Soft Tissue Characterization with Temporal Enhanced Ultrasound through Periodic Manipulation of Point Spread Function: A Feasibility Study.

Temporal enhanced ultrasound (TeUS) is a tissue characterization approach based on analysis of a temporal series of US data. Previously we demonstrated that intrinsic or external micro-motions of scatterers in the tissue contribute towards the tissue classification properties of TeUS. This property is beneficial to detect early stage cancer, for example, where changes in nuclei configuration (scatteres) dominate tissue properties. In this study, we propose an analytical derivation and experiments to acquire TeUS through manipulation of US imaging parameters, which may be simpler to translate to clinical applications. The feasibility of the proposed method is demonstrated on tissue-mimicking phantoms. Using an autoencoder classifier, we are able to classify phantoms of varying elasticities and scattering sizes.

An End-to-End Solution for Automatic Contouring of Tumor Region in Intraoperative Images of Breast Lumpectomy.

Breast-conserving surgery, also known as lumpectomy, is an early stage breast cancer treatment that aims to spare as much healthy breast tissue as possible. A risk associated with lumpectomy is the presence of cancer positive margins post operation. Surgical navigation has been shown to reduce cancer positive margins but requires manual segmentation of the tumor intraoperatively. In this paper, we propose an end-to-end solution for automatic contouring of breast tumor from intraoperative ultrasound images using two convolutional neural network architectures, the U-Net and residual U-Net. The networks are trained on annotated intraoperative breast ultrasound images and evaluated on the quality of predicted segmentations. This work brings us one step closer to providing surgeons with an automated surgical navigation system that helps reduce cancer-positive margins during lumpectomy.

Reduction of stroke assessment time for visually guided reaching task on KINARM exoskeleton robot.

Robotic technologies provide objective, highly reliable tools for assessment of brain function following stroke. KINARM is an exoskeleton device that quantifies sensorimotor brain function using a visually guided reaching task among many other behavioral tasks. As further tasks are developed to more broadly assess different aspects of behavior using the robot, techniques and approaches are required to reduce the time it takes to complete each task. The present study investigates how the value of robot-measured parameters changes under alternative schemes that significantly reduce assessment time compared to the current assessment protocol for the visually guided reaching task. Results of the study are validated by addressing an important diagnostic question using an SVM classifier, showing that the alternative schemes provide nearly identical performance in terms of classification sensitivity, specificity and accuracy.

A navigation system for shoulder arthroscopic surgery.

The general framework and experimental validation of a novel navigation system designed for shoulder arthroscopy are presented. The system was designed to improve the surgeon's perception of the three-dimensional space within the human shoulder. Prior to surgery, a surface model of the shoulder was created from computed tomography images. Intraoperatively, optically tracked arthroscopic instruments were calibrated. The surface model was then registered to the patient using tracked freehand ultrasound images taken from predefined landmark regions on the scapula. Three-dimensional models of the surgical instruments were displayed, in real time, relative to the surface model in a user interface. Laboratory experiments revealed only small registration and calibration errors, with minimal time needed to complete the intraoperative tasks.

Discrete Fourier analysis of ultrasound RF time series for detection of prostate cancer.

In this paper, we demonstrate that a set of six features extracted from the discrete Fourier transform of ultrasound Radio-Frequency (RF) time series can be used to detect prostate cancer with high sensitivity and specificity. Ultrasound RF time series refer to a series of echoes received from one spatial location of tissue while the imaging probe and the tissue are fixed in position. Our previous investigations have shown that at least one feature, fractal dimension, of these signals demonstrates strong correlation with the tissue microstructure. In the current paper, six new features that represent the frequency spectrum of the RF time series have been used, in conjunction with a neural network classification approach, to detect prostate cancer in regions of tissue as small as 0.03 cm2. Based on pathology results used as gold standard, we have acquired mean accuracy of 91%, mean sensitivity of 92% and mean specificity of 90% on seven human prostates.

A novel flow reactor for studying reactions on liquid surfaces coated by organic monolayers: methods, validation, and initial results.

A new flow reactor has been developed that allows the study of heterogeneous kinetics on an aqueous surface coated by an organic monolayer. Computational fluid dynamics simulations have been used to determine the flow characteristics for various experimental conditions. In addition a mathematical framework has been developed to derive the true first-order wall loss rate coefficient, k(1st)(w), from the experimentally observed wall loss rate, k(obs). Validation of the new flow reactor is performed by measuring the uptake of O(3) by canola oil as a function of pressure and flow velocity and the reactive uptake coefficients of N(2)O(5) by aqueous 60 wt % and 80 wt % H(2)SO(4). Using this new flow reactor, we also determined the reactive uptake coefficient of N(2)O(5) on aqueous 80 wt % H(2)SO(4) solution coated with an 1-octadecanol (C(18)H(37)OH) monolayer. The uptake coefficient was determined as (8.1 +/- 3.2) x 10-4, which is about 2 orders of magnitude lower compared to the reactive uptake coefficient on a pure aqueous 80 wt % H(2)SO(4) solution. Our measured reactive uptake coefficient can be considered as a lower limit for the reactive uptake coefficient of aqueous aerosols coated with organic monolayers in the atmosphere, because in the atmosphere organic monolayers will likely also consist of surfactants with shorter lengths and branched structures which will have a smaller overall effect.

A neural network based approach for inference and verification of transcriptional regulatory interactions.

In this paper, we present a comprehensive neural network based modeling and validation framework for reverse engineering gene regulatory interactions. We employ two approaches, Gene Set Stochastic Sampling and Sensitivity Analysis, to infer these interactions. We first apply these methods to a simulated artificial dataset to ensure their correctness and accuracy. True biological interactions are then modeled by analyzing a rat hippocampus development dataset. Finally, we present a thorough computational methodology to test the validity and robustness of the inferred regulations through novel assemblies of relevant testing datasets.

Cervical spine loading characteristics in a cadaveric C5 corpectomy model using a static and dynamic plate.

Anterior plates are used to increase the initial stability of anterior cervical spine fusions; however, plating has been suggested to cause graft stress shielding, leading to reduced fusion rates. The objectives of this study were to quantify the effects of graft size and plating (static versus dynamic) and the role of the posterior elements on load transmission in anterior cervical fusion. A C5 corpectomy was performed on six human cervical spines (C3-C7). An instrumented height-adjustable graft and dynamic cervical plate were used to measure axial load transmission. Each specimen underwent axial compressive testing with dynamic and static plate configurations, optimal and undersized graft heights, and posterior elements intact and removed. Dynamic plating allowed significantly more load transmission by the graft, particularly in the undersized graft configuration. The posterior elements play a significant role in load transmission.