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At least 109 records · Page 6Linked to original sources
PubMed2002

Phylogenetic relationships of the Asian box turtles of the genus Cuora sensu lato (Reptilia: Bataguridae) inferred from mitochondrial DNA sequences.

Phylogenetic relationships of the genus Cuora sensu lato (Cuora sensu stricto and Cistoclemmys) and other testudinoid genera were inferred from variations in 882 base positions of mitochondrial 12S and 16S rRNA genes. Results yielded a robust support to the monophyly of a group (Cuora group) consisting of Cuora sensu lato and the monotypic Pyxidea. Within the Cuora group, the continental Cuora (sensu stricto) and the two subspecies of Ci. flavomarginata constituted two well-supported monophyletic groups. Distinctly small interspecific genetic distances in the former groups suggested that in the continent speciations in Cuora took place much later than the primary divergences in the Cuora group, or speciations in other related genera, such as Mauremys. Our analyses failed to provide a substantial support to the monophyly of any other combinations of taxa within the Cuora group, including Cuora in broad and strict senses, and Cistoclemmys as consisting of Ci. galbinifrons and Ci. flavomarginata. Besides these, our results also suggested the non-monophyly for the Batagurinae and the Geoemydinae, and sister relationships of the Bataguridae with Testudinidae rather than with the Emydidae.

Animals↗
PubMed1992

[Change in the event-related skin conductivity: an indicator of the immediate importance of elaborate information processing?].

In recent psychophysiological conceptualizations of the orienting response (OR) within the framework of information processing, the OR is increasingly considered a "call for processing resources", something which is especially inferred from variations in the event-related skin conductance response (SCR). The present study, therefore, was concerned with certain implications arising from this framework or perspective, particularly in regard to the question of whether stimuli eliciting skin conductance responses obligatorily receive/evoke processing priority or not. In order to examine whether these electrodermal responses denote a capturing of attention or merely a call for processing resources, short (1 s) pure sine tones of 65 dB with sudden onset (commonly used as orienting stimuli) were inserted in a reaction time paradigm with an additional memory load. This demand was primarily given because memory processes play a key role in theories of orienting and habituation. The task was run under two different conditions of complexity, factorially combined with a novelty variation of the added auditory stimuli. The results revealed a substantial deterioration of task performance subsequent to the occurrence of the tones, which, however, was dependent on task complexity and on novelty of the tones. The task impairment is particularly remarkable as subjects were asked to avoid distractions by paying attention to the task and as the tones were introduced as subsidiary and task-irrelevant. Together with the missing effects of task complexity on phasic and tonic electrodermal activity, results suggest that information-processing conceptualizations of the OR can only be a meaningful heuristic contribution to theoretical developments about human orienting and its habituation if the setting of processing priority, its conditions, as well as its implications are adequately taken into account. In addition, it seems to be promising to consider the strength of the SCR as an index of urgency of elaborate, attention-demanding processing and not as a peripheral physiological manifestation of the OR, or, respectively, of a call for unspecific processing resources. Such a view would also do justice to the aspect of prioritization. The sufficient conditions for an OR's occurrence could, in this context, be equated with, among others, some of those which activate a mechanism subserving selective attention and, as a possible result, which lead to further and more elaborate processing of potentially important information.

Adult↗
PubMed2005

Measuring statistical literacy.

This study considers the measurement of Statistical Literacy understanding that goes beyond the basic chance and data skills and knowledge in the mathematics curriculum. This understanding requires application of mathematical skills in a range of contextual situations and draws on aspects of statistics, such as variation and inference, which may not be explicit in the school curriculum. The study reports the outcomes from tests of Statistical Literacy given to 673 students from Grades 5 to 10. It confirms the nature and structure of a previously identified construct of Statistical Literacy and proposes three subgroups of items that address aspects of Statistical Literacy that might usefully be measured by classroom teachers.

Adolescent↗
PubMed1994

Outcomes evaluation in TBI Rehabilitation. Part I: overview and system principles.

Questions of how to measure outcomes are commonly heard in rehabilitation today. In this supplement we review the current state of the art of outcomes measurement in traumatic brain injury rehabilitation, discuss key issues, and identify steps that need to be taken. The underlying question is not simply that of outcomes measurement but how to infer effective and cost-effective treatment. The validity of such inferences rests on multiple features of the entire clinical information system. Requirements for valid, feasible, outcome-oriented clinical data systems are described. Effectiveness is inferred from variations in outcomes experienced by similar persons who received differing interventions. Outcome data systems need large sample sizes and technically adequate severity adjusters. A nationwide TBI data system is needed to identify reasonably homogeneous subgroups in different programs whose outcomes can be meaningfully compared. In alliance with payors and persons with disabilities, rehabilitation professionals can create outcome data systems that will provide the knowledge necessary to improve the effectiveness and cost-effectiveness of rehabilitation programs.

Activities of Daily Living↗
PubMed2005

Inferences on the common coefficient of variation.

The coefficient of variation is often used as a measure of precision and reproducibility of data in medical and biological science. This paper considers the problem of making inference about the common population coefficient of variation when it is a priori suspected that several independent samples are from populations with a common coefficient of variation. The procedures for confidence interval estimation and hypothesis testing are developed based on the concepts of generalized variables. The coverage properties of the proposed confidence intervals and type-I errors of the proposed tests are evaluated by simulation. The proposed methods are illustrated by a real life example.

Blood↗
PubMed2001

The evolutionary history of brown trout (Salmo trutta L.) inferred from phylogeographic, nested clade, and mismatch analyses of mitochondrial DNA variation.

Phylogeographic, nested clade, and mismatch analyses of mitochondrial DNA (mtDNA) variation were used to infer the temporal dynamics of distributional and demographic history of brown trout (Salmo trutta). Both new and previously published data were analyzed for 1,794 trout from 174 populations. This combined analysis improved our knowledge of the complex evolutionary history of brown trout throughout its native Eurasian and North African range of distribution in many ways. It confirmed the existence of five major evolutionary lineages that evolved in geographic isolation during the Pleistocene and have remained largely allopatric since then. These should be recognized as the basic evolutionarily significant units within brown trout. Finer phylogeographic structuring was also resolved within major lineages. Contrasting temporal juxtaposition of different evolutionary factors and timing of major demographic expansions were observed among lineages. These unique evolutionary histories have been shaped both by the differential latitudinal impact of glaciations on habitat loss and potential for dispersal, as well as climatic impacts and landscape heterogeneity that translated in a longitudinal pattern of genetic diversity and population structuring at more southern latitudes. This study also provided evidence for the role of biological factors in addition to that of physical isolation in limiting introgressive hybridization among major trout lineages.

Animals↗
PubMed2001

Interpretability and robustness of sieve analysis models for assessing HIV strain variations in vaccine efficacy.

From data on HIV-1 characteristics measured on viruses isolated from vaccinated and unvaccinated persons infected while enrolled in preventive HIV-1 vaccine trials, interpretable inferences into strain variations of vaccine efficacy can be made with recently developed sieve analysis models. Four assumptions are needed for the parameters in these models to have meaningful interpretations in terms of vaccine-induced reductions in strain-specific per-contact transmission probabilities: (A1) vaccination impacts each strain-specific transmission probability homogeneously in vaccinated persons (leaky vaccine effect); (A2) for each strain biological susceptibility to infection given exposure is homogeneous among vaccinated trial participants and among unvaccinated trial participants; (A3) the distribution of exposure is equal in vaccinated and unvaccinated trial participants; (A4) the relative prevalence of circulating HIV-1 strains during the trial follow-up period is constant. Through theoretical considerations and simulations of an ongoing phase III HIV-1 vaccine efficacy trial in Bangkok, we evaluate the importance and necessity of these assumptions. We show that the models still provide estimates of biologically interpretable parameters when A1 is violated, but with bias the extent to which vaccine protection is heterogeneous. We also show that the models are highly robust to departures from A4, with implication that the time-independent models are adequate for applications. In addition, we suggest extensions of the sieve analysis models which incorporate random effects that account for unmeasured heterogeneity in infection risk. With these mixed models, usefully interpretable strain-specific vaccine efficacy parameters can be estimated without requiring A2. The conclusion is that A3, which is justified by randomization and blinding, is the essential assumption for the sieve models to provide reliable interpretable inferences into strain variations in vaccine efficacy.

AIDS Vaccines↗
PubMed2000

Y chromosomal DNA variation in east Asian populations and its potential for inferring the peopling of Korea.

We have examined variations of five polymorphic loci (DYS287, DXYS5Y, SRY465, DYS19, and DXYS156Y) on the Y chromosome in samples from a total of 1260 males in eight ethnic groups of East Asia. We found four unique haplotypes constructed from three biallelic markers in these samples of East Asians. The Japanese population was characterized by a relatively high frequency of either the haplotype I-2b (-/Y2/T) or II-1 (+/Y1/C). These dual patterns of the distribution of Y chromosomes (I-2b/II-1) were also found in Korea, although they were present at relatively low frequencies. The haplotype II-1 was present in Northeast Asian populations (Chinese, Japanese, Koreans, and Mongolians) only, except for one male from the Thai population among the Southeast Asian populations (Indonesians, Philippines, Thais, and Vietnamese). The Japanese were revealed to have the highest frequency of this haplotype (27.5%), followed by Koreans (2.9%), Mongolians (2.6%), and mainland Chinese (2.2%). In contrast, the frequency of the haplotype I-2b was found to be 17.1% in the Japanese, 9.5% in Indonesian, 6.3% in Korean, 3.8% in Vietnamese, and 2.7% in Thai samples. These findings suggested that the chromosomes of haplotype I-2b were likely derived from certain areas of Northeast Asia, the region closest to Southeast Asia. Phylogenetic analysis using the neighbor-joining tree also reflected a general distinction between Southeast and Northeast Asian populations. The phylogeny revealed a closer genetic relationship between Japanese and Koreans than to the other surveyed Asian populations. Based on the result of the dual patterns of the haplotype distribution, it is more likely that the population structure of Koreans may not have evolved from a single ancient population derived from Northeast Asians, but through dual infusions of Y chromosomes entering Korea from two different waves of East Asians.

Asia, Southeastern↗
PubMed2006

Genomics and conservation genetics.

In large part, the relevance of genetics to conservation rests on the premise that neutral marker variation in populations reflects levels of detrimental and adaptive genetic variation. Despite its prominence, this tenet has been difficult to evaluate, until now. As we discuss here, genome sequence information and new technological and bioinformatics platforms now enable comprehensive surveys of neutral variation and more direct inferences of detrimental and adaptive variation in species with sequenced genomes and in 'genome-enabled' endangered taxa. Moreover, conservation schemes could begin to consider specific pathological genetic variants. A new conservation genetic agenda would utilize data from enhanced surveys of genomic variation in endangered species to better manage functional genetic variation.

Animals↗
PubMed2005

Phylogeography of loaches of the genus lefua (balitoridae, cypriniformes) inferred from mitochondrial DNA sequences.

In order to elucidate phylogenetic relationships and intraspecific variations and to infer the evolutionary process of loaches of the genus Lefua, we analyzed nucleotide sequences of the mitochondrial D-loop region of 100 specimens obtained from 97 localities in Japan and Korea. The genus Lefua includes three described species, L. nikkonis, L. echigonia, and L. costata and an undescribed species, Lefua sp. Our results showed that each species of Lefua formed a monophyletic group, indicating clearly that Lefua species can be genetically distinguished from one another. Lefua nikkonis was the most closely related to L. costata, while L. sp. was the most closely related to L. echigonia. Specimens of L. sp. were grouped into two intraspecific populations and specimens of L. echigonia were grouped into six populations. These populations were well separated geographically from one another by mountain ranges and highlands. We estimated the evolutionary time for splitting of the species and intraspecific populations, and speculated on the evolutionary process of the genus Lefua. Species of Lefua are severely threatened. Fundamental genetic information is indispensable for conservation. We presented genetic background in order to protect these threatened loaches.

Animals↗
PubMed1982

Intervention effects and relative variation as dimensions in experts' use of visual inference.

Recent research indicates that when analyzing graphically presented single-subject data, subjects trained in visual inference appear to attend to large changes between phases regardless of relative variation and do not differentiate among common intervention effect patterns. In this follow-up study, experts in applied behavior analysis completed a free-sort task designed to assess the effects of these dimensions on their use of visual inference. The results indicate that they tended to differentiate among common intervention effect patterns but did not attend to relative variation in the data.

Journal Article↗
PubMed2002

Geographic pattern of genetic variation in the European globeflower Trollius europaeus L. (Ranunculaceae) inferred from amplified fragment length polymorphism markers.

The distribution of genetic variation and the phylogenetic relationships between 18 populations of the arctic-alpine plant Trollius europaeus were analysed in three main regions (Alps, Pyrenees and Fennoscandia) by using dominant AFLP markers. Analysis of molecular variance revealed that most of the genetic variability was found within populations (64%), although variation among regions (17%) and among populations within regions (19%) was highly significant (P < 0.001). Accordingly, the global fixation index FST averaged over loci was high (0.39). The among-population differentiation indicates restricted gene flow, congruent with limited dispersal of specific globeflower's pollinating flies (Chiastocheta spp.). Within-population diversity levels were significantly higher in the Alps (mean Nei's expected heterozygosity HE = 0.229) than in the Pyrenees (HE= 0.197) or in Fennoscandia (HE = 0.158). This finding is congruent with the species-richness of the associated flies, which is maximum in the Alps. We discuss the processes involved in shaping observed patterns of genetic diversity within and among T. europaeus populations. Genetic drift is the major factor acting on the small Pyrenean populations at the southern edge of T. europaeus distribution, while large Fennoscandian populations result probably from a founder effect followed by demographic expansion. The Alpine populations represent moderately fragmented relics of large southern ancestral populations. The patterns of genetic variability observed in the host plant support the hypothesis of sympatric speciation in associated flies, rather than recurrent allopatric speciations.

France↗
PubMed2006

Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments.

BACKGROUND: Molecular evolutionary studies of noncoding sequences rely on multiple alignments. Yet how multiple alignment accuracy varies across sequence types, tree topologies, divergences and tools, and further how this variation impacts specific inferences, remains unclear. RESULTS: Here we develop a molecular evolution simulation platform, CisEvolver, with models of background noncoding and transcription factor binding site evolution, and use simulated alignments to systematically examine multiple alignment accuracy and its impact on two key molecular evolutionary inferences: transcription factor binding site conservation and divergence estimation. We find that the accuracy of multiple alignments is determined almost exclusively by the pairwise divergence distance of the two most diverged species and that additional species have a negligible influence on alignment accuracy. Conserved transcription factor binding sites align better than surrounding noncoding DNA yet are often found to be misaligned at relatively short divergence distances, such that studies of binding site gain and loss could easily be confounded by alignment error. Divergence estimates from multiple alignments tend to be overestimated at short divergence distances but reach a tool specific divergence at which they cease to increase, leading to underestimation at long divergences. Our most striking finding was that overall alignment accuracy, binding site alignment accuracy and divergence estimation accuracy vary greatly across branches in a tree and are most accurate for terminal branches connecting sister taxa and least accurate for internal branches connecting sub-alignments. CONCLUSION: Our results suggest that variation in alignment accuracy can lead to errors in molecular evolutionary inferences that could be construed as biological variation. These findings have implications for which species to choose for analyses, what kind of errors would be expected for a given set of species and how multiple alignment tools and phylogenetic inference methods might be improved to minimize or control for alignment errors.

Binding Sites↗
PubMed1996

Determining linkage and mode of inheritance: mode scores and other methods.

The lod score method remains a popular approach for detecting linkage and estimating the recombination fraction theta between a marker locus and a trait locus. However, its implementation requires knowledge of all parameters of the genetic mechanism, including the number of loci involved and the genotype specific penetrance, which could depend on factors such as age. When some of the penetrance parameters phi are unknown, several methods are available, and have been reviewed by Hodge and Elston [(1994) Genet Epidemiol 11:329-342]. These include the "wrod score" (lod score maximized over theta under a wrong value of phi) and "mod score" (lod score maximized over both theta and phi) methods for inference on theta. It has further been proposed that the mod score also be used for estimating phi. In this paper, we review and assess the adequacy of these two methods for inferences on both phi and theta. In particular, all of the methods can be seen as variations on likelihood inference, using the information in the conditional likelihood for the marker data, given the trait data. The loss of efficiency of the mod is compared to that of the full likelihood, which utilizes all information available in the trait data. We also propose an alternative, based on the pseudo-likelihood, where phi is estimated via the trait information and plugged into the conditional likelihood. This method is compared to the mod score method, and the advantages and disadvantages of each are elucidated. In particular, it is seen that the pseudo-likelihood method can be more efficient than the mod score method if the ascertainment scheme can be modeled. As examples, both a random sample and a multiplex ascertainment scheme are considered. In addition, the pseudo-likelihood method leads to likelihood ratio tests for detecting linkage with a simple, known asymptotic reference distribution, a feature not shared by the mod score. Finally, we discuss the advantages of using the pseudo-likelihood method over the full likelihood method, both of which are valid when the ascertainment scheme is known.

Genetic Linkage↗
PubMed2006

SSADH variation in primates: intra- and interspecific data on a gene with a potential role in human cognitive functions.

In the present study we focus on the nucleotide and the inferred amino acid variation occurring in humans and other primate species for mitochondrial NAD(+)-dependent succinic semialdehyde dehydrogenase, a gene recently supposed to contribute to cognitive performance in humans. We determined 2527 bp of coding, intronic, and flanking sequences from chimpanzee, bonobo, gorilla, orangutan, gibbon, and macaque. We also resequenced the entire coding sequence on 39 independent chromosomes from Italian families. Four variable coding sites were genotyped in additional populations from Europe, Africa, and Asia. A test for constancy of the nonsynonymous vs. synonymous rates of nucleotide changes revealed that primates are characterized by largely variable d(N)/d(S) ratios. On a background of strong conservation, probably controlled by selective constraints, the lineage leading to humans showed a ratio increased to 0.42. Human polymorphic levels fall in the range reported for other genes, with a pattern of frequency and haplotype structure strongly suggestive of nonneutrality. The comparison with the primate sequences allowed inferring the ancestral state at all variable positions, suggesting that the c.538(C) allele and the associated functional variant is indeed a derived state that is proceeding to fixation. The unexpected pattern of human polymorphism compared to interspecific findings outlines the possibility of a recent positive selection on some variants relevant to new cognitive capabilities unique to humans.

Adaptation, Biological↗
PubMed2005

Relative vs. absolute statistical analysis of compositions: a comparative study of surface waters of a Mediterranean river.

Most hydrogeological research includes some sort of statistical study, which is generally conducted on the raw measures of chemical variables, though there are several theoretical and practical studies warning against this practice. Arguments refer mainly to the positive character of this type of data, and to the fact that they carry only information about the relative abundance of each component on the whole, what makes techniques based on correlation, like the widely used Principal Component Analysis (PCA), loose their meaning. The solution proposed by Aitchison (1982, Journal of the Royal Statistical Society, Series B 44(2), 139-177)-based on working with log-ratios of observations-is equivalent to define a new distance between compositions and to adapt usual statistical techniques to it. To illustrate its effect, our study compares the performance of the biplot-a PCA graphical technique-according to the usual Euclidean and to the Aitchison distance. The study is conducted on a set of 14 molarities measured monthly through the years 1997-1999 at 30 different stations along the Llobregat River and its tributaries (Barcelona, NE Spain). Ordinary analysis, implicitly based on an Euclidean distance, presents some deficiencies, mainly because it only captures major ion variations and the inferred relationship between them actually depends on other non-relevant variables, such as water mass. An analysis based on compositional distances captures variations of all the ions; it is robust against the inclusion of non-relevant variables in the analysis; and it offers a way to build factors expressed as equilibrium equations. In our case, two promising factors are extracted, showing the different anthropogenic and geological pollution sources of the rivers.

Environmental Monitoring↗
PubMed2000

Population subdivision in Europe's great bustard inferred from mitochondrial and nuclear DNA sequence variation.

A continent-wide survey of sequence variation in mitochondrial (mt) and nuclear (n) DNA of the endangered great bustard (Otis tarda) was conducted to assess the extent of phylogeographic structure in a morphologically monotypic bird. DNA sequence variation in a combined 809 bp segment of the mtDNA genome from 66 individuals from the last six breeding regions showed relatively low levels of intraspecific sequence diversity (n = 0.32%) but significant differences in the regional distribution of 11 haplotypes (phiST = 0.49). Despite their exceptional potential for dispersal, a complete and long-term historical separation between the populations from the Iberian Peninsula (Spain) and mainland Europe (Hungary, Slovakia, Germany, and Russia) was demonstrated. Divergence between populations based on a 3-bp insertion-deletion polymorphism within the intron region of the nuclear CHD-Z gene was geographically concordant with the primary subdivision identified within the mtDNA sequences. Inferred aspects of phylogeography were used to formulate conservation recommendations for this endangered species.

Animals↗