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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Assessment of Clonal Expansion Using CarcSeq Measurement of Lung Cancer Driver Mutations and Correlation With Mouse Strain- and Sex-Related Incidence of Spontaneous Lung Neoplasia

Quantification of variation in levels of spontaneously occurring cancer driver mutations (CDMs) was developed to assess clonal expansion and predict future risk of neoplasm development. Specifically, an error-corrected next-generation sequencing method, CarcSeq, and a mouse CarcSeq panel (analogous to human and rat panels) were developed and used to quantify low-frequency mutations in a panel of amplicons enriched in hotspot CDMs. Mutations in a subset of panel amplicons, Braf, Egfr, Kras, Stk11, and Tp53, were related to incidence of lung neoplasms at 2 years. This was achieved by correlating median absolute deviation (MAD) from the overall median mutant fraction (MF) measured in the lung DNA of 16-week-old male and female, B6C3F1 and CD-1 mice (10 mice/sex/strain) with percentages of spontaneous alveolar/bronchioloalveolar adenomas and carcinomas reported in bioassay control groups. A total of 1586 mouse lung mutants with MFs > x 10-4 were recovered. The ratio of nonsynonymous to synonymous mutations was used to assess the proportion of recovered mutations conferring a positive selective advantage. The greatest ratio was observed in what is considered the most lung tumor-sensitive model examined, male B6C3F1 mice. Of the recurrent, nonsynonymous mouse mutations recovered, 55.5% have been reported in human tumors, with many located in or around the mouse equivalent of human cancer hotspot codons. MAD for the same subset of amplicons measured in normal human lung DNA samples showed a correlation of moderate strength and borderline significance with age (a cancer risk factor), as well as age-related cumulative lung cancer risk, suggesting MAD may inform species extrapolation.

Toxicology↗
DOE OSTI2014

Strain effects and intermixing at the Si surface: Importance of long-range elastic corrections in first-principles calculations

Here we investigate Ge mixing at the Si(001) surface and characterize the 2 N Si(001) reconstruction by means of hybrid quantum and molecular mechanics calculations (QM/MM). Avoiding fake elastic dampening, this scheme allows to correctly take into account long range deformation induced by reconstructed and defective surfaces. We focus in particular on the dimer vacancy line (DVL) and its interaction with Ge adatoms. We first show that calculated formation energies for these defects are highly dependent on the choice of chemical potential and that the latter must be chosen carefully. Characterizing the effect of the DVL on the deformation field, we also find that the DVL favors Ge segregation in the fourth layer close to the DVL. Using the activation-relaxation technique (ART nouveau) and QM/MM, we show that a complex diffusion path permits the substitution of the Ge atom in the fourth layer, with barriers compatible with mixing observed at intermediate temperature. We also show that the use of QM/MM results in much more signi cant corrections at the saddle points (up to 0.5 eV) that at minima, demonstrating its importance for describing kinetics correctly.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗