SciCombinator

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Concept: Lawrence Livermore National Laboratory

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A mixed parallel scheme that combines message passing interface (MPI) and multithreading was implemented in the AutoDock Vina molecular docking program. The resulting program, named VinaLC, was tested on the petascale high performance computing (HPC) machines at Lawrence Livermore National Laboratory. To exploit the typical cluster-type supercomputers, thousands of docking calculations were dispatched by the master process to run simultaneously on thousands of slave processes, where each docking calculation takes one slave process on one node, and within the node each docking calculation runs via multithreading on multiple CPU cores and shared memory. Input and output of the program and the data handling within the program were carefully designed to deal with large databases and ultimately achieve HPC on a large number of CPU cores. Parallel performance analysis of the VinaLC program shows that the code scales up to more than 15K CPUs with a very low overhead cost of 3.94%. One million flexible compound docking calculations took only 1.4 h to finish on about 15K CPUs. The docking accuracy of VinaLC has been validated against the DUD data set by the re-docking of X-ray ligands and an enrichment study, 64.4% of the top scoring poses have RMSD values under 2.0 Å. The program has been demonstrated to have good enrichment performance on 70% of the targets in the DUD data set. An analysis of the enrichment factors calculated at various percentages of the screening database indicates VinaLC has very good early recovery of actives. © 2013 Wiley Periodicals, Inc.

Concepts: Algorithm, Parallel computing, Computer, Computer program, Input/output, Central processing unit, Supercomputer, Lawrence Livermore National Laboratory

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A prevailing way of extracting valuable information from biomedical literature is to apply text mining methods on unstructured texts. However, the massive amount of literature that needs to be analyzed poses a big data challenge to the processing efficiency of text mining. In this paper, we address this challenge by introducing parallel processing on a supercomputer. We developed paraBTM, a runnable framework that enables parallel text mining on the Tianhe-2 supercomputer. It employs a low-cost yet effective load balancing strategy to maximize the efficiency of parallel processing. We evaluated the performance of paraBTM on several datasets, utilizing three types of named entity recognition tasks as demonstration. Results show that, in most cases, the processing efficiency can be greatly improved with parallel processing, and the proposed load balancing strategy is simple and effective. In addition, our framework can be readily applied to other tasks of biomedical text mining besides NER.

Concepts: Parallel computing, Data mining, Natural language processing, Named entity recognition, Computational linguistics, Lawrence Livermore National Laboratory, Silicon Graphics

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Pyrolysis and oxidation of tri-ethyl phosphate (TEP) were carried out in the reflected shock region at temperatures of 1462-1673 K and 1213-1508 K, respectively, and at pressures near 1.3 atm. CO concentration time histories during the experiments were measured using laser absorption spectroscopy at 4580.4 nm. Experimental CO yields were compared with model predictions using the detailed organophosphorus compounds (OPC) incineration mechanism from the Lawrence Livermore National Lab (LLNL). The mechanism significantly underpredicts CO yield in TEP pyrolysis. During TEP oxidation, predicted rate of CO formation was significantly slower than the experimental results. Therefore, a new improved kinetic model for TEP combustion has been developed which was built upon the AramcoMech2.0 mechanism for C0-C2 chemistry, and the existing LLNL submechanism for phosphorous chemistry. Thermochemical data of 40 Phosphorous (P) containing species were reevaluated, either using recently published group values for P-containing species or by quantum chemical calculations (CBS-QB3). The new improved model is in better agreement with the experimental CO time histories within the temperature and pressure conditions tested in this study. Sensitivity analysis was used to identify important reactions affecting CO formation and future experimental/theoretical studies on kinetic parameters of these reactions were suggested to further improve the model. To the best of our knowledge, this is the first study of TEP kinetics in a shock tube under these conditions and the first time-resolved laser-based species time history data during its pyrolysis and oxidation.

Concepts: Chemistry, Thermodynamics, Phosphorus, United States Department of Energy National Laboratories, Los Alamos National Laboratory, University of California, Lawrence Livermore National Laboratory, Livermore, California

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After a chelation treatment, assessment of intake and doses is the primary concern of an internal dosimetrist. Using the urinary excretion data from two actual wound cases encountered at Los Alamos National Laboratory (LANL), this paper discusses several methods that can be used to interpret intakes from the urinary data collected after one or multiple chelation treatments. One of the methods uses only the data assumed to be unaffected by chelation (data collected beyond 100 d after the last treatment). This method, used by many facilities for official dose records, was implemented by employing maximum likelihood analysis and Bayesian analysis methods. The impacts of an improper assumption about the physicochemical behavior of a radioactive material and the importance of the use of a facility-specific biokinetic model when available have also been demonstrated. Another method analyzed both the affected and unaffected urinary data using an empirical urinary excretion model. This method, although case-specific, was useful in determining the actual intakes and the doses averted or the reduction in body burdens due to chelation treatments. This approach was important in determining the enhancement factors, the behavior of the chelate, and other observations that may be pertinent to several DTPA compartmental modeling approaches being conducted by the health physics community.

Concepts: Scientific method, Maximum likelihood, Model, Bayesian inference, Likelihood function, Chelation therapy, Los Alamos National Laboratory, Lawrence Livermore National Laboratory

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For radionuclides such as plutonium and americium, detection of removable activity in the nose (i.e., nasal swab measurements) are frequently used to determine whether follow-up bioassay measurements are warranted following a potential intake. For this paper, the authors analyzed 429 nasal swab measurements taken following incidents or suspicious circumstances (such as an air monitor alarming) at Los Alamos National Laboratory (LANL) for which the dose was later evaluated using in vitro bioassay. Nasal swab measurements were found to be very poor predictors of dose and should not be used as such in the field. However, nasal swab measurements can be indicative of whether a reliably detectable committed effective dose (CED) occurred. About 14% of nasal swab measurements between 1.25 and 16.7 Bq corresponded to CEDs greater than 1 mSv, so in general, positive nasal swabs always indicate that follow-up bioassay should be performed (positive nasal swabs less than 1.25 Bq are considered separately). This probability increased significantly for nasal swabs greater than 16.7 Bq. Only about 3% of nasal swabs with no detectable activity (NDA) corresponded to reliably detectable CEDs. A nasal swab with NDA is therefore necessary, but not sufficient, to negate the need for a follow-up bioassay if it was collected following other workplace indicators of a potential intake.

Concepts: Pharmacology, Effective dose, Manhattan Project, United States Department of Energy National Laboratories, Los Alamos National Laboratory, University of California, Lawrence Livermore National Laboratory, Glenn T. Seaborg

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Biologists at the Frederick National Laboratory for Cancer Research have teamed up with computer scientists and physicists at the Department of Energy to tackle the problem of “undruggable” RAS. The goal is to obtain a precise understanding of how RAS is activated by interactions with the plasma membrane; this will be illuminated through supercomputer simulations that build on structural and biochemical studies of RAS.

Concepts: Chemistry, Computer graphics, Computer, Electrical engineering, Lawrence Livermore National Laboratory, Sandia National Laboratories

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This work is focused on numerical calibrations of the body counter for in vivo measurement of pure beta emitters through the produced bremsstrahlung radiation. Calibrations were performed using the UPh-02T block whole-body phantom and the Lawrence Livermore National Laboratory (LLNL) realistic torso phantom. Neither of these physical phantoms is appropriate for such calibrations; therefore, specific (90)Sr sources have been manufactured to be used with the UPh-02T phantom for experimental measurement followed with Monte Carlo (MC) simulations. Calibrations with the LLNL torso phantom were carried out solely using MC technique. Different scenarios of the (90)Sr distribution in the human tissues were considered for the spectrometer calibrations. MC simulations with the LLNL confirmed the applicability of the UPh-02T with specific (90)Sr/(90)Y sources for experimental calibrations of the body counters for measurement of pure beta emitters. Differences in count rates in 50-200 keV for UPh-02T and LLNL were not >25% for all considered scenarios.

Concepts: Electron, Lawrence Berkeley National Laboratory, United States Department of Energy National Laboratories, Los Alamos National Laboratory, University of California, Lawrence Livermore National Laboratory, United States Department of Energy, Livermore, California

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Accelerator mass spectrometry (AMS) has been adopted as a powerful bioanalytical method for human studies in the areas of pharmacology and toxicology. The exquisite sensitivity (10(-18) mol) of AMS has facilitated studies of toxins and drugs at environmentally and physiologically relevant concentrations in humans. Such studies include risk assessment of environmental toxicants, drug candidate selection, absolute bioavailability determination, and more recently, assessment of drug-target binding as a biomarker of response to chemotherapy. Combining AMS with complementary capabilities such as high performance liquid chromatography (HPLC) can maximize data within a single experiment and provide additional insight when assessing drugs and toxins, such as metabolic profiling. Recent advances in the AMS technology at Lawrence Livermore National Laboratory have allowed for direct coupling of AMS with complementary capabilities such as HPLC via a liquid sample moving wire interface, offering greater sensitivity compared to that of graphite-based analysis, therefore enabling the use of lower (14)C and chemical doses, which are imperative for clinical testing. The aim of this review is to highlight the recent efforts in human studies using AMS, including technological advancements and discussion of the continued promise of AMS for innovative clinical based research.

Concepts: Pharmacology, Mass spectrometry, Chromatography, High performance liquid chromatography, Analytical chemistry, Accelerator mass spectrometry, United States Department of Energy National Laboratories, Lawrence Livermore National Laboratory

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Corrective optical elements form an important part of high-precision optical systems. We have developed a method to manufacture high-gradient corrective optical elements for high-power laser systems using deterministic magnetorheological finishing (MRF) imprinting technology. Several process factors need to be considered for polishing ultraprecise topographical structures onto optical surfaces using MRF. They include proper selection of MRF removal function and wheel sizes, detailed MRF tool and interferometry alignment, and optimized MRF polishing schedules. Dependable interferometry also is a key factor in high-gradient component manufacture. A wavefront attenuating cell, which enables reliable measurement of gradients beyond what is attainable using conventional interferometry, is discussed. The results of MRF imprinting a 23 μm deep structure containing gradients over 1.6 μm / mm onto a fused-silica window are presented as an example of the technique’s capabilities. This high-gradient element serves as a thermal correction plate in the high-repetition-rate advanced petawatt laser system currently being built at Lawrence Livermore National Laboratory.

Concepts: Optics, United States Department of Energy National Laboratories, Los Alamos National Laboratory, University of California, Lawrence Livermore National Laboratory, Inertial confinement fusion, National Ignition Facility, Livermore, California

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Data from animal experiments are relied upon for understanding the biokinetics of contaminant retention and excretion where insufficient human data exist. Records involving nonhuman primate experiments performed from 1973 to 1987 were collected and compiled by researchers at the Lawrence Berkeley Laboratory. These records included early blood samples that were taken after soluble plutonium was administered via intramuscular, subcutaneous, or intravenous injection. Samples were collected as early as 5 min post injection with several samples collected during the first few weeks. The NCRP 156 biokinetic model was developed primarily from animal experiments due to insufficient human data not influenced by chelation therapy. This work compared the NCRP 156 biokinetic model default transfer rate constants to the early blood excretion data from nonhuman primate experiments for Pu. These results indicated that the blood content of nonhuman primates exhibited “moderate” retention properties for simulated wound conditions. Additionally, there was no evidence of long-term retention of plutonium in the whole blood samples, confirming that plutonium was not incorporated within blood cells. Particle solubility characteristics should be considered for wounds when using the NCRP 156 wound biokinetic model.

Concepts: Mammal, Primate, Route of administration, Plutonium, Manhattan Project, Lawrence Berkeley National Laboratory, Lawrence Livermore National Laboratory, Glenn T. Seaborg