pinecone/core-2020-05-10-deduplication huggingface dataset:
Validation of a Clinical-Grade Assay to Measure Donor-Derived Cell-Free DNA in Solid Organ Transplant Recipients

The use of circulating cell-free DNA (cfDNA) as a biomarker in transplant recipients offers advantages over invasive tissue biopsy as a quantitative measure for detection of transplant rejection and immunosuppression optimization. However, the fraction of donor-derived cfDNA (dd-cfDNA) in transplant recipient plasma is low and challenging to quantify. Previously reported methods to measure dd-cfDNA require donor and recipient genotyping, which is impractical in clinical settings and adds cost. We developed a targeted next-generation sequencing assay that uses 266 single-nucleotide polymorphisms to accurately quantify dd-cfDNA in transplant recipients without separate genotyping. Analytical performance of the assay was characterized and validated using 1117 samples comprising the National Institute for Standards and Technology Genome in a Bottle human reference genome, independently validated reference materials, and clinical samples. The assay quantifies the fraction of dd-cfDNA in both unrelated and related donor-recipient pairs. The dd-cfDNA assay can reliably measure dd-cfDNA (limit of blank, 0.10%; limit of detection, 0.16%; limit of quantification, 0.20%) across the linear quantifiable range (0.2% to 16%) with across-run CVs of 6.8%. Precision was also evaluated for independently processed clinical sample replicates and is similar to across-run precision. Application of the assay to clinical samples from heart transplant recipients demonstrated increased levels of dd-cfDNA in patients with biopsy-confirmed rejection and decreased levels of dd-cfDNA after successful rejection treatment. This noninvasive clinical-grade sequencing assay can be completed within 3 days, providing the practical turnaround time preferred for transplanted organ surveillance
Financing drug discovery via dynamic leverage

We extend the megafund concept for funding drug discovery to enable dynamic leverage in which the portfolio of candidate therapeutic assets is predominantly financed initially by equity, and debt is introduced gradually as assets mature and begin generating cash flows. Leverage is adjusted so as to maintain an approximately constant level of default risk throughout the life of the fund. Numerical simulations show that applying dynamic leverage to a small portfolio of orphan drug candidates can boost the return on equity almost twofold compared with securitization with a static capital structure. Dynamic leverage can also add significant value to comparable all-equity-financed portfolios, enhancing the return on equity without jeopardizing debt performance or increasing risk to equity investors
Seizure characterisation using frequency-dependent multivariate dynamics

The characterisation of epileptic seizures assists in the design of targeted pharmaceutical seizure prevention techniques\ud
and pre-surgical evaluations. In this paper, we expand on recent use of multivariate techniques to study the crosscorrelation\ud
dynamics between electroencephalographic (EEG) channels. The Maximum Overlap Discrete Wavelet\ud
Transform (MODWT) is applied in order to separate the EEG channels into their underlying frequencies. The\ud
dynamics of the cross-correlation matrix between channels, at each frequency, are then analysed in terms of the\ud
eigenspectrum. By examination of the eigenspectrum, we show that it is possible to identify frequency dependent\ud
changes in the correlation structure between channels which may be indicative of seizure activity.\ud
The technique is applied to EEG epileptiform data and the results indicate that the correlation dynamics vary over\ud
time and frequency, with larger correlations between channels at high frequencies. Additionally, a redistribution of wavelet energy is found, with increased fractional energy demonstrating the relative importance of high frequencies\ud
during seizures. Dynamical changes also occur in both correlation and energy at lower frequencies during seizures,\ud
suggesting that monitoring frequency dependent correlation structure can characterise changes in EEG signals during\ud
these. Future work will involve the study of other large eigenvalues and inter-frequency correlations to determine\ud
additional seizure characteristics
Absolute photoionization cross sections and resonance structure of doubly ionized silicon in the region of the 2p-1 threshold: experiment and theory

We present the absolute photoionization cross section of doubly ionized silicon as a function of photon energy. These were obtained by merging a Si2+ ion beam generated in an electron cyclotron resonance source with monochromatized synchrotron radiation from an undulator. The photoion yield measurements were carried out in the photon energy range between 95 eV and 170 eV, i.e., the region corresponding to the excitation followed by the ionization (threshold ∼133.8eV) of an inner-subshell 2p electron. Resonance structure due to 2p excitation in the 2p63s3p3P metastable state was also observed with its contribution to the total cross section not exceeding 3%. Calculation of the 2p photoionization continuum cross section as a function of photon energy was carried out using the relativistic random-phase approximation (RRPA) and agreed very well with the corresponding measurements. The resonance structure in the 3s cross section below the 2p threshold was found to be in good agreement with the multiconfiguration atomic structure calculations of Sayyad et al. [J. Phys. B 28, 1715 (1995)], while the corresponding RRPA-RMQDT (relativistic multi-channel quantum-defect theory) calculations proved less successful
Rashba spin–orbit coupling effect on the quantum Hall magnetoresistivity

In this paper we analyze the influence of the Rashba spin–orbit coupling on the quantum Hall\ud
magnetoresistivity in a two-dimensional electron system (2DES). The study is based on an analytical\ud
model for the integer quantum Hall effect (IQHE) and the Shubnikov-de Haas (SdH) phenomena. This\ud
model shows the behaviour of the Hall magnetoresistivity when the Rashba parameter is varied, and\ud
reproduces Hall plateaux of a 2DES confined in a III–V heterostructure. We also discuss the Rashba and\ud
Zeeman competition and its effect on the width of the Hall magnetoresistivity plateaux
Arsenic and heavy metal uptake and accumulation in native plant species from soils polluted by mining activities

Arsenic and heavy metal (specifically Cd, Cr, Cu, Ni, Pb, and Zn) uptake, translocation, and accumulation in ten native plant species spontaneously growing in soils polluted by mining activities were studied, with a focus on future phytoremediation work in polluted soils. Plant and soil samples were collected in the vicinity of the Mónica mine (NW Madrid, Spain). Soil analysis showed the ability of native plants for growing in soils with high concentration levels of Cd, Cu, Pb, Zn, and especially As. From these elements, the highest percentage of extractable elements was found for Cd and the lowest for Pb. A highly significant correlation was observed between total and extractable element concentrations in soils, except for Cu, indicating that total concentration is the most relevant factor for element mobility in these soils. Extractable elements in soils were better correlated with concentrations in plants than total elements in soils; thus, extraction methods applied are suitable to estimate the element phytoavailable fraction in soils, which depends on the plant species and not only on the element mobility in soils. High element concentrations were found in the aboveground parts of Corrigiola telephiifolia (As and Pb), Jasione montana (Cd and Zn), and Digitalis thapsi (As, Cd, Cu, Pb and Zn). However, considering the translocation and accumulation factors, together with the concentration levels found in roots and aboveground parts, only C. telephiifolia could be considered a Pb accumulator and an As hyperaccumulator plant, which could be used for future phytoremediation work in soils polluted with As
Transport properties of CuGaSe(2)-based thin-film solar cells as a function of absorber composition

The transport properties of thin-film solar cells based on wide-gap CuGaSe(2) absorbers have been investigated as a function of the bulk [Ga]/[Cu] ratio ranging from 1.01 to 1.33. We find that (i) the recombination processes in devices prepared from absorbers with a composition close to stoichiometry ([Ga]/[Cu] = 1.01) are strongly tunnelling assisted resulting in low recombination activation energies (E(a)) of approx. 0.95 eV in the dark and 1.36 eV under illumination. (ii) With an increasing [Ga]/[Cu] ratio, the transport mechanism changes to be dominated by thermally activated Shockley-Read-Hall recombination with similar E(a) values of approx. 1.52-1.57 eV for bulk [Ga]/[Cu] ratios of 1.12-1.33. The dominant recombination processes take place at the interface between CdS buffer and CuGaSe(2) absorber independently from the absorber composition. The increase of E(a) with the [Ga]/[Cu] ratio correlates with the open circuit voltage and explains the better performance of corresponding solar cells
Evolution of vulnerability to pain in interpersonal relations as a strategic trait aiding cooperation

Why are humans so vulnerable to pain in interpersonal relations and can so easily hurt others physically and emotionally?  We theoretically examine whether being offensively strong but defensively weak can evolve as a strategic trait that fosters cooperation.  We study a population comprised of "thick-skinned" and "thin-skinned" agents by using an indirect evolution model that combines rational choice in strategic interactions with evolutionary selection across generations.  We find that (a) the relatively vulnerable and cooperative thin-skins cannot evolve under purely random matching, (b) with some assortment thin-skins evolve and can take over the entire population, (c) vulnerability to greater pain makes it easier for thin-skins to evolve, and (d) proximate pain which merely feels bad but does not lower fitness helps thin-skins evolve even more than pain which accurately reflects fitness consequences.  We draw contrast with the Hawk-Dove model and identify several ways in which rationality hinders the evolution of the relatively vulnerable and peaceful type of agent.
Numerical generation of periodic traveling wave solutions of some nonlinear dispersive wave systems.

In this paper a numerical procedure to generate approximations to periodic traveling wave profiles of some nonlinear dispersive wave systems is introduced. The method is based on a suitable modification of a fixed point algorithm of Petviashvili type and solves several drawbacks of some previous algorithms presented in the literature. By way of illustration, the method is applied to generate numerically periodic traveling waves of two problems of interest: the fractional KdV type equations and the extended Boussinesq system.Ministerio de Economía, Industria y Competitividad /FEDER (MTM2015-66330-P)Ministerio de Economía, Industria y Competitividad (MTM2014-54710-P
Comparison of CrAlN layers obtained with one (CrAl) or two targets (Cr and Al) by magnetron sputtering

The authors would like to thank the Regional Council of Burgundy, France for its funding and Michael Walock for his help in English revisionsThe aim of this study is to compare the properties of CrAlN coatings obtained by magnetron sputtering with one (CrAl) or two targets (Cr and Al). The influence of parameters such as the target bias voltage, the working pressure, the deposition time and the bias voltage applied on the Cr or Al targets on the properties of the layers was studied. We characterized the films by X-ray Diffraction, Scanning Electron Microscopy, coupled with Energy  Dispersive Spectroscopy, nanoindentation and their residual stresses were also determined.
The optimal films obtained with both methods are well crystallized, well-adherent to the substrate, and contained similar amounts of Al (20–30 at.%). The optimal coatings synthesized with one target presented properties not as good as those realized with two targets. Nevertheless, films made with one target showed a lower frictional coefficient probably due to composition control. The lack of compositional control with the use of one target limits the optimization process. With two targets, we have greater control over the film
composition. This leads to higher hardness, lower stresses, and improved Young's modulus over films produced with a single CrAl target. Additionally, the morphologies are different (columnar with CrAl and dense with Cr and Al). To conclude, it seems more justified to work if possible with two independent targets.Regional Council of Burgund
Vanadium (IV and V) Complexes of Reduced Schiff Bases Derived from the Reaction of Aromatic o -Hydroxyaldehydes and Diamines Containing Carboxyl Groups

The reduced Schiff bases of salicylaldehyde [and o-vanillin (o-van)] with D,L- and L-diaminopropionic acid (DPA), designated by salDPA, and L-2,4-diaminopentanoic acid [ornithine (Orn)], designated by salOrn, as well as the VIVO2+ and VVO2+ complexes of salDPA were prepared. The compounds were characterised in the solid state and in solution. The structure of H4salDPA+Cl- was determined by X-ray diffraction. Complexation of VIVO2+ and VVO2+ with salDPA and salOrn (only the VIVO system) in aqueous solution was studied by potentiometry, UV/Visible spectroscopy and circular dichroism, as well as by EPR spectroscopy for the VIVO-salDPA system and by 1H- and 51V NMR spectroscopy for the VVO2-salDPA system. Stoichiometries and complex formation constants were determined by potentiometry at 25 °C and I = 0.2 M KCl. Practically only 1:1 complexes were formed in both systems with composition (VO)LH2 and(VO)L in the VIVO-salDPA system, and with composition(VO2)LH and (VO2)L in the VVO2-salDPA system. Spectroscopic data provided information about the most probable binding modes of each stoichiometry. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)http://dx.doi.org/10.1002/ejic.20060030
Iron Biogeochemistry in the High Latitude North Atlantic Ocean

Iron (Fe) is an essential micronutrient for marine microbial organisms, and low supply controls productivity in large parts of the world’s ocean. The high latitude North Atlantic is seasonally Fe limited, but Fe distributions and source strengths are poorly constrained. Surface ocean dissolved Fe (DFe) concentrations were low in the study region (<0.1 nM) in summer 2010, with significant perturbations during spring 2010 in the Iceland Basin as a result of an eruption of the Eyjafjallajökull volcano (up to 2.5 nM DFe near Iceland) with biogeochemical consequences. Deep water concentrations in the vicinity of the Reykjanes Ridge system were influenced by pronounced sediment resuspension, with indications for additional inputs by hydrothermal vents, with subsequent lateral transport of Fe and manganese plumes of up to 250–300 km. Particulate Fe formed the dominant pool, as evidenced by 4–17 fold higher total dissolvable Fe compared with DFe concentrations, and a dynamic exchange between the fractions appeared to buffer deep water DFe. Here we show that Fe supply associated with deep winter mixing (up to 103 nmol m−2 d−1) was at least ca. 4–10 times higher than atmospheric deposition, diffusive fluxes at the base of the summer mixed layer, and horizontal surface ocean fluxes
Surface modification of HVOF thermal sprayed WC–CoCr coatings by laser treatment

In this work the affects of laser characteristics on microstructure and microhardness of high velocity oxygen fuel sprayed (HVOF) WC–CoCr coatings were investigated. The coating was deposited with a Sulzer Metco WokaJet™-400 kerosene fuel and the laser surface treatments were applied using CO2 laser with 10.6 μm wavelength. Large variations in surface properties were produced from variation in the laser processing parameters. In total, four levels of peak power (100, 200, 300 and 350 W), four levels of spot diameter (0.2, 0.4, 0.6 and 1 mm) and three levels of pulse repetition frequency (PRF) were investigated. An initial set of tests were followed by a more detailed 33 factorial design of experiments. Pulse repetition frequency and duty cycle were set in order to maintain the same overlap in the x and y directions for the raster scanned sample spot impact dimensions. Overlaps of 30% were used in the initial tests and 10% in the more detailed trials. The results have shown that care must be taken to keep the irradiance at a relatively low level compared to uncoated surfaces. High irradiance can in this case result in rough and porous surfaces. Lower levels of irradiance are shown to provide more uniform microstructures, reduced porosity and increased microhardness
Chemical and electrical characterisation of the segregation of Al from a CuAl alloy (90%:10% wt) with thermal anneal

A copper-aluminium (CuAl) alloy (90% : 10% wt) has been investigated in relation to segregation of the alloying element Al, from the alloy bulk during vacuum anneal treatments. X-ray photoelectron spectroscopy (XPS) measurements were used to track the surface enrichment of Al segregating from the alloy bulk during in situ ultra-high vacuum anneals. Secondary ion mass spectroscopy (SIMS) indicates a build-up of Al at the surface of the annealed alloy relative to the bulk composition. Metal oxide semiconductor (MOS) CuAl/ SiO2/Si structures show a shift in flatband voltage upon thermal anneal consistent with the segregation of the Al to the alloy/SiO2 interface. Electrical four point probe measurements indicates that the segregation of Al from the alloy bulk following thermal annealing results in a decrease in film resistivity. X-ray diffraction data shows evidence for significant changes in crystal structure upon annealing, providing further evidence for expulsion of Al from the alloy bulk
Putting Pragmatism to Work in the Cold War: Science, Technology, and Politics in the Writings of James B. Conant

This paper examines James Conant’s pragmatic theory of science – a theory that has been neglected by most commentators on the history of 20th-century philosophy of science – and it argues that this theory occupied an important place in Conant’s strategic thinking about the Cold War. Conant drew upon his wartime science policy work, the history of science, and Quine’s epistemological holism to argue that there is no strict distinction between science and technology, that there is no such thing as “the scientific method,” and that theories are better interpreted as policies rather than creeds. An important consequence that he drew from these arguments is that science is both a thoroughly value-laden, and an intrinsically social, enterprise. These results led him to develop novel proposals for reorganizing scientific and technological research – proposals that he believed could help to win the Cold War. Interestingly, the Cold War had a different impact upon Conant’s thinking than it did upon many other theorists of science in postwar America. Instead of leading him to “the icy slopes of logic,” it led him to develop a socially- and politically-engaged theory that was explicitly in the service of the American Cold War effort
Combined grazing incidence RBS and TEM analysis of luminescent nano-SiGe/SiO2 multilayers.

Multilayer structures with five periods of amorphous SiGe nanoparticles/SiO2 layers with different thickness were deposited by Low Pressure Chemical Vapor Deposition and annealed to crystallize the SiGe nanoparticles. The use of grazing incidence RBS was necessary to obtain sufficient depth resolution to separate the signals arising from the individual layers only a few nm thick. The average size and areal density of the embedded SiGe nanoparticles as well as the oxide interlayer thickness were determined from the RBS spectra. Details of eventual composition changes and diffusion processes caused by the annealing processes were also studied. Transmission Electron Microscopy was used to obtain complementary information on the structural parameters of the samples in order to check the information yielded by RBS. The study revealed that annealing at 900 °C for 60 s, enough to crystallize the SiGe nanoparticles, leaves the structure unaltered if the interlayer thickness is around 15 nm or higher
High-order methods for the numerical solution of the BiGlobal linear stability eigenvalue problem in complex geometries.

A high-order computational tool based on spectral and spectral/hp elements (J. Fluid. Mech. 2009; to appear) discretizations is employed for the analysis of BiGlobal fluid instability problems. Unlike other implementations of this type, which use a time-stepping-based formulation (J. Comput. Phys. 1994; 110(1):82–102; J. Fluid Mech. 1996; 322:215–241), a formulation is considered here in which the discretized matrix is constructed and stored prior to applying an iterative shift-and-invert Arnoldi algorithm for the solution of the generalized eigenvalue problem. In contrast to the time-stepping-based formulations, the matrix-based approach permits searching anywhere in the eigenspace using shifting. Hybrid and fully unstructured meshes are used in conjunction with the spatial discretization. This permits analysis of flow instability on arbitrarily complex 2-D geometries, homogeneous in the third spatial direction and allows both mesh (h)-refinement as well as polynomial (p)-refinement. A series of validation cases has been defined, using well-known stability results in confined geometries. In addition new results are presented for ducts of curvilinear cross-sections with rounded corners
Belt separation system under slat in fattening pig housing: Effect of belt type and extraction frequency

The efficiency of manure separation by a conveyor belt under a partially slatted floor for fattening pigs was determined for two types of belts, a flat belt with an incline of up to 6° transversely and a concave belt with an incline of up to 1° longitudinally. A 31.20% and 23.75% dry matter content of the solid fraction was obtained for the flat and concave belt, respectively. The flat belt was more efficient at 6° than other slope angles. The residence time of the manure on the two belt types influenced the separation efficiency from a live weight of 63.00 kg upwards. The quantity of residue produced with this system was reduced to 25–40% with respect to a pit system under slat. This could mean a remarkable reduction in costs of storage, transport and application of manure
Stability of vacancy clusters in FeCr alloys: A study of the Cr concentration dependence

Fe–Cr based alloys are the leading structural material candidates in the design of next generation reactors due to their high resistance to swelling and corrosion. Despite these good properties there are others, such as embrittlement, which require a higher level of understanding in order to improve aspects such as safety or lifetime of the reactors. The addition of Cr improves the behavior of the steels under irradiation, but not in a monotonic way. Therefore, understanding the changes in the Fe–Cr based alloys microstructure induced by irradiation and the role played by the alloying element (Cr) is needed in order to predict the response of these materials under the extreme conditions they are going to support. In this work we perform a study of the effect of Cr concentration in a bcc Fe–Cr matrix on formation and binding energies of vacancy clusters up to 5 units. The dependence of the calculated formation and binding energy is investigated with two empirical interatomic potentials specially developed to study radiation damage in Fe–Cr alloys. Results are very similar for both potentials showing an increase of the defect stability with the cluster size and no real dependence on Cr concentration for the binding energy