Miracle-dz/UniFAR-FTUs huggingface dataset:
"Why Polyploidy is Rarer in Animals Than in Plants" Revisited

No satisfactory explanation of the rarity of polyploidy among animals exists. In taxa possessing a degenerate Y chromosome, polyploid speciation invariably disrupts the balance of X to autosomal gene product normally maintained by dosage compensation. This dosage balance is upset whether or not sex determination is disrupted. This factor may explain the distribution of polyploidy across taxa. In particular, plants may commonly show polyploidy because degenerate sex chromosomes are rare (first, because dioecy is rare, and second, because extreme Y degeneracy is rare among dioecious plants). Animals may rarely show polyploidy because degenerate sex chromosomes are common. Several predictions are discussed.
Conformal inference of counterfactuals and individual treatment effects

Evaluating treatment effect heterogeneity widely informs treatment decision making. At the moment, much emphasis is placed on the estimation of the conditional average treatment effect via flexible machine learning algorithms. While these methods enjoy some theoretical appeal in terms of consistency and convergence rates, they generally perform poorly in terms of uncertainty quantification. This is troubling since assessing risk is crucial for reliable decision‐making in sensitive and uncertain environments. In this work, we propose a conformal inference‐based approach that can produce reliable interval estimates for counterfactuals and individual treatment effects under the potential outcome framework. For completely randomized or stratified randomized experiments with perfect compliance, the intervals have guaranteed average coverage in finite samples regardless of the unknown data generating mechanism. For randomized experiments with ignorable compliance and general observational studies obeying the strong ignorability assumption, the intervals satisfy a doubly robust property which states the following: the average coverage is approximately controlled if either the propensity score or the conditional quantiles of potential outcomes can be estimated accurately. Numerical studies on both synthetic and real data sets empirically demonstrate that existing methods suffer from a significant coverage deficit even in simple models. In contrast, our methods achieve the desired coverage with reasonably short intervals.
Bayesian reconstruction of gravitational-wave signals from binary black holes with nonzero eccentricities

We present a comprehensive study on how well gravitational-wave signals of binary black holes (BBHs) with nonzero eccentricities can be recovered with state of the art model-independent waveform reconstruction and parameter estimation techniques. For this we use BayesWave, a Bayesian algorithm used by the LIGO–Virgo Collaboration for unmodeled reconstructions of signal waveforms and parameters. We used two different waveform models to produce simulated signals of BBHs with eccentric orbits and embed them in samples of simulated noise of design-sensitivity Advanced LIGO detectors. We studied the network overlaps and point estimates of central moments of signal waveforms recovered by BayesWave as a function of e, the eccentricity of the binary at 8 Hz orbital frequency. BayesWave recovers signals of near-circular (e ≲ 0.2) and highly eccentric (e ≳ 0.7) binaries with network overlaps similar to that of circular (e = 0) ones, however it produces lower network overlaps for binaries with e ∈ [0.2, 0.7]. Estimation errors on central frequencies and bandwidths (measured relative to bandwidths) are nearly independent from e, while estimation errors on central times and durations (measured relative to durations) increase and decrease with e above e ≳ 0.5, respectively. We also tested how BayesWave performs when reconstructions are carried out using generalized wavelets with linear frequency evolution (chirplets) instead of sine-Gaussian wavelets. We have found that network overlaps improve by ∼10–20 percent when chirplets are used, and the improvement is the highest at low (e < 0.5) eccentricities. There is however no significant change in the estimation errors of central moments when the chirplet base is used.
Report from the NSF Future Directions Workshop, Toward User-Oriented Agents: Research Directions and Challenges

This USER Workshop was convened with the goal of defining future research directions for the burgeoning intelligent agent research community and to communicate them to the National Science Foundation. It took place in Pittsburgh Pennsylvania on October 24 and 25, 2019 and was sponsored by National Science Foundation Grant Number IIS-1934222. Any opinions, findings and conclusions or future directions expressed in this document are those of the authors and do not necessarily reflect the views of the National Science Foundation. The 27 participants presented their individual research interests and their personal research goals. In the breakout sessions that followed, the participants defined the main research areas within the domain of intelligent agents and they discussed the major future directions that the research in each area of this domain should take
Robust PDE Identification from Noisy Data

We propose robust methods to identify underlying Partial Differential Equation (PDE) from a given set of noisy time dependent data. We assume that the governing equation is a linear combination of a few linear and nonlinear differential terms in a prescribed dictionary. Noisy data make such identification particularly challenging. Our objective is to develop methods which are robust against a high level of noise, and to approximate the underlying noise-free dynamics well. We first introduce a Successively Denoised Differentiation (SDD) scheme to stabilize the amplified noise in numerical differentiation. SDD effectively denoises the given data and the corresponding derivatives. Secondly, we present two algorithms for PDE identification: Subspace pursuit Time evolution error (ST) and Subspace pursuit Cross-validation (SC). Our general strategy is to first find a candidate set using the Subspace Pursuit (SP) greedy algorithm, then choose the best one via time evolution or cross validation. ST uses multi-shooting numerical time evolution and selects the PDE which yields the least evolution error. SC evaluates the cross-validation error in the least squares fitting and picks the PDE that gives the smallest validation error. We present a unified notion of PDE identification error to compare the objectives of related approaches. We present various numerical experiments to validate our methods. Both methods are efficient and robust to noise.
How simplifying and flexible is the simplifying assumption in pair-copula constructions - some analytical answers in dimension three and beyond

Motivated by the increasing popularity and the seemingly broad applicability of pair-copula constructions underlined by numerous publications in the last decade, in this contribution we tackle the unavoidable question on how flexible and simplifying the commonly used 'simplifying assumption' is from an analytic perspective and provide answers to two related open questions posed by Nagler and Czado in 2016. Aiming at a simplest possible setup for deriving the main results we first focus on the three-dimensional setting. We prove flexibility of simplified copulas in the sense that they are dense in the family of all three-dimensional copulas with respect to the uniform metric $d_\infty$, show that the partial vine copula is never the optimal simplified copula approximation of a given, non-simplified copula $C$, and derive examples illustrating that the corresponding approximation error can be strikingly large and extend to more than 28\% of the diameter of the metric space. Moreover, the mapping $\psi$ assigning each three-dimensional copula its unique partial vine copula turns out to be discontinuous with respect to $d_\infty$ (but continuous with respect to other notions of convergence), implying a surprising sensitivity of partial vine copula approximations. The afore-mentioned main results are then extended to the general multivariate setting.
Promoted mass growth of multiple, distant giant planets through pebble accretion and planet–planet collision

We propose a pebble-driven planet formation scenario to form giant planets with high multiplicity and large orbital distances in the early gas disc phase. We perform N-body simulations to investigate the growth and migration of low-mass protoplanets in the disc with inner viscously heated and outer stellar irradiated regions. The key feature of this model is that the giant planet cores grow rapidly by a combination of pebble accretion and planet–planet collisions. This consequently speeds up their gas accretion. Because of efficient growth, the planet transitions from rapid type I migration to slow type II migration early, reducing the inward migration substantially. Multiple giant planets can sequentially form in this way with increasing semimajor axes. Both mass growth and orbital retention are more pronounced when a large number of protoplanets are taken into account compared to the case of single planet growth. Eventually, a few numbers of giant planets form with orbital distances of a few to a few tens of aus within 1.5–3 Myr after the birth of the protoplanets. The resulting simulated planet populations could be linked to the substructures exhibited in disc observations as well as large orbital distance exoplanets observed in radial velocity and microlensing surveys.
Unresolved Binary Exoplanet Host Stars Fit as Single Stars: Effects on the Stellar Parameters

In this work, we quantify the effect of an unresolved companion star on the derived stellar parameters of the primary star if a blended spectrum is fit assuming the star is single. Fitting tools that determine stellar parameters from spectra typically fit for a single star, but we know that up to half of all exoplanet host stars may have one or more companion stars. We use high-resolution spectra of planet host stars in the Kepler field from the California-Kepler Survey to create simulated binaries; we select eight stellar pairs and vary the contribution of the secondary star, then determine stellar parameters with SpecMatch-Emp and compare them to the parameters derived for the primary star alone. We find that, in most cases, the effective temperature, surface gravity, metallicity, and stellar radius derived from the composite spectrum are within 2–3σ of the values determined from the unblended spectrum, but the deviations depend on the properties of the two stars. Relatively bright companion stars that are similar to the primary star have the largest effect on the derived parameters; in these cases, the stellar radii can be overestimated by up to 60%. We find that metallicities are generally underestimated, with values up to eight times smaller than the typical uncertainty in [Fe/H]. Our study shows that follow-up observations are necessary to detect or set limits on stellar companions of planetary host stars so that stellar (and planet) parameters are as accurate as possible.
The variable radio counterpart of Swift J1858.6-0814

Swift J1858.6-0814 is a transient neutron star X-ray binary discovered in 2018 October. Multiwavelength follow-up observations across the electromagnetic spectrum revealed many interesting properties, such as erratic flaring on minute time-scales and evidence for wind outflows at both X-ray and optical wavelengths, strong and variable local absorption, and an anomalously hard X-ray spectrum. Here, we report on a detailed radio observing campaign consisting of one observation at 5.5/9 GHz with the Australia Telescope Compact Array, and nine observations at 4.5/7.5 GHz with the Karl G. Jansky Very Large Array. A radio counterpart with a flat to inverted radio spectrum is detected in all observations, consistent with a compact jet being launched from the system. Swift J1858.6-0814 is highly variable at radio wavelengths in most observations, showing significant variability when imaged on 3-to-5-min time-scales and changing up to factors of 8 within 20 min. The periods of brightest radio emission are not associated with steep radio spectra, implying they do not originate from the launching of discrete ejecta. We find that the radio variability is similarly unlikely to have a geometric origin, be due to scintillation, or be causally related to the observed X-ray flaring. Instead, we find that it is consistent with being driven by variations in the accretion flow propagating down the compact jet. We compare the radio properties of SwiftJ1858.6-0814 with those of Eddington-limited X-ray binaries with similar X-ray and optical characteristics, but fail to find a match in radio variability, spectrum, and luminosity.
The Copula of the Cosmological Matter Density Field is Non-Gaussian

Non-Gaussianity of the cosmological matter density field can be largely reduced by a local Gaussianization transformation (and its approximations, such as the logarithmic transformation). Such behavior can be recast as the Gaussian copula hypothesis (GCH), and has been verified to very high accuracy at a two-point level. On the other hand, statistically significant non-Gaussianities in the Gaussianized field have been detected in simulations. We point out that this apparent inconsistency is caused by the very limited degrees of freedom in the copula function, which make it misleading as a diagnosis of residual non-Gaussianity in the Gaussianized field. Using the copula density and at the two-point level, we highlight the departure from Gaussianity. We further quantify its impact in the predicted nth (n ≥ 2) order correlation functions. We explore a remedy of the GCH, which alleviates but does not completely solve the above problems.
Polar quasinormal modes of the scalarized Einstein-Gauss-Bonnet black holes

We study the polar quasinormal modes of spontaneously scalarized black holes in Einstein-Gauss-Bonnet theory. In previous works we showed that a set of nodeless solutions of the fundamental branch of the model studied in [1] are stable under both radial [2] and axial perturbations [3]. Here we calculate the polar quasinormal modes and show that this set of solutions is stable against the polar perturbations as well. Thus for a certain region of the parameter space the scalarized black holes are potentially stable physically interesting objects. The spectrum of the polar quasinormal modes differs both quantitatively and qualitatively from the Schwarzschild one which offers the possibility to test the Gauss-Bonnet theory via the future gravitational wave observations.
Borrowing From the Future: Addressing Double Sampling in Model-free Control

In model-free reinforcement learning, the temporal difference method and its variants become unstable when combined with nonlinear function approximations. Bellman residual minimization with stochastic gradient descent (SGD) is more stable, but it suffers from the double sampling problem: given the current state, two independent samples for the next state are required, but often only one sample is available. Recently, the authors of [Zhu et al, 2020] introduced the borrowing from the future (BFF) algorithm to address this issue for the prediction problem. The main idea is to borrow extra randomness from the future to approximately re-sample the next state when the underlying dynamics of the problem are sufficiently smooth. This paper extends the BFF algorithm to action-value function based model-free control. We prove that BFF is close to unbiased SGD when the underlying dynamics vary slowly with respect to actions. We confirm our theoretical findings with numerical simulations.
Pressure metrics for deformation spaces of quasifuchsian groups with parabolics

In this paper, we produce a mapping class group invariant pressure metric on the space QF(S) of quasiconformal deformations of a co-finite area Fuchsian group uniformizing a surface S. Our pressure metric arises from an analytic pressure form on QF(S) which is degenerate only on pure bending vectors on the Fuchsian locus. Our techniques also show that the Hausdorff dimension of the limit set varies analytically over QF(S).
Phase I study of vemurafenib in children with recurrent or progressive BRAFV600E mutant brain tumors: Pacific Pediatric Neuro-Oncology Consortium study (PNOC-002)

Background: BRAFV600E mutation is present in a subset of pediatric brain tumors. Vemurafenib is an oral, selective ATP-competitive inhibitor of BRAFV600E kinase. The goal of this multi-center study conducted through the Pacific Pediatric Neuro-Oncology Consortium (PNOC) was to determine the recommended phase 2 dose (RP2D) and dose limiting toxicities (DLTs) in children < 18 years with recurrent or progressive BRAFV600E mutant brain tumors. Results: Nineteen eligible patients were enrolled. Eleven patients had received three or more prior therapies. Data reported are from the start of treatment for the first patient (April 30 2014) through August 31 2019. The RP2D was defined as 550 mg/m2 twice daily after DLT criteria adjustment for rash. Related grade ≥ 3 adverse events included secondary keratoacanthoma (n = 1); rash (n =16); and fever (n = 5). Subjects received a median of 23 cycles (range 3–63). Four patients remain on treatment. Centrally reviewed best radiographic responses included 1 complete response, 5 partial responses, and 13 stable disease. The steady-state area under the curve (AUC0-∞median) was 604 mg*h/L (range 329–1052). Methods: Vemurafenib was given starting at 550 mg/m2, twice daily which corresponds to the adult RP2D. Adverse events were graded using the NIH Common Terminology Criteria for Adverse Events (CTCAE) version 4.0. Central imaging review was performed. Pharmacokinetic sampling was performed. Conclusions: Vemurafenib has promising anti-tumor activity in recurrent BRAF V600E-positive brain tumors with manageable toxicity. A phase 2 study is ongoing (NCT01748149).
Information Diffusion on Social Media During Natural Disasters

Social media analytics has drawn new quantitative insights of human activity patterns. Many applications of social media analytics, from pandemic prediction to earthquake response, require an in-depth understanding of how these patterns change when human encounter unfamiliar conditions. In this paper, we select two earthquakes in China as the social context in Sina-Weibo (or Weibo for short), the largest Chinese microblog site. After proposing a formalized Weibo information flow model to represent the information spread on Weibo, we study the information spread from three main perspectives: individual characteristics, the types of social relationships between interactive participants, and the topology of real interaction networks. The quantitative analyses draw the following conclusions. First, the shadow of Dunbar’s number is evident in the “declared friends/followers” distributions, and the number of each participant’s friends/followers who also participated in the earthquake information dissemination show the typical power-law distribution, indicating a rich-gets-richer phenomenon. Second, an individual’s number of followers is the most critical factor in user influence. Strangers are very important forces for disseminating real-time news after an earthquake. Third, two types of real interaction networks share the scale-free and small-world property, but with a looser organizational structure. In addition, correlations between different influence groups indicate that when compared with other online social media, the discussion on Weibo is mainly dominated and influenced by verified users.
Consequences of removal of exotic species (eucalyptus) on carbon and nitrogen cycles in the soil-plant system in a secondary tropical Atlantic forest in Brazil with a dual-isotope approach

The impact of exotic species on heterogeneous native tropical forest requires the understanding on which temporal and spatial scales these processes take place. Functional tracers such as carbon (δ13C) and nitrogen (δ15N) isotopic composition in the soil-plant system might help track the alterations induced by the exotic species. Thus, we assess the effects from the removal of the exotic species eucalyptus (Corymbia cytriodora) in an Atlantic forest Reserve, and eucalyptus removal on the alteration of the nutrient dynamics (carbon and nitrogen). The hypotheses were: (1) the eucalyptus permanence time altered δ13C and δ15N in leaves, soils and litter fractions (leaves, wood, flowers + fruits, and rest); and (2) eucalyptus removal furthered decomposition process of the soil organic matter. Hence, we determined the soil granulometry, the δ13C and δ15N in leaves, in the superficial soil layer, and litter in three sites: a secondary forest in the Atlantic forest, and other two sites where eucalyptus had been removed in different times: 12 and 3 months ago (M12 and M3, respectively). Litter samples presented intermediate δ13C and δ15N values in comparison with leaves and soil. In the M3, the greater δ13C values in both litter rest fraction and soil indicate the presence, cycling and soil incorporation of C, coming from the C4 photosynthesis of grassy species (Poaceae). In the secondary forest, the soil δ15N values were twice higher, compared with the eucalyptus removal sites, revealing the negative influence from these exotic species upon the ecosystem N dynamics. In the M12, the leaves presented higher δ13C mean value and lower δ15N values, compared with those from the other sites. The difference of δ13C values in the litter fractions regarding the soil led to a greater fractioning of 13C in all sites, except the flower + fruit fractions in the secondary forest, and the rest fraction in the M3 site. We conclude that the permanence of this exotic species and the eucalyptus removal have altered the C and N isotopic and elemental compositions in the soil-plant system. Our results suggest there was organic matter decomposition in all litter fractions and in all sites. However, a greater organic matter decomposition process was observed in the M3 soil, possibly because of a more intense recent input of vegetal material, as well as the presence of grassy, easily-decomposing herbaceous species, only in this site. Therefore, the dual-isotope approach generated a more integrated picture of the impact on the ecosystem after removing eucalyptus in this secondary Atlantic forest, and could be regarded as an option for future eucalyptus removal studies.
Analysis of Africanized honey bee mitochondrial DNA reveals further diversity of origin

Nos ultimos 40 anos, abelhas africanizadas se espalharam a partir do Brasil e agora ocupam a maioria das areas habitaveis pela especie Apis mellifera, da Argentina ao sudoeste dos Estados Unidos. Acredita-se que a fonte genetica primaria das abelhas africanizadas seja a subespecie subsaariana de abelha A. m. scutellata. Marcadores mitocondriais comuns em A. m. scutellata tem sido usados para classificar abelhas africanizadas em estudos de fisiologia e genetica de populacao. A avaliacao de haplotipos mitocondriais compostos em abelhas africanizadas, usando 3 enzimas de restricao e um polimorfismo de comprimento no espacador intergenico "COI-COII", evidenciou uma heranca mitocondrial mais diversa. Mais de 25% do mtDNA "africano" encontrado em populacoes africanizadas na Argentina sao derivados de fontes nao relacionadas a A. m. scutellata.