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NASA NTRS2009

International Utilization at the Threshold of "Assembly Complete"- Science Returns from the International Space Station

The European Columbus and Japanese Kibo laboratories are now fully operational on the International Space Station (ISS), bringing decades of international planning to fruition. NASA is now completing launch and activation of major research facilities that will be housed in the Destiny U.S. Laboratory, Columbus, and Kibo. These facilities include major physical sciences capabilities for combustion, fluid physics, and materials science, as well as additional multipurpose and supporting infrastructure. Expansion of the laboratory space and expansion to a 6-person crew (planned for May 2009), is already leading to significant increases in research throughput even before assembly is completed. International research on the ISS includes exchanges of results, sharing of facilities, collaboration on experiments, and joint publication and communication of accomplishments. Significant and ongoing increases in research activity on ISS have occurred over the past year. Although research results lag behind on-orbit operations by 2-5 years, the surge of early research activities following Space Shuttle return to flight in 2005 is now producing an accompanying surge in scientific publications. Evidence of scientific productivity from early utilization opportunities combined with the current pace of research activity in orbit are both important parts of the evidence base for evaluating the potential future achievements of a complete and active ISS.

Robinson, Julie A.↗

NASA NTRS2010

Serrating Nozzle Surfaces for Complete Transfer of Droplets

A method of ensuring the complete transfer of liquid droplets from nozzles in microfluidic devices to nearby surfaces involves relatively simple geometric modification of the nozzle surfaces. The method is especially applicable to nozzles in print heads and similar devices required to dispense liquid droplets having precise volumes. Examples of such devices include heads for soft printing of ink on paper and heads for depositing droplets of deoxyribonucleic acid (DNA) or protein solutions on glass plates to form microarrays of spots for analysis. The main purpose served by the present method is to ensure that droplets transferred from a nozzle have consistent volume, as needed to ensure accuracy in microarray analysis or consistent appearance of printed text and images. In soft printing, droplets having consistent volume are generated inside a print head, but in the absence of the present method, the consistency is lost in printing because after each printing action (in which a drop is ejected from a nozzle), a small residual volume of liquid remains attached to the nozzle. By providing for complete transfer of droplets (and thus eliminating residual liquid attached to the nozzle) the method ensures consistency of volume of transferred droplets. An additional benefit of elimination of residue is prevention of cross-contamination among different liquids printed through the same nozzle a major consideration in DNA microarray analysis. The method also accelerates the printing process by minimizing the need to clean a printing head to prevent cross-contamination. Soft printing involves a hydrophobic nozzle surface and a hydrophilic print surface. When the two surfaces are brought into proximity such that a droplet in the nozzle makes contact with the print surface, a substantial portion of the droplet becomes transferred to the print surface. Then as the nozzle and the print surface are pulled apart, the droplet is pulled apart and most of the droplet remains on the print surface. The basic principle of the present method is to reduce the liquid-solid surface energy of the nozzle to a level sufficiently below the intrinsic solid-liquid surface energy of the nozzle material so that the droplet is not pulled apart and, instead, the entire droplet volume becomes transferred to the print surface. In this method, the liquid-solid surface energy is reduced by introducing artificial surface roughness in the form of micromachined serrations on the inner nozzle surface (see figure). The method was tested in experiments on soft printing of DNA solutions and of deionized water through 0.5-mm-diameter nozzles, of which some were not serrated, some were partially serrated, and some were fully serrated. In the nozzles without serrations, transfer was incomplete; that is, residual liquids remained in the nozzles after printing. However, in every nozzle in which at least half the inner surface was serrated, complete transfer of droplets to the print surface was achieved.

Kim, Chang-Jin "CJ"↗

NASA NTRS2016

Successful Completion of the JWST OGSE2 Cryogenic Test at JSC Chamber-A While Managing Numerous Challenges

The James Webb Space Telescope (JWST) Optical Telescope Element (OTE) assembly is the largest optically stable infrared-optimized telescope currently being manufactured and assembled, and scheduled for launch in 2018. The JWST OTE, including the primary mirrors, secondary mirror, and the Aft Optics Subsystems (AOS) are designed to be passively cooled and operate at near 45 degrees Kelvin. Due to the size of its large sunshield in relation to existing test facilities, JWST cannot be optically or thermally tested as a complete observatory-level system at flight temperatures. As a result, the telescope portion along with its instrument complement will be tested as a single unit very late in the program, and on the program schedule critical path. To mitigate schedule risks, a set of 'pathfinder' cryogenic tests will be performed to reduce program risks by demonstrating the optical testing capabilities of the facility, characterizing telescope thermal performance, and allowing project personnel to learn valuable testing lessons off-line. This paper describes the 'pathfinder' cryogenic test program, focusing on the recently completed second test in the series called the Optical Ground Support Equipment 2 (OGSE2) test. The JWST OGSE2 was successfully completed within the allocated project schedule while faced with numerous conflicting thermal requirements during cool-down to the final cryogenic operational temperatures, and during warm-up after the cryo-stable optical tests. The challenges include developing a pre-test cool-down and warm-up profiles without a reliable method to predict the thermal behaviors in a rarified helium environment, and managing the test article hardware safety driven by the project Limits and Constraints (L&C's). Furthermore, OGSE2 test included the time critical Aft Optics Subsystem (AOS), a part of the flight Optical Telescope Element that would need to be placed back in the overall telescope assembly integrations. The OGSE2 test requirements included the strict adherence of the project contamination controls due to the presence of the contamination sensitive flight optical elements. The test operations required close coordination of numerous personnel while they being exposed and trained for the 'final' combined OTE and instrument cryo-test in 2017. This paper will also encompass the OGSE2 thermal data look-back review.

JWST OGSE2 Cryogenic Test↗

NASA NTRS2017

Kepler Planet Detection Metrics: Robovetter Completeness and Effectiveness for Data Release 25

In general, the Kepler pipeline identifies a list of Threshold Crossing Events (TCEs), which are periodic flux decrements meeting certain criteria (Jenkins, 2017). These TCEs are reviewed and those that appear consistent with astrophysically transiting or eclipsing systems are classified as Kepler Objects of Interest (KOIs). Further review is given to KOIs, which are then dispositioned as Planet Candidates (PCs) or False Positive (FPs). FPs are further denoted by four major flags that indicate if the signal is Not Transit-Like (NTL), due to a Stellar Eclipse (SS; previously referred to as Significant Secondary), and/or due to contamination from a source other than the target as evidenced by a Centroid Offset (CO) oran Ephemeris Match (EM) with another object. This entire TCE review process is known as dispositioning or vetting.In the first five Kepler mission planet candidate catalogs (Borucki et al., 2011a,b; Batalha et al., 2013; Burke et al., 2014; Rowe et al., 2015), TCEs were manually examined on an individual basis and dispositioned using various plots and quantitative diagnostic tests (see e.g., Coughlin, 2017). In the sixth catalog, Mullally et al. (2015a) employed partial automation via simple parameter cuts to automatically disposition a large fraction of TCEs as not transit-like. Mullally et al. (2015a) also used an automated technique known as the centroid Robovetter (Mullally, 2017) to automatically identify some FP KOIs due to centroid offsets - a telltale signature of light contamination from another target. The remaining targets were manually dispositioned. In the seventh catalog, Coughlin et al. (2016) automated theentire dispositioning process using what is collectively known simply as the Robovetter.In the eighth and final mission catalog, Thompson et al. (2017) use a revised Robovetter to automate the dispositioning of all TCEs with an emphasis on creating a catalog suitable for accurately determining planet occurrence rates. In order to calculate accurate occurrence rates, the completeness and effectiveness of the Robovetter must be characterized. We define these terms as applied to the Robovetter, following Thompson et al. (2017), as:1. Completeness: The fraction of transiting planets detected by the pipeline that are classified as planet candidates by the Robovetter.2. Effectiveness: The fraction of false positives detected by the pipeline that are classified as false positives by the Robovetter.The remainder of this document describes products that can be used to quantitatively assess Robovetter completeness and effectiveness for an arbitrary set of Kepler stars.

Robovetter↗

NASA NTRS2020

The Zwicky Transient Facility Bright Transient Survey. I. Spectroscopic Classification and the Redshift Completeness of Local Galaxy Catalogs

The Zwicky Transient Facility (ZTF) is performing a three-day cadence survey of the visible northern sky (∼3π) with newly found transient candidates announced via public alerts. The ZTF Bright Transient Survey (BTS) is a large spectroscopic campaign to complement the photometric survey. BTS endeavors to spectroscopically classify all extragalactic transients with m(peak) ≤ 18.5 mag in either the g(ZTF) or r(ZTF) filters, and publicly announce said classifications. BTS discoveries are predominantly supernovae (SNe), making this the largest flux-limited SN survey to date. Here we present a catalog of 761 SNe, classified during the first nine months of ZTF (2018 April 1–2018 December 31). We report BTS SN redshifts from SN template matching and spectroscopic host-galaxy redshifts when available. We analyze the redshift completeness of local galaxy catalogs, the redshift completeness fraction (RCF; the ratio of SN host galaxies with known spectroscopic redshift prior to SN discovery to the total number of SN hosts). Of the 512 host galaxies with SNe Ia, 227 had previously known spectroscopic redshifts, yielding an RCF estimate of 44% ± 4%. The RCF decreases with increasing distance and decreasing galaxy luminosity (for z < 0.05, or ∼200 Mpc, RCF ≈ 0.6). Prospects for dramatically increasing the RCF are limited to new multifiber spectroscopic instruments or wide-field narrowband surveys. Existing galaxy redshift catalogs are only ∼50% complete at r ≈ 16.9 mag. Pushing this limit several magnitudes deeper will pay huge dividends when searching for electromagnetic counterparts to gravitational wave events or sources of ultra-high-energy cosmic rays or neutrinos.

C. Fremling↗

NASA NTRSDate not supplied

Evaluation of Self-Scheduling Exercises Completed by Analog Crewmembers in NASA's Human Exploration Research Analog (HERA)

NASA human spaceflight missions are inherently dynamic and require frequent scheduling changes in order to adapt to changing mission priorities and objectives. Tactical level changes to the mission plan are traditionally made by a team of expert planners and operations specialists on the ground. However, astronauts are expected to execute missions more autonomously during future long duration missions. Astronauts will need to take on some of the responsibility of managing their own schedule while still abiding by the numerous constraints required by human spaceflight operations. This paper summarizes salient elements of crew performance in NASA’s Human Exploration Research Analog Campaign 3. Analog crewmembers completed a series of self-scheduling exercises to evaluate Playbook’s usability towards enabling self-scheduling without support from ground control. Playbook is a self-scheduling software tool designed and developed by our team. We also investigated how to best communicate self-scheduling tasks and constraints to the crew in order to facilitate efficient self-scheduling during isolation in a realistic environment. Our analysis identified that 30 minutes was sufficient to complete complex self-scheduling tasks. Our evaluation also identified differences between individual and collaborative performance; analog crewmembers completed self-scheduling exercises more quickly as a team as opposed to individually and reported lower subjective difficulty ratings overall.

HERA↗

NASA NTRSDate not supplied

Astrobee: Completed, Current, and Future Research using Free Flying Robots on the International Space Station

After four years on the International Space Station (ISS), the Astrobee Research Facility, has completed over 130 Test Sessions logging over 1000 hours of operations. Managed by the NASA ISS Program OZ office and supported by NASA Ames Research Center (ARC) in California, the Astrobee Team maintains three identical free-flying Astrobee robots for research on the ISS. As a technology demonstration platform, the Astrobee Robots are available for Guest Scientists to use for a spectrum of research capabilities. Astrobee, propelled by battery-operated fans, is designed to autonomously operate throughout most of the USOS (US Orbital Segment), with the objective of minimizing astronaut support. Astrobee carries a suite of six cameras, a two degree-of-freedom (DOF) arm with a gripper that can grasp ISS handrails and other objects, and three payload bays that provide power and data for guest science hardware. Astrobee can autonomously execute hours-long flight plans or be teleoperated from the ground or by astronauts. While the Astrobee Team continues to improve mapping and autonomous flight capabilities, one of the main goals of Astrobee Robots is to provide research opportunities for Guest Scientists. The Astrobee Robot Software (ARS) makes extensive use of the open-source Robot Operating System (ROS). The ARS can be used interchangeably with an Astrobee Simulator or as Astrobee’s onboard software. ARS features include autonomous docking and perching, real-time teleoperations from the ground, plan based autonomous tasks, multi Astrobee communication, among other capabilities. Through simulation software and ground testing laboratories, the Astrobee Team is available to support Guest Scientists during development and testing and lead real-time ISS operations. Guest Scientists can participate in this research opportunity following the Guest Science Lifecycle (GSL) shown in Figure 1: Guest Science Lifecycle below. The Astrobee Team and Guest Scientists have complete research including Gecko materials studies, RFID and sound sensing capabilities, student Robotics Programming Challenges, and Free Flyer formation flight investigations. Current science with the Astrobee Robots includes Free Flyer self-toss studies, new docking capabilities, advanced mapping resolution capabilities, and high resolution panoramic imagery. Future Guest scientists and Astrobee Team research will focus on robotics applications for future NASA missions such as Gateway and Artemis and potential experiments involving human-robot interactions. This presentation will focus on four main subjects, 1) completed, current, and future planned research using the Astrobee robots, 2) how Guest Scientist get from conception to the ISS, 3) Astrobee Facility resources available for Guest Science ground testing and real-time ISS operations support, and 4) lessons learned from four years of ISS operations.

Astrobee↗

NASA NTRSDate not supplied

Astrobee: Five years of Completed, Current, and Future Research on the International Space Station using Free Flying Robots.

After five years on the International Space Station (ISS), the Astrobee Research Facility, has completed over 160 Test Sessions logging over 1200 hours of operations. Managed by the NASA ISS Program OZ office and supported by NASA Ames Research Center (ARC) in California, the Astrobee Team currently maintains two identical free-flying Astrobee robots and a Docking Station for research on the ISS. As a technology demonstration platform, the Astrobee Robots are available for Guest Scientists to use for a spectrum of research capabilities. Using ambient air on the ISS, propelled by battery-operated fans, Astrobee is designed to autonomously operate throughout most of the USOS (US Orbital Segment), with the objective of minimizing the need for astronaut support. Astrobee carries a suite of six cameras, a two degree-of-freedom (DOF) arm with a gripper that can grasp ISS handrails and other objects, and three payload bays that provide power and data for guest science hardware. Astrobee can autonomously execute hours-long flight plans or be tele-operated from the ground. While the Astrobee Team continues to improve mapping and autonomous flight capabilities, one of the main goals of Astrobee Robots is to provide research opportunities for Guest Scientists. The Astrobee Robot Software (ARS) makes extensive use of the open-source Robot Operating System (ROS). The ARS can be used interchangeably with an Astrobee Simulator or as Astrobee’s onboard software. ARS features include autonomous docking and perching, real-time teleoperations from the ground, plan based autonomous tasks, multi Astrobee communication, among other capabilities. Through simulation software and ground testing laboratories, the Astrobee Team is available to support Guest Scientists during development and testing and lead real-time ISS operations. The Astrobee Team and Guest Scientists have completed research including Astrobatics maneuvers, RFID and sound sensing capabilities, Gecko materials studies, student Robotics Programming Challenges, and Free Flyer formation flight investigations. Current science with the Astrobee Robots is investigating new docking capabilities through software only research as well as testing new docking hardware installed on the Astrobees. The Astrobee Team and other researchers at NASA Ames continue to explore robotics applications for future NASA missions such as Gateway and potential experiments involving human-robot interactions. Continued advanced mapping resolution capabilities, and high-resolution panoramic imagery also remains areas of research. Exciting in development research involves docking for rendezvous proximity operation (CLINGERS), multi resolution 3D scanning (MRS), space debris removal in microgravity (REACCH). This presentation will mainly focus on completed research over the past year and current science being performed on the Astrobees. This presentation will also focus on how a Guest Scientist/Researcher progresses from conception to running their science on the Astrobees on the ISS, as well as discuss the Astrobee Facility resources available for supporting ground testing and real-time ISS operations.

Astrobee↗

DOE OSTI2014

Completion processing for data communications instructions

Completion processing of data communications instructions in a distributed computing environment, including receiving, in an active messaging interface (`AMI`) data communications instructions, at least one instruction specifying a callback function; injecting into an injection FIFO buffer of a data communication adapter, an injection descriptor, each slot in the injection FIFO buffer having a corresponding slot in a pending callback list; listing in the pending callback list any callback function specified by an instruction, incrementing a pending callback counter for each listed callback function; transferring payload data as per each injection descriptor, incrementing a transfer counter upon completion of each transfer; determining from counter values whether the pending callback list presently includes callback functions whose data transfers have been completed; calling by the AMI any such callback functions from the pending callback list, decrementing the pending callback counter for each callback function called.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Completion processing for data communications instructions

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

High power laser workover and completion tools and systems

Workover and completion systems, devices and methods for utilizing 10 kW or more laser energy transmitted deep into the earth with the suppression of associated nonlinear phenomena. Systems and devices for the laser workover and completion of a borehole in the earth. These systems and devices can deliver high power laser energy down a deep borehole, while maintaining the high power to perform laser workover and completion operations in such boreholes deep within the earth.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

Accelerating Nuclear Facility Mission Completion Through an Improved Chemical Hazard Control Strategy - 20460

Code of Federal Regulation (CFR) 10 CFR 830, Nuclear Safety Management [1], explicitly identifies hazardous materials in addition to radioactive materials when establishing the scope of materials that must be evaluated in Hazard Category (HC) 1, 2, and 3 nuclear facilities. This inclusion has led to a near decade-long progression of more and more rigorous application of chemical hazard controls in these facilities. The progressive addition of more rigorous chemical hazard controls has occurred across the Department of Energy (DOE) Complex, having been driven by contractors and regulators alike. However, chemical hazards in other DOE facilities have been, and continue to be, controlled using traditional industrial safety centered strategies. Thus, identical chemical hazards are controlled using dramatically different approaches based solely on the facility type. Not only are the controls different, the analysis and derivation rigor and requirements are also significantly different. In particular, chemical control derivation and application in non-nuclear facilities are much less onerous than the comprehensive hazard analysis process used in nuclear facilities, even in circumstances in which chemicals are not initiators to, or do not exacerbate a nuclear event. While the derivation and control approaches used in these two types of facilities are disparate, the safety results are similarly effective based on a review of reported chemical events from 2014 through 2018. While both approaches achieve comparable safety outcomes, the approach used in nuclear facilities results in significantly greater preparation costs and implementation costs. Furthermore, the problem with the differing approach is not relegated to the control preparation and implementation burden. The operational impact of potentially unnecessary controls slows mission completion without a corresponding increase in safety, not to mention the dilution of the importance of Technical Safety Requirements. The proposed solution must first include a critical and thorough examination of DOE Complex and top-tier chemical industry chemical hazard control practices, coupled with a similar examination of the driving facility regulatory requirements. Results from the examination can then be used to fuel a bold departure from current chemical control practices in Hazard Category 1, 2, and 3 nuclear facilities. Development of an improved and consistent chemical hazard control process would follow, one that continues to ensure safety while accelerating mission completion and significantly reducing the burden associated with chemical hazard control development and implementation. The improved process must establish a hierarchy where radiological hazards are addressed using safety class and safety significant controls and chemical hazards are addressed using overarching safety management programs (with limited unique exceptions). The improved Hazard Category 1,2, and 3 nuclear facility chemical hazard control strategy, while compliant with 10 CFR 830 [1], would be founded on the requirements in 10 CFR 851, Worker Safety and Health Program [2], and the complementary DOE O 151.1D, Comprehensive Emergency Management System [3]. In this way, the Hazard Category 1, 2, and 3 nuclear facility chemical hazard control strategy would, wherever appropriate, be the same process used at other DOE Complex facilities. Ultimately, the improved process will maintain safety and significantly reduce costs and life cycle risk through faster mission completion. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2020

Advanced Mixed Waste Treatment Project Overcomes Challenges to Complete Treatment of Debris Waste - 20616

The Advanced Mixed Waste Treatment Project (AMWTP), operated by Fluor Idaho for the Department of Energy Idaho Operations Office, completed the last of its debris waste treatment in the fall of 2019. Concluding that work-scope was certainly not without its challenges. Fluor Idaho and its employees had to adapt to treating extremely challenging waste types, such as high-fissile gram materials and potentially pyrophoric and reactive wastes coming down the stretch. It also had to complete the sizing of large waste boxes from Mound Laboratories in inner-contamination enclosures designed to capture the extremely fine, 'flighty' plutonium-238 in its high-efficiency particulate air filters. Very few waste treatment facilities in the DOE Complex have completed their missions. In fact, most large-scale waste treatment facilities are still under construction with many months or years remaining before 'hot operations' begin. AMWTP is unique because it functioned as a 'one-stop shop.' Transuranic and low-level waste characterization, treatment, certification, and shipping all occurred there. AMWTP concluded the most challenging part of its mission and will continue to ship material out of the state of Idaho for the next decade. This paper will provide a background of the AMWTP mission, and the adaptations to its operating permit, equipment, or treatment processes to address challenging waste types. AMWTP will leave behind a legacy of being one of the most successful waste treatment facilities in the history of the DOE Complex. The facility was well-conceived, well-constructed, and well-executed; it was done right from start to finish. During the course of its waste treatment mission, the facility was required to adapt to changing conditions by treating extremely challenging waste types. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

NASA NTRS2005

Optimized program completeness

Overall program completeness is optimized by selecting the ordered set of observations and targets that maximizes the efficiency for the ensemble of stars. We describe the optimization approach and report on completeness sensitivity to instrument throughput, inner working angle, instrument sensitivity, observational overhead, exo-zodiacal brightness, and target revisit constraints.

optimization↗

DOE OSTI2021

Synergistic Enzyme Mixtures to Realize Near-Complete Depolymerization in Biodegradable Polymer/Additive Blends

Embedding catalysts inside of plastics affords accelerated chemical modification with programmable latency and pathways. Nanoscopically embedded enzymes can lead to near-complete degradation of polyesters via chain-end mediated processive depolymerization. The overall degradation rate and pathways have a strong dependence on the morphology of semicrystalline polyesters. Yet, most studies to date focus on pristine polymers instead of mixtures that contain additives and other components despite their nearly universal use in plastic production. Here, for this study, additives are introduced to purposely change the morphology of polycaprolactone (PCL) by increasing the bending and twisting of crystalline lamellae. These morphological changes immobilize chain ends preferentially at the crystalline/amorphous interfaces and limit chain-end accessibility by the embedded processive enzyme. This chain-end redistribution reduces the polymer-to-monomer conversion from >95% to less than 50%, causing formation of highly crystalline plastic pieces, including microplastics. By synergizing both random chain scission and processive depolymerization, it is feasible to navigate morphological changes in polymer/additive blends and to achieve near-complete depolymerization. The random scission enzymes in the amorphous domains create new chain ends that are subsequently bound and depolymerized by processive enzymes. Present studies further highlight the importance to consider how the host polymer's morphologies affect the reactions catalyzed by embedded catalytic species.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Feeder Power Disaggregation: A Data-Efficient Matrix Completion Approach

This paper presents a data-driven algorithm for the feeder power disaggregation problem in distribution systems. Leveraging spatio-temporal power patterns in residential homes, residential power is discomposed into three components: sparse-switching loads, periodic loads, and photovoltaic (PV) generation, which are characterized through the design of two sparse matrices and a low-rank matrix. The matrix completion process is data-efficient because of the matrix sparsity and low rankness, along with the use of power system models. The proposed approach is tested using real-world residential data set on a 33-bus distribution system, demonstrating accurate power disaggregation with efficient matrix completion.

distribution system↗

DOE OSTI2021

Matrix Completion for Improved Observability in Low-Voltage Distribution Grids

This paper considers the problem of recovering missing entries in a partially observed matrix from relatively few measurements (i.e., the so-called matrix completion problem) with the aim of increasing the presently limited observability of low-voltage distribution grids. To this end, the partially observed matrix is formed using scarce voltage magnitude measurements while accounting for their spatial information. Voltage readings are assumed to be collected from distribution utility sensors and/or geographically-distributed cable television network sensors located in immediate proximity to distribution grid nodes. A matrix completion approach built on the parameter-less singular value shrinkage technique is used to estimate voltage magnitudes at otherwise non-observable low-voltage nodes using a small number of single- or multiple-snapshot data. The effectiveness of the proposed approach is demonstrated using a U.S.-style distribution test system from the synthetic SMART- DS data set under very low- to moderate-observability conditions.

low-rank matrix completion↗

DOE OSTI2013

Using phage display selected antibodies to dissect microbiomes for complete de novo genome sequencing of low abundance microbes

Background: Single cell genomics has revolutionized microbial sequencing, but complete coverage of genomes in complex microbiomes is imperfect due to enormous variation in organismal abundance and amplification bias. Empirical methods that complement rapidly improving bioinformatic tools will improve characterization of microbiomes and facilitate better genome coverage for low abundance microbes. Methods: We describe a new approach to sequencing individual species from microbiomes that combines antibody phage display against intact bacteria with fluorescence activated cell sorting (FACS). Single chain (scFv) antibodies are selected using phage display against a bacteria or microbial community, resulting in species-specific antibodies that can be used in FACS for relative quantification of an organism in a community, as well as enrichment or depletion prior to genome sequencing. Results: We selected antibodies against Lactobacillus acidophilus and demonstrate a FACS-based approach for identification and enrichment of the organism from both laboratory-cultured and commercially derived bacterial mixtures. The ability to selectively enrich for L. acidophilus when it is present at a very low abundance (<0.2%) leads to complete (>99.8%) de novo genome coverage whereas the standard single-cell sequencing approach is incomplete (<68%). We show that specific antibodies can be selected against L. acidophilus when the monoculture is used as antigen as well as when a community of 10 closely related species is used demonstrating that in principal antibodies can be generated against individual organisms within microbial communities. Conclusions: The approach presented here demonstrates that phage-selected antibodies against bacteria enable identification, enrichment of rare species, and depletion of abundant organisms making it tractable to virtually any microbe or microbial community. Combining antibody specificity with FACS provides a new approach for characterizing and manipulating microbial communities prior to genome sequencing.

59 BASIC BIOLOGICAL SCIENCES↗