pinecone/core-2020-05-10-deduplication huggingface dataset:
Lymph nodes harbor viral reservoirs that cause rebound of plasma viremia in SIV-infected macaques upon cessation of combined antiretroviral therapy.

Attempts to find a cure for HIV infection are hindered by the presence of viral reservoirs that resist highly active antiretroviral therapy. To identify the properties of these reservoirs, four SIV239-infected Rhesus macaques were treated with combined antiretroviral therapy (cART) for 1 year. While plasma viral RNA (vRNA) was effectively suppressed, a systemic analysis revealed that vRNA was distributed in the following order: lymphatic tissues>lungs and intestine>other tissues. Histochemistry yielded no cells with viral signals. To increase the chance of detection, two additional SIV-infected animals were treated and analyzed on Day 10 after the cessation of cART. These animals exhibited similar vRNA distribution patterns to the former animals, and immunohistochemistry revealed Nef-positive T lymphocytes predominantly in the follicles of mesenteric lymph nodes (MLNs). These data suggest that lymphatic tissues, including MLNs, contain major cellular reservoirs that cause rebound of plasma viremia upon cessation of therapy
Cone visual pigments.

This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.Cone visual pigments are visual opsins that are present in vertebrate cone photoreceptor cells and act as photoreceptor molecules responsible for photopic vision. Like the rod visual pigment rhodopsin, which is responsible for scotopic vision, cone visual pigments contain the chromophore 11-cis-retinal, which undergoes cis-trans isomerization resulting in the induction of conformational changes of the protein moiety to form a G protein-activating state. There are multiple types of cone visual pigments with different absorption maxima, which are the molecular basis of color discrimination in animals. Cone visual pigments form a phylogenetic sister group with non-visual opsin groups such as pinopsin, VA opsin, parapinopsin and parietopsin groups. Cone visual pigments diverged into four groups with different absorption maxima, and the rhodopsin group diverged from one of the four groups of cone visual pigments. The photochemical behavior of cone visual pigments is similar to that of pinopsin but considerably different from those of other non-visual opsins. G protein activation efficiency of cone visual pigments is also comparable to that of pinopsin but higher than that of the other non-visual opsins. Recent measurements with sufficient time-resolution demonstrated that G protein activation efficiency of cone visual pigments is lower than that of rhodopsin, which is one of the molecular bases for the lower amplification of cones compared to rods. In this review, the uniqueness of cone visual pigments is shown by comparison of their molecular properties with those of non-visual opsins and rhodopsin. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks
Constraints on mantle source and interactions from He-Sr isotope variation in Italian Plio-Quaternary volcanism

Helium isotope ratios of olivine and pyroxene phenocrysts from Plio-Quaternary volcanic rocks from Southern Italy (seven Eolian Islands, Mt. Vulture, Etna, Ustica, Pantelleria) range from 2.3 to 7.1 Ra. Importantly the phenocryst 3He/4He correlate well with whole rock Sr isotopic composition (0.70309-0.70711) reflecting the mixing of two sources. A significant contribution of He from crustal contamination is recorded only occasionally (e.g., pyroxenes from Vulcano). When merged with data from the Roman Comagmatic Province, a remarkably strong near-linear He-Sr isotope correlation is apparent. The general northward decrease in 3He/4He corresponds to an increase in 87Sr/86Sr (and decrease in 143Nd/144Nd and 206Pb/204Pb) that is due to increasing metasomatic enrichment of the mantle wedge via subduction of the Ionian-Adriatic plate. Calculations based on the ingrowth of 4He in the wedge and on the 4He content of the subducting crust show that mechanisms of enrichment in radiogenic He are effective only if the wedge is strongly depleted in He relative to best estimates of the depleted mantle. This can be accommodated if the process of metasomatism by the subduction fluids depletes the mantle wedge. The 3He/4He of Pantelleria, Etna, Iblei, Ustica, Alicudi and Filicudi basalts (7.0 ± 0.6 Ra) define the mantle composition least affected by subduction-related metasomatism. Although these volcanoes are from a variety of tectonic regimes (subduction-related, intraplate, rifting) their similarities suggest a common origin of geochemical features. Their characteristics are consistent with a HIMU-type mantle that is either younger than the Cook-Austral island end-member, or has a lower 238U/204Pb
Discovery of extended VHE gamma-ray emission from the vicinity of the young massive stellar cluster Westerlund 1

Aims. Results obtained in very-high-energy (VHE; E ≥ 100   GeV) γ-ray observations performed with the H.E.S.S. telescope array are used to investigate particle acceleration processes in the vicinity of the young massive stellar cluster Westerlund 1 (Wd 1).\ud
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Methods. Imaging of Cherenkov light from γ-ray induced particle cascades in the Earth’s atmosphere is used to search for VHE γ rays from the region around Wd 1. Possible catalogued counterparts are searched for and discussed in terms of morphology and energetics of the H.E.S.S. source.\ud
\ud
Results. The detection of the degree-scale extended VHE γ-ray source HESS J1646–458 is reported based on 45 h of H.E.S.S. observations performed between 2004 and 2008. The VHE γ-ray source is centred on the nominal position of Wd 1 and detected with a total statistical significance of  ~20σ. The emission region clearly extends beyond the H.E.S.S. point-spread function (PSF). The differential energy spectrum follows a power law in energy with an index of Γ = 2.19 ± 0.08stat ± 0.20sys and a flux normalisation at 1 TeV of Φ0 = (9.0 ± 1.4stat ± 1.8sys)    ×    10-12   TeV-1   cm-2   s-1. The integral flux above 0.2 TeV amounts to (5.2 ± 0.9)    ×    10-11   cm-2   s-1.\ud
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Conclusions. Four objects coincident with HESS J1646–458 are discussed in the search of a counterpart, namely the magnetar CXOU J164710.2 − 455216, the X-ray binary 4U 1642–45, the pulsar PSR J1648–4611 and the massive stellar cluster Wd 1. In a single-source scenario, Wd 1 is favoured as site of VHE particle acceleration. Here, a hadronic parent population would be accelerated within the stellar cluster. Beside this, there is evidence for a multi-source origin, where a scenario involving PSR J1648–4611 could be viable to explain parts of the VHE γ-ray emission of HESS J1646–458.Peer-reviewedPublisher Version10942
An ice-sheet scale comparison of eskers with modelled subglacial drainage routes.

Eskers record the signature of channelisedmeltwater drainage during deglaciation providing vital information on\ud
the nature and evolution of subglacial drainage. In this paper, we compare the spatial pattern of eskers beneath\ud
the former Laurentide Ice Sheet with subglacial drainage routes diagnosed at discrete time intervals from the\ud
results of a numerical ice-sheet model. Perhaps surprisingly,we showthat eskers predominantly occur in regions\ud
where modelled subglacial water flow is low. Eskers and modelled subglacial drainage routes were found to\ud
typically match over distances of b10 km, and most eskers show a better agreement with the routes close to\ud
the ice margin just prior to deglaciation. This supports a time-transgressive esker pattern, with formation in\ud
short (b10km) segments of conduit close behind a retreating ice margin, and probably associated with thin, stagnant\ud
or sluggish ice. Esker-forming conduits were probably dominated by supraglacially fed meltwater inputs.\ud
We also show that modelled subglacial drainage routes containing the largest concentrations of meltwater\ud
show a close correlation with palaeo-ice stream locations. The paucity of eskers along the terrestrial portion of\ud
these palaeo-ice streams and meltwater routes is probably because of the prevalence of distributed drainage\ud
and the high erosion potential of fast-flowing ice
Rate and equilibrium constants for the addition of N-heterocyclic carbenes into benzaldehydes : a remarkable 2-substituent effect.

Rate and equilibrium constants for the reaction between N-aryl triazolium N-heterocyclic carbene (NHC) precatalysts and substituted benzaldehyde derivatives to form 3-(hydroxybenzyl)azolium adducts under both catalytic and stoichiometric conditions have been measured. Kinetic analysis and reaction profile fitting of both the forward and reverse reactions, plus onwards reaction to the Breslow intermediate, demonstrate the remarkable effect of the benzaldehyde 2-substituent in these reactions and provide insight into the chemoselectivity of cross-benzoin reactions
Experimental validation of a resilient electronic logic design with autonomous fault discrimination/masking.

This paper presents the experimental validation of a novel fault-tolerant electronic logic design conducted by an automated mixed-signal fault injection procedure. The design under evaluation relies upon a novel redundant design strategy intended to provide fault discrimination and selective fault masking embedded within a functional CMOS NAND gate. The traditional logic layout is modified to include fault detection and reporting at an extremely fine-grained design level with 2x overhead as opposed to the traditional 4x overhead. The fault injection test bench procedure requires automated fault injection, programmable fault load conditions and combined analogue/digital domain verification. The device under test is implemented using discrete n- and p-FETs arranged as a modular test board together with automated fault injection and test lines. The fault response is measured and confirms the predicted intrinsic fault rate of 25% with a successful 100% masking of suck low-faults and precise identification of stuck-high via IDDQ trigger. The test procedure is shown to be extensible towards more complex logic unit designs and for evaluation of multiple simultaneous faults
The small group subtlety of using ICT for participatory governance: A South African experience

Journal Article: Government Information Quarterly (29:2) 2012, pp 203-211.The greater number of government efforts to stimulate participative governance in
communities using Information and Communication Technology (ICT) often fall short of
expectations. In South Africa extending e-government to communities has been in the form of more and/or better equipped ICT-enabled community centres, called Thusong Service Centres. In this paper, based on action research experiences, we report outcomes of interpretive research into ICT-enabled approaches to participative governance in communities. Using the Diffusion of Innovations theory as an analytic lens, the findings reveal a subtlety that is not often mentioned in the call for participative e-governance; people from communities prefer to work in groups rather than individually. The collectiveness inclination is a common denominator of many developing countries where people choose to come together to leverage the few available resources. Individuals become apprehensive when made to work on their own using the ICT. The research reveals the necessity to redesign ICT to suit small groups as part of participative e-governance rather than the normative ICT design that suits individual work styles. Additionally, the research reveals that by working in groups, communities are more willing to accept the government initiatives that are being energised with the use of ICT. Methodologically, the research revealed the ethical issue that arises from action research in its raising of unrealistic expectations in a community.School of Computin
A comparative analysis reveals weak relationships between ecological factors and beta diversity of stream insect metacommunities at two spatial levels.

The hypotheses that beta diversity should increase with decreasing latitude and increase with spatial extent of a region have rarely been tested based on a comparative analysis of multiple datasets, and no such study has focused on stream insects. We first assessed how well variability in beta diversity of stream insect metacommunities is predicted by insect group, latitude, spatial extent, altitudinal range, and dataset properties across multiple drainage basins throughout the world. Second, we assessed the relative roles of environmental and spatial factors in driving variation in assemblage composition within each drainage basin. Our analyses were based on a dataset of 95 stream insect metacommunities from 31 drainage basins distributed around the world. We used dissimilarity-based indices to quantify beta diversity for each metacommunity and, subsequently, regressed beta diversity on insect group, latitude, spatial extent, altitudinal range, and dataset properties (e.g., number of sites and percentage of presences). Within each metacommunity, we used a combination of spatial eigenfunction analyses and partial redundancy analysis to partition variation in assemblage structure into environmental, shared, spatial, and unexplained fractions. We found that dataset properties were more important predictors of beta diversity than ecological and geographical factors across multiple drainage basins. In the within-basin analyses, environmental and spatial variables were generally poor predictors of variation in assemblage composition. Our results revealed deviation from general biodiversity patterns because beta diversity did not show the expected decreasing trend with latitude. Our results also call for reconsideration of just how predictable stream assemblages are along ecological gradients, with implications for environmental assessment and conservation decisions. Our findings may also be applicable to other dynamic systems where predictability is low
Bandgap Optimization of Two-Dimensional Photonic Crystals Using Semidefinite Programming and Subspace Methods

In this paper, we consider the optimal design of photonic crystal structures for two-dimensional square lattices. The mathematical formulation of the bandgap optimization problem leads to an infinite-dimensional Hermitian eigenvalue optimization problem parametrized by the dielectric material and the wave vector. To make the problem tractable, the original eigenvalue problem is discretized using the finite element method into a series of finite-dimensional eigenvalue problems for multiple values of the wave vector parameter. The resulting optimization problem is large-scale and non-convex, with low regularity and non-differentiable objective. By restricting to appropriate eigenspaces, we reduce the large-scale non-convex optimization problem via reparametrization to a sequence of small-scale convex semidefinite programs (SDPs) for which modern SDP solvers can be efficiently applied. Numerical results are presented for both transverse magnetic (TM) and transverse electric (TE) polarizations at several frequency bands. The optimized structures exhibit patterns which go far beyond typical physical intuition on periodic media design
Towards a fitting procedure to deeply virtual meson production - the next-to-leading order case

Based on the collinear factorization approach, we present a comprehensive perturbative next-to- leading (NLO) analysis of deeply virtual meson production (DVMP). Our representation in conformal Mellin space can serve as basis for a global fitting procedure to access generalized parton distributions from experimental measurements of DVMP and deeply virtual Compton scattering (DVCS). We introduce a rather general formalism for the evaluation of conformal moments that can be developed further beyond the considered order. We also confirm previous diagrammatical findings in the pure singlet quark channel. Finally, we use the analytic properties of the hard scattering amplitudes to estimate qualitatively the size of radiative corrections and illustrate these considerations with some numerical examples. The results suggest that global NLO GPD fits, including both DVMP and DVCS data, could be more stable than often feared
Becoming a performance analyst: autoethnographic reflections on agency, and facilitated transformational growth

This paper features an autoethnographic approach in presenting and reflecting upon the story of one higher education student's rapid vocational and academic transformation. Initially an inconspicuous undergraduate student, Andrew experienced an accelerated development that catapulted him to working in elite sport performance analysis (PA) environments, within a year. PA is a sub-discipline of sports coaching that involves using the latest technological advances to influence sporting performance, through the objective analysis of performance data. This autoethnographic piece is partly Andrew’s personal reflection upon that journey towards his newfound profession, which initially grew out of his experience of a generic sports degree at a university. Through stepping out of his comfort zone, and analysing sports previously unknown to him, extraordinary progress was made, and various vocational and academic opportunities arose. The initial catalyst for this developmental journey was facilitated by coaching lecturer David, who reflects upon how Andrew’s story links to his own educational philosophies. Andrew and David explore what these stories might mean to them personally, including potential links to the metaphor of learning as becoming, and notions around the concepts of learner agency, and educational facilitation. The paper ends by exploring the theoretical frameworks that guided this paper’s structure and focus
Measurement of the production of a W boson in association with a charm quark in pp collisions at root s=7 TeV with the ATLAS detector

The production of a W boson in association with a single charm quark is studied using 4.6 fb(-1) of pp collision data at root s = 7 TeV collected with the ATLAS detector at the Large Hadron Collider. In events in which a W boson decays to an electron or muon, the charm quark is tagged either by its semileptonic decay to a muon or by the presence of a charmed meson. The integrated and differential cross sections as a function of the pseudorapidity of the lepton from the W-boson decay are measured. Results are compared to the predictions of next-to-leading-order QCD calculations obtained from various parton distribution function parameterisations. The ratio of the strange-to-down sea-quark distributions is determined to be 0.96(-0.30)(+0.26) at Q (2) = 1.9 GeV2, which supports the hypothesis of an SU(3)-symmetric composition of the light-quark sea. Additionally, the cross-section ratio sigma(W (+) +)/sigma(W (-) + c) is compared to the predictions obtained using parton distribution function parameterisations with different assumptions about the s-(s) over bar quark asymmetry
Bouc-Wen-type models with stiffness degradation: thermodynamic analysis and applications

International audienceIn this paper, a thermodynamic analysis of Bouc-Wen models endowed with both strength and stiffness degradation is provided. It is based on the relationship between the flow rules of these models and those of the endochronic plasticity theory with damage, discussed in a companion paper (Erlicher and Point, 2008). Using the theoretical framework of that extended endochronic theory, it is shown that an elastic Bouc-Wen model with damage, i.e. without plastic strains, can be formulated. Moreover, a proper definition of the dissipated energy of these Bouc-Wen models with degradation is given and some thermodynamic constraints on the parameters defining the models behavior are emphasized and discussed. In particular, some properties of the energetic linear stiffness degradation rule as well as the so-called pivot rule, well-known in the seismic engineering field, are illustrated and commented upon. An improved energetic stiffness degradation rule and a new stiffness degradation rule are proposed
Two particle-in-grid realisations on spacetrees

International audienceThe present paper studies two particle management strategies for dynamically adaptive Cartesian grids at hands of a particle-in-cell code. One holds the particles within the grid cells, the other within the grid vertices. The fundamental challenge for the algorithmic strategies results from the fact that particles may run through the grid without velocity constraints. To facilitate this, we rely on multiscale grid representations. They allow us to lift and drop particles between different spatial resolutions. We call this cell-based strategy particle in tree (PIT). Our second approach assigns particles to vertices describing a dual grid (PIDT) and augments the lifts and drops with multiscale linked cells.Our experiments validate the two schemes at hands of an electrostatic particle-in-cell code by retrieving the dispersion relation of Langmuir waves in a thermal plasma. They reveal that different particle and grid characteristics favour different realisations. The possibility that particles can tunnel through an arbitrary number of grid cells implies that most data is exchanged between neighbouring ranks, while very few data is transferred non-locally. This constraints the scalability as the code potentially has to realise global communication. We show that the merger of an analysed tree grammar with PIDT allows us to predict particle movements among several levels and to skip parts of this global communication a priori. It is capable to outperform several established implementations based upon trees and/or space-filling curves
Simple dynamics on graphs

International audienceCan the interaction graph of a finite dynamical system force this system to have a ``complex'' dynamics ? In other words, given a finite interval of integers $A$, which are the signed digraphs $G$ such that every finite dynamical system $f:A^n\to A^n$ with $G$ as interaction graph has a ``complex'' dynamics ? If $|A|\geq 3$ we prove that no such signed digraph exists. More precisely, we prove that for every signed digraph $G$ there exists a system $f:A^n\to A^n$ with $G$ as interaction graph that converges toward a unique fixed point in at most $\lfloor\log_2 n\rfloor+2$ steps. The boolean case $|A|=2$ is more difficult, and we provide partial answers instead. We exhibit large classes of unsigned digraphs which admit boolean dynamical systems which converge toward a unique fixed point in polynomial, linear or constant time
On decomposing net final values: EVA, SVA and shadow project

A decomposition model of Net Final Values (NFV), named Systemic Value Added (SVA), is proposed for decision-making purposes, based on a systemic approach introduced in Magni [Magni, C. A. (2003), Bulletin of Economic Research 55(2), 149-176; Magni, C. A. (2004) Economic Modelling 21, 595-617]. The model translates the notion of excess profit giving formal expression to a counterfactual alternative available to the decision maker. Relations with other decomposition models are studied, among which Stewart's [Stewart, G.B. (1991), The Quest for Value: The EVA (TM) Management Guide, Harper Collins, Publishers Inc]. The index here introduced differs from Stewart's Economic Value Added (EVA) in that it rests on a different interpretation of the notion of excess profit and is formally connected with the EVA model by means of a shadow project. The SVA is formally and conceptually threefold, in that it is economic, financial, accounting-flavoured. Some results are offered, providing sufficient and necessary conditions for decomposing NFV. Relations between a project's SVA and its shadow project's EVA are shown, all results of Pressacco and Stucchi [Pressacco, F. and Stucchi, P. (1997), Rivista di Matematica per le Scienze Economiche e Sociali 20, 165-185] are proved by making use of the systemic approach and the shadow counterparts of those results are also shown