How Will We Interact with the Web of Data?

The Web is currently evolving from an information space of linked documents, to a Web of linked, machine-readable data. Perhaps counter-intuitively, this shift to publishing data for machine consumption raises many challenges for human-computer interaction. In this article I will discuss some of the implications of this trend for how we interact with the Web of data and consider how familiar tools such as the Web browser may need to develop.     

The emerging landscape of bioinformatics software systems

Fusing computing and biology expertise, bioinformatics software provides a powerful tool for organizing and mining the vast amounts of data genetics researchers are accumulating. As life scientists and computational scientists interact to create useful bioinformatics software systems, several themes or lessons recur. We identify seven themes: the nature of biological data; data storage, analysis and retrieval; computational modeling and simulation; biologically meaningful information integration; data mining; image processing and visualization; and closing the loop     

Factorization of multipliers in passivity and IQC analysis

Multipliers are often used to find conditions for the absolute stability of Lur’e systems. They can be used either in conjunction with passivity theory or within the more recent framework of integral quadratic constraints (IQCs). We compare the use of multipliers in both approaches. Passivity theory requires that the multipliers have a canonical factorization and it has been suggested in the literature that this represents an advantage of the IQC theory. We consider sufficient conditions on the nonlinearity class for the associated multipliers to have a canonical factorization.     

Stereospecific synthesis of (Z,Z)-11,13-hexadecadienal,a female sex pheromone of the navel orangeworm,Amyelois transitella (Lepidoptera: Pyralidae)

A synthesis of (Z,Z)-11,13-hexadecadienal, a compound previously identified as the major component of the sex pheromone of the female navel orangeworm,Amyelois transitella (Walker), is described. The key step is the reduction of an unsymmetrical conjugated diyne with dicyclohexylborane. This reduction produced theZ,Z isomer with less than 0.5% total of other isomers.Mention of a commercial or proprietary product in this paper does not constitute endorsement of that product by the USDA.     

Electrical engineering department,Heriot-Watt university,Edinburgh, UK

This review describes research work which is just starting in the Electrical Engineering Department of Heriot-Watt University. It is based on a directed-graph method of describing the structure of a computation, and as such can be equally applied to hardware and software. It is a computer aid to the logical and program designer, rather than to the drawing office and production department, like most present day digital c.a.d. systems. The project is based on the results of various workers, and much of this paper contains a summary of their work as a necessary introduction.It is possible to write a good many pages¹ on the lack of c.a.d. for computer designers: the shortest summary is to say that it is not possible to be sure what a normal hardware logic structure will do except by simulation or exhaustive tests. The alternatives for $\text{n}$ Boolean variables must have some relation to 2²ⁿ, a number which can rapidly outstrip any speed improvement in computer simulation as $\text{n}$ increases. Since programming uses hardware-built functions there is a similar effect, and once again the structure of a program is no guarantee of correct performance-exhaustive testing or whether exhaustive testing or machine simulation is needed. Lastly, since the design methods are so different for programs and logic there is a considerable interface problem.     

High-density hybridoma perfusion culture. Limitation vs inhibition

Because our earlier work indicated a strong correlation between specific antibody productivity and cell density in perfusion culture, we conducted experiments to determine the optimum means of increasing cell density while maintaining high antibody productivity. The rates of medium supply and waste removal were varied to determine whether cell density was limited or inhibited, and whether a diffusable substance could be responsible for the correlation between antibody productivity and cell density. Nutrient supply was found to be a stronger determinant of cell density than waste removal; however, the rate of waste removal had a greater effect on cell growth at lower cell densities. Even at noninhibitory levels of ammonia and lactate, cellular metabolism was regulated to minimize their concentrations at lowered rates of waste removal. Separate step changes in glucose and glutamine resulted in increased cell density and antibody concentration. Specific antibody productivity increased following the step in glutamine, but not glucose. Both steps caused changes in cellular metabolism that prevented the levels of lactate and ammonia from reaching toxic levels.     

Targeted disruption of fibroblast growth factor (FGF) receptor 2 suggests a role for FGF signaling in pregastrulation mammalian development

We disrupted the fibroblast growth factor (FGF) receptor 2 (FGFR2) gene by introducing a neo cassette into the IIIc ligand binding exon and by deleting a genomic DNA fragment encoding its transmembrane domain and part of its kinase I domain. A recessive embryonic lethal mutation was obtained. Preimplantation development was normal until the blastocyst stage. Homozygous mutant embryos died a few hours after implantation at a random position in the uterine crypt, with collapsed yolk cavity. Mutant blastocysts hatched, adhered, and formed a layer of trophoblast giant cells in vitro, but after prolonged culture, the growth of the inner cell mass stopped, no visceral endoderm formed, and finally the egg cylinder disintegrated. It follows that FGFR2 is required for early postimplantation development between implantation and the formation of the egg cylinder. We suggest that FGFR2 contributes to the outgrowth, differentiation, and maintenance of the inner cell mass and raise the possibility that this activity is mediated by FGF4 signals transmitted by FGFR2. The role of early FGF signaling in pregastrulation development as a possible adaptation to mammalian (amniote) embryogenesis is discussed.     

Agrobacterium tumefaciens-mediated transformation of yeast

Agrobacterium tumefaciens transfers a piece of its Ti plasmid DNA (transferred DNA or T-DNA) into plant cells during crown gall tumorigenesis. A. tumefaciens can transfer its T-DNA to a wide variety of hosts, including both dicotyledonous and monocotyledonous plants. We show that the host range of A. tumefaciens can be extended to include Saccharomyces cerevisiae. Additionally, we demonstrate that while T-DNA transfer into S. cerevisiae is very similar to T-DNA transfer into plants, the requirements are not entirely conserved. The Ti plasmid-encoded vir genes of A. tumefaciens that are required for T-DNA transfer into plants are also required for T-DNA transfer into S. cerevisiae, as is vir gene induction. However, mutations in the chromosomal virulence genes of A. tumefaciens involved in attachment to plant cells have no effect on the efficiency of T-DNA transfer into S. cerevisiae. We also demonstrate that transformation efficiency is improved 500-fold by the addition of yeast telomeric sequences within the T-DNA sequence.