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	Author	David Roche; Debora Gil; Jesus Giraldo
	Title	Multiple active receptor conformation, agonist efficacy and maximum effect of the system: the conformation-based operational model of agonism,			Type	Journal Article
	Year	2013	Publication	Drug Discovery Today	Abbreviated Journal	DDT
	Volume	18	Issue	7-8	Pages	365-371
	Keywords
	Abstract	The operational model of agonism assumes that the maximum effect a particular receptor system can achieve (the Em parameter) is fixed. Em estimates are above but close to the asymptotic maximum effects of endogenous agonists. The concept of Em is contradicted by superagonists and those positive allosteric modulators that significantly increase the maximum effect of endogenous agonists. An extension of the operational model is proposed that assumes that the Em parameter does not necessarily have a single value for a receptor system but has multiple values associated to multiple active receptor conformations. The model provides a mechanistic link between active receptor conformation and agonist efficacy, which can be useful for the analysis of agonist response under different receptor scenarios.
	Address
	Corporate Author				Thesis
	Publisher	Elsevier	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; 600.057; 600.054			Approved	no
	Call Number	IAM @ iam @ RGG2013a			Serial	2190
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	Author	Sergio Vera; Debora Gil; Agnes Borras; Marius George Linguraru; Miguel Angel Gonzalez Ballester
	Title	Geometric Steerable Medial Maps			Type	Journal Article
	Year	2013	Publication	Machine Vision and Applications	Abbreviated Journal	MVA
	Volume	24	Issue	6	Pages	1255-1266
	Keywords	Medial Representations ,Medial Manifolds Comparation , Surface , Reconstruction
	Abstract	In order to provide more intuitive and easily interpretable representations of complex shapes/organs, medial manifolds should reach a compromise between simplicity in geometry and capability for restoring the anatomy/shape of the organ/volume. Existing morphological methods show excellent results when applied to 2D objects, but their quality drops across dimensions. This paper contributes to the computation of medial manifolds in two aspects. First, we provide a standard scheme for the computation of medial manifolds that avoids degenerated medial axis segments. Second, we introduce a continuous operator for accurate and efficient computation of medial structures of arbitrary dimension. We evaluate quantitatively the performance of our method with respect to existing approaches, by applying them to syn- thetic shapes of known medial geometry. We also show its higher performance for medical imaging applications in terms of simplicity of medial structures and capability for reconstructing the anatomical volume.
	Address
	Corporate Author				Thesis
	Publisher	Springer Berlin Heidelberg	Place of Publication		Editor	Mubarak Shah
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0932-8092	ISBN		Medium
	Area		Expedition		Conference
	Notes	IAM; 605.203; 600.060; 600.044			Approved	no
	Call Number	IAM @ iam @ VGB2013			Serial	2192
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	Author	Ferran Poveda; Debora Gil; Enric Marti; Albert Andaluz; Manel Ballester;Francesc Carreras Costa
	Title	Helical structure of the cardiac ventricular anatomy assessed by Diffusion Tensor Magnetic Resonance Imaging multi-resolution tractography			Type	Journal Article
	Year	2013	Publication	Revista Española de Cardiología	Abbreviated Journal	REC
	Volume	66	Issue	10	Pages	782-790
	Keywords	Heart;Diffusion magnetic resonance imaging;Diffusion tractography;Helical heart;Myocardial ventricular band.
	Abstract	Deep understanding of myocardial structure linking morphology and function of the heart would unravel crucial knowledge for medical and surgical clinical procedures and studies. Several conceptual models of myocardial fiber organization have been proposed but the lack of an automatic and objective methodology prevented an agreement. We sought to deepen in this knowledge through advanced computer graphic representations of the myocardial fiber architecture by diffusion tensor magnetic resonance imaging (DT-MRI). We performed automatic tractography reconstruction of unsegmented DT-MRI canine heart datasets coming from the public database of the Johns Hopkins University. Full scale tractographies have been build with 200 seeds and are composed by streamlines computed on the vectorial field of primary eigenvectors given at the diffusion tensor volumes. Also, we introduced a novel multi-scale visualization technique in order to obtain a simplified tractography. This methodology allowed to keep the main geometric features of the fiber tracts, making easier to decipher the main properties of the architectural organization of the heart. On the analysis of the output from our tractographic representations we found exact correlation with low-level details of myocardial architecture, but also with the more abstract conceptualization of a continuous helical ventricular myocardial fiber array. Objective analysis of myocardial architecture by an automated method, including the entire myocardium and using several 3D levels of complexity, reveals a continuous helical myocardial fiber arrangement of both right and left ventricles, supporting the anatomical model of the helical ventricular myocardial band described by Torrent-Guasp.
	Address
	Corporate Author				Thesis
	Publisher	Elsevier	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; 600.044; 600.060			Approved	no
	Call Number	IAM @ iam @ PGM2013			Serial	2194
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	Author	David Roche; Debora Gil; Jesus Giraldo
	Title	Mechanistic analysis of the function of agonists and allosteric modulators: Reconciling two-state and operational models			Type	Journal Article
	Year	2013	Publication	British Journal of Pharmacology	Abbreviated Journal	BJP
	Volume	169	Issue	6	Pages	1189-202
	Keywords
	Abstract	Two-state and operational models of both agonism and allosterism are compared to identify and characterize common pharmacological parameters. To account for the receptor-dependent basal response, constitutive receptor activity is considered in the operational models. By arranging two-state models as the fraction of active receptors and operational models as the fractional response relative to the maximum effect of the system, a one-by-one correspondence between parameters is found. The comparative analysis allows a better understanding of complex allosteric interactions. In particular, the inclusion of constitutive receptor activity in the operational model of allosterism allows the characterization of modulators able to lower the basal response of the system; that is, allosteric modulators with negative intrinsic efficacy. Theoretical simulations and overall goodness of fit of the models to simulated data suggest that it is feasible to apply the models to experimental data and constitute one step forward in receptor theory formalism.
	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	IAM; 600.044; 605.203			Approved	no
	Call Number	IAM @ iam @ RGG2013b			Serial	2195
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	Author	Joan M. Nuñez; Debora Gil; Fernando Vilariño
	Title	Finger joint characterization from X-ray images for rheymatoid arthritis assessment			Type	Conference Article
	Year	2013	Publication	6th International Conference on Biomedical Electronics and Devices	Abbreviated Journal
	Volume		Issue		Pages	288-292
	Keywords	Rheumatoid Arthritis; X-Ray; Hand Joint; Sclerosis; Sharp Van der Heijde
	Abstract	In this study we propose amodular systemfor automatic rheumatoid arthritis assessment which provides a joint space width measure. A hand joint model is proposed based on the accurate analysis of a X-ray finger joint image sample set. This model shows that the sclerosis and the lower bone are the main necessary features in order to perform a proper finger joint characterization. We propose sclerosis and lower bone detection methods as well as the experimental setup necessary for its performance assessment. Our characterization is used to propose and compute a joint space width score which is shown to be related to the different degrees of arthritis. This assertion is verified by comparing our proposed score with Sharp Van der Heijde score, confirming that the lower our score is the more advanced is the patient affection.
	Address	Barcelona; February 2013
	Corporate Author				Thesis
	Publisher	SciTePress	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	800	Expedition		Conference	BIODEVICES
	Notes	IAM;MV; 600.057; 600.054;SIAI			Approved	no
	Call Number	IAM @ iam @ NGV2013			Serial	2196
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	Author	David Roche; Debora Gil; Jesus Giraldo
	Title	Mathematical modeling of G protein-coupled receptor function: What can we learn from empirical and mechanistic models?			Type	Book Chapter
	Year	2014	Publication	G Protein-Coupled Receptors – Modeling and Simulation Advances in Experimental Medicine and Biology	Abbreviated Journal
	Volume	796	Issue	3	Pages	159-181
	Keywords	β-arrestin; biased agonism; curve fitting; empirical modeling; evolutionary algorithm; functional selectivity; G protein; GPCR; Hill coefficient; intrinsic efficacy; inverse agonism; mathematical modeling; mechanistic modeling; operational model; parameter optimization; receptor dimer; receptor oligomerization; receptor constitutive activity; signal transduction; two-state model
	Abstract	Empirical and mechanistic models differ in their approaches to the analysis of pharmacological effect. Whereas the parameters of the former are not physical constants those of the latter embody the nature, often complex, of biology. Empirical models are exclusively used for curve fitting, merely to characterize the shape of the E/[A] curves. Mechanistic models, on the contrary, enable the examination of mechanistic hypotheses by parameter simulation. Regretfully, the many parameters that mechanistic models may include can represent a great difficulty for curve fitting, representing, thus, a challenge for computational method development. In the present study some empirical and mechanistic models are shown and the connections, which may appear in a number of cases between them, are analyzed from the curves they yield. It may be concluded that systematic and careful curve shape analysis can be extremely useful for the understanding of receptor function, ligand classification and drug discovery, thus providing a common language for the communication between pharmacologists and medicinal chemists.
	Address
	Corporate Author				Thesis
	Publisher	Springer Netherlands	Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0065-2598	ISBN	978-94-007-7422-3	Medium
	Area		Expedition		Conference
	Notes	IAM; 600.075			Approved	no
	Call Number	IAM @ iam @ RGG2014			Serial	2197
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	Author	Patricia Marquez; Debora Gil; Aura Hernandez-Sabate; Daniel Kondermann
	Title	When Is A Confidence Measure Good Enough?			Type	Conference Article
	Year	2013	Publication	9th International Conference on Computer Vision Systems	Abbreviated Journal
	Volume	7963	Issue		Pages	344-353
	Keywords	Optical flow, confidence measure, performance evaluation
	Abstract	Confidence estimation has recently become a hot topic in image processing and computer vision.Yet, several definitions exist of the term “confidence” which are sometimes used interchangeably. This is a position paper, in which we aim to give an overview on existing definitions, thereby clarifying the meaning of the used terms to facilitate further research in this field. Based on these clarifications, we develop a theory to compare confidence measures with respect to their quality.
	Address	St Petersburg; Russia; July 2013
	Corporate Author				Thesis
	Publisher	Springer Link	Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title	LNCS
	Series Volume		Series Issue		Edition
	ISSN	0302-9743	ISBN	978-3-642-39401-0	Medium
	Area		Expedition		Conference	ICVS
	Notes	IAM;ADAS; 600.044; 600.057; 600.060; 601.145			Approved	no
	Call Number	IAM @ iam @ MGH2013a			Serial	2218
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	Author	Patricia Marquez; Debora Gil; R.Mester; Aura Hernandez-Sabate
	Title	Local Analysis of Confidence Measures for Optical Flow Quality Evaluation			Type	Conference Article
	Year	2014	Publication	9th International Conference on Computer Vision Theory and Applications	Abbreviated Journal
	Volume	3	Issue		Pages	450-457
	Keywords	Optical Flow; Confidence Measure; Performance Evaluation.
	Abstract	Optical Flow (OF) techniques facing the complexity of real sequences have been developed in the last years. Even using the most appropriate technique for our specific problem, at some points the output flow might fail to achieve the minimum error required for the system. Confidence measures computed from either input data or OF output should discard those points where OF is not accurate enough for its further use. It follows that evaluating the capabilities of a confidence measure for bounding OF error is as important as the definition itself. In this paper we analyze different confidence measures and point out their advantages and limitations for their use in real world settings. We also explore the agreement with current tools for their evaluation of confidence measures performance.
	Address	Lisboa; January 2014
	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	VISAPP
	Notes	IAM; ADAS; 600.044; 600.060; 600.057; 601.145; 600.076; 600.075			Approved	no
	Call Number	Admin @ si @ MGM2014			Serial	2432
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	Author	Sergio Vera; Debora Gil; Miguel Angel Gonzalez Ballester
	Title	Anatomical parameterization for volumetric meshing of the liver			Type	Conference Article
	Year	2014	Publication	SPIE – Medical Imaging	Abbreviated Journal
	Volume	9036	Issue		Pages
	Keywords	Coordinate System; Anatomy Modeling; Parameterization
	Abstract	A coordinate system describing the interior of organs is a powerful tool for a systematic localization of injured tissue. If the same coordinate values are assigned to specific anatomical landmarks, the coordinate system allows integration of data across different medical image modalities. Harmonic mappings have been used to produce parametric coordinate systems over the surface of anatomical shapes, given their flexibility to set values at specific locations through boundary conditions. However, most of the existing implementations in medical imaging restrict to either anatomical surfaces, or the depth coordinate with boundary conditions is given at sites of limited geometric diversity. In this paper we present a method for anatomical volumetric parameterization that extends current harmonic parameterizations to the interior anatomy using information provided by the volume medial surface. We have applied the methodology to define a common reference system for the liver shape and functional anatomy. This reference system sets a solid base for creating anatomical models of the patient’s liver, and allows comparing livers from several patients in a common framework of reference.
	Address	Amsterdam; September 2014
	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	SPIE-MI
	Notes	IAM; 600.075			Approved	no
	Call Number	Admin @ si @ VGG2014			Serial	2456
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	Author	Enric Marti; Antoni Gurgui; Debora Gil; Aura Hernandez-Sabate; Jaume Rocarias; Ferran Poveda
	Title	ABP on line: Seguimiento, estregas y evaluación en aprendizaje basado en proyectos			Type	Miscellaneous
	Year	2014	Publication	8th International Congress on University Teaching and Innovation	Abbreviated Journal
	Volume		Issue		Pages
	Keywords
	Abstract
	Address	Tarragona; juliol 2014
	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	CIDUI
	Notes	IAM; ADAS; 600.076; 600.063; 600.075			Approved	no
	Call Number	Admin @ si @ MGG2014			Serial	2457
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	Author	Carles Sanchez; Oriol Ramos Terrades; Patricia Marquez; Enric Marti; Jaume Rocarias; Debora Gil
	Title	Evaluación automática de prácticas en Moodle para el aprendizaje autónomo en Ingenierías			Type	Miscellaneous
	Year	2014	Publication	8th International Congress on University Teaching and Innovation	Abbreviated Journal
	Volume		Issue		Pages
	Keywords
	Abstract
	Address	Tarragona; juliol 2014
	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	CIDUI
	Notes	IAM; 600.075;DAG			Approved	no
	Call Number	Admin @ si @ SRM2014			Serial	2458
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	Author	Patricia Marquez; H. Kause; A. Fuster; Aura Hernandez-Sabate; L. Florack; Debora Gil; Hans van Assen
	Title	Factors Affecting Optical Flow Performance in Tagging Magnetic Resonance Imaging			Type	Conference Article
	Year	2014	Publication	17th International Conference on Medical Image Computing and Computer Assisted Intervention	Abbreviated Journal
	Volume	8896	Issue		Pages	231-238
	Keywords	Optical flow; Performance Evaluation; Synthetic Database; ANOVA; Tagging Magnetic Resonance Imaging
	Abstract	Changes in cardiac deformation patterns are correlated with cardiac pathologies. Deformation can be extracted from tagging Magnetic Resonance Imaging (tMRI) using Optical Flow (OF) techniques. For applications of OF in a clinical setting it is important to assess to what extent the performance of a particular OF method is stable across dierent clinical acquisition artifacts. This paper presents a statistical validation framework, based on ANOVA, to assess the motion and appearance factors that have the largest in uence on OF accuracy drop. In order to validate this framework, we created a database of simulated tMRI data including the most common artifacts of MRI and test three dierent OF methods, including HARP.
	Address	Boston; USA; September 2014
	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	0302-9743	ISBN	978-3-319-14677-5	Medium
	Area		Expedition		Conference	STACOM
	Notes	IAM; ADAS; 600.060; 601.145; 600.076; 600.075			Approved	no
	Call Number	Admin @ si @ MKF2014			Serial	2495
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	Author	Jorge Bernal; Debora Gil; Carles Sanchez; F. Javier Sanchez
	Title	Discarding Non Informative Regions for Efficient Colonoscopy Image Analysis			Type	Conference Article
	Year	2014	Publication	1st MICCAI Workshop on Computer-Assisted and Robotic Endoscopy	Abbreviated Journal
	Volume	8899	Issue		Pages	1-10
	Keywords	Image Segmentation; Polyps, Colonoscopy; Valley Information; Energy Maps
	Abstract	In this paper we present a novel polyp region segmentation method for colonoscopy videos. Our method uses valley information associated to polyp boundaries in order to provide an initial segmentation. This first segmentation is refined to eliminate boundary discontinuities caused by image artifacts or other elements of the scene. Experimental results over a publicly annotated database show that our method outperforms both general and specific segmentation methods by providing more accurate regions rich in polyp content. We also prove how image preprocessing is needed to improve final polyp region segmentation.
	Address	Boston; USA; September 2014
	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	0302-9743	ISBN	978-3-319-13409-3	Medium
	Area		Expedition		Conference	CARE
	Notes	MV; IAM; 600.044; 600.047; 600.060; 600.075			Approved	no
	Call Number	Admin @ si @ BGS2014b			Serial	2503
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	Author	Francesco Brughi; Debora Gil; Llorenç Badiella; Eva Jove Casabella; Oriol Ramos Terrades
	Title	Exploring the impact of inter-query variability on the performance of retrieval systems			Type	Conference Article
	Year	2014	Publication	11th International Conference on Image Analysis and Recognition	Abbreviated Journal
	Volume	8814	Issue		Pages	413–420
	Keywords
	Abstract	This paper introduces a framework for evaluating the performance of information retrieval systems. Current evaluation metrics provide an average score that does not consider performance variability across the query set. In this manner, conclusions lack of any statistical significance, yielding poor inference to cases outside the query set and possibly unfair comparisons. We propose to apply statistical methods in order to obtain a more informative measure for problems in which different query classes can be identified. In this context, we assess the performance variability on two levels: overall variability across the whole query set and specific query class-related variability. To this end, we estimate confidence bands for precision-recall curves, and we apply ANOVA in order to assess the significance of the performance across different query classes.
	Address	Algarve; Portugal; October 2014
	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	0302-9743	ISBN	978-3-319-11757-7	Medium
	Area		Expedition		Conference	ICIAR
	Notes	IAM; DAG; 600.060; 600.061; 600.077; 600.075			Approved	no
	Call Number	Admin @ si @ BGB2014			Serial	2559
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	Author	Debora Gil; David Roche; Agnes Borras; Jesus Giraldo
	Title	Terminating Evolutionary Algorithms at their Steady State			Type	Journal Article
	Year	2015	Publication	Computational Optimization and Applications	Abbreviated Journal	COA
	Volume	61	Issue	2	Pages	489-515
	Keywords	Evolutionary algorithms; Termination condition; Steady state; Differential evolution
	Abstract	Assessing the reliability of termination conditions for evolutionary algorithms (EAs) is of prime importance. An erroneous or weak stop criterion can negatively affect both the computational effort and the final result. We introduce a statistical framework for assessing whether a termination condition is able to stop an EA at its steady state, so that its results can not be improved anymore. We use a regression model in order to determine the requirements ensuring that a measure derived from EA evolving population is related to the distance to the optimum in decision variable space. Our framework is analyzed across 24 benchmark test functions and two standard termination criteria based on function fitness value in objective function space and EA population decision variable space distribution for the differential evolution (DE) paradigm. Results validate our framework as a powerful tool for determining the capability of a measure for terminating EA and the results also identify the decision variable space distribution as the best-suited for accurately terminating DE in real-world applications.
	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	0926-6003	ISBN		Medium
	Area		Expedition		Conference
	Notes	IAM; 600.044; 605.203; 600.060; 600.075			Approved	no
	Call Number	Admin @ si @ GRB2015			Serial	2560
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