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Phylogeny and host-plant association in the leaf beetle genus Trirhabda LeConte (Coleoptera: Chrysomelidae).

The leaf beetle genus Trirhabda contains 26 described species from the United States and Canada, feeding on host plants from the families Asteraceae and Hydrophyllaceae. In this study, we present a phylogeny for the genus that was reconstructed from mitochondrial COI and 12S rRNA fragments, nuclear ITS2 rRNA, and morphological characters. Both parsimony and mixed-model Bayesian likelihood analyses were performed. Under both methods, the mitochondrial and nuclear partitions support the same backbone phylogeny, as do the combined data. The utility of the molecular data is contrasted with the low phylogenetic signal among morphological characters. The phylogeny was used to trace the evolution of the host-plant association in Trirhabda. The recovered phylogeny shows that although the host-plant association is phylogenetically conservative, Trirhabda experienced one shift to a distantly related host-plant family, 6 shifts between host-plant tribes, and 6 between genera within tribes. The phylogeny reveals that Trirhabda were plesiomorphically adapted to tolerate complex secondary compounds of its host plants and this adaptation is retained in Trirhabda species, as evidenced by multiple shifts from chemically simpler host plants back to the more complex host plants.

Animals↗

Computerized coding of injury narrative data from the National Health Interview Survey.

OBJECTIVE: To investigate the accuracy of a computerized method for classifying injury narratives into external-cause-of-injury and poisoning (E-code) categories. METHODS: This study used injury narratives and corresponding E-codes assigned by experts from the 1997 and 1998 US National Health Interview Survey (NHIS). A Fuzzy Bayesian model was used to assign injury descriptions to 13 E-code categories. Sensitivity, specificity and positive predictive value were measured by comparing the computer generated codes with E-code categories assigned by experts. RESULTS: The computer program correctly classified 4695 (82.7%) of the 5677 injury narratives when multiple words were included as keywords in the model. The use of multiple-word predictors compared with using single words alone improved both the sensitivity and specificity of the computer generated codes. The program is capable of identifying and filtering out cases that would benefit most from manual coding. For example, the program could be used to code the narrative if the maximum probability of a category given the keywords in the narrative was at least 0.9. If the maximum probability was lower than 0.9 (which will be the case for approximately 33% of the narratives) the case would be filtered out for manual review. CONCLUSIONS: A computer program based on Fuzzy Bayes logic is capable of accurately categorizing cause-of-injury codes from injury narratives. The capacity to filter out certain cases for manual coding improves the utility of this process.

Forms and Records Control↗

Electron-beam computed tomography: a Bayesian approach to risk assessment.

The epidemic of coronary artery disease continues to affect a large number of individuals who often experience sudden and unexpected events. This underscores the need to develop more effective programs to detect silent atherosclerosis, with the ultimate goal of preventing coronary events. The use of conventional risk factors is helpful in assessing the median risk of a population, but it is often unsatisfactory in estimating the actual risk of an individual patient. As a consequence, newer imaging modalities are being developed to detect atherosclerosis in its early developmental phases. Technologies such as electron-beam computed tomography (EBCT) may render risk stratification more accurate if used in the appropriate patient populations and with the right diagnostic approach. Several studies have already demonstrated the power of coronary calcification as a strong predictor of future cardiovascular events. Nonetheless, the medical literature is currently pervaded by an animated debate, as some investigators still have concerns about the effectiveness of a preventive approach driven by technology. The use of Bayesian models to interpret data acquired with EBCT screening may provide practitioners with valuable evidence to aid in their decision making.

Bayes Theorem↗

Perception of 3D surface orientation from skew symmetry.

In this paper, we investigate how symmetry can be used to perceive 3D surface orientation. When a symmetric planar object is viewed from an angle, the projected contour has skew symmetry, which provides partial information about the 3D orientation of the object. For a given skew symmetry, this information can be characterized by a constraint curve of possible slant/tilt combinations that are consistent with a mirror-symmetric interpretation. These constraint curves move around when an object is rotated within a plane, and depend on what we will term the spin of the object: the angle between its axis of symmetry and the direction of tilt. To test the influence of symmetry constraint curves, we presented subjects with stereo images of symmetric objects that varied in spin, and had them perform an orientation-matching task. We found that the judgments showed biases that depended on the spin of the objects. Since other sources of information depend only on slant and tilt, not on spin, the biases imply that skew symmetry contributed to subjects' judgments. In a second experiment, we introduced conflicts between stereo and symmetry cues, and found that the spin-dependent biases can be modulated by selectively changing stereo slant. We propose an explanation of these results involving the optimal integration of stereo and skew symmetry, and present a Bayesian model that can account for the pattern of biases.

Analysis of Variance↗

Risk assessment for Cryptosporidium: a hierarchical Bayesian analysis of human dose response data.

Three dose-response studies were conducted with healthy volunteers using different Cryptosporidium parvum isolates (IOWA, TAMU, and UCP). The study data were previously analyzed for median infectious dose (ID50) using a simple cumulative percent endpoint method (Reed and Muench, 1938). ID50s were derived using two definitions of infection: one as subjects having oocysts detected in stool by direct fluorescence assay, and the other by a clinical finding of diarrhea with or without detected oocysts (Chappell et al., 1998; Okhuysen et al., 1999). In the present study, the data were analyzed using the broader definition of infection (i.e., presence of oocysts in stool and/or diarrheal illness characteristic of cryptosporidiosis). Maximum likelihood dose-response parameter estimates for UCP, IOWA, and TAMU were 2980, 190, and 17.5, respectively. Based on these estimates, the ID50s of the three respective isolates were 2066, 132, and 12.1. The three oocyst isolates were considered representative of a larger population of human-infecting strains and analyzed as combined data using a hierarchical Bayesian model. Hyperparameters defined the distribution of dose-response parameters for the population of strains. Output from Markov Chain Monte Carlo analysis described posterior distributions for the hyperparameters and for the parameters of the IOWA, TAMU, and UCP strains. Point estimates of dose-response parameters produced by this analysis were similar to the maximum likelihood estimates. Finally, the utility of these results for probabilistic risk assessment was evaluated. The risk of infection from single oocyst doses was derived for a mixture of the three isolates (where IOWA, TAMU, or UCP are equally likely), and for an oocyst selected at random from the larger population of strains. These estimated risks of infection were 0.018 and 0.028, respectively.

Animals↗

Prevalence estimates for paratuberculosis adjusted for test variability using Bayesian analysis.

The ELISA tests that are available to detect an infection with Mycobacterium avium subsp. paratuberculosis (MAP) have a limited validity expressed as the sensitivity (Se) and specificity (Sp). In many studies, the Se and Sp of the tests are treated as constants and this will result in an underestimation of the variability of the true prevalence (TP). Bayesian inference provided a natural framework for using information on the test variability (i.e., the uncertainty) in the estimates of test Se and Sp when estimating the TP. Data from two prevalence studies for MAP using an ELISA in several regions in two locations were available for the analyses. In location 1, all cattle of at least 3 years of age were sampled in approximately 90 randomly sampled herds in each of the four regions of the country. In location 2, in 30 randomly sampled herds in each of three regions, approximately 30 randomly selected cows were sampled. Information about the unknown test Se and Sp and MAP prevalence was incorporated into a Bayesian model by joint prior probability distributions. Posterior estimates were obtained by combining the actual likelihood with the prior distributions using Bayes' formula. The corrected cow-level TP (proportion of infected cows in a herd) was low, 5.8 and 3.6% in locations 1 and 2, respectively. Certain regions within a location differed significantly in herd-level TP (proportion of infected herds). The herd-level TP was 54.3% in location 1 (95% credible interval (CI) 46.1, 63.3%) and 32.9% in location 2 (95% CI: 14.4, 73.3%). The variation in the herd-level TP estimate for location 2 was more than three times as large as the variation in location 1 mainly because of the relatively small number of investigated herds in location 2. In future prevalence studies for MAP, sample size calculations should be based on a very low cow-level prevalence. Approximately 50 and 90% of the herds in the current study had an estimated cow-level TP below 4 and 10%, respectively.

Animals↗

Multimodality in the superior colliculus: an information theoretic analysis.

The deep superior colliculus (DSC) integrates multisensory input and triggers an orienting movement toward the source of stimulation (target). It would seem reasonable to suppose that input of an additional modality should always increase the amount of information received by a DSC neuron concerning a target. However, of all DSC neurons studied, only about one half in the cat and one-quarter in the monkey were multimodal. The rest received only unimodal input. Multimodal DSC neurons show the properties of multisensory enhancement, in which the neural response to an input of one modality is augmented by input of another modality, and of inverse effectiveness, in which weaker unimodal responses produce a higher percentage enhancement. Previously, we demonstrated that these properties are consistent with the hypothesis that DSC neurons use Bayes' rule to compute the posterior probability that a target is present given their stochastic sensory inputs. Here we use an information theoretic analysis of our Bayesian model to show that input of an additional modality may indeed increase target information, but only if input received from the initial modality does not completely reduce uncertainty concerning the presence of a target. Unimodal DSC neurons may be those whose unimodal input fully reduces target uncertainty and therefore have no need for input of another modality.

Bayes Theorem↗

Bayesian second-level analysis of functional magnetic resonance images.

We propose a new method for the second-level analysis of functional MRI data based on Bayesian statistics. Our method does not require a computationally costly Bayesian model on the first level of analysis. Rather, modeling for single subjects is realized by means of the commonly applied General Linear Model. On the basis of the resulting parameter estimates for single subjects we calculate posterior probability maps and maps of the effect size for effects of interest in groups of subjects. A comparison of this method with the conventional analysis based on t statistics shows that the new approach is more robust against outliers. Moreover, our method overcomes some of the severe problems of null hypothesis significance tests such as the need to correct for multiple comparisons and facilitates inferences which are hard to formulate in terms of classical inferences.

Algorithms↗

Reanalysis of systematic reviews: the case of invasive strategies for acute coronary syndromes.

OBJECTIVES: The objective of this study was to collect all systematic reviews on invasive strategies for acute coronary syndromes (ACS) and reanalyze the data in these reviews to reach combined estimates, as well as to make predictions on the effectiveness and risk of harm so as to facilitate relevant decision making in health care. METHODS: The data sources used were the following electronic databases, searched from 1994 to September 2004: Cochrane Database of Systematic Reviews; Cochrane Central Register of Controlled Trials; DARE, HTA, EED (NHS CRD); MEDLINE In-Process, Other Non-Indexed Citations, MEDLINE, and PubMed (2000 to 2004). References to the identified systematic reviews were checked. An ancillary search to identify recent randomized controlled trials (RCTs) covering the period from January 2003 to January 2006 was done in MEDLINE(R). We included systematic reviews of RCTs on patients with ACS. In unstable angina and non-ST-elevation myocardial infarction (UA/NSTEMI), eligible reviews had to compare early routine invasive strategy with early selective invasive strategy. In ST-elevation myocardial infarction (STEMI), a comparison between primary percutaneous coronary intervention (PCI) and thrombolytic therapy was required. The methodological quality of the reviews was assessed, and a standardized data extraction form was used. Results for the main outcomes of the RCTs in the reviews were reanalyzed. An additional search of those RCTs not included in the meta-analyses was performed for UA/NSTEMI and short-term morality data on STEMI. Bayesian models were constructed to estimate the uncertainty about a possible treatment effect and to make predictions and probability statements. Main results are based on these analyses. Mortality was considered as the primary outcome measure. RESULTS: One systematic review on invasive strategies was identified for UA/NSTEMI and nine on invasive strategies for STEMI. Five reviews of the latter that were published after the year 2000 were included for the final analysis. The median quality score was 10.5 (range, 7-13; n = 6) on a scale from 0 to 18 points. An updated literature search identified one further RCT on UA/NSTEMI. Regarding NSTEMI and mortality, the average risk difference favoring an early invasive treatment strategy compared with early conservative strategy was .6 percent (95 percent credible interval [CrI], -2.1 to 1.0). Predicted risk (relative risk/risk difference scales) of doing harm was 26.7/26.6 percent. Regarding STEMI and mortality, the absolute risk reduction in favor of primary PCI over thrombolysis was 4.1 percent (95 percent CrI, -7.1 to -1.1) when PCI was compared with streptokinase and 1.2 percent (95 percent CrI, -2.7 to .2) when compared with fibrin-specific thrombolytics. Predicted risk of harm was 8.9/5.3 percent and 8.0/13.3 percent, respectively. CONCLUSIONS: There seems to be at present no solid evidence for survival benefit on early invasive strategy for UA/NSTEMI as a broad diagnostic group, and the risk of doing harm should be considered. Also, the evidence for PCI to decrease early mortality after STEMI is scanty. Estimations of predicted harm may further aid decisions on whether to implement the new treatment over the old one. It may also give an additional dimension for interpreting the results of any meta-analysis.

Angioplasty, Balloon, Coronary↗

New Asian species of the genus Anamika (euagarics, hebelomatoid clade) based on morphology and ribosomal DNA sequences.

Two dark-spored agaric species from Asia are placed in the genus Anamika (Agaricales or euagarics clade). This result is supported by ITS and nLSU-rDNA sequences with strong measures of branch support, in addition to several morphological and ecological similarities. An inclusive ITS study was performed using a mixed model Bayesian analysis that suggests the derived status of Anamika within Hebeloma, thereby rendering Hebeloma a paraphyletic genus. However, the monophyly of Hebeloma cannot be rejected outright given ITS and nLSU-rDNA data. Thus, we propose two new Asian species in Anamika: A. angustilamellata sp. nov. from dipterocarp and fagaceous forests of southwestern China and northern Thailand; and A. lactariolens comb. nov., a Japanese species originally described in the genus Alnicola. A complete description of A. angustilamellata, including illustrations, is provided.

Agaricales↗

Will Lake Michigan lake trout meet the Great Lakes Strategy 2002 PCB reduction goal?

The Great Lakes Strategy 2002 establishes the long-term goal that all Great Lakes fish should be safe to eat without restriction. As an indicator of progress toward that goal, the Strategy specifies that lake trout PCBs will decline 25% from 2000 to 2007. We estimated the plausibility of achieving this near-term goal by examining a time-series of Lake Michigan lake trout PCB concentrations from 1972 to 2000. We used two different Bayesian approaches, Bayesian model averaging (BMA) and dynamic linear models (DLM), to model the trajectory of these historical data and forecast concentrations through 2007. Both approaches indicate that the probability of a 25% reduction from 2000 to 2007 is negligible. The most likely lake trout PCB declines predicted by the BMA and DLM over this time period are 6.8% and 8.9%, respectively. Our results suggest that declines in lake trout PCBs will be in the range of 5-10% assuming conditions similar to recent years. This rate of decline will be difficult to discern without adequate data collection. If sufficient data are not gathered to document further declines, then the relaxation of lake trout consumption advisories is indeed a long-term prospect.

Animals↗

Mortality risk perceptions: a Bayesian reassessment.

"This study uses data on perceived and actual mortality risks to test several alternative Bayesian models of the factors influencing risk beliefs. The analysis...indicates that while the hazard rate for the individual age group is an influential factor, the overall population death rate and the discounted expected number of life years lost due to the cause of death are also influential in affecting risk perceptions.... The predictive power of a linear perception model increases with the level of the risk and is least accurate for very small risks."

Behavior↗

The rat approximates an ideal detector of changes in rates of reward: implications for the law of effect.

Rats responded on 2 levers delivering brain stimulation reward on concurrent variable interval schedules. Following many successive sessions with unchanging relative rates of reward, subjects adjusted to an eventual change slowly and showed spontaneous reversions at the beginning of subsequent sessions. When changes in rates of reward occurred between and within every session, subjects adjusted to them about as rapidly as they could in principle do so, as shown by comparison to a Bayesian model of an ideal detector. This and other features of the adjustments to frequent changes imply that the behavioral effect of reinforcement depends on the subject's perception of incomes and changes in incomes rather than on the strengthening and weakening of behaviors in accord with their past effects or expected results. Models for the process by which perceived incomes determine stay durations and for the process that detects changes in rates are developed.

Animals↗

Regularization in short-term memory for serial order.

Previous research has shown that short-term memory for serial order can be influenced by background knowledge concerning regularities of sequential structure. Specifically, it has been shown that recall is superior for sequences that fit well with familiar sequencing constraints. The authors report a corresponding effect pertaining to serial recall errors. Undergraduate participants performed immediate serial recall on sequences of pseudowords generated on the basis of an artificial grammar. After extensive experience with this material, recall errors displayed a bias toward regularizing responses, response sequences more probable, with respect to the artificial grammar, than the originally presented stimulus sequence. This regularization effect squares well with recent trace redintegration and Bayesian models of serial recall, and appears to represent an analog of the schema-based error patterns observed in other domains of memory.

Adolescent↗

The subspecific origin of the inland breeding colonies of the cormorant Phalacrocorax carbo in Britain.

The establishment of cormorant breeding colonies inland within south-east Britain since 1981 is a matter of major conservation and pest management concern. This study was initiated to investigate the subspecific origin of two recently established breeding colonies. The analysis examined sequence variation of the control (D-loop) region of the mitochondrial genome. Samples of tissue were obtained from 334 individuals from across the species range in western Europe from both subspecies (Phalacrocorax carbo carbo and P. c. sinensis) and 84 birds from two inland breeding colonies in Britain. Single-strand conformation polymorphism (SSCP) was used to assess mitochondrial variation among samples, revealing four haplotypes. The samples from the traditional breeding colonies clustered into three distinct phylogeographic groupings: Norway-Scotland, Wales-England-Iles des Chausey and the rest of Continental Europe. These results only partly agree with the traditional subspecific taxonomic groupings and are slightly at variance with results using microsatellite DNA frequencies, and a hypothesis using results from both studies is advanced. The subspecific origin of the inland colonies was investigated using maximum likelihood and Bayesian models.

Animals↗

Ruling out acute myocardial infarction. A prospective multicenter validation of a 12-hour strategy for patients at low risk.

BACKGROUND: Although previous investigations have suggested that 24 hours is required to exclude acute myocardial infarction in patients who are admitted to a coronary care unit for the evaluation of acute chest pain, we hypothesized that a 12-hour period might be adequate for patients with a low probability of infarction at the time of admission. METHODS: Using a Bayesian model, we developed a strategy to identify candidates for a shorter period of observation from an analysis of a derivation set of 976 patients with acute chest pain who were admitted to three teaching and four community hospitals. In the derivation set, patients whose clinical characteristics in the emergency room predicted a low (less than or equal to 7 percent) probability of myocardial infarction had only a 0.4 percent risk of infarction if they had neither abnormal levels of cardiac enzymes nor recurrent ischemic pain during the first 12 hours of hospitalization. In an independent testing set of 2684 patients from the seven hospitals, 957 admitted patients (36 percent) were classified as candidates for this 12-hour period of observation according to a previously published multivariate algorithm. Few of these patients were actually transferred from a monitored setting at 12 hours. RESULTS: Of the 771 candidates for a 12-hour period of observation who did not have enzyme abnormalities or recurrent pain during the first 12 hours, 4 (0.5 percent) were subsequently found to have acute myocardial infarction, and only 3 (0.4 percent) died after primary cardiac arrests, all of which occurred three to five days after admission. Rates of other major cardiovascular complications were low in the patients who might have been transferred from the coronary care unit after 12 hours with this strategy. In patients with a higher initial risk of infarction, the standard strategy of 24-hour observation identified all but 11 of 739 acute myocardial infarctions (1 percent). CONCLUSIONS: Emergency room clinical data can be used to identify a large subgroup of patients for whom a 12-hour period of observation is normally sufficient to exclude acute myocardial infarction. Patient-specific evaluation and treatment can then proceed without the restrictions imposed by "rule-out" protocols for myocardial infarction.

Adult↗

Visual extrapolation of contour geometry.

Computing the shapes of object boundaries from fragmentary image contours poses a formidable problem for the visual system. We investigated the extrapolation of contour shape by human vision. Measurements of extrapolation position and orientation were taken at six distances from the point of occlusion, thereby yielding a detailed representation of the extrapolated contours. Analyses of these measurements revealed that: (i) extrapolation curvature increases linearly with the curvature of the inducing contour, although there is individual bias in the slope; (ii) the precision with which an extrapolated contour is represented is roughly constant, in angular terms, with increasing distance from the point of occlusion; (iii) there is a substantial cost of curvature, in that the overall precision of an extrapolated contour decreases systematically with curvature; (iv) the shapes of visually extrapolated contours are characterized by a nonlinear decrease in curvature, asymptoting to zero; and (v) this decaying pattern of curvature is explained by a Bayesian model in which, with increasing distance from the point of occlusion, the prior tendency to minimize curvature gradually dominates the likelihood tendency to minimize variation in curvature.

Bayes Theorem↗

Recombination and mutation during long-term gastric colonization by Helicobacter pylori: estimates of clock rates, recombination size, and minimal age.

The bacterium Helicobacter pylori colonizes the gastric mucosa of half of the human population, resulting in chronic gastritis, ulcers, and cancer. We sequenced ten gene fragments from pairs of strains isolated sequentially at a mean interval of 1.8 years from 26 individuals. Several isolates had acquired small mosaic segments from other H. pylori or point mutations. The maximal mutation rate, the import size, and the frequency of recombination were calculated by using a Bayesian model. The calculations indicate that the last common ancestor of H. pylori existed at least 2,500-11,000 years ago. Imported mosaics have a median size of 417 bp, much smaller than for other bacteria, and recombination occurs frequently (60 imports spanning 25,000 bp per genome per year). Thus, the panmictic population structure of H. pylori results from very frequent recombination during mixed colonization by unrelated strains.

Bayes Theorem↗