Atomic force microscopy assisted with electron and ion beam microscopy for the direct measurement of biostructures and DNA samples

Dissertation to obtain a Master degree in Biotechnology

The economic valuation of noise reduction projects: A cost-benefit analysis approach

The main purpose of this Work Project consists in performing a practical Cost-Benefit Analysis from a social perspective of two noise reduction projects in industrial sites that aim at complying with the existing regulation. By doing so, one may expect a more comprehensive view of the benefits and costs of both projects, as well as relevant insight to the way noise exposure regulation must be optimally defined in Portugal and within the EU area.

Comparison of the fluorescent polarization (TDx) and the enzymatic competitive (EMIT 2000) immune assays for the measurement of cyclosporin A blood concentration

Evaluation of Cyclosporin A (CyA) blood concentration is imperative in solid organ transplantation in order to achieve maximal immunosuppression with the least side effects. We compared the results of whole blood concentrations of CyA in 50 blood samples simultaneously evaluated by the fluorescent polarization immune assay (TDx) and the enzymatic competitive immune assay (EMIT 2000). There was a strong correlation between both kits for any range of CyA blood concentration (R=0.99, p<0.001). The within-run and between-days coefficient of variation were less than 4% for both assays. The cost for each CyA measurement was 50% lower for the EMIT assay when compared to the TDx assay. We concluded that the EMIT is as accurate as the TDx in measuring CyA blood concentration and has the advantage of a lower cost, as well as the possibility of widespread access to the EMIT methodology in contrast to the TDx equipment, allowing the laboratory to perform several routines within a working day.

Measurement of the top pair production cross-section in 8 TeV proton-proton collisions using kinematic information in the lepton+jets final state with ATLAS

A measurement is presented of the tt¯ inclusive production cross section in pp collisions at a center-of-mass energy of s√=8  TeV using data collected by the ATLAS detector at the CERN Large Hadron Collider. The measurement was performed in the lepton+jets final state using a data set corresponding to an integrated luminosity of 20.3  fb−1. The cross section was obtained using a likelihood discriminant fit and b-jet identification was used to improve the signal-to-background ratio. The inclusive tt¯ production cross section was measured to be 260±1(stat)+22−23(stat)±8(lumi)±4(beam)  pb assuming a top-quark mass of 172.5 GeV, in good agreement with the theoretical prediction of 253+13−15  pb. The tt¯→(e,μ)+jets production cross section in the fiducial region determined by the detector acceptance is also reported.

Measurement of Spin Correlation in Top-Antitop Quark Events and Search for Top Squark Pair Production in pp Collisions at s√=8 TeV Using the ATLAS Detector

A measurement of spin correlation in tt¯ production is presented using data collected with the ATLAS detector at the Large Hadron Collider in proton-proton collisions at a center-of-mass energy of 8 TeV, corresponding to an integrated luminosity of 20.3 fb−1. The correlation between the top and antitop quark spins is extracted from dilepton tt¯ events by using the difference in azimuthal angle between the two charged leptons in the laboratory frame. In the helicity basis the measured degree of correlation corresponds to Ahelicity=0.38±0.04, in agreement with the Standard Model prediction. A search is performed for pair production of top squarks with masses close to the top quark mass decaying to predominantly right-handed top quarks and a light neutralino, the lightest supersymmetric particle. Top squarks with masses between the top quark mass and 191 GeV are excluded at the 95% confidence level.

Measurement of the transverse polarization of Λ and Λ ¯ hyperons produced in proton-proton collisions at s =7TeV using the ATLAS detector

The transverse polarization of Λ and Λ¯ hyperons produced in proton--proton collisions at a center-of-mass energy of 7 TeV is measured. The analysis uses 760 μb−1 of minimum bias data collected by the ATLAS detector at the LHC in the year 2010. The measured transverse polarization averaged over Feynman xF from 5×10−5 to 0.01 and transverse momentum pT from 0.8 to 15 GeV is −0.010±0.005(stat)±0.004(syst) for Λ and 0.002±0.006(stat)±0.004(syst) for Λ¯. It is also measured as a function of xF and pT, but no significant dependence on these variables is observed. Prior to this measurement, the polarization was measured at fixed-target experiments with center-of-mass energies up to about 40 GeV. The ATLAS results are compatible with the extrapolation of a fit from previous measurements to the xF range covered by this mesurement.

Observation and measurement of Higgs boson decays to WW∗ with the ATLAS detector

We report the observation of Higgs boson decays to WW∗ based on an excess over background of 6.1 standard deviations in the dilepton final state, where the Standard Model expectation is 5.8 standard deviations. Evidence for the vector-boson fusion (VBF) production process is obtained with a significance of 3.2 standard deviations. The results are obtained from a data sample corresponding to an integrated luminosity of 25 pb−1 from s√=7 and 8 TeV pp collisions recorded by the ATLAS detector at the LHC. For a Higgs boson mass of 125.36 GeV, the ratio of the measured value to the expected value of the total production cross section times branching fraction is 1.09+0.16−0.15 (stat.)+0.17−0.14 (syst.). The corresponding ratios for the gluon fusion and vector-boson fusion production mechanisms are 1.02±0.19 (stat.)+0.22−0.18 (syst.) and 1.27+0.44−0.40 (stat.)+0.30−0.21 (syst.), respectively. At s√=8 TeV, the total production cross sections are measured to be σ(gg→ H→WW∗)=4.6±0.9(stat.)+0.8−0.7(syst.)pb and σ(VBF H→WW∗)=0.51+0.17−0.15(stat.)+0.13−0.08(syst.)pb. The fiducial cross section is determined for the gluon-fusion process in exclusive final states with zero or one associated jet.

Observation of top-quark pair production in association with a photon and measurement of the t t ¯ γ production cross section in pp collisions at s =7 TeV using the ATLAS detector

A search is performed for top-quark pairs (tt¯) produced together with a photon (γ) with transverse momentum >20 GeV using a sample of tt¯ candidate events in final states with jets, missing transverse momentum, and one isolated electron or muon. The dataset used corresponds to an integrated luminosity of 4.59 fb−1 of proton--proton collisions at a center-of-mass energy of 7 TeV recorded by the ATLAS detector at the CERN Large Hadron Collider. In total 140 and 222 tt¯γ candidate events are observed in the electron and muon channels, to be compared to the expectation of 79±26 and 120±39 non-tt¯γ background events respectively. The production of tt¯γ events is observed with a significance of 5.3 standard deviations away from the null hypothesis. The tt¯γ production cross section times the branching ratio (BR) of the single-lepton decay channel is measured in a fiducial kinematic region within the ATLAS acceptance. The measured value is σfidtt¯γ=63±8(stat.)+17−13(syst.)±1(lumi.) fb per lepton flavor, in good agreement with the leading-order theoretical calculation normalized to the next-to-leading-order theoretical prediction of 48±10 fb.

Ergosterol as a rapid measurement of Ganoderma rot of oil palm

Palm oil (PO) is a very important commodity for many countries and especially Indonesia and Malaysia who are the predominant producers. PO is used in ca. 30% of supermarket foods, cosmetics, cooking and as biodiesel. The growth of oil palms in plantations is controversial as the production methods contribute to climate change and cause environmental damage [1]. The plant is subjected to a devastating disease in these two countries caused by the white rot fungus Ganoderma. There are no satisfactory methods to diagnose the disease in the plant as they are too slow and/or inaccurate. The lipid compound ergosterol is unique to fungi and is used to measure growth especially in solid substrates. We report here on the use of ergosterol to measure the growth of Ganoderma in oil palms using HPLC and TLC methods [2]. The method is rapid and correlates well with other methods and is capable of being used on-site, hence improving the speed of analysis and allowing remedial action. Climate change will affect the health of OP [1] and rapid detection methods will be increasingly required to control the disease. [1] Paterson, RRM, Kumar, L, Taylor, S, Lima N. Future climate effects on suitability for growth of oil palms in Malaysia and Indonesia. Scientific Reports, 5, 2015, 14457. [2] Muniroh, MS, Sariah M, Zainal Abidin, MA, Lima, N, Paterson, RRM. Rapid detection of Ganoderma-infected oil palms by microwave ergosterol extraction with HPLC and TLC. Journal of Microbiological Methods, 100, 2014, 143–147.

Measurement of charged-particle spectra in Pb+Pb collisions at √sNN = 2.76TeV with the ATLAS detector at the LHC

Charged-particle spectra obtained in 0.15nb−1 of Pb+Pb interactions at sNN−−−√=2.76TeV and 4.2pb−1 of pp interactions at s√=2.76TeV with the ATLAS detector at the LHC are presented in a wide transverse momentum (0.5of collision centrality, which is determined by the response of the forward calorimeter located on both sides of the interaction point. The nuclear modification factors RAA and RCP are presented in detail as function of centrality, pT and η. They show a distinct pT-dependence with a pronounced minimum at about 7GeV. Above 60GeV, RAA is consistent with a plateau at a centrality-dependent value, within the uncertainties. The value is 0.55±0.01(stat.)±0.04(syst.) in the most central collisions. The RAA distribution is consistent with flat |η| dependence over the whole transverse momentum range in all centrality classes.

Measurement of the forward-backward asymmetry of electron and muon pair-production in pp collisions at s√ = 7 TeV with the ATLAS detector

This paper presents measurements from the ATLAS experiment of the forward-backward asymmetry in the reaction pp→Z/γ∗→l+l−, with l being electrons or muons, and the extraction of the effective weak mixing angle. The results are based on the full set of data collected in 2011 in pp collisions at the LHC at s√ = 7 TeV, corresponding to an integrated luminosity of 4.8 fb−1. The measured asymmetry values are found to be in agreement with the corresponding Standard Model predictions. The combination of the muon and electron channels yields a value of the effective weak mixing angle of 0.2308±0.0005(stat.)±0.0006(syst.)±0.0009(PDF), where the first uncertainty corresponds to data statistics, the second to systematic effects and the third to knowledge of the parton density functions. This result agrees with the current world average from the Particle Data Group fit.

Measurement of exclusive γγ→ℓ+ℓ− production in proton--proton collisions at s√=7 TeV with the ATLAS detector

This Letter reports a measurement of the exclusive γγ→ℓ+ℓ−(ℓ=e,μ) cross-section in proton--proton collisions at a centre-of-mass energy of 7 TeV by the ATLAS experiment at the LHC, based on an integrated luminosity of 4.6 fb−1. For the electron or muon pairs satisfying exclusive selection criteria, a fit to the dilepton acoplanarity distribution is used to extract the fiducial cross-sections. The cross-section in the electron channel is determined to be σexcl.γγ→e+e−=0.428±0.035(stat.)±0.018(syst.) pb for a phase-space region with invariant mass of the electron pairs greater than 24 GeV, in which both electrons have transverse momentum pT>12 GeV and pseudorapidity |η|<2.4. For muon pairs with invariant mass greater than 20 GeV, muon transverse momentum pT>10 GeV and pseudorapidity |η|<2.4, the cross-section is determined to be σexcl.γγ→μ+μ−=0.628±0.032(stat.)±0.021(syst.) pb. When proton absorptive effects due to the finite size of the proton are taken into account in the theory calculation, the measured cross-sections are found to be consistent with the theory prediction.

Combined Measurement of the Higgs Boson Mass in pp Collisions at root s=7 and 8 TeV with the ATLAS and CMS Experiments

A measurement of the Higgs boson mass is presented based on the combined data samples of the ATLAS and CMS experiments at the CERN LHC in the H→γγ and H→ZZ→4ℓ decay channels. The results are obtained from a simultaneous fit to the reconstructed invariant mass peaks in the two channels and for the two experiments. The measured masses from the individual channels and the two experiments are found to be consistent among themselves. The combined measured mass of the Higgs boson is mH=125.09±0.21(stat.)±0.11(syst.) GeV.

Measurement of the charge asymmetry in dileptonic decays of top quark pairs in pp collisions at s√=7 TeV using the ATLAS detector

A measurement of the top--antitop (tt¯) charge asymmetry is presented using data corresponding to an integrated luminosity of 4.6 fb−1 of LHC pp collisions at a centre-of-mass energy of 7 TeV collected by the ATLAS detector. Events with two charged leptons, at least two jets and large missing transverse momentum are selected. Two observables are studied: AℓℓC based on the identified charged leptons, and Att¯C, based on the reconstructed tt¯ final state. The asymmetries are measured to be AℓℓC=0.024±0.015 (stat.)±0.009 (syst.), Att¯C=0.021±0.025 (stat.)±0.017 (syst.). The measured values are in agreement with the Standard Model predictions.

Measurement of the inclusive jet cross-section in proton--proton collisions at s√=7 TeV using 4.5 fb−1 of data with the ATLAS detector

The inclusive jet cross-section is measured in proton--proton collisions at a centre-of-mass energy of 7 TeV using a data set corresponding to an integrated luminosity of 4.5 fb−1 collected with the ATLAS detector at the Large Hadron Collider in 2011. Jets are identified using the anti-kt algorithm with radius parameter values of 0.4 and 0.6. The double-differential cross-sections are presented as a function of the jet transverse momentum and the jet rapidity, covering jet transverse momenta from 100 GeV to 2 TeV. Next-to-leading-order QCD calculations corrected for non-perturbative effects and electroweak effects, as well as Monte Carlo simulations with next-to-leading-order matrix elements interfaced to parton showering, are compared to the measured cross-sections. A quantitative comparison of the measured cross-sections to the QCD calculations using several sets of parton distribution functions is performed.