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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Spatial top-down proteomics for the functional characterization of human kidney

Background: The Human Proteome Project has credibly detected nearly 93% of the roughly 20,000 proteins which are predicted by the human genome. However, the proteome is enigmatic, where alterations in amino acid sequences from polymorphisms and alternative splicing, errors in translation, and post-translational modifications result in a proteome depth estimated at several million unique proteoforms. Recently mass spectrometry has been demonstrated in several landmark efforts mapping the human proteoform landscape in bulk analyses. Herein, we developed an integrated workflow for characterizing proteoforms from human tissue in a spatially resolved manner by coupling laser capture microdissection, nanoliter-scale sample preparation, and mass spectrometry imaging. Results: Using healthy human kidney sections as the case study, we focused our analyses on the major functional tissue units including glomeruli, tubules, and medullary rays. After laser capture microdissection, these isolated functional tissue units were processed with microPOTS (microdroplet processing in one-pot for trace samples) for sensitive top-down proteomics measurement. This provided a quantitative database of 616 proteoforms that was further leveraged as a library for mass spectrometry imaging with near-cellular spatial resolution over the entire section. Notably, several mitochondrial proteoforms were found to be differentially abundant between glomeruli and convoluted tubules, and further spatial contextualization was provided by mass spectrometry imaging confirming unique differences identified by microPOTS, and further expanding the field-of-view for unique distributions such as enhanced abundance of a truncated form (1-74) of ubiquitin within cortical regions. Conclusions: We developed an integrated workflow to directly identify proteoforms and reveal their spatial distributions. Where of the 20 differentially abundant proteoforms identified as discriminate between tubules and glomeruli by microPOTS, the vast majority of tubular proteoforms were of mitochondrial origin (8 of 10) where discriminate proteoforms in glomeruli were primarily hemoglobin subunits (9 of 10). These trends were also identified within ion images demonstrating spatially resolved characterization of proteoforms that has the potential to reshape discovery-based proteomics because the proteoforms are the ultimate effector of cellular functions. Applications of this technology have the potential to unravel etiology and pathophysiology of disease states, informing on biologically active proteoforms, which remodel the proteomic landscape in chronic and acute disorders.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1971

On the timing problem in optical PPM communications.

Investigation of the effects of imperfect timing in a direct-detection (noncoherent) optical system using pulse-position-modulation bits. Special emphasis is placed on specification of timing accuracy, and an examination of system degradation when this accuracy is not attained. Bit error probabilities are shown as a function of timing errors, from which average error probabilities can be computed for specific synchronization methods. Of significant importance is shown to be the presence of a residual, or irreducible error probability, due entirely to the timing system, that cannot be overcome by the data channel.

Gagliardi, R. M.↗
NASA NTRS1975

Nearshore coastal mapping

Two test sites of different water quality and bottom topography were used to test for maximum water depth penetration using the Skylab S-192 MSS for measurement of nearshore coastal bathymetry. Sites under investigation lie along the Lake Michigan coastline where littoral transport acts to erode sand bluffs and endangers developments along 1,200 miles of shore, and on the west coast of Puerto Rico where unreliable shoal location and depth information constitutes a safety hazard to navigation. The S-192 and S-190A and B provide data on underwater features because of water transparency in the blue/green portion of the spectrum. Depth of 20 meters were measured with the S-192 in the Puerto Rico test site. The S-190B photography with its improved spatial resolution clearly delineates the triple sand bar topography in the Lake Michigan test site. Several processing techniques were employed to test for maximum depth measurement with least error. The results are useful for helping to determine an optimum spectral bandwidth for future space sensors that will increase depth measurements for different water attenuation conditions where a bottom reflection is detectable.

Polcyn, F. C.↗
NASA NTRS1977

Performance and sensitivity analysis of the generalized likelihood ratio method for failure detection

Results of the generalized likelihood ratio (GLR) technique for the detection of failures in aircraft application are presented, and its relationship to the properties of the Kalman-Bucy filter is examined. Under the assumption that the system is perfectly modeled, the detectability and distinguishability of four failure types are investigated by means of analysis and simulations. Detection of failures is found satisfactory, but problems in identifying correctly the mode of a failure may arise. These issues are closely examined as well as the sensitivity of GLR to modeling errors. The advantages and disadvantages of this technique are discussed, and various modifications are suggested to reduce its limitations in performance and computational complexity.

Bueno, R. A.↗
NASA NTRS1978

Extensions of the Wilson-Bappu effect among very luminous stars

It has been stated that the technique used by Wilson and Bappu (1957) in their study of the observational correlation of M sub V and the logarithm of the full width at half maximum of the Ca II K-line central emission for G, K, and M stars has a plus or minus 0.5 mag accuracy. A tabulation by Wilson (1976) suggests, however, that the error may be only plus or minus 0.3 mag. This accuracy makes the approach valuable for late-type supergiants since other methods suffer from comparable errors. A description is in this connection presented of a new class of emission lines in late-type giant and supergiant spectra that exhibit M sub V correlated widths, yet are detectable among the brightest stars.

Stencel, R. E.↗
NASA NTRS1985

Stochastic response analysis, order reduction, and output feedback controllers for flexible spacecraft

Real disturbances and real sensors have finite bandwidths. The first objective of this paper is to incorporate this finiteness in the 'open-loop modal cost analysis' as applied to a flexible spacecraft. Analysis based on residue calculus shows that among other factors, significance of a mode depends on the power spectral density of disturbances and the response spectral density of sensors at the modal frequency. The second objective of this article is to compare performances of an optimal and a suboptimal output feedback controller, the latter based on 'minimum error excitation' of Kosut. Both the performances are found to be nearly the same, leading us to favor the latter technique because it entails only linear computations. Our final objective is to detect an instability due to truncated modes by representing them as a multiplicative and an additive perturbation in a nominal transfer function. In an example problem it is found that this procedure leads to a narrow range of permissible controller gains, and that it labels a wrong mode as a cause of instability. A free beam is used to illustrate the analysis in this work.

Hablani, H. B.↗
NASA NTRS1988

Sources of error in heterodyne moire deflectometry

Alignment problems, and the accompanying errors, in heterodyne moire deflectometry are considered. A change in the x-directed offset between two states of a phase object causes a constant phase error, and it is noted that the relative x coordinate of the two photographic plates (the two states of the phase object) must be positioned typically within 1 micron to avoid a detectable offset. Possible solutions for assuring the relative alignment of the two deflectograms are considered, including a sandwich technique and a two-color double-exposure implementation.

Decker, Arthur J.↗
NASA NTRS1989

Reflections on human error - Matters of life and death

The last two decades have witnessed a rapid growth in the introduction of automatic devices into aircraft cockpits, and eleswhere in human-machine systems. This was motivated in part by the assumption that when human functioning is replaced by machine functioning, human error is eliminated. Experience to date shows that this is far from true, and that automation does not replace humans, but changes their role in the system, as well as the types and severity of the errors they make. This altered role may lead to fewer, but more critical errors. Intervention strategies to prevent these errors, or ameliorate their consequences include basic human factors engineering of the interface, enhanced warning and alerting systems, and more intelligent interfaces that understand the strategic intent of the crew and can detect and trap inconsistent or erroneous input before it affects the system.

Wiener, Earl L.↗
NASA NTRS1990

Accuracy requirements of optical linear algebra processors in adaptive optics imaging systems

A ground-based adaptive optics imaging telescope system attempts to improve image quality by detecting and correcting for atmospherically induced wavefront aberrations. The required control computations during each cycle will take a finite amount of time. Longer time delays result in larger values of residual wavefront error variance since the atmosphere continues to change during that time. Thus an optical processor may be well-suited for this task. This paper presents a study of the accuracy requirements in a general optical processor that will make it competitive with, or superior to, a conventional digital computer for the adaptive optics application. An optimization of the adaptive optics correction algorithm with respect to an optical processor's degree of accuracy is also briefly discussed.

Downie, John D.↗
NASA NTRS1995

Discovery of a transient MeV range gamma-ray source

The University of California, San Diego (UCSD)/MIT hard X-ray and gamma-ray instrument on the HEAO 1 surveyed the region near the Galactic center 3 times during its lifetime in 1977-1979. During the 1977 September-October scan, a gamma-ray source was detected south of the Galactic center. The source was below the threshold sensitivity in the spring and fall of 1978. The source was detected with the medium energy phoswich scintillation counters which operated over the 80 keV-2 MeV range, had an area of 42 sq cm each, and a 17 deg FWHM aperture. The error box for the source is centered on l = 2.4 deg, b = -12.2 deg, with a 90% confidence error circle of approximately 3.5 deg radius. The flux in the 333-635 keV range was (1.89 +/- 0.29) x 10(exp -5) photons/(sq cm s keV) and was constant within statistics during the 1 month period the source was in the field of view. The spectrum can be characterized as a Gaussian in the range 300 less than or = E less than or = 650 keV, with a FWHM of 249 +/- 51 keV centered on 461 +/- 22 keV. The flux of this broad Gaussian is (6.6 +/- 1.1) x 10(exp -3) photons/(sq cm s). The source is tentatively identified with the 5.57 hr period low-mass X-ray-emitting binary system 1H 1822-371. Assuming this is correct, the ratio of gamma-ray to X-ray luminosity during the outburst was about 5; at a distance of 8 kpc, the gamma ray luminosity is 4 x 10(exp 37) ergs. The emission may be interpreted as a positron-pair plasma ejected from a compact object, possibly a black hole, and annihilating in a thick accretion disk surrounding the object.

Briggs, M. S.↗
NASA NTRS1999

A Search for Simultaneous Optical Counterparts of Gamma-Ray Bursts (LOTIS: Livermore Optical Transient Imaging System)

Under this grant the UC Berkeley PI, K. Hurley, joined the LOTIS collaboration. His task was to provide precise localization data on cosmic gamma-ray bursts, so that the LOTIS automated camera data could be searched more efficiently for evidence of optical emission from gamma-ray burst sources. This was accomplished. A program is now in place which automatically sends Interplanetary Network data on bursts via e-mail to H.S. Park, for every burst detected by the GRB experiment aboard the Ulysses spacecraft (for which K. Hurley is the P.I.). The data consist either of triangulation annuli (obtained when just two spacecraft observe the burst) or error boxes (when three widely separated spacecraft observe it). These define a locus of possible burst positions. The annuli intersect the large error circles of the CGRO-BATSE experiment, and reduce their areas by a factor of approximately 25 or more. The error boxes reduce the areas by factors of several hundred. This in turn reduces the area which must be searched for an optical counterpart. No such counterparts have been observed to date by the LOTIS experiment, but several interesting upper limits have been obtained.

Park, H.-S.↗
NASA NTRS2001

BATSE Observations of the Piccinotti Sample of AGN II: Variability and Spectral Analysis

The Piccinotti sample is the hard x-ray-selected sample of active galactic nuclei (AGNs) best studied at energies below approximately 10 keV. It represents the only unbiased and complete high-energy survey of the sky down to a limiting flux of 3.1 x 10(exp -11) per square erg per second. As such, it has been used to study AGN properties such as X-ray spectral characteristics, log N-log S relation, and luminosity function. The BATSE data provide, for the first time, a systematic coverage of the whole sample at high energies. BATSE data from nearly four years of observations (1993 November - 1997 September) were analyzed using standard BATSE occultation analysis software to extract a signal from sources in the Piccinotti sample. Although the BATSE sensitivity for individual source measurements is relatively poor on short time scales, the near all-sky coverage and long CGRO lifetime allows us to improve our sensitivity considerably by sumrr~ng data over many years. This significantly reduces our statistical errors at the expense of loss of temporal information. However, the systematic errors associated with the summation of data over such a long period are not negligible, and the study of systematic effects was a major part of our effort. We evaluated two types of systematic error: those affecting the overall normalization (which are important for comparison with other instruments) and those affecting the size of the fluctuations (which are relevant for estimating the confidence level of a detection). The former was studied by comparison of BATSE data with other instruments, primarily CGRO/OSSE. The results indicate that our absolute flux values maybe overestimated by as much as 35% for some sources. However, since this does not affect our estimation of the detection confidence, we made no corrections to our flux estimates.

Paciesas, William S.↗
NASA NTRS2003

Effect of Clouds on Apertures of Space-based Air Fluorescence Detectors

Space-based ultra-high-energy cosmic ray detectors observe fluorescence light from extensive air showers produced by these particles in the troposphere. Clouds can scatter and absorb this light and produce systematic errors in energy determination and spectrum normalization. We study the possibility of using IR remote sensing data from MODIS and GOES satellites to delimit clear areas of the atmosphere. The efficiency for detecting ultra-high-energy cosmic rays whose showers do not intersect clouds is determined for real, night-time cloud scenes. We use the MODIS SST cloud mask product to define clear pixels for cloud scenes along the equator and use the OWL Monte Carlo to generate showers in the cloud scenes. We find the efficiency for cloud-free showers with closest approach of three pixels to a cloudy pixel is 6.5% exclusive of other factors. We conclude that defining a totally cloud-free aperture reduces the sensitivity of space-based fluorescence detectors to unacceptably small levels.

Sokolsky, P.↗
NASA NTRS2011

On-Orbit Solar Dynamics Observatory (SDO) Star Tracker Warm Pixel Analysis

This paper describes the process of identification and analysis of warm pixels in two autonomous star trackers on the Solar Dynamics Observatory (SDO) mission. A brief description of the mission orbit and attitude regimes is discussed and pertinent star tracker hardware specifications are given. Warm pixels are defined and the Quality Index parameter is introduced, which can be explained qualitatively as a manifestation of a possible warm pixel event. A description of the algorithm used to identify warm pixel candidates is given. Finally, analysis of dumps of on-orbit star tracker charge coupled devices (CCD) images is presented and an operational plan going forward is discussed. SDO, launched on February 11, 2010, is operated from the NASA Goddard Space Flight Center (GSFC). SDO is in a geosynchronous orbit with a 28.5 inclination. The nominal mission attitude points the spacecraft X-axis at the Sun, with the spacecraft Z-axis roughly aligned with the Solar North Pole. The spacecraft Y-axis completes the triad. In attitude, SDO moves approximately 0.04 per hour, mostly about the spacecraft Z-axis. The SDO star trackers, manufactured by Galileo Avionica, project the images of stars in their 16.4deg x 16.4deg fields-of-view onto CCD detectors consisting of 512 x 512 pixels. The trackers autonomously identify the star patterns and provide an attitude estimate. Each unit is able to track up to 9 stars. Additionally, each tracker calculates a parameter called the Quality Index, which is a measure of the quality of the attitude solution. Each pixel in the CCD measures the intensity of light and a warns pixel is defined as having a measurement consistently and significantly higher than the mean background intensity level. A warns pixel should also have lower intensity than a pixel containing a star image and will not move across the field of view as the attitude changes (as would a dim star image). It should be noted that the maximum error introduced in the star tracker attitude solution during suspected warm pixel corruptions is within the specified 36 attitude error budget requirement of [35, 70, 70] arcseconds. Thus, the star trackers provided attitude accuracy within the specification for SDO. The star tracker images are intentionally defocused so each star image is detected in more than one CCD pixel. The position of each star is calculated as an intensity-weighted average of the illuminated pixels. The exact method of finding the positions is proprietary to the tracker manufacturer. When a warm pixel happens to be in the vicinity of a star, it can corrupt the calculation of the position of that particular star, thereby corrupting the estimate of the attitude.

Felikson, Denis↗
NASA NTRS2012

QuakeSim 2.0

QuakeSim 2.0 improves understanding of earthquake processes by providing modeling tools and integrating model applications and various heterogeneous data sources within a Web services environment. QuakeSim is a multisource, synergistic, data-intensive environment for modeling the behavior of earthquake faults individually, and as part of complex interacting systems. Remotely sensed geodetic data products may be explored, compared with faults and landscape features, mined by pattern analysis applications, and integrated with models and pattern analysis applications in a rich Web-based and visualization environment. Integration of heterogeneous data products with pattern informatics tools enables efficient development of models. Federated database components and visualization tools allow rapid exploration of large datasets, while pattern informatics enables identification of subtle, but important, features in large data sets. QuakeSim is valuable for earthquake investigations and modeling in its current state, and also serves as a prototype and nucleus for broader systems under development. The framework provides access to physics-based simulation tools that model the earthquake cycle and related crustal deformation. Spaceborne GPS and Inter ferometric Synthetic Aperture (InSAR) data provide information on near-term crustal deformation, while paleoseismic geologic data provide longerterm information on earthquake fault processes. These data sources are integrated into QuakeSim's QuakeTables database system, and are accessible by users or various model applications. UAVSAR repeat pass interferometry data products are added to the QuakeTables database, and are available through a browseable map interface or Representational State Transfer (REST) interfaces. Model applications can retrieve data from Quake Tables, or from third-party GPS velocity data services; alternatively, users can manually input parameters into the models. Pattern analysis of GPS and seismicity data has proved useful for mid-term forecasting of earthquakes, and for detecting subtle changes in crustal deformation. The GPS time series analysis has also proved useful as a data-quality tool, enabling the discovery of station anomalies and data processing and distribution errors. Improved visualization tools enable more efficient data exploration and understanding. Tools provide flexibility to science users for exploring data in new ways through download links, but also facilitate standard, intuitive, and routine uses for science users and end users such as emergency responders.

Donnellan, Andrea↗
NASA NTRS2010

SIM-Lite Mission Spectral Calibration Sensitivities and Refinements

SIM-Lite missions will perform astrometry at microarcsecond accuracy using star light interferometry. For typical baselines that are shorter than 10 meters, this requires to measure optical path difference (OPD) accurate to tens of picometers calling for highly accurate calibration. A major challenge is to calibrate the star spectral dependency in fringe measurements -- the spectral calibration. Previously, we have developed a spectral calibration and estimation scheme achieving picometer level accuracy. In this paper, we present the improvements regarding the application of this scheme from sensitivity studies. Data from the SIM Spectral Calibration Development Unit (SCDU) test facility shows that the fringe OPD is very sensitive to pointings of both beams from the two arms of the interferometer. This sensitivity coupled with a systematic pointing error provides a mechanism to explain the bias changes in 2007. Improving system alignment can effectively reduce this sensitivity and thus errors due to pointing errors. Modeling this sensitivity can lead to further improvement in data processing. We then investigate the sensitivity to a model parameter, the bandwidth used in the fringe model, which presents an interesting trade between systematic and random errors. Finally we show the mitigation of calibration errors due to system drifts by interpolating instrument calibrations. These improvements enable us to use SCDU data to demonstrate that SIM-Lite missions can meet the 1pm noise floor requirement for detecting earth-like exoplanets.

wave front aberration↗
NASA NTRS2023

Optimal Estimation Inversion of Ionospheric Electron Density from GNSS-POD Limb Measurements: Part II-Validation and Comparison Using NmF2 and hmF2

A growing number of SmallSat/CubeSat constellations with high-rate (50–100 Hz) global navigation satellite system radio occultations (GNSS-RO) as well as low-rate (1 Hz) precise orbit determination (GNSS-POD) limb-viewing capabilities provide unprecedented spatial and temporal sampling rates for ionospheric studies. In the F-region electron density (N 𝑒 ) retrieval process, instead of the conventional onion-peeling (OP) inversion, an optimal estimation (OE) inversion technique was recently developed using total electron content measurements acquired by GNSS-POD link. The new technique is applied to data acquired from the COSMIC-1, COSMIC-2, and Spire constellations. Although both OE and OP techniques use the Abel weighting function in N 𝑒 inversion, OE significantly differs in its performance, especially in the lower F- and E-regions. In this work, we evaluate and compare newly derived data sets using F2 peak properties with other space-based and ground-based observations. We determine the F2 peak N 𝑒 (NmF2) and its altitude (hmF2), and compare them with the OP-retrieved values. Good agreement is observed between the two techniques for both NmF2 and hmF2. In addition, we also utilize autoscaled F2 peak measurements from a number of worldwide Digisonde stations (∼30). The diurnal sensitivity and latitudinal variability of the F2 peak between the two techniques are carefully studied at these locations. Good agreement is observed between OE-retrieved NmF2 and Digisonde-measured NmF2. However, significant differences appear between OE-retrieved hmF2 and Digisonde-measured hmF2. During the daytime, Digisonde-measured hmF2 remains ∼25–45 km below the OE-retrieved hmF2, especially at mid and high latitudes. We also incorporate F-region N 𝑒 measurements from two incoherent scatter radar observations at high latitudes, located in the North American (Millstone Hill) and European (EISCAT at Tromso) sectors. The radar measurements show good agreement with OE-retrieved values. Although there are several possible sources of error in the ionogram-derived N 𝑒 profiles, our further analysis on F1 and F2 layers indicates that the low Digisonde hmF2 is caused by the autoscaled method, which tends to detect a height systematically below the F2 peak when the F1 layer is present.

GNSS radio occultation↗
NASA NTRS1973

Digital data detection and synchronization

The primary accomplishments have been in the analysis and simulation of receivers and bit synchronizers. It has been discovered that tracking rate effects play, a rather fundamental role in both receiver and synchronizer performance, but that data relating to recorder time-base-error, for the proper characterization of this phenomenon, is in rather short supply. It is possible to obtain operationally useful tape recorder time-base-error data from high signal-to-noise ratio tapes using synchronizers with relatively wideband tracking loops. Low signal-to-noise ratio tapes examined in the same way would not be synchronizable. Additional areas of interest covered are receiver false lock, cycle slipping, and other unusual phenomena, which have been described to some extent in this and earlier reports and simulated during the study.

Noack, T. L.↗