The Experts below are selected from a list of 117 Experts worldwide ranked by ideXlab platform
Mariaesther Vidal - One of the best experts on this subject based on the ideXlab platform.
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Decomposing federated queries in presence of replicated fragments
Journal of Web Semantics, 2016Co-Authors: Gabriela Montoya, Hala Skaf-molli, Pascal Molli, Mariaesther VidalAbstract:Abstract Federated query engines allow for linked data consumption using SPARQL endpoints. Replicating data fragments from different sources enables data re-organization and provides the basis for more effective and efficient federated query processing. However, existing federated query engines are not designed to support replication. In this paper, we propose a replication-aware framework named LILAC , sparqL query decomposItion against federations of repLicAted data sourCes, that relies on replicated fragment descriptions to accurately identify sources that provide replicated data. We defined the query decomposition problem with fragment replication (QDP-FR). QDP-FR corresponds to the problem of finding the sub-queries to be sent to the endpoints that allows the federated query engine to compute the query answer, while the number of tuples to be transferred from endpoints to the federated query engine is minimized. An approximation of QDP-FR is implemented by the LILAC replication-aware query decomposition algorithm. Further, LILAC techniques have been included in the state-of-the-art federated query engines FedX and Anapsid to evaluate the benefits of the proposed source selection and query decomposition techniques in different engines. Experimental results suggest that LILAC efficiently solves QDP-FR and is able to reduce the number of transferred tuples and the execution time of the studied engines.
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International Semantic Web Conference (1) - Federated SPARQL Queries Processing with Replicated Fragments
The Semantic Web - ISWC 2015, 2015Co-Authors: Gabriela Montoya, Hala Skaf-molli, Pascal Molli, Mariaesther VidalAbstract:Federated query engines provide a unified query interface to federations of SPARQL endpoints. Replicating data fragments from different Linked Data sources facilitates data re-organization to better fit federated query processing needs of data consumers. However, existing federated query engines are not designed to support replication and replicated data can negatively impact their performance. In this paper, we formulate the source selection problem with fragment replication SSP-FR. For a given set of endpoints with replicated fragments and a SPARQL query, the problem is to select the endpoints that minimize the number of tuples to be transferred. We devise the Fedra source selection algorithm that approximates SSP-FR. We implement Fedra in the state-of-the-art federated query engines FedX and Anapsid, and empirically evaluate their performance. Experimental results suggest that Fedra efficiently solves SSP-FR, reducing the number of selected SPARQL endpoints as well as the size of query intermediate results.
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Efficient Query Processing for SPARQL Federations with Replicated Fragments
arXiv: Databases, 2015Co-Authors: Gabriela Montoya, Hala Skaf-molli, Pascal Molli, Mariaesther VidalAbstract:Low reliability and availability of public SPARQL endpoints prevent real-world applications from exploiting all the potential of these querying infras-tructures. Fragmenting data on servers can improve data availability but degrades performance. Replicating fragments can offer new tradeoff between performance and availability. We propose FEDRA, a framework for querying Linked Data that takes advantage of client-side data replication, and performs a source selection algorithm that aims to reduce the number of selected public SPARQL endpoints, execution time, and intermediate results. FEDRA has been implemented on the state-of-the-art query engines Anapsid and FedX, and empirically evaluated on a variety of real-world datasets.
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Anapsid an adaptive query processing engine for sparql endpoints
International Semantic Web Conference, 2011Co-Authors: Maribel Acosta, Mariaesther Vidal, Tomas Lampo, Julio Castillo, Edna RuckhausAbstract:Following the design rules of Linked Data, the number of available SPARQL endpoints that support remote query processing is quickly growing; however, because of the lack of adaptivity, query executions may frequently be unsuccessful. First, fixed plans identified following the traditional optimize-thenexecute paradigm, may timeout as a consequence of endpoint availability. Second, because blocking operators are usually implemented, endpoint query engines are not able to incrementally produce results, and may become blocked if data sources stop sending data. We present Anapsid, an adaptive query engine for SPARQL endpoints that adapts query execution schedulers to data availability and run-time conditions. Anapsid provides physical SPARQL operators that detect when a source becomes blocked or data traffic is bursty, and opportunistically, the operators produce results as quickly as data arrives from the sources. Additionally, Anapsid operators implement main memory replacement policies to move previously computed matches to secondary memory avoiding duplicates. We compared Anapsid performance with respect to RDF stores and endpoints, and observed that Anapsid speeds up execution time, in some cases, in more than one order of magnitude.
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International Semantic Web Conference (1) - Anapsid: an adaptive query processing engine for SPARQL endpoints
The Semantic Web – ISWC 2011, 2011Co-Authors: Maribel Acosta, Mariaesther Vidal, Tomas Lampo, Julio Castillo, Edna RuckhausAbstract:Following the design rules of Linked Data, the number of available SPARQL endpoints that support remote query processing is quickly growing; however, because of the lack of adaptivity, query executions may frequently be unsuccessful. First, fixed plans identified following the traditional optimize-thenexecute paradigm, may timeout as a consequence of endpoint availability. Second, because blocking operators are usually implemented, endpoint query engines are not able to incrementally produce results, and may become blocked if data sources stop sending data. We present Anapsid, an adaptive query engine for SPARQL endpoints that adapts query execution schedulers to data availability and run-time conditions. Anapsid provides physical SPARQL operators that detect when a source becomes blocked or data traffic is bursty, and opportunistically, the operators produce results as quickly as data arrives from the sources. Additionally, Anapsid operators implement main memory replacement policies to move previously computed matches to secondary memory avoiding duplicates. We compared Anapsid performance with respect to RDF stores and endpoints, and observed that Anapsid speeds up execution time, in some cases, in more than one order of magnitude.
Axel Meyer - One of the best experts on this subject based on the ideXlab platform.
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The evolutionary position of turtles revised
Naturwissenschaften, 2001Co-Authors: Rafael Zardoya, Axel MeyerAbstract:Consensus on the evolutionary position of turtles within the amniote phylogeny has eluded evolutionary biologists for more than a century. This phylogenetic problem has remained unsolved partly because turtles have such a unique morphology that only few characters can be used to link them with any other group of amniotes. Among the many alternative hypotheses that have been postulated to explain the origin and phylogenetic relationships of turtles, a general agreement among paleontologists emerged in favoring the placement of turtles as the only living survivors of the Anapsid reptiles (those that lack temporal fenestrae in the skull). However, recent morphological and molecular studies have radically changed our view of amniote phylogenetic relationships, and evidence is accumulating that supports the diapsid affinities of turtles. Molecular studies favor archosaurs (crocodiles and birds) as the living sister group of turtles, whereas morphological studies support lepidosaurs (tuatara, lizards, and snakes) as the closest living relatives of turtles. Accepting these hypotheses implies that turtles cannot be viewed any longer as primitive reptiles, and that they might have lost the temporal holes in the skull secondarily rather than never having had them.
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complete mitochondrial genome suggests diapsid affinities of turtles
Proceedings of the National Academy of Sciences of the United States of America, 1998Co-Authors: Rafael Zardoya, Axel MeyerAbstract:Despite more than a century of debate, the evolutionary position of turtles (Testudines) relative to other amniotes (reptiles, birds, and mammals) remains uncertain. One of the major impediments to resolving this important evolutionary problem is the highly distinctive and enigmatic morphology of turtles that led to their traditional placement apart from diapsid reptiles as sole descendants of presumably primitive Anapsid reptiles. To address this question, the complete (16,787-bp) mitochondrial genome sequence of the African side-necked turtle (Pelomedusa subrufa) was determined. This molecule contains several unusual features: a (TA)n microsatellite in the control region, the absence of an origin of replication for the light strand in the WANCY region of five tRNA genes, an unusually long noncoding region separating the ND5 and ND6 genes, an overlap between ATPase 6 and COIII genes, and the existence of extra nucleotides in ND3 and ND4L putative ORFs. Phylogenetic analyses of the complete mitochondrial genome sequences supported the placement of turtles as the sister group of an alligator and chicken (Archosauria) clade. This result clearly rejects the Haematothermia hypothesis (a sister-group relationship between mammals and birds), as well as rejecting the placement of turtles as the most basal living amniotes. Moreover, evidence from both complete mitochondrial rRNA genes supports a sister-group relationship of turtles to Archosauria to the exclusion of Lepidosauria (tuatara, snakes, and lizards). These results challenge the classic view of turtles as the only survivors of primary Anapsid reptiles and imply that turtles might have secondarily lost their skull fenestration.
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complete mitochondrial genome suggests diapsid affinities of turtles pelomedusa subrufayphylogenyyamniotayAnapsids
1998Co-Authors: Rafael Zardoya, Axel MeyerAbstract:Despite more than a century of debate, the evolutionary position of turtles (Testudines) relative to other amniotes (reptiles, birds, and mammals) remains uncertain. One of the major impediments to resolving this important evolutionary problem is the highly distinctive and enigmatic morphology of turtles that led to their traditional placement apart from diapsid reptiles as sole descendants of presumably primitive Anapsid reptiles. To address this question, the complete (16,787-bp) mitochondrial genome sequence of the African side-necked turtle (Pelomedusa subrufa) was deter- mined. This molecule contains several unusual features: a (TA)n microsatellite in the control region, the absence of an origin of replication for the light strand in the WANCY region of five tRNA genes, an unusually long noncoding region separating the ND5 and ND6 genes, an overlap between ATPase 6 and COIII genes, and the existence of extra nucle- otides in ND3 and ND4L putative ORFs. Phylogenetic analyses of the complete mitochondrial genome sequences supported the placement of turtles as the sister group of an alligator and chicken (Archosauria) clade. This result clearly rejects the Haematothermia hypothesis (a sister-group relationship be- tween mammals and birds), as well as rejecting the placement of turtles as the most basal living amniotes. Moreover, evi- dence from both complete mitochondrial rRNA genes sup- ports a sister-group relationship of turtles to Archosauria to the exclusion of Lepidosauria (tuatara, snakes, and lizards). These results challenge the classic view of turtles as the only survivors of primary Anapsid reptiles and imply that turtles might have secondarily lost their skull fenestration.
Edna Ruckhaus - One of the best experts on this subject based on the ideXlab platform.
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Anapsid an adaptive query processing engine for sparql endpoints
International Semantic Web Conference, 2011Co-Authors: Maribel Acosta, Mariaesther Vidal, Tomas Lampo, Julio Castillo, Edna RuckhausAbstract:Following the design rules of Linked Data, the number of available SPARQL endpoints that support remote query processing is quickly growing; however, because of the lack of adaptivity, query executions may frequently be unsuccessful. First, fixed plans identified following the traditional optimize-thenexecute paradigm, may timeout as a consequence of endpoint availability. Second, because blocking operators are usually implemented, endpoint query engines are not able to incrementally produce results, and may become blocked if data sources stop sending data. We present Anapsid, an adaptive query engine for SPARQL endpoints that adapts query execution schedulers to data availability and run-time conditions. Anapsid provides physical SPARQL operators that detect when a source becomes blocked or data traffic is bursty, and opportunistically, the operators produce results as quickly as data arrives from the sources. Additionally, Anapsid operators implement main memory replacement policies to move previously computed matches to secondary memory avoiding duplicates. We compared Anapsid performance with respect to RDF stores and endpoints, and observed that Anapsid speeds up execution time, in some cases, in more than one order of magnitude.
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International Semantic Web Conference (1) - Anapsid: an adaptive query processing engine for SPARQL endpoints
The Semantic Web – ISWC 2011, 2011Co-Authors: Maribel Acosta, Mariaesther Vidal, Tomas Lampo, Julio Castillo, Edna RuckhausAbstract:Following the design rules of Linked Data, the number of available SPARQL endpoints that support remote query processing is quickly growing; however, because of the lack of adaptivity, query executions may frequently be unsuccessful. First, fixed plans identified following the traditional optimize-thenexecute paradigm, may timeout as a consequence of endpoint availability. Second, because blocking operators are usually implemented, endpoint query engines are not able to incrementally produce results, and may become blocked if data sources stop sending data. We present Anapsid, an adaptive query engine for SPARQL endpoints that adapts query execution schedulers to data availability and run-time conditions. Anapsid provides physical SPARQL operators that detect when a source becomes blocked or data traffic is bursty, and opportunistically, the operators produce results as quickly as data arrives from the sources. Additionally, Anapsid operators implement main memory replacement policies to move previously computed matches to secondary memory avoiding duplicates. We compared Anapsid performance with respect to RDF stores and endpoints, and observed that Anapsid speeds up execution time, in some cases, in more than one order of magnitude.
Bhart-anjan S. Bhullar - One of the best experts on this subject based on the ideXlab platform.
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the amniote temporal roof and the diapsid origin of the turtle skull
Zoology, 2016Co-Authors: Tyler R. Lyson, Gaberiel Bever, Daniel J. Field, Bhart-anjan S. BhullarAbstract:Fossils provide a glimpse into the architecturally complex origins of modern vertebrate body plans. One such origin that has been long debated is that of turtles. Although much attention has been directed toward the origin of the shell, the enigmatic evolution of the turtle skull and its Anapsid temporal region has long clouded our understanding of reptile phylogeny. Two taxa, Eunotosaurus africanus and Pappochelys rosinae, were recently and independently described as long-anticipated stem turtles whose diapsid skulls would cement the evolutionary link between turtles and other modern reptile lineages. Detailed μCT analysis of the stratigraphically older and phylogenetically stemward of the two, Eunotosaurus, provides empirical insight into changing developmental trajectories that may have produced the Anapsid cranial form of modern turtles and sets the stage for more comprehensive studies of early amniote cranial evolution.
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Evolutionary origin of the turtle skull
Nature, 2015Co-Authors: Gaberiel Bever, Tyler R. Lyson, Daniel J. Field, Bhart-anjan S. BhullarAbstract:Computed tomography and phylogenetic analysis of the Eunotosaurus africanus skull suggests that not only is Eunotosaurus an early relative of the group that eventually evolved into turtles, but that it is also a diapsid caught in the act of evolving towards a secondarily Anapsid state. Transitional fossils informing the origin of turtles are among the most sought-after discoveries in palaeontology^ 1 , 2 , 3 , 4 , 5 . Despite strong genomic evidence indicating that turtles evolved from within the diapsid radiation (which includes all other living reptiles^ 6 , 7 ), evidence of the inferred transformation between an ancestral turtle with an open, diapsid skull to the closed, Anapsid condition of modern turtles remains elusive. Here we use high-resolution computed tomography and a novel character/taxon matrix to study the skull of Eunotosaurus africanus , a 260-million-year-old fossil reptile from the Karoo Basin of South Africa, whose distinctive postcranial skeleton shares many unique features with the shelled body plan of turtles^ 2 , 3 , 4 . Scepticism regarding the status of Eunotosaurus as the earliest stem turtle arises from the possibility that these shell-related features are the products of evolutionary convergence. Our phylogenetic analyses indicate strong cranial support for Eunotosaurus as a critical transitional form in turtle evolution, thus fortifying a 40-million-year extension to the turtle stem and moving the ecological context of its origin back onto land^ 8 , 9 . Furthermore, we find unexpected evidence that Eunotosaurus is a diapsid reptile in the process of becoming secondarily Anapsid. This is important because categorizing the skull based on the number of openings in the complex of dermal bone covering the adductor chamber has long held sway in amniote systematics^ 10 , and still represents a common organizational scheme for teaching the evolutionary history of the group. These discoveries allow us to articulate a detailed and testable hypothesis of fenestral closure along the turtle stem. Our results suggest that Eunotosaurus represents a crucially important link in a chain that will eventually lead to consilience in reptile systematics, paving the way for synthetic studies of amniote evolution and development. The evolution of the early reptiles is a complicated story and one particular event — the inferred transformation between an ancestral turtle with a diapsid skull (with openings in the skull behind each eye) to the closed, Anapsid condition of modern turtles — has remained elusive in the fossil record. Eunotosaurus africanus is an unusual reptile that lived 260 million years ago in what is now South Africa. Its oddities include flared and expanded ribs, which some have suggested represent the early stirrings of testudinates (turtles and tortoises). Computed tomography and phylogenetic analysis of the E. africanus skull now suggests that not only is Eunotosaurus an early relative of the group, but that it is a diapsid caught in the act of evolving towards a secondarily Anapsid state.
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Evolutionary origin of the turtle skull
Nature, 2015Co-Authors: Gaberiel Bever, Tyler R. Lyson, Daniel J. Field, Bhart-anjan S. BhullarAbstract:Transitional fossils informing the origin of turtles are among the most sought-after discoveries in palaeontology. Despite strong genomic evidence indicating that turtles evolved from within the diapsid radiation (which includes all other living reptiles), evidence of the inferred transformation between an ancestral turtle with an open, diapsid skull to the closed, Anapsid condition of modern turtles remains elusive. Here we use high-resolution computed tomography and a novel character/taxon matrix to study the skull of Eunotosaurus africanus, a 260-million-year-old fossil reptile from the Karoo Basin of South Africa, whose distinctive postcranial skeleton shares many unique features with the shelled body plan of turtles. Scepticism regarding the status of Eunotosaurus as the earliest stem turtle arises from the possibility that these shell-related features are the products of evolutionary convergence. Our phylogenetic analyses indicate strong cranial support for Eunotosaurus as a critical transitional form in turtle evolution, thus fortifying a 40-million-year extension to the turtle stem and moving the ecological context of its origin back onto land. Furthermore, we find unexpected evidence that Eunotosaurus is a diapsid reptile in the process of becoming secondarily Anapsid. This is important because categorizing the skull based on the number of openings in the complex of dermal bone covering the adductor chamber has long held sway in amniote systematics, and still represents a common organizational scheme for teaching the evolutionary history of the group. These discoveries allow us to articulate a detailed and testable hypothesis of fenestral closure along the turtle stem. Our results suggest that Eunotosaurus represents a crucially important link in a chain that will eventually lead to consilience in reptile systematics, paving the way for synthetic studies of amniote evolution and development.
Rafael Zardoya - One of the best experts on this subject based on the ideXlab platform.
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The evolutionary position of turtles revised
Naturwissenschaften, 2001Co-Authors: Rafael Zardoya, Axel MeyerAbstract:Consensus on the evolutionary position of turtles within the amniote phylogeny has eluded evolutionary biologists for more than a century. This phylogenetic problem has remained unsolved partly because turtles have such a unique morphology that only few characters can be used to link them with any other group of amniotes. Among the many alternative hypotheses that have been postulated to explain the origin and phylogenetic relationships of turtles, a general agreement among paleontologists emerged in favoring the placement of turtles as the only living survivors of the Anapsid reptiles (those that lack temporal fenestrae in the skull). However, recent morphological and molecular studies have radically changed our view of amniote phylogenetic relationships, and evidence is accumulating that supports the diapsid affinities of turtles. Molecular studies favor archosaurs (crocodiles and birds) as the living sister group of turtles, whereas morphological studies support lepidosaurs (tuatara, lizards, and snakes) as the closest living relatives of turtles. Accepting these hypotheses implies that turtles cannot be viewed any longer as primitive reptiles, and that they might have lost the temporal holes in the skull secondarily rather than never having had them.
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complete mitochondrial genome suggests diapsid affinities of turtles
Proceedings of the National Academy of Sciences of the United States of America, 1998Co-Authors: Rafael Zardoya, Axel MeyerAbstract:Despite more than a century of debate, the evolutionary position of turtles (Testudines) relative to other amniotes (reptiles, birds, and mammals) remains uncertain. One of the major impediments to resolving this important evolutionary problem is the highly distinctive and enigmatic morphology of turtles that led to their traditional placement apart from diapsid reptiles as sole descendants of presumably primitive Anapsid reptiles. To address this question, the complete (16,787-bp) mitochondrial genome sequence of the African side-necked turtle (Pelomedusa subrufa) was determined. This molecule contains several unusual features: a (TA)n microsatellite in the control region, the absence of an origin of replication for the light strand in the WANCY region of five tRNA genes, an unusually long noncoding region separating the ND5 and ND6 genes, an overlap between ATPase 6 and COIII genes, and the existence of extra nucleotides in ND3 and ND4L putative ORFs. Phylogenetic analyses of the complete mitochondrial genome sequences supported the placement of turtles as the sister group of an alligator and chicken (Archosauria) clade. This result clearly rejects the Haematothermia hypothesis (a sister-group relationship between mammals and birds), as well as rejecting the placement of turtles as the most basal living amniotes. Moreover, evidence from both complete mitochondrial rRNA genes supports a sister-group relationship of turtles to Archosauria to the exclusion of Lepidosauria (tuatara, snakes, and lizards). These results challenge the classic view of turtles as the only survivors of primary Anapsid reptiles and imply that turtles might have secondarily lost their skull fenestration.
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complete mitochondrial genome suggests diapsid affinities of turtles pelomedusa subrufayphylogenyyamniotayAnapsids
1998Co-Authors: Rafael Zardoya, Axel MeyerAbstract:Despite more than a century of debate, the evolutionary position of turtles (Testudines) relative to other amniotes (reptiles, birds, and mammals) remains uncertain. One of the major impediments to resolving this important evolutionary problem is the highly distinctive and enigmatic morphology of turtles that led to their traditional placement apart from diapsid reptiles as sole descendants of presumably primitive Anapsid reptiles. To address this question, the complete (16,787-bp) mitochondrial genome sequence of the African side-necked turtle (Pelomedusa subrufa) was deter- mined. This molecule contains several unusual features: a (TA)n microsatellite in the control region, the absence of an origin of replication for the light strand in the WANCY region of five tRNA genes, an unusually long noncoding region separating the ND5 and ND6 genes, an overlap between ATPase 6 and COIII genes, and the existence of extra nucle- otides in ND3 and ND4L putative ORFs. Phylogenetic analyses of the complete mitochondrial genome sequences supported the placement of turtles as the sister group of an alligator and chicken (Archosauria) clade. This result clearly rejects the Haematothermia hypothesis (a sister-group relationship be- tween mammals and birds), as well as rejecting the placement of turtles as the most basal living amniotes. Moreover, evi- dence from both complete mitochondrial rRNA genes sup- ports a sister-group relationship of turtles to Archosauria to the exclusion of Lepidosauria (tuatara, snakes, and lizards). These results challenge the classic view of turtles as the only survivors of primary Anapsid reptiles and imply that turtles might have secondarily lost their skull fenestration.
