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At least 109 records · Page 6

CryoDRGN-AI: neural ab initio reconstruction of challenging cryo-EM and cryo-ET datasets

Proteins and other biomolecules form dynamic macromolecular machines that are tightly orchestrated to move, bind, and perform chemistry. Cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) can access the intrinsic heterogeneity of these complexes and are therefore key tools for understanding their function. However, 3D reconstruction of the collected imaging data presents a challenging computational problem, especially without any starting information, a setting termed ab initio reconstruction. Here, in this study, we introduce cryoDRGN-AI, a method leveraging an expressive neural representation and combining an exhaustive search strategy with gradient-based optimization to process challenging heterogeneous datasets. Using cryoDRGN-AI, we reveal new conformational states in large datasets, reconstruct previously unresolved motions from unfiltered datasets, and demonstrate ab initio reconstruction of biomolecular complexes from in situ data. With this expressive and scalable model for structure determination, we hope to unlock the full potential of cryo-EM and cryo-ET as a high-throughput tool for structural biology and discovery.

Levy, Axel [Stanford Univ., CA (United States); SL↗

Imaging in Diagnostic Nuclear Medicine

Single-photon emission computed tomography (SPECT) and positron emission tomography (PET) are modern methods for visualization in diagnostic nuclear medicine. SPECT is known as a workhorse in cardiology, and PET is the gold standard in oncology. The development of nuclear medicine is provided by cooperation of physicists, mathematicians, biologists, medical doctors, and radio-chemists. In spite of extensive clinical applications, several problems may lead to false diagnoses. In particular, the correction of attenuation of gamma radiation in human organs must be taken into account. For interpretation and evaluation of such an effect on the clinical results, we perform physico-mathematical simulation of the SPECT diagnostics in cardiology in the absence and presence of the correction of attenuation. A brief review of the state-of-the art is presented. The simulation employs the first Russian anthropomorphic mathematical phantom that describes the distribution of radio-pharmacological agent ({sup 99m }Tc-methoxyisobutylisonitrile) in chest organs of a typical male patient. A model for calculation of raw images is developed with allowance for attenuation of radiation in biological tissues and the effect of collimator and detector. The results of the proposed models and calculated images are compared with clinical images obtained at the Meshalkin Institute of Circulation Pathology (Novosibirsk) and Myasnikov Institute of Clinical Cardiology (Moscow). Statistical algorithms are developed for the solution of the inverse problem of image reconstruction based on the entropy principle. The clinical and physico-mathematical approaches are compared in the evaluation of the effect of correction on the quality of reconstructed images of the left ventricle of myocardium.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Joint ptycho-tomography with deep generative priors

Abstract Joint ptycho-tomography is a powerful computational imaging framework to recover the refractive properties of a 3D object while relaxing the requirements for probe overlap that is common in conventional phase retrieval. We use an augmented Lagrangian scheme for formulating the constrained optimization problem and employ an alternating direction method of multipliers (ADMM) for the joint solution. ADMM allows the problem to be split into smaller and computationally more efficient subproblems: ptychographic phase retrieval, tomographic reconstruction, and regularization of the solution. We extend our ADMM framework with plug-and-play (PnP) denoisers by replacing the regularization subproblem with a general denoising operator based on machine learning. While the PnP framework enables integrating such learned priors as denoising operators, tuning of the denoiser prior remains challenging. To overcome this challenge, we propose a denoiser parameter to control the effect of the denoiser and to accelerate the solution. In our simulations, we demonstrate that our proposed framework with parameter tuning and learned priors generates high-quality reconstructions under limited and noisy measurement data.

97 MATHEMATICS AND COMPUTING↗

Methods for analysing the quality of the element base of quantum information technologies

Methods for analysing the quality of the element base of quantum information technologies are considered. Methods for simulating quantum operations with allowance for quantum noise, based on the formalism of quantum operations (operator sum method and Choi – Jamiolkowski isomorphism), are described. Results of simulating some one- and two-qubit quantum transformations with allowance for the amplitude and phase relaxation and the presence of depolarising noise are reported. The quantum state tomography, based on the root approach and maximum likelihood method, is considered. The method of guaranteed estimation of quantum tomography accuracy, which implies quantitative estimation of measurement results, is described. Tomography of a single-qubit transformation on a superconducting quantum processor (IBM) is performed. The practical purpose of the study is to provide high quality and efficiency of quantum information technologies. The results obtained can be used to improve the quality of logic gates of quantum computers and debug the procedures of quantum state control in quantum cryptography problems. The bibliography includes 28 references. (quantum technology)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Efficacy of perfusion CT in differentiating of pancreatic ductal adenocarcinoma from mass-forming chronic pancreatitis and characterization of isoattenuating pancreatic lesions

Purpose: Multidetector computed tomography (MDCT) is routinely used in the diagnosis of pancreatic ductal adenocarcinoma (PDAC), but it may be inadequate in some cases, especially mass-forming chronic pancreatitis (MFCP) and isoattenuating pancreatic lesions. Perfusion CT (pCT) may help resolve this problem. The aim of this study was to evaluate whether pCT could help differentiating PDAC from MFCP and in characterization of isoattenuating pancreatic lesions. Materials and methods: This prospective study included 89 cases of pancreatic lesions detected by MDCT and further analyzed with pCT. Sixty-one cases with final pathological diagnosis PDAC and 12 cases with MFCP were included from the study. Blood volume (BV), blood flow (BF), mean transit time (MTT), and permeability surface area product (PS) maps were obtained. Perfusion values obtained from the lesions and normal parenchyma were compared. Results: Compared with normal parenchyma, BV, BF, PS were lower and MTT was longer in PDAC and MFCP (p < 0.05). Compared with MFCP, BV, BF, PS were lower and MTT was longer in PDAC (p < 0.001). Compared with normal parenchyma, BV, BF, PS were lower and MTT was longer in isoattenuating lesions, (p < 0.001). Cutoff values of 7.60 mL/100 mL, 64.43 mL/100 mL/min, 28.08 mL/100 mL/min for BV, BF, PS, respectively, provided 100% sensitivity and specificity and 7.47 s for MTT provided 98.3% sensitivity, 80% specificity for distinguishing PDAC from MFCP. Conclusion: pCT is a useful technology that can be helpful in overcoming the limitations of routine MDCT in diagnosing PDAC and characterization of isoattenuating lesions.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Laminography as a tool for imaging large-size samples with high resolution

Despite the increased brilliance of the new generation synchrotron sources, there is still a challenge with high-resolution scanning of very thick and absorbing samples, such as a whole mouse brain stained with heavy elements, and, extending further, brains of primates. Samples are typically cut into smaller parts, to ensure a sufficient X-ray transmission, and scanned separately. Compared with the standard tomography setup where the sample would be cut into many pillars, the laminographic geometry operates with slab-shaped sections significantly reducing the number of sample parts to be prepared, the cutting damage and data stitching problems. In this work, a laminography pipeline for imaging large samples (>1 cm) at micrometre resolution is presented. The implementation includes a low-cost instrument setup installed at the 2-BM micro-CT beamline of the Advanced Photon Source. Additionally, sample mounting, scanning techniques, data stitching procedures, a fast reconstruction algorithm with low computational complexity, and accelerated reconstruction on multi-GPU systems for processing large-scale datasets are presented. The applicability of the whole laminography pipeline was demonstrated by imaging four sequential slabs throughout an entire mouse brain sample stained with osmium, in total generating approximately 12 TB of raw data for reconstruction.

47 OTHER INSTRUMENTATION↗

Cross-Plane Acquisitions in Electrical Capacitance Volume Tomography

Electrical capacitance tomography (ECT) is a widely used imaging modality to image two-dimensional cross sections of multiphase flows. Recent developments in electrical capacitance volume tomography (ECVT) have made it possible to directly obtain volumetric images from measured data. An ECVT is instrumental for obtaining accurate phase hold up information and velocity information that are needed for the optimization of certain flow processes. However, compared to ECT, the high correlation between the measurements in ECVT exacerbates the ill-conditioning of the associated image reconstruction problem. Previous studies have suggested that neglecting mutual capacitance data between the ECVT electrodes located at cross-planes that are well separated along the sensor axis can be done without significantly affecting the reconstructed image. In addition, this may help constrain the ill-conditioning of the reconstruction problem. Here, we examine in detail and quantify the effect of reduced cross-plane acquisition strategies for optimizing the image reconstruction and constraining the ill-conditioning of typical ECVT settings.

20 FOSSIL-FUELED POWER PLANTS↗

Momentum informed muon scattering tomography for monitoring spent nuclear fuels in dry storage cask

Development of an effective monitoring method for spent nuclear fuel (SNF) in a dry storage cask (DSC) is important to meet the increasing demand for dry storage investigations. The DSC investigation should provide information about the quantity of stored SNF, and quality assurance of materials should be possible without opening the cask. However, traditional nondestructive examination (NDE) methods such as x-rays are difficult to deploy for DSC investigation because a typical DSC is intentionally designed to shield against radiation. To address this challenge, cosmic ray muons (CRMs) are used as an alternative NDE radiation probe because they can easily penetrate an entire DSC system; however, a wide application of muons is often hindered due to the naturally low CRM flux (~10 4 muons/m 2 /min). This paper introduces a newly proposed imaging algorithm, momentum-informed muon scattering tomography (MMST) , and presents how a limitation of the current muon scattering tomography technique has been addressed by measuring muon momentum. To demonstrate its functionality, a commercial DSC with 24 pressurized light water reactor fuel assemblies (FAs) and the MMST system were designed in GEANT4. Three noticeable improvements were observed for MMST system as a DSC investigation tool: (1) a signal stabilization, (2) an enhanced capability to differentiate various materials, and (3) statistically increased precision to identify and locate missing FAs. The results show that MMST improves the investigation accuracy from 79 to 98% when one FA is missing and 51% to 88% when one-half FA is missing. The advancement of the NDE technique using CRM for DSC verification is expected to resolve long-standing problems in increasing demand for DSC inspections and nuclear security.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Probing quantum processor performance with pyGSTi

PyGSTi is a Python software package for assessing and characterizing the performance of quantum computing processors. It can be used as a standalone application, or as a library, to perform a wide variety of quantum characterization, verification, and validation (QCVV) protocols on as-built quantum processors. In this work, we outline pyGSTi's structure, and what it can do, using multiple examples. We cover its main characterization protocols with end-to-end implementations. These include gate set tomography, randomized benchmarking on one or many qubits, and several specialized techniques. We also discuss and demonstrate how power users can customize pyGSTi and leverage its components to create specialized QCVV protocols and solve user-specific problems.

97 MATHEMATICS AND COMPUTING↗

The Coupled Adjoint-State Equation in forward and inverse linear elasticity: Incompressible plane stress

A persistent challenge present in inverse or parameter estimation problems with interior data is how to deal with uncertainty in the boundary conditions employed in the forward or state model. In this work we focus on a linear plane stress inverse elasticity problem with measured displacement data where one component of the measured displacement field is known with considerably greater precision than the other. This situation is commonly encountered when the displacement field is measured using ultrasound or optical coherence tomography. We present a novel computational formulation in which no displacement or traction boundary conditions are assumed. The formulation results in coupling the state and adjoint equations, that are typically uncoupled when a well-posed state model is available. Two variants of residual-based stabilization are added. Our approach is applied to a simulated data set and experimental data from an ultrasound phantom.

42 ENGINEERING↗

Detection of System Drift for the Health Monitoring of an X-ray CT Scientific Instrument

This SE296 Capstone Project technical report is being submitted as a final requirement of the UCSD Master of Science in Structural Engineering with specialization in Structural Health Monitoring (SHM) and Nondestructive Evaluation (NDE). The Capstone provides students the opportunity to apply knowledge in their technology areas towards the solution of an SHM or NDE problem. As an employee of the Lawrence Livermore National Laboratory and NDE/NCI team member, I chose to apply the SHM design paradigm taught at UCSD to improve the health monitoring of the X-ray Micro-Computed Tomography (MCT) system. I would like to thank LLNL’s Dr. Harry Martz for serving as my mentor during this project and the entire LLNL MCT technical team for answering my questions and contributing to my knowledge. I would also like to thank Prof. Michael Todd for recruiting me to the UCSD NDE/SHM program and serving as my graduate advisor.

42 ENGINEERING↗

Iterative Nonlinear Tikhonov Algorithm with Constraints for Electromagnetic Tomography

Low frequency electromagnetic tomography such as the capacitance tomography (ECT) has been proposed for monitoring and mass-gauging of gas-liquid two-phase system under microgravity condition in NASA's future long-term space missions. Due to the ill-posed inverse problem of ECT, images reconstructed using conventional linear algorithms often suffer from limitations such as low resolution and blurred edges. Hence, new efficient high resolution nonlinear imaging algorithms are needed for accurate two-phase imaging. The proposed Iterative Nonlinear Tikhonov Regularized Algorithm with Constraints (INTAC) is based on an efficient finite element method (FEM) forward model of quasi-static electromagnetic problem. It iteratively minimizes the discrepancy between FEM simulated and actual measured capacitances by adjusting the reconstructed image using the Tikhonov regularized method. More importantly, it enforces the known permittivity of two phases to the unknown pixels which exceed the reasonable range of permittivity in each iteration. This strategy does not only stabilize the converging process, but also produces sharper images. Simulations show that resolution improvement of over 2 times can be achieved by INTAC with respect to conventional approaches. Strategies to further improve spatial imaging resolution are suggested, as well as techniques to accelerate nonlinear forward model and thus increase the temporal resolution.

Xu, Feng↗

Sharpness-Aware Low-Dose CT Denoising Using Conditional Generative Adversarial Network

Low-dose computed tomography (LDCT) has offered tremendous benefits in radiation-restricted applications, but the quantum noise as resulted by the insufficient number of photons could potentially harm the diagnostic performance. Current image-based denoising methods tend to produce a blur effect on the final reconstructed results especially in high noise levels. In this paper, a deep learning-based approach was proposed to mitigate this problem. An adversarially trained network and a sharpness detection network were trained to guide the training process. Experiments on both simulated and real dataset show that the results of the proposed method have very small resolution loss and achieves better performance relative to state-of-the-art methods both quantitatively and visually.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Digital Radiography and Computed Tomography (DRCT) of Recovered Chemical Warfare Materiel

The Digital Radiography and Computed Tomography (DRCT) of recovered chemical warfare material (RCWM) project is an ongoing effort to provide the following to the U.S. Army Chemical Materiel Activity (CMA): 1. Development of field-portable and transportable digital x-ray inspection capabilities including radiography and computed tomography. 2. Continuous maintenance and product development to maintain state of the art in x-ray inspection. 3. Evaluation and incorporation of advanced technologies. 4. Deployment of capabilities to selected U.S. Army designated sites. 5. Training of personnel in the use of x-ray inspection equipment. 6. Development of user guides and related documentation for inspection systems. 7. Operations support to field personnel to assess and resolve problems in the field. Support includes both remote (from Idaho) and on-site depending on the problem. These systems have been used to inspect thousands of containers ranging from bare and overpacked munitions to drums and ton containers. This in-progress program review showcases prospective efforts and updates to project systems that are in the developmental stage.

36 MATERIALS SCIENCE↗

Titanium porous-transport layers for PEM water electrolysis prepared by tape casting

While the porous-transport layer (PTL) is a key component in PEM electrolyzers, it is one of the most underexplored due to limited available structures. In this work, we present a novel PTL design for PEM water electrolyzers enabled by a cost-effective, scalable tape-casting technique. Here, a precise control of the PTL pore structure is achieved by incorporating poreformers of various sizes, and by varying the titanium and poreformer ratio. The structures are characterized with SEM and synchrotron X-ray computed tomography imaging techniques. Comprehensive electrochemical performance analysis demonstrates that higher titanium loading provides improved contact at the catalyst-layer/PTL interface but suffers from severe mass-transport losses due to gas bubbles. We solve this mass-transport problem by mixing in large poreformer beads that produce a highly porous structure with excellent gas removal properties yet still maintaining mechanical integrity. The PTL fabricated with 60:40 Ti:PMMA ratio and 60 μm PMMA bead size outperformed the standard commercial Ti powder-based PTL by 62 mV at 4 A/cm 2 .

25 ENERGY STORAGE↗

Geomagnetic Secular Variation Prediction with Thermal Heterogeneous Boundary Conditions

It has long been conjectured that thermal heterogeneity at the core-mantle boundary (CMB) affects the geodynamo substantially. The observed two pairs of steady and strong magnetic flux lobes near the Polar Regions and the low secular variation in the Pacific over the past 400 years (and perhaps longer) are likely the consequences of this CMB thermal heterogeneity. There are several studies on the impact of the thermal heterogeneity with numerical geodynamo simulations. However, direct correlation between the numerical results and the observations is found very difficult, except qualitative comparisons of certain features in the radial component of the magnetic field at the CMB. This makes it difficult to assess accurately the impact of thermal heterogeneity on the geodynamo and the geomagnetic secular variation. We revisit this problem with our MoSST_DAS system in which geomagnetic data are assimilated with our geodynamo model to predict geomagnetic secular variations. In this study, we implement a heterogeneous heat flux across the CMB that is chosen based on the seismic tomography of the lowermost mantle. The amplitude of the heat flux (relative to the mean heat flux across the CMB) varies in the simulation. With these assimilation studies, we will examine the influences of the heterogeneity on the forecast accuracies, e.g. the accuracies as functions of the heterogeneity amplitude. With these, we could be able to assess the model errors to the true core state, and thus the thermal heterogeneity in geodynamo modeling.

Kuang, Weijia↗

Adaptive Error Estimation in Linearized Ocean General Circulation Models

Data assimilation methods are routinely used in oceanography. The statistics of the model and measurement errors need to be specified a priori. This study addresses the problem of estimating model and measurement error statistics from observations. We start by testing innovation based methods of adaptive error estimation with low-dimensional models in the North Pacific (5-60 deg N, 132-252 deg E) to TOPEX/POSEIDON (TIP) sea level anomaly data, acoustic tomography data from the ATOC project, and the MIT General Circulation Model (GCM). A reduced state linear model that describes large scale internal (baroclinic) error dynamics is used. The methods are shown to be sensitive to the initial guess for the error statistics and the type of observations. A new off-line approach is developed, the covariance matching approach (CMA), where covariance matrices of model-data residuals are "matched" to their theoretical expectations using familiar least squares methods. This method uses observations directly instead of the innovations sequence and is shown to be related to the MT method and the method of Fu et al. (1993). Twin experiments using the same linearized MIT GCM suggest that altimetric data are ill-suited to the estimation of internal GCM errors, but that such estimates can in theory be obtained using acoustic data. The CMA is then applied to T/P sea level anomaly data and a linearization of a global GFDL GCM which uses two vertical modes. We show that the CMA method can be used with a global model and a global data set, and that the estimates of the error statistics are robust. We show that the fraction of the GCM-T/P residual variance explained by the model error is larger than that derived in Fukumori et al.(1999) with the method of Fu et al.(1993). Most of the model error is explained by the barotropic mode. However, we find that impact of the change in the error statistics on the data assimilation estimates is very small. This is explained by the large representation error, i.e. the dominance of the mesoscale eddies in the T/P signal, which are not part of the 21 by 1" GCM. Therefore, the impact of the observations on the assimilation is very small even after the adjustment of the error statistics. This work demonstrates that simult&neous estimation of the model and measurement error statistics for data assimilation with global ocean data sets and linearized GCMs is possible. However, the error covariance estimation problem is in general highly underdetermined, much more so than the state estimation problem. In other words there exist a very large number of statistical models that can be made consistent with the available data. Therefore, methods for obtaining quantitative error estimates, powerful though they may be, cannot replace physical insight. Used in the right context, as a tool for guiding the choice of a small number of model error parameters, covariance matching can be a useful addition to the repertory of tools available to oceanographers.

Chechelnitsky, Michael Y.↗