Quantitative Viscoelastic Response (QVisR): Direct Estimation of Viscoelasticity with Neural Networks.

We present a machine learning method to directly estimate viscoelastic moduli from displacement time-series profiles generated by Viscoelastic Response (VisR) ultrasound excitations. VisR uses two colocalized acoustic radiation force pushes to approximate tissue viscoelastic creep response and tracks displacements on-axis to measure the material relaxation. A fully-connected neural network is trained to learn a nonlinear mapping from VisR displacements, the push focal depth, and the measurement axial depth to the material elastic and viscous moduli. In this work, we assess the validity of Quantitative Viscoelastic Response (QVisR) in simulated materials, propose a method of domain adaption to phantom VisR displacements, and show in vivo estimates from a clinically acquired dataset.

It's the little THANGS: Recording frequently unreported errors for dosimetry quality improvement.

The reporting of errors resulting in dose deviations are well-studied. Less studied is the amount of inconsequential errors that will not harm the patient but could lead to inefficiency. This paper reports an institutional effort to quantify and reduce these less significant errors. Dosimetry items discovered during physicist plan/record and verify (R&V) check prior to treatment were recorded in a shared document and called Therapy Anomaly Gathering System (THANGS) and individual items were called a "thang." Items were categorized to 1 of 4 types: Treatment Plan, Plan Document, R&V, and Secondary MU. The aggregate numbers were presented to the dosimetry staff at regular staff meetings. It was emphasized to the staff that this was a Quality Improvement (QI) study and would not be used punitively. Thangs were tracked over a 4-year period. In Q1 of year 1 of the study, the average number of errors identified was 179/month. This was reduced to 114/month by Q4 of year 1 and 68/month by the end of year 4, a 62% reduction. The number of errors/plan in Q1 Year 1 was 1.25, and that was reduced by Q4 Year 4 to 0.4, a 68% reduction. The percentage of errors by type did not vary much over the 4 years. By far, R&V errors were the most common, and QI efforts were primarily aimed at them. We have developed a simple method to identify areas in dosimetric work that are vulnerable to minor errors and, through consistent reminders, drastically reduce them. This leads to a seamless throughput for a given plan ultimately resulting in improved physics, therapist, and most importantly patient satisfaction.

A kilonova following a long-duration gamma-ray burst at 350 Mpc.

Gamma-ray bursts (GRBs) are divided into two populations1,2; long GRBs that derive from the core collapse of massive stars (for example, ref. 3) and short GRBs that form in the merger of two compact objects4,5. Although it is common to divide the two populations at a gamma-ray duration of 2 s, classification based on duration does not always map to the progenitor. Notably, GRBs with short (≲2 s) spikes of prompt gamma-ray emission followed by prolonged, spectrally softer extended emission (EE-SGRBs) have been suggested to arise from compact object mergers6-8. Compact object mergers are of great astrophysical importance as the only confirmed site of rapid neutron capture (r-process) nucleosynthesis, observed in the form of so-called kilonovae9-14. Here we report the discovery of a possible kilonova associated with the nearby (350 Mpc), minute-duration GRB 211211A. The kilonova implies that the progenitor is a compact object merger, suggesting that GRBs with long, complex light curves can be spawned from merger events. The kilonova of GRB 211211A has a similar luminosity, duration and colour to that which accompanied the gravitational wave (GW)-detected binary neutron star (BNS) merger GW170817 (ref. 4). Further searches for GW signals coincident with long GRBs are a promising route for future multi-messenger astronomy.

Development of a Robotic Shear Wave Elastography System for Noninvasive Staging of Liver Disease in Murine Models.

Shear wave elastography (SWE) is an ultrasound-based stiffness quantification technology that is used for noninvasive liver fibrosis assessment. However, despite widescale clinical adoption, SWE is largely unused by preclinical researchers and drug developers for studies of liver disease progression in small animal models due to significant experimental, technical, and reproducibility challenges. Therefore, the aim of this work was to develop a tool designed specifically for assessing liver stiffness and echogenicity in small animals to better enable longitudinal preclinical studies. A high-frequency linear array transducer (12-24 MHz) was integrated into a robotic small animal ultrasound system (Vega; SonoVol, Inc., Durham, NC) to perform liver stiffness and echogenicity measurements in three dimensions. The instrument was validated with tissue-mimicking phantoms and a mouse model of nonalcoholic steatohepatitis. Female C57BL/6J mice (n = 40) were placed on choline-deficient, L-amino acid-defined, high-fat diet and imaged longitudinally for 15 weeks. A subset was sacrificed after each imaging timepoint (n = 5) for histological validation, and analyses of receiver operating characteristic (ROC) curves were performed. Results demonstrated that robotic measurements of echogenicity and stiffness were most strongly correlated with macrovesicular steatosis (R2  = 0.891) and fibrosis (R2  = 0.839), respectively. For diagnostic classification of fibrosis (Ishak score), areas under ROC (AUROCs) curves were 0.969 for ≥Ishak1, 0.984 for ≥Ishak2, 0.980 for ≥Ishak3, and 0.969 for ≥Ishak4. For classification of macrovesicular steatosis (S-score), AUROCs were 1.00 for ≥S2 and 0.997 for ≥S3. Average scanning and analysis time was <5 minutes/liver. Conclusion: Robotic SWE in small animals is feasible and sensitive to small changes in liver disease state, facilitating in vivo staging of rodent liver disease with minimal sonographic expertise.

Validation of a combined ultrasound and bioluminescence imaging system with magnetic resonance imaging in orthotopic pancreatic murine tumors.

Preclinical mouse solid tumor models are widely used to evaluate efficacy of novel cancer therapeutics. Recent reports have highlighted the need for utilizing orthotopic implantation to represent clinical disease more accurately, however the deep tissue location of these tumors makes longitudinal assessment challenging without the use of imaging techniques. The purpose of this study was to evaluate the performance of a new multi-modality high-throughput in vivo imaging system that combines bioluminescence imaging (BLI) with robotic, hands-free ultrasound (US) for evaluating orthotopic mouse models. Long utilized in cancer research as independent modalities, we hypothesized that the combination of BLI and US would offer complementary advantages of detection sensitivity and quantification accuracy, while mitigating individual technological weaknesses. Bioluminescent pancreatic tumor cells were injected into the pancreas tail of C57BL/6 mice and imaged weekly with the combination system and magnetic resonance imaging (MRI) to serve as a gold standard. BLI photon flux was quantified to assess tumor activity and distribution, and US and MRI datasets were manually segmented for gross tumor volume. Robotic US and MRI demonstrated a strong agreement (R2 = 0.94) for tumor volume measurement. BLI showed a weak overall agreement with MRI (R2 = 0.21), however, it offered the greatest sensitivity to detecting the presence of tumors. We conclude that combining BLI with robotic US offers an efficient screening tool for orthotopic tumor models.

Use of 3D Robotic Ultrasound for In Vivo Analysis of Mouse Kidneys.

Common modalities for in vivo imaging of rodents include positron emission tomography (PET), computed tomography (CT), magnetic resonance imaging (MRI), and ultrasound (US). Each method has limitations and advantages, including availability, ease of use, cost, size, and the use of ionizing radiation or magnetic fields. This protocol describes the use of 3D robotic US for in vivo imaging of rodent kidneys and heart, subsequent data analysis, and possible research applications. Practical applications of robotic US are the quantification of total kidney volume (TKV), as well as the measurement of cysts, tumors, and vasculature. Although the resolution is not as high as other modalities, robotic US allows for more practical high throughput data collection. Furthermore, using US M-mode imaging, cardiac function may be quantified. Since the kidneys receive 20%-25% of the cardiac output, assessing cardiac function is critical to the understanding of kidney physiology and pathophysiology.

Testing general relativity with gravitational-wave catalogs: The insidious nature of waveform systematics.

Gravitational-wave observations of binary black holes allow new tests of general relativity (GR) to be performed on strong, dynamical gravitational fields. These tests require accurate waveform models of the gravitational-wave signal; otherwise waveform errors can erroneously suggest evidence for new physics. Existing waveforms are generally thought to be accurate enough for current observations, and each of the events observed to date appears to be individually consistent with GR. In the near future, with larger gravitational-wave catalogs, it will be possible to perform more stringent tests of gravity by analyzing large numbers of events together. However, there is a danger that waveform errors can accumulate among events: even if the waveform model is accurate enough for each individual event, it can still yield erroneous evidence for new physics when applied to a large catalog. This paper presents a simple linearized analysis, in the style of a Fisher matrix calculation that reveals the conditions under which the apparent evidence for new physics due to waveform errors grows as the catalog size increases. We estimate that, in the worst-case scenario, evidence for a deviation from GR might appear in some tests using a catalog containing as few as 10 - 30 events above a signal-to-noise ratio of 20. This is close to the size of current catalogs and highlights the need for caution when performing these sorts of experiments.

Substrate-dependent effects of quaternary structure on RNase E activity.

RNase E is an essential, multifunctional ribonuclease encoded in E. coli by the rne gene. Structural analysis indicates that the ribonucleolytic activity of this enzyme is conferred by rne-encoded polypeptide chains that (1) dimerize to form a catalytic site at the protein-protein interface, and (2) multimerize further to generate a tetrameric quaternary structure consisting of two dimerized Rne-peptide chains. We identify here a mutation in the Rne protein's catalytic region (E429G), as well as a bacterial cell wall peptidoglycan hydrolase (Amidase C [AmiC]), that selectively affect the specific activity of the RNase E enzyme on long RNA substrates, but not on short synthetic oligonucleotides, by enhancing enzyme multimerization. Unlike the increase in specific activity that accompanies concentration-induced multimerization, enhanced multimerization associated with either the E429G mutation or interaction of the Rne protein with AmiC is independent of the substrate's 5' terminus phosphorylation state. Our findings reveal a previously unsuspected substrate length-dependent regulatory role for RNase E quaternary structure and identify cis-acting and trans-acting factors that mediate such regulation.

Constraining the Lensing of Binary Black Holes from Their Stochastic Background.

Gravitational waves (GWs) are subject to gravitational lensing in the same way as electromagnetic radiation. However, to date, no unequivocal observation of a lensed GW transient has been reported. Independently, GW observatories continue to search for the stochastic GW signal that is produced by many transient events at high redshift. We exploit a surprising connection between the lensing of individual transients and limits to the background radiation produced by the unresolved population of binary back hole mergers: we show that it constrains the fraction of individually resolvable lensed binary black holes to less than ∼4×10^{-5} at present sensitivity. We clarify the interpretation of existing, low redshift GW observations (obtained assuming no lensing) in terms of their apparent lensed redshifts and masses and explore constraints from GW observatories at future sensitivity. Based on our results, recent claims of observations of lensed events are statistically disfavored.

Recognition of Dimeric Lewis X by Anti-Dimeric Lex Antibody SH2.

The carbohydrate antigen dimeric Lewis X (DimLex), which accumulates in colonic and liver adenocarcinomas, is a valuable target to develop anti-cancer therapeutics. Using the native DimLex antigen as a vaccine would elicit an autoimmune response against the Lex antigen found on normal, healthy cells. Thus, we aim to study the immunogenic potential of DimLex and search internal epitopes displayed by DimLex that remain to be recognized by anti-DimLex monoclonal antibodies (mAbs) but no longer possess epitopes recognized by anti-Lex mAbs. In this context, we attempted to map the epitope recognized by anti-DimLex mAb SH2 by titrations and competitive inhibition experiments using oligosaccharide fragments of DimLex as well as Lex analogues. We compare our results with that reported for anti-Lex mAb SH1 and anti-polymeric Lex mAbs 1G5F6 and 291-2G3-A. While SH1 recognizes an epitope localized to the non-reducing end Lex trisaccharide, SH2, 1G5F6, and 291-2G3-A have greater affinity for DimLex conjugates than for Lex conjugates. We show, however, that the Lex trisaccharide is still an important recognition element for SH2, which (like 1G5F6 and 291-2G3-A) makes contacts with all three sugar units of Lex. In contrast to mAb SH1, anti-polymeric Lex mAbs make contact with the GlcNAc acetamido group, suggesting that epitopes extend further from the non-reducing end Lex. Results with SH2 show that this epitope is only recognized when DimLex is presented by glycoconjugates. We have reported that DimLex adopts two conformations around the ß-d-GlcNAc-(1→3)-d-Gal bond connecting the Lex trisaccharides. We propose that only one of these conformations is recognized by SH2 and that this conformation is favored when the hexasaccharide is presented as part of a glycoconjugate such as DimLex-bovine serum albumin (DimLex-BSA). Proper presentation of the oligosaccharide candidate via conjugation to a protein or lipid is essential for the design of an anti-cancer vaccine or immunotherapeutic based on DimLex.

Divergent rRNAs as regulators of gene expression at the ribosome level.

It is generally assumed that each organism has evolved to possess a unique ribosomal RNA (rRNA) species optimal for its physiological needs. However, some organisms express divergent rRNAs, the functional roles of which remain unknown. Here, we show that ribosomes containing the most variable rRNAs, encoded by the rrnI operon (herein designated as I-ribosomes), direct the preferential translation of a subset of mRNAs in Vibrio vulnificus, enabling the rapid adaptation of bacteria to temperature and nutrient shifts. In addition, genetic and functional analyses of I-ribosomes and target mRNAs suggest that both I-ribosomal subunits are required for the preferential translation of specific mRNAs, the Shine-Dalgarno sequences of which do not play a critical role in I-ribosome binding. This study identifies genome-encoded divergent rRNAs as regulators of gene expression at the ribosome level, providing an additional level of regulation of gene expression in bacteria in response to environmental changes.

Corrections to "On the Quantitative Potential of Viscoelastic Response (VisR) Ultrasound Using the One-Dimensional Mass-Spring-Damper Model".

In the original publication of this paper [1], equation (3) contained sign errors for the amplitude of the third and fourth Heaviside functions. The corrected equation is shown in the following: [Formula: see text].

In Vivo Viscoelastic Response (VisR) Ultrasound for Characterizing Mechanical Anisotropy in Lower-Limb Skeletal Muscles of Boys with and without Duchenne Muscular Dystrophy.

Our group has previously found that in silico, mechanical anisotropy may be interrogated by exciting transversely isotropic materials with geometrically asymmetric acoustic radiation force excitations and then monitoring the associated induced displacements in the region of excitation. We now translate acoustic radiation force-based anisotropy assessment to human muscle in vivo and investigate its clinical relevance to monitoring muscle degeneration in Duchenne muscular dystrophy (DMD). Clinical anisotropy assessments were performed using Viscoelastic Response ultrasound, with a degree of anisotropy reflected by the ratios of Viscoelastic Response relative elasticity (RE) or relative viscosity (RV) measured with the asymmetric radiation force oriented parallel versus perpendicular to muscle fiber alignment. In vivo results from rectus femoris and gastrocnemius muscles of boys aged ∼7.9-10.4 y indicate that RE and RV anisotropy ratios in rectus femoris muscles of boys with DMD were significantly higher than those of healthy control boys (RE: DMD = 1.51 ± 0.87, control = 0.99 ± 0.69, p = 0.04, Wilcoxon rank sum test; RV: DMD = 1.04 ± 0.71, control = 0.74 ± 0.22, p = 0.02). In the gastrocnemius muscle, only the RV anisotropy ratio was significantly higher in dystrophic than control patients (DMD = 1.23 ± 0.35, control = 0.88 ± 0.31, p = 0.04). In the dystrophic rectus femoris muscle, the RE anisotropy ratio was inversely correlated (slope = -0.03/lbf, r = -0.43, p = 0.07, Pearson correlation) with quantitative muscle testing functional output measures but was not correlated with quantitative muscle testing in the dystrophic gastrocnemius. These results suggest that Viscoelastic Response RE and RV measures reflect differences in mechanical anisotropy associated with functional impairment with dystrophic degeneration that are relevant to monitoring DMD clinically.

Results from a clinical trial evaluating the efficacy of real-time body surface visual feedback in reducing patient motion during lung cancer radiotherapy.

INTRODUCTION: Optical surface measurement devices are a maturing technology in radiotherapy. The challenge for such devices is to demonstrate how they can improve clinical care. We present results from a phase 1 clinical trial designed to test the hypothesis that if presented with live data from a novel optical measurement device, showing their deviation from an ideal radiotherapy treatment position, patients will be able to better control their motion and increase their geometrical conformance. METHOD AND MATERIALS: Fourteen lung cancer patients were enrolled in a prospective clinical study and asked to use a variety of visual feedback schema from a novel in-house developed optical surface measurement device. The magnitude and regularity of their body surface motion using the different schema was compared to that when free-breathing at three time-points throughout their radiotherapy treatment schedule. Additionally, 4D Cone Beam CT data, acquired simultaneously with the optical measurements, was used to test if improvements in external motion are reflected in changes in internal tumor motion. RESULTS: The primary endpoint of the trial, device tolerability assessed by the fraction of participants completing all study sessions, was 86%. Secondary endpoints showed that use of the visual feedback device was found to statistically significantly decrease body surface motion magnitude by an average of 17% over the study cohort, although not universally. Similarly body surface motion variability was decreased by 18% on average. Internal tumor motion magnitude was also found to be statistically significantly decreased by an average of 14% when using the feedback device. Reduction in external motion was predictive of reduced internal motion but no evidence of a simple correlation between changes in internal and external motion magnitude was found. CONCLUSIONS: Visual feedback of live motion is well tolerated by lung cancer patients and can reduce both body surface and tumor motion.

Long-Lived Inverse Chirp Signals from Core-Collapse in Massive Scalar-Tensor Gravity.

This Letter considers stellar core collapse in massive scalar-tensor theories of gravity. The presence of a mass term for the scalar field allows for dramatic increases in the radiated gravitational wave signal. There are several potential smoking gun signatures of a departure from general relativity associated with this process. These signatures could show up within existing LIGO-Virgo searches.

Acoustic Radiation Force Impulse (ARFI)-Induced Peak Displacements Reflect Degree of Anisotropy in Transversely Isotropic Elastic Materials.

In transversely isotropic (TI) materials, mechanical properties (Young's modulus, shear modulus, and Poisson's ratio) are different along versus across the axis of symmetry (AoS). In this work, the feasibility of interrogating such directional mechanical property differences using acoustic radiation force impulse (ARFI) imaging is investigated. We herein test the hypotheses that 1) ARFI-induced peak displacements (PDs) vary with TI material orientations when an asymmetrical ARFI excitation point spread function (PSF) is used, but not when a symmetrical ARFI PSF is employed; and 2) the ratio of PDs induced with the long axis of an asymmetrical ARFI PSF oriented along versus across the material's AoS is related to the degree of anisotropy of the material. These hypotheses were tested in silico using finite element method (FEM) models and Field II. ARFI excitations had F/1.5, 3, 4, or 5 focal configurations, with the F/1.5 and F/5 cases having the most asymmetrical and symmetrical PSFs at the focal depth, respectively. These excitations were implemented for ARFI imaging in 52 different simulated TI materials with varying degrees of anisotropy, and the ratio of ARFI-induced PDs was calculated. The change in the ratio of PDs with respect to the anisotropy of the materials was highest for the F/1.5, indicating that PD was most strongly impacted by the material orientation when the ARFI excitation was the most asymmetrical. On the contrary, the ratio of PDs did not depend on the anisotropy of the material for the F/5 ARFI excitation, suggesting that PD did not depend on material orientation when the ARFI excitation was symmetrical. Finally, the ratio of PDs achieved using asymmetrical ARFI PSF reflected the degree of anisotropy in TI materials. These results support that symmetrical ARFI focal configurations are desirable when the orientation of the ARFI excitation to the AoS is not specifically known and measurement standardization is important, such as for longitudinal or cross-sectional studies of anisotropic organs. However, asymmetrical focal configurations are useful for exploiting anisotropy, which may be diagnostically relevant. Feasibility for future experimental implementation is demonstrated by simulating ultrasonic displacement tracking and by varying the ARF duration.

Astrometric Search Method for Individually Resolvable Gravitational Wave Sources with Gaia.

Gravitational waves (GWs) cause the apparent position of distant stars to oscillate with a characteristic pattern on the sky. Astrometric measurements (e.g., those made by Gaia) provide a new way to search for GWs. The main difficulty facing such a search is the large size of the data set; Gaia observes more than one billion stars. In this Letter the problem of searching for GWs from individually resolvable supermassive black hole binaries using astrometry is addressed for the first time; it is demonstrated how the data set can be compressed by a factor of more than 10^{6}, with a loss of sensitivity of less than 1%. This technique was successfully used to recover artificially injected GW signals from mock Gaia data and to assess the GW sensitivity of Gaia. Throughout the Letter the complementarity of Gaia and pulsar timing searches for GWs is highlighted.

Black Hole Kicks as New Gravitational Wave Observables.

Generic black hole binaries radiate gravitational waves anisotropically, imparting a recoil, or kick, velocity to the merger remnant. If a component of the kick along the line of sight is present, gravitational waves emitted during the final orbits and merger will be gradually Doppler shifted as the kick builds up. We develop a simple prescription to capture this effect in existing waveform models, showing that future gravitational wave experiments will be able to perform direct measurements, not only of the black hole kick velocity, but also of its accumulation profile. In particular, the eLISA space mission will measure supermassive black hole kick velocities as low as ∼500 km s^{-1}, which are expected to be a common outcome of black hole binary coalescence following galaxy mergers. Black hole kicks thus constitute a promising new observable in the growing field of gravitational wave astronomy.

On the Quantitative Potential of Viscoelastic Response (VisR) Ultrasound Using the One-Dimensional Mass-Spring-Damper Model.

Viscoelastic response (VisR) ultrasound is an acoustic radiation force (ARF)-based imaging method that fits induced displacements to a one-dimensional (1-D) mass-spring-damper (MSD) model to estimate the ratio of viscous to elastic moduli, τ, in viscoelastic materials. Error in VisR τ estimation arises from inertia and acoustic displacement underestimation. These error sources are herein evaluated using finite-element method (FEM) simulations, error correction methods are developed, and corrected VisR τ estimates are compared with true simulated τ values to assess VisR's relevance to quantifying viscoelasticity. With regard to inertia, adding a mass term in series with the Voigt model, to achieve the MSD model, accounts for inertia due to tissue mass when ideal point force excitations are used. However, when volumetric ARF excitations are applied, the induced complex system inertia is not described by the single-degree-of-freedom MSD model, causing VisR to overestimate τ. Regarding acoustic displacement underestimation, associated deformation of ARF-induced displacement profiles further distorts VisR τ estimates. However, median error in VisR τ is reduced to approximately -10% using empirically derived error correction functions applied to simulated viscoelastic materials with viscous and elastic properties representative of tissue. The feasibility of corrected VisR imaging is then demonstrated in vivo in the rectus femoris muscle of an adult with no known neuromuscular disorders. These results suggest VisR's potential relevance to quantifying viscoelastic properties clinically.