pinecone/core-2020-05-10-deduplication huggingface dataset:
How cells tune viral mechanics-insights from biophysical measurements of influenza virus

During replication, the physical state of a virus is controlled by assembly and disassembly processes, when particles are put together and dismantled by cellular cues, respectively. A fundamental question has been how a cell can assemble an infectious virus, and dismantle a virus entering an uninfected cell and thereby trigger a new round of infection. This apparent paradox might be explained by considering that infected and uninfected cells are functionally different, or that assembly and disassembly take place along different cellular pathways. A third possibility is that the physical properties of newly assembled viruses are different from the infection-ready viruses. Recent biophysical experiments measured the stiffness of single Influenza viruses and combined this with biochemical measurements and cell biological assays. Besides inducing the fusogenic state of hemagglutinin, low pH cues softened the virus and precluded aggregation of viral ribonucleoprotein particles with the matrix protein M1. The recent experiments suggest a two-step model for Influenza virus entry and uncoating involving low pH in early and late endosomes, respectively. I conclude with a short outlook into how combined biophysical and cell biological approaches might lead to the identification of new cellular cues controlling viral uncoating and infection
Quadratures associated with pseudo-orthogonal rational functions on the real half line with poles in [-∞,0]

We consider a positive measure on [0,∞) and a sequence of nested spaces ℒ_0 ⊂ ℒ_1 ⊂ ℒ_2 ... of rational functions with prescribed poles in [-∞,0]. Let {φ_k : k = 0..∞}, with φ_0 ∈ ℒ_0 and φ_k ∈ ℒ_k ∖ ℒ_{k-1}, k = 1,2,... be the associated sequence of orthogonal rational functions. The zeros of φ_n can be used as the nodes of a rational Gauss quadrature formula that is exact for all functions in ℒ_n . ℒ_{n-1}, a space of dimension 2n. Quasi- and pseudo-orthogonal functions are functions in ℒ_n that are orthogonal to some subspace of ℒ_{n-1}. Both of them are generated from φ_n and φ_{n-1} and depend on a real parameter τ. Their zeros can be used as the nodes of a rational Gauss-Radau quadrature formula where one node is fixed in advance and the others are chosen to maximize the subspace of ℒ_n . ℒ_{n-1} where the quadrature is exact. The parameter τ is used to fix a node at a pre-assigned point. The space where the quadratures are exact has dimension 2n-1 in both cases but it is in ℒ_{n-1} . ℒ_{n-1} in the quasi-orthogonal case and it is in ℒ_n . ℒ_{n-2} in the pseudo-orthogonal case.status: publishe
Subcortical volumetric abnormalities in bipolar disorder

Considerable uncertainty exists about the defining brain changes associated with bipolar disorder (BD). Understanding and quantifying the sources of uncertainty can help generate novel clinical hypotheses about etiology and assist in the development of biomarkers for indexing disease progression and prognosis. Here we were interested in quantifying case-control differences in intracranial volume (ICV) and each of eight subcortical brain measures: nucleus accumbens, amygdala, caudate, hippocampus, globus pallidus, putamen, thalamus, lateral ventricles. In a large study of 1710 BD patients and 2594 healthy controls, we found consistent volumetric reductions in BD patients for mean hippocampus (Cohen's d=-0.232; P=3.50 × 10(-7)) and thalamus (d=-0.148; P=4.27 × 10(-3)) and enlarged lateral ventricles (d=-0.260; P=3.93 × 10(-5)) in patients. No significant effect of age at illness onset was detected. Stratifying patients based on clinical subtype (BD type I or type II) revealed that BDI patients had significantly larger lateral ventricles and smaller hippocampus and amygdala than controls. However, when comparing BDI and BDII patients directly, we did not detect any significant differences in brain volume. This likely represents similar etiology between BD subtype classifications. Exploratory analyses revealed significantly larger thalamic volumes in patients taking lithium compared with patients not taking lithium. We detected no significant differences between BDII patients and controls in the largest such comparison to date. Findings in this study should be interpreted with caution and with careful consideration of the limitations inherent to meta-analyzed neuroimaging comparisons.Molecular Psychiatry advance online publication, 9 February 2016; doi:10.1038/mp.2015.227.status: publishe
8D likelihood effective Higgs couplings extraction framework in h → 4 ℓ

We present an overview of a comprehensive analysis framework aimed at performing direct extraction of all possible effective Higgs couplings to neutral electroweak gauge bosons in the decay to electrons and muons, the so called ‘golden channel’. Our framework is based primarily on a maximum likelihood method constructed from analytic expressions of the fully differential cross sections for h → 4 ℓ and for the dominant irreducible q q ¯ $$ q\overline{q} $$ → 4 ℓ background, where 4 ℓ = 2 e 2 μ, 4 e, 4 μ . Detector effects are included by an explicit convolution of these analytic expressions with the appropriate transfer function over all center of mass variables. Utilizing the full set of observables, we construct an unbinned detector-level likelihood which is continuous in the effective couplings. We consider possible ZZ , Zγ , and γγ couplings simultaneously, allowing for general CP odd/even admixtures. A broad overview is given of how the convolution is performed and we discuss the principles and theoretical basis of the framework. This framework can be used in a variety of ways to study Higgs couplings in the golden channel using data obtained at the LHC and other future colliders
Lifetime measurements of the first 2+ states in 104,106 Zr: Evolution of ground-state deformations

The first fast-timing measurements from nuclides produced via the in-flight fission mechanism are reported. The lifetimes of the first 2+ states in 104,106 Zr nuclei have been measured via β -delayed γ -ray timing of stopped radioactive isotope beams. An improved precision for the lifetime of the 21+ state in 104 Zr was obtained, τ(21+)=2.90−20+25 ns , as well as a first measurement of the 21+ state in 106 Zr, τ(21+)=2.60−15+20 ns , with corresponding reduced transition probabilities of B(E2;21+→0g.s.+)=0.39(2) e2b2 and 0.31(1) e2b2 , respectively. Comparisons of the extracted ground-state deformations, β2=0.39(1) ( 104 Zr) and β2=0.36(1) ( 106 Zr) with model calculations indicate a persistence of prolate deformation. The data show that 104 Zr is the most deformed of the neutron-rich Zr isotopes measured so far
Towards ( 3+1 ) gravity through Drinfel'd doubles with cosmological constant

We present the generalisation to ( 3+1 ) dimensions of a quantum deformation of the ( 2+1 ) (Anti)-de Sitter and Poincaré Lie algebras that is compatible with the conditions imposed by the Chern–Simons formulation of ( 2+1 ) gravity. Since such compatibility is automatically fulfilled by deformations coming from Drinfel'd double structures, we believe said structures are worth being analysed also in the ( 3+1 ) scenario as a possible guiding principle towards the description of ( 3+1 ) gravity. To this aim, a canonical classical r -matrix arising from a Drinfel'd double structure for the three ( 3+1 ) Lorentzian algebras is obtained. This r -matrix turns out to be a twisted version of the one corresponding to the ( 3+1 ) κ -deformation, and the main properties of its associated noncommutative spacetime are analysed. In particular, it is shown that this new quantum spacetime is not isomorphic to the κ -Minkowski one, and that the isotropy of the quantum space coordinates can be preserved through a suitable change of basis of the quantum algebra generators. Throughout the paper the cosmological constant appears as an explicit parameter, thus allowing the (flat) Poincaré limit to be straightforwardly obtained
Chern–Simons–Higgs theory with visible and hidden sectors and its N=2 SUSY extension

We study vortex solutions in Abelian Chern–Simons–Higgs theories with visible and hidden sectors. We first consider the case in which the two sectors are connected through a BF-like gauge mixing term with no explicit interaction between the two scalars. Since first order Bogomolny equations do not exist in this case, we derive the second order field equations. We then proceed to an N=2 supersymmetric extension including a Higgs portal mixing among the visible and hidden charged scalars. As expected, Bogomolny equations do exist in this case and we study their string-like solutions numerically
Search for resonances in the dilepton mass distribution in pp collisions at root s=7 TeV

A search for narrow resonances at high mass in the dimuon and dielectron channels has been performed by the CMS experiment at the CERN LHC, using pp collision data recorded at ps = 7TeV. The event samples correspond to integrated luminosities of 40 pb−1 in the dimuon channel and 35 pb−1 in the dielectron channel. Heavy dilepton resonances are predicted in theoretical models with extra gauge bosons (Z′) or as Kaluza-Klein graviton excitations (GKK) in the Randall-Sundrum model. Upper limits on the inclusive cross section of Z′(GKK) -- ℓ+ℓ− relative to Z -- ℓ+ℓ− are presented. These limits exclude at 95% confidence level a Z′ with standard-model-like couplings below 1140 GeV, the superstring-inspired Z′ ψ below 887 GeV, and, for values of the coupling parameter k/MPl of 0.05 (0.1), Kaluza-Klein gravitons below 855 (1079) GeV.Peer Reviewe
Particle swarm optimization for MEG source localization

The estimation of three-dimension neural active sources from the magnetoencephalography (MEG) record is a very critical issue for both clinical neurology and brain functions research. Nowadays multiple signal classification (MUSIC) algorithm and recursive MUSIC algorithm are widely used to locate dipolar sources from MEG data. The drawback of these algorithms is that they need excessive calculation and is quite time-consuming when scanning a three-dimensional space. In order to solve this problem, we propose a MEG sources localization scheme based on an improved Particle Swarm Optimization (PSO). This scheme uses the advantage of global searching ability of PSO to estimate the rough source location. Then combining with grids search in small area, the accurate dipolar source localization is performed. In addition, we compare the results of our method with those based on Genetic Algorithm (GA). Computer simulation results show that our PSO strategy is an effective and precise approach to dipole localization which can improve the speed greatly and localize the sources accurately.PRIB 2008 proceedings found at: http://dx.doi.org/10.1007/978-3-540-88436-
Dimensions of Oppositionalay in a Brazilian Communiiy Sample: Testing the DSM-5 Proposal and Etiological Links

Objective: Investigating dimensions of oppositional symptoms may help to explain heterogeneity of etiology and outcomes for mental disorders across development and provide further empirical justification for the DSM-5-proposed modifications of oppositional defiant disorder (ODD). However, dimensions of oppositionality have not previously been tested in samples outside Europe or the United States. in this study, we used a large Brazilian community sample to compare the fit of different models for dimensions of oppositional symptoms; to examine the association of psychiatric diagnoses and symptoms with dimensions of oppositionality; and to examine the associations between dimensions of oppositionality and parental history of mental disorders. Method: A Brazilian community sample of 2,512 children 6 through 12 years old were investigated in this study. Confirmatory factorial analyses were performed to compare the fit of alternative models, followed by linear and logistic regression analyses of associations with psychiatric diagnosis and parental history of psychopathology. Results: A three-factor model with irritable, headstrong, and hurtful dimensions fitted best. the irritable dimension showed a strong association with emotional disorders in the child (p < .001) and history of depression (p < .01) and suicidality (p < .05) in the mother. the headstrong dimension was uniquely associated with attention-deficit/hyperactivity disorder (ADHD) in the child (p < .001) and with maternal history of ADHD symptoms (p < .05). the hurtful dimension was specifically associated with conduct disorder (p < .05). Conclusions: Our findings from a large community sample of Brazilian children support a distinction between dimensions of oppositionality consistent with current DSM-5 recommendations and provide further evidence for etiological distinctions between these dimensions. J. Am. Acad. Child Adolesc. Psychiatry; 201352(4):389-400.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)NovartisAbbottEli Lilly and Co.Janssen-CilagShireWellcome TrustU.K. Department of HealthUniv São Paulo, BR-05403903 São Paulo, BrazilKings Coll London, Inst Psychiat, London WC2R 2LS, EnglandUniv São Paulo, Res Support Ctr Neurodev & Mental Hlth, BR-05403903 São Paulo, BrazilUniv Fed Rio Grande do Sul, BR-90046900 Porto Alegre, RS, BrazilUniversidade Federal de São Paulo, São Paulo, BrazilUniversidade Federal de São Paulo, São Paulo, BrazilWeb of Scienc
Drug delivery into microneedle-porated nails from nanoparticle reservoirs

This study demonstrates the potential of polymeric nanoparticles as drug reservoirs for sustained topical drug delivery into microneedle-treated human nail. Laser scanning confocal microscopy was used to image the delivery of a fluorescent model compound from nanoparticles into the nail. A label-free imaging technique, stimulated Raman scattering microscopy, was applied, in conjunction with two-photon fluorescence imaging, to probe the disposition of nanoparticles and an associated lipophilic 'active' in a microneedle-porated nail. The results provide clear evidence that the nanoparticles function as immobile reservoirs, sequestered on the nail surface and in the microneedle-generated pores, from which the active payload can be released and diffuse laterally into the nail over an extended period of time
H.E.S.S. observations of the binary system PSR B1259–63/LS 2883 around the 2010/2011 periastron passage

Aims. We present very high energy (VHE; E > 100 GeV) data from the -ray binary system PSR B1259-63/LS 2883 taken around its periastron passage on 15th of December 2010 with the High Energy Stereoscopic System (H.E.S.S.) of Cherenkov Telescopes. We aim to search for a possible TeV counterpart of the GeV flare detected by the Fermi LAT. In addition, we aim to study the current periastron passage in the context of previous observations taken at similar orbital phases, testing the repetitive behaviour of the source.
Methods. Observations at VHEs were conducted with H.E.S.S. from 9th to 16th of January 2011. The total dataset amounts to _6 h of observing time. The data taken around the 2004 periastron passage were also re-analysed with the current analysis techniques in order to extend the energy spectrum above 3 TeV to fully compare observation results from 2004 and 2011. Results. The source is detected in the 2011 data at a significance level of 11:5_ revealing an averaged integral flux above 1 TeV of (1:01 _0:18stat _ 0:20sys) _ 1012 cm2 s1. The di_erential energy spectrum follows a power-law shape with a spectral index  = 2:92 _ 0:30stat _ 0:20sys and a flux normalisation at 1 TeV of N0 = (1:95 _ 0:32stat _ 0:39sys) _ 1012 TeV1 cm2 s1. The measured light curve does not show any evidence for variability of the source on the daily scale. The re-analysis of the 2004 data yields results compatible with the published ones. The di_erential energy spectrum measured up to _10 TeV is consistent with a power law with a spectral index  = 2:81_0:10stat _0:20sys and a flux normalisation at 1 TeV of N0 = (1:29 _ 0:08stat _ 0:26sys) _ 1012 TeV1 cm2 s1. Conclusions. The measured integral flux and the spectral shape of the 2011 data are compatible with the results obtained around previous periastron passages. The absence of variability in the H.E.S.S. data indicates that the GeV flare observed by Fermi LAT in the time period covered also by H.E.S.S. observations originates in a di_erent physical scenario than the TeV emission. Moreover, the comparison of the new results to the results from the 2004 observations made at a similar orbital phase provides a stronger evidence of the repetitive behaviour of the source.http://www.aanda.org/index.php?option=com_toc&url=/articles/aa/abs/2013/03/contents/contents.htmlhttp://www.aanda.org/http://dx.doi.org/10.1051/0004-6361/20122061
Yang–Baxter sigma models based on the CYBE

It is known that Yang–Baxter sigma models provide a systematic way to study integrable deformations of both principal chiral models and symmetric coset sigma models. In the original proposal and its subsequent development, the deformations have been characterized by classical r-matrices satisfying the modified classical Yang–Baxter equation (mCYBE). In this article, we propose the Yang–Baxter sigma models based on the classical Yang–Baxter equations (CYBE) rather than the mCYBE. This generalization enables us to utilize various kinds of solutions of the CYBE to classify integrable deformations. In particular, it is straightforward to realize partial deformations of the target space without loss of the integrability of the parent theory
Ligand binding mechanism in steroid receptors; from conserved plasticity to differential evolutionary constraints

Steroid receptor drugs have been available for more than half a century, but details 24 of the ligand binding mechanism has remained elusive. We solved X-ray structures of 25 the glucocorticoid and mineralocorticoid receptors to identify a conserved plasticity at 26 helix 6-7 region that extend the ligand binding pocket towards the receptor surface. 27 Since none of the endogenous ligands exploit this region, we hypothesized that it 28 constitutes an integral part of the binding event. Extensive all atom unbiased ligand 29 exit and entrance simulations corroborate a ligand binding pathway that gives the 30 observed structural plasticity a key functional role. Kinetic measurements reveal that 31 the receptor residence time correlate with structural rearrangements observed in both 32 structures and simulations. Ultimately, our findings reveal why nature has conserved 33 the capacity to open up this region and highlight how differences in the details of the 34 ligand entry process result in differential evolutionary constraints across the steroid 35 receptors.This study was supported by The European Research Council (2009-Adg25027-535 PELE) to V.G and by the SEV-2011-00067 grant of the Severo Ochoa Program. We 536 would like to acknowledge our AstraZeneca colleagues J. Hartleib, R.Unwin and 537 R.Knöll for helpful discussions. We also thank N. Blomberg (ELIXIR) and R. Neutze 538 (University of Gothenburg) for careful reading of the manuscript.Peer ReviewedPostprint (author's final draft
5-HTTLPR-environment interplay and its effects on neural reactivity in adolescents

It is not known how 5-HTTLPR genotype × childhood adversity (CA) interactions that are associated with an increased risk for affective disorders in population studies operate at the neural systems level. We hypothesized that healthy adolescents at increased genetic and environmental risk for developing mood disorders (depression and anxiety) would demonstrate increased amygdala reactivity to emotional stimuli compared to those with only one such risk factor or those with none. Participants (n = 67) were classified into one of 4 groups dependent on being homozygous for the long or short alleles within the serotonin-transporter-linked polymorphic region (5-HTTLPR) of the SLC6A4 gene and exposure to CA in the first 11. years of life (present or absent). A functional magnetic resonance imaging investigation was undertaken which involved viewing emotionally-salient face stimuli. In addition, we assessed the role of other variables hypothesized to influence amygdala reactivity, namely recent negative life-events (RNLE) assessed at ages 14 and 17, current anxiety symptoms and psychiatric history. We replicated prior findings demonstrating moderation by gene variants in 5-HTTLPR, but found no support for an effect of CA on amygdala reactivity. We also found a significant effect of RNLE aged 17 with amygdala reactivity demonstrating additive, but not interactive effects with 5-HTTLPR. A whole-brain analysis found a 5-HTTLPR × CA interaction in the lingual gyrus whereby CA appears to differentially modify neural reactivity depending on genotype. These results demonstrate that two different forms of environmental adversities interplay with 5-HTTLPR and thereby differentially impact amygdala and cortical reactivity
Terrestrial and submarine evidence for the extent and timing of the Last Glacial Maximum and the onset of deglaciation on the maritime-Antarctic and sub-Antarctic islands.

This paper is the maritime and sub–Antarctic contribution to the Scientific Committee for Antarctic Research (SCAR) Past Antarctic Ice Sheet Dynamics (PAIS) community Antarctic Ice Sheet reconstruction. The overarching aim for all sectors of Antarctica was to reconstruct the Last Glacial Maximum (LGM) ice sheet extent and thickness, and map the subsequent deglaciation in a series of 5000 year time slices. However, our review of the literature found surprisingly few high quality chronological constraints on changing glacier extents on these timescales in the maritime and sub–Antarctic sector. Therefore, in this paper we focus on an assessment of the terrestrial and offshore evidence for the LGM ice extent, establishing minimum ages for the onset of deglaciation, and separating evidence of deglaciation from LGM limits from those associated with later Holocene glacier fluctuations. Evidence included geomorphological descriptions of glacial landscapes, radiocarbon dated basal peat and lake sediment deposits, cosmogenic isotope ages of glacial features and molecular biological data. We propose a classification of the glacial history of the maritime and sub–Antarctic islands based on this assembled evidence. These include: (Type I) islands which accumulated little or no LGM ice; (Type II) islands with a limited LGM ice extent but evidence of extensive earlier continental shelf glaciations; (Type III) seamounts and volcanoes unlikely to have accumulated significant LGM ice cover; (Type IV) islands on shallow shelves with both terrestrial and submarine evidence of LGM (and/or earlier) ice expansion; (Type V) Islands north of the Antarctic Polar Front with terrestrial evidence of LGM ice expansion; and (Type VI) islands with no data. Finally, we review the climatological and geomorphological settings that separate the glaciological history of the islands within this classification scheme