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At least 793 records · Page 44

Leveraging AI for Productive and Trustworthy HPC Software: Challenges and Research Directions

We discuss the challenges and propose research directions for using AI to revolutionize the development of high-performance computing (HPC) software. AI technologies, in particular large language models, have transformed every aspect of software development. For its part, HPC software is recognized as a highly specialized scientific field of its own. We discuss the challenges associated with leveraging state-of-the-art AI technologies to develop such a unique and niche class of software and outline our research directions in the two US Department of Energy–funded projects for advancing HPC Software via AI: Ellora and Durban.

Teranishi, Keita [ORNL] (ORCID:0000000166472690)↗

Benchmarking Initiatives

Benchmarking has been recognized as an efficient tool for model validation as well as scientific collaboration. Several workshop series have been established to foster the benchmarking idea: setting up test cases with increasing complexity for method development and code comparison. In addition to representing model complexity, one of the key efforts is to develop codes that are suitable for modern HPC platforms such as PetaFlop supercomputers. It has been realized that those challenges are beyond single team capabilities. The Subsurface Environmental Simulation Benchmarking (SSBench) working group was initiated to develop, publish, and make publicly available well-described benchmark problems that could be used to demonstrate simulator conformance with norms established by the subsurface science and engineering community. SSBench supports the development of environmentally-relevant benchmark problem sets that provide rigorous tests for process model conceptualization, numerical implementation, process coupling, and accuracy. The initial SSBench focus on multicomponent reactive transport modeling reflects the expanding range of mechanisms and increasing complexity needed to address issues relevant to climate change, nuclear waste management, contaminant remediation, and pollution prevention.

benchmarking↗

An Emerging Role for Polystores in Precision Medicine

Medical data is organically heterogeneous, and it usually varies significantly in both size and composition. Yet, this data is also a key for the recent and promising field of precision medicine, which focuses on identifying and tailoring appropriate medical treatments for the needs of the individual patients, based on their specific conditions, their medical history, lifestyle, genetic, and other individual factors. As we, and a database community at large, recognize that a “one size does not fit all” solution is required to work with such data, we present in this paper our observations based on our experiences, and the applications in the field of precision medicine. Finally, we make the case for the use of polystore architecture; how it applies for precision medicine; we discuss the reference architecture; describe some of its critical components (array database); and discuss the specific types of analysis that directly benefit from this database architecture, and the ways it serves the data.

60 APPLIED LIFE SCIENCES↗

Frequency Domain Reflectometry Modeling and Measurement for Nondestructive Evaluation of Nuclear Power Plant Cables

Cable insulation polymers are among the more susceptible materials to age-related degradation within a nuclear power plant. This is recognized by both regulators and utilities, so all plants have developed cable aging management programs to detect damage before critical component failure in compliance with regulatory guidelines. Although a wide range of tools are available to evaluate cables and cable systems, cable aging management programs vary in how condition monitoring and NDE is conducted as utilities search for the most reliable and cost-effective ways to assess cable system condition. Frequency domain reflectometry (FDR) is emerging as one valuable tool to locate and assess damaged portions of a cable system with minimal cost and only requires access in most cases to one of the cable terminal ends. This work examines a physics-based model of a cable system and relates it to FDR measurements for a better understanding of specific damage influences on defect detectability.

cable↗

Scattering forms and the positive geometry of kinematics, color and the worldsheet

The search for a theory of the S-Matrix over the past five decades has revealed surprising geometric structures underlying scattering amplitudes ranging from the string worldsheet to the amplituhedron, but these are all geometries in auxiliary spaces as opposed to the kinematical space where amplitudes actually live. Motivated by recent advances providing a reformulation of the amplituhedron and planar N = 4 SYM amplitudes directly in kinematic space, we propose a novel geometric understanding of amplitudes in more general theories. The key idea is to think of amplitudes not as functions, but rather as differential forms on kinematic space. We explore the resulting picture for a wide range of massless theories in general spacetime dimensions. For the bi-adjoint Φ3 scalar theory, we establish a direct connection between its “scattering form” and a classic polytope — the associahedron — known to mathematicians since the 1960’s. We find an associahedron living naturally in kinematic space, and the tree level amplitude is simply the “canonical form” associated with this “positive geometry”. Fundamental physical properties such as locality and unitarity, as well as novel “soft” limits, are fully determined by the combinatorial geometry of this polytope. Furthermore, the moduli space for the open string worldsheet has also long been recognized as an associahedron. We show that the scattering equations act as a diffeomorphism between the interior of this old “worldsheet associahedron” and the new “kinematic associahedron”, providing a geometric interpretation and simple conceptual derivation of the bi-adjoint CHY formula. We also find “scattering forms” on kinematic space for Yang-Mills theory and the Non-linear Sigma Model, which are dual to the fully color-dressed amplitudes despite having no explicit color factors. This is possible due to a remarkable fact—“Color is Kinematics”— whereby kinematic wedge products in the scattering forms satisfy the same Jacobi relations as color factors. Finally, all our scattering forms are well-defined on the projectivized kinematic space, a property which can be seen to provide a geometric origin for color-kinematics duality.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Kinematic focus point method for particle mass measurements in missing energy events

We investigate the solvability of the event kinematics in missing energy events at hadron colliders, as a function of the particle mass ansatz. To be specific, we reconstruct the neutrino momenta in dilepton tt¯-like events, without assuming any prior knowledge of the mass spectrum. We identify a class of events, which we call extreme events, with the property that the kinematic boundary of their allowed region in mass parameter space passes through the true mass point. We develop techniques for recognizing extreme events in the data and demonstrate that they are abundant in a realistic data sample, due to expected singularities in phase space. We propose a new method for mass measurement whereby we obtain the true values of the mass parameters as the focus point of the kinematic boundaries for all events in the data sample. Since the masses are determined from a relatively sharp peak structure (the density of kinematic boundary curves), the method avoids some of the systematic errors associated with other techniques. We show that this new approach is complementary to previously considered methods in the literature where one studies the solvability of the kinematic constraints throughout the mass parameter space. In particular, we identify a problematic direction in mass space of nearly 100% solvability, and then show that the focus point method is effective in lifting the degeneracy.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Traversable wormholes as quantum channels: exploring CFT entanglement structure and channel capacity in holography

We interpret the traversable wormhole in AdS/CFT in the context of quantum information theory. In particular, we investigate its properties as both a quantum channel and entanglement witness. We define protocols that allow either the bounding of the channel’s entanglement capacity or the determination of aspects of the entanglement structure between the two boundary CFTs. Such protocols and connections allow for the use of quantum channel techniques in the study of gravitational physics and vice versa. More generally, our results suggest a purely quantum information-theoretic criterion for recognizing when the product of two boundary theories has a classical bulk interpretation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Probing energetic light dark matter with multi-particle tracks signatures at DUNE

The search for relativistic scattering signals of cosmogenic light dark matter at terrestrial detectors has received increasing attention as an alternative approach to probe dark-sector physics. Large-volume neutrino experiments are well motivated for searches of dark matter that interacts very weakly with Standard Model particles and/or that exhibits a small incoming flux. We perform a dedicated signal sensitivity study for a detector similar to the one proposed by the DUNE Collaboration for cosmogenic dark-matter signals resulting from a non-minimal multi-particle dark-sector scenario. The liquid argon time projection chamber technology adopted for the DUNE detectors is particularly suited for searching for complicated signatures owing to good measurement resolution and particle identification, as well as dE/dx measurements to recognize merged tracks. Taking inelastic boosted dark matter as our benchmark scenario that allows for multiple visible particles in the final state, we demonstrate that the DUNE far detectors have a great potential for probing scattering signals induced by relativistic light dark matter. Detector effects and backgrounds have been estimated and taken into account. Model-dependent and model-independent expected sensitivity limits for a DUNE-like detector are presented.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Comprehensive characterization of hepatocyte-derived extracellular vesicles identifies direct miRNA-based regulation of hepatic stellate cells and DAMP-based hepatic macrophage IL-1ß and IL-17 upregulation in alcoholic hepatitis mice.

Extracellular vesicles (EVs) have been growingly recognized as biomarkers and mediators of alcoholic liver disease (ALD) in human and mice. Here we characterized hepatocyte-derived EVs (HC-EVs) and their cargo for their biological functions in a novel murine model that closely resembles liver pathology observed in patients with alcoholic hepatitis (AH), the most severe spectrum of ALD. The number of circulating EVs and HC-EVs were significantly increased by 10-fold in AH mice compared to control mice. The miRNA(miR)-seq analysis detected 20 up-regulated and 4 down-regulated miRNAs (P < 0.001-0.05) in AH-HC-EVs. Treatment of murine primary hepatic stellate cells (HSCs) with AH-HC-EVs induced ?-SMA (P < 0.05) and Col1a1 (P < 0.001). Smad7, Nr1d2, and Rora genes which regulate HSC activation were predicted targets of 17 miRs up-regulated in AH-HC-EVs. Among them were miR-27a and miR-181 which upon transfection in HSCs, repressed Nr1d2, the HSC quiescence marker. AH-HC-EVs were also enriched in organelle proteins and mitochondrial DNA (10-fold, P < 0.05) and upregulated IL-1??and IL-17 production by hepatic macrophages (HMs) from AH mice in a TLR9-dependent manner. These results demonstrate HC-EV release is intensified in AH and suggest that AH-HC-EVs orchestrate liver fibrogenesis by directly targeting HSC quiescence transcripts via a unique set of miRNAs and by amplifying HSC activation via DAMP-based induction of profibrogenic IL-1? and IL-17 by HMs.

AH, hepatocyte-derived EVs, miRNAs, DAMPs, HSC act↗

Ultrasmall sample biochemical analysis

Richard Feynman’s landmark lecture from 1959 titled BThere’s Plenty of Room at the Bottom: An Invitation to Enter a New Field of Physics^ is widely known for encouraging research into the field we now refer to as nanotechnology. In that same lecture, he also presciently recognized that many fundamental questions in biology could be answered through miniaturization, particularly using microscopy, noting that many knowledge gaps could be readily addressed if we could Bjust look at the thing!^ Indeed, increasing the resolution with which biological systems are investigated, whether it be through cryoelectron microscopy, flow cytometry, or singlecell RNA-Seq, has revolutionized many aspects of biological inquiry. In this themed topical collection of Analytical and Bioanalytical Chemistry, we emphasize that there is still Bplenty of room at the bottom^ when it comes to biochemical analysis. Great strides have been made in biology and medicine as chemical measurements that have historically been applied to bulk tissues are extended to the scale at which the biology is occurring, which is often at the cellular or subcellular level.

Kelly, Ryan T.↗

Mercury Concentrations in the Two-Toed Amphiuma ( Amphiuma means ) and the Lesser Siren ( Siren intermedia ): Validating Non-lethal Sampling Methods in Southeastern Aquatic Salamanders

The global decline of amphibians is a major conservation issue. Many stressors are recognized for this decline including exposure to environmental contaminants. Mercury (Hg) is an environmental contaminant that bioaccumulates in wildlife and can cause a variety of negative impacts across taxa, including amphibians. Amphiuma and Siren spp. can comprise a large portion of biomass within their respective ecosystems, and thus, likely serve as important predators or prey in wetland communities. However, due to their cryptic nature, little is known about their ecology, diet, and accumulation potential. Here, we sought to validate a non-lethal sampling method to quantify total mercury (THg) in two enigmatic species of aquatic salamanders: the two-toed amphiuma (Amphiuma means) and the lesser siren (Siren intermedia). We examined relationships between THg content in lethal (whole-body) and non-lethal (tail clip) samples. Tail clips were significant predictors of whole body THg (all p < 0.001), explaining 84-89% of variation in whole body THg. Average whole-body THg (mg/kg did not significantly differ between the two species (p = 0.97), and overall, they had similar whole body THg content (LESI = 0.330 ± 0.04, n = 18; AMME = 0.333 ± 0.07, n = 11). To our knowledge, these data represent the first reported Hg burdens in A. means and S. intermedia.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

A case of immunoglobulin G4-related inflammatory pseudotumor mimicking renal cell carcinoma

In a 69-year-old woman with a history of Mikulicz’s disease, a hypoechoic solitary renal mass was identified on routine ultrasound examination. Based on the findings of computed tomography (CT) and magnetic resonance imaging (MRI), renal cell carcinoma was a possible diagnosis. Subsequent partial nephrectomy revealed a mass characterized by an increased number of blood vessels, internal hemorrhage, and a thick fibrous capsule. Immunohistochemically, the mass comprised of tubulointerstitial nephritis with increased immunoglobulin (Ig)G4-positive plasma cells and fibrosis. Generally, diagnosis of IgG4-related kidney disease (IgG4-RKD) is not difficult when the kidney is involved together with other systemic involvements. However, diagnosis becomes harder when a solitary renal mass appears as a single-organ involvement. On precise review of our imaging findings, MRI signals were markedly affected by hemorrhage, so the mass showed hypointensity on both T1- and T2-weighted imaging, and the signal of in-phase images decreased. Dynamic MRI showed no apparent enhancement of the mass, while CT showed an apparent enhancement effect. Capsule formation was another key finding for IgG4-RKD and was recognized as a gradually enhancing boundary zone surrounding the mass on both CT and MRI. When a solitary renal mass is associated with hemorrhage and thick capsule formation, inflammatory pseudotumor should be considered as differential diagnosis.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Magnetic resonance imaging of the placenta and gravid uterus: a pictorial essay

The placenta is commonly overlooked on magnetic resonance imaging of the pregnant patient, which is frequently performed for alternative reasons such as to characterize fetal or uterine anomalies or to investigate the etiology of acute pelvic pain in pregnancy. Placental disorders have potential for significant maternal and fetal morbidity and peripartum complications if not recognized and treated in a timely manner. The radiologist must be familiar with normal placental variants and the spectrum of benign to life-threatening conditions affecting the placenta so that the Obstetrician can be promptly notified and patient management altered, if necessary. In this pictorial essay, we will describe our MR protocol for placental imaging, provide an image-rich review of the normal placenta, placental variants, and a variety of pathological conditions affecting the placenta and gravid uterus.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Imaging post-stereotactic body radiation therapy responses for hepatocellular carcinoma: typical imaging patterns and pitfalls

Stereotactic body radiation therapy (SBRT) has increased utility in the management of hepatocellular carcinoma (HCC) ranging from local therapy in early-stage HCC not suitable for other focal therapies to end-stage HCC. As the indications for the use of SBRT in HCC expand, diagnostic imaging is being increasingly used to assess response to treatment. The imaging features of tumor response do not parallel those of other focal therapies such as radiofrequency ablation or trans-arterial chemoembolization that immediately devascularize the tumor. The tumor response to SBRT on imaging takes much longer and often shows gradual changes including the reduction of enhancement and size over several months. It is essential to recognize the typical imaging patterns of response, as well as the appearance of focal liver reaction in the non-target liver that can confound image interpretation. The timing of treatment response assessment imaging is fundamental to minimize the potential for false negative response. The purpose of this article is to review the variable post-SBRT imaging features of HCC and adjacent liver parenchyma and discuss the potential pitfalls of imaging evaluation after SBRT for HCC.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Abdominal manifestations of hereditary hemorrhagic telangiectasia: a series of 333 patients over 15 years

Purpose: Hereditary hemorrhagic telangiectasia (HHT) is an autosomal dominant multi-organ vascular disorder that commonly affects the gastrointestinal tract and the liver resulting in telangiectasias and arteriovenous malformations (AVMs). Previous studies looking at the prevalence of liver and abdominal organ involvement in HHT have been limited by differing imaging techniques and sample size limitations. We sought to define the prevalence of HHT related abdominal vascular abnormalities using optimized multiphasic contrast-enhanced abdominal computed tomography (CT) exams in a large cohort of HHT patients. Methods: Between January 2001 and May 2015; we identified a total of 333 consecutive HHT patients who had undergone a dedicated HHT protocol multiphase abdominal CT at our institution. The CT exams were reviewed by three board certified abdominal radiologists for the presence of vascular abnormalities involving the liver, pancreas, spleen, and other abdominal organs. Vascular abnormalities involving the liver were further categorized as telangiectasias, large confluent vascular masses, perfusion abnormalities, or hepatic shunts. Results: In patients with abdominal vascular abnormalities, the liver was the most commonly involved organ, with 180 out of 333 (54.1%) patients demonstrating at least one hepatic vascular abnormality (telangiectasia, confluent vascular mass, transient perfusion abnormalities, and hepatic shunts), with most (70.0%) demonstrating multiple hepatic vascular abnormalities. The other most common organs involved included the pancreas (18.0%), spleen (6.3%), and small bowel (4.5%). Conclusion: In patients with the clinical diagnosis of HHT, greater than half demonstrate an abdominal vascular abnormality, with the most commonly involved organ being the liver. These may be under recognized on routine or single phase contrast-enhanced CT of the abdomen. This supports the use of optimized multiphasic abdominal CT exams as an important tool for the evaluation and screening of patients with HHT.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

The inferior vena cava: a pictorial review of embryology, anatomy, pathology, and interventions

The inferior vena cava (IVC) is the largest venous conduit below the diaphragm. Although this structure is often overlooked both clinically and radiographically, it can be involved in many different pathologic processes. A thorough understanding of the IVC will assist the radiologist in recognizing anatomic variants, identifying abnormalities, and providing accurate differential diagnoses. In this comprehensive pictorial review of the IVC, we depict embryology behind anatomic variants, present a wide range of pathology with a focus on diagnostic imaging, and describe relevant endovascular interventions.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Imaging of transgender patients: expected findings and complications of gender reassignment therapy

Objectives: Gender dysphoria is defined as a conflict between the biological gender and the gender with which the person identifies. Gender reassignment therapy can alter external sexual features to resemble those of the desired gender and are broadly classified into two types, female to male (FTM) and male to female (MTF). In this paper we describe expected findings and complications of gender reassignment therapy. Methods: Collaborative multi-institutional project supported by Ovarian and Uterine Cancer Disease Focused panel of Society of Abdominal Radiology. Results: Gender dysphoria is defined as a conflict between the biological gender and the gender with which the person identifies. Gender reassignment therapy can alter external sexual features to resemble those of the desired gender and are broadly classified into two types, female to male (FTM) and male to female (MTF). These therapies include hormonal treatment as well as surgical procedures. FTM genital reconstructive therapy includes creation of a neophallus, which can be achieved by metoidioplasty or phalloplasty with mastectomy, along with testosterone administration. MTF gender reassignment surgery includes complete removal of external genitalia with penectomy and orchiectomy, with vaginoplasty, clitoroplasty, labiaplasty, and breast augmentation along with estrogen supplements. Conclusion: Surgical techniques alter the standard anatomy and make imaging interpretation challenging if radiologists are unfamiliar with expected post-operative appearances. It is important to recognize the complications related to surgical and non-surgical treatment of gender dysphoria to avoid interpretation errors. Furthermore, increasing the prevalence of transgender patients requires increased sensitivity when interpreting imaging studies to reduce the potential for misdiagnoses in reporting due to frequently incomplete available clinical history.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Anorectal pitfalls in computed tomography colonography

There is a wide array of pathological lesions seen in the anorectal region with CT colonography (CTC), much of which is unique to this location. Many relatively common findings in the anorectal region are typically benign, but can be misinterpreted as malignant. There are also technique-related pitfalls that can impede accurate diagnosis of anorectal findings at CTC. Understanding common and uncommon lesions in the anorectal region as well as recognizing technical pitfalls will optimize interpretation of CTC and decrease the number of missed cancers and false positives. This review will systematically cover that they key pitfalls confronting the radiologist at CTC interpretation of the anorectal region, primarily dividing them into those related to underlying anatomy and those related to technique. Tips for how to effectively handle these potential pitfalls will also be discussed.

62 RADIOLOGY AND NUCLEAR MEDICINE↗