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At least 1,171 records · Page 65

Structural Mechanism of the Pan-BCR-ABL Inhibitor Ponatinib (AP24534): Lessons for Overcoming Kinase Inhibitor Resistance

The BCR-ABL inhibitor imatinib has revolutionized the treatment of chronic myeloid leukemia. However, drug resistance caused by kinase domain mutations has necessitated the development of new mutation-resistant inhibitors, most recently against the T315I gatekeeper residue mutation. Ponatinib (AP24534) inhibits both native and mutant BCR-ABL, including T315I, acting as a pan-BCR-ABL inhibitor. Here, we undertook a combined crystallographic and structure-activity relationship analysis on ponatinib to understand this unique profile. While the ethynyl linker is a key inhibitor functionality that interacts with the gatekeeper, virtually all other components of ponatinib play an essential role in its T315I inhibitory activity. The extensive network of optimized molecular contacts found in the DFG-out binding mode leads to high potency and renders binding less susceptible to disruption by single point mutations. The inhibitory mechanism exemplified by ponatinib may have broad relevance to designing inhibitors against other kinases with mutated gatekeeper residues.

59 BASIC BIOLOGICAL SCIENCES↗

Agent-based modeling and simulation for the circular economy: Lessons learned and path forward

Circular economy aims at decoupling human activities from resource use and creating wealth. However, many have questioned the link between increased circularity and sustainability, resulting in several methodological approaches being developed to answer that question. This article analyzes and discusses the insights gained from applying agent-based modeling and simulation to study the techno-economic and social conditions promoting circularity and sustainability. This article analyzes the benefits and limitations of this technology and discusses future methodology developments within the circular economy context. Moreover, six limits of the circular economy concept are used to interpret insights from the literature: thermodynamic limits, system boundary limits, limits posed by the physical scale of the economy, limits posed by path dependencies and lock-in, limits of governance and management, and limits of social and cultural definitions. Promising research avenues are to use this methodology with machine learning, industrial ecology methods, and detailed geographic information.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Shock compaction heating and collisional processes in the production of type 3 ordinary chondrites: Lessons from the (nearly) unique L3 chondrite melt breccia Northwest Africa 8709

Abstract Northwest Africa (NWA) 8709 is a rare example of a type 3 ordinary chondrite melt breccia and provides critical information for the shock compaction histories of chondrites. An L3 protolith for NWA 8709 is inferred on the basis of oxygen isotope composition, elemental composition, diverse mineral chemistry, and overall texture. NWA 8709 is among the most strongly shocked type 3 chondrites known, and experienced complete melting of the matrix and partial melting of chondrules. Unmelted phases underwent FeO reduction and partial homogenization, with reduction possibly occurring by reaction of olivine and low‐Ca pyroxene with an S‐bearing gas that was produced by vaporization. Chondrules and metal grains became foliated by uniaxial compaction, and during compression, chondrules and fragments became attached to form larger clumps. This process, and possibly also melt incorporation into chondrules to cause “inflation,” may have contributed to anomalously large chondrule sizes in NWA 8709. The melt breccia character is attributed to strong shock affecting a porous precursor. Data‐model comparisons suggest that a precursor with 23% porosity that was impacted by a 3 km/s projectile could have produced the meteorite. The rarity of other type 3 ordinary chondrite melt breccias implies that the immediate precursors to such chondrites were lower in porosity than the NWA 8709 precursor, or experienced weaker shocks. Altogether, the data imply a predominantly “quiet” dynamical environment to form most type 3 ordinary chondrites, with compaction occurring in a series of relatively weak shock events.

Ruzicka, Alex M.↗

Unveiling the transferability of PLSR models for leaf trait estimation: lessons from a comprehensive analysis with a novel global dataset

Leaf traits are essential for understanding many physiological and ecological processes. Partial least squares regression (PLSR) models with leaf spectroscopy are widely applied for trait estimation, but their transferability across space, time, and plant functional types (PFTs) remains unclear. We compiled a novel dataset of paired leaf traits and spectra, with 47 393 records for >700 species and eight PFTs at 101 globally distributed locations across multiple seasons. Using this dataset, we conducted an unprecedented comprehensive analysis to assess the transferability of PLSR models in estimating leaf traits. While PLSR models demonstrate commendable performance in predicting chlorophyll content, carotenoid, leaf water, and leaf mass per area prediction within their training data space, their efficacy diminishes when extrapolating to new contexts. Specifically, extrapolating to locations, seasons, and PFTs beyond the training data leads to reduced R 2 (0.12–0.49, 0.15–0.42, and 0.25–0.56) and increased NRMSE (3.58–18.24%, 6.27–11.55%, and 7.0–33.12%) compared with nonspatial random cross-validation. The results underscore the importance of incorporating greater spectral diversity in model training to boost its transferability. These findings highlight potential errors in estimating leaf traits across large spatial domains, diverse PFTs, and time due to biased validation schemes, and provide guidance for future field sampling strategies and remote sensing applications.

59 BASIC BIOLOGICAL SCIENCES↗

Third national inventory of nuclear liabilities - main findings, lessons learned

The safe management of a country's radioactive substances in both the short and the long term implies a cost to its present society and necessitates financial resources to cover these costs. Once they are needed, these financial resources may prove to be insufficient or even completely lacking, leading to a nuclear liability. By virtue of article 9 of the Belgian law of 12 December 1997, the Belgian Government wishes to avoid the occurrence of such nuclear liabilities. This law charges ONDRAF/NIRAS, the Belgian Agency for Radioactive Waste and Enriched Fissile Materials with the mission to draw up a register of the localisation and the state of all nuclear sites and all sites containing radioactive substances, to estimate the costs of their decommissioning and remediation, to evaluate the existence and adequacy of the provisions for financing these future or current operations and to update the resulting inventory of nuclear liabilities on a five-yearly basis. This paper outlines the methodology put in place by ONDRAF/NIRAS to accomplish this assignment and highlights some of the results of this third inventory. It then focuses on the main recommendations ONDRAF/NIRAS made to the Belgian Government on the field of avoiding potential nuclear liabilities. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Belgian regulatory framework for decontamination and decommissioning - lessons learned and new initiatives

Belgium can rely on significant experience in the field of decontamination and decommissioning of nuclear facilities. Several projects are ongoing and include research reactors (BR3, Thetis), uranium and MOX fuel fabrication plants (FBFC International, Belgonucleaire), fuel reprocessing facilities (Eurochemic) and radwaste processing facilities (Belgoprocess). Additional projects are expected in the coming years with the planned final shutdown of the oldest nuclear power reactor units. Two national authorities are involved in the decontamination and decommissioning process of nuclear facilities. The FANC (together with its subsidiary Bel V) is concerned for all matters related to nuclear safety and radiation protection, while NIRAS/ONDRAF is concerned for all matters related to radioactive waste and fuel management and financial provisions. These attributions ensure that all safety and material concerns are addressed and that both the licensees and the national authorities bear their own responsibilities. They rely on an existing regulatory framework covering both the procedural and the technical aspects of the decontamination and decommissioning activities. However, opportunities for regulatory improvement were raised after some recent events in Belgium, among which the bankruptcy of a nuclear company producing radioisotopes, involving numerous additional interested parties in a complex judiciary context. Amendments in the current regulations are considered to increase the prerogatives of the authorities regarding the management of radioactive waste by a licensee, the transfer of an operating license from an operator to another, and the general decommissioning strategy of a facility. Furthermore, a dedicated 'waste and decommissioning' working group within WENRA defined new reference levels applying to the decontamination and decommissioning of nuclear facilities. Belgium committed to include these requirements explicitly in its national legislation, even though most of them were already included in the existing decommissioning authorizations. Amendments will cover the safety provisions inherent to the decontamination and decommissioning phase, such as the decommissioning strategy, the qualification of techniques, the experience feedback valorization, the periodic safety reviews, the radioactive waste management, or the final characterization of the sites. Additionally, requirements regarding the authorization process will be detailed, such as the content of the licensee's application file or the structure of the safety report covering the decontamination and decommissioning phase. These changes will contribute to a more secure regulatory framework for all interested parties. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Rocky flats closure project - lessons learned in worker stakeholder engagement

The Rocky Flats Environmental Technology Site (EPA Superfund site near Denver, Colorado) produced plutonium components for nuclear weapons for the U.S. defense program. The facility shut down in 1989 and clean up began in 1992. To ensure safe remediation of inactive nuclear sites, site owners have begun to consult stakeholders more widely in recent years. The closure of Rocky Flats aimed to set the standard for stakeholder involvement in doing the work safely, complying with regulations/standards, in a cost-effective manner. We have studied, using ethnographic methods, the extent to which workers at Rocky Flats were involved in communication and decision making strategies. Our results point out that workers can have perceptions of the site remediation process that differ from management and even other workers and that a significant number of workers questioned the commitment by management to engage the worker as stakeholder. The most effective remediation efforts should involve careful consideration of the insights and observations of all workers, particularly those who face immediate and high-level health and safety risks. (authors)

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

WE-A-BRC-02: Lessons Learned: Clinical Trials and Operations

Quality and safety in healthcare are inextricably linked. There are compelling data that link poor quality radiation therapy to inferior patient survival. Radiation Oncology clinical trial protocol deviations often involve incorrect target volume delineation or dosing, akin to radiotherapy incidents which also often involve partial geometric miss or improper radiation dosing. When patients with radiation protocol variations are compared to those without significant protocol variations, clinical outcome is negatively impacted. Traditionally, quality assurance in radiation oncology has been driven largely by new technological advances, and safety improvement has been driven by reactive responses to past system failures and prescriptive mandates recommended by professional organizations and promulgated by regulators. Prescriptive approaches to quality and safety alone often do not address the huge variety of process and technique used in radiation oncology. Risk-based assessments of radiotherapy processes provide a mechanism to enhance quality and safety, both for new and for established techniques. It is imperative that we explore such a paradigm shift at this time, when expectations from patients as well as providers are rising while available resources are falling. There is much we can learn from our past experiences to be applied towards the new risk-based assessments. Learning Objectives: Understand the impact of clinical and technical quality on outcomes Understand the importance of quality care in radiation oncology Learn to assess the impact of quality on clinical outcomes D. Followill, NIH Grant CA180803.

60 APPLIED LIFE SCIENCES↗

WE-A-BRC-03: Lessons Learned: IROC Audits

Quality and safety in healthcare are inextricably linked. There are compelling data that link poor quality radiation therapy to inferior patient survival. Radiation Oncology clinical trial protocol deviations often involve incorrect target volume delineation or dosing, akin to radiotherapy incidents which also often involve partial geometric miss or improper radiation dosing. When patients with radiation protocol variations are compared to those without significant protocol variations, clinical outcome is negatively impacted. Traditionally, quality assurance in radiation oncology has been driven largely by new technological advances, and safety improvement has been driven by reactive responses to past system failures and prescriptive mandates recommended by professional organizations and promulgated by regulators. Prescriptive approaches to quality and safety alone often do not address the huge variety of process and technique used in radiation oncology. Risk-based assessments of radiotherapy processes provide a mechanism to enhance quality and safety, both for new and for established techniques. It is imperative that we explore such a paradigm shift at this time, when expectations from patients as well as providers are rising while available resources are falling. There is much we can learn from our past experiences to be applied towards the new risk-based assessments. Learning Objectives: Understand the impact of clinical and technical quality on outcomes Understand the importance of quality care in radiation oncology Learn to assess the impact of quality on clinical outcomes D. Followill, NIH Grant CA180803.

60 APPLIED LIFE SCIENCES↗

TH-B-BRC-00: How to Identify and Resolve Potential Clinical Errors Before They Impact Patients Treatment: Lessons Learned

Radiation treatment consists of a chain of events influenced by the quality of machine operation, beam data commissioning, machine calibration, patient specific data, simulation, treatment planning, imaging and treatment delivery. There is always a chance that the clinical medical physicist may make or fail to detect an error in one of the events that may impact on the patient’s treatment. In the clinical scenario, errors may be systematic and, without peer review, may have a low detectability because they are not part of routine QA procedures. During treatment, there might be errors on machine that needs attention. External reviews of some of the treatment delivery components by independent reviewers, like IROC, can detect errors, but may not be timely. The goal of this session is to help junior clinical physicists identify potential errors as well as the approach of quality assurance to perform a root cause analysis to find and eliminate an error and to continually monitor for errors. A compilation of potential errors will be presented by examples of the thought process required to spot the error and determine the root cause. Examples may include unusual machine operation, erratic electrometer reading, consistent lower electron output, variation in photon output, body parts inadvertently left in beam, unusual treatment plan, poor normalization, hot spots etc. Awareness of the possibility and detection of error in any link of the treatment process chain will help improve the safe and accurate delivery of radiation to patients. Four experts will discuss how to identify errors in four areas of clinical treatment. D. Followill, NIH grant CA 180803.

60 APPLIED LIFE SCIENCES↗

Optimizing metaproteomics database construction: lessons from a study of the vaginal microbiome

Metaproteomics, a method for untargeted, high-throughput identification of proteins in complex samples, provides functional information about microbial communities and can tie functions to specific taxa. Metaproteomics often generates less data than other omics techniques, but analytical workflows can be improved to increase usable data in metaproteomic outputs. Identification of peptides in the metaproteomic analysis is performed by comparing mass spectra of sample peptides to a reference database of protein sequences. Although these protein databases are an integral part of the metaproteomic analysis, few studies have explored how database composition impacts peptide identification. Here, we used cervicovaginal lavage (CVL) samples from a study of bacterial vaginosis (BV) to compare the performance of databases built using six different strategies. We evaluated broad versus sample-matched databases, as well as databases populated with proteins translated from metagenomic sequencing of the same samples versus sequences from public repositories. Smaller sample-matched databases performed significantly better, driven by the statistical constraints on large databases. Additionally, large databases attributed up to 34% of significant bacterial hits to taxa absent from the sample, as determined orthogonally by 16S rRNA gene sequencing. We also tested a set of hybrid databases which included bacterial proteins from NCBI RefSeq and translated bacterial genes from the samples. These hybrid databases had the best overall performance, identifying 1,068 unique human and 1,418 unique bacterial proteins, ~30% more than a database populated with proteins from typical vaginal bacteria and fungi. Our findings can help guide the optimal identification of proteins while maintaining statistical power for reaching biological conclusions.

59 BASIC BIOLOGICAL SCIENCES↗

37 Years with the light scalar mesons. The learned lessons

Attention is paid to the production mechanisms of light scalars that reveal their nature. We reveal the chiral shielding of the σ(600) meson. We show that the kaon loop mechanism of the ϕ radiative decays, ratified by experiment, is four-quark transition and points to the four-quark nature of light scalars. We show also that the light scalars are produced in the two photon collisions via four-quark transitions in contrast to the classic P wave tensor qq̅ mesons that are produced via two-quark transitions γγ → qq̅. We study the mechanism of production of the light scalar mesons in the D{sup +}{sub s }→ π{sup +}π{sup −} e {sup +}ν decays: D{sup +}{sub s }→ ss̅e {sup +}ν → [σ(600) + f {sub 0}(980)]e {sup +}ν → π{sup +}π{sup −} e {sup +}ν, and compare it with the mechanism of production of the light pseudoscalar mesons in the D{sup +}{sub s }→ (η/η′)e {sup +}ν decays: D{sup +}{sub s }→ ss̅e {sup +}ν → (η/η′)e {sup +}ν. As a result we find support to four-quark nature of light scalars. In the end, we outline the future research program.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Lessons from black hole quasinormal modes in modified gravity

Quasinormal modes (QNMs) of perturbed black holes have recently gained much interest because of their tight relations with the gravitational wave signals emitted during the post-merger phase of a binary black hole coalescence. One of the intriguing features of these modes is that they respect the no-hair theorem, and hence, they can be used to test black hole spacetimes and the underlying gravitational theory. In this paper, we exhibit three different aspects of how black hole QNMs could be altered in theories beyond Einstein’s general relativity (GR). These aspects are (i) the direct alterations of QNM spectra as compared with those in GR, (ii) the violation of the geometric correspondence between the high-frequency QNMs and the photon geodesics around the black hole, and (iii) the breaking of the isospectrality between the axial and polar gravitational perturbations. Several examples will be provided in each individual case. The prospects and possible challenges associated with future observations will be also discussed.

79 ASTRONOMY AND ASTROPHYSICS↗

Application Characterization at Scale: Lessons learned from developing a distributed Open Community Runtime system for High Performance Computing

Since 2012, the U.S. Department of Energy’s X-Stack program has been developing solutions including runtime systems, programming models, languages, compilers, and tools for the Exascale system software to address crucial performance and power requirements. Fine grain programming models and runtime systems show a great potential to efficiently utilize the underlying hardware. Thus, they are essential to many X-Stack efforts. An abundant amount of small tasks can better utilize the vast parallelism available on current and future machines. Moreover, finer tasks can recover faster and adapt better, due to a decrease in state and control. Nevertheless, current applications have been written to exploit old paradigms (such as Communicating Sequential Processor and Bulk Synchronous Parallel processing). To fully utilize the advantages of these new systems, applications need to be adapted to these new paradigms. As part of the applications’ porting process, in-depth characterization studies, focused on both application characteristics and runtime features, need to take place to fully understand the application performance bottlenecks and how to resolve them. This paper presents a characterization study for a novel high performance runtime system, called the Open Community Runtime, using key HPC kernels as its vehicle. This study has the following contributions: one of the first high performance, fine grain, distributed memory runtime system implementing the OCR standard (version 0.99a); and a characterization study of key HPC kernels in terms of runtime primitives running on both intra and inter node environments. Running on a general purpose cluster, we have found up to 1635x relative speed-up for a parallel tiled Cholesky Kernels on 128 nodes with 16 cores each and a 1864x relative speed-up for a parallel tiled Smith-Waterman kernel on 128 nodes with 30 cores.

Application characterization↗

Scientific Open-Source Software Is Less Likely to Become Abandoned Than One Might Think! Lessons from Curating a Catalog of Maintained Scientific Software

Scientific software is essential to scientific innovation and in many ways it is distinct from other types of software. Abandoned (or unmaintained), buggy, and hard to use software, a perception often associated with scientific software can hinder scientific progress, yet, in contrast to other types of software, its longevity is poorly understood. Existing data curation efforts are fragmented by science domain and/or are small in scale and lack key attributes. We use large language models to classify public software repositories in World of Code into distinct scientific domains and layers of the software stack, curating a large and diverse collection of over 18,000 scientific software projects. Using this data, we estimate survival models to understand how the domain, infrastructural layer, and other attributes of scientific software affect its longevity. We further obtain a matched sample of non-scientific software repositories and investigate the differences. We find that infrastructural layers, downstream dependencies, mentions of publications, and participants from government are associated with a longer lifespan, while newer projects with participants from academia had shorter lifespan. Against common expectations, scientific projects have a longer lifetime than matched non-scientific open-source software projects. We expect our curated attribute-rich collection to support future research on scientific software and provide insights that may help extend longevity of both scientific and other projects.

Malviya Thakur, Addi [ORNL] (ORCID:000000022681999↗

TECHNOLOGY: A Lesson In LED Adoption: Understanding the hurdles faced by K–12 schools

PK-12 schools lag in upgrading fluorescent lighting. Surprised? So were we; spurring a journey to understand the reasons for lagging adoption of LED. During conversations with school facility managers and other lighting professionals the reasons became clearer. What follows is a synopsis of what has been uncovered so far, yet there remains much to learn. Here, these stories are not the product of imagination; they represent real experiences, real decisions, and real concerns from 9 school districts in 7 states from coast to coast.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Commercial Vehicle Driver Behaviors and Decision Making: Lessons Learned from Urban Ridealongs

As e-commerce and urban deliveries spike, cities grapple with managing urban freight more actively. In order to effectively manage urban deliveries, city planners and policy makers need to better understand driver behaviors and the challenges they experience in performing deliveries. In this study, we collected data on commercial vehicle (CV) driver behaviors by performing ridealongs with various logistics carriers. Ridealongs were performed in Seattle, Washington, covering a range of vehicles (cars, vans, and trucks), goods (parcels, mail, beverages, and printed materials), and customer types (residential, office, large and small retail). Observers collected qualitative observations and quantitative data on trip and dwell times, while also tracking vehicles through GPS devices. The results showed that, on average, urban CVs spent 80 percent of their daily operating time parked. The study also found that, unlike the common belief, drivers (especially those operating heavier vehicles) parked in authorized parking locations, with only less than 5 percent of stops occurring in the travel lane. Dwell times associated with authorized parking locations were significantly longer than those of other parking locations, and mail and heavy goods deliveries generally had longer dwell times. We also identified three main criteria CV drivers used for choosing a parking location: avoiding unsafe maneuvers, minimizing conflicts with other users of the road, and coopetition with other commercial drivers. Here, the results provide estimates for trip times, dwell times, and parking choice types, as well as insights into why those decisions are made and the factors affecting driver choices.

33 ADVANCED PROPULSION SYSTEMS↗