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NASA NTRS2012

I/O Performance Characterization of Lustre and NASA Applications on Pleiades

In this paper we study the performance of the Lustre file system using five scientific and engineering applications representative of NASA workload on large-scale supercomputing systems such as NASA s Pleiades. In order to facilitate the collection of Lustre performance metrics, we have developed a software tool that exports a wide variety of client and server-side metrics using SGI's Performance Co-Pilot (PCP), and generates a human readable report on key metrics at the end of a batch job. These performance metrics are (a) amount of data read and written, (b) number of files opened and closed, and (c) remote procedure call (RPC) size distribution (4 KB to 1024 KB, in powers of 2) for I/O operations. RPC size distribution measures the efficiency of the Lustre client and can pinpoint problems such as small write sizes, disk fragmentation, etc. These extracted statistics are useful in determining the I/O pattern of the application and can assist in identifying possible improvements for users applications. Information on the number of file operations enables a scientist to optimize the I/O performance of their applications. Amount of I/O data helps users choose the optimal stripe size and stripe count to enhance I/O performance. In this paper, we demonstrate the usefulness of this tool on Pleiades for five production quality NASA scientific and engineering applications. We compare the latency of read and write operations under Lustre to that with NFS by tracing system calls and signals. We also investigate the read and write policies and study the effect of page cache size on I/O operations. We examine the performance impact of Lustre stripe size and stripe count along with performance evaluation of file per process and single shared file accessed by all the processes for NASA workload using parameterized IOR benchmark.

Saini, Subhash↗

NASA NTRS2007

Object Oriented Modeling and Design

The Object Oriented Modeling and Design seminar is intended for software professionals and students, it covers the concepts and a language-independent graphical notation that can be used to analyze problem requirements, and design a solution to the problem. The seminar discusses the three kinds of object-oriented models class, state, and interaction. The class model represents the static structure of a system, the state model describes the aspects of a system that change over time as well as control behavior and the interaction model describes how objects collaborate to achieve overall results. Existing knowledge of object oriented programming may benefit the learning of modeling and good design. Specific expectations are: Create a class model, Read, recognize, and describe a class model, Describe association and link, Show abstract classes used with multiple inheritance, Explain metadata, reification and constraints, Group classes into a package, Read, recognize, and describe a state model, Explain states and transitions, Read, recognize, and describe interaction model, Explain Use cases and use case relationships, Show concurrency in activity diagram, Object interactions in sequence diagram.

Shaykhian, Gholam Ali↗

NASA NTRS2013

ESD Test Apparatus for Soldering Irons

ESDA (Electrostatic Discharge Association) ESD STM 13.1-2000 requires frequent testing of the voltage leakage from the tip of a soldering iron and the resistance from the tip of the soldering iron to the common point ground. Without this test apparatus, the process is time-consuming and requires several wires, alligator clips, or test probes, as well as additional equipment. Soldering iron tips must be tested for electrostatic discharge risks frequently, and this typically takes a lot of time in setup and testing. This device enables the operator to execute the full test in one minute or less. This innovation is a simple apparatus that plugs into a digital multimeter (DMM) and the Common Point Ground (CPG) reference. It enables the user to perform two of the electrostatic discharge tests required in ESD STM 13.1-2000. The device consists of a small black box with two prongs sticking out of one end, two inputs on the opposite end (one of the inputs is used to connect the reference CPG to the DMM), and a metal tab on one side. Inside the box are wires, several washers of various materials, and assembly hardware (nuts and screws/bolts). The device is a passive electronic component that is plugged into a DMM. The operator sets the DMM to read voltage. The operator places the heated tip of the soldering iron onto the metal tab with a small amount of solder to ensure a complete connection. The voltage is read and recorded. The operator switches the DMM to read resistance. The operator places the heated tip of the soldering iron onto the metal tab with a small amount of solder to ensure a complete connection. The resistance is recorded. If the recorded voltage and resistance are below a number stated in ESDA ESD STM 13.1-2000, the test is considered to pass. The device includes all the necessary wiring internal to its body so the operator does not need to do any independent wiring, except for grounding. It uses a stack of high-thermal-resistance washers to minimize the heat transfer from the soldering iron to the wiring used to measure the resistance and voltages. This minimizes thermal error. The device allows very rapid execution of a test that is performed frequently.

Sancho, Jose↗

NASA NTRS2014

Portable Simulator for On-Board International Space Station Emergency Training

The crew on-board the International Space Station (ISS) have to be prepared for any possible emergency. The emergencies of most concern are a fire, depressurization or a toxic atmosphere. The crew members train on the ground before launch but also need to practice their emergency response skills while they are on orbit for 6 months. On-Board Training (OBT) events for emergency response proficiency used to require the crew and ground teams to use paper "scripts" that showed the path through the emergency procedures. This was not very realistic since the participants could read ahead and never deviate from this scripted path. The new OBT emergency simulator allows the crew to view dynamic information on an iPad only when it would become available during an event. The simulator interface allows the crew member to indicate hatch closures, don and doff masks, read pressures, and sample smoke or atmosphere levels. As the crew executes their actions using the on-board simulator, the ground teams are able to monitor those actions via ground display data flowing through the ISS Ku Band communication system which syncs the on-board simulator software with a ground simulator which is accessible in all the control centers. The OBT Working Group (OBT WG), led by the Chief Training Office (CTO) at Johnson Space center is a Multilateral working group with partners in Russia, Japan, Germany and U.S.A. The OBTWG worked together to create a simulator based on these principles: (a) Create a dynamic simulation that gives real-time data feedback; (b) Maintain real-time interface between Mission Control Centers and crew during OBTs; (c) Provide flexibility for decision making during drill execution; (d) Materially reduce Instructor and Flight Control Team man-hour costs involved with developing, updating, and maintaining emergency OBT cases/scenarios; and (e) Introduce an element of surprise to emergency scenarios so the team can't tell the outcome of the case by reading ahead in a paper script. This paper details some of the background as the project evolved with the International Partners. It also provides more details on how the simulator information for the crew is also shared with the ground teams. Finally, the paper will discuss how this remote simulator concept can be useful for future, longer term space missions.

Bolt, Kathy↗

NASA NTRS1951

Viscous Effects on Impact Probes in a Subsonic Rarified Gas Flow

The problem of time response of pressure gaging systems used with low density flows has been discussed in Ref ]4, and the effect of outgassing on pressure magnitudes was indicated in the same reference. Briefly, gases or vapors adhering to the internal walls of the pressure gaging system behave like gas sources and produce a pressure rise in the gage system which has no relation to the external flow. The effect can also occur in the reverse direction, with "in-gassing" or the action of an effective sink in the gage system as gases entering through the probe orifice are adsorbed to the walls. For given surface conditions, the magnitude of the pressure error to be expected due to out-gassing depends on the dimensions of the probe system. In the present tests, it was desirable to use the smallest possible probe to yield the lowest possible Reynolds number. The lower limit on size was fixed by outgassing effects, evaluated by the following procedure. 2.0 PROCEDURE The pumping system was adjusted to give a pressure, measured at the reservoir, of 9 microns Hg with no flow into the wind tunnel. The upstream metering valve was then opened and the air flow rate adjusted to give a pressure of 100 microns in the reservoir under steady flow conditions, The pressure read by one of the impact tubes, inserted into the flow, was measured. The upstream metering valve was then closed rapid)y, and the reservoir pressure, p0, and the impact probe pressure, Pj, were measured simultaneously at definite time intervals. Another probe was inserted into the flow and the procedure repeated, until the pressure-time data had been obtained for each probe investigated. The results for a series of tests Involving probe Nos.l, 2 and 3 are shown on HYD 2616 300 RESULTS From HYD 2616, It is clear that the smallest probe (No.3) requires the longest time to reach equilibrium. After a sufficient time has elapsed (about 180 seconds), this probe read the same, within the accuracy of measurement, as the other two, When a similar experiment was performed utilizing a probe which was one-half the size of probe No.2, it indicated a pressure, after 180 seconds, which was almost 10 microns Hg higher than the other probes. Accordingly, only probe Nos. 1, 2, 3 and 4 were employed in the experiments, and a time of at least 180 seconds was allowed to elapse between a change of setting and the reading of the instruments0

Kane, E. D.↗

NASA NTRS2016

The HEXITEC Hard X-Ray Pixelated CdTe Imager for Fast Solar Observations

There is an increasing demand in solar and astrophysics for high resolution X-ray spectroscopic imaging. Such observations would present ground breaking opportunities to study the poorly understood high energy processes in our solar system and beyond, such as solar flares, X-ray binaries, and active galactic nuclei. However, such observations require a new breed of solid state detectors sensitive to high energy X-rays with fine independent pixels to sub-sample the point spread function (PSF) of the X-ray optics. For solar observations in particular, they must also be capable of handling very high count rates as photon fluxes from solar flares often cause pile up and saturation in present generation detectors. The Rutherford Appleton Laboratory (RAL) has recently developed a new cadmium telluride (CdTe) detector system, called HEXITEC (High Energy X-ray Imaging Technology). It is an 80 x 80 array of 250 micron independent pixels sensitive in the 2-200 keV band and capable of a high full frame read out rate of 10 kHz. HEXITEC provides the smallest independently read out CdTe pixels currently available, and are well matched to the few arcsecond PSF produced by current and next generation hard X-ray focusing optics. NASA's Goddard and Marshall Space Flight Centers are collaborating with RAL to develop these detectors for use on future space borne hard X-ray focusing telescopes. We show the latest results on HEXITEC's imaging capability, energy resolution, high read out rate, and reveal it to be ideal for such future instruments.

Baumgartner, Wayne H.↗

NASA NTRS2017

Beyond Nanopore Sequencing in Space: Identifying the Unknown

Astronaut Kate Rubins sequenced DNA on the International Space Station (ISS) for the first time in August 2016 (Figure 1A). A 2D sequencing library containing an equal mixture of lambda bacteriophage, Escherichia coli, and Mus musculus was prepared on the ground with a SQK_MAP006 kit and sent to the ISS frozen and loaded into R7.3 flow cells. After a total of 9 on-orbit sequencing runs over 6 months, it was determined that there was no decrease in sequencing performance on-orbit compared to ground controls (1). A total of ~280,000 and ~130,000 reads generated on-orbit and on the ground, respectively, identified 90% of reads that were attributed to 30% lambda bacteriophage, 30% Escherichia coli, and 30% M. musculus (Figure 1B). Extensive bioinformatics analysis determined comparable 2D and 1D read accuracies between flight and ground runs (Figure 1C), and data collected from the ISS were able to construct directed assemblies of E.coli and lambda genomes at 100% and M. musculus mitochondrial genome at 96.7%. These findings validate sequencing as a viable option for potential on-orbit applications such as environmental microbial monitoring and disease diagnosis. Current microbial monitoring of the ISS applies culture-based techniques that provide colony forming unit (CFU) data for air, water, and surface samples. The identity of the cultured microorganisms in unknown until sample return and ground-based analysis, a process that can take up to 60 days. For sequencing to benefit ISS applications, spaceflight-compatible sample preparation techniques are required. Subsequent to the testing of the MinION on-orbit, a sample-to-sequence method was developed using miniPCR™ and basic pipetting, which was only recently proven to be effective in microgravity. The work presented here details the in- flight sample preparation process and the first application of DNA sequencing on the ISS to identify unknown ISS-derived microorganisms.

Stahl, Sarah E.↗

NASA NTRS2003

Design of an event-driven random-access-windowing CCD-based camera

Commercially available cameras are not designed for the combination of single frame and high-speed streaming digital video with real-time control of size and location of multiple regions-of-interest (ROI). A new control paradigm is defined to eliminate the tight coupling between the camera logic and the host controller. This functionality is achieved by defining the indivisible pixel read out operation on a per ROI basis with in-camera time keeping capability. This methodology provides a Random Access, Real-time, Event-driven (RARE) camera for adaptive camera control and is well suited for target tracking applications requiring autonomous control of multiple ROIs. This methodology additionally provides for reduced ROI read out time and higher frame rates compared to the original architecture by avoiding external control intervention during the ROI read out process.

Ortiz, Gerardo G.↗

NASA NTRSDate not supplied

Conversion of Environment Files from ORDEM 3 & MEM 3 to STENVI

To perform Micrometeoroid and Orbital Debris (MMOD) analyses, NASA describes the orbital debris particle environment using the ORDEM 3 tool and the micrometeoroid environment using the MEM 3 tool. Both output files that detail the flux of particles as a function of several parameters. European MMOD analyses use different tools to perform similar functions, including the Meteoroid And Space debris Terrestrial Environment Reference (MASTER) environment model, which outputs flux data in the Standard Environment Interface (STENVI) format. The NASA Johnson Space Center Hypervelocity Impact Technology Group was asked to create a converter to translate flux data from the output file formats used by ORDEM 3.x and MEM 3 into the STENVI file format. Validation was performed to ensure that the converter was reproducing the input data correctly. The Bumper 3 MMOD risk assessment tool has a capability for reading ORDEM 3.x, MEM 3, and STENVI environment file formats and was used to compare MMOD risk results generated using the converter’s output STENVI files to the risk results generated using the input ORDEM 3.x and MEM 3 igloo files. Specific point comparisons validated that the converter translated the environment data correctly, producing the intended output. However, realistic risk assessments showed that the bin methodology employed by Bumper for determining particle flux as a function of particle size when reading files in STENVI format produces much higher MMOD risk than the point-interpolation methodology used in Bumper risk assessments using ORDEM and MEM. Modifications to how Bumper 3 reads STENVI files during analyses are considered to improve Bumper’s ability to perform useful analyses with environment files in this format.

STENVI↗

NASA NTRS2023

Conversion of ORDEM 3.X & MEM 3 Into STENVI File Format

STENVI↗

NASA NTRS2024

Celebrating 10 Years of the Sub-Seasonal to Seasonal Prediction Project and Looking to the Future

The conference clearly demonstrated the increasing interest and growth of the scientific community working on the development and application of sub-seasonal to seasonal prediction since the start of the World Weather Research Programme (WWRP)/World Climate Research Programme (WCRP) sub-seasonal to seasonal (S2S) prediction project in 2013. The conference, which was held at the University of Reading (United Kingdom), was organized into three main themes as briefly summarized below, with eleven invited talks, 74 oral contributed talks, and 101 posters. The conference also included a two-hour breakout session, wherein eight groups discussed the current state and prospect for S2S prediction, and an early career researcher event. A summary of these discussions and recommendations is presented below. The conference web page (https://research.reading.ac.uk/s2s-summit2023/) is archived at the University of Reading. Introductory comments by representatives of the World Meteorological Organization (WMO) WWRP and WCRP emphasized the importance of the weather–climate linkage, targeted by S2S forecasts (from 2 weeks to a season ahead), addressing the challenges of creating “end-to-end” forecasts that encompass the entire climate-services chain from the prediction science and forecast, to the development and issuing of forecast products tailored to informing user-decisions. They also emphasized the efficacy of multi-model ensemble efforts and databases to foster collaborations internationally and between operational centres and academia. Although the WWRP/WCRP S2S project comes to an end in 2023, S2S prediction will remain an important focus for WWRP and WCRP. In WWRP, a new project called SAGE (Sub-seasonal to seasonal predictions for Agriculture and Environment) will start in 2024. Another important legacy of the S2S project will be the maintenance of the S2S database (Vitart et al. 2017) and the establishment of a WMO Lead Center for sub-seasonal prediction multi-model ensemble (LC-SSPMME) which will provide real-time multi-model S2S climate information. In two keynote presentations, Prof. Brian Hoskins (University of Reading) and Dr. Gilbert Brunet (Australian Bureau of Meteorology) discussed the potential of S2S predictability and the ongoing journey for understanding and improving these predictions. This conference was a sequel to the International Conference on Sub-seasonal to Seasonal Prediction (Robertson et al., 2014) which took place in College Park (Maryland, USA) in February 2014 to celebrate the start of the WWRP/WCRP S2S project, and to WCRP and WWRP conferences in Boulder, USA, in 2018 (Merryfield et al., 2020). A significant development compared to the previous S2S conferences was the large number of presentations on research to operation (R2O) and S2S applications and on the use of artificial intelligence and machine learning (AI/ML) methods for S2S prediction. Some of these methods provide empirical S2S forecasts which are competitive with state-of-the-art dynamical models. Other presentations demonstrated that AI/ML can provide alternative calibration of dynamical model outputs to traditional methods. Several talks and posters highlighted the increasing use of AI/ML, including deep learning, in S2S forecast post-processing and using AI to identify higher flow-dependent skill. Finally, some presentations demonstrated the value of AI/ML methods for a better understanding of S2S sources of predictability and attribution of extreme events.

S. J. Woolnough↗

NASA NTRSDate not supplied

Spectral Measurement Errors due to CCD Serial Pixel-to-Pixel Readout Interference in the Ocean Color Instrument of the NASA PACE Mission

The Ocean Color Instrument on NASA’s PACE mission is a hyperspectral imager with a spatial resolution of 1km x 1km and spectral resolution of 5nm in 2.5nm steps over 320-890nm. The detection system is based on two Charge-Coupled Devices (CCDs) operating in Time Delay Integration (TDI) mode to achieve high signal-to-noise ratio. The front-end optical imager is a rotating mirror-based system that images the ground-scene onto a slit with a field of view of 16km x 1km. The slit-image is re-imaged and wavelength dispersed on the CCDs. As the ground-scene moves through the slit, it moves along the CCD columns as charge is moved along with it. The accumulated charge at the end of each column is collected in a serial pixel. Each of the 16 CCD outputs read out 32 columns of the same ground scene spaced 0.625nm apart. The 32-pixel serial register is swiftly read out before the next TDI cycle. The telescope is spinning at 5.77Hz to achieve the required spatial resolution. This results in a serial pixel readout speed of 8.5MHz. Each serial read-cycle goes through a reset and video period that are each sampled to create a low-noise correlated double sample value. This only allows 59ns for the reset and video to be asserted and settled before sampling. Due to the short time period, the response of the CCD exhibits serial pixel-to-pixel readout interference as the reset and video signals do not have time to fully settle before sampling. Each serial pixel value therefore has a dependence on the value of the preceding pixel value. This leads to a spectral measurement error of up to 0.3%. We explain the operation of the detection system, the behavior of the interference and the resulting wavelength error with results from ground testing and on-orbit characterization.

Ulrik B Gliese↗

NASA NTRSDate not supplied

Benchmarking Computational Tools for Calling SNPs and Indels in Complex Microbial Populations

The NASA BioNutrients missions seek to understand the suitability of microorganisms for bioproduction during space flight. One topic of interest is the stability of microbial genomes during long-term ambient storage and subsequent rehydration and growth. To address these questions, samples from 8 species were flown to ISS for 5 years of desiccated storage at ambient temperature (Stasis Packs) and 2 species were packaged along with powdered media inside a bioreactor system to allow hydration and growth in microgravity (Production Packs). For both systems, Whole Genome Sequencing (WGS) of the DNA extracted from the returned samples and paired ground controls will be conducted to identify changes in genome stability due to time, storage conditions and growth in space. Across the technical replicates, ground controls, 10 timepoints, and multiple experimental conditions, ~300 samples have been selected for initial analysis with WGS sequencing to 100x coverage. A flexible and resource efficient mutation calling pipeline is needed to process this large dataset and allow for comparisons between species. Many bioinformatics tools for calling Indels and Single Nucleotide Variants (SNVs) are designed for use with pure isolates, where true variations from the reference genome are expected to dominate the reads aligning to the location of mutation. In contrast, DNA from the Stasis Pack (SP) samples was collected directly after recovery from desiccated storage and the Production Pack (PP) samples were collected after fermentation. In this context, reads with mutations are expected to be less frequent than reads that align with the reference genome, as each sample will include multiple lines of cells. Thus, BioNutrients samples are expected to be similar to samples from cancer cell or “pooled” sequencing approaches. In preparation for the analysis of the BioNutrients samples, we have tested three mutation calling tools (GATK for Microbes, BreSeq and DiscoSNP) designed for complex samples. A challenge of validating mutation identification pipelines is a lack of “Ground Truth” datasets, especially for complex samples. To compare these three tools, we sought to identify mutations in pre-existing WGS data collected from populations of Chlamydomonas reinhardtii that were exposed to UV mutagenesis and growth in LEO as part of the Space Algae-1 mission. Here we present a summary of these tools against the analysis originally conducted using the CRISP tool. Critical metrics are compared such as runtime, the number of SNPs, the number and size of Indels, and patterns of transversion and transitions identified by each tool are reported. By sharing these benchmarking results collected in support of the BioNutrients mission, we aim to guide others seeking to identify SNVs in similarly complex microbial samples.

Biology↗

NASA NTRSDate not supplied

Improving Satellite-Based Hotspot Detection Through Deep Learning-Enabled Smoke Recognition

While geostationary satellites, such as the GOES-R series, provide wildland fire hotspot readings at a high temporal resolution, they are prone to false negative readings and decreased confidence. One cause of decreased hotspot confidence is cloud contamination. Smoke produced from wildfire is often misinterpreted as cloud contamination, resulting in inaccurate and unsure sensor readings. To this end, we built a deep learning image segmentation model to identify smoke and cloud in true color satellite images. The model is pre-trained using self-supervised learning on over 10,000 GOES-R images to learn the underlying structure of satellite imagery. Then, the model is fine-tuned on a set of 130 labeled documents using supervised learning. The resulting model performs multi-class image segmentation with 85% accuracy and runs in under a minute on a standard personal computer. When paired alongside hotspot data, the model’s outputs can help increase confidence in wildfire location by identifying cases of cloud contamination that are due to smoke. The resulting model can be deployed in a stand-alone application or bundled in an Open Data Integration for wildland fire management (ODIN) application.

Earth observation↗

NASA NTRSDate not supplied

Toward Large Field-of-view X-ray Spectrometers with Magnetic Microcalorimeters

A future X-ray telescope mission like Lynx, a X-ray flagship mission concept, requires a large field of view, high energy resolution, and high spatial resolution. The Magnetic Microcalorimeter (MMC) detectors we are developing for such a mission feature a 5-arcminute field of view, approximately 100,000 pixels, each spanning 0.5–1 arcsecond. These detectors require the readout of 8,000 sensors. Three different array types have been designed to meet scientific goals, two of which utilize thermal multiplexing to reduce the number of readout channels in a scheme called “Hydra.” We are currently fabricating detectors on a recently completed buried wiring wafer with connections to every sensor. The sensors are read out using a microwave multiplexer (μMUX) with flux ramp modulation. A single μMUX can read out approximately 1,000 sensors with only two feed lines. We will report on the test of the first two-dimensional μMUX chip, consisting of 78 resonators. μMUX chips that pass screening will be directly bonded to MMC array chips using indium bump bonding. In parallel, we have tested a kinetic inductance traveling wave parametric amplifier (KI-TWPA) to amplify signals at low temperatures. The KI-TWPA exhibits extremely low internal noise, approaching the standard quantum limit. Since the energy resolution of an MMC is primarily limited by the readout system, the KI-TWPA is an ideal amplifier for MMCs with μMUX readout. We recently measured the readout noise of a μMUX with a KI-TWPA, demonstrating its capability for reading out MMC arrays. We present the design and fabrication of the latest MMC detectors, along with its readout performance.

Magntic Microcalorimeters↗

NASA NTRS2002

A correction to a highly accurate voight function algorithm

An algorithm for rapidly computing the complex Voigt function was published by Shippony and Read. Its claimed accuracy was 1 part in 10^8. It was brought to our attention by Wells that Shippony and Read was not meeting its claimed accuracy for extremely small but non zero y values. Although true, the fix to the code is so trivial to warrant this note for those who use this algorithm.

voight integral faddeeva function↗

DOE OSTI2024

Applying queueing theory to evaluate wait-time-savings of triage algorithms

Abstract In the past decade, artificial intelligence (AI) algorithms have made promising impacts in many areas of healthcare. One application is AI-enabled prioritization software known as computer-aided triage and notification (CADt). This type of software as a medical device is intended to prioritize reviews of radiological images with time-sensitive findings, thus shortening the waiting time for patients with these findings. While many CADt devices have been deployed into clinical workflows and have been shown to improve patient treatment and clinical outcomes, quantitative methods to evaluate the wait-time-savings from their deployment are not yet available. In this paper, we apply queueing theory methods to evaluate the wait-time-savings of a CADt by calculating the average waiting time per patient image without and with a CADt device being deployed. We study two workflow models with one or multiple radiologists (servers) for a range of AI diagnostic performances, radiologist’s reading rates, and patient image (customer) arrival rates. To evaluate the time-saving performance of a CADt, we use the difference in the mean waiting time between the diseased patient images in the with-CADt scenario and that in the without-CADt scenario as our performance metric. As part of this effort, we have developed and also share a software tool to simulate the radiology workflow around medical image interpretation, to verify theoretical results, and to provide confidence intervals for the performance metric we defined. We show quantitatively that a CADt triage device is more effective in a busy, short-staffed reading setting, which is consistent with our clinical intuition and simulation results. Although this work is motivated by the need for evaluating CADt devices, the evaluation methodology presented in this paper can be applied to assess the time-saving performance of other types of algorithms that prioritize a subset of customers based on binary outputs.

Thompson, Yee Lam Elim (ORCID:0000000196537707)↗

DOE OSTI2024

Anaerobic fungi contain abundant, diverse, and transcriptionally active Long Terminal Repeat retrotransposons

Long Terminal Repeat (LTR) retrotransposons are a class of repetitive elements that are widespread in the genomes of plants and many fungi. LTR retrotransposons have been associated with rapidly evolving gene clusters in plants and virulence factor transfer in fungal-plant parasite-host interactions. We report here the abundance and transcriptional activity of LTR retrotransposons across several species of the early-branching Neocallimastigomycota, otherwise known as the anaerobic gut fungi (AGF). The ubiquity of LTR retrotransposons in these genomes suggests key evolutionary roles in these rumen-dwelling biomass degraders, whose genomes also contain many enzymes that are horizontally transferred from other rumen-dwelling prokaryotes. Up to 10% of anaerobic fungal genomes consist of LTR retrotransposons, and the mapping of sequences from LTR retrotransposons to transcriptomes shows that the majority of clusters are transcribed, with some exhibiting expression greater than 104 reads per kilobase million mapped reads (rpkm). Many LTR retrotransposons are strongly differentially expressed upon heat stress during fungal cultivation, with several exhibiting a nearly three-log10 fold increase in expression, whereas growth substrate variation modulated transcription to a lesser extent. We show that some LTR retrotransposons contain carbohydrate-active enzymes (CAZymes), and the expansion of CAZymes within genomes and among anaerobic fungal species may be linked to retrotransposon activity. We further discuss how these widespread sequences may be a source of promoters and other parts towards the bioengineering of anaerobic fungi.

Genetics & Heredity↗