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PubMed2000

Predictors of adverse events with intramuscular ketamine sedation in children.

STUDY OBJECTIVE: Ketamine is a safe and effective sedative for emergency department procedures in children. However, the use of ketamine sometimes is associated with airway complications, emesis, and recovery agitation. We wished to identify predictors of these adverse events that clinicians might use to risk-stratify children who are candidates for ketamine sedation. METHODS: We analyzed data from 1,021 ED intramuscular ketamine sedations in children 15 years of age or younger at a university medical center and an affiliated county hospital over a 9-year period. Five potential predictor variables (age, gender, American Society of Anesthesiologists' [ASA] risk classification, quantity of first ketamine dose, and number of ketamine doses administered) were compared between children with and without complications. We used multiple logistic regression analyses to determine the association of these 5 variables with emesis and recovery agitation, and validated these analyses with bootstrap resampling techniques. We compared children with and without airway complications using univariate statistics alone, as there were too few patients with airway complications to support a multivariate analysis. RESULTS: No study variables had significant univariate associations with airway complications (all P values >.40). We found emesis to be associated with increasing age in multivariate analysis (odds ratio [OR] 1.25 per year, bias-corrected 95% confidence interval [CI] 1.17 to 1.34, P<.001). The incidence of emesis was 12. 1% in children aged 5 years or older, and 3.5% in those younger than 5 years (Delta8.6%, 95% CI 4.9% to 12.1%). Recovery agitation was associated with the presence of an underlying medical condition (ie, ASA class > or =2, OR 3.05, bias-corrected 95% CI 1.65 to 7.30, P=.004) and inversely associated with increasing age (OR 0.79 per year, bias-corrected 95% CI 0.69 to 0.89, P<.001). The incidence of recovery agitation was 17.9% in ASA class 1 children and 33.3% in children in ASA class 2 or greater (Delta-15.4%, 95% CI 0.0% to -30. 7%). The incidence of recovery agitation was 12.1% in children aged 5 years or older, and 22.5% in those younger than 5 years (Delta-10. 4%, 95% CI -3.0% to -17.7%). Bootstrap resampling techniques validated the importance of the significant variables identified in the regression analyses. CONCLUSION: No study variable was predictive of ketamine-associated airway complications. Emesis that occurred after ketamine administration was modestly associated with increasing age. Recovery agitation was modestly associated with decreasing age and the presence of an underlying medical condition. The discriminatory power of these variables was low enough as to be unlikely to alter clinical decisions regarding patient selection for ketamine administration. No evidence of a significant ketamine dose relationship was noted for airway complications, emesis, or recovery agitation.

Adolescent↗

PubMed2001

Analyzing the radiation of the proenkephalin gene in tetrapods: cloning of a Bombina orientalis proenkephalin cDNA.

Analyzing the Radiation of the Proenkephalin Gene in Tetrapods: Cloning of a Bombina orientalis Proenkephalin cDNA: A proenkephalin cDNA was cloned from the brain of the anuran amphibian, Bombina orientalis (Family: Discoglossidae). This cDNA is 1358 nucleotides in length, and contains an open reading frame that codes for 251 amino acids. Within the open reading frame there are seven opioid (YGGF) sequences. There were five Met-enkephalin (YGGFM) sequences that are flanked by sets of paired basic amino acid proteolytic cleavage sites and two C-terminally extended Met-enkephalin sequences: YGGFMRGY and YGGFMRF. No Leu-enkephalin sequences were found in B. orientalis proenkephalin. It was possible to align the amino acid sequences of proenkephalin from several vertebrate taxa (human, Australian lungfish, B. orientalis, Xenopus laevis, Spea multiplicatus) by inserting a minimum of nine gaps. This alignment was then used to analyze the corresponding nucleotides for each proenkephalin sequence using maximum likelihood. This analysis yielded a single tree. In this tree, the Australian lungfish sequence was the outgroup or the tetrapod ingroup. The amphibian sequences form a clade separate from the human sequence. The bootstrap value for the amphibian clade was 100%. Within the amphibian clade the Bombina sequence was the sister group to a clade composed of the X. laevis and S. multiplicatus sequences. The bootstrap value for the X. laevis/S. multiplicatus clade was 94%. Collectively, these data indicate that the sequence of Bombina proenkephalin may be more similar to the proposed ancestral anuran proenkephalin sequence, than either X. laevis or S. multiplicatus proenkephalin.

Amino Acid Sequence↗

PubMed1997

Self-organized marginal stability resulting from inconsistency between fuzzy logic and deterministic logic: an application to biological systems.

Complex systems in which internal agents (observers) interact with each other with finite velocity of information propagation cannot be described with a single consistent logic. We have proposed the bootstrapping system of cellular automata for describing such complex systems using two types of complementary logic: Boolean and non-Boolean. We extend this in this paper to a system of time-discrete continuous maps using fuzzy logic in place of non-Boolean logic. Fuzziness implies the intrinsic ambiguity of internal measurement. The bootstrapping system evolves, changing the dynamics perpetually, so that the discrepancy between the two types of complementary logic may be minimized. The equilibration force defined from the strength of discrepancy forms a landscape for self-organization which is similar to the fitness landscape for evolution. Though they appear similar, the former is derived from the internal dynamics. The goal of evolution, when applied to the map of the Belousov-Zabochinsky reaction, is demonstrated to be near the border between periodicity and chaos. The behavior depends on the degree of fuzziness and the extent of noise. When fuzziness increases too much, the system becomes unstable. Near the boundary, it exhibits intermittent chaos with a background of 1/f noise.

Animals↗

PubMed1999

Molecular phylogenetic studies on Theileria parasites based on small subunit ribosomal RNA gene sequences.

Classification of Theileria parasites of south-east Asian countries is still ambiguous due to the lack of basic studies, especially their molecular genetic information. In this study, we included 6 known species and 14 unclassified Theileria parasite isolates: Theileria annulata, Theileria parva, Theileria taurotragi, Theileria sergenti, Theileria buffeli, Theileria types Sable, Theileria types A, B, B1, B2, C, D, E, F, G, G1, Theileria type Medan (Indonesia), Theileria type Ipoh (Malaysia) and Theileria type Thong Song (Thailand). Small subunit ribosomal RNA (srRNA) nucleotide sequence data were collected by PCR, cloning and dideoxy sequencing. The srRNA nucleotide sequences were aligned and analyzed by distance methods, maximum parsimony algorithms and maximum likelihood methods to construct phylogenetic trees. Bootstrap analysis was used to test the strength of the different phylogenetic reconstructions. The data indicated that all of the tree-building methods gave very similar results. This study identified two groups of Theileria, the pathogenic and benign groups, which are strongly supported by bootstrap analysis. The analysis also indicated that three subgroups (A, B and C) were generated within the benign Theileria group whereas the classification of Theileria type D and Thong Song is questionable. However, more basic information such as life cycle differences, vectors, modes of transmission, virulent and genetic/sexual compatability is essential for clearer taxonomic definition of the benign Theileria parasites.

Animals↗

PubMed2000

Regrowth delay analysis of irradiated tumors in the curative dose region.

PURPOSE: To develop a method to analyze regrowth delay times, including cured tumors. METHODS AND MATERIALS: Regrowth delay measured in the in vitro squamous cell carcinoma megacolony system following fractionated irradiation was analyzed using two different approaches. A conventional regrowth delay analysis based on means or medians of dose groups was contrasted with a one-step procedure using the inverse of individual regrowth delay times, where cured tumors are represented by an infinite delay time. Two data sets with different proportions of cured tumors were compared in this way. In addition, for both approaches, confidence limits were also generated by the bootstrap technique. RESULTS: The parameter estimated was the alpha/beta ratio. The inverse analysis yielded similar results as the conventional analysis, but with much smaller confidence limits. When the dataset was stripped by stepwise removal of lower dose groups with no cures, the estimates of the alpha/beta ratio remained definitely more robust in inverse analysis. Results of the bootstrap procedure confirmed the accuracy of the calculated confidence intervals. CONCLUSION: Regrowth delay analysis using reciprocal regrowth delay times is a useful tool, especially when the data shows large variations, or a substantial fraction of the dataset falls into the curative dose region.

Animals↗

PubMed1998

Neural learning of embodied interaction dynamics.

This paper presents our approach towards realizing a robot which can bootstrap itself towards higher complexity through embodied interaction dynamics with the environment including other agents. First, the elements of interaction dynamics are extracted from conceptual analysis of embodied interaction and its emergence, especially of behavioral imitation. Then three case studies are made, presenting our neural architecture and the robotic experiments on some of the important elements discussed above: self-exploration and entrainment, emergent coordination, and categorizing self-behavior. Finally, we propose that integrating all these elements will be an important step towards realizing the bootstrapping agent envisaged above.

Journal Article↗

PubMed2002

Allostatic load as a predictor of functional decline. MacArthur studies of successful aging.

Allostatic load has been proposed as a cumulative measure of dysregulation across multiple physiological systems, and has been postulated to impact health risks. In the allostatic load model, increased risk is hypothesized to result not only from large and clinically significant dysregulation in individual systems, but also from more modest dysregulation, if present in multiple systems. Our objective was to construct an allostatic load score by optimally combining several physiologic measurements, and to examine its association with future functional decline. We analyzed data from a 7-year longitudinal study of a community-based cohort, whose age at baseline was between 70 and 79 years. Canonical correlation analysis was used to study the association of 10 biological measurements representing allostatic load with declines in scores on five tests each of physical and cognitive function over two follow-up periods: 1998-1991 and 1991-1995. We used bootstrapping to evaluate the stability of the canonical correlation and canonical weights. The canonical correlation between allostatic load and the 20 decline scores was 0.43 (P =.03) and the [25th, 75th] percentile interval of its distribution over 200 bootstrapped subsamples of the cohort was [0.48, 0.53]. These findings were not substantially affected by adjusting for covariates and cardiovascular disease. We conclude that a summary measure of physiologic dysregulation, such as allostatic load, is an independent predictor of functional decline in elderly men and women.

Adaptation, Physiological↗

PubMed1998

Approximate standard errors and confidence intervals for indices of positive and negative agreement.

Indices of positive and negative agreement for observer reliability studies, in which neither observer can be regarded as the standard, have been proposed. In this article, it is demonstrated by means of an example and a small simulation study that a recently published method for constructing confidence intervals for these indices leads to intervals that are too wide. Appropriate asymptotic (i.e., large sample) variance estimates and confidence intervals for the positive and negative agreement indices are presented and compared with bootstrap confidence intervals. We also discuss an alternative method of interval estimation motivated from a Bayesian viewpoint. The asymptotic intervals performed adequately for sample sizes of 200 or more. For smaller samples, alternative confidence intervals such as bootstrap intervals or Bayesian intervals should be considered.

Confidence Intervals↗

PubMed1998

Event-related potentials during digit recognition tasks.

OBJECTIVE: An event-related potential (ERP) correlate of visual short-term memory (VMP) has been identified in our laboratory. This study aims to determine how stimulus load modulates recognition processing of digits. METHODS: ERPs were recorded from 117 healthy right-handed subjects during a delayed matching-to-sample paradigm, using number stimuli that were either low load (three digits long) or high load (five digits long). The bootstrap method [R. Srebro, A bootstrap method to compare the shapes of two scalp fields, Electroenceph. Clin. Neurophysiol. 100 (1996) 25-32.] was employed to evaluate the topographic features of the VMP revealed in the current source density (CSD) maps. RESULTS: Response times were significantly shorter for matching stimuli than for non-matching stimuli only for low loads; longer response times were related to higher loads compared to low loads only for matching stimuli. The high loads were related to larger ERP responses. The ERP was significantly smaller for matching than for non-matching three-digit numbers, but not for five-digit numbers. The ERP was also reduced to the test stimuli compared to sample stimuli regardless of stimulus load. Both temporal and frontal regions were involved in the recognition of the digit stimuli, and the left hemisphere was more active in the non-matching processing of digits. CONCLUSIONS: The VMP spatial pattern in addition to its amplitude is sensitive to stimulus load in the encoding process.

Adult↗

PubMed2003

Comparison of simulated cumulative drug versus time data sets with indices.

The objectives of this study were twofold. First, to clarify the applicability of the similarity factor, f(2), the difference factor, f(1), and the Rescigno index, xi(i), in the comparison of cumulative drug vs. time data sets. Second, to assess the possibility for these indices to be used on a confidence interval basis. Theoretical profiles as well as errorless and errant cumulative % data sets were simulated using the Weibull function. At various variability levels, 12-fold and 3-fold replicated reference and test data sets were generated from the errant data sets. The 90% confidence intervals were constructed for the median of the index (non-parametric confidence intervals, NPCIs) and for the evaluated index based on the 5th and 95th percentiles of 1000 index values estimated from bootstrapped samples (bootstrapped confidence intervals, BSCIs). It was observed that at low variability levels, i.e. when mean data sets can be used, all indices could be used for the comparison of cumulative data sets. At high variability levels, only the BSCIs of f(2) included the actual index value for the 12-fold replicated data sets. However, deviations of the low limits of NPCIs of f(2) from the actual index values were similar to corresponding deviations of BSCIs. When 3-fold replicated data sets were used, both NPCIs and BSCIs of all indices were generally reliable but much larger than that of 12 replications. In conclusion, the time period for the evaluation of the indices cannot be theoretically justified because indices change continuously with time. Cutoff points for their evaluation must be decided on a case-by-case basis. If theoretically possible, evaluation of the indices should be done by using areas. With highly variable data, BSCIs are preferred because compared to NPCIs they are less dependent on the number of replications. When n=12, BSCIs of f(2) are comparatively more reliable. When n=3, BSCIs of the indices tested in this study have similar performances.

Computer Simulation↗

PubMed2002

Phylogeny of the Gyalectales and Ostropales (Ascomycota, Fungi): among and within order relationships based on nuclear ribosomal RNA small and large subunits.

Despite various morphological and anatomical similarities, the two orders Gyalectales (lichenized ascomycetes) and Ostropales (lichenized and non-lichenized ascomycetes) have been considered to be distantly related to each other and their position within the Ascomycota was unsettled. To estimate relationships within these groups and their respective phylogenenetic placement within the Ascomycota, we analyzed DNA sequences from the nuclear small and large subunit ribosomal RNA genes using Maximum Parsimony, Maximum Likelihood, and Bayesian statistics with Markov chain Monte Carlo algorithms. Support for internal branches estimated with bootstrap was compared to Bayesian posterior probabilities. We report here that the Ostropales, in their current circumscription, are paraphyletic, and that the Ostropales s.l. include the Gyalectales and Trapeliaceae. The Unitunicate Ascohymenials are redelineated to include the Ostropales s.l., as defined here, and the Baeomycetaceae. Dimerella and Coenogonium are congeneric, and Petractis thelotremella and P. hypoleuca are reunited with members of the genus Gyalecta. In addition to requiring less computational time, Bayesian inference of phylogeny recovered the same topology as a conventional heuristic search using Maximum Likelihood as the optimization criterion and seems superior to bootstrapping in estimating support for short internal branches.

Ascomycota↗

PubMed2002

Relationships within Cornales and circumscription of Cornaceae-matK and rbcL sequence data and effects of outgroups and long branches.

Phylogenetic relationships in Cornales were assessed using sequences rbcL and matK. Various combinations of outgroups were assessed for their suitability and the effects of long branches and outgroups on tree topology were examined using RASA 2.4 prior to conducting phylogenetic analyses. RASA identified several potentially problematic taxa having long branches in individual data sets that may have obscured phylogenetic signal, but when data sets were combined RASA no longer detected long branch problems. t(RASA) provides a more conservative measurement for phylogenetic signal than the PTP and skewness tests. The separate matK and rbcL sequence data sets were measured as not containing phylogenetic signal by RASA, but PTP and skewness tests suggested the reverse [corrected]. Nonetheless, the matK and rbcL sequence data sets suggested relationships within Cornales largely congruent with those suggested by the combined matK-rbcL sequence data set that contains significant phylogenetic signal as measured by t(RASA), PTP, and skewness tests. Our analyses also showed that a taxon having a long branch on the tree may not be identified as a "long-branched" taxon by RASA. The long branches identified by RASA had little effect on the arrangement of other taxa in the tree, but the placements of the long-branched taxa themselves were often problematic. Removing the long-branched taxa from analyses generally increased bootstrap support, often substantially. Use of non-optimal outgroups (as identified by RASA) decreased phylogenetic resolution in parsimony analyses and suggested different relationships in maximum likelihood analyses, although usually weakly supported clades (less than 50% support) were impacted. Our results do not recommend using t(RASA) as a sole criterion to discard data or taxa in phylogenetic analyses, but t(RASA) and the taxon variance ratio obtained from RASA may be useful as a guide for improved phylogenetic analyses. Results of parsimony and ML analyses of the sequence data using optimal outgroups suggested by RASA revealed four major clades within Cornales: (1) Curtisia-Grubbia, (2) Cornus-Alangium, (3) Nyssa-Camptotheca-Davidia-Mastixia-Diplopanax, and (4) Hydrangeaceae-Loasaceae, with clades (2) and (3) forming a monophyletic group sister to clade (4) and clade (1) sister to the remainder of Cornales. However, there was not strong bootstrap support for relationships among the major clades. The placement of Hydrostachys could not be reliably determined, although most analyses place the genus within Hydrangeaceae; ML analyses, for example, placed the genus as the sister of Hydrangeeae. Our results supported a Cornales including the systematically problematic Hydrostachys, a Cornaceae consisting of Cornus and Alangium, a Nyssaceae consisting of Nyssa and Camptotheca, a monogeneric Davidiaceae, a Mastixiaceae consisting of Mastixia and Diplopanax, and an expanded Grubbiaceae consisting of Grubbia and Curtisia, and two larger families, Hydrangeaceae and Loasaceae.

Cornaceae↗

PubMed2002

Phylogeographic analysis of the cornsnake (Elaphe guttata) complex as inferred from maximum likelihood and Bayesian analyses.

Most phylogeographic studies have used maximum likelihood or maximum parsimony to infer phylogeny and bootstrap analysis to evaluate support for trees. Recently, Bayesian methods using Marlov chain Monte Carlo to search tree space and simultaneously estimate tree support have become popular due to its fast search speed and ability to create a posterior distribution of parameters of interest. Here, I present a study that utilizes Bayesian methods to infer phylogenetic relationships of the cornsnake (Elaphe guttata) complex using cytochrome b sequences. Examination of the posterior probability distributions confirms the existence of three geographic lineages. Additionally, there is no support for the monophyly of the subspecies of E. guttata. Results suggest the three geographic lineages partially conform to the ranges of previously defined subspecies, although Shimodaira-Hasegawa tests suggest that subspecies-constrained trees produce significantly poorer likelihood estimates than the most likely trees reflecting the evolution of three geographic assemblages. Based on molecular support, these three geographic assemblages are recognized as species using evolutionary species criteria: E. guttata, Elaphe slowinskii, and Elaphe emoryi [phylogeographic, maximum likelihood, maximum parsimony, bootstrap, Bayesian, Markov chain Monte Carlo, cornsnake, Cytochrome b, geographic lineages, E. guttta, E. slowinskii, and E. emoryi].

Animals↗

PubMed2003

A new phylogenetic marker, apolipoprotein B, provides compelling evidence for eutherian relationships.

Higher-level relationships within, and the root of Placentalia, remain contentious issues. Resolution of the placental tree is important to the choice of mammalian genome projects and model organisms, as well as for understanding the biogeography of the eutherian radiation. We present phylogenetic analyses of 63 species representing all extant eutherian mammal orders for a new molecular phylogenetic marker, a 1.3kb portion of exon 26 of the apolipoprotein B (APOB) gene. In addition, we analyzed a multigene concatenation that included APOB sequences and a previously published data set (Murphy et al., 2001b) of three mitochondrial and 19 nuclear genes, resulting in an alignment of over 17kb for 42 placentals and two marsupials. Due to computational difficulties, previous maximum likelihood analyses of large, multigene concatenations for placental mammals have used quartet puzzling, less complex models of sequence evolution, or phylogenetic constraints to approximate a full maximum likelihood bootstrap. Here, we utilize a Unix load sharing facility to perform maximum likelihood bootstrap analyses for both the APOB and concatenated data sets with a GTR+Gamma+I model of sequence evolution, tree-bisection and reconnection branch-swapping, and no phylogenetic constraints. Maximum likelihood and Bayesian analyses of both data sets provide support for the superordinal clades Boreoeutheria, Euarchontoglires, Laurasiatheria, Xenarthra, Afrotheria, and Ostentoria (pangolins+carnivores), as well as for the monophyly of the orders Eulipotyphla, Primates, and Rodentia, all of which have recently been questioned. Both data sets recovered an association of Hippopotamidae and Cetacea within Cetartiodactyla, as well as hedgehog and shrew within Eulipotyphla. APOB showed strong support for an association of tarsier and Anthropoidea within Primates. Parsimony, maximum likelihood and Bayesian analyses with both data sets placed Afrotheria at the base of the placental radiation. Statistical tests that employed APOB to examine a priori hypotheses for the root of the placental tree rejected rooting on myomorphs and hedgehog, but did not discriminate between rooting at the base of Afrotheria, at the base of Xenarthra, or between Atlantogenata (Xenarthra+Afrotheria) and Boreoeutheria. An orthologous deletion of 363bp in the aligned APOB sequences proved phylogenetically informative for the grouping of the order Carnivora with the order Pholidota into the superordinal clade Ostentoria. A smaller deletion of 237-246bp was diagnostic of the superordinal clade Afrotheria.

Amino Acid Sequence↗

PubMed2003

Nuclear gene sequences provide evidence for the monophyly of australidelphian marsupials.

Relationships among the seven extant orders of marsupials remain poorly understood. Most classifications recognize a fundamental split between Ameridelphia, which contains the American orders Didelphimorphia and Paucituberculata, and Australidelphia, which contains four Australasian orders (Dasyuromorphia, Diprotodontia, Notoryctemorphia, and Peramelina) and the South American order Microbiotheria, represented by Dromiciops gliroides. Ameridelphia and Australidelphia are each supported by key morphological characters with dichotomous character states. To date, molecular studies indexing all marsupial orders have reported inconclusive results. However, several studies have suggested that Dromiciops is nested within Australidelphia. This result has important implications for understanding the biogeographic history of living marsupials. To address questions in higher-level marsupial systematics, we sequenced portions of five nuclear genes (Apolipoprotein B gene; Breast and Ovarian cancer susceptibility gene 1; Recombination activating gene 1; Interphotoreceptor retinoid binding protein gene; and von Willebrand factor gene) for representatives of all orders of marsupials, as well as placental outgroups. The resulting 6.4kb concatenation was analyzed using maximum parsimony, distance methods, maximum likelihood, and Bayesian methods. tests were used to examine a priori hypotheses. All analyses provided robust support for the monophyly of Australidelphia (bootstrap support=99-100%; posterior probability=1.00). Ameridelphia received much lower support, although this clade was not rejected in statistical tests. Within Diprotodontia, both Vombatiformes and Phalangeriformes were supported at the 100% bootstrap level and with posterior probabilities of 1.00.

Animals↗

PubMed2001

Analysis of uncertainties in estimates of components of variance in multivariate ROC analysis.

RATIONALE AND OBJECTIVES: Solutions have previously been presented to the problem of estimating the components of variance in the general linear model used for multivariate receiver operating characteristic (ROC) analysis. The case where the variance components do not change across the modalities under comparison was first treated, followed by the case where they are permitted to change. No analysis of uncertainties in these estimates has been presented previously. MATERIALS AND METHODS: For the case where the variance components do not change across modalities, the "jackknife-after-bootstrap" resampling procedure can be used together with conventional linear propagation of variance to solve for the uncertainties in estimates of the components. For the case where the components are permitted to change across modalities, a slight elaboration of this procedure is presented. RESULTS: The approach was validated by Monte Carlo simulations, where uncertainties in estimates of the variance components calculated by the jackknife-after-bootstrap procedure were found to converge in the mean to the Monte Carlo results over many independent trials. The method is exemplified with data from a study of readers-with and without the aid of a computer-assist modality-given the task of discriminating benign from malignant masses in mammography. CONCLUSION: The present approach is relevant to a broad class of problems where estimates of multiple contributions to the variance observed in ROC assessment of diagnostic modalities are desired, in particular, for the assessment of multiple-reader studies of computer-aided diagnosis in radiology where the variance components may change across reading modalities (eg, unaided vs computer-aided reading).

Analysis of Variance↗

PubMedDate not supplied

Assessing uncertainty in DNA evidence caused by sampling effects.

Sampling error estimation in forensic DNA testimony was discussed. Is an estimate necessary and how should it be made? The authors find that all modern methods have areas of strength and weakness. The assessment of which is the 'best' is subjective and depends on the performance of the method, the type of problem (criminal work or paternity), the database size and availability of computing software and support. The authors preferred the highest posterior density approach for performance, however the other methods all have areas where their performance is adequate. For single-contributor stains normal approximation methods are suitable, also the bootstrap and the highest posterior density method. For multiple-contributor stains or other complex situations the match probability expressions become quite complex and it may not be possible to derive the necessary variance expressions. The highest posterior density or the bootstrap provide a better general method, with non-zero theta. The size-bias correction and the factor of 10 approaches may be considered acceptable by many forensic scientists as long as their limitations are understood.

DNA↗

PubMed1999

Phylogenetic analysis of the SSU rRNA from members of the Chrysophyceae.

The nucleotide sequence for the nuclear-encoded small subunit ribosomal RNA gene (SSU rRNA) was determined for 24 species of the Chrysophyceae sensu stricto. These sequences were aligned, using primary and secondary structure, with nine previously published sequences for the Chrysophyceae, 14 for the Synurophyceae, and five for the Eustigmatophyceae (outgroup). Data analyses were the substitution rate calibration distance method using neighbor-joining (TREECON), Kimura 2-parameter neighbor-joining method (PAUP) and the maximum parsimony method (PAUP, PHYLIP). Trees from the analyses were largely congruent, but bootstrap support was weak at many nodes. The analyses recovered clades of uniflagellate and biflagellate organisms associated with current higher level taxonomy (e.g., subclass, order). The genus Ochromonas was polyphyletic, and O. tuberculata in particular was distantly related to the other Ochromonas species in the analysis. The family Paraphysomonadaceae occupied a basal position in three of four analyses. The class Synurophyceae appeared to be embedded within the Chrysophyceae, but bootstrap support was weak (< 50%) in all analyses except the PHYLIP parsimony analysis (= 81%). It was considered premature to place the Synurophyceae back into the Chrysophyceae based upon the analysis of one gene, especially given the ultrastructural and pigment differences between the two groups, but the relationship of these two groups deserves further study.

Biological Evolution↗