A pattern based approach to defining the dynamic infrastructure of UML 2.0.

The 2U Consortium has recently submitted a proposal for the definition of the UML 2.0 infrastructure. This uses an innovative technique of rapidly “stamping out” the definition using a small number of patterns commonly found in software architecture. The patterns, their instantiation, and any further language details are described using precise class diagrams and OCL, this enables the definition to be easily understood. The main focus of the 2U approach is on the static part of the definition. A further concern when modelling software, using languages such as the UML, is describing the dynamic behaviour of the system over time. The contribution of this paper is to provide a template that can be used to “stamp out” the dynamic part of the UML 2.0 infrastructure. We argue for the suitability of the dynamic template because it makes little commitment to concrete abstractions and can, therefore, be used to support a broad spectrum of behavioural languages

Unambiguous UML submission to UML 2 infrastructure RFP (ad/00-09-01).

This is a response to the UML 2.0 Request for Proposals on Infrastructure (ad/00-09-01). We propose an architecture for the definition of UML 2.0 which supports the layered and extensible definition of UML as a family of languages, and depends on the use of package extension (composition) and package template mechanisms in the metamodelling language. This submission defines that architecture and populates it with the definition of a core foundation for the definition of structural and behavioural modelling constructs for UML. Chapter 3 (“Language Architecture”) identifies all those parts of the architecture defined in any given version of this document

Farming experiments and transfer of technology of bivalve culture along the southwest coast of India

The Central Marine Fisheries Research Institute (CMFRI) in India developed bivalve farming technologies in the 1970s. but these were not widely adopted at the time. In 1993, CMFRI undertook an action research program to encourage farming of edible oysters, mussels, clams and pearls along the southwest coast of India. Successful demonstration of the viability of bivalve farming led to the initiation of commercial farming of mussels and generated interest among farmers and entrepreneurs in developing production of pearls and farming of edible oysters. Given the high potential for mollusc aquacultu re, both for the local and export markets, issues such as demarcation and issuance of lease rights on aquaculture zones in public waterbodies by the government, organization of marketing systems and provisions for technical and fin ancial support to farmers need to be addressed

Revised submission for MOF 2.0 query / views / transformations RFP.

This submission presents the QVT-Partners proposal for the MOF 2.0 QVT standard. The proposal consists of a number of key ingredients which we briefly discuss in this section. -Specification and implementation: A common scenario in the development of any artifact is to first create a specification of the form and behaviour of the the artifact, and then realise an implementation which satisfies the specification. The specification is characterised by a lack of implementation details, but having a close correspondence to the requirements; conversely an implementation may lack close correspondence to the requirements. This submission maintains this important distinction. Relations provide a specification oriented view of the relationship between models and are specified in a language that can be easily understood. They say what it means to translate between several models but without saying precisely how the translation is achieved. Those details are realised by mappings which characterise the means by which models are translated. It should be noted though, that while the mappings language is rich enough to provide an implementation of relations it also manages to maintain a requirements oriented focus. This may give rise to a scenario where developers prefer to omit relations and directly define mappings. -Scalability and reuse: Decomposition is a key approach to managing complexity. This submission provides a number of composition mechanisms whereby relations and mappings can be composed to form more complex specifications. These mechanisms also aid reuse since mappings and relations can be treated as reusable components which are composed for specific contexts. -Usability: Diagrammatic notations have been important to the success of many OMG standards. This proposal presents a diagrammatic notation which is an extension of collaboration object diagrams and is therefore familiar to many end users. A criticism often levelled at diagrammatic notations is their scalability. This submission also presents a textual syntax, constructs of the diagrammatic notations are closely aligned with its textual counterpart. Considering the domains of relations and mappings at the generic type level is often too limiting. Instead it often is specific-types of things that are of interest. This submission uses patterns to describe the domains of both relations and mappings. Patterns are a means of succinctly describing specific-types of model elements and enable domains of interest to be rapidly stated with ease. -Semantic soundness: By definition a standard should give rise to consistency across differing implementations. It is important that an end user can get the same results on two different implementations. For this reason, this submission goes to some effort to ensure that all the constructs have a well-defined semantic basis. This is achieved by treating the submission in two parts. The infrastructure part has a small number of constructs which can be easily and consistently understood from informal descriptions (although a mathematical semantics is given in Appendix B for the sake of completeness and rigour). The superstructure part uses the infrastructure as its semantic basis and defines the syntax that the end user deals with. The relationship between the superstructure and the infrastructure is expressed as a translation

Clam resource in the Astamudi Lake, a tropical estuary in sourthern India: Managment and conservation concerns

Clam resources form the livelihood of more than five hundred families in and around Ashtamudi Lake, situated between latitude 8°45' - 9°28' N and 76°28 - 77" 17' E. The alarming increase in the exploitation of Paphia malabarica in the recent years forced the Government of Kerala to impose ban on the fishing activities during its breeding season based on the recommendations of CMFRI in 1993

INCF/OCNS Software Working Group

Neuroscience cannot exist without its ecosystem of community-developed software tools that many of us rely heavily upon. The newly established Software Working Group, a community working group shared by the International Neuroinformatics Coordinating Facility (INCF) and the Organization for Computational Neurosciences (OCNS), aims to undertake activities that focus on these software tools. Members of the working group will find and discuss relevant software tools, learn and teach how to use them, test and review them, and report bugs to inform tool developers of issues when required. The working group will also strive to learn how these tools work to get involved in their development and maintenance. The aim is to ensure that the tools that our community depends on continue to be maintained by actively engaged community members, and to bring end users into close collaboration with tool developers. Since the working group includes many tool developers, it also serves as a platform to exchange design and development ideas, and will assist in improving interoperability between related tools. Another related goal of the working group is to help members define, improve, and teach transferable skills in the area of modern research software development, particularly in but not limited to, computational neuroscience. The working group is designed to be flexible, instead of being linked to a particular goal. This approach allows the group to pursue timely projects that its members value and are interested in working on. The current goals of the working group are: - To set up and maintain a living document of the current best practices in research software development to serve as a reference for the research community, especially tool developers - To host regular “developer sessions” where developer teams of various tools discuss their development pipelines (or workflows)—to disseminate various development practices, and help potential contributors get started. The activities of the working group can be followed on its website at https://ocns.github.io/SoftwareWG

Cephalopod resources in southeast and northeast coasts of India and Andaman - Nicobar waters

During 1988-'90, FORV Sagar Sampada has made 28 exclusive cruises to three regions in the Bay of Bengal covering different seasons of the year. Cephalopods formed one of the components of the demersal fishery resources of these regions, with the pelagic resources remaining insignificant. The commercially important neritic species of squids (Loligo duvauceli, Doryteuthis sibogae and Doryteuthis singhalensis), and cuttlefish (Sepia aculeata) were comparatively more in number and quantity than the species of oceanic squid Symplectoteuthis oualaniensis and other less important oceanic squids. The former groups of cephalopods were taken in demersal trawl and the latter in pelagic trawl. The distribution and relative abundance of various neritic and oceanic group of cephalopods by area and depth is given in the paper

Biosorption and Biomineralization of U(VI) by the Marine Bacterium Idiomarina loihiensis MAH1: Effect of Background Electrolyte and pH

The main goal of this study is to compare the effects of pH, uranium concentration, and background electrolyte (seawater and NaClO4 solution) on the speciation of uranium(VI) associated with the marine bacterium Idiomarina loihiensis MAH1. This was done at the molecular level using a multidisciplinary approach combining X-ray Absorption Spectroscopy (XAS), Time-Resolved Laser-Induced Fluorescence Spectroscopy (TRLFS), and High Resolution Transmission Electron Microscopy (HRTEM). We showed that the U(VI)/bacterium interaction mechanism is highly dependent upon pH but also the nature of the used background electrolyte played a role. At neutral conditions and a U concentration ranging from 5·10−4 to 10−5 M (environmentally relevant concentrations), XAS analysis revealed that uranyl phosphate mineral phases, structurally resembling meta-autunite [Ca(UO2)2(PO4)2 2–6H2O] are precipitated at the cell surfaces of the strain MAH1. The formation of this mineral phase is independent of the background solution but U(VI) luminescence lifetime analyses demonstrated that the U(VI) speciation in seawater samples is more intricate, i.e., different complexes were formed under natural conditions. At acidic conditions, pH 2, 3 and 4.3 ([U] = 5·10−4 M, background electrolyte = 0.1 M NaClO4), the removal of U from solution was due to biosorption to Extracellular Polysaccharides (EPS) and cell wall components as evident from TEM analysis. The LIII-edge XAS and TRLFS studies showed that the biosorption process observed is dependent of pH. The bacterial cell forms a complex with U through organic phosphate groups at pH 2 and via phosphate and carboxyl groups at pH 3 and 4.3, respectively. The differences in the complexes formed between uranium and bacteria on seawater compared to NaClO4 solution demonstrates that the actinide/microbe interactions are influenced by the three studied factors, i.e., the pH, the uranium concentration and the chemical composition of the solution.This work was funded by the grants CGL2009-09760 and CGL2012-36505 (Ministerio de Ciencia e Innovación), and RNM 3943 (Junta de Andalucía), Spain

The Related Transcriptional Enhancer Factor-1 Isoform, TEAD4216, Can Repress Vascular Endothelial Growth Factor Expression in Mammalian Cells

Increased cellular production of vascular endothelial growth factor (VEGF) is responsible for the development and progression of multiple cancers and other neovascular conditions, and therapies targeting post-translational VEGF products are used in the treatment of these diseases. Development of methods to control and modify the transcription of the VEGF gene is an alternative approach that may have therapeutic potential. We have previously shown that isoforms of the transcriptional enhancer factor 1-related (TEAD4) protein can enhance the production of VEGF. In this study we describe a new TEAD4 isoform, TEAD4216, which represses VEGF promoter activity. The TEAD4216 isoform inhibits human VEGF promoter activity and does not require the presence of the hypoxia responsive element (HRE), which is the sequence critical to hypoxia inducible factor (HIF)-mediated effects. The TEAD4216 protein is localized to the cytoplasm, whereas the enhancer isoforms are found within the nucleus. The TEAD4216 isoform can competitively repress the stimulatory activity of the TEAD4434 and TEAD4148 enhancers. Synthesis of the native VEGF165 protein and cellular proliferation is suppressed by the TEAD4216 isoform. Mutational analysis indicates that nuclear or cytoplasmic localization of any isoform determines whether it acts as an enhancer or repressor, respectively. The TEAD4216 isoform appears to inhibit VEGF production independently of the HRE required activity by HIF, suggesting that this alternatively spliced isoform of TEAD4 may provide a novel approach to treat VEGF-dependent diseases

Prediction of cis-regulatory elements controlling genes differentially expressed by retinal and choroidal vascular endothelial cells

Cultured endothelial cells of the human retina and choroid demonstrate distinct patterns of gene expression. We hypothesized that differential gene expression reflected differences in the interactions of transcription factors and respective cis-regulatory motifs(s) in these two endothelial cell subpopulations, recognizing that motifs often exist as modules. We tested this hypothesis in silico by using TRANSFAC Professional and CisModule to identify cis-regulatory motifs and modules in genes that were differentially expressed by human retinal versus choroidal endothelial cells, as identified by analysis of a microarray data set. Motifs corresponding to eight transcription factors were significantly (p < 0.05) differentially abundant in genes that were relatively highly expressed in retinal (i.e., glucocorticoid receptor, high mobility group AT-hook 1, heat shock transcription factor 1, p53, vitamin D receptor) or choroidal (i.e., transcription factor E2F, Yin Yang 1, zinc finger 5) endothelial cells. Predicted cis-regulatory modules were quite different for these two groups of genes. Our findings raise the possibility of exploiting specific cis-regulatory motifs to target therapy at the ocular endothelial cells subtypes responsible for neovascular age-related macular degeneration or proliferative diabetic retinopathy