A regional paediatric hospital dental service

Stewart, D J; Elliott, Rogers; Kernohan, D. C.; Pielou, W D; Saunders, I D

doi:10.1016/s0300-5712(77)80027-4

Cited by 4 publications

(4 citation statements)

References 2 publications

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“…1). The second method is the Hopkins and Skellam (H&S) index [25,27], which compares the average distance from an epitope to its nearest epitope with the average distance from a random amino acid to the nearest epitope within proteins (Eq. 2).…”

Section: Resultsmentioning

confidence: 99%

“…These methods consider two features of a clustering: the 'intensity' and the 'grain'. The intensity reflects the difference in object density between the rich and poor regions, and the grain describes how frequently rich and poor regions alternate [25]. In this paper we will use two methods: the cumulative binomial probability (CBP) method [26], and the Hopkins and Skellam index (H&S) [25,27].…”

Section: Methodsmentioning

confidence: 99%

“…Regarding the Hopkins and Skellam index (H&S) [25,27]: this method is based on the observation that in a fully random distribution (of an infinite size), the distance from a starting point to the nearest object of interest is not influenced by the presence or absence of such an object at the starting point. In an over-dispersed distribution, the presence of an object at the starting point will mean that the nearest object is on average further away than when starting at a random location, while in a clustered distribution, the reverse is true.…”

Section: Methodsmentioning

confidence: 99%

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The distribution of CTL epitopes in HIV-1 appears to be random, and similar to that of other proteomes

2009

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BackgroundHIV-1 viruses are highly capable of mutating their proteins to escape the presentation of CTL epitopes in their current host. Upon transmission to another host, some escape mutations revert, but other remain stable in the virus sequence for at least several years. Depending on the rate of accumulation and reversion of escape mutations, HIV-1 could reach a high level of adaptation to the human population. Yusim et. al. hypothesized that the apparent clustering of CTL epitopes in the conserved regions of HIV-1 proteins could be an evolutionary signature left by large-scale adaptation of HIV-1 to its human/simian host.ResultsIn this paper we quantified the distribution of CTL epitopes in HIV-1 and found that that in 99% of the HIV-1 protein sequences, the epitope distribution was indistinguishable from random. Similar percentages were found for HCV, Influenza and for three eukaryote proteomes (Human, Drosophila, Yeast).ConclusionWe conclude that CTL epitopes in HIV-1 are randomly distributed, and that this distribution is similar to the distribution of CTL epitopes in proteins from other proteomes. Therefore, the visually apparent clustering of CTL epitopes in epitope maps should not be interpreted as a signature of a past large-scale adaptation of HIV-1 to the human cellular immune response.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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The distribution of CTL epitopes in HIV-1 appears to be random, and similar to that of other proteomes

2009

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“…On the stand level we used Simpson's index C of concentration (see [ 29 ], p. 309) for measuring the degree to which a stand results from clonal reproduction. This parameter calculates the probability that two individuals (drawn randomly from a population of N individuals without replacement) are identical in their multilocus genotypes: C = {[ n i ( n i - 1)]/[ N ( N - 1)]}, where n i is the number of individuals of genotype i and N is the total number of individuals in the population.…”

Section: Methodsmentioning

confidence: 99%

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Höltken¹,

Gregorius²

2006

BMC Ecol

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BackroundP. avium, a pioneer tree species that colonizes early forest successional stages, is assumed to require an effective strategy allowing stably repeatable rounds of local establishment, dispersal and local extinction. Consequently, the early replacement of cherry by climax tree species makes the establishment of several local generations very unlikely, especially in central European continuous cover forests. This has to be seen in connection with the mixed reproduction system involving asexual reproduction as a complementary adaptational strategy. Tests of the local establishment of wild cherry must therefore consider the possibility of first generation establishment via seedling recruitment potentially followed by an asexual generation (root suckering). Successful establishment can therefore be determined only among adult individuals with the option of detecting vegetative reproduction at these stages. To test the implied suggestion about local establishment strategies of wild cherry, nuclear microsatellites were used to analyse patterns of asexual propagation among adult stages that have been subjected to one of two major types of forest management. These management types, the historical "coppice with standards system" (CWS) and the "high forest system" (HFS), can be reasonably assumed to have affected the reproduction system of P. avium.ResultsClear differences were found in the reproduction pattern between two stands representing the two forest management types: 1) Clonal propagation is observed in both management systems, but with a distinctly higher frequency in the CWS. Hence, sexual recruitment as a first local generation is followed by a second asexual generation in both, whereas in the CWS there is evidence for an additional clonal generation. 2) The estimation of amounts of clonal reproduction critically depends on the assumptions about multilocus gene associations. This is revealed by the application of newly developed methods of quantifying gene associations. 3) Haplotype diversities are higher in the CWS and found to be associated with a large degree of heterozygosity for the second largest clonal group. 4) Seed set was sparse over the last eight years of observation in the CWS stand.ConclusionThis study provides useful guidelines for more comprehensive investigations, particularly on the interrelationships between degrees of cloning and capacity of sexual reproduction, amounts of multilocus gene associations, effects of heterozygosity on cloning success, and sustainability of different forest management types.

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