pinecone/core-2020-05-10-deduplication huggingface dataset:
Development of a candidate reference material for adventitious virus detection in vaccine and biologicals manufacturing by deep sequencing

AbstractBackgroundUnbiased deep sequencing offers the potential for improved adventitious virus screening in vaccines and biotherapeutics. Successful implementation of such assays will require appropriate control materials to confirm assay performance and sensitivity.MethodsA common reference material containing 25 target viruses was produced and 16 laboratories were invited to process it using their preferred adventitious virus detection assay.ResultsFifteen laboratories returned results, obtained using a wide range of wet-lab and informatics methods. Six of 25 target viruses were detected by all laboratories, with the remaining viruses detected by 4–14 laboratories. Six non-target viruses were detected by three or more laboratories.ConclusionThe study demonstrated that a wide range of methods are currently used for adventitious virus detection screening in biological products by deep sequencing and that they can yield significantly different results. This underscores the need for common reference materials to ensure satisfactory assay performance and enable comparisons between laboratories
Genetic characterization of Escherichia coli RecN protein as a member of SMC family of proteins

AbstractThe proteins of SMC family are characterized by having Walker A and B sites. The Escherichia coli RecN protein is a prokaryotic member of SMC family that involved in the induced excision of Tn10 and the repair of the DNA double strand breaks. In this work, the Walker A nucleotide binding site of the E. coli RecN protein was mutated by changing the highly conserved lysine residue 35 to the aspartic acid (D), designated as recNK35D. Reverse genetics was utilized to delete the entire recN gene (ΔrecN108) or introduce the recNK35D gene into the E. coli chromosomal DNA. The recNK35D cells showed decrease in the frequency of excision of Tn10 from gal76::Tn10 after treatment with mitomycin C compared to recN+ cells. The ΔrecN108 cells showed an un-induced increase in the frequency of Tn10 excision from gal76::Tn10 in rec+ background while, recBC sbcBC ΔrecN108 cells are completely deficient in Tn10 excision. The recombination proficiency is reduced in cells carrying recBC sbcBC cells in addition recNK35D mutation. We observed that the Walker A nucleotide binding site is important for the RecN protein. Strains that deleted recN gene are recombination deficient and more sensitive to mitomycin C than strains carrying recNK35D
Decay constants of charm and beauty pseudoscalar heavy–light mesons on fine lattices

AbstractWe compute decay constants of heavy–light mesons in quenched lattice QCD with a lattice spacing of a≃0.04 fm using non-perturbatively O(a) improved Wilson fermions and O(a) improved currents. We obtain fDs=220(6)(5)(11) MeV, fD=206(6)(3)(22) MeV, fBs=205(7)(26)(17) MeV and fB=190(8)(23)(25) MeV, using the Sommer parameter r0=0.5 fm to set the scale. The first error is statistical, the second systematic and the third from assuming a ±10% uncertainty in the experimental value of r0. A detailed discussion is given in the text. We also present results for the meson decay constants fK and fπ and the ρ meson mass
Generation and Characterization of Severe Combined Immunodeficiency Rats

SummarySevere combined immunodeficiency (SCID) mice, the most widely used animal model of DNA-PKcs (Prkdc) deficiency, have contributed enormously to our understanding of immunodeficiency, lymphocyte development, and DNA-repair mechanisms, and they are ideal hosts for allogeneic and xenogeneic tissue transplantation. Here, we use zinc-finger nucleases to generate rats that lack either the Prkdc gene (SCID) or the Prkdc and Il2rg genes (referred to as F344-scid gamma [FSG] rats). SCID rats show several phenotypic differences from SCID mice, including growth retardation, premature senescence, and a more severe immunodeficiency without “leaky” phenotypes. Double-knockout FSG rats show an even more immunocompromised phenotype, such as the abolishment of natural killer cells. Finally, xenotransplantation of human induced pluripotent stem cells, ovarian cancer cells, and hepatocytes shows that SCID and FSG rats can act as hosts for xenogeneic tissue grafts and stem cell transplantation and may be useful for preclinical testing of new drugs
Theoretical uncertainties on quasielastic charged-current neutrino–nucleus cross sections

AbstractWe estimate the theoretical uncertainties of the model developed in [J. Nieves, J.E. Amaro, M. Valverde, Phys. Rev. C 70 (2004) 055503] for inclusive quasielastic charged-current neutrino–nucleus reactions at intermediate energies. Besides we quantify the deviations of the predictions of this many body framework from those obtained within a simple Fermi gas model. A special attention has been paid to the ratio σ(μ)/σ(e) of interest for experiments on atmospheric neutrinos. We show that uncertainties affecting this ratio are likely smaller than 5%
QTC3D: Extending the qualitative trajectory calculus to three dimensions

AbstractSpatial interactions between agents (humans, animals, or machines) carry information of high value to human or electronic observers. However, not all the information contained in a pair of continuous trajectories is important and thus the need for qualitative descriptions of interaction trajectories arises. The Qualitative Trajectory Calculus (QTC) (Van de Weghe, 2004) is a promising development towards this goal. Numerous variants of QTC have been proposed in the past and QTC has been applied towards analyzing various interaction domains. However, an inherent limitation of those QTC variations that deal with lateral movements is that they are limited to two-dimensional motion; therefore, complex three-dimensional interactions, such as those occurring between flying planes or birds, cannot be captured. Towards that purpose, in this paper QTC3D is presented: a novel qualitative trajectory calculus that can deal with full three-dimensional interactions. QTC3D is based on transformations of the Frenet–Serret frames accompanying the trajectories of the moving objects. Apart from the theoretical exposition, including definition and properties, as well as computational aspects, we also present an application of QTC3D towards modeling bird flight. Thus, the power of QTC is now extended to the full dimensionality of physical space, enabling succinct yet rich representations of spatial interactions between agents
Erdős–Hajnal-type theorems in hypergraphs

AbstractThe Erdős–Hajnal conjecture states that if a graph on n vertices is H-free, that is, it does not contain an induced copy of a given graph H, then it must contain either a clique or an independent set of size nδ(H), where δ(H)>0 depends only on the graph H. Except for a few special cases, this conjecture remains wide open. However, it is known that an H-free graph must contain a complete or empty bipartite graph with parts of polynomial size.We prove an analogue of this result for 3-uniform hypergraphs, showing that if a 3-uniform hypergraph on n vertices is H-free, for any given H, then it must contain a complete or empty tripartite subgraph with parts of order c(logn)12+δ(H), where δ(H)>0 depends only on H. This improves on the bound of c(logn)12, which holds in all 3-uniform hypergraphs, and, up to the value of the constant δ(H), is best possible.We also prove that, for k⩾4, no analogue of the standard Erdős–Hajnal conjecture can hold in k-uniform hypergraphs. That is, there are k-uniform hypergraphs H and sequences of H-free hypergraphs which do not contain cliques or independent sets of size appreciably larger than one would normally expect
Real-time Monitoring of Wind Turbine Generator Shaft Alignment Using Laser Measurement

AbstractShaft Misalignment is one of the most common sources of trouble of wind turbine drive train when rigid couplings connect the shafts. Ideal alignment of the shaft is difficult to be obtained and the couplings attached to the shaft may present angular or parallel misalignment defined also as lateral and axially misalignment. Despite misalignment is often observed in the practice, there are relatively few studies on wind turbine shaft misalignment in the literature and their results are sometimes conflicting. The aim of this research is to use laser based metrology techniques to capture the positional changes of wind turbines in service and aligning drivelines in wind turbine. By using sets of lasers on a shaft alignment rig, and then determining the average and periodic amplitude from an ensemble averaged signal, the degree of misalignment can be found and the necessary corrective action found
Pkd1 Regulates Lymphatic Vascular Morphogenesis during Development

SummaryLymphatic vessels arise during development through sprouting of precursor cells from veins, which is regulated by known signaling and transcriptional mechanisms. The ongoing elaboration of vessels to form a network is less well understood. This involves cell polarization, coordinated migration, adhesion, mixing, regression, and shape rearrangements. We identified a zebrafish mutant, lymphatic and cardiac defects 1 (lyc1), with reduced lymphatic vessel development. A mutation in polycystic kidney disease 1a was responsible for the phenotype. PKD1 is the most frequently mutated gene in autosomal dominant polycystic kidney disease (ADPKD). Initial lymphatic precursor sprouting is normal in lyc1 mutants, but ongoing migration fails. Loss of Pkd1 in mice has no effect on precursor sprouting but leads to failed morphogenesis of the subcutaneous lymphatic network. Individual lymphatic endothelial cells display defective polarity, elongation, and adherens junctions. This work identifies a highly selective and unexpected role for Pkd1 in lymphatic vessel morphogenesis during development
The emergence and growth of a submarine volcano: The Kameni islands, Santorini (Greece)

AbstractThe morphology of a volcanic edifice reflects the integrated eruptive and evolutionary history of that system, and can be used to reconstruct the time-series of prior eruptions. We present a new high-resolution merged LiDAR-bathymetry grid, which has enabled detailed mapping of both onshore and offshore historic lava flows of the Kameni islands, emplaced in the centre of the Santorini caldera since at least AD 46. We identify three new submarine lava flows: two flows, of unknown age, lie to the east of Nea Kameni and a third submarine flow, located north of Nea Kameni appears to predate the 1925–1928 lava flows but was emplaced subsequent to the 1707–1711 lava flows. Yield strength estimates derived from the morphology of the 1570/1573 lobe suggest that submarine lava strengths are approximately two times greater than those derived from the onshore flows. To our knowledge this is the first documented yield strength estimate for submarine flows. This increase in strength is likely related to cooling and thickening of the dacite lava flows as they displace sea water. Improved lava volume estimates derived from the merged LiDAR-Bathymetry grid suggest typical lava extrusion rates of ∼2–3m3s−1 during four of the historic eruptions on Nea Kameni (1707–1711, 1866–1870, 1925–1928 and 1939–1941). They also reveal a linear relationship between the pre-eruption interval and the volume of extruded lava. These observations may be used to estimate the size of future dome-building eruptions at Santorini volcano, based on the time interval since the last significant eruption
Masses of excited heavy baryons in the relativistic quark–diquark picture

AbstractThe mass spectra of the excited heavy baryons consisting of two light (u,d,s) and one heavy (c,b) quarks are calculated in the heavy-quark–light-diquark approximation within the constituent quark model. The light quarks, forming the diquark, and the light diquark in the baryon are treated completely relativistically. The expansion in v/c up to the second order is used only for the heavy (b and c) quarks. The internal structure of the diquark is taken into account by inserting the diquark–gluon interaction form factor. An overall good agreement of the obtained predictions with available experimental data is found
Absence of gravitational contributions to the running Yang–Mills coupling

AbstractThe question of a modification of the running gauge coupling of (non-)Abelian gauge theories by an incorporation of the quantum gravity contribution has recently attracted considerable interest. In this Letter we perform an involved diagrammatical calculation in the full Einstein–Yang–Mills system both in cut-off and dimensional regularization at one-loop order. It is found that all gravitational quadratic divergencies cancel in cut-off regularization and are trivially absent in dimensional regularization so that there is no alteration to asymptotic freedom at high energies. This settles the previously open question of a potential regularization scheme dependence of the one-loop β function traditionally computed in the background field approach. Furthermore we show that the remaining logarithmic divergencies give rise to an extended effective Einstein–Yang–Mills Lagrangian with a counterterm of dimension six
α-Lactalbumin:Oleic Acid Complex Spontaneously Delivers Oleic Acid to Artificial and Erythrocyte Membranes

AbstractHuman α-lactalbumin made lethal to tumor cells (HAMLET) is a tumoricidal complex consisting of human α-lactalbumin and multiple oleic acids (OAs). OA has been shown to play a key role in the activity of HAMLET and its related complexes, generally known as protein–fatty acid (PFA) complexes. In contrast to what is known about the fate of the protein component of such complexes, information about what happens to OA during their action is still lacking. We monitored the membrane, OA and protein components of bovine α-lactalbumin complexed with OA (BLAOA; a HAMLET-like substance) and how they associate with each other. Using ultracentrifugation, we found that the OA and lipid components follow each other closely. We then firmly identify a transfer of OA from BLAOA to both artificial and erythrocyte membranes, indicating that natural cells respond similarly to BLAOA treatment as artificial membranes. Uncomplexed OA is unable to similarly affect membranes at the conditions tested, even at elevated concentrations. Thus, BLAOA can spontaneously transfer OA to a lipid membrane. After the interaction with the membrane, the protein is likely to have lost most or all of its OA. We suggest a mechanism for passive import of mainly uncomplexed protein into cells, using existing models for OA's effect on membranes. Our results are consistent with a membrane destabilization mediated predominantly by OA insertion being a significant contribution to PFA cytotoxicity
A class of hierarchical graphs as topologies for interconnection networks

AbstractWe study some topological and algorithmic properties of a recently defined hierarchical interconnection network, the hierarchical crossed cube HCC(k,n), which draws upon constructions used within the well-known hypercube and also the crossed cube. In particular, we study: the construction of shortest paths between arbitrary vertices in HCC(k,n); the connectivity of HCC(k,n); and one-to-all broadcasts in parallel machines whose underlying topology is HCC(k,n) (with both one-port and multi-port store-and-forward models of communication). Moreover, some of our proofs are applicable not just to hierarchical crossed cubes but to hierarchical interconnection networks formed by replacing crossed cubes with other families of interconnection networks. As such, we provide a generic construction with accompanying generic results relating to some topological and algorithmic properties of a wide range of hierarchical interconnection network
Altered Backbone and Side-Chain Interactions Result in Route Heterogeneity during the Folding of Interleukin-1β (IL-1β)

AbstractDeletion of the β-bulge trigger-loop results in both a switch in the preferred folding route, from the functional loop packing folding route to barrel closure, as well as conversion of the agonist activity of IL-1β into antagonist activity. Conversely, circular permutations of IL-1β conserve the functional folding route as well as the agonist activity. These two extremes in the folding-functional interplay beg the question of whether mutations in IL-1β would result in changes in the populations of heterogeneous folding routes and the signaling activity. A series of topologically equivalent water-mediated β-strand bridging interactions within the pseudosymmetric β-trefoil fold of IL-1β highlight the backbone water interactions that stabilize the secondary and tertiary structure of the protein. Additionally, conserved aromatic residues lining the central cavity appear to be essential for both stability and folding. Here, we probe these protein backbone-water molecule and side chain-side chain interactions and the role they play in the folding mechanism of this geometrically stressed molecule. We used folding simulations with structure-based models, as well as a series of folding kinetic experiments to examine the effects of the F42W core mutation on the folding landscape of IL-1β. This mutation alters water-mediated backbone interactions essential for maintaining the trefoil fold. Our results clearly indicate that this perturbation in the primary structure alters a structural water interaction and consequently modulates the population of folding routes accessed during folding and signaling activity
Evaluating summarised radionuclide concentration ratio datasets for wildlife

AbstractConcentration ratios (CRwo-media) are used in most radioecological models to predict whole-body radionuclide activity concentrations in wildlife from those in environmental media. This simplistic approach amalgamates the various factors influencing transfer within a single generic value and, as a result, comparisons of model predictions with site-specific measurements can vary by orders of magnitude. To improve model predictions, the development of ‘condition-specific’ CRwo-media values has been proposed (e.g. for a specific habitat). However, the underlying datasets for most CRwo-media value databases, such as the wildlife transfer database (WTD) developed within the IAEA EMRAS II programme, include summarised data. This presents challenges for the calculation and subsequent statistical evaluation of condition-specific CRwo-media values. A further complication is the common use of arithmetic summary statistics to summarise data in source references, even though CRwo-media values generally tend towards a lognormal distribution and should, therefore, be summarised using geometric statistics. In this paper, we propose a statistically-defensible and robust method for reconstructing underlying datasets to calculate condition-specific CRwo-media values from summarised data and deriving geometric summary statistics. This method is applied to terrestrial datasets from the WTD. Statistically significant differences in sub-category CRwo-media values (e.g. mammals categorised by feeding strategy) were identified, which may justify the use of these CRwo-media values for specific assessment contexts. However, biases and limitations within the underlying datasets of the WTD explain some of these differences. Given the uncertainty in the summarised CRwo-media values, we suggest that the CRwo-media approach to estimating transfer is used with caution above screening-level assessments
Formation of an unusually short hydrogen bond in photoactive yellow protein

AbstractThe photoactive chromophore of photoactive yellow protein (PYP) is p-coumaric acid (pCA). In the ground state, the pCA chromophore exists as a phenolate anion, which is H-bonded by protonated Glu46 (OGlu46–OpCA=~2.6Å) and protonated Tyr42. On the other hand, the OGlu46–OpCA H-bond was unusually short (OGlu46–OpCA=2.47Å) in the intermediate pRCW state observed in time-resolved Laue diffraction studies. To understand how the existence of the unusually short H-bond is energetically possible, we analyzed the H-bond energetics adopting a quantum mechanical/molecular mechanical (QM/MM) approach based on the atomic coordinates of the PYP crystal structures. In QM/MM calculations, the OGlu46–OpCA bond is 2.60Å in the ground state, where Tyr42 donates an H-bond to pCA. In contrast, when the hydroxyl group of Tyr42 is flipped away from pCA, the H-bond was significantly shortened to 2.49Å in the ground state. The same H-bond pattern reproduced the unusually short H-bond in the pRCW structure (OGlu46–OpCA=2.49Å). Intriguingly, the potential-energy profile resembles that of a single-well H-bond, suggesting that the pKa values of the donor (Glu46) and acceptor (pCA) moieties are nearly equal. The present results indicate that the “equal pKa” requirement for formation of single-well or low-barrier H-bond (LBHB) is satisfied only when Tyr42 does not donate an H-bond to pCA, and argue against the possibility that the OGlu46–OpCA bond is an LBHB in the ground state, where Tyr42 donates an H-bond to pCA
The role of field redefinition on renormalisability of a general N=12 supersymmetric gauge theories

AbstractWe investigate some issues on renormalisability of non-anticommutative supersymmetric gauge theory related to field redefinitions. We study one loop corrections to N=12 supersymmetric SU(N)×U(1) gauge theory coupled to chiral matter in component formalism, and show the procedure which has been introduced for renormalisation is problematic because some terms which are needed for the renormalisability of theory are missed from the Lagrangian. In order to prove the theory is renormalisable, we redefine the gaugino and the auxiliary fields (λ,F¯), which result in a modified form of the Lagrangian in the component formalism. Then, we show the modified Lagrangian has extra terms which are necessary for renormalisability of non-anticommutative supersymmetric gauge field theories. Finally, we prove N=12 supersymmetric gauge theory is renormalisable up to one loop corrections using standard method of renormalisation; besides, it is shown the effective action is gauge invariant
Computing vertex-surjective homomorphisms to partially reflexive trees

AbstractA homomorphism from a graph G to a graph H is a vertex mapping f:VG→VH such that f(u) and f(v) form an edge in H whenever u and v form an edge in G. The H-Coloring problem is that of testing whether a graph G allows a homomorphism to a given graph H. A well-known result of Hell and Nešetřil determines the computational complexity of this problem for any fixed graph H. We study a natural variant of this problem, namely the SurjectiveH-Coloring problem, which is that of testing whether a graph G allows a homomorphism to a graph H that is (vertex-)surjective. We classify the computational complexity of this problem for when H is any fixed partially reflexive tree. Thus we identify the first class of target graphs H for which the computational complexity of SurjectiveH-Coloring can be determined. For the polynomial-time solvable cases we show a number of parameterized complexity results, including in particular ones on graph classes with (locally) bounded expansion