A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers

Background: The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily. Results: The mapping population parents ('IAC66-6' and 'TUC71-7') contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs). Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56) were positioned on 21 CGs, but were not regularly distributed. Interestingly, the distance between adjacent scIvana_1-based markers was less than 5 cM, and was observed on five CGs, suggesting a clustered organization. Conclusions: Results indicated the use of a NBS-profiling technique was efficient to develop retrotransposon-based markers in sugarcane. The simultaneous maximum-likelihood estimates of linkage and linkage phase based strategies confirmed the suitability of its approach to estimate linkage, and construct the linkage map. Interestingly, using our genetic data it was possible to calculate the number of retrotransposonscIvana_1 (similar to 60) copies in the sugarcane genome, confirming previously reported molecular results. In addition, this research possibly will have indirect implications in crop economics e. g., productivity enhancement via QTL studies, as the mapping population parents differ in response to an important fungal disease.

A molecular linkage map for Drosophila mediopunctata confirms synteny with Drosophila melanogaster and suggests a region that controls the variation in the number of abdominal spots

The classic approach to gene discovery relies on the construction of linkage maps. We report the first molecular-based linkage map for Drosophila mediopunctata, a neotropical species of the tripunctata group. Eight hundred F2 individuals were genotyped at 49 microsatellite loci, resulting in a map that is approximate to 450 centimorgans long. Five linkage groups were detected, and the species' chromosomes were identified through cross-references to BLASTn searches and Muller elements. Strong synteny was observed when compared with the Drosophila melanogaster chromosome arms, but little conservation in the gene order was seen. The incorporation of morphological data corresponding to the number of central abdominal spots on the map was consistent with the expected location of a genomic region responsible for the phenotype on the second chromosome.

Assessment of SNPs for linkage mapping in Eucalyptus: construction of a consensus SNP/microsatellite map from two unrelated pedigrees

Financial support. Brazilian Ministry of Science and Technology (CNPq Grant 577047-2008-6), FAP-DF NEXTREE Grant 193.000.570/2009 and EMBRAPA Macroprogram 2 project grant 02.07.01.004.

Direct estimation of the backward flow

[EN] The aim of this work is to propose a new method for estimating the backward flow directly from the optical flow. We assume that the optical flow has already been computed and we need to estimate the inverse mapping. This mapping is not bijective due to the presence of occlusions and disocclusions, therefore it is not possible to estimate the inverse function in the whole domain. Values in these regions has to be guessed from the available information. We propose an accurate algorithm to calculate the backward flow uniquely from the optical flow, using a simple relation. Occlusions are filled by selecting the maximum motion and disocclusions are filled with two different strategies: a min-fill strategy, which fills each disoccluded region with the minimum value around the region; and a restricted min-fill approach that selects the minimum value in a close neighborhood. In the experimental results, we show the accuracy of the method and compare the results using these two strategies.

Measurement of the forward-backward asymmetry of Z boson decays in electron-positron pairs with the ATLAS detector in proton-proton collisions at root out s = 7TeV at the LHC

In this thesis the measurement of the effective weak mixing angle wma in proton-proton collisions is described. The results are extracted from the forward-backward asymmetry (AFB) in electron-positron final states at the ATLAS experiment at the LHC. The AFB is defined upon the distribution of the polar angle between the incoming quark and outgoing lepton. The signal process used in this study is the reaction pp to zgamma + X to ee + X taking a total integrated luminosity of 4.8\,fb^(-1) of data into account. The data was recorded at a proton-proton center-of-mass energy of sqrt(s)=7TeV. The weak mixing angle is a central parameter of the electroweak theory of the Standard Model (SM) and relates the neutral current interactions of electromagnetism and weak force. The higher order corrections on wma are related to other SM parameters like the mass of the Higgs boson.rnrnBecause of the symmetric initial state constellation of colliding protons, there is no favoured forward or backward direction in the experimental setup. The reference axis used in the definition of the polar angle is therefore chosen with respect to the longitudinal boost of the electron-positron final state. This leads to events with low absolute rapidity have a higher chance of being assigned to the opposite direction of the reference axis. This effect called dilution is reduced when events at higher rapidities are used. It can be studied including electrons and positrons in the forward regions of the ATLAS calorimeters. Electrons and positrons are further referred to as electrons. To include the electrons from the forward region, the energy calibration for the forward calorimeters had to be redone. This calibration is performed by inter-calibrating the forward electron energy scale using pairs of a central and a forward electron and the previously derived central electron energy calibration. The uncertainty is shown to be dominated by the systematic variations.rnrnThe extraction of wma is performed using chi^2 tests, comparing the measured distribution of AFB in data to a set of template distributions with varied values of wma. The templates are built in a forward folding technique using modified generator level samples and the official fully simulated signal sample with full detector simulation and particle reconstruction and identification. The analysis is performed in two different channels: pairs of central electrons or one central and one forward electron. The results of the two channels are in good agreement and are the first measurements of wma at the Z resonance using electron final states at proton-proton collisions at sqrt(s)=7TeV. The precision of the measurement is already systematically limited mostly by the uncertainties resulting from the knowledge of the parton distribution functions (PDF) and the systematic uncertainties of the energy calibration.rnrnThe extracted results of wma are combined and yield a value of wma_comb = 0.2288 +- 0.0004 (stat.) +- 0.0009 (syst.) = 0.2288 +- 0.0010 (tot.). The measurements are compared to the results of previous measurements at the Z boson resonance. The deviation with respect to the combined result provided by the LEP and SLC experiments is up to 2.7 standard deviations.

Equazioni stocastiche backward nel mercato delle emissioni

In questa tesi viene esposto il modello EU ETS (European Union Emission Trading Scheme) per la riduzione delle emissoni di gas serra, il quale viene formalizzato matematicamente da un sistema di FBSDE (Forward Backward Stochastic Differential Equation). Da questo sistema si ricava un'equazione differenziale non lineare con condizione al tempo finale non continua che viene studiata attraverso la teoria delle soluzioni viscosità. Inoltre il modello viene implementato numericamente per ottenere alcune simulazioni dei processi coinvolti.

Outcomes in patients waiting for antiretroviral treatment in the Free State Province, South Africa: prospective linkage study

Objective: In South Africa, many HIV-infected patients experience delays in accessing antiretroviral therapy (ART). We examined pretreatment mortality and access to treatment in patients waiting for ART. Design: Cohort of HIV-infected patients assessed for ART eligibility at 36 facilities participating in the Comprehensive HIV and AIDS Management (CHAM) program in the Free State Province. Methods: Proportion of patients initiating ART, pre-ART mortality and risk factors associated with these outcomes were estimated using competing risks survival analysis. Results: Forty-four thousand, eight hundred and forty-four patients enrolled in CHAM between May 2004 and December 2007, of whom 22 083 (49.2%) were eligible for ART; pre-ART mortality was 53.2 per 100 person-years [95% confidence interval (CI) 51.8–54.7]. Median CD4 cell count at eligibility increased from 87 cells/ml in 2004 to 101 cells/ml in 2007. Two years after eligibility an estimated 67.7% (67.1–68.4%) of patients had started ART, and 26.2% (25.6–26.9%) died before starting ART. Among patients with CD4 cell counts below 25 cells/ml at eligibility, 48% died before ART and 51% initiated ART. Men were less likely to start treatment and more likely to die than women. Patients in rural clinics or clinics with low staffing levels had lower rates of starting treatment and higher mortality compared with patients in urban/peri-urban clinics, or better staffed clinics. Conclusions: Mortality is high in eligible patients waiting for ART in the Free State Province. The most immunocompromised patients had the lowest probability of starting ART and the highest risk of pre-ART death. Prioritization of these patients should reduce waiting times and pre-ART mortality.