Search

Harmonizing serology measurements is critical for identifying reference materials that permit standardization and comparison of results across different diagnostic platforms. However, the theoretical foundations of such tasks have yet to be fully explored in the context of antibody thermodynamics and uncertainty quantification (UQ). This has restricted the usefulness of standards currently deployed and limited the scope of materials considered as viable reference material. To address these problems, we develop rigorous theories of antibody normalization and harmonization, as well as formulate a probabilistic framework for defining correlates of protection. We begin by proposing a mathematical definition of harmonization equipped with structure needed to quantify uncertainty associated with the choice of standard, assay, etc. We then show how a thermodynamic description of serology measurements (i) relates this structure to the Gibbs free-energy of antibody binding, and thereby (ii) induces a regression analysis that directly harmonizes measurements. We supplement this with a novel, optimization-based normalization (not harmonization!) method that checks for consistency between reference and sample dilution curves. Last, we relate these analyses to uncertainty propagation techniques to estimate correlates of protection. A key result of these analyses is that under physically reasonable conditions, the choice of reference material does not increase uncertainty associated with harmonization or correlates of protection. We provide examples and validate main ideas in the context of an interlab study that lays the foundation for using monoclonal antibodies as a reference for SARS-CoV-2 serology measurements.

Cerebral vasospasm, a prolonged constriction of cerebral arteries, is the first cause of morbidity and mortality for patients who survive hospitalisation after aneurysmal subarachnoid haemorrhage. The recent finding that stent-retrievers can successfully treat the disease has challenged the viewpoint that damage to the extracellular matrix is necessary. We apply a 3D finite element rate-based constrained mixture model (rb-CMM) to simulate vasospasm, remodelling and treatment with stents. The artery is modelled as a thick-walled fibre-reinforced constrained mixture subject to physiological pressure and axial stretch. The model accounts for distributions of collagen fibre homeostatic stretches, VSMC active response, remodelling and damage. After simulating vasospasm and subsequent remodelling of the artery to a new homeostatic state, we simulate treatment with commonly available stent-retrievers. We perform a parameter study to examine how arterial diameter and thickness affect the success of stent treatment. The model predictions on the pressure required to mechanically resolve the constriction are consistent with stent-retrievers. In agreement with clinical observations, our model predicts that stent-retrievers tend to be effective in arteries of up to 3mm diameter, but fail in larger ones. Variations in arterial wall thickness significantly affect stent pressure requirements. We have developed a novel rb-CMM that accounts for VSMC active response, remodelling and damage. Consistently with clinical observations, simulations predict that stent-retrievers can mechanically resolve vasospasm. Moreover, accounting for a patient's arterial properties is important for predicting likelihood of stent success. This in silico tool has the potential to support clinical decision-making and guide the development and evaluation of dedicated stents for personalised treatment of vasospasm., Comment: 32 pages, 10 figures

This is the second manuscript in a two-part series that uses diagnostic testing to understand the connection between prevalence (i.e. number of elements in a class), uncertainty quantification (UQ), and classification theory. Part I considered the context of supervised machine learning (ML) and established a duality between prevalence and the concept of relative conditional probability. The key idea of that analysis was to train a family of discriminative classifiers by minimizing a sum of prevalence-weighted empirical risk functions. The resulting outputs can be interpreted as relative probability level-sets, which thereby yield uncertainty estimates in the class labels. This procedure also demonstrated that certain discriminative and generative ML models are equivalent. Part II considers the extent to which these results can be extended to tasks in unsupervised learning through recourse to ideas in linear algebra. We first observe that the distribution of an impure population, for which the class of a corresponding sample is unknown, can be parameterized in terms of a prevalence. This motivates us to introduce the concept of linearly independent populations, which have different but unknown prevalence values. Using this, we identify an isomorphism between classifiers defined in terms of impure and pure populations. In certain cases, this also leads to a nonlinear system of equations whose solution yields the prevalence values of the linearly independent populations, fully realizing unsupervised learning as a generalization of supervised learning. We illustrate our methods in the context of synthetic data and a research-use-only SARS-CoV-2 enzyme-linked immunosorbent assay (ELISA).

Electronic $K$ x rays emitted by muonic Ar atoms in the gas phase were observed using a superconducting transition-edge-sensor microcalorimeter. The high-precision energy spectra provided a clear signature of the presence of muonic atoms accompanied by a few electrons, which have never been observed before. One-, two-, and three-electron bound, i.e., H-like, He-like, and Li-like, muonic Ar atoms were identified from electronic $K$ x rays and hyper-satellite $K$ x rays. These $K$ x rays are emitted after the charge transfer process by the collisions with surrounding Ar atoms. With the aid of theoretical calculations, we confirmed that the peak positions are consistent with the x-ray energies from highly charged Cl ions, and the intensities reflecting deexcitation dynamics were successfully understood by taking into account the interaction between the muon and bound electrons.

The calcium isotopes are an ideal system to investigate the evolution of shell structure and magic numbers. Although the properties of surface nucleons in calcium have been well studied, probing the structure of deeply bound nucleons remains a challenge. Here, we report on the first measurement of unbound states in $^{53}$Ca and $^{55}$Ca, populated from \ts{54,56}Ca($p,pn$) reactions at a beam energy of around 216 MeV/nucleon at the RIKEN Radioactive Isotopes Beam Factory. The resonance properties, partial cross sections, and momentum distributions of these unbound states were analyzed. Orbital angular momentum $l$ assignments were extracted from momentum distributions based on calculations using the distorted wave impulse approximation (DWIA) reaction model. The resonances at excitation energies of 5516(41)\,keV in $^{53}$Ca and 6000(250)\,keV in $^{55}$Ca indicate a significant $l$\, =\,3 component, providing the first experimental evidence for the $\nu 0f_{7/2}$ single-particle strength of unbound hole states in the neutron-rich Ca isotopes. The observed excitation energies and cross-sections point towards extremely localized and well separated strength distributions, with some fragmentation for the $\nu 0f_{7/2}$ orbital in $^{55}$Ca. These results are in good agreement with predictions from shell-model calculations using the effective GXPF1Bs interaction and \textit{ab initio} calculations and diverge markedly from the experimental distributions in the nickel isotones at $Z=28$., Comment: 13 pages, 7 figures

Doubly robust estimators have gained popularity in the field of causal inference due to their ability to provide consistent point estimates when either an outcome or exposure model is correctly specified. However, the influence function based variance estimator frequently used with doubly robust estimators is only consistent when both the outcome and exposure models are correctly specified. Here, use of M-estimation and the empirical sandwich variance estimator for doubly robust point and variance estimation is demonstrated. Simulation studies illustrate the properties of the influence function based and empirical sandwich variance estimators. Estimators are applied to data from the Improving Pregnancy Outcomes with Progesterone (IPOP) trial to estimate the effect of maternal anemia on birth weight among women with HIV. In the example, birth weights if all women had anemia were estimated to be lower than birth weights if no women had anemia, though estimates were imprecise. Variance estimates were more stable under varying model specifications for the empirical sandwich variance estimator than the influence function based variance estimator., Comment: 19 pages, 5 figures, 6 tables

Studies intended to estimate the effect of a treatment, like randomized trials, may not be sampled from the desired target population. To correct for this discrepancy, estimates can be transported to the target population. Methods for transporting between populations are often premised on a positivity assumption, such that all relevant covariate patterns in one population are also present in the other. However, eligibility criteria, particularly in the case of trials, can result in violations of positivity when transporting to external populations. To address nonpositivity, a synthesis of statistical and mathematical models can be considered. This approach integrates multiple data sources (e.g. trials, observational, pharmacokinetic studies) to estimate treatment effects, leveraging mathematical models to handle positivity violations. This approach was previously demonstrated for positivity violations by a single binary covariate. Here, we extend the synthesis approach for positivity violations with a continuous covariate. For estimation, two novel augmented inverse probability weighting estimators are proposed. Both estimators are contrasted with other common approaches for addressing nonpositivity. Empirical performance is compared via Monte Carlo simulation. Finally, the competing approaches are illustrated with an example in the context of two-drug versus one-drug antiretroviral therapy on CD4 T cell counts among women with HIV.

Diagnostic testing provides a unique setting for studying and developing tools in classification theory. In such contexts, the concept of prevalence, i.e. the number of individuals with a given condition, is fundamental, both as an inherent quantity of interest and as a parameter that controls classification accuracy. This manuscript is the first in a two-part series that studies deeper connections between classification theory and prevalence, showing how the latter establishes a more complete theory of uncertainty quantification (UQ) for certain types of machine learning (ML). We motivate this analysis via a lemma demonstrating that general classifiers minimizing a prevalence-weighted error contain the same probabilistic information as Bayes-optimal classifiers, which depend on conditional probability densities. This leads us to study relative probability level-sets $B^\star (q)$, which are reinterpreted as both classification boundaries and useful tools for quantifying uncertainty in class labels. To realize this in practice, we also propose a numerical, homotopy algorithm that estimates the $B^\star (q)$ by minimizing a prevalence-weighted empirical error. The successes and shortcomings of this method motivate us to revisit properties of the level sets, and we deduce the corresponding classifiers obey a useful monotonicity property that stabilizes the numerics and points to important extensions to UQ of ML. Throughout, we validate our methods in the context of synthetic data and a research-use-only SARS-CoV-2 enzyme-linked immunosorbent (ELISA) assay.

Gamma decays were observed in $^{56}$Ca and $^{58}$Ca following quasi-free one-proton knockout reactions from $^{57,59}$Sc beams at $\approx 200$ MeV/nucleon. For $^{56}$Ca, a $\gamma$ ray transition was measured to be 1456(12) keV, while for $^{58}$Ca an indication for a transition was observed at 1115(34) keV. Both transitions were tentatively assigned as the $2^+_1 \rightarrow 0^+_{gs}$ decays, and were compared to results from ab initio and conventional shell-model approaches. A shell-model calculation in a wide model space with a marginally modified effective nucleon-nucleon interaction depicts excellent agreement with experiment for $2^+_1$ level energies, two-neutron separation energies, and reaction cross sections, corroborating the formation of a new nuclear shell above the $N$ = 34 shell. Its constituents, the $0f_{5/2}$ and $0g_{9/2}$ orbitals, are almost degenerate. This degeneracy precludes the possibility for a doubly magic $^{60}$Ca and potentially drives the dripline of Ca isotopes to $^{70}$Ca or even beyond., Comment: 8 pages, 3 figures

We report on the first production of an antihydrogen beam by charge exchange of 6.1 keV antiprotons with a cloud of positronium in the GBAR experiment at CERN. The antiproton beam was delivered by the AD/ELENA facility. The positronium target was produced from a positron beam itself obtained from an electron linear accelerator. We observe an excess over background indicating antihydrogen production with a significance of 3-4 standard deviations.

Iterated conditional expectation (ICE) g-computation is an estimation approach for addressing time-varying confounding for both longitudinal and time-to-event data. Unlike other g-computation implementations, ICE avoids the need to specify models for each time-varying covariate. For variance estimation, previous work has suggested the bootstrap. However, bootstrapping can be computationally intense. Here, we present ICE g-computation as a set of stacked estimating equations. Therefore, the variance for the ICE g-computation estimator can be consistently estimated using the empirical sandwich variance estimator. Performance of the variance estimator was evaluated empirically with a simulation study. The proposed approach is also demonstrated with an illustrative example on the effect of cigarette smoking on the prevalence of hypertension. In the simulation study, the empirical sandwich variance estimator appropriately estimated the variance. When comparing runtimes between the sandwich variance estimator and the bootstrap for the applied example, the sandwich estimator was substantially faster, even when bootstraps were run in parallel. The empirical sandwich variance estimator is a viable option for variance estimation with ICE g-computation., Comment: 18 pages, 1 figure, 6 tables

While randomized controlled trials (RCTs) are critical for establishing the efficacy of new therapies, there are limitations regarding what comparisons can be made directly from trial data. RCTs are limited to a small number of comparator arms and often compare a new therapeutic to a standard of care which has already proven efficacious. It is sometimes of interest to estimate the efficacy of the new therapy relative to a treatment that was not evaluated in the same trial, such as a placebo or an alternative therapy that was evaluated in a different trial. Such multi-study comparisons are challenging because of potential differences between trial populations that can affect the outcome. In this paper, two bridging estimators are considered that allow for comparisons of treatments evaluated in different trials using data fusion methods to account for measured differences in trial populations. A "multi-span'' estimator leverages a shared arm between two trials, while a "single-span'' estimator does not require a shared arm. A diagnostic statistic that compares the outcome in the standardized shared arms is provided. The two estimators are compared in simulations, where both estimators demonstrate minimal empirical bias and nominal confidence interval coverage when the identification assumptions are met. The estimators are applied to data from the AIDS Clinical Trials Group 320 and 388 to compare the efficacy of two-drug versus four-drug antiretroviral therapy on CD4 cell counts among persons with advanced HIV. The single-span approach requires fewer identification assumptions and was more efficient in simulations and the application.

When estimating an effect of an action with a randomized or observational study, that study is often not a random sample of the desired target population. Instead, estimates from that study can be transported to the target population. However, transportability methods generally rely on a positivity assumption, such that all relevant covariate patterns in the target population are also observed in the study sample. Strict eligibility criteria, particularly in the context of randomized trials, may lead to violations of this assumption. Two common approaches to address positivity violations are restricting the target population and restricting the relevant covariate set. As neither of these restrictions are ideal, we instead propose a synthesis of statistical and simulation models to address positivity violations. We propose corresponding g-computation and inverse probability weighting estimators. The restriction and synthesis approaches to addressing positivity violations are contrasted with a simulation experiment and an illustrative example in the context of sexually transmitted infection testing uptake. In both cases, the proposed synthesis approach accurately addressed the original research question when paired with a thoughtfully selected simulation model. Neither of the restriction approaches were able to accurately address the motivating question. As public health decisions must often be made with imperfect target population information, model synthesis is a viable approach given a combination of empirical data and external information based on the best available knowledge.