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At least 1,117 records · Page 62

Assessing correlated truncation errors in modern nucleon-nucleon potentials

We test the BUQEYE model of correlated effective field theory (EFT) truncation errors on Reinert, Krebs, and Epelbaum's semilocal momentum-space implementation of the chiral EFT (𝜒⁢EFT ) expansion of the nucleon-nucleon (NN) potential. This Bayesian model hypothesizes that dimensionless coefficient functions extracted from the order-by-order corrections to NN observables can be treated as draws from a Gaussian process (GP). We combine a variety of graphical and statistical diagnostics to assess when predicted observables have a 𝜒⁢EFT convergence pattern consistent with the hypothesized GP statistical model. Our conclusions are that, first, the BUQEYE model is generally applicable to the potential investigated here, which enables statistically principled estimates of the impact of higher EFT orders on observables. Second, parameters defining the extracted coefficients such as the expansion parameter 𝑄 must be well chosen for the coefficients to exhibit a regular convergence pattern—a property we exploit to obtain posterior distributions for such quantities. Third, the assumption of GP stationarity across lab energy and scattering angle is not generally met; this necessitates adjustments in future work. We provide a workflow and interpretive guide for our analysis framework, and show what can be inferred about probability distributions for 𝑄, the EFT breakdown scale Λ 𝑏 , the scale associated with soft physics in the 𝜒⁢EFT potential 𝑚 eff , and the GP hyperparameters. All our results can be reproduced using a publicly available Jupyter notebook, which can be straightforwardly modified to analyze other 𝜒⁢EFT NN potentials.

Bayesian methods↗

Cellular, molecular, and therapeutic characterization of pilocarpine-induced temporal lobe epilepsy

Animal models have expanded our understanding of temporal lobe epilepsy (TLE). However, translating these to cell-specific druggable hypotheses is not explored. Herein, we conducted an integrative insilico-analysis of an available transcriptomics dataset obtained from animals with pilocarpine-induced-TLE. A set of 119 genes with subtle-to-moderate impact predicted most forms of epilepsy with ~ 97% accuracy and characteristically mapped to upregulated homeostatic and downregulated synaptic pathways. The deconvolution of cellular proportions revealed opposing changes in diverse cell types. The proportion of nonneuronal cells increased whereas that of interneurons, except for those expressing vasoactive intestinal peptide (Vip), decreased, and pyramidal neurons of the cornu-ammonis (CA) subfields showed the highest variation in proportion. A probabilistic Bayesian-network demonstrated an aberrant and oscillating physiological interaction between nonneuronal cells involved in the blood–brain-barrier and Vip interneurons in driving seizures, and their role was evaluated insilico using transcriptomic changes induced by valproic-acid, which showed opposing effects in the two cell-types. Additionally, we revealed novel epileptic and antiepileptic mechanisms and predicted drugs using causal inference, outperforming the present drug repurposing approaches. These well-powered findings not only expand the understanding of TLE and seizure oscillation, but also provide predictive biomarkers of epilepsy, cellular and causal micro-circuitry changes associated with it, and a drug-discovery method focusing on these events.

60 APPLIED LIFE SCIENCES↗

Modeling Images of Natural 3D Surfaces: Overview and Potential Applications

Generative models of natural images have long been used in computer vision. However, since they only describe the of 2D scenes, they fail to capture all the properties of the underlying 3D world. Even though such models are sufficient for many vision tasks a 3D scene model is when it comes to inferring a 3D object or its characteristics. In this paper, we present such a generative model, incorporating both a multiscale surface prior model for surface geometry and reflectance, and an image formation process model based on realistic rendering, the computation of the posterior model parameter densities, and on the critical aspects of the rendering. We also how to efficiently invert the model within a Bayesian framework. We present a few potential applications, such as asteroid modeling and Planetary topography recovery, illustrated by promising results on real images.

Jalobeanu, Andre↗

Probabilistic inference in very large universes

Our current favored cosmological theories allow for the striking and controversial possibility that the observable universe is just a small part of a much larger universe in which parameters that describe the effective, low-energy laws of physics vary from one region to another. The controversy is largely driven by the fact that such a “very large universe” is mostly observationally inaccessible to us, so the issue arises of how we can reasonably assess a theory that describes such a universe. In this paper, we propose a Bayesian method for theory assessment based on theory-generated probability distributions for our observations. We focus on the principles that define this method, leaving aside concerns about how, in practice, one would carry out the required calculations. (One important issue that we set aside is the measure problem.) We argue that cosmological theories can be tested by the standard method of Bayesian updating, but we need to use theoretical predictions for “first-person” probabilities—that is, probabilities that we should use for our observations, taking into account all relevant selection effects. These selection effects can vary from one observer to another and can vary with time, so, in principle, first-person probabilities are defined for each observer instant—an observer at a specific instant of time. Calculations of first-person probabilities should take into account everything that the observer believes about herself and her surroundings, which we refer to as her subjective state. If the universe is very large, a theory might predict that there are many observer instants in the same subjective state; we argue that first-person probabilities should be calculated using a principle of self-locating indifference (PSLI), the assumption that any real observer should make predictions for her future as if she were chosen randomly and uniformly from the theoretically predicted observer instants that share her subjective state. We believe the PSLI is intuitively very reasonable, but we also argue that, if the theory is correct, the use of this principle maximizes the expected fraction of observers who will make correct predictions. A further complication is that cosmological theories are not expected to fully predict the detailed properties of the universe, but rather will predict a set of possible universes, each with a probability. Different possible universes will generically have different numbers of observers. We argue that, in the calculation of first-person probabilities, the probability for each possible universe should be weighted by the number of observer instants in the specified subjective state that it contains. These issues have been controversial in the literature, so we also provide a rebuttal to the claim that principles like the PSLI involve a “selection fallacy”; a rebuttal to what we dub the principle of required certainty; an argument rejecting theories that predict a preponderance of Boltzmann brains; a rebuttal to a parable about humans and Jovians used by Hartle and Srednicki to argue that assumptions of typicality can lead to absurd consequences; and, finally, a discussion about how the use of “old evidence” can be fit into a Bayesian mold.

Azhar, Feraz [University of Notre Dame, IN (United↗

Flood Hazard Assessment from Storm Tides, Rain and Sea Level Rise for a Tidal River Estuary

Cities and towns along the tidal Hudson River are highly vulnerable to flooding through the combination of storm tides and high streamflows, compounded by sea level rise. Here a three-dimensional hydrodynamic model, validated by comparing peak water levels for 76 historical storms, is applied in a probabilistic flood hazard assessment. In simulations, the model merges streamflows and storm tides from tropical cyclones (TCs), offshore extratropical cyclones (ETCs) and inland "wet extratropical" cyclones (WETCs). The climatology of possible ETC and WETC storm events is represented by historical events (1931-2013), and simulations include gauged streamflows and inferred ungauged streamflows (based on watershed area) for the Hudson River and its tributaries. The TC climatology is created using a stochastic statistical model to represent a wider range of storms than is contained in the historical record. TC streamflow hydrographs are simulated for tributaries spaced along the Hudson, modeled as a function of TC attributes (storm track, sea surface temperature, maximum wind speed) using a statistical Bayesian approach. Results show WETCs are important to flood risk in the upper tidal river (e.g., Albany, New York), ETCs are important in the estuary (e.g., New York City) and lower tidal river, and TCs are important at all locations due to their potential for both high surge and extreme rainfall. The raising of floods by sea level rise is shown to be reduced by approximately 30-60 percent at Albany due to the dominance of streamflow for flood risk. This can be explained with simple channel flow dynamics, in which increased depth throughout the river reduces frictional resistance, thereby reducing the water level slope and the upriver water level.

Tidal river↗

HELIOS–RETRIEVAL: An Open-source, Nested Sampling Atmospheric Retrieval Code; Application to the HR 8799 Exoplanets and Inferred Constraints for Planet Formation

We present an open-source retrieval code named HELIOS–RETRIEVAL, designed to obtain chemical abundances and temperature–pressure profiles by inverting the measured spectra of exoplanetary atmospheres. In our forward model, we use an exact solution of the radiative transfer equation, in the pure absorption limit, which allows us to analytically integrate over all of the outgoing rays. Two chemistry models are considered: unconstrained chemistry and equilibrium chemistry (enforced via analytical formulae). The nested sampling algorithm allows us to formally implement Occam’s Razor based on a comparison of the Bayesian evidence between models. We perform a retrieval analysis on the measured spectra of the four HR 8799 directly imaged exoplanets. Chemical equilibrium is disfavored for HR 8799b and c. We find supersolar C/H and O/H values for the outer HR 8799b and c exoplanets, while the inner HR 8799d and e exoplanets have a range of C/H and O/H values. The C/O values range from being superstellar for HR 8799b to being consistent with stellar for HR 8799c and being substellar for HR 8799d and e. If these retrieved properties are representative of the bulk compositions of the exoplanets, then they are inconsistent with formation via gravitational instability (without late-time accretion) and consistent with a core accretion scenario in which late-time accretion of ices occurred differently for the inner and outer exoplanets. For HR 8799e, we find that spectroscopy in the K band is crucial for constraining C/O and C/H. HELIOS–RETRIEVAL is publicly available as part of the Exoclimes Simulation Platform (http://www.exoclime.org).

79 ASTRONOMY AND ASTROPHYSICS↗

Using discrete Bayesian networks for diagnosing and isolating cross-level faults in HVAC systems

Fault detection and diagnosis (FDD) technologies are critical to ensure satisfactory building performance, such as reducing energy wastes and negative impacts on occupant comfort and productivity. Existing FDD technologies mainly focus on component-level FDD solutions, which could lead to mis-diagnosis of cross-level faults in heating, ventilating, and air-conditioning (HVAC) systems. Cross-level faults are those faults that occur in one component or subsystem, but cause operational abnormalities in other components or subsystems, and result in a building level performance degradation. How to effectively diagnose the root cause of a cross-level fault is the focus of this study. Here, this paper presents a novel discrete Bayesian Network (DisBN)-based method for diagnosing cross-level faults in an HVAC system commonly used in commercial buildings. A two-level DisBN structure model is developed in this study. The parameters used in the DisBN model are obtained either from expert knowledge or through machine-learning strategies from normal system operation data. Meanwhile, the probability parameters are discretized to incorporate the uncertainties associated with typical expert knowledge. Thus, the developed DisBN method addresses the challenges many other BN based FDD methods face, i.e., the lack of fault data for BN parameter training. The developed DisBN represents causal relationships between a fault and its cross-level system impacts (i.e., fault symptoms or fault indicators) by considering how fault impacts propagate across different levels in an HVAC system. A weather and schedule information-based Pattern Matching (WPM) method is employed to automatically create WPM baseline data sets for each incoming real time snapshot data from the building systems. Consequently, BN inference and real-time diagnostics are achieved by comparing incoming snapshot data and the WPM baseline data set. The proposed method is evaluated using experimental fault data collected in a campus building. Fault diagnosis results demonstrate that the WPM-DisBN method is effective at locating the root causes of cross-level faults in an HVAC system.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Asteroid orbit determination using Bayesian probabilities

Bayesian a priori and a posteriori probability densities are employed to determine asteroid orbital elements from optical astrometric observations. For near-earth asteroids and Jupiter Trojans, the two-body approximation can yield grossly erroneous uncertainty estimates because of the scattering effect of close planetary encounters or prolonged weak planetary perturbations. For main-belt asteroids, the two-body approximation works efficiently, from which it is inferred that, although the ephemeris must be computed from an integrated orbit, only approximate partial derivatives are needed to attain sufficient accuracy in predicting ephemeris uncertainties. The semimajor and semiminor axes of the 2D 1-sigma sky-plane uncertainty ellipse during the years 1993 to 2005 in the many-body and two-body linear approximations are shown.

Muinonen, Karri↗

Ground Heat Flux Reconstruction Using Bayesian Uncertainty Quantification Machinery and Surrogate Modeling

Ground heat flux (G 0 ) is a key component of the land-surface energy balance of high-latitude regions. Despite its crucial role in controlling permafrost degradation due to global warming, G 0 is sparsely measured and not well represented in the outputs of global scale model simulation. In this study, an analytical heat transfer model is tested to reconstruct G 0 across seasons using soil temperature series from field measurements, Global Climate Model, and climate reanalysis outputs. The probability density functions of ground heat flux and of model parameters are inferred using available G 0 data (measured or modeled) for snow-free period as a reference. When observed G 0 is not available, a numerical model is applied using estimates of surface heat flux (dependent on parameters) as the top boundary condition. These estimates (and thus the corresponding parameters) are verified by comparing the distributions of simulated and measured soil temperature at several depths. Aided by state-of-the-art uncertainty quantification methods, the developed G 0 reconstruction approach provides novel means for assessing the probabilistic structure of the ground heat flux for regional permafrost change studies.

54 ENVIRONMENTAL SCIENCES↗

Cosmological Evidence Modelling: a new simulation-based approach to constrain cosmology on non-linear scales

Extracting accurate cosmological information from galaxy–galaxy and galaxy–matter correlation functions on non-linear scales (${\lesssim } 10 \, h^{-1}{\rm {Mpc}}$) requires cosmological simulations. Additionally, one has to marginalize over several nuisance parameters of the galaxy–halo connection. However, the computational cost of such simulations prohibits naive implementations of stochastic posterior sampling methods like Markov chain Monte Carlo (MCMC) that would require of order $\mathcal {O}(10^6)$ samples in cosmological parameter space. Several groups have proposed surrogate models as a solution: a so-called emulator is trained to reproduce observables for a limited number of realizations in parameter space. Afterwards, this emulator is used as a surrogate model in an MCMC analysis. In this work, we demonstrate a different method called Cosmological Evidence Modelling (CEM). First, for each simulation, we calculate the Bayesian evidence marginalized over the galaxy–halo connection by repeatedly populating the simulation with galaxies. We show that this Bayesian evidence is directly related to the posterior probability of cosmological parameters. Finally, we build a physically motivated model for how the evidence depends on cosmological parameters as sampled by the simulations. We demonstrate the feasibility of CEM by using simulations from the Aemulus simulation suite and forecasting cosmological constraints from BOSS CMASS measurements of redshift-space distortions. Our analysis includes exploration of how galaxy assembly bias affects cosmological inference. Overall, CEM has several potential advantages over the more common approach of emulating summary statistics, including the ability to easily marginalize over highly complex models of the galaxy–halo connection and greater accuracy, thereby reducing the number of simulations required.

79 ASTRONOMY AND ASTROPHYSICS↗

Statistical Uncertainty in Paleoclimate Proxy Reconstructions

A quantitative analysis of any environment older than the instrumental record relies on proxies. Uncertainties associated with proxy reconstructions are often underestimated, which can lead to artificial conflict between different proxies, and between data and models. In this paper, using ordinary least squares linear regression as a common example, we describe a simple, robust and generalizable method for quantifying uncertainty in proxy reconstructions. We highlight the primary controls on the magnitude of uncertainty, and compare this simple estimate to equivalent estimates from Bayesian, nonparametric and fiducial statistical frameworks. We discuss when it may be possible to reduce uncertainties, and conclude that the unexplained variance in the calibration must always feature in the uncertainty in the reconstruction. This directs future research toward explaining as much of the variance in the calibration data as possible. We also advocate for a “data-forward” approach, that clearly decouples the presentation of proxy data from plausible environmental inferences.

58 GEOSCIENCES↗

Automatic Calibration of a Geomechanical Model from Sparse Data for Estimating Stress in Deep Geological Formations

Summary In this study, we demonstrate geomechanical modeling with fully automatic parameter calibration to estimate the full geomechanical stress fields of a prospective US carbon dioxide (CO2) storage site, based on sparse measurement data. The goal is to compute full stress tensor field estimates (principal stresses and orientations) that are maximally compatible with observations within the constraints of the model assumptions, thereby extending pointwise, incomplete partial stress measurement to a simulated full formation stress field, as well as a rough assessment of the associated error. We use the Perch site, located in Otsego County, Michigan, USA, as our case study. The input data consist of partial stress tensor information inferred from in-situ borehole tests, geophysical well logs, and processing of seismic data. A static earth model (SEM) of the site was developed, and geomechanical simulation functionality of the open-source MATLAB Reservoir Simulation Toolbox (MRST) was used to model the stress field. Adjoint-based nonlinear optimization was used to adjust boundary conditions and material properties to calibrate simulated results of observations. Results were interpreted through a Bayesian framework. The focus of this paper is to demonstrate how the fully automatic calibration procedure works and discuss the results obtained; it does not attempt a detailed analysis of the stress field in the context of the proposed CO2 storage initiatives. Our work is part of a larger effort to noninvasively determine in-situ stresses in deep formations considered for CO2 storage. Guided by previously published research on geomechanical model calibration, our work presents a novel calibration approach supporting a potentially large number of linear or nonlinear calibration parameters to produce results optimally agreeing with available measurements and thus extend partial pointwise estimates to full tensor fields compatible with the physics of the site.

Engineering↗

Modeling Stochastic Variability in Multiband Time-series Data

In preparation for the era of time-domain astronomy with upcoming large-scale surveys, we propose a state-space representation of a multivariate damped random walk process as a tool to analyze irregularly-spaced multifilter light curves with heteroscedastic measurement errors. We adopt a computationally efficient and scalable Kalman filtering approach to evaluate the likelihood function, leading to maximum O(k 3 n) complexity, where k is the number of available bands and n is the number of unique observation times across the k bands. This is a significant computational advantage over a commonly used univariate Gaussian process that can stack up all multiband light curves in one vector with maximum O(k 3 n 3 ) complexity. Using such efficient likelihood computation, we provide both maximum likelihood estimates and Bayesian posterior samples of the model parameters. Three numerical illustrations are presented: (i) analyzing simulated five-band light curves for a comparison with independent single-band fits; (ii) analyzing five-band light curves of a quasar obtained from the Sloan Digital Sky Survey Stripe 82 to estimate short-term variability and timescale; (iii) analyzing gravitationally lensed g- and r-band light curves of Q0957+561 to infer the time delay. Two R packages, Rdrw and timedelay, are publicly available to fit the proposed models.

79 ASTRONOMY AND ASTROPHYSICS↗

Compactly‐Supported Nonstationary Kernels for Computing Exact Gaussian Processes on Big Data

The Gaussian process (GP) is a widely used method for analyzing large-scale data sets, including spatio-temporal measurements of nonlinear processes that are now commonplace in the environmental sciences. Traditional implementations of GPs involve stationary kernels (also termed covariance functions) that limit their flexibility, and exact methods for inference that prevent application to data sets with more than about 10,000 points. Modern approaches to address stationarity assumptions generally fail to accommodate large data sets, while all attempts to address scalability focus on approximating the Gaussian likelihood, which can involve subjectivity and lead to inaccuracies. In this work, we explicitly derive an alternative kernel that can discover and encode both sparsity and nonstationarity. We embed the kernel within a fully Bayesian GP model and leverage high-performance computing resources to enable the analysis of massive data sets. We demonstrate the favorable performance of our novel kernel relative to existing exact and approximate GP methods across a variety of synthetic data examples. Furthermore, we conduct space–time prediction based on more than 1 million measurements of daily maximum temperature and verify that our results outperform state-of-the-art methods in the Earth sciences. More broadly, having access to exact GPs that use ultra-scalable, sparsity-discovering, nonstationary kernels allows GP methods to truly compete with a wide variety of machine learning methods.

Gaussian processes↗

On the Bayesian calibration of computer model mixtures through experimental data, and the design of predictive models

For many real systems, several computer models may exist with different physics and predictive abilities. To achieve more accurate simulations/predictions, it is desirable for these models to be properly combined and calibrated. Here, we propose the Bayesian calibration of computer model mixture method which relies on the idea of representing the real system output as a mixture of the available computer model outputs with unknown input dependent weight functions. The method builds a fully Bayesian predictive model as an emulator for the real system output by combining, weighting, and calibrating the available models in the Bayesian framework. Moreover, it fits a mixture of calibrated computer models that can be used by the domain scientist as a mean to combine the available computer models, in a flexible and principled manner, and perform reliable simulations. It can address realistic cases where one model may be more accurate than the others at different input values because the mixture weights, indicating the contribution of each model, are functions of the input. Inference on the calibration parameters can consider multiple computer models associated with different physics. The method does not require knowledge of the fidelity order of the models. We provide a technique able to mitigate the computational overhead due to the consideration of multiple computer models that is suitable to the mixture model framework. We implement the proposed method in a real-world application involving the Weather Research and Forecasting large-scale climate model.

97 MATHEMATICS AND COMPUTING↗

Cosmology From CMB Lensing and Delensed EE Power Spectra Using 2019-2020 SPT-3G Polarization Data

From CMB polarization data alone we reconstruct the CMB lensing power spectrum, comparable in overall constraining power to previous temperature-based reconstructions, and an unlensed E -mode power spectrum, with clear detections of the third through tenth acoustic peaks. The observations, taken in 2019 and 2020 with the South Pole Telescope (SPT) and the SPT-3G camera, cover 1500 deg 2 at 95, 150, and 220 GHz with arcminute resolution and roughly 4.9 µ K-arcmin coadded noise in polarization. The power spectrum estimates, together with systematic parameter estimates and a joint covariance matrix, follow from a Bayesian analysis using the Marginal Unbiased Score Expansion (MUSE) method. The E -mode spectrum at ℓ > 2000 and lensing spectrum at L > 350 are the most precise to date. Assuming the ΛCDM model, and using only these SPT data and priors on τ and absolute calibration from Planck, we find H 0 = 66.81 ± 0.81 km/s/Mpc, comparable in precision to the Planck determination and in 5.4 σ tension with the most precise H 0 inference derived via the distance ladder. We also find S 8 ≡ σ 8 (Ω m /0.3) 0.5 = 0.850 ± 0.017, providing further independent evidence of a slight tension with low-redshift structure probes. The ΛCDM model provides a good simultaneous fit to the combined Planck, ACT, and SPT data, and thus passes a powerful test. Combining these CMB datasets with BAO observations, we explore extensions to the ΛCDM model. We find that the effective number of neutrino species, spatial curvature, and primordial helium fraction are consistent with standard model values, and that the 95% confidence upper limit on the neutrino mass sum is 0.075 eV, close to the minimum sum expected from observations of solar and atmospheric neutrino oscillations. The SPT data are consistent with the somewhat weak (< 3 σ ) preference for excess lensing power seen in Planck and ACT data relative to predictions of the ΛCDM model given the combined Planck, ACT, and BAO data sets. Finally, we also detect at greater than 3 σ the influence of non-linear evolution in the CMB lensing power spectrum and discuss it in the context of the S 8 tension. Forthcoming SPT-3G analyses will feature deeper and wider observations in temperature and polarization, providing even tighter constraints and more powerful tests of the ΛCDM model.

79 ASTRONOMY AND ASTROPHYSICS↗

A fully Bayesian method for jointly fitting instrumental calibration and X-ray spectral models

Owing to a lack of robust principled methods, systematic instrumental uncertainties have generally been ignored in astrophysical data analysis despite wide recognition of the importance of including them. Ignoring calibration uncertainty can cause bias in the estimation of source model parameters and can lead to underestimation of the variance of these estimates. We previously introduced a pragmatic Bayesian method to address this problem. The method is 'pragmatic' in that it introduced an ad hoc technique that simplified computation by neglecting the potential information in the data for narrowing the uncertainty for the calibration product. Following that work, we use a principal component analysis to efficiently represent the uncertainty of the effective area of an X-ray (or γ-ray) telescope. Here, however, we leverage this representation to enable a principled, fully Bayesian method that coherently accounts for the calibration uncertainty in high-energy spectral analysis. In this setting, the method is compared with standard analysis techniques and the pragmatic Bayesian method. The advantage of the fully Bayesian method is that it allows the data to provide information not only for estimation of the source parameters but also for the calibration product—here the effective area, conditional on the adopted spectral model. In this way, it can yield more accurate and efficient estimates of the source parameters along with valid estimates of their uncertainty. Provided that the source spectrum can be accurately described by a parameterized model, this method allows rigorous inference about the effective area by quantifying which possible curves are most consistent with the data.

79 ASTRONOMY AND ASTROPHYSICS↗

BP-Quant

Here, we present the implementation of a Bayesian model (BP-Quant) that uses statistically derived peptides signatures to identify peptides that are outside the dominant pattern, or the existence of multiple over-expressed patterns to improve relative protein abundance estimates. It is a research-driven approach that utilizes the objectives of the experiment, defined in the context of a standard statistical hypothesis, to identify a set of peptides exhibiting similar statistical behavior relating to a protein. This approach infers that changes in relative protein abundance can be used as a surrogate for changes in function, without necessarily taking into account the effect of differential post-translational modifications, processing, or splicing in altering protein function. BP-Quant is available as MatLab ® and R packages here.

Bramer, Lisa↗