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At least 73 records · Page 4

Reducing Interprocessor Dependence in Recoverable Distributed Shared Memory

Checkpointing techniques in parallel systems use dependency tracking and/or message logging to ensure that a system rolls back to a consistent state. Traditional dependency tracking in distributed shared memory (DSM) systems is expensive because of high communication frequency. In this paper we show that, if designed correctly, a DSM system only needs to consider dependencies due to the transfer of blocks of data, resulting in reduced dependency tracking overhead and reduced potential for rollback propagation. We develop an ownership timestamp scheme to tolerate the loss of block state information and develop a passive server model of execution where interactions between processors are considered atomic. With our scheme, dependencies are significantly reduced compared to the traditional message-passing model.

Janssens, Bob

Integrating Cache Performance Modeling and Tuning Support in Parallelization Tools

With the resurgence of distributed shared memory (DSM) systems based on cache-coherent Non Uniform Memory Access (ccNUMA) architectures and increasing disparity between memory and processors speeds, data locality overheads are becoming the greatest bottlenecks in the way of realizing potential high performance of these systems. While parallelization tools and compilers facilitate the users in porting their sequential applications to a DSM system, a lot of time and effort is needed to tune the memory performance of these applications to achieve reasonable speedup. In this paper, we show that integrating cache performance modeling and tuning support within a parallelization environment can alleviate this problem. The Cache Performance Modeling and Prediction Tool (CPMP), employs trace-driven simulation techniques without the overhead of generating and managing detailed address traces. CPMP predicts the cache performance impact of source code level "what-if" modifications in a program to assist a user in the tuning process. CPMP is built on top of a customized version of the Computer Aided Parallelization Tools (CAPTools) environment. Finally, we demonstrate how CPMP can be applied to tune a real Computational Fluid Dynamics (CFD) application.

Waheed, Abdul

A Capability to Generate Physics-based Mass Estimating Relationships for Conceptual Space Vehicle Design

This paper is written in support of the on-going research into conceptual space vehicle design conducted at the Space Systems Design Laboratory (SSDL) at the Georgia Institute of Technology. Research at the SSDL follows a sequence of a number of the traditional aerospace disciplines. The sequence of disciplines and interrelationship among them is shown in the Design Structure Matrix (DSM). The discipline of Weights and Sizing occupies a central location in the design of a new space vehicle. Weights and Sizing interact, either in a feed forward or feed back manner, with every other discipline in the DSM. Because of this principle location, accuracy in Weights and Sizing is integral to producing an accurate model of a space vehicle concept. Instead of using conceptual level techniques, a simplified Finite Element Analysis (FEA) technique is described as applied to the problem of the Liquid Oxygen (LOX) tank bending loads applied to the forward Liquid Hydrogen (LH2) tank of the Georgia Tech Air Breathing Launch Vehicle (ABLV).

Olds, John R.

Bacillus nealsonii sp. nov., isolated from a spacecraft-assembly facility, whose spores are gamma-radiation resistant

One of the spore-formers isolated from a spacecraft-assembly facility, belonging to the genus Bacillus, is described on the basis of phenotypic characterization, 16S rDNA sequence analysis and DNA-DNA hybridization studies. It is a Gram-positive, facultatively anaerobic, rod-shaped eubacterium that produces endospores. The spores of this novel bacterial species exhibited resistance to UV, gamma-radiation, H2O2 and desiccation. The 18S rDNA sequence analysis revealed a clear affiliation between this strain and members of the low G+C Firmicutes. High 16S rDNA sequence similarity values were found with members of the genus Bacillus and this was supported by fatty acid profiles. The 16S rDNA sequence similarity between strain FO-92T and Bacillus benzoevorans DSM 5391T was very high. However, molecular characterizations employing small-subunit 16S rDNA sequences were at the limits of resolution for the differentiation of species in this genus, but DNA-DNA hybridization data support the proposal of FO-92T as Bacillus nealsonii sp. nov. (type strain is FO-92T =ATCC BAAM-519T =DSM 15077T).

Non-programmatic

Nozzle Aerodynamic Stability During a Throat Shift

An experimental investigation was conducted on the internal aerodynamic stability of a family of two-dimensional (2-D) High Speed Civil Transport (HSCT) nozzle concepts. These nozzles function during takeoff as mixer-ejectors to meet acoustic requirements, and then convert to conventional high-performance convergent-divergent (CD) nozzles at cruise. The transition between takeoff mode and cruise mode results in the aerodynamic throat and the minimum cross-sectional area that controls the engine backpressure shifting location within the nozzle. The stability and steadiness of the nozzle aerodynamics during this so called throat shift process can directly affect the engine aerodynamic stability, and the mechanical design of the nozzle. The objective of the study was to determine if pressure spikes or other perturbations occurred during the throat shift process and, if so, identify the caused mechanisms for the perturbations. The two nozzle concepts modeled in the test program were the fixed chute (FC) and downstream mixer (DSM). These 2-D nozzles differ principally in that the FC has a large over-area between the forward throat and aft throat locations, while the DSM has an over-area of only about 10 percent. The conclusions were that engine mass flow and backpressure can be held constant simultaneously during nozzle throat shifts on this class of nozzles, and mode shifts can be accomplished at a constant mass flow and engine backpressure without upstream pressure perturbations.

Kawecki, Edwin J.

Pi-Sat: A Low Cost Small Satellite and Distributed Spacecraft Mission System Test Platform

Current technology and budget trends indicate a shift in satellite architectures from large, expensive single satellite missions, to small, low cost distributed spacecraft missions. At the center of this shift is the SmallSatCubesat architecture. The primary goal of the Pi-Sat project is to create a low cost, and easy to use Distributed Spacecraft Mission (DSM) test bed to facilitate the research and development of next-generation DSM technologies and concepts. This test bed also serves as a realistic software development platform for Small Satellite and Cubesat architectures. The Pi-Sat is based on the popular $35 Raspberry Pi single board computer featuring a 700Mhz ARM processor, 512MB of RAM, a flash memory card, and a wealth of IO options. The Raspberry Pi runs the Linux operating system and can easily run Code 582s Core Flight System flight software architecture. The low cost and high availability of the Raspberry Pi make it an ideal platform for a Distributed Spacecraft Mission and Cubesat software development. The Pi-Sat models currently include a Pi-Sat 1U Cube, a Pi-Sat Wireless Node, and a Pi-Sat Cubesat processor card.The Pi-Sat project takes advantage of many popular trends in the Maker community including low cost electronics, 3d printing, and rapid prototyping in order to provide a realistic platform for flight software testing, training, and technology development. The Pi-Sat has also provided fantastic hands on training opportunities for NASA summer interns and Pathways students.

Software

Ground-Level Digital Terrain Model (DTM) Construction from Tandem-X InSAR Data and Worldview Stereo-Photogrammetric Images

The ground-level digital elevation model (DEM) or digital terrain model (DTM) information are invaluable for environmental modeling, such as water dynamics in forests, canopy height, forest biomass, carbon estimation, etc. We propose to extract the DTM over forested areas from the combination of interferometric complex coherence from single-pass TanDEM-X (TDX) data at HH polarization and Digital Surface Model (DSM) derived from high-resolution WorldView (WV) image pair by means of random volume over ground (RVoG) model. The RVoG model is a widely and successfully used model for polarimetric SAR interferometry (Pol-InSAR) technique for vertical forest structure parameter retrieval [1][2][3][4]. The ground-level DEM have been obtained by complex volume decorrelation in the RVoG model with the DSM using stereo-photogrammetric technique. Finally, the airborne lidar data were used to validate the ground-level DEM and forest canopy height results.

Lee, Seung-Kuk

Trade-Space Analysis Tool for Designing Constellations (TAT-C)

While there is growing interest in implementing future NASA Earth Science missions as Distributed Spacecraft Missions (DSMs), there are currently no tool to help in the design of DSMs. The objective of our project is to provide a framework that facilitates DSM Pre-Phase A investigations and optimizes DSM designs with respect to a-priori Science goals. Our Trade-space Analysis Tool for Constellations (TAT-C) allows to investigate questions such as: "Which type of constellations should be chosen? How many spacecraft should be included in the constellation? Which design has the best cost/risk value?" This paper provides a description of the TAT-C tool and its components.

Image Processing

Streamlining the Design Tradespace for Earth Imaging Constellations

Distributed Spacecraft Missions (DSMs) are gaining momentum in their application to Earth Observation (EO) missions owing to their unique ability to increase observation sampling in spatial, spectral, angular and temporal dimensions simultaneously. DSM design includes a much larger number of variables than its monolithic counterpart, therefore, Model-Based Systems Engineering (MBSE) has been often used for preliminary mission concept designs, to understand the trade-offs and interdependencies among the variables. MBSE models are complex because the various objectives a DSM is expected to achieve are almost always conflicting, non-linear and rarely analytical. NASA Goddard Space Flight Center is developing a pre-Phase A tool called "Trade-space Analysis Tool for Constellations" (TAT-C) to initiate constellation mission design. The tool will allow users to explore the tradespace between various performance, cost and risk metrics (as a function of their science mission) and select Pareto optimal architectures that meet their requirements. This paper focuses on the tradespace search and how it can be streamlined by combining physical rules, as well as well-designed orbit and coverage computations, thus yielding significant speed-ups. Two use cases are shown as representative examples of the utility of TAT-C generated trades, and results are preliminarily validated against AGI's Systems Tool Kit.

Science Data Processing

Navigating the Deployment and Downlink Tradespace for Earth Imaging Constellations

Distributed Spacecraft Missions (DSMs) are gaining momentum in their application to Earth Observation (EO) missions owing to their unique ability to increase observation sampling in spatial, spectral, angular and temporal dimensions simultaneously. DSM design includes a much larger number of variables than its monolithic counterpart, therefore, Model-Based Systems Engineering (MBSE) has been often used for preliminary mission concept designs, to understand the trade-offs and interdependencies among the variables. MBSE models are complex because the various objectives a DSM is expected to achieve are almost always conflicting, non-linear and rarely analytical. NASA Goddard Space Flight Center (GSFC) is developing a pre-Phase A tool called Tradespace Analysis Tool for Constellations (TAT-C) to initiate constellation mission design. The tool will allow users to explore the tradespace between various performance, cost and risk metrics (as a function of their science mission) and select Pareto optimal architectures that meet their requirements. This paper will describe the different types of constellations that TAT-C’s Tradespace Search Iterator is capable of enumerating (homogeneous Walker, heterogeneous Walker, precessing type, ad-hoc) and their impact on key performance metrics such as revisit statistics, time to global access and coverage. We will also discuss the ability to simulate phased deployment of the given constellations, as a function of launch availabilities and/or vehicle capability, and show the impact on performance. All performance metrics are calculated by the Data Reduction and Metric Computation module within TAT-C, which issues specific requests and processes results from the Orbit and Coverage module. Our TSI is also capable of generating tradespaces for downlinking imaging data from the constellation, based on permutations of available ground station networks - known (default) or customized (by the user). We will show the impact of changing ground station options for any given constellation, on data latency and required communication bandwidth, which in turn determines the responsiveness of the space system.

Nag, Sreeja

Dynamic Smagorinsky Modeled Large-Eddy Simulations of Turbulence Using Tetrahedral Meshes

Eddy-resolving numerical computations of turbulent flows are emerging as viable alternatives to Reynolds Averaged Navier-Stokes (RANS) calculations for flows with an intrinsically steady mean state due to the advances in large-scale parallel computing. In these computations, medium to large turbulent eddies are resolved by the numerics while the smaller or subgrid scales are either modeled or taken care of by the inherent numerical dissipation. To advance the state of the art of unstructured-mesh turbulence simulation capabilities, large eddy simulations (LES) using the dynamic Smagorinsky model (DSM) on tetrahedral meshes are carried out with the space-time conservation element, solution element (CESE) method. In contrast to what has been reported in the literature, the present implementation of dynamic models allows for active backscattering without any ad-hoc limiting of the eddy viscosity calculated from the subgrid-scale model. For the benchmark problems involving compressible isotropic turbulence decay as well as the shock/turbulent boundary layer interaction benchmark problems, no numerical instability associated with kinetic energy growth is observed and the volume percentage of the backscattering portion accounts for about 38-40% of the simulation domain. A slip-wall model in conjunction with the implemented DSM is used to simulate a relatively high Reynolds number Mach 2.85 turbulent boundary layer over a 30° ramp with several tetrahedral meshes and a wall-normal spacing of either Δγ& = 10 or Δγ& = 20. The computed mean wall pressure distribution, separation region size, mean velocity profiles, and Reynolds stress agree reasonably well with experimental data.

CESE method

Boreal canopy surfaces from spaceborne stereogrammetry

Surface elevation estimates from high resolution spaceborne image (HRSI) stereogrammetry are used to examine fine-scaled structure of boreal forest canopies. These data can depict detailed spatial patterns of vertical forest structure at remote sites across the circumpolar domain where these estimates would otherwise be unavailable. This work examines where these estimates are most effective at describing vertical forest structure to explain which canopy surfaces they represent. We evaluated the variation in canopy surface estimates captured from four general types of HRSI digital surface models (DSMs) across the full range of boreal canopy cover. These DSMs, classified into 4 types by grouping them according to the acquisition's (1) sun elevation angle (low or high) and (2) seasonality-driven ground surface condition (snow presence/absence), vary with acquisition characteristics and the details of this variation continues to be studied. We explored some of this variation by comparing the distributions of differences in boreal canopy percentile heights derived from reference small footprint lidar in Tanana Valley, Alaska with canopy surface elevations derived from these 4 types of HRSI DSMs. We examined how canopy surface estimates from HRSI DSMs differ according to acquisition characteristics and canopy cover, and ultimately which canopy surfaces are represented in these DSMs. Our results help clarify which boreal canopy surfaces are representative of those captured with HRSI DSMs. They show that in the Tanana Valley (1) DSMs grouped by sun elevation angle and ground surface condition provide different surface estimates of boreal canopies; (2) the two DSM types that appear to most differently capture boreal forest canopy surfaces are DSMs from snow-free images acquired at sun elevation angles <30° (Low sun elev. & snow-free) and those with snow-cover at sun elevation angles ≥30° (High sun elev. & snow-free); (3) DSMs with snow most often do not capture upper canopy surfaces; (4) the “Low sun elev. & snow-free” DSMs resolve surfaces that are most representative of upper canopy surfaces (dense forests >60% cover, 70th–80th percentile heights); and (5) in the most dense forests (>80% cover) where canopy gaps are least likely to bias downward the average surface estimates, the snow-free DSM types are representative of 70th - 80th percentile heights (“Low sun elev. & snow-free”) and 60th–70th percentile heights (“High sun elev. & snow-free”). The combination of horizontal structure (canopy cover) and acquisition characteristics affect the boreal vertical structure (canopy surface height) estimates from spaceborne stereogrammetry. These effects should be considered when analyzing products derived from HRSI DSMs, and as part of a comprehensive approach to spaceborne remote sensing of circumpolar boreal forests.

forest structure

Modelling above-ground biomass stock over Norway using national forest inventory data with ArcticDEM and Sentinel-2 data

Boreal forests constitute a large portion of the global forest area, yet they are undersampled through field surveys, and only a few remotely sensed data sources provide structural information wall-to-wall throughout the boreal domain. ArcticDEM is a collection of high-resolution (2 m) space-borne stereogrammetric digital surface models (DSM) covering the entire land area north of 60° of latitude. The free-availability of ArcticDEM data offers new possibilities for aboveground biomass mapping (AGB) across boreal forests, and thus it is necessary to evaluate the potential for these data to map AGB over alternative open-data sources (i.e., Sentinel-2). This study was performed over the entire land area of Norway north of 60° of latitude, and the Norwegian national forest inventory (NFI) was used as a source of field data composed of accurately geolocated field plots (n=7710) systematically distributed across the study area. Separate random forest models were fitted using NFI data, and corresponding remotely sensed data consisting of either: i) a canopy height model (ArcticCHM) obtained by subtracting a high-quality digital terrain model (DTM) from the ArcticDEM DSM height values, ii) Sentinel-2 (S2), or iii) a combination of the two (ArcticCHM+S2). Furthermore, we assessed the effect of the forest- and terrain-specific factors on the models’ predictive accuracy. The best model (,i.e., ArcticCHM+S2) explained nearly 60% of the variance of the training set, which translated in the largest accuracy in terms of root mean square error (RMSE=41.4 t/ha). This result highlights the synergy between 3D and multispectral data in AGB modelling. Furthermore, this study showed that despite the importance of ArcticCHM variables, the S2 model performed slightly better than ArcticCHM model. This finding highlights some of the limitations of ArcticDEM, which, despite the unprecedented spatial resolution, is highly heterogeneous due to the blending of multiple acquisitions across different years and seasons. We found that both forest- and terrain-specific characteristics affected the uncertainty of the ArcticCHM+S2 model and concluded that the combined use of ArcticCHM and Sentinel-2 represents a viable solution for AGB mapping across boreal forests. The synergy between the two data sources allowed for a reduction of the saturation effects typical of multispectral data while ensuring the spatial consistency in the output predictions due to the removal of artifacts and data voids present in ArcticCHM data. While the main contribution of this study is to provide the first evidence of the best-case-scenario (i.e., availability of accurate terrain models) that ArcticDEM data can provide for large-scale AGB modelling, it remains critically important for other studies to investigate how ArcticDEM may be used in areas where no DTMs are available as is the case for large portions of the boreal zone.

space-borne imagery

High-Resolution Forest Canopy Height Estimation in an African Blue Carbon Ecosystem

Mangrove forests are one of the most productive and carbon dense ecosystems that are only found at tidally inundated coastal areas. Forest canopy height is an important measure for modeling carbon and biomass dynamics, as well as land cover change. By taking advantage of the flat terrain and dense canopy cover, the present study derived digital surface models (DSMs) using stereophotogrammetric techniques on high-resolution spaceborne imagery (HRSI) for southern Mozambique. A mean-weighted ground surface elevation factor was subtracted from the HRSI DSM to accurately estimate the canopy height in mangrove forests in southern Mozambique. The mean and H100 tree height measured in both the field and with the digital canopy model provided the most accurate results with a vertical error of 1.18-1.84 m, respectively. Distinct patterns were identified in the HRSI canopy height map that could not be discerned from coarse shuttle radar topography mission canopy maps even though the mode and distribution of canopy heights were similar over the same area. Through further investigation, HRSI DSMs have the potential of providing a new type of three-dimensional dataset that could serve as calibration/validation data for other DSMs generated from spaceborne datasets with much larger global coverage. HSRI DSMs could be used in lieu of Lidar acquisitions for canopy height and forest biomass estimation, and be combined with passive optical data to improve land cover classifications.

HRSI

MjCyc: Rediscovering the pathway-genome landscape of the first sequenced archaeon, Methanocaldococcus (Methanococcus) jannaschii

The genome of Methanocaldococcus (Methanococcus) jannaschii DSM 2661 was the first Archaeal genome to be sequenced in 1996. Subsequent sequence-based annotation cycles led to its first metabolic reconstruction in 2005. Leveraging new experimental results and function assignments, we have now re-annotated M. jannaschii, creating an updated resource with novel information and testable predictions in a pathway-genome database available at BioCyc.org. This reannotation effort has resulted in 652 function assignments with enzyme roles, accounting for a third of the total protein-coding entries for this genome. The updated resource includes 883 reactions, 540 enzymes, and 142 individual pathways. Despite notable progress in computational genomics, more than a third of the genome remains functionally uncharacterized. The publicly available MjCyc pathway-genome database holds great potential for the wider community to conduct research on the biology of methanogenic Archaea.

59 BASIC BIOLOGICAL SCIENCES

Nitrogen fixation in Pampinifervens , a new species-rich genus of Aquificaceae that inhabits a wide pH range in terrestrial hot springs

Members of the Aquificota play important roles in hydrogen, sulfur, and carbon cycles in geothermal systems as ubiquitous and abundant chemolithoautotrophs; however, their roles in the nitrogen cycle are poorly defined. Here, we show that Aquificaceae isolate T-2 T from Tengchong, China, fixes nitrogen based on growth with dinitrogen as the sole nitrogen source and incorporation of 15 N atoms when grown with 15 N 2 . We further show evidence that suggests its nitrogen fixation (nif) genes are transcribed in situ in a nearby spring. We propose the name Pampinifervens diazotrophicum gen. et sp. nov., with strain T-2 T (= JCM 35475 T = DSM 116324 T ) as the nomenclatural type. Its close relative designated Pampinifervens florentissimum sp. nov. T-8 T (= CGMC 1.5214 T = JCM 33569 T ) does not fix nitrogen but respires nitrate. Analysis of 104 metagenome-assembled genomes from 84 metagenomes allowed us to circumscribe the genus Pampinifervens and identify at least 16 sympatric Pampinifervens species that dominate the Aquificaceae populations in diverse hot springs in southwest China, with distinct species globally. Analysis of these Pampinifervens genomes revealed variable presence of nif and denitrification genes and frequent gene loss and horizontal transfer. Genes for pH homeostasis were also present in Pampinifervens genomes, with a proliferation in species from Tengchong, consistent with the wide pH growth range of both Pampinifervens isolates and the prevalence of Pampinifervens in both alkaline and acidic springs. The dynamic evolution of nif and denitrification genes, along with pH homeostasis genes, may facilitate the diversification of Pampinifervens into diverse springs with different nitrogen availability.

Aquificae

Author Correction: Genome-guided isolation of the hyperthermophilic aerobe Fervidibacter sacchari reveals conserved polysaccharide metabolism in the Armatimonadota

Correction to: Nature Communicationshttps://doi.org/10.1038/s41467-024-53784-3, published online 4 November 2024 In the version of this article initially published, Table 1 did not include the properties of the taxa being proposed or refer directly to another location in the main manuscript describing the properties. As such, the original manuscript did not comply with Rule 27 (2)(c) of the ICNP. Also, Table 1 listed the order Fervidibacterales as the nomenclatural type for the class Fervidibacteria, which violates latest emended version of Rule 15 stating that the nomenclatural type for a class must be a genus. Below we provide a modification of Table 1 containing protologues with these errors corrected. We have also changed the order of the taxa in the table to meet the most common ordering. (Table presented.) Taxon names proposed under the ICNP Proposed taxon Etymology Description Genus Fervidibacter Fer.vi.di.bac’ter. L. masc. adj. fervidus, hot, steaming; N.L. masc. n. bacter, a rod; N.L. masc. n. Fervidibacter, a hot rod Thermophilic or hyperthermophilic inhabitants of freshwater thermal environments. All members are likely polysaccharide-degrading chemoheterotrophs with numerous carbohydrate-active enzymes encoded in their genomes. Aerobic, with high-affinity and/or low-affinity terminal oxidases present in the genomes. The oxidative pentose phosphate pathway and the tricarboxylic acid cycle are complete in genomes belonging to the genus. Gram-stain-negative and diderm cell envelope structure. Ovoid- to rod-shaped morphology. Spores are not formed. The genus is a distinct phylogenetic lineage in the family Fervidibacteraceae, the order Fervidibacterales, and the class Fervidibacteria in the phylum Armatimonadota. The type species is Fervidibacter sacchariT. Species Fervidibacter sacchari sac’cha.ri. N.L. gen. n. sacchari, of sugar Hyperthermophilic, microaerophilic, facultatively anaerobic, and grows chemoheterotrophically on monosaccharides and polysaccharides. Cells are ovoid- to rod-shaped, Gram-stain negative, and are 0.9–1.3 µm in width and 1.6–3.6 µm in length. Grows between 65 and 87.5 °C and an optimum temperature of 80 °C, and a pH range of 6.5–8.6 with an optimum pH of 7.5. Grows at an optimum O2 concentration of 5–10%. Grows on D-arabinose, D-galactose, D-glucose, D-rhamnose, D-ribose, D-xylose, chondroitin sulfate, colloidal chitin, galactan, gellan gum, guar gum, karaya gum, locust bean gum, xantham gum, xyloglucan, β-glucan, glycogen, starch, AFEX-pretreated corn stover, miscanthus, sugarcane bagasse, acetate and casamino acids. Grows weakly on xyloglucan under fermentation conditions. The major fatty acids (>10%) are C16:0, C18:0 and/or cyclo-C17:0, and iso-C16:0. The major respiratory quinones (>10%) are MK-8 and MK-9. The isolate and genomes of the species have been recovered from geothermal springs in the Great Basin, Nevada, USA. GC content of genomes range between 51–52%. Subunits for both the high-affinity and low-affinity terminal oxidases are encoded in the genomes. Genomes also encode a Group 3d [NiFe] hydrogenase, which produces hydrogen as an electron sink for NAD+ regeneration. The type strain PD1T (= JCM 39283T = DSM 113467T) was isolated from Great Boiling Spring in Nevada, USA. Family Fervidibacteraceae Fer.vi.di.bac.te.ra’ce.ae. N.L. masc. n. Fervidibacter type genus of the family; L. suff. -aceae ending to denote a family; N.L. fem. pl. n. Fervidibacteraceae the family of the genus Fervidibacter Thermophilic or hyperthermophilic inhabitants of freshwater thermal environments. All members are likely polysaccharide-degrading chemoheterotrophs with numerous carbohydrate-active enzymes encoded in their genomes. Aerobic, with high-affinity and/or low-affinity terminal oxidases present in the genomes. The oxidative pentose phosphate pathway and the tricarboxylic acid cycle are complete in genomes belonging to the family. The family is a distinct phylogenetic lineage in the order Fervidibacterales and the class Fervidibacteria in the phylum Armatimonadota. The type genus is Fervidibacter. Order Fervidibacterales Fer.vi.di.bac.te.ra’les. N.L. masc. n. Fervidibacter type genus of the order; L. suff. -ales ending to denote an order; N.L. fem. pl. n. Fervidibacterales the order of the genus Fervidibacter Thermophilic or hyperthermophilic inhabitants of freshwater thermal environments. All members are likely polysaccharide-degrading chemoheterotrophs with numerous carbohydrate-active enzymes encoded in their genomes. Aerobic or strictly anaerobic. Phylogenomic placement of this lineage within the Fervidibacteria and relative evolutionary divergence supports delineation of this lineage as an order within the class Fervidibacteria and phylum Armatimonadota. The type genus is Fervidibacter. Class Fervidibacteria Fer.vi.di.bac.te’ri.a. N.L. masc. n. Fervidibacter type genus of the type order of the class; L. suff. -ia ending to denote a class; N.L. neut. pl. n. Fervidibacteria the class of the order Fervidibacterales Thermophilic or hyperthermophilic inhabitants of freshwater thermal environments. All members are likely polysaccharide-degrading chemoheterotrophs with numerous carbohydrate-active enzymes encoded in their genomes. Aerobic or strictly anaerobic. Phylogenomic placement of this lineage within the Armatimonadota and relative evolutionary divergence supports delineation of this lineage as a class within the Armatimonadota. The type genus is Fervidibacter. The error has not been corrected in the PDF or HTML versions of the Article.

Nou, Nancy O

Decoding substance use disorder severity from clinical notes using a large language model

Substance use disorder (SUD) poses a major concern due to its detrimental effects on health and society. SUD identification and treatment depend on a variety of factors such as severity, co-determinants (e.g., withdrawal symptoms), and social determinants of health. Existing diagnostic coding systems used by insurance providers, like the International Classification of Diseases (ICD-10), lack granularity for certain diagnoses, but American clinicians will add this granularity (as that found within the Diagnostic and Statistical Manual of Mental Disorders classification or DSM-5) as supplemental unstructured text in clinical notes. Traditional natural language processing (NLP) methods face limitations in accurately parsing such diverse clinical language. Large language models (LLMs) offer promise in overcoming these challenges by adapting to diverse language patterns. This study investigates the application of LLMs for extracting severity-related information for various SUD diagnoses from clinical notes. We propose a workflow employing zero-shot learning of LLMs with carefully crafted prompts and post-processing techniques. Through experimentation with Flan-T5, an open-source LLM, we demonstrate its superior recall compared to the rule-based approach. Focusing on 11 categories of SUD diagnoses, we show the effectiveness of LLMs in extracting severity information, contributing to improved risk assessment and treatment planning for SUD patients.

60 APPLIED LIFE SCIENCES