Cost-efficient design and production of flexible and re-usable near real-time tactical human-machine interfaces

International audienceMaking complex systems accessible to human operators supposes to design HMIs that provide the operator with means to manage the complexity in an efficient manner. This is particularly true in the aeronautics domain for tactical HMIs where complexity is present in many dimensions. Current technical requirements, such as being able to display thousands of objects updated on the basis of time intervals inferior to half a second, coupled with economic requirements such as manning and cost reductions, make this issue even more crucial. We present our approach to the design and production of near real-time tactical HMIs, that enables us to devise HMIs that meet such requirements while being flexible enough to be re- used in a wide variety of contexts and produced at a reasonable cost

Institutional requirements for optimal water quality management in arid urban areas

Summarizes Completion reports no. 45-47.AER72-73WRW-GVS-RCW-TLH28.Funded in part by the United States Department of the Interior, Office of Water Resources Research, as authorized by the Water Resources Research Act of 1964, and pursuant to Grant Agreement no. 14-31-0001-3567

Evaluation of simulated soil carbon dynamics in Arctic-Boreal ecosystems

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Huntzinger, D. N., Schaefer, K., Schwalm, C., Fisher, J. B., Hayes, D., Stofferahn, E., Carey, J., Michalak, A. M., Wei, Y., Jain, A. K., Kolus, H., Mao, J., Poulter, B., Shi, X., Tang, J., & Tian, H. Evaluation of simulated soil carbon dynamics in Arctic-Boreal ecosystems. Environmental Research Letters, 15(2), (2020): 025005, doi:10.1088/1748-9326/ab6784.Given the magnitude of soil carbon stocks in northern ecosystems, and the vulnerability of these stocks to climate warming, land surface models must accurately represent soil carbon dynamics in these regions. We evaluate soil carbon stocks and turnover rates, and the relationship between soil carbon loss with soil temperature and moisture, from an ensemble of eleven global land surface models. We focus on the region of NASA's Arctic-Boreal vulnerability experiment (ABoVE) in North America to inform data collection and model development efforts. Models exhibit an order of magnitude difference in estimates of current total soil carbon stocks, generally under- or overestimating the size of current soil carbon stocks by greater than 50 PgC. We find that a model's soil carbon stock at steady-state in 1901 is the prime driver of its soil carbon stock a hundred years later—overwhelming the effect of environmental forcing factors like climate. The greatest divergence between modeled and observed soil carbon stocks is in regions dominated by peat and permafrost soils, suggesting that models are failing to capture the frozen soil carbon dynamics of permafrost regions. Using a set of functional benchmarks to test the simulated relationship of soil respiration to both soil temperature and moisture, we find that although models capture the observed shape of the soil moisture response of respiration, almost half of the models examined show temperature sensitivities, or Q10 values, that are half of observed. Significantly, models that perform better against observational constraints of respiration or carbon stock size do not necessarily perform well in terms of their functional response to key climatic factors like changing temperature. This suggests that models may be arriving at the right result, but for the wrong reason. The results of this work can help to bridge the gap between data and models by both pointing to the need to constrain initial carbon pool sizes, as well as highlighting the importance of incorporating functional benchmarks into ongoing, mechanistic modeling activities such as those included in ABoVE.This work was supported by NASA'S Arctic Boreal Vulnerability Experiment (ABoVE; https://above.nasa.gov); NNN13D504T. Funding for the Multi-scale synthesis and Terrestrial Model Intercomparison Project (MsTMIP; https://nacp.ornl.gov/MsTMIP.shtml) activity was provided through NASA ROSES Grant #NNX10AG01A. Data management support for preparing, documenting, and distributing model driver and output data was performed by the Modeling and Synthesis Thematic Data Center at Oak Ridge National Laboratory (MAST-DC; https://nacp.ornl.gov), with funding through NASA ROSES Grant #NNH10AN681. Finalized MsTMIP data products are archived at the ORNL DAAC (https://daac.ornl.gov). We also acknowledge the modeling groups that provided results to MsTMIP. The synthesis of site-level soil respiration, temperature, and moisture data reported in Carey et al 2016a, 2016b) was funded by the US Geological Survey (USGS) John Wesley Powell Center for Analysis and Synthesis Award G13AC00193. Additional support for that work was also provided by the USGS Land Carbon Program. JBF carried out the research at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration. California Institute of Technology. Government sponsorship acknowledged

North America's net terrestrial CO2 exchange with the atmosphere 1990–2009

Scientific understanding of the global carbon cycle is required for developing national and international policy to mitigate fossil fuel CO2 emissions by managing terrestrial carbon uptake. Toward that understanding and as a contribution to the REgional Carbon Cycle Assessment and Processes (RECCAP) project, this paper provides a synthesis of net land–atmosphere CO2 exchange for North America (Canada, United States, and Mexico) over the period 1990–2009. Only CO2 is considered, not methane or other greenhouse gases. This synthesis is based on results from three different methods: atmospheric inversion, inventory-based methods and terrestrial biosphere modeling. All methods indicate that the North American land surface was a sink for atmospheric CO2, with a net transfer from atmosphere to land. Estimates ranged from −890 to −280 Tg C yr−1, where the mean of atmospheric inversion estimates forms the lower bound of that range (a larger land sink) and the inventory-based estimate using the production approach the upper (a smaller land sink). This relatively large range is due in part to differences in how the approaches represent trade, fire and other disturbances and which ecosystems they include. Integrating across estimates, "best" estimates (i.e., measures of central tendency) are −472 ± 281 Tg C yr−1 based on the mean and standard deviation of the distribution and −360 Tg C yr−1 (with an interquartile range of −496 to −337) based on the median. Considering both the fossil fuel emissions source and the land sink, our analysis shows that North America was, however, a net contributor to the growth of CO2 in the atmosphere in the late 20th and early 21st century. With North America's mean annual fossil fuel CO2 emissions for the period 1990–2009 equal to 1720 Tg C yr−1 and assuming the estimate of −472 Tg C yr−1 as an approximation of the true terrestrial CO2 sink, the continent's source : sink ratio for this time period was 1720:472, or nearly 4:1

Carbon cycle uncertainty in the Alaskan Arctic

Climate change is leading to a disproportionately large warming in the high northern latitudes, but the magnitude and sign of the future carbon balance of the Arctic are highly uncertain. Using 40 terrestrial biosphere models for the Alaskan Arctic from four recent model intercomparison projects – NACP (North American Carbon Program) site and regional syntheses, TRENDY (Trends in net land atmosphere carbon exchanges), and WETCHIMP (Wetland and Wetland CH4 Inter-comparison of Models Project) – we provide a baseline of terrestrial carbon cycle uncertainty, defined as the multi-model standard deviation (o) for each quantity that follows. Mean annual absolute uncertainty was largest for soil carbon (14.0±9.2 kgCm−2), then gross primary production (GPP) (0.22±0.50 kgCm−2 yr−1), ecosystem respiration (Re) (0.23±0.38 kgCm−2 yr−1), net primary production (NPP) (0.14±0.33 kgCm−2 yr−1), autotrophic respiration (Ra) (0.09±0.20 kgCm−2 yr−1), heterotrophic respiration (Rh) (0.14±0.20 kgCm−2 yr−1), net ecosystem exchange (NEE) (−0.01±0.19 kgCm−2 yr−1), and CH4 flux (2.52±4.02 g CH4 m−2 yr−1). There were no consistent spatial patterns in the larger Alaskan Arctic and boreal regional carbon stocks and fluxes, with some models showing NEE for Alaska as a strong carbon sink, others as a strong carbon source, while still others as carbon neutral. Finally, AmeriFlux data are used at two sites in the Alaskan Arctic to evaluate the regional patterns; observed seasonal NEE was captured within multi-model uncertainty. This assessment of carbon cycle uncertainties may be used as a baseline for the improvement of experimental and modeling activities, as well as a reference for future trajectories in carbon cycling with climate change in the Alaskan Arctic and larger boreal region

Staphylococcus aureus RNAIII Binds to Two Distant Regions of coa mRNA to Arrest Translation and Promote mRNA Degradation

Staphylococcus aureus RNAIII is the intracellular effector of the quorum sensing system that temporally controls a large number of virulence factors including exoproteins and cell-wall-associated proteins. Staphylocoagulase is one major virulence factor, which promotes clotting of human plasma. Like the major cell surface protein A, the expression of staphylocoagulase is strongly repressed by the quorum sensing system at the post-exponential growth phase. Here we used a combination of approaches in vivo and in vitro to analyze the mechanism used by RNAIII to regulate the expression of staphylocoagulase. Our data show that RNAIII represses the synthesis of the protein through a direct binding with the mRNA. Structure mapping shows that two distant regions of RNAIII interact with coa mRNA and that the mRNA harbors a conserved signature as found in other RNAIII-target mRNAs. The resulting complex is composed of an imperfect duplex masking the Shine-Dalgarno sequence of coa mRNA and of a loop-loop interaction occurring downstream in the coding region. The imperfect duplex is sufficient to prevent the formation of the ribosomal initiation complex and to repress the expression of a reporter gene in vivo. In addition, the double-strand-specific endoribonuclease III cleaves the two regions of the mRNA bound to RNAIII that may contribute to the degradation of the repressed mRNA. This study validates another direct target of RNAIII that plays a role in virulence. It also illustrates the diversity of RNAIII-mRNA topologies and how these multiple RNAIII-mRNA interactions would mediate virulence regulation

Intra-fraction setup variability: IR optical localization vs. X-ray imaging in a hypofractionated patient population

<p>Abstract</p> <p>Background</p> <p>The purpose of this study is to investigate intra-fraction setup variability in hypo-fractionated cranial and body radiotherapy; this is achieved by means of integrated infrared optical localization and stereoscopic kV X-ray imaging.</p> <p>Method and Materials</p> <p>We analyzed data coming from 87 patients treated with hypo-fractionated radiotherapy at cranial and extra-cranial sites. Patient setup was realized through the ExacTrac X-ray 6D system (BrainLAB, Germany), consisting of 2 infrared TV cameras for external fiducial localization and X-ray imaging in double projection for image registration. Before irradiation, patients were pre-aligned relying on optical marker localization. Patient position was refined through the automatic matching of X-ray images to digitally reconstructed radiographs, providing 6 corrective parameters that were automatically applied using a robotic couch. Infrared patient localization and X-ray imaging were performed at the end of treatment, thus providing independent measures of intra-fraction motion.</p> <p>Results</p> <p>According to optical measurements, the size of intra-fraction motion was (<it>median ± quartile</it>) 0.3 ± 0.3 mm, 0.6 ± 0.6 mm, 0.7 ± 0.6 mm for cranial, abdominal and lung patients, respectively. X-ray image registration estimated larger intra-fraction motion, equal to 0.9 ± 0.8 mm, 1.3 ± 1.2 mm, 1.8 ± 2.2 mm, correspondingly.</p> <p>Conclusion</p> <p>Optical tracking highlighted negligible intra-fraction motion at both cranial and extra-cranial sites. The larger motion detected by X-ray image registration showed significant inter-patient variability, in contrast to infrared optical tracking measurement. Infrared localization is put forward as the optimal strategy to monitor intra-fraction motion, featuring robustness, flexibility and less invasivity with respect to X-ray based techniques.</p

Operon structure of Staphylococcus aureus

In bacteria, gene regulation is one of the fundamental characteristics of survival, colonization and pathogenesis. Operons play a key role in regulating expression of diverse genes involved in metabolism and virulence. However, operon structures in pathogenic bacteria have been determined only by in silico approaches that are dependent on factors such as intergenic distances and terminator/promoter sequences. Knowledge of operon structures is crucial to fully understand the pathophysiology of infections. Presently, transcriptome data obtained from growth curves in a defined medium were used to predict operons in Staphylococcus aureus. This unbiased approach and the use of five highly reproducible biological replicates resulted in 93.5% significantly regulated genes. These data, combined with Pearson’s correlation coefficients of the transcriptional profiles, enabled us to accurately compile 93% of the genome in operon structures. A total of 1640 genes of different functional classes were identified in operons. Interestingly, we found several operons containing virulence genes and showed synergistic effects for two complement convertase inhibitors transcribed in one operon. This is the first experimental approach to fully identify operon structures in S. aureus. It forms the basis for further in vitro regulation studies that will profoundly advance the understanding of bacterial pathophysiology in vivo

Initial clinical experience with frameless optically guided stereotactic radiosurgery/radiotherapy in pediatric patients

The objective of this study is to report our initial experience treating pediatric patients with central nervous system tumors using a frameless, optically guided linear accelerator. Pediatric patients were selected for treatment after evaluation by a multidisciplinary neuro-oncology team including neurosurgery, neurology, pathology, oncology, and radiation oncology. Prior to treatment, all patients underwent treatment planning using magnetic resonance imaging (MRI) and treatment simulation on a standard computed tomography scanner (CT). For CT simulation, patients were fitted with a customized plastic face mask with a bite block attached to an optical array with four reflective markers. After ensuring adequate reproducibility, these markers were tracked during treatment by an infra-red camera. All treatments were delivered on a Varian Trilogy linear accelerator. The follow-up period ranges from 1–18 months, with a median follow-up of 6 months. Nine patients, ages ranging from 12 to 19 years old (median age 15 years old), with a variety of tumors have been treated. Patients were treated for juvenile pilocytic astrocytoma (JPA; n = 2), pontine low-grade astrocytoma (n = 1), pituitary adenoma (n = 3), metastatic medulloblastoma (n = 1), acoustic neuroma (n = 1), and pineocytoma (n = 1). We followed patients for a median of 12 months (range 3–18 months) with no in-field failures and were able to obtain encouraging toxicity profiles. Frameless stereotactic optically guided radiosurgery and radiotherapy provides a feasible and accurate tool to treat a number of benign and malignant tumors in children with minimal treatment-related morbidity

MiR-200c Regulates Noxa Expression and Sensitivity to Proteasomal Inhibitors

The pro-apoptotic p53 target Noxa is a BH3-only protein that antagonizes the function of selected anti-apoptotic Bcl-2 family members. While much is known regarding the transcriptional regulation of Noxa, its posttranscriptional regulation remains relatively unstudied. In this study, we therefore investigated whether Noxa is regulated by microRNAs. Using a screen combining luciferase reporters, bioinformatic target prediction analysis and microRNA expression profiling, we identified miR-200c as a negative regulator of Noxa expression. MiR-200c was shown to repress basal expression of Noxa, as well as Noxa expression induced by various stimuli, including proteasomal inhibition. Luciferase reporter experiments furthermore defined one miR-200c target site in the Noxa 3′UTR that is essential for this direct regulation. In spite of the miR-200c:Noxa interaction, miR-200c overexpression led to increased sensitivity to the clinically used proteasomal inhibitor bortezomib in several cell lines. This apparently contradictory finding was reconciled by the fact that in cells devoid of Noxa expression, miR-200c overexpression had an even more pronounced positive effect on apoptosis induced by proteasomal inhibition. Together, our data define miR-200c as a potentiator of bortezomib-induced cell death. At the same time, we show that miR-200c is a novel negative regulator of the pro-apoptotic Bcl-2 family member Noxa