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	Author	Debora Gil; Agnes Borras; Sergio Vera; Miguel Angel Gonzalez Ballester
	Title	A Validation Benchmark for Assessment of Medial Surface Quality for Medical Applications			Type	Conference Article
	Year	2013	Publication	9th International Conference on Computer Vision Systems	Abbreviated Journal
	Volume	7963	Issue		Pages	334-343
	Keywords	Medial Surfaces; Shape Representation; Medical Applications; Performance Evaluation
	Abstract	Confident use of medial surfaces in medical decision support systems requires evaluating their quality for detecting pathological deformations and describing anatomical volumes. Validation in the medical imaging field is a challenging task mainly due to the difficulties for getting consensual ground truth. In this paper we propose a validation benchmark for assessing medial surfaces in the context of medical applications. Our benchmark includes a home-made database of synthetic medial surfaces and volumes and specific scores for evaluating surface accuracy, its stability against volume deformations and its capabilities for accurate reconstruction of anatomical volumes.
	Address	Sant Petersburg; Russia; July 2013
	Corporate Author				Thesis
	Publisher	Springer Berlin Heidelberg	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; 600.044; 600.060			Approved	no
	Call Number	Admin @ si @ GBV2013			Serial	2300
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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	Detecting loss of diversity for an efficient termination of EAs			Type	Conference Article
	Year	2013	Publication	15th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing	Abbreviated Journal
	Volume		Issue		Pages	561 - 566
	Keywords	EA termination; EA population diversity; EA steady state
	Abstract	Termination of Evolutionary Algorithms (EA) at its steady state so that useless iterations are not performed is a main point for its efficient application to black-box problems. Many EA algorithms evolve while there is still diversity in their population and, thus, they could be terminated by analyzing the behavior some measures of EA population diversity. This paper presents a numeric approximation to steady states that can be used to detect the moment EA population has lost its diversity for EA termination. Our condition has been applied to 3 EA paradigms based on diversity and a selection of functions covering the properties most relevant for EA convergence. Experiments show that our condition works regardless of the search space dimension and function landscape.
	Address	Timisoara; Rumania;
	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	978-1-4799-3035-7	Medium
	Area		Expedition		Conference	SYNASC
	Notes	IAM; 600.044; 600.060; 605.203			Approved	no
	Call Number	Admin @ si @ RGG2013c			Serial	2299
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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	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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	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	H. Martin Kjer; Jens Fagertun; Sergio Vera; Debora Gil; Miguel Angel Gonzalez Ballester; Rasmus R. Paulsena
	Title	Free-form image registration of human cochlear uCT data using skeleton similarity as anatomical prior			Type	Journal Article
	Year	2016	Publication	Patter Recognition Letters	Abbreviated Journal	PRL
	Volume	76	Issue	1	Pages	76-82
	Keywords
	Abstract
	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; 600.060			Approved	no
	Call Number	Admin @ si @ MFV2017b			Serial	2941
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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	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	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	Carles Sanchez
	Title	Tracheal Structure Characterization using Geometric and Appearance Models for Efficient Assessment of Stenosis in Videobronchoscopy			Type	Book Whole
	Year	2014	Publication	PhD Thesis, Universitat Autonoma de Barcelona-CVC	Abbreviated Journal
	Volume		Issue		Pages
	Keywords
	Abstract	Recent advances in endoscopic devices have increased their use for minimal invasive diagnostic and intervention procedures. Among all endoscopic modalities, bronchoscopy is one of the most frequent with around 261 millions of procedures per year. Although the use of bronchoscopy is spread among clinical facilities it presents some drawbacks, being the visual inspection for the assessment of anatomical measurements the most prevalent of them. In particular, inaccuracies in the estimation of the degree of stenosis (the percentage of obstructed airway) decreases its diagnostic yield and might lead to erroneous treatments. An objective computation of tracheal stenosis in bronchoscopy videos would constitute a breakthrough for this non-invasive technique and a reduction in treatment cost. This thesis settles the first steps towards on-line reliable extraction of anatomical information from videobronchoscopy for computation of objective measures. In particular, we focus on the computation of the degree of stenosis, which is obtained by comparing the area delimited by a healthy tracheal ring and the stenosed lumen. Reliable extraction of airway structures in interventional videobronchoscopy is a challenging task. This is mainly due to the large variety of acquisition conditions (positions and illumination), devices (different digitalizations) and in videos acquired at the operating room the unpredicted presence of surgical devices (such as probe ends). This thesis contributes to on-line stenosis assessment in several ways. We propose a parametric strategy for the extraction of lumen and tracheal rings regions based on the characterization of their geometry and appearance that guide a deformable model. The geometric and appearance characterization is based on a physical model describing the way bronchoscopy images are obtained and includes local and global descriptions. In order to ensure a systematic applicability we present a statistical framework to select the optimal parameters of our method. Experiments perform on the first public annotated database, show that the performance of our method is comparable to the one provided by clinicians and its computation time allows for a on-line implementation in the operating room.
	Address
	Corporate Author				Thesis	Ph.D. thesis
	Publisher	Ediciones Graficas Rey	Place of Publication		Editor	F. Javier Sanchez;Debora Gil;Jorge Bernal
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN	978-84-940902-9-5	Medium
	Area		Expedition		Conference
	Notes	IAM; 600.075			Approved	no
	Call Number	Admin @ si @ San2014			Serial	2575
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	Author	Antonio Esteban Lansaque
	Title	3D reconstruction and recognition using structured ligth			Type	Report
	Year	2014	Publication	CVC Technical Report	Abbreviated Journal
	Volume	179	Issue		Pages
	Keywords
	Abstract	This work covers the problem of 3D reconstruction, recognition and 6DOF pose estimation. The goal of this project is to reconstruct a 3D scene and to align an object model of the industrial pieces onto the reconstructed scene. The reconstruction algorithm is based on stereo techniques and the recognition algorithm is based on SHOT descriptors computed on a set of uniform keypoints. Correspondences are used to estimate a first 6DOF transformation that maps the model onto the scene and then ICP algorithm is used to refine the transformation. In order to check the effectiveness of the proposed algorithm, several experiments were performed. These experiments were conducted on a lab environment in order to get results under the same conditions in all of them. Although obtained results are not real time results, the proposed algorithm ends up with high rates of object recognition.
	Address	UAB; September 2014
	Corporate Author				Thesis	Master's 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; 600.075			Approved	no
	Call Number	Admin @ si @ Est2014			Serial	2578
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	Author	Antoni Gurgui; Debora Gil; Enric Marti
	Title	Laplacian Unitary Domain for Texture Morphing			Type	Conference Article
	Year	2015	Publication	Proceedings of the 10th International Conference on Computer Vision Theory and Applications VISIGRAPP2015	Abbreviated Journal
	Volume	1	Issue		Pages	693-699
	Keywords	Facial; metamorphosis;LaplacianMorphing
	Abstract	Deformation of expressive textures is the gateway to realistic computer synthesis of expressions. By their good mathematical properties and flexible formulation on irregular meshes, most texture mappings rely on solutions to the Laplacian in the cartesian space. In the context of facial expression morphing, this approximation can be seen from the opposite point of view by neglecting the metric. In this paper, we use the properties of the Laplacian in manifolds to present a novel approach to warping expressive facial images in order to generate a morphing between them.
	Address	Munich; Germany; February 2015
	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	978-989-758-089-5	Medium
	Area		Expedition		Conference	VISAPP
	Notes	IAM; 600.075			Approved	no
	Call Number	Admin @ si @ GGM2015			Serial	2614
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	Author	Sergio Vera; Miguel Angel Gonzalez Ballester; Debora Gil
	Title	A Novel Cochlear Reference Frame Based On The Laplace Equation			Type	Conference Article
	Year	2015	Publication	29th international Congress and Exhibition on Computer Assisted Radiology and Surgery	Abbreviated Journal
	Volume	10	Issue	1	Pages	1-312
	Keywords
	Abstract	Poster
	Address	Barcelona; Spain; June 2015
	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	CARS
	Notes	IAM; 600.075			Approved	no
	Call Number	Admin @ si @ VGG2015			Serial	2615
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	Author	David Roche
	Title	A Statistical Framework for Terminating Evolutionary Algorithms at their Steady State			Type	Book Whole
	Year	2015	Publication	PhD Thesis, Universitat Autonoma de Barcelona-CVC	Abbreviated Journal
	Volume		Issue		Pages
	Keywords
	Abstract	As any iterative technique, it is a necessary condition a stop criterion for terminating Evolutionary Algorithms (EA). In the case of optimization methods, the algorithm should stop at the time it has reached a steady state so it can not improve results anymore. Assessing the reliability of termination conditions for EAs is of prime importance. A wrong or weak stop criterion can negatively aect both the computational eort and the nal result. In this Thesis, we introduce a statistical framework for assessing whether a termination condition is able to stop EA at its steady state. In one hand a numeric approximation to steady states to detect the point in which EA population has lost its diversity has been presented for EA termination. This approximation has been applied to dierent EA paradigms based on diversity and a selection of functions covering the properties most relevant for EA convergence. Experiments show that our condition works regardless of the search space dimension and function landscape and Dierential Evolution (DE) arises as the best paradigm. On the other hand, 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 xspace. Our theoretical framework is analyzed across several benchmark test functions and two standard termination criteria based on function improvement in f-space and EA population x-space distribution for the DE paradigm. Results validate our statistical framework as a powerful tool for determining the capability of a measure for terminating EA and select the x-space distribution as the best-suited for accurately stopping DE in real-world applications.
	Address	July 2015
	Corporate Author				Thesis	Ph.D. thesis
	Publisher	Ediciones Graficas Rey	Place of Publication		Editor	Debora Gil;Jesus Giraldo
	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; 600.075			Approved	no
	Call Number	Admin @ si @ Roc2015			Serial	2686
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