pinecone/core-2020-05-10-deduplication huggingface dataset:
Disordered regions in transmembrane proteins

AbstractThe functions of transmembrane proteins in living cells are widespread; they range from various transport processes to energy production, from cell–cell adhesion to communication. Structurally, they are highly ordered in their membrane-spanning regions, but may contain disordered regions in the cytosolic and extra-cytosolic parts. In this study, we have investigated the disordered regions in transmembrane proteins by a stringent definition of disordered residues on the currently available largest experimental dataset, and show a significant correlation between the spatial distributions of positively charged residues and disordered regions. This finding suggests a new role of disordered regions in transmembrane proteins by providing structural flexibility for stabilizing interactions with negatively charged head groups of the lipid molecules. We also find a preference of structural disorder in the terminal – as opposed to loop – regions in transmembrane proteins, and survey the respective functions involved in recruiting other proteins or mediating allosteric signaling effects. Finally, we critically compare disorder prediction methods on our transmembrane protein set. While there are no major differences between these methods using the usual statistics, such as per residue accuracies, Matthew's correlation coefficients, etc.; substantial differences can be found regarding the spatial distribution of the predicted disordered regions. We conclude that a predictor optimized for transmembrane proteins would be of high value to the field of structural disorder
Exclusive c→s,d semileptonic decays of ground-state spin-1/2 doubly charmed baryons

AbstractWe evaluate exclusive semileptonic decays of ground-state spin-1/2 doubly heavy charmed baryons driven by a c→s,d transition at the quark level. Our results for the form factors are consistent with heavy quark spin symmetry constraints which are valid in the limit of an infinitely massive charm quark and near zero recoil. Only a few exclusive semileptonic decay channels have been theoretically analyzed before. For those cases we find that our results are in a reasonable agreement with previous calculations
Fractional angular momentum in non-commutative spaces

AbstractIn noncommutative spaces to maintain Bose–Einstein statistics for identical particles at the non-perturbation level described by deformed annihilation-creation operators when the state vector space of identical bosons is constructed by generalizing one-particle quantum mechanics it is explored that the consistent ansatz of commutation relations of phase space variables should simultaneously include space–space non-commutativity and momentum–momentum non-commutativity, and a new type of boson commutation relations at the deformed level is obtained. Consistent perturbation expansions of deformed annihilation-creation operators are obtained. The influence of the new boson commutation relations on dynamics is discussed. The non-perturbation and perturbation property of the orbital angular momentum of two-dimensional system are investigated. Its spectrum possesses fractional eigen values and fractional intervals
Search for single production of a vector-like quark via a heavy gluon in the 4b final state with the ATLAS detector in pp collisions at s=8 TeV

AbstractA search is performed for the process pp→G⁎→BHb¯/B¯Hb→Hbb¯→bb¯bb¯, predicted in composite Higgs scenarios, where G⁎ is a heavy colour octet vector resonance and BH a vector-like quark of charge −1/3. The data were obtained from pp collisions at a centre-of-mass energy of 8 TeV corresponding to an integrated luminosity of 19.5 fb−1, recorded by the ATLAS detector at the LHC. The largest background, multijet production, is estimated using a data-driven method. No significant excess of events with respect to Standard Model predictions is observed, and upper limits on the production cross section times branching ratio are set. Comparisons to the predictions from a specific benchmark model are made, resulting in lower mass limits in the two-dimensional mass plane of mG⁎ vs. mBH
Dimensions, matroids, and dense pairs of first-order structures

AbstractA structure M is pregeometric if the algebraic closure is a pregeometry in all structures elementarily equivalent to M. We define a generalisation: structures with an existential matroid. The main examples are superstable groups of Lascar U-rank a power of ω and d-minimal expansion of fields. Ultraproducts of pregeometric structures expanding an integral domain, while not pregeometric in general, do have a unique existential matroid.Generalising previous results by van den Dries, we define dense elementary pairs of structures expanding an integral domain and with an existential matroid, and we show that the corresponding theories have natural completions, whose models also have a unique existential matroid. We also extend the above result to dense tuples of structures
Restriction categories I: categories of partial maps

AbstractGiven a category with a stable system of monics, one can form the corresponding category of partial maps. To each map in this category there is, on the domain of the map, an associated idempotent, which measures the degree of partiality. This structure is captured abstractly by the notion of a restriction category, in which every arrow is required to have such an associated idempotent. Categories with a stable system of monics, functors preserving this structure, and natural transformations which are cartesian with respect to the chosen monics, form a 2-category which we call MCat. The construction of categories of partial maps provides a 2-functor Par:MCat→Cat. We show that Par can be made into an equivalence of 2-categories between MCat and a 2-category of restriction categories. The underlying ordinary functor Par0:MCat0→Cat0 of the above 2-functor Par turns out to be monadic, and, from this, we deduce the completeness and cocompleteness of the 2-categories of M-categories and of restriction categories. We also consider the problem of how to turn a formal system of subobjects into an actual system of subobjects. A formal system of subobjects is given by a functor into the category sLat of semilattices. This structure gives rise to a restriction category which, via the above equivalence of 2-categories, gives an M-category. This M-category contains the universal realization of the given formal subobjects as actual subobjects
Temperature Coefficients of Compensated Silicon Solar Cells – Influence of Ingot Position and Blend-in-ratio

AbstractSolar-grade silicon made from a metallurgical route presents boron and phosphorus compensation. Earlier work has shown that cells made from such material produce more energy than reference polysilicon modules when the temperature and irradiance is high. In the present study, solar cells from two different ingots with different blend-in-ratios were made from wafers at varying ingot heights in order to investigate how the temperature coefficients vary with compensation level and ingot height. The results suggest that solar modules made with solar cells from different ingot heights will perform differently at high temperature. It was also observed that the compensation level seems to have a smaller impact on the temperature coefficients than the ingot height
Treatment of full thickness focal cartilage lesions with a metallic resurfacing implant in a sheep animal model, 1 year evaluation

SummaryBackgroundFull depth focal cartilage lesions do not heal spontaneously and while some of these lesions are asymptomatic they might progress to osteoarthritis. Treatment for these lesions is warranted and the gold standard treatment at younger age remains biological healing by cell stimulation. In the middle-age patient the success rate of biologic treatment varies, hence the surge of non-biological alternatives. Our objective was to evaluate the efficacy and safety of a metallic implant for treatment of these lesions with respect to the long-term panarticular cartilage homeostasis.MethodsThe medial femoral condyle of 16 sheep was operated unilaterally. A metallic implant was inserted in the weight-bearing surface at an aimed height of 0.5 mm recessed. Euthanasia was performed at 6 or 12 months. Implant height and tilt was analyzed using a laser-scanning device. Damage to cartilage surfaces was evaluated macroscopically and microscopically according to the Osteoarthritis Research Society International (OARSI) recommendations.ResultsThirteen sheep were available for evaluation and showed a varying degree of cartilage damage linearly increasing with age. Cartilage damage of the medial tibial plateau opposing the implant was increased compared to the non-operated knee by 1.77 units (p = 0.041; 95% CI: 0.08, 3.45) on a 0–27 unit scale. Remaining joint compartments were unaffected. Implant position averaged 0.54 recessed (95% CI: 0.41, 0.67).ConclusionsOur results showed a consistent and accurate placement of these implants at a defined zone. At this position cartilage wear of opposing and surrounding joint cartilage is limited. Thus expanded animal and human studies are motivated
A convenient implementation of the overlap between arbitrary Hartree–Fock–Bogoliubov vacua for projection

AbstractOverlap between Hartree–Fock–Bogoliubov (HFB) vacua is very important in the beyond mean-field calculations. However, in the HFB transformation, the U,V matrices are sometimes singular due to the exact emptiness (vi=0) or full occupation (ui=0) of some single-particle orbits. This singularity may cause some problem in evaluating the overlap between HFB vacua through Pfaffian. We found that this problem can be well avoided by setting those zero occupation numbers ui, vi to some tiny values denoted by ε(>0), which numerically satisfies 1+ε2=1 (e.g., ε=10−8 when using the double precision data type). This treatment does not change the HFB vacuum state because ui2,vi2=ε2 are numerically zero relative to 1. Therefore, for arbitrary HFB transformation, we say that the U, V matrices can always be nonsingular. From this standpoint, we present a new convenient Pfaffian formula for the overlap between arbitrary HFB vacua, which is especially suitable for symmetry restoration. Testing calculations have been performed for this new formula. It turns out that our method is reliable and accurate in evaluating the overlap between arbitrary HFB vacua
Student's Experiences with Traditional Bullying and Cyberbullying: Findings from a Romanian Sample

AbstractThe field of cyberbullying is relatively new and there is no universal consensus on its definition, measurement and intervention. Authors agree that bullying has entered into the digital domain and professionals require the skills to help identify and prevent these behaviours. Ninety two students were surveyed to determine their experience with different types of bullying behaviors (face-to-face, cyberbullying or both), as bully, victim or witness. Our objective was to explore the association between those types of bullying and anxiety. The results suggest a significant association between face-to-face bullying and anxiety. Similarly, there was significant association between experiencing both types of bullying and anxiety. Further studies are required with larger and more diverse samples in order to verify current fidings and to test for additional associations
A finite volume method for scalar conservation laws with stochastic time–space dependent flux functions

AbstractWe propose a new finite volume method for scalar conservation laws with stochastic time–space dependent flux functions. The stochastic effects appear in the flux function and can be interpreted as a random manner to localize the discontinuity in the time–space dependent flux function. The location of the interface between the fluxes can be obtained by solving a system of stochastic differential equations for the velocity fluctuation and displacement variable. In this paper we develop a modified Rusanov method for the reconstruction of numerical fluxes in the finite volume discretization. To solve the system of stochastic differential equations for the interface we apply a second-order Runge–Kutta scheme. Numerical results are presented for stochastic problems in traffic flow and two-phase flow applications. It is found that the proposed finite volume method offers a robust and accurate approach for solving scalar conservation laws with stochastic time–space dependent flux functions
T Lymphocytes Orient against the Direction of Fluid Flow during LFA-1-Mediated Migration

AbstractAs they leave the blood stream and travel to lymph nodes or sites of inflammation, T lymphocytes are captured by the endothelium and migrate along the vascular wall to permissive sites of transmigration. These processes take place under the influence of hemodynamic shear stress; therefore, we investigated how migrational speed and directionality are influenced by variations in shear stress. We examined human effector T lymphocytes on intercellular adhesion molecule 1 (ICAM-1)-coated surfaces under the influence of shear stresses from 2 to 60 dyn.cm−2. T lymphocytes were shown to respond to shear stress application by a rapid (30 s) and fully reversible orientation of their migration against the fluid flow without a change in migration speed. Primary T lymphocytes migrating on ICAM-1 in the presence of uniformly applied SDF-1α were also found to migrate against the direction of shear flow. In sharp contrast, neutrophils migrating in the presence of uniformly applied fMLP and leukemic HSB2 T lymphocytes migrating on ICAM-1 alone oriented their migration downstream, with the direction of fluid flow. Our findings suggest that, in addition to biochemical cues, shear stress is a contributing factor to leukocyte migration directionality
Sox2 expression effects on direct reprogramming efficiency as determined by alternative somatic cell fate

AbstractInduced pluripotent stem cells (iPSCs) are generated by directly reprogramming somatic cells by forcing them to express the exogenous transcription factors, Oct4, Sox2, Klf4 and c-Myc (OSKM). These cells could potentially be used in clinical applications and basic research. Here, we explored the molecular role of Sox2 by generating iPSCs that expressed Sox2 at various levels. Low Sox2 (LS) expression increased the efficiency of generating partially reprogrammed iPSCs in combination with OKM. Notably, we detected a significant increase in the number of fully reprogrammed iPSCs with three factors of OK and LS. LS expression was linked with the reduced expression of ectoderm and mesoderm marker genes. This indicates that cell differentiation into the ectoderm and mesoderm lineages was impeded during reprogramming. The quality of the iPSCs that was generated by using OK and LS was comparable to that of iPSCs that were produced via conventional OSK as seen by pluripotent marker gene expression and chimera formation. We conclude that Sox2 plays a crucial role in a dose-dependent manner in direct reprogramming of somatic cells to iPSCs
On the stability of multiscale models of dynamical symmetry breaking from holography

AbstractWe consider two classes of backgrounds of Type IIB supergravity obtained by wrapping D5-branes on a two-cycle inside the conifold. The field theory dual exhibits confinement and, in addition, a region in which the dynamics is walking, at least in the weak sense that the running of the coupling is anomalously slow. We introduce quenched matter in the fundamental, modeled by probe D7-branes which wrap an internal three-dimensional manifold and lie at the equator of the transverse two-sphere. In the space spanned by the remaining internal angle and the radial coordinate, the branes admit two embeddings. The first one is U-shaped: the branes merge at some finite value of the radius. The second one is disconnected and extends along the entire radial direction at fixed angular separation. We interpret these two configurations as corresponding to chiral-symmetry breaking and preserving phases, respectively.We present a simple diagnostic tool to examine the classical stability of the embedding, based on the concavity/convexity conditions for the relevant thermodynamic potentials. We use this criterion to show that U-shaped probes that explore the walking region are unstable, hence providing a dynamical origin for the tachyonic mode found in the literature. Whenever this occurs, the disconnected solution becomes favored energetically. We find that in one of the two classes of backgrounds the U-shaped embedding is always unstable, and thus never realized dynamically. Consequently, these models cannot be used to describe chiral-symmetry breaking. In the second category of solutions, our analysis reveals the presence of a first-order phase transition between chiral-symmetry broken and restored phases. Interestingly, this is in the same class that contains a parametrically light scalar in the spectrum of glueballs of the dual field theory
On the rationality of Case

AbstractCase marking has long resisted rationalization in terms of language-external systems of cognition, representing a classical illustration in the generative tradition for an apparently purely ‘formal’ or ‘syntactic’ aspect of grammatical organization. I argue that this impasse derives from the prevailing absence of a notion of grammatical meaning, i.e. meaning unavailable lexically or in non-linguistic cognition and uniquely dependent on grammatical forms of organization. In particular, propositional forms of reference, contrary to their widespread designation as ‘semantic’, are arguably not only grammar-dependent but depend on relations designated as structural ‘Cases’. I further argue that these fail to reduce to thematic structure, Person, Tense, or Agreement. Therefore, Case receives a rationalization in terms of how lexical memory is made referential and propositional in language. Structural Case is ‘uninterpretable’ (bereft of content) only if a non-grammatical notion of meaning is employed, and sapiens-specific cognition is (implausibly) regarded as unmediated by language
Higher-order calculations of electron–deuteron scattering in nuclear effective theory

AbstractMotivated by recent advances in the application of effective field theory techniques to light nuclei we revisit the problem of electron–deuteron scattering in these approaches. Applying Weinberg's power counting for two-nucleon processes to this reaction leads, in the first instance, to an effective field theory expansion that does not converge for virtual photon momenta of order 300 MeV. However, here we show that this breakdown is not the result of an inability to describe deuteron physics: instead it results from the effective field theory's failure to describe the nucleon's isoscalar electromagnetic form factor once these momentum transfers are reached. Analyzing ratios of deuteron to (isoscalar) nucleon form factors within the effective field theory overcomes this difficulty. We show that when such an analysis is performed the effective theory expansion for deuteron physics converges well up to virtual photon momenta of order 700 MeV, and agrees with experimental data for the deuteron charge and quadrupole form factors over a similar range
Guaranteed and robust discontinuous Galerkin a posteriori error estimates for convection–diffusion–reaction problems

AbstractWe propose and study a posteriori error estimates for convection–diffusion–reaction problems with inhomogeneous and anisotropic diffusion approximated by weighted interior-penalty discontinuous Galerkin methods. Our twofold objective is to derive estimates without undetermined constants and to analyze carefully the robustness of the estimates in singularly perturbed regimes due to dominant convection or reaction. We first derive locally computable estimates for the error measured in the energy (semi)norm. These estimates are evaluated using H(div,Ω)-conforming diffusive and convective flux reconstructions, thereby extending the previous work on pure diffusion problems. The resulting estimates are semi-robust in the sense that local lower error bounds can be derived using suitable cutoff functions of the local Péclet and Damköhler numbers. Fully robust estimates are obtained for the error measured in an augmented norm consisting of the energy (semi)norm, a dual norm of the skew-symmetric part of the differential operator, and a suitable contribution of the interelement jumps of the discrete solution. Numerical experiments are presented to illustrate the theoretical results
Unconventional supersymmetry and its breaking

AbstractWe present a gauge theory for a superalgebra that includes an internal gauge (G) and local Lorentz (so(1,D−1)) algebras. These two symmetries are connected by fermionic supercharges. The field content of the system includes a (non-)abelian gauge potential A, a spin-1/2 Dirac spinor ψ, the Lorentz connection ωab, and the vielbein eμa. The connection one-form A is in the adjoint representation of G, while ψ is in the fundamental. In contrast to standard supersymmetry and supergravity, the metric is not a fundamental field and is in the center of the superalgebra: it is not only invariant under the internal gauge group, G, and under Lorentz transformations, SO(1,D−1), but is also invariant under supersymmetry.The distinctive features of this theory that mark the difference with standard supersymmetries are: i) the number of fermionic and bosonic states is not necessarily the same; ii) there are no superpartners with equal mass; iii) although this supersymmetry originates in a local gauge theory and gravity is included, there is no gravitino; iv) fermions acquire mass from their coupling to the background or from higher order self-couplings, while bosons remain massless. In odd dimensions, the Chern–Simons (CS) form provides an action that is (quasi-)invariant under the entire superalgebra. In even dimensions, the Yang–Mills (YM) form is the only natural option and the symmetry breaks down to G⊗SO(1,D−1). In four dimensions, the construction follows the Townsend–Mac Dowell–Mansouri approach, starting with an osp(4|2)∼usp(2,2|1) connection. Due to the absence of osp(4|2)-invariant traces in four dimensions, the resulting Lagrangian is only invariant under u(1)⊕so(3,1), which includes a Nambu–Jona-Lasinio (NJL) term. In this case, the Lagrangian depends on a single dimensionful parameter that fixes Newton's constant, the cosmological constant and the NJL coupling
Upper limits on the Peccei–Quinn scale and on the reheating temperature in axino dark matter scenarios

AbstractConsidering axino cold dark matter scenarios with a long-lived charged slepton, we study constraints on the Peccei–Quinn scale fa and on the reheating temperature TR imposed by the dark matter density and by big bang nucleosynthesis (BBN). For an axino mass compatible with large-scale structure, ma˜≳100 keV, temperatures above 109 GeV become viable for fa>3×1012 GeV. We calculate the slepton lifetime in hadronic axion models. With the dominant decay mode being two-loop suppressed, this lifetime can be sufficiently large to allow for primordial bound states leading to catalyzed BBN of lithium-6 and beryllium-9. This implies new upper limits on fa and on TR that depend on quantities which will be probed at the Large Hadron Collider