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At least 109 records · Page 6

Real-time Multi-granular Analytics Framework for HIT Systems

Streaming analytics is the process of ingesting and digesting live data from multiple data sources. In the healthcare domain, as the importance of extracting immediate insights while data are streaming into the system grows, the focus is shifting from batch processing to streaming analytics. With data increasing dramatically at high speeds, many informatics designs have been proposed to adapt healthcare domain into this new environment. In our previous work, we introduced a prototype of health informatics technology (HIT) framework that aims to address challenges in adopting state-of-the-art technologies to enable advanced healthcare analytic tasks in new streaming environments. We recently made major updates to the framework so that anomaly from multiple streaming data sources at different granularity levels can be detected in near real-time. In this paper, we detail the implementation and deployment of the framework in Kubernetes clusters and report its performances when tested on electronic health record (EHR) data of Veterans Affairs.

Park, Byung↗

Advanced Methods for Immersed Domain Multi-physics Computations

This is the final report on the project, and describes the main accomplishments in the development of the Shifted Boundary Method (SBM), a new computational framework for embedded/immersed computational mechanics applications.

97 MATHEMATICS AND COMPUTING↗

57Fe Mössbauer isomer shift of pure iron and iron oxides at high pressure—An experimental and theoretical study

The 57Fe isomer shift (IS) of pure iron has been measured up to 100 GPa using synchrotron Mössbauer spectroscopy in the time domain. Apart from the expected discontinuity due to the α→ε structural and spin transitions, the IS decreases monotonically with increasing pressure. The absolute shifts were reproduced without semi-empirical calibrations by periodic density functional calculations employing extensive localized basis sets with several common density functionals. However, the best numerical agreement is obtained with the B1WC hybrid functional. Extension of the calculations to 350 GPa, a pressure corresponding to the Earth’s inner core, predicted the IS range of 0.00 to -0.85 mm/s, covering the span from Fe(0) to Fe(VI) compounds measured at ambient pressure. The calculations also reproduced the pressure trend from polymorphs of prototypical iron oxide minerals, FeO and Fe2O3. Analysis of the electronic structure shows a strong donation of electrons from oxygen to iron at high pressure. The assignment of formal oxidation to the Fe atom becomes ambiguous under this condition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

SIDDA: SInkhorn Dynamic Domain Adaptation for image classification with equivariant neural networks

Modern neural networks (NNs) often do not generalize well in the presence of a ‘covariate shift’; that is, in situations where the training and test data distributions differ, but the conditional distribution of classification labels given the data remains unchanged. In such cases, NN generalization can be reduced to a problem of learning more robust, domain-invariant features. Domain adaptation (DA) methods include a broad range of techniques aimed at achieving this; however, these methods have struggled with the need for extensive hyperparameter tuning, which then incurs significant computational costs. In this work, we introduce SInkhorn Dynamic Domain Adaptation (SIDDA), an out-of-the-box DA training algorithm built upon the Sinkhorn divergence, that can achieve effective domain alignment with minimal hyperparameter tuning and computational overhead. We demonstrate the efficacy of our method on multiple simulated and real datasets of varying complexity, including simple shapes, handwritten digits, real astronomical observations, and remote sensing data. These datasets exhibit covariate shifts due to noise, blurring, differences between telescopes, and variations in imaging wavelengths. SIDDA is compatible with a variety of NN architectures, and it works particularly well in improving classification accuracy and model calibration when paired with symmetry-aware equivariant NNs (ENNs). We find that SIDDA consistently enhances the generalization capabilities of NNs, achieving up to a ${\approx}40\%$ improvement in classification accuracy on unlabeled target data, while also providing a more modest performance gain of $\lesssim 1\%$ on labeled source data. We also study the efficacy of DA on ENNs with respect to the varying group orders of the dihedral group DN, and find that the model performance improves as the degree of equivariance increases. Finally, if SIDDA achieves proper domain alignment, it also enhances model calibration on both source and target data, with the most significant gains in the unlabeled target domain—achieving over an order of magnitude improvement in the expected calibration error and Brier score. SIDDA’s versatility across various NN models and datasets, combined with its automated approach to domain alignment, has the potential to significantly advance multi-dataset studies by enabling the development of highly generalizable models.

79 ASTRONOMY AND ASTROPHYSICS↗

The second-generation Shifted Boundary Method and its numerical analysis

Recently, the Shifted Boundary Method (SBM) was proposed within the class of unfitted (or immersed, or embedded) finite element methods. By reformulating the original boundary value problem over a surrogate (approximate) computational domain, the SBM avoids integration over cut cells and the associated problematic issues regarding numerical stability and matrix conditioning. Accuracy is maintained by modifying the original boundary conditions using Taylor expansions. Hence the name of the method, that shifts the location and values of the boundary conditions. In this article, we present enhanced variational SBM formulations for the Poisson and Stokes problems with improved flexibility and robustness. These simplified variational forms allow to relax some of the assumptions required by the mathematical proofs of stability and convergence of earlier implementations. First, we show that these new SBM implementations can be proved asymptotically stable and convergent even without the rather restrictive assumption that the inner product between the normals to the true and surrogate boundaries is positive. Second, we show that it is not necessary to introduce a stabilization term involving the tangential derivatives of the solution at Dirichlet boundaries, therefore avoiding the calibration of an additional stabilization parameter. Finally, we prove enhanced L 2 -estimates without the cumbersome assumption – of earlier proofs – that the surrogate domain is convex. Instead we rely on a conventional assumption that the boundary of the true domain is smooth, which can also be replaced by requiring convexity of the true domain. The aforementioned improvements open the way to a more general and efficient implementation of the Shifted Boundary Method, particularly in complex three-dimensional geometries. We complement these theoretical developments with numerical experiments in two and three dimensions.

42 ENGINEERING↗

Celeritas Midterm SciDAC Report

Celeritas is a new Monte Carlo (MC) code that helps satisfy the increasing demand for high energy physics (HEP) detector simulation, using Graphics Processing Unit (GPU) hardware on high performance computing (HPC) systems to model Large Hadron Collider (LHC) experiments and beyond. This report details the project’s progress midway through its SciDAC funding period, highlighting the first complete implementation of standard electromagnetic (EM) physics on GPUs, initial results for performance and scalability on Leadership Computing Facilities (LCFs), and preliminary integration into the CMS and ATLAS experiments. By integrating HEP domain knowledge with expertise in MC transport, Celeritas has catalyzed a shift in the HEP community’s perception of GPU platforms as the future for HPC simulations.

97 MATHEMATICS AND COMPUTING↗

Two-phase accurate multiplexed structured image capture (2pAc-MUSIC)

Multiplexed Structural Image Capture (MUSIC) technique uses modulation of light from a scene prior to imaging to encode the temporal evolution of target into spatial frequency shifts, with each shift corresponding to a unique time and resulting in individual distinct snapshots. Computational-processing of the multiplexed single-shot image can recover the nanosecond-resolution scene evolution. One of the limitations is the loss of spatial resolution of the recovered image due to limitations of the low-pass spatial frequency filtering depth. Here we demonstrated that two images with complementary spatial phases can be used to enhance the spatial resolutions. For this application, 2 Phase Accurate (2pAc)-MUSIC is implemented that a scene is encoded with two complementary phases. The increased spatial information captured reduces the lower frequency noise in the Fourier domain found in single-phase MUSIC. A recovery algorithm combines the 180-degree spatial frequency shifted images into a single scene and applies a spatial filter in the Fourier domain that has a larger depth than previously possible to achieve a scene with increased spatial resolution. The 2pAc-MUSIC can effectively enhance the spatial resolution by removing the overlapping zero-order spatial frequencies.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Composites of (C4F)n and (CF)n Synthesized by Uncatalyzed Fluorination of Graphite

A new solid-state 19F magic-angle spinning NMR signal at an isotropic 19F chemical shift of −53 ppm is measured from graphite fluoride synthesized by reaction of graphite with F2 at temperatures above 750 K with no catalyst. Two-dimensional NMR suggests the −53 ppm 19F NMR signal originates from covalent fluoromethanetriyl groups belonging to ordered (CyF)n bulk domains composited with the major (CF)n domains. Quantitative 19F and 13C NMR find y=4.32±0.64. DFT calculations of NMR chemical shifts for unsaturated fluorographene models show that a (C4F)n phase with fluorine bound covalently to a single side of the carbon layer best explains the observed NMR chemical shifts. We assign the new phase to this (C4F)n structure, which constitutes up to 15% of the carbon in our graphite fluoride composites. The (C4F)n content of the composite affects bulk electrochemical properties in a manner similar to graphite fluorides produced by conventional, catalyzed fluorination processes.

Walder, Brennan J. (ORCID:0000000274539143)↗

Quantifying and visualizing the microscopic degrees of freedom of grain boundaries in the Wigner–Seitz cell of the displacement-shift-complete lattice

Here we introduce a grain boundary (GB) translation vector, t ws , to describe and quantify the domain of the microscopic degrees of freedom of GBs. It has long been recognized that for fixed macroscopic degrees of freedom of a GB there exists a large multiplicity of states characterized by different relative grain translations. More recently another degree of freedom, [n], the number of GB atoms, has emerged and is now recognized as an equally important component of GB structural multiplicity. In this work, we show that all GB microstates can be uniquely characterized by their value of t ws , which is located within the Wigner–Seitz (WS) cell of the Displacement-Shift-Complete lattice (DSCL) of the GB. The GB translation vector captures information about both the translation state and the number of GB atoms. We show that the density of GB microstates inside the WS cell of the DSCL is not uniform and can form clusters that correspond to different GB phases. Further, the vectors connecting the centers of the clusters correspond to the Burgers vectors of GB phase junctions, which can be predicted without building the junctions. Using t ws , we quantify GB excess shear and argue that it is defined up to a DSCL vector, which has implications for thermodynamic equilibrium conditions. Additionally, this work generalizes the definition of the number of GB atoms [n] to asymmetric boundaries.

36 MATERIALS SCIENCE↗

Measurements of plasma parameters in the divertor island of Wendelstein 7-X through line-ratio spectroscopy on helium

We report electron temperature T e and density n e have been measured in the divertor island of Wendelstein 7-X by means of a new thermal He-beam system utilizing line-ratio spectroscopy. This system is equipped with a poloidal arrangement of five gas valves that allows to infer 2D plasma profiles T e ( R,Z ) and n e ( R,Z ) across the magnetic island forming the island divertor. A local maximum in T e ( R,Z ) was measured along the flux surfaces located between the island center and the outer separatrix. In the island center, characterized by closed field lines, a clear local minimum in T e was measured, indicating that no direct heat deposition occurs in this region and that the perpendicular heat flux from the core plasma into this domain is small. Increasing the island size leads to a reduction of the connection length in the scrape-off layer (SOL) and to a shift of the island center towards the divertor target. In this scenario, the T e ( R,Z ) are reduced in the entire island domain. Density profiles are found flat across the divertor island for both island size scenarios. These findings are supported by similar observations made with a reciprocating probe plunging through the same SOL island at the mid-plane of W7-X representing the upstream position in this 3D divertor geometry.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Comparisons of Montane Snow Water Equivalent Projections: Calculating Total Snow Mass in Regions with Projection Agreement and Divergence in the Western United States

Montane snowpack is a vital source of water in the western United States. Here, we use a large-ensemble approach to evaluate the agreement across 124 snow water equivalent (SWE) projections with statistically downscaled forcing between end-of-century (2076–95) and early twenty-first century (2106–35) periods. Comparisons were performed on dates corresponding with the end of winter (15 April) and midspring snowmelt (15 May) in five western U.S. domains. Using 1) the percent change to end-of-century SWE across different ensembles of snow projections and 2) the shift between early twenty-first century and end-of-century SWE distributions for each snow projection, we identified relationships between projections that were consistent across each domain. In low to midelevations, end-of-century SWE decreases were 48% and larger on 15 April. These regions had projected changes to SWE that were both high confidence and in relative agreement across projections. Despite this, the majority of 15 April SWE volume existed in higher elevations where the magnitude and direction (positive or negative) of SWE changes were most uncertain. The results of this study show that large-ensemble approaches can be used to measure coherence between snow projections and identify 1) the highest confidence changes to future snow water resources and 2) the locations and periods where and when improvements to snow projections would most benefit estimates of future snow water resources.

Climate models↗

Distinguishing Potassium Channel Resting State Conformations in Live Cells with Environment-Sensitive Fluorescence

Ion channels are polymorphic membrane proteins whose high-resolution structures offer images of individual conformations, giving us starting points for identifying the complex and transient allosteric changes that give rise to channel physiology. Here, we report live-cell imaging of voltage-dependent structural changes of voltage-gated Kv2.1 channels using peptidyl tarantula toxins labeled with an environment-sensitive fluorophore, whose spectral shifts enable identification of voltage-dependent conformation changes in the resting voltage sensing domain (VSD) of the channel. We synthesize a new environment-sensitive, far-red fluorophore, julolidine phenoxazone (JP) azide, and conjugate it to tarantula toxin GxTX to characterize Kv2.1 VSD allostery during membrane depolarization. JP has an inherent response to the polarity of its immediate surroundings, offering site-specific structural insight into each channel conformation. Using voltage-clamp spectroscopy to collect emission spectra as a function of membrane potential, we find that they vary with toxin labeling site, the presence of Kv2 channels, and changes in membrane potential. With a high-affinity conjugate in which the fluorophore itself interacts closely with the channel, the emission shift midpoint is 50 mV more negative than the Kv2.1 gating current midpoint. This suggests that substantial conformational changes at the toxin-channel interface are associated with early gating charge transitions and these are not concerted with VSD motions at more depolarized potentials. These fluorescent probes enable study of conformational changes that can be correlated with electrophysiology, putting channel structures and models into a context of live-cell membranes and physiological states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The influence of cooling rates on strain phase diagrams and domain structures of ferroelectric thin films: A case study of PbTiO 3

Strain engineering has been established as an effective approach to control phase equilibria, domain configurations, and functional properties of ferroelectric thin films. Temperature-strain phase diagrams have been used as powerful tools for providing insights into strain engineering. However, almost all existing phase diagrams established using the phase-field approach assume quenching conditions without considering actual cooling rates during the post-deposition annealing process of ferroelectric thin films. Within this work, we systematically investigate the influence of cooling rates on domain structures and the strain-phase diagram of ferroelectric thin films using phase-field simulations, taking PbTiO 3 thin films as a model system. We found that both the position of phase boundaries in the strain phase diagrams and the domain morphology are significantly influenced by the cooling rates. It is revealed that while the paraelectric-ferroelectric phase boundary remains invariant, the phase boundaries between single-phase and multi-phase regions tend to shift toward the corresponding multi-phase region as the cool rate reduces. Slow cooling generally leads to more ordered domain structures with increased domain size. Using the obtained equilibrium domain structures, we calculated effective thermal conductivities and found significant variations that can be tuned by the cooling rates. In conclusion, this work reveals an underexplored yet critical impact of cooling rates on phase equilibria and domain structures in ferroelectric thin films, which may inspire further fine-tuning of domains and domain walls in low-dimensional ferroelectrics for multifunctional applications.

Domain structures↗

Summer Convective Precipitation Changes Over the Great Lakes Region Under a Warming Scenario

To understand future summer precipitation changes over the Great Lakes Region (GLR), we performed an ensemble of regional climate simulations through the Pseudo-Global Warming (PGW) approach. We found that different types of convective precipitation respond differently to the PGW signal. Isolated deep convection (IDC), usually concentrated in the southern domain, shows an increase in precipitation to the north of the GLR. Mesoscale convective systems (MCSs), usually concentrated upwind of the GLR, shift to the downwind region with increased precipitation. Thermodynamic variables such as convective available potential energy (CAPE) and convective inhibition energy (CIN) are found to increase across almost the entire studied domain, creating a potential environment more favorable for stronger convection systems and less favorable for weaker ones. Meanwhile, changes in the lifting condensation level (LCL) and level of free convection (LFC) show a strong correlation with variations in convective precipitation, highlighting the significance of these thermodynamic factors in controlling precipitation over the domain. Our results indicate that the decrease in LCL and LCF in areas with increased convective precipitation is mainly due to increased atmospheric moisture. In response to the prescribed warming perturbation, MCSs occur more frequently downwind, while localized IDCs exhibit more intense rain rates, longer durations, and larger rainfall area.

54 ENVIRONMENTAL SCIENCES↗

Comparison of the Forward and Reverse Photocycle Dynamics of Two Highly Similar Canonical Red/Green Cyanobacteriochromes Reveals Unexpected Differences

Cyanobacteriochromes (CBCRs) are cyanobacterial photoreceptors that exhibit photochromism between two states: a thermally stable dark-adapted state and a metastable light-adapted state with bound linear tetrapyrrole (bilin) chromophores possessing 15Z and 15E configurations, respectively. The photodynamics of canonical red/green CBCRs have been extensively studied; however, the time scales of their excited-state lifetimes and subsequent ground-state evolution rates widely differ and, at present, remain difficult to predict. Here, we compare the photodynamics of two closely related red/green CBCRs that have substantial sequence identity (~68%) and similar chromophore environments: AnPixJg2 from Anabaena sp. PCC 7120 and NpR6012g4 from Nostoc punctiforme. Using broadband transient absorption spectroscopy on the primary (125 fs to 7 ns) and secondary (7 ns to 10 ms) time scales together with global analysis modeling, our studies revealed that AnPixJg2 and NpR6012g4 have comparable quantum yields for initiating the forward ( 15Z P r → 15E P g ) and reverse ( 15E P g → 15Z P r ) reactions, which proceed through monotonic and nonmonotonic mechanisms, respectively. In addition to small discrepancies in the kinetics, the secondary reverse dynamics resolved unique features for each domain: intermediate shunts in NpR6012g4 and a Meta-Gf intermediate red-shifted from the 15Z P r photoproduct in AnPixJg2. Altogether, this study supports the conclusion that sequence similarity is a useful criterion for predicting pathways of the light-induced evolution and quantum yield of generating primary intermediate Φ p within subfamilies of CBCRs, but more studies are still needed to develop a comprehensive molecular level understanding of these processes.

59 BASIC BIOLOGICAL SCIENCES↗

An FDA-approved drug structurally and phenotypically corrects the K210del mutation in genetic cardiomyopathy models

Dilated cardiomyopathy (DCM) due to genetic disorders results in decreased myocardial contractility, leading to high morbidity and mortality rates. There are several therapeutic challenges in treating DCM, including poor understanding of the underlying mechanism of impaired myocardial contractility and the difficulty of developing targeted therapies to reverse mutation-specific pathologies. In this report, we focused on K210del, a DCM-causing mutation, due to 3-nucleotide deletion of sarcomeric troponin T (TnnT), resulting in loss of Lysine210. We resolved the crystal structure of the troponin complex carrying the K210del mutation. K210del induced an allosteric shift in the troponin complex resulting in distortion of activation Ca 2+ -binding domain of troponin C (TnnC) at S69, resulting in calcium discoordination. Next, we adopted a structure-based drug repurposing approach to identify bisphosphonate risedronate as a potential structural corrector for the mutant troponin complex. Cocrystallization of risedronate with the mutant troponin complex restored the normal configuration of S69 and calcium coordination. Risedronate normalized force generation in K210del patient-induced pluripotent stem cell–derived (iPSC-derived) cardiomyocytes and improved calcium sensitivity in skinned papillary muscles isolated from K210del mice. Systemic administration of risedronate to K210del mice normalized left ventricular ejection fraction. Collectively, these results identify the structural basis for decreased calcium sensitivity in K210del and highlight structural and phenotypic correction as a potential therapeutic strategy in genetic cardiomyopathies.

Research & Experimental Medicine↗

Class imbalance in out-of-distribution datasets: Improving the robustness of the TextCNN for the classification of rare cancer types

In the last decade, the widespread adoption of electronic health record documentation has created huge opportunities for information mining. Natural language processing (NLP) techniques using machine and deep learning are becoming increasingly widespread for information extraction tasks from unstructured clinical notes. Disparities in performance when deploying machine learning models in the real world have recently received considerable attention. In the clinical NLP domain, the robustness of convolutional neural networks (CNNs) for classifying cancer pathology reports under natural distribution shifts remains understudied. In this research, we aim to quantify and improve the performance of the CNN for text classification on out-of-distribution (OOD) datasets resulting from the natural evolution of clinical text in pathology reports. We identified class imbalance due to different prevalence of cancer types as one of the sources of performance drop and analyzed the impact of previous methods for addressing class imbalance when deploying models in real-world domains. Our results show that our novel class-specialized ensemble technique outperforms other methods for the classification of rare cancer types in terms of macro F1 scores. We also found that traditional ensemble methods perform better in top classes, leading to higher micro F1 scores. Based on our findings, we formulate a series of recommendations for other ML practitioners on how to build robust models with extremely imbalanced datasets in biomedical NLP applications.

60 APPLIED LIFE SCIENCES↗

Crystal structure of a seven-substitution mutant of hydroxynitrile lyase from rubber tree

The α/β-hydrolase fold superfamily includes esterases and hydroxynitrile lyases which, despite catalyzing different reactions, share a Ser–His–Asp catalytic triad. We report a 1.99 Å resolution crystal structure of HNL6V, an engineered variant of hydroxynitrile lyase fromHevea brasiliensis(HbHNL) containing seven amino-acid substitutions (T11G, E79H, C81L, H103V, N104A, G176S and K236M). The structure reveals that HNL6V maintains the characteristic α/β-hydrolase fold while exhibiting systematic shifts in backbone and catalytic atom positions. Compared with wild-typeHbHNL, the C α positions in HNL6V differ by a mean of 0.2 ± 0.1 Å, representing a statistically significant displacement. Importantly, the catalytic triad and oxyanion-hole atoms have moved 0.2–0.8 Å closer to their corresponding positions in SABP2, although they remain 0.3–1.1 Å from fully achieving the configuration of SABP2. The substitutions also increase local flexibility, particularly in the lid domain covering the active site. This structural characterization demonstrates that targeted amino-acid substitutions can systematically shift catalytic geometries towards those of evolutionarily related enzymes.

Biochemistry & Molecular Biology↗