On the formalization and reuse of scientific research

The reuse of scientific knowledge obtained from one investigation in another investigation is basic to the advance of science. Scientific investigations should therefore be recorded in ways that promote the reuse of the knowledge they generate. The use of logical formalisms to describe scientific knowledge has potential advantages in facilitating such reuse. Here, we propose a formal framework for using logical formalisms to promote reuse. We demonstrate the utility of this framework by using it in a worked example from biology: demonstrating cycles of investigation formalization [F] and reuse [R] to generate new knowledge. We first used logic to formally describe a Robot scientist investigation into yeast (Saccharomyces cerevisiae) functional genomics [f₁]. With Robot scientists, unlike human scientists, the production of comprehensive metadata about their investigations is a natural by-product of the way they work. We then demonstrated how this formalism enabled the reuse of the research in investigating yeast phenotypes [r₁ = R(f₁)]. This investigation found that the removal of non-essential enzymes generally resulted in enhanced growth. The phenotype investigation was then formally described using the same logical formalism as the functional genomics investigation [f₂ = F(r₁)]. We then demonstrated how this formalism enabled the reuse of the phenotype investigation to investigate yeast systems-biology modelling [r₂ = R(f₂)]. This investigation found that yeast flux-balance analysis models fail to predict the observed changes in growth. Finally, the systems biology investigation was formalized for reuse in future investigations [f₃ = F(r₂)]. These cycles of reuse are a model for the general reuse of scientific knowledge.     

Using lactic acid bacteria for developing novel fish food products

Lactic acid bacteria‐induced fermentation of fish was tested with the purpose of developing a novel fish food product with desired meat properties. Three selected lactic acid bacteria strains, isolated from lightly preserved fish products, were inoculated into minced frozen fillet of yellowfin tuna, and changes in fish properties were observed during 52 days of storage at 8 °C. Organoleptic, bacteriological and biochemical studies (pH, histamine, TVB‐N, malonaldehyde) and shelf‐life measurements suggest that Leuconostoc mesenteroides could be considered as a possible starter culture for fish fermentation, but additional experiments should be performed. © 2000 Society of Chemical Industry     

The reliability and limits of the MTT reduction assay for carbon nanotubes-cell interaction

The unique physical and chemical properties of carbon nanotubes (CNTs) suggest enormous potential for many areas of research and application. The urgent need for toxicological studies on CNTs has arisen from the steadily increasing production volume. 2-(4,5-dimethyl-2-thiazolyl)-3,5-diphenyl-2H-tetrazolium bromide (MTT) assay is among the most versatile and popular assays used for in vitro toxicology. For particulate samples like CNTs the applicability and limits of various tests including the MTT assay have to be defined. Two MTT assays were applied to study the effect of single-walled CNTs (SWCNTs) on A549 cells. Both assays revealed significant and comparable loss of cell functionality that was confirmed by DNA assay. However, using a cell-free system, we have found that polyoxyethylene sorbitan monooleate-suspended SWCNTs interfere less with MTT assay than sodium dodecyl sulfate-suspended SWCNTs. Moreover, depending on the purification procedure of SWCNTs, they were able to convert MTT into its MTT-formazan insoluble form in the absence of any living system. In summary, a careful validation of MTT assay procedures is therefore suggested in experiments where CNTs are one of the constituents, to avoid a potential bias in concluding results of cytotoxicity studies.     

Phase transition on the Si(001) clean surface prepared in UHV MBE chamber: a study by high-resolution STM and <Emphasis Type="Italic">in situ</Emphasis> RHEED

The Si(001) surface deoxidized by short annealing at T ~ 925°C in the ultrahigh vacuum molecuar beam epitaxy chamber has been in situ investigated using high-resolution scanning tunneling microscopy (STM)and redegreesected high-energy electron diffraction (RHEED. RHEED patterns corresponding to (2 × 1) and (4 × 4) structures were observed during sample treatment. The (4 × 4) reconstruction arose at T ≲ 600°C after annealing. The reconstruction was observed to be reversible: the (4 × 4) structure turned into the (2 × 1) one at T ≳ 600°C, the (4 × 4) structure appeared again at recurring cooling. The c (8 × 8) reconstruction was revealed by STM at room temperature on the same samples. A fraction of the surface area covered by the c (8 × 8) structure decreased, as the sample cooling rate was reduced. The (2 × 1) structure was observed on the surface free of the c (8 × 8) one. The c (8 × 8) structure has been evidenced to manifest itself as the (4 × 4) one in the RHEED patterns. A model of the c (8 × 8) structure formation has been built on the basis of the STM data. Origin of the high-order structure on the Si(001) surface and its connection with the epinucleation phenomenon are discussed.     

Single Au Atoms on the Surface of N-Free and N-Doped Carbon: Interaction with Formic Acid and Methanol Molecules

Topics in Catalysis - Formic acid and methanol are considered as liquid organic hydrogen carriers and could be produced sustainably from biomass or by CO2 hydrogenation using catalysts. The choice...