The Emu Bay Shale: A unique early Cambrian Lagerstätte from a tectonically active basin.

The Emu Bay Shale (EBS) of South Australia is anomalous among Cambrian Lagerstätten because it captures anatomical information that is rare in Burgess Shale-type fossils, and because of its inferred nearshore setting, the nature of which has remained controversial. Intensive study, combining outcrop and borehole data with a compilation of >25,000 fossil specimens, reveals that the EBS biota inhabited a fan delta complex within a tectonically active basin. Preservation of soft-bodied organisms in this setting is unexpected and further underscores differences between the EBS and other Cambrian Lagerstätten. Environmental conditions, including oxygen fluctuations, slope instability, high suspended sediment concentrations, and episodic high-energy events, inhibited colonization of the lower prodelta by all but a few specialist species but favored downslope transportation and preservation of other largely endemic, shallow-water benthos. The EBS provides extraordinary insight into early Cambrian animal diversity from Gondwana. These results demonstrate how environmental factors determined community composition and provide a framework for understanding this unique Konservat-Lagerstätte.

Three-Dimensional Multi-Frequency Shear Wave Absolute Vibro-Elastography (3D S-WAVE) With a Matrix Array Transducer: Implementation and Preliminary In Vivo Study of the Liver.

Magnetic resonance elastography (MRE) is commonly regarded as the imaging-based gold-standard for liver fibrosis staging, comparable to biopsy. While ultrasound-based elastography methods for liver fibrosis staging have been developed, they are confined to a 1D or a 2D region of interest and to a limited depth. 3D Shear Wave Absolute Vibro-Elastography (S-WAVE) is a steady-state, external excitation, volumetric elastography technique that is similar to MRE, but has the additional advantage of multi-frequency excitation. We present a novel ultrasound matrix array implementation of S-WAVE that takes advantage of 3D imaging. We use a matrix array transducer to sample axial multi-frequency steady-state tissue motion over a volume, using a Color Power Angiography sequence. Tissue motion with the frequency components {40,50,60} and {45,55,65} Hz are acquired over a (90° lateral) × (40° elevational) × (16 cm depth) sector with an acquisition time of 12 seconds. We compute the elasticity map in 3D using local spatial frequency estimation. We characterize this new approach in tissue phantoms against measurements obtained with transient elastography and MRE. Six healthy volunteers and eight patients with chronic liver disease were imaged. Their MRE and S-WAVE volumes were aligned using T1 to B-mode registration for direct comparison in common regions of interest. S-WAVE and MRE results are correlated with R2 = 0.92, while MRE and TE results are correlated with R2 = 0.71. Our findings show that S-WAVE with matrix array has the potential to deliver a similar assessment of liver fibrosis as MRE in a more accessible, inexpensive way, to a broader set of patients.

Comparison of Variations Between Spectral Doppler and Gaussian Surface Integration Methods for Umbilical Vein Blood Volume Flow.

OBJECTIVES: We are studying a new method for estimating blood volume flow that uses 3-dimensional ultrasound to measure the total integrated flux through an ultrasound-generated Gaussian surface that intersects the umbilical cord. This method makes none of the assumptions typically required with standard 1-dimensional spectral Doppler volume flow estimates. We compared the variations in volume flow estimates between techniques in the umbilical vein. METHODS: The study was Institutional Review Board approved, and all 12 patients gave informed consent. Because we had no reference standard for the true umbilical vein volume flow, we compared the variations of the measurements for the flow measurement techniques. At least 3 separate spectral Doppler and 3 separate Gaussian surface measurements were made along the umbilical vein. Means, standard deviations, and coefficients of variation (standard deviation/mean) for the flow estimation techniques were calculated for each patient. P < .05 was considered significant. RESULTS: The ranges of the mean volume flow estimates were 174 to 577 mL/min for the spectral Doppler method and 100 to 341 mL/min for the Gaussian surface integration (GSI) method. The mean standard deviations (mean ± SD) were 161 ± 95 and 45 ± 48 mL/min for the spectral Doppler and GSI methods, respectively (P < .003). The mean coefficients of variation were 0.46 ± 0.17 and 0.18 ± 0.14 for the spectral Doppler and GSI methods respectively (P < 0.002). CONCLUSIONS: The new volume flow estimation method using 3-dimensional ultrasound appears to have significantly less variation in estimates than the standard 1-dimensional spectral Doppler method.

Partial Volume Effect and Correction for 3-D Color Flow Acquisition of Volumetric Blood Flow.

Blood volume flow (VF) estimation is becoming an integral part of quantitative medical imaging. Three-dimensional color flow can be used to measure volumetric flow, but partial volume correction (PVC) is essential due to finite beamwidths and lumen diameters. Color flow power was previously assumed to be directly proportional to the perfused fractional color flow beam area (voxel). We investigate the relationship between color flow power and fractionally perfused voxels. We simulate 3-D color flow imaging using Field II based on a 3.75-MHz mechanically swept linear array. A 16-mm-diameter tube with laminar flow was embedded into soft tissue. We investigated two study scenarios where soft tissue backscatter is 1) 40 dB higher and 2) 40 dB lower, relative to blood. Velocity and power were computed from color flow packets ( n = 16 ) using autocorrelation. Study 1 employed a convolution-based wall filter. Study 2 did not employ a wall filter. VF was computed from the resulting color flow data, as published previously. Partial volume voxels in Study 1 show lesser power than those in Study 2, likely due to wall filter effects. An "S"-shaped relationship was found between color flow power and fractionally perfused voxel area in Study 2, which could be due to an asymmetric lateral-elevational point spread function. Flow computation is biased low by 7.3% and 7.9% in Study 1 and Study 2, respectively. Uncorrected simulation estimates are biased high by 41.5% and 12.5% in Study 1 and Study 2, respectively. Our findings show that PVC improves 3-D VF estimation and that wall filter processing alters the proportionality between color flow power and fractionally perfused voxel area.

Pilot study of the potential of 3D ultrasound to measure tonsillar volume and hypertrophy.

OBJECTIVE: Obstructive sleep apnea (OSA), results in approximately 4-5 million outpatient visits per year in the United States. In pediatric patients, OSA is primarily caused by adenotonsillar hypertrophy, and therefore, adenotonsillectomy remains an effective surgical treatment. We investigate whether 3D ultrasound (3DUS) imaging can accurately and objectively assess tonsillar hypertrophy for the potential identification and stratification of candidates for adenotonsillectomy. METHODS: A prospective study was performed evaluating pediatric patients (N = 17) between the ages of 4-14 years who were undergoing adenotonsillectomy for OSA symptoms. On the day of surgery, tonsillar ultrasound was performed by a single attending radiologist. Tonsillectomy was performed and each tonsils' principal axes and physical volume by water submergence were measured. The findings were compared using paired T-test, Pearson correlation coefficient and Bland-Altman analysis. RESULTS: The average tonsillar physical measurements of length, width and height were 1.54 ± 0.28, 2.0 ± 0.31 cm and 2.72 ± 0.41 cm, and 1.73 ± 0.17, 1.61 ± 0.21 mm and 2.98 ± 0.28 mm from physical and 3DUS estimations, respectively (P < 0.001 for all measurements). The average tonsillar volume was 3.84 ± 1.23 ml and 4.30 ± 1.15 ml from physical and 3DUS measurements, respectively (p = 0.04). The Bland-Altman mean difference ±â€¯95% limit of agreement between length, width, height, and volume results from the two measurements were -0.186 ± 2.01 cm, -0.393 ± 6.33 cm, 0.25 ± 7.71 cm, and 0.45 ± 2.32 ml, respectively. CONCLUSION: While 3DUS is feasible, it may not be an accurate estimate of tonsillar volume for assessing hypertrophy. A larger study will be required to establish the accuracy of 3DUS measurements of tonsillar volume.

In Vivo Validation of Volume Flow Measurements of Pulsatile Flow Using a Clinical Ultrasound System and Matrix Array Transducer.

The goal of this study was to evaluate the accuracy of a non-invasive C-plane Doppler estimation of pulsatile blood flow in the lower abdominal vessels of a porcine model. Doppler ultrasound measurements from a matrix array transducer system were compared with invasive volume flow measurements made on the same vessels with a surgically implanted ultrasonic transit-time flow probe. For volume flow rates ranging from 60 to 750 mL/min, agreement was very good, with a Pearson correlation coefficient of 0.97 (p < 0.0001) and a mean bias of -4.2%. The combination of 2-D matrix array technology and fast processing gives this Doppler method clinical potential, as many of the user- and system-dependent parameters of previous methods, including explicit vessel angle and diameter measurements, are eliminated.

Renal Segmentation From 3D Ultrasound via Fuzzy Appearance Models and Patient-Specific Alpha Shapes.

Ultrasound (US) imaging is the primary imaging modality for pediatric hydronephrosis, which manifests as the dilation of the renal collecting system (CS). In this paper, we present a new framework for the segmentation of renal structures, kidney and CS, from 3DUS scans. First, the kidney is segmented using an active shape model-based approach, tailored to deal with the challenges raised by US images. A weighted statistical shape model allows to compensate the image variation with the propagation direction of the US wavefront. The model is completed with a new fuzzy appearance model and a multi-scale omnidirectional Gabor-based appearance descriptor. Next, the CS is segmented using an active contour formulation, which combines contour- and intensity-based terms. The new positive alpha detector presented here allows to control the propagation process by means of a patient-specific stopping function created from the bands of adipose tissue within the kidney. The performance of the new segmentation approach was evaluated on a dataset of 39 cases, showing an average Dice's coefficient of 0.86±0.05 for the kidney, and 0.74 ± 0.10 for the CS segmentation, respectively. These promising results demonstrate the potential utility of this framework for the US-based assessment of the severity of pediatric hydronephrosis.

A hierarchical model for automated breast lesion detection from ultrasound 3D data.

Ultrasound imaging plays an important role in breast cancer screening for which early and accurate lesion detection is crucial for clinical practice. Many researches were performed on supporting the breast lesion detection based on ultrasound data. In the paper, a novel hierarchical model is proposed to automatically detect breast lesion from ultrasound 3D data. The model simultaneously considers the data information from low-level to high-level for the detection by processing with a joint probability. For each layer of the model, the corresponding algorithm is performed to denote the certain level image information. A dynamic programming approach is applied to efficiently obtain the optimal solution. With a preliminary dataset, the superior performance of the proposed model has been demonstrated for the automated detection of breast lesion with 0.375 false positive per case at 91.7% sensitivity.

Quantification of kidneys from 3D ultrasound in pediatric hydronephrosis.

This paper introduces a complete framework for the quantification of renal structures (parenchyma, and collecting system) in 3D ultrasound (US) images. First, the segmentation of the kidney is performed using Gabor-based appearance models (GAM), a variant of the popular active shape models, properly tailored to the imaging physics of US image data. The framework also includes a new graph-cut based method for the segmentation of the collecting system, including brightness and contrast normalization, and positional prior information. The significant advantage (p = 0.03) of the new method over previous approaches in terms of segmentation accuracy has been successfully verified on clinical 3DUS data from pediatric cases with hydronephrosis. The promising results obtained in the estimation of the volumetric hydronephrosis index demonstrate the potential of our new framework to quantify anatomy in US and asses the severity of hydronephrosis.

A new vetulicolian from Australia and its bearing on the chordate affinities of an enigmatic Cambrian group.

BACKGROUND: Vetulicolians are one of the most problematic and controversial Cambrian fossil groups, having been considered as arthropods, chordates, kinorhynchs, or their own phylum. Mounting evidence suggests that vetulicolians are deuterostomes, but affinities to crown-group phyla are unresolved. RESULTS: A new vetulicolian from the Emu Bay Shale Konservat-Lagerstätte, South Australia, Nesonektris aldridgei gen. et sp. nov., preserves an axial, rod-like structure in the posterior body region that resembles a notochord in its morphology and taphonomy, with notable similarity to early decay stages of the notochord of extant cephalochordates and vertebrates. Some of its features are also consistent with other structures, such as a gut or a coelomic cavity. CONCLUSIONS: Phylogenetic analyses resolve a monophyletic Vetulicolia as sister-group to tunicates (Urochordata) within crown Chordata, and this holds even if they are scored as unknown for all notochord characters. The hypothesis that the free-swimming vetulicolians are the nearest relatives of tunicates suggests that a perpetual free-living life cycle was primitive for tunicates. Characters of the common ancestor of Vetulicolia + Tunicata include distinct anterior and posterior body regions - the former being non-fusiform and used for filter feeding and the latter originally segmented - plus a terminal mouth, absence of pharyngeal bars, the notochord restricted to the posterior body region, and the gut extending to the end of the tail.

Acute vision in the giant Cambrian predator Anomalocaris and the origin of compound eyes.

Until recently, intricate details of the optical design of non-biomineralized arthropod eyes remained elusive in Cambrian Burgess-Shale-type deposits, despite exceptional preservation of soft-part anatomy in such Konservat-Lagerstätten. The structure and development of ommatidia in arthropod compound eyes support a single origin some time before the latest common ancestor of crown-group arthropods, but the appearance of compound eyes in the arthropod stem group has been poorly constrained in the absence of adequate fossils. Here we report 2-3-cm paired eyes from the early Cambrian (approximately 515 million years old) Emu Bay Shale of South Australia, assigned to the Cambrian apex predator Anomalocaris. Their preserved visual surfaces are composed of at least 16,000 hexagonally packed ommatidial lenses (in a single eye), rivalling the most acute compound eyes in modern arthropods. The specimens show two distinct taphonomic modes, preserved as iron oxide (after pyrite) and calcium phosphate, demonstrating that disparate styles of early diagenetic mineralization can replicate the same type of extracellular tissue (that is, cuticle) within a single Burgess-Shale-type deposit. These fossils also provide compelling evidence for the arthropod affinities of anomalocaridids, push the origin of compound eyes deeper down the arthropod stem lineage, and indicate that the compound eye evolved before such features as a hardened exoskeleton. The inferred acuity of the anomalocaridid eye is consistent with other evidence that these animals were highly mobile visual predators in the water column. The existence of large, macrophagous nektonic predators possessing sharp vision--such as Anomalocaris--within the early Cambrian ecosystem probably helped to accelerate the escalatory 'arms race' that began over half a billion years ago.

Modern optics in exceptionally preserved eyes of Early Cambrian arthropods from Australia.

Despite the status of the eye as an "organ of extreme perfection", theory suggests that complex eyes can evolve very rapidly. The fossil record has, until now, been inadequate in providing insight into the early evolution of eyes during the initial radiation of many animal groups known as the Cambrian explosion. This is surprising because Cambrian Burgess-Shale-type deposits are replete with exquisitely preserved animals, especially arthropods, that possess eyes. However, with the exception of biomineralized trilobite eyes, virtually nothing is known about the details of their optical design. Here we report exceptionally preserved fossil eyes from the Early Cambrian (∼ 515 million years ago) Emu Bay Shale of South Australia, revealing that some of the earliest arthropods possessed highly advanced compound eyes, each with over 3,000 large ommatidial lenses and a specialized 'bright zone'. These are the oldest non-biomineralized eyes known in such detail, with preservation quality exceeding that found in the Burgess Shale and Chengjiang deposits. Non-biomineralized eyes of similar complexity are otherwise unknown until about 85 million years later. The arrangement and size of the lenses indicate that these eyes belonged to an active predator that was capable of seeing in low light. The eyes are more complex than those known from contemporaneous trilobites and are as advanced as those of many living forms. They provide further evidence that the Cambrian explosion involved rapid innovation in fine-scale anatomy as well as gross morphology, and are consistent with the concept that the development of advanced vision helped to drive this great evolutionary event.

On the stability of the effective apodization of the nonlinearly generated second harmonic with respect to range.

The concept of an effective apodization was introduced to describe the field pattern for the nonlinearly generated second harmonic (2f) within the focal zone using a linear propagation model. Our objective in this study was to investigate the validity of the concept of an effective apodization at 2f as an approach to approximating the field of the second harmonic over a wide range of depths. Two experimental setups were employed: a vascular imaging array with a water path and an adult cardiac imaging array with an attenuating liver path. In both cases the spatial dependencies of the ultrasonic fields were mapped by scanning a point-like hydrophone within a series of planes orthogonal to the propagation direction. The sampling distances were located before, within, and beyond the focal zone. The signals were Fourier transformed and the complex values at 2f were linearly backpropagated to the transmit plane in order to obtain an effective apodization. The measured results demonstrated a relatively constant effective apodization at 2f as a function of propagation distance. Finite amplitude computer simulations were found to be in agreement with these measurements. Thus the measure of the effective apodization at 2f provides an approximation to the second harmonic field outside the focal zone.

Spatial coherence of backscatter for the nonlinearly produced second harmonic for specific transmit apodizations.

To be successful, correlation-based, phase-aberration correction requires a high correlation among backscattered signals. For harmonic imaging, the spatial coherence of backscatter for the second harmonic component is different than the spatial coherence of backscatter for the fundamental component. The purpose of this work was to determine the effect of changing the transmit apodization on the spatial coherence of backscatter for the nonlinearly generated second harmonic. Our approach was to determine the effective apodizations for the fundamental and second harmonic using both experimental measurements and simulations. Two-dimensional measurements of the transverse cross sections of the finite-amplitude ultrasonic fields generated by rectangular and circular apertures were acquired with a hydrophone. Three different one-dimensional transmit apodization functions were investigated: uniform, Riesz, and trapezoidal. An effective apodization was obtained for each transmit apodization by backpropagating the values measured from within the transmit focal zone using a linear angular spectrum approach. Predictions of the spatial coherence of backscatter were obtained using the pulse-echo Van Cittert-Zernike theorem. In all cases the effective apodization at 2f was narrower than the transmit apodization. We demonstrate that certain transmit apodizations result in a greater spatial coherence of backscatter at the second harmonic than at the fundamental.

Spatial coherence of the nonlinearly generated second harmonic portion of backscatter for a clinical imaging system.

Correlation-based approaches to phase aberration correction rely on the spatial coherence of backscattered signals. The spatial coherence of backscatter from speckle-producing targets is predicted by the auto correlation of the transmit apodization (Van Cittert-Zernike theorem). Work by others indicates that the second harmonic beam has a wider mainlobe with lower sidelobes than a beam transmitted at 2f. The purpose of this paper is to demonstrate that the spatial coherence of backscatter for the second harmonic is different from that of the fundamental, as would be anticipated from applying the Van Cittert-Zernike theorem to the reported measurements of the second harmonic field. Another objective of this work is to introduce the concept of the effective apodization and to verify that the effective apodization of the second harmonic is narrower than the transmit apodization. The spatial coherence of backscatter was measured using three clinical arrays with a modified clinical imaging system. The spatial coherence results were verified using a pseudo-array scan in a transverse plane of the transmitted field with a hydrophone. An effective apodization was determined by backpropagating these values using a linear angular spectrum approach. The spatial coherence for the harmonic portion of backscatter differed systematically and significantly from the auto correlation of the transmit apodization.