Towards a neighborhood simplification of tile systems: From Moore to quasi-linear dependencies

Self-assembly is the process by which objects aggregate independently and form complex structures. One of the theoretical frameworks in which the process of self-assembly can be embedded and formally studied is that of tile systems. A Wang tile is a square unit, with glues on its edges, attaching to other tiles which have matching glues, and forming larger and larger structures. In this paper we concentrate over two basic, but essential, self-assembling structures done by Wang tiles. The first one, called ribbon, is a non-self-crossing wire-like structure, in which successive tiles are adjacent along an edge, and where tiles are glued to their predecessor and successor by use of matching glues. The second one, called zipper, is a similar contiguous structure, only that here, all touching tiles must have matching glues on their abutting edges, independently of their position in the structure. In case of Wang tiles, it has been shown that these two structures are equivalent. Here we generalize this result for the case when the tiles have eight glues, four on their edges and four on their corners. Thus we show that an eight neighborhood dependency, namely the Moore neighborhood, can be simulated by a quasi-linear dependency.     

Polyominoes simulating arbitrary-neighborhood zippers and tilings

This paper provides a bridge between the classical tiling theory and the complex-neighborhood self-assembling situations that exist in practice.The neighborhood of a position in the plane is the set of coordinates which are considered adjacent to it. This includes classical neighborhoods of size four, as well as arbitrarily complex neighborhoods. A generalized tile system consists of a set of tiles, a neighborhood, and a relation which dictates which are the “admissible” neighboring tiles of a given tile. Thus, in correctly formed assemblies, tiles are assigned positions of the plane in accordance with this relation.We prove that any validly tiled path defined in a given but arbitrary neighborhood (a zipper) can be simulated by a simple “ribbon” of microtiles. A ribbon is a special kind of polyomino, consisting of a non-self-crossing sequence of tiles on the plane, in which successive tiles stick along their adjacent edge.Finally, we extend this construction to the case of traditional tilings, proving that we can simulate arbitrary-neighborhood tilings by simple-neighborhood tilings, while preserving some of their essential properties.     

An approach for incorporating quality-based cost–benefit analysis in data warehouse design

Data are considered to be important organizational assets because of their assumed value, including their potential to improve the organizational decision-making processes. Such potential value, however, comes with various costs, including those of acquiring, storing, securing and maintaining the given assets at appropriate quality levels. Clearly, if these costs outweigh the value that results from using the data, it would be counterproductive to acquire, store, secure and maintain the data. Thus cost–benefit assessment is particularly important in data warehouse (DW) development; yet very few techniques are available for determining the value that the organization will derive from storing a particular data table and hence determining which data set should be loaded in the DW. This research seeks to address the issue of identifying the set of data with the potential for producing the greatest net value for the organization by offering a model that can be used to perform a cost–benefit analysis on the decision support views that the warehouse can support and by providing techniques for estimating the parameters necessary for this model.     

Two-step purification strategy for enhanced recovery of recombinant hepatitis B surface antigen from Pichia pastoris

Univariate screening on factors affecting the purification performance of recombinant hepatitis B surface antigen (HBsAg) on ion exchange chromatography (IEC) and size exclusion chromatography (SEC) and the establishment of a two-step purification strategy were performed. Amongst four IEC adsorbents examined, the use of Q Sepharose XL IEC adsorbent under optimized conditions together with optimized SEC purification was able to efficiently purify HBsAg. An established purification strategy comprising the two techniques further demonstrated adaptability for scale-up operations with a final total purification factor (PF) of 94.82 ± 16.20, HBsAg purity of 95.48% and recovery yield of 78.07%.     

Effect of sarsaponin on ruminal fermentation with particular reference to methane production in vitro

This experiment was designed to investigate the effects of different concentrations (0, 1.2, 1.8, 2.4, and 3.2 g/L) of sarsaponin on ruminal microbial methane production using the substrates soluble potato starch, cornstarch, or hay plus concentrate (1.5:1). Ruminal fluid was collected from a dairy cow, mixed with phosphate buffer (1:2) and incubated (30 ml) anaerobically at 38 degrees C for 6 and 24 h with or without sarsaponin. Excluding the lower level of sarsaponin, pH of the medium was slightly decreased. Ammonia-N concentration and numbers of protozoa were decreased in a dose-dependent manner. Total volatile fatty acids and total gas production were increased. Molar proportion of acetate was decreased and propionate was increased with a corresponding decrease in acetate:propionate ratio. Hydrogen production was decreased. As the concentration of sarsaponin increased from 1.2 to 3.2 g/L, fermentation of soluble potato starch, cornstarch, or hay plus concentrate decreased methane production from 20 to 60% (6 h) and 17 to 50% (24 h), 21 to 58% (6 h) and 18 to 52% (24 h), and 23 to 53% (6 h) and 15 to 44% (24 h), respectively. Excluding the lower dose concentration (1.2 g/L) of sarsaponin, in vitro disappearance of dry matter of hay plus concentrate was decreased after 24 h. In conclusion, these results show that sarsaponin stimulated the mixed ruminal microorganism fermentation as well as to inhibit methane production in vitro.     

Sticky-free and overhang-free DNA languages

An essential step of any DNA computation is encoding the input data on single or double DNA strands. Due to the biochemical properties of DNA, complementary single strands can bind to one another forming double-stranded DNA. Consequently, data-encoding DNA strands can sometimes interact in undesirable ways when used in computations. It is crucial thus to analyze properties that guard against such phenomena and study sets of sequences that ensure that no unwanted bindings occur during any computation. This paper formalizes and investigates properties of DNA languages that guarantee their robusteness during computations. After defining and investigating several types of DNA languages possessing good encoding properties, such as sticky-free and overhang-free languages, we give algorithms for deciding whether regular DNA languages are invariant under bio-operations. We also give a method for constructing DNA languages that, in addition to being invariant and sticky-free, possess error-detecting properties. Finally, we present the results of running tests that check whether several known gene languages (the set of genes of a given organism) as well as the input DNA languages used in Adlemans DNA computing experiment, have the defined properties.Received: 6 February 2003, Published online: 2 September 2003Research partially supported by Grants R2824A01 and R220259 of the Natural Sciences and Engineering Research Council of Canada.     

Modulation of Lumen Formation by Microgeometrical Bioactive Cues and Migration Mode of Actin Machinery

How endothelial cells (ECs) express the particular filopodial or lamellipodial form of the actin machinery is critical to understanding EC functions such as angiogenesis and sprouting. It is not known how these mechanisms coordinately promote lumen formation of ECs. Here, adhesion molecules (RGD peptides) and inductor molecules (BMP‐2 mimetic peptides) are micropatterned onto polymer surfaces by a photolithographic technique to induce filopodial and lamellipodial migration modes. Firstly, the effects of peptide microgeometrical distribution on EC adhesion, orientation and morphogenesis are evaluated. Large micropatterns (100 μm) promote EC orientation without lumen formation, whereas small micropatterns (10–50 μm) elicit a collective cell organization and induce EC lumen formation, in the case of RGD peptides. Secondly, the correlation between EC actin machinery expression and EC self‐assembly into lumen formation is addressed. Only the filopodial migration mode (mimicked by RGD) but not lamellipodial migration mode (mimicked by BMP‐2) promotes EC lumen formation. This work gives a new concept for the design of biomaterials for tissue engineering and may provide new insight for angiogenesis inhibition on tumors.     

The metabolism and analysis of isoflavones and other dietary polyphenols in foods and biological systems

Polyphenols in dietary and botanical matrices are usually present as simple and complex O-glycosides. In fermented dietary materials, the glycosidic moiety is removed and accompanied in some cases by more complex changes to the polyphenol. As for most xenobiotics, polyphenols undergo phase II conjugation in the intestinal wall during their absorption from the gut. In contrast, a few polyphenols, such as puerarin in the kudzu vine, are C-glycosides and are stable in the gut and during absorption, distribution and excretion. Large bowel bacteria reduce polyphenol aglycones, causing opening of the heterocyclic B-ring and ring cleavage. The products are mostly absorbed and enter the bloodstream. Phase I and II metabolism events occur in the intestine and the liver - most polyphenols predominantly circulate as β-glucuronides and sulfate esters with very little as the aglycones, the presumed active forms. In addition, metabolism can occur in non-hepatic tissues and cells including breast tumor cells that have variable amounts of cytochrome P450s, sulfatase and sulfotransferase activities. Inflammatory cells produce chemical oxidants (HOCl, HOBr, ONO(2)(-)) that will react with polyphenols. The isoflavones daidzein and genistein and the flavonol quercetin form mono- and dichlorinated products in reaction with HOCl. Genistein is converted to 3'-nitrogenistein in the lung tissue of lipopolysaccharide-treated rats. Whereas polyphenols that can be converted to quinones or epoxides react with glutathione (GSH) to form adducts, chlorinated isoflavones do not react with GSH; instead, they are converted to β-glucuronides and are excreted in bile. Analysis of polyphenols and their metabolites is routinely carried out with great sensitivity, specificity and quantification by LC-tandem mass spectrometry. Critical questions about the absorption and tissue uptake of complex polyphenols such as the proanthocyanins can be answered by labeling these polyphenols with (14)C-sucrose in plant cell culture and then purifying them for use in animal experiments. The (14)C signature is quantified using accelerator mass spectrometry, a technique capable of detecting one (14)C atom in 10(15) carbon atoms. This permits the study of the penetration of the polyphenols into the interstitial fluid, the fluid that is actually in contact with non-vascular cells.     

Effect of seed treatments on the chemical composition and properties of two amaranth species: starch and protein

The seeds of two Amaranth species were studied. The starch contents were 543 and 623 g kg^?1 while crude protein contents were 154 and 169 g kg^?1 for Amaranthus caudatus and Amaranthus cruentus seeds, respectively. The effect of several treatments, including cooking, popping and germination and flour air classification on the protein and starch properties were studied. Air classification decreased the starch content and increased the protein content, while heating increased the protein but did not affect the starch content. Germination decreased both starch and protein contents. Amylose content was increased by air classification and heating, but was not affected by germination. It was found that all treatments increased the starch swelling power and reduced the falling number. The resistant starch content was increased in the high protein flour (HPF) fraction and germinated flour compared with the raw flour, while its content decreased in the heat treated seed flours. These processes also affected the starch gelatinization temperature and peak viscosity. The thermal properties of the starch flour were not affected by air classification while gelatinization energy was decreased significantly (by 52.0 and 90.0% and by 70.0 and 95.0%) in cooked and popped A caudatus and A cruentus seed flours, respectively. The gelatinization energy was highest in germinated seeds dried at 90 °C with values of 2.67 and 3.87 J g^?1. Air classification reduced the level of all protein fractions. Thermal treatment decreased the water‐soluble fraction (albumins + globulins) and alcohol‐soluble fraction (prolamins) in both species. The levels of all fractions except the water‐soluble fraction (albumins + globulins) were reduced significantly in both species by germination, which mainly increased the amount of aspartic acid, serine and alanine, while the amounts of threonine, arginine and tyrosine decreased in both species. The polypeptide bands of the HPF in both species were unchanged compared with the raw seed flours, but more intensive coloured bands were observed. Thermal treatments eliminated major and minor bands above 35.0 KDa in both species. Copyright © 2004 Society of Chemical Industry