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  • Articles  (58)
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  • Oxford University Press  (58)
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  • Articles  (58)
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  • 1
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    Forgetting complex propositions (2015)
    Oxford University Press
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    Publication Date: 2015-11-25
    Description: This article uses possible-world semantics to model the changes that may occur in an agent's knowledge as she loses information. This builds on previous work in which the agent may forget the truth-value of an atomic proposition, to a more general case where she may forget the truth-value of a propositional formula. The generalization poses some challenges, since in order to forget whether a complex proposition is the case, the agent must also lose information about the propositional atoms that appear in it, and there is no unambiguous way to go about this. We resolve this situation by considering expressions of the form [] , which quantify over all possible (but ‘minimal’) ways of forgetting whether . Propositional atoms are modified non-deterministically, although uniformly, in all possible worlds. We then represent this within action model logic in order to give a sound and complete axiomatization for a logic with knowledge and forgetting. Finally, some variants are discussed, such as when an agent forgets (rather than forgets whether ) and when the modification of atomic facts is done non-uniformly throughout the model.
    Print ISSN: 1367-0751
    Electronic ISSN: 1368-9894
    Topics: Mathematics
    Published by Oxford University Press
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  • 2
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    The Degradome database: expanding roles of mammalian proteases in life and disease (2016)
    Oxford University Press
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    Publication Date: 2016-01-07
    Description: Since the definition of the degradome as the complete repertoire of proteases in a given organism, the combined effort of numerous laboratories has greatly expanded our knowledge of its roles in biology and pathology. Once the genomic sequences of several important model organisms were made available, we presented the Degradome database containing the curated sets of known protease genes in human, chimpanzee, mouse and rat. Here, we describe the updated Degradome database, featuring 81 new protease genes and 7 new protease families. Notably, in this short time span, the number of known hereditary diseases caused by mutations in protease genes has increased from 77 to 119. This increase reflects the growing interest on the roles of the degradome in multiple diseases, including cancer and ageing. Finally, we have leveraged the widespread adoption of new webtools to provide interactive graphic views that show information about proteases in the global context of the degradome. The Degradome database can be accessed through its web interface at http://degradome.uniovi.es .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    On the asymptotic hyperstability of switched systems under integral-type feedback regulation Popovian constraints (2015)
    Oxford University Press
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    Publication Date: 2015-06-17
    Description: This paper deals with the asymptotic hyperstability of switched time-varying dynamic systems involving switching actions among linear time-invariant parametrizations in the feed-forward loop for any feedback regulator controller potentially being also subject to switching through time while being within a class which satisfies a Popov-type integral inequality. Asymptotic hyperstability is proved to be achievable under very generic switching laws if at least one of the feed-forward parametrization possesses a strictly positive real transfer function, a minimum residence time interval is respected for each activation time interval of such a parametrization and a maximum allowable residence time interval is simultaneously maintained for all active parametrizations which are not positive real, if any. In the case where all the feed-forward parametrizations possess a common Lyapunov function, asymptotic hyperstability of the switched closed-loop system is achieved under arbitrary switching.
    Print ISSN: 0265-0754
    Electronic ISSN: 1471-6887
    Topics: Mathematics
    Published by Oxford University Press
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  • 4
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    Birth-and-Death of KLK3 and KLK2 in Primates: Evolution Driven by Reproductive Biology (2012)
    Oxford University Press
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    Publication Date: 2012-12-26
    Description: The kallikrein ( KLK ) gene family comprises the largest uninterrupted locus of serine proteases in the human genome and represents a notable case for studying the evolutionary fate of duplicated genes. In primates, a recent duplication event gave rise to KLK2 and KLK3 , both encoding essential proteins for the cascade of seminal plasma liquefaction. We reconstructed the evolutionary history of KLK2 and KLK3 by comparative analysis of the orthologous sequences from 22 primate species, calculated d N / d S ratios, and addressed the hypothesis of coevolution with their substrates, the semenogelins (SEMG1 and SEMG2). Our findings support the placement of the KLK2–KLK3 duplication in the Catarrhini ancestor and unveil the frequent loss of KLK2 throughout primate evolution by different genomic mechanisms, including unequal crossing-over, deletions, and pseudogenization. We provide evidences for an adaptive evolution of KLK3 toward an expanded enzymatic spectrum, with an effect on the hydrolysis of semen coagulum. Furthermore, we found associations between mating system, the number of SEMG repeat units, and the number of functional KLK2 and KLK3 , suggesting complex evolutionary dynamics shaped by reproductive biology.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Overwintering populations of Anabaena, Aphanizomenon and Microcystis as potential inocula for summer blooms (2013)
    Oxford University Press
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    Publication Date: 2013-10-26
    Description: Overwintering cyanobacterial populations of Nostocales and Microcystis were investigated in six freshwater reservoirs in Northwestern Spain during two consecutive winters. Surface sediments hosted 10 3 –10 5 akinetes mL –1 and 10 2 –10 4 Microcystis colonies mL –1 . Sediments from deeper areas close to dam accumulated 2-fold ( Microcystis ) and 11-fold (akinetes) greater concentrations than those at the shallower upstream areas. Anabaena spp. and Microcystis aeruginosa dominated the sediment pool, with minor amounts of akinetes of Aphanizomenon ( Aph. flos-aquae , Aph. gracile ) and benthic Nostocales ( Cylindrospermum , Nostoc and Trichormus ). Our study confirms the dual benthic-pelagic overwintering of Anabaena, Aphanizomenon and Microcystis , found in the pelagial at 7.5–9.8°C. This study also provides an insight into the little known annual cycle of potential cyanotoxin-producers Aph. gracile and Anabaena circinalis . Our estimates show that: (i) only a small fraction (〈1%) of the sediment pool of akinetes and Microcystis was resupended in the bottom water during winter which, however, may be sufficient inocula to build up the summer maxima under realistic in situ growth rates; and (ii) the time required for the development of summer populations is mainly driven by growth rates, and therefore by the environmental conditions faced by the inoculum, with a lower influence (although greater for Microcystis than for Nostocales) of the inoculum size.
    Print ISSN: 0142-7873
    Electronic ISSN: 1464-3774
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Metagenomic analysis of lacustrine viral diversity along a latitudinal transect of the Antarctic Peninsula (2016)
    Oxford University Press
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    Publication Date: 2016-04-29
    Description: Environmental viruses constitute the most abundant biological entities on earth, and harbor an enormous genetic diversity. While their strong influence on the ecosystem is widely acknowledged, current knowledge about their diversity and distribution remains limited. Here we present the metagenomic study of viral communities from freshwater bodies located along a transect of the Antarctic Peninsula. These ecosystems were chosen on the basis of environmental and biogeographical variation. The results obtained indicate that the virus assemblages were diverse, and that the larger fraction represented viruses with no close relatives in the databases. Comparisons to existing metaviromes showed that the communities studied were dissimilar to other freshwater viromes including those from the Arctic. Finally, we observed no indication of there being a reduction in either viral richness or diversity estimates with increasing latitude along the studied transect, further adding to the controversy regarding the possible existence of latitudinal gradients of diversity in the microbial world.
    Print ISSN: 0168-6496
    Electronic ISSN: 1574-6941
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Functional analysis of sucrase-isomaltase mutations from chronic lymphocytic leukemia patients (2013)
    Oxford University Press
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    Publication Date: 2013-05-14
    Description: Next-generation sequencing techniques have emerged as powerful tools for the understanding of cancer genomes. In recent years, whole-exome and whole-genome sequencing strategies have enabled the annotation of a comprehensive mutation landscape of chronic lymphocytic leukemia (CLL), the most frequent leukemia in western countries. Several recurrently mutated genes have been identified, with a subset being validated as neoplastic drivers. Still, a main challenge remains for the differentiation between driver and passenger mutations among candidates as well as for the functional description of the newly discovered leukemogenic genes that could be utilized for personalized anti-tumor strategies. In this scenario, we have identified the metabolic enzyme sucrase–isomaltase (SI) as one of the most frequently mutated genes in a cohort of 105 CLL patients. Here, we demonstrate that these SI mutations result in loss of enzyme function by preventing the biosynthesis of catalytically competent SI at the cell surface. Transcriptome analyses of RNA from CLL patients with SI loss-of-function mutations have uncovered gene expression patterns that depict ample metabolic reprogramming, pinpointing SI as a putative player in the cancer-associated metabolic switch. These results highlight SI as a relevant target for clinical evaluation in future CLL studies.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 8
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    The RCSB Protein Data Bank: new resources for research and education (2012)
    Oxford University Press
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    Publication Date: 2012-12-20
    Description: The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) develops tools and resources that provide a structural view of biology for research and education. The RCSB PDB web site ( http://www.rcsb.org ) uses the curated 3D macromolecular data contained in the PDB archive to offer unique methods to access, report and visualize data. Recent activities have focused on improving methods for simple and complex searches of PDB data, creating specialized access to chemical component data and providing domain-based structural alignments. New educational resources are offered at the PDB-101 educational view of the main web site such as Author Profiles that display a researcher’s PDB entries in a timeline. To promote different kinds of access to the RCSB PDB, Web Services have been expanded, and an RCSB PDB Mobile application for the iPhone/iPad has been released. These improvements enable new opportunities for analyzing and understanding structure data.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    An epistemic and dynamic approach to abductive reasoning: selecting the best explanation (2013)
    Oxford University Press
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    Publication Date: 2013-11-25
    Description: Previous works have discussed how to represent abductive reasoning in a dynamic epistemic logic framework. It has been discussed how to define an abductive problem, how to define an abductive solution and what to do with the best solution, once this one has been selected. The present work discusses two possible ways in which the agent can select ‘the best’ explanation.
    Print ISSN: 1367-0751
    Electronic ISSN: 1368-9894
    Topics: Mathematics
    Published by Oxford University Press
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  • 10
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    Overlap and diversity in antimicrobial peptide databases: compiling a non-redundant set of sequences (2015)
    Oxford University Press
    Details
    Publication Date: 2015-07-26
    Description: Motivation: The large variety of antimicrobial peptide (AMP) databases developed to date are characterized by a substantial overlap of data and similarity of sequences. Our goals are to analyze the levels of redundancy for all available AMP databases and use this information to build a new non-redundant sequence database. For this purpose, a new software tool is introduced. Results: A comparative study of 25 AMP databases reveals the overlap and diversity among them and the internal diversity within each database. The overlap analysis shows that only one database (Peptaibol) contains exclusive data, not present in any other, whereas all sequences in the LAMP_Patent database are included in CAMP_Patent. However, the majority of databases have their own set of unique sequences, as well as some overlap with other databases. The complete set of non-duplicate sequences comprises 16 990 cases, which is almost half of the total number of reported peptides. On the other hand, the diversity analysis identifies the most and least diverse databases and proves that all databases exhibit some level of redundancy. Finally, we present a new parallel-free software, named Dover Analyzer, developed to compute the overlap and diversity between any number of databases and compile a set of non-redundant sequences. These results are useful for selecting or building a suitable representative set of AMPs, according to specific needs. Availability and implementation: The regularly updated non-redundant sequence databases and the Dover Analyzer software to perform custom analysis are available at http://mobiosd-hub.com/doveranalyzer/ . Contact: ymarrero77@yahoo.es Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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