Pedro de Alarcon - Academia.edu (original) (raw)
Uploads
Papers by Pedro de Alarcon
Journal of Structural Biology, 1999
Nowadays we are experiencing a remarkable growth in the number of databases that have become acce... more Nowadays we are experiencing a remarkable growth in the number of databases that have become accessible over the Web. However, in a certain number of cases, for example, in the case of BioImage, this information is not of a textual nature, thus posing new challenges in the design of tools to handle these data. In this work, we concentrate on the development of new mechanisms aimed at ''querying'' these databases of complex data sets by their intrinsic content, rather than by their textual annotations only. We concentrate our efforts on a subset of BioImage containing 3D images (volumes) of biological macromolecules, implementing a first prototype of a ''query-bycontent'' system. In the context of databases of complex data types the term query-by-content makes reference to those data modeling techniques in which userdefined functions aim at ''understanding'' (to some extent) the informational content of the data sets. In these systems the matching criteria introduced by the user are related to intrinsic features concerning the 3D images themselves, hence, complementing traditional queries by textual key words only. Efficient computational algorithms are required in order to ''extract'' structural information of the 3D images prior to storing them in the database. Also, easy-to-use interfaces should be implemented in order to obtain feedback from the expert. Our query-by-content prototype is used to construct a concrete query, making use of basic structural features, which are then evaluated over a set of three-dimensional images of biological macromolecules. This experimental implementation can be accessed via the Web at the BioImage server in Madrid
Biophysical Journal, 2002
In the present work we develop an efficient way of representing the geometry and topology of volu... more In the present work we develop an efficient way of representing the geometry and topology of volumetric datasets of biological structures from medium to low resolution, aiming at storing and querying them in a database framework. We make use of a new vector quantization algorithm to select the points within the macromolecule that best approximate the probability density function of the original volume data. Connectivity among points is obtained with the use of the alpha shapes theory. This novel data representation has a number of interesting characteristics, such as 1) it allows us to automatically segment and quantify a number of important structural features from low-resolution maps, such as cavities and channels, opening the possibility of querying large collections of maps on the basis of these quantitative structural features; 2) it provides a compact representation in terms of size; 3) it contains a subset of three-dimensional points that optimally quantify the densities of medium resolution data; and 4) a general model of the geometry and topology of the macromolecule (as opposite to a spatially unrelated bunch of voxels) is easily obtained by the use of the alpha shapes theory.
Tesis inédita de la Universidad Autónoma de Madrid, Escuela Politécnica Superior, 2002
El envejecimiento poblacional es un problema cada vez más acuciante para las sociedades desarroll... more El envejecimiento poblacional es un problema cada vez más acuciante para las sociedades desarrolladas dado el incremento en el gasto socio-sanitario que conlleva para las Administraciones Públicas. La aplicación de las TIC en el ámbito de la salud puede contribuir a paliar los efectos de esta situación. En el presente artículo se describe la Plataforma Virtual de Rehabilitación implementada en el marco del proyecto "Telerehabilitación en personas mayores". Dicha plataforma permite, a través de las TIC, la realización y seguimiento de terapias de rehabilitación de forma remota para pacientes con prótesis total de rodilla, una patología con elevada incidencia entre el colectivo de personas mayores. La Plataforma se basa en una arquitectura modular y escalable, preparada para ofrecer tratamiento a nuevas patologías.
Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003
Object recognition supported by user interaction for service robots
Lecture Notes in Computer Science, 2002
We describe a system for querying 3D model databases using the spin image representation as a sha... more We describe a system for querying 3D model databases using the spin image representation as a shape signature for objects depicted as triangular meshes. The spin image representation facilitates the task of aligning the query object with respect to matched models (coarsegrain registration). The main contribution of this work is the introduction of a three-level indexing schema based on artificial neural networks. The indexing schema improves significantly the efficiency in matching query spin images against those stored in the database. Our results are suitable for content-based retrieval in 3D general object databases. A particular application to molecular databases is also presented.
Nucleic Acids Research, 1999
Nowadays it is possible to unravel complex information at all levels of cellular organization by ... more Nowadays it is possible to unravel complex information at all levels of cellular organization by obtaining multi-dimensional image information. At the macromolecular level, three-dimensional (3D) electron microscopy, together with other techniques, is able to reach resolutions at the nanometer or subnanometer level. The information is delivered in the form of 3D volumes containing samples of a given function, for example, the electron density distribution within a given macromolecule. The same situation happens at the cellular level with the new forms of light microscopy, particularly confocal microscopy, all of which produce biological 3D volume information. Furthermore, it is possible to record sequences of images over time (videos), as well as sequences of volumes, bringing key information on the dynamics of living biological systems. It is in this context that work on BioImage started two years ago, and that its first version is now presented here. In essence, BioImage is a database specifically designed to contain multi-dimensional images, perform queries and interactively work with the resulting multi-dimensional information on the World Wide Web, as well as accomplish the required cross-database links. Two sister home pages of BioImage can be accessed at http://www.bioimage.org and http://www-embl.bioimage.org
The Journal of Pathology, 2007
Testicular germ cell tumours (GCTs) of adolescents and adults can be subdivided into seminomas (r... more Testicular germ cell tumours (GCTs) of adolescents and adults can be subdivided into seminomas (referred to as dysgerminomas of the ovary) and non-seminomas, all referred to as type II GCTs. They originate from carcinoma in situ (CIS), being the malignant counterparts of primordial germ cells (PGCs)/gonocytes. The invasive components mimic embryogenesis, including the stem cell component embryonal carcinoma (EC), the somatic lineage teratoma (TE), and the extra-embryonic tissues yolk sac tumour (YST) and choriocarcinoma (CH). The other type is the so-called spermatocytic seminomas (SS, type III GCT), composed of neoplastic primary spermatocytes. We reported previously that the miRNAs hsa-miR 371-373 cluster is involved in overruling cellular senescence induced by oncogenic stress, allowing cells to become malignant. Here we report the first high-throughput screen of 156 microRNAs in a series of type II and III GCTs (n = 69, in duplicate) using a quantitative PCR-based approach. After normalization to allow inter-sample analysis, the technical replicates clustered together, and the previous hsa-miRNA 371-373 cluster finding was confirmed. Unsupervised cluster analysis demonstrated that the cell lines are different from the in vivo samples. The in vivo samples, both normal and malignant, clustered predominantly based on their maturation status. This parallels normal embryogenesis, rather than chromosomal anomalies in the tumours. miRNAs within a single cluster showed a similar expression pattern, implying common regulatory mechanisms. Normal testicular tissue expressed most discriminating miRNAs at a higher level than SE and SS. Moreover, differentiated non-seminomas showed overexpression of discriminating miRNAs. These results support the model that miRNAs are involved in regulating differentiation of stem cells, retained in GCTs.
Journal of Structural Biology, 1999
The BioImage database is a new scientific database for multidimensional microscopic images of bio... more The BioImage database is a new scientific database for multidimensional microscopic images of biological specimens, which is available through the World Wide Web (WWW). The development of this database has followed an iterative approach, in which requirements and functionality have been revised and extended. The complexity and innovative use of the data meant that technical and biological expertise has been crucial in the initial design of the data model. A controlled vocabulary was introduced to ensure data consistency. Pointers are used to reference information stored in other databases. The data model was built using InfoModeler as a database design tool. The database management system is the Informix Dynamic Server with Universal Data Option. This object-relational system allows the handling of complex data using features such as collection types, inheritance, and userdefined data types. Informix datablades are used to provide additional functionality: the Web Integration Option enables WWW access to the database; the Video Foundation Blade provides functionality for video handling. 1999 Academic Press
Journal of Structural Biology, 1999
Nowadays we are experiencing a remarkable growth in the number of databases that have become acce... more Nowadays we are experiencing a remarkable growth in the number of databases that have become accessible over the Web. However, in a certain number of cases, for example, in the case of BioImage, this information is not of a textual nature, thus posing new challenges in the design of tools to handle these data. In this work, we concentrate on the development of new mechanisms aimed at ''querying'' these databases of complex data sets by their intrinsic content, rather than by their textual annotations only. We concentrate our efforts on a subset of BioImage containing 3D images (volumes) of biological macromolecules, implementing a first prototype of a ''query-bycontent'' system. In the context of databases of complex data types the term query-by-content makes reference to those data modeling techniques in which userdefined functions aim at ''understanding'' (to some extent) the informational content of the data sets. In these systems the matching criteria introduced by the user are related to intrinsic features concerning the 3D images themselves, hence, complementing traditional queries by textual key words only. Efficient computational algorithms are required in order to ''extract'' structural information of the 3D images prior to storing them in the database. Also, easy-to-use interfaces should be implemented in order to obtain feedback from the expert. Our query-by-content prototype is used to construct a concrete query, making use of basic structural features, which are then evaluated over a set of three-dimensional images of biological macromolecules. This experimental implementation can be accessed via the Web at the BioImage server in Madrid
Biophysical Journal, 2002
In the present work we develop an efficient way of representing the geometry and topology of volu... more In the present work we develop an efficient way of representing the geometry and topology of volumetric datasets of biological structures from medium to low resolution, aiming at storing and querying them in a database framework. We make use of a new vector quantization algorithm to select the points within the macromolecule that best approximate the probability density function of the original volume data. Connectivity among points is obtained with the use of the alpha shapes theory. This novel data representation has a number of interesting characteristics, such as 1) it allows us to automatically segment and quantify a number of important structural features from low-resolution maps, such as cavities and channels, opening the possibility of querying large collections of maps on the basis of these quantitative structural features; 2) it provides a compact representation in terms of size; 3) it contains a subset of three-dimensional points that optimally quantify the densities of medium resolution data; and 4) a general model of the geometry and topology of the macromolecule (as opposite to a spatially unrelated bunch of voxels) is easily obtained by the use of the alpha shapes theory.
Tesis inédita de la Universidad Autónoma de Madrid, Escuela Politécnica Superior, 2002
El envejecimiento poblacional es un problema cada vez más acuciante para las sociedades desarroll... more El envejecimiento poblacional es un problema cada vez más acuciante para las sociedades desarrolladas dado el incremento en el gasto socio-sanitario que conlleva para las Administraciones Públicas. La aplicación de las TIC en el ámbito de la salud puede contribuir a paliar los efectos de esta situación. En el presente artículo se describe la Plataforma Virtual de Rehabilitación implementada en el marco del proyecto "Telerehabilitación en personas mayores". Dicha plataforma permite, a través de las TIC, la realización y seguimiento de terapias de rehabilitación de forma remota para pacientes con prótesis total de rodilla, una patología con elevada incidencia entre el colectivo de personas mayores. La Plataforma se basa en una arquitectura modular y escalable, preparada para ofrecer tratamiento a nuevas patologías.
Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003
Object recognition supported by user interaction for service robots
Lecture Notes in Computer Science, 2002
We describe a system for querying 3D model databases using the spin image representation as a sha... more We describe a system for querying 3D model databases using the spin image representation as a shape signature for objects depicted as triangular meshes. The spin image representation facilitates the task of aligning the query object with respect to matched models (coarsegrain registration). The main contribution of this work is the introduction of a three-level indexing schema based on artificial neural networks. The indexing schema improves significantly the efficiency in matching query spin images against those stored in the database. Our results are suitable for content-based retrieval in 3D general object databases. A particular application to molecular databases is also presented.
Nucleic Acids Research, 1999
Nowadays it is possible to unravel complex information at all levels of cellular organization by ... more Nowadays it is possible to unravel complex information at all levels of cellular organization by obtaining multi-dimensional image information. At the macromolecular level, three-dimensional (3D) electron microscopy, together with other techniques, is able to reach resolutions at the nanometer or subnanometer level. The information is delivered in the form of 3D volumes containing samples of a given function, for example, the electron density distribution within a given macromolecule. The same situation happens at the cellular level with the new forms of light microscopy, particularly confocal microscopy, all of which produce biological 3D volume information. Furthermore, it is possible to record sequences of images over time (videos), as well as sequences of volumes, bringing key information on the dynamics of living biological systems. It is in this context that work on BioImage started two years ago, and that its first version is now presented here. In essence, BioImage is a database specifically designed to contain multi-dimensional images, perform queries and interactively work with the resulting multi-dimensional information on the World Wide Web, as well as accomplish the required cross-database links. Two sister home pages of BioImage can be accessed at http://www.bioimage.org and http://www-embl.bioimage.org
The Journal of Pathology, 2007
Testicular germ cell tumours (GCTs) of adolescents and adults can be subdivided into seminomas (r... more Testicular germ cell tumours (GCTs) of adolescents and adults can be subdivided into seminomas (referred to as dysgerminomas of the ovary) and non-seminomas, all referred to as type II GCTs. They originate from carcinoma in situ (CIS), being the malignant counterparts of primordial germ cells (PGCs)/gonocytes. The invasive components mimic embryogenesis, including the stem cell component embryonal carcinoma (EC), the somatic lineage teratoma (TE), and the extra-embryonic tissues yolk sac tumour (YST) and choriocarcinoma (CH). The other type is the so-called spermatocytic seminomas (SS, type III GCT), composed of neoplastic primary spermatocytes. We reported previously that the miRNAs hsa-miR 371-373 cluster is involved in overruling cellular senescence induced by oncogenic stress, allowing cells to become malignant. Here we report the first high-throughput screen of 156 microRNAs in a series of type II and III GCTs (n = 69, in duplicate) using a quantitative PCR-based approach. After normalization to allow inter-sample analysis, the technical replicates clustered together, and the previous hsa-miRNA 371-373 cluster finding was confirmed. Unsupervised cluster analysis demonstrated that the cell lines are different from the in vivo samples. The in vivo samples, both normal and malignant, clustered predominantly based on their maturation status. This parallels normal embryogenesis, rather than chromosomal anomalies in the tumours. miRNAs within a single cluster showed a similar expression pattern, implying common regulatory mechanisms. Normal testicular tissue expressed most discriminating miRNAs at a higher level than SE and SS. Moreover, differentiated non-seminomas showed overexpression of discriminating miRNAs. These results support the model that miRNAs are involved in regulating differentiation of stem cells, retained in GCTs.
Journal of Structural Biology, 1999
The BioImage database is a new scientific database for multidimensional microscopic images of bio... more The BioImage database is a new scientific database for multidimensional microscopic images of biological specimens, which is available through the World Wide Web (WWW). The development of this database has followed an iterative approach, in which requirements and functionality have been revised and extended. The complexity and innovative use of the data meant that technical and biological expertise has been crucial in the initial design of the data model. A controlled vocabulary was introduced to ensure data consistency. Pointers are used to reference information stored in other databases. The data model was built using InfoModeler as a database design tool. The database management system is the Informix Dynamic Server with Universal Data Option. This object-relational system allows the handling of complex data using features such as collection types, inheritance, and userdefined data types. Informix datablades are used to provide additional functionality: the Web Integration Option enables WWW access to the database; the Video Foundation Blade provides functionality for video handling. 1999 Academic Press