Database Engineering Processes with DB-MAIN

Software engineering needs more and more to be supported by CASE tools. Since databases are at the heart of information systems, they deserve a particular attention. More and more CASE tools allow method engineers to implement their own methodology and they allow users to record all their actions, with their rationales, in order to improve the quality of the design and the quality of the documentation of the design. DBMAIN is such a database oriented tool with a method description and a documentation generation facilities. But it has its particularities like its procedural non-deterministic Method Description Language, its well integrated multilevel histories and its userfriendly methodological engine

Global Phylogenomic Assessment of \u3ci\u3eLeptoseris\u3c/i\u3e and \u3ci\u3eAgaricia\u3c/i\u3e Reveals Substantial Undescibed Diversity at Mesophotic Depths

Background: Mesophotic coral communities are increasingly gaining attention for the unique biological diversity they host, exemplified by the numerous mesophotic fish species that continue to be discovered. In contrast, many of the photosynthetic scleractinian corals observed at mesophotic depths are assumed to be depth-generalists, with very few species characterised as mesophotic-specialists. This presumed lack of a specialised community remains largely untested, as phylogenetic studies on corals have rarely included mesophotic samples and have long suffered from resolution issues associated with traditional sequence markers. Results: Here, we used reduced-representation genome sequencing to conduct a phylogenomic assessment of the two dominant mesophotic genera of plating corals in the Indo-Pacific and Western Atlantic, respectively, Leptoseris and Agaricia. While these genome-wide phylogenies broadly corroborated the morphological taxonomy, they also exposed deep divergences within the two genera and undescribed diversity across the current taxonomic species. Five of the eight focal species consisted of at least two sympatric and genetically distinct lineages, which were consistently detected across different methods. Conclusions: The repeated observation of genetically divergent lineages associated with mesophotic depths highlights that there may be many more mesophotic-specialist coral species than currently acknowledged and that an urgent assessment of this largely unstudied biological diversity is warranted

Evaluation of Microorganisms Cultured from Injured and Repressed Tissue Regeneration Sites in Endangered Giant Aquatic Ozark Hellbender Salamanders

Investigation into the causes underlying the rapid, global amphibian decline provides critical insight into the effects of changing ecosystems. Hypothesized and confirmed links between amphibian declines, disease, and environmental changes are increasingly represented in published literature. However, there are few long-term amphibian studies that include data on population size, abnormality/injury rates, disease, and habitat variables to adequately assess changes through time. We cultured and identified microorganisms isolated from abnormal/injured and repressed tissue regeneration sites of the endangered Ozark Hellbender, Cryptobranchus alleganiensis bishopi, to discover potential causative agents responsible for their significant decline in health and population. This organism and our study site were chosen because the population and habitat of C. a. bishopi have been intensively studied from 1969–2009, and the abnormality/injury rate and apparent lack of regeneration were established. Although many bacterial and fungal isolates recovered were common environmental organisms, several opportunistic pathogens were identified in association with only the injured tissues of C.a. bishopi. Bacterial isolates included Aeromonas hydrophila, a known amphibian pathogen, Granulicetella adiacens, Gordonai terrae, Stenotrophomonas maltophilia, Aerococcus viridans, Streptococcus pneumoniae and a variety of Pseudomonads, including Pseudomonas aeruginosa, P. stutzeri, and P. alcaligenes. Fungal isolates included species in the genera Penicillium, Acremonium, Cladosporium, Curvularia, Fusarium, Streptomycetes, and the Class Hyphomycetes. Many of the opportunistic pathogens identified are known to form biofilms. Lack of isolation of the same organism from all wounds suggests that the etiological agent responsible for the damage to C. a. bishopi may not be a single organism. To our knowledge, this is the first study to profile the external microbial consortia cultured from a Cryptobranchid salamander. The incidence of abnormalities/injury and retarded regeneration in C. a. bishopi may have many contributing factors including disease and habitat degradation. Results from this study may provide insight into other amphibian population declines

Reference Manual Version

Preface We believe that programs 1 like emacs, AutoCAD 2, Word 3 and TEX owe their success partially to the existence of a language 4 allowing the user to write macros or even programs. Indeed, such languages fill a gap between built-in functionalities and those expected by the user. This argument suffices to explain why we choose to define and to implement such a language for the DB-MAIN tool. Because small steps are more secure than large ones, at the beginning – when Voyager did not exist yet – this language had to be a simple script facility for generating reports. Now, this language shares the characteristics of its big brothers and even has a name: Voyager 2. This last issue was the most difficult to settle! This manual was written as a reference manual and therefore is quite concise in order to give the reader a maximum of detail economically. We are conscious that the examples are rather scarce, especially regarding the use of the repository. For this reason, this document is only a first version of what will ultimately become a series of manuals: reference manual; users’s guide; and tutorial. I thank the DB-MAIN, DB-MAIN/01, INTER-DB, PROAGEC research groups and —last but not least — the Professor J.-L. Hainaut for their support in my work. 1 TEX is a sophisticated program designed to produce high-quality typesetting, especially for mathematical text. It was created by Donald Knuth. This manual was produced with LATEX. 2 AutoCad and AutoLisp are trademarks of Autodesk

Attribute-Based Refinement of Software Architectures

This paper aims to show the usefulness of attaching attributes to pieces of software architectures, in order to direct a transformation and refinement process. These attributes are properties that can be considered as abstract ways to express architectural structures, and characteristics that constrain the refinement process. Then we define a methodology that consists in refining and transforming an architecture on the basis of the attributes attached to it. The methodology will be illustrated on a case study

Attribute-Based Refinement of Software Architectures

This paper aims to show the usefulness of attaching attributes to pieces of software architectures, in order to direct a transformation and refinement process. These attributes ways to express architectural structures, and characteristics that constrain the refinement process. Then we define a methodology that consists in refining and transforming an architecture on the basis of the attributes attached to it. The methodology will be illustrated on a case study. 1. Introduction an