pinecone/core-2020-05-10-deduplication huggingface dataset:
Reaction-diffusion systems for spatio-temporal intracellular protein networks: a beginner's guide with two examples

International audienceSpatio-temporal dynamics of a variety of proteins is, among other things, regulated by posttranslational modifications of these proteins. Such modifications can thus influence stability and biochemical activities of the proteins, activity and stability of their upstream targets within specific signalling pathways. Commonly used mathematical tools for such protein-protein (and/or protein-mRNA) interactions in single cells, namely, Michaelis-Menten and Hill kinetics, yielding a system of ordinary differential equations, are extended here into (non-linear) partial differential equations by taking into account a more realistic spatial representation of the environment where these reactions occur. In the modelling framework under consideration, all interactions occur in a cell divided into two compartments, the nucleus and the cytoplasm, connected by the semipermeable nuclear membrane and bounded by the impermeable cell membrane. Passive transport mechanism, modelled by the so-called Kedem-Katchalsky boundary conditions, is used here to represent migration of species throughout the nuclear membrane. Nonlinear systems of partial differential equations are solved by the semi-implicit Rothe method. Examples of two spatial oscillators are shown. Namely, these are the circadian rhythm for concentration of the FRQ protein in Neurospora crassa and oscillatory dynamics observed in the activation and regulation of the p53 protein following DNA damage
Search for high-mass resonances decaying to dilepton final states in pp collisions at root s=7 TeV with the ATLAS detector

The ATLAS detector at the Large Hadron Collider is used to search for high-mass resonances decaying to an electron-positron pair or a muon-antimuon pair. The search is sensitive to heavy neutral Z' gauge bosons, Randall-Sundrum gravitons, Z* bosons, techni-mesons, Z/gamma bosons, and bosons predicted by Torsion models. Results are presented based on an analysis of pp collisions at a center-of-mass energy of 7 TeV corresponding to an integrated luminosity of 4.9 fb(-1) in the e(+)e(-) channel and 5.0 fb(-1) in the mu(+)mu(-) channel. A Z' boson with Standard Model-like couplings is excluded at 95% confidence level for masses below 2.22 TeV. A Randall-Sundrum graviton with coupling k root M-P1 = 0.1 is excluded at 95% confidence level for masses below 2.16 Tev. Limits on the other models are also presented, including Technicolor and Minimal Z' Models
Evolution of the upper and lower landing site after endovascular aortic aneurysm repair.

International audienceBACKGROUND: The evolution and correlation between the aortic neck and distally located iliac necks after endovascular treatment of abdominal aortic aneurysms (AAAs) was studied. METHODS: Of 179 patients who had undergone AAA repair between 2003 and 2007, 61 received the same radiologic follow-up and were included in this retrospective study. Data for 61 aortic necks and 115 iliac arteries were analyzed using the preoperative scan, 1-month visit, and final follow-up, with a minimum mean follow-up of 24 ± 15.2 months. Three measurements were taken of the aortic neck: subrenal (D1a), 15 mm below the lowest renal artery (D1b), and at the origin of the aneurysm (D1c). Three measurements were taken at the level of the iliac arteries: origin (Da), middle (Db), and the iliac bifurcation (Dc). These measurements were analyzed using analysis of variance and Spearman correlation coefficient. The results were evaluated for subsequent endoleaks, migrations, and reinterventions. All diameters were compared between patients with a regression of >10% in the greatest diameter of AAA at last follow-up (group A, n = 35) and those without (group B, n = 26). RESULTS: All diameters (in mm) increased significantly over time at the level of the proximal neck (D1a = 3.7 ± 2.8, P = .018; D1b = 4.4 ± 2.5, P = .016; D1c = 4.3 ± 3.1, P = .036) and iliac arteries (Da = 2.1 ± 0.2, P = .0006; Db = 2.5 ± 0.5, P = .0006; Dc = 3 ± 0.7, P = .007). The increase in diameters at the proximal neck and iliac arteries evolved independently (insignificant correlation), with the exception of D1b and Dc (P = .006), which showed a weak correlation (r = 0.363). The group A patients presented increases in all diameters, although to a less significant extent (P < .05) than group B patients. During follow-up, a proximal endoleak and a distal endoleak occurred, both requiring reintervention. CONCLUSIONS: Our results show a trend toward dilatation of the aortic neck and iliac arteries, with no correlation between the two levels, even in patients with a regression of the aneurysm sac during follow-up. Although this study found no correlation with the occurrence of endoleaks, our results suggest the need for a longer follow-up, especially on the landing sites
A transformation-driven approach to generate a DSML verification framework

International audienceThe integration of formal verification methods in modeling ac- tivities is a key issue to ensure the correctness of complex system design models. In this purpose, the most common approach consists in defining a translational semantics mapping the abstract syntax of the designer dedi- cated Domain-Specific Modeling Language (DSML) to a formal verification dedicated semantic domain in order to reuse the available powerful verifica- tion technologies. Formal verification is thus usually achieved using model transformations. However, the verification results are available in the formal domain which significantly impairs their use by the system designer which is usually not an expert of the formal technologies. In this paper, we introduce a novel approach based on Higher-Order trans- formations that analyze and instrument the transformation that expresses the semantics in order to produce traceability data to automatize the back propagation of verification results to the DSML end-user
Vibration measurement-based simple technique for damage detection of truss bridges: A case study.

(C) 2015 The Author. Published by Elsevier Ltd in Case Studies in Engineering Failure Analysis, vol. 4. This is an open access article under the CC
BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).The bridges experience increasing traffic volume and weight, deteriorating of components
and large number of stress cycles. Therefore, assessment of the current condition of steel
railway bridges becomes necessary. Most of the commonly available approaches for
structural health monitoring are based on visual inspection and non-destructive testing
methods. The visual inspection is unreliable as those depend on uncertainty behind
inspectors and their experience. Also, the non-destructive testing methods are found to be
expensive. Therefore, recent researches have noticed that dynamic modal parameters or
vibration measurement-based structural health monitoring methods are economical and
may also provide more realistic predictions to damage state of civil infrastructure.
Therefore this paper proposes a simple technique to locate the damage region of railway
truss bridges based on measured modal parameters. The technique is discussed with a case
study. Initially paper describes the details of considered railway bridge. Then observations
of visual inspection, material testing and in situ load testing are discussed under separate
sections. Development of validated finite element model of the considered bridge is
comprehensively discussed. Hence, variations of modal parameters versus position of the
damage are plotted. These plots are considered as the main reference for locating the
damage of the railway bridge in future periodical inspection by comparing the measured
corresponding modal parameters. Finally the procedure of periodical vibration measure-
ment and damage locating technique are clearly illustrated
$N^3$ entropy of M5 branes from dielectric effect

We observe that the $N^3$ entropy behavior of near-extermal M5 branes can be
reproduced from SYM side with the role of Myers' terms. We start by
generalizing the Klebanov-Tseytlin (KT) supergravity solution that displays the
$N^3$ entropy behavior. The new feature of the general solution is visibility
of the "internal" degrees of the M5 branes, i.e., the M0 branes and the M2
branes. With the rationale provided by the supergravity analysis, we consider a
D0 brane quantum mechanical setup with Myers' terms. Using localization
technique, we show that the leading $N^3$ behavior of the free energy comes
from the "classical contribution" with the rest sub-leading.Comment: latex, 21 pages, missing figure adde
Electron paramagnetic resonance characterization of tetrahydrobiopterin radical formation in bacterial nitric oxide synthase compared to mammalian nitric oxide synthase.

International audienceH(4)B is an essential catalytic cofactor of the mNOSs. It acts as an electron donor and activates the ferrous heme-oxygen complex intermediate during Arg oxidation (first step) and NOHA oxidation (second step) leading to nitric oxide and citrulline as final products. However, its role as a proton donor is still debated. Furthermore, its exact involvement has never been explored for other NOSs such as NOS-like proteins from bacteria. This article proposes a comparative study of the role of H(4)B between iNOS and bsNOS. In this work, we have used freeze-quench to stop the arginine and NOHA oxidation reactions and trap reaction intermediates. We have characterized these intermediates using multifrequency electron paramagnetic resonance. For the first time, to our knowledge, we report a radical formation for a nonmammalian NOS. The results indicate that bsNOS, like iNOS, has the capacity to generate a pterin radical during Arg oxidation. Our current electron paramagnetic resonance data suggest that this radical is protonated indicating that H(4)B may not transfer any proton. In the 2nd step, the radical trapped for iNOS is also suggested to be protonated as in the 1st step, whereas it was not possible to trap a radical for the bsNOS 2nd step. Our data highlight potential differences for the catalytic mechanism of NOHA oxidation between mammalian and bacterial NOSs
Differential asteroseismic study of seismic twins observed by            CoRoT

International audienceContext. The CoRoT short asteroseismic runs give us the opportunity to          observe a large variety of late-type stars through their solar-like oscillations. We          report the observation and modeling of the F5V star HD 175272.Aims. Our aim is to define a method for extracting as much information          as possible from a noisy oscillation spectrum. Methods. We followed a differential approach that consists of using a          well-known star as a reference to characterize another star. We used classical tools such          as the envelope autocorrelation function to derive the global seismic parameters of the          star. We compared HD 175272 with HD 181420 through a linear approach, because they appear          to be asteroseismic twins.Results. The comparison with the reference star enables us to          substantially enhance the scientific output for HD 175272. First, we determined its global          characteristics through a detailed seismic analysis of HD 181420. Second, with our          differential approach, we measured the difference of mass, radius and age between          HD 175272 and HD 181420.Conclusions. We have developed a general method able to derive          asteroseismic constraints on a star even in case of low-quality data. This method can be          applied to stars with interesting properties but low signal-to-noise ratio oscillation          spectrum, such as stars hosting an exoplanet or members of a binary system
A preconditioning approach to the pagerank\ud
computation problem

Some spectral properties of the transition matrix of an oriented graph indicate the preconditioning of Euler-Richardson (ER) iterative scheme as a good way to compute efficiently the vertexrank vector associated with such graph. We choose the preconditioner from an algebra U of matrices, thereby obtaining an ERU method, and we observe that ERU can outperform ER in terms of rate of convergence. The proposed preconditioner can be updated at a very low cost whenever the graph changs, as is the case when it represents a generic set of information. The particular U utilized requires a surplus of operations per step and memory allocations, which make ERU superior to ER for not too wide graphs. However , the observed high improvement in convergence rate obtained by preconditining and the general theory developed, are a reason for investigating different choices of U, more efficient for huge graphs
Optimal networks for mass transportation problems

In the framework of transport theory, we are interested in the following optimization problem: given the distributions mu(+) of working people and mu(-) of their working places in an urban area, build a transportation network (such as a railway or an underground system) which minimizes a functional depending on the geometry of the network through a particular cost function. The functional is defined as the Wasserstein distance of mu(+) from mu(-) with respect to a metric which depends on the transportation network
Measurement of the high-mass Drell--Yan differential cross-section in pp collisions at sqrt(s)=7 TeV with the ATLAS detector

This Letter reports a measurement of the high-mass Drell–Yan differential cross-section in proton–proton collisions at a centre-of-mass energy of 7 TeV at the LHC. Based on an integrated luminosity of 4.9 fb−1, the differential cross-section in the Z/γ⁎→e+e− channel is measured with the ATLAS detector as a function of the invariant mass, mee, in the range 116<mee<1500 GeV, for a fiducial region in which both the electron and the positron have transverse momentum pT>25 GeV and pseudorapidity |η|<2.5. A comparison is made to various event generators and to the predictions of perturbative QCD calculations at next-to-next-to-leading order.We acknowledge the support of ANPCyT, Argentina; YerPhI, Armenia; ARC, Australia; BMWF and FWF, Austria; ANAS, Azerbaijan; SSTC, Belarus; CNPq and FAPESP, Brazil; NSERC, NRC and CFI, Canada; CERN; CONICYT, Chile; CAS, MOST and NSFC, China; COLCIENCIAS, Colombia; MSMT CR, MPO CR and VSC CR, Czech Republic; DNRF, DNSRC and Lundbeck Foundation, Denmark; EPLANET, ERC and NSRF, European Union; IN2P3-CNRS, CEA-DSM/IRFU, France; GNSF, Georgia; BMBF, DFG, HGF, MPG and AvH Foundation, Germany; GSRT and NSRF, Greece; ISF, MINERVA, GIF, DIP and Benoziyo Center, Israel; INFN, Italy; MEXT and JSPS, Japan; CNRST, Morocco; FOM and NWO, Netherlands; BRF and RCN, Norway; MNiSW, Poland; GRICES and FCT, Portugal; MERYS (MECTS), Romania; MES of Russia and ROSATOM, Russian Federation; JINR; MSTD, Serbia; MSSR, Slovakia; ARRS and MIZS, Slovenia; DST/NRF, South Africa; MICINN, Spain; SRC and Wallenberg Foundation, Sweden; SER, SNSF and Cantons of Bern and Geneva, Switzerland; NSC, Taiwan; TAEK, Turkey; STFC, the Royal Society and Leverhulme Trust, United Kingdom; DOE and NSF, United States of America
Search for s-channel single top-quark production in proton-proton collisions at s√=8 TeV with the ATLAS detector

This Letter presents a search at the LHC for s-channel single top-quark production in proton-proton collisions at a centre-of-mass energy of 8 TeV. The analyzed data set was recorded by the ATLAS detector and corresponds to an integrated luminosity of 20.3 fb−1. Selected events contain one charged lepton, large missing transverse momentum and exactly two b-tagged jets. A multivariate event classifier based on boosted decision trees is developed to discriminate s-channel single top-quark events from the main background contributions. The signal extraction is based on a binned maximum-likelihood fit of the output classifier distribution. The analysis leads to an upper limit on the s-channel single top-quark production cross-section of 14.6 pb at the 95% confidence level. The fit gives a cross-section of σs=5.0±4.3 pb, consistent with the Standard Model expectation.We acknowledge the support of ANPCyT, Argentina; YerPhI, Armenia; ARC, Australia; BMWFW and FWF, Austria; ANAS, Azerbaijan; SSTC, Belarus; CNPq and FAPESP, Brazil; NSERC, NRC and CFI, Canada; CERN; CONICYT, Chile; CAS, MOST and NSFC, China; COLCIENCIAS, Colombia; MSMT CR, MPO CR and VSC CR, Czech Republic; DNRF, DNSRC and Lundbeck Foundation, Denmark; EPLANET, ERC and NSRF, European Union; IN2P3-CNRS, CEA-DSM/IRFU, France; GNSF, Georgia; BMBF, DFG, HGF, MPG and AvH Foundation, Germany; GSRT and NSRF, Greece; ISF, MINERVA, GIF, I-CORE and Benoziyo Center, Israel; INFN, Italy; MEXT and JSPS, Japan; CNRST, Morocco; FOM and NWO, Netherlands; BRF and RCN, Norway; MNiSW and NCN, Poland; GRICES and FCT, Portugal; MNE/IFA, Romania; MES of Russia and ROSATOM, Russian Federation; JINR; MSTD, Serbia; MSSR, Slovakia; ARRS and MIZS, Slovenia; DST/NRF, South Africa; MINECO, Spain; SRC and Wallenberg Foundation, Sweden; SER, SNSF and Cantons of Bern and Geneva, Switzerland; NSC, Taiwan; TAEK, Turkey; STFC, the Royal Society and Leverhulme Trust, United Kingdom; DOE and NSF, United States of America
HALOGAS : H I observations and modeling of the nearby edge-on spiral galaxy NGC 4565

We present 21 cm observations and models of the neutral hydrogen in NGC 4565, a nearby, edge-on spiral galaxy, as part of the Westerbork Hydrogen Accretion in LOcal GAlaxieS survey. These models provide insight concerning both the morphology and kinematics of Hi above, as well as within, the disk. NGC 4565 exhibits a distinctly warped and asymmetric disk with a flaring layer. Our modeling provides no evidence for a massive, extended Hi halo. We see evidence for a bar and associated radial motions. Additionally, there are indications of radial motions within the disk, possibly associated with a ring of higher density. We see a substantial decrease in rotational velocity with height above the plane of the disk (a lag) of -40(-20)(+5) km s(-1) kpc(-1) and -30(-30)(+5) km s(-1) kpc(-1) in the approaching and receding halves, respectively. This lag is only seen within the inner similar to 4'.75 (14.9 kpc) on the approaching half and similar to 4'.25 (13.4 kpc) on the receding half, making this a radially shallowing lag, which is now seen in the Hi layers of several galaxies. When comparing results for NGC 4565 and those for other galaxies, there are tentative indications of high star formation rate per unit area being associated with the presence of a halo. Finally, Hi is found in two companion galaxies, one of which is clearly interacting with NGC 4565
Dietary inorganic nitrate : role in exercise physiology, cardiovascular and metabolic regulation

Nitric oxide (NO) is a ubiquitous signaling molecule with a vast number of tasks in the body, including regulation of cardiovascular and metabolic function. A decreased bioavailability of NO is a central event in disorders such as hypertension and metabolic syndrome. NO is also important in the regulation of blood flow and metabolism during exercise. The production of NO has previously been thought to be under the exclusive control of the nitric oxide synthases (NOS) but this view is now being seriously challenged. Recent lines of research suggest the existence of an NO-synthase independent pathway in which the supposedly inert NO oxidation products nitrate (NO3-) and nitrite (NO2-) can be reduced back to NO in blood and tissues. An important additional source of nitrate is our everyday diet and certain vegetables are particularly rich in this anion. In this thesis the possibility that dietary derived nitrate is metabolized in vivo to form reactive nitrogen oxides with NO-like bioactivity has been explored.
It is shown that nitrate in amounts easily achieved via the diet, increases the systemic levels of nitrite and reduces blood pressure in healthy humans. Moreover, nitrate reduces whole body oxygen cost during submaximal and maximal exercise; a surprising effect involving improvement in mitochondrial efficiency and reduced expression of specific mitochondrial proteins regulating proton conductance. Alterations in the mitochondrial affinity for oxygen can explain this reduction in both submaximal and maximal oxygen consumption and predicts basal metabolic rate in humans. Finally, in mice lacking endothelial NO synthase, dietary supplementation with nitrate could reverse several features of the metabolic syndrome that develop in these animals. These studies demonstrate that dietary nitrate can fuel a nitrate-nitrite-NO pathway with important implications for cardiovascular and metabolic functions in health and disease
Entropy of Reissner-Nordstr\"om-de Sitter black hole

Based on the consideration that the black hole horizon and the cosmological
horizon of Reissner-Nordstr\"om black hole in de Sitter space are not
independent each other, we conjecture the total entropy of the system should
have an extra term contributed from the entanglement between the two horizons,
except for the sum of the two horizon entropies. Making use of the globally
effective first law and the effective thermodynamic quantities, we derive the
total entropy and find that it will diverge as the two horizons tends to
coincide.Comment: 3 pages, 2 figures. In the published version, there are some errors
  in the equations (13-15). We correct them in this version. The conclusion is
  not affecte
Mirror Symmetry for $G_2$-Manifolds: Twisted Connected Sums and Dual
  Tops

Recently, at least 50 million of novel examples of compact $G_2$ holonomy
manifolds have been constructed as twisted connected sums of asymptotically
cylindrical Calabi-Yau threefolds. The purpose of this paper is to study mirror
symmetry for compactifications of Type II superstrings in this context. We
focus on $G_2$ manifolds obtained from building blocks constructed from dual
pairs of tops, which are the closest to toric CY hypersurfaces, and formulate
the analogue of the Batyrev mirror map for this class of $G_2$ holonomy
manifolds, thus obtaining several millions of novel dual superstring
backgrounds. In particular, this leads us to conjecture a plethora of novel
exact dualities among the corresponding 2d N=1 sigma models.Comment: 34 pages, comments welcom
Access to financial services: The case of the 'Mzansi' account in South Africa

© 2015 Africagrowth Institute. Production and hosting by Elsevier B.V. All rights reserved. The presence of rationing of financial services in the developing countries is a major obstacle to achieving sustainable growth. In recent years there have been co-ordinated efforts to increase the level of financial inclusion, i.e. to reduce the supply-side constraints restricting access to finance. This paper aims to understand household's latent behaviour decision making in accessing financial services, by analysing an entry level Mzansi account in South Africa. The willingness to access financial services is not taken as given, but it is instead defined by perceptions and attitudes. The Mzansi intervention is appealing to individuals with basic but insufficient financial education. Aspirations seem to be very influential in revealing the choice of financial services and to this end, Mzansi is perceived as a pre-entry account not meeting the aspirations of individuals aiming to climb up the financial services ladder