Advanced Design Concepts for Open Distributed Systems Development

Experience with the engineering of large scale open distributed systems has shown that their design should be specified at several well-defined levels of abstraction, in which each level aims at satisfying specific user, architectural, and implementation needs. Therefore, designers should dispose of a comprehensive design methodology, which allows them to conceive a specification at a certain abstraction level and transform this specification into a conforming specification at a lower abstraction level. The collection of these transformations should abridge the total design trajectory from initial user requirements to final implementation. The authors present and discuss some advanced design concepts that provide a basis for such a design methodolog

What makes industries believe in formal methods

The introduction of formal methods in the design and development departments of an industrial company has far reaching and long lasting consequences. In fact it changes the whole environment of methods, tools and skills that determine the design culture of that company. A decision to replace current design practice by formal methods, therefore, appears a vital one and is not lightly taken. The past has shown that efforts to introduce formal methods in industry has faced a lot of controversy and opposition at various hierarchical levels in companies, resulting in a marginal spread of such methods. This paper revisits the requirements for formal description techniques and identifies some critical success and inhibiting factors associated with the introduction of formal methods in the industrial practice. One of the inhibiting factors is the often encountered lack of appropriateness of the formal model to express and manipulate the design concerns that determine the world of the engineer. This factor motivated our research in the area of architectural and implementation design concepts. The last two sections of this paper report on some results of this research

Advances in architectural concepts to support distributed systems design

This paper presents and discusses some architectural concepts for distributed systems design. These concepts are derived from an analysis of limitations of some currently available standard design languages. We conclude that language design should be based upon the careful consideration of architectural concepts. This paper aims at supporting designers by presenting a methodological design framework in which they can reason about the design and implementation of distributed systems. The paper is also meant for language developers and formalists by presenting a collection of architectural concepts which deserve consideration for formal support

A design model for Open Distributed Processing systems

This paper proposes design concepts that allow the conception, understanding and development of complex technical structures for open distributed systems. The proposed concepts are related to, and partially motivated by, the present work on Open Distributed Processing (ODP). As opposed to the current ODP approach, the concepts are aimed at supporting a design trajectory with several, related abstraction levels. Simple examples are used to illustrate the proposed concepts

A 331 WIMPy Dark Radiation Model

Recent observations suggest that the number of relativistic degrees of freedom in the early universe might exceed what is predicted in the standard cosmological model. If even a small, percent-level fraction of dark matter particles are produced relativistically, they could mimic the effect of an extra realistic species at matter-radiation equality while obeying BBN, CMB and Structure Formation bounds. We show that this scenario is quite naturally realized with a weak-scale dark matter particle and a high-scale ``mother'' particle within a well motivated 3-3-1 gauge model, which is particularly interesting for being consistent with electroweak precision measurements, with recent LHC results, and for offering a convincing explanation for the number of generations in the Standard Model.Comment: 10 pages,7 figures. Matches Published EPJC versio

Shallow Genome Sequencing for Phylogenomics of Mycorrhizal Fungi from Endangered Orchids

ABSTRACT Most plant species form symbioses with mycorrhizal fungi and this relationship is especially important for orchids. Fungi in the genera Tulasnella, Ceratobasidium, and Serendipita are critically important for orchid germination, growth and development. The goals of this study are to understand the phylogenetic relationships of mycorrhizal fungi and to improve the taxonomic resources for these groups. We identified 32 fungal isolates with the internal transcribed spacer region and used shallow genome sequencing to functionally annotate these isolates. We constructed phylogenetic trees from 408 orthologous nuclear genes for 50 taxa representing 14 genera, 11 families, and five orders in Agaricomycotina. While confirming relationships among the orders Cantharellales, Sebacinales, and Auriculariales, our results suggest novel relationships between families in the Cantharellales. Consistent with previous studies, we found the genera Ceratobasidium and Thanatephorus of Cerabotasidiaceae to not be monophyletic. Within the monophyletic genus Tulasnella , we found strong phylogenetic signals that suggest a potentially new species and a revision of current species boundaries (e.g. Tulasnella calospora ); however it is premature to make taxonomic revisions without further sampling and morphological descriptions. There is low resolution of Serendipita isolates collected. More sampling is needed from areas around the world before making evolutionary-informed changes in taxonomy. Our study adds value to an important living collection of fungi isolated from endangered orchid species, but also informs future investigations of the evolution of orchid mycorrhizal fungi

Phylogeny of Agavaceae Based on ndhF, rbcL, and its Sequences

Great advances have been made in our understanding of the phylogeny and classification of Agavaceae in the last 20 years. In older systems Agavaceae were paraphyletic due to overemphasis of ovary position or habit. Discovery of a unique bimodal karyotype in Agave and Yucca eventually led to a reexamination of concepts and relationships in all the lilioid monocots, which continues to the present day. Developments in cytogenetics, microscopy, phylogenetic systematics, and most recently DNA technology have led to remarkable new insights. Large-scale rbcL sequence studies placed Agavaceae with the core Asparagales and identified closely related taxa. Analysis of cpDNA restriction sites, rbcL, and ITS nrDNA sequences all supported removal of Dracaenaceae, Nolinaceae, and clarified relationships. Agavaceae s.s. presently consists of Agave, Beschorneria, Furcraea, Hesperaloe, Hesperoyucca, Manfreda, Polianthes, Prochnyanthes, and Yucca. In this paper we analyze recently obtained ndhF sequence data from Agavaceae and Asparagales and discuss the implications for classification. Parsimony analysis of ndhF data alone resolves most genera of Agavaceae and supports the inclusion of Camassia, Chlorogalum, Hesperocallis, and Hosta within Agavaceae s.l. Analysis of combined ndhF and rbcL data sets of selected Asparagales results in better resolution and stronger bootstrap support for many relationships. Combination of all available ndhF, rbcL, and ITS data in a single analysis results in the best resolution currently available for Agavaceae s.l. Implications for classification schemes past and present are discussed

Effect of transgene introgression site on gene migration from transgenic b. napus to b. rapa [abstract]

Abstract only availableThere is a growing concern of the possible transgenic introgression from GM plants into agricultural weeds, which has stimulated research in the process of crop to weed gene flow. Crop to weed gene flow often involves the hybridization of a polyploidy crop to a diploid weed. An example is canola (Brassica napus with AACC genomes) which can hybridize with B. rapa (AA) to produce fertile triploid F1 hybrids (ACC) in the wild. It is hypothesized that there are "safe sites" on the C genome because the C genome is likely to be lost from wild populations after a few generations of repeated backcrossing with B. rapa. However, there is homoeology between the A and C genomes of Brassica, which allows potential recombination between genomes and the movement of transgenes from the C to A genomes by chromosomal rearrangements. Recent advances in molecular markers and fluorescent in situ hybridization (FISH) now allow us to observe the frequency of homoeologous exchanges following hybridization. Our research is focused on finding safe sites within the B. napus genome which are least likely to be transferred into B. napus and B. rapa hybrids and their progeny. To test this, we have crossed a transgenic B. napus with a natural B. rapa three times to make three different F1events. Then we backcrossed each of the three F1 three times with B. rapa. We are measuring the germination rate of each generation and using transgene specific PCR primers to check the presence or absence of the transgene in hybrids. We will also use molecular cytogenetics (FISH) to count chromosome numbers. This study will help determine the possibilities of a "safe" site in B. napus and offer insight in the mechanisms of crop to weed transgene introgression in B. napus x B. rapa hybrids.MU Monsanto Undergraduate Research Fellowshi

Escape from Preferential Retention Following Repeated Whole Genome Duplications in Plants

The well supported gene dosage hypothesis predicts that genes encoding proteins engaged in dose–sensitive interactions cannot be reduced back to single copies once all interacting partners are simultaneously duplicated in a whole genome duplication. The genomes of extant flowering plants are the result of many sequential rounds of whole genome duplication, yet the fraction of genomes devoted to encoding complex molecular machines does not increase as fast as expected through multiple rounds of whole genome duplications. Using parallel interspecies genomic comparisons in the grasses and crucifers, we demonstrate that genes retained as duplicates following a whole genome duplication have only a 50% chance of being retained as duplicates in a second whole genome duplication. Genes which fractionated to a single copy following a second whole genome duplication tend to be the member of a gene pair with less complex promoters, lower levels of expression, and to be under lower levels of purifying selection. We suggest the copy with lower levels of expression and less purifying selection contributes less to effective gene-product dosage and therefore is under less dosage constraint in future whole genome duplications, providing an explanation for why flowering plant genomes are not overrun with subunits of large dose–sensitive protein complexes

Formal description techniques for distributed computing systems:the challenges for the 1990's

Initially FDTs where developed within IS0 and CCITT for specification, at a high-level of abstraction, of distributed systems. Research is now being performed on the use of FDTs to support the complete implementation trajectory. In this paper we discuss a number of such research activities that are conducted within the framework of the Lotosphere project(*). The paper discusses aspects of design methodology, correctness preserving transformation, the reflection of design criteria, the role of pre-defined specification and implementation constructs, and formal approaches to conformance testing. Furthermore some insight is given in the development of a comprehensive toolset that supports these aspects of design methodology. The paper concludes with some experience obtained from the application of these methods and tools to some realistic pilot implementations: an ISDN and MHS application and a Transaction Processing application