Multispectral signatures in relation to ground control signatures using nested sampling approach
There are no author-identified significant results in this report.
Lyon, R. J. P.↗
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Multispectral signatures in relation to ground control signatures using nested-sampling approach
There are no author-identified significant results in this report.
Lyon, R. J. P.↗
Multispectral signatures in relation to ground control signature using nested sampling approach
The author has identified the following significant results. Principal effort has been on the development of a PDP-10 software package to read the CCT tapes more cheaply and rapidly. This is 90% completed and debugged. A shade print example of Treasure Island is provided. Stanford area was overflown with the U-2 as an add-on photographic mission to help fill in record-gaps in ERTS-1 overpass which was clouded out.
Lyon, R. J. P.↗
Multispectral signatures in relation to ground control signature using nested sampling approach
There are no author-identified significant results in this report.
Lyon, R. J. P.↗
Multispectral signatures in relation to ground control signature using nested sampling approach
There are no author-identified significant results in this report.
Lyon, R. J. P.↗
Multispectral signatures in relation to ground control signature using nested sampling approach
The author has identified the following significant results. In a cooperative study with USGS personnel, it has been possible to detect a 1.5 by 1 mile anomaly on ERTS CCT data, in the pine-covered mountains of western Nevada. This anomalous area is about 3-5 times larger than that of the known geobotanical anomaly which lies centrally within the area. The site has been studied on the ground and bi-directional reflectances, relative to BaS04 obtained for 40 trees, using both in-vivo techniques (similar to cherry picker operations) and field determinations of cut branches. The anomaly can be seen best by color transparencies made from 5/4, 6/4, 7/4 ratioed digital data, the 3 ratios each being coded by one of 3 colors (blue, green, and red).
Lyon, R. J. P.↗
Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor
Mutational signature analysis is commonly performed in cancer genomic studies. Here, we present SigProfilerExtractor, an automated tool for de novo extraction of mutational signatures, and benchmark it against another 13 bioinformatics tools by using 34 scenarios encompassing 2,500 simulated signatures found in 60,000 synthetic genomes and 20,000 synthetic exomes. For simulations with 5% noise, reflecting high-quality datasets, SigProfilerExtractor outperforms other approaches by elucidating between 20% and 50% more true-positive signatures while yielding 5-fold less false-positive signatures. Applying SigProfilerExtractor to 4,643 whole-genome- and 19,184 whole-exome-sequenced cancers reveals four novel signatures. Two of the signatures are confirmed in independent cohorts, and one of these signatures is associated with tobacco smoking. In summary, this report provides a reference tool for analysis of mutational signatures, a comprehensive benchmarking of bioinformatics tools for extracting signatures, and several novel mutational signatures, including one putatively attributed to direct tobacco smoking mutagenesis in bladder tissues.
59 BASIC BIOLOGICAL SCIENCES↗
The Dual Nature of Entrainment-Mixing Signatures Revealed through Large-Eddy Simulations of a Convection-Cloud Chamber
Abstract Entrainment of subsaturated air into a cloud can influence its optical and microphysical properties in various ways, depending on the droplet evaporation and turbulent mixing time scales. Previous experiments in the Pi convection-cloud chamber have revealed that, given a fixed entrained air property, the mixing of entrained subsaturated air results in complete evaporation of some cloud droplets, with the rest remaining unchanged. This is a signature of inhomogeneous mixing. While comparing the results of entrainment with varying air properties, the mixing signature appears as if the subsaturated air is well mixed with the cloud to evenly reduce the droplets’ size. In other words, taken together, the experiments appear to have the signature of homogeneous mixing. To explore these results in a greater depth, we conduct large-eddy simulations combined with a bin microphysics scheme. Our results reproduce the similar signatures of inhomogeneous and homogeneous mixing, implying that LES can resolve the inhomogeneous mixing when the grid spacing is smaller than the entrained air parcel. Additionally, we observe that increasing the aerosol injection rate enhances the signature of inhomogeneous mixing, while coarser grid spacing diminishes it. Finally, the change in wall fluxes in response to various entrained air properties confirms that the homogeneous signature seen in the analysis of an ensemble of simulations is the result of various equilibrium states. This further strengthens the suggestion that the homogeneous mixing signature found in aircraft observations near the cloud top may result from combining entrainment events of different intensities, possibly caused by various-sized eddies. Significance Statement Large-eddy simulation and size-resolved microphysics can resolve time scales for turbulent mixing and evaporation and, therefore, are well suited for reproducing, extending, and interpreting the entrainment experiment in the Pi convection-cloud chamber. Our simulation results confirm (i) the inhomogeneous mixing signature for an individual entrainment event and (ii) the appearance of homogeneous mixing in an ensemble of entrainment episodes. Furthermore, we demonstrate that the inhomogeneous mixing signature is more pronounced in a polluted cloud, but coarser grid spacing in simulations may compromise the accuracy of this signature. Last, the homogeneous mixing signature results from various equilibrium states established for different entrainment intensities and adjusted wall fluxes, which are challenging to measure experimentally but can be easily analyzed in the simulations.
54 ENVIRONMENTAL SCIENCES↗
Ground-recorded sonic boom signatures of F-18 aircraft formation flight
Two F-18 aircraft were flown, one above the other, in two formations, in order for the shock systems of the two aircraft to merge and propagate to the ground. The first formation had the canopy of the lower F-18 in the inlet shock of the upper F-18 (called inlet-canopy). The flight conditions were Mach 1.22 and an altitude of 23,500 ft. An array of five sonic boom recorders was used on the ground to record the sonic boom signatures. This paper describes the flight test technique and the ground level sonic boom signatures. The tail-canopy formation resulted in two, separated, N-wave signatures. Such signatures probably resulted from aircraft positioning error. The inlet-canopy formation yielded a single modified signature; two recorders measured an approximate flattop signature. Loudness calculations indicated that the single inlet-canopy signatures were quieter than the two, separated tail-canopy signatures. Significant loudness occurs after a sonic boom signature. Such loudness probably comes from the aircraft engines.
Bahm, Catherine M.↗
Theoretical Basis for Finite Difference Extrapolation of Sonic Boom Signatures
Calculation of sonic boom signatures for aircraft has traditionally followed the methods of Whitham' and Walkden. The wave disturbance generated by the vehicle is obtained by area rule linearized supersonic flow methods, which yield a locally axisymmetric asymptotic solution. This solution is acoustic in nature, i.e., first order in disturbance quantities, and corresponds to ray acoustics. Cumulative nonlinear distortion of the signature is incorporated by using this solution to adjust propagation speed to first order, thus yielding a solution second order in disturbance quantities. The effects of atmospheric gradients are treated by Blokhintzov's method of geometrical acoustics. Both nonlinear signature evolution and ray tracing are applied as if the pressure field very close to the vehicle were actually that given by the source term (the 'F-function') of the asymptotic linearized flow solution. The viewpoint is thus that the flow solution exists at a small radius near the vehicle, and may be treated as an input to an extrapolation procedure consisting of ray tracing and nonlinear aging. The F-function is often regarded as a representation of a near-field pressure signature, and it is common for computational implementations to treat it interchangeably with the pressure signature. There is a 'matching radius' between the source function and the subsequent propagation extrapolation. This viewpoint has been supported by wind tunnel tests of simple models, and very typically yields correct results for actual flight vehicles. The assumption that the F-function and near-field signature are interchangeable is generally not correct. The flowfield of a vehicle which is not axisymmetric contains crossflow components which are very significant at small radii and less so at larger distances. From an acoustical viewpoint, the crossflow is equivalent to source diffraction portions of the wave field. Use of the F-function as a near field signature effectively assumes that the diminution of the crossflow/diffraction component may be applied all at once at the matching radius noted above. This approximation, though not rigorously validated, is responsible for the usual correct far-field results. On the other hand, if an actual near-field signature (either from wind tunnel or CFD data) is used at a starting point rather than one based on th effective source distribution, the predicted far-field signature is generally wrong.
Plotkin, Kenneth J.↗
Ground-Recorded Sonic Boom Signatures of F-18 Aircraft in Formation Flight
Two F-18 aircraft were flown, one above the other, in two formations, in order for the shock systems of the two aircraft to merge and propagate to the ground. The first formation had the canopy of the lower F-18 in the tail shock of the upper F-18 (called tail-canopy). The second formation had the canopy of the lower F- 18 in the inlet shock of the upper F-18 (called inlet-canopy). The flight conditions were Mach 1.22 and an altitude of 23,500 ft . An array of five sonic boom recorders was used on the ground to record the sonic boom signatures. This paper describes the flight test technique and the ground level sonic boom signatures. The tail-canopy formation resulted in two, separated, N-wave signatures. Such signatures probably resulted from aircraft positioning error. The inlet-canopy formation yielded a single modified signature; two recorders measured an approximate flattop signature. Loudness calculations indicated that the single inlet-canopy signatures were quieter than the two, separated tail-canopy signatures. Significant loudness occurs after a sonic boom signature. Such loudness probably comes from the aircraft engines.
Bahm, Catherine M.↗
Analysis of Plume Effects on Sonic Boom Signature for Isolated Nozzle Configurations
Computational fluid dynamics (CFD) analysis has been performed to study the plume effects on sonic boom signature for isolated nozzle configurations. The objectives of these analyses were to provide comparison to past work using modern CFD analysis tools, to investigate the differences of high aspect ratio nozzles to circular (axisymmetric) nozzles, and to report the effects of underexpanded nozzle operation on boom signature. CFD analysis was used to address the plume effects on sonic boom signature from a baseline exhaust nozzle. Near-field pressure signatures were collected for nozzle pressure ratios (NPRs) between 6 and 10. A computer code was used to extrapolate these signatures to a ground-observed sonic boom N-wave. Trends show that there is a reduction in sonic boom N-wave signature as NPR is increased from 6 to 10. The performance curve for this supersonic nozzle is flat, so there is not a significant loss in thrust coefficient as the NPR is increased. As a result, this benefit could be realized without significant loss of performance. Analyses were also collected for a high aspect ratio nozzle based on the baseline design for comparison. Pressure signatures were collected for nozzle pressure ratios from 8 to 12. Signatures were nearly twice as strong for the two-dimensional case, and trends also show a reduction in sonic boom signature as NPR is increased from 8 to 12. As low boom designs are developed and improved, there will be a need for understanding the interaction between the aircraft boat tail shocks and the exhaust nozzle plume. These CFD analyses will provide a baseline study for future analysis efforts.
Castner, Raymond S.↗
Analysis of Plume Effects on Sonic Boom Signature for Isolated Nozzle Configurations
Computational fluid dynamics (CFD) analysis has been performed to study the plume effects on sonic boom signature for isolated nozzle configurations. The objectives of these analyses were to provide comparison to past work using modern CFD analysis tools, to investigate the differences of high aspect ratio nozzles to circular (axisymmetric) nozzles, and to report the effects of underexpanded nozzle operation on boom signature. CFD analysis was used to address the plume effects on sonic boom signature from a baseline exhaust nozzle. Near-field pressure signatures were collected for nozzle pressure ratios (NPRs) between 6 and 10. A computer code was used to extrapolate these signatures to a ground-observed sonic boom N-wave. Trends show that there is a reduction in sonic boom N-wave signature as NPR is increased from 6 to 10. The performance curve for this supersonic nozzle is flat, so there is not a significant loss in thrust coefficient as the NPR is increased. As a result, this benefit could be realized without significant loss of performance. Analyses were also collected for a high aspect ratio nozzle based on the baseline design for comparison. Pressure signatures were collected for nozzle pressure ratios from 8 to 12. Signatures were nearly twice as strong for the two-dimensional case, and trends also show a reduction in sonic boom signature as NPR is increased from 8 to 12. As low boom designs are developed and improved, there will be a need for understanding the interaction between the aircraft boat tail shocks and the exhaust nozzle plume. These CFD analyses will provide a baseline study for future analysis efforts.
Castner, Raymond S.↗
Entanglement-based quantum digital signatures over a deployed campus network
The quantum digital signature protocol offers a replacement for most aspects of public-key digital signatures ubiquitous in today’s digital world. A major advantage of a quantum-digital-signatures protocol is that it can have information-theoretic security, whereas public-key cryptography cannot. Here we demonstrate and characterize hardware to implement entanglement-based quantum digital signatures over our campus network. Over 25 hours, we collect measurements on our campus network, where we measure sufficiently low quantum bit error rates (<5% in most cases) which in principle enable quantum digital signatures at over 50 km as shown through rigorous simulation accompanied by a noise model developed specifically for our implementation. These results show quantum digital signatures can be successfully employed over deployed fiber. Moreover, our reported method provides great flexibility in the number of users, but with reduced entanglement rate per user. Finally, while the current implementation of our entanglement-based approach has a low signature rate, feasible upgrades would significantly increase the signature rate.
97 MATHEMATICS AND COMPUTING↗
Numerical Predictions of Sonic Boom Signatures for a Straight Line Segmented Leading Edge Model
A sonic boom wind tunnel test was conducted on a straight-line segmented leading edge (SLSLE) model in the NASA Langley 4- by 4- Foot Unitary Plan Wind Tunnel (UPWT). The purpose of the test was to determine whether accurate sonic boom measurements could be obtained while continuously moving the SLSLE model past a conical pressure probe. Sonic boom signatures were also obtained using the conventional move-pause data acquisition method for comparison. The continuous data acquisition approach allows for accurate signatures approximately 15 times faster than a move-pause technique. These successful results provide an incentive for future testing with greatly increased efficiency using the continuous model translation technique with the single probe to measure sonic boom signatures. Two widely used NASA codes, USM3D (Navier-Stokes) and CART3D-AERO (Euler, adjoint-based adaptive mesh), were used to compute off-body sonic boom pressure signatures of the SLSLE model at several different altitudes below the model at Mach 2.0. The computed pressure signatures compared well with wind tunnel data. The effect of the different altitude for signature extraction was evaluated by extrapolating the near field signatures to the ground and comparing pressure signatures and sonic boom loudness levels.
Elmiligui, Alaa A.↗
Circulating miRNA Signature Predicts Health Risks Associated with Radiation and Microgravity
The many known health risks currently associated with space travel include increased risk of cardiovascular disease, cancer, central nervous system related diseases, muscle degeneration, and changes with host-gut microbiome interactions that can have profound impact with these and other health risks. The majority of the risk from space travel stem of the two components of the space environment which are microgravity and radiation. From our earlier work (Beheshti et al, PLOS One, 2018), we predicted that there is a systemic component of the host that causes general increased health risks due to spaceflight driven by a circulating microRNA (miRNA) signature consisting of 13 miRNAs that directly regulates both p53 and TGF1. MiRNAs are small non-coding RNA molecules with a negative and post-transcriptional regulation on gene expression) are increasingly recognized as major systemic regulators of responses to stressors, including microgravity, oxidative stress, and DNA damage. In addition, due to the size and stability of miRNAs, it is known that miRNAs can circulate throughout the body and have been found in the majority of the bodily fluids including blood, urine, saliva, and tears. Here, we start to dissect the actual impact of this miRNA signature on both the radiation and microgravity components and prove that this miRNA signature actually exists in the circulation of a host. To achieve this, we obtained multiple tissues including, serum, liver, and spleen and utilizing droplet digital PCR (ddPCR), we start to show how this circulating miRNA signature impacts which component of the spaceflight. The tissue was obtained from experiments performed on C57BL/6 male mice (N=10 for each condition) that were hindlimb unloaded (HU) to simulated microgravity, irradiated with 2Gy gamma (IR), HU plus IR, and control mice under normal conditions. It was shown that these miRNAs were present in the serum as predicted by the in silico prediction from our earlier predictions. The HU vs Controls show significant increases of the predicted miRNAs in the serum for more than half of the miRNA signature, with remaining miRNAs increasing comparing to the controls close to statistical significance. IR vs control mice showed increases for the miRNAs, but not has pronounced as the HU conditions. Finally, the combination of the HU+IR vs controls showed increases for the majority of the miRNA signature. The data indicates that the miRNA signature originally predicted through in silico methods is mainly associated with the microgravity component and is circulating throughout the host resulting in a systemic impact of the miRNAs on the host. These miRNAs are shown in the literature to potentially increase health risks associated with several diseases. In addition, we have begun testing the potential of utilizing antagonists to this miRNA signature to act as a potential countermeasure to mitigate radiation impact on the organism. This work demonstrates for the first time the potential of a minimally invasive novel biomarker and countermeasure that can be used to mitigate both radiation and microgravity effects.
Beheshti, Afshin↗
Unique genetic signatures in HIV-1 subtype A1 and A1D recombinant envelope glycoprotein distinguish contemporary transmitted/founder viruses from historical strains in East Africa
Introduction: The envelope glycoprotein (Env) of HIV-1 Transmitted/Founder (T/F) viruses in subtypes B and C carries distinct genetic signatures that enhance transmission fitness, augment infectivity and immune evasion. However, there is limited data on such signatures in T/F subtypes A1, D and A1D recombinants that predominate East Africa’s HIV epidemic.Methods: We used phylogenetically corrected approaches to detect distinct genetic signatures by comparing 44 contemporary HIV-1 T/F Envs with 229 historical Envs of the same subtype in East Africa.Results and Discussion: Subtype analysis based on the full-length Env gene of contemporary T/F viruses revealed a high proportion of subtype A1, followed by A1D recombinants, and fewer subtype D. Signature analysis revealed that the contemporary subtype A1 T/Fs were more likely to select distinct amino acids, including M22 in the signal peptide, R82 in gp120, A172 in the V2 loop, E230 in the glycosite 230, K275 in the D loop, Y317 in the V3 loop, K476 and N477 in the CD4 contact site, when compared with the historical Envs (q-value < 0.2). Conversely, the contemporary subtype A1 T/F Envs were less likely to carry the amino acids Q432 in the CD4 contact site, and the L784 signature within the LLP-2 (q-value < 0.2). The A1D recombinant T/Fs were more likely to select the D620 in the C-helix, but under selected the L34 in gp120, P299 in the V3 loop and Y643 in the Heptad repeat-2, compared to the historical Envs (q-value < 0.2). The distinct signature sites reported in this study may contribute to the successful establishment of acute infection as well as the persistence of long-term infection. Therefore, effective therapeutics and vaccines may target these distinct amino acid signatures especially for the East African region as it may be necessary to employ subtype-specific vaccines according to the subtype distribution.
59 BASIC BIOLOGICAL SCIENCES↗
Longitudinal analysis of host protein serum signatures of treatment and recovery in pulmonary tuberculosis
A better understanding of treatment progression and recovery in pulmonary tuberculosis (TB) infectious disease is crucial. This study analyzed longitudinal serum samples from pulmonary TB patients undergoing interventional treatment to identify surrogate markers for TB-related outcomes. Serum that was collected at baseline and 8, 17, 26, and 52 weeks from 30 TB patients experiencing durable cure were evaluated and compared using a sensitive LC-MS/MS proteomic platform for the detection and quantification of differential host protein signatures relative to timepoint. The global proteome signature was analyzed for statistical differences across the time course and between disease severity and treatment groups. A total of 676 proteins showed differential expression in the serum over these timepoints relative to baseline. Comparisons to understand serum protein dynamics at 8 weeks, treatment endpoints at 17 and 26 weeks, and post-treatment at 52 weeks were performed. The largest protein abundance changes were observed at 8 weeks as the initial effects of antibiotic treatment strongly impacted inflammatory and immune modulated responses. However, the largest number of proteome changes was observed at the end of treatment time points 17 and 26 weeks respectively. Post-treatment 52-week results showed an abatement of differential proteome signatures from end of treatment, though interestingly those proteins uniquely significant at post-treatment were almost exclusively downregulated. Patients were additionally stratified based upon disease severity and compared across all timepoints, identifying 461 discriminating proteome signatures. These proteome signatures collapsed into discrete expression profiles with distinct pathways across immune activation and signaling, hemostasis, and metabolism annotations. Insulin-like growth factor (IGF) and Integrin signaling maintained a severity signature through 52 weeks, implying an intrinsic disease severity signature well into the post-treatment timeframe. Previous proteome studies have primarily focused on the 8-week timepoint in relation to culture conversion status. While this study confirms previous observations, it also highlights some differences. The inclusion of additional end of treatment and post-treatment time points offers a more comprehensive assessment of treatment progression within the serum proteome. Examining the expression dynamics at these later time periods will help in the investigation of relapse patients and has provided indicative markers of response and recovery.
59 BASIC BIOLOGICAL SCIENCES↗