Computational design of mixed chirality peptide macrocycles with internal symmetry
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Mulligan, Vikram Khipple↗
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Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria
Armillaria species are both devastating forest pathogens and some of the largest terrestrial organisms on Earth. They forage for hosts and achieve immense colony sizes via rhizomorphs, root-like multicellular structures of clonal dispersal. Here, we sequenced and analysed the genomes of four Armillaria species and performed RNA sequencing and quantitative proteomic analysis on the invasive and reproductive developmental stages of A. ostoyae. Comparison with 22 related fungi revealed a significant genome expansion in Armillaria, affecting several pathogenicity-related genes, lignocellulose-degrading enzymes and lineage-specific genes expressed during rhizomorph development. Rhizomorphs express an evolutionarily young transcriptome that shares features with the transcriptomes of both fruiting bodies and vegetative mycelia. Several genes show concomitant upregulation in rhizomorphs and fruiting bodies and share cis-regulatory signatures in their promoters, providing genetic and regulatory insights into complex multicellularity in fungi. Our results suggest that the evolution of the unique dispersal and pathogenicity mechanisms of Armillaria might have drawn upon ancestral genetic toolkits for wood-decay, morphogenesis and complex multicellularity.
59 BASIC BIOLOGICAL SCIENCES↗
Agulhas Current Properties Shape Microbial Community Diversity and Potential Functionality
Understanding the impact of oceanographic features on marine microbial ecosystems remains a major ecological endeavour. Here we assess microbial diversity, community structure and functional capacity along the Agulhas current system and the Subtropical convergence in the South Indian Ocean (SIO). Samples collected from the epipelagic, oxygen minimum and bathypelagic zones were analysed by 16S rRNA gene amplicon and metagenomic sequencing. In contrast to previous studies, we found high taxonomic richness in surface and deep water samples, but generally low richness for oxygen minimum zone communities. Beta-diversity analysis revealed significant dissimilarity between the three water depths. Most microbial communities were dominated by marine Gammaproteobacteria, with strikingly low levels of picocyanobacteria. Community composition was strongly influenced by specific environmental factors including depth, salinity, and the availability of both oxygen and light. Carbon, nitrogen and sulphur cycling capacity is the SIO was linked to several autotrophic and copiotrophic Alphaproteobacteria and Gammaproteobacteria. Taken together, our data suggest that the environmental conditions in the Agulhas current system, particularly depth-related parameters, substantially influence microbial community structure. While the capacity for biogeochemical cycling of nitrogen and sulphur is linked primarily by the dominant Gammaproteobacterial taxa, ecologically rare taxa drive carbon cycling.
59 BASIC BIOLOGICAL SCIENCES↗
The MG-RAST Metagenomics Database and Portal in 2015
MG-RAST (http://metagenomics.anl.gov) is an opensubmission data portal for processing, analyzing, sharing and disseminating metagenomic datasets. Currently, the system hosts over 200 000 datasets and is continuously updated. The volume of submissions has increased 4-fold over the past 24 months, now averaging 4 terabasepairs per month. In addition to several new features, we report changes to the analysis workflow and the technologies used to scale the pipeline up to the required throughput levels. Lastly, to show possible uses for the data from MG-RAST, we present several examples integrating data and analyses from MG-RAST into popular third-party analysis tools or sequence alignment tools.
96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
Dimensionality Reduction of SDSS Spectra with Variational Autoencoders
High-resolution galaxy spectra contain much information about galactic physics, but the high dimensionality of these spectra makes it difficult to fully utilize the information they contain. We apply variational autoencoders (VAEs), a nonlinear dimensionality reduction technique, to a sample of spectra from the Sloan Digital Sky Survey (SDSS). In contrast to principal component analysis (PCA), a widely used technique, VAEs can capture nonlinear relationships between latent parameters and the data. We find that a VAE can reconstruct the SDSS spectra well with only six latent parameters, outperforming PCA with the same number of components. Different galaxy classes are naturally separated in this latent space, without class labels having been given to the VAE. The VAE latent space is interpretable because the VAE can be used to make synthetic spectra at any point in latent space. For example, making synthetic spectra along tracks in latent space yields sequences of realistic spectra that interpolate between two different types of galaxies. Using the latent space to find outliers may yield interesting spectra: in our small sample, we immediately find unusual data artifacts and stars misclassified as galaxies. In this exploratory work, we show that VAEs create compact, interpretable latent spaces that capture nonlinear features of the data. While a VAE takes substantial time to train (≈1 day for 48,000 spectra), once trained, VAEs can enable the fast exploration of large astronomical data sets.
79 ASTRONOMY AND ASTROPHYSICS↗
Imbrian-age highland volcanism on the moon - The Gruithuisen and Mairan domes
The Gruithuisen and Mairan domes on the moon represent morphologically and spectrally distinct nonmare extrusive volcanic features of Imbrian age. The composition, morphology, and age relationships of the domes indicate that nonmare extrusive volcanism in the northern Procellarum region of the moon continued until about 3.3 x 10 to the 9th to 3.6 x 10 to the 9th years ago and was partially contemporaneous with the emplacement of the main sequence of mare deposits.
Head, J. W., III↗
A manufacturer's approach to ensure long term structural integrity
In the present paper we are as a manufacturer of airliners, certified according to the FAR 25 regulations, describing what considerations in terms of design, sizing, verification, maintenance, etc., that are essential to ensure long term structural integrity. In the first part we are describing the main features of the design concepts of Saab 340 and Saab 2000 aircraft with respect to structural integrity and high reliability. Secondly we are describing the approach we have adopted at Saab Aircraft to ensure structural integrity and high reliability of Saab Aircraft products. We are describing the concepts of global and local loads and sequences, the fatigue and damage tolerance sizing and its verification. We are also describing the quality assurance in production and the structural maintenance programme according to the MSG-3. Structural repair and feedback from operators are also covered.
Aging Aircraft↗
Spacecraft Modeling, Attitude Determination, and Control: Quaternion-Based Approach
Spacecraft attitude determination and control is an important part of a spacecraft to achieve its designed mission. As of today, many spacecrafts have been successfully launched, and most of them have performed well as they were designed. Many research papers have been published to address the attitude determination and control design problems. Several text books are available for students to learn the technology and for engineers to use as references. The most popular spacecraft models for attitude determination algorithms and control design methods are the Euler angle models and the quaternion models . The Euler angle models have been proved very efficient as the linearized models are controllable, and all standard linear control system design methods are directly applicable. The drawbacks related to the Euler angle methods are (a) the designs based on linearized models may not globally stabilize the original nonlinear spacecraft, i.e., the design may not work when the attitude of the spacecraft is far away from the point where the linearization is performed; (b) the models depend on the rotational sequences, this can be error prone if several teams work on the same project and they use different rotational sequences; (c) for any rotational sequence, there is a singular point where the model is not applicable; and (d) since most attitude determination methods use quaternion to represent the spacecraft attitude, there is a need to transform quaternion into Euler angles. On the other hand, for quaternion models, people have found controllers that can globally stabilize nonlinear spacecraft systems; the models do not depend on rotational sequences and they have no singular point; and the quaternion is provided by attitude determination system and ready to use. The main problem with the quaternion model based control system design is that the linearized quaternion model is not controllable. Therefore, most published design methods heavily rely on Lyapunov functions for the nonlinear spacecraft system. But there is no systematic way to obtain a desired Lyapunov functions. Moreover, the Lyapunov function based designs focus on the closed-loop system stability but pay little attention to the closed-loop system performance. In a series of papers, the author proposed some reduced quaternion models which lead to some controllable linearized spacecraft models. Therefore, all standard linear system theory can be directly applied to analyze and design the spacecraft control systems. We showed that, in some cases, the designed control system is not only optimal for the linearized system, but also globally stabilize the original nonlinear system . Clearly, the reduced quaternion models do not depend on rotational sequences. Due to the special structure of the linearized spacecraft model, some most important design methods, such as LQR design and robust pole assignment design are very simple, enjoy the analytical solutions for some problems, have direct connection to the performance measures, such as settling time, rising time , and percentage of overshoot . All these features are attractive for high quality control system designs. The idea mentioned above is then extended to more spacecraft control problems using specific actuators such as magnetic torque bars and control momentum gyroscopes. These types of actuators may not provide exactly desired torques. Most existing methods use different conversions to get approximate solutions, meaning that these actuators may generate a torque close to but not equal to the desired one. Using the reduced quaternion models that incorporate the actuators into the system model, the control inputs are not torques but the operational parameters. The main benefit of this idea is that the control actions are not approximate but accurate. As all actuators have their operational limit, design with input constraints are also considered in this book by using recently developed interior-point optimization techniques. This book grows up from my research on the spacecraft attitude determination and control design methods in more than a decade which is focused on using reduced quaternion models because of their merits stated above. The book provides all necessary background materials on orbital dynamics, rotations and quaternion, frequently used reference frames, transformations between reference frames, space environment and disturbance torques, ephemeris astronomical vector calculations and measurement instruments, spacecraft control actuators and their models, so that the readers will get a global picture and can apply all these information into the spacecraft system modeling, attitude determination, and spacecraft control system designs, which is the main purpose of this book. This book is different from existing books in that we focus on quaternion based spacecraft control system designs and we consider only attitude control system design related problems, from spacecraft modeling, to attitude determination and estimation, to control system design method selection, to control algorithm development, and to the simulation of the control system designs. Moreover, this book addresses different attitude control tasks in the spacecraft life cycle, including spacecraft maneuver, orbit raising, attitude control, and rendezvous. Finally, this book emphasizes the state space design methods rather than the classical frequency design methods.
Attitude determination and control↗
DL-TODA: A Deep Learning Tool for Omics Data Analysis
Metagenomics is a technique for genome-wide profiling of microbiomes; this technique generates billions of DNA sequences called reads. Given the multiplication of metagenomic projects, computational tools are necessary to enable the efficient and accurate classification of metagenomic reads without needing to construct a reference database. The program DL-TODA presented here aims to classify metagenomic reads using a deep learning model trained on over 3000 bacterial species. A convolutional neural network architecture originally designed for computer vision was applied for the modeling of species-specific features. Using synthetic testing data simulated with 2454 genomes from 639 species, DL-TODA was shown to classify nearly 75% of the reads with high confidence. The classification accuracy of DL-TODA was over 0.98 at taxonomic ranks above the genus level, making it comparable with Kraken2 and Centrifuge, two state-of-the-art taxonomic classification tools. DL-TODA also achieved an accuracy of 0.97 at the species level, which is higher than 0.93 by Kraken2 and 0.85 by Centrifuge on the same test set. Application of DL-TODA to the human oral and cropland soil metagenomes further demonstrated its use in analyzing microbiomes from diverse environments. Compared to Centrifuge and Kraken2, DL-TODA predicted distinct relative abundance rankings and is less biased toward a single taxon.
59 BASIC BIOLOGICAL SCIENCES↗
First-Principles Molecular Dynamics of Monomethylhydrazine and Nitrogen Dioxide
The exploration of chemical reactions preceding ignition is essential for the development of ideal hypergolic propellants. Unexpected reaction pathways of a hypergolic mixture composed of monomethylhydrazine and nitrogen dioxide are predicted through a cooperative combination of (i) spin-unrestricted ab initio molecular dynamics (AIMD) and (ii) wave packet dynamics of protons. Ensembles of AIMD trajectories reveal a sequence of reaction steps for proton transfer and rupture of the C–N bond. The details of proton transfer are explored by wave packet dynamics on the basis of ab initio potential energy surfaces from AIMD trajectories. Finally, the possibility of spontaneous ignition of this hypergolic mixture at room temperature is predicted as a quantized feature of proton-transfer dynamics.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Microtopography Matters: Belowground CH 4 Cycling Regulated by Differing Microbial Processes in Peatland Hummocks and Lawns
Water table depth and vegetation are key controls of methane (CH 4 ) emissions from peatlands. Microtopography integrates these factors into features called microforms. Microforms often differ in CH 4 emissions, but microform-dependent patterns of belowground CH 4 cycling remain less clearly resolved. Here, to investigate the impact of microtopography on belowground CH 4 cycling, we characterized depth profiles of the community composition and activity of CH 4 -cycling microbes using 16S rRNA amplicon sequencing, incubations, and measurements of porewater CH 4 concentration and isotopic composition from hummocks and lawns at Sallie's Fen in NH, USA. Geochemical proxies of methanogenesis and methanotrophy indicated that microforms differ in dominant microbial CH 4 cycling processes. Hummocks, where water table depth is lower, had higher porewater redox potential (Eh) and higher porewater δ 13 C-CH 4 values in the upper 30 cm than lawns, where water table depth is closer to the peat surface. Porewater δ 13 C-CH 4 and δD-CH 3 D values were highest at the surface of hummocks where the ratio of methanotrophs to methanogens was also greatest. These results suggest that belowground CH 4 cycling in hummocks is more strongly regulated by methanotrophy, while in lawns methanogenesis is more dominant. We also investigated controls of porewater CH 4 chemistry. The ratio of the relative abundance of methanotrophs to methanogens was the strongest predictor of porewater CH 4 concentration and δ 13 C-CH 4 , while vegetation composition had minimal influence. As microbial community composition was strongly influenced by redox conditions but not vegetation, we conclude that water table depth is a stronger control of belowground CH 4 cycling across microforms than vegetation.
59 BASIC BIOLOGICAL SCIENCES↗
Clusters have edges: the projected phase-space structure of SDSS redMaPPer clusters
ABSTRACT We study the distribution of line-of-sight velocities of galaxies in the vicinity of Sloan Digital Sky Survey (SDSS) red-sequence Matched-filter Probabilistic Percolation (redMaPPer) galaxy clusters. Based on their velocities, galaxies can be split into two categories: galaxies that are dynamically associated with the cluster, and random line-of-sight projections. Both the fraction of galaxies associated with the galaxy clusters, and the velocity dispersion of the same, exhibit a sharp feature as a function of radius. The feature occurs at a radial scale Redge ≈ 2.2Rλ, where Rλ is the cluster radius assigned by redMaPPer. We refer to Redge as the ‘edge radius’. These results are naturally explained by a model that further splits the galaxies dynamically associated with a galaxy cluster into a component of galaxies orbiting the halo and an infalling galaxy component. The edge radius Redge constitutes a true ‘cluster edge’, in the sense that no orbiting structures exist past this radius. A companion paper tests whether the ‘halo edge’ hypothesis holds when investigating the full three-dimensional phase-space distribution of dark matter substructures in numerical simulations, and demonstrates that this radius coincides with a suitably defined splashback radius.
79 ASTRONOMY AND ASTROPHYSICS↗
Profiles of upcoming HPC Applications and their Impact on Reservation Strategies
With the expected convergence between HPC, BigData and AI, new applications with different profiles are coming to HPC infrastructures. Here, we aim at better understanding the features and needs of these applications in order to be able to run them efficiently on HPC platforms. The approach followed is bottom-up: we study thoroughly an emerging application from the neuroscience community (SLANT) to understand its behavior. Based on these observations, we derive a generic, yet simple, application model (namely, a linear sequence of stochastic jobs). We expect this model to be representative for a large set of upcoming applications that require the computational power of HPC clusters without fitting the typical behavior of large-scale traditional applications. In a second step, we show how one can manipulate this generic model in a scheduling framework. Specifically we consider the problem of making reservations (both time and memory) for an execution on an HPC platform. We derive solutions using the model of the first step of this work. We experimentally show the robustness of the model, even with very few data or with another application, to generate the model, and provide performance gains with regards to standard and more recent approaches used in the neuroscience community.
97 MATHEMATICS AND COMPUTING↗
Accuracy of UTE-MRI-based patient setup for brain cancer radiation therapy
Purpose: Radiation therapy simulations solely based on MRI have advantages compared to CT-based approaches. One feature readily available from computed tomography (CT) that would need to be reproduced with MR is the ability to compute digitally reconstructed radiographs (DRRs) for comparison against on-board radiographs commonly used for patient positioning. In this study, the authors generate MR-based bone images using a single ultrashort echo time (UTE) pulse sequence and quantify their 3D and 2D image registration accuracy to CT and radiographic images for treatments in the cranium. Methods: Seven brain cancer patients were scanned at 1.5 T using a radial UTE sequence. The sequence acquired two images at two different echo times. The two images were processed using an in-house software to generate the UTE bone images. The resultant bone images were rigidly registered to simulation CT data and the registration error was determined using manually annotated landmarks as references. DRRs were created based on UTE-MRI and registered to simulated on-board images (OBIs) and actual clinical 2D oblique images from ExacTrac™. Results: UTE-MRI resulted in well visualized cranial, facial, and vertebral bones that quantitatively matched the bones in the CT images with geometric measurement errors of less than 1 mm. The registration error between DRRs generated from 3D UTE-MRI and the simulated 2D OBIs or the clinical oblique x-ray images was also less than 1 mm for all patients. Conclusions: UTE-MRI-based DRRs appear to be promising for daily patient setup of brain cancer radiotherapy with kV on-board imaging.
61 RADIATION PROTECTION AND DOSIMETRY↗
Genetic stability of foot-and-mouth disease virus during long-term infections in natural hosts
Foot-and-mouth disease (FMD) is a severe infection caused by a picornavirus that affects livestock and wildlife. Persistence in ruminants is a well-documented feature of Foot-andmouth disease virus (FMDV) pathogenesis and a major concern for disease control. Persistently infected animals harbor virus for extended periods, providing a unique opportunity to study within-host virus evolution. This study investigated the genetic dynamics of FMDV during persistent infections of naturally infected Asian buffalo. Using next-generation sequencing (NGS) we obtained 21 near complete FMDV genome sequences from 12 sub-clinically infected buffalo over a period of one year. Four animals yielded only one virus isolate and one yielded two isolates of different serotype suggesting a serial infection. Seven persistently infected animals yielded more than one virus of the same serotype showing a longterm intra-host viral genetic divergence at the consensus level of less than 2.5%. Quasi-species analysis showed few nucleotide variants and non-synonymous substitutions of progeny virus despite intra-host persistence of up to 152 days. Phylogenetic analyses of serotype Asia-1 VP1 sequences clustered all viruses from persistent animals with Group VII viruses circulating in Pakistan in 2011, but distinct from those circulating on 2008–2009. Furthermore, signature amino acid (aa) substitutions were found in the antigenically relevant VP1 of persistent viruses compared with viruses from 2008–2009. Intra-host purifying selective pressure was observed, with few codons in structural proteins undergoing positive selection. However, FMD persistent viruses did not show a clear pattern of antigenic selection. Our findings provide insight into the evolutionary dynamics of FMDV populations within naturally occurring subclinical and persistent infections that may have implications to vaccination strategies in the region.
60 APPLIED LIFE SCIENCES↗
Using Stage Level Microseismic Analysis to Gain Insight into Fracture Efficiency and Completion Effectiveness
Microseismic event density heat maps at sequential time intervals during the treatment of individual completion stages have been developed to better understand fracture behavior on a stage level. Animating these heat maps through time on a single stage provides fascinating visual insights into the dynamic sequencing of populations of events, event timing and their likely genesis, providing a new way of visualizing and interpreting microseismic data sets. This technique leverages heat-map benefits from URTEC 2674376, excluding microseismic event clusters that may obscure or skew statistical analysis of the event densities, thus allowing for more accurate assessment of geologic features, stimulated rock volume, near-field concentration of events due to varying cluster spacing, fracture efficiency and stress shadowing. Far-field microseismic events prior to ramp up of treatment pressure are clearly indicated from this technique that cannot be observed with standard heat maps with certain completion designs. Unambiguous changes in microseismic event character from these far-field pre-ramp up events to those near-field events occurring at the onset of pressure are also observed. Applying a stage by stage approach on packages of wells and different locations provides robust statistical conclusions pertaining to reservoir behavior during well completion.
Wang, Iris↗
The Voyager spacecraft /James Watt International Gold Medal Lecture/
The Voyager Project background is reviewed with emphasis on selected features of the Voyager spacecraft. Investigations by the Thermo-electric Outer Planets Spacecraft Project are discussed, including trajectories, design requirements, and the development of a Self Test and Repair computer, and a Computer Accessed Telemetry System. The design and configuration of the spacecraft are described, including long range communications, attitude control, solar independent power, sequencing and control data handling, and spacecraft propulsion. The development program, maintained by JPL, experienced a variety of problems such as design deficiencies, and process control and manufacturing problems. Finally, the spacecraft encounter with Jupiter is discussed, and expectations for the Saturn encounter are expressed.
Heacock, R. L.↗
Zonal motion and structure in Jupiter's upper troposphere from Voyager infrared and imaging observations
Global digital maps of Jupiter's upper-tropospheric temperature have been generated at the 270- and 150-mb pressure levels, together with IR cloud optical depths at 5 and 45 microns and the ammonia abundance near the 680-mb pressure level, on the basis of Voyager IRIS north-south mapping sequences. Attention is given to the 270-mb and 45 micron data; global digital maps are presented for violet and orange reflectivities. The dominant upper tropospheric thermal structures move at a rate far different from that of the cloud indicators, and are noted to remain stationary relative to the planet's bulk rotation. Strong stationary features are found at a zonal wavenumber of 9 near 15 deg N latitude and of 11 near 20 deg latitude.
Magalhaes, Julio A.↗