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  • 1
    Electronic Resource
    Electronic Resource
    Promoter prediction analysis on the whole human genome (2004)
    [s.l.] : Nature Publishing Group
    Nature biotechnology 22 (2004), S. 1467-1473 
    Details
    ISSN: 1546-1696
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: [Auszug] Promoter prediction programs (PPPs) are important for in silico gene discovery without support from expressed sequence tag (EST)/cDNA/mRNA sequences, in the analysis of gene regulation and in genome annotation. Contrary to previous expectations, a comprehensive analysis of PPPs reveals that no ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nbt1032
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  • 2
    Electronic Resource
    Electronic Resource
    Stability analysis of singular systems (1989)
    Springer
    Circuits, systems and signal processing 8 (1989), S. 267-287 
    Details
    ISSN: 1531-5878
    Source: Springer Online Journal Archives 1860-2000
    Topics: Electrical Engineering, Measurement and Control Technology
    Notes: Abstract This paper deals with a refined qualitative analysis of motions of a broad class of continuous time-varying nonlinear singular differential systems. These systems consist of a finite number of first-order differential equations that cannot be set into the normal form. Some novel qualitative concepts, convenient for the description of solutions of singular systems, are introduced and analyzed. These concepts involve some inherent properties of singular systems. General sufficient conditions for these concepts are derived in terms of the existence of a suitable Lyapunov function. Also, for the subclass of singular systems considered, the construction of a Lyapunov function candidate that can be effectively applied in the analysis is proposed. The results obtained generalize some known results in stability theory.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01598415
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  • 3
    Electronic Resource
    Electronic Resource
    Some properties of solutions of the semi-state model for nonlinear nonstationary systems (1986)
    Springer
    Circuits, systems and signal processing 5 (1986), S. 109-123 
    Details
    ISSN: 1531-5878
    Source: Springer Online Journal Archives 1860-2000
    Topics: Electrical Engineering, Measurement and Control Technology
    Notes: Abstract Certain properties of solutions similar to set invariance, set attractivity, boundedness, BIBO stability, etc. are investigated for the semistate model $$P(t)\dot x = M(t,x)x + D(t,x)u,y = q(t,x,u).$$ For systems considered, it is assumed that the reduction to a normal form of lower order is not possible. Using the direct method of Liapunov, the properties of solutions are investigated without actual knowledge of solutions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01600190
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  • 4
    Electronic Resource
    Electronic Resource
    Qualitative analysis of motion properties of semistate models of large-scale systems (1987)
    Springer
    Circuits, systems and signal processing 6 (1987), S. 315-334 
    Details
    ISSN: 1531-5878
    Source: Springer Online Journal Archives 1860-2000
    Topics: Electrical Engineering, Measurement and Control Technology
    Notes: Abstract This paper studies the behavior of motions of large-scale (LS) semistate systems (SSS) governed byP i (t)x i =M i (t,x i )x i +f i (t)+h i (t, x), i=1,2,...,s, =(x 1 T x 2 T ⋯x s T )T, where matricesP i (t) are singular. Using Lyapunov's approach and the tools for LS system analysis, a variant of attractivity and ultimate boundedness of appropriate time-variable sets are investigated. The results are based on a specific choice of the aggregate functions. It is assumed that the reduction of equations to a normal form of lower order is inconvenient. The aggregation-decomposition approach used in this paper reduces the dimensionality of an aggregate matrix of the system to the number of its systems. Motion properties of LS systems are deduced from the properties of its isolated subsystems, the character of interconnections, and the conditions imposed on the system aggregate matrix. Sufficient algebraic conditions for the above-mentioned motion properties are developed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01599997
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  • 5
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    Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies (2014)
    In:  EPIC3PLoS ONE, 9(3), pp. e89606, ISSN: 1932-6203
    Details
    Publication Date: 2017-01-30
    Description: The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev , info:eu-repo/semantics/article
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  • 6
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    Toward an understanding of the molecular mechanisms of barnacle larval settlement : a comparative transcriptomic approach (2011)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e22913, doi:10.1371/journal.pone.0022913.
    Description: The barnacle Balanus amphitrite is a globally distributed biofouler and a model species in intertidal ecology and larval settlement studies. However, a lack of genomic information has hindered the comprehensive elucidation of the molecular mechanisms coordinating its larval settlement. The pyrosequencing-based transcriptomic approach is thought to be useful to identify key molecular changes during larval settlement. Using 454 pyrosequencing, we collected totally 630,845 reads including 215,308 from the larval stages and 415,537 from the adults; 23,451 contigs were generated while 77,785 remained as singletons. We annotated 31,720 of the 92,322 predicted open reading frames, which matched hits in the NCBI NR database, and identified 7,954 putative genes that were differentially expressed between the larval and adult stages. Of these, several genes were further characterized with quantitative real-time PCR and in situ hybridization, revealing some key findings: 1) vitellogenin was uniquely expressed in late nauplius stage, suggesting it may be an energy source for the subsequent non-feeding cyprid stage; 2) the locations of mannose receptors suggested they may be involved in the sensory system of cyprids; 3) 20 kDa-cement protein homologues were expressed in the cyprid cement gland and probably function during attachment; and 4) receptor tyrosine kinases were expressed higher in cyprid stage and may be involved in signal perception during larval settlement. Our results provide not only the basis of several new hypotheses about gene functions during larval settlement, but also the availability of this large transcriptome dataset in B. amphitrite for further exploration of larval settlement and developmental pathways in this important marine species.
    Description: This work was supported by grants (N-HKUST602/09 and AoE/P-04/04-II) from the Research Grants Council of the Hong Kong Special Administrative Region and an award (SA-C0040/UK-C0016) made by KAUST to P-Y Qian.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 7
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    Unique prokaryotic consortia in geochemically distinct sediments from Red Sea Atlantis II and Discovery Deep brine pools (2012)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 7 (2012): e42872, doi:10.1371/journal.pone.0042872.
    Description: The seafloor is a unique environment, which allows insights into how geochemical processes affect the diversity of biological life. Among its diverse ecosystems are deep-sea brine pools - water bodies characterized by a unique combination of extreme conditions. The ‘polyextremophiles’ that constitute the microbial assemblage of these deep hot brines have not been comprehensively studied. We report a comparative taxonomic analysis of the prokaryotic communities of the sediments directly below the Red Sea brine pools, namely, Atlantis II, Discovery, Chain Deep, and an adjacent brine-influenced site. Analyses of sediment samples and high-throughput pyrosequencing of PCR-amplified environmental 16S ribosomal RNA genes (16S rDNA) revealed that one sulfur (S)-rich Atlantis II and one nitrogen (N)-rich Discovery Deep section contained distinct microbial populations that differed from those found in the other sediment samples examined. Proteobacteria, Actinobacteria, Cyanobacteria, Deferribacteres, and Euryarchaeota were the most abundant bacterial and archaeal phyla in both the S- and N-rich sections. Relative abundance-based hierarchical clustering of the 16S rDNA pyrotags assigned to major taxonomic groups allowed us to categorize the archaeal and bacterial communities into three major and distinct groups; group I was unique to the S-rich Atlantis II section (ATII-1), group II was characteristic for the N-rich Discovery sample (DD-1), and group III reflected the composition of the remaining sediments. Many of the groups detected in the S-rich Atlantis II section are likely to play a dominant role in the cycling of methane and sulfur due to their phylogenetic affiliations with bacteria and archaea involved in anaerobic methane oxidation and sulfate reduction.
    Description: This work was supported by King Abdullah University for Science and Technology Global Collaborative Partners (GCR) program.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 8
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    Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses (2014)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e97338, doi:10.1371/journal.pone.0097338.
    Description: Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.
    Description: This work was supported by King Abdullah University for Science and Technology Global Collaborative Partners (GCR) program.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 9
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    Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments (2016)
    Elsevier
    Details
    Publication Date: 2016-08-01
    Print ISSN: 2095-9273
    Electronic ISSN: 2095-9281
    Topics: Natural Sciences in General
    Published by Elsevier
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  • 10
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    Genomic Anatomy of the Hippocampus (2008)
    Cell Press
    Details
    Publication Date: 2008-12-01
    Print ISSN: 0896-6273
    Electronic ISSN: 1097-4199
    Topics: Biology , Medicine
    Published by Cell Press
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