nils-herrmann/clean_scirepeval huggingface dataset:
THE PROPERTIES AND FATE OF THE GALACTIC CENTER G2 CLOUD

The object G2 was recently discovered descending into the gravitational potential of the supermassive black hole (BH) Sgr A*. We test the photoionized cloud scenario, determine the cloud properties, and estimate the emission during the pericenter passage. The incident radiation is computed starting from the individual stars at the locations of G2. The radiative transfer calculations are conducted with CLOUDY code and 2011 broadband and line luminosities are fitted. The spherically symmetric, tidally distorted, and magnetically arrested cloud shapes are tested with both the interstellar medium dust and 10 nm graphite dust. The best-fitting magnetically arrested model has the initial density ninit = 1.8 × 105 cm−3, initial radius Rinit = 2.2 × 1015 cm = 17 mas, mass mcloud = 4 MEarth, and dust relative abundance A = 0.072. It provides a good fit to 2011 data, is consistent with the luminosities in 2004 and 2008, and reaches an agreement with the observed size. We revise down the predicted radio and X-ray bow shock luminosities to be below the quiescent level of Sgr A*, which readily leads to non-detection in agreement to observations. The magnetic energy dissipation in the cloud at the pericenter coupled with more powerful irradiation may lead to an infrared source with an apparent magnitude . No shock into the cloud and no X-rays are expected from cloud squeezing by the ambient gas pressure. Larger than previously estimated cloud mass mcloud = (4–20) MEarth may produce a higher accretion rate and a brighter state of Sgr A* as the debris descend onto the BH.
Geometric massive gravity in multiconnection framework

What is the right way to interpret a massive graviton? We generalize the kinematical framework of general relativity to multiple connections. The average of the connections is itself a connection and plays the role of the canonical connection in standard General Relativity. At the level of dynamics, the simplest choice of the Einstein-Hilbert action is indistinguishable from the single-connection case. However, inspired by Weyl geometry, we show how one can construct massive gravity to all orders in perturbation theory compatible with the de Rham-Gabadadze-Tolley ghost-free model. We conclude that the mass of the graviton can be interpreted as a geometrical property of spacetime arising from two connections. Furthermore in the multi-connection framework there is no ambiguity in the definition of physical metric and consequently coupling to matter.
Infrared absorption by graphene–hBN heterostructures

We propose a theory of optical absorption in monolayer graphene–hexagonal boron nitride (hBN) heterostructures. In highly oriented heterostructures, the hBN underlay produces a long-range moiré superlattice potential for the graphene electrons which modifies the selection rules for absorption of incoming photons in the infrared to visible frequency range. The details of the absorption spectrum modification depend on the relative strength of the various symmetry-allowed couplings between the graphene electrons and the hBN, and the resulting nature of the reconstructed band structure.
Adatoms and Anderson Localization in Graphene

In this letter, we address the nature of the disordered state that results from the adsorption of adatoms in graphene. For adatoms that sit at the center of the honeycomb plaquette, as in the case of most transition metals, we show that the ones that form a zero-energy resonant state lead to Anderson localization in the vicinity of the Dirac point. Among those, we show that there is a symmetry class of adatoms where Anderson localization is suppressed, leading to an exotic quantum critical metallic state with large charge puddles, that localizes only at the Dirac point. We identify the experimental conditions for the observation of the Anderson transition for adatoms in graphene.
A MOSAIC of methods: Improving ortholog detection through integration of algorithmic diversity

A  Improving ortholog detection through integration of algorithmic diversity M. Cyrus Maher and Ryan D. Hernandez Department of Epidemiology and Biostatistics, University of California, San Francisco, 185 Berry Street, Lobby 5, Suite 5700 San Francisco, CA 94107 Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics, Institute for Quantitative Biosciences (QB3), University of California, San Francisco, 1700 4th Street San Francisco, California 94158
Equivalences of the Multi-Indexed Orthogonal Polynomials

Multi-indexed orthogonal polynomials describe eigenfunctions of exactly solvable shape-invariant quantum mechanical systems in one dimension obtained by the method of virtual states deletion. Multi-indexed orthogonal polynomials are labeled by a set of degrees of polynomial parts of virtual state wavefunctions. For multi-indexed orthogonal polynomials of Laguerre, Jacobi, Wilson, and Askey-Wilson types, two different index sets may give equivalent multi-indexed orthogonal polynomials. We clarify these equivalences. Multi-indexed orthogonal polynomials with both type I and II indices are proportional to those of type I indices only (or type II indices only) with shifted parameters.
Software for Science: Some Personal Reflections

As computer systems become more and more complex, software and tools lag more and more behind. This is especially true for scientific software that often demands high performance, and thus needs to take advantage of parallelisms, memory hierarchies and other software and systems. How do we help bridge this ever-increasing gap? 
This paper describes some of my experiences and thoughts regarding licensing, code sharing, code maintenance, open access publishing, and educations and training. Details include my recent experiences with getting industrial funding for GPL licensed software, BSD issues, sharing code on GitHub, and how I inspire students to take my 4th year Parallel Computing elective which this semester has over 50 students enrolled. Some thoughts and comments regarding why both optimization and data locality are such a central issue for scientific software is also included.
On lower and upper bounds for Asian-type options: a unified approach

In the context of dealing with financial risk management problems it is desirable to have accurate bounds for option prices in situations when pricing formulae do not exist in the closed form. A unified approach for obtaining upper and lower bounds for Asian-type options, including options on VWAP, is proposed in this paper. The bounds obtained are applicable to the continuous and discrete-time frameworks for the case of time-dependent interest rates. Numerical examples are provided to illustrate the accuracy of the bounds.
The Google scholar experiment: How to index false papers and manipulate bibliometric indicators

Google Scholar has been well received by the research community. Its promises of free, universal, and easy access to scientific literature coupled with the perception that it covers the social sciences and the humanities better than other traditional multidisciplinary databases have contributed to the quick expansion of Google Scholar Citations and Google Scholar Metrics: 2 new bibliometric products that offer citation data at the individual level and at journal level. In this article, we show the results of an experiment undertaken to analyze Google Scholar's capacity to detect citation‐counting manipulation. For this, we uploaded 6 documents to an institutional web domain that were authored by a fictitious researcher and referenced all the publications of the members of the EC3 research group at the University of Granada. The detection by Google Scholar of these papers caused an outburst in the number of citations included in the Google Scholar Citations profiles of the authors. We discuss the effects of such an outburst and how it could affect the future development of such products, at both the individual level and the journal level, especially if Google Scholar persists with its lack of transparency.
Just Google It - Digital Research Practices of Humanities Scholars

The transition from analogue to digital archives and the recent explosion of online content offers researchers novel ways of engaging with data. The crucial question for ensuring a balance between the supply and demand-side of data, is whether this trend connects to existing scholarly practices and to the average search skills of researchers. To gain insight into this process we conducted a survey among nearly three hundred (N= 288) humanities scholars in the Netherlands and Belgium with the aim of finding answers to the following questions: 1) To what extent are digital databases and archives used? 2) What are the preferences in search functionalities 3) Are there differences in search strategies between novices and experts of information retrieval? Our results show that while scholars actively engage in research online they mainly search for text and images. General search systems such as Google and JSTOR are predominant, while large-scale collections such as Europeana are rarely consulted. Searching with keywords is the dominant search strategy and advanced search options are rarely used. When comparing novice and more experienced searchers, the first tend to have a more narrow selection of search engines, and mostly use keywords. Our overall findings indicate that Google is the key player among available search engines. This dominant use illustrates the paradoxical attitude of scholars toward Google: while provenance and context are deemed key academic requirements, the workings of the Google algorithm remain unclear. We conclude that Google introduces a black box into digital scholarly practices, indicating scholars will become increasingly dependent on such black boxed algorithms. This calls for a reconsideration of the academic principles of provenance and context.
Statistical mechanics of multiedge networks.

Statistical properties of binary complex networks are well understood and recently many attempts have been made to extend this knowledge to weighted ones. There are, however, subtle yet important considerations to be made regarding the nature of the weights used in this generalization. Weights can be either continuous or discrete magnitudes, and in the latter case, they can additionally have undistinguishable or distinguishable nature. This fact has not been addressed in the literature insofar and has deep implications on the network statistics. In this work we face this problem introducing multiedge networks as graphs where multiple (distinguishable) connections between nodes are considered. We develop a statistical mechanics framework where it is possible to get information about the most relevant observables given a large spectrum of linear and nonlinear constraints including those depending both on the number of multiedges per link and their binary projection. The latter case is particularly interesting as we show that binary projections can be understood from multiedge processes. The implications of these results are important as many real-agent-based problems mapped onto graphs require this treatment for a proper characterization of their collective behavior.
Inferring Selective Constraint from Population Genomic Data Suggests Recent Regulatory Turnover in the Human Brain

The comparative genomics revolution of the past decade has enabled the discovery of functional elements in the human genome via sequence comparison. While that is so, an important class of elements, those specific to humans, is entirely missed by searching for sequence conservation across species. Here we present an analysis based on variation data among human genomes that utilizes a supervised machine learning approach for the identification of human-specific purifying selection in the genome. Using only allele frequency information from the complete low-coverage 1000 Genomes Project data set in conjunction with a support vector machine trained from known functional and nonfunctional portions of the genome, we are able to accurately identify portions of the genome constrained by purifying selection. Our method identifies previously known human-specific gains or losses of function and uncovers many novel candidates. Candidate targets for gain and loss of function along the human lineage include numerous putative regulatory regions of genes essential for normal development of the central nervous system, including a significant enrichment of gain of function events near neurotransmitter receptor genes. These results are consistent with regulatory turnover being a key mechanism in the evolution of human-specific characteristics of brain development. Finally, we show that the majority of the genome is unconstrained by natural selection currently, in agreement with what has been estimated from phylogenetic methods but in sharp contrast to estimates based on transcriptomics or other high-throughput functional methods.
Representation of Dormant and Active Microbial Dynamics for Ecosystem Modeling

Dormancy is an essential strategy for microorganisms to cope with environmental stress. However, global ecosystem models typically ignore microbial dormancy, resulting in notable model uncertainties. To facilitate the consideration of dormancy in these large-scale models, we propose a new microbial physiology component that works for a wide range of substrate availabilities. This new model is based on microbial physiological states and the major parameters are the maximum specific growth and maintenance rates of active microbes and the ratio of dormant to active maintenance rates. A major improvement of our model over extant models is that it can explain the low active microbial fractions commonly observed in undisturbed soils. Our new model shows that the exponentially-increasing respiration from substrate-induced respiration experiments can only be used to determine the maximum specific growth rate and initial active microbial biomass, while the respiration data representing both exponentially-increasing and non-exponentially-increasing phases can robustly determine a range of key parameters including the initial total live biomass, initial active fraction, the maximum specific growth and maintenance rates, and the half-saturation constant. Our new model can be incorporated into existing ecosystem models to account for dormancy in microbially-driven processes and to provide improved estimates of microbial activities.
CLASSIFYING SUPERNOVAE USING ONLY GALAXY DATA

We present a new method for probabilistically classifying supernovae (SNe) without using SN spectral or photometric data. Unlike all previous studies to classify SNe without spectra, this technique does not use any SN photometry. Instead, the method relies on host-galaxy data. We build upon the well-known correlations between SN classes and host-galaxy properties, specifically that core-collapse SNe rarely occur in red, luminous, or early-type galaxies. Using the nearly spectroscopically complete Lick Observatory Supernova Search sample of SNe, we determine SN fractions as a function of host-galaxy properties. Using these data as inputs, we construct a Bayesian method for determining the probability that an SN is of a particular class. This method improves a common classification figure of merit by a factor of >2, comparable to the best light-curve classification techniques. Of the galaxy properties examined, morphology provides the most discriminating information. We further validate this method using SN samples from the Sloan Digital Sky Survey and the Palomar Transient Factory. We demonstrate that this method has wide-ranging applications, including separating different subclasses of SNe and determining the probability that an SN is of a particular class before photometry or even spectra can. Since this method uses completely independent data from light-curve techniques, there is potential to further improve the overall purity and completeness of SN samples and to test systematic biases of the light-curve techniques. Further enhancements to the host-galaxy method, including additional host-galaxy properties, combination with light-curve methods, and hybrid methods, should further improve the quality of SN samples from past, current, and future transient surveys.
Single-photon nonlinear optics with graphene plasmons.

We show that it is possible to realize significant nonlinear optical interactions at the few photon level in graphene nanostructures. Our approach takes advantage of the electric field enhancement associated with the strong confinement of graphene plasmons and the large intrinsic nonlinearity of graphene. Such a system could provide a powerful platform for quantum nonlinear optical control of light. As an example, we consider an integrated optical device that exploits this large nonlinearity to realize a single photon switch.
Spyhoppers and Stargazers: Can Whales See the Stars?

In Moby Dick, Herman Melville wondered how - or what - whales see with eyes on opposite sides of their heads. "It is plain that he can never see an object which is exactly ahead... Is his brain so much more comprehensive, combining and subtle than man's that he can at the same moment of time attentively examine two distinct prospects, one on one side of him, and the other in an exactly opposite direction?" he asked. It's a good question. But if Melville were alive today he might have pondered something perhaps even more intriguing: Can whales see the stars?
Revealing the Intricate Effect of Collaboration on Innovation

We studied the Japan and U.S. patent records of several decades to demonstrate the effect of collaboration on innovation. We found that statistically inventor teams slightly outperform solo inventors while company teams perform equally well as solo companies. By tracking the performance record of individual teams, we found that inventor teams’ performance generally degrades with more repeat collaborations. Though company teams’ performance displays strongly bursty behavior, long-term collaboration does not significantly help innovation. To systematically study the effect of repeat collaboration, we defined the repeat collaboration number of a team as the average number of collaborations over all the teammate pairs. We found that mild repeat collaboration improves the performance of Japanese inventor teams and U.S. company teams. Yet, excessive repeat collaboration does not significantly help innovation at both the inventor and company levels in both countries. To control for unobserved heterogeneity, we performed a detailed regression analysis and the results were consistent with our simple observations. The presented results revealed the intricate effect of collaboration on innovation, which may also be observed in other creative projects.
Radial forcing and Edgar Allan Poe's lengthening pendulum

Inspired by Edgar Allan Poe's The Pit and the Pendulum, we investigate a radially driven, lengthening pendulum. We first show that increasing the length of an undriven pendulum at a uniform rate does not amplify the oscillations in a manner consistent with the behavior of the scythe in Poe's story. We discuss parametric amplification and the transfer of energy (through the parameter of the pendulum's length) to the oscillating part of the system. In this manner, radial driving can easily and intuitively be understood, and the fundamental concept applied in many other areas. We propose and show by a numerical model that appropriately timed radial forcing can increase the oscillation amplitude in a manner consistent with Poe's story. Our analysis contributes a computational exploration of the complex harmonic motion that can result from radially driving a pendulum and sheds light on a mechanism by which oscillations can be amplified parametrically. These insights should prove especially valuable in the unde...
Exoplanet transit variability: bow shocks and winds around HD 189733b

By analogy with the solar system, it is believed that stellar winds will form bow shocks around exoplanets. For hot Jupiters the bow shock will not form directly between the planet and the star, causing an asymmetric distribution of mass around the exoplanet and hence an asymmetric transit. As the planet orbits thorough varying wind conditions, the strength and geometry of its bow shock will change, thus producing transits of varying shape. We model this process using magnetic maps of HD 189733 taken one year apart, coupled with a 3D stellar wind model, to determine the local stellar wind conditions throughout the orbital path of the planet. We predict the time-varying geometry and density of the bow shock that forms around the magnetosphere of the planet and simulate transit light curves. Depending on the nature of the stellar magnetic field, and hence its wind, we find that both the transit duration and ingress time can vary when compared to optical light curves. We conclude that consecutive near-UV transit light curves may vary significantly and can therefore provide an insight into the structure and evolution of the stellar wind.
A bosonic multi-state two-well model

Inspired by the increasing possibility of experimental control in ultracold atomic physics, we introduce a new Lax operator and use it to construct and solve models with two wells and two on-well states together with its generalization for n on-well states. The models are solved by the algebraic Bethe ansatz method and can be viewed as describing two Bose–Einstein condensates allowing for an exchange interaction through Josephson tunnelling.
Dynamic fisheye grids for binary black hole simulations

We present a new warped gridding scheme adapted to simulating gas dynamics in binary black hole spacetimes. The grid concentrates grid points in the vicinity of each black hole to resolve the smaller scale structures there, and rarefies grid points away from each black hole to keep the overall problem size at a practical level. In this respect, our system can be thought of as a ‘double’ version of the fisheye coordinate system, used before in numerical relativity codes for evolving binary black holes. The gridding scheme is constructed as a mapping between a uniform coordinate system—in which the equations of motion are solved—to the distorted system representing the spatial locations of our grid points. Since we are motivated to eventually use this system for circumbinary disc calculations, we demonstrate how the distorted system can be constructed to asymptote to the typical spherical polar coordinate system, amenable to efficiently simulating orbiting gas flows about central objects with little numerical diffusion. We discuss its implementation in the Harm3d code, tailored to evolve the magnetohydrodynamics equations in curved spacetimes. We evaluate the performance of the system’s implementation in Harm3d with a series of tests, such as the advected magnetic field loop test, magnetized Bondi accretion, and evolutions of hydrodynamic discs about a single black hole and about a binary black hole. Like we have done with Harm3d, this gridding scheme can be implemented in other unigrid codes as a (possibly) simpler alternative to adaptive mesh refinement.