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At least 847 records · Page 47

Mapping the Interstellar Reddening and Extinction toward Baade's Window Using Minimum Light Colors of ab-type RR Lyrae Stars: Revelations from the De-reddened Color–Magnitude Diagrams

We have obtained repeated images of six fields toward the Galactic bulge in five passbands (u, g, r, i, z) with the DECam imager on the Blanco 4 m telescope at CTIO. From more than 1.6 billion individual photometric measurements in the field centered on Baade’s window, we have detected 4877 putative variable stars. A total of 474 of these have been confirmed as fundamental mode RR Lyrae stars, whose colors at minimum light yield line-of- sight reddening determinations, as well as a reddenning law toward the Galactic Bulge, which differs significantly from the standard R(V) = 3.1 formulation. Assuming that the stellar mix is invariant over the 3 square-degree field, we are able to derive a line-of-sight reddening map with sub-arcminute resolution, enabling us to obtain de-reddened and extinction corrected color–magnitude diagrams (CMDs) of this bulge field using up to 2.5 million well-measured stars. The corrected CMDs show unprecedented detail and expose sparsely populated sequences: for example, delineation of the very wide red giant branch, structure within the red giant clump, the full extent of the horizontal branch, and a surprising bright feature that is likely due to stars with ages younger than 1 Gyr. We use the RR Lyrae stars to trace the spatial structure of the ancient stars and find an exponential decline in density with Galactocentric distance. We discuss ways in which our data products can be used to explore the age and metallicity properties of the bulge, and how our larger list of all variables is useful for learning to interpret future LSST alerts.

Abhijit Saha↗

Nuclear Safety [Vol. 37, No. 1, January-March 1996]

Nuclear Safety is a journal that covers significant issues in the field of nuclear safety. Its primary scope is safety in the design, construction, operation, and decommissioning of nuclear power reactors worldwide and the research and analysis activities that promote this goal, but it also encompasses the safety aspects of the entire nuclear fuel cycle, including fuel fabrication, spent-fuel processing and handling, and nuclear waste disposal, the handling of fissionable materials and radioisotopes, and the environmental effects of all these activities. Table of Contents for this issue follows. GENERAL SAFETY CONSIDERATIONS: 1 A Decision Support System for Maintenance Management of a Boiling-Water Reactor Power Plant, J. H. Shen, A. Ray, and S. Levine; ACCIDENT ANALYSIS: 12 On Prediction of the Ignition Potential of Uranium Metal and Hydride, M. Epstein, W. Luangdilok, M. G. Plys, and H. K. Fauske; 26 An Overview of the Primary Parameters and Methods for Determining Condensation Heat Transfer to Containment Structures, J. Green and K. Almenas; DESIGN FEATURES: 49 Modem Tornado Design of Nuclear and Other Potentially Hazardous Facilities, J. D. Stevenson and Y. Zaho; U.S. NUCLEAR REGULATORY COMMISSION INFORMATION AND ANALYSES: 73 1994 Accident Sequence Precursor Program Results, R. J. Belles, J. W. Cletcher, D. A. Copinger, B. W. Dolan, J. W. Minarick, and P. D. O'Reilly; ANNOUNCEMENTS: 93 American Institute of Chemical Engineers (AlChE) Spring 1997 National Meeting; 94 European Safety and Reliability Association International Conference on Safety and Reliability ESREL ’97; 95 Criticality Safety Challenges in the Next Decade; 96 21st International Symposium on the Scientific Basis for Nuclear Waste Management; 84 The Authors; 88 Letter to the Editor; 90 Indexes to Nuclear Safety, Volume 36.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Model for Simulating a Spiral Software-Development Process

A discrete-event simulation model, and a computer program that implements the model, have been developed as means of analyzing a spiral software-development process. This model can be tailored to specific development environments for use by software project managers in making quantitative cases for deciding among different software-development processes, courses of action, and cost estimates. A spiral process can be contrasted with a waterfall process, which is a traditional process that consists of a sequence of activities that include analysis of requirements, design, coding, testing, and support. A spiral process is an iterative process that can be regarded as a repeating modified waterfall process. Each iteration includes assessment of risk, analysis of requirements, design, coding, testing, delivery, and evaluation. A key difference between a spiral and a waterfall process is that a spiral process can accommodate changes in requirements at each iteration, whereas in a waterfall process, requirements are considered to be fixed from the beginning and, therefore, a waterfall process is not flexible enough for some projects, especially those in which requirements are not known at the beginning or may change during development. For a given project, a spiral process may cost more and take more time than does a waterfall process, but may better satisfy a customer's expectations and needs. Models for simulating various waterfall processes have been developed previously, but until now, there have been no models for simulating spiral processes. The present spiral-process-simulating model and the software that implements it were developed by extending a discrete-event simulation process model of the IEEE 12207 Software Development Process, which was built using commercially available software known as the Process Analysis Tradeoff Tool (PATT). Typical inputs to PATT models include industry-average values of product size (expressed as number of lines of code), productivity (number of lines of code per hour), and number of defects per source line of code. The user provides the number of resources, the overall percent of effort that should be allocated to each process step, and the number of desired staff members for each step. The output of PATT includes the size of the product, a measure of effort, a measure of rework effort, the duration of the entire process, and the numbers of injected, detected, and corrected defects as well as a number of other interesting features. In the development of the present model, steps were added to the IEEE 12207 waterfall process, and this model and its implementing software were made to run repeatedly through the sequence of steps, each repetition representing an iteration in a spiral process. Because the IEEE 12207 model is founded on a waterfall paradigm, it enables direct comparison of spiral and waterfall processes. The model can be used throughout a software-development project to analyze the project as more information becomes available. For instance, data from early iterations can be used as inputs to the model, and the model can be used to estimate the time and cost of carrying the project to completion.

Mizell, Carolyn↗

MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters

Abstract With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.

59 BASIC BIOLOGICAL SCIENCES↗

Pseudomonas atagosis sp. nov., and Pseudomonas akappagea sp. nov., New Soil Bacteria Isolated from Samples on the Volcanic Island Izu Oshima, Tokyo

During the exploration of microbial natural resources, two strains of Pseudomonas, PS14 T and PS24 T , were isolated from samples taken from Izu Oshima, a volcanic island located 120 km southwest of central Tokyo. Phylogenetic analysis based on 16S rRNA gene sequences showed that PS14 T was most similar to Pseudomonas baetica a390T (99.6%) and Pseudomonas helmanticensis OHA11 T (99.5%), and that PS24T was most similar to Pseudomonas qingdaonensis JJ3 T (98.8%) and Pseudomonas lutea OK2 T (98.7%). The major fatty acids of these two strains were C 16:0 and C 17:0 cyclo, summed feature 3 (C 16:1 ω6c and/or C 16:1 ω7c), and summed feature 8 (C18:1 ω7c and/or 18:1 ω6c). The phylogenetic analyses, DNA-DNA hybridization results and phenotypic traits indicated that PS14 T and PS24 T constitute two novel species, Pseudomonas atagosis sp. nov. (type strain PS14 T = CECT 9940 T , = LMG 31496 T ) and Pseudomonas akappagea sp. nov. (type strain PS24T = CECT 9941T, = LMG 31497T), respectively. The sequence data of the draft genomes of PS14 T and PS24 T were deposited in the GenBank database under accession numbers VXCA00000000 and VXCP00000000, respectively, and the sequence data of their 16S rRNA genes were deposited in the GenBank database under accession numbers MN396717 and MN382268, respectively.

59 BASIC BIOLOGICAL SCIENCES↗

Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae

Geodermatophilaceae (order Geodermatophilales , class Actinobacteria ) form a comparatively isolated family within the phylum Actinobacteria and harbor many strains adapted to extreme ecological niches and tolerant against reactive oxygen species. Clarifying the evolutionary history of Geodermatophilaceae was so far mainly hampered by the insufficient resolution of the main phylogenetic marker in use, the 16S rRNA gene. In conjunction with the taxonomic characterisation of a motile and aerobic strain, designated YIM M13156 T and phylogenetically located within the family, we here carried out a phylogenetic analysis of the genome sequences now available for the type strains of Geodermatophilaceae and re-analyzed the previously assembled phenotypic data. The results indicated that the largest genus, Geodermatophilus , is not monophyletic, hence the arrangement of the genera of Geodermatophilaceae must be reconsidered. Taxonomic markers such as polar lipids and fatty-acids profile, cellular features and temperature ranges are indeed heterogeneous within Geodermatophilus . In contrast to previous studies, we also address which of these features can be interpreted as apomorphies of which taxon, according to the principles of phylogenetic systematics. We thus propose a novel genus, Klenkia, with the type species Klenkia marina sp. nov. and harboring four species formerly assigned to Geodermatophilus , G. brasiliensis , G. soli , G. taihuensis , and G. terrae . Emended descriptions of all species of Geodermatophilaceae are provided for which type-strain genome sequences are publicly available. Our study again demonstrates that the principles of phylogenetic systematics can and should guide the interpretation of both genomic and phenotypic data.

59 BASIC BIOLOGICAL SCIENCES↗

Development of chemometric models to classify solid-state U materials by micro-Raman spectroscopy

Discerning uranium (U) particles found in environmental sampling is of interest for monitoring the peaceful use of nuclear material. In this study, a soft independent modeling of class analogy (SIMCA) library was successfully developed for the classification of a four-class system consisting of α-U 3 O 8 , UO 2 , UO 2 (NO 3 ) 2 ·6H 2 O (UNH), and UO 2 O 2 ·4H 2 O (studtite) by Raman spectroscopy in the presence of matrix particulates and additional outliers. Spectral variability between numerous particles of each type revealed appreciable differences as a function of particle size with respect to hydration state and potential oxide phase within each class. Interclass variability was accounted for using both unsupervised and supervised chemometric models. The supervised SIMCA model displayed reasonable sensitivity for each U class and a high degree of specificity by returning whether a spectrum belonged to one class or not. This work demonstrates how Raman spectral features and chemometrics can be used to distinguish U materials from one another and from matrix materials such as flint clay. Combining the outlined chemometric approach with Raman mapping sequences could provide a rapid, nondestructive technique to characterize the chemical composition of a diverse collection of U compounds amid background samples for environmental sampling, nuclear forensics, and industrial applications.

Actinide↗

Crystal Structure of Cocosin, A Potential Food Allergen from Coconut ( Cocos nucifera )

Coconut ( Cocos nucifera ) is an important palm tree. Coconut fruit is widely consumed. The most abundant storage protein in coconut fruit is cocosin (a likely food allergen), which belongs to the 11S globulin family. Cocosin was crystallized near a century ago, but its structure remains unknown. By optimizing crystallization conditions and cryoprotectant solutions, we were able to obtain cocosin crystals that diffracted to 1.85 Å. The cocosin gene was cloned from genomic DNA isolated from dry coconut tissue. The protein sequence deduced from the predicted cocosin coding sequence was used to guide model building and structure refinement. We report the structure of cocosin was determined for the first time, and it revealed a typical 11S globulin feature of a double layer doughnut-shaped hexamer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Evolution and comparative genomics of the most common Trichoderma species

Background: The growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding of its biology and evolution. Many Trichoderma species are used as biofertilizers and biofungicides and T. reesei is the model organism for industrial production of cellulolytic enzymes. In addition, some highly opportunistic species devastate mushroom farms and can become pathogens of humans. A comparative analysis of the first three whole genomes revealed mycoparasitism as the innate feature of Trichoderma. However, the evolution of these traits is not yet understood. Results: We selected 12 most commonly occurring Trichoderma species and studied the evolution of their genome sequences. Trichoderma evolved in the time of the Cretaceous-Palaeogene extinction event 66 (±15) mya, but the formation of extant sections (Longibrachiatum, Trichoderma) or clades (Harzianum/Virens) happened in Oligocene. The evolution of the Harzianum clade and section Trichoderma was accompanied by significant gene gain, but the ancestor of section Longibrachiatum experienced rapid gene loss. The highest number of genes gained encoded ankyrins, HET domain proteins and transcription factors. We also identified the Trichoderma core genome, completely curated its annotation, investigated several gene families in detail and compared the results to those of other fungi. Eighty percent of those genes for which a function could be predicted were also found in other fungi, but only 67% of those without a predictable function. Conclusions: Our study presents a time scaled pattern of genome evolution in 12 Trichoderma species from three phylogenetically distant clades/sections and a comprehensive analysis of their genes. The data offer insights in the evolution of a mycoparasite towards a generalist.

59 BASIC BIOLOGICAL SCIENCES↗

Anomalous Stellar Populations in Low-surface-brightness Galaxies

We present new Hubble Space Telescope WFC3 near-IR observations of the color–magnitude diagrams (CMDs) in two low-surface-brightness galaxies, F575-3 and F615-1, notable for having no current star formation based on a lack of Hα emission. Key features of the near-IR CMDs are resolved, such as the red giant branch (RGB), the asymptotic giant branch (AGB) region, and the top of the blue main sequence. F575-3 has the bluest RGB of any CMD in the literature, indicating an extremely low mean metallicity. F615-1 has unusually wide RGB and AGB sequences, suggesting multiple episodes of star formation from metal-poor gas, and possibly infalling material. Both galaxies have an unusual population of stars to the red of the RGB and lower in luminosity than typical AGB stars. These stars have normal optical colors but abnormal near-IR colors. We suggest that this population of stars might be analogous to local peculiar stars like Be stars with strong near-IR excesses owing to a surrounding disk of hot gas.

47 OTHER INSTRUMENTATION↗

Different Formation Scenarios for Counterrotating Stellar Disks in Nearby Galaxies

Using the integral field unit data from the Mapping Nearby Galaxies at Apache Point Observatory survey, we select a sample of 101 galaxies with counterrotating stellar disks and regularly rotating ionized gas disks. We classify the 101 galaxies into four types based on the features of their stellar velocity fields. The relative fractions and stellar population age radial gradients of the four types are different in the blue cloud, green valley, and red sequence populations. We suggest different formation scenarios for counterrotating stellar disks; the key factors in the formation of counterrotating stellar disks include (1) the abundance of preexisting gas in the progenitor and (2) the efficiency in angular momentum consumption.

79 ASTRONOMY AND ASTROPHYSICS↗

The geology and geophysics of Mars

The current state of knowledge concerning the regional geology and geophysics of Mars is summarized. Telescopic observations of the planet are reviewed, pre-Mariner models of its interior are discussed, and progress achieved with the Mariner flybys, especially that of Mariner 9, is noted. A map of the Martian geological provinces is presented to provide a summary of the surface geology and morphology. The contrast between the northern and southern hemispheres is pointed out, and the characteristic features of the surface are described in detail. The global topography of the planet is examined along with its gravitational field, gravity anomalies, and moment of inertia. The general sequence of events in Martian geological history is briefly outlined.

Saunders, R. S.↗

Ocean-ice interaction in the marginal ice zone using synthetic aperture radar imagery

Ocean-ice interaction processes in the marginal ice zone (MIZ) by wind, waves, and mesoscale features, such as up/downwelling and eddies are studied using Earth Remote-Sensing Satellite (ERS) 1 synthetic aperture radar (SAR) images and an ocean-ice interaction model. A sequence of seven SAR images of the MIZ in the Chukchi Sea with 3 or 6 days interval are investigated for ice edge advance/retreat. Simultaneous current measurements from the northeast Chukchi Sea, as well as the Barrow wind record, are used to interpret the MIZ dynamics. SAR spectra of waves in ice and ocean waves in the Bering and Chukchi Sea are compared for the study of wave propagation and dominant SAR imaging mechanism. By using the SAR-observed ice edge configuration and wind and wave field in the Chukchi Sea as inputs, a numerical simulation has been performed with the ocean-ice interaction model. After 3 days of wind and wave forcing the resulting ice edge configuration, eddy formation, and flow velocity field are shown to be consistent with SAR observations.

Liu, Antony K.↗

Identification of Novel Desiccation-Tolerant S. cerevisiae Strains for Deep Space Biosensors

NASA's BioSentinel mission, a secondary payload that will fly on the Space Launch Systems first Exploration Mission (EM-1), utilizes the budding yeast S. cerevisiae to study the biological response to the deep space radiation environment. Yeast samples are desiccated prior to launch to suspend growth and metabolism while the spacecraft travels to its target heliocentric orbit beyond Low Earth Orbit. Each sample is then rehydrated at the desired time points to reactivate the cells. A major risk in this mission is the loss of cell viability that occurs in the recovery period following the desiccation and rehydration process. Cell survival is essential for the detection of the biological response to features in the deep space environment, including ionizing radiation.The aim of this study is to mitigate viable cell loss in future biosensors by identifying mutations and genes that confer tolerance to desiccation stress in rad51, a radiation-sensitive yeast strain. We initiated a screen for desiccation-tolerance after rehydrating cells that were desiccated for three years, and selected various clones exhibiting robust growth. To verify retention of radiation sensitivity in the isolated clonesa crucial feature for a successful biosensorwe exposed them to ionizing radiation. Finally, to elucidate the genetic and molecular bases for observed desiccation-tolerance, we will perform whole-genome sequencing of those rad51 clones that exhibit both robust growth and radiation sensitivity following desiccation. The identification and characterization of desiccation-tolerant strains will allow us to engineer a biological model that will be resilient in face of the challenges of the deep space environment, and will thus ensure the experimental success of future biosensor missions.

S. cerevisiae↗

CyBERT: Cybersecurity Claim Classification by Fine-Tuning the BERT Language Model

We introduce CyBERT, a cybersecurity feature claims classifier based on bidirectional encoder representations from transformers and a key component in our semi-automated cybersecurity vetting for industrial control systems (ICS). To train CyBERT, we created a corpus of labeled sequences from ICS device documentation collected across a wide range of vendors and devices. This corpus provides the foundation for fine-tuning BERT’s language model, including a prediction-guided relabeling process. We propose an approach to obtain optimal hyperparameters, including the learning rate, the number of dense layers, and their configuration, to increase the accuracy of our classifier. Fine-tuning all hyperparameters of the resulting model led to an increase in classification accuracy from 76% obtained with BertForSequenceClassification’s original architecture to 94.4% obtained with CyBERT. Furthermore, we evaluated CyBERT for the impact of randomness in the initialization, training, and data-sampling phases. CyBERT demonstrated a standard deviation of ±0.6% during validation across 100 random seed values. Finally, we also compared the performance of CyBERT to other well-established language models including GPT2, ULMFiT, and ELMo, as well as neural network models such as CNN, LSTM, and BiLSTM. The results showed that CyBERT outperforms these models on the validation accuracy and the F1 score, validating CyBERT’s robustness and accuracy as a cybersecurity feature claims classifier.

97 MATHEMATICS AND COMPUTING↗

Whole-genome relationships among Francisella bacteria of diverse origins define new species and provide specific regions for detection

Francisella tularensis is a highly virulent zoonotic pathogen that causes tularemia and, because of weaponization efforts in past world wars, is considered a tier 1 biothreat agent. Detection and surveillance of F. tularensis may be confounded by the presence of uncharacterized, closely related organisms. Through DNA-based diagnostics and environmental surveys, novel clinical and environmental Francisella isolates have been obtained in recent years. Here we present 7 new Francisella genomes and a comparison of their characteristics to each other and to 24 publicly available genomes as well as a comparative analysis of 16S rRNA and sdhA genes from over 90 Francisella strains. Delineation of new species in bacteria is challenging, especially when isolates having very close genomic characteristics exhibit different physiological features—for example, when some are virulent pathogens in humans and animals while others are nonpathogenic or are opportunistic pathogens. Species resolution within Francisella varies with analyses of single genes, multiple gene or protein sets, or whole-genome comparisons of nucleic acid and amino acid sequences. Analyses focusing on single genes (16S rRNA, sdhA ), multiple gene sets (virulence genes, lipopolysaccharide [LPS] biosynthesis genes, pathogenicity island), and whole-genome comparisons (nucleotide and protein) gave congruent results, but with different levels of discrimination confidence. We designate four new species within the genus; Francisella opportunistica sp. nov. (MA06-7296), Francisella salina sp. nov. (TX07-7308), Francisella uliginis sp. nov. (TX07-7310), and Francisella frigiditurris sp. nov. (CA97-1460). Lastly, this study provides a robust comparative framework to discern species and virulence features of newly detected Francisella bacteria.

59 BASIC BIOLOGICAL SCIENCES↗

On the effects of reactant stratification and wall curvature in non-premixed rotating detonation combustors

The optimization of non-premixed rotating detonation combustors (RDCs) requires improved understanding of the coupled effects of reactant stratification, fluid property gradients, and complex shock-wave interactions on the detonation wave structure within annular geometries. In the current work, simultaneous orthogonal views of chemiluminescence and hydroxyl planar laser-induced fluorescence (PLIF) are utilized to establish the existence of a dual-wave system characterized by leading and trailing detonation waves that are closely coupled by the local flow physics. These features are persistent over a wide range of mass flow rates and are consistent with prior observations of non-premixed rotating detonations in annular geometries. The detailed instantaneous time sequences are compared with a 3D reactive unsteady Reynolds averaged Navier-Stokes (URANS) simulation to more clearly elucidate the in-situ combustion dynamics and the sensitivity to reactant inlet conditions. It is found that the dual-wave system results from unburned reactants that survive the leading detonation wave in the injector near field and are consumed within a trailing azimuthal reflected-shock combustion (ARSC) zone. By contrast, the injector far field is characterized by rapid mixing due to a sudden drop to subsonic conditions, and the bifurcated detonation wave structure collapses into a stronger, single-wave detonation front with higher overall pressure ratio as compared with the dual-wave system. While each RDC will have different inflow, mixing, and combustion characteristics, the underlying interactions between the stratified reactants and azimuthal wave dynamics identified through the combination of advanced MHz-rate diagnostics and 3D numerical simulations have important implications for the study of detonation wave stability, mode transition, and combustion efficiency in non-premixed annular RDCs.

3D URANS↗

Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils

Co-occurrence networks allow for the identification of potential associations among species, which may be important for understanding community assembly and ecosystem functions. We employed this strategy to examine prokaryotic co-occurrence patterns in the Amazon soils and the response of these patterns to land use change to pasture, with the hypothesis that altered microbial composition due to deforestation will mirror the co-occurrence patterns across prokaryotic taxa. In this study, we calculated Spearman correlations between operational taxonomic units (OTUs) as determined by 16S rRNA gene sequencing, and only robust correlations were considered for network construction (-0.80 ≥ ρ ≥ 0.80, adjusted P <0.01). The constructed network represents distinct forest and pasture components, with altered compositional and topological features. A comparative analysis between two representative modules of these contrasting ecosystems revealed novel information regarding changes to metabolic pathways related to nitrogen cycling. Our results showed that soil physicochemical properties such as temperature, C/N and H + +Al 3+ had a significant impact on prokaryotic communities, with alterations to network topologies. Taken together, changes in co-occurrence patterns and physicochemical properties may contribute to ecosystem processes including nitrification and denitrification, two important biogeochemical processes occurring in tropical forest systems.

54 ENVIRONMENTAL SCIENCES↗