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221.
Background
Application of phenetic methods to gene expression analysis proved to be a successful approach. Visualizing the results in a 3-dimentional space may further enhance these techniques. 相似文献222.
Davide?Baú Alberto?JM?Martin Catherine?Mooney Alessandro?Vullo Ian?Walsh Gianluca?PollastriEmail author 《BMC bioinformatics》2006,7(1):402
Background
We describe Distill, a suite of servers for the prediction of protein structural features: secondary structure; relative solvent accessibility; contact density; backbone structural motifs; residue contact maps at 6, 8 and 12 Angstrom; coarse protein topology. The servers are based on large-scale ensembles of recursive neural networks and trained on large, up-to-date, non-redundant subsets of the Protein Data Bank. Together with structural feature predictions, Distill includes a server for prediction of C α traces for short proteins (up to 200 amino acids). 相似文献223.
Roel GW Verhaak Frank JT Staal Peter JM Valk Bob Lowenberg Marcel JT Reinders Dick de Ridder 《BMC bioinformatics》2006,7(1):105-15
Background
Intensity values measured by Affymetrix microarrays have to be both normalized, to be able to compare different microarrays by removing non-biological variation, and summarized, generating the final probe set expression values. Various pre-processing techniques, such as dChip, GCRMA, RMA and MAS have been developed for this purpose. This study assesses the effect of applying different pre-processing methods on the results of analyses of large Affymetrix datasets. By focusing on practical applications of microarray-based research, this study provides insight into the relevance of pre-processing procedures to biology-oriented researchers. 相似文献224.
The presence or absence of antibodies to citrullinated peptides/proteins (ACPA) is an important parameter that helps a clinician
set a diagnosis of early rheumatoid arthritis and, hence, initiate treatment. There are several commercial tests available
to measure ACPA levels, although it can be difficult to decide what the best test for a given clinical question is. We analyzed
literature data in which the diagnostic and other properties of various ACPA tests are compared. The results show that for
diagnostic purposes the CCP2 test has the highest specificity, the highest sensitivity in stratified studies and the highest
positive predictive value. For the prediction of future joint destruction the CCP2, MCV, and CCP3 tests may be used. The ability
to predict the likelihood of not achieving sustained disease-modifying antirheumatic drug-free remission was highest for the
CCP2 test. Finally, the levels of anti-CCP2 and anti-CCP3 (and possibly anti-mutated citrullinated vimentin) in rheumatoid
arthritis patients are not significantly influenced by TNFα blocking agents. 相似文献
225.
Ernst JM Helmreich 《Cell communication and signaling : CCS》2010,8(1):1-15
As one of the disciplines of systems biology, proteomics is central to enabling the elucidation of protein function within the cell; furthermore, the question of how to deduce protein structure and function from the genetic readout has gained new significance. This problem is of particular relevance for proteins engaged in cell signalling. In dealing with this question, I shall critically comment on the reliability and predictability of transmission and translation of the genetic blue print into the phenotype, the protein. Based on this information, I will then evaluate the intentions and goals of today's proteomics and gene-networking and appraise their chances of success. Some of the themes commented on in this publication are explored in greater detail with particular emphasis on the historical roots of concepts and techniques in my forthcoming book, published in German: Von Molekülen zu Zellen. 100 Jahre experimentelle Biologie. Betrachtungen eines Biochemikers. 相似文献
226.
227.
Short term effect of ploughing a permanent pasture on N2O production from nitrification and denitrification 总被引:1,自引:1,他引:0
Estavillo JM Merino P Pinto M Yamulki S Gebauer G Sapek A Corré W 《Plant and Soil》2002,239(2):253-265
Soils are an important source of N2O, which can be produced both in the nitrification and the denitrification processes. Grassland soils in particular have a high potential for mineralization and subsequent nitrification and denitrification. When ploughing long term grassland soils, the resulting high supply of mineral N may provide a high potential for N2O losses. In this work, the short-term effect of ploughing a permanent grassland soil on gaseous N production was studied at different soil depths. Fertiliser and irrigation were applied in order to observe the effect of ploughing under a range of conditions. The relative proportions of N2O produced from nitrification and denitrification and the proportion of N2 gas produced from denitrification were determined using the methyl fluoride and acetylene specific inhibitors. Irrespectively to ploughing, fertiliser application increased the rates of N2O production, N2O production from nitrification, N2O production from denitrification and total denitrification (N2O + N2). Application of fertiliser also increased the denitrification N2O/N2 ratio both in the denitrification potential and in the gaseous N productions by denitrification. Ploughing promoted soil organic N mineralization which led to an increase in the rates of N2O production, N2O production from nitrification, N2O production from denitrification and total denitrification (N2O + N2). In both the ploughed and unploughed treatments the 0–10 cm soil layer was the major contributing layer to gaseous N production by all the above processes. However, the contribution of this layer decreased by ploughing, gaseous N productions from the 10 to 30 cm layer being significantly increased with respect to the unploughed treatment. Ploughing promoted both nitrification and denitrification derived N2O production, although a higher proportion of N2O lost by denitrification was observed as WFPS increased. Recently ploughed plots showed lower denitrification derived N2O percentages than those ploughed before as a result of the lower soil water content in the former plots. Similarly, a lower mean nitrification derived N2O percentage was found in the 10–30 cm layer compared with the 0–10 cm. 相似文献
228.
The advent of molecular markers has created opportunities for a better understanding of quantitative inheritance and for developing novel strategies for genetic improvement of agricultural species, using information on quantitative trait loci (QTL). A QTL analysis relies on accurate genetic marker maps. At present, most statistical methods used for map construction ignore the fact that molecular data may be read with error. Often, however, there is ambiguity about some marker genotypes. A Bayesian MCMC approach for inferences about a genetic marker map when random miscoding of genotypes occurs is presented, and simulated and real data sets are analyzed. The results suggest that unless there is strong reason to believe that genotypes are ascertained without error, the proposed approach provides more reliable inference on the genetic map. 相似文献
229.
Zirconyl hematoxylin stains acidic mucins darkly and specifically using a solution of 100 mg hematoxylin, 5 ml ethanol, 5 ml 0.5% sodium iodate, 400 mg zirconyl chloride octahydrate, and 30 ml 25% aqueous glycerol. The stain is especially advantageous for studying goblet cells and Paget cells. 相似文献
230.