Results for “false positive analysis” — Page 5

NASA NTRS2019

Lipid Decontamination Procedures for Life Detection Missions

Molecular biosignatures are key targets for current, proposed, and future life detection missions. With the high accuracy and low limit of detection (LOD) that new and future instruments will require, decontamination of life detection hardware is necessary to prevent false positives. Lipids are a molecular biosignature of interest, as they are ubiquitous to all life as we know it, can survive unaltered in the geologic record for longer than any other biomolecule (i.e. billions of years), and form through both biotic and abiotic processes. Lipids display origin-diagnostic molecular patterns that can reveal biotic or abiotic synthesis, so finding them and ascertaining their molecular features is important for potentially detecting evidence of life elsewhere. Traditional methods of decontamination, or contamination control (CC), primarily clean hardware through fabrication in sterile (cleanroom) environments, killing microbes, and removing/flushing contaminants off instrument and spacecraft components. However, research suggests that some standard cleaning methods are either unlikely to remove lipid contaminants or are incompatible with life detection instrument materials. To solve this problem, I propose to find, test, and verify a decontamination method that thoroughly cleans instruments by destroying lipid molecules, but is simultaneously compatible with major materials used in these instruments. I will study the effects of traditional CC methods (including Dry Heat Microbial Reduction and Vapor phase Hydrogen Peroxide) and experimental CC methods (Electron Beam Irradiation) on lipid molecules for application to life detection instrumentation. I will then develop a CC plan for a novel lipid detector (ExCALiBR, Extractor for Chemical Analysis of Lipid Biomarkers in Regolith) searching for lipids in either soil or icy world scenarios. This plan will uphold planetary protection regulation requirements and validate experimental analyses of in-situ life detection tests.

Decontamination↗

NASA NTRS2017

Kepler Planet Detection Metrics: Per-Target Flux-Level Transit Injection Tests of TPS for Data Release 25

Quantifying the ability of a transiting planet survey to recover transit signals has commonly been accomplished through Monte-Carlo injection of transit signals into the observed data and subsequent running of the signal search algorithm (Gilliland et al., 2000; Weldrake et al., 2005; Burke et al., 2006). In order to characterize the performance of the Kepler pipeline (Twicken et al., 2016; Jenkins et al., 2017) on a sample of over 200,000 stars, two complementary injection and recovery tests are utilized:1. Injection of a single transit signal per target into the image or pixel-level data, hereafter referred to as pixel-level transit injection (PLTI), with subsequent processing through the Photometric Analysis (PA), Presearch Data Conditioning (PDC), Transiting Planet Search (TPS), and Data Validation (DV) modules of the Kepler pipeline. The PLTI quantification of the Kepler pipeline's completeness has been described previously by Christiansen et al. (2015, 2016); the completeness of the final SOC 9.3 Kepler pipeline acting on the Data Release 25 (DR25) light curves is described by Christiansen (2017).2. Injection of multiple transit signals per target into the normalized flux time series data with a subsequent transit search using a stream-lined version of the Transiting Planet Search (TPS) module. This test, hereafter referred to as flux-level transit injection (FLTI), is the subject of this document. By running a heavily modified version of TPS, FLTI is able to perform many injections on selected targets and determine in some detail which injected signals are recoverable. Significant numerical efficiency gains are enabled by precomputing the data conditioning steps at the onset of TPS and limiting the search parameter space (i.e., orbital period, transit duration, and ephemeris zero-point) to a small region around each injected transit signal.The PLTI test has the advantage that it follows transit signals through all processing steps of the Kepler pipeline, and the recovered signals can be further classified as planet candidates or false positives in the exact same manner as detections from the nominal (i.e., observed) pipeline run (Twicken et al., 2016, Thompson et al., in preparation). To date, the PLTI test has been the standard means of measuring pipeline completeness averaged over large samples of targets (Christiansen et al., 2015, 2016; Christiansen, 2017). However, since the PLTI test uses only one injection per target, it does not elucidate individual-target variations in pipeline completeness due to differences in stellar properties or astrophysical variability. Thus, we developed the FLTI test to provide a numerically efficient way to fully map individual targets and explore the performance of the pipeline in greater detail. The FLTI tests thereby allow a thorough validation of the pipeline completeness models (such as window function (Burke and Catanzarite, 2017a), detection efficiency (Burke Catanzarite, 2017b), etc.) across the spectrum of Kepler targets (i.e., various astrophysical phenomena and differences in instrumental noise). Tests during development of the FLTI capability revealed that there are significant target-to-target variations in the detection efficiency.

DR25↗

NASA NTRS2018

Kepler Data Validation I: Architecture, Diagnostic Tests, and Data Products for Vetting Transiting Planet Candidates

The Kepler Mission was designed to identify and characterize transiting planets in the Kepler Field of View and to determine their occurrence rates. Emphasis was placed on identification of Earth-size planets orbiting in the Habitable Zone of their host stars. Science data were acquired for a period of four years. Long-cadence data with 29.4 min sampling were obtained for approx. 200,000 individual stellar targets in at least one observing quarter in the primary Kepler Mission. Light curves for target stars are extracted in the Kepler Science Data Processing Pipeline, and are searched for transiting planet signatures. A Threshold Crossing Event is generated in the transit search for targets where the transit detection threshold is exceeded and transit consistency checks are satisfied. These targets are subjected to further scrutiny in the Data Validation (DV) component of the Pipeline. Transiting planet candidates are characterized in DV, and light curves are searched for additional planets after transit signatures are modeled and removed. A suite of diagnostic tests is performed on all candidates to aid in discrimination between genuine transiting planets and instrumental or astrophysical false positives. Data products are generated per target and planet candidate to document and display transiting planet model fit and diagnostic test results. These products are exported to the Exoplanet Archive at the NASA Exoplanet Science Institute, and are available to the community. We describe the DV architecture and diagnostic tests, and provide a brief overview of the data products. Transiting planet modeling and the search for multiple planets on individual targets are described in a companion paper. The final revision of the Kepler Pipeline code base is available to the general public through GitHub. The Kepler Pipeline has also been modified to support the Transiting Exoplanet Survey Satellite (TESS) Mission which is expected to commence in 2018.

data analysis↗

NASA NTRSDate not supplied

The Air Quality Monitor “Benzene” Anomaly: Ground Testing and On-going Effects

The International Space Station (ISS) Air Quality Monitors (AQMs) have provided targeted in-flight analysis of volatile organic compounds (VOCs) in the ISS atmosphere since early 2013. During their initial half decade of use covering multiple sets of units, the AQMs performed well, meeting their validation criteria and showing excellent accuracy compared to archival samples. In addition to routine environmental monitoring, the AQMs have also been used during a number of contingency situations and investigations related to Environmental Control and Life Support Systems (ECLSS). These include a potential ammonia leak, increases in atmospheric ethanol, and efforts to locate potential sources of polydimethylsiloxanes that lead to the production of dimethylsilanediol (DMSD) in the US Water Processor Assembly (WPA). As the fleet of AQMs has aged, several issues have arisen. These have ranged from pervasive problems on electronics boards to loss of sensitivity due to operating in an elevated CO2 environment. The most notable issue encountered during on-orbit operations was incorrect identification of compounds. This initially occurred in mid-2020, when AQM1 reported the presence of benzene. While the AQM team questioned the validity of these results, the concentration of the “benzene” continued to increase and eventually exceeded the 30- and 180-day Spacecraft Maximum Allowable Concentration (SMAC). This led to wide-ranging efforts by a number of groups aimed at understanding the situation and identifying the source of the “benzene.” AQM1 failed after being relocated to the Russian Segment as part of the investigation, and the unit was returned for evaluation. When archive samples collected while the AQM was measuring elevated benzene showed no detectable benzene, the focus of the investigation shifted to determining the cause of the false positive readings. Here, we will discuss the results of this investigation by the AQM team, potential causes of the interference, and subsequent reporting of AQM1 results.

W T Wallace↗

NASA NTRS2024

The Air Quality Monitor “Benzene” Anomaly: Ground Testing and On-going Effects

The International Space Station (ISS) Air Quality Monitors (AQMs) have provided targeted in-flight analysis of volatile organic compounds (VOCs) in the ISS atmosphere since early 2013. During their initial half decade of use covering multiple sets of units, the AQMs performed well, meeting their validation criteria and showing excellent accuracy compared to archival samples. In addition to routine environmental monitoring, the AQMs have also been used during a number of contingency situations and investigations related to Environmental Control and Life Support Systems (ECLSS). These include a potential ammonia leak, increases in atmospheric ethanol, and efforts to locate potential sources of polydimethylsiloxanes that lead to the production of dimethylsilanediol (DMSD) in the US Water Processor Assembly (WPA). As the fleet of AQMs has aged, several issues have arisen. These have ranged from pervasive problems on electronics boards to loss of sensitivity due to operating in an elevated CO2 environment. The most notable issue encountered during on-orbit operations was incorrect identification of compounds. This initially occurred in mid-2020, when AQM1 reported the presence of benzene. While the AQM team questioned the validity of these results, the concentration of the “benzene” continued to increase and eventually exceeded the 30- and 180-day Spacecraft Maximum Allowable Concentration (SMAC). This led to wide-ranging efforts by a number of groups aimed at understanding the situation and identifying the source of the “benzene.” AQM1 failed after being relocated to the Russian Segment as part of the investigation, and the unit was returned for evaluation. When archive samples collected while the AQM was measuring elevated benzene showed no detectable benzene, the focus of the investigation shifted to determining the cause of the false positive readings. Here, we will discuss the results of this investigation by the AQM team, potential causes of the interference, and subsequent reporting of AQM1 results.

W T Wallace↗

NASA NTRSDate not supplied

The Air Quality Monitor “Benzene” Anomaly: Ground Testing and On-going Effects

The International Space Station (ISS) Air Quality Monitors (AQMs) have provided targeted in-flight analysis of volatile organic compounds (VOCs) in the ISS atmosphere since early 2013. During their initial half decade of use covering multiple sets of units, the AQMs performed well, meeting their validation criteria and showing excellent accuracy compared to archival samples. In addition to routine environmental monitoring, the AQMs have also been used during a number of contingency situations and investigations related to Environmental Control and Life Support Systems (ECLSS). These include a potential ammonia leak, increases in atmospheric ethanol, and efforts to locate potential sources of polydimethylsiloxanes that lead to the production of dimethylsilanediol (DMSD) in the US Water Processor Assembly (WPA). As the fleet of AQMs has aged, several issues have arisen. These have ranged from pervasive problems on electronics boards to loss of sensitivity due to operating in an elevated CO2 environment. The most notable issue encountered during on-orbit operations was incorrect identification of compounds. This initially occurred in mid-2020, when AQM1 reported the presence of benzene. While the AQM team questioned the validity of these results, the concentration of the “benzene” continued to increase and eventually exceeded the 30- and 180-day Spacecraft Maximum Allowable Concentration (SMAC). This led to wide-ranging efforts by a number of groups aimed at understanding the situation and identifying the source of the “benzene.” AQM1 failed after being relocated to the Russian Segment as part of the investigation, and the unit was returned for evaluation. When archive samples collected while the AQM was measuring elevated benzene showed no detectable benzene, the focus of the investigation shifted to determining the cause of the false positive readings. Here, we will discuss the results of this investigation by the AQM team, potential causes of the interference, and subsequent reporting of AQM1 results.

William T Wallace↗

NASA NTRS2018

Exoplanet Biosignatures: At the Dawn of a New Era of Planetary Observations

The rapid rate of discoveries of exoplanets has expanded the scope of the science possible for the remote detection of life beyond Earth. The Exoplanet Biosignatures Workshop-Without-Walls (EBWWW) held in 2016 engaged the international scientific community across diverse scientific disciplines, to assess the state of the science and technology in the search for life on exoplanets, and to identify paths for progress. The workshop activities resulted in five (5) major review papers which provide: 1) an encyclopedic review of known and proposed biosignatures and models used to ascertain them; 2) an in-depth review of O2 as a biosignature, rigorously examining the nuances of false positives and negatives for evidence of life; 3) a Bayesian framework to comprehensively organize current understanding to quantify confidence in biosignature assessments; 4) an extension of that Bayesian framework in anticipation of increasing planetary data and novel concepts of biosignatures, and 5) a review of the upcoming telescope capabilities to characterize exoplanets and their environment. Because of the immense content of these review papers, this summary provides a guide to their complementary scope and highlights salient features. Strong themes that emerged from the workshop were that biosignatures must be interpreted in the context of their environment, and that frameworks must be developed to link diverse forms of scientific understanding of that context to quantify the likelihood that a biosignature has been observed. Models are needed to explore the parameter space where measurements will be widespread but sparse in detail. Given the technological prospects for large ground-based telescopes and direct imaging from space-based observatories, the detection of atmospheric signatures of a few potentially habitable planets may come before 2030.

spectral imaging↗

NASA NTRS1994

Correlation approach to identify coding regions in DNA sequences

Recently, it was observed that noncoding regions of DNA sequences possess long-range power-law correlations, whereas coding regions typically display only short-range correlations. We develop an algorithm based on this finding that enables investigators to perform a statistical analysis on long DNA sequences to locate possible coding regions. The algorithm is particularly successful in predicting the location of lengthy coding regions. For example, for the complete genome of yeast chromosome III (315,344 nucleotides), at least 82% of the predictions correspond to putative coding regions; the algorithm correctly identified all coding regions larger than 3000 nucleotides, 92% of coding regions between 2000 and 3000 nucleotides long, and 79% of coding regions between 1000 and 2000 nucleotides. The predictive ability of this new algorithm supports the claim that there is a fundamental difference in the correlation property between coding and noncoding sequences. This algorithm, which is not species-dependent, can be implemented with other techniques for rapidly and accurately locating relatively long coding regions in genomic sequences.

Non-NASA Center↗

NASA NTRS2007

Benchtop Detection of Proteins

A process, and a benchtop-scale apparatus for implementing the process, have been developed to detect proteins associated with specific microbes in water. The process and apparatus may also be useful for detection of proteins in other, more complex liquids. There may be numerous potential applications, including monitoring lakes and streams for contamination, testing of blood and other bodily fluids in medical laboratories, and testing for microbial contamination of liquids in restaurants and industrial food-processing facilities. A sample can be prepared and analyzed by use of this process and apparatus within minutes, whereas an equivalent analysis performed by use of other processes and equipment can often take hours to days. The process begins with the conjugation of near-infrared-fluorescent dyes to antibodies that are specific to a particular protein. Initially, the research has focused on using near-infrared dyes to detect antigens or associated proteins in solution, which has proven successful vs. microbial cells, and streamlining the technique in use for surface protein detection on microbes would theoretically render similar results. However, it is noted that additional work is needed to transition protein-based techniques to microbial cell detection. Consequently, multiple such dye/antibody pairs could be prepared to enable detection of multiple selected microbial species, using a different dye for each species. When excited by near-infrared light of a suitable wavelength, each dye fluoresces at a unique longer wavelength that differs from those of the other dyes, enabling discrimination among the various species. In initial tests, the dye/antibody pairs are mixed into a solution suspected of containing the selected proteins, causing the binding of the dye/antibody pairs to such suspect proteins that may be present. The solution is then run through a microcentrifuge that includes a membrane that acts as a filter in that it retains the dye/antibody/protein complexes while allowing any remaining unbound dye/antibody pairs to flow away. The retained dye/antibody/protein complexes are transferred to a cuvette, wherein they are irradiated with light from a miniature near-infrared laser delivered via a fiber-optic cable. The resulting fluorescence from the dye(s) is measured by use of a miniature spectrometer, the output of which is digitized, then analyzed by laptop computer. The software running in the computer identifies the protein species by the wavelengths of their spectral peaks and determines the amounts of the proteins, and thus, one day, microbes of the various species from the intensities of the peaks. The abovementioned removal of the unbound dye/antibody pairs during centrifugation prevents false positive readings. The process proves successful in detecting proteins in solution and thus can now be employed for use in microbe detection.

Scardelletti, Maximilian C.↗

NASA NTRS2019

ISEP: A Joint SRAG/CCMC Collaboration to Improve Mitigation of Space Weather Effects on Crew Health in the Exo-LEO Era

The Space Radiation Analysis Group (SRAG) at Johnson Space Center (JSC) is tasked with monitoring changes to space weather and mitigating any resultant impacts to crew health and safety. As human spaceflight goals extend from Low-Earth Orbit (LEO) missions like the International Space Station (ISS) to the moon, Mars and beyond, SRAG will need to update their current approach for crew monitoring of and protection from radiation exposure due to energetic Solar Particle Events (ESPEs). Challenges faced in planning exo-LEO missions include the lack of protection from the Earth’s geomagnetic field employed by the ISS in addition to limited communication capability between the crew and the ground. In the event of an ESPE, the current ISS trajectory ensures that the vehicle is only traveling through fields of higher radiation exposure for a brief period of time; the Earth’s geomagnetic field prevents the penetration of the high-energy particles of concern throughout the majority of the orbit. Exo-LEO missions, on the other hand, require that the vehicle travel through free space, exposing vehicle and crew to the full impact of the ESPE. NASA has combined multiple approaches to resolve this radiation exposure issue. New vehicles are designed to take advantage of advances in particle transport modeling capabilities and shielding technology, allowing redistribution of mass throughout the vehicle to areas of thinner shielding when the energetic particle flux has increased to levels of concern. Although vehicle shielding is an important aspect of radiation exposure protection, there is a continued requirement to monitor and predict the space weather environment. To this end, SRAG maintains a console position in Mission Control with 24/7 mission support capability. In the event of increased solar activity, SRAG collaborates with the Flight Control Team (FCT) to determine if crew action (i.e., shelter) is required. During any increase in solar activity, the FCT needs three pieces of information to effectively decide the crew response in light of other required mission tasks: if an event (ESPE) will occur, how ‘intense’ an observed event will be, and how long will an observed event will last. An ideal alert system limits false alarms, therefore causing the crew to take action unnecessarily, without ignoring events that pose a hazard to the crew. SRAG’s current operational concept for ISS missions focuses on short-term forecasts, best described as ‘now-casting’. Console operators are in daily communication with the Space Weather Prediction Center (SWPC) for situational awareness purposes. When conditions exist that may lead to increased solar activity, operators receive notifications from SWPC. In the case of a well-connected ESPE, the console operator may only have on the order of minutes to several hours to notify the FCT of the event and provide a recommendation for crew action. As NASA shifts to exo-LEO missions, the increased time in free space as well as the reduced ability to communicate with the crew will force a transition in crew protection strategy that emphasizes improvments to both the accuracy and the lead time in forecasting capabilities.

Barzilla, Janet E.↗

NASA NTRSDate not supplied

Does Collection Time Bias the Ecology of Cleanroom Air Samples?

Microbial monitoring of astromaterials collections has taken on increased importance with the return of biologically sensitive samples from the asteroids Ryugu and Bennu and the initiation of the Mars Sample Return Program. Terrestrial bacteria and fungi can alter the mineralogy and organic composition of our collections causing irreversible contamination of pristine samples and increasing the risk of false positives for life detection measurements. NASA has conducted routine microbial monitoring of its existing collections since 20181. Initial monitoring focused on surface samples collected with foam swabs. Although, airborne microbiology is often decoupled from surface microbiology in the built environment2 culture-based air sampling techniques like impactors were not compliant with existing contamination control requirements. Bringing organic rich media, gelatin or liquids into curation cleanrooms presents an unacceptable risk to pristine samples. In 2022 NASA purchased a materials complaint air sampler and began collecting air samples from the cleanrooms in addition to surface samples3. The new instrument uses an electret filter to collect samples that are suitable for cultivating organisms or for direct DNA sequencing. Preliminary DNA sequencing results appeared to indicate that longer sampling times biased the microbial community in favor of hearty, spore-forming bacteria3. We present the results of a study comparing overnight sampling (17 hours) to short (1 hour) sampling of unoccupied curation cleanrooms. The results will help us optimize our monitoring protocols and develop a more detailed inventory of the ecology of astromaterials curation cleanrooms. Methods: We analyzed 72 paired air samples from six different cleanrooms including the meteorite processing lab (ISO 7 equivalent, 16 samples), the lunar lab (ISO 6 equivalent, 10 samples), the stardust lab (ISO 5 equivalent 14 samples), the OSIRIS-REx lab (ISO 5 equivalent, 12 samples), the Hayabusa2 lab (ISO 5 equivalent, 14 samples), and the Genesis lab (ISO 4 equivalent, 6 samples). All the samples were collected with an InnovaPrep Bobcat air sampler operating at a sampling rate of 200 L/min. The sampler operates for 5 minutes out of every 20 minute period. Half of the samples were collected by filtering 3,000L (15 min. of active sampling) of air across an electret filter for one hour. The rest of the samples were collected by filtering approximately 51,000 L air across the filter overnight (~17 hours, 255 min. of active sampling). Cells were eluted from the filter using 6-7 ml of pressurized 0.15% tween 20 in PBS (phosphate buffered saline). This liquid was used to cultivate bacteria according to previously published methods1,4,5 and for DNA extraction and next generation sequencing. DNA was extracted with a Qiagen MagAttract PowerMicrobiome kit6. To identify bacteria and archaea, the 16S rRNA gene was amplified using Earth Microbiome primers for the V4 region 7. The amplified DNA was sequenced on an Illumina MiSeq using a V3 reagent kit. The resulting sequences were processed using DADA2 and QIIME2 as implemented on the EDGE bioinformatics platform8–10. Results: Only two of the 72 samples had no amplifiable DNA. Amplified DNA concentrations ranged from 2.67 – 0.272 ng/µl. The median concentration of amplified DNA for the 1 hour samples was 0.770 ± 0.368 ng/µl. The median concentration of amplified DNA for the overnight samples was 0.877 ± 0.434 ng/µl. On average the overnight samples had slightly more sequences (58,960 vs. 59,456) and ASV’s (amplicon sequence variants) (60 vs 64.5) than the one hour samples, but these differences are not statistically significant. The most abundant ASV in every sample mapped to the genus Cupravidus. ASV’s mapping to the genuses Bacillus, Schlegelella, Thermus, and Staphylococcus were also common. Discussion and Future Work: Alpha diversity statistics like Shannon Entropy and Faith Phylogenetic Diversity are used to describe the diversity of organisms in a single sample. If a longer sampling time was biasing the data, we would expect to see a change in these diversity statistics vs. sample time. However, we did not observe this in our data. The median Shannon entropy was slightly higher for the overnight samples (3.773 vs 3.611) as was the Faith Phylogenetic Diversity (4.042 vs 3.596), but both values were within a standard deviation of each other for the two sampling times (Fig. 1). It is unlikely, that the longer sampling time is introducing bias into our data. We do observe a significant decrease in diversity when comparing the air samples by lab. The Genesis lab (ISO 4 equivalent) has a lower median number of ASV’s (45.5) than the other labs (62). Median values for Shannon Entropy (3.717 vs. 3.430) and Faith Phylogenetic Diversity (3.796 vs. 3.548) are also lower for Genesis, but those values are with one standard deviation of each other for the different sampling times. This is consistent with previous culture-based results suggesting that the environment in cleanrooms tends to select for a core group of organisms capable of surviving under dry, low nutrient, conditions. The presence of the ASV’s mapping to Cupravidus and Thermus in our sequencing blanks and controls suggests that several of the most common organisms in our samples represent contaminants from the reagents used to perform the DNA extractions and sequencing. Further work is needed to identify these contaminants, remove them from our data and recalculate the diversity statistics. This is a systematic error. Therefore, we do not expect removing the sequencing contaminants to change our conclusions. Longer air sample collection times appear to result in slightly higher diversity and do not bias the results towards “hardy” bacteria like spore-formers. Based on these preliminary results we conclude that sampling at least 3,000 liters of air is sufficient to capture the microbial diversity of cleanrooms, and that air samples can also be collected overnight without negatively impacting diversity. These results allow us to be flexible when designing microbial monitoring plans so that they do not interfere with routine lab activity. References: 1. Regberg, A. B. et al. 49th Lunar and Planetary Science Conference (2018). 2. The United States Pharmacopeial Convention. USP General Chapter <1116> (2013). 3. Regberg, A. B., et al. 54th Lunar and Planetary Science Conference (2023). 4. Regberg, A. B. et al. 53rd Lunar and Planetary Science Conference ( 2022). 5. Davis, R. E.,et al. 50th Lunar and Planetary Science Conference (2019). 6. Qiagen. MagAttract® PowerMicrobiome® DNA/RNA EP Kit Handbook. (2018). 7. Walters, W. et al. mSystems 1, (2015). 8. Callahan, B. J. et al. Nat. Methods 13, 581–583 (2016). 9. Hall, M. & Beiko, R. G. Microbiome Analysis: Methods and Protocols113–129 (Springer, 2018). 10. Philipson, C. et al. Bio-Protoc. 7, e2622 (2017).

A. B. Regberg↗