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Author |
Sergio Vera; Miguel Angel Gonzalez Ballester; Debora Gil |
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Title |
A medial map capturing the essential geometry of organs |
Type |
Conference Article |
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Year |
2012 |
Publication |
ISBI Workshop on Open Source Medical Image Analysis software |
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Pages |
1691 - 1694 |
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Keywords |
Medial Surface Representation, Volume Reconstruction,Geometry , Image reconstruction , Liver , Manifolds , Shape , Surface morphology , Surface reconstruction |
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Abstract |
Medial representations are powerful tools for describing and parameterizing the volumetric shape of anatomical structures. Accurate computation of one pixel wide medial surfaces is mandatory. Those surfaces must represent faithfully the geometry of the volume. Although morphological methods produce excellent results in 2D, their complexity and quality drops across dimensions, due to a more complex description of pixel neighborhoods. This paper introduces a continuous operator for accurate and efficient computation of medial structures of arbitrary dimension. Our experiments show its higher performance for medical imaging applications in terms of simplicity of medial structures and capability for reconstructing the anatomical volume |
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Barcelona,Spain |
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IEEE |
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1945-7928 |
ISBN |
978-1-4577-1857-1 |
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ISBI |
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IAM |
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IAM @ iam @ VGG2012a |
Serial |
1989 |
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Author |
Patricia Marquez;Debora Gil;Aura Hernandez-Sabate |
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Title |
A Complete Confidence Framework for Optical Flow |
Type |
Conference Article |
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Year |
2012 |
Publication |
12th European Conference on Computer Vision – Workshops and Demonstrations |
Abbreviated Journal |
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Volume |
7584 |
Issue |
2 |
Pages |
124-133 |
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Keywords |
Optical flow, confidence measures, sparsification plots, error prediction plots |
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Abstract |
Medial representations are powerful tools for describing and parameterizing the volumetric shape of anatomical structures. Existing 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 avoid degenerated medial axis segments; second, we introduce an energy based method which performs independently of the dimension. We evaluate quantitatively the performance of our method with respect to existing approaches, by applying them to synthetic shapes of known medial geometry. Finally, we show results on shape representation of multiple abdominal organs, exploring the use of medial manifolds for the representation of multi-organ relations. |
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Springer-Verlag |
Place of Publication |
Florence, Italy, October 7-13, 2012 |
Editor |
Andrea Fusiello, Vittorio Murino ,Rita Cucchiara |
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LNCS |
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978-3-642-33867-0 |
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ECCVW |
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IAM;ADAS; |
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Call Number |
IAM @ iam @ MGH2012b |
Serial |
1991 |
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Author |
Sergio Vera; Debora Gil; Agnes Borras; F. Javier Sanchez; Frederic Perez; Marius G. Linguraru |
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Title |
Computation and Evaluation of Medial Surfaces for Shape Representation of Abdominal Organs |
Type |
Conference Article |
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Year |
2011 |
Publication |
Workshop on Computational and Clinical Applications in Abdominal Imaging |
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Volume |
7029 |
Issue |
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Pages |
223-230 |
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Abstract |
Medial representations are powerful tools for describing and parameterizing the volumetric shape of anatomical structures. Existing 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 avoid degenerated medial axis segments; second, we introduce an energy based method which performs independently of the dimension. We evaluate quantitatively the performance of our method with respect to existing approaches, by applying them to synthetic shapes of known medial geometry. Finally, we show results on shape representation of multiple abdominal organs, exploring the use of medial manifolds for the representation of multi-organ relations. |
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Nice, France |
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Springer Berlin Heidelberg |
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In H. Yoshida et al |
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ABDI |
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IAM; MV |
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no |
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Call Number |
VGB2011 |
Serial |
2036 |
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Author |
Carles Sanchez; Debora Gil; Antoni Rosell; Albert Andaluz; F. Javier Sanchez |
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Title |
Segmentation of Tracheal Rings in Videobronchoscopy combining Geometry and Appearance |
Type |
Conference Article |
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Year |
2013 |
Publication |
Proceedings of the International Conference on Computer Vision Theory and Applications |
Abbreviated Journal |
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Volume |
1 |
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Pages |
153--161 |
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Keywords |
Video-bronchoscopy, tracheal ring segmentation, trachea geometric and appearance model |
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Abstract |
Videobronchoscopy is a medical imaging technique that allows interactive navigation inside the respiratory pathways and minimal invasive interventions. Tracheal procedures are ordinary interventions that require measurement of the percentage of obstructed pathway for injury (stenosis) assessment. Visual assessment of stenosis in videobronchoscopic sequences requires high expertise of trachea anatomy and is prone to human error. Accurate detection of tracheal rings is the basis for automated estimation of the size of stenosed trachea. Processing of videobronchoscopic images acquired at the operating room is a challenging task due to the wide range of artifacts and acquisition conditions. We present a model of the geometric-appearance of tracheal rings for its detection in videobronchoscopic videos. Experiments on sequences acquired at the operating room, show a performance close to inter-observer variability |
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Barcelona; February 2013 |
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SciTePress |
Place of Publication |
Portugal |
Editor |
Sebastiano Battiato and José Braz |
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978-989-8565-47-1 |
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800 |
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Conference |
VISAPP |
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Notes |
IAM;MV; 600.044; 600.047; 600.060; 605.203 |
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no |
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Call Number |
IAM @ iam @ SGR2013 |
Serial |
2123 |
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Author |
David Roche; Debora Gil; Jesus Giraldo |
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Title |
Multiple active receptor conformation, agonist efficacy and maximum effect of the system: the conformation-based operational model of agonism, |
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Journal Article |
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Year |
2013 |
Publication |
Drug Discovery Today |
Abbreviated Journal |
DDT |
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Volume |
18 |
Issue |
7-8 |
Pages |
365-371 |
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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. |
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Elsevier |
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IAM; 600.057; 600.054 |
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no |
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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 |
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Title |
Geometric Steerable Medial Maps |
Type |
Journal Article |
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Year |
2013 |
Publication |
Machine Vision and Applications |
Abbreviated Journal |
MVA |
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Volume |
24 |
Issue |
6 |
Pages |
1255-1266 |
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Keywords |
Medial Representations ,Medial Manifolds Comparation , Surface , Reconstruction |
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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. |
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Publisher |
Springer Berlin Heidelberg |
Place of Publication |
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Editor |
Mubarak Shah |
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0932-8092 |
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Notes |
IAM; 605.203; 600.060; 600.044 |
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no |
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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 |
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Title |
Helical structure of the cardiac ventricular anatomy assessed by Diffusion Tensor Magnetic Resonance Imaging multi-resolution tractography |
Type |
Journal Article |
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Year |
2013 |
Publication |
Revista Española de Cardiología |
Abbreviated Journal |
REC |
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Volume |
66 |
Issue |
10 |
Pages |
782-790 |
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Keywords |
Heart;Diffusion magnetic resonance imaging;Diffusion tractography;Helical heart;Myocardial ventricular band. |
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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. |
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Elsevier |
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IAM; 600.044; 600.060 |
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no |
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IAM @ iam @ PGM2013 |
Serial |
2194 |
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Author |
David Roche; Debora Gil; Jesus Giraldo |
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Title |
Mechanistic analysis of the function of agonists and allosteric modulators: Reconciling two-state and operational models |
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Journal Article |
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Year |
2013 |
Publication |
British Journal of Pharmacology |
Abbreviated Journal |
BJP |
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Volume |
169 |
Issue |
6 |
Pages |
1189-202 |
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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. |
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Notes |
IAM; 600.044; 605.203 |
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no |
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Call Number |
IAM @ iam @ RGG2013b |
Serial |
2195 |
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Author |
Joan M. Nuñez; Debora Gil; Fernando Vilariño |
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Title |
Finger joint characterization from X-ray images for rheymatoid arthritis assessment |
Type |
Conference Article |
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Year |
2013 |
Publication |
6th International Conference on Biomedical Electronics and Devices |
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Pages |
288-292 |
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Keywords |
Rheumatoid Arthritis; X-Ray; Hand Joint; Sclerosis; Sharp Van der Heijde |
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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. |
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Address |
Barcelona; February 2013 |
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SciTePress |
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800 |
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BIODEVICES |
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Notes |
IAM;MV; 600.057; 600.054;SIAI |
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no |
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Call Number |
IAM @ iam @ NGV2013 |
Serial |
2196 |
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Author |
David Roche; Debora Gil; Jesus Giraldo |
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Title |
Mathematical modeling of G protein-coupled receptor function: What can we learn from empirical and mechanistic models? |
Type |
Book Chapter |
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Year |
2014 |
Publication |
G Protein-Coupled Receptors – Modeling and Simulation Advances in Experimental Medicine and Biology |
Abbreviated Journal |
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Volume |
796 |
Issue |
3 |
Pages |
159-181 |
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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 |
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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. |
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Springer Netherlands |
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0065-2598 |
ISBN |
978-94-007-7422-3 |
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IAM; 600.075 |
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Call Number |
IAM @ iam @ RGG2014 |
Serial |
2197 |
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