nils-herrmann/clean_scirepeval huggingface dataset:
Maximum likelihood evidence for Neandertal admixture in Eurasian populations from three genomes

Although there has been much interest in estimating divergence and admixture from genomic data, it has proven difficult to distinguish gene flow after divergence from alternative histories involving structure in the ancestral population. The lack of a formal test to distinguish these scenarios has sparked recent controversy about the possibility of interbreeding between Neandertals and modern humans in Eurasia. We derive the probability of mutational configurations in non-recombining sequence blocks under alternative histories of divergence with admixture and ancestral structure. Dividing the genome into short blocks makes it possible to compute maximum likelihood estimates of parameters under both models. We apply this method to triplets of human Neandertal genomes and quantify the relative support for models of long-term population structure in the ancestral African popuation and admixture from Neandertals into Eurasian populations after their expansion out of Africa. Our analysis allows us -- for the first time -- to formally reject a history of ancestral population structure and instead reveals strong support for admixture from Neandertals into Eurasian populations at a higher rate (3.4%-7.9%) than suggested previously.
SlopMap: a software application tool for quick and flexible identification of similar sequences using exact k-mer matching.

With the advent of Next-Generation (NG) sequencing, it has become possible to sequence a entire genomes quickly and inexpensively. However, in some experiments one only needs to extract and assembly a portion of the sequence reads, for example when performing transcriptome studies, sequencing mitochondrial genomes, or characterizing exomes. With the raw DNA-library of a complete genome it would appear to be a trivial problem to identify reads of interest. But it is not always easy to incorporate well-known tools such as BLAST, BLAT, Bowtie, and SOAP directly into a bioinformatics pipelines before the assembly stage, either due to incompatibility with the assembler's file inputs, or because it is desirable to incorporate information that must be extracted separately. For example, in order to incorporate flowgrams from a Roche 454 sequencer into the Newbler assembler it is necessary to first extract them from the original SFF files. We present SlopMap, a bioinformatics software utility that allows quickly identification similar to the provided reference reads from either Roche 454 or Illumnia DNA library. With simple and intuitive command-line interface along with file output formats compatible to assembly programs, SlopMap can be directly embedded to biological data processing pipeline without any additional programming work. In addition, SlopMap preserves flowgram information needed for Roche 454 assembler.
Efficient, uninformative sampling of limb darkening coefficients for two-parameter laws

Stellar limb darkening affects a wide range of astronomical measurements and is frequently modelled with a parametric model using polynomials in the cosine of the angle between the line of sight and the emergent intensity. Two-parameter laws are particularly popular for cases where one wishes to fit freely for the limb darkening coefficients (i.e. an uninformative prior) due to the compact prior volume and the fact that more complex models rarely obtain unique solutions with present data. In such cases, we show that the two limb darkening coefficients are constrained by three physical boundary conditions, describing a triangular region in the two-dimensional parameter space. We show that uniformly distributed samples may be drawn from this region with optimal efficiency by a technique developed by computer graphical programming: triangular sampling. Alternatively, one can make draws using a uniform, bivariate Dirichlet distribution. We provide simple expressions for these parametrizations for both techniques applied to the case of quadratic, square-root and logarithmic limb darkening laws. For example, in the case of the popular quadratic law, we advocate fitting for q1 ≡ (u1 + u2) 2 and q2 ≡ 0.5u1(u1 + u2) −1 with uniform priors in the interval [0, 1] to implement triangular sampling easily. Employing these parametrizations allows one to derive model parameters which fully account for our ignorance about the intensity profile, yet never explore unphysical solutions, yielding robust and realistic uncertainty estimates. Furthermore, in the case of triangular sampling with the quadratic law, our parametrization leads to significantly reduced mutual correlations and provides an alternative geometric explanation as to why naively fitting the quadratic limb darkening coefficients precipitates strong correlations in the first place.
Interpretation of the Weyl tensor

According to folklore in general relativity, the Weyl tensor can be decomposed into parts corresponding to Newton-like, incoming and outgoing wavelike field components. It is shown here that this one-to-one correspondence does not hold for space-time geometries with cylindrical isometries. This is done by investigating some well-known exact solutions of Einstein's field equations with whole-cylindrical symmetry, for which the physical interpretation is very clear, but for which the standard Weyl interpretation would give contradictory results. For planar or spherical geometries, however, the standard interpretation works for both, static and dynamical space-times. It is argued that one reason for the failure in the cylindrical case is that for waves spreading in two spatial dimensions there is no local criterion to distinguish incoming and outgoing waves already at the linear level. It turns out that Thorne's local energy notion, subject to certain qualifications, provides an efficient diagnostic tool to extract the proper physical interpretation of the space-time geometry in the case of cylindrical configurations.
FAILED SUPERNOVAE EXPLAIN THE COMPACT REMNANT MASS FUNCTION

One explanation for the absence of higher mass red supergiants (16.5 M☉ ≲ M ≲ 25 M☉) as the progenitors of Type IIP supernovae (SNe) is that they die in failed SNe creating black holes. Simulations show that such failed SNe still eject their hydrogen envelopes in a weak transient, leaving a black hole with the mass of the star's helium core (5–8 M☉). Here we show that this naturally explains the typical masses of observed black holes and the gap between neutron star and black hole masses without any fine-tuning of stellar mass loss, binary mass transfer, or the SN mechanism, beyond having it fail in a mass range where many progenitor models have density structures that make the explosions more likely to fail. There is no difficulty including this ∼20% population of failed SNe in any accounting of SN types over the progenitor mass function. And, other than patience, there is no observational barrier to either detecting these black hole formation events or limiting their rates to be well below this prediction.
Highly efficient, dual state emission from an organic semiconductor

We report highly efficient, simultaneous fluorescence and phosphorescence (74% yield) at room temperature from a single molecule ensemble of (BzP)PB [N,N′-bis(4-benzoyl-phenyl)-N,N′-diphenyl-benzidine] dispersed into a polymer host. The slow phosphorescence (208 ms lifetime) is very efficient (50%) at room temperature and only possible because the non-radiative rate for the triplet state is extremely low (2.4 × 100 s−1). The ability of an organic molecule to function as an efficient dual state emitter at room temperature is unusual and enables a wide range of applications including the use as broadband down-conversion emitters, optical sensors and attenuators, exciton probes, and spin-independent intermediates for Forster resonant energy transfer.
The Casimir Forces in a Single Conducting Cylindrical Cavity

We want to study the Casimir effect for a single conducting microscopic cylindrical cavity. The mathematical technique is based on the Green function of the geometry of the inside of the cavity, and the integral regularization is based on the plasma frequency cutoff for real conductors. Using the symmetric electromagnetic energy-momentum tensor, in terms of four potential, the total Casimir energy for the inside of the Cavity is calculated. Neglecting the contribution of the external (outside of the cavity) Casimir energy based on the reason recently presented in , the forces experienced by the lateral surface of the cavity and its circular bases are calculated. The resulting expressions show that these forces are repulsive. The numerical computation is done for the real problem of a cavity with a basis of a radius in the same order of its height at the scale of 100 nanometers made of the best conducting materials already known.
Scrutinizing the 125 GeV Higgs boson in two Higgs doublet models at the LHC, ILC, and Muon Collider

The discovery at the LHC of a scalar particle with properties that are so far consistent with the SM Higgs boson is one of the most important advances in the history of particle physics. The challenge of future collider experiments is to determine whether its couplings will show deviations from the SM Higgs, as this would indicate new physics at the TeV scale, and also to probe the flavor structure of the Yukawa couplings. As a benchmark alternative to the SM Higgs, we consider a generic two Higgs doublet model (2HDM) and analyze the precision to which the LHC14, an ILC250, 500, 1000 GeV and a 125 GeV Muon Collider (MC) can determine the gauge and Yukawa couplings. We allow for correlations among the couplings. We include the impact of a Higgs total width measurement, indirectly at the LHC and ILC and by a direct scan at the MC. We also discuss pattern relations among the couplings that can test for singlet or doublet Higgs extensions of 2HDMs.
On the accuracy of N -body simulations at very large scales

We examine the deviation of Cold Dark Matter particle trajectories from the Newtonian result as the size of the region under study becomes comparable to or exceeds the particle horizon. To first order in the gravitational potential, the general relativistic result coincides with the Zel'dovich approximation and hence the Newtonian prediction on all scales. At second order, General Relativity predicts corrections which overtake the corresponding second order Newtonian terms above a certain scale of the order of the Hubble radius. However, since second order corrections are very much suppressed on such scales, we conclude that simulations which exceed the particle horizon but use Newtonian equations to evolve the particles, reproduce the correct trajectories very well. The dominant relativistic corrections to the power spectrum on scales close to the horizon are at most of the order of $\sim 10^{-5}$ at $z=49$ and $\sim 10^{-3}$ at $z=0$. The differences in the positions of real space features are affected at a level below $10^{-6}$ at both redshifts. Our analysis also clarifies the relation of N-body results to relativistic considerations.
Collider Constraints on the Dark Matter Interpretation of the CDMS II Results

The recent observation of three events by the CDMS II experiment can be interpreted as a 8.6 GeV dark matter scatters elastically with the nucleons inside the silicon detectors with a spin-independent cross section of 1.9 x 10^-41 cm^2. We employ the effective dark matter interaction approach to fit to the interpreted cross section, and make predictions for monojet and monophoton production at the LHC with the fitted parameters. We show that some of the operators are already ruled out by current data while the others can be further probed in the upcoming 14 TeV run of the LHC.
High-spin structures of 36 88 Kr 52 and 37 89 Rb 52 : Evolution from collective to single-particle behavior

The high-spin states of the two neutron-rich nuclei ${}^{88}$Kr${}_{52}$ and ${}^{89}$Rb${}_{52}$ have been studied from the ${}^{18}$O+${}^{208}$Pb fusion-fission reaction. Their level schemes were built from triple $\ensuremath{\gamma}$-ray coincidence data, and $\ensuremath{\gamma}\ensuremath{-}\ensuremath{\gamma}$ angular correlations were analyzed in order to assign spin and parity values to most of the observed states. The two level schemes evolve from collective structures to single-particle excitations as a function of the excitation energy. Comparison with results of shell-model calculations gives the specific proton and neutron configurations which are involved to generate the angular momentum along the yrast lines.
Effect of fluctuations on the QCD critical point in a finite volume

We investigate the effect of a finite volume on the critical behavior of the theory of the strong interaction (QCD) by means of a quark-meson model for two quark flavors. In particular, we analyze the effect of a finite volume on the location of the critical point in the phase diagram existing in our model. In our analysis, we take into account the effect of long-range fluctuations with the aid of renormalization group techniques. We find that these quantum and thermal fluctuations, absent in mean-field studies, play an import role for the dynamics in a finite volume. We show that the critical point is shifted towards smaller temperatures and larger values of the quark chemical potential if the volume size is decreased. This behavior persists for antiperiodic as well as periodic boundary conditions for the quark fields as used in many lattice QCD simulations.
A Time and Space Efficient Junction Tree Architecture

The junction tree algorithm is a way of computing marginals of boolean multivariate probability distributions that factorise over sets of random variables. The junction tree algorithm first constructs a tree called a junction tree who's vertices are sets of random variables. The algorithm then performs a generalised version of belief propagation on the junction tree. The Shafer-Shenoy and Hugin architectures are two ways to perform this belief propagation that tradeoff time and space complexities in different ways: Hugin propagation is at least as fast as Shafer-Shenoy propagation and in the cases that we have large vertices of high degree is significantly faster. However, this speed increase comes at the cost of an increased space complexity. This paper first introduces a simple novel architecture, ARCH-1, which has the best of both worlds: the speed of Hugin propagation and the low space requirements of Shafer-Shenoy propagation. A more complicated novel architecture, ARCH-2, is then introduced which has, up to a factor only linear in the maximum cardinality of any vertex, time and space complexities at least as good as ARCH-1 and in the cases that we have large vertices of high degree is significantly faster than ARCH-1.
Gold, Oil, and Stocks

We employ a wavelet approach and conduct a time-frequency analysis of dynamic correlations between pairs of key traded assets (gold, oil, and stocks) covering the period from 1987 to 2012. The analysis is performed on both intra-day and daily data. We show that heterogeneity in correlations across a number of investment horizons between pairs of assets is a dominant feature during times of economic downturn and financial turbulence for all three pairs of the assets under research. Heterogeneity prevails in correlations between gold and stocks. After the 2008 crisis, correlations among all three assets increase and become homogenous: the timing differs for the three pairs but coincides with the structural breaks that are identified in specific correlation dynamics. A strong implication emerges: during the period under research, and from a different-investment-horizons perspective, all three assets could be used in a well-diversified portfolio only during relatively short periods.
Metropolis Monte Carlo integration on the Lefschetz thimble: Application to a one-plaquette model

We propose a new algorithm based on the Metropolis sampling method to perform Monte Carlo integration for path integrals in the recently proposed formulation of quantum field theories on the Lefschetz thimble. The algorithm is based on a mapping between the curved manifold defined by the Lefschetz thimble of the full action and the flat manifold associated with the corresponding quadratic action. We discuss an explicit method to calculate the residual phase due to the curvature of the Lefschetz thimble. Finally, we apply this new algorithm to a simple one-plaquette model where our results are in perfect agreement with the analytic integration. We also show that for this system the residual phase does not represent a sign problem.
Modeling the Rise in Internet-based Petitions

Contemporary collective action, much of which involves social media and other Internet-based platforms, leaves a digital imprint which may be harvested to better understand the dynamics of mobilization. Petition signing is an example of collective action which has gained in popularity with rising use of social media and provides such data for the whole population of petition signatories for a given platform. This paper tracks the growth curves of all 20,000 petitions to the UK government over 18 months, analyzing the rate of growth and outreach mechanism. Previous research has suggested the importance of the first day to the ultimate success of a petition, but has not examined early growth within that day, made possible here through hourly resolution in the data. The analysis shows that the vast majority of petitions do not achieve any measure of success; over 99 percent fail to get the 10,000 signatures required for an official response and only 0.1 percent attain the 100,000 required for a parliamentary debate. We analyze the data through a multiplicative process model framework to explain the heterogeneous growth of signatures at the population level. We define and measure an average outreach factor for petitions and show that it decays very fast (reducing to 0.1% after 10 hours). After 24 hours, a petition's fate is virtually set. The findings seem to challenge conventional analyses of collective action from economics and political science, where the production function has been assumed to follow an S-shaped curve.
Noether gauge symmetry for the Bianchi type I model in f(T) gravity

In this paper, we present the Noether symmetries of a class of the Bianchi type I anisotropic model in the context of f(T) gravity. By solving the system of equations obtained from the Noether symmetry condition, we obtain the form of f(T) as a teleparallel form. This analysis shows that teleparallel gravity has the maximum number of Noether symmetries. We derive the symmetry generators and show that there are five kinds of symmetries, including time and scale invariance under metric coefficients. We classify the symmetries and we obtain the corresponding invariants.
Novel Compact Accelerator-Based Neutron and Gamma Sources for Future Detector Calibration

Novel ultra-compact, electrically switchable, time-structured/pulsed, ~1-14 MeV-level neutron and photon generators have application embedded into large detector systems, especially calorimeters, for energy and operational calibration. The small sizes are applicable to permanent in-situ deployment, or able to be conveniently inserted into large high energy physics detector systems. For bench- testing of prototypes, or for detector module production testing, these compact n and gamma generators offer advantages.
DWARF GALAXIES WITH OPTICAL SIGNATURES OF ACTIVE MASSIVE BLACK HOLES

We present a sample of 151 dwarf galaxies (108.5 ≲ M⋆ ≲ 109.5 M☉) that exhibit optical spectroscopic signatures of accreting massive black holes (BHs), increasing the number of known active galaxies in this stellar-mass range by more than an order of magnitude. Utilizing data from the Sloan Digital Sky Survey Data Release 8 and stellar masses from the NASA-Sloan Atlas, we have systematically searched for active BHs in ∼25,000 emission-line galaxies with stellar masses comparable to the Magellanic Clouds and redshifts z < 0.055. Using the narrow-line [O iii]/Hβ versus [N ii]/Hα diagnostic diagram, we find photoionization signatures of BH accretion in 136 galaxies, a small fraction of which also exhibit broad Hα emission. For these broad-line active galactic nucleus (AGN) candidates, we estimate BH masses using standard virial techniques and find a range of 105 ≲ MBH ≲ 106 M☉ and a median of MBH ∼ 2 × 105 M☉. We also detect broad Hα in 15 galaxies that have narrow-line ratios consistent with star-forming galaxies. Follow-up observations are required to determine if these are true type 1 AGN or if the broad Hα is from stellar processes. The median absolute magnitude of the host galaxies in our active sample is Mg = −18.1 mag, which is ∼1–2 mag fainter than previous samples of AGN hosts with low-mass BHs. This work constrains the smallest galaxies that can form a massive BH, with implications for BH feedback in low-mass galaxies and the origin of the first supermassive BH seeds.
Topological Flat Band Models and Fractional Chern Insulators

Topological insulators and their intriguing edge states can be understood in a single-particle picture and can as such be exhaustively classified. Interactions significantly complicate this picture and can lead to entirely new insulating phases, with an altogether much richer and less explored phenomenology. Most saliently, lattice generalizations of fractional quantum Hall states, dubbed fractional Chern insulators, have recently been predicted to be stabilized by interactions within nearly dispersionless bands with non-zero Chern number, $C$. Contrary to their continuum analogues, these states do not require an external magnetic field and may potentially persist even at room temperature, which make these systems very attractive for possible applications such as topological quantum computation. This review recapitulates the basics of tight-binding models hosting nearly flat bands with non-trivial topology, $C\neq 0$, and summarizes the present understanding of interactions and strongly correlated phases within these bands. Emphasis is made on microscopic models, highlighting the analogy with continuum Landau level physics, as well as qualitatively new, lattice specific, aspects including Berry curvature fluctuations, competing instabilities as well as novel collective states of matter emerging in bands with $|C|>1$. Possible experimental realizations, including oxide interfaces and cold atom implementations as well as generalizations to flat bands characterized by other topological invariants are also discussed.
Field theory of the d +t→n+α reaction dominated by a 5 He * unstable particle

An effective, nonrelativistic quantum field theory for the $dt\ensuremath{\rightarrow}n\ensuremath{\alpha}$ fusion reaction in the low-energy, resonance region is presented. The theory assumes that the reaction is dominated by an intermediate ${}^{5}{\mathrm{He}}^{*}$ unstable spin-$3/{2}^{+}$ resonance. It involves two parameters in the coupling of the $dt$ and $n\ensuremath{\alpha}$ particles to the unstable resonant state and the resonance energy level\char22{}only three real parameters in all. All Coulomb corrections to this process are computed. The resultant field theory is exactly solvable and provides an excellent description of the $dt$ fusion process.