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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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150 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Structural insights reveal interplay between LAG-3 homodimerization, ligand binding, and function

Lymphocyte activation gene-3 (LAG-3) is an inhibitory receptor expressed on activated T cells and an emerging immunotherapy target. Domain 1 (D1) of LAG-3, which has been purported to directly interact with major histocompatibility complex class II (MHCII) and fibrinogen-like protein 1 (FGL1), has been the major focus for the development of therapeutic antibodies that inhibit LAG-3 receptor-ligand interactions and restore T cell function. Here, we present a high-resolution structure of glycosylated mouse LAG-3 ectodomain, identifying that cis-homodimerization, mediated through a network of hydrophobic residues within domain 2 (D2), is critically required for LAG-3 function. Additionally, we found a previously unidentified key protein-glycan interaction in the dimer interface that affects the spatial orientation of the neighboring D1 domain. Mutation of LAG-3 D2 residues reduced dimer formation, dramatically abolished LAG-3 binding to both MHCII and FGL1 ligands, and consequentially inhibited the role of LAG-3 in suppressing T cell responses. Intriguingly, we showed that antibodies directed against D1, D2, and D3 domains are all capable of blocking LAG-3 dimer formation and MHCII and FGL-1 ligand binding, suggesting a potential allosteric model of LAG-3 function tightly regulated by dimerization. Furthermore, our work reveals unique epitopes, in addition to D1, that can be targeted for immunotherapy of cancer and other human diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Profiles of upcoming HPC Applications and their Impact on Reservation Strategies

With the expected convergence between HPC, BigData and AI, new applications with different profiles are coming to HPC infrastructures. Here, we aim at better understanding the features and needs of these applications in order to be able to run them efficiently on HPC platforms. The approach followed is bottom-up: we study thoroughly an emerging application from the neuroscience community (SLANT) to understand its behavior. Based on these observations, we derive a generic, yet simple, application model (namely, a linear sequence of stochastic jobs). We expect this model to be representative for a large set of upcoming applications that require the computational power of HPC clusters without fitting the typical behavior of large-scale traditional applications. In a second step, we show how one can manipulate this generic model in a scheduling framework. Specifically we consider the problem of making reservations (both time and memory) for an execution on an HPC platform. We derive solutions using the model of the first step of this work. We experimentally show the robustness of the model, even with very few data or with another application, to generate the model, and provide performance gains with regards to standard and more recent approaches used in the neuroscience community.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Cell Cycle-Dependent Recruitment of FtsN to the Divisome in Escherichia coli

Cell division in Escherichia coli starts with the formation of an FtsZ protofilament network at midcell, the Z ring. However, only after a considerable lag period does the cell start to form a midcell constriction. The onset of constriction depends upon the arrival of so-called late divisome proteins, among which, FtsN is the last essential one. The timing and dependency of FtsN arrival to the divisome, along with genetic evidence, suggests it triggers cell division. In this study, we used high-throughput fluorescence microscopy to determine the arrival of FtsN and the early divisome protein ZapA to midcell at a single-cell level during the cell cycle. Our data show while the recruitment of ZapA/FtsZ is gradual in the cell cycle, recruitment of FtsN is rapid and begins at about the onset of constriction. At this time, the fraction of ZapA/FtsZ in the Z ring approaches its peak value. We also find a second increase in FtsN recruitment to the divisome, which begins once the amount of ZapA/FtsZ at midcell starts decreasing. Increasing hypermorphic FtsA* (FtsA R286W), but not FtsA, accelerates FtsN recruitment but not constriction. This finding is consistent with FtsA* recruiting FtsN with some other divisome component being rate-limiting for constriction under these conditions. Finally, our data support the recently proposed idea that ZapA/FtsZ and FtsN are part of physically separate complexes in midcell throughout the whole septation process.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Demystifying asynchronous I/O Interference in HPC applications

With increasing complexity of HPC workflows, data management services need to perform expensive I/O operations asynchronously in the background, aiming to overlap the I/O with the application runtime. However, this may cause interference due to competition for resources: CPU, memory/network bandwidth. The advent of multi-core architectures has exacerbated this problem, as many I/O operations are issued concurrently, thereby competing not only with the application but also among themselves. Furthermore, the interference patterns can dynamically change as a response to variations in application behavior and I/O subsystems (e.g. multiple users sharing a parallel file system). Without a thorough understanding, I/O operations may perform suboptimally, potentially even worse than in the blocking case. To fill this gap, here we investigate the causes and consequences of interference due to asynchronous I/O on HPC systems. Specifically, we focus on multi-core CPUs and memory bandwidth, isolating the interference due to each resource. Then, we perform an in-depth study to explain the interplay and contention in a variety of resource sharing scenarios such as varying priority and number of background I/O threads and different I/O strategies: sendfile, read/write, mmap/write underlining trade-offs. The insights from this study are important both to enable guided optimizations of existing background I/O, as well as to open new opportunities to design advanced asynchronous I/O strategies.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Challenges and the Evolving Landscape of Assessing Blood-Based PD-L1 Expression as a Biomarker for Anti-PD-(L)1 Immunotherapy

While promising, PD-L1 expression on tumor tissues as assessed by immunohistochemistry has been shown to be an imperfect biomarker that only applies to a limited number of cancers, whereas many patients with PD-L1-negative tumors still respond to anti-PD-(L)1 immunotherapy. Recent studies using patient blood samples to assess immunotherapeutic responsiveness suggests a promising approach to the identification of novel and/or improved biomarkers for anti-PD-(L)1 immunotherapy. In this review, we discuss the advances in our evolving understanding of the regulation and function of PD-L1 expression, which is the foundation for developing blood-based PD-L1 as a biomarker for anti-PD-(L)1 immunotherapy. We further discuss current knowledge and clinical study results for biomarker identification using PD-L1 expression on tumor and immune cells, exosomes, and soluble forms of PD-L1 in the peripheral blood. Finally, we discuss key challenges for the successful development of the potential use of blood-based PD-L1 as a biomarker for anti-PD-(L)1 immunotherapy.

59 BASIC BIOLOGICAL SCIENCES↗