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We enhance situational awareness in any domain with technologies and systems that enable chemical sensing and unique observation methods.
“We’re not doing experiments for experiments’ sake, or building things that only work under certain lab conditions. Real people rely on our products to work in the field when they need them under pressure .”
President, Integrated Systems and Solutions
Development of a biodosimeter for radiation triage using novel blood protein biomarker panels in humans and non-human primates
Purpose : In a significant nuclear event, hundreds of thousands of individuals will require rapid triage for absorbed radiation to ensure effective medical treatment and efficient use of medical resources. We are developing a rapid screening method to assess whether an individual received an absorbed dose of ≥2 Gy based on the analysis of a specific panel of blood proteins in a fingerstick blood sample. Materials and methods : We studied a data set of 1051 human blood samples obtained from radiotherapy patients, normal healthy individuals, and several special population groups. We compared the findings in humans with those from irradiation studies in non-human primates (NHPs). Results : We identified a panel of three protein biomarkers, salivary alpha amylase (AMY1), Flt3 ligand (FLT3L), and monocyte chemotactic protein 1 (MCP1), which are upregulated in human patients receiving fractionated doses of total body irradiation (TBI) therapy as a treatment for cancer. These proteins exhibited a similar radiation response in NHPs after single acute or fractionated doses of ionizing radiation. Conclusion : Our work provides confidence in this biomarker panel for biodosimetry triage using fingerstick blood samples and in the use of NHPs as a model for irradiated humans.
Completion of genome-scale flux-balance models using computational reaction gap-filling is a widely used approach, but its accuracy is not well known. We report on computational experiments of reaction gap filling in which we generated degraded versions of the EcoCyc-20.0-GEM model by randomly removing flux-carrying reactions from a growing model. We gap-filled the degraded models and compared the resulting gap-filled models with the original model. Gap-filling was performed by the Pathway Tools MetaFlux software using its General Development Mode (GenDev) and its Fast Development Mode (FastDev). We explored 12 GenDev variants including two linear solvers (SCIP and CPLEX) for solving the Mixed Integer Linear Programming (MILP) problems for gap filling; three different sets of linear constraints were applied; and two MILP methods were implemented. We compared these 13 variants according to accuracy, speed, and amount of information returned to the user. We observed large variation among the performance of the 13 gap-filling variants. Although no variant was best in all dimensions, we found one variant that was fast, accurate, and returned more information to the user. Some gap-filling variants were inaccurate, producing solutions that were non-minimum or invalid (did not enable model growth). The best GenDev variant showed a best average precision of 87% and a best average recall of 61%. FastDev showed an average precision of 71% and an average recall of 59%. Thus, using the most accurate variant, approximately 13% of the gap-filled reactions were incorrect (were not the reactions removed from the model), and 39% of gap-filled reactions were not found, suggesting that curation is still an important aspect of metabolic-model development.
Reaction gap filling is a computational technique for proposing the addition of reactions to genome-scale metabolic models to permit those models to run correctly. Gap filling completes what are otherwise incomplete models that lack fully connected metabolic networks. The models are incomplete because they are derived from annotated genomes in which not all enzymes have been identified. Here we compare the results of applying an automated likelihood-based gap filler within the Pathway Tools software with the results of manually gap filling the same metabolic model. Both gap-filling exercises were applied to the same genome-derived qualitative metabolic reconstruction for Bifidobacterium longum subsp. longum JCM 1217, and to the same modeling conditions — anaerobic growth under four nutrients producing 53 biomass metabolites. The solution computed by the gap-filling program GenDev contained 12 reactions, but closer examination showed that solution was not minimal; two of the twelve reactions can be removed to yield a set of ten reactions that enable model growth. The manually curated solution contained 13 reactions, eight of which were shared with the 12-reaction computed solution. Thus, GenDev achieved recall of 61.5% and precision of 66.6%. These results suggest that although computational gap fillers are populating metabolic models with significant numbers of correct reactions, automatically gap-filled metabolic models also contain significant numbers of incorrect reactions. Our conclusion is that manual curation of gap-filler results is needed to obtain high-accuracy models. Many of the differences between the manual and automatic solutions resulted from using expert biological knowledge to direct the choice of reactions within the curated solution, such as reactions specific to the anaerobic lifestyle of B. longum.
Cyber-security has emerged as a pressing issue for transportation systems. Studies have shown that attackers can attack modern vehicles from a variety of interfaces and gain access to the most safety-critical components. Such threats become even broader and more challenging with the emergence of vehicle-to-vehicle (V2V) and vehicle-to-infrastructure (V2I) communication technologies. Addressing the security issues in transportation systems requires comprehensive approaches that encompass considerations of security mechanisms, safety properties, resource constraints, and other related system metrics. In this work, we propose an integrated framework that combines hybrid modeling, formal verification, and automated synthesis techniques for analyzing the security and safety of transportation systems and carrying out design space exploration of both in-vehicle electronic control systems and vehicle-to-vehicle communications. We demonstrate the ideas of our framework through a case study of cooperative adaptive cruise control.
Evaluation of OMI Operational Standard NO2 Column Retrievals Using in Situ and Surface-Based NO2 Observations
We assess the standard operational nitrogen dioxide (NO2) data product (OMNO2, version 2.1) retrieved from the Ozone Monitoring Instrument (OMI) onboard NASA’s Aura satellite using a combination of aircraft and surface in situ measurements as well as ground-based column measurements at several locations and a bottom-up NOx emission inventory over the continental US. Despite considerable sampling differences, NO2 vertical column densities from OMI are modestly correlated (r = 0.3–0.8) with in situ measurements of tropospheric NO2 from aircraft, ground-based observations of NO2 columns from MAX-DOAS and Pandora instruments, in situ surface NO2measurements from photolytic converter instruments, and a bottom-up NOx emission inventory. Overall, OMI retrievals tend to be lower in urban regions and higher in remote areas, but generally agree with other measurements to within ± 20%. No consistent seasonal bias is evident. Contrasting results between different data sets reveal complexities behind NO2 validation. Monthly mean vertical NO2 profile shapes from the Global Modeling Initiative (GMI) chemistry-transport model (CTM) used in the OMI retrievals are highly consistent with in situ aircraft measurements, but these measured profiles exhibit considerable day-to-day variation, affecting the retrieved daily NO2 columns by up to 40%. This assessment of OMI tropospheric NO2 columns, together with the comparison of OMI-retrieved and model-simulated NO2columns, could offer diagnostic evaluation of the model.
As part of this special issue on control systems for the energy sector, guest editors Sean Peisert and Jonathan Margulies put together a roundtable discussion so readers can learn about the security challenges facing the industrial control system/SCADA world from those who are on the front lines. The discussion touches on some of the hard problems of securing mission-critical systems in the real world, including the challenges of securing 20-year-old legacy infrastructures, defining vendors’ roles and responsibilities in security, and where research and new technologies are needed to fill today’s security gaps.