Hybrid Adaptive Ray-Moment Method (HARM2): A highly parallel method for radiation hydrodynamics on adaptive grids
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A.L. Rosen↗
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Results for “Adaptive radiation”
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Heavy-ion induced genetic changes and evolution processes
On Moon and Mars, there will be more galactic cosmic rays and higher radiation doses than on Earth. Our experimental studies showed that heavy ion radiation can effectively cause mutation and chromosome aberrations and that high Linear Energy Transfer (LET) heavy-ion induced mutants can be irreversible. Chromosome translocations and deletions are common in cells irradiated by heavy particles, and ionizing radiations are effective in causing hyperploidy. The importance of the genetic changes in the evolution of life is an interesting question. Through evolution, there is an increase of DNA content in cells from lower forms of life to higher organisms. The DNA content, however, reached a plateau in vertebrates. By increasing DNA content, there can be an increase of information in the cell. For a given DNA content, the quality of information can be changed by rearranging the DNA. Because radiation can cause hyperploidy, an increase of DNA content in cells, and can induce DNA rearrangement, it is likely that the evolution of life on Mars will be effected by its radiation environment. A simple analysis shows that the radiation level on Mars may cause a mutation frequency comparable to that of the spontaneous mutation rate on Earth. To the extent that mutation plays a role in adaptation, radiation alone on Mars may thus provide sufficient mutation for the evolution of life.
Yang, C. H.↗
Sensing device and method for measuring emission time delay during irradiation of targeted samples
An apparatus for measuring emission time delay during irradiation of targeted samples by utilizing digital signal processing to determine the emission phase shift caused by the sample is disclosed. The apparatus includes a source of electromagnetic radiation adapted to irradiate a target sample. A mechanism generates first and second digital input signals of known frequencies with a known phase relationship, and a device then converts the first and second digital input signals to analog sinusoidal signals. An element is provided to direct the first input signal to the electromagnetic radiation source to modulate the source by the frequency thereof to irradiate the target sample and generate a target sample emission. A device detects the target sample emission and produces a corresponding first output signal having a phase shift relative to the phase of the first input signal, the phase shift being caused by the irradiation time delay in the sample. A member produces a known phase shift in the second input signal to create a second output signal. A mechanism is then provided for converting each of the first and second analog output signals to digital signals. A mixer receives the first and second digital output signals and compares the signal phase relationship therebetween to produce a signal indicative of the change in phase relationship between the first and second output signals caused by the target sample emission. Finally, a feedback arrangement alters the phase of the second input signal based on the mixer signal to ultimately place the first and second output signals in quadrature. Mechanisms for enhancing this phase comparison and adjustment technique are also disclosed.
Danielson, J. D. Sheldon↗
Sensing device and method for measuring emission time delay during irradiation of targeted samples utilizing variable phase tracking
An apparatus for measuring emission time delay during irradiation of targeted samples by utilizing digital signal processing to determine the emission phase shift caused by the sample is disclosed. The apparatus includes a source of electromagnetic radiation adapted to irradiate a target sample. A mechanism generates first and second digital input signals of known frequencies with a known phase relationship, and a device then converts the first and second digital input signals to analog sinusoidal signals. An element is provided to direct the first input signal to the electromagnetic radiation source to modulate the source by the frequency thereof to irradiate the target sample and generate a target sample emission. A device detects the target sample emission and produces a corresponding first output signal having a phase shift relative to the phase of the first input signal, the phase shift being caused by the irradiation time delay in the sample. A member produces a known phase shift in the second input signal to create a second output signal. A mechanism is then provided for converting each of the first and second analog output signals to digital signals. A mixer receives the first and second digital output signals and compares the signal phase relationship therebetween to produce a signal indicative of the change in phase relationship between the first and second output signals caused by the target sample emission. Finally, a feedback arrangement alters the phase of the second input signal based on the mixer signal to ultimately place the first and second output signals in quadrature. Mechanisms for enhancing this phase comparison and adjustment technique are also disclosed.
Danielson, J. D. Sheldon↗
Discovery of additional ancient genome duplications in yeasts
Whole-genome duplication (WGD) has had profound macroevolutionary impacts on diverse lineages, preceding adaptive radiations in vertebrates, teleost fish, and angiosperms. In contrast to the many known ancient WGDs in animals, and especially plants, we are aware of evidence for only four WGDs in fungi. The oldest of these occurred ∼100 million years ago (mya) and is shared by ∼60 extant Saccharomycetales species, including the baker’s yeast Saccharomyces cerevisiae. Notably, this is the only known ancient WGD event in the yeast subphylum Saccharomycotina. The dearth of ancient WGD events in fungi remains a mystery. Some studies have suggested that fungal lineages that experience chromosome and genome duplication quickly go extinct, leaving no trace in the genomic record, while others contend that the lack of known WGDs is due to an absence of data. Under the second hypothesis, additional sampling and deeper sequencing of fungal genomes should lead to the discovery of more WGD events. Coupling hundreds of recently published genomes from nearly every described Saccharomycotina species, with three additional long-read assemblies, we discovered three novel WGD events. Although the functions of retained duplicate genes originating from these events are broad, they bear similarities to the well-known WGD that occurred in the Saccharomycetales. In conclusion, our results suggest that WGD may be a more common evolutionary force in fungi than previously believed.
convergent evolution↗
Patterns of Care, Tolerability, and Safety of the First Cohort of Patients Treated on a Novel High-Field MR-Linac Within the MOMENTUM Study: Initial Results From a Prospective Multi-Institutional Registry
High-field magnetic resonance-linear accelerators (MR-Linacs), linear accelerators combined with a diagnostic magnetic resonance imaging (MRI) scanner and online adaptive workflow, potentially give rise to novel online anatomic and response adaptive radiation therapy paradigms. The first high-field (1.5T) MR-Linac received regulatory approval in late 2018, and little is known about clinical use, patient tolerability of daily high-field MRI, and toxicity of treatments. Herein we report the initial experience within the MOMENTUM Study (NCT04075305), a prospective international registry of the MR-Linac Consortium.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Patterns of Initial Relapse from a Phase 3 Study of Response-Based Therapy for High-Risk Hodgkin Lymphoma (AHOD0831): A Report from the Children's Oncology Group
The Children's Oncology Group protocol AHOD0831, for pediatric patients with high-risk classical Hodgkin lymphoma (cHL), used response-adapted radiation fields, rather than larger involved-field radiation therapy (IFRT) that were historically used. This retrospective analysis of patterns of relapse among patients enrolled in the study was conducted to study the potential effect of a reduction in RT exposure.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Recent progress on coarse graining simulations
We focus on coarse graining simulations based on the primary conservation equations, effectively codesigned physics and algorithms, and low-Mach-number corrected (LMC) hydrodynamics. Simulation methods involve LANL’s x-Radiation-Adaptive-Grid-Eulerian Large-Eddy Simulation, Besnard-Harlow-Rauenzahn (BHR) Reynolds-Averaged Navier-Stokes (RANS) approach, and Dynamic BHR – a paradigm bridging RANS and LES. A relevant question addressed relates to whether 3D RANS and RANS/LES hybrids – the industry standards for aerospace and automotive research, are presently relevant for practical variable-density applications involving shocked and accelerated interface instabilities. Furthermore, recent simulations of the GaTECH inclined mixing-layer shock-tube and NIF ICF-capsule experiments are used to demonstrate issues, challenges, and potential for 3D coarse grained LMC simulation strategies for robustly simulating complex transitional and coupled hydrodynamics-multiphysics with coarser resolution. Present LES readiness to provide accurate predictions at scale is demonstrated – whereas 3D RANS and RANS/LES bridging do not appear impactful in this context.
42 ENGINEERING↗
Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea
Ammonia-oxidizing archaea (AOA) are among the most abundant and ubiquitous microorganisms in the ocean, exerting primary control on nitrification and nitrogen oxides emission. Although united by a common physiology of chemoautotrophic growth on ammonia, a corresponding high genomic and habitat variability suggests tremendous adaptive capacity. Here, we compared 44 diverse AOA genomes, 37 from species cultivated from samples collected across diverse geographic locations and seven assembled from metagenomic sequences from the mesopelagic to hadopelagic zones of the deep ocean. Comparative analysis identified seven major marine AOA genotypic groups having gene content correlated with their distinctive biogeographies. Phosphorus and ammonia availabilities as well as hydrostatic pressure were identified as selective forces driving marine AOA genotypic and gene content variability in different oceanic regions. Notably, AOA methylphosphonate biosynthetic genes span diverse oceanic provinces, reinforcing their importance for methane production in the ocean. Together, our combined comparative physiological, genomic, and metagenomic analyses provide a comprehensive view of the biogeography of globally abundant AOA and their adaptive radiation into a vast range of marine and terrestrial habitats.
59 BASIC BIOLOGICAL SCIENCES↗
Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past
Abstract Although the phylum Chloroflexota is ubiquitous, its biology and evolution are poorly understood due to limited cultivability. Here, we isolated two motile, thermophilic bacteria from hot spring sediments belonging to the genus Tepidiforma and class Dehalococcoidia within the phylum Chloroflexota. A combination of cryo-electron tomography, exometabolomics, and cultivation experiments using stable isotopes of carbon revealed three unusual traits: flagellar motility, a peptidoglycan-containing cell envelope, and heterotrophic activity on aromatics and plant-associated compounds. Outside of this genus, flagellar motility has not been observed in Chloroflexota, and peptidoglycan-containing cell envelopes have not been described in Dehalococcoidia. Although these traits are unusual among cultivated Chloroflexota and Dehalococcoidia, ancestral character state reconstructions showed flagellar motility and peptidoglycan-containing cell envelopes were ancestral within the Dehalococcoidia, and subsequently lost prior to a major adaptive radiation of Dehalococcoidia into marine environments. However, despite the predominantly vertical evolutionary histories of flagellar motility and peptidoglycan biosynthesis, the evolution of enzymes for degradation of aromatics and plant-associated compounds was predominantly horizontal and complex. Together, the presence of these unusual traits in Dehalococcoidia and their evolutionary histories raise new questions about the timing and selective forces driving their successful niche expansion into global oceans.
59 BASIC BIOLOGICAL SCIENCES↗
Kingdom-Wide Analysis of Fungal Protein-Coding and tRNA Genes Reveals Conserved Patterns of Adaptive Evolution
Protein-coding genes evolved codon usage bias due to the combined but uneven effects of adaptive and nonadaptive influences. Studies in model fungi agree on codon usage bias as an adaptation for fine-tuning gene expression levels; however, such knowledge is lacking for most other fungi. Our comparative genomics analysis of over 450 species supports codon usage and transfer RNAs (tRNAs) as coadapted for translation speed and this is most likely a realization of convergent evolution. Rather than drift, phylogenetic reconstruction inferred adaptive radiation as the best explanation for the variation of interspecific codon usage bias. Although the phylogenetic signals for individual codon and tRNAs frequencies are lower than expected by genetic drift, we found remarkable conservation of highly expressed genes being codon optimized for translation by the most abundant tRNAs, especially by inosine-modified tRNAs. As an application, we present a sequence-to-expression neural network that uses codons to reliably predict highly expressed transcripts. The kingdom Fungi, with over a million species, includes many key players in various ecosystems and good targets for biotechnology. Collectively, our results have implications for better understanding the evolutionary success of fungi, as well as informing the biosynthetic manipulation of fungal genes.
59 BASIC BIOLOGICAL SCIENCES↗
Convergent evolution of tree hydraulic traits in Amazonian habitats: implications for community assemblage and vulnerability to drought
Amazonian droughts are increasing in frequency and severity. However, little is known about how this may influence species-specific vulnerability to drought across different ecosystem types. We measured 16 functional traits for 16 congeneric species from six families and eight genera restricted to floodplain, swamp, white-sand or plateau forests of Central Amazonia. We investigated whether habitat distributions can be explained by species hydraulic strategies, and if habitat specialists differ in their vulnerability to embolism that would make water transport difficult during drought periods. We found strong functional differences among species. Nonflooded species had higher wood specific gravity and lower stomatal density, whereas flooded species had wider vessels, and higher leaf and xylem hydraulic conductivity. The P 50 values (water potential at 50% loss of hydraulic conductivity) of nonflooded species were significantly more negative than flooded species. However, we found no differences in hydraulic safety margin among species, suggesting that all trees may be equally likely to experience hydraulic failure during severe droughts. Water availability imposes a strong selection leading to differentiation of plant hydraulic strategies among species and may underlie patterns of adaptive radiation in many tropical tree genera. Our results have important implications for modeling species distribution and resilience under future climate scenarios.
59 BASIC BIOLOGICAL SCIENCES↗
Gas particle radiator
A gas particle radiator adapted to operate in a microgravity space environment having a transparent boundary which transmits energy in the infrared spectrum, and a gas particle mixture that yields high absorption and emittances are described.
Donald L Chubb↗
The fossil record of evolution: Data on diversification and extinction
Understanding of the evolution of complex life, and of the roles that changing terrestrial and extraterrestrial environments played in life's history, is dependent upon synthetic knowledge of the fossil record. Paleontologists have been describing fossils for more that two centuries. However, much of this information is dispersed in monographs and journal articles published throughout the world. Over the past several years, this literature was surveyed, and a data base on times of origination and extinction of fossil genera was compiled. The data base, which now holds approximately 32,000 genera, covers all taxonomic groups of marine animals, incorporates the most recent taxonomic assignments, and uses a detailed global time framework that can resolve originations and extinctions to intervals averaging three million years in duration. These data can be used to compile patterns of global biodiversity, measure rates of taxic evolution, and test hypotheses concerning adaptive radiations, mass extinctions, etc. Thus far, considerable effort was devoted to using the data to test the hypothesis of periodicity of mass extinction. Rates of extinction measured from the data base have also been used to calibrate models of evolutionary radiations in marine environments. It was observed that new groups, or clades of animals (i.e., orders and classes) tend to reach appreciable diversity first in nearshore environments and then to radiate in more offshore environments; during decline, these clades may disappear from the nearshore while persisting in offshore, deep water habitats. These observations have led to suggestions that there is something special about stressful or perturbed environments that promotes the evolution of novel kinds of animals that can rapidly replace their predecessors. The numerical model that is being investigated to study this phenomenon treats environments along onshore-offshore gradients as if they were discrete habitats. Other aspects of this investigation are presented.
Sepkoski, J. J., Jr.↗
National Space Biomedical Research Institute
This report summarizes the activities of the National Space Biomedical Research Institute (NSBRI) during FY 1999, the second full year of existence of the NSBRI's research program, and is prepared in accordance with Cooperative Agreement NCC9-58 between NASA's Lyndon B. Johnson Space Center and Baylor College of Medicine (NSBRI). The report consists of progress reports on projects related to the effects of microgravity and space on physiology. The research is broken up in nine areas: (1) Bone loss, (2) Cardiovascular alterations, (3) human performance, (3) immunology, infection and hematology, (4) muscle alterations and atrophy,(5) Neurovestibular adaptation, radiation effects, (6) technology development, and (7) synergy projects.
Source record↗
Characteristics of Monolithically Integrated InGaAs Active Pixel Imager Array
Switching and amplifying characteristics of a newly developed monolithic InGaAs Active Pixel Imager Array are presented. The sensor array is fabricated from InGaAs material epitaxially deposited on an InP substrate. It consists of an InGaAs photodiode connected to InP depletion-mode junction field effect transistors (JFETs) for low leakage, low power, and fast control of circuit signal amplifying, buffering, selection, and reset. This monolithically integrated active pixel sensor configuration eliminates the need for hybridization with silicon multiplexer. In addition, the configuration allows the sensor to be front illuminated, making it sensitive to visible as well as near infrared signal radiation. Adapting the existing 1.55 micrometer fiber optical communication technology, this integration will be an ideal system of optoelectronic integration for dual band (Visible/IR) applications near room temperature, for use in atmospheric gas sensing in space, and for target identification on earth. In this paper, two different types of small 4 x 1 test arrays will be described. The effectiveness of switching and amplifying circuits will be discussed in terms of circuit effectiveness (leakage, operating frequency, and temperature) in preparation for the second phase demonstration of integrated, two-dimensional monolithic InGaAs active pixel sensor arrays for applications in transportable shipboard surveillance, night vision, and emission spectroscopy.
Kim, Q.↗
Verification and Validation of the RAGE Hydrocode in Preparation for Investigation of Impacts into a Volatile-rich Target
Before a hydrocode is used to investigate a question of scientific interest, it should be tested against analogous laboratory experiments and problems with analytical solutions. The Radiation Adaptive Grid Eulerian (RAGE) hydrocode[1], developed by Los Alamos National Laboratory (LANL) and Science Applications International Corporation (SAIC)[2,3] has been subjected to many tests during its development.[4,5] We extend and review this work, emphasizing tests relevant to impact cratering into volatile-rich targets.
Plesko, C. S.↗
Analytical investigation of adaptive control of radiated inlet noise from turbofan engines
An analytical model has been developed to predict the resulting far field radiation from a turbofan engine inlet. A feedforward control algorithm was simulated to predict the controlled far field radiation from the destructive combination of fan noise and secondary control sources. Numerical results were developed for two system configurations, with the resulting controlled far field radiation patterns showing varying degrees of attenuation and spillover. With one axial station of twelve control sources and error sensors with equal relative angular positions, nearly global attenuation is achieved. Shifting the angular position of one error sensor resulted in an increase of spillover to the extreme sidelines. The complex control inputs for each configuration was investigated to identify the structure of the wave pattern created by the control sources, giving an indication of performance of the system configuration. It is deduced that the locations of the error sensors and the control source configuration are equally critical to the operation of the active noise control system.
Risi, John D.↗