nils-herrmann/clean_scirepeval huggingface dataset:
Effective field theory for proton halo nuclei

We use halo effective field theory to analyze the universal features of proton halo nuclei bound due to a large S-wave scattering length. Our work provides a fully field-theoretical treatment of bound halo nuclei in the presence of a repulsive Coulomb interaction. With a Lagrangian built from effective core and valence-proton fields, we derive a leading-order expression for the charge form factor. Within the same framework we also calculate the radiative proton capture cross section. We present general results at leading order that can be applied to any one-proton halo system bound in a relative S wave. We illustrate the method by studying the excited 1/2(+) state of fluorine 17, for which we give results for the charge radius and the astrophysical S factor.
From nuclear structure to neutron stars

Recent progress in quantum Monte Carlo with modern nucleon-nucleon interactions have enabled the successful description of properties of light nuclei and neutronrich matter. As a demonstration, we show that the agreement between theoretical calculations of the charge form factor of 12 C and the experimental data is excellent. Applying similar methods to isospin-asymmetric systems allows one to describe neutrons confined in an external potential and homogeneous neutron-rich matter. Of particular interest is the nuclear symmetry energy, the energy cost of creating an isospin asymmetry. Combining these advances with recent observations of neutron star masses and radii gives insight into the equation of state of neutron-rich matter near and above the saturation density. In particular, neutron star radius measurements constrain the derivative of the symmetry energy.
Exploration and retrieval of whole-metagenome sequencing samples

Over the recent years, the field of whole-metagenome shotgun sequencing has witnessed significant growth owing to the high-throughput sequencing technologies that allow sequencing genomic samples cheaper, faster and with better coverage than before. This technical advancement has initiated the trend of sequencing multiple samples in different conditions or environments to explore the similarities and dissimilarities of the microbial communities. Examples include the human microbiome project and various studies of the human intestinal tract. With the availability of ever larger databases of such measurements, finding samples similar to a given query sample is becoming a central operation.  In this article, we develop a content-based exploration and retrieval method for whole-metagenome sequencing samples. We apply a distributed string mining framework to efficiently extract all informative sequence k-mers from a pool of metagenomic samples and use them to measure the dissimilarity between two samples. We evaluate the performance of the proposed approach on two human gut metagenome datasets as well as human microbiome project metagenomic samples. We observe significant enrichment for diseased gut samples in results of queries with another diseased sample and high accuracy in discriminating between different body sites even though the method is unsupervised. Availability and implementation: A software implementation of the DSM framework is available at https://github.com/HIITMetagenomics/dsm-framework.  sohan.seth@hiit.fi or antti.honkela@hiit.fi Supplementary information: Supplementary data are available at Bioinformatics online.
Tsallis entropy and hyperbolicity

Some preliminary evidence suggests the conjecture that the collective behaviour of systems having long-range interactions may be described more effectively by the Tsallis rather than by the Boltzmann/Gibbs/Shannon entropy. To this end, we examine consequences of the biggest difference between these two entropies: their composition properties. We rely on a metric formalism that establishes the "hyperbolic" nature of Tsallis entropy and explore some of its consequences for the underlying systems. We present some recent and some forthcoming results of our work
Detrended cross-correlation analysis consistently extended to multifractality.

We propose an algorithm, multifractal cross-correlation analysis (MFCCA), which constitutes a consistent extension of the detrended cross-correlation analysis and is able to properly identify and quantify subtle characteristics of multifractal cross-correlations between two time series. Our motivation for introducing this algorithm is that the already existing methods, like multifractal extension, have at best serious limitations for most of the signals describing complex natural processes and often indicate multifractal cross-correlations when there are none. The principal component of the present extension is proper incorporation of the sign of fluctuations to their generalized moments. Furthermore, we present a broad analysis of the model fractal stochastic processes as well as of the real-world signals and show that MFCCA is a robust and selective tool at the same time and therefore allows for a reliable quantification of the cross-correlative structure of analyzed processes. In particular, it allows one to identify the boundaries of the multifractal scaling and to analyze a relation between the generalized Hurst exponent and the multifractal scaling parameter λ(q). This relation provides information about the character of potential multifractality in cross-correlations and thus enables a deeper insight into dynamics of the analyzed processes than allowed by any other related method available so far. By using examples of time series from the stock market, we show that financial fluctuations typically cross-correlate multifractally only for relatively large fluctuations, whereas small fluctuations remain mutually independent even at maximum of such cross-correlations. Finally, we indicate possible utility of MFCCA to study effects of the time-lagged cross-correlations.
First studies with the Resistive-Plate WELL gaseous multiplier

We present the results of first studies of the Resistive Plate WELL (RPWELL): a single-faced THGEM coupled to a copper anode via a resistive layer of high bulk resistivity. We explored various materials of different bulk resistivity (10 9 − 10 12 Ωcm) and thickness (0.4 − 4 mm). Our most successful prototype, with a 0.6 mm resistive plate of ∼ 10 9 Ωcm, achieved gains of up to 10 5 with 8 keV x-ray in Ne/5%CH4; a minor 30% gain drop occurred with a rate increase from 10 to 10 4 Hz/mm 2 . The detector displayed a full "discharge-free" operation—even when exposed to high primary ionization events. We present the RPWELL detector concept and compare its performance to that of other previously explored THGEM configurations—in terms of gain, its curves, dependence on rate, and the response to high ionization. The robust Resistive Plate WELL concept is a step forward in the Micro-Pattern Gas-Detector family, with numerous potential applications.
Probing the cosmic-ray content of galaxy clusters by stacking Fermi-LAT count maps

Observation in radio have shown that galaxy clusters are giant reservoirs of cosmic rays (CR). Although a gammaray signal from the cluster volume is expected to arise through interactions of CR protons with the ambient plasma, a confirming observation is still missing.  We search for a cumulative gamma-ray emission in direction of galaxy clusters by analysing a collection of stacked Fermi-LAT count maps. Additionally, we investigate possible systematic differences in the emission between cool-core and non-cool core cluster populations.  Making use of a sample of 53 clusters selected from the HIFLUGCS catalog, we do not detect a significant signal from the stacked sample. The upper limit on the average flux per cluster derived for the total stacked sample is at the level of a few 10 11 phcm 2 s 1 at 95% confidence level in the 1-300 GeV band, assuming power-law spectra with photon indices 2.0, 2.4, 2.8 and 3.2. Separate stacking of the cool core and non-cool core clusters in the sample lead to similar values of around 5 × 10 11 phcm 2 s 1 and 2 × 10 11 phcm 2 s 1 , respectively.  Under the assumption that decaying π 0 , produced in collisions between CRs and the ambient thermal gas, are responsible for the gamma-ray emission, we set upper limits on the average CR content in galaxy clusters. For the entire cluster population, our upper limit on the gamma-ray flux translates into an upper limit on the average CR-to-thermal energy ratio of 4.6% for a photon index of 2.4, although it is possible for individual systems to exceed this limit. Our 95% upper limits are at the level expected from numerical simulations, which likely suggests that the injection of CR at cosmological shocks is less efficient than previously assumed.
On the frequency of planetary systems around G-dwarfs

We determine the fraction of G-dwarf stars that could host stable planetary systems based on the observed properties of binaries in the Galactic field, and in various postulated primordial binary populations, which assume that the primordial binary fraction is higher than that in the field. We first consider the frequency of Solar System analogues – planetary systems that form either around a single G-dwarf star, or a binary containing a G-dwarf where the binary separation exceeds 100–300au. If the primordial binary fraction and period distribution is similar to that in the field, then up to 63per cent of G-dwarf systems could potentially host a Solar System analogue. However, if the primordial binary fraction is higher, the fraction of G-dwarf systems that could host a planetary system like our own is lowered to 38per cent. We extend our analysis to consider the fraction of G-dwarf systems (both single and binary) that can host either circumprimary planets (orbiting the primary star of the binary) or circumbinary planets (orbiting both stars in the binary) for fiducial planetary separations between 1 – 100au. Depending on the assumed binary population, in the circumprimary case between 65 and 95per cent of systems can host a planet at 1au, decreasing to between 20 and 65per cent of systems that can host a planet at 100au. In the circumbinary case, between 5 and 59per cent of systems can host a planet at 1au, increasing to between 34 and 75per cent of systems that can host a planet at 100au. Our results suggest that the assumed binary fraction is the key parameter in determining the fraction of potentially stable planetary systems in G-dwarf systems and that using the present-day value may lead to significant overestimates if the binary fraction was initially higher.
Single top quark cross section measurement in the t-channel at the high-luminosity LHC

We study the precision with which the t-channel single top quark production cross section is expected to be measured in future LHC runs at 14 TeV. The single top final state has a lepton and neutrino from the top quark decay plus two jets, one of which is required to be b-tagged. This measurement is done in the context of the Snowmass 2013 study for the low-luminosity 14 TeV and the high-luminosity 14 TeV LHC as well as for high-luminosity 33 TeV LHC.
Magnetotunneling spectroscopy of chiral two-dimensional electron systems

We present a theoretical study of momentum-resolved tunneling between parallel two-dimensional conductors whose charge carriers have a (pseudo-)spin-1/2 degree of freedom that is strongly coupled to their linear orbital momentum. Specific examples are single and bilayer graphene as well as single-layer molybdenum disulphide. Resonant behavior of the differential tunneling conductance exhibited as a function of an in-plane magnetic field and bias voltage is found to be strongly affected by the (pseudo-)spin structure of the tunneling matrix. We discuss ramifications for the direct measurement of electronic properties such as Fermi surfaces and the dispersion curves. Furthermore, using a graphene double-layer structure as an example, we show how magneto-tunneling transport can be used to measure the pseudo-spin structure of tunnel matrix elements, thus enabling electronic characterization of the barrier material.
Pressure-induced phase transitions of multiferroic BiFeO3

Pressure-induced phase transitions of multiferroic BiFeO3 have been investigated using synchrotron radiation X-ray diffraction with diamond anvil cell technique at room temperature. Present experimental data clearly show that rhombohedral (R3c) phase of BiFeO3 first transforms to monoclinic (C2/m) phase at 7 GPa, then to orthorhombic (Prima) phase at 11 GPa, which is consistent with recent theoretical ab initio calculation. However, we observe another peak at 2 theta=7 degrees in the pressure range of 5-7 GPa that has not been reported previously. Further analysis reveals that this reflection peak is attributed to the orthorhombic (Pbam) phase, indicating the coexistance of monoclinic phase with orthorhombic phase in low pressure range.
Can spontaneous symmetry breaking order develop in a topological phase

Landau's symmetry breaking theory is the basis of modern condensed matter physics, from which most phases can be understood. The recent discovery of topological insulators simulates the study on the topological phase which is beyond this theory. An interesting question is whether the topological phase and spontaneous symmetry breaking order can coexist. We study this problem based on the topological phase in the Haldane model. Firstly by including a staggered potential, we show that if the system is subjected to the symmetry needed by the charge density wave (CDW) order in advance, the topological phase can coexist with the CDW order, realizing the topological CDW phase. While when the nearest neighor interaction which preserves the symmetry of the origin Hamiltonian is included, the CDW order can not develop from spontaneous symmetry breaking in the topological phase. The results imply that a spontaneous symmetry breaking order may not develop in a topological phase.
Spin-orbit coupling and quantum spin Hall effect for neutral atoms without spin flips.

We propose a scheme which realizes spin-orbit coupling and the quantum spin Hall effect for neutral atoms in optical lattices without relying on near resonant laser light to couple different spin states. The spin-orbit coupling is created by modifying the motion of atoms in a spin-dependent way by laser recoil. The spin selectivity is provided by Zeeman shifts created with a magnetic field gradient. Alternatively, a quantum spin Hall Hamiltonian can be created by all-optical means using a period-tripling, spin-dependent superlattice.
Interface-induced topological insulator transition in GaAs/Ge/GaAs quantum wells.

We demonstrate theoretically that interface engineering can drive germanium, one of the most commonly used semiconductors, into a topological insulating phase. Utilizing giant electric fields generated by charge accumulation at GaAs/Ge/GaAs opposite semiconductor interfaces and band folding, the new design can reduce the sizable gap in Ge and induce large spin-orbit interaction, which leads to a topological insulator transition. Our work provides a new method to realize topological insulators in commonly used semiconductors and suggests a promising approach to integrate it in well-developed semiconductor electronic devices.
Efficient hedging in general Black-Scholes model

An investor faced with a contingent claim may eliminate risk by perfect hedging, but as it is often quite expensive, he seeks partial hedging (quantile hedging or efficient hedging) that requires less capital and reduces the risk. Efficient hedging for European call option was considered in the standard Black-Scholes model with constant drift and volatility coefficients. In this paper we considered the efficient hedging for European call option in general Black-Scholes model $dX_t=X_t(m(t)dt+\sigma (t)dw(t))$ with time-varying drift and volatility coefficients and in fractional Black-Scholes model $dX_t=X_t(\sigma B_H(t)+mdt)$ with constant coefficients.
Cauchy problem for fractional diffusion-wave equations with variable coefficients

We consider an evolution equation with the Caputo-Dzhrbashyan fractional derivative of order with respect to the time variable, and the second order uniformly elliptic operator with variable coefficients acting in spatial variables. This equation describes the propagation of stress pulses in a viscoelastic medium. Its properties are intermediate between those of parabolic and hyperbolic equations. In this paper, we construct and investigate a fundamental solution of the Cauchy problem, prove existence and uniqueness theorems for such equations.
Optimal payoffs under state-dependent preferences

Most decision theories, including expected utility theory, rank-dependent utility theory and cumulative prospect theory, assume that investors are only interested in the distribution of returns and not in the states of the economy in which income is received. Optimal payoffs have their lowest outcomes when the economy is in a downturn, and this feature is often at odds with the needs of many investors. We introduce a framework for portfolio selection within which state-dependent preferences can be accommodated. Specifically, we assume that investors care about the distribution of final wealth and its interaction with some benchmark. In this context, we are able to characterize optimal payoffs in explicit form. Furthermore, we extend the classical expected utility optimization problem of Merton to the state-dependent situation. Some applications in security design are discussed in detail and we also solve some stochastic extensions of the target probability optimization problem.
Spectral community detection in sparse networks

Spectral methods based on the eigenvectors of matrices are widely used in the analysis of network data, particularly for community detection and graph partitioning. Standard methods based on the adjacency matrix and related matrices, however, break down for very sparse networks, which includes many networks of practical interest. As a solution to this problem it has been recently proposed that we focus instead on the spectrum of the non-backtracking matrix, an alternative matrix representation of a network that shows better behavior in the sparse limit. Inspired by this suggestion, we here make use of a relaxation method to derive a spectral community detection algorithm that works well even in the sparse regime where other methods break down. Interestingly, however, the matrix at the heart of the method, it turns out, is not exactly the non-backtracking matrix, but a variant of it with a somewhat different definition. We study the behavior of this variant matrix for both artificial and real-world networks and find it to have desirable properties, especially in the common case of networks with broad degree distributions, for which it appears to have a better behaved spectrum and eigenvectors than the original non-backtracking matrix.
Dirac quasinormal modes in spherically symmetric regular black holes

Using the WKB approximation, massless and massive Dirac quasinormal modes (QNMs) are studied in spherically symmetric regular spacetimes. We analyze the relationships between QNM frequencies and the parameters (angular momentum number $l$, magnetic monopole charge $\beta$ and the mass of the field $m$), and discuss the extreme charge of magnetic monopole $\beta_{e}$ for spherically symmetric regular black holes (BHs). Furthermore, we apply an expansion method to expand QNMs in inverse powers of $L=l+1/2$, and confirm good precision with $l>n$. Finally, we improve traditional finite difference method to be available in massive Dirac case, and illuminate the dynamical evolution of massive Dirac field.
General relativistic N -body simulations in the weak field limit

We develop a formalism for general relativistic $N$-body simulations in the weak field regime, suitable for cosmological applications. The problem is kept tractable by retaining the metric perturbations to first order, the first derivatives to second order, and second derivatives to all orders, thus taking into account the most important nonlinear effects of Einstein gravity. It is also expected that any significant ``backreaction'' should appear at this order. We show that the simulation scheme is feasible in practice by implementing it for a plane-symmetric situation and running two test cases, one with only cold dark matter, and one which also includes a cosmological constant. For these plane-symmetric situations, the deviations from the usual Newtonian $N$-body simulations remain small and, apart from a nontrivial correction to the background, can be accurately estimated within the Newtonian framework. The correction to the background scale factor, which is a genuine backreaction effect, can be robustly obtained with our algorithm. Our numerical approach is also naturally suited for the inclusion of extra relativistic fields and thus for dark energy or modified gravity simulations.
A diffraction effect in X-ray area detectors

When an X-ray area detector based on a single-crystalline material, for instance a state-of-the-art hybrid pixel detector, is illuminated from a point source by monochromatic radiation, a pattern of lines appears which overlays the detected image. These lines are easily seen in scattering experiments with smooth patterns, such as small-angle X-ray scattering. The origin of this effect is Bragg reflection within the sensor layer of the detector. Experimental images are presented over a photon energy range from 3.4 to 10 keV, together with a theoretical analysis. The intensity of the detected signal is decreased by up to 20% on this pattern, which can affect the evaluation of scattering and diffraction experiments. The patterns can be exploited to check the alignment of the detector surface with the direct beam, and the alignment of individual detector modules with each other in the case of modular detectors, as well as for energy calibration of the radiation.
Percolation on random networks with arbitrary k-core structure.

The k-core decomposition of a network has thus far mainly served as a powerful tool for the empirical study of complex networks. We now propose its explicit integration in a theoretical model. We introduce a hard-core random network (HRN) model that generates maximally random networks with arbitrary degree distribution and arbitrary k-core structure. We then solve exactly the bond percolation problem on the HRN model and produce fast and precise analytical estimates for the corresponding real networks. Extensive comparison with real databases reveals that our approach performs better than existing models, while requiring less input information.
Quartz Plate Calorimetry for CMS HE Upgrade

Analysis of the CMS data and the simulation prediction based on these results indicate that the performance of the current scintillators in the CMS Hadron Endcap Calorimeter (HE) tiles will degrade dramatically in the High Luminosity LHC (HL-LHC) era. In order to continue the physics program in this region, the HE tiles will need to be replaced. The new tiles should have comparable/improved performance, be radiation hard, reliable and robust.