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At least 685 records · Page 38Linked to original sources

PubMed2004

Evaluation of once daily tobramycin dosing in critically ill patients through Bayesian simulation.

OBJECTIVE: To evaluate if once-daily dose (ODD) regimens of tobramycin attain pharmacodynamic goals using individualized pharmacokinetic monitoring of critically ill patients with creatinine clearance (Clcr) over 60 mL/min. METHODS: Fifty-one adult critically ill patients treated with intravenous tobramycin with ODD were included in the study. The effect of dosing using the proposed method was compared with a weight-based (7 mg/kg) dosing method. Pharmacokinetics parameters, peak concentration (Cpeak), minimum concentration (Cmin) and the time below the minimum inhibitory concentration (MIC) were estimated using Bayesian analysis. Pharmacodynamic parameters used to evaluate both dosing regimens were Cpeak/MIC ratio and, secondly, time below MIC (T< MIC). RESULTS: The median dose of tobramycin administrated in our hospital was too low for achieving pharmacodynamic goals. In contrast, the weight-based (7 mg/kg) method produced an adequate Cpeak/MIC ratio but an increase of the dose would not reduce the secondary pharmacodynamic index T 60 mL/min achieved the Cpeak/MIC target values of 10. However in critically ill patients with Clcr>80 mL/min, T<MIC is greater than the aminoglycoside post-antibiotic effect, so these patients do not attain the secondary pharmacodynamic index. These data show the need for rapid pharmacokinetic optimization with individualized aminoglycoside dosing. Additional studies are necessary to better define the best tobramycin regimen for critically ill patients.

Anti-Bacterial Agents↗

PubMed2005

Range expansions in the flightless longhorn cactus beetles, Moneilema gigas and Moneilema armatum, in response to Pleistocene climate changes.

Pollen cores and plant and animal fossils suggest that global climate changes at the end of the last glacial period caused range expansions in organisms indigenous to the North American desert regions, but this suggestion has rarely been investigated from a population genetic perspective. In order to investigate the impact of Pleistocene climate changes and glacial/interglacial cycling on the distribution and population structure of animals in North American desert communities, biogeographical patterns in the flightless, warm-desert cactus beetles, Moneilema gigas and Moneilema armatum, were examined using mitochondrial DNA (mtDNA) sequence data from the cytochrome oxidase I (COI) gene. Gene tree relationships between haplotypes were inferred using parsimony, maximum-likelihood, and Bayesian analysis. Nested clade analysis and coalescent modelling using the programs mdiv and fluctuate were used to identify demographically independent populations, and to test the hypothesis that Pleistocene climate changes caused recent range expansions in these species. A sign test was used to evaluate the probability of observing concerted population growth across multiple, independent populations. The phylogeographical and nested clade analyses reveal a history of northward expansion in both of these species, as well as a history of past range fragmentation, followed by expansion from refugia. The coalescent analyses provide highly significant evidence for independent range expansions from multiple refugia, but also identify biogeographical patterns that predate the most recent glacial period. The results indicate that widespread desert environments are more ancient than has been suggested in the past.

Animals↗

PubMed2005

Mitochondrial and nuclear DNA phylogeography of European grayling (Thymallus thymallus): evidence for secondary contact zones in central Europe.

Mitochondrial and microsatellite DNA markers were applied to infer the phylogeography, intraspecific diversity and dynamics of the distributional history of European grayling (Thymallus thymallus) with focus on its central and northern European distribution range. Phylogenetic and nested clade analyses revealed at least four major mtDNA lineages, which evolved in geographical isolation during the Pleistocene. These lineages should be recognized as the basic evolutionary significant units (ESUs) for grayling in central and northern Europe. In addition, and in contrast to previous work on grayling, the results of Bayesian analysis of individual admixture coefficients, two-dimensional scaling analysis and spatial analysis of molecular variance provided evidence for a high level of admixture among major lineages in contact zones between drainages (e.g. the low mountain range of Germany), most likely resulting from glacial perturbations and ancient river connections between drainages during the Pleistocene glaciations. Even within river systems, a high level of differentiation among populations was revealed as indicated by the microsatellite data. Grayling sampled from 29 sites displayed high levels of differentiation (overall F(ST) = 0.367), a high number of private alleles and high bootstrap support for the genetic distance-based population clusters across 12 loci. We specifically discuss our results in context of phylogeograpic studies on other European freshwater fish species with habitat preferences similar to those of grayling. Our study shows that both large-scale phylogeographical and detailed genetic analyses on a fine scale are mandatory for developing appropriate conservation guidelines of endangered species.

Animals↗

PubMed2005

Phylogeography of the longhorn cactus beetle Moneilema appressum LeConte (Coleoptera: Cerambycidae): was the differentiation of the Madrean sky islands driven by Pleistocene climate changes?

Although it has been suggested that Pleistocene climate changes drove population differentiation and speciation in many groups of organisms, population genetic evidence in support of this scenario has been ambiguous, and it has often been difficult to distinguish putative vicariance from simple isolation by distance. The sky island communities of the American Southwest present an ideal system in which to compare late Pleistocene range fragmentations documented by palaeoenvironmental studies with population genetic data from organisms within these communities. In order to elucidate the impact of Pleistocene climate fluctuations on these environments, biogeographic patterns in the flightless longhorn cactus beetle, Moneilema appressum were examined using mitochondrial DNA sequence data. Gene tree relationships between haplotypes were inferred using parsimony, maximum-likelihood, and Bayesian analysis. Nested clade analysis, Mantel tests, and coalescent modelling were employed to examine alternative biogeographic scenarios, and to test the hypothesis that Pleistocene climate changes drove population differentiation in this species. The program mdiv was used to estimate migration and divergence times between populations, and to measure the statistical support for isolation over ongoing migration. These analyses showed significant geographic structure in genetic relationships, and implicated topography as a key determinant of isolation. However, although the coalescent analyses suggested that a history of past habitat fragmentation underlies the observed geographic patterns, the nested clade analysis indicated that the pattern was consistent with isolation by distance. Estimated divergence times indicated that range fragmentation in M. appressum is considerably older than the end of the most recent glacial, but coincided with earlier interglacial warming events and with documented range expansions in other, desert-dwelling species of Moneilema.

Animals↗

PubMed2005

Bayesian inference of evolutionary history from chloroplast microsatellites in the cosmopolitan weed Capsella bursa-pastoris (Brassicaceae).

Besides showing an extraordinary degree of phenotypic variability, Capsella bursa-pastoris (Brassicaceae) is also one of the world's most common plant species and a serious weed in many countries. We have employed a coalescent-based Bayesian analysis of chloroplast microsatellite data to infer demographic and evolutionary parameters of this species. Two different demographic models applied to data from seven chloroplast microsatellite loci among 59 accessions show that the effective population size of C. bursa-pastoris is very small indicating a rapid expansion of the species, a result that is in accordance with fossil and historical data. Against this background, analysis of flowering time variation among accessions suggests that ecotypic differentiation in flowering time has occurred recently in the species' history. Finally, our results also indicate that mononucleotide repeat loci in the chloroplast genome can deteriorate in relatively short periods of evolutionary time.

Base Sequence↗

PubMed2006

Genetic and karyotypic structure in the shrews of the Sorex araneus group: are they independent?

The species of the common shrew (Sorex araneus) group are morphologically very similar but exhibit high levels of karyotypic variation. Here we used genetic variation at 10 microsatellite markers in a data set of 212 individuals mostly sampled in the western Alps and composed of five karyotypic taxa (Sorex coronatus, Sorex antinorii and the S. araneus chromosome races Cordon, Bretolet and Vaud) to investigate the concordance between genetic and karyotypic structure. Bayesian analysis confirmed the taxonomic status of the three sampled species since individuals consistently grouped according to their taxonomical status. However, introgression can still be detected between S. antinorii and the race Cordon of S. araneus. This observation is consistent with the expected low karyotypic complexity of hybrids between these two taxa. Geographically based cryptic substructure was discovered within S. antinorii, a pattern consistent with the different postglaciation recolonization routes of this species. Additionally, we detected two genetic groups within S. araneus notwithstanding the presence of three chromosome races. This pattern can be explained by the probable hybrid status of the Bretolet race but also suggests a relatively low impact of chromosomal differences on genetic structure compared to historical factors. Finally, we propose that the current data set (available at http://www.unil.ch/dee/page7010_en.html#1) could be used as a reference by those wanting to identify Sorex individuals sampled in the western Alps.

Animals↗

PubMed2006

Hybridization between subspecies of waterbuck (Kobus ellipsiprymnus) in zones of overlap with limited introgression.

Two subspecies of waterbuck (Kobus ellipsiprymnus), common (Kobus ellipsiprymnus ellipsiprymnus) and defassa (Kobus ellipsiprymnus defassa), are recognized based on differences in rump pattern, coat colour and geographical distribution. These forms are parapatrically distributed with an area of range overlap in East Africa, where phenotypically intermediate populations occur. Variation in 478 bp of the mitochondrial DNA control region and 14 polymorphic microsatellite loci were used to describe the genetic structure and phylogeographical pattern of the species, and to assess if the intermediate populations are the results of hybridization. In total, 186 individuals from 11 localities were analysed. A high degree of genetic differentiation was found between subspecies, although this was most evident from the microsatellite data. Hybridization was suggested in the phenotypically and geographically intermediate Nairobi NP population in Kenya. A neighbour-joining (NJ) tree based on microsatellite population genetic distances grouped Nairobi between the common and defassa populations, and a Bayesian analysis clearly showed introgression. Individuals sampled in Samburu NP, Kenya, had a common waterbuck phenotype, but introgression was suggested by both markers. Although a high degree of maternal defassa input was indicated from the sequence data, the Samburu population grouped with the common waterbuck in the microsatellite population genetic distance tree, with high support. Analyses of linkage disequilibrium and maximum-likelihood estimates of genetic drift suggested that admixture between subspecies is a recent event. The fact that introgression is limited between subspecies could be caused by chromosomal differences, hindering gene flow between common and defassa waterbuck.

Africa, Eastern↗

PubMed2007

Linked vs unlinked markers: multilocus microsatellite haplotype-sharing as a tool to estimate gene flow and introgression.

We have explored the use of multilocus microsatellite haplotypes to study introgression from cultivated (Malus domestica) into wild apple (Malus sylvestris), and to study gene flow among remnant populations of M. sylvestris. A haplotype consisted of alleles at microsatellite loci along one chromosome. As destruction of haplotypes through recombination occurs much faster than loss of alleles due to genetic drift, the lifespan of a multilocus haplotype is much shorter than that of the underlying alleles. When different populations share the same haplotype, this may indicate recent gene flow between populations. Similarly, haplotypes shared between two species would be a strong signal for introgression. As the expected lifespan of a haplotype depends on the strength of the linkage, the length [in centiMorgans (cM)] of the haplotype shared contains information on the number of generations passed. This application of shared haplotypes is distinct from using haplotype-sharing to detect association between markers and a certain trait. We inferred haplotypes for four to eight microsatellite loci on Linkage Group 10 of apple from genotype data using the program phase, and then identified those haplotypes shared between populations and species. Compared with a Bayesian analysis of unlinked microsatellite loci using the program structure, haplotype-sharing detected a partially different set of putative hybrids. Cultivated haplotypes present in M. sylvestris were short (< 1.5 cM), indicating that introgression had taken place many generations ago, except for two Belgian plants that contained a haplotype of 47.1 cM, indicating recent introgression. In the estimation of gene flow, F(ST) based on unlinked loci indicated small (0.032-0.058) but statistically significant differentiation between some populations only. However, various M. sylvestris haplotypes were shared in nearly all pairwise comparisons of populations, and their length indicated recent gene flow. Hence, all Dutch populations should be considered as one conservation unit. The added value of using sharing of multilocus microsatellite haplotypes as a source of population genetic information is discussed.

Belgium↗

PubMed2005

The value of prior information for detection of QTL affecting longitudinal traits: an example using Von Bertalanffy growth function.

A Bayesian procedure is presented for detecting quantitative trait loci (QTL) affecting longitudinal traits. The statistical model assumes a QTL affecting the prior distribution of the parameters of a given production function, under a hierarchical Bayesian scheme. Marginal posterior distributions for the effects associated with the QTL are calculated using Markov chain Monte Carlo methods. Furthermore, the Bayesian analysis allows the use of some available relevant information that can improve the detection of the QTL substantially. To illustrate the procedure, an example of QTL detection using the Von Bertalanffy growth function is presented with a F2 pig population bred from Iberian boars and Landrace sows. Animals of the F2 population were genotyped for seven markers in chromosome 2 (SSC2). Two prior distributions for the mean effect of the parameters related with birth and adult weight were compared. On the one hand, vague prior distributions were used, and, on the other, there were assumed univariate Gaussian distributions that ensure biologically meaningful adult and birth weights on the posterior growth curves. Results from the second prior distribution supported the presence of QTL, by showing that individuals with both alleles of Iberian origin had lower rates of maturation. On the contrary, when vague priors were used, the procedure was not able to detect QTL.

Animals↗

PubMed2005

Frequency distribution of a Cys430Ser polymorphism in peroxisome proliferator-activated receptor-gamma coactivator-1 (PPARGC1) gene sequence in Chinese and Western pig breeds.

Identification of major genes, that genetically impact fat tissue formation is important for successful selection of lean animals with good meat quality. Because of its central role in fat cell differentiation and muscle fibre type determination, PPARGC1 is a potential candidate gene affecting fattening traits and pig meat quality. In this study, a T/A substitution at position 1378 (GenBank accession no. AY346131) in the porcine PPARGC1 gene causing a Cys430Ser amino acid substitution at position 430 was genotyped on a total of 239 animals, including 101 from seven Chinese and 138 from six Western pig breeds. Bayesian analysis revealed that the mean frequency of allele T (Cys) was 92.64 +/- 4.82% in Chinese pigs, and 45.99 +/- 4.13% in Western pigs. The 95% interval of the posterior mean frequency of allele T was 0.82-1.00 in Chinese pigs and 0.38-0.54 in Western pigs, indicating these two groups of pigs diverged at this locus during genetic evolution of the breed. Because marked differences in fat and lean tissue deposition exist between Western and Chinese pig breeds, this Cys430Ser exchange in the PPARGC1 gene deserves further evaluation to determine its phenotypic effect on fattening and carcass traits in commercial pig populations.

Amino Acid Substitution↗

PubMed2005

Estimation of heritability for Tying-up syndrome in the Thoroughbred racehorse by Gibbs sampling.

Tying-up is a condition that primarily affects the muscles of horses. In this study, the heritability of the Tying-up syndrome in the Thoroughbred racehorse was estimated by Bayesian analysis with Gibbs sampling based on the threshold model for binary traits. The data used were the clinical data in racehorses diagnosed by veterinarians of the Racehorse Clinics of Japan Racing Association from 2000 to 2003. The health status of the Tying-up was treated as a binary trait. In the genetic analysis, the effect of changing the amount of the pedigree or inbreeding information on the estimation of heritability was investigated, too. The heritability estimates with non-zero probability in the posterior densities were approximately 0.16-0.18 in minimum, suggesting that the heritability of the Tying-up is not zero at least. The posterior density distributions of the heritability estimates were generally more pointed and sharp with using inbreeding coefficients than without using it, suggesting that more stable estimations were obtained when inbreeding coefficients were used. Among the different amounts of pedigree and inbreeding information, the heritabilities obtained with three or four generations of pedigree using inbreeding coefficients seems to be preferable, i.e. heritability of 0.42 or 0.43 for Tying-up.

Animals↗

PubMed2005

Comparison of BSE prevalence estimates from EU countries for the period July to December 2001 to the OIE and EU GBR classifications.

Consequent upon the bovine spongiform encephalopathy (BSE) crisis, the European Union (EU) Commission enacted various decisions, which demanded that all bovine animals over 30 months of age should be examined by one of the approved rapid tests when slaughtered for human consumption. All cattle over 24 months of age subject to 'special emergency slaughtering' or died on the farm or in transit or suspect of BSE infection should also be examined by one of the approved rapid tests. According to a specific commission decision, Sweden and Finland were to test only a sample of bovine animals over 30 months of age subject to normal slaughter. Testing commenced on 1 January 2001. The authors evaluate the results of more than 5 million tests performed in the second semester 2001 from across the EU. The prevalence of BSE in the risk categories considered (emergency slaughter, fallen stock and healthy slaughtered), and the probability distribution of true-positive, false-positive and false-negative results are estimated by second-order Bayesian analysis. The results of the validation of tests performed in the EU are also considered by estimation of the probability distribution of their sensitivity and specificity. The prevalence of infection estimated in the cattle population of each EU country is compared against the criteria given in the OIE Terrestrial Animal Health Code and is also used to evaluate the consistency of the results of EU Geographical BSE Risk with the actual infection levels in the countries. Finally, the capability of the two current approaches to BSE surveillance (i.e. the testing of all slaughtered and dead cattle as applied in the EU and a surveillance system targeted at animals in risk categories only) to detect the infection in a given population are discussed.

Animals↗

PubMed2004

Sputum carcinoembryonic antigen, neuron-specific enolase and cytokeratin fragment 19 levels in lung cancer diagnosis.

OBJECTIVE: The aim of the present study was to examine the impact of sputum carcinoembryonic antigen (CEA), neuron-specific enolase (NSE) and cytokeratin fragment 19 (CYFRA 21-1) levels in lung cancer diagnosis and to compare the diagnostic usefulness of sputum assays with that of serum assays. METHODOLOGY: Forty-seven patients with lung cancer and 62 with benign lung disease were studied. Tumour marker levels in sputum (sp.) and serum (ser) were measured by immunoradiometric assays. RESULTS: Sputum and serum tumour marker levels were significantly higher in lung cancer than in benign disease. When the specificity was 95%, the sensitivity was 57%, 43%, 36%, 30%, 28% and 19%, for spCEA, serCYFRA 21-1, spCYFRA 21-1, serCEA, serNSE, and spNSE, respectively. Bayesian analysis showed that the best predictive values correspond to spCEA and serCYFRA 21-1. The maximum overall gain was obtained in pretest probability of 0.35 for both spCEA and serCYFRA 21-1, with predictive values of 84% and 80% for spCEA and serCYFRA 21-1, respectively. CONCLUSION: Sputum tumour marker levels were no more useful than the serum levels in lung cancer diagnosis. SpCEA offered the best predictive values but these were still not sufficiently satisfactory for spCEA to be proposed for routine use.

Adult↗

PubMed1987

Acute appendicitis in childhood: a feasibility study of computer-assisted diagnosis.

The case records of 169 children admitted to hospital with suspected appendicitis were subjected to Bayesian analysis in order to determine whether computer-assisted diagnosis would be likely to reduce the negative laparotomy rate. The results suggest that the negative laparotomy rate could be reduced from 27% to 18% if computer-assisted diagnosis was used.

Acute Disease↗

PubMed1996

Detection of carriers of haemophilia A: use of bioassays and restriction fragment length polymorphisms (RFLP).

BACKGROUND: Haemophilia A is a sex-linked bleeding disorder carried by unaffected females. Currently, the two main methods used for the determination of carrier status in women from families with haemophilia A are bioassays and DNA-based assays using restriction fragment length polymorphisms (RFLP). AIM: The aim of this paper was to assess the current usefulness of these two methods. METHODS: Bioassays measured factor VIII coagulation activity by a two-stage coagulation assay and von Willebrand antigen by immunoelectrophoresis. RFLP were determined with two intragenic probes (p114 and p486) and two linked probes (St14 and DX13). Data were analysed using a Bayesian analysis to allow for all possible recombination events. We also incorporated an estimate for the risk of mosaicism into calculations in isolated haemophilia families. Both bioassays and RFLP were used to determine carrier status in 63 women, 31 from known haemophilia families and 32 from families of isolated cases. The techniques were assessed for their ability to classify the patients as normal (p < 0.2) or carrier (p > 0.7). Where applicable, intron 22 inversion was also tested. RESULTS: In the known families, six women could not be classified after bioassay, but all could be classified by RFLP. Of the 32 women from families of isolated cases, eight were unclassified by bioassay and 12 were not definitely classified using RFLP. However, RFLP was useful in determining that a recent mutation had occurred in six of the eight families in which DNA from the grandparents was available. CONCLUSION: For diagnosis of carriers of haemophilia, RFLP is the preferred method in familial haemophilia, but is less useful in isolated haemophilia.

Blood Coagulation Tests↗

PubMed2005

Stochastically modeling Listeria monocytogenes growth in farm tank milk.

This article presents a Listeria monocytogenes growth model in milk at the farm bulk tank stage. The main objective was to judge the feasibility and value to risk assessors of introducing a complex model, including a complete thermal model, within a microbial quantitative risk assessment scheme. Predictive microbiology models are used under varying temperature conditions to predict bacterial growth. Input distributions are estimated based on data in the literature, when it is available. If not, reasonable assumptions are made for the considered context. Previously published results based on a Bayesian analysis of growth parameters are used. A Monte Carlo simulation that forecasts bacterial growth is the focus of this study. Three scenarios that take account of the variability and uncertainty of growth parameters are compared. The effect of a sophisticated thermal model taking account of continuous variations in milk temperature was tested by comparison with a simplified model where milk temperature was considered as constant. Limited multiplication of bacteria within the farm bulk tank was modeled. The two principal factors influencing bacterial growth were found to be tank thermostat regulation and bacterial population growth parameters. The dilution phenomenon due to the introduction of new milk was the main factor affecting the final bacterial concentration. The results show that a model that assumes constant environmental conditions at an average temperature should be acceptable for this process. This work may constitute a first step toward exposure assessment for L. monocytogenes in milk. In addition, this partly conceptual work provides guidelines for other risk assessments where continuous variation of a parameter needs to be taken into account.

Animals↗

PubMed2006

A statistical test of the hypothesis that polyclonal intestinal tumors arise by random collision of initiated clones.

The random collision hypothesis is a mathematical idealization of intestinal tumor formation that can account for the polyclonal origin of tumors without requiring a mechanistic description of clonal interaction. Using data from recent polyclonality studies in mice, we develop a statistical procedure to test the random collision hypothesis. Elements from stochastic geometry and approximations due to Armitage (1949, Biometrika 36, 257-266) support a statistical model of tumor count data. Bayesian analysis yields the posterior distribution of the number of heterotypic tumors, from which p-values are computed to test random collision.

Animals↗

PubMed1995

Computer Program for Diagnosing and Teaching Geographic Medicine.

One of the unique aspects of infectious disease is its wide variety, both in time and place. The specialist practicing in India may have little or no expertise in Peruvian disease. A colleague in New York may be called upon to diagnose and treat conditions originating in Africa, Asia, South America, Fiji and Papua, New Guinea. At the same time, this colleague must be familiar with the pathogens that originate in Texas, Hawaii, and Canada. Indeed, even the full-time infectious diseases specialist may not be conversant in diseases such as lagochilascariasis, louping ill, and lobomycosis. War, famine, education, immigration, and business travel have contributed to the advent of specialists in Geographic Medicine and Emporiatrics, otherwise known as Travel medicine. The "art" of diagnosis is largely an ability (albeit subconscious) to rank probabilities based on the incidences of likely diseases and the chance of encountering given clinical features within each disease. In theory, Bayesian analysis could be employed to diagnose disease accurately when given proper input. A multicenter study was undertaken to test a comprehensive computer driven-software program that incorporates worldwide epidemiologic and clinical parameters.

Journal Article↗