Showing papers by "Roma Tre University published in 2016"

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

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. For example, 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 versus those that measure flux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase 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. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. 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. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagy-related protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. 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 assays, we hope to encourage technical innovation in the field.

Neutrino Physics with JUNO

Abstract: The Jiangmen Underground Neutrino Observatory (JUNO), a 20 kton multi-purpose underground liquid scintillator detector, was proposed with the determination of the neutrino mass hierarchy (MH) as a primary physics goal. The excellent energy resolution and the large fiducial volume anticipated for the JUNO detector offer exciting opportunities for addressing many important topics in neutrino and astro-particle physics. In this document, we present the physics motivations and the anticipated performance of the JUNO detector for various proposed measurements. Following an introduction summarizing the current status and open issues in neutrino physics, we discuss how the detection of antineutrinos generated by a cluster of nuclear power plants allows the determination of the neutrino MH at a 3–4σ significance with six years of running of JUNO. The measurement of antineutrino spectrum with excellent energy resolution will also lead to the precise determination of the neutrino oscillation parameters ${\mathrm{sin}}^{2}{\theta }_{12}$, ${\rm{\Delta }}{m}_{21}^{2}$, and $| {\rm{\Delta }}{m}_{{ee}}^{2}| $ to an accuracy of better than 1%, which will play a crucial role in the future unitarity test of the MNSP matrix. The JUNO detector is capable of observing not only antineutrinos from the power plants, but also neutrinos/antineutrinos from terrestrial and extra-terrestrial sources, including supernova burst neutrinos, diffuse supernova neutrino background, geoneutrinos, atmospheric neutrinos, and solar neutrinos. As a result of JUNO's large size, excellent energy resolution, and vertex reconstruction capability, interesting new data on these topics can be collected. For example, a neutrino burst from a typical core-collapse supernova at a distance of 10 kpc would lead to ∼5000 inverse-beta-decay events and ∼2000 all-flavor neutrino–proton ES events in JUNO, which are of crucial importance for understanding the mechanism of supernova explosion and for exploring novel phenomena such as collective neutrino oscillations. Detection of neutrinos from all past core-collapse supernova explosions in the visible universe with JUNO would further provide valuable information on the cosmic star-formation rate and the average core-collapse neutrino energy spectrum. Antineutrinos originating from the radioactive decay of uranium and thorium in the Earth can be detected in JUNO with a rate of ∼400 events per year, significantly improving the statistics of existing geoneutrino event samples. Atmospheric neutrino events collected in JUNO can provide independent inputs for determining the MH and the octant of the ${\theta }_{23}$ mixing angle. Detection of the (7)Be and (8)B solar neutrino events at JUNO would shed new light on the solar metallicity problem and examine the transition region between the vacuum and matter dominated neutrino oscillations. Regarding light sterile neutrino topics, sterile neutrinos with ${10}^{-5}\,{{\rm{eV}}}^{2}\lt {\rm{\Delta }}{m}_{41}^{2}\lt {10}^{-2}\,{{\rm{eV}}}^{2}$ and a sufficiently large mixing angle ${\theta }_{14}$ could be identified through a precise measurement of the reactor antineutrino energy spectrum. Meanwhile, JUNO can also provide us excellent opportunities to test the eV-scale sterile neutrino hypothesis, using either the radioactive neutrino sources or a cyclotron-produced neutrino beam. The JUNO detector is also sensitive to several other beyondthe-standard-model physics. Examples include the search for proton decay via the $p\to {K}^{+}+\bar{ u }$ decay channel, search for neutrinos resulting from dark-matter annihilation in the Sun, search for violation of Lorentz invariance via the sidereal modulation of the reactor neutrino event rate, and search for the effects of non-standard interactions. The proposed construction of the JUNO detector will provide a unique facility to address many outstanding crucial questions in particle and astrophysics in a timely and cost-effective fashion. It holds the great potential for further advancing our quest to understanding the fundamental properties of neutrinos, one of the building blocks of our Universe.

Water: A Tale of Two Liquids

Abstract: Water is the most abundant liquid on earth and also the substance with the largest number of anomalies in its properties. It is a prerequisite for life and as such a most important subject of current research in chemical physics and physical chemistry. In spite of its simplicity as a liquid, it has an enormously rich phase diagram where different types of ices, amorphous phases, and anomalies disclose a path that points to unique thermodynamics of its supercooled liquid state that still hides many unraveled secrets. In this review we describe the behavior of water in the regime from ambient conditions to the deeply supercooled region. The review describes simulations and experiments on this anomalous liquid. Several scenarios have been proposed to explain the anomalous properties that become strongly enhanced in the supercooled region. Among those, the second critical-point scenario has been investigated extensively, and at present most experimental evidence point to this scenario. Starting from very low ...

Muon reconstruction performance of the ATLAS detector in proton–proton collision data at √ s =13 TeV

Abstract: This article documents the performance of the ATLAS muon identification and reconstruction using the first LHC dataset recorded at s√ = 13 TeV in 2015. Using a large sample of J/ψ→μμ and Z→μμ decays from 3.2 fb−1 of pp collision data, measurements of the reconstruction efficiency, as well as of the momentum scale and resolution, are presented and compared to Monte Carlo simulations. The reconstruction efficiency is measured to be close to 99% over most of the covered phase space (|η| 2.2, the pT resolution for muons from Z→μμ decays is 2.9% while the precision of the momentum scale for low-pT muons from J/ψ→μμ decays is about 0.2%.

Performance of $b$-Jet Identification in the ATLAS Experiment

Abstract: The identification of jets containing b hadrons is important for the physics programme of the ATLAS experiment at the Large Hadron Collider. Several algorithms to identify jets containing b hadrons are described, ranging from those based on the reconstruction of an inclusive secondary vertex or the presence of tracks with large impact parameters to combined tagging algorithms making use of multi-variate discriminants. An independent b-tagging algorithm based on the reconstruction of muons inside jets as well as the b-tagging algorithm used in the online trigger are also presented. The b-jet tagging efficiency, the c-jet tagging efficiency and the mistag rate for light flavour jets in data have been measured with a number of complementary methods. The calibration results are presented as scale factors defined as the ratio of the efficiency (or mistag rate) in data to that in simulation. In the case of b jets, where more than one calibration method exists, the results from the various analyses have been combined taking into account the statistical correlation as well as the correlation of the sources of systematic uncertainty.

Large deformations of planar extensible beams and pantographic lattices: Heuristic homogenization, experimental and numerical examples of equilibrium

Abstract: The aim of this paper is to find a computationally efficient and predictive model for the class of systems that we call ‘pantographic structures’. The interest in these materials was increased by the possibilities opened by the diffusion of technology of three-dimensional printing. They can be regarded, once choosing a suitable length scale, as families of beams (also called fibres) interconnected to each other by pivots and undergoing large displacements and large deformations. There are, however, relatively few ‘ready-to-use’ results in the literature of nonlinear beam theory. In this paper, we consider a discrete spring model for extensible beams and propose a heuristic homogenization technique of the kind first used by Piola to formulate a continuum fully nonlinear beam model. The homogenized energy which we obtain has some peculiar and interesting features which we start to describe by solving numerically some exemplary deformation problems. Furthermore, we consider pantographic structures, find the corresponding homogenized second gradient deformation energies and study some planar problems. Numerical solutions for these two-dimensional problems are obtained via minimization of energy and are compared with some experimental measurements, in which elongation phenomena cannot be neglected.

Performance of pile-up mitigation techniques for jets in pp collisions at √s = 8 TeV using the ATLAS detector

Abstract: The large rate of multiple simultaneous protonproton interactions, or pile-up, generated by the Large Hadron Collider in Run 1 required the development of many new techniques to mitigate the advers ...

Luminosity determination in pp collisions at √s = 8 TeV using the ATLAS detector at the LHC

Abstract: The luminosity determination for the ATLAS detector at the LHC during pp collisions at s√= 8 TeV in 2012 is presented. The evaluation of the luminosity scale is performed using several luminometers ...

Observation of Long-Range Elliptic Azimuthal Anisotropies in s =13 and 2.76 TeV pp Collisions with the ATLAS Detector

Abstract: ATLAS has measured two-particle correlations as a function of relative azimuthal-angle, $\Delta \phi$, and pseudorapidity, $\Delta \eta$, in $\sqrt{s}$=13 and 2.76 TeV $pp$ collisions at the LHC using charged particles measured in the pseudorapidity interval $|\eta|$<2.5. The correlation functions evaluated in different intervals of measured charged-particle multiplicity show a multiplicity-dependent enhancement at $\Delta \phi \sim 0$ that extends over a wide range of $\Delta\eta$, which has been referred to as the "ridge". Per-trigger-particle yields, $Y(\Delta \phi)$, are measured over 2<$|\Delta\eta|$<5. For both collision energies, the $Y(\Delta \phi)$ distribution in all multiplicity intervals is found to be consistent with a linear combination of the per-trigger-particle yields measured in collisions with less than 20 reconstructed tracks, and a constant combinatoric contribution modulated by $\cos{(2\Delta \phi)}$. The fitted Fourier coefficient, $v_{2,2}$, exhibits factorization, suggesting that the ridge results from per-event $\cos{(2\phi)}$ modulation of the single-particle distribution with Fourier coefficients $v_2$. The $v_2$ values are presented as a function of multiplicity and transverse momentum. They are found to be approximately constant as a function of multiplicity and to have a $p_{\mathrm{T}}$ dependence similar to that measured in $p$+Pb and Pb+Pb collisions. The $v_2$ values in the 13 and 2.76 TeV data are consistent within uncertainties. These results suggest that the ridge in $pp$ collisions arises from the same or similar underlying physics as observed in $p$+Pb collisions, and that the dynamics responsible for the ridge has no strong $\sqrt{s}$ dependence.

Search for an additional, heavy Higgs boson in the H → ZZ decay channel at √s = 8 TeV in pp collision data with the ATLAS detector

Abstract: A search is presented for a high-mass Higgs boson in the , , , and decay modes using the ATLAS detector at the CERN Large Hadron Collider. The search uses proton-proton collision data at a centre-of-mass energy of 8 TeV corresponding to an integrated luminosity of 20.3 fb. The results of the search are interpreted in the scenario of a heavy Higgs boson with a width that is small compared with the experimental mass resolution. The Higgs boson mass range considered extends up to for all four decay modes and down to as low as 140 , depending on the decay mode. No significant excess of events over the Standard Model prediction is found. A simultaneous fit to the four decay modes yields upper limits on the production cross-section of a heavy Higgs boson times the branching ratio to boson pairs. 95 % confidence level upper limits range from 0.53 pb at GeV to 0.008 pb at GeV for the gluon-fusion production mode and from 0.31 pb at GeV to 0.009 pb at GeV for the vector-boson-fusion production mode. The results are also interpreted in the context of Type-I and Type-II two-Higgs-doublet models.

Measurement of the inelastic proton-proton cross section at √s=13 TeV with the ATLAS detector at the LHC

Abstract: This Letter presents a measurement of the inelastic proton-proton cross section using 60 μb^{-1} of pp collisions at a center-of-mass energy sqrt[s] of 13 TeV with the ATLAS detector at the LHC. Inelastic interactions are selected using rings of plastic scintillators in the forward region (2.07 10^{-6}, where M_{X} is the larger invariant mass of the two hadronic systems separated by the largest rapidity gap in the event. In this ξ range the scintillators are highly efficient. For diffractive events this corresponds to cases where at least one proton dissociates to a system with M_{X}>13 GeV. The measured cross section is compared with a range of theoretical predictions. When extrapolated to the full phase space, a cross section of 78.1±2.9 mb is measured, consistent with the inelastic cross section increasing with center-of-mass energy.

Environmental, social and governance disclosure, integrated reporting, and the accuracy of analyst forecasts ☆

Abstract: The International Integrated Reporting Council advocates that integrated reporting (IR) should become the worldwide norm for corporate reporting aimed at serving the needs of investors. Nonetheless, only in South Africa has IR been mandated. We study the impact of the reporting regime change in South Africa on analyst forecast accuracy over the period 2008 to 2012, as a way of evaluating users’ perceptions of the usefulness of IR. We theorise that any effects of IR will be greater the greater is the level of disclosures of environmental, social and governance performance. We find results consistent with those who support IR and our theory that the level of environmental, social and governance disclosures is a mediating variable in determining the effectiveness of IR. The results are driven by the levels of environmental disclosure and, to a lesser extent, governance disclosure. Our results provide some support for those who advocate the virtues of integrated reporting.

XIPE: the x-ray imaging polarimetry explorer

Abstract: XIPE, the X-ray Imaging Polarimetry Explorer, is a mission dedicated to X-ray Astronomy. At the time of writing XIPE is in a competitive phase A as fourth medium size mission of ESA (M4). It promises to reopen the polarimetry window in high energy Astrophysics after more than 4 decades thanks to a detector that efficiently exploits the photoelectric effect and to X-ray optics with large effective area. XIPE uniqueness is time-spectrally-spatially- resolved X-ray polarimetry as a breakthrough in high energy astrophysics and fundamental physics. Indeed the payload consists of three Gas Pixel Detectors at the focus of three X-ray optics with a total effective area larger than one XMM mirror but with a low weight. The payload is compatible with the fairing of the Vega launcher. XIPE is designed as an observatory for X-ray astronomers with 75 % of the time dedicated to a Guest Observer competitive program and it is organized as a consortium across Europe with main contributions from Italy, Germany, Spain, United Kingdom, Poland, Sweden.

Photonic Maxwell's Demon

Abstract: We report an experimental realization of Maxwell's demon in a photonic setup. We show that a measurement at the few-photons level followed by a feed-forward operation allows the extraction of work from intense thermal light into an electric circuit. The interpretation of the experiment stimulates the derivation of an equality relating work extraction to information acquired by measurement. We derive a bound using this relation and show that it is in agreement with the experimental results. Our work puts forward photonic systems as a platform for experiments related to information in thermodynamics.

Clostridium difficile Toxins A and B: Insights into Pathogenic Properties and Extraintestinal Effects

Abstract: Clostridium difficile infection (CDI) has significant clinical impact especially on the elderly and/or immunocompromised patients. The pathogenicity of Clostridium difficile is mainly mediated by two exotoxins: toxin A (TcdA) and toxin B (TcdB). These toxins primarily disrupt the cytoskeletal structure and the tight junctions of target cells causing cell rounding and ultimately cell death. Detectable C. difficile toxemia is strongly associated with fulminant disease. However, besides the well-known intestinal damage, recent animal and in vitro studies have suggested a more far-reaching role for these toxins activity including cardiac, renal, and neurologic impairment. The creation of C. difficile strains with mutations in the genes encoding toxin A and B indicate that toxin B plays a major role in overall CDI pathogenesis. Novel insights, such as the role of a regulator protein (TcdE) on toxin production and binding interactions between albumin and C. difficile toxins, have recently been discovered and will be described. Our review focuses on the toxin-mediated pathogenic processes of CDI with an emphasis on recent studies.

Role of Iron Uptake Systems in Pseudomonas aeruginosa Virulence and Airway Infection

Abstract: Pseudomonas aeruginosa is a leading cause of hospital-acquired pneumonia and chronic lung infections in cystic fibrosis patients. Iron is essential for bacterial growth, and P. aeruginosa expresses multiple iron uptake systems, whose role in lung infection deserves further investigation. P. aeruginosa Fe(3+) uptake systems include the pyoverdine and pyochelin siderophores and two systems for heme uptake, all of which are dependent on the TonB energy transducer. P. aeruginosa also has the FeoB transporter for Fe(2+) acquisition. To assess the roles of individual iron uptake systems in P. aeruginosa lung infection, single and double deletion mutants were generated in P. aeruginosa PAO1 and characterized in vitro, using iron-poor media and human serum, and in vivo, using a mouse model of lung infection. The iron uptake-null mutant (tonB1 feoB) and the Fe(3+) transport mutant (tonB1) did not grow aerobically under low-iron conditions and were avirulent in the mouse model. Conversely, the wild type and the feoB, hasR phuR (heme uptake), and pchD (pyochelin) mutants grew in vitro and caused 60 to 90% mortality in mice. The pyoverdine mutant (pvdA) and the siderophore-null mutant (pvdA pchD) grew aerobically in iron-poor media but not in human serum, and they caused low mortality in mice (10 to 20%). To differentiate the roles of pyoverdine in iron uptake and virulence regulation, a pvdA fpvR double mutant defective in pyoverdine production but expressing wild-type levels of pyoverdine-regulated virulence factors was generated. Deletion of fpvR in the pvdA background partially restored the lethal phenotype, indicating that pyoverdine contributes to the pathogenesis of P. aeruginosa lung infection by combining iron transport and virulence-inducing capabilities.

Measurement of the transverse momentum and phi(eta)*. distributions of Drell-Yan lepton pairs in proton-proton collisions at root s=8 TeV with the ATLAS detector

Abstract: Distributions of transverse momentum [Formula: see text] and the related angular variable [Formula: see text] of DrellΓCoYan lepton pairs are measured in 20.3┬afb[Formula: see text] of protonΓCoproton collisions at [Formula: see text]┬aTeV with the ATLAS detector at the LHC. Measurements in electron-pair and muon-pair final states are corrected for detector effects and combined. Compared to previous measurements in protonΓCoproton collisions at [Formula: see text]┬aTeV, these new measurements benefit from a larger data sample and improved control of systematic uncertainties. Measurements are performed in bins of lepton-pair mass above, around and below the Z-boson mass peak. The data are compared to predictions from perturbative and resummed QCD calculations. For values of [Formula: see text] the predictions from the Monte Carlo generator ResBos are generally consistent with the data within the theoretical uncertainties. However, at larger values of [Formula: see text] this is not the case. Monte Carlo generators based on the parton-shower approach are unable to describe the data over the full range of [Formula: see text] while the fixed-order prediction of Dynnlo falls below the data at high values of [Formula: see text]. ResBos and the parton-shower Monte Carlo generators provide a much better description of the evolution of the [Formula: see text] and [Formula: see text] distributions as a function of lepton-pair mass and rapidity than the basic shape of the data.

Search for supersymmetry at √s= 13 TeV in final states with jets and two same-sign leptons or three leptons with the ATLAS detector

Abstract: A search for strongly produced supersymmetric particles is conducted using signatures involving multiple energetic jets and either two isolated leptons (e or μ) with the same electric charge or at ...

Magmas near the critical degassing pressure drive volcanic unrest towards a critical state

Abstract: During the reawaking of a volcano, magmas migrating through the shallow crust have to pass through hydrothermal fluids and rocks. The resulting magma-hydrothermal interactions are still poorly understood, which impairs the ability to interpret volcano monitoring signals and perform hazard assessments. Here we use the results of physical and volatile saturation models to demonstrate that magmatic volatiles released by decompressing magmas at a critical degassing pressure (CDP) can drive volcanic unrest towards a critical state. We show that, at the CDP, the abrupt and voluminous release of H2O-rich magmatic gases can heat hydrothermal fluids and rocks, triggering an accelerating deformation that can ultimately culminate in rock failure and eruption. We propose that magma could be approaching the CDP at Campi Flegrei, a volcano in the metropolitan area of Naples, one of the most densely inhabited areas in the world, and where accelerating deformation and heating are currently being observed.

Search for resonances in diphoton events at √s=13 TeV with the ATLAS detector

Abstract: Searches for new resonances decaying into two photons in the ATLAS experiment at the CERN Large Hadron Collider are described. The analysis is based on protonproton collision data corresponding to ...

Lactoferrin from Milk: Nutraceutical and Pharmacological Properties.

Abstract: Lactoferrin is an iron-binding protein present in large quantities in colostrum and in breast milk, in external secretions and in polymorphonuclear leukocytes. Lactoferrin’s main function is non-immune protection. Among several protective activities shown by lactoferrin, those displayed by orally administered lactoferrin are: (i) antimicrobial activity, which has been presumed due to iron deprivation, but more recently attributed also to a specific interaction with the bacterial cell wall and extended to viruses and parasites; (ii) immunomodulatory activity, with a direct effect on the development of the immune system in the newborn, together with a specific antinflammatory effects; (iii) a more recently discovered anticancer activity. It is worth noting that most of the protective activities of lactoferrin have been found, sometimes to a greater extent, also in peptides derived from limited proteolysis of lactoferrin that could be generated after lactoferrin ingestion. Lactoferrin could therefore be considered an ideal nutraceutic product because of its relatively cheap production from bovine milk and of its widely recognized tolerance after ingestion, along with its well demonstrated protective activities. The most important protective activities shown by orally administered bovine lactoferrin are reviewed in this article.