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Very Practical (very + practical)
Selected AbstractsSelective sampling for approximate clustering of very large data setsINTERNATIONAL JOURNAL OF INTELLIGENT SYSTEMS, Issue 3 2008Liang Wang A key challenge in pattern recognition is how to scale the computational efficiency of clustering algorithms on large data sets. The extension of non-Euclidean relational fuzzy c-means (NERF) clustering to very large (VL = unloadable) relational data is called the extended NERF (eNERF) clustering algorithm, which comprises four phases: (i) finding distinguished features that monitor progressive sampling; (ii) progressively sampling from a N × N relational matrix RN to obtain a n × n sample matrix Rn; (iii) clustering Rn with literal NERF; and (iv) extending the clusters in Rn to the remainder of the relational data. Previously published examples on several fairly small data sets suggest that eNERF is feasible for truly large data sets. However, it seems that phases (i) and (ii), i.e., finding Rn, are not very practical because the sample size n often turns out to be roughly 50% of n, and this over-sampling defeats the whole purpose of eNERF. In this paper, we examine the performance of the sampling scheme of eNERF with respect to different parameters. We propose a modified sampling scheme for use with eNERF that combines simple random sampling with (parts of) the sampling procedures used by eNERF and a related algorithm sVAT (scalable visual assessment of clustering tendency). We demonstrate that our modified sampling scheme can eliminate over-sampling of the original progressive sampling scheme, thus enabling the processing of truly VL data. Numerical experiments on a distance matrix of a set of 3,000,000 vectors drawn from a mixture of 5 bivariate normal distributions demonstrate the feasibility and effectiveness of the proposed sampling method. We also find that actually running eNERF on a data set of this size is very costly in terms of computation time. Thus, our results demonstrate that further modification of eNERF, especially the extension stage, will be needed before it is truly practical for VL data. © 2008 Wiley Periodicals, Inc. [source] g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbationJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2010Maarten G. Wolf Abstract To efficiently insert a protein into an equilibrated and fully hydrated membrane with minimal membrane perturbation we present a computational tool, called g_membed, which is part of the Gromacs suite of programs. The input consists of an equilibrated membrane system, either flat or curved, and a protein structure in the right position and orientation with respect to the lipid bilayer. g_membed first decreases the width of the protein in the xy -plane and removes all molecules (generally lipids and waters) that overlap with the narrowed protein. Then the protein is grown back to its full size in a short molecular dynamics simulation (typically 1000 steps), thereby pushing the lipids away to optimally accommodate the protein in the membrane. After embedding the protein in the membrane, both the lipid properties and the hydration layer are still close to equilibrium. Thus, only a short equilibration run (less then 1 ns in the cases tested) is required to re-equilibrate the membrane. Its simplicity makes g_membed very practical for use in scripting and high-throughput molecular dynamics simulations. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] EFFECT OF ARTIFICIAL FEEDING ON DIGESTIVE EFFICIENCY, GROWTH AND QUALITIES OF MUSCLE AND OOCYTE OF MATURING ATLANTIC MACKEREL (SCOMBER SCOMBRUS L.)JOURNAL OF FOOD BIOCHEMISTRY, Issue 6 2007KRISNA RUNGRUANGSAK-TORRISSEN ABSTRACT Maturing Atlantic mackerel with and without artificial feeding, kept in sea pens (September to May), showed differences in digestive efficiency (protease activity ratio of trypsin to chymotrypsin), muscle growth (concentrations of RNA, protein, RNA/protein ratio and free amino acids [FAA]) and oocyte quality (trypsin-like specific activity, and concentrations of RNA, RNA/protein ratio and FAA). The artificially fed mackerel had higher body weights (1.7 times) but with less white muscle protein concentration (0.5 time), compared to the control group. Both groups showed higher levels of capacity for protein synthesis in the oocytes than in the white muscle, but it was about two times higher in the artificially fed fish whereas about four times higher in the control group. This indicated that, during maturation, development of oocytes and muscle for growth occurred concurrently in higher growth mackerel, while development of oocytes dominated in slower growth fish. A higher trypsin-like specific activity with higher FAA levels in the oocytes from females fed with an artificial diet, compared to the control group, suggested differences in development and quality between the gametes of the fish with different feedings. PRACTICAL APPLICATIONS The work illustrates differences in digestive efficiency and the quality of growth performance (growth and protein metabolism in muscle and oocytes) in fish with different feedings. The use of various methods for evaluating digestive efficiency and the quality of fish growth performance could provide reasonable information for some important biological differences between fish groups, especially when the number of samples are low. It is more advantageous to apply different methods simultaneously than using growth parameter alone in order to study for precise evaluation of the quality of fish growth performance. The methods are very practical for studying food utilization and growth quality of fish in different environmental conditions and with different behaviors in aquaculture as well as in natural ecosystem where food consumption rate and feeding regime cannot be under control. [source] HPLC determinations of enantiomeric ratiosCHIRALITY, Issue 1 2007Peter Wipf Abstract Evaporative light-scattering detection (ELSD) is widely applied in the HPLC analysis of organic compounds lacking a UV chromophore. However, this detection method is generally unsuitable for determination of enantiomeric ratios (er). The er calculated from a UV trace and an ELS trace of the same compound differs significantly. Because of the nonlinear concentration response of the ELS detector, a compound with an er of 95:5 appears to be enantiomerically pure by ELS detection. It is possible to obtain a calibration curve and to calculate a correction factor, but this procedure is time consuming and therefore not very practical for routine analyses. In contrast, a charged aerosol detector allows a very accurate determination of the enantiomeric ratios. Like the ELS detection, the CA detection is independent of the chromophore properties of the substrate. Therefore, we recommend the use of CA instead of ELS detection for determination of the enantiomeric ratios of non-UV active compounds. Chirality, 2006. © 2006 Wiley-Liss, Inc. [source] | ||||||||||