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	Author	Sergio Escalera; Vassilis Athitsos; Isabelle Guyon
	Title	Challenges in multimodal gesture recognition			Type	Journal Article
	Year	2016	Publication	Journal of Machine Learning Research	Abbreviated Journal	JMLR
	Volume	17	Issue		Pages	1-54
	Keywords	Gesture Recognition; Time Series Analysis; Multimodal Data Analysis; Computer Vision; Pattern Recognition; Wearable sensors; Infrared Cameras; KinectTM
	Abstract	This paper surveys the state of the art on multimodal gesture recognition and introduces the JMLR special topic on gesture recognition 2011-2015. We began right at the start of the KinectTMrevolution when inexpensive infrared cameras providing image depth recordings became available. We published papers using this technology and other more conventional methods, including regular video cameras, to record data, thus providing a good overview of uses of machine learning and computer vision using multimodal data in this area of application. Notably, we organized a series of challenges and made available several datasets we recorded for that purpose, including tens of thousands of videos, which are available to conduct further research. We also overview recent state of the art works on gesture recognition based on a proposed taxonomy for gesture recognition, discussing challenges and future lines of research.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor	Zhuowen Tu
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	HuPBA;MILAB;			Approved	no
	Call Number	Admin @ si @ EAG2016			Serial	2764
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	Author	Cristina Palmero; Jordi Esquirol; Vanessa Bayo; Miquel Angel Cos; Pouya Ahmadmonfared; Joan Salabert; David Sanchez; Sergio Escalera
	Title	Automatic Sleep System Recommendation by Multi-modal RBG-Depth-Pressure Anthropometric Analysis			Type	Journal Article
	Year	2017	Publication	International Journal of Computer Vision	Abbreviated Journal	IJCV
	Volume	122	Issue	2	Pages	212–227
	Keywords	Sleep system recommendation; RGB-Depth data Pressure imaging; Anthropometric landmark extraction; Multi-part human body segmentation
	Abstract	This paper presents a novel system for automatic sleep system recommendation using RGB, depth and pressure information. It consists of a validated clinical knowledge-based model that, along with a set of prescription variables extracted automatically, obtains a personalized bed design recommendation. The automatic process starts by performing multi-part human body RGB-D segmentation combining GrabCut, 3D Shape Context descriptor and Thin Plate Splines, to then extract a set of anthropometric landmark points by applying orthogonal plates to the segmented human body. The extracted variables are introduced to the computerized clinical model to calculate body circumferences, weight, morphotype and Body Mass Index categorization. Furthermore, pressure image analysis is performed to extract pressure values and at-risk points, which are also introduced to the model to eventually obtain the final prescription of mattress, topper, and pillow. We validate the complete system in a set of 200 subjects, showing accurate category classification and high correlation results with respect to manual measures.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	HuPBA;MILAB; 303.100			Approved	no
	Call Number	Admin @ si @ PEB2017			Serial	2765
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	Author	Pejman Rasti; Salma Samiei; Mary Agoyi; Sergio Escalera; Gholamreza Anbarjafari
	Title	Robust non-blind color video watermarking using QR decomposition and entropy analysis			Type	Journal Article
	Year	2016	Publication	Journal of Visual Communication and Image Representation	Abbreviated Journal	JVCIR
	Volume	38	Issue		Pages	838-847
	Keywords	Video watermarking; QR decomposition; Discrete Wavelet Transformation; Chirp Z-transform; Singular value decomposition; Orthogonal–triangular decomposition
	Abstract	Issues such as content identification, document and image security, audience measurement, ownership and copyright among others can be settled by the use of digital watermarking. Many recent video watermarking methods show drops in visual quality of the sequences. The present work addresses the aforementioned issue by introducing a robust and imperceptible non-blind color video frame watermarking algorithm. The method divides frames into moving and non-moving parts. The non-moving part of each color channel is processed separately using a block-based watermarking scheme. Blocks with an entropy lower than the average entropy of all blocks are subject to a further process for embedding the watermark image. Finally a watermarked frame is generated by adding moving parts to it. Several signal processing attacks are applied to each watermarked frame in order to perform experiments and are compared with some recent algorithms. Experimental results show that the proposed scheme is imperceptible and robust against common signal processing attacks.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	HuPBA;MILAB;			Approved	no
	Call Number	Admin @ si @RSA2016			Serial	2766
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	Author	Cristina Palmero; Albert Clapes; Chris Bahnsen; Andreas Møgelmose; Thomas B. Moeslund; Sergio Escalera
	Title	Multi-modal RGB-Depth-Thermal Human Body Segmentation			Type	Journal Article
	Year	2016	Publication	International Journal of Computer Vision	Abbreviated Journal	IJCV
	Volume	118	Issue	2	Pages	217-239
	Keywords	Human body segmentation; RGB ; Depth Thermal
	Abstract	This work addresses the problem of human body segmentation from multi-modal visual cues as a first stage of automatic human behavior analysis. We propose a novel RGB–depth–thermal dataset along with a multi-modal segmentation baseline. The several modalities are registered using a calibration device and a registration algorithm. Our baseline extracts regions of interest using background subtraction, defines a partitioning of the foreground regions into cells, computes a set of image features on those cells using different state-of-the-art feature extractions, and models the distribution of the descriptors per cell using probabilistic models. A supervised learning algorithm then fuses the output likelihoods over cells in a stacked feature vector representation. The baseline, using Gaussian mixture models for the probabilistic modeling and Random Forest for the stacked learning, is superior to other state-of-the-art methods, obtaining an overlap above 75 % on the novel dataset when compared to the manually annotated ground-truth of human segmentations.
	Address
	Corporate Author				Thesis
	Publisher	Springer US	Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	HuPBA;MILAB;			Approved	no
	Call Number	Admin @ si @ PCB2016			Serial	2767
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	Author	Gerard Canal; Sergio Escalera; Cecilio Angulo
	Title	A Real-time Human-Robot Interaction system based on gestures for assistive scenarios			Type	Journal Article
	Year	2016	Publication	Computer Vision and Image Understanding	Abbreviated Journal	CVIU
	Volume	149	Issue		Pages	65-77
	Keywords	Gesture recognition; Human Robot Interaction; Dynamic Time Warping; Pointing location estimation
	Abstract	Natural and intuitive human interaction with robotic systems is a key point to develop robots assisting people in an easy and effective way. In this paper, a Human Robot Interaction (HRI) system able to recognize gestures usually employed in human non-verbal communication is introduced, and an in-depth study of its usability is performed. The system deals with dynamic gestures such as waving or nodding which are recognized using a Dynamic Time Warping approach based on gesture specific features computed from depth maps. A static gesture consisting in pointing at an object is also recognized. The pointed location is then estimated in order to detect candidate objects the user may refer to. When the pointed object is unclear for the robot, a disambiguation procedure by means of either a verbal or gestural dialogue is performed. This skill would lead to the robot picking an object in behalf of the user, which could present difficulties to do it by itself. The overall system — which is composed by a NAO and Wifibot robots, a KinectTM v2 sensor and two laptops — is firstly evaluated in a structured lab setup. Then, a broad set of user tests has been completed, which allows to assess correct performance in terms of recognition rates, easiness of use and response times.
	Address
	Corporate Author				Thesis
	Publisher	Elsevier B.V.	Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	HuPBA;MILAB;			Approved	no
	Call Number	Admin @ si @ CEA2016			Serial	2768
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	Author	Debora Gil; Sergio Vera; Agnes Borras; Albert Andaluz; Miguel Angel Gonzalez Ballester
	Title	Anatomical Medial Surfaces with Efficient Resolution of Branches Singularities			Type	Journal Article
	Year	2017	Publication	Medical Image Analysis	Abbreviated Journal	MIA
	Volume	35	Issue		Pages	390-402
	Keywords	Medial Representations; Shape Recognition; Medial Branching Stability ; Singular Points
	Abstract	Medial surfaces are powerful tools for shape description, but their use has been limited due to the sensibility existing methods to branching artifacts. Medial branching artifacts are associated to perturbations of the object boundary rather than to geometric features. Such instability is a main obstacle for a condent application in shape recognition and description. Medial branches correspond to singularities of the medial surface and, thus, they are problematic for existing morphological and energy-based algorithms. In this paper, we use algebraic geometry concepts in an energy-based approach to compute a medial surface presenting a stable branching topology. We also present an ecient GPU-CPU implementation using standard image processing tools. We show the method computational eciency and quality on a custom made synthetic database. Finally, we present some results on a medical imaging application for localization of abdominal pathologies.
	Address
	Corporate Author				Thesis
	Publisher	Elsevier B.V.	Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	IAM; 600.060; 600.096; 600.075; 600.145			Approved	no
	Call Number	Admin @ si @ GVB2017			Serial	2775
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	Author	Daniel Hernandez; Alejandro Chacon; Antonio Espinosa; David Vazquez; Juan Carlos Moure; Antonio Lopez
	Title	Stereo Matching using SGM on the GPU			Type	Report
	Year	2016	Publication	Programming and Tuning Massively Parallel Systems	Abbreviated Journal	PUMPS
	Volume		Issue		Pages
	Keywords	CUDA; Stereo; Autonomous Vehicle
	Abstract	Dense, robust and real-time computation of depth information from stereo-camera systems is a computationally demanding requirement for robotics, advanced driver assistance systems (ADAS) and autonomous vehicles. Semi-Global Matching (SGM) is a widely used algorithm that propagates consistency constraints along several paths across the image. This work presents a real-time system producing reliable disparity estimation results on the new embedded energy efficient GPU devices. Our design runs on a Tegra X1 at 42 frames per second (fps) for an image size of 640x480, 128 disparity levels, and using 4 path directions for the SGM method.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference	PUMPS
	Notes	ADAS; 600.085; 600.087; 600.076			Approved	no
	Call Number	ADAS @ adas @ HCE2016b			Serial	2776
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	Author	Joan M. Nuñez; Jorge Bernal; F. Javier Sanchez; Fernando Vilariño
	Title	Growing Algorithm for Intersection Detection (GRAID) in branching patterns			Type	Journal Article
	Year	2015	Publication	Machine Vision and Applications	Abbreviated Journal	MVAP
	Volume	26	Issue	2	Pages	387-400
	Keywords	Bifurcation ; Crossroad; Intersection ;Retina ; Vessel
	Abstract	Analysis of branching structures represents a very important task in fields such as medical diagnosis, road detection or biometrics. Detecting intersection landmarks Becomes crucial when capturing the structure of a branching pattern. We present a very simple geometrical model to describe intersections in branching structures based on two conditions: Bounded Tangency condition (BT) and Shortest Branch (SB) condition. The proposed model precisely sets a geometrical characterization of intersections and allows us to introduce a new unsupervised operator for intersection extraction. We propose an implementation that handles the consequences of digital domain operation that,unlike existing approaches, is not restricted to a particular scale and does not require the computation of the thinned pattern. The new proposal, as well as other existing approaches in the bibliography, are evaluated in a common framework for the first time. The performance analysis is based on two manually segmented image data sets: DRIVE retinal image database and COLON-VESSEL data set, a newly created data set of vascular content in colonoscopy frames. We have created an intersection landmark ground truth for each data set besides comparing our method in the only existing ground truth. Quantitative results confirm that we are able to outperform state-of-the-art performancelevels with the advantage that neither training nor parameter tuning is needed.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	;SIAI			Approved	no
	Call Number	Admin @ si @MBS2015			Serial	2777
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	Author	Gloria Fernandez Esparrach; Jorge Bernal; Maria Lopez Ceron; Henry Cordova; Cristina Sanchez Montes; Cristina Rodriguez de Miguel; F. Javier Sanchez
	Title	Exploring the clinical potential of an automatic colonic polyp detection method based on the creation of energy maps			Type	Journal Article
	Year	2016	Publication	Endoscopy	Abbreviated Journal	END
	Volume	48	Issue	9	Pages	837-842
	Keywords
	Abstract	Background and aims: Polyp miss-rate is a drawback of colonoscopy that increases significantly in small polyps. We explored the efficacy of an automatic computer vision method for polyp detection. Methods: Our method relies on a model that defines polyp boundaries as valleys of image intensity. Valley information is integrated into energy maps which represent the likelihood of polyp presence. Results: In 24 videos containing polyps from routine colonoscopies, all polyps were detected in at least one frame. Mean values of the maximum of energy map were higher in frames with polyps than without (p<0.001). Performance improved in high quality frames (AUC= 0.79, 95%CI: 0.70-0.87 vs 0.75, 95%CI: 0.66-0.83). Using 3.75 as maximum threshold value, sensitivity and specificity for detection of polyps were 70.4% (95%CI: 60.3-80.8) and 72.4% (95%CI: 61.6-84.6), respectively. Conclusion: Energy maps showed a good performance for colonic polyp detection. This indicates a potential applicability in clinical practice.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	MV;			Approved	no
	Call Number	Admin @ si @FBL2016			Serial	2778
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	Author	Jordina Torrents-Barrena; Aida Valls; Petia Radeva; Meritxell Arenas; Domenec Puig
	Title	Automatic Recognition of Molecular Subtypes of Breast Cancer in X-Ray images using Segmentation-based Fractal Texture Analysis			Type	Book Chapter
	Year	2015	Publication	Artificial Intelligence Research and Development	Abbreviated Journal
	Volume	277	Issue		Pages	247 - 256
	Keywords
	Abstract	Breast cancer disease has recently been classified into four subtypes regarding the molecular properties of the affected tumor region. For each patient, an accurate diagnosis of the specific type is vital to decide the most appropriate therapy in order to enhance life prospects. Nowadays, advanced therapeutic diagnosis research is focused on gene selection methods, which are not robust enough. Hence, we hypothesize that computer vision algorithms can offer benefits to address the problem of discriminating among them through X-Ray images. In this paper, we propose a novel approach driven by texture feature descriptors and machine learning techniques. First, we segment the tumour part through an active contour technique and then, we perform a complete fractal analysis to collect qualitative information of the region of interest in the feature extraction stage. Finally, several supervised and unsupervised classifiers are used to perform multiclass classification of the aforementioned data. The experimental results presented in this paper support that it is possible to establish a relation between each tumor subtype and the extracted features of the patterns revealed on mammograms.
	Address
	Corporate Author				Thesis
	Publisher	IOS Press	Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title	Frontiers in Artificial Intelligence and Applications	Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	MILAB			Approved	no
	Call Number	Admin @ si @TVR2015			Serial	2780
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	Author	E. Tavalera; Mariella Dimiccoli; Marc Bolaños; Maedeh Aghaei; Petia Radeva
	Title	Regularized Clustering for Egocentric Video Segmentation			Type	Book Chapter
	Year	2015	Publication	Pattern Recognition and Image Analysis	Abbreviated Journal
	Volume		Issue		Pages	327-336
	Keywords	Temporal video segmentation ; Egocentric videos ; Clustering
	Abstract	In this paper, we present a new method for egocentric video temporal segmentation based on integrating a statistical mean change detector and agglomerative clustering(AC) within an energyminimization framework. Given the tendency of most AC methods to oversegment video sequences when clustering their frames, we combine the clustering with a concept drift detection technique (ADWIN) that has rigorous guarantee of performances. ADWIN serves as a statistical upper bound for the clustering-based video segmentation. We integrate techniques in an energy-minimization framework that serves disambiguate the decision of both techniques and to complete the segmentation taking into account the temporal continuity of video frames We present experiments over egocentric sets of more than 13.000 images acquired with different wearable cameras, showing that our method outperforms state-of-the-art clustering methods.
	Address
	Corporate Author				Thesis
	Publisher	Springer International Publishing	Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title	LNCS
	Series Volume		Series Issue		Edition
	ISSN		ISBN	978-3-319-19390-8	Medium
	Area		Expedition		Conference
	Notes	MILAB			Approved	no
	Call Number	Admin @ si @TDB2015a			Serial	2781
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	Author	Francesco Ciompi; Simone Balocco; Juan Rigla; Xavier Carrillo; J. Mauri; Petia Radeva
	Title	Computer-Aided Detection of Intra-Coronary Stent in Intravascular Ultrasound Sequences			Type	Journal Article
	Year	2016	Publication	Medical Physics	Abbreviated Journal	MP
	Volume	43	Issue	10	Pages
	Keywords
	Abstract	Purpose: An intraluminal coronary stent is a metal mesh tube deployed in a stenotic artery during Percutaneous Coronary Intervention (PCI), in order to prevent acute vessel occlusion. The identication of struts location and the denition of the stent shape are relevant for PCI planning 15 and for patient follow-up. We present a fully-automatic framework for Computer-Aided Detection (CAD) of intra-coronary stents in Intravascular Ultrasound (IVUS) image sequences. The CAD system is able to detect stent struts and estimate the stent shape. Methods: The proposed CAD uses machine learning to provide a comprehensive interpretation of the local structure of the vessel by means of semantic classication. The output of the classication 20 stage is then used to detect struts and to estimate the stent shape. The proposed approach is validated using a multi-centric data-set of 1,015 images from 107 IVUS sequences containing both metallic and bio-absorbable stents. Results: The method was able to detect structs in both metallic stents with an overall F-measure of 77.7% and a mean distance of 0.15 mm from manually annotated struts, and in bio-absorbable 25 stents with an overall F-measure of 77.4% and a mean distance of 0.09 mm from manually annotated struts. Conclusions: The results are close to the inter-observer variability and suggest that the system has the potential of being used as method for aiding percutaneous interventions.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	MILAB			Approved	no
	Call Number	Admin @ si @ CBR2016			Serial	2819
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	Author	Mariella Dimiccoli
	Title	Fundamentals of cone regression			Type	Journal
	Year	2016	Publication	Journal of Statistics Surveys	Abbreviated Journal
	Volume	10	Issue		Pages	53-99
	Keywords	cone regression; linear complementarity problems; proximal operators.
	Abstract	Cone regression is a particular case of quadratic programming that minimizes a weighted sum of squared residuals under a set of linear inequality constraints. Several important statistical problems such as isotonic, concave regression or ANOVA under partial orderings, just to name a few, can be considered as particular instances of the cone regression problem. Given its relevance in Statistics, this paper aims to address the fundamentals of cone regression from a theoretical and practical point of view. Several formulations of the cone regression problem are considered and, focusing on the particular case of concave regression as an example, several algorithms are analyzed and compared both qualitatively and quantitatively through numerical simulations. Several improvements to enhance numerical stability and bound the computational cost are proposed. For each analyzed algorithm, the pseudo-code and its corresponding code in Matlab are provided. The results from this study demonstrate that the choice of the optimization approach strongly impacts the numerical performances. It is also shown that methods are not currently available to solve efficiently cone regression problems with large dimension (more than many thousands of points). We suggest further research to fill this gap by exploiting and adapting classical multi-scale strategy to compute an approximate solution.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1935-7516	ISBN		Medium
	Area		Expedition		Conference
	Notes	MILAB;			Approved	no
	Call Number	Admin @ si @Dim2016a			Serial	2783
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	Author	Jean-Pascal Jacob; Mariella Dimiccoli; L. Moisan
	Title	Active skeleton for bacteria modelling			Type	Journal Article
	Year	2017	Publication	Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualization	Abbreviated Journal	CMBBE
	Volume	5	Issue	4	Pages	274-286
	Keywords
	Abstract	The investigation of spatio-temporal dynamics of bacterial cells and their molecular components requires automated image analysis tools to track cell shape properties and molecular component locations inside the cells. In the study of bacteria aging, the molecular components of interest are protein aggregates accumulated near bacteria boundaries. This particular location makes very ambiguous the correspondence between aggregates and cells, since computing accurately bacteria boundaries in phase-contrast time-lapse imaging is a challenging task. This paper proposes an active skeleton formulation for bacteria modelling which provides several advantages: an easy computation of shape properties (perimeter, length, thickness and orientation), an improved boundary accuracy in noisy images and a natural bacteria-centred coordinate system that permits the intrinsic location of molecular components inside the cell. Starting from an initial skeleton estimate, the medial axis of the bacterium is obtained by minimising an energy function which incorporates bacteria shape constraints. Experimental results on biological images and comparative evaluation of the performances validate the proposed approach for modelling cigar-shaped bacteria like Escherichia coli. The Image-J plugin of the proposed method can be found online at http://fluobactracker.inrialpes.fr.
	Address
	Corporate Author				Thesis
	Publisher	Taylor & Francis Group	Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes	MILAB;			Approved	no
	Call Number	Admin @ si @JDM2017			Serial	2784
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	Author	A.S. Coquel; Jean-Pascal Jacob; M. Primet; A. Demarez; Mariella Dimiccoli; T. Julou; L. Moisan; A. Lindner; H. Berry
	Title	Localization of protein aggregation in Escherichia coli is governed by diffusion and nucleoid macromolecular crowding effect			Type	Journal Article
	Year	2013	Publication	Plos Computational Biology	Abbreviated Journal	PCB
	Volume	9	Issue	4	Pages
	Keywords
	Abstract	Aggregates of misfolded proteins are a hallmark of many age-related diseases. Recently, they have been linked to aging of Escherichia coli (E. coli) where protein aggregates accumulate at the old pole region of the aging bacterium. Because of the potential of E. coli as a model organism, elucidating aging and protein aggregation in this bacterium may pave the way to significant advances in our global understanding of aging. A first obstacle along this path is to decipher the mechanisms by which protein aggregates are targeted to specific intercellular locations. Here, using an integrated approach based on individual-based modeling, time-lapse fluorescence microscopy and automated image analysis, we show that the movement of aging-related protein aggregates in E. coli is purely diffusive (Brownian). Using single-particle tracking of protein aggregates in live E. coli cells, we estimated the average size and diffusion constant of the aggregates. Our results provide evidence that the aggregates passively diffuse within the cell, with diffusion constants that depend on their size in agreement with the Stokes-Einstein law. However, the aggregate displacements along the cell long axis are confined to a region that roughly corresponds to the nucleoid-free space in the cell pole, thus confirming the importance of increased macromolecular crowding in the nucleoids. We thus used 3D individual-based modeling to show that these three ingredients (diffusion, aggregation and diffusion hindrance in the nucleoids) are sufficient and necessary to reproduce the available experimental data on aggregate localization in the cells. Taken together, our results strongly support the hypothesis that the localization of aging-related protein aggregates in the poles of E. coli results from the coupling of passive diffusion-aggregation with spatially non-homogeneous macromolecular crowding. They further support the importance of “soft” intracellular structuring (based on macromolecular crowding) in diffusion-based protein localization in E. coli.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor	: Stanislav Shvartsman, Princeton University, United States of America
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	no
	Call Number	Admin @ si @CJP2013			Serial	2786
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