pinecone/core-2020-05-10-deduplication huggingface dataset:
The input-output relationship approach to structural identifiability analysis

Analysis of the identifiability of a given model system is an essential prerequisite to the determination of model parameters from physical data. However, the tools available for the analysis of non-linear systems can be limited both in applicability and by computational intractability for any but the simplest of models. The input-output relation of a model summarises the input-output structure of the whole system and as such provides the potential for an alternative approach to this analysis. However for this approach to be valid it is necessary to determine whether the monomials of a differential polynomial are linearly independent. A simple test for this property is presented in this work. The derivation and analysis of this relation can be implemented symbolically within Maple. These techniques are applied to analyse classical models from biomedical systems modelling and those of enzyme catalysed reaction schemes.Peer-reviewedPost-prin
Causal holographic information.

We propose a measure of holographic information based on a causal wedge construction. The motivation behind this comes from an attempt to understand how boundary field theories can holographically reconstruct spacetime. We argue that given the knowledge of the reduced density matrix in a spatial region of the boundary, one should be able to reconstruct at least the corresponding bulk causal wedge. In attempt to quantify the ‘amount of information’ contained in a given spatial region in field theory, we consider a particular bulk surface (specifically a co-dimension two surface in the bulk spacetime which is an extremal surface on the boundary of the bulk causal wedge), and propose that the area of this surface, measured in Planck units, naturally quantifies the information content. We therefore call this area the causal holographic information. We also contrast our ideas with earlier studies of holographic entanglement entropy. In particular, we establish that the causal holographic information, whilst not being a von Neumann entropy, curiously enough agrees with the entanglement entropy in all cases where one has a microscopic understanding of entanglement entropy
Infrared structure at NNLO using antenna subtraction.

We consider the infrared structure of hadron-hadron collisions at next-to-next-to leading order using the antenna subtraction method. The general form of the subtraction terms is presented for double real, real-virtual and double virtual contributions. At NLO and NNLO it is shown that the virtual and double virtual subtraction terms can be written in terms of integrated dipoles, formed by systematically combining the mass factorisation contributions and integrated antenna functions. The integrated dipoles describing ℓ unresolved partons, denoted J(ℓ)2, are related to Catani’s IR singularity operators, I(ℓ)ij(∈). It is shown that the IR pole structure of the virtual and double virtual contributions can be written as a sum over integrated dipoles within the antenna subtraction formalism and the master expressions analogous to Catani’s one- and two-loop factorisation formulae are derived. To demonstrate the techniques described in this paper, we apply antenna subtraction to the production of two gluon jets via quark-antiquark scattering at NLO and NNLO. Double real, real-virtual and double virtual subtraction terms are explicitly derived for the leading colour NNLO contribution
The association of defensin HNP-2 with negatively charged membranes : a combined fluorescence and linear dichroism study.

The association of defensin HNP-2 with negatively charged membranes has been studied using a new approach that combines fluorescence and linear dichroism (LD) spectroscopies with simulated LD spectra in order to characterise the binding kinetics and bound configurations of the peptide. Binding to membranes composed of mixtures of diacylglycerophosphocholines (PC) with either diacylglycerophosphoglycerol (PG) or diacylglycerophosphoserine (PS) was conducted at lipid:peptide ratios that yielded binding, but not membrane fusion. HNP-2 association with membranes under these conditions was a 2 stage-process, with both stages exhibiting first order kinetics. The fast initial step, with a half-life of < 1 min, was followed by a slower step with a half-life of > 3 min. Conversion between the states was estimated to have an enthalpy of activation of approximately 10 kJ mol− 1 and an entropy of activation of − 0.2 kJ K mol− 1. LD spectra corresponding to each of the membrane bound states were generated by non-linear regression using a standard kinetic model. These spectra are interpreted in comparison with spectra calculated using the program Dichrocalc and reveal that the peptide associates with membranes in a small number of stable configurations. All of these configurations have a significant proportion of β-sheet structure residing in the plane of the membrane. Two configurations support structures previously proposed for defensins in membranes
One night's CPAP withdrawal in otherwise compliant OSA patients: marked driving impairment but good awareness of increased sleepiness

The final publication is available at Springer via http://dx.doi.org/10.1007/s11325-011-0588-8.PURPOSE. OSA patients effectively treated by and compliant with CPAP occasionally miss a night’s\ud
treatment. The purpose of this study was to use a real car interactive driving simulator to assess\ud
the effects of such an occurrence on the next day’s driving, including the extent to which these\ud
drivers are aware of increased sleepiness.\ud
METHODS. 11 long-term compliant CPAP treated 50-75y male OSA participants completed a 2h\ud
afternoon, simulated, realistic monotonous drive in an instrumented car, twice, following one night:\ud
i) normal sleep with CPAP ii) nil CPAP. Drifting out of road lane (‘incidents’), subjective sleepiness\ud
every 200sec and continuous EEG activities indicative of sleepiness and compensatory effort were\ud
monitored.\ud
RESULTS. Withdrawal of CPAP markedly increased sleep disturbance, and led to significantly more\ud
incidents, a shorter ‘safe’ driving duration, increased alpha and theta EEG power and greater\ud
subjective sleepiness. However, increased EEG beta activity indicated more compensatory effort\ud
was being applied. Importantly, under both conditions there was a highly significant correlation\ud
between subjective and EEG measures of sleepiness, to the extent that participants were well\ud
aware of the effects of nil CPAP. CONCLUSIONS. Patients should be aware that compliance with treatment every night is crucial for\ud
safe driving
Decision-centric adaptation appraisal for water management across Colorado's Continental Divide

This article was published by Elsevier as an open access article under the CC BY-NC-ND\ud
license (http://creativecommons.org/licenses/by-nc-nd/4.0/).A multi-step decision support process was developed and applied to the physically and legally complex case of water diversions from the Upper Colorado River across the Continental Divide to serve cities and farms along Colorado's Front Range. We illustrate our approach by simulating the performance of an existing drought-response measure, the Shoshone Call Relaxation Agreement (SCRA) [the adaptation measure], using the Water Evaluation and Planning (WEAP) tool [the hydrologic cycle and water systems model]; and the Statistical DownScaling Model (SDSM-DC) [the stochastic climate scenario generator]. Scenarios relevant to the decision community were analyzed and results indicate that this drought management measure would provide only a small storage benefit in offsetting the impacts of a shift to a warmer and drier future climate coupled with related environmental changes. The analysis demonstrates the importance of engaging water managers in the development of credible and computationally efficient decision support tools that accurately capture the physical, legal and contractual dimensions of their climate risk management problems
Determination of $m_c$ and $m_b$ from quarkonium 1S energy levels in
  perturbative QCD

We update determination of the $\overline{\rm MS}$ masses of the charm and
bottom quarks, from comparisons of the masses of the charmonium and bottomonium
$1S$ states with their perturbative predictions up to
next-to-next-to-next-to-leading order in $\varepsilon$ expansion and using the
$\overline{\rm MS}$ masses. Effects of non-zero charm-quark mass in the
bottomonium masses are incorporated up to next-to-next-to-leading order. We
obtain $\overline m_c=1246\pm 2 (d_3) \pm 4 (\alpha_s) \pm 23 (\text{h.o.}
)~{\rm MeV} $ and $\overline m_b=4197\pm 2 (d_3) \pm 6 (\alpha_s) \pm 20
(\text{h.o.} )\pm 5 (m_c)~ {\rm MeV} $, which agree with the current Particle
Data Group values.Comment: 12 pages, 5 figures, 1 table. v2: Typo corrected in Eq.(3); no change
  of final result
Neutrino masses and mixings: Status of known and unknown $3\nu$
  parameters

Within the standard 3nu mass-mixing framework, we present an up-to-date
global analysis of neutrino oscillation data (as of January 2016), including
the latest available results from experiments with atmospheric neutrinos
(Super-Kamiokande and IceCube DeepCore), at accelerators (first T2K anti-nu and
NOvA nu runs in both appearance and disappearance mode), and at short-baseline
reactors (Daya Bay and RENO far/near spectral ratios), as well as a reanalysis
of older KamLAND data in the light of the "bump" feature recently observed in
reactor spectra. We discuss improved constraints on the five known oscillation
parameters (delta m^2, |Delta m^2|, sin^2theta_12, sin^2theta_13,
sin^2theta_23), and the status of the three remaining unknown parameters: the
mass hierarchy, the theta_23 octant, and the possible CP-violating phase delta.
With respect to previous global fits, we find that the reanalysis of KamLAND
data induces a slight decrease of both delta m^2 and sin^2theta_12, while the
latest accelerator and atmospheric data induce a slight increase of |Delta
m^2|. Concerning the unknown parameters, we confirm the previous intriguing
preference for negative values of sin(delta) [with best-fit values around
sin(delta) ~ -0.9], but we find no statistically significant indication about
the theta_23 octant or the mass hierarchy (normal or inverted). Assuming an
alternative (so-called LEM) analysis of NOvA data, some delta ranges can be
excluded at >3 sigma, and the normal mass hierarchy appears to be slightly
favored at 90% C.L. We also describe in detail the covariances of selected
pairs of oscillation parameters. Finally, we briefly discuss the implications
of the above results on the three non-oscillation observables sensitive to the
(unknown) absolute nu mass scale: the sum of nu masses, the effective nu_e
mass, and the effective Majorana mass.Comment: 15 pages, 9 figures, 2 tables. Invited contribution prepared for the
  Nuclear Physics B Special Issue on "Neutrino Oscillations" celebrating the
  Nobel Prize in Physics 201
Reproducibility of arterial stiffness and wave reflections in chronic obstructive pulmonary disease: the contribution of lung hyperinflation and a comparison of techniques.

Significant cardiovascular morbidity and mortality exists in chronic obstructive pulmonary disease (COPD). Arterial stiffness is raised in COPD and may be a mechanistic link. Non-invasive assessment of arterial stiffness has the potential to be a surrogate outcome measure, although no reproducibility data exists in COPD patients. Two studies (23 and 33 COPD patients) were undertaken to 1) assess the Vicorder reproducibility of carotid-femoral pulse wave velocity and Augmentation index in COPD; 2) compare it to SphygmoCor; and 3) assess the contribution of lung hyperinflation to measurement variability. There were excellent correlations and good agreement between repeat Vicorder measurements for carotid-femoral pulse wave velocity (rÂ =Â 0.96 (pÂ <Â 0.001); mean difference Â±SDÂ =Â -0.03Â Â±Â 0.36Â m/s (pÂ =Â 0.65); co-efficient of reproducibilityÂ =Â 4.02%; limits of agreementÂ =Â -0.68-0.75Â m/s). Augmentation index significantly correlated (rÂ =Â 0.736 (pÂ <Â 0.001); mean difference Â±SDÂ =Â 0.72Â Â±Â 4.86% (pÂ =Â 0.48), however limits of agreement were only 10.42-9.02%, with co-efficient of reproducibility of 27.93%. Comparing devices, Vicorder values were lower but there was satisfactory agreement. There were no correlation between lung hyperinflation (as measured by residual volume percent predicted, total lung capacity percent predicted or the ratio of inspiratory capacity to residual volume) and variability of measurements in either study. In COPD, measurement of carotid-femoral pulse wave velocity is highly reproducible, not affected by lung hyperinflation and suitable as a surrogate endpoint in research studies. Day-to-day variation in augmentation index highlights the importance of such studies prior to the planning and undertaking of clinical COPD research
Mammalian Target of Rapamycin Complex 2 Controls CD8 T Cell Memory Differentiation in a Foxo1-Dependent Manner

Upon infection, antigen-specific naive CD8 T cells are activated and differentiate into short-lived effector cells (SLECs) and memory precursor cells (MPECs). The underlying signaling pathways remain largely unresolved. We show that Rictor, the core component of mammalian target of rapamycin complex 2 (mTORC2), regulates SLEC and MPEC commitment. Rictor deficiency favors memory formation and increases IL-2 secretion capacity without dampening effector functions. Moreover, mTORC2-deficient memory T cells mount more potent recall responses. Enhanced memory formation in the absence of mTORC2 was associated with Eomes and Tcf-1 upregulation, repression of T-bet, enhanced mitochondrial spare respiratory capacity, and fatty acid oxidation. This transcriptional and metabolic reprogramming is mainly driven by nuclear stabilization of Foxo1. Silencing of Foxo1 reversed the increased MPEC differentiation and IL-2 production and led to an impaired recall response of Rictor KO memory T cells. Therefore, mTORC2 is a critical regulator of CD8 T cell differentiation and may be an important target for immunotherapy interventions
Biogeochemical and contaminant cycling in sediments from a human-impacted coastal lagoon â Introduction and summary

International audienceFrom 2001 to 2003, the Microbent project (ââBiogeochemical processes at the water sediment interface in eutrophic environmentââ) was carried out within the framework of the Programme National Environnement CoËtier, the French contribution to LandeOcean Interaction in the Coastal Zone (LOICZ). The Microbent programme was focused on the study of sediment biogeochemical cycles of carbon, oxygen, sulphur, iron, nitrogen, and phosphorus in relation to the faunal activity in the sediment and their relation with the mobility of metallic contaminants at the sedimentewater interface (SWI) in a Mediterranean coastal lagoon (Thau lagoon, France; Fig. 1). The aim of Microbent was to set up an interdisciplinary study bringing together geochemists, sedimentologists, and biologists in order to understand and quantify the main reaction pathways, and the fluxes of contaminants at the SWI, including those related to benthic fauna. Work was focused on the processes which generate contaminant fluxes: (1) early diagenetic processes, which generate the chemical conditions of the environment; (2) processes leading to the transfer of contaminants from particles toward biofilms, water column, and organisms; and (3) processes of sediment mixing by organisms and sediment accumulation
Hopf algebra structure on packed square matrices

International audienceWe construct a new bigraded Hopf algebra whose bases are indexed by square matrices with entries in the alphabet {0, 1,. .. , k}, k 1, without null rows or columns. This Hopf algebra generalizes the one of permutations of Malvenuto and Reutenauer, the one of k-colored permutations of Novelli and Thibon, and the one of uniform block permutations of Aguiar and Orellana. We study the algebraic structure of our Hopf algebra and show, by exhibiting multiplicative bases, that it is free. We moreover show that it is self-dual and admits a bidendriform bialgebra structure. Besides, as a Hopf subalgebra, we obtain a new one indexed by alternating sign matrices. We study some of its properties and algebraic quotients defined through alternating sign matrices statistics
An interactive 3D medical visualization system based on a light ﬁeld display

This paper presents a prototype medical data visualization system exploiting a light field display and custom direct volume rendering techniques to enhance understanding of massive volumetric data, such as CT, MRI, and PET scans. The system can be integrated with standard medical image archives and extends the capabilities of current radiology workstations by supporting real-time rendering of volumes of potentially unlimited size on light field displays generating dynamic observer-independent light fields. The system allows multiple untracked naked-eye users in a sufficiently large interaction area to coherently perceive rendered volumes as real objects, with stereo and motion parallax cues. In this way, an effective collaborative analysis of volumetric data can be achieved. Evaluation tests demonstrate the usefulness of the generated depth cues and the improved performance in understanding complex spatial structures with respect to standard techniques.883-893Pubblicat
Observing extended sources with the Herschel          SPIRE Fourier Transform Spectrometer

International audienceThe Spectral and Photometric Imaging Receiver (SPIRE) on the European Space Agency’s            Herschel Space Observatory utilizes a pioneering design for its imaging          spectrometer in the form of a Fourier Transform Spectrometer (FTS). The standard FTS data          reduction and calibration schemes are aimed at objects with either a spatial extent that          is much larger than the beam size or a source that can be approximated as a point source          within the beam. However, when sources are of intermediate spatial extent, neither of          these calibrations schemes is appropriate and both the spatial response of the instrument          and the source’s light profile must be taken into account and the coupling between them          explicitly derived. To that end, we derive the necessary corrections using an observed          spectrum of a fully extended source with the beam profile and considering the source’s          light profile. We apply the derived correction to several observations of planets and          compare the corrected spectra with their spectral models to study the beam coupling          efficiency of the instrument in the case of partially extended sources. We find that we          can apply these correction factors for sources with angular sizes up to            θD ~ 17′′. We demonstrate how the angular size of          an extended source can be estimated using the difference between the subspectra observed          at the overlap bandwidth of the two frequency channels in the spectrometer, at            959 < ν < 989   GHz.          Using this technique on an observation of Saturn, we estimate a size of 17.2′′,          which is 3% larger than its true size on the day of observation. Finally, we show the          results of the correction applied on observations of a nearby galaxy, M82, and the compact          core of a Galactic molecular cloud, Sgr B2
Ephemeris, orbital decay, and masses of ten eclipsing high-mass X-ray binaries

International audienceWe update the ephemeris of the eclipsing high-mass X-ray binary (HMXB) systems LMC X-4, Cen X-3, 4U 1700-377, 4U 1538-522, SMC X-1, IGR J18027-2016, Vela X-1,IGR J17252-3616, XTE J1855-026, and OAO 1657-415 with the help of more than ten years of monitoring these sources with the All Sky Monitor onboard RXTE and with the Integral Soft Gamma-Ray Imager onboard INTEGRAL. These results are used to refine previous measurements of the orbital period decay of all sources (where available) and provide the first accurate values of the apsidal advance in Vela X-1 and 4U 1538-522. Updated values for the masses of the neutron stars hosted in the ten HMXBs are also provided, as well as the long-term light curves folded on the best determined orbital parameters of the sources. These light curves reveal complex eclipse ingresses and egresses that are understood mostly as being caused by accretion wakes. Our results constitute a database to be used for population and evolutionary studies of HMXBs and for theoretical modeling of long-term accretion in wind-fed X-ray binaries
Screening of ARHSP-TCC patients expands the spectrum of SPG11 mutations and includes a large scale gene deletion

Autosomal recessive spastic paraplegia with thinning of corpus callosum (ARHSP-TCC) is a complex form of HSP initially described in Japan but subsequently reported to have a worldwide distribution with a particular high frequency in multiple families from the Mediterranean basin. We recently showed that ARHSP-TCC is commonly associated with mutations in SPG11/KIAA1840 on chromosome 15q. We have now screened a collection of new patients mainly originating from Italy and Brazil, in order to further ascertain the spectrum of mutations in SPG11, enlarge the ethnic origin of SPG11 patients, determine the relative frequency at the level of single Countries (i.e., Italy), and establish whether there is one or more common mutation. In 25 index cases we identified 32 mutations; 22 are novel, including 9 nonsense, 3 small deletions, 4 insertions, 1 in/del, 1 small duplication, 1 missense, 2 splice-site, and for the first time a large genomic rearrangement. This brings the total number of SPG11 mutated patients in the SPATAX collection to 111 cases in 44 families and in 17 isolated cases, from 16 Countries, all assessed using homogeneous clinical criteria. While expanding the spectrum of mutations in SPG11, this larger series also corroborated the notion that even within apparently homogeneous population a molecular diagnosis cannot be achieved without full gene sequencing. Â© 2008 Wiley-Liss, Inc
Long-range and short-range dihadron angular correlations in central PbPb collisions at √sNN = 2.76 TeV

Artículo escrito por un elevado número de autores, solo se referencian el que aparece en primer lugar, el nombre del grupo de colaboración, si le hubiere, y los autores pertenecientes a la UAMJournal of High Energy Physics 2011.7 (2011): 076 reproduced by permission of Scuola Internazionale Superiore di Studi Avanzati (SISSA)First measurements of dihadron correlations for charged particles are presented for central PbPb collisions at a nucleon-nucleon center-of-mass energy of 2.76TeV over a broad range in relative pseudorapidity (Δη) and the full range of relative azimuthal angle (Δø). The data were collected with the CMS detector, at the LHC. A broadening of the away-side (Δø y≈ π) azimuthal correlation is observed at all Δη, as compared to the measurements in pp collisions. Furthermore, long-range dihadron correlations in Δη are observed for particles with similar ø values. This phenomenon, also known as the "ridge", persists up to at least IΔηI = 4. For particles with transverse momenta (pT) of 2-4 GeV/c, the ridge is found to be most prominent when these particles are correlated with particles of pT = 2-6 GeV/c, and to be much reduced when paired with particles of pT = 10-12 GeV/