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| Author | Mariano Vazquez; Ruth Aris; Guillaume Hozeaux; R.Aubry; P.Villar;Jaume Garcia ; Debora Gil; Francesc Carreras | ||||
| Title | A massively parallel computational electrophysiology model of the heart | Type | Journal Article | ||
| Year | 2011 | Publication | International Journal for Numerical Methods in Biomedical Engineering | Abbreviated Journal | IJNMBE |
| Volume | 27 | Issue | Pages | 1911-1929 | |
| Keywords | computational electrophysiology; parallelization; finite element methods | ||||
| Abstract | This paper presents a patient-sensitive simulation strategy capable of using the most efficient way the high-performance computational resources. The proposed strategy directly involves three different players: Computational Mechanics Scientists (CMS), Image Processing Scientists and Cardiologists, each one mastering its own expertise area within the project. This paper describes the general integrative scheme but focusing on the CMS side presents a massively parallel implementation of computational electrophysiology applied to cardiac tissue simulation. The paper covers different angles of the computational problem: equations, numerical issues, the algorithm and parallel implementation. The proposed methodology is illustrated with numerical simulations testing all the different possibilities, ranging from small domains up to very large ones. A key issue is the almost ideal scalability not only for large and complex problems but also for medium-size meshes. The explicit formulation is particularly well suited for solving this highly transient problems, with very short time-scale. | ||||
| Address | Swansea (UK) | ||||
| Corporate Author | John Wiley & Sons, Ltd. | Thesis | |||
| Publisher | John Wiley & Sons, Ltd. | Place of Publication | Editor | ||
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IAM | Approved | no | ||
| Call Number | IAM @ iam @ VAH2011 | Serial | 1198 | ||
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| Author | Albert Andaluz; Francesc Carreras; Debora Gil; Jaume Garcia | ||||
| Title | Una aplicació amigable pel càlcul de indicadors clínics del ventricle esquerre | Type | Miscellaneous | ||
| Year | 2010 | Publication | Forum Biocat 2010 | Abbreviated Journal | |
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| Address | Lonja de Mar,Barcelona (Spain) | ||||
| Corporate Author | CVC | Thesis | |||
| Publisher | Biocat | Place of Publication | Barcelona | Editor | |
| Language | Catalan | Summary Language | Original Title | ||
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IAM | Approved | no | ||
| Call Number | IAM @ iam @ ACG2010 | Serial | 1483 | ||
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| Author | J.L.Bruguera; R.Casado; M.Martinez; I.Corral; Enric Marti; L.A.Branda | ||||
| Title | El apoyo institucional como elemento favorecedor de la coordinación docente: experiencias en diferentes universidades | Type | Miscellaneous | ||
| Year | 2009 | Publication | Revista Red-U | Abbreviated Journal | |
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IAM | Approved | no | ||
| Call Number | IAM @ iam @ BCM2009 | Serial | 1490 | ||
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| Author | G.Estape; Enric Marti | ||||
| Title | L’ús d’aplicacions de visualització 3D com a eina d’aprenenetatge en activitats formatives dirigides i autònomes: el cas del programa Bluestar | Type | Miscellaneous | ||
| Year | 2008 | Publication | V Jornades d’Innovació Docent UAB | Abbreviated Journal | |
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IAM | Approved | no | ||
| Call Number | IAM @ iam @ ESM2008 | Serial | 1495 | ||
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| Author | Paula Fritzsche; C.Roig; Ana Ripoll; Emilio Luque; Aura Hernandez-Sabate | ||||
| Title | A Performance Prediction Methodology for Data-dependent Parallel Applications | Type | Conference Article | ||
| Year | 2006 | Publication | Proceedings of the IEEE International Conference on Cluster Computing | Abbreviated Journal | |
| Volume | Issue | Pages | 1-8 | ||
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| Abstract | The increase in the use of parallel distributed architectures in order to solve large-scale scientific problems has generated the need for performance prediction for both deterministic applications and non-deterministic applications. In particular, the performance prediction of data dependent programs is an extremely challenging problem because for a specific issue the input datasets may cause different execution times. Generally, a parallel application is characterized as a collection of tasks and their interrelations. If the application is time-critical it is not enough to work with only one value per task, and consequently knowledge of the distribution of task execution times is crucial. The development of a new prediction methodology to estimate the performance of data-dependent parallel applications is the primary target of this study. This approach makes it possible to evaluate the parallel performance of an application without the need of implementation. A real data-dependent arterial structure detection application model is used to apply the methodology proposed. The predicted times obtained using the new methodology for genuine datasets are compared with predicted times that arise from using only one execution value per task. Finally, the experimental study shows that the new methodology generates more precise predictions. | ||||
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IAM | Approved | no | ||
| Call Number | IAM @ iam @ FRR2006 | Serial | 1497 | ||
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| Author | Jaume Garcia | ||||
| Title | Statistical Models of the Architecture and Function of the Left Ventricle | Type | Book Whole | ||
| Year | 2009 | Publication | PhD Thesis, Universitat Autonoma de Barcelona-CVC | Abbreviated Journal | |
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| Abstract | Cardiovascular Diseases, specially those affecting the Left Ventricle (LV), are the leading cause of death in developed countries with approximately a 30% of all global deaths. In order to address this public health concern, physicians focus on diagnosis and therapy planning. On one hand, early and accurate detection of Regional Wall Motion Abnormalities (RWMA) significantly contributes to a quick diagnosis and prevents the patient to reach more severe stages. On the other hand, a thouroughly knowledge of the normal gross anatomy of the LV, as well as, the distribution of its muscular fibers is crucial for designing specific interventions and therapies (such as pacemaker implanction). Statistical models obtained from the analysis of different imaging modalities allow the computation of the normal ranges of variation within a given population. Normality models are a valuable tool for the definition of objective criterions quantifying the degree of (anomalous) deviation of the LV function and anatomy for a given subject. The creation of statistical models involve addressing three main issues: extraction of data from images, definition of a common domain for comparison of data across patients and designing appropriate statistical analysis schemes. In this PhD thesis we present generic image processing tools for the creation of statistical models of the LV anatomy and function. On one hand, we use differential geometry concepts to define a computational framework (the Normalized Parametric Domain, NPD) suitable for the comparison and fusion of several clinical scores obtained over the LV. On the other hand, we present a variational approach (the Harmonic Phase Flow, HPF) for the estimation of myocardial motion that provides dense and continuous vector fields without overestimating motion at injured areas. These tools are used for the creation of statistical models. Regarding anatomy, we obtain an atlas jointly modelling, both, LV gross anatomy and fiber architecture. Regarding function, we compute normality patterns of scores characterizing the (global and local) LV function and explore, for the first time, the configuration of local scores better suited for RWMA detection. | ||||
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| Corporate Author | Thesis | Ph.D. thesis | |||
| Publisher | Ediciones Graficas Rey | Place of Publication | Editor | Debora Gil | |
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IAM | Approved | no | ||
| Call Number | IAM @ iam @ Gar2009a | Serial | 1499 | ||
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| Author | Jaume Garcia; Debora Gil; Francesc Carreras ; Sandra Pujades; R.Leta; Xavier Alomar; Guillem Pons-LLados | ||||
| Title | Un Model 3D del Ventricle Esquerre Integrant Anatomia i Funcionalitat | Type | Conference Article | ||
| Year | 2008 | Publication | XX Congrés de la Societat Catalana de Cardiologia, Actes del Congres | Abbreviated Journal | |
| Volume | Issue | Pages | 122 | ||
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| Abstract | Els canvis en la dinàmica del Ventricle Esquerre (VE) reflecteixen la majoria de malalties cardiovasculars . Els avenços en imatge mèdica han impulsat la recerca en models i simulacions de la dinàmica 3D del VE . La majoria dels models existents sols consideren l’anatomia externa del VE i no permeten una avaluació de l’acoblament electromecànic . Donat que la mecànica d’un muscle depèn de la orientació de les seves fibres, un model realista hauria d’incloure la disposició espacial de la banda ventricular helicoidal (BVH) .
Proposem desenvolupar un model del VE adaptat a cada pacient que integri, per primer cop, l’anatomia de la banda ventricular, l’anatomia externa del VE i la seva funcionalitat, per a una millor determinació del patró d’activació electromecànica |
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| Publisher | Place of Publication | Barcelona | Editor | ||
| Language | catalan | Summary Language | catalan | Original Title | |
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IAM | Approved | no | ||
| Call Number | IAM @ iam @ GGC2008c | Serial | 1504 | ||
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| Author | Jaume Garcia; Debora Gil; Francesc Carreras; Sandra Pujades; R.Leta | ||||
| Title | Modelització 4-Dimensional de la Funció Siatólica del Ventricle Esquerre | Type | Conference Article | ||
| Year | 2007 | Publication | XIX Congrés de la Societat Catalana de Cardiologia de Barcelona | Abbreviated Journal | |
| Volume | Issue | Pages | 133-134 | ||
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| Abstract | L’evolució tecnològica en el tractament de les imatges mèdiques permet reconstruir, amb el software apropiat, imatges tridimensionals de les estructures cardiovasculars i dotar-les de moviment. Les imatges 4D resultants faciliten l’estudi de la fisiopatologia de la insuficiència cardíaca en base als transtorns de l’activació electromecànica ventricular, el que pot ser d’interès en el procés de selecció de pacients candidats a teràpies de resincronització. Presentem els resultats preliminars de la reconstrucció 4D del ventricle esquerre (VE) a partir de les seqüències de tagging miocàrdic del VE. | ||||
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| Publisher | Place of Publication | Barcelona (Spain) | Editor | ||
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IAM | Approved | no | ||
| Call Number | IAM @ iam @ GGC2007 | Serial | 1505 | ||
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| Author | Jaume Garcia; Debora Gil; Luis Badiella; Aura Hernandez-Sabate; Francesc Carreras; Sandra Pujades; Enric Marti | ||||
| Title | A Normalized Framework for the Design of Feature Spaces Assessing the Left Ventricular Function | Type | Journal Article | ||
| Year | 2010 | Publication | IEEE Transactions on Medical Imaging | Abbreviated Journal | TMI |
| Volume | 29 | Issue | 3 | Pages | 733-745 |
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| Abstract | A through description of the left ventricle functionality requires combining complementary regional scores. A main limitation is the lack of multiparametric normality models oriented to the assessment of regional wall motion abnormalities (RWMA). This paper covers two main topics involved in RWMA assessment. We propose a general framework allowing the fusion and comparison across subjects of different regional scores. Our framework is used to explore which combination of regional scores (including 2-D motion and strains) is better suited for RWMA detection. Our statistical analysis indicates that for a proper (within interobserver variability) identification of RWMA, models should consider motion and extreme strains. | ||||
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| ISSN | 0278-0062 | ISBN | Medium | ||
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| Notes |
IAM | Approved | no | ||
| Call Number | IAM @ iam @ GGH2010b | Serial | 1507 | ||
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| Author | Jaume Garcia; Debora Gil; A.Bajo; M.J.Ledesma-Carbayo; C.SantaMarta | ||||
| Title | Influence of the temporal resolution on the quantification of displacement fields in cardiac magnetic resonance tagged images | Type | Conference Article | ||
| Year | 2008 | Publication | Proc. Computers in Cardiology | Abbreviated Journal | |
| Volume | 35 | Issue | Pages | 785-788 | |
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| Abstract | It is difficult to acquire tagged cardiac MR images with a high temporal and spatial resolution using clinical MR scanners. However, if such images are used for quantifying scores based on motion, it is essential a resolution as high as possible. This paper explores the influence of the temporal resolution of a tagged series on the quantification of myocardial dynamic parameters. To such purpose we have designed a SPAMM (Spatial Modulation of Magnetization) sequence allowing acquisition of sequences at simple and double temporal resolution. Sequences are processed to compute myocardial motion by an automatic technique based on the tracking of the harmonic phase of tagged images (the Harmonic Phase Flow, HPF). The results have been compared to manual tracking of myocardial tags. The error in displacement fields for double resolution sequences reduces 17%. | ||||
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| Publisher | Place of Publication | Editor | Alan Murray | ||
| Language | Summary Language | Original Title | |||
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| Notes |
IAM | Approved | no | ||
| Call Number | IAM @ iam @ GGB2008 | Serial | 1508 | ||
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| Author | Jaume Garcia; Francesc Carreras; Sandra Pujades; Debora Gil | ||||
| Title | Regional motion patterns for the Left Ventricle function assessment | Type | Conference Article | ||
| Year | 2008 | Publication | Proc. 19th Int. Conf. Pattern Recognition ICPR 2008 | Abbreviated Journal | |
| Volume | Issue | Pages | 1-4 | ||
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| Abstract | Regional scores (e.g. strain, perfusion) of the Left Ventricle (LV) functionality are playing an increasing role in the diagnosis of cardiac diseases. A main limitation is the lack of normality models for complementary scores oriented to assessment of the LV integrity. This paper introduces an original framework based on a parametrization of the LV domain, which allows comparison across subjects of local physiological measures of different nature. We compute regional normality patterns in a feature space characterizing the LV function. We show the consistency of the model for the regional motion on healthy and hypokinetic pathological cases | ||||
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IAM | Approved | no | ||
| Call Number | IAM @ iam @ GCP2008 | Serial | 1510 | ||
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| Author | Jaume Garcia; Albert Andaluz; Debora Gil; Francesc Carreras | ||||
| Title | Decoupled External Forces in a Predictor-Corrector Segmentation Scheme for LV Contours in Tagged MR Images | Type | Conference Article | ||
| Year | 2010 | Publication | 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society | Abbreviated Journal | |
| Volume | Issue | Pages | 4805-4808 | ||
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| Abstract | Computation of functional regional scores requires proper identification of LV contours. On one hand, manual segmentation is robust, but it is time consuming and requires high expertise. On the other hand, the tag pattern in TMR sequences is a problem for automatic segmentation of LV boundaries. We propose a segmentation method based on a predictorcorrector (Active Contours – Shape Models) scheme. Special stress is put in the definition of the AC external forces. First, we introduce a semantic description of the LV that discriminates myocardial tissue by using texture and motion descriptors. Second, in order to ensure convergence regardless of the initial contour, the external energy is decoupled according to the orientation of the edges in the image potential. We have validated the model in terms of error in segmented contours and accuracy of regional clinical scores. | ||||
| Address | Buenos Aires (Argentina) | ||||
| Corporate Author | IEEE EMB | Thesis | |||
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| ISSN | 1557-170X | ISBN | 978-1-4244-4123-5 | Medium | |
| Area | Expedition | Conference | EMBC | ||
| Notes |
IAM | Approved | no | ||
| Call Number | IAM @ iam @ GAG2010 | Serial | 1514 | ||
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| Author | Jaume Garcia; Debora Gil; Aura Hernandez-Sabate | ||||
| Title | Endowing Canonical Geometries to Cardiac Structures | Type | Book Chapter | ||
| Year | 2010 | Publication | Statistical Atlases And Computational Models Of The Heart | Abbreviated Journal | |
| Volume | 6364 | Issue | Pages | 124-133 | |
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| Abstract | International conference on Cardiac electrophysiological simulation challenge
In this paper, we show that canonical (shape-based) geometries can be endowed to cardiac structures using tubular coordinates defined over their medial axis. We give an analytic formulation of these geometries by means of B-Splines. Since B-Splines present vector space structure PCA can be applied to their control points and statistical models relating boundaries and the interior of the anatomical structures can be derived. We demonstrate the applicability in two cardiac structures, the 3D Left Ventricular volume, and the 2D Left-Right ventricle set in 2D Short Axis view. |
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| Publisher | Springer Berlin / Heidelberg | Place of Publication | Editor | Camara, O.; Pop, M.; Rhode, K.; Sermesant, M.; Smith, N.; Young, A. | |
| Language | Summary Language | Original Title | |||
| Series Editor | Series Title | Lecture Notes in Computer Science | Abbreviated Series Title | LNCS | |
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IAM | Approved | no | ||
| Call Number | IAM @ iam @ GGH2010b | Serial | 1515 | ||
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| Author | Debora Gil; Jaume Garcia; Ruth Aris; Guillaume Houzeaux; Manuel Vazquez | ||||
| Title | A Riemmanian approach to cardiac fiber architecture modelling | Type | Conference Article | ||
| Year | 2009 | Publication | 1st International Conference on Mathematical & Computational Biomedical Engineering | Abbreviated Journal | |
| Volume | Issue | Pages | 59-62 | ||
| Keywords | cardiac fiber architecture; diffusion tensor magnetic resonance imaging; differential (Rie- mannian) geometry. | ||||
| Abstract | There is general consensus that myocardial fiber architecture should be modelled in order to fully understand the electromechanical properties of the Left Ventricle (LV). Diffusion Tensor magnetic resonance Imaging (DTI) is the reference image modality for rapid measurement of fiber orientations by means of the tensor principal eigenvectors. In this work, we present a mathematical framework for across subject comparison of the local geometry of the LV anatomy including the fiber architecture from the statistical analysis of DTI studies. We use concepts of differential geometry for defining a parametric domain suitable for statistical analysis of a low number of samples. We use Riemannian metrics to define a consistent computation of DTI principal eigenvector modes of variation. Our framework has been applied to build an atlas of the LV fiber architecture from 7 DTI normal canine hearts. | ||||
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| Publisher | Place of Publication | Swansea (UK) | Editor | Nithiarasu, R.L.R.V.L. | |
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| Area | Expedition | Conference | CMBE | ||
| Notes |
IAM | Approved | no | ||
| Call Number | IAM @ iam @ FGA2009 | Serial | 1520 | ||
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| Author | Debora Gil; Jaume Garcia; Manuel Vazquez; Ruth Aris; Guillaume Houzeaux | ||||
| Title | Patient-Sensitive Anatomic and Functional 3D Model of the Left Ventricle Function | Type | Conference Article | ||
| Year | 2008 | Publication | 8th World Congress on Computational Mechanichs (WCCM8)/5th European Congress on Computational Methods in Applied Sciences and Engineering (ECCOMAS 2008) | Abbreviated Journal | |
| Volume | Issue | Pages | |||
| Keywords | Left Ventricle; Electromechanical Models; Image Processing; Magnetic Resonance. | ||||
| Abstract | Early diagnosis and accurate treatment of Left Ventricle (LV) dysfunction significantly increases the patient survival. Impairment of LV contractility due to cardiovascular diseases is reflected in its motion patterns. Recent advances in medical imaging, such as Magnetic Resonance (MR), have encouraged research on 3D simulation and modelling of the LV dynamics. Most of the existing 3D models consider just the gross anatomy of the LV and restore a truncated ellipse which deforms along the cardiac cycle. The contraction mechanics of any muscle strongly depends on the spatial orientation of its muscular fibers since the motion that the muscle undergoes mainly takes place along the fibers. It follows that such simplified models do not allow evaluation of the heart electro-mechanical function and coupling, which has recently risen as the key point for understanding the LV functionality . In order to thoroughly understand the LV mechanics it is necessary to consider the complete anatomy of the LV given by the orientation of the myocardial fibres in 3D space as described by Torrent Guasp. We propose developing a 3D patient-sensitive model of the LV integrating, for the first time, the ven- tricular band anatomy (fibers orientation), the LV gross anatomy and its functionality. Such model will represent the LV function as a natural consequence of its own ventricular band anatomy. This might be decisive in restoring a proper LV contraction in patients undergoing pace marker treatment. The LV function is defined as soon as the propagation of the contractile electromechanical pulse has been modelled. In our experiments we have used the wave equation for the propagation of the electric pulse. The electromechanical wave moves on the myocardial surface and should have a conductivity tensor oriented along the muscular fibers. Thus, whatever mathematical model for electric pulse propa- gation [4] we consider, the complete anatomy of the LV should be extracted. The LV gross anatomy is obtained by processing multi slice MR images recorded for each patient. Information about the myocardial fibers distribution can only be extracted by Diffusion Tensor Imag- ing (DTI), which can not provide in vivo information for each patient. As a first approach, we have computed an average model of fibers from several DTI studies of canine hearts. This rough anatomy is the input for our electro-mechanical propagation model simulating LV dynamics. The average fiber orientation is updated until the simulated LV motion agrees with the experimental evidence provided by the LV motion observed in tagged MR (TMR) sequences. Experimental LV motion is recovered by applying image processing, differential geometry and interpolation techniques to 2D TMR slices [5]. The pipeline in figure 1 outlines the interaction between simulations and experimental data leading to our patient-tailored model. | ||||
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| Publisher | Place of Publication | Venezia (Italia) | Editor | ||
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| Series Volume | Series Issue | Edition | |||
| ISSN | B-31470-08 | ISBN | Medium | ||
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| Notes |
IAM | Approved | no | ||
| Call Number | IAM @ iam @ GGV2008c | Serial | 1521 | ||
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