Use of Contrast-Enhanced MRI in Management of Discordant Core Biopsy Results.

OBJECTIVE. Evaluating concordance between core biopsy results and imaging findings is an integral component of breast intervention. Pathologic results deemed benign discordant reflect concern that a malignancy may have been incorrectly sampled. Standard of care currently is surgical excision, although a large percentage of these lesions will be benign at final pathologic analysis. The purpose of this study was to determine whether inclusion of contrast-enhanced MRI would optimize patient care. MATERIALS AND METHODS. Forty-five patients with 46 lesions were identified who underwent contrast-enhanced MRI after receiving discordant ultrasound or stereotactic biopsy results between 2012 and mid 2018. These findings were classified BI-RADS category 4 at diagnostic imaging. Disease-positive was defined as all malignancies and borderline lesions. RESULTS. Fourteen patients had suspicious MRI findings; 31 patients did not. Negative or benign MRI findings were validated by stability at imaging follow-up of at least 1 year in 27 patients (28 lesions) and at least 6 months in four patients. Eight of the total of 46 discordant lesions were ultimately malignant, a rate of 17.3%, an expected result for BI-RADS 4 lesions. Sensitivity, specificity, positive predictive value, and negative predictive value of MRI calculated in the group of 41 patients (42 lesions) with documented stability for at least 1 year were 100%, 93.3%, 85.7%, and 100%. The false-negative rate of MRI was 0%; the false-positive rate was 2 of 30 (6.7%). CONCLUSION. In the management of discordant benign core biopsy results, contrast-enhanced MRI facilitated successful triage of patients to surgery; 31 of the original 45 patients (68.9%) avoided surgery.

Bayesian inference for duplication-mutation with complementarity network models.

We observe an undirected graph G without multiple edges and self-loops, which is to represent a protein-protein interaction (PPI) network. We assume that G evolved under the duplication-mutation with complementarity (DMC) model from a seed graph, G0, and we also observe the binary forest Γ that represents the duplication history of G. A posterior density for the DMC model parameters is established, and we outline a sampling strategy by which one can perform Bayesian inference; that sampling strategy employs a particle marginal Metropolis-Hastings (PMMH) algorithm. We test our methodology on numerical examples to demonstrate a high accuracy and precision in the inference of the DMC model's mutation and homodimerization parameters.

A simulation approach for change-points on phylogenetic trees.

We observe n sequences at each of m sites and assume that they have evolved from an ancestral sequence that forms the root of a binary tree of known topology and branch lengths, but the sequence states at internal nodes are unknown. The topology of the tree and branch lengths are the same for all sites, but the parameters of the evolutionary model can vary over sites. We assume a piecewise constant model for these parameters, with an unknown number of change-points and hence a transdimensional parameter space over which we seek to perform Bayesian inference. We propose two novel ideas to deal with the computational challenges of such inference. Firstly, we approximate the model based on the time machine principle: the top nodes of the binary tree (near the root) are replaced by an approximation of the true distribution; as more nodes are removed from the top of the tree, the cost of computing the likelihood is reduced linearly in n. The approach introduces a bias, which we investigate empirically. Secondly, we develop a particle marginal Metropolis-Hastings (PMMH) algorithm, that employs a sequential Monte Carlo (SMC) sampler and can use the first idea. Our time-machine PMMH algorithm copes well with one of the bottle-necks of standard computational algorithms: the transdimensional nature of the posterior distribution. The algorithm is implemented on simulated and real data examples, and we empirically demonstrate its potential to outperform competing methods based on approximate Bayesian computation (ABC) techniques.