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1.
Background
The Brief Infant-Toddler Social and Emotional Assessment (BITSEA) is a promising questionnaire for the early detection of psychosocial problems in toddlers. The screening accuracy and clinical application were evaluated.Methods
In a community sample of 2-year-olds (N = 2060), screening accuracy of the BITSEA Problem scale was examined regarding a clinical CBCL1.5-5 Total Problem score. For the total population and subgroups by child’s gender and ethnicity Receiver Operating Characteristic (ROC) curves were calculated, and across a range of BITSEA Problem scores, sensitivity, specificity, likelihood ratio’s, diagnostic odds ratio and Youden’s index. Clinical application of the BITSEA was examined by evaluating the relation between the scale scores and the clinical decision of the child health professional.Results
The area under the ROC curve (95% confidence interval) of the Problem scale was 0.97(0.95–0.98), there were no significant differences between subgroups. The association between clinical decision and BITSEA Problem score (B = 2.5) and Competence score (B = −0.7) was significant (p<0.05).Conclusions
The results indicate that the BITSEA Problem scale has good discriminative power to differentiate children with and without psychosocial problems. Referred children had less favourable scores compared to children that were not referred. The BITSEA may be helpful in the early detection of psychosocial problems. 相似文献2.
Objectives
Rotator cuff tear is a common cause of shoulder diseases. Correct diagnosis of rotator cuff tears can save patients from further invasive, costly and painful tests. This study used predictive data mining and Bayesian theory to improve the accuracy of diagnosing rotator cuff tears by clinical examination alone.Methods
In this retrospective study, 169 patients who had a preliminary diagnosis of rotator cuff tear on the basis of clinical evaluation followed by confirmatory MRI between 2007 and 2011 were identified. MRI was used as a reference standard to classify rotator cuff tears. The predictor variable was the clinical assessment results, which consisted of 16 attributes. This study employed 2 data mining methods (ANN and the decision tree) and a statistical method (logistic regression) to classify the rotator cuff diagnosis into “tear” and “no tear” groups. Likelihood ratio and Bayesian theory were applied to estimate the probability of rotator cuff tears based on the results of the prediction models.Results
Our proposed data mining procedures outperformed the classic statistical method. The correction rate, sensitivity, specificity and area under the ROC curve of predicting a rotator cuff tear were statistical better in the ANN and decision tree models compared to logistic regression. Based on likelihood ratios derived from our prediction models, Fagan''s nomogram could be constructed to assess the probability of a patient who has a rotator cuff tear using a pretest probability and a prediction result (tear or no tear).Conclusions
Our predictive data mining models, combined with likelihood ratios and Bayesian theory, appear to be good tools to classify rotator cuff tears as well as determine the probability of the presence of the disease to enhance diagnostic decision making for rotator cuff tears. 相似文献3.
Shu-Hwa Chen Sheng-Yao Su Chen-Zen Lo Kuei-Hsien Chen Teng-Jay Huang Bo-Han Kuo Chung-Yen Lin 《PloS one》2009,4(12)
Background
Selecting an appropriate substitution model and deriving a tree topology for a given sequence set are essential in phylogenetic analysis. However, such time consuming, computationally intensive tasks rely on knowledge of substitution model theories and related expertise to run through all possible combinations of several separate programs. To ensure a thorough and efficient analysis and avert tedious manipulations of various programs, this work presents an intuitive framework, the phylogenetic reconstruction with automatic likelihood model selectors (PALM), with convincing, updated algorithms and a best-fit model selection mechanism for seamless phylogenetic analysis.Methodology
As an integrated framework of ClustalW, PhyML, MODELTEST, ProtTest, and several in-house programs, PALM evaluates the fitness of 56 substitution models for nucleotide sequences and 112 substitution models for protein sequences with scores in various criteria. The input for PALM can be either sequences in FASTA format or a sequence alignment file in PHYLIP format. To accelerate the computing of maximum likelihood and bootstrapping, this work integrates MPICH2/PhyML, PalmMonitor and Palm job controller across several machines with multiple processors and adopts the task parallelism approach. Moreover, an intuitive and interactive web component, PalmTree, is developed for displaying and operating the output tree with options of tree rooting, branches swapping, viewing the branch length values, and viewing bootstrapping score, as well as removing nodes to restart analysis iteratively.Significance
The workflow of PALM is straightforward and coherent. Via a succinct, user-friendly interface, researchers unfamiliar with phylogenetic analysis can easily use this server to submit sequences, retrieve the output, and re-submit a job based on a previous result if some sequences are to be deleted or added for phylogenetic reconstruction. PALM results in an inference of phylogenetic relationship not only by vanquishing the computation difficulty of ML methods but also providing statistic methods for model selection and bootstrapping. The proposed approach can reduce calculation time, which is particularly relevant when querying a large data set. PALM can be accessed online at http://palm.iis.sinica.edu.tw. 相似文献4.
Background
Continuity of care (COC) is a widely accepted core principle of primary care and has been associated with patient satisfaction, healthcare utilization and mortality in many, albeit small, studies.Objective
To assess the relationship between longitudinal continuity with a primary care physician (PCP) and likelihood of death in the French general population.Design
Observational study based on reimbursement claims from the French national health insurance (NHI) database for salaried workers (2007–2010).Setting
Primary care.Patients
We extracted data on the number and pattern of visits made to a PCP and excluded all patients who did not visit a PCP at least twice within 6 months. We recorded age, gender, comorbidities, social status, and deaths.Main outcome measures
The primary endpoint was death by all causes. We measured longitudinal continuity of care (COC) with a PCP twice a year between 2007 and 2010, using the COC index developed by Bice and Boxerman. We introduced the COC index as time-dependent variables in a survival analysis after adjustment for age, gender and stratifying on comorbidities and social status.Results
A total of 325 742 patients were included in the analysis. The average COC index ranged from 0.74 (SD: 0.35) to 0.76 (0.35) (where 1.0 is perfect continuity). Likelihood of death was lower in patients with higher continuity (hazard ratio for an increase in 0.1 of continuity, adjusted for age, sex, and stratified on comorbidities and social status: 0.96 [0.95–0.96]).Conclusion
Higher longitudinal continuity was associated with a reduced likelihood of death. 相似文献5.
Importance
Emergency treatment options in myocardial infarction are guided by presence or absence of ST-elevations in electrocardiography. Occurrence and factors associated with ST-presentation in different population groups are however inadequately known.Objective
To determine likelihood and patient features associated with ST-elevations in myocardial infarction.Design
Nationwide registry study including 22 hospitals with angiolaboratory during an eight year period in Finland.Setting
Hospitalized care.Participants
68,162 consecutive patients aged ≥30 with myocardial infarction.Measures
Likelihood and patient features associated with presence of ST-elevations.Results
Myocardial infarction presented with ST-elevation in 37.5% (CI 37.0–37.9%) and without in 62.5% (CI 61.9–63.1%) of patients, p<0.0001. Majority of patients aged 30–59 years with myocardial infarction had ST-elevation, but among octogenarians ST-elevations were present in only 24.7%. Presence of ST-elevations decreased with age by estimated 15.6% (CI 15.0–16.2%) per 10 year increase (p<0.0001). Men aged 40–79 years had significantly higher rate for ST-elevation myocardial infarction compared to women. Sex-based difference in presentation of myocardial infarction declined with increasing age. Overall, men had a 13% (CI 11–15%, p<0.0001) higher relative risk for ST-elevations compared to women when adjusted for age and co-morbidities. Diabetes, atrial fibrillation, peripheral or cerebral artery disease, chronic pulmonary disease, malignancy, and renal insufficiency were associated with absence of ST-elevations in myocardial infarction in multivariate analysis.Conclusions and Relevance
Myocardial infarction presents with ST-elevations more commonly in men. Presence of ST-elevations decreases with increasing age. Diabetes, atrial fibrillation, peripheral or cerebral artery disease, chronic pulmonary disease, malignancy, and renal insufficiency are associated with absence of ST-elevations in myocardial infarction. These findings may help to predict likelihood of ST-elevations in a patient with myocardial infarction. 相似文献6.
Background
Ecologists are collecting extensive data concerning movements of animals in marine ecosystems. Such data need to be analysed with valid statistical methods to yield meaningful conclusions.Principal Findings
We demonstrate methodological issues in two recent studies that reached similar conclusions concerning movements of marine animals (Nature 451∶1098; Science 332∶1551). The first study analysed vertical movement data to conclude that diverse marine predators (Atlantic cod, basking sharks, bigeye tuna, leatherback turtles and Magellanic penguins) exhibited “Lévy-walk-like behaviour”, close to a hypothesised optimal foraging strategy. By reproducing the original results for the bigeye tuna data, we show that the likelihood of tested models was calculated from residuals of regression fits (an incorrect method), rather than from the likelihood equations of the actual probability distributions being tested. This resulted in erroneous Akaike Information Criteria, and the testing of models that do not correspond to valid probability distributions. We demonstrate how this led to overwhelming support for a model that has no biological justification and that is statistically spurious because its probability density function goes negative. Re-analysis of the bigeye tuna data, using standard likelihood methods, overturns the original result and conclusion for that data set. The second study observed Lévy walk movement patterns by mussels. We demonstrate several issues concerning the likelihood calculations (including the aforementioned residuals issue). Re-analysis of the data rejects the original Lévy walk conclusion.Conclusions
We consequently question the claimed existence of scaling laws of the search behaviour of marine predators and mussels, since such conclusions were reached using incorrect methods. We discourage the suggested potential use of “Lévy-like walks” when modelling consequences of fishing and climate change, and caution that any resulting advice to managers of marine ecosystems would be problematic. For reproducibility and future work we provide R source code for all calculations. 相似文献7.
Background
Marginal posterior genotype probabilities need to be computed for genetic analyses such as geneticcounseling in humans and selective breeding in animal and plant species.Methods
In this paper, we describe a peeling based, deterministic, exact algorithm to compute efficiently genotype probabilities for every member of a pedigree with loops without recourse to junction-tree methods from graph theory. The efficiency in computing the likelihood by peeling comes from storing intermediate results in multidimensional tables called cutsets. Computing marginal genotype probabilities for individual i requires recomputing the likelihood for each of the possible genotypes of individual i. This can be done efficiently by storing intermediate results in two types of cutsets called anterior and posterior cutsets and reusing these intermediate results to compute the likelihood.Examples
A small example is used to illustrate the theoretical concepts discussed in this paper, and marginal genotype probabilities are computed at a monogenic disease locus for every member in a real cattle pedigree. 相似文献8.
Dong Yang Stefan James Ulf de Faire Lars Alfredsson Tomas Jernberg Tahereh Moradi 《PloS one》2013,8(4)
Objective
To examine the relationship between sex, country of birth, level of education as an indicator of socioeconomic position, and the likelihood of treatment in a coronary care unit (CCU) for a first-time myocardial infarction.Design
Nationwide register based study.Setting
Sweden.Patients
199 906 patients (114 387 men and 85,519 women) of all ages who were admitted to hospital for first-time myocardial infarction between 2001 and 2009.Main outcome measures
Admission to a coronary care unit due to myocardial infarction.Results
Despite the observed increasing access to coronary care units over time, the proportion of women treated in a coronary care unit was 13% less than for men. As compared with men, the multivariable adjusted odds ratio among women was 0.80 (95% confidence interval 0.77 to 0.82). This lower proportion of women treated in a CCU varied by age and year of diagnosis and country of birth. Overall, there was no evidence of a difference in likelihood of treatment in a coronary care unit between Sweden-born and foreign-born patients. As compared with patients with high education, the adjusted odds ratio among patients with a low level of education was 0.93 (95% confidence interval 0.89 to 0.96).Conclusions
Foreign-born and Sweden-born first-time myocardial infarction patients had equal opportunity of being treated in a coronary care unit in Sweden; this is in contrast to the situation in many other countries with large immigrant populations. However, the apparent lower rate of coronary care unit admission after first-time myocardial infarction among women and patients with low socioeconomic position warrants further investigation. 相似文献9.
Background and Aims
A great deal of money is spent controlling invasive weeds as part of international and national policies. It is essential that the funded treatments work across the region in which the policies operate. We argue that experiments across multiple sites are required to validate these programs as results from single sites may be misleading. Here, the control of Pteridium aquilinum (bracken) is used as a test example to address the following four questions. (1) Does the effectiveness of P. aquilinum-control treatments vary across sites? (2) Is the best treatment identified in previous research (cutting twice per year) consistent at all sites, and if not why not? (3) Is treatment performance related to P. aquilinum rhizome mass, litter cover or litter depth at the various sites? (4) Does successful P. aquilinum control influence species richness?Methods
Pteridium aquilinum‐control treatments were monitored for 10 years using six replicated experiments and analysed using meta-analysis. Meta-regressions were used to explore heterogeneity between sites.Key Results
The effectiveness of treatments varied between sites depending on the measure used to assess P. aquilinum performance. In general, cutting twice per year was the most successful treatment but on some sites other, less expensive treatments were as good. The effectiveness of treatments at different sites was not related to rhizome mass, but the effectiveness of most applied treatments were inversely related to post-control litter. Effective treatment was also associated with high species richness.Conclusions
It is concluded that successful development of national weed control programs requires multi-site experimental approaches. Here, meta-analyses demonstrate that variation in effectiveness between sites could be explained in part by pre-specified variables. Reliance on data from a single site for policy formulation is therefore clearly dangerous.Key words: Bracken, Pteridium aquilinum, weed, control, herbicide, litter dynamics, species diversity, meta-analysis 相似文献10.
Bas E Dutilh Cristiane C Thompson Ana CP Vicente Michel A Marin Clarence Lee Genivaldo GZ Silva Robert Schmieder Bruno GN Andrade Luciane Chimetto Daniel Cuevas Daniel R Garza Iruka N Okeke Aaron Oladipo Aboderin Jessica Spangler Tristen Ross Elizabeth A Dinsdale Fabiano L Thompson Timothy T Harkins Robert A Edwards 《BMC genomics》2014,15(1)
Background
Vibrio cholerae is a globally dispersed pathogen that has evolved with humans for centuries, but also includes non-pathogenic environmental strains. Here, we identify the genomic variability underlying this remarkable persistence across the three major niche dimensions space, time, and habitat.Results
Taking an innovative approach of genome-wide association applicable to microbial genomes (GWAS-M), we classify 274 complete V. cholerae genomes by niche, including 39 newly sequenced for this study with the Ion Torrent DNA-sequencing platform. Niche metadata were collected for each strain and analyzed together with comprehensive annotations of genetic and genomic attributes, including point mutations (single-nucleotide polymorphisms, SNPs), protein families, functions and prophages.Conclusions
Our analysis revealed that genomic variations, in particular mobile functions including phages, prophages, transposable elements, and plasmids underlie the metadata structuring in each of the three niche dimensions. This underscores the role of phages and mobile elements as the most rapidly evolving elements in bacterial genomes, creating local endemicity (space), leading to temporal divergence (time), and allowing the invasion of new habitats. Together, we take a data-driven approach for comparative functional genomics that exploits high-volume genome sequencing and annotation, in conjunction with novel statistical and machine learning analyses to identify connections between genotype and phenotype on a genome-wide scale.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-654) contains supplementary material, which is available to authorized users. 相似文献11.
Background
Phylogenetic study of protein sequences provides unique and valuable insights into the molecular and genetic basis of important medical and epidemiological problems as well as insights about the origins and development of physiological features in present day organisms. Consensus phylogenies based on the bootstrap and other resampling methods play a crucial part in analyzing the robustness of the trees produced for these analyses.Methodology
Our focus was to increase the number of bootstrap replications that can be performed on large protein datasets using the maximum parsimony, distance matrix, and maximum likelihood methods. We have modified the PHYLIP package using MPI to enable large-scale phylogenetic study of protein sequences, using a statistically robust number of bootstrapped datasets, to be performed in a moderate amount of time. This paper discusses the methodology used to parallelize the PHYLIP programs and reports the performance of the parallel PHYLIP programs that are relevant to the study of protein evolution on several protein datasets.Conclusions
Calculations that currently take a few days on a state of the art desktop workstation are reduced to calculations that can be performed over lunchtime on a modern parallel computer. Of the three protein methods tested, the maximum likelihood method scales the best, followed by the distance method, and then the maximum parsimony method. However, the maximum likelihood method requires significant memory resources, which limits its application to more moderately sized protein datasets. 相似文献12.
Imad Cherkaoui Radia Sabouni Iraqi Ghali Darya Kizub Alexander C. Billioux Kenza Bennani Jamal Eddine Bourkadi Abderrahmane Benmamoun Ouafae Lahlou Rajae El Aouad Kelly E. Dooley 《PloS one》2014,9(4)
Setting
Public tuberculosis (TB) clinics in urban Morocco.Objective
Explore risk factors for TB treatment default and develop a prediction tool. Assess consequences of default, specifically risk for transmission or development of drug resistance.Design
Case-control study comparing patients who defaulted from TB treatment and patients who completed it using quantitative methods and open-ended questions. Results were interpreted in light of health professionals’ perspectives from a parallel study. A predictive model and simple tool to identify patients at high risk of default were developed. Sputum from cases with pulmonary TB was collected for smear and drug susceptibility testing.Results
91 cases and 186 controls enrolled. Independent risk factors for default included current smoking, retreatment, work interference with adherence, daily directly observed therapy, side effects, quick symptom resolution, and not knowing one’s treatment duration. Age >50 years, never smoking, and having friends who knew one’s diagnosis were protective. A simple scoring tool incorporating these factors was 82.4% sensitive and 87.6% specific for predicting default in this population. Clinicians and patients described additional contributors to default and suggested locally-relevant intervention targets. Among 89 cases with pulmonary TB, 71% had sputum that was smear positive for TB. Drug resistance was rare.Conclusion
The causes of default from TB treatment were explored through synthesis of qualitative and quantitative data from patients and health professionals. A scoring tool with high sensitivity and specificity to predict default was developed. Prospective evaluation of this tool coupled with targeted interventions based on our findings is warranted. Of note, the risk of TB transmission from patients who default treatment to others is likely to be high. The commonly-feared risk of drug resistance, though, may be low; a larger study is required to confirm these findings. 相似文献13.
Background
The Wolbachia strategy aims to manipulate mosquito populations to make them incapable of transmitting dengue viruses between people. To test its efficacy, this strategy requires field trials. Public consultation and engagement are recognized as critical to the future success of these programs, but questions remain regarding how to proceed. This paper reports on a case study where social research was used to design a community engagement framework for a new dengue control method, at a potential release site in central Vietnam.Methodology/Principal Findings
The approach described here, draws on an anthropological methodology and uses both qualitative and quantitative methods to design an engagement framework tailored to the concerns, expectations, and socio-political setting of a potential trial release site for Wolbachia-infected Aedes aegypti mosquitoes. The process, research activities, key findings and how these were responded to are described. Safety of the method to humans and the environment was the most common and significant concern, followed by efficacy and impact on local lives. Residents expected to be fully informed and engaged about the science, the project, its safety, the release and who would be responsible should something go wrong. They desired a level of engagement that included regular updates and authorization from government and at least one member of every household at the release site.Conclusions/Significance
Results demonstrate that social research can provide important and reliable insights into public concerns and expectations at a potential release site, as well as guidance on how these might be addressed. Findings support the argument that using research to develop more targeted, engagement frameworks can lead to more sensitive, thorough, culturally comprehensible and therefore ethical consultation processes. This approach has now been used successfully to seek public input and eventually support for releases Wolbachia-infected mosquitoes, in two different international settings - Australia and Vietnam. 相似文献14.
Haixia Chen Malin Strand Jon L. Norenburg Shichun Sun Hiroshi Kajihara Alexey V. Chernyshev Svetlana A. Maslakova Per Sundberg 《PloS one》2010,5(9)
Background
It has been suggested that statistical parsimony network analysis could be used to get an indication of species represented in a set of nucleotide data, and the approach has been used to discuss species boundaries in some taxa.Methodology/Principal Findings
Based on 635 base pairs of the mitochondrial protein-coding gene cytochrome c oxidase I (COI), we analyzed 152 nemertean specimens using statistical parsimony network analysis with the connection probability set to 95%. The analysis revealed 15 distinct networks together with seven singletons. Statistical parsimony yielded three networks supporting the species status of Cephalothrix rufifrons, C. major and C. spiralis as they currently have been delineated by morphological characters and geographical location. Many other networks contained haplotypes from nearby geographical locations. Cladistic structure by maximum likelihood analysis overall supported the network analysis, but indicated a false positive result where subnetworks should have been connected into one network/species. This probably is caused by undersampling of the intraspecific haplotype diversity.Conclusions/Significance
Statistical parsimony network analysis provides a rapid and useful tool for detecting possible undescribed/cryptic species among cephalotrichid nemerteans based on COI gene. It should be combined with phylogenetic analysis to get indications of false positive results, i.e., subnetworks that would have been connected with more extensive haplotype sampling. 相似文献15.
Tao Ding Michèle Bergeron Peggy Seely Xuefen Yang Tamsir O. Diallo Margot Plews Paul Sandstrom T. Blake Ball Adrienne F. A. Meyers 《PloS one》2014,9(8)
Background
CD4 T cell enumeration is the most widely used prognostic marker for management of HIV disease. Internal quality control and external quality assessment (EQA) programs are critical to ensure reliability of clinical measurements. The utility of stabilized whole blood products (SWBP) as a test reagent for EQA programs such as Quality Assessment and Standardization for Immunological measures relevant to HIV/AIDS (QASI) program have been demonstrated previously. Since then, several new commercial SWBPs and alternative CD4 enumeration technologies have become available. Seven SWBPs were evaluated on seven different enumeration platforms to determine which product(s) are most suitable for EQA programs that support multiple analytical technologies.Method
Assessment of SWBPs was based on two criteria: (1) accuracy of CD4 T cell measurements and; (2) stability under sub optimal storage conditions.Results
Three SWBPs (Multi-Check, StatusFlow and CD4 Count) showed accurate CD4 T-cell absolute count and percentage values across six of the enumeration platforms. All products retain stability up to 18 days at 21–23°C with the exception of Multi-Check-high on FacsCount and Multi-Check-Low and StatusFlow-Low on Pima. One of the products (CD4 Count) retained stability for three days on all platforms tested when stored at 37°C.Conclusion
This study demonstrated that the characteristics of commercially available SWBPs vary across multiple CD4 platforms. The compatibility of testing panels for EQA programs with multiple analytical platforms needs to be carefully considered, especially in large multiplatform CD4 EQA programs. The selection of a suitable cross-platform SWBP is an increasing challenge as more reagents and platforms are introduced for CD4 T-cell enumeration. 相似文献16.
17.
18.
Kiki M. J. M. H. Lombarts Maas Jan Heineman Albert J. J. A. Scherpbier Onyebuchi A. Arah 《PloS one》2014,9(1)
Background
To understand teaching performance of individual faculty, the climate in which residents’ learning takes place, the learning climate, may be important. There is emerging evidence that specific climates do predict specific outcomes. Until now, the effect of learning climate on the performance of the individual faculty who actually do the teaching was unknown.Objectives
This study: (i) tested the hypothesis that a positive learning climate was associated with better teaching performance of individual faculty as evaluated by residents, and (ii) explored which dimensions of learning climate were associated with faculty’s teaching performance.Methods and Materials
We conducted two cross-sectional questionnaire surveys amongst residents from 45 residency training programs and multiple specialties in 17 hospitals in the Netherlands. Residents evaluated the teaching performance of individual faculty using the robust System for Evaluating Teaching Qualities (SETQ) and evaluated the learning climate of residency programs using the Dutch Residency Educational Climate Test (D-RECT). The validated D-RECT questionnaire consisted of 11 subscales of learning climate. Main outcome measure was faculty’s overall teaching (SETQ) score. We used multivariable adjusted linear mixed models to estimate the separate associations of overall learning climate and each of its subscales with faculty’s teaching performance.Results
In total 451 residents completed 3569 SETQ evaluations of 502 faculty. Residents also evaluated the learning climate of 45 residency programs in 17 hospitals in the Netherlands. Overall learning climate was positively associated with faculty’s teaching performance (regression coefficient 0.54, 95% confidence interval: 0.37 to 0.71; P<0.001). Three out of 11 learning climate subscales were substantially associated with better teaching performance: ‘coaching and assessment’, ‘work is adapted to residents’ competence’, and ‘formal education’.Conclusions
Individual faculty’s teaching performance evaluations are positively affected by better learning climate of residency programs. 相似文献19.
Background
Microsatellite loci have high mutation rates and thus are indicative of mutational processes within the genome. By concentrating on the symbiotic and aposymbiotic cnidarians, we investigated if microsatellite abundances follow a phylogenetic or ecological pattern. Individuals from eight species were shotgun sequenced using 454 GS-FLX Titanium technology. Sequences from the three available cnidarian genomes (Nematostella vectensis, Hydra magnipapillata and Acropora digitifera) were added to the analysis for a total of eleven species representing two classes, three subclasses and eight orders within the phylum Cnidaria.Results
Trinucleotide and tetranucleotide repeats were the most abundant motifs, followed by hexa- and dinucleotides. Pentanucleotides were the least abundant motif in the data set. Hierarchical clustering and log likelihood ratio tests revealed a weak relationship between phylogeny and microsatellite content. Further, comparisons between cnidaria harboring intracellular dinoflagellates and those that do not, show microsatellite coverage is higher in the latter group.Conclusions
Our results support previous studies that found tri- and tetranucleotides to be the most abundant motifs in invertebrates. Differences in microsatellite coverage and composition between symbiotic and non-symbiotic cnidaria suggest the presence/absence of dinoflagellates might place restrictions on the host genome.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-939) contains supplementary material, which is available to authorized users. 相似文献20.
Kevin A. Brown Laurie J. Lambert James M. Brophy James Nasmith Stéphane Rinfret Eli Segal Simon Kouz Dave Ross Richard Harvey Sébastien Maire Lucy J. Boothroyd Peter Bogaty 《PloS one》2014,9(8)