Modeling COVID-19 Outbreaks in Long-Term Care Facilities Using an Agent-Based Modeling and Simulation Approach.

The elderly, especially those individuals with pre-existing health problems, have been disproportionally at a higher risk during the COVID-19 pandemic. Residents of long-term care facilities have been gravely affected by the pandemic and resident death numbers have been far above those of the general population. To better understand how infectious diseases such as COVID-19 can spread through long-term care facilities, we developed an agent-based simulation tool that uses a contact matrix adapted from previous infection control research in these types of facilities. This matrix accounts for the average distinct daily contacts between seven different agent types that represent the roles of individuals in long-term care facilities. The simulation results were compared to actual COVID-19 outbreaks in some of the long-term care facilities in Ontario, Canada. Our analysis shows that this simulation tool is capable of predicting the number of resident deaths after 50 days with a less than 0.1 variation in death rate. We modeled and predicted the effectiveness of infection control measures by utilizing this simulation tool. We found that to reduce the number of resident deaths, the effectiveness of personal protective equipment must be above 50%. We also found that daily random COVID-19 tests for as low as less than 10% of a long-term care facility's population will reduce the number of resident deaths by over 75%. The results further show that combining several infection control measures will lead to more effective outcomes.

Robust Alignment for Panoramic Stitching Via an Exact Rank Constraint.

We study the problem of image alignment for panoramic stitching. Unlike most existing approaches that are feature-based, our algorithm works on pixels directly, and accounts for errors across the whole images globally. Technically, we formulate the alignment problem as rank-1 and sparse matrix decomposition over transformed images, and develop an efficient algorithm for solving this challenging non-convex optimization problem. The algorithm reduces to solving a sequence of subproblems, where we analytically establish exact recovery conditions, convergence and optimality, together with convergence rate and complexity. We generalize it to simultaneously align multiple images and recover multiple homographies, extending its application scope toward vast majority of practical scenarios. The experimental results demonstrate that the proposed algorithm is capable of more accurately aligning the images and generating higher quality stitched images than the state-of-the-art methods.

Prior Information Guided Regularized Deep Learning for Cell Nucleus Detection.

Cell nuclei detection is a challenging research topic because of limitations in cellular image quality and diversity of nuclear morphology, i.e., varying nuclei shapes, sizes, and overlaps between multiple cell nuclei. This has been a topic of enduring interest with promising recent success shown by deep learning methods. These methods train convolutional neural networks (CNNs) with a training set of input images and known, labeled nuclei locations. Many such methods are supplemented by spatial or morphological processing. Using a set of canonical cell nuclei shapes, prepared with the help of a domain expert, we develop a new approach that we call shape priors (SPs) with CNNs (SPs-CNN). We further extend the network to introduce an SP layer and then allowing it to become trainable (i.e., optimizable). We call this network as tunable SP-CNN (TSP-CNN). In summary, we present new network structures that can incorporate "expected behavior" of nucleus shapes via two components: learnable layers that perform the nucleus detection and a fixed processing part that guides the learning with prior information. Analytically, we formulate two new regularization terms that are targeted at: 1) learning the shapes and 2) reducing false positives while simultaneously encouraging detection inside the cell nucleus boundary. Experimental results on two challenging datasets reveal that the proposed SP-CNN and TSP-CNN can outperform the state-of-the-art alternatives.

Projection onto Epigraph Sets for Rapid Self-Tuning Compressed Sensing MRI.

The compressed sensing (CS) framework leverages the sparsity of MR images to reconstruct from the undersampled acquisitions. CS reconstructions involve one or more regularization parameters that weigh sparsity in transform domains against fidelity to acquired data. While parameter selection is critical for reconstruction quality, the optimal parameters are subject and dataset specific. Thus, commonly practiced heuristic parameter selection generalizes poorly to independent datasets. Recent studies have proposed to tune parameters by estimating the risk of removing significant image coefficients. Line searches are performed across the parameter space to identify the parameter value that minimizes this risk. Although effective, these line searches yield prolonged reconstruction times. Here, we propose a new self-tuning CS method that uses computationally efficient projections onto epigraph sets of the l1 and total-variation norms to simultaneously achieve parameter selection and regularization. In vivo demonstrations are provided for balanced steady-state free precession, time-of-flight, and T1-weighted imaging. The proposed method achieves an order of magnitude improvement in computational efficiency over line-search methods while maintaining near-optimal parameter selection.

Quadrature RF Coil for In Vivo Brain MRI of a Macaque Monkey in a Stereotaxic Head Frame.

We present a quadrature volume coil designed for brain imaging of a macaque monkey fixed in a sphinx position (facing down the bore) within a stereotactic frame at 3 T, where the position of the monkey and presence of the frame preclude use of existing coils. Requirements include the ability to position and remove the coil without disturbing the position of the monkey in the frame. A saddle coil and a solenoid were combined on a modified cylindrical former and connected in quadrature as to produce a homogeneous circularly polarized field throughout the brain. To allow the loops of the saddle coil to encompass the ear posts, partial disassembly and reassembly were facilitated by embedding pin and socket contacts into separate pieces of the former. Coil design included simulation of the electromagnetic fields for the coil containing a 3D model of a monkey's head. The resulting coil produced adequate homogeneity and signal-to-noise ratio throughout the brain.