A probabilistic approach to microRNA-target binding

Elucidation of microRNA activity is a crucial step in understanding gene regulation. One key problem in this effort is how to model the pairwise interactions of microRNAs with their targets. As this interaction is strongly mediated by their sequences, it is desired to set-up a probabilistic model to explain the binding preferences between a microRNA sequence and the sequence of a putative target. To this end, we introduce a new model of microRNA-target binding, which transforms an aligned duplex to a new sequence and defines the likelihood of this sequence using a Variable Length Markov Chain. It offers a complementary representation of microRNA–mRNA pairs for microRNA target prediction tools or other probabilistic frameworks of integrative gene regulation analysis. The performance of present model is evaluated by its ability to predict microRNA–target mRNA interaction given a mature microRNA sequence and a putative mRNA binding site. In regard to classification accuracy, it outperforms two recent methods based on thermodynamic stability and sequence complementarity. The experiments can also unveil the effects of base pairing types and non-seed region in duplex formation.     

A two-stage probabilistic approach to multiple-community similarity indices

SUMMARY: A traditional approach for assessing similarity among N (N > 2) communities is to use multiple pairwise comparisons. However, pairwise similarity indices do not completely characterize multiple-community similarity because the information shared by at least three communities is ignored. We propose a new and intuitive two-stage probabilistic approach, which leads to a general framework to simultaneously compare multiple communities based on abundance data. The approach is specifically used to extend the commonly used Morisita index and NESS (normalized expected species shared) index to the case of N communities. For comparing N communities, a profile of N- 1 indices is proposed to characterize similarity of species composition across communities. Based on sample abundance data, nearly unbiased estimators of the proposed indices and their variances are obtained. These generalized NESS and Morisita indices are applied to comparison of three size classes of plant data (seedling, saplings, and trees) within old-growth and secondary rain forest plots in Costa Rica.     

A probabilistic approach to the assessment of some life history pattern parameters in a Middle Pleistocene human population

Parameters of a Middle Pleistocene human population such as the expected length of the female reproductive period (E(Y)), the expected interbirth interval (E(X)), the survival rate (tau) for females after the expected reproductive period, the rate (phi(2)) of women who, given that they reach first birth, do not survive to the end of the expected reproductive period, and the female infant plus juvenile mortality rate (phi(1)) have been assessed from a probabilistic standpoint provided that such a population were stationary. The hominid sample studied, the Sima de los Huesos (SH) cave site, Sierra de Atapuerca (Spain), is the most exhaustive human fossil sample currently available. Results suggest that the Atapuerca (SH) sample can derive from a stationary population. Further, in the case that the expected reproductive period ends between 37 and 40 yr of age, then 24 less, similarE(Y) less, similar27 yr, E(X)=3 yr, 0.224相似文献   

Welcoming uncertainty: A probabilistic approach to measure sustainability

Current efforts to build Sustainable Development Measurements have stumbled with problems of arbitrary structure, valuation,artificial ignorance suppression, and democratic illegitimacy. This paper proposes a new method to track and compare the Sustainable Development (SD) of countries, building an Interval of Sustainable Development (ISD). The ISD is capable of overcoming these problems by reporting all possible structures instead of only one, by relying on a variety of existing economic, social, and environmental variables, by embodying confidence levels in the measurement itself, and by facilitating democratic deliberation. By doing this, the ISD is capable of showing, subject to a confidence level, how a country is performing with respect to SD. This paper also applies this method specifying parameters and using available data for 180 countries during 1990–2011. During this 22-year period, results for a selection of countries are presented to illustrate the advantages and limitations of this proposal.     

A probabilistic approach to protein backbone tracing in electron density maps

One particularly time-consuming step in protein crystallography is interpreting the electron density map; that is, fitting a complete molecular model of the protein into a 3D image of the protein produced by the crystallographic process. In poor-quality electron density maps, the interpretation may require a significant amount of a crystallographer's time. Our work investigates automating the time-consuming initial backbone trace in poor-quality density maps. We describe ACMI (Automatic Crystallographic Map Interpreter), which uses a probabilistic model known as a Markov field to represent the protein. Residues of the protein are modeled as nodes in a graph, while edges model pairwise structural interactions. Modeling the protein in this manner allows the model to be flexible, considering an almost infinite number of possible conformations, while rejecting any that are physically impossible. Using an efficient algorithm for approximate inference--belief propagation--allows the most probable trace of the protein's backbone through the density map to be determined. We test ACMI on a set of ten protein density maps (at 2.5 to 4.0 A resolution), and compare our results to alternative approaches. At these resolutions, ACMI offers a more accurate backbone trace than current approaches.     

A quantum-theoretic approach to genetic problems

A quantum-theoretic picture of the transfer of genetic information is described. The advantage of such an approach is that a number of genetic effects appear to be explicable on the basis of general microphysical laws, independent of any specific model (such as DNA-protein coding) for the transmission of genetic information. It is assumed that the genetic information is carried by a family of numerical observables belonging to a specific microphysical system; it is shown that a single observable is theoretically sufficient to carry this information. The various types of structure that this observable can possess are then described in detail, and the possible genetic effects which can airse from each such structure are discussed. For example, it is shown how the assumption that the genetic observable possesses degenerate eigenvalues may lead to a theory of allelism. To keep the treatment self-contained, the basic quantum-theoretical principles to be used are discussed in some detail. Finally, the relation of the present approach to current biochemical ideas and to earlier quantum-theoretic treatments of genetic systems is discussed.     

A probabilistic approach to the construction of competing-risk life tables

"This paper aims to identify net and partial-crude probabilities in the competing-risk life table context, by using probabilistic approaches. Five types of lifelength random variables are defined to formulate these nonidentifiable probabilities. General expressions for net and partial-crude probabilities are first derived under independent risks assumptions. Two sets of explicit formulas for estimating the net and partial-crude probabilities are then derived in terms of the identifiable overall and crude probabilities by making the additional assumption of piecewise uniform distribution of the lifelength random variables. A study of the degree to which nonidentifiability can affect the net and partial-crude probabilities in a variety of situations is developed. An example from cross-sectional studies is employed to illustrate the methodology developed."     

A note on the probabilistic approach to the cancer problem

Assuming that the initiation of cancer growth is due to a purely accidental fluctuation of some physicochemical condition, it is possible to derive the equation for the cancer incidence as a function of age. The final result depends on whether it is assumed that a single accidental fluctuation in a cell is sufficient to produce cancer, or that a finite number,k, of repetitions of the accidental fluctuation must occur in the same cell. In principle it is possible to determine from observed incidence curves the numberk. Actually, however, this cannot be done at present, because the difference of the theoretical curves for differentk's is rather small, and the available cancer statistics are not accurate enough to show such differences.     

A probabilistic approach to compact steady-state kinetic equations for enzymic reactions

We describe a method for deriving kinetic equations based on the simplification of a complex graphical scheme of steady-state enzymic reactions to one that is comprised of an unbranched pathway. It entails compressing unbranched multi-step sequences into one step, and fusing some graph nodes into a single node. The final form of the equations is compact and well structured, and it simplifies the choice of independent kinetic parameters. The approach is illustrated by an analysis of representative two- and three-substrate reactions.     

A probabilistic approach to estimating species pools from large compositional matrices

Abstract. Species pools are increasingly recognized as important controls of local plant community structure and diversity. While existing approaches to estimate their content and size either rely on phytosociological expert knowledge or on simple response models across environmental gradients, the proposed application of phytosociological smoothing according to Beals exploits the full information of plant co‐occurrence patterns statistically. Where numerous representative compositional data are available, the new method yields robust estimates of the potential of sites to harbour plant species. To test the new method, a large phytosociological databank covering the forested regions of Oregon (US) was subsampled randomly and evenly across strata defined by geographic regions and elevation belts. The resulting matrix of species presence/absence in 874 plots was smoothed by calculating Beals' index of sociological favourability, which estimates the probability of encountering each species at each site from the actual plot composition and the pattern of species co‐occurrence in the matrix. In a second step, the resulting lists of sociologically probable species were intersected with complete species lists for each of 14 geographical subregions. Species pools were compared to observed species composition and richness. Species pool size exhibited much clearer spatial trends than plot richness and could be modelled much better as a function of climatic factors. In this framework the goal of modelling species pools is not to test a hypothesis, but to bridge the gap between manageable scales of empirical observation and the spatio‐temporal hierarchy of diversity patterns.     

A frequency matrix for probabilistic identification of some bacilli

A matrix comprising frequencies for positive results for 44 Bacillus taxa for 30 characters has been constructed. The 44 taxa include most of the common species and several clusters of environmental isolates including those described as B. firmus-B. lentus intermediates. The tests, which were chosen for their high diagnostic value, included some of the traditional tests used for identification of bacilli supplemented with a range of sugar fermentations and other characterization tests. The matrix was evaluated by identifying hypothetical median organisms, cluster representatives and a panel of 23 reference strains. All reference strains achieved Willcox probabilities above 0.995. Fifty-eight environmental isolates were also subjected to the 30 tests and identification was attempted. Forty-one strains (70%) achieved a Willcox probability greater than 0.95, which was considered an acceptable identification, and were assigned to 12 taxa. If the SE of taxonomic distance was also considered in the identification score (an acceptable value being less than 7.0), the number of acceptable identifications was reduced to 34 (59%). It was encouraging that bacteria from garden soils identified to the common species such as B. subtilis, B. cereus and B. licheniformis whereas some of the bacteria from an estuarine habitat were identified as species such as B. firmus which are normally identified with that habitat.     

A probabilistic approach for estimating water permeability in pressure-driven membranes

A probabilistic approach is proposed to estimate water permeability in a cellulose triacetate (CTA) membrane. Water transport across the membrane is simulated in reverse osmosis mode by means of non-equilibrium molecular dynamics (MD) simulations. Different membrane configurations obtained by an annealing MD simulation are considered and simulation results are analyzed by using a hierarchical Bayesian model to obtain the permeability of the different membranes. The estimated membrane permeability is used to predict full-scale water flux by means of a process-level Monte Carlo simulation. Based on the results, the parameters of the model are observed to converge within 5-ns total simulation time. The results also indicate that the use of unique structural configurations in MD simulations is essential to capture realistic membrane properties at the molecular scale. Furthermore, the predicted full-scale water flux based on the estimated permeability is within the same order of magnitude of bench-scale experimental measurement of 1.72×10^?5 m/s.     

A biomimetic approach to some specifically functionalized cyclic terpenoids

The paper relates on the current advancements in the synthesis of complex cyclic terpenoids by superacidic induced cyclization of open chain precursors. It is shown that functional groups disposal in the initial substrate strongly influences the reaction outcome. Possible variations of the investigated compound structures include particularly alpha-functionalization and alpha,omega-bifunctionalization. This approach allowed a selective initiation of cyclization sequence from an internal double bond or suspending the ring closure cascade to partially cyclized compounds. The reported synthetic schemes are attempts to mimic the biogenetical processes postulated in the living systems.     

Brief communication: A probabilistic approach to age estimation from infracranial sequences of maturation

Infracranial sequences of maturation are commonly used to estimate the age at death of nonadult specimens found in archaeological, paleoanthropological, or forensic contexts. Typically, an age assessment is made by comparing the degree of long‐bone epiphyseal fusion in the target specimen to the age ranges for different stages of fusion in a reference skeletal collection. While useful as a first approximation, this approach has a number of shortcomings, including the potential for “age mimicry,” being highly dependent on the sample size of the reference sample and outliers, not using the entire fusion distribution, and lacking a straightforward quantitative way of combining age estimates from multiple sites of fusion. Here we present an alternative probabilistic approach based on data collected on 137 individuals, ranging in age from 7‐ to 29‐years old, from a documented skeletal collection from Coimbra, Portugal. We then use cross validation to evaluate the accuracy of age estimation from epiphyseal fusion. While point estimates of age can, at least in some circumstances, be both accurate and precise based on the entire skeleton, or many sites of fusion, there will often be substantial error in these estimates when they derive from one or only a few sites. Because a probabilistic approach to age estimation from epiphyseal fusion is computationally intensive, we make available a series of spreadsheets or computer programs that implement the approach presented here. Am J Phys Anthropol 142:655–664, 2010. © 2010 Wiley‐Liss, Inc.