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At least 19 recordsLinked to original sources
PubMed2003

Phonetic diversity, statistical learning, and acquisition of phonology.

In learning to perceive and produce speech, children master complex language-specific patterns. Daunting language-specific variation is found both in the segmental domain and in the domain of prosody and intonation. This article reviews the challenges posed by results in phonetic typology and sociolinguistics for the theory of language acquisition. It argues that categories are initiated bottom-up from statistical modes in use of the phonetic space, and sketches how exemplar theory can be used to model the updating of categories once they are initiated. It also argues that bottom-up initiation of categories is successful thanks to the perception-production loop operating in the speech community. The behavior of this loop means that the superficial statistical properties of speech available to the infant indirectly reflect the contrastiveness and discriminability of categories in the adult grammar. The article also argues that the developing system is refined using internal feedback from type statistics over the lexicon, once the lexicon is well-developed. The application of type statistics to a system initiated with surface statistics does not cause a fundamental reorganization of the system. Instead, it exploits confluences across levels of representation which characterize human language and make bootstrapping possible.

Child, Preschool↗
PubMed2003

Statistical approaches for estimating actinobacterial diversity in marine sediments.

Bacterial diversity in a deep-sea sediment was investigated by constructing actinobacterium-specific 16S ribosomal DNA (rDNA) clone libraries from sediment sections taken 5 to 12, 15 to 18, and 43 to 46 cm below the sea floor at a depth of 3,814 m. Clones were placed into operational taxonomic unit (OTU) groups with >/= 99% 16S rDNA sequence similarity; the cutoff value for an OTU was derived by comparing 16S rRNA homology with DNA-DNA reassociation values for members of the class Actinobacteria. Diversity statistics were used to determine how the level of dominance, species richness, and genetic diversity varied with sediment depth. The reciprocal of Simpson's index (1/D) indicated that the pattern of diversity shifted toward dominance from uniformity with increasing sediment depth. Nonparametric estimation of the species richness in the 5- to 12-, 15- to 18-, and 43- to 46-cm sediment sections revealed a trend of decreasing species number with depth, 1,406, 308, and 212 OTUs, respectively. Application of the LIBSHUFF program indicated that the 5- to 12-cm clone library was composed of OTUs significantly (P = 0.001) different from those of the 15- to 18- and 43- to 46-cm libraries. F(ST) and phylogenetic grouping of taxa (P tests) were both significant (P < 0.00001 and P < 0.001, respectively), indicating that genetic diversity decreased with sediment depth and that each sediment community harbored unique phylogenetic lineages. It was also shown that even nonconservative OTU definitions result in severe underestimation of species richness; unique phylogenetic clades detected in one OTU group suggest that OTUs do not correspond to real ecological groups sensu Palys (T. Palys, L. K. Nakamura, and F. M. Cohan, Int. J. Syst. Bacteriol. 47:1145-1156, 1997). Mechanisms responsible for diversity and their implications are discussed.

Actinobacteria↗
PubMed2006

Simple allelic-phenotype diversity and differentiation statistics for allopolyploids.

The analysis of genetic diversity within and between populations is a routine task in the study of diploid organisms. However, population genetic studies of polyploid organisms have been hampered by difficulties associated with scoring and interpreting molecular data. This occurs because the presence of multiple alleles at each locus often precludes the measurement of genotype or allele frequencies. In allopolyploids, the problem is compounded because genetically distinct isoloci frequently share alleles. As a result, analysis of genetic diversity patterns in allopolyploids has tended to rely on the interpretation of phenotype frequencies, which loses information available from allele composition. Here, we propose the use of a simple allelic-phenotype diversity statistic (H') that measures diversity as the average number of alleles by which pairs of individuals differ. This statistic can be extended to a population differentiation measure (F'ST), which is analogous to FST. We illustrate the behaviour of these statistics using coalescent computer simulations that show that F'ST behaves in a qualitatively similar way to FST, thus providing a useful way to quantify population differentiation in allopolyploid species.

Alleles↗
PubMed2003

Statistical hypothesis testing--how exact are exact p-values?

OBJECTIVES AND BACKGROUND: When testing a hypothesis statistically, a principle is generally accepted that exact p values shall be stated in the treatise. Researchers have the choice of many statistical computer programmes with implemented hypothesis tests. Are exact p values calculated in the same statistical tests by diverse statistical programmes identical? METHODS: The respective zero hypothesis were tested in 5 artificially created data sets by the parametric unpaired t-test, non-parametric Mann-Whitney test, two-tailed F-test. The calculations were carried out by the following programmes: Statistix, version 7.1 (source www.statistix.com), Analyse-it, version 1.62 (source www.analyse-it.com), MedCalc, version 6.14 (source www.medcalc.be). The p values in the same tests were mutually compared. RESULTS: All three programmes calculated identical exact p values for the t-test. In the remaining two tests in case of 26 out of 44 calculations (59.1 per cent; 95 per cent confidence interval 43-73 per cent) different p values were calculated. The greatest difference was 18.35 per cent. In two cases the values oscillated about 0.05 and this fact caused essentially different interpretation of results. CONCLUSIONS: Using the significance test in the biomedical research has been subject to criticism for a longer period of time. The testing of the zero hypothesis on the arbitrary significance level of 0.05 should be substituted by other methods. Our discoveries should undermine the ungrounded belief of the users of statistical tests--physicians in ununderminable accuracy of mathematical procedures. The use of confidence intervals deems much more suitable although there are objections against them as well. (Tab. 4, Fig. 1, Ref. 19.).

Confidence Intervals↗
PubMed2000

Microsatellite evolution in modern humans: a comparison of two data sets from the same populations.

We genotyped 64 dinucleotide microsatellite repeats in individuals from populations that represent all inhabited continents. Microsatellite summary statistics are reported for these data, as well as for a data set that includes 28 out of 30 loci studied by Bowcock et al. (1994) in the same individuals. For both data sets, diversity statistics such as heterozygosity, number of alleles per locus, and number of private alleles per locus produced the highest values in Africans, intermediate values in Europeans and Asians, and low values in Americans. Evolutionary trees of populations based on genetic distances separated groups from different continents. Corresponding trees were topologically similar for the two data sets, with the exception that the (deltamu)2 genetic distance reliably distinguished groups from different continents for the larger data set, but not for the smaller one. Consistent with our results from diversity statistics and from evolutionary trees, population growth statistics S k and beta, which seem particularly useful for indicating recent and ancient population size changes, confirm a model of human evolution in which human populations expand in size and through space following the departure of a small group from Africa.

Alleles↗
PubMed2005

Use of 16S rRNA gene terminal restriction fragment analysis to assess the impact of solids retention time on the bacterial diversity of activated sludge.

Terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes was used to investigate the reproducibility and stability in the bacterial community structure of laboratory-scale sequencing batch bioreactors (SBR) and to assess the impact of solids retention time (SRT) on bacterial diversity. Two experiments were performed. In each experiment two sets of replicate SBRs were operated for a periods of three times the SRT. One set was operated at an SRT of 2 days and another set was operated at an SRT of 8 days. Samples for T-RFLP analysis were collected from the two sets of replicate reactors. HhaI, MspI, and RsaI T-RFLP profiles were analyzed using cluster analysis and diversity statistics. Cluster analysis with Ward's method using Jaccard distance and Hellinger distance showed that the bacterial community structure in both sets of reactors from both experimental runs was dynamic and that replicate reactors were clustered together and evolved similarly from startup. Richness (S), evenness (E), the Shannon-Weaver index (H), and the reciprocal of Simpson's index (1/D) were calculated, and the values were compared between the two sets of reactors. Evenness values were higher for reactors operated at an SRT of 2 days. Statistically significant differences in diversity (H and D) between the two sets of reactors were tested using a randomization procedure, and the results showed that reactors from both experimental runs that were operated at an SRT of 2 days had higher diversity (H and D) at the 5% level. T-RFLP analysis with diversity indices proved to be a powerful tool to analyze changes in the bacterial community diversity in response to changes in the operational parameters of activated-sludge systems.

Bacteria↗
PubMed2006

Genetic diversity and population structure of Elytrigia pycnantha (Godr.) (Triticeae) in Mont Saint-Michel Bay using microsatellite markers.

During the last decade, an invasive wheatgrass species (Elytrigia pycnantha) has colonized the low salt marshes of the Mont Saint Michel Bay resulting in an accelerated change in the vegetation. This study was conducted using microgeographical genetic diversity in order to understand the genetic structure of this invasive and clonal species. Genetic variation and population structure of fifteen populations collected in high and low marsh habitats around the Bay were analyzed using five microsatellite loci. Because E. pycnantha is an allohexaploid, the application of standard genetic diversity statistics was not possible; we chose to summarize genetic diversity using statistics calculated from banding phenotypes. The mean number of alleles per locus was 10.2, the mean number of different alleles per sample was 6.87. The mean number of allelic phenotypes across all populations was 7.21. The mean value of genetic diversity for the species, calculated as the average number of alleles by which pairs of individuals differ, was H's = 1.91 and H't = 2.04. Little genetic differentiation among populations was detected (0.067). The association between pairwise genetic differentiation and geographic distances exhibited no evidence for isolation by distance. A geographical pattern of population differentiation, where a single population GI was clearly separated from the remaining population groups (considered as a metapopulation), was revealed by principal component analysis (PCA), and we propose that this is because GI represents a new genotype.

Ecosystem↗
PubMed2025

SURROGATE SELECTION OVERSAMPLES EXPANDED T CELL CLONOTYPES.

Surrogate selection is an experimental design that without sequencing any DNA can restrict a sample of cells to those carrying certain genomic mutations. In immunological disease studies, this design may provide a relatively easy approach to enrich a lymphocyte sample with cells relevant to the disease response because the emergence of neutral mutations associates with the proliferation history of clonal subpopulations. A statistical analysis of clonotype sizes provides a structured, quantitative perspective on this useful property of surrogate selection. Our model specification couples within-clonotype birth-death processes with an exchangeable model across clonotypes. Beyond enrichment questions about the surrogate selection design, our framework enables a study of sampling properties of elementary sample diversity statistics; it also points to new statistics that may usefully measure the burden of somatic genomic alterations associated with clonal expansion. We examine statistical properties of immunological samples governed by the coupled model specification, and we illustrate calculations in surrogate selection studies of melanoma and in single-cell genomic studies of T cell repertoires.

Bayes&#x2019;s rule↗
PubMed2003

Molecular variability of sunflower downy mildew, Plasmopara halstedii, from different continents.

Downy mildew of sunflower (Helianthus annuus L.), caused by the pathogen Plasmopara halstedii, is a potentially devastating disease. Seventy-seven isolates of P. halstedii collected in twelve countries from four continents were investigated for RAPD polymorphism with 21 primers. The study led to a binary matrix, which was subjected to various complementary analyses. This is the first report on the international genetic diversity of the pathogen. Similarity indices ranged from 89% to 100%. Neither a consensus unweighted pair group method with arithmetic means (UPGMA) tree constructed after bootstrap resampling of markers nor a principal component analysis based on distance matrix revealed very consistent clusterings of the isolates, and groups did not fit race or geographical origins. Phylogenies were probably obscured by limited diversity. Analysis of molecular variance (AMOVA) and Nei's genetic diversity statistics gave similar conclusions. Most of the genetic diversity was attributable to individual differences. The most differentiated races also had the lowest within-diversity indices, which suggest that they appeared recently with strong bottleneck effects. Our analyses suggest that this pathogen is probably homothallic or has an asexual mode of reproduction and that gene flow among countries can occur through commercial exchanges. Knowledge of the downy mildew populations' structure at the international level will help to devise strategies for controlling this potentially devastating disease.

DNA↗
PubMed2005

An analysis of genetic diversity across the maize genome using microsatellites.

How domestication bottlenecks and artificial selection shaped the amount and distribution of genetic variation in the genomes of modern crops is poorly understood. We analyzed diversity at 462 simple sequence repeats (SSRs) or microsatellites spread throughout the maize genome and compared the diversity observed at these SSRs in maize to that observed in its wild progenitor, teosinte. The results reveal a modest genome-wide deficit of diversity in maize relative to teosinte. The relative deficit of diversity is less for SSRs with dinucleotide repeat motifs than for SSRs with repeat motifs of more than two nucleotides, suggesting that the former with their higher mutation rate have partially recovered from the domestication bottleneck. We analyzed the relationship between SSR diversity and proximity to QTL for domestication traits and observed no relationship between these factors. However, we did observe a weak, although significant, spatial correlation for diversity statistics among SSRs within 2 cM of one another, suggesting that SSR diversity is weakly patterned across the genome. Twenty-four of 462 SSRs (5%) show some evidence of positive selection in maize under multiple tests. Overall, the pattern of genetic diversity at maize SSRs can be explained largely by a bottleneck effect with a smaller effect from selection.

DNA, Plant↗
PubMed1979

Conduit urinary diversion and urinary-tract infection. II. Raised serum antibody titers against Escherichia coli and Proteus mirabilis in relation to bacteriologic findings.

Elevated serum antibody titers against Escherichia coli and/or Proteus mirabilis were found in 35% of 89 patients with a conduit urinary diversion. Statistical analysis showed significant correlation between the titers and growth of E. coli or P. mirabilis in conduit urine. But 17 (24%) of 72 patients without E. coli in urine cultures had raised E. coli antibody titer. Only 3 (4%) of 68 patients without growth of P. mirabilis had raised P. mirabilis antibody titer. When the post-diversion observation period was more than five years, the frequency of antibody titer elevation was greater than in patients with shorter post-diversion follow-up. The volume of residual urine in the conduit showed statistically significant correlation with presence of bacteriuria and with the antibody titer level against P. mirabilis. Patients with high antibody titers tended to have high readings of serum creatinine. Antibiotic therapy reduced elevated E. coli and P. mirabilis antibody titers. Titration of antibodies to E. coli and P. mirabilis is recommended in the follow-up care of patients with conduit urinary diversion.

Adolescent↗
PubMed2004

[A review of basic statistics concepts,research design and statistical analysis methods].

Statistics is a methodology involving a great number of statistical methods. It results in confusion of many clinicians and researchers while they are meditating on how to analyze the collected data in their studies, selecting an appropriate statistical method from all. In fact, the statistical methods are closely correlated to the research design and the data types. Therefore only with a full comprehension of the design methods and the data types can we figure out a simple and practical means from diverse statistical analysis methods. Through the systematic illustration in this review, several statistical concepts, data types, design methods, and the proper way of explaining results with statistical tables and graphs will be demonstrated elaborately. It intends to help the clinicians and researchers select appropriate statistical methods and furthermore, interpret the statistical outcomes accurately in their research.

Humans↗
PubMed2006

Virtual anatomy: an anatomist's playground.

Virtual anatomy presents significant advantages over the reality of a cadaver as it can provide different views and perspectives, portability, longevity, standardization, diversity and most importantly the opportunity to learn the anatomy of the living human body instead of the corpse. Virtual anatomy is the life-like appearance of visible anatomy, a good example of which is the evolution of the Visible Human. Racial and statistical diversity is already developing as the population of photographic "Visible Humans" is now at least 10. Virtual anatomy should include additional diversity and therefore, consideration should be given to the preparation of more visible anatomy that will better support the virtual integration of all areas of physiology, kinematics, pathology and pathophysiology, development and evolution. Integration of anatomists with mathematicians, computer scientists, information scientists, physiologists, pathologists and clinicians (and LIST other basic scientist) is needed in order to facilitate this development. As this unfolds it is proposed, or challenged, that anatomists should maintain their position of responsibility for building anatomy as the foundation for all medical and healthcare education. In order to maintain that position they must understand and participate in this development and enjoy the rewards of teaching more visually empowering, functional, and clinical anatomy. The trip is a long one and is only about to begin but the train is leaving. Are you on board?

Anatomy↗
PubMed1991

Intraspecific variation in population gene diversity and effective population size correlates with the mating system in plants.

Published data on allele frequencies at isozyme loci in inbreeding and outbreeding plant species were analyzed to examine intraspecific variation in gene diversity and effective population size (Ne). Compared with outbreeders, inbreeding species showed markedly greater variation among populations in average values of Nei's gene diversity statistic. Effective population size was estimated by assuming that the variation observed at isozyme loci is selectively neutral. Inbreeding species showed greater levels of variation in Ne than did outbreeders, although the upper range of Ne was similar in the two classes of species. The results suggest that there may be considerable genetic variation and potential for evolutionary change in some but not all populations of inbreeders. Moreover, these findings are important with respect to the conservation of genetic resources. In particular, that the amount of intraspecific variation in population genetic diversity and Ne differs between inbreeding and outbreeding species should be taken into account in sampling efforts designed to optimize the diversity of germplasm collections.

Journal Article↗
PubMed2002

Geographic structure of genetic variation in the widespread woodland grass Milium effusum L. A comparison between two regions with contrasting history and geomorphology.

Allozyme variation in the forest grass Milium effusum L. was studied in 21-23 populations within each of two equally sized densely sampled areas in northern and southern Sweden. In addition, 25 populations from other parts of Eurasia were studied for comparison. The structure of variation was analysed with both diversity statistics and measures based on allelic richness at a standardised sample size. The species was found to be highly variable, but no clear geographic patterns in the distribution of alleles or in overall genetic differentiation were found, either within the two regions or within the whole sample. Thus, no inferences about the direction of postglacial migration could be made. Obviously, migration and gene flow must have taken place in a manner capable of randomising the distribution of alleles. However, there were clear differences in levels and structuring of the variation between the two regions. Levels of variation, both in terms of genetic diversity and allelic richness, were lower in northern Sweden as compared with southern Sweden. In contrast, different measures of geographic structure all showed higher levels of population differentiation in the northern region. This is interpreted as due to different geomorphological conditions in the two regions, creating a relatively continuous habitat and gene flow in the southern region as compared with the northern region where the species, although common, is confined to narrow and mutually isolated corridors in the landscape.

Alleles↗
PubMed2005

[Research on cytokines gene express of rats alcoholic liver disease affected by tea polyphenol].

OBJECTIVE: To evaluate the effect of tea polyphenol(TP) on the rat with alcoholic liver damage. METHOD: Rats were divided into 3 groups, in which 2 groups were stomach perfused with alcohol to result in ALD, and 1 group of them stomach perfused with TP simultaneously. Another group was normal control groups (stomach perfused with drinking water). In the end of 12 weeks, the liver specimen of each rat was observed by anglicizing its tissue damage, and all data collected was performed by statistical analysis in quantum and semi-quantum. Meanwhile cytokines gene express of each group is determined. RESULT: In the end of 12 weeks, alcoholic hepatitis appeared in rat liver. Hepatic injury in alcohol group and TP group were found, but could not be found in normal group. Compared with pure alcohol group, alcoholic liver damage mainly showing with steatosis in TP group were slight, in addition showing liver cellular swelling with small area, with less spot and focal necrosis, none bridging necrosis. Steatosis were slight relatively, mega-bubble steatosis were less found. Collagen deposition of TP group were less than those of pure alcohol group. Gene expression of. cytokine have diversity statistically such as IL-3, IL-4, IL-1R2, IL-6R, IL-7R2, IL-3Ra, IL-R1, IL-13, IL-1R1, IL-7R2, EPO-R, LIFR, IL-1R2, IL-5R2, CSF1, CD27, IL-6R. CONCLUSION: TP is able to attenuate alcoholic liver damage. It's mechanism is possibly due to modulating cytokines gene expression of cytokine.

Animals↗
PubMed2006

Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs).

Twenty-four simple sequence repeat (SSR) markers were used to detect molecular polymorphisms among 370 mostly sexually derived Citrus accessions from the collection of citrus germplasm maintained at the University of California, Riverside. A total of 275 alleles were detected with an average of 11.5 alleles per locus and an average polymorphism information content of 0.625. Genetic diversity statistics were calculated for each individual SSR marker, the entire population, and for specified Citrus groups. Phylogenetic relationships among all citrus accessions and putative non-hybrid Citrus accessions were determined by constructing neighbor-joining trees. There was strong support for monophyly at the species level when hybrid taxa were removed from the data set. Both of these trees indicate that Fortunella clusters within the genus Citrus but Poncirus is a sister genus to Citrus. Additionally, Citrus accessions were probabilistically assigned to populations or multiple populations if their genotype indicated an admixture by a model-based clustering approach. This approach identified five populations in this data set. These separate analyses (distance and model based) both support the hypothesis that there are only a few naturally occurring species of Citrus and most other types of Citrus arose through various hybridization events between these naturally occurring forms.

Alleles↗