BUbble Flow Field: a Simulation Framework for Evaluating Ultrasound Localization Microscopy Algorithms

Ultrasound contrast enhanced imaging has seen widespread uptake in research and clinical diagnostic imaging. This includes applications such as vector flow imaging, functional ultrasound and super-resolution Ultrasound Localization Microscopy (ULM). All of these require testing and validation during development of new algorithms with ground truth data. In this work we present a comprehensive simulation platform BUbble Flow Field (BUFF) that generates contrast enhanced ultrasound images in vascular tree geometries with realistic flow characteristics and validation algorithms for ULM. BUFF allows complex micro-vascular network generation of random and user-defined vascular networks. Blood flow is simulated with a fast Computational Fluid Dynamics (CFD) solver and allows arbitrary input and output positions and custom pressures. The acoustic field simulation is combined with non-linear Microbubble (MB) dynamics and simulates a range of point spread functions based on user-defined MB characteristics. The validation combines both binary and quantitative metrics. BFF's capacity to generate and validate user-defined networks is demonstrated through its implementation in the Ultrasound Localisation and TRacking Algorithms for Super Resolution (ULTRA-SR) Challenge at the International Ultrasonics Symposium (IUS) 2022 of the Institute of Electrical and Electronics Engineers (IEEE). The ability to produce ULM images, and the availability of a ground truth in localisation and tracking enables objective and quantitative evaluation of the large number of localisation and tracking algorithms developed in the field. BUFF can also benefit deep learning based methods by automatically generating datasets for training. BUFF is a fully comprehensive simulation platform for testing and validation of novel ULM techniques and is open source.Comment: 10 Pages, 9 Figure

Kinematics of individual muscle units in natural contractions measured in vivo using ultrafast ultrasound

Objective. The study of human neuromechanical control at the motor unit (MU) level has predominantly focussed on electrical activity and force generation, whilst the link between these, i.e. the muscle deformation, has not been widely studied. To address this gap, we analysed the kinematics of muscle units in natural contractions. Approach. We combined high-density surface electromyography (HDsEMG) and ultrafast ultrasound (US) recordings, at 1000 frames per second, from the tibialis anterior muscle to measure the motion of the muscular tissue caused by individual MU contractions. The MU discharge times were identified online by decomposition of the HDsEMG and provided as biofeedback to 12 subjects who were instructed to keep the MU active at the minimum discharge rate (9.8 ± 4.7 pulses per second; force less than 10% of the maximum). The series of discharge times were used to identify the velocity maps associated with 51 single muscle unit movements with high spatio-temporal precision, by a novel processing method on the concurrently recorded US images. From the individual MU velocity maps, we estimated the region of movement, the duration of the motion, the contraction time, and the excitation–contraction (E–C) coupling delay. Main results. Individual muscle unit motions could be reliably identified from the velocity maps in 10 out of 12 subjects. The duration of the motion, total contraction time, and E–C coupling were 17.9 $\pm$ 5.3 ms, 56.6 $\pm$ 8.4 ms, and 3.8 $\pm$ 3.0 ms (n = 390 across ten participants). The experimental measures also provided the first evidence of muscle unit twisting during voluntary contractions and MU territories with distinct split regions. Significance. The proposed method allows for the study of kinematics of individual MU twitches during natural contractions. The described measurements and characterisations open new avenues for the study of neuromechanics in healthy and pathological conditions

Characterization of myeloperoxidase and its contribution to antimicrobial effect on extracellular traps in flounder (Paralichthys olivaceus)

Myeloperoxidase (MPO) is a cationic leukocyte haloperoxidase and together with other proteins, they possess activities against various microorganisms and are involved in extracellular trap (ET) formation. The present work describes the gene and deduced protein sequences, and functions of MPO in flounder (PoMPO). The PoMPO possesses a 2313 bp open reading frame (ORF) that encodes a protein of 770 amino acids. The highest PoMPO mRNA expression levels were found in the head kidney, followed by peritoneal cells, gill, spleen, skin, muscle, and liver. PoMPO was expressed in MHCII+ and GCSFR+ cells which indicated that PoMPO mainly is expressed in flounder macrophages and granulocytes. Bacterial lipopolysaccharide-stimulated peritoneal leukocytes showed an increased protein level of PoMPO while it seemed that LPS also promoted the migration of MPO+ cells from the head kidney into the peripheral blood and peritoneal cavity. After phorbol 12-myristate 13-acetate (PMA) or bacterial stimulation, flounder leukocytes produced typical ET structures containing DNA with decoration by MPO. The ETs containing DNA and PoMPO effectively inhibited the proliferation of ET-trapped bacteria. Blocking PoMPO with antibodies decreased the enzymatic activity, which attenuated the antibacterial activity of ETs. This study pinpoints the involvement of ETs in flounder innate responses to pathogens

Rapid short-pulse sequences enhance the spatiotemporal uniformity of acoustically driven microbubble activity during flow conditions

Despite the promise of microbubble-mediated focused ultrasound therapies, in vivo findings have revealed over-treated and under-treated regions distributed throughout the focal volume. This poor distribution cannot be improved by conventional pulse shapes and sequences, due to their limited ability to control acoustic cavitation dynamics within the ultrasonic focus. This paper describes the design of a rapid short-pulse (RaSP) sequence which is comprised of short pulses separated by μs off-time intervals. Improved acoustic cavitation distribution was based on the hypothesis that microbubbles can freely move during the pulse off-times. Flowing SonoVue® microbubbles (flow velocity: 10 mm/s) were sonicated with a 0.5 MHz focused ultrasound transducer using RaSP sequences (peak-rarefactional pressures: 146–900 kPa, pulse repetition frequency: 1.25 kHz, and pulse lengths: 5–50 cycles). The distribution of cavitation activity was evaluated using passive acoustic mapping. RaSP sequences generated uniform distributions within the focus in contrast to long pulses (50 000 cycles) that produced non-uniform distributions. Fast microbubble destruction occurred for long pulses, whereas microbubble activity was sustained for longer durations for shorter pulses. High-speed microscopy revealed increased mobility in the direction of flow during RaSP sonication. In conclusion, RaSP sequences produced spatiotemporally uniform cavitation distributions and could result in efficient therapies by spreading cavitation throughout the treatment area

Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2

Previous work found that the co-occurring mutations R203K/G204R on the SARS-CoV-2 nucleocapsid (N) protein are increasing in frequency among emerging variants of concern or interest. Through a combination of in silico analyses, this study demonstrates that R203K/G204R are adaptive, while large-scale phylogenetic analyses indicate that R203K/G204R associate with the emergence of the high-transmissibility SARS-CoV-2 lineage B.1.1.7. Competition experiments suggest that the 203K/204R variants possess a replication advantage over the preceding R203/G204 variants, possibly related to ribonucleocapsid (RNP) assembly. Moreover, the 203K/204R virus shows increased infectivity in human lung cells and hamsters. Accordingly, we observe a positive association between increased COVID-19 severity and sample frequency of 203K/204R. Our work suggests that the 203K/204R mutations contribute to the increased transmission and virulence of select SARS-CoV-2 variants. In addition to mutations in the spike protein, mutations in the nucleocapsid protein are important for viral spreading during the pandemic

Prediction of the Lymph Node Status in Patients with Intrahepatic Cholangiocarcinoma: Analysis of 320 Surgical Cases

Purpose: This study was conducted to identify factors involved in lymph node metastasis (LNM) and evaluate their role in predicting LNM in clinically lymph node negative (clinical stage I–III) intrahepatic cholangiocarcinoma (ICC). Materials and Methods: We selected 320 patients who were diagnosed with ICC with no apparent clinical LNM (T1–3N0M0). Age, gender, tumor boundary, histological differentiation, tumor size, and carbohydrate antigen 19-9 value were the studied factors. Univariate and multivariate logistic analysis were conducted. Receiver operating characteristics curve analysis was used to test the predicting value of each factor and a test which combined the associated factors was used to predict LNM. Results: LNM was observed in 76 cases (76/320, 23.8%). Univariate and multivariate analysis showed that histological differentiation as well as tumor boundary and tumor size significantly correlated with LNM. The sensitivity and negative predictive value for LNM for the three factors when combined was 96.1 and 95% respectively. This means that 5% of the patients who did not have the risk factors mentioned above developed LNM. Conclusion: This model used the combination of three factors (low-graded histological differentiation, distinct tumor boundary, small tumor size) and they proved to be useful in predicting LNM in ICC with clinically lymph node negative cases. In patients with these criteria, lymph node dissection or lymph node irradiation may be omitted and such cases may also be good candidates for stereotactic body radiotherapy (SBRT)