pinecone/core-2020-05-10-deduplication huggingface dataset:
A theoretical multiscale treatment of protein-protein electron transfer: the ferredoxin/ferredoxin-NADP+ reductase and flavodoxin/ferredoxin-NADP+ reductase systems

In the photosynthetic electron transfer (ET) chain, two electrons transfer from photosystem I to the flavin-\ud
dependent ferredoxin-NADP+ reductase (FNR) via two sequential independent ferredoxin (Fd) electron carriers.\ud
In some algae and cyanobacteria (as Anabaena), under low iron conditions, flavodoxin (Fld) replaces Fd as single electron carrier. Extensive mutational studies have characterized the protein–protein interaction in FNR/Fd and\ud
FNR/Fldcomplexes.Interestingly,eventhoughFd and Fldsharethe interaction site on FNR,individual residueson FNR do not participate to the same extent in the interaction with each of the protein partners, pointing to different electron transfer mechanisms. Despite of extensive mutational studies, only FNR/Fd X-ray structures from Anabaena and maize have been solved; structural data for FNR/Fld remains elusive. Here, we present a multiscale modelling approach including coarse-grained and all-atom protein–protein docking, the QM/MM e-Pathway analysis and electronic coupling calculations, allowing for a molecular and electronic comprehensive analysis of the ET process in both complexes. Our results, consistent with experimental mutational data, reveal the ET in FNR/Fd proceeding through a bridge-mediated mechanism in a dominant protein–protein complex, where transfer of the electron is facilitated by Fd loop-residues 40–\ud
49. In FNR/Fld, however, we observe a direct transfer between redox cofactors and less complex specificity than in Fd; more than one orientation in the encounter complex can be efficient in ET.Work was supported by computational time from the Barcelona Supercomputer Center and funds from theSpanishMinistry ofEconomy\ud
and Competitiveness through the projects CTQ2013-48287 (to V.G.) and BIO2013-42978-P (to M.M.) and a Beatriu de Pinos grant BP-B-00252 from the Catalan Government (to S.S.).Peer ReviewedPostprint (author's final draft
Last millennium northern hemisphere summer temperatures from tree rings: Part I: The long term context

Large-scale millennial length Northern Hemisphere (NH) temperature reconstructions have been progressively improved over the last 20 years as new datasets have been developed. This paper, and its companion (Part II, Anchukaitis et al. in prep), details the latest tree-ring (TR) based NH land air temperature reconstruction from a temporal and spatial perspective. This work is the first product of a consortium called N-TREND (Northern Hemisphere Tree-Ring Network Development) which brings together dendroclimatologists to identify a collective strategy for improving large-scale summer temperature reconstructions. The new reconstruction, N-TREND2015, utilises 54 records, a significant expansion compared with previous TR studies, and yields an improved reconstruction with stronger statistical calibration metrics. N-TREND2015 is relatively insensitive to the compositing method and spatial weighting used and validation metrics indicate that the new record portrays reasonable coherence with large scale summer temperatures and is robust at all time-scales from 918 to 2004 where at least 3 TR records exist from each major continental mass. N-TREND2015 indicates a longer and warmer medieval period (∼900–1170) than portrayed by previous TR NH reconstructions and by the CMIP5 model ensemble, but with better overall agreement between records for the last 600 years. Future dendroclimatic projects should focus on developing new long records from data-sparse regions such as North America and eastern Eurasia as well as ensuring the measurement of parameters related to latewood density to complement ring-width records which can improve local based calibration substantially
Is it pleasure or health from leisure that we benefit from most?:An analysis of well-being alternatives and implications for policy

International policy now constantly advocates a need for populations to engage in more physical activity to promote health and to reduce society’s health care costs. Such policy has developed guidelines on recommended levels and intensity of physical activity and implicitly equates health with well-being. It is assumed that individual, and hence social welfare will be enhanced if the activity guidelines are met. This paper challenges that claim and raises questions for public policy priorities. Using an instrumental variable analysis to value the well-being from active leisure, it is shown that the well-being experienced from active leisure that is not of a recommended intensity to generate health benefits, perhaps due to its social, recreational or fun purpose, has a higher value of well-being than active leisure that does meet the guidelines. This suggests rethinking the motivation and foundation of existing policy and perhaps a realignment of priorities towards activity that has a greater contribution to social welfare through its intrinsic fun and possibly social interaction
Non-homogeneous random walks on a semi-infinite strip.

We study the asymptotic behaviour of Markov chains (Xn,ηn) on Z+×S, where Z+ is the non-negative integers and S is a finite set. Neither coordinate is assumed to be Markov. We assume a moments bound on the jumps of Xn, and that, roughly speaking, ηn is close to being Markov when Xn is large. This departure from much of the literature, which assumes that ηn is itself a Markov chain, enables us to probe precisely the recurrence phase transitions by assuming asymptotically zero drift for Xn given ηn. We give a recurrence classification in terms of increment moment parameters for Xn and the stationary distribution for the large- X limit of ηn. In the null case we also provide a weak convergence result, which demonstrates a form of asymptotic independence between Xn (rescaled) and ηn. Our results can be seen as generalizations of Lamperti’s results for non-homogeneous random walks on Z+ (the case where S is a singleton). Motivation arises from modulated queues or processes with hidden variables where ηn tracks an internal state of the system
Serum-free process development: improving the yield and consistency of human mesenchymal stem cell production

This is an Open Access Article. It is published by Elsevier under the Creative Commons Attribution 4.0 Unported Licence (CC BY). Full details of this licence are available at: http://creativecommons.org/licenses/by/4.0/Background: The cost effective production of hMSCs for off-the-shelf and patient specific therapies will require an increasing focus on improving product yield and driving manufacturing consistency.\ud
Methods: Bone-marrow derived hMSCs from two donors were expanded for 36 days in monolayer with medium supplemented with either fetal bovine serum (FBS) or PRIME-XV® Serum-free Medium (SFM). Cells were assessed throughout culture for proliferation, mean cell diameter, colony forming potential, osteogenic potential, gene expression and metabolites.\ud
Results: Expansion of BM-hMSCs in PRIME-XV® SFM resulted in a significantly higher growth rate (p < 0.001) and increased consistency between donors compared with FBS-based culture. FBS-based culture showed an inter batch production range of 0.9 and 5 days per dose compared with 0.5 and 0.6 days in SFM for each BM-hMSC donor line. The consistency between donors was also improved by the use of PRIME-XV® SFM, with a production range of 0.9 days compared with 19.4 days in FBS-based culture. Mean cell diameter has also been demonstrated as a process metric for BM-hMSC growth rate and senescence via a correlation (R2 = 0.8705) across all conditions. PRIME-XV® SFM has also shown increased consistency in BM-hMSC characteristics such as per cell metabolite utilisation, in vitro colony forming potential and osteogenic potential despite the higher number of population doublings.\ud
Conclusions: We have increased the yield and consistency of BM-hMSC expansion between donors, demonstrating a level of control over the product, which has the potential to increase the cost effectiveness and reduce the risk in these manufacturing processes
The Energy-Momentum Tensor(s) in Classical Gauge Theories

We give an introduction to, and review of, the energy-momentum tensors in
classical gauge field theories in Minkowski space, and to some extent also in
curved space-time. For the canonical energy-momentum tensor of non-Abelian
gauge fields and of matter fields coupled to such fields, we present a new and
simple improvement procedure based on gauge invariance for constructing a gauge
invariant, symmetric energy-momentum tensor. The relationship with the
Einstein-Hilbert tensor following from the coupling to a gravitational field is
also discussed.Comment: 34 pages; v2: Slightly expanded version with some improvements of
  presentation; Contribution to Mathematical Foundations of Quantum Field
  Theory, special issue in memory of Raymond Stora, Nucl. Phys.
Globally enhanced mercury deposition during the end-Pliensbachian extinction and Toarcian OAE: A link to the Karoo-Ferrar Large Igneous Province

The Mesozoic Era featured emplacement of a number of Large Igneous Provinces (LIPs), formed by the outpouring of millions of cubic kilometres of basaltic magma. The radiometric ages of several Mesozoic LIPs coincide with the dates of Oceanic Anoxic Events (OAEs). As a result of these coincidences, a causal link has been suggested, but never conclusively proven. This study explores the use of mercury as a possible direct link between the Karoo-Ferrar LIP and the coeval Toarcian OAE (T-OAE). Mercury is emitted to the atmosphere as a trace constituent of volcanic gas, and may be distributed globally before being deposited in sediments. Modern marine deposits show a strong linear correlation between mercury and organic-matter content. Results presented here indicate departures from such a simple linear relationship in sediments deposited during the T-OAE, and also during the Pliensbachian-Toarcian transition (an event that saw elevated benthic extinctions and carbon-cycle perturbations prior to the T-OAE). A number of depositional settings illustrate an increased mercury concentration in sediments that record one or both events, suggesting a rise in the depositional flux of this element. Complications to this relationship may arise from very organic-rich sediments potentially overprinting any Hg/TOC signal, whereas environments preserving negligible organic matter may leave no record of mercury deposition. However, the global distribution of coevally elevated Hg-rich levels suggests enhanced atmospheric mercury availability during the Early Toarcian, potentially aided by the apparent affinity of Hg for terrestrial organic matter, although the relative importance of aquatic vs terrestrial fixation of Hg in governing these enrichments remains uncertain. A perturbation in atmospheric Hg is most easily explained by enhanced volcanic output. It is suggested that extrusive igneous activity caused increased mercury flux to the Early Toarcian sedimentary realm, supporting the potential of this element as a proxy for ancient volcanism. This interpretation is consistent with a relationship between LIP formation and a perturbed carbon cycle during the Pliensbachian-Toarcian transition and T-OAE. The recording of these two distinct Hg excursions may also indicate that the Karoo-Ferrar LIP released volatiles in temporally distinct episodes, due either to multiple phases of magmatic emplacement or sporadic release of thermogenic gaseous products from intrusion of igneous material into volatile-rich lithologies.We acknowledge NERC (NE/G01700X/1) and the Leverhulme Trust for funding
Turbulence characteristics of the B\"{o}dewadt layer in a large enclosed rotor-stator system

A three-dimensional (3D) direct numerical simulation is combined with a laboratory study to describe the turbulent flow in an enclosed annular rotor-stator cavity characterized by a large aspect ratio G=(b-a)/h=18.32 and a small radius ratio a/b=0.152, where a and b are the inner and outer radii of the rotating disk and h is the interdisk spacing. The rotation rate Omega under consideration is equivalent to the rotational Reynolds number Re=Omegab2/nu=9.5 x 104, where nu is the kinematic viscosity of the fluid. This corresponds to a value at which an experiment carried out at the laboratory has shown that the stator boundary layer is turbulent, whereas the rotor boundary layer is still laminar. Comparisons of the 3D computed solution with velocity measurements have given good agreement for the mean and turbulent fields. The results enhance evidence of weak turbulence at this Reynolds number, by comparing the turbulence properties with available data in the literature. An approximately self-similar boundary layer behavior is observed along the stator side. The reduction of the structural parameter a1 under the typical value 0.15 and the variation in the wall-normal direction of the different characteristic angles show that this boundary layer is three-dimensional. A quadrant analysis of conditionally averaged velocities is performed to identify the contributions of different events (ejections and sweeps) on the Reynolds shear stress producing vortical structures. The asymmetries observed in the conditionally averaged quadrant analysis are dominated by Reynolds stress-producing events in this B\"{o}dewadt layer. Moreover, case 1 vortices (with a positive wall induced velocity) are found to be the major source of generation of special strong events, in agreement with the conclusions of Lygren and Andersson
Numerical Study of a Monolithic Fluid-Structure Formulation

International audienceThe conservation laws of continuum mechanic are naturally written in an Eulerian frame where the difference between a fluid and a solid is only in the expression of the stress tensors, usually with Newton's hypothesis for the fluids and Helmholtz potentials of energy for hyperelastic solids. There are currently two favored approaches to Fluid Structured Interactions (FSI) both working with the equations for the solid in the initial domain; one uses an ALE formulation for the fluid and the other matches the fluid-structure interfaces using Lagrange multipliers and the immersed boundary method. By contrast the proposed formulation works in the frame of physically deformed solids and proposes a discretization where the structures have large displacements computed in the deformed domain together with the fluid in the same; in such a monolithic formulation velocities of solids and fluids are computed all at once in a single variational formulation by a semi-implicit in time and the finite element method. Besides the simplicity of the formulation the advantage is a single algorithm for a variety of problems including multi-fluids, free boundaries and FSI. The idea is not new but the progress of mesh generators renders this approach feasible and even reasonably robust. In this article the method and its discretization are presented, stability is discussed showing in a loose fashion were are the difficulties and why one is able to show convergence of monolithic algorithms on fixed domains for fluids in compliant shell vessels restricted to small displacements. A numerical section discusses implementation issues and presents a few simple tests
Search for new particles decaying to zz using final states with leptons and jets with the ATLAS detector in root s=7 TeV proton-proton collisions

A search is presented for a narrow resonance decaying to a pair of Z bosons using data corresponding to 1.02 fb(-1) of integrated luminosity collected by the ATLAS experiment from pp collisions at root s= 7 TeV. Events containing either four charged leptons (llll) or two charged leptons and two jets (lljj) are analyzed and found to be consistent with the Standard Model background expectation. Lower limits on a resonance mass are set using the Randall-Sundrum (RS1) graviton model as a benchmark. Using both llll and lljj events, an RS1 graviton with k/(m) over bar (pl) = 0.1 and mass between 325 and 845 GeV is excluded at 95% confidence level. In addition, the llll events are used to set a model-independent fiducial cross section limit of sigma(fid)(pp -> X -> ZZ) < 0.92 pb at 95% confidence level for any new sources of ZZ production with m(ZZ) greater than 300 GeV
What Drives the International Transfer of Climate Change Mitigation Technologies? Empirical Evidence from Patent Data

CERNA WORKING PAPER SERIES 2010-03International audienceArticle Abstract : Technology transfer plays a key role in global efforts to reduce greenhouse gas emissions. In this paper, we characterize the factors that promote or hinder the international diffusion of climate-friendly technologies using detailed patent data from 96 countries for the period 1995-2007. The data provide strong evidence that lax Intellectual Property regimes have a strong and negative impact on the international diffusion of patented knowledge. Restrictions on international trade and foreign direct investment also hinder the diffusion of climate-friendly technologies. Surprisingly, local technological capabilities tend to discourage transfers. While broad indicators of technology capabilities are expected to facilitate transfers, this latter result stems from our technology-specific definition of local capabilities, which makes it possible to capture a substitution effect between local and foreign inventions.<br/>Working paper abstract: Using patent data from 66 countries for the period 1990-2003, we characterize the factors which promote or hinder the international diffusion of climate-friendly technologies on a global scale. Regression results show that technology-specific capabilities of the recipient countries are determinant factors. In contrast, the general level of education is less important. We also show that restrictions to international trade--e.g., high tariff rates--and to a lesser extent lax intellectual property regimes negatively influence the international diffusion of patented knowledge. A counter-intuitive result is that barriers to foreign direct investments can promote transfers. We discuss different possible interpretations
Limbic versus cognitive target for deep brain stimulation in treatment-resistant depression: accumbens more promising than caudate.

International audienceHigh-frequency deep brain stimulation (DBS) represents a major stake for treatment for treatment-resistant depression (TRD). We describe a preliminary trial of DBS of two potential brain targets in chronic TRD: the nucleus accumbens (Acb) and, in the event of failure, the caudate nucleus. Patients were followed for 6 months before surgery (M0). From M1 to M5, they underwent stimulation of the Acb target. PET scans allowed us to track metabolic modifications resulting from this stimulation. The caudate target of nonresponders was stimulated between M5 and M9. Patients then entered an extension phase, in which it was possible to adapt stimulation parameters and treatments. Six patients were included and four were operated on. At M5, none of the patients were either responders or remitters, but we did observe a decrease in Hamilton Depression Rating Scale (HDRS) scores. Three patients were switched to caudate stimulation, but no improvement was observed. During the extension phase, the Acb target was stimulated for all patients, three of whom exhibited a significant response. A decrease in glucose metabolism was observed after Acb stimulation, in the posterior cingulate gyrus, left frontal lobe, superior and medial gyrus, and bilateral cerebellum. An increase in metabolism was observed in the bilateral frontal lobe (superior gyrus), left frontal lobe (medial gyrus), and right limbic lobe (anterior cingulate gyrus). The results of this trial suggest that Acb is a more promising target than the caudate. NCT01569711
PETRA : Process Evolution using a TRAce‐based system on a Maintenance Platform.

International audienceTo meet increasing needs in the field of maintenance, we studied the dynamic aspect of process and services on a maintenance platform, a major challenge in process mining and knowledge engineering. Hence, we propose a dynamic experience feedback approach to exploit maintenance process behaviors in real execution of the maintenance platform. An active learning process exploiting event log is introduced by taking into account the dynamic aspect of knowledge using trace engineering. Our proposal makes explicit the underlying knowledge of platform users by means of a trace-based system called "PETRA". The goal of this system is to extract new knowledge rules about transitions and activities in maintenance processes from previous platform executions as well as its user (i.e. maintenance operators) interactions. While following a Knowledge Traces Discovery process and handling the maintenance ontology IMAMO, "PETRA" is composed of three main subsystems: tracking, learning and knowledge capitalization. The capitalized rules are shared in the platform knowledge base in order to be reused in future process executions. The feasibility of this method is proven through concrete use cases involving four maintenance processes and their simulation
Vapour - Liquid Equilibrium measurements of CO2 based mixtures: Experimental apparatus and testing procedures

At present, the accurate evaluation of the thermo-physical behaviour of multicomponent fluids represents a crucial element for studying and simulating low CO2 emission energy conversion technologies. In order to extend the range of application of the available thermodynamic models, an intense experimental research activity has been performed in recent years. The main purpose of this paper is to describe the experimental and modelling procedures applied by the authors to measure and to analyse data extracted from the Vapour-Liquid Equilibrium apparatus recently installed at LEAP laboratory. This test rig allows the characterization of mixture phase equilibrium properties on the basis of the static-analytical method, within the pressure and temperature ranges of 0-20 MPa and -60-200°C. Finally, the paper reports the most relevant features and the main guidelines for the instruments calibration procedures. © 2013 The Authors
Search for top quark decays t→qH with H→γγ using the ATLAS detector

A search is performed for flavour-changing neutral currents in the decay of a top quark to an up-type (c, u) quark and a Higgs boson, where the Higgs boson decays to two photons. The proton-proton collision data set used corresponds to 4.7 fb−1 at s√ = 7TeV and 20.3fb−1 at s√ = 8TeV collected by the ATLAS experiment at the LHC. Top quark pair events are searched for in which one top quark decays to qH and the other decays to bW. Both the hadronic and the leptonic decay modes of the W boson are used. No significant signal is observed and an upper limit is set on the t → qH branching ratio of 0.79 at the 95% confidence level. The corresponding limit on the tqH coupling combination λ2tcH+λ2tuH [...] √ is 0.17.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, 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 MIZ. S, 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