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.     

Comparison of the Determination of Eight Cholesterol Oxides in Dry�CCured Shoulder by GC�CFID, GC�CMS, and GC Tandem Mass Spectrometry

The analysis of eight cholesterol oxidation products: 7α–hydroxycholesterol, 7β–hydroxycholesterol, α–epoxycholesterol, β–epoxycholesterol, 20α–hydroxycholesterol, cholestanetriol, 25–hydroxycholesterol, and 7–ketocholesterol in dry–cured shoulder was carried out. The extraction of lipids was performed by using the Bligh and Dyer method (1959). Interferences were removed by solid-phase extraction (SPE) in two steps with silica and aminipropylsilica SPE columns. The separation of the eight cholesterol oxidation products was done by gas chromatography, and the detection was performed by flame ionization detection (FID) and mass spectrometry (MS). The results obtained from the use of both systems of detection were compared. The results showed that gas chromatography-mass spectrometry (GC–MS) was the most suitable technique to obtain reliable quantitative data, and significant differences (p < 0.05) between FID and MS determining 7α–hydroxycholesterol, 20α–hydroxycholesterol, and 25–hydroxycholesterol were observed. For the determination of cholesterol oxidation products, it was necessary to apply gas chromatography-tandem mass spectrometry to increase the sensitivity and to avoid interference from other compounds.     

AES for multiscale localization modeling in granular media

This work presents a multiscale strong discontinuity approach to tackle key challenges in modeling localization behavior in granular media: accommodation of discontinuities in the kinematic fields, and direct linkage to the underlying grain-scale information. Assumed enhanced strain (AES) concepts are borrowed to enhance elements for post-localization analysis, but are reformulated within a recently-proposed hierarchical multiscale computational framework. Unlike classical AES methods, where material properties are usually constants or assumed to evolve with some arbitrary phenomenological laws, this framework provides a bridge to extract evolutions of key material parameters, such as friction and dilatancy, based on grain scale computational or experimental data. More importantly, the phenomenological softening modulus typically used in AES methods is no longer required. Numerical examples of plane strain compression tests are presented to illustrate the applicability of this method and to analyze its numerical performance.     

Natural and human forcing in recent geomorphic change; case studies in the Rio de la Plata basin

An analysis of geomorphic system's response to change in human and natural drivers in some areas within the Río de la Plata basin is presented. The aim is to determine whether an acceleration of geomorphic processes has taken place in recent years and, if so, to what extent it is due to natural (climate) or human (land-use) drivers. Study areas of different size, socio-economic and geomorphic conditions have been selected: the Río de la Plata estuary and three sub-basins within its watershed. Sediment cores were extracted and dated (²¹⁰Pb) to determine sedimentation rates since the end of the 19th century. Rates were compared with time series on rainfall as well as human drivers such as population, GDP, livestock load, crop area, energy consumption or cement consumption, all of them related to human capacity to disturb land surface. Data on river discharge were also gathered. Results obtained indicate that sedimentation rates during the last century have remained essentially constant in a remote Andean basin, whereas they show important increases in the other two, particularly one located by the São Paulo metropolitan area. Rates in the estuary are somewhere in between. It appears that there is an intensification of denudation/sedimentation processes within the basin.Rainfall remained stable or varied very slightly during the period analysed and does not seem to explain increases of sedimentation rates observed. Human drivers, particularly those more directly related to capacity to disturb land surface (GDP, energy or cement consumption) show variations that suggest human forcing is a more likely explanation for the observed change in geomorphic processes. It appears that a marked increase in denudation, of a “technological” nature, is taking place in this basin and leading to an acceleration of sediment supply. This is coherent with similar increases observed in other regions.     

An in-vitro method for prediction of the digestible crude protein content in pig feeds

An in-vitro method using commercially available enzymes for the prediction of the in-vivo digestible crude protein content was developed and tested on seven feedstuffs and 16 diets for pigs. Fat-extracted feed samples were consecutively incubated with pepsin at pH 1 and pancreatin at pH 6.8. From the nitrogen content of the feed sample and of the residue after incubation the in-vitro digestibility of the crude protein was calculated. Using the linear regression of in-vitro on in-vivo digestible crude protein of samples obtained in feeding trials, the in-vivo digestible crude protein content (DXP_p) in g kg^?1 dry matter could be predicted. For feedstuffs and diets the correlation was 0.99 and 0.95 and the residual standard deviation 17 and 6 g kg^?1 dry matter, respectively. In a similar procedure the nitrogen solubilised during incubation with enzymes was analysed. The regression value was similar to that of the original procedure. However, this procedure was abandoned because it was more laborious.     

Integrated Inductors Modeling for Library Development and Layout Generation

In this work we propose a modification to the conventional lumped equivalent circuit model for integrated inductors. Also the widely used parametric model is modified. The proposed models expand the frequency range where the integrated inductor behavior is accurately predicted. They are useful in developing automatic tools to assist the designers in selecting and automatically laying-out integrated inductors [1]. This work is based on measurements from integrated inductors fabricated in a standard silicon process.