Effect of pooling samples on the efficiency of comparative studies using microarrays

Motivation: Many biomedical experiments are carried out by pooling individual biological samples. However, pooling samples can potentially hide biological variance and give false confidence concerning the data significance. In the context of microarray experiments for detecting differentially expressed genes, recent publications have addressed the problem of the efficiency of sample pooling, and some approximate formulas were provided for the power and sample size calculations. It is desirable to have exact formulas for these calculations and have the approximate results checked against the exact ones. We show that the difference between the approximate and the exact results can be large.

Desulfurisation of oils using ionic liquids: selection of cationic and anionic components to enhance extraction efficiency

Extraction of dibenzothiophene from dodecane using ionic liquids as the extracting phase has been investigated for a range of ionic liquids with varying cation classes (imidazolium, pyridinium, and pyrrolidinium) and a range of anion types using liquid-liquid partition studies and QSPR (quantitative structure-activity relationship) analysis. The partition ratio of dibenzothiophene to the ionic liquids showed a clear variation with cation class (dimethylpyridinium > methylpyridinium > pyridinium approximate to imidazolium approximate to pyrrolidinium), with much less significant variation with anion type. Polyaromatic quinolinium-based ionic liquids showed even greater extraction potential, but were compromised by higher melting points. For example, 1-butyl-6-methylquinolinium bis{(trifluoromethyl)sulfonyl} amide (mp 47 degrees C) extracted 90% of the available dibenzothiophene from dodecane at 60 degrees C.

In situ measurement of UHF wearable antenna radiation efficiency using a reverberation chamber

The radiation efficiency and resonance frequency of five compact antennas worn by nine individual test subjects was measured at 2.45 GHz in a reverberation chamber. The results show that, despite significant differences in body mass, wearable antenna radiation efficiency had a standard deviation less than 0.6 dB and the resonance frequency shift was less than 1% between test subjects. Variability in the radiation efficiency and resonance frequency shift between antennas was largely dependant on body tissue coupling which is related to both antenna geometry and radiation characteristics. The reverberation chamber measurements were validated using a synthetic tissue phantom and compared with results obtained in a spherical near field chamber and finite-difference time-domain (FDTD) simulation.

Lanthanide(III) nitrobenzenesulfonates as new nitration catalysts: The role of the metal and of the counterion in the catalytic efficiency

Lanthanide(III) complexes of p-nitrobenzenesulfonic acid, Ln(p-NBSA)(3), m-nitrobenzenesulfonic acid, Ln(m-NBSA)(3), and 2,4-nitrobenzenesulfonic acid, Ln(2,4-NBSA)(3), were prepared, characterized and examined as catalyst for the nitration of benzene, toluene, xylenes, naphthalene, bromobenzene and chlorobenzene. The initial screening of the catalysts showed that lanthanum(III) complexes were more effective than the corresponding ytterbium(III) complexes, and that catalysts containing the bulky 2,4-NBSA ligand were less effective than the catalyst containing p-NBSA (nosylate) or m-NBSA ligands. Examination of a series of Ln(p-NBSA)(3) and Ln(m-NBSA)(3) catalysts revealed that there is a clear correlation between the ionic radii of the lanthanide(III) ions and the yields of nitration, with the lighter lanthanides being more effective. The X-ray single crystal structure of Yb(m-NBSA)(3).6H(2)O shows that two m-NBSA ligands are directly bound to the metal centre while the third ligand is not located in the first coordination sphere, but it is hydrogen bonded to one of the water molecules which is coordinated to ytterbium(III). NMR studies suggest that this structure is preserved under the conditions used in the nitration reaction. The structure of Yb(m-NBSA)(3) is markedly different from the structure of the well-known ytterbium(III) triflate catalyst. The coordination of the nitrobenzenesulfonate counterion to the lanthanide(III) ion suggests that steric effects might play an important role in determining the efficiency of these novel nitration catalysts. ((C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004).

The settlement performance of stone column foundations

Vibrated stone columns are frequently used as a method of reinforcing soft ground as they provide increased bearing capacity and reduce foundation settlements. Their performance in relation to bearing capacity is well documented, but there is also a need for enhanced understanding of their settlement characteristics, particularly in relation to small-group configurations. This paper presents results obtained from physical model tests on triaxial specimens 300 mm in diameter and 400 mm high. Parameters investigated include column length to diameter ratio, area replacement ratio and single/group configuration. The findings of the work are as follows. The design is flexible: settlement can equally be controlled using short columns at relatively high area replacement ratios, or longer columns at smaller area replacement ratios. An optimum area replacement ratio of 30-40% exists for the control of settlement. The settlement performance of a small column group is highly influenced by inter-column and footing interaction effects.

Direct and indirect effects of species displacements; an invading freshwater amphipod can disrupt leaf litter processing and shredder efficiency

Invasive species may threaten the fundamental role played by native macroinvertebrate shredders in determining energy flow and the trophic dynamics of freshwater ecosystems. Functionally, amphipods have long been regarded as mainly shredders, but they are increasingly recognized as major predators of other macroinvertebrate taxa. Furthermore, intraguild predation (IGP) between native and invasive amphipods underlies many species displacements. We used laboratory mesocosms to investigate what might happen to shredders and leaf-litter processing in water bodies invaded by the highly predatory Ponto-Caspian amphipod Dikerogammarus villosus, which is spreading rapidly throughout Europe and may soon invade the North American Great Lakes. The leaf-shredding efficiency of D. villosus was significantly lower than that of 3 Gammarus species (2 native and 1 invasive) that D. villosus has either already displaced or may be currently displacing in The Netherlands. In addition, D. villosus was a major predator of all of these native and invasive amphipod shredders and of a common isopod shredder Asellus aquaticus. Leaf processing in Gammarus and Asellus mesocosms declined rapidly in the presence of D. villosus and ceased altogether within 4 d because by then, all potential shredders had been killed and consumed. Furthermore, the shredding efficiency of surviving amphipods and isopods declined significantly within 2 d of the release of D. villosus, a result indicating that predator-avoidance behavior may override leaf processing. We discuss the implications of these direct and indirect effects of D. villosus invasions and species displacements on community structure and litter processing in aquatic ecosystems. © 2011 The North American Benthological Society.


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The pressure distribution along the stone column in soft clay when subjected to consolidation and foundation loading

The mechanism whereby the foundation loading is transmitted through stone the column (included in soft clay) has received less attention from researchers. This paper reports on some interesting findings obtained from a laboratory-based model study in respect of this issue. The stone column, included in the soft clay bed was subjected to foundation loading under drained conditions. The results show, probably for the first time, how the foundation loadings are transmitted through the column and indeed the existence of “negative skin friction” (a widely accepted phenomena in solid piles) in granular columns in soft clays.

The application of colloidal gas aphrons in the recovery of fine cellulose fibres from paper mill wastewater

Colloidal gas aphrons (CGAs) are micron-sized gas bubbles of 25–30 µm in diameter produced by a high-speed stirrer in a vessel containing dilute surfactant solution. These bubbles, because of their small size, exhibit some colloidal properties. In this work, CGAs were used to separate fine fibres from a lean slurry of cellulosic pulp in a flotation column. The pulp fibres were recovered as foamate from the top. Sodium dodecyl sulphate at a concentration of 2.0 kg/m3 was used as a surfactant to generate the CGAs in a spinning disc apparatus. The results indicated that up to 70% flotation efficiency could be obtained within a short column height of 0.3–0.35 m. This technique can be applied to recover fine cellulosic pulp from paper-machine backwater.

Maximising capture efficiency and specificity of magnetic separation for Mycobacterium avium subsp. paratuberculosis cells

In order to introduce specificity for Mycobacterium avium subsp. paratuberculosis prior to a phage amplification assay, various magnetic-separation approaches, involving either antibodies or peptides, were evaluated in terms of the efficiency of capture (expressed as a percentage) of M. avium subsp. paratuberculosis cells and the percentage of nonspecific binding by other Mycobacterium spp. A 50:50 mixture of MyOne Tosylactivated Dynabeads coated with the chemically synthesized M. avium subsp. paratuberculosis-specific peptides biotinylated aMp3 and biotinylated aMptD (i.e., peptide-mediated magnetic separation [PMS]) proved to be the best magnetic-separation approach for achieving 85 to 100% capture of M. avium subsp. paratuberculosis and minimal (<1%) nonspecific recovery of other Mycobacterium spp. (particularly if beads were blocked with 1% skim milk before use) from broth samples containing 103 to 104 CFU/ml. When PMS was coupled with a recently optimized phage amplification assay and used to detect M. avium subsp. paratuberculosis in 50-ml volumes of spiked milk, the mean 50% limit of detection (LOD50) was 14.4 PFU/50 ml of milk (equivalent to 0.3 PFU/ml). This PMS-phage assay represents a novel, rapid method for the detection and enumeration of viable M. avium subsp. paratuberculosis organisms in milk, and potentially other sample matrices, with results available within 48 h.