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At least 703 records · Page 39

The Number and Pattern of Viral Genomic Reassortments are not Necessarily Identifiable from Segment Trees

Reassortment is an evolutionary process common in viruses with segmented genomes. These viruses can swap whole genomic segments during cellular co-infection, giving rise to novel progeny formed from the mixture of parental segments. Since large-scale genome rearrangements have the potential to generate new phenotypes, reassortment is important to both evolutionary biology and public health research. However, statistical inference of the pattern of reassortment events from phylogenetic data is exceptionally difficult, potentially involving inference of general graphs in which individual segment trees are embedded. In this paper, we argue that, in general, the number and pattern of reassortment events are not identifiable from segment trees alone, even with theoretically ideal data. We call this fact the fundamental problem of reassortment, which we illustrate using the concept of the “first-infection tree,” a potentially counterfactual genealogy that would have been observed in the segment trees had no reassortment occurred. Further, we illustrate four additional problems that can arise logically in the inference of reassortment events and show, using simulated data, that these problems are not rare and can potentially distort our observation of reassortment even in small data sets. Finally, we discuss how existing methods can be augmented or adapted to account for not only the fundamental problem of reassortment, but also the four additional situations that can complicate the inference of reassortment.

59 BASIC BIOLOGICAL SCIENCES↗

A Group of O-Acetyltransferases Catalyze Xyloglucan Backbone Acetylation and Can Alter Xyloglucan Xylosylation Pattern and Plant Growth When Expressed in Arabidopsis

Abstract Xyloglucan is a major hemicellulose in plant cell walls and exists in two distinct types, XXXG and XXGG. While the XXXG-type xyloglucan from dicot species only contains O-acetyl groups on side-chain galactose (Gal) residues, the XXGG-type xyloglucan from Poaceae (grasses) and Solanaceae bears O-acetyl groups on backbone glucosyl (Glc) residues. Although O-acetyltransferases responsible for xyloglucan Gal acetylation have been characterized, the biochemical mechanism underlying xyloglucan backbone acetylation remains to be elucidated. In this study, we showed that recombinant proteins of a group of DUF231 members from rice and tomato were capable of transferring acetyl groups onto O-6 of Glc residues in cello-oligomer acceptors, indicating that they are xyloglucan backbone 6-O-acetyltransferases (XyBATs). We further demonstrated that XyBAT-acetylated cellohexaose oligomers could be readily xylosylated by AtXXT1 (Arabidopsis xyloglucan xylosyltransferase 1) to generate acetylated, xylosylated cello-oligomers, whereas AtXXT1-xylosylated cellohexaose oligomers were much less effectively acetylated by XyBATs. Heterologous expression of a rice XyBAT in Arabidopsis led to a severe reduction in cell expansion and plant growth and a drastic alteration in xyloglucan xylosylation pattern with the formation of acetylated XXGG-type units, including XGG, XGGG, XXGG, XXGG,XXGGG and XXGGG (G denotes acetylated Glc). In addition, recombinant proteins of two Arabidopsis XyBAT homologs also exhibited O-acetyltransferase activity toward cellohexaose, suggesting their possible role in mediating xyloglucan backbone acetylation in vivo. Our findings provide new insights into the biochemical mechanism underlying xyloglucan backbone acetylation and indicate the importance of maintaining the regular xyloglucan xylosylation pattern in cell wall function.

Cell Biology↗

A Single Xyloglucan Xylosyltransferase Is Sufficient for Generation of the XXXG Xylosylation Pattern of Xyloglucan

ABSTRACT Xyloglucan is the most abundant hemicellulose in the primary cell walls of dicots. Dicot xyloglucan is the XXXG type consisting of repeating units of three consecutive xylosylated Glc residues followed by one unsubstituted Glc. Its xylosylation is catalyzed by xyloglucan 6-xylosyltransferases (XXTs) and there exist five XXTs (AtXXT1-5) in Arabidopsis. While AtXXT1 and AtXXT2 have been shown to add the first two Xyl residues in the XXXG repeat, which XXTs are responsible for the addition of the third Xyl residue remains elusive although AtXXT5 was a proposed candidate. In this report, we generated recombinant proteins of all five Arabidopsis XXTs and one rice XXT (OsXXT1) in the mammalian HEK293 cells and investigated their ability to sequentially xylosylate Glc residues to generate the XXXG xylosylation pattern. We found that like AtXXT1/2, AtXXT4 and OsXXT1 could efficiently xylosylate the cellohexaose (G6) acceptor to produce mono- and di-xylosylated G6, whereas AtXXT5 was only barely capable of adding one Xyl onto G6. When AtXXT1-catalyzed products were used as acceptors, AtXXT1/2/4 and OsXXT1, but not AtXXT5, were able to xylosylate additional Glc residues to generate tri- and tetra-xylosylated G6. Further characterization of the tri- and tetra-xylosylated G6 revealed that they had the sequence of GXXXGG and GXXXXG with three and four consecutive xylosylated Glc residues, respectively. In addition, we have found that although tri-xylosylation occurred on G6, cello-oligomers with a degree of polymerization of 3 to 5 could only be mono- and di-xylosylated. Together, these results indicate that each of AtXXT1/2/4 and OsXXT1 is capable of sequentially adding Xyl onto three contiguous Glc residues to generate the XXXG xylosylation pattern and these findings provide new insight into the biochemical mechanism underlying xyloglucan biosynthesis.

Cell Biology↗

Metabolic patterns in Septoria canker resistant and susceptible Populus trichocarpa genotypes 24 hours post-inoculation

Sphaerulina musiva is an economically and ecologically important fungal pathogen that causes Septoria stem canker and leaf spot disease of Populus species. Here, to bridge the gap between genetic markers and structural barriers previously found to be linked to Septoria (Sphaerulina musiva) canker disease resistance in poplar, we employed hydrophilic interaction liquid chromatography (HILIC) and tandem mass spectrometry (MS/MS) to identify and quantify metabolites involved with signaling and cell wall re-modelling. Fluctuations in signaling molecules, organic acids, amino acids, sterols, phenolics, and saccharides in resistant and susceptible Populus trichocarpa inoculated with Sphaerulina musiva, were observed. The patterns of 222 metabolites in the resistant host implicates systemic acquired resistance (SAR), cell wall apposition, and lignin deposition as modes of resistance to this hemibiotrophic pathogen. This pattern is consistent with the expected response to the biotrophic phase of S. musiva colonization during the first 24 hours post-inoculation. The fungal pathogen metabolized key regulatory signals of SAR, other phenolics, and precursors of lignin biosynthesis which were depleted in the susceptible host. This is the first study to characterize metabolites associated with the response to initial colonization by S. musiva between resistant and susceptible hosts.

59 BASIC BIOLOGICAL SCIENCES↗

Local Ferromagnetic Resonance Measurements of Mesoscopically Patterned Ferromagnets Using Deterministically Placed Nanodiamonds

Nitrogen-vacancy centers in diamond have recently been established as effective sensors of the magnetization dynamics in vicinal ferromagnetic materials. Here, we demonstrate sub-100-nm placement accuracy of nitrogen-vacancy-containing nanodiamonds and use these as local sensors that probe optically detected ferromagnetic resonance in mesoscopically patterned Permalloy islands. These measurements reveal variations in the ferromagnetic resonance signal at different sites on these structures with distinct behavior in the edge and the bulk of patterned features. These test measurements establish an easily implemented approach for spatially targeted measurements of spin dynamics in mesoscale ferromagnets. In principle, the methodology can also be extended to local studies of nanoscale ferromagnets, such as single magnetic nanowires and nanoparticles.

30 DIRECT ENERGY CONVERSION↗

Nanoscale dynamics during self-organized ion beam patterning of Si. II. Kr + bombardment

Understanding the self-organized ion beam nanopatterning of elemental semiconductors, particularly silicon, is of intrinsic scientific and technological interest. This is the second component of a two-part coherent x-ray scattering and x-ray photon correlation spectroscopy (XPCS) investigation of the kinetics and fluctuation dynamics of nanoscale ripple development on silicon during 1 keV Ar + (part I) and Kr + bombardment at 65° polar angle. Here it is found that the ion-enhanced viscous flow relaxation is essentially equal for Kr + -induced patterning as previously found for Ar + patterning despite the difference in ion masses. However, the magnitude of the surface curvature-dependent roughening rate in the early-stage kinetics is larger for Kr + than for Ar + , consistent with expectations that the heavier ion gives an increased mass redistributive contribution to the initial surface instability. As with the Ar + case, fluctuation dynamics in the late stage show a peak in correlation times at the length scale corresponding to the dominant structural feature on the surface—the ripples. Finally, it is shown that speckle motion during the surface evolution can be analyzed to determine spatial inhomogeneities in erosion rate and ripple velocity. This allows the direction and speed of ripple motion to be measured in a real time experiment. In the present case, ripple motion is found to be into the projected direction of the ion source, in contrast to expectations from an existing sputter erosion driven model with parameters derived from binary collision approximation simulations.

36 MATERIALS SCIENCE↗

Complete β-decay patterns of 142 Cs, 142 Ba, and 142 La determined using total absorption spectroscopy

Background: The β decays of fission products produced in nuclear fuel are important for nuclear energy applications and fundamental science of reactor antineutrinos. In particular, nuclear reactor safety is related to the decay modes of radioactive neutron-rich nuclei, primarily via the emission of γ rays, neutrons, and electrons. Additionally nuclear reactors are the most powerful man-made source of antineutrinos emitted during the β decay of fission products. These antineutrinos are used to inspect fundamental properties of leptons as well as informing reactor operation. However, the majority of data on complex decays of fission products collected in the evaluated nuclear data repositories like Evaluated Nuclear Structure Data File (ENSDF) and Evaluated Nuclear Data Files (ENDF) are based on low-efficiency and often incomplete measurements resulting in questionable reference reactor antineutrino flux predictions, see the analysis by [Nichols, J. Nucl. Sci. Technol. 52, 17 (2015)]. Various assessments like the one done under the auspices of the [Yoshida et al., Assessment of Fission Product Decay Data for Decay Heat Calculations: A report by the Working Party on International Evaluation Co-operation of the Nuclear Energy Agency Nuclear Science Committee (Nuclear Energy Agency, Organization for Economic Co-operation and Development, Paris, France, 2007), Vol. 25], as well as by [Sonzogni, Johnson, and McCutchan, Phys. Rev. C 91, 011301(R) (2015)] and [Dwyer and Langford, Phys. Rev. Lett. 114, 012502 (2015)], list the A = 142 isobars with high cumulative fission yield among the important nuclei where data for reactor decay heat and/or antineutrino production should be verified and/or improved. Purpose: Here, our goal is to improve the quality of β -decay measurements and evaluate the impact of modified decay schemes on reactor decay heat and antineutrino energy spectra, for fission products along the A = 142 isobaric chain. This work is an in depth follow-up on [Rasco et al., Phys. Rev. Lett. 117, 092501 (2016)]. which presented briefly the impact of the corrected decay scheme of 142 Cs . Here, we extend the data to full isobaric decay chain including the daughter nuclei, 142 Ba and 142 La, and present more details on the 142 Cs results. Method: The decays of neutron-rich isobars of mass A = 142 produced by means of proton-induced fission of 238 U were measured using the Modular Total Absorption Spectrometer (MTAS) array on-line at the mass separator and Tandem accelerator at Oak Ridge National Laboratory. Results: The β -decay schemes for 142 Cs and 142 La were modified with respect to the nuclear data repositories. A small β-delayed neutron branching ratio for 142 Cs emitter was remeasured as $0.10^{+5}_{–3}% %. Improved precision on the measured half-lives is reported. Small corrections to the low-energy decay of 142 Ba are made. The β-decay patterns for 142 La and 142 Cs are presented. The decay heat release and cross section for the detection of reactor antineutrinos are deduced and compared to earlier results. Conclusions: The β-feeding pattern for 142 Cs having decay energy value $Q_β$ of over 7 MeV was substantially modified with respect to the current ENSDF entry. Smaller changes were encountered for 142 La, but since this A = 142 isobar also has a large cumulative yield in fission, the changes influence both decay heat and the antineutrino spectra. The previously known β intensities for 142 Ba decay ($Q_β$ value of 2.2 MeV) were verified and slightly modified. Overall, increased decay heat values and lower flux of antineutrinos interacting with matter are presented.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Towards a machine-readable literature: finding relevant papers based on an uploaded powder diffraction pattern

A prototype application for machine-readable literature is investigated. The program is called pyDataRecognition and serves as an example of a data-driven literature search, where the literature search query is an experimental data set provided by the user. The user uploads a powder pattern together with the radiation wavelength. The program compares the user data to a database of existing powder patterns associated with published papers and produces a rank ordered according to their similarity score. The program returns the digital object identifier and full reference of top-ranked papers together with a stack plot of the user data alongside the top-five database entries. The paper describes the approach and explores successes and challenges.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spot pattern welding scanning strategy for sensor embedding and residual stress reduction in laser-foil-printing additive manufacturing

Here, this paper aims to present spot pattern welding (SPW) as a scanning strategy for laser-foil-printing (LFP) additive manufacturing (AM) in place of the previously used continuous pattern welding (CPW) (line-raster scanning). The SPW strategy involves generating a sequence of overlapping spot welds on the metal foil, allowing the laser to form dense and uniform weld beads. This in turn reduces thermal gradients, promotes material consolidation and helps mitigate process-related risks such as thermal cracking, porosity, keyholing and Marangoni effects. 304L stainless steel (SS) feedstock is used to fabricate test specimens using the LFP system. Imaging techniques are used to examine the melt pool dimensions and layer bonding. In addition, the parts are evaluated for residual stresses, mechanical strength and grain size. Compared to CPW, SPW provides a more reliable heating/cooling relationship that is less dependent on part geometry. The overlapping spot welds distribute heat more evenly, minimizing the risk of elevated temperatures during the AM process. In addition, the resulting dense and uniform weld beads contribute to lower residual stresses in the printed part. To the best of the authors’ knowledge, this is the first study to thoroughly investigate SPW as a scanning strategy using the LFP process. In general, SPW presents a promising strategy for securing embedded sensors into LFP parts while minimizing residual stresses.

36 MATERIALS SCIENCE↗

Spaced Orthocyclic Winding Pattern for Improved Die Compressed Coils

Winding fill, coil fill, or packing factor, is critical to the performance of many types of electromagnetic devices from electric machines to actuators, transformers, inductors, etc. One technique to increase the packing of conductors in the winding area is to compress round magnet wire conductors in a die, so that they deform and air voids between coil turns are removed. The winding layout of the coil turns on a bobbin before compression has a direct impact on the achievable coil fill and the damage to the coil insulation or conductors after compression. It is thought that winding the turns in an orthocyclic pattern on the bobbin before compression would minimize damage to the turns. This however causes turns to displace during the winding compression process. A new pre-compression winding pattern is proposed, a spaced orthocyclic winding, to minimize turn displacement and damage. A design of experiments study has been carried out to optimize this winding method and to compare it to the traditional orthocyclic winding.

33 ADVANCED PROPULSION SYSTEMS↗

Analyzing File Access Patterns on Large-Scale HPC Systems: Opportunities for File Prefetching

This paper explores the potential opportunities for implementing file prefetching techniques on large-scale high-performance computing (HPC) systems. Specifically, we investigate the file access patterns of various applications across multiple scientific domains using two years' worth of Darshan I/O traces obtained from the Summit supercomputer. We identify recurring trends and patterns which indicate that prefetching can be effectively leveraged to improve data access performance on HPC systems. This study serves as a valuable reference for system architects and developers in the HPC community, providing insights into the opportunities and challenges associated with enabling file prefetching on large-scale HPC systems.

Karimi, Ahmad Maroof↗

Numerical and Visual Representations of Uncertainty Lead to Different Patterns of Decision Making

Although visualizations are a useful tool for helping people to understand information, they can also have unintended effects on human cognition. This is especially true for uncertain information, which is difficult for people to understand. Prior work has found that different methods of visualizing uncertain information can produce different patterns of decision making from users. However, uncertainty can also be represented via text or numerical information, and few studies have systematically compared these types of representations to visualizations of uncertainty. We present two experiments that compared visual representations of risk (icon arrays) to numerical representations (natural frequencies) in a wildfire evacuation task. Like prior studies, we found that different types of visual cues led to different patterns of decision making. In addition, our comparison of visual and numerical representations of risk found that people were more likely to evacuate when they saw visualizations than when they saw numerical representations. These experiments reinforce the idea that design choices are not neutral: seemingly minor differences in how information is represented can have important impacts on human risk perception and decision making.

97 MATHEMATICS AND COMPUTING↗

A Comparative Study of Straight-Strip and Zigzag-Interleaved Anode Patterns for MPGD Readouts

Due to their simplicity and versatility of design, straight strip or rectangular pad anode structures are frequently employed with micro-pattern gas detectors to reconstruct high precision space points for various tracking applications. The particle impact point is typically determined by interpolating the charge collected by several neighboring strips. However, to effectively extract the inherent positional information, the lateral spacing of the straight strips must be comparable to or preferably smaller than the full extent of the incident charge cloud. In contrast, highly interleaved anode patterns, such as zigzags, can adequately sample the incident charge with a pitch appreciably larger than the charge cloud.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Propagation Pattern for Moment Representation of the Lattice Boltzmann Method

A propagation pattern for the moment representation of the regularized lattice Boltzmann method (LBM) in three dimensions is presented. Using effectively lossless compression, the simulation state is stored as a set of moments of the lattice Boltzmann distribution function, instead of the distribution function itself. An efficient cache-aware propagation pattern for this moment representation has the effect of substantially reducing both the storage and memory bandwidth required for LBM simulations. This article extends recent work with the moment representation by expanding the performance analysis on central processing unit (CPU) architectures, considering how boundary conditions are implemented, and demonstrating the effectiveness of the moment representation on a graphics processing unit (GPU) architecture.

42 ENGINEERING↗

Steelhead ( Oncorhynchus mykiss ) lineages and sexes show variable patterns of association of adult migration timing and age‐at‐maturity traits with two genomic regions

Abstract As life history diversity plays a critical role in supporting the resilience of exploited populations, understanding the genetic basis of those life history variations is important for conservation management. However, effective application requires a robust understanding of the strength and universality of genetic associations. Here, we examine genetic variation of single nucleotide polymorphisms in genomic regions previously associated with migration phenology and age‐at‐maturity in steelhead ( Oncorhynchus mykiss ) from the Columbia River. We found chromosome 28 markers (GREB1L, ROCK1 genes) explained significant variance in migration timing in both coastal and inland steelhead. However, strength of association was much greater in coastal than inland steelhead ( R 2 0.51 vs. 0.08), suggesting that genomic background and challenging inland migration pathways may act to moderate effects of this region. Further, we found that chromosome 25 candidate markers (SIX6 gene) were significantly associated with age and size at first return migration for inland steelhead, and this pattern was mediated by sex in a predictable pattern (males R 2 = 0.139–0.170; females R 2 = 0.096–0.111). While this encourages using these candidate regions in predicting life history characteristics, we suggest that stock‐specific associations and haplotype frequencies will be useful in guiding implementation of genetic assays to inform management.

Willis, Stuart C.↗

Contrasting patterns of sequence variation in steelhead populations reflect distinct evolutionary processes

Abstract Multiple evolutionary processes influence genome‐wide allele frequencies and quantifying effects of genetic drift, and multiple forms of selection remain challenging in natural populations. Here, we investigate variation at major effect loci in contrast to patterns of neutral drift across a wide collection of steelhead ( Oncorhynchus mykiss ) populations that have declined in abundance due to anthropogenic impacts. Whole‐genome resequencing of 74 populations of steelhead revealed genome‐wide patterns (~8 million SNPs) consistent with expected neutral population structure. However, allelic variation at major effect loci associated with adult migration timing (chromosome 28: GREB1L / ROCK1 ) and age at maturity (chromosome 25: SIX6 ) reflected how selection has acted on phenotypic variation in contrast with neutral structure. Variation at major effect loci was influenced by evolutionary processes with differing signals between the strongly divergent Coastal and Inland lineages, while allele frequencies within and among populations within the Inland lineage have been driven by local natural selection as well as recent anthropogenic influences. Recent anthropogenic effects appeared to have influenced the frequency of major effect alleles including artificial selection for specific traits in hatchery stocks with subsequent gene flow into natural populations. Selection from environmental factors at various scales has also likely influenced variation for major effect alleles. These results reveal evolutionary mechanisms that influence allele frequencies at major effect loci that are critical for conservation of phenotypic traits and life history variation of this protected species.

Willis, Stuart↗

Biological mechanisms may contribute to soil carbon saturation patterns

Increasing soil organic carbon (SOC) storage is a key strategy to mitigate rising atmospheric CO 2 , yet SOC pools often appear to saturate, or increase at a declining rate, as carbon (C) inputs increase. Soil C saturation is commonly hypothesized to result from the finite amount of reactive mineral surface area available for retaining SOC, and is accordingly represented in SOC models as a physicochemically determined SOC upper limit. However, mineral-associated SOC is largely microbially generated. In this perspective, we present the hypothesis that apparent SOC saturation patterns could emerge as a result of ecological constraints on microbial biomass—for example, via competition or predation—leading to reduced C flow through microbes and a reduced rate of mineral-associated SOC formation as soil C inputs increase. Microbially explicit SOC models offer an opportunity to explore this hypothesis, yet most of these models predict linear microbial biomass increases with C inputs and insensitivity of SOC to input rates. Synthesis of 54 C addition studies revealed constraints on microbial biomass as C inputs increase. Different hypotheses limiting microbial density were embedded in a three-pool SOC model without explicit limits on mineral surface area. As inputs increased, the model demonstrated either no change, linear, or apparently saturating increases in mineral-associated and particulate SOC pools. Taken together, our results suggest that microbial constraints are common and could lead to reduced mineral-associated SOC formation as input rates increase. We conclude that SOC responses to altered C inputs—or any environmental change—are influenced by the ecological factors that limit microbial populations, allowing for a wider range of potential SOC responses to stimuli. Understanding how biotic versus abiotic factors contribute to these patterns will better enable us to predict and manage soil C dynamics.

54 ENVIRONMENTAL SCIENCES↗

The auxin efflux carrier PIN1a regulates vascular patterning in cereal roots

Barley (Hordeum vulgare) is an important global cereal crop and a model in genetic studies. Despite advances in characterising barley genomic resources, few mutant studies have identified genes controlling root architecture and anatomy, which plays a critical role in capturing soil resources. Our phenotypic screening of a TILLING mutant collection identified line TM5992 exhibiting a short-root phenotype compared with wild-type (WT) Morex background. Outcrossing TM5992 with barley variety Proctor and subsequent SNP array-based bulk segregant analysis, fine mapped the mutation to a cM scale. Exome sequencing pinpointed a mutation in the candidate gene HvPIN1a, further confirming this by analysing independent mutant alleles. Detailed analysis of root growth and anatomy in Hvpin1a mutant alleles exhibited a slower growth rate, shorter apical meristem and striking vascular patterning defects compared to WT. Expression and mutant analyses of PIN1 members in the closely related cereal brachypodium (Brachypodium distachyon) revealed that BdPIN1a and BdPIN1b were redundantly expressed in root vascular tissues but only Bdpin1a mutant allele displayed root vascular defects similar to Hvpin1a. We conclude that barley PIN1 genes have sub-functionalised in cereals, compared to Arabidopsis (Arabidopsis thaliana), where PIN1a sequences control root vascular patterning.

59 BASIC BIOLOGICAL SCIENCES↗