Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Checkpointing”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
NASA NTRS1992

Scheduling message processing for reducing rollback propagation

Traditional checkpointing and rollback recovery techniques for parallel systems have typically assumed the communication pattern is specified by program behavior. In this paper we exploit the property that the communication pattern can often be changed at run-time without affecting program correctness. A scheduling algorithm for message processing and its implementation for reducing rollback propagation are described. The algorithm incorporates a user-transparent prioritized scheme based upon the run-time communication and checkpointing history. Communication trace-driven simulation for several parallel programs written in the Chare Kernel language demonstrates that the probability of rollback propagation can be reduced at the cost of slight additional performance degradation.

Wang, Yi-Min↗
NASA NTRS1995

Ensuring correct rollback recovery in distributed shared memory systems

Distributed shared memory (DSM) implemented on a cluster of workstations is an increasingly attractive platform for executing parallel scientific applications. Checkpointing and rollback techniques can be used in such a system to allow the computation to progress in spite of the temporary failure of one or more processing nodes. This paper presents the design of an independent checkpointing method for DSM that takes advantage of DSM's specific properties to reduce error-free and rollback overhead. The scheme reduces the dependencies that need to be considered for correct rollback to those resulting from transfers of pages. Furthermore, in-transit messages can be recovered without the use of logging. We extend the scheme to a DSM implementation using lazy release consistency, where the frequency of dependencies is further reduced.

Janssens, Bob↗
NASA NTRS2001

Evidence for factors modulating radiation-induced G2-delay: potential application as radioprotectors

Manipulation of checkpoint response to DNA damage can be developed as a means for protecting astronauts from the adverse effects of unexpected, or background exposures to ionizing radiation. To achieve this goal reagents need to be developed that protect cells from radiation injury by prolonging checkpoint response, thus promoting repair. We present evidence for a low molecular weight substance excreted by cells that dramatically increases the duration of the G2-delay. This compound is termed G2-Arrest Modulating Activity (GAMA). A rat cell line (A1-5) generated by transforming rat embryo fibroblasts with a temperature sensitive form of p53 plus H-ras demonstrates a dramatic increase in radiation resistance after exposure to low LET radiation that is not associated with an increase in the efficiency of rejoining of DNA double strand breaks. Radioresistance in this cell line correlates with a dramatic increase in the duration of the G2 arrest that is modulated by a GAMA produced by actively growing cells. The properties of GAMA suggest that it is a low molecular weight heat-stable peptide. Further characterization of this substance and elucidation of its mechanism of action may allow the development of a biological response modifier with potential applications as a radioprotector. GAMA may be useful for protecting astronauts from radiation injury as preliminary evidence suggests that it is able to modulate the response of cells exposed to heavy ion radiation, similar to that encountered in outer space.

NASA Discipline Radiation Health↗
NASA NTRS2017

Radiation Hardening by Software Techniques on FPGAs: Flight Experiment Evaluation and Results

We present our work on implementing Radiation Hardening by Software (RHBSW) techniques on the Xilinx Virtex5 FPGAs PowerPC 440 processors on the SpaceCube 2.0 platform. The techniques have been matured and tested through simulation modeling, fault emulation, laser fault injection and now in a flight experiment, as part of the Space Test Program- Houston 4-ISS SpaceCube Experiment 2.0 (STP-H4-ISE 2.0). This work leverages concepts such as heartbeat monitoring, control flow assertions, and checkpointing, commonly used in the High Performance Computing industry, and adapts them for use in remote sensing embedded systems. These techniques are extremely low overhead (typically <1.3%), enabling a 3.3x gain in processing performance as compared to the equivalent traditionally radiation hardened processor. The recently concluded STP-H4 flight experiment was an opportunity to upgrade the RHBSW techniques for the Virtex5 FPGA and demonstrate them on-board the ISS to achieve TRL 7. This work details the implementation of the RHBSW techniques, that were previously developed for the Virtex4-based SpaceCube 1.0 platform, on the Virtex5-based SpaceCube 2.0 flight platform. The evaluation spans the development and integration with flight software, remotely uploading the new experiment to the ISS SpaceCube 2.0 platform, and conducting the experiment continuously for 16 days before the platform was decommissioned. The experiment was conducted on two PowerPCs embedded within the Virtex5 FPGA devices and the experiment collected 19,400 checkpoints, processed 253,482 status messages, and incurred 0 faults. These results are highly encouraging and future work is looking into longer duration testing as part of the STP-H5 flight experiment.

Hybrid Flight Architectures↗
DOE OSTI2024

Techniques for recovering from errors when executing software applications on parallel processors

In various embodiments, a software program uses hardware features of a parallel processor to checkpoint a context associated with an execution of a software application on the parallel processor. The software program uses a preemption feature of the parallel processor to cause the parallel processor to stop executing instructions in accordance with the context. The software program then causes the parallel processor to collect state data associated with the context. After generating a checkpoint based on the state data, the software program causes the parallel processor to resume executing instructions in accordance with the context.

Hukerikar, Saurabh↗
DOE OSTI2022

A mouse pancreatic organoid model to compare PD-L1 blocking antibodies

Immune checkpoint inhibitors (ICIs) have changed the therapeutic landscape for cancer patients, but diabetes, a rare, severe immune-related endocrinopathy, is linked to ICI therapy. It is unclear whether glycosylation of ICIs may play a role in the development of this adverse event and how the physiological effects of different ICIs on pancreatic cells should be evaluated. We used a mouse pancreatic organoid model to compare three PD-L1 blocking antibodies in the presence or absence of IFNγ using a metabolic bioanalyzer. Modulation of ICI glycosylation altered its metabolic effects on mouse pancreatic organoids, suggesting that this model could be used to monitor and compare ICIs and to study the mechanisms underlying the development of IC-mediated diabetes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Comprehensive analysis of the human ESCRT-III-MIT domain interactome reveals new cofactors for cytokinetic abscission

The 12 related human ESCRT-III proteins form filaments that constrict membranes and mediate fission, including during cytokinetic abscission. The C-terminal tails of polymerized ESCRT-III subunits also bind proteins that contain Microtubule-Interacting and Trafficking (MIT) domains. MIT domains can interact with ESCRT-III tails in many different ways to create a complex binding code that is used to recruit essential cofactors to sites of ESCRT activity. Here, we have comprehensively and quantitatively mapped the interactions between all known ESCRT-III tails and 19 recombinant human MIT domains. We measured 228 pairwise interactions, quantified 60 positive interactions, and discovered 18 previously unreported interactions. We also report the crystal structure of the SPASTIN MIT domain in complex with the IST1 C-terminal tail. Three MIT enzymes were studied in detail and shown to: (1) localize to cytokinetic midbody membrane bridges through interactions with their specific ESCRT-III binding partners (SPASTIN-IST1, KATNA1-CHMP3, and CAPN7-IST1), (2) function in abscission (SPASTIN, KATNA1, and CAPN7), and (3) function in the ‘NoCut’ abscission checkpoint (SPASTIN and CAPN7). Our studies define the human MIT-ESCRT-III interactome, identify new factors and activities required for cytokinetic abscission and its regulation, and provide a platform for analyzing ESCRT-III and MIT cofactor interactions in all ESCRT-mediated processes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Performance and power modeling and prediction using MuMMI and 10 machine learning methods

Energy-efficient scientific applications require insight into how high performance computing system features impact the applications' power and performance. This insight can result from the development of performance and power models. Here, in this article, we use the modeling and prediction tool MuMMI (Multiple Metrics Modeling Infrastructure) and 10 machine learning methods to model and predict performance and power consumption and compare their prediction error rates. We use an algorithm-based fault-tolerant linear algebra code and a multilevel checkpointing fault-tolerant heat distribution code to conduct our modeling and prediction study on the Cray XC40 Theta and IBM BG/Q Mira at Argonne National Laboratory and the Intel Haswell cluster Shepard at Sandia National Laboratories. Our experimental results show that the prediction error rates in performance and power using MuMMI are less than 10% for most cases. By utilizing the models for runtime, node power, CPU power, and memory power, we identify the most significant performance counters for potential application optimizations, and we predict theoretical outcomes of the optimizations. Based on two collected datasets, we analyze and compare the prediction accuracy in performance and power consumption using MuMMI and 10 machine learning methods.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D

Abstract Now in its 52nd year of continuous operations, the Protein Data Bank (PDB) is the premiere open‐access global archive housing three‐dimensional (3D) biomolecular structure data. It is jointly managed by the Worldwide Protein Data Bank (wwPDB) partnership. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is funded by the National Science Foundation, National Institutes of Health, and US Department of Energy and serves as the US data center for the wwPDB. RCSB PDB is also responsible for the security of PDB data in its role as wwPDB‐designated Archive Keeper. Every year, RCSB PDB serves tens of thousands of depositors of 3D macromolecular structure data (coming from macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro‐electron diffraction). The RCSB PDB research‐focused web portal ( RCSB.org ) makes PDB data available at no charge and without usage restrictions to many millions of PDB data consumers around the world. The RCSB PDB training, outreach, and education web portal ( PDB101.RCSB.org ) serves nearly 700 K educators, students, and members of the public worldwide. This invited Tools Issue contribution describes how RCSB PDB (i) is organized; (ii) works with wwPDB partners to process new depositions; (iii) serves as the wwPDB‐designated Archive Keeper; (iv) enables exploration and 3D visualization of PDB data via RCSB.org ; and (v) supports training, outreach, and education via PDB101.RCSB.org . New tools and features at RCSB.org are presented using examples drawn from high‐resolution structural studies of proteins relevant to treatment of human cancers by targeting immune checkpoints.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Fragme∩t: An Open‐Source Framework for Multiscale Quantum Chemistry Based on Fragmentation

Fragment-based quantum chemistry offers a means to circumvent the nonlinear computational scaling of conventional electronic structure calculations, by partitioning a large calculation into smaller subsystems then considering the many-body interactions between them. Variants of this approach have been used to parameterize classical force fields and machine learning potentials, applications that benefit from interoperability between quantum chemistry codes. However, there is a dearth of software that provides interoperability yet is purpose-built to handle the combinatorial complexity of fragment-based calculations. To fill this void we introduce “Fragme∩t”, an open-source software application that provides a tool for community validation of fragment-based methods, a platform for developing new approximations, and a framework for analyzing many-body interactions. Fragme∩t includes algorithms for automatic fragment generation and structure modification, and for distance- and energy-based screening of the requisite subsystems. Checkpointing, database management, and parallelization are handled internally and results are archived in a portable database. Interfaces to various quantum chemistry engines are easy to write and exist already for Q-Chem, PySCF, xTB, Orca, CP2K, MRCC, Psi4, NWChem, GAMESS, and MOPAC. Applications reported here demonstrate parallel efficiencies around 96% on more than 1000 processors but also showcase that the code can handle large-scale protein fragmentation using only workstation hardware, all with a codebase that is designed to be usable by non-experts. Fragme∩t conforms to modern software engineering best practices and is built upon well established technologies including Python, SQLite, and Ray. The source code is available under the Apache 2.0 license.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Cohort-based pan-cancer analysis and experimental studies reveal ISG15 gene as a novel biomarker for prognosis and immunotherapy efficacy prediction

Abstract ISG15, an interferon-stimulated ubiquitin-like protein, plays a multifaceted role in tumorigenesis and immune regulation. This study comprehensively evaluates ISG15 as a prognostic biomarker and predictor of immunotherapy response through pan-cancer bioinformatics analysis and experimental validation. By integrating multiomics data from TCGA, GEO, and clinical cohorts, we found that ISG15 is significantly overexpressed in multiple cancers and generally correlates with poor prognosis. Elevated ISG15 expression is associated with increased immune checkpoint gene expression, particularly PD-L1, and immune infiltration, notably M2-like tumor-associated macrophages. Immunohistochemistry and multiplexed immunofluorescence confirmed a strong positive correlation between ISG15, PD-L1, and M2-TAM infiltration in lung and gastric cancer samples. Functional analysis at the single-cell level revealed significant associations between ISG15 and tumor proliferation, angiogenesis, and immune suppression. Immunotherapy cohort analysis demonstrated that tumors with high ISG15 expression responded favorably to PD-L1 inhibitors but exhibited resistance to CTLA-4 blockade, findings further validated in lung cancer patients receiving anti-PD-1 therapy. These results suggest that ISG15 is a promising biomarker for prognosis and immunotherapy response prediction across cancers. Its integration into clinical decision-making may enhance personalized treatment strategies, improve immunotherapy outcomes, and provide new insights into the tumor immune microenvironment, cancer progression, and potential therapeutic targets for future drug development.

Immunology↗
DOE OSTI2026

Memory-efficient nonsmooth dynamic optimization using adaptive randomized compression

Dynamic optimization problems arise in many applications including flow control, full waveform inversion, and medical imaging. These problems are plagued by significant computational challenges. One such challenge — and the focus of this work — is the memory limitation induced by the size of the underlying dynamical system. In particular, the entire dynamic trajectory is required for derivative computation and therefore must be stored or recomputed using, e.g., checkpointing. Although recent work demonstrated the use of adaptive randomized sketching to overcome the memory challenge, that work only applies to smooth unconstrained problems, prohibiting its use for nonsmooth regularized and constrained problems. The inclusion of nonsmooth regularizers and constraints is critical as they often arise in an attempt to preserve certain physical properties or to promote sparsity. To solve these problems, we introduce a trust-region algorithm for minimizing the sum of a smooth nonconvex function and a nonsmooth convex function that leverages randomized sketching to compress the dynamical system trajectories and adaptively adjust the sketch rank to satisfy a gradient inexactness condition. We prove convergence of this algorithm and demonstrate that it achieves substantial memory reduction on three discretized PDE-constrained optimization applications.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Pan-cancer proteogenomics characterization of tumor immunity

Despite the successes of immunotherapy in cancer treatment over recent decades, less than <10%–20% cancer cases have demonstrated durable responses from immune checkpoint blockade. To enhance the efficacy of immunotherapies, combination therapies suppressing multiple immune evasion mechanisms are increasingly contemplated. To better understand immune cell surveillance and diverse immune evasion responses in tumor tissues, we comprehensively characterized the immune landscape of more than 1,000 tumors across ten different cancers using CPTAC pan-cancer proteogenomic data. We identified seven distinct immune subtypes based on integrative learning of cell type compositions and pathway activities. We then thoroughly categorized unique genomic, epigenetic, transcriptomic, and proteomic changes associated with each subtype. Further leveraging the deep phosphoproteomic data, we studied kinase activities in different immune subtypes, which revealed potential subtype-specific therapeutic targets. Insights from this work will facilitate the development of future immunotherapy strategies and enhance precision targeting with existing agents.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

A prognostic risk model for glioma patients by systematic evaluation of genomic variations

The overall survival rate of gliomas has not significantly improved despite new effective treatments, mainly due to tumor heterogeneity and drug delivery. Here, we perform an integrated clinic-genomic analysis of 1, 477 glioma patients from a Chinese cohort and a TCGA cohort and propose a potential prognostic model for gliomas. We identify that SBS11 and SBS23 mutational signatures are associated with glioma recurrence and indicate worse prognosis only in low-grade type of gliomas and IDH-Mut subtype. We also identify 42 genomic features associated with distinct clinical outcome and successfully used ten of these to develop a prognostic risk model of gliomas. The high-risk glioma patients with shortened survival were characterized by high level of frequent copy number alterations including PTEN, CDKN2A/B deletion, EGFR amplification, less IDH1 or CIC gene mutations, high infiltration levels of immunosuppressive cells and activation of G2M checkpoint and Oxidative phosphorylation oncogenic pathway.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Radiation portal monitor data file format for comprehensive background radiation monitoring

Radiation portal monitors (RPMs) are widely used at border security checkpoints to detect the presence of radioactive materials in people, vehicles, and cargo. Typically, RPM detection systems consist of two pillars equipped with gamma and neutron detectors. To improve detection efficiency, RPMs employ techniques such as a limited energy window, dynamic alarm thresholds, and lead shielding. However, without continuous monitoring of background radiation, signal interpretation can be compromised, because environmental factors and mechanical failures can cause fluctuations. Here, we introduce a daily file format that logs gamma background and neutron background radiation levels continuously over a 24 h period; this format is different from traditional formats that record data only when the RPM is active or occupied. The approach enables RPM operators and analysts to (1) identify and diagnose malfunctioning components, (2) adjust system settings to account for dynamic environmental factors, and (3) use the recorded data to characterize outer space phenomena. Continuous background reporting is essential for identifying issues such as faulty connections, voltage divider failures, and errors in background updates. Continuous background reporting also enables the detection of external influences, including nearby X-ray scanners, temperature fluctuations, rainfall, cosmic radiation, and lunar phase changes. These data files are designed to be easily evaluated and parsed using common tools, and a quick review by an expert is often sufficient for problem diagnosis. We anticipate that continuous background radiation monitoring and these new strategies will significantly improve the accuracy and reliability of RPM systems, reducing the rate of false alarms and enhancing overall system performance.

Background radiation monitoring↗
DOE OSTI2023

Standoff trace explosives vapor detection at meter distances

Vapor detection is a noncontact sampling method, which is a less invasive means of explosives screening than physical swiping. Explosive vapor detection is a challenge due to the low levels of vapors available for detection. This study demonstrates that the parts-per-quadrillion sensitivity of atmospheric flow tube-mass spectrometry (AFT-MS) combined with a high-volume air sampler enables standoff detection of trace explosives vapor at distances of centimeters to meters. Standoff detection of explosives vapor was possible both upstream and downstream of the vapor source relative to room air currents. RDX vapor from a saturated source was detected at up to 2.5 m. Vapors from RDX residue and nitroglycerin residue were detected at distances up to 0.5 m. The sampling can be optimized by accounting for air movement in the room or environment, which could further extend standoff detection distances. In conclusion, using AFT-MS with a high-volume sampler could also be effective for standoff vapor detection of drugs and additional chemical threats and could be useful for security screening applications such as at mail facilities, border crossings, and security checkpoints.

47 OTHER INSTRUMENTATION↗
DOE OSTI2026

Ambient ion focusing from a field-free region to a detector: enhanced signal for explosives and drug detection with mass spectrometry

This study demonstrates ion focusing at ambient pressure and increased ion signal by creating a voltage gradient from a field-free region to a detector, thereby improving the detection of chemicals, such as explosives and drugs. At ambient pressure, ion loss and resulting signal reduction pose challenges that limit detection sensitivity in analytical instruments. Techniques to increase sensitivity, such as atmospheric flow tube-mass spectrometry (AFT-MS), extend ion-molecule reaction times but result in significant overall ion loss due to diffusion. Ion manipulation techniques, though challenging at ambient pressure, can mitigate these losses by concentrating ions toward the detector inlet. Using SIMION, ion trajectories were modeled with a voltage gradient applied between a flow tube and a detector, revealing ion focusing at ambient pressure. Experimental verification with an atmospheric flow tube employed both mass spectrometry and Faraday plate detectors to measure ion beam profiles across varying flow rates, tube diameters, and voltage gradients. Application of a voltage gradient effectively directed ions to the axial center of the flow tube, narrowed ion beam width, and increased signal intensity by 5 to 10 times compared to conditions without a voltage gradient. This ion focusing approach shows promise for improving sensitivity in ambient-pressure instruments. This technique has the potential to enhance detection levels in security and forensic applications, with particular benefits for field-portable devices used at checkpoints to identify explosives and drugs.

ambient pressure↗
DOE OSTI2023

rRNA methylation by Spb1 regulates the GTPase activity of Nog2 during 60S ribosomal subunit assembly

Biogenesis of the large ribosomal (60S) subunit involves the assembly of three rRNAs and 46 proteins, a process requiring approximately 70 ribosome biogenesis factors (RBFs) that bind and release the pre-60S at specific steps along the assembly pathway. The methyltransferase Spb1 and the K-loop GTPase Nog2 are essential RBFs that engage the rRNA A-loop during sequential steps in 60S maturation. Spb1 methylates the A-loop nucleotide G2922 and a catalytically deficient mutant strain ( spb 1 D52A ) has a severe 60S biogenesis defect. However, the assembly function of this modification is currently unknown. Here, we present cryo-EM reconstructions that reveal that unmethylated G2922 leads to the premature activation of Nog2 GTPase activity and capture a Nog2-GDP-AlF 4 - transition state structure that implicates the direct involvement of unmodified G2922 in Nog2 GTPase activation. Genetic suppressors and in vivo imaging indicate that premature GTP hydrolysis prevents the efficient binding of Nog2 to early nucleoplasmic 60S intermediates. We propose that G2922 methylation levels regulate Nog2 recruitment to the pre-60S near the nucleolar/nucleoplasmic phase boundary, forming a kinetic checkpoint to regulate 60S production. Our approach and findings provide a template to study the GTPase cycles and regulatory factor interactions of the other K-loop GTPases involved in ribosome assembly.

59 BASIC BIOLOGICAL SCIENCES↗