291 research outputs found

    Tentacle : a graph-based database system

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    With the advent of large and complex applications and the emergence of semi-structured information repositories such as the World Wide Web, new demands are being made on database systems. The TENTACLE database system is an experimental database system which provides facilities capable of meeting some of these demands. The distinguishing features of the system are that it: uses a graph-based data model (and storage subsystem) to provide a flexible means of representing poorly structured information, integrates a path expression-based query language with a general purpose language to query and manipulate the graph structures, thereby eliminating the impedance mismatch encountered in a two language system, and provides a programmable database kernel capable of executing the combined query and utility language, allowing the construction of domain specific applications inside the database without the assistance of wrappers or gateways. As a demonstration of the utility of the system, I have constructed a hypertext server inside the TENTACLE database without making use of external mediators or gateways. Since the hypertext server program is part of the database content, database facilities may be used to assist in the creation and maintenance of the hypertext server itself. In addition, the close integration of hypertext server and database simplifies tasks such as the management of associations between hypertext entities or the maintenance of different document views

    Exploiting Data Locality in Dynamic Web Applications

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    The Internet has grown from a static document retrieval system to a dynamic medium where users are both consumers and producers of information. Users may experience above-average website latencies due to the physical distances information must travel. Because user satisfaction is related to a website\u27s responsiveness, e-commerce may be hindered and prevent online businesses from reaching their full potential. This dissertation analyzes how temporal and relational dependencies in web applications limit their ability to become distributed. Two contributions are made, the first showing the location of data inside a datacenter influences the web system\u27s performance, and secondly, that relaxing strict consistency inside the web application at a fine- grained level can greatly lower latencies for geographically diverse users. Experiments are used to show when and how much these optimizations can benefit a dynamic web application

    The Evolutionary Origin of the Runx/CBFbeta Transcription Factors – Studies of the Most Basal Metazoans

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    BACKGROUND. Members of the Runx family of transcriptional regulators, which bind DNA as heterodimers with CBFβ, are known to play critical roles in embryonic development in many triploblastic animals such as mammals and insects. They are known to regulate basic developmental processes such as cell fate determination and cellular potency in multiple stem-cell types, including the sensory nerve cell progenitors of ganglia in mammals. RESULTS. In this study, we detect and characterize the hitherto unexplored Runx/CBFβ genes of cnidarians and sponges, two basal animal lineages that are well known for their extensive regenerative capacity. Comparative structural modeling indicates that the Runx-CBFβ-DNA complex from most cnidarians and sponges is highly similar to that found in humans, with changes in the residues involved in Runx-CBFβ dimerization in either of the proteins mirrored by compensatory changes in the binding partner. In situ hybridization studies reveal that Nematostella Runx and CBFβ are expressed predominantly in small isolated foci at the base of the ectoderm of the tentacles in adult animals, possibly representing neurons or their progenitors. CONCLUSION. These results reveal that Runx and CBFβ likely functioned together to regulate transcription in the common ancestor of all metazoans, and the structure of the Runx-CBFβ-DNA complex has remained extremely conserved since the human-sponge divergence. The expression data suggest a hypothesis that these genes may have played a role in nerve cell differentiation or maintenance in the common ancestor of cnidarians and bilaterians.National Science Foundation (IBN-0212773, FP-91656101-0); Boston University SPRInG (20-202-8103-9); Israel Science Foundation (825/07

    Toward a Formal Semantics for Autonomic Components

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    Autonomic management can improve the QoS provided by parallel/ distributed applications. Within the CoreGRID Component Model, the autonomic management is tailored to the automatic - monitoring-driven - alteration of the component assembly and, therefore, is defined as the effect of (distributed) management code. This work yields a semantics based on hypergraph rewriting suitable to model the dynamic evolution and non-functional aspects of Service Oriented Architectures and component-based autonomic applications. In this regard, our main goal is to provide a formal description of adaptation operations that are typically only informally specified. We contend that our approach makes easier to raise the level of abstraction of management code in autonomic and adaptive applications.Comment: 11 pages + cover pag

    Integrating genomic, transcriptomic and developmental approaches to investigate coloniality and life cycle evolution in the Hydractiniidae (Hydrozoa: Cnidaria)

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    Integrative approaches to evolutionary biology yield rich data through which we can truly begin to understand the marvels of life. This dissertation integrates genomic, transcriptomic, and developmental approaches to understand the evolution of prominent life history characters of the cnidarian class Hydrozoa, including the transition from solitary to colonial forms, an elaboration of coloniality known as polyp polymorphism, and medusae (jellyfish) evolution and loss. While these characters have been repeatedly explored phylogenetically, recognizing interesting and complex evolutionary patterns of character transitions, understanding of these complex patterns of character evolution will ultimately come from insight into their development. In this dissertation, I have developed workflows for analyzing RNA-Seq data in both an intra- and interspecific comparative context. Using next-generation sequencing I not only characterize entire transcriptomic expression profiles in various tissues of two hydractiniid hydrozoans, Hydractinia symbiolongicarpus and Podocoryna carnea, but also assess and accurately characterize intra- and interspecific changes in gene expression. Using these unbiased differential expression analyses, I identify correlated changes in expression and propose candidate genes and gene pathways that are potentially involved in these key transitions. Furthermore, using whole mount in situ hybridization to characterize the spatial expression of various candidates genes, I validated each approach showing expression consistent with their role in the development of a particular tissue or life cycle stage. Results presented in this dissertation suggest that the differential regulation of gene expression, as well as novel gene gain and loss appear to have played an important role in hydrozoan life cycle transitions. Moreover, these results reveal the power of these unbiased genomic/transcriptomic methods over traditional comparative candidate gene approaches to address longstanding questions of hydrozoan morphology and evolution

    Cryptic diversity in the leptothecate genera Laodicea and Tiaropsis (Cnidaria: Hydrozoa)

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    Postponed access: the file will be accessible after 2022-09-01Although they are an ecologically and economically important group of animals, hydrozoans are understudied because of their difficult identification due to their small size and fragility. Hydrozoans as a group show a great diversity in life strategies, and often include both a polyp and a medusa stage in their life cycle, which complicates their taxonomy because both stages may be needed for a correct identification. For the two leptothecate hydrozoan genera Laodicea (Family Laodiceidae) and Tiaropsis (Family Tiaropsidae), the polyp stage is very small and easy to overlook, while the medusa stage is conspicuous and relatively straightforward to identify, at least to genus level. Only one species of each of these genera is believed to occur in Norwegian waters, Laodicea undulata (Forbes &Goodsir, 1853) and Tiaropsis multicirrata (M. Sars, 1835), but preliminary data suggest that the diversity of these taxa in the region is higher than previously thought. In this study, I used DNA barcoding and different molecular species delimitation methods (based on mitochondrial markers 16S and COI and the nuclear marker ITS) in combination with a detailed morphological analysis of both the hydroid and medusa stages to assess the species diversity of the genera Laodicea and Tiaropsis in Norway. Based on molecular evidence, Laodicea undulatais shown to comprise two molecularly distinct Norwegian clades, which appear not to be sister species. Specimens morphologically identified as T. multicirrata split up into three distinct clades in Norway according to the evaluated molecular markers, indicating cryptic diversity in Tiaropsis for the studied region. For both Tiaropsis and Laodicea, the results suggest that the observed clades correspond to undescribed species, but further work is necessary to place them in a broader phylogenetic perspective and to identify any potential morphological characters that define them.Master's Thesis in BiologyBIO399MAMN-BIOMAMN-HAVS

    Verkkosovellusten jatkuva kehitys ja julkaisuautomaatio

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    Software development methods have evolved towards more agile practices for getting changes implemented more quickly. While the new features are finished faster, the release processes are also made more automated to get the changes in production environment reliably, repeatably and rapid. This thesis examines the practices used for continuous software development and web application release automation. The main objective is to find out and implement a way for making changes agilely and getting them tested and released in several environments effortlessly. After the research, different tools are sought for, compared and suitable tools are selected. Lean software development is chosen as the working practice for the development. GitHub enterprise is used for version control, JetBrains TeamCity for continuous integration and Octopus Deploy for deployment automation. SonarQube is used for static code analysis and UseTrace for automated functionality testing. The lean development practice is found well fit for real world use. The deployment pipeline is also well operational, founding issues early and deployments are enabled steady, effortless and fast. Some issues with code analysis are found due to the decisions in the application implementation. UseTrace tests have occasionally some false positives in the failing test results but overall they worked as expected.Sovelluskehitysmenetelmät ovat kehittyneet ketterämmiksi, jotta muutokset saataisiin toteutettua nopeammin. Kun uudet ominaisuudet valmistuvat nopeammin, myös julkaisuprosesseista tehdään automatisoidumpia, jotta muutokset saadaan tuotantoon luotettavasti, toistettavasti ja nopeasti. Tässä työssä tutkitaan menetelmiä, joita käytetään jatkuvaan sovelluskehitykseen ja verkkosovellusten julkaisuautomaatioon. Pääasiallisena tavoitteena on selvittää ja toteuttaa tapa, jolla muutoksia voidaan tehdä ketterästi ja julkaista testattuina moniin ympäristöihin pienellä vaivalla. Tutkimuksen jälkeen etsitään erilaisia työkaluja, joita vertaillaan keskenään ja soveltuvat työkalut valitaan. Lean-malli valitaan sovelluskehityksessä käytettäväksi tavaksi. GitHub enterprise:a käytetään versionhallintaan, JetBrains TeamCity:ä jatkuvaan integraatioon ja Octopus Deploy:ta jatkuvaan toimittamiseen. SonarQube:a käytetään staattiseen koodianalyysiin ja UseTrace:a automaattiseen funktionaalisuustestaamiseen. Lean-sovelluskehitysmalli todetaan hyvin toimivaksi todellisessa käytössä. Julkaisuputki on myös hyvin toimiva, löytäen ongelmat ajoissa ja mahdollistaen julkaisut luotettavasti, vaivattomasti ja nopeasti. Koodianalyysin osalta joitain ongelmia ilmenee sovellustoteutukseen liittyvistä päätöksistä johtuen. UseTrace-automaattitestit tuottavat satunnaisesti virheellisiä ongelmia testituloksissa, mutta yleisesti ottaen ne toimivat odotetusti

    On symbolic semantics for name-decorated contexts

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    Under several regards, various of the recently proposed computational paradigms are open-ended, i.e. they may comprise components whose behaviour is not or cannot be fully specified. For instance, applications can be distributed across different administration domains that do not fully disclose their internal business processes to each other, or the dynamics of the system may allow reconfigurations and dynamic bindings whose specification is not available at design time. While a large set of mature design and analysis techniques for closed systems have been developed, their lifting to the open case is not always straightforward. Some existing approaches in the process calculi community are based on the need of proving properties for components that may hold in any, or significantly many, execution environments. Dually, frameworks describing the dynamics of systems with unspecified components have also been presented. In this paper we lay some preliminary ideas on how to extend a symbolic semantics model for open systems in order to deal with name-based calculi. Moreover, we also discuss how the use of a simple type system based on name-decoration for unknown components can improve the expressiveness of the framework. The approach is illustrated on a simple, paradigmatic calculus of web crawlers, which can be understood as a term representation of a simple class of graphs

    Transcriptome and venom proteome of the box jellyfish Chironex fleckeri

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    Background: The box jellyfish, Chironex fleckeri, is the largest and most dangerous cubozoan jellyfish to humans. It produces potent and rapid-acting venom and its sting causes severe localized and systemic effects that are potentially life-threatening. In this study, a combined transcriptomic and proteomic approach was used to identify C. fleckeri proteins that elicit toxic effects in envenoming. Results: More than 40,000,000 Illumina reads were used to de novo assemble ~34,000 contiguous cDNA sequences and ~20,000 proteins were predicted based on homology searches, protein motifs, gene ontology and biological pathway mapping. More than 170 potential toxin proteins were identified from the transcriptome on the basis of homology to known toxins in publicly available sequence databases. MS/MS analysis of C. fleckeri venom identified over 250 proteins, including a subset of the toxins predicted from analysis of the transcriptome. Potential toxins identified using MS/MS included metalloproteinases, an alpha-macroglobulin domain containing protein, two CRISP proteins and a turripeptide-like protease inhibitor. Nine novel examples of a taxonomically restricted family of potent cnidarian pore-forming toxins were also identified. Members of this toxin family are potently haemolytic and cause pain, inflammation, dermonecrosis, cardiovascular collapse and death in experimental animals, suggesting that these toxins are responsible for many of the symptoms of C. fleckeri envenomation. Conclusions: This study provides the first overview of a box jellyfish transcriptome which, coupled with venom proteomics data, enhances our current understanding of box jellyfish venom composition and the molecular structure and function of cnidarian toxins. The generated data represent a useful resource to guide future comparative studies, novel protein/peptide discovery and the development of more effective treatments for jellyfish stings in humans. (Length: 300)
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