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Showing papers by "Federal University of Rio de Janeiro published in 2012"


Journal ArticleDOI
Georges Aad1, T. Abajyan2, Brad Abbott3, Jalal Abdallah4  +2964 moreInstitutions (200)
TL;DR: In this article, a search for the Standard Model Higgs boson in proton-proton collisions with the ATLAS detector at the LHC is presented, which has a significance of 5.9 standard deviations, corresponding to a background fluctuation probability of 1.7×10−9.

9,282 citations


Journal ArticleDOI
TL;DR: These guidelines are presented for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes.
Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.

4,316 citations


Journal ArticleDOI
TL;DR: In this paper, the authors presented the first spectroscopic data from the Baryon Oscillation Spectroscopic Survey (BOSS) for the Sloan Digital Sky Survey III (SDSS-III) dataset.
Abstract: The Sloan Digital Sky Survey III (SDSS-III) presents the first spectroscopic data from the Baryon Oscillation Spectroscopic Survey (BOSS). This ninth data release (DR9) of the SDSS project includes 535,995 new galaxy spectra (median z ~ 0.52), 102,100 new quasar spectra (median z ~ 2.32), and 90,897 new stellar spectra, along with the data presented in previous data releases. These spectra were obtained with the new BOSS spectrograph and were taken between 2009 December and 2011 July. In addition, the stellar parameters pipeline, which determines radial velocities, surface temperatures, surface gravities, and metallicities of stars, has been updated and refined with improvements in temperature estimates for stars with T eff -0.5. DR9 includes new stellar parameters for all stars presented in DR8, including stars from SDSS-I and II, as well as those observed as part of the SEGUE-2. The astrometry error introduced in the DR8 imaging catalogs has been corrected in the DR9 data products. The next data release for SDSS-III will be in Summer 2013, which will present the first data from the APOGEE along with another year of data from BOSS, followed by the final SDSS-III data release in 2014 December.

1,623 citations


Journal ArticleDOI
20 Dec 2012-Nature
TL;DR: It is shown that an abrupt five- to sixfold ploidy increase approximately 60 million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1–2 Myr ago, conferred about 30–36-fold duplication of ancestral angiosperm genes in elite cottons, genetic complexity equalled only by Brassica among sequenced angiosperms.
Abstract: Polyploidy often confers emergent properties, such as the higher fibre productivity and quality of tetraploid cottons than diploid cottons bred for the same environments. Here we show that an abrupt five- to sixfold ploidy increase approximately 60 million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1-2 Myr ago, conferred about 30-36-fold duplication of ancestral angiosperm (flowering plant) genes in elite cottons (Gossypium hirsutum and Gossypium barbadense), genetic complexity equalled only by Brassica among sequenced angiosperms. Nascent fibre evolution, before allopolyploidy, is elucidated by comparison of spinnable-fibred Gossypium herbaceum A and non-spinnable Gossypium longicalyx F genomes to one another and the outgroup D genome of non-spinnable Gossypium raimondii. The sequence of a G. hirsutum A(t)D(t) (in which 't' indicates tetraploid) cultivar reveals many non-reciprocal DNA exchanges between subgenomes that may have contributed to phenotypic innovation and/or other emergent properties such as ecological adaptation by polyploids. Most DNA-level novelty in G. hirsutum recombines alleles from the D-genome progenitor native to its New World habitat and the Old World A-genome progenitor in which spinnable fibre evolved. Coordinated expression changes in proximal groups of functionally distinct genes, including a nuclear mitochondrial DNA block, may account for clusters of cotton-fibre quantitative trait loci affecting diverse traits. Opportunities abound for dissecting emergent properties of other polyploids, particularly angiosperms, by comparison to diploid progenitors and outgroups.

1,015 citations


Journal ArticleDOI
TL;DR: PrEP using oral FTC-TDF tablets is a robust intervention for preventing HIV acquisition among men who have sex with men, and specific drug concentrations associated with protection from HIV-1 acquisition in the iPrEx trial are estimated.
Abstract: Drug concentrations associated with protection from HIV-1 acquisition have not been determined. We evaluated drug concentrations among men who have sex with men in a substudy of the iPrEx trial (1). In this randomized placebo-controlled trial, daily oral doses of emtricitabine/tenofovir disoproxil fumarate were used as pre-exposure prophylaxis (PrEP) in men who have sex with men. Drug was detected less frequently in blood plasma and in viable cryopreserved peripheral blood mononuclear cells (PBMCs) in HIV-infected cases at the visit when HIV was first discovered compared with controls at the matched time point of the study (8% versus 44%; P < 0.001) and in the 90 days before that visit (11% versus 51%; P < 0.001). An intracellular concentration of the active form of tenofovir, tenofovir-diphosphate (TFV-DP), of 16 fmol per million PBMCs was associated with a 90% reduction in HIV acquisition relative to the placebo arm. Directly observed dosing in a separate study, the STRAND trial, yielded TFV-DP concentrations that, when analyzed according to the iPrEx model, corresponded to an HIV-1 risk reduction of 76% for two doses per week, 96% for four doses per week, and 99% for seven doses per week. Prophylactic benefits were observed over a range of doses and drug concentrations, suggesting ways to optimize PrEP regimens for this population.

800 citations


Journal ArticleDOI
TL;DR: It is shown that serine phosphorylation of IRS-1 (IRS-1pSer) is common to both diseases, and establishes molecular links between the dysregulated insulin signaling in AD and diabetes.
Abstract: Defective brain insulin signaling has been suggested to contribute to the cognitive deficits in patients with Alzheimer's disease (AD). Although a connection between AD and diabetes has been suggested, a major unknown is the mechanism(s) by which insulin resistance in the brain arises in individuals with AD. Here, we show that serine phosphorylation of IRS-1 (IRS-1pSer) is common to both diseases. Brain tissue from humans with AD had elevated levels of IRS-1pSer and activated JNK, analogous to what occurs in peripheral tissue in patients with diabetes. We found that amyloid-β peptide (Aβ) oligomers, synaptotoxins that accumulate in the brains of AD patients, activated the JNK/TNF-α pathway, induced IRS-1 phosphorylation at multiple serine residues, and inhibited physiological IRS-1pTyr in mature cultured hippocampal neurons. Impaired IRS-1 signaling was also present in the hippocampi of Tg mice with a brain condition that models AD. Importantly, intracerebroventricular injection of Aβ oligomers triggered hippocampal IRS-1pSer and JNK activation in cynomolgus monkeys. The oligomer-induced neuronal pathologies observed in vitro, including impaired axonal transport, were prevented by exposure to exendin-4 (exenatide), an anti-diabetes agent. In Tg mice, exendin-4 decreased levels of hippocampal IRS-1pSer and activated JNK and improved behavioral measures of cognition. By establishing molecular links between the dysregulated insulin signaling in AD and diabetes, our results open avenues for the investigation of new therapeutics in AD.

712 citations


Journal ArticleDOI
TL;DR: This article showed that the percentage of the total phytoplankton biovolume attributable to cyanobacteria increases steeply with temperature, indicating a synergistic effect of nutrients and climate.
Abstract: Dominance by cyanobacteria hampers human use of lakes and reservoirs worldwide. Previous studies indicate that excessive nutrient loading and warmer conditions promote dominance by cyanobacteria, but evidence from global scale field data has so far been scarce. Our analysis, based on a study of 143 lakes along a latitudinal transect ranging from subarctic Europe to southern South America, shows that although warmer climates do not result in higher overall phytoplankton biomass, the percentage of the total phytoplankton biovolume attributable to cyanobacteria increases steeply with temperature. Our results also reveal that the percent cyanobacteria is greater in lakes with high rates of light absorption. This points to a positive feedback because restriction of light availability is often a consequence of high phytoplankton biovolume, which in turn may be driven by nutrient loading. Our results indicate a synergistic effect of nutrients and climate. The implications are that in a future warmer climate, nutrient concentrations may have to be reduced substantially from present values in many lakes if cyanobacterial dominance is to be controlled.

674 citations


Journal ArticleDOI
TL;DR: This study provides Class II evidence that 20 mg tafamidis QD was associated with no difference in clinical progression in patients with TTR-FAP, as measured by the NIS-LL and the Norfolk QOL-DN score, supporting the hypothesis that preventing TTR dissociation can delay peripheral neurologic impairment.
Abstract: Objectives: To evaluate the efficacy and safety of 18 months of tafamidis treatment in patients with early-stage V30M transthyretin familial amyloid polyneuropathy (TTR-FAP). Methods: In this rando ...

626 citations


Journal ArticleDOI
TL;DR: These two phase 3 studies show the efficacy and safety of canakinumab in systemic JIA with active systemic features, and among the 100 patients who underwent randomization in the withdrawal phase, the risk of flare was lower among patients who continued to receive canakinUMab than among those who were switched to placebo.
Abstract: A B S T R AC T BACKGROUND Interleukin-1 is pivotal in the pathogenesis of systemic juvenile idiopathic arthritis (JIA). We assessed the efficacy and safety of canakinumab, a selective, fully human, anti–interleukin-1β monoclonal antibody, in two trials. METHODS In trial 1, we randomly assigned patients, 2 to 19 years of age, with systemic JIA and active systemic features (fever; ≥2 active joints; C-reactive protein, >30 mg per liter; and glucocorticoid dose, ≤1.0 mg per kilogram of body weight per day), in a double-blind fashion, to a single subcutaneous dose of canakinumab (4 mg per kilo gram) or placebo. The primary outcome, termed adapted JIA ACR 30 response, was defined as improvement of 30% or more in at least three of the six core criteria for JIA, worsening of more than 30% in no more than one of the criteria, and resolution of fever. In trial 2, after 32 weeks of open-label treatment with canakinumab, pa tients who had a response and underwent glucocorticoid tapering were randomly assigned to continued treatment with canakinumab or to placebo. The primary outcome was time to flare of systemic JIA. RESULTS At day 15 in trial 1, more patients in the canakinumab group had an adapted JIA ACR 30 response (36 of 43 [84%], vs. 4 of 41 [10%] in the placebo group; P<0.001). In trial 2, among the 100 patients (of 177 in the open-label phase) who underwent randomization in the withdrawal phase, the risk of flare was lower among patients who continued to receive canakinumab than among those who were switched to pla cebo (74% of patients in the canakinumab group had no flare, vs. 25% in the pla

611 citations


Journal ArticleDOI
TL;DR: It is shown that the requirements for obtaining secure keys are much easier to meet than for DI-QKD, which opens promising experimental opportunities and clarifies the link between the security of this one-sided DI- QKD scenario and the demonstration of quantum steering, in analogy to the links between DI-ZKD and the violation of Bell inequalities.
Abstract: We analyze the security and feasibility of a protocol for quantum key distribution (QKD) in a context where only one of the two parties trusts his measurement apparatus. This scenario lies naturally between standard QKD, where both parties trust their measurement apparatuses, and device-independent QKD (DI-QKD), where neither do, and can be a natural assumption in some practical situations. We show that the requirements for obtaining secure keys are much easier to meet than for DI-QKD, which opens promising experimental opportunities. We clarify the link between the security of this one-sided DI-QKD scenario and the demonstration of quantum steering, in analogy to the link between DI-QKD and the violation of Bell inequalities.

610 citations


Journal ArticleDOI
Georges Aad1, Brad Abbott2, Jalal Abdallah3, S. Abdel Khalek  +3081 moreInstitutions (197)
TL;DR: A combined search for the Standard Model Higgs boson with the ATLAS experiment at the LHC using datasets corresponding to integrated luminosities from 1.04 fb(-1) to 4.9 fb(1) of pp collisions is described in this paper.

Journal ArticleDOI
Georges Aad, B. Abbott1, Jalal Abdallah2, A. A. Abdelalim3  +3013 moreInstitutions (174)
TL;DR: In this article, detailed measurements of the electron performance of the ATLAS detector at the LHC were reported, using decays of the Z, W and J/psi particles.
Abstract: Detailed measurements of the electron performance of the ATLAS detector at the LHC are reported, using decays of the Z, W and J/psi particles. Data collected in 2010 at root s = 7 TeV are used, corresponding to an integrated luminosity of almost 40 pb(-1). The inter-alignment of the inner detector and the electromagnetic calorimeter, the determination of the electron energy scale and resolution, and the performance in terms of response uniformity and linearity are discussed. The electron identification, reconstruction and trigger efficiencies, as well as the charge misidentification probability, are also presented.

Journal ArticleDOI
TL;DR: The results indicate the need for improving pre-employment strategies to select the most resilient individuals for rescue work, to implement continuous preventive measures for personnel, and to promote educational campaigns about PTSD and its therapeutic possibilities.
Abstract: Purpose We sought to estimate the pooled current prevalence of posttraumatic stress disorder (PTSD) among rescue workers and to determine the variables implicated in the heterogeneity observed among the prevalences of individual studies.

Journal ArticleDOI
TL;DR: In combination with commercial antimicrobials, ciprofloxacin plus (+)-a-pinene or (+)-β- pinene presented synergistic activity against MRSA whereas an indifferent effect against all fungi was detected when amphotericin B was combined with the positive enantiomers of pinene.
Abstract: The antimicrobial activities of the isomers and enantiomers of pinene were evaluated against bacterial and fungal cells. The agar diffusion test showed that only the positive enantiomers of the a- and β-isomers of pinene were active. The minimal inhibitory concentration (MIC) and minimal microbicidal concentration (MMC) of these monoterpenes were also determined, confirming that the positive enantiomers exhibited microbicidal activity against all fungi and bacteria tested with MICs ranging from 117 to 4,150 µg/mL. However, no antimicrobial activity was detected with the negative enantiomers up to 20 mg/mL. Time-kill curves showed that (+)-a-pinene and (+)-β-pinene were highly toxic to Candida albicans, killing 100% of inoculum within 60 min. By contrast, the bactericidal effect occurred after 6 h in methicillin-resistant Staphylococcus aureus (MRSA). In combination with commercial antimicrobials, ciprofloxacin plus (+)-a-pinene or (+)-β-pinene presented synergistic activity against MRSA whereas an indifferent effect against all fungi was detected when amphotericin B was combined with the positive enantiomers of pinene. The potential of (+)-a-pinene and (+)-β-pinene to inhibit phospholipase and esterase activities was also evaluated, and the best inhibition results were obtained with Cryptococcus neoformans. C. albicans biofilm formation was prevented with the MIC concentration of (+)-a-pinene and twice the MIC value of (+)-β-pinene. Finally, the cytotoxicity of the positive enantiomers of pinene to murine macrophages was evaluated, and 250 µg/mL of (+)-a-pinene and (+)-β-pinene reduced the cell viability to 66.8% and 57.7%, respectively.

Journal ArticleDOI
TL;DR: It is argued that the human brain is a scaled-up primate brain in its cellular composition and metabolic cost, with a relatively enlarged cerebral cortex that does not have a relatively larger number of brain neurons yet is remarkable in its cognitive abilities and metabolism simply because of its extremely large number of neurons.
Abstract: Neuroscientists have become used to a number of “facts” about the human brain: It has 100 billion neurons and 10- to 50-fold more glial cells; it is the largest-than-expected for its body among primates and mammals in general, and therefore the most cognitively able; it consumes an outstanding 20% of the total body energy budget despite representing only 2% of body mass because of an increased metabolic need of its neurons; and it is endowed with an overdeveloped cerebral cortex, the largest compared with brain size These facts led to the widespread notion that the human brain is literally extraordinary: an outlier among mammalian brains, defying evolutionary rules that apply to other species, with a uniqueness seemingly necessary to justify the superior cognitive abilities of humans over mammals with even larger brains These facts, with deep implications for neurophysiology and evolutionary biology, are not grounded on solid evidence or sound assumptions, however Our recent development of a method that allows rapid and reliable quantification of the numbers of cells that compose the whole brain has provided a means to verify these facts Here, I review this recent evidence and argue that, with 86 billion neurons and just as many nonneuronal cells, the human brain is a scaled-up primate brain in its cellular composition and metabolic cost, with a relatively enlarged cerebral cortex that does not have a relatively larger number of brain neurons yet is remarkable in its cognitive abilities and metabolism simply because of its extremely large number of neurons

Journal ArticleDOI
TL;DR: How the fine structural characteristics of glycosaminoglycans, and enzymes involved in their biosynthesis and degradation, are involved in cell signaling, cell function and cancer progression is summarized.
Abstract: Glycosaminoglycans are natural heteropolysaccharides that are present in every mammalian tissue. They are composed of repeating disaccharide units that consist of either sulfated or non-sulfated monosaccharides. Their molecular size and the sulfation type vary depending on the tissue, and their state either as part of proteoglycan or as free chains. In this regard, glycosaminoglycans play important roles in physiological and pathological conditions. During recent years, cell biology studies have revealed that glycosaminoglycans are among the key macromolecules that affect cell properties and functions, acting directly on cell receptors or via interactions with growth factors. The accumulated knowledge regarding the altered structure of glycosaminoglycans in several diseases indicates their importance as biomarkers for disease diagnosis and progression, as well as pharmacological targets. This review summarizes how the fine structural characteristics of glycosaminoglycans, and enzymes involved in their biosynthesis and degradation, are involved in cell signaling, cell function and cancer progression. Prospects for glycosaminoglycan-based therapeutic targeting in cancer are also discussed.

Journal ArticleDOI
TL;DR: The North American Regional Climate Change Assessment Program (NARCCAP) is an international effort designed to investigate the uncertainties in regional-scale projections of future climate and produce highresolution climate change scenarios using multiple regional climate models (RCMs) nested within atmosphere-ocean general circulation models (AOGCMs) forced with the Special Report on Emission Scenarios (SRES) A2 scenario, with a common domain covering the conterminous United States, northern Mexico, and most of Canada as discussed by the authors.
Abstract: The North American Regional Climate Change Assessment Program (NARCCAP) is an international effort designed to investigate the uncertainties in regional-scale projections of future climate and produce highresolution climate change scenarios using multiple regional climate models (RCMs) nested within atmosphere–ocean general circulation models (AOGCMs) forced with the Special Report on Emission Scenarios (SRES) A2 scenario, with a common domain covering the conterminous United States, northern Mexico, and most of Canada. The program also includes an evaluation component (phase I) wherein the participating RCMs, with a grid spacing of 50 km, are nested within 25 years of National Centers for Environmental Prediction–Department of Energy (NCEP–DOE) Reanalysis II. This paper provides an overview of evaluations of the phase I domain-wide simulations focusing on monthly and seasonal temperature and precipitation, as well as more detailed investigation of four subregions. The overall quality of the simulations i...

Journal ArticleDOI
TL;DR: In this article, the authors measured the Milky Way rotation curve over the Galactocentric range 4 kpc R 14 kpc from the first year of data from the Apache Point Observatory Galactic Evolution Experiment.
Abstract: We measure the Milky Way's rotation curve over the Galactocentric range 4 kpc R 14 kpc from the first year of data from the Apache Point Observatory Galactic Evolution Experiment. We model the line-of-sight velocities of 3365 stars in 14 fields with b = 0? between 30? ? l ? 210? out to distances of 10 kpc using an axisymmetric kinematical model that includes a correction for the asymmetric drift of the warm tracer population (? R 35 km s?1). We determine the local value of the circular velocity to be Vc (R 0) = 218 ? 6 km s?1 and find that the rotation curve is approximately flat with a local derivative between ?3.0 km s?1 kpc?1 and 0.4 km s?1 kpc?1. We also measure the Sun's position and velocity in the Galactocentric rest frame, finding the distance to the Galactic center to be 8 kpc 99 % confidence. We find an offset between the Sun's rotational velocity and the local circular velocity of 26 ? 3 km s?1, which is larger than the locally measured solar motion of 12 km s?1. This larger offset reconciles our value for Vc with recent claims that Vc 240 km s?1. Combining our results with other data, we find that the Milky Way's dark-halo mass within the virial radius is ~8 ? 1011 M ?.

Journal ArticleDOI
Georges Aad1, Brad Abbott2, J. Abdallah3, S. Abdel Khalek4  +3073 moreInstitutions (193)
TL;DR: In this paper, a Fourier analysis of the charged particle pair distribution in relative azimuthal angle (Delta phi = phi(a)-phi(b)) is performed to extract the coefficients v(n,n) =.
Abstract: Differential measurements of charged particle azimuthal anisotropy are presented for lead-lead collisions at root sNN = 2.76 TeV with the ATLAS detector at the LHC, based on an integrated luminosity of approximately 8 mu b(-1). This anisotropy is characterized via a Fourier expansion of the distribution of charged particles in azimuthal angle relative to the reaction plane, with the coefficients v(n) denoting the magnitude of the anisotropy. Significant v(2)-v(6) values are obtained as a function of transverse momentum (0.5 = 3 are found to vary weakly with both eta and centrality, and their p(T) dependencies are found to follow an approximate scaling relation, v(n)(1/n)(p(T)) proportional to v(2)(1/2)(p(T)), except in the top 5% most central collisions. A Fourier analysis of the charged particle pair distribution in relative azimuthal angle (Delta phi = phi(a)-phi(b)) is performed to extract the coefficients v(n,n) = . For pairs of charged particles with a large pseudorapidity gap (|Delta eta = eta(a) - eta(b)| > 2) and one particle with p(T) < 3 GeV, the v(2,2)-v(6,6) values are found to factorize as v(n,n)(p(T)(a), p(T)(b)) approximate to v(n) (p(T)(a))v(n)(p(T)(b)) in central and midcentral events. Such factorization suggests that these values of v(2,2)-v(6,6) are primarily attributable to the response of the created matter to the fluctuations in the geometry of the initial state. A detailed study shows that the v(1,1)(p(T)(a), p(T)(b)) data are consistent with the combined contributions from a rapidity-even v(1) and global momentum conservation. A two-component fit is used to extract the v(1) contribution. The extracted v(1) isobserved to cross zero at pT approximate to 1.0 GeV, reaches a maximum at 4-5 GeV with a value comparable to that for v(3), and decreases at higher p(T).

Journal ArticleDOI
01 Feb 2012-Energy
TL;DR: In this article, the authors present a review of the impacts that climate change may have throughout the energy chain and identify current knowledge gaps and areas for future research development, concluding that one of the greatest challenges is how to assess impacts which may occur as a consequence of the projected increase in the intensity of extreme weather events.

Journal ArticleDOI
Georges Aad1, Georges Aad2, Brad Abbott1, Brad Abbott3  +5592 moreInstitutions (189)
TL;DR: The ATLAS trigger system as discussed by the authors selects events by rapidly identifying signatures of muon, electron, photon, tau lepton, jet, and B meson candidates, as well as using global event signatures, such as missing transverse energy.
Abstract: Proton-proton collisions at root s = 7 TeV and heavy ion collisions at root(NN)-N-s = 2.76 TeV were produced by the LHC and recorded using the ATLAS experiment's trigger system in 2010. The LHC is designed with a maximum bunch crossing rate of 40 MHz and the ATLAS trigger system is designed to record approximately 200 of these per second. The trigger system selects events by rapidly identifying signatures of muon, electron, photon, tau lepton, jet, and B meson candidates, as well as using global event signatures, such as missing transverse energy. An overview of the ATLAS trigger system, the evolution of the system during 2010 and the performance of the trigger system components and selections based on the 2010 collision data are shown. A brief outline of plans for the trigger system in 2011 is presented.

Journal ArticleDOI
TL;DR: Empirical TMFs are likely to be useful for understanding the food web biomagnification potential of chemicals, but may be less useful in species- and site-specific risk assessments, where the goal is to predict absolute contaminant concentrations in organisms in relation to threshold levels.
Abstract: Recent reviews by researchers from academia, industry, and government have revealed that the criteria used by the Stockholm Convention on persistent organic pollutants under the United Nations Environment Programme are not always able to identify the actual bioaccumulative capacity of some substances, by use of chemical properties such as the octanol–water partitioning coefficient. Trophic magnification factors (TMFs) were suggested as a more reliable tool for bioaccumulation assessment of chemicals that have been in commerce long enough to be quantitatively measured in environmental samples. TMFs are increasingly used to quantify biomagnification and represent the average diet-to-consumer transfer of a chemical through food webs. They differ from biomagnification factors, which apply to individual species and can be highly variable between predator–prey combinations. The TMF is calculated from the slope of a regression between the chemical concentration and trophic level of organisms in the food web. The trophic level can be determined from stable N isotope ratios (δ15N). In this article, we give the background for the development of TMFs, identify and discuss impacts of ecosystem and ecological variables on their values, and discuss challenges and uncertainties associated with contaminant measurements and the use of δ15N for trophic level estimations. Recommendations are provided for experimental design, data treatment, and statistical analyses, including advice for users on reporting and interpreting TMF data. Interspecies intrinsic ecological and organismal properties such as thermoregulation, reproductive status, migration, and age, particularly among species at higher trophic levels with high contaminant concentrations, can influence the TMF (i.e., regression slope). Following recommendations herein for study design, empirical TMFs are likely to be useful for understanding the food web biomagnification potential of chemicals, where the target is to definitively identify if chemicals biomagnify (i.e., TMF > or < 1). TMFs may be less useful in species- and site-specific risk assessments, where the goal is to predict absolute contaminant concentrations in organisms in relation to threshold levels. Integr Environ Assess Manag 2012;8:64–84. © 2011 SETAC

Journal ArticleDOI
TL;DR: In this paper, Andrieu et al. show that a fully adapted auxiliary particle filter is unbiased and can drastically decrease computing time compared to a standard particle filter, and introduce a new estimator of the likelihood based on the output of the auxiliary particle filters.

Journal ArticleDOI
TL;DR: It is found that infection of epithelial cells with Shigella and Salmonella triggers acute intracellular amino acid (AA) starvation due to host membrane damage, and AA starvation induced by bacterial pathogens is sensed by the host to trigger protective innate immune and stress responses.

Journal ArticleDOI
TL;DR: A review examines the commonalities in this growing subgroup of Burkholderia species and discusses their prospective biotechnological applications.
Abstract: The genus Burkholderia comprises more than 60 species isolated from a wide range of niches. Although they have been shown to be diverse and ubiquitously distributed, most studies have thus far focused on the pathogenic species due to their clinical importance. However, the increasing number of recently described Burkholderia species associated with plants or with the environment has highlighted the division of the genus into two main clusters, as suggested by phylogenetical analyses. The first cluster includes human, animal, and plant pathogens, such as Burkholderia glumae, Burkholderia pseudomallei, and Burkholderia mallei, as well as the 17 defined species of the Burkholderia cepacia complex, while the other, more recently established cluster comprises more than 30 non-pathogenic species, which in most cases have been found to be associated with plants, and thus might be considered to be potentially beneficial. Several species from the latter group share characteristics that are of use when associating with plants, such as a quorum sensing system, the presence of nitrogen fixation and/or nodulation genes, and the ability to degrade aromatic compounds. This review examines the commonalities in this growing subgroup of Burkholderia species and discusses their prospective biotechnological applications.

Journal ArticleDOI
TL;DR: This work tunes the BR pathway response to establish how plant cells can generate functionally different cellular outputs in response to MAMPs and pathogens, and proposes that tradeoffs associated with plasticity in the face of infection are layered atop plant steroid developmental programs.
Abstract: Metazoans and plants use pattern recognition receptors (PRRs) to sense conserved microbial-associated molecular patterns (MAMPs) in the extracellular environment. In plants, the bacterial MAMPs flagellin and elongation factor Tu (EF-Tu) activate distinct, phylogenetically related cell surface pattern recognition receptors of the leucine-rich repeat receptor kinase (LRR-RK) family called FLS2 and EF-Tu receptor, respectively. BAK1 is an LRR-RK coreceptor for both FLS2 and EF-Tu receptor. BAK1 is also a coreceptor for the plant brassinosteroid (BR) receptor, the LRR-RK BRI1. Binding of BR to BRI1 primarily promotes cell elongation. Here, we tune the BR pathway response to establish how plant cells can generate functionally different cellular outputs in response to MAMPs and pathogens. We demonstrate that BR can act antagonistically or synergistically with responses to MAMPs. We further show that the synergistic activities of BRs on MAMP responses require BAK1. Our results highlight the importance of plant steroid homeostasis as a critical step in the establishment of plant immunity. We propose that tradeoffs associated with plasticity in the face of infection are layered atop plant steroid developmental programs.

Journal ArticleDOI
TL;DR: In this paper, the authors studied the self-healing potential of cement-based materials incorporating calcium sulfoaluminate based expansive additive (CSA) and crystalline additive (CA).
Abstract: This research studies the self-healing potential of cement-based materials incorporating calcium sulfoaluminate based expansive additive (CSA) and crystalline additive (CA). Mortar specimens were used throughout the study. At the age of 28 days, specimens were pre-cracked to introduce a surface crack width of between 100 and 400 μm. Thereafter, the specimens were submerged in water to create a self-healing process. The experimental results indicated that the mixtures with CSA and CA showed favorable surface crack closing ability. The optimal mix design was found to be a ternary blend of Portland cement, 10 wt.% CSA and 1.5 wt.% CA, by which a surface crack width up to about 400 μm was completely closed, and the rate of water passing was dropped to zero within 28 days. It was hypothesized that the amount of leached Ca 2+ from the matrix plays an important role on the precipitation of calcium carbonate which is the major healing product. The analyses showed that those specimens with CSA/CA additions released more Ca 2+ than that control specimen. Moreover, those specimens with additives had higher pH value which would favor calcium carbonate precipitation.

Journal ArticleDOI
Georges Aad1, Georges Aad2, Brad Abbott1, Brad Abbott3  +5559 moreInstitutions (188)
TL;DR: In this paper, the performance of the missing transverse momentum reconstruction was evaluated using data collected in pp collisions at a centre-of-mass energy of 7 TeV in 2010.
Abstract: The measurement of missing transverse momentum in the ATLAS detector, described in this paper, makes use of the full event reconstruction and a calibration based on reconstructed physics objects. The performance of the missing transverse momentum reconstruction is evaluated using data collected in pp collisions at a centre-of-mass energy of 7 TeV in 2010. Minimum bias events and events with jets of hadrons are used from data samples corresponding to an integrated luminosity of about 0.3 nb(-1) and 600 nb(-1) respectively, together with events containing a Z boson decaying to two leptons (electrons or muons) or a W boson decaying to a lepton (electron or muon) and a neutrino, from a data sample corresponding to an integrated luminosity of about 36 pb(-1). An estimate of the systematic uncertainty on the missing transverse momentum scale is presented.

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TL;DR: In this paper, the authors demonstrate the feasibility of alignment-free quantum key distribution and perform proof-of-principle demonstrations of alignment free entanglement distribution and Bell-inequality violation.
Abstract: Quantum communication employs the counter-intuitive features of quantum physics for tasks that are impossible in the classical world. It is crucial for testing the foundations of quantum theory and promises to revolutionize information and communication technologies. However, to execute even the simplest quantum transmission, one must establish, and maintain, a shared reference frame. This introduces a considerable overhead in resources, particularly if the parties are in motion or rotating relative to each other. Here we experimentally show how to circumvent this problem with the transmission of quantum information encoded in rotationally invariant states of single photons. By developing a complete toolbox for the efficient encoding and decoding of quantum information in such photonic qubits, we demonstrate the feasibility of alignment-free quantum key-distribution, and perform proof-of-principle demonstrations of alignment-free entanglement distribution and Bell-inequality violation. The scheme should find applications in fundamental tests of quantum mechanics and satellite-based quantum communication.

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TL;DR: In this paper, the use of two groups of solid acid catalysts (sulfated oxides and zeolites with different pore structures) in the esterification of levulinc acid with ethanol aiming for ethyl levulinate production was explored.
Abstract: Levulinic acid is considered as a versatile building block because it can be used for the synthesis of several organic chemicals. In particular, its esterification with ethanol produces ethyl levulinate that can be used as diesel miscible biofuel (DMB), preventing global warming by decreasing atmospheric CO2 generated from the consumption of fossil fuels. This article explores the use of two groups of solid acid catalysts (sulfated oxides and zeolites with different pore structures) in the esterification of levulinc acid with ethanol aiming for ethyl levulinate production. It was found that while there is a correlation between the number of acidic sites and activity for the sulfated oxides, the same is not true for the studied zeolites where the pore channels play a more important role. Among the catalysts tested, Amberlyst-15 and sulfated SnO2 showed a remarkable high yield of ethyl levulinate that was probably due to the strong acidity provided by SO3H functional groups and SO4 species, respectively.