A Computational Method for the Rate Estimation of Evolutionary Transpositions

Genome rearrangements are evolutionary events that shuffle genomic architectures. Most frequent genome rearrangements are reversals, translocations, fusions, and fissions. While there are some more complex genome rearrangements such as transpositions, they are rarely observed and believed to constitute only a small fraction of genome rearrangements happening in the course of evolution. The analysis of transpositions is further obfuscated by intractability of the underlying computational problems. We propose a computational method for estimating the rate of transpositions in evolutionary scenarios between genomes. We applied our method to a set of mammalian genomes and estimated the transpositions rate in mammalian evolution to be around 0.26.Comment: Proceedings of the 3rd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO), 2015. (to appear

Estudio agroeconomico del proceso de produccion de frijol (Phaseolus vulgaris) en Colombia

A methodology is presented on how to study bean production processes and its on-farm application in Colombia. The main objectives are to identify the factors limiting production and productivity, availability and use of resources, credit, technical assistance, markets, pest and weed distribution and intensity, production costs, and crop profit. The study consists of various stages: definition of the problem, antecedents, interviews with technicians and administrators, bibliographic review, definition of objectives and variables, questionnaires, pilot and final surveys, selection of areas (Antioquia, Huila, Narino, and Valle del Cauca), municipalities, and producers (177 farms with an av. of 25 ha). The av. area of bean crops is 6 ha with great differences among states; more than 60 percent of the cultivation is shared with other crops such as maize, coffee, plantain, soybeans, cassava, aracacha, peas and potatoes. Except farmers of the Valle, and to a lesser extent, those that only cultivate beans in Huila, the great majority of cultivators did not have adequate mechanical equipment for preparation, planting, harvesting, and irrigation. Seventy percentage are landowners, 10 percent tenants, and 17 percent sharecroppers. It is considered that beans need less irrigation, should be harvested quickly, and that it is the crop that produces the greatest profit; however, it is considered to be the crop representing the highest risk. Planting systems are described: on flat rows; multiple cropping on ridges; multiple cropping without rows; multiple cropping in the same flat row; multiple cropping in different rows, and mixed multiple cropping. Only 12 percent of the cultivators use improved seed and during the study, 86, 48 and 34 percent planted red, black, and both types of beans, resp. Data are presented on the intensity of land use; principle pests, diseases, and weeds are evaluated. Information on costs, storage, and marketing are also included. (CIAT

Measuring the νμ\nu_{\mu} to νμˉ\bar{\nu_{\mu}} Ratio in a High Statistics Atmospheric Neutrino Experiment

By exploiting differences in muon lifetimes it is possible to distinguish $\nu_{\mu}$ from $\bar{\nu_{\mu}}$ charged current interactions in underground neutrino detectors. Such observations would be a useful tool in understanding the source of the atmospheric neutrino anomaly.Comment: 6 pages no figure

System-size scan of dihadron azimuthal correlations in ultra-relativistic heavy ion collisions

System-size dependence of dihadron azimuthal correlations in ultra-relativistic heavy ion collision is simulated by a multi-phase transport model. The structure of correlation functions and yields of associated particles show clear participant path-length dependences in collision systems with a partonic phase. The splitting parameter and root-mean-square width of away-side correlation functions increase with collision system size from $^{14}$N+$^{14}$N to $^{197}$Au+$^{197}$Au collisions. The double-peak structure of away-side correlation functions can only be formed in sufficient "large" collision systems under partonic phase. The contrast between the results with partonic phase and with hadron gas could suggest some hints to study onset of deconfinment.Comment: 8 pages, 4 figures, 1 table; Nucl. Phys. A (accepted

Cost-sensitive Bayesian network learning using sampling

A significant advance in recent years has been the development of cost-sensitive decision tree learners, recognising that real world classification problems need to take account of costs of misclassification and not just focus on accuracy. The literature contains well over 50 cost-sensitive decision tree induction algorithms, each with varying performance profiles. Obtaining good Bayesian networks can be challenging and hence several algorithms have been proposed for learning their structure and parameters from data. However, most of these algorithms focus on learning Bayesian networks that aim to maximise the accuracy of classifications. Hence an obvious question that arises is whether it is possible to develop cost-sensitive Bayesian networks and whether they would perform better than cost-sensitive decision trees for minimising classification cost? This paper explores this question by developing a new Bayesian network learning algorithm based on changing the data distribution to reflect the costs of misclassification. The proposed method is explored by conducting experiments on over 20 data sets. The results show that this approach produces good results in comparison to more complex cost-sensitive decision tree algorithms

Single gluino production in the R-parity lepton number violating MSSM at the LHC

We examine the $R_{p}$-violating signal of single gluino production associated with a charged lepton or neutrino at the large hadron collider (LHC), in the model of R-parity relaxed supersymmetric model. If the parameters in the ${\rlap/R}_p$ supersymmetric interactions are not too small, and the mass of gluino is considered in the range from several GeV (as the Lightest Supersymmetric Particle) to 800 GeV, the cross section of the single gluino production via Drell-Yan processes can be in the order of $10^2 \sim 10^3$ femto barn, and that via gluon fusion in the order of $10^{-1} \sim 10^3$ femto barn. If the gluino decay can be well detected in the CERN LHC, this process provides a prospective way to probe supersymmetry and $R_p$ violation.Comment: LaTex, 22 pages, 5 EPS file

Longitudinal broadening of near side jets due to parton cascade

Longitudinal broadening along $\Delta\eta$ direction on near side in two-dimensional ($\Delta\phi \times \Delta\eta$) di-hadron correlation distribution has been studied for central Au+Au collisions at $\sqrt{s_{NN}}$ = 200 GeV, within a dynamical multi-phase transport model. It was found that the longitudinal broadening is generated by a longitudinal flow induced by strong parton cascade in central Au+Au collisions, in comparison with p+p collisions at $\sqrt{s_{NN}}$ = 200 GeV. The longitudinal broadening may shed light on the information about strongly interacting partonic matter at RHIC.Comment: 5 pages, 4 figures; accepted by Eur. Phys. J.

Three-Particle Correlations from Parton Cascades in Au+Au Collisions

We present a study of three-particle correlations among a trigger particle and two associated particles in Au + Au collisions at $\sqrt{s_{NN}}$ = 200 GeV using a multi-phase transport model (AMPT) with both partonic and hadronic interactions. We found that three-particle correlation densities in different angular directions with respect to the triggered particle (`center', `cone', `deflected', `near' and `near-away') increase with the number of participants. The ratio of `deflected' to `cone' density approaches to 1.0 with the increasing of number of participants, which indicates that partonic Mach-like shock waves can be produced by strong parton cascades in central Au+Au collisions.Comment: 9 pages, 6 figures; Final version to appear in Physics Letters

Immediate reward reinforcement learning for clustering and topology preserving mappings

We extend a reinforcement learning algorithm which has previously been shown to cluster data. Our extension involves creating an underlying latent space with some pre-defined structure which enables us to create a topology preserving mapping. We investigate different forms of the reward function, all of which are created with the intent of merging local and global information, thus avoiding one of the major difficulties with e.g. K-means which is its convergence to local optima depending on the initial values of its parameters. We also show that the method is quite general and can be used with the recently developed method of stochastic weight reinforcement learning [14]