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81.
J Steinbuch AC van Dijk FHBM Schreuder MTB Truijman J Hendrikse PJ Nederkoorn A van der Lugt E Hermeling APG Hoeks WH Mess 《Cardiovascular ultrasound》2017,15(1):9
Background
Mean or maximal intima-media thickness (IMT) is commonly used as surrogate endpoint in intervention studies. However, the effect of normalization by surrounding or median IMT or by diameter is unknown. In addition, it is unclear whether IMT inhomogeneity is a useful predictor beyond common wall parameters like maximal wall thickness, either absolute or normalized to IMT or lumen size. We investigated the interrelationship of common carotid artery (CCA) thickness parameters and their association with the ipsilateral internal carotid artery (ICA) stenosis degree.Methods
CCA thickness parameters were extracted by edge detection applied to ultrasound B-mode recordings of 240 patients. Degree of ICA stenosis was determined from CT angiography.Results
Normalization of maximal CCA wall thickness to median IMT leads to large variations. Higher CCA thickness parameter values are associated with a higher degree of ipsilateral ICA stenosis (p?<?0.001), though IMT inhomogeneity does not provide extra information. When the ratio of wall thickness and diameter instead of absolute maximal wall thickness is used as risk marker for having moderate ipsilateral ICA stenosis (>50%), 55 arteries (15%) are reclassified to another risk category.Conclusions
It is more reasonable to normalize maximal wall thickness to end-diastolic diameter rather than to IMT, affecting risk classification and suggesting modification of the Mannheim criteria.Trial registration
Clinical trials.gov NCT01208025.82.
Cecilia Wieder Clment Frainay Nathalie Poupin Pablo Rodríguez-Mier Florence Vinson Juliette Cooke Rachel PJ Lai Jacob G. Bundy Fabien Jourdan Timothy Ebbels 《PLoS computational biology》2021,17(9)
Over-representation analysis (ORA) is one of the commonest pathway analysis approaches used for the functional interpretation of metabolomics datasets. Despite the widespread use of ORA in metabolomics, the community lacks guidelines detailing its best-practice use. Many factors have a pronounced impact on the results, but to date their effects have received little systematic attention. Using five publicly available datasets, we demonstrated that changes in parameters such as the background set, differential metabolite selection methods, and pathway database used can result in profoundly different ORA results. The use of a non-assay-specific background set, for example, resulted in large numbers of false-positive pathways. Pathway database choice, evaluated using three of the most popular metabolic pathway databases (KEGG, Reactome, and BioCyc), led to vastly different results in both the number and function of significantly enriched pathways. Factors that are specific to metabolomics data, such as the reliability of compound identification and the chemical bias of different analytical platforms also impacted ORA results. Simulated metabolite misidentification rates as low as 4% resulted in both gain of false-positive pathways and loss of truly significant pathways across all datasets. Our results have several practical implications for ORA users, as well as those using alternative pathway analysis methods. We offer a set of recommendations for the use of ORA in metabolomics, alongside a set of minimal reporting guidelines, as a first step towards the standardisation of pathway analysis in metabolomics. 相似文献
83.
84.
Improved analyses of human mtDNA sequences support a recent African origin for Homo sapiens 总被引:3,自引:1,他引:2
New quantitative methods are applied to the 135 human mitochondrial
sequences from the Vigilant et al. data set. General problems in analyzing
large numbers of short sequences are discussed, and an improved strategy is
suggested. A key feature is to focus not on individual trees but on the
general "landscape" of trees. Over 1,000 searches were made from random
starting trees with only one tree (a local optimum) being retained each
time, thereby ensuring optima were found independently. A new tree
comparison metric was developed that is unaffected by rearrangements of
trees around many very short internal edges. Use of this metric showed that
downweighting hypervariable sites revealed more evolutionary structure than
studies that weighted all sites equally. Our results are consistent with
convergence toward a global optimum. Crucial features are that the best
optima show very strong regional differentiation, a common group of 49
African sequences is found in all the best optima, and the best optima
contain the 16 !Kung sequences in a separate group of San people. The other
86 sequences form a heterogeneous mixture of Africans, Europeans,
Australopapuans, and Asians. Thus all major human lineages occur in Africa,
but only a subset occurs in the rest of the world. The existence of these
African-only groups strongly contradicts multiregional theories for the
origin of Homo sapiens that require widespread migration and interbreeding
over the entire range of H. erectus. Only when the multiregional model is
rejected is it appropriate to consider the root, based on a single locus,
to be the center of origin of a population (otherwise different loci could
give alternative geographic positions for the root). For this data, several
methods locate the root within the group of 49 African sequences and are
thus consistent with the recent African origin of H. sapiens. We
demonstrate that the time of the last common ancestor cannot be the time of
major expansion in human numbers, and our results are thus also consistent
with recent models that differentiate between the last common ancestor,
expansion out of Africa, and the major expansion in human populations. Such
a two-phase model is consistent with a wide range of molecular and
archeological evidence.
相似文献
85.
A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages 总被引:17,自引:13,他引:4
Lockhart PJ; Steel MA; Barbrook AC; Huson DH; Charleston MA; Howe CJ 《Molecular biology and evolution》1998,15(9):1183-1188
The aims of the work were (1) to develop statistical tests to identify
whether substitution takes place under a covariotide model in sequences
used for phylogenetic inference and (2) to determine the influence of
covariotide substitution on phylogenetic trees inferred for photosynthetic
and other organisms. (Covariotide and covarion models are ones in which
sites that are variable in some parts of the underlying tree are invariable
in others and vice versa.) Two tests were developed. The first was a
contingency test, and the second was an inequality test comparing the
expected number of variable sites in two groups with the observed number.
Application of these tests to 16S rDNA and tufA sequences from a range of
nonphotosynthetic prokaryotes and oxygenic photosynthetic prokaryotes and
eukaryotes suggests the occurrence of a covariotide mechanism. The degree
of support for partitioning of taxa in reconstructed trees involving these
organisms was determined in the presence or absence of sites showing
particular substitution patterns. This analysis showed that the support for
splits between (1) photosynthetic eukaryotes and prokaryotes and (2)
photosynthetic and nonphotosynthetic organisms could be accounted for by
patterns arising from covariotide substitution. We show that the additional
problem of compositional bias in sequence data needs to be considered in
the context of patterns of covariotide/covarion substitution. We argue that
while covariotide or covarion substitution may give rise to
phylogenetically informative patterns in sequence data, this may not always
be so.
相似文献
86.
87.
Heat shock response of germinating embryos of wheat : effects of imbibition time and seed vigor 总被引:2,自引:2,他引:0
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Seeds frequently face a hostile environment during early germination. In order to determine whether seeds have evolved unique mechanisms to deal with such environments, a survey of the heat shock response in isolated embryos of wheat (Triticum aestivum L.) was undertaken. Embryos simultaneously heat shocked and labeled following several different periods of prior imbibition up to 12 hours synthesized many groups of heat shock proteins (hsps) typical of other plant and animal systems. Also, five developmentally dependent hsps, present only in treatments imbibed less than 6 hours prior to heat shock, were detected. These proteins have relative molecular masses of 14, 40, 46, 58, and 60 kilodaltons. One of the developmentally dependent hsps is among the most highly labeled hsps found in early imbibed embryos. The possibility that this protein is the Em protein is discussed. The hypothesis that the capacity for hsp synthesis is affected by seed vigor was also tested. The heat shock responses of embryos from two high and two low vigor seed lots were compared using one- and two-dimensional electrophoresis of labelled protein extracts. The results indicate that both of the low vigor lots tested had weaker heat shock responses than their high vigor counterparts overall. Not all hsps were relatively less abundant in low vigor embryos. The developmentally dependent hsps showed little relationship to vigor. Some of the developmentally dependent hsps were actually made in greater amounts, relative to other proteins, in the low vigor seed lots. The results presented here demonstrate that imbibing embryos are capable of expressing an enhanced heat shock response, and that this response is related to seed vigor. 相似文献
88.
Sheldon R. Simon Igor L. Paul Joseph Mansour Michael Munro Peter J. Abernethy Eric L. Radin 《Journal of biomechanics》1981,14(12):817-819
Studies were made of the forces generated at heel stroke in human gait using both force plates having a high resonant frequencies (capable of picking up high frequency components in the contact force) as well as a force transducer inserted into the heel of the shoe of the subjects. The output traces were analyzed for the existence of high frequency impulsive loads during a normal walking cycle. The effect of the complicance of the foot and floor was studied with the force transducers. The results showed that during normal human gait the lower limb is subjected to a high frequency impulsive load at heel strike. The severity of this impulse varied with the individual, the velocity and angle with which the limb aproached the ground and the compliance of the two materials coming in contact at heel strike. The magnitude of this peak force varied from 0.5 to 1.25 times body weight and its frequency components from 10 to 75 Hz. 相似文献
89.
Y Wang J L Abernethy A E Eckhardt R L Hill 《The Journal of biological chemistry》1992,267(18):12709-12716
A UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase from porcine submaxillary glands was purified to electrophoretic homogeneity. IgG prepared from antisera against the pure enzyme immunoprecipitated the transferase in Triton X-100 extracts of submaxillary glands. The submaxillary transferase is a membrane-bound enzyme in contrast to the pure bovine colostrum enzyme, which is soluble in the absence of detergents. Both transferases have similar properties but also differ significantly. Examination of the acceptor substrate specificity of the submaxillary gland transferase showed that it specifically transferred N-acetylgalactosamine from UDP-GalNAc to the hydroxyl group of threonine and was devoid of transferase activity toward serine-containing peptides. These results imply that more than one transferase is involved in forming the GalNAc-threonine and the GalNAc-serine linkages found in O-linked oligosaccharides in glycoproteins. The amino acid sequence adjacent to glycosylated threonine residues may influence the rate of glycosylation by the pure transferase. For example, the second threonine residue in the sequence, Thr-Thr, appears to be glycosylated about twice as fast as the first and more rapidly than single, isolated threonine residues. However, no unique consensus sequence for glycosylation of threonine residues is evident, and any accessible threonine residue appears to be a potential acceptor substrate. 相似文献
90.
The reactions of [M(CC6H2Me3-2,4,6)X(CO)2(L)2] (M = Mo, W; X = Cl, Br; L = pyridine, 3,5-dimethylpyrazole) with Na[H2B(mt)2] (mt = methimazolyl) are metal dependent, providing either the alkylidyne complex [Mo(CC6H2Me3-2,4, 6)(CO)2{κ3-H,S,S′-H2B(mt)2}] or the bis(chelate) complex [W(CO){κ2-S,S′-H2B(mt)2}{κ3-H,S,S′-H2B(mt)2}], the latter featuring both bi and tridentate coordination modes for the H2B(mt)2 ligand. 相似文献