External validation of a deep learning algorithm for automated echocardiographic strain measurements

Aims

Echocardiographic strain imaging reflects myocardial deformation and is a sensitive measure of cardiac function and wall-motion abnormalities. Deep learning (DL) algorithms could automate the interpretation of echocardiographic strain imaging.

Methods and results

We developed and trained an automated DL-based algorithm for left ventricular (LV) strain measurements in an internal dataset. Global longitudinal strain (GLS) was validated externally in (i) a real-world Taiwanese cohort of participants with and without heart failure (HF), (ii) a core-lab measured dataset from the multinational prevalence of microvascular dysfunction-HF and preserved ejection fraction (PROMIS-HFpEF) study, and regional strain in (iii) the HMC-QU-MI study of patients with suspected myocardial infarction. Outcomes included measures of agreement [bias, mean absolute difference (MAD), root-mean-squared-error (RMSE), and Pearson's correlation (R)] and area under the curve (AUC) to identify HF and regional wall-motion abnormalities. The DL workflow successfully analysed 3741 (89%) studies in the Taiwanese cohort, 176 (96%) in PROMIS-HFpEF, and 158 (98%) in HMC-QU-MI. Automated GLS showed good agreement with manual measurements (mean ± SD): -18.9 ± 4.5% vs. -18.2 ± 4.4%, respectively, bias 0.68 ± 2.52%, MAD 2.0 ± 1.67, RMSE = 2.61, R = 0.84 in the Taiwanese cohort; and -15.4 ± 4.1% vs. -15.9 ± 3.6%, respectively, bias -0.65 ± 2.71%, MAD 2.19 ± 1.71, RMSE = 2.78, R = 0.76 in PROMIS-HFpEF. In the Taiwanese cohort, automated GLS accurately identified patients with HF (AUC = 0.89 for total HF and AUC = 0.98 for HF with reduced ejection fraction). In HMC-QU-MI, automated regional strain identified regional wall-motion abnormalities with an average AUC = 0.80.

Conclusion

DL algorithms can interpret echocardiographic strain images with similar accuracy as conventional measurements. These results highlight the potential of DL algorithms to democratize the use of cardiac strain measurements and reduce time-spent and costs for echo labs globally.

The Complex, Unique, and Powerful Imaging Instrument for Dynamics (CUPI2D) at the Spallation Neutron Source (invited)

The Oak Ridge National Laboratory is planning to build the Second Target Station (STS) at the Spallation Neutron Source (SNS). STS will host a suite of novel instruments that complement the First Target Station's beamline capabilities by offering an increased flux for cold neutrons and a broader wavelength bandwidth. A novel neutron imaging beamline, named the Complex, Unique, and Powerful Imaging Instrument for Dynamics (CUPI2D), is among the first eight instruments that will be commissioned at STS as part of the construction project. CUPI2D is designed for a broad range of neutron imaging scientific applications, such as energy storage and conversion (batteries and fuel cells), materials science and engineering (additive manufacturing, superalloys, and archaeometry), nuclear materials (novel cladding materials, nuclear fuel, and moderators), cementitious materials, biology/medical/dental applications (regenerative medicine and cancer), and life sciences (plant-soil interactions and nutrient dynamics). The innovation of this instrument lies in the utilization of a high flux of wavelength-separated cold neutrons to perform real time in situ neutron grating interferometry and Bragg edge imaging-with a wavelength resolution of δλ/λ ≈ 0.3%-simultaneously when required, across a broad range of length and time scales. This manuscript briefly describes the science enabled at CUPI2D based on its unique capabilities. The preliminary beamline performance, a design concept, and future development requirements are also presented.

Experimental Search for Neutron to Mirror Neutron Oscillations as an Explanation of the Neutron Lifetime Anomaly

An unexplained >4σ discrepancy persists between "beam" and "bottle" measurements of the neutron lifetime. A new model proposed that conversions of neutrons n into mirror neutrons n^{'}, part of a dark mirror sector, can increase the apparent neutron lifetime by 1% via a small mass splitting Δm between n and n^{'} inside the 4.6 T magnetic field of the National Institute of Standards and Technology Beam Lifetime experiment. A search for neutron conversions in a 6.6 T magnetic field was performed at the Spallation Neutron Source which excludes this explanation for the neutron lifetime discrepancy.

Multiplexed serotype-specific real time PCR assays - a valuable tool to support large scale surveillance for bluetongue virus infection

In the last decade, real time PCR has been increasingly adopted for bluetongue diagnosis with both broadly reactive and serotype-specific assays widely used. The use of these assays and nucleic acid sequencing technologies have enhanced bluetongue virus detection, resulting in the identification of a number of new serotypes. As a result, 27 different serotypes are officially recognised and at least 3 more are proposed. Rapid identification of the virus serotype is essential for matching of antigens used in vaccines and to undertake surveillance and epidemiological studies to assist risk management. However, it is not uncommon for multiple serotypes to circulate in a region either concurrently or in successive years. It is therefore necessary to have a large suite of assays available to ensure that the full spectrum of viruses is detected. Nevertheless, covering a large range of virus serotypes is demanding from both a time and resource perspective. To overcome these challenges, real time PCR assays were optimised to match local virus strains and then combined in a panel of quadriplex assays, resulting in 3 assays to detect 12 serotypes directly from blood samples from cattle and sheep. These multiplex assays have been used extensively for bluetongue surveillance in both sentinel animals and opportunistically collected samples. A protocol to adapt these assays to capture variations in local strains of bluetongue virus and to expand the panel is described. Collectively these assays provide powerful tools for surveillance and the rapid identification of bluetongue virus serotypes directly from animal blood samples. This article is protected by copyright. All rights reserved.

A concept of a broadband inverted geometry spectrometer for the Second Target Station at the Spallation Neutron Source

BWAVES is an acronym for Broadband Wide-Angle VElocity Selector spectrometer, indicating that a novel WAVES (Wide-Angle VElocity Selector) device will be used to select the velocity/wavelength of the detected neutrons after they are scattered by the sample. We describe a conceptual design of BWAVES, a time-of-flight broadband inverted-geometry neutron spectrometer for the Second Target Station at the Spallation Neutron Source operated by Oak Ridge National Laboratory. Being the first inverted geometry spectrometer where the energy of the detected neutrons can be chosen by a WAVES device mechanically, irrespective of the limitations imposed by the crystal analyzers or filters, BWAVES will feature a uniquely broad, continuous dynamic range of measurable energy transfers, spanning 4.5 decades. This will enable measurements of both vibrational and relaxational excitations within the same, continuous scattering spectra. Novel approaches that are necessary for the implementation of a WAVES device at the BWAVES spectrometer will result in a spectrometer with the design and characteristics much different from those displayed by the neutron spectrometers in existence today.

How to design a focusing guide: The large moderator case1

As continuously shaped super-mirrors are becoming available, the conceptual design of focusing guides should explore a wider range of possibilities to accomplish an efficient neutron beam extraction. Starting from a desired phase-space volume at the sample position and using an upstream ray-tracing approach, the acceptance diagram of any focusing guide can be calculated at the moderator position. To ensure high brilliance transfer and homogeneous coverage, the acceptance diagram should be fully included in the neutron source emission phase-space volume. Following this idea, the guide system can be scaled into dimensionless geometric figures that convey performance limits for a desired cross-section reduction. Moreover, if we impose a monotonic increase of the reflection angle with divergence angle at the sample position, the shape of the mirror is analytically determined. This approach was applied in the design of a focusing guide for SNAP instrument at SNS, at ORNL, USA. The results of McStas simulations are presented with different options included. Our approach facilitates finding an optimal solution for connecting multiple guide pieces to avoid excessive losses and ensure a homogeneous phase space coverage.

The Macromolecular Neutron Diffractometer MaNDi at the Spallation Neutron Source

The Macromolecular Neutron Diffractometer (MaNDi) is located on beamline 11B of the Spallation Neutron Source at Oak Ridge National Laboratory. The instrument is a neutron time-of-flight wavelength-resolved Laue diffractometer optimized to collect diffraction data from single crystals. The instrument has been designed to provide flexibility in several instrumental parameters, such as beam divergence and wavelength bandwidth, to allow data collection from a range of macromolecular systems.

Identification of a novel virus in pigs--Bungowannah virus: a possible new species of pestivirus

In 2003 an outbreak of sudden deaths occurred in 3-4-week-old piglets on a farm in New South Wales, Australia. There was a marked increase in the birth of stillborn foetuses. Pathological changes consisted of a multifocal non-suppurative myocarditis. A viral infection was suspected but a wide range of known agents were excluded. A modified sequence independent single primer amplification (SISPA) method was used to identify a novel virus associated with this outbreak. Conserved 5'UTR motifs, the presence of a putative N(pro) coding region and limited antigenic cross-reactivity with other members of the Pestivirus genus, support the placement of this virus in the Pestivirus genus. Phylogenetic analysis of the 5'UTR, N(pro) and E2 coding regions showed this virus to be the most divergent pestivirus identified to date.

A single amino acid is critical for the expression of B-cell epitopes on the helicase domain of the pestivirus NS3 protein

Truncated NS3 proteins, expressed by recombinant baculoviruses, were used to investigate the location of conserved B-cell epitopes on this non-structural bovine viral diarrhoea virus (BVDV) protein. A goat anti-pestivirus antiserum, and a panel of anti-NS3 monoclonal antibodies, including the BVDV-1 specific antibody P1D8, were used to verify the presence or absence of the epitopes. Interestingly, the monoclonal antibodies reacted only with the truncated protein encompassing the helicase domain of NS3. Expression of the B-cell epitopes was dependent on, but not within, a 57 amino acid sequence at the carboxy-terminal end of this protein, supporting observations that these conserved epitopes are conformational in nature. A comparison of deduced amino acid sequences of the helicase domain from BVDV-1, BVDV-2, BDV and CSFV isolates highlighted a single amino acid that appeared to be unique to P1D8-reactive BVDV-1 isolates. Site-directed mutagenesis studies confirmed that this amino acid is critical for the expression of the BVDV-1 specific NS3 epitope recognised by the P1D8 monoclonal antibody. Surprisingly, the amino acid was also important for an epitope recognised by two group-specific monoclonal antibodies, P1H11 and P4A11. Protein modelling studies, based on the structure of the hepatitis C NS3 helicase domain, indicated that this amino acid occupies a prominent position on the surface of the protein.

Extraction and preliminary characterization of a human bronchogenic carcinoma antigen

Saline extracts of human bronchogenic tumours, soluble in 50% saturated ammonium sulphate and also fractions from Sephadex G-200 chromatography were used to raise antisera in rabbits. After absorbing the antisera with normal tissue extracts, direct Ouchterlony tests were performed against tumour (adenocarcinomata and squamous cell carcinomata) and normal extracts. A precipitin reaction was given with all 11 tumour extracts tested at a concentration of 5 mg/ml whereas all the 9 normal lung control extracts did not react at concentrations up to 100 mg/ml. The possibility that this reaction could be related to histocompatibility differences between individuals is ruled out by the fact that in two cases tumour and normal tissue were obtained from the same patient. These studies and also precipitin-inhibition experiments have confirmed the existence of antigen associated with bronchial carcinomata and have shown that, although the antigen or a cross-reacting antigen is present in normal lung tissue, the amounts are small in comparison with the amounts extracted from tumour. Antigenic activity was contained in a single absorbance peak when fractionated by Sephadex G-200 chromatography and its elution volume indicated a molecular weight of approximately 4-0 times 10(4)D. Further purification was achieved using isotachophoresis. Preliminary characterization of the antigen has shown it to be stable at pH 4-5, resistant to heating at 50 degrees C for 30 min, to migrate on immunoelectrophoresis with a cationic mobility at PH 8-5 and to be immunologically distinct from carcinoembryonic antigen.