MUMAL: multivariate analysis in shotgun proteomics using machine learning techniques.

BACKGROUND: The shotgun strategy (liquid chromatography coupled with tandem mass spectrometry) is widely applied for identification of proteins in complex mixtures. This method gives rise to thousands of spectra in a single run, which are interpreted by computational tools. Such tools normally use a protein database from which peptide sequences are extracted for matching with experimentally derived mass spectral data. After the database search, the correctness of obtained peptide-spectrum matches (PSMs) needs to be evaluated also by algorithms, as a manual curation of these huge datasets would be impractical. The target-decoy database strategy is largely used to perform spectrum evaluation. Nonetheless, this method has been applied without considering sensitivity, i.e., only error estimation is taken into account. A recently proposed method termed MUDE treats the target-decoy analysis as an optimization problem, where sensitivity is maximized. This method demonstrates a significant increase in the retrieved number of PSMs for a fixed error rate. However, the MUDE model is constructed in such a way that linear decision boundaries are established to separate correct from incorrect PSMs. Besides, the described heuristic for solving the optimization problem has to be executed many times to achieve a significant augmentation in sensitivity. RESULTS: Here, we propose a new method, termed MUMAL, for PSM assessment that is based on machine learning techniques. Our method can establish nonlinear decision boundaries, leading to a higher chance to retrieve more true positives. Furthermore, we need few iterations to achieve high sensitivities, strikingly shortening the running time of the whole process. Experiments show that our method achieves a considerably higher number of PSMs compared with standard tools such as MUDE, PeptideProphet, and typical target-decoy approaches. CONCLUSION: Our approach not only enhances the computational performance, and thus the turn around time of MS-based experiments in proteomics, but also improves the information content with benefits of a higher proteome coverage. This improvement, for instance, increases the chance to identify important drug targets or biomarkers for drug development or molecular diagnostics

Quadrupole Pairing Interaction and Signature Inversion

The signature inversion in the \pi h11/2 \otimes \nu h11/2 rotational bands of odd-odd Cs and La isotopes and the \pi h11/2 \otimes \nu i13/2 bands of odd-odd Tb, Ho and Tm nuclei is investigated using pairing and deformation self consistent mean field calculations. The model can rather satisfactorily account for the anomalous signature splitting, provided that spin assignments in som of the bands are revised. Our calculations show that signature inversioncan appear already at axially symmetric shapes. It is found that this is due to the contribution of the \lambda\mu=22 component of the quadrupole pairing interaction to the mean field potential.Comment: 17 pages, 14 figures, Nuclear Physics A in prin

Trans-sialidase from Trypanosoma cruzi enhances the adhesion properties and fibronectin-driven migration of thymocytes

In experimental Trypanosoma cruzi infections, severe thymic atrophy leads to release of activated CD4+CD8+ double-positive (DP) T cells to the periphery. In humans, activated DP T cells are found in the blood in association with severe cardiac forms of human chronic Chagas disease. The mechanisms underlying the premature thymocyte release during the chagasic thymic atrophy remain elusive. We tested whether the migratory properties of intrathymic thymocytes are modulated by the parasite trans-sialidase (TS). We found that TS affected the dynamics of thymocytes undergoing intrathymic maturation, and these changes were accompanied by an increase in the number of recent DP thymic emigrants in the peripheral lymphoid organs. We demonstrated that increased percentages of blood DP T cell subsets were associated with augmented antibody titers against TS in chagasic patients with chronic cardiomyopathy. In vitro studies showed that TS was able to activate the MAPK pathway and actin filament mobilization in thymocytes. These effects were correlated with its ability to modulate the adhesion of thymocytes to thymic epithelial cells and their migration toward extracellular matrix. These findings point to effects of TS that could influence the escape of immature thymocytes in Chagas disease.Fil: Nardy, Ana Flávia F.R.. Universidade Federal do Rio de Janeiro; BrasilFil: Silva Filho, Joao Luiz da. Universidade Federal do Rio de Janeiro; BrasilFil: Perez, Ana Rosa. Universidad Nacional de Rosario. Facultad de Ciencias Médicas. Instituto de Inmunología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Meis, Juliana de. Instituto Oswaldo Cruz; BrasilFil: Farias de Oliveira, Désio Aurélio. Instituto Oswaldo Cruz; BrasilFil: Penha, Luciana. Universidade Federal do Rio de Janeiro; BrasilFil: Oliveira, Isadora de Araújo. Universidade Federal do Rio de Janeiro; BrasilFil: Dias, Wagner B.. Universidade Federal do Rio de Janeiro; BrasilFil: Todeschini, Adriane. Universidade Federal do Rio de Janeiro; BrasilFil: Freire de Lima, Célio Geraldo. Universidade Federal do Rio de Janeiro; BrasilFil: Bellio, Maria. Universidade Federal do Rio de Janeiro; BrasilFil: Caruso Neves, Celso. Universidade Federal do Rio de Janeiro; BrasilFil: Pinheiro, Ana Acácia. Universidade Federal do Rio de Janeiro; BrasilFil: Takiya, Christina Maeda. Universidade Federal do Rio de Janeiro; BrasilFil: Bottasso, Oscar Adelmo. Universidad Nacional de Rosario. Facultad de Ciencias Médicas. Instituto de Inmunología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Savino, Wilson. Instituto Oswaldo Cruz; BrasilFil: Morrot, Alexandre. Universidade Federal do Rio de Janeiro; Brasi

Dilatonic current-carrying cosmic strings

We investigate the nature of ordinary cosmic vortices in some scalar-tensor extensions of gravity. We find solutions for which the dilaton field condenses inside the vortex core. These solutions can be interpreted as raising the degeneracy between the eigenvalues of the effective stress-energy tensor, namely the energy per unit length U and the tension T, by picking a privileged spacelike or timelike coordinate direction; in the latter case, a phase frequency threshold occurs that is similar to what is found in ordinary neutral current-carrying cosmic strings. We find that the dilaton contribution for the equation of state, once averaged along the string worldsheet, vanishes, leading to an effective Nambu-Goto behavior of such a string network in cosmology, i.e. on very large scales. It is found also that on small scales, the energy per unit length and tension depend on the string internal coordinates in such a way as to permit the existence of centrifugally supported equilibrium configuration, also known as vortons, whose stability, depending on the very short distance (unknown) physics, can lead to catastrophic consequences on the evolution of the Universe.Comment: 10 pages, ReVTeX, 2 figures, minor typos corrected. This version to appear in Phys. Rev.

Measurement of the top quark-pair production cross section with ATLAS in pp collisions at \sqrt{s}=7\TeV

A measurement of the production cross-section for top quark pairs(\ttbar) in $pp$ collisions at \sqrt{s}=7 \TeV is presented using data recorded with the ATLAS detector at the Large Hadron Collider. Events are selected in two different topologies: single lepton (electron $e$ or muon $\mu$) with large missing transverse energy and at least four jets, and dilepton ($ee$, $\mu\mu$ or $e\mu$) with large missing transverse energy and at least two jets. In a data sample of 2.9 pb-1, 37 candidate events are observed in the single-lepton topology and 9 events in the dilepton topology. The corresponding expected backgrounds from non-\ttbar Standard Model processes are estimated using data-driven methods and determined to be $12.2 \pm 3.9$ events and $2.5 \pm 0.6$ events, respectively. The kinematic properties of the selected events are consistent with SM \ttbar production. The inclusive top quark pair production cross-section is measured to be \sigmattbar=145 \pm 31 ^{+42}_{-27} pb where the first uncertainty is statistical and the second systematic. The measurement agrees with perturbative QCD calculations.Comment: 30 pages plus author list (50 pages total), 9 figures, 11 tables, CERN-PH number and final journal adde

Inclusive search for same-sign dilepton signatures in pp collisions at root s=7 TeV with the ATLAS detector

An inclusive search is presented for new physics in events with two isolated leptons (e or mu) having the same electric charge. The data are selected from events collected from p p collisions at root s = 7 TeV by the ATLAS detector and correspond to an integrated luminosity of 34 pb(-1). The spectra in dilepton invariant mass, missing transverse momentum and jet multiplicity are presented and compared to Standard Model predictions. In this event sample, no evidence is found for contributions beyond those of the Standard Model. Limits are set on the cross-section in a fiducial region for new sources of same-sign high-mass dilepton events in the ee, e mu and mu mu channels. Four models predicting same-sign dilepton signals are constrained: two descriptions of Majorana neutrinos, a cascade topology similar to supersymmetry or universal extra dimensions, and fourth generation d-type quarks. Assuming a new physics scale of 1 TeV, Majorana neutrinos produced by an effective operator V with masses below 460 GeV are excluded at 95% confidence level. A lower limit of 290 GeV is set at 95% confidence level on the mass of fourth generation d-type quarks

Impact of a Tutored Theoretical-Practical Training to Develop Undergraduate Students’ Skills for the Detection of Caries Lesions: Study Protocol for a Multicenter Controlled Randomized Study

Background: Tutored laboratorial activities could be a manner of improving the competency development of students. However, its impact over conventional theoretical classes has not yet been tested. Additionally, different university contexts could influence this issue and should be explored. Objective: To assess the impact of a tutored theoretical-practical training for teaching undergraduate students to detect caries lesions as compared with theoretical teaching activities. The impact of these teaching/learning activities will be assessed in terms of efficacy, cost/benefit, retention of knowledge/acquired competences, and student acceptability. Methods: Sixteen centers (7 centers from Brazil and 9 centers from other countries throughout the world) are involved in the inclusion of subjects for this protocol. A randomized controlled study with parallel groups will be conducted. One group (control) will be exposed to a 60- to 90-minute conventional theoretical class and the other group (test) will be exposed to the same theoretical class and also a 90-minute laboratory class, including exercises and discussions based on the evaluation of a pool of images and extracted teeth. The mentioned outcomes will be evaluated immediately after the teaching activities and also in medium- and long-term analyses. To compare the long-term outcomes, students who enrolled in the university before the participating students will be interviewed for data collection and these data will be used as a control and compared with the trained group. This stage will be a nonrandomized phase of this study, nested in the main study. Appropriate statistical analysis will be performed according to the aims of this study. Variables related to the centers will also be analyzed and used to model adjustment as possible sources of variability among results. Results: This ongoing study is funded by a Brazilian national funding agency (CNPq- 400736/2014-4). We expect that the tutored theoretical-practical training will improve the undergraduate students’ performance in the detection of caries lesions and subsequent treatment decisions, mainly in terms of long-term retention of knowledge. Our hypothesis is that tutored theoretical-practical training is a more cost-effective option for teaching undergraduate students to detect caries lesions. Conclusions: If our hypothesis is confirmed, the use of laboratory training in conjunction with theoretical classes could be used as an educational strategy in Cariology to improve the development of undergraduate students’ skills in the detection of caries lesions and clinical decision-making

Standalone vertex finding in the ATLAS muon spectrometer

A dedicated reconstruction algorithm to find decay vertices in the ATLAS muon spectrometer is presented. The algorithm searches the region just upstream of or inside the muon spectrometer volume for multi-particle vertices that originate from the decay of particles with long decay paths. The performance of the algorithm is evaluated using both a sample of simulated Higgs boson events, in which the Higgs boson decays to long-lived neutral particles that in turn decay to bbar b final states, and pp collision data at √s = 7 TeV collected with the ATLAS detector at the LHC during 2011

Thermal Density Functional Theory in Context

This chapter introduces thermal density functional theory, starting from the ground-state theory and assuming a background in quantum mechanics and statistical mechanics. We review the foundations of density functional theory (DFT) by illustrating some of its key reformulations. The basics of DFT for thermal ensembles are explained in this context, as are tools useful for analysis and development of approximations. We close by discussing some key ideas relating thermal DFT and the ground state. This review emphasizes thermal DFT's strengths as a consistent and general framework.Comment: Submitted to Spring Verlag as chapter in "Computational Challenges in Warm Dense Matter", F. Graziani et al. ed

Measurement of inclusive two-particle angular correlations in pp collisions with the ATLAS detector at the LHC

We present a measurement of two-particle angular correlations in proton- proton collisions at s√=900 GeV and 7 TeV. The collision events were collected during 2009 and 2010 with the ATLAS detector at the Large Hadron Collider using a single-arm minimum bias trigger. Correlations are measured for charged particles produced in the kinematic range of transverse momentum p T  > 100 MeV and pseudorapidity |η| < 2.5. A complex structure in pseudorapidity and azimuth is observed at both collision energies. Results are compared to pythia 8 and herwig++ as well as to the AMBT2B, DW and Perugia 2011 tunes of pythia 6. The data are not satisfactorily described by any of these models