of publication: en



K. Zhang, J. Lu, G. Lafruit, R. Lauwereins, L. Van Gool,
Accurate and efficient stereo matching with robust piecewise voting
IEEE International Conference on Multimedia & Expo - ICME, pp. 93-96, 2009
Bibtex
Bibtex : info:hdl:2013/186798
Note : Language of publication: en



P. Van Dale, A. De Greef, C. Lenders, N. Warzée,
Biomedical Engineer and Phlebologist: A Midship Frame
International Angiology - Proceedings of the XVI World Congress of the Union Internationale de Phlebologie, pp. 138, 31 August - 4 September 2009, 2009
Bibtex
Bibtex : info:hdl:2013/71595
Note : Language of publication: en



E. Wolff, O. Debeir, E. Hanson, C. Leignel, C. Simler, C. Beumier, N. Warzée,
Comparaison et évaluation de méthodes de segmentation avec contrainte en vue d’une classification du b{\^a}ti et des routes
Proceedings of JIGOT, Toulouse, France, 2009
Bibtex
Bibtex : info:hdl:2013/52997
Note : Language of publication: fr



S. Rogmans, M. Dumont, T. Cuypers, G. Lafruit, P. Bekaert,
Complexity reduction of real-time depth scanning on graphics hardware
4th International Conference on Computer Vision Theory and Applications - VISAPP, pp. 547-550, 2009
Bibtex
Bibtex : info:hdl:2013/186796
Note : Language of publication: en



N. Wauthoz, P. Deleuze, J. Hecq, I. Roland, S. Saussez, I. Adanja, O. Debeir, C. Decaestecker, V. Mathieu, R. Kiss, K. Amighi,
In vivo assessment of temozolomide delivery systems for inhalation therapy of lung cancer
Conference: Journée doctorale Pôle Santé (17/12/2009: Campus Erasme), 2009
Bibtex
Bibtex : info:hdl:2013/85223
Note : Language of publication: fr
Abstract : In Vivo Assessment of Temozolomide Local Delivery for Lung Cancer Inhalation Therapy Nathalie Wauthoz, Philippe Deleuze, Julien Hecq, Isabelle Roland, Sven Saussez, Ivan Adanja, Olivier Debeir, Christine Decaestecker, Véronique Mathieu, Karim Amighi Laboratoire de Pharmacie Galénique et de Biopharmacie Director : Karim Amighi Abstract The aim of this study was to compare the efficacy of local drug delivery by inhalation to intravenous delivery in a B16F10 melanoma metastatic lung model. Temozolomide was formulated as a suspension, which was elaborated and evaluated in terms of particle size, shape and agglomeration. An endotracheal administration device was used to aerosolize the suspension. This mode of delivery was evaluated at different temozolomide concentrations and was optimized for the uniformity of delivered dose, the droplet size distribution and the distribution of droplets in vivo. Of the particles in the stabilized suspension, 79\% were compatible with the human respirable size range, and this formulation retained 100\% in vitro anticancer activity as compared to temozolomide alone in three distinct cancer cell lines. The pulmonary delivery device provided good reproducibility in terms of both the dose delivered and the droplet size distribution. Most of the lung tissues that were exposed to aerosol droplets contained the particles, as revealed by fluorescent microscopy techniques. The global in vivo antitumor activity of the inhaled temozolomide provided a median survival period similar to that for intravenous temozolomide delivery, and three out of twenty-seven mice (11\%) survived with almost complete eradication of the lung tumours. The present study thus shows that inhalation of a simple liquid formulation is well tolerated and active against a very biologically aggressive mouse melanoma pulmonary pseudo-metastatic model. This inhalation delivery could be used to deliver other types of anticancer drugs.



S. Safin, A. Defays, A. Billon, C. Decaestecker, N. Warzée,
Influence d’images évocatrices et distractrices sur une t{\^a}che de jugement en acoustique des salles
IHM 2009, ACM International Conference Proceeding Series, pp. 241-248, 2009
Bibtex
Bibtex : info:hdl:2013/71594
Note : Language of publication: en



J. Lu, Q. Yang, G. Lafruit,
Interpolation error as a quality metric for stereo: robust, or not?
34th International Conference on Acoustics, pp. 977-980, 2009
Bibtex
Bibtex : info:hdl:2013/186800
Note : Language of publication: en



S. Rogmans, M. Dumont, G. Lafruit, P. Bekaert,
Migrating real-time depth image-based rendering from traditional to next-gen GPGPU
3DTV-CON: The True Vision - Capture, pp. 1-4, 2009
Bibtex
Bibtex : info:hdl:2013/186801
Note : Language of publication: en



N. Warzée, M. Groenen, J. Rosoux, O. Debeir, R. Ercek, C. Reichling,
Numérisation 3D de la grotte d'El Castillo (Puente Viesgo)
Actes du colloque Virtual Retrospect 2007, pp. 221-229, 2009
Bibtex
Bibtex : info:hdl:2013/71566
Note : Consultable à l'adresse suivante : http://archeovision.cnrs.fr/spip.php?article91



F. Morel, M. Cammaerts Tricot, N. Warzée,
Orientation, vitesse et sinuosité de trajets quantifiées par un logiciel 'O.V.S. nouvelle génération'
Conference: IUSSI (September 2009: Bondy, France), 2009
Bibtex
Bibtex : info:hdl:2013/71599
Note : Language of publication: fr



K. Zhang, J. Lu, G. Lafruit, R. Lauwereins, L. Van Gool,
Real-time accurate stereo with bitwise fast voting on CUDA
5th IEEE Workshop on Embedded Computer Vision, pp. 794-800, 2009
Bibtex
Bibtex : info:hdl:2013/186803
Note : Language of publication: en



J. Lu, K. Zhang, G. Lafruit, F. Catthoor,
Real-time stereo matching: a cross-based local approach
IEEE International Conference on Acoustics, pp. 733-736, 2009
Bibtex
Bibtex : info:hdl:2013/186797
Note : Language of publication: en



R. Ercek, D. Viviers, N. Warzée,
Reconstruction and Digitalization of an archaeological site, Itanos, Crete
International Meeting on Archaeology and Graphic Informatics, ARQUEOLOGICA 2.0, pp. 6, Sevilla (Spain), 2009
Bibtex
Bibtex : info:hdl:2013/127110
Note : Language of publication: en



K. Zhang, J. Lu, G. Lafruit, R. Lauwereins, L. Van Gool,
Robust stereo matching with fast normalized cross-correlation over shape-adaptive regions
IEEE International Conference on Image Processing - ICIP, pp. 2357-2360, 2009
Bibtex
Bibtex : info:hdl:2013/186799
Note : Language of publication: en



V. Megalizzi, F. Lefranc, O. Debeir, C. Decaestecker, R. Kiss,
Screening of sigma-1 ligand-induced effects on glioma cell aggressiveness in vitro and in vivo: new therapeutic potential of old anti-psychotic medicines.
Conference: 100th American Association for Cancer Research Annual Meeting (Abstract 852: Denver - CO - USA), 2009
Bibtex
Bibtex : info:hdl:2013/71528
Note : Language of publication: en



O. Debeir, H. Atoui, C. Simler, N. Warzée, E. Wolff,
Weakened watershed assembly for remote sensing image segmentation and change detection
VISAPP 2009 : International Conference on Computer Vision Theory and Applications, 2009
Bibtex
Bibtex : info:hdl:2013/53011
Note : Language of publication: en



Books chapters

G. Lafruit, W. Van Raemdonck, K. Tack, E. Delfosse,
JPEG2000 in 3D Graphics Terrain Rendering
Wiley, pp. 421-439, 2009
Bibtex
Bibtex : info:hdl:2013/187410
Note : Language of publication: na



Thesis

J. Lu, G. Lafruit,
Complexity-Aware Advanced Visual Computing for Multi-View Video. Computer Engineering
2009
Bibtex
Bibtex : info:hdl:2013/188500
Note : Language of publication: na



B. Haibe-Kains,
Identification and assessment of gene signatures in human breast cancer
2009
Bibtex
Bibtex : info:hdl:2013/210348
Note : Doctorat en Sciences
Abstract : This thesis addresses the use of machine learning techniques to develop clinical diagnostic tools for breast cancer using molecular data. These tools are designed to assist physicians in their evaluation of the clinical outcome of breast cancer (referred to as prognosis).<p>The traditional approach to evaluating breast cancer prognosis is based on the assessment of clinico-pathologic factors known to be associated with breast cancer survival. These factors are used to make recommendations about whether further treatment is required after the removal of a tumor by surgery. Treatment such as chemotherapy depends on the estimation of patients' risk of relapse. Although current approaches do provide good prognostic assessment of breast cancer survival, clinicians are aware that there is still room for improvement in the accuracy of their prognostic estimations.<p>In the late nineties, new high throughput technologies such as the gene expression profiling through microarray technology emerged. Microarrays allowed scientists to analyze for the first time the expression of the whole human genome ("transcriptome"). It was hoped that the analysis of genome-wide molecular data would bring new insights into the critical, underlying biological mechanisms involved in breast cancer progression, as well as significantly improve prognostic prediction. However, the analysis of microarray data is a difficult task due to their intrinsic characteristics: (i) thousands of gene expressions are measured for only few samples; (ii) the measurements are usually "noisy"; and (iii) they are highly correlated due to gene co-expressions. Since traditional statistical methods were not adapted to these settings, machine learning methods were picked up as good candidates to overcome these difficulties. However, applying machine learning methods for microarray analysis involves numerous steps, and the results are prone to overfitting. Several authors have highlighted the major pitfalls of this process in the early publications, shedding new light on the promising but overoptimistic results. <p>Since 2002, large comparative studies have been conducted in order to identify the key characteristics of successful methods for class discovery and classification. Yet methods able to identify robust molecular signatures that can predict breast cancer prognosis have been lacking. To fill this important gap, this thesis presents an original methodology dealing specifically with the analysis of microarray and survival data in order to build prognostic models and provide an honest estimation of their performance. The approach used for signature extraction consists of a set of original methods for feature transformation, feature selection and prediction model building. A novel statistical framework is presented for performance assessment and comparison of risk prediction models.<p>In terms of applications, we show that these methods, used in combination with a priori biological knowledge of breast cancer and numerous public microarray datasets, have resulted in some important discoveries. In particular, the research presented here develops (i) a robust model for the identification of breast molecular subtypes and (ii) a new prognostic model that takes into account the molecular heterogeneity of breast cancers observed previously, in order to improve traditional clinical guidelines and state-of-the-art gene signatures./Cette thèse concerne le développement de techniques d'apprentissage (machine learning) afin de mettre au point de nouveaux outils cliniques basés sur des données moleculaires. Nous avons focalisé notre recherche sur le cancer du sein, un des cancers les plus fréquemment diagnostiqués. Ces outils sont développés dans le but d'aider les médecins dans leur évaluation du devenir clinique des patients cancéreux (cf. le pronostique).<p>Les approches traditionnelles d'évaluation du pronostique d'un patient cancéreux se base sur des critères clinico-pathologiques connus pour être prédictifs de la survie. Cette évaluation permet aux médecins de décider si un traitement est nécessaire après l'extraction de la tumeur. Bien que les outils d'évaluation traditionnels sont d'une aide importante, les cliniciens sont conscients de la nécessité d'améliorer de tels outils.<p>Dans les années 90, de nouvelles technologies à haut-débit, telles que le profilage de l'expression génique par biopuces à ADN (microarrays), ont été mises au point afin de permettre aux scientifiques d'analyser l'expression de l'entièreté du génôme de cellules cancéreuses. Ce nouveau type de données moléculaires porte l'espoir d'améliorer les outils pronostiques traditionnels et d'approfondir nos connaissances concernant la génèse du cancer du sein. Cependant ces données sont extrêmement difficiles à analyser à cause (i) de leur haute dimensionalité (plusieurs dizaines de milliers de gènes pour seulement quelques centaines d'expériences); (ii) du bruit important dans les mesures; (iii) de la collinéarité entre les mesures d{\^u}e à la co-expression des gènes.<p>Depuis 2002, des études comparatives à grande échelle ont permis d'identifier les méthodes performantes pour l'analyse de groupements et la classification de données microarray, négligeant l'analyse de survie pertinente pour le pronostique dans le cancer du sein. Pour pallier ce manque, cette thèse présente une méthodologie originale adaptée à l'analyse de données microarray et de survie afin de construire des modèles pronostiques performants et robustes. <p>En termes d'applications, nous montrons que cette méthodologie, utilisée en combinaison avec des connaissances biologiques a priori et de nombreux ensembles de données publiques, a permis d'importantes découvertes. En particulier, il résulte de la recherche presentée dans cette thèse, le développement d'un modèle robuste d'identification des sous-types moléculaires du cancer du sein et de plusieurs signatures géniques améliorant significativement l'état de l'art au niveau pronostique.



L. Mundeleer,
Modélisation d'un système de navigation chirurgicale pour le traitement par radio-fréquences des tumeurs du foie
2009
Bibtex
Bibtex : info:hdl:2013/210264
Note : Doctorat en Sciences de l'ingénieur
Abstract : Radiofrequency ablation (RFA) is a minimally invasive treatment for either hepatocellular carcinoma or metastasis liver carcinoma. In order to resect large lesions, the surgeon has to perform multiple time-consuming destruction cycles and reposition the RFA needle for each of them. The critical step in handling a successful ablation and preventing local recurrence is the correct positioning of the needle. For small tumors, the surgeon places the middle of the active needle tip in the center of the tumor under intra-operative ultrasound guidance. When one application is not enough to cover the entire tumor, the surgeon needs to repeat the treatment after repositioning of the needle, but US guidance is obstructed by the opacity stemming from the first RFA application. In this case the surgeon can only rely on anatomical knowledge and the repositioning of the RFA needle becomes a subjective task limiting the treatment accuracy. We have developed a computer assisted surgery guidance application for this repositioning procedure. Our software application handles the complete process from preoperative image analysis to tool tracking in the operating room. Our framework is mostly used for this RFA procedure, but is also suitable for any other medical or surgery application.



Technical report

O. Debeir,
Projet ARMURS : Automatic Recognition for Map Update by Remote Sensing: Deuxième rapport d'activité
2009
Bibtex
Bibtex : info:hdl:2013/74449
Note : Language of publication: en



O. Debeir,
Projet ARMURS : Automatic Recognition for Map Update by Remote Sensing: Deuxième rapport opérationnel
2009
Bibtex
Bibtex : info:hdl:2013/74448
Note : Language of publication: fr




2008

S. Scheurmans, G. Lafruit,
Advanced Real-Time Video Processing on Graphics Hardware for Image-Based Rendering Systems. Ingénieur Industriel
2008
Bibtex
Bibtex : info:hdl:2013/188487
Note : Language of publication: na



N. Gabriels, G. Lafruit,
Robust Self-Calibration in Multi-Camera Setup. Ingénieur Industriel
2008
Bibtex
Bibtex : info:hdl:2013/188486
Note : Language of publication: na



Papers

T. Leloup, W. El Kazzi, F. Schuind, N. Warzée,
A novel technique for distal locking of intramedullary nail based on two non-constrained fluoroscopic images and navigation.
IEEE transactions on medical imaging, Vol. 27, 9, pp. 1202-1212, 2008
Bibtex
Bibtex : info:hdl:2013/70568
Note : SCOPUS: ar.j



N. Sadeghi-Meibodi, N. D'Haene, C. Decaestecker, M. Levivier, T. Metens, C. Maris, D. Wikler, D. Balériaux, I. Salmon, S. Goldman,
Apparent diffusion coefficient and cerebral blood volume in brain gliomas: relation to tumor cell density and tumor microvessel density based on stereotactic biopsies.
American journal of neuroradiology, Vol. 29, 3, pp. 476-482, 2008
Bibtex
Bibtex : info:hdl:2013/51761
Note : Journal Article
Abstract : BACKGROUND AND PURPOSE: MR imaging-based apparent diffusion coefficient (ADC) and regional cerebral blood volume (rCBV) measurements have been related respectively to both cell and microvessel density in brain tumors. However, because of the high degree of heterogeneity in gliomas, a direct correlation between these MR imaging-based measurements and histopathologic features is required. The purpose of this study was to correlate regionally ADC and rCBV values with both cell and microvessel density in gliomas, by using coregistered MR imaging and stereotactic biopsies. MATERIALS AND METHODS: Eighteen patients (9 men, 9 women; age range, 19-78 years) with gliomas underwent diffusion-weighted and dynamic susceptibility contrast-enhanced MR imaging before biopsy. Eighty-one biopsy samples were obtained and categorized as peritumoral, infiltrated tissue, or bulk tumor, with quantification of cell and microvessel density. ADC and rCBV values were measured at biopsy sites and were normalized to contralateral white matter on corresponding maps coregistered with a 3D MR imaging dataset. ADC and rCBV ratios were compared with quantitative histologic features by using the Spearman correlation test. RESULTS: The highest correlations were found within bulk tumor samples between rCBV and cell density (r=0.57, P < .001) and rCBV and microvessel density (r=0.46, P < .01). An inverse correlation was found between ADC and microvessel density within bulk tumor (r=-0.36, P < .05), whereas no significant correlation was found between ADC and cell density. CONCLUSION: rCBV regionally correlates with both cell and microvessel density within gliomas, whereas no regional correlation was found between ADC and cell density.



A. Pozdzik, I. Salmon, F. Debelle, C. Decaestecker, C. Van den Branden, D. Verbeelen, M. Deschodt Lanckman, J. Vanherweghem, J. Nortier,
Aristolochic acid induces proximal tubule apoptosis and epithelial to mesenchymal transformation.
Kidney international, Vol. 73, 5, pp. 595-607, 2008
Bibtex
Bibtex : info:hdl:2013/53619
Note : Journal Article
Abstract : Aristolochic acid contamination in herbal remedies leads to interstitial fibrosis, tubular atrophy, and renal failure in humans. To study the cellular mechanisms contributing to the pathophysiology of this renal disease, we studied Wistar rats treated with aristolochic acid and measured tubular and interstitial cell proliferation, epithelial/mesenchymal cell marker expression, tubular membrane integrity, myofibroblast accumulation, oxidative stress, mitochondrial damage, tubular apoptosis, and fibrosis. Oxidative stress, a loss of cadherin concomitant with vimentin expression, basement membrane denudation with active caspase-3 expression, and mitochondrial injury within tubular cells were evident within 5 days of administration of the toxin. During the chronic phase, interstitial mesenchymal cells accumulated in areas of collagen deposits. Impaired regeneration and apoptosis of proximal tubular cells resulted in tubule atrophy with a near absence of dedifferentiated cell transmembrane migration. We suggest that resident fibroblast activation plays a critical role in the process of renal fibrosis during aristolochic acid toxicity.



P. Malarme, D. Wikler, N. Warzée,
Centralized control for surgical informatics systems in an integrated digital operating theater
International Journal of Computer Assisted Radiology and Surgery, Vol. 3, 1, pp. 145-148, 2008
Bibtex
Bibtex : info:hdl:2013/71565
Note : Language of publication: en



L. Mundeleer, D. Wikler, T. Leloup, N. Warzée,
Development of a computer assisted system aimed at RFA liver surgery
Computerized medical imaging and graphics, Vol. 32, 7, pp. 611-621, 2008
Bibtex
Bibtex : info:hdl:2013/70567
Note : SCOPUS: ar.j
Abstract : Radio frequency ablation (RFA) is a minimally invasive treatment for either hepatocellular carcinoma or metastasis liver carcinoma. In order to resect large lesions, the surgeon has to perform multiple time-consuming destruction cycles and reposition the RFA needle for each of them. The critical step in handling a successful ablation and preventing local recurrence is the correct positioning of the needle. For small tumors, the surgeon places the middle of the active needle tip in the center of the tumor under intra-operative ultrasound guidance. When one application is not enough to cover the entire tumor, the surgeon needs to repeat the treatment after repositioning of the needle, but US guidance is obstructed by the opacity stemming from the first RFA application. In this case the surgeon can only rely on anatomical knowledge and the repositioning of the RFA needle becomes a subjective task limiting the treatment accuracy. We have developed a computer assisted surgery guidance application for this repositioning procedure. Our software application handles the complete process from preoperative image analysis to tool tracking in the operating room. Our framework is mostly used for this RFA procedure, but is also suitable for any other medical or surgery application. © 2008 Elsevier Ltd. All rights reserved.



N. D'Haene, X. Catteau, C. Maris, B. Martin, I. Salmon, C. Decaestecker,
Endothelial hyperplasia and endothelial galectin-3 expression are prognostic factors in primary central nervous system lymphomas.
British journal of haematology, Vol. 140, 4, pp. 402-410, 2008
Bibtex
Bibtex : info:hdl:2013/53617
Note : Journal Article
Abstract : Recently, considerable attention has been focused on the identification of clinically relevant prognostic markers for primary central nervous system lymphomas (PCNSL). The present study investigated whether three morphological features, i.e. necrosis, reactive perivascular T-cell infiltrate and endothelial hyperplasia, and galectin-1 and galectin-3 immunohistochemical expression have prognostic roles in a series of 58 PCNSL samples from 44 immunocompetent and 14 immunocompromised patients. The presence of endothelial hyperplasia (identified in 21\% of the assessable cases) was identified as a bad prognostic factor for immunocompetent PCNSL patients, whereas the other morphological features were not associated with any prognostic value. Lymphomatous cells of eight PCNSL cases expressed galectin-3 without any prognostic value, and lymphomatous cells did not express galectin-1. In contrast, endothelial expression of galectin-3 was identified (by means of uni- and multi-variate analyses) as a bad prognostic factor for immunocompetent PCNSL patients. In addition, a combination of endothelial hyperplasia and/or endothelial galectin-3 expression was shown to be an independent prognostic factor for immunocompetent PCNSL patients treated with methotrexate-based chemotherapy. In summary, this study suggests that endothelial-related markers can identify risk groups of PCNSL patients and indicates that galectin-3 could be involved in PCNSL angiogenesis.



X. Ji, S. Pollin, G. Lafruit, I. Moccagatta, A. Dejonghe, F. Catthoor,
Energy-efficient bandwidth allocation for multiuser scalable video streaming over WLAN
EURASIP Journal on wireless communications and networking, 2008
Bibtex
Bibtex : info:hdl:2013/186281
Note : Language of publication: en



M. Le Mercier, F. Lefranc, T. Mijatovic, O. Debeir, B. Haibe-Kains, G. Bontempi, C. Decaestecker, R. Kiss, V. Mathieu,
Evidence of galectin-1 involvement in glioma chemoresistance.
Toxicology and applied pharmacology, Vol. 229, 2, pp. 172-183, 2008
Bibtex
Bibtex : info:hdl:2013/51198
Note : Journal Article
Abstract : Glioblastomas (GBMs) are resistant to apoptosis but less so to autophagy; a fact that may at least partly explain the therapeutic benefits of the pro-autophagic drug temozolomide in the treatment of GBM patients. Galectin-1 (Gal1) whose expression is stimulated by hypoxia is a potent modulator of GBM cell migration and a pro-angiogenic molecule. Hypoxia is also known to confer cancer cells with resistance to chemotherapy and radiotherapy and to modulate the unfolded protein response (UPR) during endoplasmic reticulum (ER) stress. The present study investigates whether decreasing Gal1 expression (by means of a siRNA approach) in human Hs683 GBM cells increases their sensitivity to pro-autophagic or pro-apoptotic drugs. The data reveal that temozolomide, the standard treatment for glioma patients, increases Gal1 expression in Hs683 cells both in vitro and in vivo. However, reducing Gal1 expression in these cells by siRNA increases the anti-tumor effects of various chemotherapeutic agents, in particular temozolomide both in vitro and in vivo. This decrease in Gal1 expression in Hs683 cells does not induce apoptotic or autophagic features, but is found to modulate p53 transcriptional activity and decrease p53-targeted gene expression including DDIT3/GADD153/CHOP, DUSP5 ATF3 and GADD45A. The decrease in Gal1 expression also impairs the expression levels of seven other genes implicated in chemoresistance: ORP150, HERP, GRP78/Bip, TRA1, BNIP3L, GADD45B and CYR61, some of which are located in the ER and whose expression is also known to be modified by hypoxia. This novel facet of Gal1 involvement in glioblastoma biology may be amenable to therapeutic manipulation.



P. Dumont, A. Berton, N. Nagy, F. Sandras, S. Tinton, P. Demetter, F. Mascart, A. Allaoui, C. Decaestecker, I. Salmon,
Expression of galectin-3 in the tumor immune response in colon cancer.
Laboratory investigation, Vol. 88, 8, pp. 896-906, 2008
Bibtex
Bibtex : info:hdl:2013/50112
Note : Journal Article
Abstract : The role of tumor-associated macrophages (TAMs) is controversial. Although most studies on different cancer types associate them with a poorer prognosis, interestingly in colon cancer, most articles indicate that TAMs prevent tumor development; patients with high TAMs have better prognosis and survival rate. M1-polarized macrophages produce high level of tumor necrosis factor-alpha, interleukin-1 beta or reactive oxygen species, which can effectively kill susceptible tumor cells. In contrast, M2-polarized macrophages can secrete different factors that promote tumor cell growth and survival or favor angiogenesis and tissue invasion. Considering the beneficial role of TAMs in colon cancer, we speculated that they may not display the M2 polarization commonly observed in tumor microenvironment, but rather develop M1 properties. Therefore, we used an in vitro model to analyze the effects of supernatants from M1-polarized macrophages on DLD-1 colon cancer cells. Our data indicate that the conditioned medium from LPS-activated macrophages (CM-LAM) contains a high level of granulocyte-macrophage colony-stimulating factor, interleukins-1 beta, -6, -8 and tumor necrosis factor-alpha, and that it exerts a marked growth inhibitory activity on DLD-1 cells. Prolonged exposure to CM-LAM results in cell death by apoptosis. Such exposure to CM-LAM leads to the modulation of gal-3 expression: we observed a marked downregulation of gal-3 mRNA and protein expression following CM-LAM treatment. We also describe that the knockdown of gal-3 sensitizes DLD-1 cells to CM-LAM. These data suggest an involvement of gal-3 in the response of colon cancer cells to proinflammatory stimuli, such as the conditioned medium from activated macrophages.



A. Mathieu, N. Nagy, C. Decaestecker, L. Ferdinande, K. Vandenbroucke, P. Rottiers, C. Cuvelier, I. Salmon, P. Demetter,
Expression of galectins-1, -3 and -4 varies with strain and type of experimental colitis in mice.
International journal of experimental pathology, Vol. 89, 6, pp. 438-446, 2008
Bibtex
Bibtex : info:hdl:2013/54123
Note : Comparative Study
Abstract : Galectins are increasingly the focus of biomedical research. Although they are involved at different stages in inflammation, data on galectins in colitis remain scarce. The aim of this study was to determine and compare the expression of galectins in acute and chronic experimental colitis in mice. Immunohistochemistry for galectins-1, -3 and -4 was performed on colon tissue from C57BL/6 and BALB/c mice with acute dextran sodium sulphate colitis and from 129 Sv/Ev IL-10 knock-out (IL-10(-/-)) mice. From these three mouse strains, we first detected major differences in galectin expression related to the genetic background in the control animals. With regard to inflammation, chronic colitis in IL-10(-/-) mice was associated with increased galectin-4 expression; in contrast with the two other models, no galectin-1 and -3 alterations were observed in IL-10(-/-) mice. Acute colitis in C57BL/6 and BALB/c mice showed increased galectin-3 expression in the lamina propria and the crypt epithelium, together with a decreased nuclear expression. These results suggest an involvement of galectins in the development and perpetuation of colonic inflammation and illustrate that the choice of the mouse strain for studying galectins might influence the outcome of the experiments.



S. Saussez, C. Decaestecker, V. Mahillon, S. Cludts, A. Capouillez, D. Chevalier, H. Vet, S. André, G. Toubeau, X. Leroy, H. Gabius,
Galectin-3 upregulation during tumor progression in head and neck cancer.
The Laryngoscope, Vol. 118, 9, pp. 1583-1590, 2008
Bibtex
Bibtex : info:hdl:2013/75908
Note : Comparative Study
Abstract : To examine the level of expression of galectin-3 in relation to neoplastic progression of hypopharyngeal squamous cell carcinomas (HSCCs) and laryngeal squamous cell carcinomas (LSCCs).



A. Capouillez, C. Decaestecker, O. Filleul, D. Chevalier, F. Coppee, X. Leroy, A. Belayew, S. Saussez,
Helicase-like transcription factor exhibits increased expression and altered intracellular distribution during tumor progression in hypopharyngeal and laryngeal squamous cell carcinomas.
Virchows Archiv, Vol. 453, 5, pp. 491-499, 2008
Bibtex
Bibtex : info:hdl:2013/75907
Note : Journal Article
Abstract : The helicase-like transcription factor (HLTF) belongs to the SWI/SNF family of proteins that use the energy from adenosine triphosphate hydrolysis to remodel chromatin during a variety of cellular processes. HLTF is also involved in DNA repair. Using computer-assisted microscopy, the immunohistochemical expression of HLTF was determined using a series of 100 hypopharyngeal and 56 laryngeal squamous cell carcinomas (SCCs) compared to tumor-free epithelia (60 cases) and dysplasias (92 cases). In hypopharyngeal SCC tumor progression, increased HLTF expression was associated with the percentage of immunopositive epithelial tissue areas (p = 0.02) and the staining intensity of the positive area (p = 0.0005). In the cases of laryngeal lesions, the immunolabeling intensity of HLTF significantly decreased with malignancy (p = 0.01). We also observed a significant shift of HLTF expression from the cytoplasm toward the nuclear compartment (p = 0.0007). Our data reveal an association between the presence of HLTF and neoplastic progression of hypopharyngeal and laryngeal SCCs.



S. Saussez, C. Decaestecker, F. Lorfevre, D. Chevalier, G. Mortuaire, H. Kaltner, S. André, G. Toubeau, H. Gabius, X. Leroy,
Increased expression and altered intracellular distribution of adhesion/growth-regulatory lectins galectins-1 and -7 during tumour progression in hypopharyngeal and laryngeal squamous cell carcinomas.
Histopathology, Vol. 52, 4, pp. 483-493, 2008
Bibtex
Bibtex : info:hdl:2013/75909
Note : Comparative Study
Abstract : To examine the level of expression of the pleiotropic regulators galectins-1 and -7 in relation to neoplastic progression of hypopharyngeal (HSCCs) and laryngeal (LSCCs) squamous cell carcinomas.



M. Le Mercier, V. Mathieu, B. Haibe-Kains, G. Bontempi, T. Mijatovic, C. Decaestecker, R. Kiss, F. Lefranc,
Knocking down galectin 1 in human hs683 glioblastoma cells impairs both angiogenesis and endoplasmic reticulum stress responses.
Journal of neuropathology and experimental neurology, Vol. 67, 5, pp. 456-469, 2008
Bibtex
Bibtex : info:hdl:2013/51203
Note : Journal Article
Abstract : Galectin (Gal) 1 is a hypoxia-regulated proangiogenic factor that also directly participates in glioblastoma cell migration. To determine how Gal-1 exerts its proangiogenic effects, we investigated Gal-1 signaling in the human Hs683 glioblastoma cell line. Galectin 1 signals through the endoplasmic reticulum transmembrane kinase/ribonuclease inositol-requiring 1alpha, which regulates the expression of oxygen-regulated protein 150. Oxygen-regulated protein 150 controls vascular endothelial growth factor maturation. Galectin 1 also modulates the expression of 7 other hypoxia-related genes (i.e. CTGF, ATF3, PPP1R15A, HSPA5, TRA1, and CYR61) that are implicated in angiogenesis. Decreasing Gal-1 expression in Hs683 orthotopic xenografts in mouse brains by siRNA administration impaired endoplasmic reticulum stress and enhanced the therapeutic benefits of the proautophagic drug temozolomide. These results suggest that decreasing Gal-1 expression (e.g. through brain delivery of nonviral infusions of anti-Gal-1 siRNA in patients) can represent an additional therapeutic strategy for glioblastoma.



A. Lemy, K. Wissing, S. Rorive, A. Zlotta, T. Roumeguere, M. Muniz Martinez, C. Decaestecker, I. Salmon, D. Abramowicz, J. Vanherweghem, J. Nortier,
Late onset of bladder urothelial carcinoma after kidney transplantation for end-stage aristolochic acid nephropathy: a case series with 15-year follow-up.
American journal of kidney diseases, Vol. 51, 3, pp. 471-477, 2008
Bibtex
Bibtex : info:hdl:2013/53618
Note : Journal Article
Abstract : BACKGROUND: Aristolochic acids are nephrotoxins and predispose to upper-tract urothelial carcinoma. The risk of bladder urothelial carcinoma after kidney transplantation and its relationship to upper-tract urothelial carcinoma is not well defined. STUDY DESIGN: Case series. SETTING & PARTICIPANTS: Single-center cohort of 38 women given kidney transplants for end-stage aristolochic acid nephropathy. OUTCOMES & MEASUREMENTS: The prevalence of upper urinary tract urothelial carcinoma was determined by collecting pathological results of specimens obtained by means of bilateral ureteronephrectomy. We also established the cumulative incidence of bladder urothelial carcinoma in biopsies performed during prospective screening cystoscopies during a 15-year follow-up. RESULTS: Upper-tract urothelial carcinoma was found in 17 patients with aristolochic acid nephropathy (44.7\%). During follow-up, bladder urothelial carcinoma was diagnosed in 15 patients 68 to 169 months after cessation of aristolochic acid exposure (39.5\%): 8 urothelial carcinoma in situ, 4 noninvasive low-grade papillary urothelial carcinoma, and 3 infiltrating urothelial carcinoma. 12 of 17 patients (71\%) with a history of upper-tract urothelial carcinoma developed bladder urothelial carcinoma during follow-up, whereas this occurred in only 3 of 21 patients (14\%) without upper-tract urothelial carcinoma (P < 0.01). Despite local and/or systemic chemotherapy, 3 patients died and 2 radical cystectomies were performed. LIMITATIONS: Small sample size of this case series. CONCLUSIONS: Upper-tract and bladder urothelial carcinoma are dramatic complications in kidney transplant recipients with aristolochic acid nephropathy, confirming the carcinogenic properties of aristolochic acids. We identified upper-tract urothelial carcinoma as a potent risk factor for the subsequent development of bladder urothelial carcinoma after kidney transplantation for aristolochic acid nephropathy. Because this complication may occur years after aristolochic acid discontinuation, we suggest regular cystoscopies in addition to the bilateral ureteronephrectomy in kidney transplant recipients with aristolochic acid nephropathy.



S. Rorive, A. Berton, N. D'Haene, C. Takacs, O. Debeir, C. Decaestecker, I. Salmon,
Matrix metalloproteinase-9 interplays with the IGFBP2-IGFII complex to promote cell growth and motility in astrocytomas.
GLIA, Vol. 56, 15, pp. 1679-1690, 2008
Bibtex
Bibtex : info:hdl:2013/52950
Note : Journal Article
Abstract : Insulin-like growth factor II (IGFII) acts as a potent mitogen for several tumor types and has been reported to positively influence astrocytoma cell growth and motility. In the central nervous system, IGFII bioavailability is mainly modulated by insulin-like growth factor binding protein 2 (IGFBP2), which sequestrates IGFII and therefore prevents its interaction with the type-1 IGF receptor (IGF-IR). Proteolysis of IGFBP2 is the predominant mechanism recognized to reduce the binding affinity of IGFBP2 for IGFII, thus favoring dissociation of IGFII from the IGFBP2-IGFII complex. It is known that certain proteases involved in astrocytoma malignancy, such as matrix metalloproteinase-7 (MMP-7), plasmin, and cathepsin D, are able to proteolyze IGFBP2 in vitro. The present study aims to investigate whether other proteases expressed by astrocytomas, specifically MMP-2, MMP-9, and membrane-type 1 matrix metalloprotease (MT1-MMP), are able to proteolyze the IGFBP2-IGFII complex. Our results show the following: (i) MMP-9 proteolyzes the IGFBP2-IGFII complex in vitro, while MMP-2 and MT1-MMP do not; (ii) this MMP-9-induced IGFBP2-IGFII complex proteolysis releases free IGFII, which contributes to enhance the motility and the growth of LN229 astrocytoma cells. Furthermore, this study also highlights that the formation of the IGFBP2-IGFII complex inhibits IGFBP2's cell motility promoting effect by reducing the pool of free IGFBP2. In conclusion, MMP-9-induced IGFBP2 proteolysis may be regarded as an important post-translational event involved in astrocytoma aggressiveness. These new findings support drug targeting of MMP-9 as an interesting approach in the treatment of astrocytoma.



M. Cammaerts Tricot, A. Vandenbussche, O. Debeir,
Méthode d'étude de la forme d'une structure microscopique, opaque et solide, appliquée à l'oeil d'une fourmi
Belgian Journal of Entomology, Vol. 10, pp. 67-79, 2008
Bibtex
Bibtex : info:hdl:2013/52958
Note : Language of publication: fr



Z. Rachidi, M. Cammaerts Tricot, O. Debeir,
Morphometric study of the eye of three species of Myrmica (Formicidae)
Belgian Journal of Entomology, Vol. 10, pp. 81-91, 2008
Bibtex
Bibtex : info:hdl:2013/52959
Note : Language of publication: en



T. Mijatovic, N. De Nève, P. Gailly, V. Mathieu, B. Haibe-Kains, G. Bontempi, J. Lapeira, C. Decaestecker, V. Facchini, R. Kiss,
Nucleolus and c-Myc: potential targets of cardenolide-mediated antitumor activity.
Molecular cancer therapeutics, Vol. 7, 5, pp. 1285-1296, 2008
Bibtex
Bibtex : info:hdl:2013/52071
Note : Journal Article
Abstract : The use of cardenolides like ouabain, digitoxin, or oleandrin has been reported previously many times as a means of potentially combating human refractory prostate cancer by inducing apoptosis through an increase in intracellular calcium concentrations. The aims of the current study were to investigate if part of the antitumor effects mediated by cardenolides concerned disorganization of nucleolar structure and whether this was further associated with a marked decrease in c-Myc expression. Accordingly, the antitumor activity of a novel hemisynthetic cardenolide [1R,3aS,3bR,5aS,6aR,7aS,9R,12aR,13aR,15aR]-3a,11a-dihydroxy-13a-(hydroxymethyl)-9,15a-dimethyl-1-(5-oxo-2,5-dihydrofuran-3-yl)icosahydro-1H,4'H-spiro[cyclopenta [7,8]phenanthro[2,3-b]pyrano[3,2-e][1,4]dioxine-11,2'-[1,3]thiazolidin]-4'-one (UNBS1450)] was compared with that of classic cardenolides and reference anticancer agents in prostate cancer cell lines in vitro and in vivo following s.c. and orthotopic prostate cancer cell grafting into mice. The present study indicates that UNBS1450 markedly decreases the in vitro viability/proliferation of human prostate cancer cell lines but not of normal cells. The induced effects are not linked to an increase in intracellular calcium concentrations and subsequent induction of apoptosis. Rather, they appear to relate to the compound's capacity to disorganize nucleolar structure and function (through an impairment of cyclin-dependent kinase and c-Myc expression and related signaling pathways; paralleled by the disorganization of cancer cell-specific perinucleolar bodies as revealed by disruption of Sam68). This nonapoptotic cancer cell death mediated by severe nucleolar targeting and down-regulation of c-Myc expression is a completely new cardenolide-induced mechanism of antitumor action.



A. Pozdzik, I. Salmon, C. Husson, C. Decaestecker, E. Rogier, M. Bourgeade, M. Deschodt Lanckman, J. Vanherweghem, J. Nortier,
Patterns of interstitial inflammation during the evolution of renal injury in experimental aristolochic acid nephropathy.
Nephrology, dialysis, transplantation, Vol. 23, 8, pp. 2480-2491, 2008
Bibtex
Bibtex : info:hdl:2013/53622
Note : Journal Article
Abstract : BACKGROUND: Interstitial inflammation is a prominent feature associated with the severity of renal injury and progressive kidney failure. We utilized an animal model of aristolochic acid (AA)-induced nephropathy (AAN) to assess patterns of infiltration and inflammation during the evolution of tubulointerstitial damage and to relate them to the development of fibrosis. METHODS: Male Wistar rats receiving sc daily AA or vehicle were sacrificed between Days 1 and 35. Infiltrating mononuclear cells were characterized by immunohistochemistry. The kidney infiltrating T lymphocytes were phenotyped by flow cytometry. Urinary levels of Th-1/ Th-2 cytokines, of monocyte chemoattractant protein-1 and of active transforming growth factor-beta (TGF-beta) were measured. Tissue expression of phosphorylated smad 2/3 protein was used to examine the TGF-beta signalling pathway. RESULTS: In AA rats, monocytes/macrophages and T lymphocytes predominantly infiltrated areas of necrotic proximal tubular cells. The coexpressions of ED1 and/or Ki-67/MHCII by infiltrating cells reflected monocyte/macrophage proliferation and their activation, respectively. The accumulation of cytotoxic T lymphocytes was attested by severe signs of CD8+ cell tubulitis. The CD8/E-cadherin costaining confirmed intrarenal homing of CD8+CD103+ cells. Urinary levels of proinflammatory cytokines and of active TGF-beta significantly increased at Days 10 and 35. An early and persistent nuclear overexpression of phosphorylated smad 2/3 protein was detected in tubular and interstitial compartments. CONCLUSION: An early and massive interstitial inflammation characterized by activated monocytes/macrophages and cytotoxic CD8+CD103+ T lymphocytes is demonstrated for the first time during the progression of experimental AAN. The involvement in an interstitial fibrosis onset of active TGF-beta is highly suggested, at least via the psmad 2/3 intracellular signalling pathway.



F. Lefranc, T. Mijatovic, Y. Kondo, S. Sauvage, I. Roland, O. Debeir, D. Krstic, V. Vasic, P. Gailly, S. Kondo, G. Blanco, R. Kiss,
Targeting the alpha 1 subunit of the sodium pump to combat glioblastoma cells.
Neurosurgery, Vol. 62, 1, pp. 211-21; discussion 221-2, 2008
Bibtex
Bibtex : info:hdl:2013/51204
Note : Journal Article
Abstract : OBJECTIVE: Ion transporters play pivotal roles in cancer cell migration in general and in glioblastomas (GBMs) in particular. However, the specific role of Na/K-ATPase (the sodium pump) and, in particular, its alpha1 subunit, has remained unexplored in GBMs. MATERIALS AND METHODS: The expression of Na+/K+ -ATPase alpha1 in GBM clinical samples, normal brain tissue, and a human GBM cell line has been investigated. Using the novel cardenolide UNBS1450 (Unibioscreen, Brussels, Belgium), which is a ligand of the sodium pump, we have characterized the effects of inhibiting Na+/K+ -ATPase alpha1 in human GBM cells with respect to cell proliferation; morphology; impact on intracellular Na+, Ca2+, and adenosine triphosphate; and changes in the actin cytoskeleton. We have investigated the mechanism by which UNBS1450 overcomes the apoptosis resistance of GBMs and determined its anti-tumor effects in comparative studies in vitro in GBM cell viability assays and in vivo using an orthotopic human GBM xenograft model. RESULTS: Overall, the alpha1 subunit of Na+/K+ -ATPase is highly expressed in a majority of glioblastomas compared with normal brain tissues, and by binding to this subunit in human U373-MG GBM cells, UNBS1450 impairs cell proliferation and migration via an intracellular adenosine triphosphate decrease-mediated disorganization of the actin cytoskeleton and cytotoxic proautophagic effects. UNBS1450 also significantly increases the in vivo survival of mice orthotopically grafted with U373-MG GBM cells. CONCLUSION: Inhibition of the Na+/K+ -ATPase alpha1 subunit in human GBM cells impairs both cell migration and cell proliferation.



C. Maris, S. Rorive, F. Sandras, N. D'Haene, N. Sadeghi-Meibodi, I. Bièche, M. Vidaud, C. Decaestecker, I. Salmon,
Tenascin-C expression relates to clinicopathological features in pilocytic and diffuse astrocytomas.
Neuropathology and applied neurobiology, Vol. 34, 3, pp. 316-329, 2008
Bibtex
Bibtex : info:hdl:2013/53624
Note : Journal Article
Abstract : AIMS: Tenascin-C (TN-C) is an extracellular matrix brain glycoprotein for which conflicting in vitro and in vivo results are reported in the literature dealing with its involvement in astrocytoma aggressiveness, in particular astrocytoma invasion. In view of these conflicting results and the lack of data available on low-grade astrocytomas, the present study focuses on pilocytic World Health Organization (WHO) grade I, and diffuse WHO grade II astrocytomas, that is, two histological entities associated with very different invasive abilities. METHODS: Using real-time reverse transcription polymerase chain reaction and immunohistochemistry, we analysed the TN-C expression in normal brain tissue as well as in a series of 54 pilocytic and 53 grade II astrocytomas. CONCLUSIONS: Our data on normal brain showed that while TN-C is largely expressed in supratentorial white matter, it was largely absent in infratentorial white matter. Paralleling these observations, we showed that TN-C expression in low-grade astrocytomas similarly varies according to tumour site. Cox regression analysis evidenced that TN-C provided an independent prognostic value which is enhanced in the case of grade II astrocytomas for which positive TN-C expression is associated with a higher risk of recurrence. We also analysed TN-C expression specifically in vascular areas of low-grade astrocytomas without demonstrating any prognostic value for this additional feature. RESULTS: Similarly to normal brain, low-grade astrocytomas exhibit variations in TN-C expression with site, and this expression is associated with an independent prognostic value in terms of recurrence.



S. Saussez, F. Lorfevre, T. Lequeux, G. Laurent, G. Chantrain, F. Vertongen, G. Toubeau, C. Decaestecker, R. Kiss,
The determination of the levels of circulating galectin-1 and -3 in HNSCC patients could be used to monitor tumor progression and/or responses to therapy.
Oral oncology, Vol. 44, 1, pp. 86-93, 2008
Bibtex
Bibtex : info:hdl:2013/52093
Note : Journal Article
Abstract : To evaluate galectin-1, -3 and -7 serum levels as diagnostic and/or prognostic markers for head and neck squamous cell carcinomas (HNSCCs). ELISA was employed to test sera from 102 patients with HNSCCs and from 38 healthy control volunteers for galectin-1, -3 and -7 serum levels. Serum galectin levels were assayed by ELISA and the levels of galectin expression in HNSCCs were determined by means of immunohistochemistry. HNSCCs display significant immunohistochemical amounts of galectin-7, but this galectin cannot be detected in the blood of HNSCC patients. Galectin-3 levels differ significantly (p=0.03) in healthy volunteers and HNSCC patients. Using a threshold value of 4.3 ng/ml, galectin-3 serum level enabled a significant level of discrimination (p=0.03) to be established between the cancer patients and the healthy volunteers, with 90\% level of specificity and 36\% level of sensitivity. The discrimination was even better when using a threshold value of 13.5 ng/ml for galectin-1 (p=0.001), with 100\% level of specificity and 22\% level of sensitivity. A subgroup of stage IV HNSCC patients displayed significantly reduced levels of circulating galectin-1 (p=0.003) and galectin-3 (p=0.001) after treatment as opposed to before. Galectin-3 concentrations in sera from the patients with a metastatic disease were significantly (p=0.01) higher than in sera from the patients with localized tumors. The determination of circulating levels of galectin-1 and -3 could be used to monitor the progression of their disease or their response to therapy.



P. Demetter, N. Nagy, B. Martin, A. Mathieu, P. Dumont, C. Decaestecker, I. Salmon,
The galectin family and digestive disease.
Journal of pathology, Vol. 215, 1, pp. 1-12, 2008
Bibtex
Bibtex : info:hdl:2013/53621
Note : Journal Article
Abstract : The soluble-type lectins or galectins constitute a family of proteins defined by shared consensus amino acid sequence and affinity for beta-galactose-containing oligosaccharides. These molecules are widely distributed in the animal kingdom; to date, 15 mammalian galectins have been described but more are likely to be discovered. These proteins are involved in many biological processes including cell-cell and cell-matrix adhesion, growth regulation, signaling, and cytokine secretion. Over the last decade, a vast amount of reports has shown the importance of several galectins in the development and progression of malignancies in the digestive tract, mainly colorectal cancers. More recent data indicate that some of these molecules are also involved in inflammatory bowel diseases. This review focuses on the current knowledge of galectin expression and putative functions in the oesophagus, stomach, small intestine, and colon. It also highlights that the rapid accumulation of research data promises future scenarios in which individual members of the galectin family and/or their ligands will be used as diagnostic and therapeutic modalities for neoplastic as well as inflammatory disorders. However, the concretization of these potential modalities requires substantial improvements in terms of standardization of galectin expression evaluation together with prospective validation of the present data.



T. Mijatovic, T. Mahieu, C. Bruyère, N. De Nève, J. Dewelle, G. Simon, M. Dehoux, E. van der Aar, B. Haibe-Kains, G. Bontempi, C. Decaestecker, E. Van Quaquebeke, F. Darro, R. Kiss,
UNBS5162, a novel naphthalimide that decreases CXCL chemokine expression in experimental prostate cancers.
Neoplasia (New York, N.Y.), Vol. 10, 6, pp. 573-586, 2008
Bibtex
Bibtex : info:hdl:2013/52069
Note : Journal Article
Abstract : Several naphthalimides have been evaluated clinically as potential anticancer agents. UNBS3157, a naphthalimide that belongs to the same class as amonafide, was designed to avoid the specific activating metabolism that induces amonafide's hematotoxicity. The current study shows that UNBS3157 rapidly and irreversibly hydrolyzes to UNBS5162 without generating amonafide. In vivo UNBS5162 after repeat administration significantly increased survival in orthotopic human prostate cancer models. Results obtained by the National Cancer Institute (NCI) using UNBS3157 and UNBS5162 against the NCI 60 cell line panel did not show a correlation with any other compound present in the NCI database, including amonafide, thereby suggesting a unique mechanism of action for these two novel naphthalimides. Affymetrix genome-wide microarray analysis and enzyme-linked immunosorbent assay revealed that in vitro exposure of PC-3 cells to UNBS5162 (1 microM for 5 successive days) dramatically decreased the expression of the proangiogenic CXCL chemokines. Histopathology additionally revealed antiangiogenic properties in vivo for UNBS5162 in the orthotopic PC-3 model. In conclusion, the present study reveals UNBS5162 to be a pan-antagonist of CXCL chemokine expression, with the compound displaying antitumor effects in experimental models of human refractory prostate cancer when administered alone and found to enhance the activity of taxol when coadministered with the taxoid.



O. Debeir, V. Megalizzi, N. Warzée, R. Kiss, C. Decaestecker,
Videomicroscopic extraction of specific information on cell proliferation and migration in vitro.
Experimental cell research, Vol. 314, 16, pp. 2985-2998, 2008
Bibtex
Bibtex : info:hdl:2013/52065
Note : Journal Article
Abstract : In vitro cell imaging is a useful exploratory tool for cell behavior monitoring with a wide range of applications in cell biology and pharmacology. Combined with appropriate image analysis techniques, this approach has been shown to provide useful information on the detection and dynamic analysis of cell events. In this context, numerous efforts have been focused on cell migration analysis. In contrast, the cell division process has been the subject of fewer investigations. The present work focuses on this latter aspect and shows that, in complement to cell migration data, interesting information related to cell division can be extracted from phase-contrast time-lapse image series, in particular cell division duration, which is not provided by standard cell assays using endpoint analyses. We illustrate our approach by analyzing the effects induced by two sigma-1 receptor ligands (haloperidol and 4-IBP) on the behavior of two glioma cell lines using two in vitro cell models, i.e., the low-density individual cell model and the high-density scratch wound model. This illustration also shows that the data provided by our approach are suggestive as to the mechanism of action of compounds, and are thus capable of informing the appropriate selection of further time-consuming and more expensive biological evaluations required to elucidate a mechanism.



Conferences

S. Rogmans, J. Lu, G. Lafruit,
A scalable end-to-end optimized real-time image-based rendering framework on graphics hardware
Proceedings of 3DTV Conference, pp. 129-132, 2008
Bibtex
Bibtex : info:hdl:2013/186807
Note : Language of publication: en



L. Engels, X. De Tiege, M. Op De Beeck, N. Warzée,
Accuracy study of electromagnetic tracking system for the spatial localization of electrodes
Conference: BIOMAG : International Conference on Biomagnetism (August 2008), 2008
Bibtex
Bibtex : info:hdl:2013/71598
Note : Language of publication: en



J. Lu, G. Lafruit, F. Catthoor,
Anisotropic local high-confidence voting for accurate stereo correpondence
Image Processing: Algorithms and Systems VII, 2008
Bibtex
Bibtex : info:hdl:2013/186804
Note : Language of publication: en



Y. Guan, G. Lafruit, R. Stahl, H. Corporaal, P. Schelkens,
Applying SIMD to optical character recognition (OCR)
Optical and Digital Image Processing, 2008
Bibtex
Bibtex : info:hdl:2013/186810
Note : Language of publication: en



E. Perez-Careta, M. Torres-Cisneros, G. Avina-Cervantes, O. Debeir, O. Ibarra-Manzano, E. Aguilera-Gomez, E. Perez-Pantoja, G. Negrete-Romero,
Cell recognition and tracking using nonlinear cross-correlation
Digest of the IEEE/LEOS Summer Topical Meetings, pp. 45-46, Acapulco, Mexico, 2008
Bibtex
Bibtex : info:hdl:2013/53017
Note : Language of publication: en



E. Perez-Careta, M. Torres-Cisneros, O. Debeir, J. Sanchez-Mondragon, G. Avina-Cervantes, O. Ibarra-Manzano, D. May-Arrioja, E. Perez-Pantoja, G. Negrete-Romero,
Cell tracking by normalized cross-correlation with image processing
Digest of the IEEE-LEOS Summer Topical Meetings, pp. 43-44, 21-23 July 2008, 2008
Bibtex
Bibtex : info:hdl:2013/53016
Note : Language of publication: en
Abstract : Here, cell tracking task involves normalized cross correlation of the cell target and microscope images. The sensibility of this method was improved applying image processing algorithms prior to the cross correlation task. © 2008 IEEE.



J. Perez-Careta, G. Avina-Cervantes, M. Torres-Cisneros, O. Ibarra-Manzano, O. Debeir, E. Aguilera-Gomez, E. Perez-Pantoja, G. Negrete-Romero,
Cells Tracking by Snakes
Medical physics : tenth Mexican Symposium on Medical Physics, pp. 124-128, México City, México, 2008
Bibtex
Bibtex : info:hdl:2013/53019
Note : DOI : 10.1063/1.2979246
Abstract : In this paper, a cells detection method based on active contours is presented. Active contours or snakes are widely use in image segmentation and tracking problems. Traditionally, active contours initialization is performance manually, this method provides an automatic initialization based on cross correlation. Cell tracking based on active contours provide a faster method to performance this task to multitarget problem. External and internal forces on the image are computed to determinate the action area of the active contours, this task is performance by the Vector Field Convolution (VFC) algorithm.



T. Gan, A. Dejonghe, G. Lenoir, K. Denolf, G. Lafruit, I. Moccagatta,
Cross-layer optimization for multi-user video streaming over IEEE 802.11E HCCA wireless networks
IEEE International Conference on Multimedia and Expo - ICME, pp. 505-508, 2008
Bibtex
Bibtex : info:hdl:2013/186808
Note : Language of publication: en



T. Leloup, A. De Greef, S. Bantuelle, W. El Kazzi, G. Mannaert, N. Warzée, A. Delchambre, F. Schuind,
Design of an articulated mini-fixation device for proximal interphalangeal joint finger fractures
Brussels International Symposium: Bone Vascularization and Fracture Healing in the Upper Extremity, pp. 155-156, 2008
Bibtex
Bibtex : info:hdl:2013/71587
Note : Language of publication: en



P. Malarme, D. Wikler, N. Warzée,
Digital Integrated Operating Room
Proceedings of Seventh Belgian Day on Biomedical Engineering, pp. 58, 2008
Bibtex
Bibtex : info:hdl:2013/71590
Note : Language of publication: en



N. Warzée,
Master in Biomedical Engineering at the U.L.B.
Conference: Med-e-Tel 2008 (April 2008: Luxembourg), 2008
Bibtex
Bibtex : info:hdl:2013/71597
Note : Language of publication: en



O. Debeir, I. Adanja, N. Warzée, P. Van Ham, C. Decaestecker,
Phase contrast image segmentation by weak watershed transform assembly
Proceedings of 5th IEEE International Symposium on Biomedical Imaging : From Nano to Macro (ISBI), pp. 724-727, ISBI)(Paris, France, 2008
Bibtex
Bibtex : info:hdl:2013/53020
Note : Language of publication: en



C. Krykwinski, K. Chellaoui, V. Nicolas, A. Parraga, J. Orban, J. Lee, P. Castadot, N. Warzée, T. Leloup, J. Verly, B. Macq, V. Grégoire,
Registration and segmentation of head and neck volumes in IMRT applications
Conference proceedings of Liège Image Days 2008: Medical Imaging, pp. 17, 2008
Bibtex
Bibtex : info:hdl:2013/71591
Note : Language of publication: en



K. Zhang, J. Lu, G. Lafruit,
Scalable stereo matching with locally adaptive polygon approximation
IEEE International Conference on Image Processing - ICIP, pp. 313-316, 2008
Bibtex
Bibtex : info:hdl:2013/186806
Note : Language of publication: en



B. Geelen, A. Ferentinos, F. Catthoor, G. Lafruit, D. Verkest,
Spatial locality trade-offs of wavelet-based applications in dynamic execution environments
pp. 1461-1464, 2008
Bibtex
Bibtex : info:hdl:2013/186805
Note : Language of publication: en



F. Lefranc, S. Spiegl-Kreinecker, B. Haibe-Kains, G. Bontempi, C. Decaestecker, W. Berger, R. Kiss,
Temozolomide displays anti-migratory effects in human glioblastoma cells through neuregulin down-regulation.
Conference: American Association for Cancer Research Annual Meeting (99th: April 12-16: San Diego - USA), 2008
Bibtex
Bibtex : info:hdl:2013/71771
Note : Language of publication: en



K. Denolf, K. Tack, G. Lafruit,
Triple A philosophy applied to multimedia SoC design
2008
Bibtex
Bibtex : info:hdl:2013/186809
Note : Language of publication: en



P. Malarme, D. Wikler, N. Warzée,
Un projet d'ingénierie biomédicale à double objectif pédagogique
Colloque sur l'Enseignement des Technologies et des Sciences de l'Information et des Systèmes (CETSIS), pp. 6, October 2008, 2008
Bibtex
Bibtex : info:hdl:2013/71593
Note : Résumé page 49



F. De Groef, X. Baele, N. Warzée,
Using a Pocket PC as an interaction peripheral for Virtual Realty
Proceedings of IEEE VRIC 2008, pp. 57-63, 10, 2008
Bibtex
Bibtex : info:hdl:2013/71592
Note : Language of publication: en



Books chapters

O. Debeir, I. Adanja, R. Kiss, C. Decaestecker,
Models of cancer cell migration and cellular imaging and analysis
Anja Lambrechts, Christophe Ampe (Eds). The Motile Actin System in Health and Disease, pp. 123-156, 2008
Bibtex
Bibtex : info:hdl:2013/99600
Note : Language of publication: en



Thesis

X. Ji, G. Lafruit,
Energy efficient video transmission over multi-user wireless networks. Computer engineering
2008
Bibtex
Bibtex : info:hdl:2013/188501
Note : Language of publication: na



B. Geelen, G. Lafruit,
Low-Power, Wavelet-based applications in Dynamic Environments. Computer Engineering
2008
Bibtex
Bibtex : info:hdl:2013/188502
Note : Language of publication: na



Technical report

O. Debeir,
Projet ARMURS : Automatic Recognition for Map Update by Remote Sensing: Premier rapport d'activité
2008
Bibtex
Bibtex : info:hdl:2013/74447
Note : Language of publication: fr



O. Debeir,
Projet ARMURS : Automatic Recognition for Map Update by Remote Sensing: Premier rapport opérationnel
2008
Bibtex
Bibtex : info:hdl:2013/74446
Note : 69 p.



Misc

R. Osorio, G. Lafruit, E. Delfosse, J. Bormans,
Method and system for transmitting digital signals between nodes of a network for optimized processing at the receiving node
Language of publication: na, 2008
Bibtex
Bibtex : info:hdl:2013/188507
Note : Language of publication: na




2007

S. Rogmans, G. Lafruit,
A Generic Framework for Implementing Real-Time Stereo Matching Algorithms on the Graphics Processing Unit. Ingénieur Industriel
2007
Bibtex
Bibtex : info:hdl:2013/188488
Note : Language of publication: na



Papers

F. Moran, M. Preda, G. Lafruit, P. Villegas, R. Berretty,
3D game content distributed adaptation in heterogeneous environments
Eurasip Journal on Advances in Signal Processing, Vol. 2007, 2, pp. 31, 2007
Bibtex
Bibtex : info:hdl:2013/186282
Note : Language of publication: en



V. Megalizzi, V. Mathieu, T. Mijatovic, P. Gailly, O. Debeir, N. De Nève, M. Van Damme, G. Bontempi, B. Haibe-Kains, C. Decaestecker, Y. Kondo, R. Kiss, F. Lefranc,
4-IBP, a sigma1 receptor agonist, decreases the migration of human cancer cells, including glioblastoma cells, in vitro and sensitizes them in vitro and in vivo to cytotoxic insults of proapoptotic and proautophagic drugs.
Neoplasia (New York, N.Y.), Vol. 9, 5, pp. 358-369, 2007
Bibtex
Bibtex : info:hdl:2013/51212
Note : Journal Article
Abstract : Although the molecular function of sigma receptors has not been fully defined and the natural ligand(s) is still not known, there is increasing evidence that these receptors and their ligands might play a significant role in cancer biology. 4-(N-benzylpiperidin-4-yl)-4-iodobenzamide (4-IBP), a selective sigma1 agonist, has been used to investigate whether this compound is able to modify: 1) in vitro the migration and proliferation of human cancer cells; 2) in vitro the sensitivity of human glioblastoma cells to cytotoxic drugs; and 3) in vivo in orthotopic glioblastoma and non-small cell lung carcinoma (NSCLC) models the survival of mice co-administered cytotoxic agents. 4-IBP has revealed weak antiproliferative effects on human U373-MG glioblastoma and C32 melanoma cells but induced marked concentration-dependent decreases in the growth of human A549 NSCLC and PC3 prostate cancer cells. The compound was also significantly antimigratory in all four cancer cell lines. This may result, at least in U373-MG cells, from modifications to the actin cytoskeleton. 4-IBP modified the sensitivity of U373-MG cells in vitro to proapoptotic lomustin and proautophagic temozolomide, and markedly decreased the expression of two proteins involved in drug resistance: glucosylceramide synthase and Rho guanine nucleotide dissociation inhibitor. In vivo, 4-IBP increased the antitumor effects of temozolomide and irinotecan in immunodeficient mice that were orthotopically grafted with invasive cancer cells.



C. Decaestecker, O. Debeir, P. Van Ham, R. Kiss,
Can anti-migratory drugs be screened in vitro? A review of 2D and 3D assays for the quantitative analysis of cell migration.
Medicinal research reviews, Vol. 27, 2, pp. 149-176, 2007
Bibtex
Bibtex : info:hdl:2013/51824
Note : Journal Article
Abstract : The aim of the present review is to detail and analyze the pros and cons of in vitro tests available to quantify the anti-migratory effects of anti-cancer drugs for their eventual use in combating the dispersal of tumor cells, a clinical need which currently remains unsatisfied. We therefore briefly sum up why anti-migratory drugs constitute a promising approach in oncology while at the same time emphasizing that migrating cancer cells are resistant to apoptosis. To analyze the pros and cons of the various in vitro tests under review we also briefly sum up the molecular and cellular stages of cancer cell migration, an approach that enables us to argue both that no single in vitro test is sufficient to characterize the anti-migratory potential of a drug and that standardization is needed for the efficient quantitative analysis of cell locomotion in a 3D environment. Before concluding our review we devote the final two parts (i) to the description of new prototypes which, in the near future, could enter the screening process with a view to identifying novel anti-migratory compounds, and (ii) to the anti-migratory compounds currently developed against cancer, with particular emphasis on how these compounds were selected before entering the clinical trial phase.



T. Mijatovic, E. Van Quaquebeke, B. Delest, O. Debeir, F. Darro, R. Kiss,
Cardiotonic steroids on the road to anti-cancer therapy.
Biochimica et biophysica acta, Vol. 1776, 1, pp. 32-57, 2007
Bibtex
Bibtex : info:hdl:2013/51817
Note : Journal Article
Abstract : The sodium pump, Na(+)/K(+)-ATPase, could be an important target for the development of anti-cancer drugs as it serves as a versatile signal transducer, it is a key player in cell adhesion and its aberrant expression and activity are implicated in the development and progression of different cancers. Cardiotonic steroids, known ligands of the sodium pump have been widely used for the treatment of heart failure. However, early epidemiological evaluations and subsequent demonstration of anti-cancer activity in vitro and in vivo have indicated the possibility of developing this class of compound as chemotherapeutic agents in oncology. Their development to date as anti-cancer agents has however been impaired by a narrow therapeutic margin resulting from their potential to induce cardiovascular side-effects. The review will thus discuss (i) sodium pump structure, function, expression in diverse cancers and its chemical targeting and that of its sub-units, (ii) reported in vitro and in vivo anti-cancer activity of cardiotonic steroids, (iii) managing the toxicity of these compounds and the limitations of existing preclinical models to adequately predict the cardiotoxic potential of new molecules in man and (iv) the potential of chemical modification to reduce the cardiovascular side-effects and improve the anti-cancer activity of new molecules.



T. Leloup, A. De Greef, S. Bantuelle, W. El Kazzi, G. Mannaert, N. Warzée, F. Schuind, A. Delchambre,
Design of an articulated mini-fixation device for proximal interphalangeal joint finger fractures
Proceedings of the annual conference of the IEEE/Engineering in Medicine and Biology Society, pp. 100-103, 2007
Bibtex
Bibtex : info:hdl:2013/71589
Note : Language of publication: en



S. Saussez, C. Decaestecker, F. Lorfevre, D. Cucu, G. Mortuaire, D. Chevalier, A. Wacreniez, H. Kaltner, S. André, G. Toubeau, I. Camby, H. Gabius, R. Kiss,
High level of galectin-1 expression is a negative prognostic predictor of recurrence in laryngeal squamous cell carcinomas.
International journal of oncology, Vol. 30, 5, pp. 1109-1117, 2007
Bibtex
Bibtex : info:hdl:2013/52089
Note : Journal Article
Abstract : Monitoring of gene-expression profiles is assumed to refine tumor characterization of laryngeal squamous cell carcinomas (LSCCs) with a therapeutic perspective. This is especially expected for adhesion/growth-regulatory effectors such as galectins, a class of endogenous lectins. Using computer-assisted microscopy, we investigated the prognostic value contributed by the quantitative determination of the immunohistochemical levels of expression of galectin-1, -3 and -7 in a series of 62 LSCCs including 42 low- and 20 high-stage LSCCs. As galectin-1 may have a key role leading to a tumor escape from immune surveillance, we also investigated whether or not the level of galectin-1 expression correlated with lymphocyte infiltration in LSCCs. The immunohistochemical determination of expression of galectin-1 is of prognostic value in human squamous laryngeal cancers. LSCCs that display high levels of galectin-1 have worse prognoses than laryngeal cancers with low levels of galectin-1 expression. Elevation of galectin-1 levels in laryngeal cancers can contribute to the process of tumor immune escape by killing the activated T-cells and other protumoral activities such as promoting motility or activity of oncogenic H-Ras proteins. The quantitative determination of galectin-1 in LSCCs is an independent prognostic marker when opposed to TNM staging. It has the potential to identify patients unlikely to benefit from T-cell-mediated immunotherapy, although the definitive effector function from its pro- and antitumoral activity profile has not been delineated.



O. Debeir, P. Dunham, L. Engels, T. Leloup, N. Warzée,
High resolution 3D acquisition of the Olivier Strebelle's sculpture 'Athletes' Alley in Beijing 2008'
International Review on Computer and Software, Vol. 2, 5, pp. 541-545, 2007
Bibtex
Bibtex : info:hdl:2013/71564
Note : Language of publication: en



C. Krykwinski, T. Leloup, N. Warzée,
Lymph node and organs at risk segmentation on 3D CT images for head and neck radiotherapy
Proceedings of the annual conference of the IEEE/Engineering in Medicine and Biology Society, pp. 88, 2007
Bibtex
Bibtex : info:hdl:2013/71588
Note : Language of publication: en



T. Mijatovic, P. Gailly, V. Mathieu, N. De Nève, P. Yeaton, R. Kiss, C. Decaestecker,
Neurotensin is a versatile modulator of in vitro human pancreatic ductal adenocarcinoma cell (PDAC) migration.
Cellular oncology, Vol. 29, 4, pp. 315-326, 2007
Bibtex
Bibtex : info:hdl:2013/52082
Note : Journal Article
Abstract : BACKGROUND: While the neurotensin (NT) roles in pancreatic cancer growth are well documented, its effects on pancreatic cancer cell migration have not been described. METHODS: The NT-induced effects on the migration process of human pancreatic ductal adenocarcinoma cells (PDACs) were characterized by means of various assays including computer-assisted video-microscopy, fluorescence microscopy, ELISA-based, small GTPase pull-down and phosphorylation assays. RESULTS: The NT-induced modifications on in vitro PDACs migration largely depended on the extra-cellular matrix environment and cell propensity to migrate collectively or individually. While NT significantly reduced the level of migration of collectively migrating PDACs on vitronectin, it significantly increased the level of individually migrating PDACs. These effects were mainly mediated through the sortilin/NTR3 receptor. Neurotensin both induced altered expression of alphaV and beta5 integrin subunits in PDACs cultured on vitronectin resulting in modified adhesion abilities, and caused modifications to the organization of the actin cytoskeleton through the NT-mediated activation of small Rho GTPases. While the NT effects on individually migrating PDACs were mediated at least through the EGFR/ERK signaling pathways, those on collectively migrating PDACs appeared highly dependent on the PI 3-kinase pathway. CONCLUSION: This study strongly suggests the involvement of neurotensin in the modulation of human PDAC migration.



N. Sadeghi-Meibodi, I. Salmon, C. Decaestecker, M. Levivier, T. Metens, D. Wikler, V. Denolin, S. Rorive, N. Massager, D. Balériaux, S. Goldman,
Stereotactic comparison among cerebral blood volume, methionine uptake, and histopathology in brain glioma.
American journal of neuroradiology, Vol. 28, 3, pp. 455-461, 2007
Bibtex
Bibtex : info:hdl:2013/51732
Note : Comparative Study
Abstract : BACKGROUND AND PURPOSE: Vascularity, metabolism, and histologic grade are related in gliomas but the exact determinants of these relationships are not fully defined. We used image coregistration and stereotactic biopsies to regionally compare cerebral blood volume (CBV) and (11)C-methionine (MET) uptake measurements in brain gliomas and to assess their relationship by histopathologic examination. MATERIALS AND METHODS: Fourteen patients with brain gliomas underwent MR imaging, including dynamic susceptibility contrast-enhanced MR and positron-emission tomography (PET) using MET acquired in identical stereotactic conditions before biopsy. MR-based CBV maps were calculated and both CBV maps and PET images were coregistered to anatomic images. Sixty-five biopsy samples were obtained on trajectories targeted toward high MET uptake area. The following histopathologic features were semiquantified in each sample: mitotic activity, endothelial proliferation, cellular pleomorphism, and tumor necrosis. CBV and MET uptake values were measured in the biopsy area and normalized to contralateral white matter. CBV ratios were compared with MET uptake ratios, and both measurements were compared with histologic features of each sample. RESULTS: CBV ratios ranged from 0.08 to 10.24 (median = 1.73), and MET uptake ratios ranged from 0.30 to 4.91 (median = 1.67). There was a positive correlation between CBV ratios and MET uptake ratios (r = 0.65, P < .001). Both CBV and MET uptake ratios were found to be significantly related to endothelial proliferation and mitotic activity (P < .01). CONCLUSION: Within glial tumors, there is a local relationship between CBV and MET uptake measurements. Both provide indices of focal malignant activity.



Conferences

L. Engels, D. Milojevic, N. Warzée,
3D and Virtual Reality: Tools For Archaeological Hypothesis Verification
Proceedings of IEEE VRIC 2007, pp. 203-208, 9, 2007
Bibtex
Bibtex : info:hdl:2013/71586
Note : Language of publication: en



A. Ferentinos, B. Geelen, F. Catthoor, G. Lafruit, T. Stouraitis, R. Lauwereins, D. Verkest,
Adaptive mapping to resource availability for dynamic wavelet-based applications
IEEE/ACM/IFIP Workshop on Embedded Systems for Real-Time Multimedia - ESTIMedia, pp. 53-58, 2007
Bibtex
Bibtex : info:hdl:2013/186818
Note : Language of publication: en



M. Torres-Cisneros, G. Avina-Cervantes, O. Debeir, J. Sanchez-Mondragon,
Cell tracking by border-optical hybrid model
Frontiers in Optics : Proceedings Frontiers in Optics 2007/Laser Science XXIII/Organic Materials and Devices for Displays and Energy Conversion, San Jose, CA; United States, 2007
Bibtex
Bibtex : info:hdl:2013/227889
Note : Language of publication: en
Abstract : We propose an hybrid (image processing-correlation) method to obtain cells detection and cells migration tracking in order to analyze cells behaviors under different conditions. © 2007 OSA.



C. Blanch, S. Pollin, G. Lafruit, A. Dejonghe, G. Lenoir,
Channel-aware rate adaptation for energy optimization and congestion avoidance
Proceedings IEEE International Conference on Acoustics, pp. I-821, 2007
Bibtex
Bibtex : info:hdl:2013/186811
Note : Language of publication: en



M. Le Mercier, Y. Kondo, V. Mathieu, I. Camby, C. Decaestecker, R. Kiss, F. Lefranc,
Decreasing galectin-1 expression in human experimental glioblastomas impairs the endoplasmic reticulum stress (ERS) response and increases temozolomide anti-tumor effects.
Conference: American Association for Cancer Research Annual Meeting (97th: April 14-18: Los Angeles - USA), 2007
Bibtex
Bibtex : info:hdl:2013/71805
Note : Abstract 1967



M. Le Mercier, I. Camby, V. Mathieu, P. Dumont, N. De Nève, I. Roland, B. Haibe-Kains, G. Bontempi, T. Mijatovic, Y. Kondo, C. Decaestecker, R. Kiss, F. Lefranc,
Decreasing Galectin-1 Expression in Human Hs683 Glioblastoma Cells Impairs their Response to Endoplasmic Reticulum Stress
Conference: Belgium Society for Cell and Developmental Biology Autumn Meeting 2006(14 October 2006: Ghent), 2007
Bibtex
Bibtex : info:hdl:2013/158305
Note : Language of publication: en
Abstract : Glioblastomas (GBMs) are resistant to apoptosis, but not to autophagy, a fact that can, at least partly, explain the therapeutic benefits of the pro-autophagic drug temozolomide in the treatment of GBM patients. Galectin-1 is a potent modulator of GBM cell migration and a close partner of Ras, whose importance as a signaling molecule in the case of GBMs has already been highlighted. The data in the present study show that the depletion by anti-galectin-1 siRNA of galectin-1 expression in human Hs683 GBM cells does not induce apoptotic or autophagic features. In contrast, this galectin-1 depletion decreases the levels of expression of several genes involved in the response to the endoplasmic reticulum (ER) stress (ERS), and including DUSP5, HERP, DNAJB9/MDG1/Erdj4 and ORP150/HYOU1, the latter of which modulates angiogenesis via the processing of VEGF. The depletion of galectin-1 expression in Hs683 tumor cells leads to sustained decreases in VEGF expression, with severe in vivo impairments of angiogenesis in Hs683 orthotopic xenografts. The in vivo delivery of a non-viral infusion of anti-galectin-1 siRNA into the ventricular system of the brains of adult mice orthotopically grafted with Hs683 GBM cells increases the anti-tumor effects of temozolomide. This novel facet of galectin-1 involvement in glioblastoma biology may be amenable to therapeutic manipulation.



P. Dunham, O. Debeir, N. Warzée, M. Groenen, J. Rosoux,
Documentation of the El Castillo (Puente Viesgo) cave using 3D scanning
Informations sur la publication Virtual Retrospect 2007 : Archéologie & Réalité Virtuelle, 2007
Bibtex
Bibtex : info:hdl:2013/107652
Note : Language of publication: en



A. Pozdzik, I. Salmon, F. Debelle, E. De Prez, C. Decaestecker, C. Van den Branden, D. Verbeelen, M. Deschodt Lanckman, J. Vanherweghem, J. Nortier,
Early intratubular epithelial to mesenchymal transition (EMT) after aristolochic acid intoxication
Conference: Annual meeting of the Belgian Society of Nephrology (8 mars 2007: Bruxelles), 2007
Bibtex
Bibtex : info:hdl:2013/99454
Note : Language of publication: en



X. Ji, S. Pollin, G. Lafruit, I. Moccagatta, A. Dejonghe, F. Catthoor,
Energy-Efficient Bandwidth Allocation for Multi-user Video streaming over WLAN
International Conference on Acoustics, pp. II-817 – II, 2007
Bibtex
Bibtex : info:hdl:2013/186828
Note : Language of publication: en



X. Ji, S. Pollin, G. Lafruit, I. Moccagatta, A. Dejonghe, F. Catthoor,
Energy-efficient bandwidth allocation for multi-user video streaming over WLAN
Proceedings IEEE International Conference on Acoustics, pp. II-817 – II, 2007
Bibtex
Bibtex : info:hdl:2013/186812
Note : Language of publication: en



J. Lu, G. Lafruit, F. Catthoor,
Fast reliable multi-scale motion region detection in video processing
International Conference on Acoustics, pp. I-689 – I, 2007
Bibtex
Bibtex : info:hdl:2013/186813
Note : Language of publication: en



J. Lu, G. Lafruit, F. Catthoor,
Fast Variable Center-Biased windowing For High-Speed Stereo on Programmable Graphics Hardware
International Conference on Image Processing, pp. VI-568 – VI, 2007
Bibtex
Bibtex : info:hdl:2013/186825
Note : Language of publication: en



J. Lu, G. Lafruit, F. Catthoor,
Fast variable center-biased windowing for high-speed stereo on programmable graphics hardware
Proceedings IEEE International Conference on Image Processing - ICIP, pp. VI-568 – VI, 2007
Bibtex
Bibtex : info:hdl:2013/186817
Note : Language of publication: en



A. Pozdzik, I. Salmon, C. Husson, C. Decaestecker, E. Rogier, M. Bourgeade, M. Deschodt Lanckman, J. Vanherweghem, J. Nortier,
From aristolochic acid intoxication to renal fibrosis: activated macrophages and CD8+CD103+ T lymphocytes are key effectors
Conference: Annual meeting of the Belgian Society of Nephrology (8 mars 2007: Bruxelles), 2007
Bibtex
Bibtex : info:hdl:2013/99457
Note : Language of publication: en



M. Le Mercier, F. Lefranc, T. Mijatovic, O. Debeir, B. Haibe-Kains, G. Bontempi, C. Decaestecker, R. Kiss, V. Mathieu,
Galectin-1 regulates p53 and is implicated in glioma cell resistance to cytotoxic drugs
Conference: Belgium Society for Cell and Developmental Biology Autumn Meeting(Louvain-la-Neuve), 2007
Bibtex
Bibtex : info:hdl:2013/158306
Note : Language of publication: en
Abstract : Purpose: Glioblastomas (GBMs) are resistant to apoptosis but less so to autophagy, a fact that may at least partly explain the therapeutic benefits of the pro-autophagic drug temozolomide in the treatment of GBM patients. Galectin-1 (Gal1) is a potent modulator of GBM cell migration and a pro-angiogenic molecule whose expression is stimulated by hypoxia. The present study investigates whether decreasing galectin-1 expression in human Hs683 GBM cells increases their sensitivity to pro-autophagic or pro-apoptotic drugs.Experimental design: A siRNA approach was used to decrease Gal1 expression in Hs683 GBM cells. The effects of temozolomide and of pro-apoptotic drugs in this model in vitro and in vivo were studied. Additionally genome-wide microarray analysis was employed to identify chemoresistance-related genes.Results: Temozolomide treatment increased Gal1 expression in Hs683 cells both in vitro and in vivo. Reducing Gal1 expression in these cells increased the anti-tumor effects of chemotherapeutical agents, in particular temozolomide both in vitro and in vivo. Decreasing Gal1 expression in Hs683 cells did not induce apoptotic or autophagic features, but decreased p53 transcriptional activity along with p53-targeted gene expression including DDIT3/GADD153/CHOP, DUSP5, ATF3 and GADD45A. The reduction in Gal1 expression also paralleled decreases in the expression levels of seven other genes implicated in chemoresistance: ORP150, HERP, Grp78/Bip, TRA1, BNIP3L, GADD45B and CYR61.Conclusions: This novel facet of Gal1 involvement in the chemoresistance of GBM cells may be amenable to therapeutic manipulation.



L. Yen, F. Fouss, C. Decaestecker, P. Francq, M. Saerens,
Graph Nodes Clustering based on the Commute-Time Kernel
Proceedings of the 11th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD 2007): Lecture Notes in Computer Science, pp. pp. 1037-1045, 2007
Bibtex
Bibtex : info:hdl:2013/70191
Note : Language of publication: en



O. Debeir, R. Van Ginckel, I. Adanja, F. Darro, R. Kiss, C. Decaestecker,
High throughput characterization of anticancer compounds by means of cellular imaging and automatic image analysis.
Conference: (April 14-18: Los Angeles - USA), 2007
Bibtex
Bibtex : info:hdl:2013/71810
Note : Présentation orale (abstract 4965)



J. Lu, S. Rogmans, G. Lafruit, F. Catthoor,
High-Speed Dense Stereo Via Directional Center-Biased Support Windows on Programmable Graphics Hardware
3DTV conference, pp. 1-4, 2007
Bibtex
Bibtex : info:hdl:2013/186826
Note : Language of publication: en



J. Lu, S. Rogmans, G. Lafruit, F. Catthoor,
High-speed dense stereo via directional center-biased windows on graphics hardware
3DTV Conference, pp. 1-4, 2007
Bibtex
Bibtex : info:hdl:2013/186814
Note : Language of publication: en



J. Lu, S. Rogmans, G. Lafruit, F. Catthoor,
High-speed stream-centric dense stereo and view synthesis on graphics hardware
IEEE International Workshop on Multimedia Signal Processing - MMSP, pp. 243-246, 2007
Bibtex
Bibtex : info:hdl:2013/186819
Note : Language of publication: en



J. Perez-Careta, G. Avina-Cervantes, O. Debeir, J. Sanchez-Mondragon, D. May-Arrioja, M. Torres-Cisneros,
Image Processing for in Vitro Cell Tracking
IV Latin American Congress on Biomedical Engineering 2007, Bioengineering Solutions for Latin America Health, pp. 1148-1151, Margarita Island, Venezuela, 2007
Bibtex
Bibtex : info:hdl:2013/53039
Note : Language of publication: en
Abstract : In this paper, we propose an image processing method able to detect cells trough in vitro phase-contrast video microscopy. Bodies of the cells and image background are very similar; it does not allow having a good performance of tracking process. The proposed method normalizes original image to obtain better object-background contrast, image is equalized to highlight the object to be tracked, and image is threshold in order to obtain a better object-background contrast. Gray Level Morphological Gradient is applied to obtain more defined contours in the areas surrounded by Halos. Dilatation and Erosion were combined to achieve this goal. A subtraction process was applied after dilation of image to obtain borders. © Springer-Verlag Berlin Heidelberg 2007.



T. Gan, K. Denolf, G. Lafruit, I. Moccagatta, A. Dejonghe, G. Lenoir,
Modelling energy consumption of an ASIC MPEG-4 simple profile encoder
IEEE International Conference on Multimedia and Expo, pp. 1922-1925, 2007