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PubMed2006

Left-ventricle myocardium segmentation using a coupled level-set with a priori knowledge.

This paper presents a coupled level-set segmentation of the myocardium of the left ventricle of the heart using a priori information. From a fast marching initialisation, two fronts representing the endocardium and epicardium boundaries of the left ventricle are evolved as the zero level-set of a higher dimension function. We introduce a novel and robust stopping term using both gradient and region-based information. The segmentation is supervised both with a coupling function and using a probabilistic model built from training instances. The robustness of the segmentation scheme is evaluated by performing a segmentation on four unseen data-sets containing high variation and the performance of the segmentation is quantitatively assessed.

Heart Ventricles↗
PubMed2006

The difference between drug money and a "lifetime's savings".

In many countries, monies suspected of being associated with drug trafficking can be seized by the authorities. One of the ways of investigating this association is through the analysis of seized banknotes for traces of controlled drugs. We report three studies which may assist the expert in assessing whether banknotes contaminated with diamorphine are part of the general population of notes in circulation or whether they show unusual contamination patterns which require explanation. Study 1 is based on three plausible contamination scenarios as they may occur during the various stages of an illicit drug transaction and seizure. It shows that notes which have been in direct contact with visible traces of diamorphine show significantly higher contamination to those in more indirect contact with the drug. Study 2 investigates the transfer of diamorphine from one highly contaminated note to other notes in a bundle over a period of 10 weeks with and without agitation. It was found that the total amount of drug transferred was smaller than 6% and no more than 4 out of a bundle of 10 previously clean notes became lightly contaminated. Based on extensive background data, study 3 proposes a probabilistic model to assess whether an observed proportion of diamorphine bearing banknotes is likely to have been contaminated by chance. The model predicts that there is only a 0.3% chance that a bundle of 100 notes from the general banknote population contains more than six contaminated specimens. Jointly, the three studies give useful indications for the spread of contamination throughout a sample and the amounts of heroin which may be expected given plausible contamination scenarios.

Journal Article↗
PubMed2006

A risk assessment approach applied to the growth of Erwinia carotovora in vegetable juice for variable temperature conditions.

Risk assessment for food spoilage relies on probabilistic models of microbial growth to predict the likelihood that microbial populations will exceed predefined spoilage levels. To assist in the design and management of industrial food quality systems, predictive microbiological models have to incorporate major risk factors such as the variability in the microbial strain, environment and initial contamination levels. In addition, the application of results measured under laboratory conditions to the less controlled environment of an industrial process usually also involves uncertainty. Extra information regarding this uncertainty must be factored into industrial microbial risk assessment. In this paper, based on our previous analysis of the growth of Erwinia carotovora we show how different factors contribute to the risk of microbial spoilage of vegetable juice and we demonstrate an effective way of including these factors into risk assessment models. The association of risk components with different unavoidable and manageable factors is also valuable for the development of optimal strategies for reducing microbial risk.

Beverages↗
PubMed2004

Estimation of potential impacts and natural resource damages of oil.

Methods were developed to estimate the potential impacts and natural resource damages resulting from oil spills using probabilistic modeling techniques. The oil fates model uses wind data, current data, and transport and weathering algorithms to calculate mass balance of fuel components in various environmental compartments (water surface, shoreline, water column, atmosphere, sediments, etc.), oil pathway over time (trajectory), surface distribution, shoreline oiling, and concentrations of the fuel components in water and sediments. Exposure of aquatic habitats and organisms to whole oil and toxic components is estimated in the biological model, followed by estimation of resulting acute mortality and ecological losses. Natural resource damages are based on estimated costs to restore equivalent resources and/or ecological services, using Habitat Equivalency Analysis (HEA) and Resource Equivalency Analysis (REA) methods. Oil spill modeling was performed for two spill sites in central San Francisco Bay, three spill sizes (20th, 50th, and 95th percentile volumes from tankers and larger freight vessels, based on an analysis of likely spill volumes given a spill has occurred) and four oil types (gasoline, diesel, heavy fuel oil, and crude oil). The scenarios were run in stochastic mode to determine the frequency distribution, mean and standard deviation of fates, impacts, and damages. This work is significant as it demonstrates a statistically quantifiable method for estimating potential impacts and financial consequences that may be used in ecological risk assessment and cost-benefit analyses. The statistically-defined spill volumes and consequences provide an objective measure of the magnitude, range and variability of impacts to wildlife, aquatic organisms and shorelines for potential spills of four oil/fuel types, each having distinct environmental fates and effects.

Animals↗
PubMed2005

Interstrand pairing patterns in beta-barrel membrane proteins: the positive-outside rule, aromatic rescue, and strand registration prediction.

beta-Barrel membrane proteins are found in the outer membrane of Gram-negative bacteria, mitochondria, and chloroplasts. Little is known about how residues in membrane beta-barrels interact preferentially with other residues on adjacent strands. We have developed probabilistic models to quantify propensities of residues for different spatial locations and for interstrand pairwise contact interactions involving strong H-bonds, side-chain interactions, and weak H-bonds. Using the reference state of exhaustive permutation of residues within the same beta-strand, the propensity values and p-values measuring statistical significance are calculated exactly by analytical formulae we have developed. Our findings show that there are characteristic preferences of residues for different membrane locations. Contrary to the "positive-inside" rule for helical membrane proteins, beta-barrel membrane proteins follow a significant albeit weaker "positive-outside" rule, in that the basic residues Arg and Lys are disproportionately favored in the extracellular cap region and disfavored in the periplasmic cap region. We find that different residue pairs prefer strong backbone H-bonded interstrand pairings (e.g. Gly-aromatic) or non-H-bonded pairings (e.g. aromatic-aromatic). In addition, we find that Tyr and Phe participate in aromatic rescue by shielding Gly from polar environments. We also show that these propensities can be used to predict the registration of strand pairs, an important task for the structure prediction of beta-barrel membrane proteins. Our accuracy of 44% is considerably better than random (7%). It also significantly outperforms a comparable registration prediction for soluble beta-sheets under similar conditions. Our results imply several experiments that can help to elucidate the mechanisms of in vitro and in vivo folding of beta-barrel membrane proteins. The propensity scales developed in this study will also be useful for computational structure prediction and for folding simulations.

Amino Acids, Aromatic↗
PubMed2006

Sequence motifs and antimotifs in beta-barrel membrane proteins from a genome-wide analysis: the Ala-Tyr dichotomy and chaperone binding motifs.

Beta-barrel membrane proteins are found in the outer membrane of gram-negative bacteria, mitochondria, and chloroplasts. Although sequence motifs have been studied in alpha-helical membrane proteins and have been shown to play important roles in their assembly, it is not clear whether over-represented motifs and under-represented anti-motifs exist in beta-barrel membrane proteins. We have developed probabilistic models to identify sequence motifs of residue pairs on the same strand separated by an arbitrary number of residues. A rigorous statistical model is essential for this study because of the difficulty associated with the short length of the strands and the small amount of structural data. By comparing to the null model of exhaustive permutation of residues within the same beta-strand, propensity values of sequence patterns of two residues and p-values measuring statistical significance are calculated exactly by several analytical formulae we have developed or by enumeration. We find that there are characteristic sequence motifs and antimotifs in transmembrane (TM) beta-strands. The amino acid Tyr plays an important role in several such motifs. We find a general dichotomy consisting of favorable Aliphatic-Tyr sequence motifs and unfavorable Tyr-Aliphatic antimotifs. Tyr is also part of a terminal motif, YxF, which is likely to be important for chaperone binding. Our results also suggest several experiments that can help to elucidate the mechanisms of in vitro and in vivo folding of beta-barrel membrane proteins.

Amino Acid Motifs↗
PubMedDate not supplied

Bayesian approach to feature selection and parameter tuning for support vector machine classifiers.

A Bayesian point of view of SVM classifiers allows the definition of a quantity analogous to the evidence in probabilistic models. By maximizing this one can systematically tune hyperparameters and, via automatic relevance determination (ARD), select relevant input features. Evidence gradients are expressed as averages over the associated posterior and can be approximated using Hybrid Monte Carlo (HMC) sampling. We describe how a Nyström approximation of the Gram matrix can be used to speed up sampling times significantly while maintaining almost unchanged classification accuracy. In experiments on classification problems with a significant number of irrelevant features this approach to ARD can give a significant improvement in classification performance over more traditional, non-ARD, SVM systems. The final tuned hyperparameter values provide a useful criterion for pruning irrelevant features, and we define a measure of relevance with which to determine systematically how many features should be removed. This use of ARD for hard feature selection can improve classification accuracy in non-ARD SVMs. In the majority of cases, however, we find that in data sets constructed by human domain experts the performance of non-ARD SVMs is largely insensitive to the presence of some less relevant features. Eliminating such features via ARD then does not improve classification accuracy, but leads to impressive reductions in the number of features required, by up to 75%.

Algorithms↗
PubMed2006

Factors affecting sensitivity and specificity of pooled-sample testing for diagnosis of low prevalence infections.

Testing of pooled samples has been proposed as a low-cost alternative for diagnostic screening and surveillance for infectious agents in situations where the prevalence of infection is low and most samples can be expected to test negative. The present study extends our previous work in pooled-sample testing (PST) to evaluate effects of the following factors on the overall PST sensitivity (SE(k)) and specificity (SP(k)): dilution (pool size), cross-contamination, and cross-reaction. A probabilistic model, in conjunction with Monte Carlo simulations, was used to calculate SE(k) and SP(k), as applied to detection of bovine viral diarrhea virus (BVDV) persistently infected (PI) animals using RT-PCR. For an average prevalence of BVDV PI of 0.01 and viremia in each animal between 10(2) and 10(7)virusparticles/mL, the pool size associated with the lowest number of tests, and lowest cost, corresponded to eight samples/pool. However, the least-cost pool size (lowest number of tests) was associated with a SE(k) of 0.90 (0.75-1), which corresponded to a decrease of 0.04, relative to the assay sensitivity for a single sample. The SP(k) for the same pool size, considering the effect of detection of BVDV acutely infected animals and cross-contamination as source of false positive results, was 0.90 (0.85-0.95). The effect of a hypothetical cross-reacting agent was to markedly decrease SP(k), especially as the prevalence of the cross-reacting agent increased. For a pool size of eight samples and a prevalence of the cross-reacting agent of 0.3, SP(k) ranged from 0.67 to 0.86, depending on the probability that the assay would detect the cross-reacting agent. The methods presented offer a means of evaluating and understanding the various factors that can influence overall accuracy of PST procedures.

Animals↗
PubMed2004

Statistical analysis of the fluctuating counts of fecal bacteria in the water of Lake Kinneret.

Counts of E. coli, Enteroccoci and fecal coliforms in four sites around Lake Kinneret (The Sea of Galilee), collected every 2-4 weeks for about 5 years during 1995-2002 showed irregular fluctuations punctuated by aperiodic outbursts of variable magnitude. Because of the haphazard nature of fecal contamination and large intervals between successive counts, these patterns were described by probabilistic models, based on the truncated Laplace or Extreme Value distribution. Their applicability was tested by comparing the predicted frequencies of counts exceeding different levels calculated from the first half of each record with those actually observed in its second half. Despite the records imperfections and minor violations of the underlying models' assumptions, there was a reasonable agreement between the estimated and actual frequencies. This demonstrated that it is possible to translate the irregular fluctuation pattern into a set of probabilities of future high counts. In principle, such probabilities can be used to quantify the water's fecal contamination pattern and as a tool to assess the efficacy of preventive measures to reduce it.

Enterobacteriaceae↗
PubMed2001

Use of probabilistic methods in exposure assessment in Germany.

Over the last two decades, quantitative risk assessment has received increasing attention in Germany. By now it is also acknowledged that probabilistic techniques in risk assessment seem to be superior to the conventional point estimate approach. An important prerequisite for the use of probabilistic techniques is seen in the provision of 'standard' probability density functions for key exposure factors. For such exposure factors like body weight, time budget, etc., default probability density functions which are representative for Germany need to be developed. Guidance on probabilistic modelling will be needed, too.

Body Weight↗
PubMed1995

Anaphase chromatid motion: involvement of type II DNA topoisomerases.

Sister chromatids are topologically intertwined at the onset of anaphase: their segregation during anaphase is known to require strand-passing activity by type II DNA topoisomerase. We propose that the removal of the intertwinings involves at the same time the traction of the mitotic spindle and the activity of topoisomerases. This implies that the velocity of the chromatids is compatible with the kinetic constraints imposed by the enzymatic reaction. We show that the greatest observed velocities (about 0.1 microns s-1) are close to the theoretical upper bound compatible with both the diffusion rate (calculated here within a probabilistic model) and the measured reaction rate of the enzyme.

Anaphase↗
PubMed2003

Higher-order interhelical spatial interactions in membrane proteins.

Higher-order interactions are important for protein folding and assembly. We introduce the concept of interhelical three-body interactions as derived from Delaunay triangulation and alpha shapes of protein structures. In addition to glycophorin A, where triplets are strongly correlated with protein stability, we found that tight interhelical triplet interactions exist extensively in other membrane proteins, where many types of triplets occur far more frequently than in soluble proteins. We developed a probabilistic model for estimating the value of membrane helical interaction triplet (MHIT) propensity. Because the number of known structures of membrane proteins is limited, we developed a bootstrap method for determining the 95% confidence intervals of estimated MHIT values. We identified triplets that have high propensity for interhelical interactions and are unique to membrane proteins, e.g. AGF, AGG, GLL, GFF and others. A significant fraction (32%) of triplet types contains triplets that may be involved in interhelical hydrogen bond interactions, suggesting the prevalent and important roles of H-bond in the assembly of TM helices. There are several well-defined spatial conformations for triplet interactions on helices with similar parallel or antiparallel orientations and with similar right-handed or left-handed crossing angles. Often, they contain small residues and correspond to the regions of the closest contact between helices. Sequence motifs such as GG4 and AG4 can be part of the three-body interactions that have similar conformations, which in turn can be part of a higher-order cooperative four residue spatial motif observed in helical pairs from different proteins. In many cases, spatial motifs such as serine zipper and polar clamp are part of triplet interactions. On the basis of the analysis of the archaeal rhodopsin family of proteins, tightly packed triplet interactions can be achieved with several different choices of amino acid residues.

Amino Acid Motifs↗
PubMed1991

A probabilistic view on steady-state enzyme reactions.

A new theoretical description of steady-state enzyme reactions is proposed. The description is based on the concepts of the probability theory instead of the conventional formalism of chemical kinetics. A general steady-state rate equation is obtained using a probabilistic model of the catalytic act. As a result, the classical problems of enzyme kinetics can be formulated and considered in a different aspect. It is shown that the new theory presents a clearer treatment of some commonly obscure questions, such as the steady-state establishment. The theory also gives additional possibilities in the interpretation of the experimental results of traditional methods and proposes certain new ways in experimental investigations of enzymes.

Animals↗
PubMed1983

Sterility and fecundability estimation.

The percentage of steriles and the fecundability of non-steriles among a given population can be estimated by a probabilistic model from observations made on delays to first conception. The maximum likelihood method of estimation that was used takes into account all available information, though some of these observations may be incomplete due to a variable follow-up amongst the couples. The model is illustrated with data provided by a prospective study.

Female↗
PubMed2000

Combinatorics of giant hexagonal bilayer hemoglobins.

The paper discusses combinatorial and probabilistic models allowing to characterize various aspects of spacial symmetry and structural heterogeneity of the giant hexagonal bilayer hemoglobins (HBL Hb). Linker-dodecamer configurations of HBL are described for two and four linker types (occurring in the two most studied HBL Hb of Arenicola and Lumbricus, respectively), and the most probable configurations are found. It is shown that, for HBL with marked dodecamers, the number of 'normal-marked' pairs of dodecamers in homological position follows a binomial distribution. The group of symmetries of the dodecamer substructure of HBL is identified with the dihedral group D6. Under natural symmetry assumptions, the total dipole moment of the dodecamer substructure of HBL is shown to be zero. Biological implications of the mathematical findings are discussed.

Animals↗
PubMed1997

Curvilinearity, covariance, and regularity in perceptual groups.

A curvilinear pattern among a series of visual items (e.g., dots) can be regarded as a kind of probabilistic inference, in which each consecutive angle, regarded independently, is more nearly collinear than would be expected by chance alone. This paper investigates judgments of curvilinearity as a function of the joint distribution of successive inter-dot angles. Subjects were asked to classify 4- and 5-dot configurations as having been generated by a curvilinear generating process, vs independently. Their results are distributed as a gaussian over the inter-dot angles with mean 0 deg (collinear), with a negative correlation between successive angles, but negligible correlation between non-successive angles. This suggests that curvilinearity is evaluated in a 4-dot window moving along the chain of dots, evaluating collinearity and smoothness but ignoring higher-order relationships. Moreover, the probabilistic model provides a remarkably precise numeric prediction of the magnitude of the correlation. Subjects also showed a reliable preference for equal spacing of dots along the virtual curve.

Humans↗
PubMed2000

Mother-to-child transmission of hepatitis C virus: evidence for preventable peripartum transmission.

BACKGROUND: Little information is available about the timing of mother-to-child transmission of hepatitis C virus (HCV), and no interventions to decrease transmission rates have been identified. We examined the effect of risk factors, including mode of delivery, on the vertical transmission rate. METHODS: Data from HCV-infected women and their infants from three hospitals in Ireland and from a British Paediatric Surveillance Unit study of infants born to HCV-infected mothers were used to estimate the vertical transmission rate and risk factors for transmission. We used a probabilistic model using methods that simultaneously estimated the time to HCV-antibody loss in uninfected infants and the diagnostic accuracy of PCR tests for HCV RNA. FINDINGS: 441 mother-child pairs from the UK (227) and Ireland (214) were included. 50% of uninfected children became HCV-antibody negative by 8 months and 95% by 13 months. The estimated specificity of PCR for HCV RNA was 97% (95% CI 96-99) and was unrelated to age; sensitivity was only 22% (7-46) in the first month but rose sharply to 97% (85-100) thereafter. The vertical transmission rate was 6.7% (4.1-10.2) overall, and 3.8 times higher in HIV coinfected (n=22) than in HIV-negative women after adjustment for other factors (p=0.06). No effect of breastfeeding on transmission was observed, although only 59 women breastfed. However, delivery by elective caesarean section before membrane rupture was associated with a lower transmission risk than vaginal or emergency caesarean-section delivery (odds ratio 0 [0-0.87], p=0.04, after adjustment for other factors). INTERPRETATION: The low sensitivity of HCV RNA soon after birth and the finding of a lower transmission rate after delivery by elective caesarean section suggest that HCV transmission occurs predominantly around the time of delivery. If the findings on elective caesarean section are confirmed in other studies, the case for antenatal HCV testing should be reconsidered.

Age Factors↗
PubMed2002

Using noise signature to optimize spike-sorting and to assess neuronal classification quality.

We have developed a simple and expandable procedure for classification and validation of extracellular data based on a probabilistic model of data generation. This approach relies on an empirical characterization of the recording noise. We first use this noise characterization to optimize the clustering of recorded events into putative neurons. As a second step, we use the noise model again to assess the quality of each cluster by comparing the within-cluster variability to that of the noise. This second step can be performed independently of the clustering algorithm used, and it provides the user with quantitative as well as visual tests of the quality of the classification.

Action Potentials↗