pinecone/core-2020-05-10-deduplication huggingface dataset:
Direct prediction of the profile of sequences compatible to a protein structure by neural networks with fragment-based local and energy-based nonlocal profiles

Locating sequences compatible with a protein structural fold is the well-known inverse protein-folding problem. While significant progress has been made, the success rate of protein design remains low. As a result, a library of designed sequences or profile of sequences is currently employed for guiding experimental screening or directed evolution. Sequence profiles can be computationally predicted by iterative mutations of a random sequence to produce energy-optimized sequences, or by combining sequences of structurally similar fragments in a template library. The latter approach is computationally more efficient but yields less accurate profiles than the former because of lacking tertiary structural information. Here we present a method called SPIN that predicts Sequence Profiles by Integrated Neural network based on fragment-derived sequence profiles and structure-derived energy profiles. SPIN improves over the fragment-derived profile by 6.7% (from 23.6 to 30.3%) in sequence identity between predicted and wild-type sequences. The method also reduces the number of residues in low complex regions by 15.7% and has a significantly better balance of hydrophilic and hydrophobic residues at protein surface. The accuracy of sequence profiles obtained is comparable to those generated from the protein design program RosettaDesign 3.5. This highly efficient method for predicting sequence profiles from structures will be useful as a single-body scoring term for improving scoring functions used in protein design and fold recognition. It also complements protein design programs in guiding experimental design of the sequence library for screening and directed evolution of designed sequences.Full Tex
Planck intermediate results. XXVII. High-redshift infrared galaxy overdensity candidates and lensed sources discovered by Planck and confirmed by Herschel-SPIRE

We have used the Planck all-sky submillimetre and millimetre maps to search for rare sources distinguished by extreme brightness, a few hundred millijanskies, and their potential for being situated at high redshift. These "cold" Planck sources, selected using the High Frequency Instrument (HFI) directly from the maps and from the Planck Catalogue of Compact Sources (PCCS), all satisfy the criterion of having their rest-frame far-infrared peak redshifted to the frequency range 353-857 GHz. This colour-selection favours galaxies in the redshift range z = 2-4, which we consider as cold peaks in the cosmic infrared background. With a 4.'5 beam at the four highest frequencies, our sample is expected to include overdensities of galaxies in groups or clusters, lensed galaxies, and chance line-of-sight projections. We perform a dedicated Herschel-SPIRE follow-up of 234 such Planck targets, finding a significant excess of red 350 and 500 mu m sources, in comparison to reference SPIRE fields. About 94% of the SPIRE sources in the Planck fields are consistent with being overdensities of galaxies peaking at 350 mu m, with 3% peaking at 500 mu m, and none peaking at 250 mu m. About 3% are candidate lensed systems, all 12 of which have secure spectroscopic confirmations, placing them at redshifts z > 2.2. Only four targets are Galactic cirrus, yielding a success rate in our search strategy for identifying extragalactic sources within the Planck beam of better than 98%. The galaxy overdensities are detected with high significance, half of the sample showing statistical significance above 10 sigma. The SPIRE photometric redshifts of galaxies in overdensities suggest a peak at z similar or equal to 2, assuming a single common dust temperature for the sources of T-d = 35 K. Under this assumption, we derive an infrared (IR) luminosity for each SPIRE source of about 4x10(12) L-circle dot, yielding star formation rates of typically 700 M-circle dot yr(-1). If the observed overdensities are actual gravitationally-bound structures, the total IR luminosity of all their SPIRE-detected sources peaks at 4 x 10(13) L-circle dot, leading to total star formation rates of perhaps 7 x 10(3) M-circle dot yr(-1) per overdensity. Taken together, these sources show the signatures of high-z (z > 2) protoclusters of intensively star-forming galaxies. All these observations confirm the uniqueness of our sample compared to reference samples and demonstrate the ability of the all-sky Planck-HFI cold sources to select populations of cosmological and astrophysical interest for structure formation studies
Local relevancy evaluation in the accreditation bodies for engineering master's programs

Accreditation models in the international context mainly consider the evaluation of learning outcomes and the ability of programs (or higher education institutions) to achieve the educational objectives stated in their mission. However, it is not clear if these objectives and therefore their outcomes satisfy real national and regional needs, a critical point in engineering master's programs, especially in developing countries. The aim of this paper is to study the importance of the local relevancy evaluation of these programs and to analyze the main models of quality assurance and accreditation bodies of USA, Europe and Latin America, in order to ascertain whether the relevancy is evaluated or not. After a literature review, we found that in a free-market economic context and international education, the accreditation of master’s programs follows an international accreditation model, and doesn´t take in account in most cases criteria and indicators for local relevancy. It concludes that it is necessary both, international accreditation to ensure the effectiveness of the program (achievement of learning outcomes) and the national accreditation through which it could ensure local relevancy of programs, for which we are giving some indicators
Triage nurse perceptions of the use, reliability and acceptability of the Toowoomba adult triage trauma tool (TATTT)

The \u27Toowoomba Adult Triage Trauma Tool\u27 (TATTT) is a computerised clinical decision support tool developed to provide an evidence-based, valid and consistent method of triage assessment and categorisation. The objective of this study was to determine the most appropriate training and testing strategy for implementing the TATTT and to evaluate its acceptability for assisting in the triage prioritisation process. Triage nurses (15) from two hospitals underwent training in the TATTT and were tested on its application. Semi-structured interviews gathered their perceptions of the training, the methods for testing and the acceptability of the TATTT for assisting in triage. The TATTT was viewed positively by all but one of the nurses. Participants believed that it provided clear direction in the triage assessment process, increased their confidence in reaching a decision and would be comfortable in adopting the TATTT in clinical practice. The study has shown that the TATTT is acceptable to users and is viewed as a viable alternative to current triage practice
Integrated Fractionation-Hydrolysis Process using Sub- and Supercritical Water for Lignocellulosic Biomass Valorization

A novel process coupling the fractionation and hydrolysis reactors is presented. Holm oak was used as real lignocellulosic biomass to be treated. In the fractionation reactor, hemicellulose and cellulose were solubilized and partially hydrolyzed in different stages with the aim of feeding the hydrolysis reactor with high C5 concentrations or C6 concentrations. The fractionation was performed in two stages: at 180°C optimizing the hemicellulose extraction and at 260°C extracting cellulose and hard hemicellulose remaining in the biomass structure. Three water flows were tested: 11, 17 and 26 cm³/min. Sugar yields from 71 to 75% were reached, mainly composed of xylose and glucose oligomers and lower amounts of other chemicals, like retro-aldol products, acetic acid or 5-HMF. The outlet stream from the fractionation reactor was directly mixed with sub or supercritical water at the inlet mixer of a SHR where the reaction time was precisely controlled. The temperature, pressure and reaction time were modified to get an insight of their effect on the yield of retro-aldol condensation products. Yields of 24% for glycolaldehyde, and pyruvaldehyde were found at 8.3 s, 350°C and 162 bar (hydrolysis reactor conditions). On other hand, 25% of lactic acid was found at 0.23 s, 396°C and 245 bar. A discussion based on a known reaction pathway is proposed. Moreover, a kinetic model for the hydrolysis reactor was proposed, being able to reproduce the experimental data with deviations lower than 10% for sugars and other products extracted. This combined process performs a selective valorization of real lignocellulosic biomass, avoiding the costly process of extreme grinding needed for the fluidization in a continuous hydrothermal process.CTQ2015-64892-R (MINECO/FEDER
Measurement of the ratio of branching fractions and difference in CP asymmetries of the decays $B^+ \to J/\psi\pi^+$ and $B^+ \to J/\psi K^+$

The ratio of branching fractions and the difference in CP asymmetries of the decays $B^+ \to J/\psi\pi^+$ and $B^+ \to J/\psi K^+$ are measured using a data sample of pp collisions collected by the LHCb experiment, corresponding to an integrated luminosity of 3 fb$^{−1}$ at centre-of-mass energies of 7 and 8 TeV. The results are\ud
$\frac{\mathcal{B} (B^+ \to J/\psi\pi^+)} {\mathcal{B} (B^+ \to J/psi K^+)} = (3.83 \pm 0.03 \pm 0.03) \times 10^{−2}$,\ud
\ud
$\mathcal{A}^{CP} (B^+ \to J/\psi\pi^+) − \mathcal{A}^{CP} (B^+ \to J/\psi K^+) = (1.82 \pm 0.86 \pm 0.14) \times 10^{−2}$,\ud
where the first uncertainties are statistical and the second are systematic. Combining this result with a recent LHCb measurement of $\mathcal{A}^{CP} (B^+ \to J/\psi K^+)$ provides the most precise estimate to date of CP violation in the decay $B^+ \to J/\psi\pi^+$,\ud
$\mathcal{A}^{CP}(B^+ \to J/\psi\pi^+) = (1.91 \pm 0.89 \pm 0.16) \times 10^{−2}$
Strain distribution in GaN hexagons measured by Raman spectroscopy

Epitaxial growth of GaN layers normally starts in a three-dimensional growth mode at nucleation sites. Growth islands are formed which coalesce when a certain layer thickness is achieved. In our samples these islands show hexagonal structure and in some cases a flat surface plane perpendicular to the (0001) growth direction. We studied these hexagons by spatially resolved Raman spectroscopy. Raman spectroscopy is a powerful tool to determine strain in GaN layers, because the E2 Raman modes are very sensitive to the change of the elastic properties of the material. In all cases we found that the centre of the hexagons is nearly strain free whereas at the edges there is a tensile strain. This tensile strain, however, is not as high as in the surrounding film.FCT - Praxis XXI/BD/16284/98Brite-Euram Project Rainbow (BRPR-CT96-0340)
A novel subset of putative stem/progenitor CD34⁺Oct-4⁺ cells is the major target for SARS coronavirus in human lung

Identification of the nature of severe acute respiratory syndrome (SARS)-infected cells is crucial toward understanding the pathogenesis. Using multicolor colocalization techniques, we previously reported that SARS+ cells in the lung of fatally infected patients expressed the only known functional receptor, angiotensin-converting enzyme 2, and also a binding receptor, liver/lymph node–specific ICAM-3–grabbing non-integrin (CD209L). In this study, we show that SARS-infected cells also express the stem/progenitor cell markers CD34 and Oct-4, and do not express cytokeratin or surfactant. These putative lung stem/progenitor cells can also be identified in some non-SARS individuals and can be infected by SARS-coronavirus ex vivo. Infection of these cells may contribute to the loss of lung repair capacity that leads to respiratory failure as clinically observed
Predicting Emotional Reaction in Social Networks

Online content has shifted from static and document-oriented to dy- namic and discussion-oriented, leading users to spend an increasing amount of time navigating online discussions in order to participate in their social network. Recent work on emotional contagion in social networks has shown that information is not neutral and affects its receiver. In this work, we present an approach to detect the emotional impact of news, using a dataset extracted from the Face- book pages of a major news provider. The results of our approach significantly outperform our selected baselines
Intersection of world-lines on curved surfaces and path-ordering of the Wilson loop.

We study contact interactions for long world-lines on a curved surface, focusing on the average number of times two world-lines intersect as a function of their end-points. The result can be used to extend the concept of path-ordering, as employed in the Wilson loop, from a closed curve into the interior of a surface spanning the curve. Taking this surface as a string world-sheet yields a generalisation of the string contact interaction previously used to represent the Abelian Wilson loop as a tensionless string. We also describe a supersymmetric generalisation
Not in our backyard : spectroscopic support for the CLASH z=11 candidate MACS 0647-JD

We report on our first set of spectroscopic Hubble Space Telescope observations of the z approximate to 11 candidate galaxy, which is strongly lensed by the MACSJ 0647.7+7015 galaxy cluster. The three lensed images are faint and we show that these early slitless grism observations are of sufficient depth to investigate whether this high-redshift candidate, identified by its strong photometric break at approximate to 1.5 mu m, could possibly be an emission line galaxy at a much lower redshift. While such an interloper would imply the existence of a rather peculiar object, we show here that such strong emission lines would clearly have been detected. Comparing realistic, two-dimensional simulations to these new observations, we would expect the necessary emission lines to be detected at >5 sigma, though we see no evidence for such lines in the dispersed data of any of the three lensed images. We therefore exclude that this object could be a low-redshift emission line interloper, which significantly increases the likelihood of this candidate being a bona fide z approximate to 11 galaxy
Search for massive resonances decaying into WW, WZ or ZZ bosons in proton-proton collisions at √s=13 TeV

A search is presented for new massive resonances decaying to WW, WZ or ZZ bosons in ℓνq[¯ over q] and q[¯ over q]q[¯   over q] final states. Results are based on data corresponding to an integrated luminosity of 2.3-2.7 fb[superscript −1] recorded in proton-proton collisions at √s=13 TeV with the CMS detector at the LHC. Decays of spin-1 and spin-2 resonances into two vector bosons are sought in the mass range 0.6-4.0 TeV. No significant excess over the standard model background is observed. Combining the results of the ℓνq[¯ over q] and q[¯ over q] q[¯ over q] final states, cross section and mass exclusion limits are set for models that predict heavy spin-1 and spin-2 resonances. This is the first search for a narrow-width spin-2 resonance at √s=13 TeV. Keywords: Beyond Standard Model, Hadron-Hadron scattering (experiments), Particle and resonance production, proton-proton scatteringNational Science Foundation (U.S.)United States. Department of Energ
Quantitative Holocene climatic reconstructions for the lower Yangtze region of China

Quantitative proxy-based and high-resolution palaeoclimatic datasets are scarce for the lower reaches of the Yangtze River (LYR) basin. This region is in a transitional vegetation zone which is climatologically sensitive; and as a birthplace for prehistorical civilization in China, it is important to understand how palaeoclimatic dynamics played a role in affecting cultural development in the region. We present a pollen-based and regionally-averaged Holocene climatic twin-dataset for mean total annual precipitation (PANN) and mean annual temperature (TANN) covering the last 10,000 years for the LYR region. This is based on the technique of weighted averaging-partial least squares regression to establish robust calibration models for obtaining reliable climatic inferences. The pollen-based reconstructions generally show an early Holocene climatic optimum with both abundant monsoonal rainfall and warm thermal conditions, and a declining pattern of both PANN and TANN values in the middle to late Holocene. The main driving forces behind the Holocene climatic changes in the LYR area are likely summer solar insolation associated with tropical or subtropical macro-scale climatic circulations such as the Intertropical Convergence Zone (ITCZ), Western Pacific Subtropical High (WPSH), and El Nio/Southern Oscillation (ENSO). Regional multi-proxy comparisons indicate that the Holocene variations in precipitation and temperature for the LYR region display an in-phase relationship with other related proxy records from southern monsoonal China and the Indian monsoon-influenced regions, but are inconsistent with the Holocene moisture or temperature records from northern monsoonal China and the westerly-dominated region in northwestern China. Overall, our comprehensive palaeoclimatic dataset and models may be significant tools for understanding the Holocene Asian monsoonal evolution and for anticipating its future dynamics in eastern Asia
Random breath testing in Queensland and Western Australia : Examination of how the random breath testing rate influences alcohol related traffic crash rates

In this paper we explore the relationship between monthly random breath testing (RBT) rates (per 1000 licensed drivers) and alcohol-related traffic crash (ARTC) rates over time, across two Australian states: Queensland and Western Australia. We analyse the RBT, ARTC and licensed driver rates across 12 years; however, due to administrative restrictions, we model ARTC rates against RBT rates for the period July 2004 to June 2009.\ud
\ud
The Queensland data reveals that the monthly ARTC rate is almost flat over the five year period. Based on the results of the analysis, an average of 5.5 ARTCs per 100,000 licensed drivers are observed across the study period. For the same period, the monthly rate of RBTs per 1000 licensed drivers is observed to be decreasing across the study with the results of the analysis revealing no significant variations in the data.\ud
\ud
The comparison between Western Australia and Queensland shows that Queensland's ARTC monthly percent change (MPC) is 0.014 compared to the MPC of 0.47 for Western Australia. While Queensland maintains a relatively flat ARTC rate, the ARTC rate in Western Australia is increasing. Our analysis reveals an inverse relationship between ARTC RBT rates, that for every 10% increase in the percentage of RBTs to licensed driver there is a 0.15 decrease in the rate of ARTCs per 100,000 licenced drivers. Moreover, in Western Australia, if the 2011 ratio of 1:2 (RBTs to annual number of licensed drivers) were to double to a ratio of 1:1, we estimate the number of monthly ARTCs would reduce by approximately 15.\ud
\ud
Based on these findings we believe that as the number of RBTs conducted increases the number of drivers willing to risk being detected for drinking driving decreases, because the perceived risk of being detected is considered greater. This is turn results in the number of ARTCs diminishing. The results of this study provide an important evidence base for policy decisions for RBT operations
Cross sections for hard exclusive electroproduction of pi+ mesons on a
  hydrogen target

The exclusive electroproduction of pi+ mesons was studied with the Hermes
spectrometer at the DESY laboratory by scattering 27.6 GeV positron and
electron beams off an internal hydrogen gas target. The virtual-photon cross
sections were measured as a function of the Mandelstam variable t and the
squared four momentum -Q^2 of the exchanged virtual photon. A model calculation
based on Generalized Parton Distributions is in fair agreement with the data at
low values of |t| if power corrections are included. A model calculation based
on the Regge formalism gives a good description of the magnitude and the t and
Q^2 dependences of the cross section.Comment: 7 pages, 5 figures, revised tex
Relativistic description of BCS-BEC crossover in nuclear matter

We study theoretically the di-neutron spatial correlations and the crossover
from superfluidity of neutron Cooper pairs in the $^1S_0$ pairing channel to
Bose-Einstein condensation (BEC) of di-neutron pairs for both symmetric and
neutron matter in the microscopic relativistic pairing theory. We take the bare
nucleon-nucleon interaction Bonn-B in the particle-particle channel and the
effective interaction PK1 of the relativistic mean-field approach in the
particle-hole channel. It is found that the spatial structure of neutron Cooper
pair wave function evolves continuously from BCS-type to BEC-type as density
decreases. We see a strong concentration of the probability density revealed
for the neutron pairs in the fairly small relative distance around $1.5 {\rm
fm}$ and the neutron Fermi momentum $k_{Fn}\in[0.6,1.0] {\rm fm^{-1}}$.
However, from the effective chemical potential and the quasiparticle excitation
spectrum, there is no evidence for the appearance of a true BEC state of
neutron pairs at any density. The most BEC-like state may appear at
$k_{Fn}\thicksim0.2 {\rm fm^{-1}}$ by examining the density correlation
function. From the coherence length and the probability distribution of neutron
Cooper pairs as well as the ratio between the neutron pairing gap and the
kinetic energy at the Fermi surface, some features of the BCS-BEC crossover are
seen in the density regions, $0.05 {\rm fm^{-1}}<k_{Fn}<0.7 (0.75) {\rm
fm^{-1}}$, for the symmetric nuclear (pure neutron) matter.Comment: 7 pages, 6 figures, Accepted by Physics Letters
The Spin-dependent Structure Function of the Proton g_1^p and a Test of
  the Bjorken Sum Rule

The inclusive double-spin asymmetry, A_1^p, has been measured at COMPASS in
deepinelastic polarised muon scattering off a large polarised NH3 target. The
data, collected in the year 2007, cover the range Q2 > 1 (GeV/c)^2, 0.004 < x <
0.7 and improve the statistical precision of g_1^p(x) by a factor of two in the
region x < 0.02. The new proton asymmetries are combined with those previously
published for the deuteron to extract the non-singlet spin-dependent structure
function g_1^NS(x,Q2). The isovector quark density, Delta_q_3(x,Q2), is
evaluated from a NLO QCD fit of g_1^NS. The first moment of Delta_q3 is in good
agreement with the value predicted by the Bjorken sum rule and corresponds to a
ratio of the axial and vector coupling constants g_A/g_V =
1.28+-0.07(stat)+-0.10(syst).Comment: 12 pages, 5 figure
Exploring correlations in the stochastic Yang-Mills vacuum

The correlation lengths of nonperturbative-nonconfining and confining
stochastic background Yang-Mills fields are obtained by means of a direct
analytic path-integral evaluation of the Green functions of the so-called one-
and two-gluon gluelumps. Numerically, these lengths turn out to be in a good
agreement with those known from the earlier, Hamiltonian, treatment of such
Green functions. It is also demonstrated that the correlation function of
nonperturbative-nonconfining fields decreases with the deviation of the path in
this correlation function from the straight-line one.Comment: 14 pages, 3 figures; an Appendix is included, which addresses the
  path-dependence of the correlation function; version to appear in Phys. Lett.