nils-herrmann/clean_scirepeval huggingface dataset:
Towards inverse modeling of intratumor heterogeneity

Development of resistance limits efficiency of present anticancer therapies and preventing it remains a big challenge in cancer research. It is accepted, at the intuitive level, that resistance emerges as a consequence of the heterogeneity of cancer cells at the molecular, genetic and cellular levels. Produced by many sources, tumor heterogeneity is extremely complex time dependent statistical characteristics which may be quantified by measures defined in many different ways, most of them coming from statistical mechanics. In this paper, we apply the Markovian framework to relate population heterogeneity to the statistics of the environment. As, from an evolutionary viewpoint, therapy corresponds to a purposeful modi- fication of the cells’ fitness landscape, we assume that understanding general relationship between the spatiotemporal statistics of a tumor microenvironment and intratumor heterogeneity will allow to conceive the therapy as an inverse problem and to solve it by optimization techniques. To account for the inherent stochasticity of biological processes at cellular scale, the generalized distancebased concept was applied to express distances between probabilistically described cell states and environmental conditions, respectively.
Cycle-flow–based module detection in directed recurrence networks

We present a new cycle-flow–based method for finding fuzzy partitions of weighted directed networks coming from time series data. We show that this method overcomes essential problems of most existing clustering approaches, which tend to ignore important directional information by considering only one-step, one-directional node connections. Our method introduces a novel measure of communication between nodes using multi-step, bidirectional transitions encoded by a cycle decomposition of the probability flow. Symmetric properties of this measure enable us to construct an undirected graph that captures the information flow of the original graph seen by the data and apply clustering methods designed for undirected graphs. Finally, we demonstrate our algorithm by analyzing earthquake time series data, which naturally induce (time-)directed networks.
Galactic PeV neutrinos from dark matter annihilation

The IceCube Neutrino Observatory has observed highly energetic neutrinos in excess of the expected atmospheric neutrino background. It is intriguing to consider the possibility that such events are probing physics beyond the standard model. In this context, $\mathcal{O}$(PeV) dark matter particles decaying to neutrinos have been considered while dark matter annihilation has been dismissed invoking the unitarity bound as a limiting factor. However, the latter claim was done ignoring the contribution from dark matter substructure, which for PeV Cold Dark Matter would extend down to a free streaming mass of $\mathcal{O}$($10^{-18}$M$_\odot$). Since the unitarity bound is less stringent at low velocities, ($\sigma_{\rm ann}$v)$\leq4\pi/m_\chi^2v$, then, it is possible that these cold and dense subhalos would contribute dominantly to a dark-matter-induced neutrino flux and easily account for the events observed by IceCube. A Sommerfeld-enhanced dark matter model can naturally support such scenario. Interestingly, the spatial distribution of the events shows features that would be expected in a dark matter interpretation. Although not conclusive, 9 of the 37 events appear to be clustered around a region near the Galactic Center while 6 others spatially coincide, within the reported angular errors, with 5 of 26 Milky Way satellites. However, a simple estimate of the probability of the latter occurring by chance is $\sim35\%$. More events are needed to statistically test this hypothesis. PeV dark matter particles are massive enough that their abundance as standard thermal relics would overclose the Universe. This issue can be solved in alternative scenarios, for instance if the decay of new massive unstable particles generates significant entropy reheating the Universe to a slightly lower temperature than the freeze-out temperature, $T_{\rm RH} \lesssim T_{\rm f}\sim4\times10^4$~GeV.
Price of anarchy is maximized at the percolation threshold.

When many independent users try to route traffic through a network, the flow can easily become suboptimal as a consequence of congestion of the most efficient paths. The degree of this suboptimality is quantified by the so-called price of anarchy (POA), but so far there are no general rules for when to expect a large POA in a random network. Here I address this question by introducing a simple model of flow through a network with randomly placed congestible and incongestible links. I show that the POA is maximized precisely when the fraction of congestible links matches the percolation threshold of the lattice. Both the POA and the total cost demonstrate critical scaling near the percolation threshold.
Quantum cosmology of (loop) quantum gravity condensates: an example

Spatially homogeneous universes can be described in (loop) quantum gravity as condensates of elementary excitations of space. Their treatment is easiest in the second-quantized group field theory formalism, which allows the adaptation of techniques from the description of Bose–Einstein condensates in condensed matter physics. Dynamical equations for the states can be derived directly from the underlying quantum gravity dynamics. The analogue of the Gross–Pitaevskii equation defines an anisotropic quantum cosmology model, in which the condensate wavefunction becomes a quantum cosmology wavefunction on minisuperspace. To illustrate this general formalism, we give a mapping of the gauge-invariant geometric data for a tetrahedron to a minisuperspace of homogeneous anisotropic three-metrics. We then study an example for which we give the resulting quantum cosmology model in the general anisotropic case and derive the general analytical solution for isotropic universes. We discuss the interpretation of these solutions. We suggest that the WKB approximation used in previous studies, corresponding to semiclassical fundamental degrees of freedom of quantum geometry, should be replaced by a notion of semiclassicality that refers to large-scale observables instead.
Total three-dimensional imaging of phase objects using defocusing microscopy: Application to red blood cells

We introduce Defocusing Microscopy (DM), a bright-field optical microscopy technique able to perform total three-dimensional (3D) imaging of transparent objects. By total 3D imaging, we mean the determination of the actual shapes of the upper and lower surfaces of a phase object. We propose a methodology using DM and apply it to red blood cells subject to different osmolality conditions: hypotonic, isotonic, and hypertonic solutions. For each situation, the shapes of the upper and lower cell surface-membranes (lipid bilayer/cytoskeleton) are completely recovered, displaying the deformation of red blood cell (RBC) surfaces due to adhesion on the glass-substrate. The axial resolution of our technique allowed us to image surface-membranes separated by distances as small as 300 nm. Finally, we determine the volume, surface area, sphericity index, and RBC refractive index for each osmotic condition.
Light fan driven by a relativistic laser pulse.

When a relativistic laser pulse with a high photon density interacts with a specially tailored thin foil target, a strong torque is exerted on the resulting spiral-shaped foil plasma, or "light fan." Because of its structure, the latter can gain significant orbital angular momentum (OAM), and the opposite OAM is imparted to the reflected light, creating a twisted relativistic light pulse. Such an interaction scenario is demonstrated by particle-in-cell simulation as well as analytical modeling, and should be easily verifiable in the laboratory. As an important characteristic, the twisted relativistic light pulse has a strong torque and ultrahigh OAM density.
Couple Control Model Implementation on Antagonistic Mono- and Bi-Articular Actuators

Recently, robot assisted therapy devices are increasingly used for spinal cord injury (SCI) rehabilitation in assisting handicapped patients to regain their impaired movements. Assistive robotic systems may not be able to cure or fully compensate impairments, but it should be able to assist certain impaired functions and ease movements. In this study, a couple control model for lower-limb orthosis of a body weight support gait training system is proposed. The developed leg orthosis implements the use of pneumatic artificial muscle as an actuation system. The pneumatic muscle was arranged antagonistically to form two pair of mono-articular muscles (i.e., hip and knee joints), and a pair of bi-articular actuators (i.e., rectus femoris and hamstring). The results of the proposed couple control model showed that, it was able to simultaneously control the antagonistic mono- and bi-articular actuators and sufficiently performed walking motion of the leg orthosis.
Asymptotics for d-Dimensional Levy-Type Processes

We consider a general d-dimensional Levy-type process with killing. Combining the classical Dyson series approach with a novel polynomial expansion of the generator A(t) of the Levy-type process, we derive a family of asymptotic approximations for transition densities and European-style options prices. Examples of stochastic volatility models with jumps are provided in order to illustrate the numerical accuracy of our approach. The methods described in this paper extend the results from Corielli et al. (2010), Pagliarani and Pascucci (2013) and Lorig et al. (2013a) for Markov diffusions to Markov processes with jumps.
Pricing of Basket Options Using Polynomial Approximations

In this paper we use Bernstein and Chebyshev polynomials to approximate the price of some basket options under a bivariate Black-Scholes model. The method consists in expanding the price of a univariate related contract after conditioning on the remaining underlying assets and calculating the mixed exponential-power moments of a Gaussian distribution that arise as a consequence of such approximation. Our numerical implementation on spread contracts shows the method is as accurate as a standard Monte Carlo approach at considerable lesser computational effort.
A Dynamical Model of the Industrial Economy of the Humber Region

The Humber region in the UK is a large and diverse industrial area centred around oil refining, chemical industries and energy production. However there is currently a desire to see the region transition towards a more bio-based economy. New bio-related industries are being situated in the region as a consequence of policy and economic incentives. Many of these industries are connected through their supply chains, either directly, or by sharing common suppliers or customers and the growth or decline of one industry can hence have impacts on many others. Therefore an important question to consider is what effect this movement towards bio-based industry will actually have on the regional economy as a whole. In this paper we develop a general abstract dynamical model for the metabolic interactions of firms or industries. This dynamical model has been applied to the Humber region in order to gain a deeper understanding of how the region may develop. The model suggests that the transition to a bio-based economy will occur with oil refining losing its dominance to bioethanol production and biological chemical production, whilst anaerobic digestion grows as a major source of electricity, in turn driving up the value of regional waste aggregators and arable farming in the overall economy.
Effect of contacts on spin lifetime measurements in graphene

Injection, transmission, and detection of spins in a conducting channel are the basic ingredients of spintronic devices. Long spin lifetimes during transit are an important ingredient in realizing this technology. An attractive platform for this purpose is graphene, which has high mobilities and low spin-orbit coupling. Unfortunately, measured spin lifetimes are orders of magnitude smaller than theoretically expected. A source of spin loss is the resistance mismatch between the ferromagnetic electrodes and graphene. While this has been studied numerically, here we provide a closed form expression for Hanle spin precession which is the standard method of measuring spin lifetimes. This allows for a detailed characterization of the nonlocal spin valve device.
Estimating nonlinear regression errors without doing regression

A method for estimating nonlinear regression errors and their distributions without performing regression is presented. Assuming continuity of the modeling function the variance is given in terms of conditional probabilities extracted from the data. For N data points the computational demand is N2. Comparing the predicted residual errors with those derived from a linear model assumption provides a signal for nonlinearity. The method is successfully illustrated with data generated by the Ikeda and Lorenz maps augmented with noise. As a by-product the embedding dimensions of these maps are also extracted.
A single impurity in an ideal atomic Fermi gas: current understanding and some open problems

We briefly review some current theoretical and experimental aspects of the problem of a single spinless impurity in a 3D polarised atomic Fermi gas at zero temperature where the interactions can be tuned using a wide Feshbach resonance. We show that various few-body states in vacuum composed of the impurity and background gas atoms (single impurity, dimer, trimer, tetramer) give rise to corresponding dressed states (, , , ) in the gas and inherit many of their characteristics. We study the ground state focussing on the choice of wave function and its properties. We raise a few unsolved problems: whether the polaron and dimeron are really separate branches, what other few-body states might exist, the nature of the groundstate for large numbers of particle-hole pairs and why is the polaron ansatz so good. We then turn to the excited states, and to the calculation of the effective mass. We examine the bounds on the effective mass and raise a conjecture about that of composite quasiparticle states.
Interplay between boundaries and disorder in coupled optical waveguides

We investigate the effects of weak disorder on the time evolution of a wave packet in an array of optical waveguides with parity-symmetric evanescent coupling and, open or periodic boundary conditions. For an open array, when the disorder is unable to suppress the ballistic expansion, we find that the light partially localizes to its initial waveguide and the parity-symmetric waveguide when a single waveguide is excited. For an array with periodic boundary condition, the light localizes in the initial waveguide and its antipodal waveguide. Through a model where the boundaries of the array are only partially reflective, we quantify and investigate the continuous crossover between these two regimes. Our results show that disorder-induced localization in finite arrays with very weak disorder is strongly affected by the boundary effects that have been hitherto ignored.
Design and operation of a cryogenic charge-integrating preamplifier for the MuSun experiment

The central detector in the MuSun experiment is a pad-plane time projection ionization chamber that operates without gas amplification in deuterium at 31 K; it is used to measure the rate of the muon capture process μ−+d→n+n+νμ. A new charge-sensitive preamplifier, operated at 140 K, has been developed for this detector. It achieved a resolution of 4.5 keV(D2) or 120 e− RMS with zero detector capacitance at 1.1 μ s integration time in laboratory tests. In the experimental environment, the electronic resolution is 10 keV(D2) or 250 e− RMS at a 0.5 μ s integration time. The excellent energy resolution of this amplifier has enabled discrimination between signals from muon-catalyzed fusion and muon capture on chemical impurities, which will precisely determine systematic corrections due to these processes. It is also expected to improve the muon tracking and determination of the stopping location.
Are Supernovae Recorded in Indigenous Astronomical Traditions

Novae and supernovae are rare astronomical events that would have had an influence on the sky-watching peoples who witnessed them. Although several bright novae/supernovae have been visible during recorded human history, there are many proposed but no confirmed accounts of supernovae in oral traditions or material culture. Criteria are established for confirming novae/supernovae in oral and material culture, and claims from around the world are discussed to determine if they meet these criteria. Australian Aboriginal traditions are explored for possible descriptions of novae/supernovae. Although representations of supernovae may exist in Indigenous traditions, and an account of a nova in Aboriginal traditions has been confirmed, there are currently no confirmed accounts in Indigenous oral or material traditions.
Mode-locked ultrashort pulse generation from on-chip normal dispersion microresonators.

We describe generation of stable mode-locked pulse trains from on-chip normal dispersion microresonators. The excitation of hyperparametric oscillation is facilitated by the local dispersion disruptions induced by mode interactions. The system is then driven from hyperparametric oscillation to the mode-locked state with over 200 nm spectral width by controlled pump power and detuning. With the continuous-wave-driven nonlinearity, the pulses sit on a pedestal, akin to a cavity soliton. We identify the importance of pump detuning and wavelength-dependent quality factors in stabilizing and shaping the pulse structure, to achieve a single pulse inside the cavity. We examine the mode-locking dynamics by numerically solving the master equation and provide analytic solutions under appropriate approximations.
The University of Washington Mobile Planetarium Do-it-Yourself Guide

The UW Mobile Planetarium Project is a student driven effort to bring astronomy to high schools and the Seattle community. We designed and built an optics solution to project WorldWide Telescope in an inflatable planetarium from a laptop and off-the-shelf HD projector. In our first six months of operation, undergraduates at the UW gave planetarium shows to over 1500 people and 150 high school students created and presented their own astronomy projects in our dome, at their school. This document aims to share the technical aspects behind the project in order for others to replicate or adapt our model to their needs. This UW Mobile Planetarium was made possible thanks to a Hubble Space Telescope Education/Public Outreach Grant.
Stability and Identification with Optimal Macroprudential Policy Rules

This paper investigates the identification, the determinacy and the stability of ad hoc, "quasi-optimal" and optimal policy rules augmented with financial stability indicators (such as asset prices deviations from their fundamental values) and minimizing the volatility of the policy interest rates, when the central bank precommits to financial stability. Firstly, ad hoc and quasi-optimal rules parameters of financial stability indicators cannot be identified. For those rules, non zero policy rule parameters of financial stability indicators are observationally equivalent to rule parameters set to zero in another rule, so that they are unable to inform monetary policy. Secondly, under controllability conditions, optimal policy rules parameters of financial stability indicators can all be identified, along with a bounded solution stabilizing an unstable economy as in Woodford (2003), with determinacy of the initial conditions of non- predetermined variables.
Genetic Influences on Brain Gene Expression in Rats Selected for Tameness and Aggression

Interindividual differences in many behaviors are partly due to genetic differences, but the identification of the genes and variants that influence behavior remains challenging. Here, we studied an F2 intercross of two outbred lines of rats selected for tame and aggressive behavior toward humans for >64 generations. By using a mapping approach that is able to identify genetic loci segregating within the lines, we identified four times more loci influencing tameness and aggression than by an approach that assumes fixation of causative alleles, suggesting that many causative loci were not driven to fixation by the selection. We used RNA sequencing in 150 F2 animals to identify hundreds of loci that influence brain gene expression. Several of these loci colocalize with tameness loci and may reflect the same genetic variants. Through analyses of correlations between allele effects on behavior and gene expression, differential expression between the tame and aggressive rat selection lines, and correlations between gene expression and tameness in F2 animals, we identify the genes Gltscr2, Lgi4, Zfp40, and Slc17a7 as candidate contributors to the strikingly different behavior of the tame and aggressive animals.
The configuration multi-edge model: Assessing the effect of fixing node strengths on weighted network magnitudes

Complex networks grow subject to structural constraints which affect their measurable properties. Assessing the effect that such constraints impose on their observables is thus a crucial aspect to be taken into account in their analysis. To this end, we examine the effect of fixing the strength sequence in multi-edge networks on several network observables such as degrees, disparity, average neighbor properties and weight distribution using an ensemble approach. We provide a general method to calculate any desired weighted network metric and we show that several features detected in real data could be explained solely by structural constraints. We thus justify the need of analytical null models to be used as basis to assess the relevance of features found in real data represented in weighted network form.
Answering Query Workloads with Optimal Error under Blowfish Privacy

Recent work has proposed a privacy framework, called Blowfish, that generalizes differential privacy in order to generate principled relaxations. Blowfish privacy definitions take as input an additional parameter called a policy graph, which specifies which properties about individuals should be hidden from an adversary. An open question is to characterize when Blowfish privacy definitions permit mechanisms that incur significantly lower error for query answering compared to differentially private mechanisms. In this paper, we answer this question and explore error bounds for answering sets of linear counting queries under different instantiations of Blowfish privacy. We first develop theoretical tools relating query answering under Blowfish to query answering under differential privacy. In particular, we prove a surprising equivalence between the minimum error required to answer a workload W under a Blowfish policy G and the minimum error required to answer a workload WG (constructed using W and G) under differential privacy. We provide applications of these tools by finding strategies for answering multidimensional range queries under different Blowfish policy graphs. We believe the tools we develop will be useful for finding strategies to answer many other classes of queries with low error under Blowfish. Next, we generalize the matrix mechanism lower bound of Li and Miklau (called the SVD bound) for differential privacy to find an analogous lower bound for Blowfish, and illustrate our bounds using multidimensional range queries.