MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

Miniature inverted-repeat transposable elements (MITEs) are a special type of Class 2 non-autonomous transposable element (TE) that are abundant in the non-coding regions of the genes of many plant and animal species. The accurate identification of MITEs has been a challenge for existing programs because they lack coding sequences and, as such, evolve very rapidly. Because of their importance to gene and genome evolution, we developed MITE-Hunter, a program pipeline that can identify MITEs as well as other small Class 2 non-autonomous TEs from genomic DNA data sets. The output of MITE-Hunter is composed of consensus TE sequences grouped into families that can be used as a library file for homology-based TE detection programs such as RepeatMasker. MITE-Hunter was evaluated by searching the rice genomic database and comparing the output with known rice TEs. It discovered most of the previously reported rice MITEs (97.6%), and found sixteen new elements. MITE-Hunter was also compared with two other MITE discovery programs, FINDMITE and MUST. Unlike MITE-Hunter, neither of these programs can search large genomic data sets including whole genome sequences. More importantly, MITE-Hunter is significantly more accurate than either FINDMITE or MUST as the vast majority of their outputs are false-positives

Measurement of transverse energy at midrapidity in Pb-Pb collisions at root s(NN)=2.76 TeV

We report the transverse energy (ET) measured with ALICE at midrapidity in Pb-Pb collisions at root s(NN) = 2.76 TeV as a function of centrality. The transverse energy was measured using identified single-particle tracks. The measurement was cross checked using the electromagnetic calorimeters and the transverse momentum distributions of identified particles previously reported by ALICE. The results are compared to theoretical models as well as to results from other experiments. The mean ET per unit pseudorapidity (eta), , in 0%-5% central collisions is 1737 +/- 6(stat.) +/- 97(sys.) GeV. We find a similar centrality dependence of the shape of as a function of the number of participating nucleons to that seen at lower energies. The growth in at the LHC energies exceeds extrapolations of low-energy data. We observe a nearly linear scaling of with the number of quark participants. With the canonical assumption of a 1 fm/c formation time, we estimate that the energy density in 0%-5% central Pb-Pb collisions at root s(NN) = 2.76 TeV is 12.3 +/- 1.0 GeV/fm(3) and that the energy density at the most central 80 fm(2) of the collision is at least 21.5 +/- 1.7 GeV/fm(3). This is roughly 2.3 times that observed in 0%-5% central Au-Au collisions at root s(NN) = 200 GeV.Peer reviewe

Azimuthally Differential Pion Femtoscopy in Pb-Pb Collisions at root s(NN)=2.76 TeV

We present the first azimuthally differential measurements of the pion source size relative to the second harmonic event plane in Pb-Pb collisions at a center-of-mass energy per nucleon-nucleon pair of root(NN)-N-s = 2.76 TeV. The measurements have been performed in the centrality range 0%-50% and for pion pair transverse momenta 0.2 <k(T) <0.7 GeV/c. We find that the R-side and R-out radii, which characterize the pion source size in the directions perpendicular and parallel to the pion transverse momentum, oscillate out of phase, similar to what was observed at the Relativistic Heavy Ion Collider. The final-state source eccentricity, estimated via R-side oscillations, is found to be significantly smaller than the initial-state source eccentricity, but remains positive-indicating that even after a stronger expansion in the in-plane direction, the pion source at the freeze-out is still elongated in the out-of-plane direction. The 3 + 1D hydrodynamic calculations are in qualitative agreement with observed centrality and transverse momentum R-side oscillations, but systematically underestimate the oscillation magnitude.Peer reviewe

Hypertriton Production in p-Pb Collisions at √sNN = 5.02 TeV

The study of nuclei and antinuclei production has proven to be a powerful tool to investigate the formation mechanism of loosely bound states in high-energy hadronic collisions. The first measurement of the production of ${\rm ^{3}_{\Lambda}\rm H}$ in p-Pb collisions at $\sqrt{s_{\rm{NN}}}$ = 5.02 TeV is presented in this Letter. Its production yield measured in the rapidity interval -1 < y < 0 for the 40% highest multiplicity p-Pb collisions is ${\rm d} N /{\rm d} y =[\mathrm{6.3 \pm 1.8 (stat.) \pm 1.2 (syst.) ] \times 10^{-7}}$. The measurement is compared with the expectations of statistical hadronisation and coalescence models, which describe the nucleosynthesis in hadronic collisions. These two models predict very different yields of the hypertriton in small collision systems such as p-Pb and therefore the measurement of ${\rm d} N /{\rm d} y$ is crucial to distinguish between them. The precision of this measurement leads to the exclusion with a significance larger than 6$\sigma$ of some configurations of the statistical hadronisation, thus constraining the production mechanism of loosely bound states

J/Psi suppression at forward rapidity in Pb-Pb collisions at root s(NN)=5.02 TeV

The inclusive J/Psi production has been studied in Pb-Pb and pp collisions at the centre-of-mass energy per nucleon pair root sNN= 5.02TeV, using the ALICE detector at the CERN LHC. The J/Psi meson is reconstructed, in the centre-of-mass rapidity interval 2.5 <y <4and in the transverse- momentum range p(T)<12GeV/c, via its decay to a muon pair. In this Letter, we present results on the inclusive J/Psi cross section in pp collisions at root s= 5.02TeV and on the nuclear modification factor R-AA. The latter is presented as a function of the centrality of the collision and, for central collisions, as a function of the transverse momentum p(T) of the J/Psi. The measured R-AA values indicate a suppression of the J/Psi in nuclear collisions and are then compared to our previous results obtained in Pb-Pb collisions at root sNN= 2.76TeV. The ratio of the R-AA values at the two energies is also computed and compared to calculations of statistical and dynamical models. The numerical value of the ratio for central events (0-10% centrality) is 1.17 +/- 0.04( stat)+/- 0.20(syst). In central events, as a function of p(T), a slight increase of R-AA with collision energy is visible in the region 2 <p(T)<6GeV/c. Theoretical calculations qualitatively describe the measurements, within uncertainties. (C) 2017 The Author. Published by Elsevier B.V.Peer reviewe

D-meson production in p-Pb collisions at root S-NN=5.02 TeV and in pp collisions at root S=7 TeV

Peer reviewe

Correlated Event-by-Event Fluctuations of Flow Harmonics in Pb-Pb Collisions at root S-NN=2.76 TeV

Peer reviewe

Advances in the biological control of the whitefly Bemisia tabaci in the Neotropical region

6 tab. Bib.La importancia econ?mica de la mosca blanca Bemisia tabaci en la regi?n Neotropical, principalmente como vector de geminivirus en varios cultivos agr?colas, y los problemas surgidos del uso de insecticidas sint?ticos, han motivado la investigaci?n sobre control biol?gico de esta plaga. Se han realizado estudios para conocer los enemigos naturales de esta plaga, existentes en la mayor?a de los pa?ses y como resultado se han identificado diversas especies de parasitoides de los g?neros Encarsia, Eretmocerus (Hymenoptera: Aphelinidae) y Amitus ((Hymenoptera: Platygasteriidae) depredadores de los g?neros Chrysopa, Nodita (Neuroptera:Chrysopidae), Coleomegilla, Cycloneda, Hyppodamia, Delphastus, Nephaspis, Scymnus (Coleoptera:Coccinellidae), Cyrtopeltis, (Hemiptera: Miridae), Orius (Heteroptera: Anthocoridae), Condylostillus (Diptera: Dolichopodidae), Syrphidae (Diptera), Theridula (Araneae:Theridulidae) y entomopat?genos de los g?neros Paecilomyces, Verticillium, Metarhizium, Aschersonia, Cladosporium y Beauveria. Los m?s estudiados para su utilizaci?n en programas de control biol?gico han sido los parasitoides de los g?neros Encarsia y Eretmocerus, predadores del g?nero Chrysopa y entomopat?genos de los g?neros Paecilomyces, Verticillium y Beauveria. En la pr?ctica, algunos pa?ses liberan entom?fagos de forma inoculativa y, aplica bioplaguicidas y muchos integran elementos del control biol?gico al manejo integrado de plagas. The economic importance of the whitefly Bemisia tabaci in the Neotropical region, mainly as vector of geminivirus in several agricultural crops and the problems that arise with the use of synthetic insecticides, have motivated research on the biological control of this pest. Studies have been carried out to find out the natural enemies in most of the countries, and as a result diverse species of parasitoids of Encarsia and Eretmocerus (Hymenoptera: Aphelinidae), and Amitus (Hymenoptera: Platygasteriidae) predators of the genus Chrysopa, Nodita (Neuroptera: Chrysopidae), Coleomegilla, Cycloneda, Hyppodamia, Delphastus, Nephaspis, Scymnus (Coleoptera: Coccinellidae), Cyrtopeltis (Hemiptera: Miridae), Orius (Heteroptera: Anthocoridae), Condylostillus (Diptera: Dolichopodidae), Syrphidae (Diptera), Theridula (Araneae:Theridulidae), and entomopatogenic fungus of the genus Paecilomyces, Verticillium, Metarhizium, Aschersonia, Cladosporium and Beauveria genera have been identified. The most widely researched for their use in programs of biological control have been parasitoids of the genus Encarsia and Eretmocerus, predators of the genus Chrysopa, and entomopatogenic fungus of the genus Paecilomyces, Verticillium and Beauveria. In the practice, some of the countries release entomophagous insects in inoculative ways, and apply biopesticides, and many integrate biological control elements into integrated pest management programs

Patricio Cardin Pe?arredonda: precursor del manejo de plagas en Cuba

1 ilus. 7 ref

A Deterministic Method For Establishing The Initial Conditions In The Rce Algorithm

. The RCE algorithm, which can be considered as belonging to the category of the Region of Influence (ROI) incremental algorithms, is one of the first and most widely used incremental algorithms. It is well known that the performance of this algorithm is limited by constraints affecting the initial parameter settings: order in which input patterns are presented during the training phase and initial radius to be used for the generated hyperspheres. In this paper, we propose a deterministic method for obtaining automatically the suitable initial radius for a given input problem. The method is based on the definition of several functions which give a quantitative measure of the geometrical relations between the different categories defined in the input space. As the simulation results show, this method improves significantly the performance (in terms of number of units generated and generalization capability) of the RCE algorithm. 1. Introduction In the last years there has been an increa..