BiplotGUI: Interactive Biplots in R

Biplots simultaneously provide information on both the samples and the variables of a data matrix in two- or three-dimensional representations. The BiplotGUI package provides a graphical user interface for the construction of, interaction with, and manipulation of biplots in R. The samples are represented as points, with coordinates determined either by the choice of biplot, principal coordinate analysis or multidimensional scaling. Various transformations and dissimilarity metrics are available. Information on the original variables is incorporated by linear or non-linear calibrated axes. Goodness-of-fit measures are provided. Additional descriptors can be superimposed, including convex hulls, alpha-bags, point densities and classification regions. Amongst the interactive features are dynamic variable value prediction, zooming and point and axis drag-and-drop. Output can easily be exported to the R workspace for further manipulation. Three-dimensional biplots are incorporated via the rgl package. The user requires almost no knowledge of R syntax.

Differential Effects of Buffer pH On Ca\u3csup\u3e2+\u3c/sup\u3e-Induced ROS Emission with Inhibited Mitochondrial Complexes I and III

Excessive mitochondrial reactive oxygen species (ROS) emission is a critical component in the etiology of ischemic injury. Complex I and complex III of the electron transport chain are considered the primary sources of ROS emission during cardiac ischemia and reperfusion (IR) injury. Several factors modulate ischemic ROS emission, such as an increase in extra-matrix Ca2+, a decrease in extra-matrix pH, and a change in substrate utilization. Here we examined the combined effects of these factors on ROS emission from respiratory complexes I and III under conditions of simulated IR injury. Guinea pig heart mitochondria were suspended in experimental buffer at a given pH and incubated with or without CaCl2. Mitochondria were then treated with either pyruvate, a complex I substrate, followed by rotenone, a complex I inhibitor, or succinate, a complex II substrate, followed by antimycin A, a complex III inhibitor. H2O2 release rate and matrix volume were compared with and without adding CaCl2 and at pH 7.15, 6.9, or 6.5 with pyruvate + rotenone or succinate + antimycin A to simulate conditions that may occur during in vivo cardiac IR injury. We found a large increase in H2O2 release with high [CaCl2] and pyruvate + rotenone at pH 6.9, but not at pHs 7.15 or 6.5. Large increases in H2O2 release rate also occurred at each pH with high [CaCl2] and succinate + antimycin A, with the highest levels observed at pH 7.15. The increases in H2O2 release were associated with significant mitochondrial swelling, and both H2O2 release and swelling were abolished by cyclosporine A, a desensitizer of the mitochondrial permeability transition pore (mPTP). These results indicate that ROS production by complex I and by complex III is differently affected by buffer pH and Ca2+ loading with mPTP opening. The study suggests that changes in the levels of cytosolic Ca2+ and pH during IR alter the relative amounts of ROS produced at mitochondrial respiratory complex I and complex III

A bioinformatics approach to the development of immunoassays for specified risk material in canned meat products

A bioinformatics approach to developing antibodies to specific proteins has been evaluated for the production of antibodies to heat-processed specified risk tissues from ruminants (brain and eye tissue). The approach involved the identification of proteins specific to ruminant tissues by interrogation of the annotation fields within the Swissprot database. These protein sequences were then interrogated for peptide sequences that were unique to the protein. Peptides were selected that met these criteria as close as possible and that were also theoretically resistant to either pepsin or trypsin. The selected peptides were synthesised and used as immunogens to raise monoclonal antibodies. Antibodies specific for the synthetic peptides were raised to half of the selected peptides. These antibodies have each been incorporated into a competitive enzyme-linked immunosorbent assay (ELISA) and shown to be able to detect the heat-processed parent protein after digestion with either pepsin or trypsin. One antibody, specific for alpha crystallin peptide (from bovine eye tissue), was able to detect the peptide in canned meat products spiked with 10% eye tissue. These results, although preliminary in nature, show that bioinformatics in conjunction with enzyme digestion can be used to develop ELISA for proteins in high-temperature processed foods and demonstrate that the approach is worth further stud

Mean curvature flow in asymptotically flat product spacetimes

We consider the long-time behaviour of the mean curvature flow of spacelike hypersurfaces in the Lorentzian product manifold $M\times\mathbb{R}$, where $M$ is asymptotically flat. If the initial hypersurface $F_0\subset M\times\mathbb{R}$ is uniformly spacelike and asymptotic to $M\times\left\{s\right\}$ for some $s\in\mathbb{R}$ at infinity, we show that a mean curvature flow starting at $F_0$ exists for all times and converges uniformly to $M\times\left\{s\right\}$ as $t\to \infty$.Comment: 23 pages, final versio

Cannabinoid CB1 receptor binding and acetylcholinesterase inhibitory activity of Sceletium tortuosum L.

The whole plant extract of plant Sceletium tortuosum, plant native to South Africa, has been known traditionally to have mood enhancing and stimulant properties. These properties have been confirmed before by proving serotonin-uptake inhibition activity. A further confirmation by using CB1 receptor binding assay has been performed in this study. The unfermented alkaloid extract was proved to posses a higher activity to bind CB1 receptor compared to that of the fermented one. GC-MS analysis confirmed that unfermented alkoloid extract contain more alkaloids than the fermented one. The methanol extract was also more active than the fermented one, suggesting that non-alkaloid compounds in this extract could posses this activity. An additional test to check wether this extract can improve cognitive function and memory was performed by acetylcholinesterase inhibitory assay. Both fermented and unfermented alkaloid extracts could inhibit acetylcholinesterase with IC 50 being 0.303 mg/ml and 0.330 mg/ml, respectively. However, the major alkaloid in the extract, mesembrine, did not show inhibition of the enzyme. A TLC based test proved that other alkaloids in the extract were responsible to the activity

Context-dependent motor skill and the role of practice

Research has shown that retrieval of learned information is better when the original learning context is reinstated during testing than when this context is changed. Recently, such contextual dependencies have also been found for perceptual-motor behavior. The current study investigated the nature of context-dependent learning in the discrete sequence production task, and in addition examined whether the amount of practice affects the extent to which sequences are sensitive to contextual alterations. It was found that changing contextual cues—but not the removal of such cues—had a detrimental effect on performance. Moreover, this effect was observed only after limited practice, but not after extensive practice. Our findings support the notion of a novel type of context-dependent learning during initial motor skill acquisition and demonstrate that this context-dependence reduces with practice. It is proposed that a gradual development with practice from stimulus-driven to representation-driven sequence execution underlies this practice effect