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At least 379 records · Page 21

Decomposing a San Francisco estuary microbiome using long-read metagenomics reveals species- and strain-level dominance from picoeukaryotes to viruses

ABSTRACT Although long-read sequencing has enabled obtaining high-quality and complete genomes from metagenomes, many challenges still remain to completely decompose a metagenome into its constituent prokaryotic and viral genomes. This study focuses on decomposing an estuarine metagenome to obtain a more accurate estimate of microbial diversity. To achieve this, we developed a new bead-based DNA extraction method, a novel bin refinement method, and obtained 150 Gbp of Nanopore sequencing. We estimate that there are ~500 bacterial and archaeal species in our sample and obtained 68 high-quality bins (>90% complete, <5% contamination, ≤5 contigs, contig length of >100 kbp, and all ribosomal and tRNA genes). We also obtained many contigs of picoeukaryotes, environmental DNA of larger eukaryotes such as mammals, and complete mitochondrial and chloroplast genomes and detected ~40,000 viral populations. Our analysis indicates that there are only a few strains that comprise most of the species abundances. IMPORTANCE Ocean and estuarine microbiomes play critical roles in global element cycling and ecosystem function. Despite the importance of these microbial communities, many species still have not been cultured in the lab. Environmental sequencing is the primary way the function and population dynamics of these communities can be studied. Long-read sequencing provides an avenue to overcome limitations of short-read technologies to obtain complete microbial genomes but comes with its own technical challenges, such as needed sequencing depth and obtaining high-quality DNA. We present here new sampling and bioinformatics methods to attempt decomposing an estuarine microbiome into its constituent genomes. Our results suggest there are only a few strains that comprise most of the species abundances from viruses to picoeukaryotes, and to fully decompose a metagenome of this diversity requires 1 Tbp of long-read sequencing. We anticipate that as long-read sequencing technologies continue to improve, less sequencing will be needed.

Lui, Lauren M.↗

Exploring the Birth and Evolution of the Universe: How Detectors Have Revolutionized Space Astronomy

The past century has seen tremendous advances in the capability of instruments used for astronomical imaging and spectroscopy. Capabilities of instruments have expanded in many dimensions; the scale of telescopes has grown tremendously, the wavelengths used for astronomy have grown from visible light to the full electromagnetic spectrum, extending from gamma rays to low frequency radio waves. Additional advances have been enabled by the availability of space facilities, which eliminate the effects of the earths atmosphere and magnetosphere, and allow cooling of instruments to avoid instrumental thermal radiation. Even with all these advances, the increase in capability of detection systems has produced truly revolutionary improvements in capability. Today, I will describe the advances in astronomical detection from the photographic plates of the early 20th century to the giant high efficiency focal planes being developed for modern space and ground based astronomical instrument. I will review the demanding performance requirements set by space astronomy, and show how the detector community has risen to the challenge in producing high performance detectors for the Hubble Space Telescope, the Spitzer Space Telescope, and the James Webb Space Telescope, now under development.

Moseley, Samuel H.↗

The Prospective Search for Highly Ionized Technetium in Hot (pre-) White Dwarfs

The discovery of technetium (Tc) in the atmospheres of red giants by Merrill (1952, ApJ, 116, 21) constituted convincing proof that s-process nucleosynthesis is indeed occurring in evolved stars. In principle, Tc should still be present in the atmospheres of hot post-AGB stars and (pre-) white dwarfs although, due to radioactive decay, it should be present in decreasing quantities along post-AGB evolution. The recent discovery of a large number of trans-iron group elements in hot white dwarfs with atomic numbers in the range A = 30-56 (Zn to Ba) raises the prospect that Tc (A = 43) may also be detected. However, this is currently not feasible because no atomic data exist for ionization stages beyond Tc ii. As an initial step, we calculated atomic energy levels and oscillator strengths of Tc iv-vi and used these data to compute non-local thermodynamic equilibrium (NLTE) model atmospheres to estimate at which minimum abundance level Tc could be detected. We show that Tc lines can be found in ultraviolet spectra of hot white dwarfs provided Tc is as abundant as other detected trans-Fe elements. We find that radiative levitation can keep Tc in large, easily detectable quantities in the atmosphere. A direct identification of Tc lines is still not feasible because wavelength positions cannot be computed with necessary precision. Laboratory measurements are necessary to overcome this problem. Our results suggest that such efforts are beneficial to the astrophysical community.

prospective↗

NASA Disasters Program: A Partner for Coastal Disaster Response, Resiliency, and Risk Reduction

Summary: The NASA Applied Sciences: Disasters Program has kicked off a pilot project as “Mid-Atlantic Resiliency Demonstration Study, Communities at Intensive Risk” in FY17 and FY18; Efforts focus on a holistic, interdisciplinary approach to integrate a full suite of capabilities from numerical weather prediction, tide and surge modeling at high spatial resolution and urban/neighborhood scales, and remote sensing capabilities for water detection and depth estimation; Future efforts - Partner with Federal Agencies, academia professional societies to complement and augment ongoing work using Earth observations unique to NASA - Translate hazards to risk in order to understand local and regional impacts and minimize vulnerability.

Bell, Jordan↗

Detection Thresholds of Falling Snow from Satellite-Borne Active and Passive Sensors

Precipitation, including rain and snow, is a critical part of the Earth's energy and hydrology cycles. Precipitation impacts latent heating profiles locally while global circulation patterns distribute precipitation and energy from the equator to the poles. For the hydrological cycle, falling snow is a primary contributor in northern latitudes during the winter seasons. Falling snow is the source of snow pack accumulations that provide fresh water resources for many communities in the world. Furthermore, falling snow impacts society by causing transportation disruptions during severe snow events. In order to collect information on the complete global precipitation cycle, both liquid and frozen precipitation must be collected. The challenges of estimating falling snow from space still exist though progress is being made. These challenges include weak falling snow signatures with respect to background (surface, water vapor) signatures for passive sensors over land surfaces, unknowns about the spherical and non-spherical shapes of the snowflakes, their particle size distributions (PSDs) and how the assumptions about the unknowns impact observed brightness temperatures or radar reflectivities, differences in near surface snowfall and total column snow amounts, and limited ground truth to validate against. While these challenges remain, knowledge of their impact on expected retrieval results is an important key for understanding falling snow retrieval estimations. Since falling snow from space is the next precipitation measurement challenge from space, information must be determined in order to guide retrieval algorithm development for these current and future missions. This information includes thresholds of detection for various sensor channel configurations, snow event system characteristics, snowflake particle assumptions, and surface types. For example, can a lake effect snow system with low (approx 2.5 km) cloud tops having an ice water content (IWC) at the surface of 0.25 g / cubic m and dendrite snowflakes be detected? If this information is known, we can focus retrieval efforts on detectable storms and concentrate advances on achievable results. Here, the focus is to determine thresholds of detection for falling snow for various snow conditions over land and lake surfaces. The results rely on simulated Weather Research Forecasting (WRF) simulations of falling snow cases since simulations provide all the information to determine the measurements from space and the ground truth. Sensitivity analyses were performed to better ascertain the relationships between multifrequency microwave and millimeter-wave sensor observations and the falling snow/underlying field of view. In addition, thresholds of detection for various sensor channel configurations, snow event system characteristics, snowflake particle assumptions, and surface types were studied. Results will be presented for active radar at Ku, Ka, and W-band and for passive radiometer channels from 10 to 183 GHz.

Gail Skofronick-Jackson↗

Listening for Neutrinos with Quantum Acoustics

Many low-threshold superconducting detectors rely on athermal phonon sensing, in which meV-scale phonons from a DM scatter are sensed via their ability to break Cooper pairs in superconducting films. While detectors based on such pairbreaking sensors are highly advantageous and scalable, their sensor threshold is ultimately limited by the energy needed to break a Cooper pair, 2Δ. We present a novel detector architecture for single phonon detection at the O(10μeV) scale, the qubit-coupled hBAR, that does not share this limitation. This architecture, composed of a superconducting qubit piezoelectrically coupled to a high-overtone bulk acoustic resonator, was originally developed in the context of the quantum acoustics community and has a sensor threshold ultimately limited by thermal noise. Such ultra-low-threshold detectors have a wide range of fundamental science applications, including reactor monitoring via neutrinos.

Baxter, Daniel Stephen [Fermilab] (ORCID:000000030↗

A Cloud Mask for AIRS

With the preliminary release of AIRS Level 1 and 2 data to the scientific community, there is a growing need for an accurate AIRS cloud mask for data assimilation studies and in producing products derived from cloud free radiances. Current cloud information provided with the AIRS data are limited or based on simplified threshold tests. A multispectral cloud detection approach has been developed for AIRS that utilizes the hyper-spectral capabilities to detect clouds based on specific cloud signatures across the short wave and long wave infrared window regions. This new AIRS cloud mask has been validated against the existing AIRS Level 2 cloud product and cloud information derived from MODIS. Preliminary results for both day and night applications over the continental U.S. are encouraging. Details of the cloud detection approach and validation results will be presented at the conference.

Brubaker, N.↗

A First Look at the DGEN380 Engine Acoustic Data from a Core-Noise Perspective

This work is a first look at acoustic data acquired in the NASA Glenn Research Center Aero-Acoustic Propulsion Laboratory using the Price Induction DGEN380 small turbofan engine, with particular emphasis on broadband combustor (core) noise. Combustor noise is detected by using a two-signal source separation technique employing one engine-internal sensor and one semi-far-field microphone. Combustor noise is an important core-noise component and is likely to become a more prominent contributor to overall airport community noise due to turbofan design trends, expected aircraft configuration changes, and advances in fan-noise-mitigation techniques. This work was carried out under the NASA Fundamental Aeronautics Program, Fixed Wing Project, Quiet Performance Subproject

Combustor Noise↗

PERISCOPE: PERIapsis Subsurface Cave OPtical Explorer

In this NIAC report we present a new technique enabling a practical option for mapping these structures at a relatively low cost: Photon Time-of-Flight (PTOF) imaging. Consider a scene with a surface that is in a camera's line of sight, with unknown geometry beyond the line of sight. PTOF works by directing laser pulses onto the visible surface and detecting the returned light after it reflects off the visible surface, onto the hidden surfaces, and back to the detector. An algorithm then reconstructs a 3d model of the hidden surface. The information gained has a wide variety of applications across NASA, the scientific community, the burgeoning commercial space industry, and in commercial and industrial use here on Earth.

Exploration↗

New York Ecological Forecasting: Utilizing NASA Earth Observations to Map Ash Distribution and Inform Emerald Ash Borer Control

Since their first sightings in the U.S. in 2002, emerald ash borer beetles (Agrilus planipennis; EAB) have killed millions of native ash (Fraxinus spp.) trees across 35 states. Infected ash stands frequently exhibit complete mortality, with the predicted result being the functional extinction of native ash in U.S. forests. In August of 2020, EAB was discovered in the 6.1-million-acre Adirondack Park. The team’s partners at the Adirondack Park Invasive Plant Program (APIPP) desired ash tree distribution and EAB susceptibility information to help improve EAB bio-control efficiency and apply the methodology to future invasive programs. To assist, the team mapped ash tree distribution using NASA Earth observations from Landsat 7 Enhanced Thematic Mapper Plus (ETM+) and Shuttle Radar Topography Mission (SRTM), along with hyperspectral imagery from the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS). Field data from the Monitoring and Managing Ash (MaMA) project, iMapInvasives and iNaturalist databases, and the New York State Department of Environmental Conservation (NYSDEC) provided ground truthing for mapping and modeling. Results indicate that for ash detection, the team’s Spectral Angle Mapping (SAM) hyperspectral classification is slightly more sensitive but less accurate than multispectral Random Forest (RF) classification, though neither method was above a ~20% detection rate. End products include maps of ash extent derived from both imagery types, a model forecasting future spread scenarios based on current EAB presence, and outreach materials. These products inform APIPP’s management decisions and facilitate public awareness of EAB’s threat to communities within the region.

Liam Megraw↗

Long-Term field testing of the accuracy and HVAC energy savings potential of occupancy presence sensors in A Single-Family home

The energy-saving potential of occupancy-centric smart thermostats has been extensively explored in simulations but lacked field testing for energy savings quantification and sensor performance assessment in real buildings. This paper presents a long-term field study conducted in a single-family home in Texas, U.S. to evaluate the performance of occupancy-centric controls (OCC) of HVAC (heating, ventilation, and air-conditioning) system in terms of energy savings, sensor accuracy, and impact on electric peak demand. The test site was equipped with a commercial off-the-shelf (COTS) smart thermostat and multiple occupancy presence sensors for OCC implementation. Additionally, a sub-metering system was installed to monitor electricity consumption of various end-use equipment, including the HVAC system. A supplementary device was installed to track the ground-truth occupancy for the accuracy evaluation of the occupancy presence sensor. Scenarios of baseline and OCC controls were alternated weekly over the 20-month testing period. The results indicated an effective OCC execution, as evidenced by indoor temperature profiles. During the 2023 cooling season, OCC achieved total energy savings of 1,958 kWh, corresponding to a 17.6% energy savings ratio. Under certain conditions, daily HVAC energy savings reached as high as 17 kWh, with a savings ratio of 35%. Sensor performance showed an overall accuracy of 83.8%, a False Positive Rate (FPR) of 12.8%, and a False Negative Rate (FNR) of 47.4%. A key limitation was the sensor’s inability to detect stationary occupants during sleep, leading to a midnight FNR of nearly 100% and significantly compromising thermal comfort. Additionally, the implementation of OCC resulted in extended periods of high electricity demand on summer afternoons, affecting occupant’s thermal comfort and posing potential challenges to community-level grid operations if OCC were widely adopted. Furthermore, this study addresses a critical research gap by empirically investigating energy-saving potential and occupancy sensor performance in residential buildings. Through a comprehensive field-testing study, the research examines the interrelationship between sensor accuracy, energy savings, and thermal comfort, an area that has received limited attention in the current literature.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Flightspeed Integral Image Analysis Toolkit

The Flightspeed Integral Image Analysis Toolkit (FIIAT) is a C library that provides image analysis functions in a single, portable package. It provides basic low-level filtering, texture analysis, and subwindow descriptor for applications dealing with image interpretation and object recognition. Designed with spaceflight in mind, it addresses: Ease of integration (minimal external dependencies) Fast, real-time operation using integer arithmetic where possible (useful for platforms lacking a dedicated floatingpoint processor) Written entirely in C (easily modified) Mostly static memory allocation 8-bit image data The basic goal of the FIIAT library is to compute meaningful numerical descriptors for images or rectangular image regions. These n-vectors can then be used directly for novelty detection or pattern recognition, or as a feature space for higher-level pattern recognition tasks. The library provides routines for leveraging training data to derive descriptors that are most useful for a specific data set. Its runtime algorithms exploit a structure known as the "integral image." This is a caching method that permits fast summation of values within rectangular regions of an image. This integral frame facilitates a wide range of fast image-processing functions. This toolkit has applicability to a wide range of autonomous image analysis tasks in the space-flight domain, including novelty detection, object and scene classification, target detection for autonomous instrument placement, and science analysis of geomorphology. It makes real-time texture and pattern recognition possible for platforms with severe computational restraints. The software provides an order of magnitude speed increase over alternative software libraries currently in use by the research community. FIIAT can commercially support intelligent video cameras used in intelligent surveillance. It is also useful for object recognition by robots or other autonomous vehicles

Thompson, David R.↗

Cluster Analysis of Thermal Icequakes Using the Seismometer to Investigate Ice and Ocean Structure (SIIOS): Implications for Ocean World Seismology

Ocean Worlds are of high interest to the planetary community due to the potential habitability of their subsurface oceans. Over the next few decades several missions will be sent to ocean worlds including the Europa Clipper, Dragonfly, and possibly a Europa lander. The Dragonfly and Europa lander missions will carry seismic payloads tasked with detecting and locating seismic sources. The Seismometer to Investigate Ice and Ocean Structure (SIIOS) is a NASA PSTAR funded project that investigates ocean world seismology using terrestrial analogs. The goals of the SIIOS experiment include quantitatively comparing flight-candidate seismometers to traditional instruments, comparing single-station approaches to a small-aperture array, and characterizing the local seismic environment of our field sites. Here we present an analysis of detected local events at our field sites at Gulkana Glacier in Alaska and in Northwest Greenland approximately 80 km North of Qaanaaq, Greenland. Both field sites passively recorded data for about two weeks. We deployed our experiment on Gulkana Glacier in September 2017 and in Greenland in June 2018. At Gulkana there was a nearby USGS weather station which recorded wind data. Temperature data was collected using the MERRA satellite. In Greenland we deployed our own weather station to collect temperature and wind data. Gulkana represents a noisier and more active environment. Temperatures fluctuated around 0°C, allowing for surface runoff to occur during the day. The glacier had several moulins, and during deployment we heard several rockfalls from nearby mountains. In addition to the local environment, Gulkana is located close to an active plate boundary (relative to Greenland). This meant that there were more regional events recorded over two weeks, than in Greenland. Greenland’s local environment was also quieter, and less active. Temperatures remained below freezing. The Greenland ice was much thicker than Gulkana (~850 m versus ~100 m) and our stations were above a subglacial lake. Both conditions can reduce event detections from basal motion. Lastly, we encased our Greenland array in an aluminum vault and buried it beneath the surface unlike our array in Gulkana where the instruments were at the surface and covered with plastic bins. The vault further insulated the array from thermal and atmospheric events.

Marusiak, A. G.↗

Data Center Waste Heat as an Emerging Urban Thermal Hazard: First Field Measurements of Neighborhood-Scale Air Temperature Impacts

Data centers are among the fastest-growing sources of concentrated anthropogenic heat in urban environments. Despite heat flux densities that exceed peak solar irradiance by a factor of 2–6, their thermal impacts on adjacent communities have never been directly measured or reported in the peer-reviewed literature. This short communication addresses that gap by presenting the first vehicle-based traverse measurements of air temperature in residential neighborhoods downwind of operational data centers. Five traverses at four facilities in the Phoenix, Arizona metropolitan area, ranging from a 36 MW single-building data center in Mesa to a 169 MW colocation campus in Chandler, reveal downwind air temperature warming as high as 2.2 °C, with average downwind air temperatures 0.7–0.9 °C warmer than corresponding upwind areas. Thermal signatures were detectable at distances up to 500 m from facility perimeters. The 36 MW Mesa facility rejects waste heat equivalent to the electricity consumption of approximately 40,000 households, while the 169 MW Chandler campus is equivalent to over 180,000 households, both concentrated into footprints smaller than a single residential subdivision. With U.S. data center capacity projected to more than double by 2030, these findings establish data center anthropogenic waste heat as a previously undocumented urban thermal hazard demanding attention from the data center and urban planning communities.

Phoenix↗

Measurement of the 252 Cf ⁢(sf) prompt fission neutron spectrum utilizing 12 C ⁡(𝑛, 𝑛) and 9 Be ⁢(𝑛, 𝑛) neutron scattering reference measurements

The 252 Cf spontaneous fission (sf), prompt fission neutron spectrum (PFNS) is a fundamental quantity for nuclear physics measurements of neutron-emitting reactions. This energy distribution of neutrons emitted from fission has been considered a neutron data standard for decades and has been utilized as a reference for neutron detection efficiency, validation of Monte Carlo simulations, benchmarking of dosimetry standards, and more. A significant portion of the global collection of nuclear data on neutron-induced reactions is correlated with the 252 Cf ⁢(sf) PFNS. Despite the reliance on this quantity by the nuclear physics community, the historical collection of 252 Cf PFNS measurements display systematic disagreements that are not understood or easily explained. These experimental discrepancies could potentially bias the 252 Cf PFNS Standard evaluation. On top of this, these past experiments frequently employed correlated experimental measurement or analysis methods. The artificial intelligence (AI)/machine learning (ML)-informed californium chi-nuclear data experiment (AIACHNE) project was formed to (a) investigate these discrepancies utilizing AI/ML methods to identify outlying regions of literature data, assign these regions to features of the experiment itself, and perform an improved evaluation of the 252 Cf PFNS and (b) perform a new experimental measurement of this quantity designed to improve upon the existing literature database. Here, in this work, we report on the AIACHNE 252 Cf PFNS experiment utilizing a new analysis method uncorrelated with all previous measurements: neutron efficiency determinations based on elastic neutron scattering on 12 C and 9 Be . This new method provides an independent test of the existing literature data and evaluation of the 252 Cf ⁢(sf) PFNS. The method is described with detailed covariance quantification procedures, as well as a direct discussion of the sources of uncertainty described as requirements in the “Templates” series of papers. The 252 Cf ⁢(sf) PFNS reported in this work agrees well with the overall shape of the existing standard PFNS evaluation as well as many literature measurements, thus verifying the current evaluation utilizing new techniques. However, the results suggest that there are deficiencies in the angle-differential 12 C and 9 Be ⁢(𝑛, 𝑛) evaluated nuclear data, which produce unphysical structures in the reported result. While these structures are relatively minor, they become obvious because of the high statistical precision of the data and the expected smooth continuity of the 252 Cf ⁢(sf) PFNS.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

The future scientific CCD

Since the first introduction of charge-coupled devices (CCDs) in 1970, CCDs have been considered for applications related to memories, logic circuits, and the detection of visible radiation. It is pointed out, however, that the mass market orientation of CCD development has left largely untapped the enormous potential of these devices for advanced scientific instrumentation. The present paper has, therefore, the objective to introduce the CCD characteristics to the scientific community, taking into account prospects for further improvement. Attention is given to evaluation criteria, a summary of current CCDs, CCD performance characteristics, absolute calibration tools, quantum efficiency, aspects of charge collection, charge transfer efficiency, read noise, and predictions regarding the characteristics of the next generation of silicon scientific CCD imagers.

Janesick, J. R.↗

Primary studies of trace quantities of green vegetation in Mono Lake area using 1990 AVIRIS data

Our primary results in Jasper Ridge Biological Preserve indicate that high spectral resolution Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) data may provide a substantial advantage in vegetation, based on the chlorophyll red edge feature from 700-780 nm. The chlorophyll red edge was detected for green vegetation cover as low as 4.8 percent. The objective of our studies in Mono Lake area is to continue the experiments performed in Jasper Ridge and to examine the persistence of red edge feature of trace quantities of green vegetation for different plant communities with non-uniform soil backgrounds.

Chen, Zhi-Kang↗

Laser light scattering instrument advanced technology development

The objective of this advanced technology development (ATD) project has been to provide sturdy, miniaturized laser light scattering (LLS) instrumentation for use in microgravity experiments. To do this, we assessed user requirements, explored the capabilities of existing and prospective laser light scattering hardware, and both coordinated and participated in the hardware and software advances needed for a flight hardware instrument. We have successfully breadboarded and evaluated an engineering version of a single-angle glove-box instrument which uses solid state detectors and lasers, along with fiber optics, for beam delivery and detection. Additionally, we have provided the specifications and written verification procedures necessary for procuring a miniature multi-angle LLS instrument which will be used by the flight hardware project which resulted from this work and from this project's interaction with the laser light scattering community.

Wallace, J. F.↗