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At least 1,549 records · Page 86

SU-C-17A-02: Sirius MRI Markers for Prostate Post-Implant Assessment: MR Protocol Development

Purpose: Currently, CT is used to visualize prostate brachytherapy sources, at the expense of accurate structure contouring. MRI is superior to CT for anatomical delineation, but the sources appear as voids on MRI images. Previously we have developed Sirius MRI markers (C4 Imaging) to replace spacers to assist source localization on MRI images. Here we develop an MRI pulse sequence protocol that enhances the signal of these markers to enable MRI-only post-implant prostate dosimetric analysis. Methods: To simulate a clinical scenario, a CIRS multi-modality prostate phantom was implanted with 66 markers and 86 sources. The implanted phantom was imaged on both 1.5T and 3.0T GE scanners under various conditions, different pulse sequences (2D fast spin echo [FSE], 3D balanced steadystate free precession [bSSFP] and 3D fast spoiled gradient echo [FSPGR]), as well as varying amount of padding to simulate various patient sizes and associated signal fall-off from the surface coil elements. Standard FSE sequences from the current clinical protocols were also evaluated. Marker visibility, marker size, intra-marker distance, total scan time and artifacts were evaluated for various combinations of echo time, repetition time, flip angle, number of excitations, bandwidth, slice thickness and spacing, fieldof- view, frequency/phase encoding steps and frequency direction. Results: We have developed a 3D FSPGR pulse sequence that enhances marker signal and ensures the integrity of the marker shape while maintaining reasonable scan time. For patients contraindicated for 3.0T, we have also developed a similar sequence for 1.5T scanners. Signal fall-off with distance from prostate to coil can be compensated mainly by decreasing bandwidth. The markers are not visible using standard FSE sequences. FSPGR sequences are more robust for consistent marker visualization as compared to bSSFP sequences. Conclusion: The developed MRI pulse sequence protocol for Sirius MRI markers assists source localization to enable MRIonly post-implant prostate dosimetric analysis. S.J. Frank is a co-founder of C4 Imaging (manufactures the MRI markers)

60 APPLIED LIFE SCIENCES↗

Deep Packet/Flow Analysis using GPUs

Deep packet inspection (DPI) faces severe performance challenges in high-speed networks (40/100 GE) as it requires a large amount of raw computing power and high I/O throughputs. Recently, researchers have tentatively used GPUs to address the above issues and boost the performance of DPI. Typically, DPI applications involve highly complex operations in both per-packet and per-flow data level, often in real-time. The parallel architecture of GPUs fits exceptionally well for per-packet network traffic processing. However, for stateful network protocols such as TCP, their data stream need to be reconstructed in a per-flow level to deliver a consistent content analysis. Since the flow-centric operations are naturally antiparallel and often require large memory space for buffering out-of-sequence packets, they can be problematic for GPUs, whose memory is normally limited to several gigabytes. In this work, we present a highly efficient GPU-based deep packet/flow analysis framework. The proposed design includes a purely GPU-implemented flow tracking and TCP stream reassembly. Instead of buffering and waiting for TCP packets to become in sequence, our framework process the packets in batch and uses a deterministic finite automaton (DFA) with prefix-/suffix- tree method to detect patterns across out-of-sequence packets that happen to be located in different batches. In conclusion, evaluation shows that our code can reassemble and forward tens of millions of packets per second and conduct a stateful signature-based deep packet inspection at 55 Gbit/s using an NVIDIA K40 GPU.

97 MATHEMATICS AND COMPUTING↗

MAGI: A Method for Metabolite Annotation and Gene Integration

Metabolomics is a widely used technology for obtaining direct measures of metabolic activities from diverse biological systems. However, ambiguous metabolite identifications are a common challenge and biochemical interpretation is often limited by incomplete and inaccurate genome-based predictions of enzyme activities (that is, gene annotations). Metabolite Annotation and Gene Integration (MAGI) generates a metabolite-gene association score using a biochemical reaction network. This is calculated by a method that emphasizes consensus between metabolites and genes via biochemical reactions. To demonstrate the potential of this method, we applied MAGI to integrate sequence data and metabolomics data collected from Streptomyces coelicolor A3(2), an extensively characterized bacterium that produces diverse secondary metabolites. Our findings suggest that coupling metabolomics and genomics data by scoring consensus between the two increases the quality of both metabolite identifications and gene annotations in this organism. MAGI also made biochemical predictions for poorly annotated genes that were consistent with the extensive literature on this important organism. Furthermore, this limited analysis suggests that using metabolomics data has the potential to improve annotations in sequenced organisms and also provides testable hypotheses for specific biochemical functions.

59 BASIC BIOLOGICAL SCIENCES↗

Do genome-scale models need exact solvers or clearer standards?

Constraint-based analysis of genome-scale models (GEMs) arose shortly after the first genome sequences became available. As numerous reviews of the field show, this approach and methodology has proven to be successful in studying a wide range of biological phenomena (McCloskey et al, 2013; Bordbar et al, 2014). However, efforts to expand the user base are impeded by hurdles in correctly formulating these problems to obtain numerical solutions. In particular, in a study entitled “An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models” (Chindelevitch et al, 2014), the authors apply an exact solver to 88 genome-scale constraint-based models of metabolism. The authors claim that COBRA calculations (Orth et al, 2010) are inconsistent with their results and that many published and actively used (Lee et al, 2007; McCloskey et al, 2013) genome-scale models do support cellular growth in existing studies only because of numerical errors. They base these broad claims on two observations: (i) three reconstructions ( i AF1260, i IT341, and i NJ661) compute feasibly in COBRA, but are infeasible when exact numerical algorithms are used by their software (entitled MONGOOSE); (ii) linear programs generated by MONGOOSE for i IT341 were submitted to the NEOS Server (a Web site that runs linear programs through various solvers) and gave inconsistent results. They further claim that a large percentage of these COBRA models are actually unable to produce biomass flux. Here, we demonstrate that the claims made by Chindelevitch et al (2014) stem from an incorrect parsing of models from files rather than actual problems with numerical error or COBRA computations.

59 BASIC BIOLOGICAL SCIENCES↗

Sulfono-g-AApeptides as a New Class of Nonnatural Helical Foldamer

Foldamers offer an attractive opportunity for the design of novel molecules that mimic the structures and functions of proteins and enzymes including biocatalysis and biomolecular recognition. Herein we report a new class of nonnatural helical sulfono-g-AApeptide foldamers of varying lengths. The crystal structure of the sulfono-g-AApeptide monomer S6 illustrates the intrinsic folding propensity of sulfono-g-AApeptides, which likely originates from the bulkiness of tertiary sulfonamide moiety. The two-dimensional solution NMR spectroscopy data for the longest sequence S1 demonstrates a 10/16 right-handed helical structure. Optical analysis using circular dichroism further supports welldefined helical conformation of sulfono-g-AApeptides in solution containing as few as five building blocks. Future development of sulfono-g-AApeptides may lead to new foldamers with discrete functions, enabling expanded application in chemical biology and biomedical sciences.

2D NMR spectroscopy↗

Molecular remodeling in Populus PdKOR RNAi roots profiled using LC-MS/MS proteomics

Plant endo-β-1,4-glucanases belonging to the Glycoside Hydrolase Family 9 have functional roles in cell wall biosynthesis and remodeling via endohydrolysis of (1→4)-β-D-glucosidic linkages. Modification of cell wall chemistry via RNAi-mediated downregulation of Populus deltoides KOR1 (PdKOR), a endo-β-1,4-glucanase gene, in Populus deltoides has been shown to have functional consequences for the composition of secondary metabolome and the ability of modified roots to interact with beneficial microbes. The molecular remodeling that underlies the observed differences at metabolic, physiological, and morphological levels in roots is not well understood. Here we used a LC-MS/MS-based proteome profiling approach to survey the molecular remodeling in root tissues of PdKOR and control plants. A total of 14316 peptides were identified and these mapped to 7139 P. deltoides proteins. Based on 90% sequence identity, the measured protein accessions represent 1187 functional protein groups. Analysis of GO categories and specific individual proteins showed differential expression of proteins relevant to plant-microbe interactions, cell wall chemistry, and metabolism. The new proteome dataset serves as a useful resource for deriving new hypotheses and empirical testing pertaining to functional roles of proteins and pathways in differential priming of plant roots to interactions with microbes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Understanding the Performance of Automotive Catalysts via Spatial Resolution of Reactions inside Honeycomb Monoliths

By directly resolving spatial and temporal species distributions within operating honeycomb monolith catalysts, spatially resolved capillary inlet mass spectrometry (SpaciMS) provides a uniquely enabling perspective for advancing automotive catalysis. Specifically, the ability to follow the spatiotemporal evolution of reactions throughout the catalyst is a significant advantage over inlet-and-effluent-limited analysis. Intracatalyst resolution elucidates numerous catalyst details including the network and sequence of reactions, clarifying reaction pathways; the relative rates of different reactions and impacts of operating conditions and catalyst state; and reaction dynamics and intermediate species that exist only within the catalyst. These details provide a better understanding of how the catalyst functions and have basic and practical benefits; e.g., catalyst system design; strategies for on-road catalyst state assessment, control, and on-board diagnostics; and creating robust and accurate predictive catalyst models. Moreover, such spatiotemporally distributed data provide for critical model assessment, and identification of improvement opportunities that might not be apparent from effluent assessment; i.e., while an incorrectly formulated model may provide correct effluent predictions, one that can accurately predict the spatiotemporal evolution of reactions along the catalyst channels will be more robust, accurate, and reliable. In such ways, intracatalyst diagnostics comprehensively enable improved design and development tools, and faster and lower-cost development of more efficient and durable automotive catalyst systems. Beyond these direct contributions, SpaciMS has spawned and been applied to enable other analytical techniques for resolving transient distributed intracatalyst performance. This chapter focuses on SpaciMS applications and associated catalyst insights and improvements, with specific sections related to lean NOx traps, selective catalytic reduction catalysts, oxidation catalysts, and particulate filters. The objective is to promote broader use and development of intracatalyst analytical methods, and thereby expand the insights resulting from this detailed perspective for advancing automotive catalyst technologies.

Partridge Jr, William↗

Characteristics of persistent spin current components in a quasi-periodic Fibonacci ring with spin–orbit interactions: Prediction of spin–orbit coupling and on-site energy

In the present work we investigate the behavior of all three components of persistent spin current in a quasi-periodic Fibonacci ring subjected to Rashba and Dresselhaus spin–orbit interactions. Analogous to persistent charge current in a conducting ring where electrons gain a Berry phase in presence of magnetic flux, spin Berry phase is associated during the motion of electrons in presence of a spin–orbit field which is responsible for the generation of spin current. The interplay between two spin–orbit fields along with quasi-periodic Fibonacci sequence on persistent spin current is described elaborately, and from our analysis, we can estimate the strength of any one of two spin–orbit couplings together with on-site energy, provided the other is known. - Highlights: • Determination of Rashba and Dresselhaus spin–orbit fields is discussed. • Characteristics of all three components of spin current are explored. • Possibility of estimating on-site energy is given. • Results can be generalized to any lattice models.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A PerR-like protein involved in response to oxidative stress in the extreme bacterium Deinococcus radiodurans

Highlights: • We report a novel PerR-like protein of Fur family in D. radiodurans that is not annotated in the current database. • drperR responses to H{sub 2}O{sub 2} and functions as a negative regulator of katE and dps. • We provided implications on how to utilize sequenced genome data and the importance of genome data mining. • This study adds knowledge to complicated regulatory network that responds to ROS stress in D. radiodurans. - Abstract: Response and defense systems against reactive oxygen species (ROS) contribute to the remarkable resistance of Deinococcus radiodurans to oxidative stress induced by oxidants or radiation. However, mechanisms involved in ROS response and defense systems of D. radiodurans are not well understood. Fur family proteins are important in ROS response. Only a single Fur homolog is predicted by sequence similarity in the current D. radiodurans genome database. Our bioinformatics analysis demonstrated an additional guanine nucleotide in the genome of D. radiodurans that is not in the database, leading to the discovery of another Fur homolog DrPerR. Gene disruption mutant of DrPerR showed enhanced resistance to hydrogen peroxide (H{sub 2}O{sub 2}) and increased catalase activity in cell extracts. Real-time PCR results indicated that DrPerR functions as a repressor of the catalase gene katE. Meanwhile, derepression of dps (DNA-binding proteins from starved cells) gene under H{sub 2}O{sub 2} stress by DrPerR point to its regulatory role in metal ions hemostasis. Thus, DrPerR might function as a Fur homolog protein which is involved in ROS response and defense. These results help clarify the complicated regulatory network that responds to ROS stress in D. radiodurans.

60 APPLIED LIFE SCIENCES↗

Nuclear Data Sheets for A=266,270,274,278,282,286,290,294,298☆

Spectroscopic information such as production, identification, half-lives, decay modes and possible excited states for experimentally known nuclides of mass numbers 266, 270, 274, 278, 282, 286, 290, 294, and 298 are presented together with the recommended values, superseding information and data in the previous ENSDF and NDS evaluation by 2005Gu33. No nuclides have yet been identified for A=302. In the last 14 years, large amounts of new and definitive data on the superheavy nuclides (SHN) have become available, thus changing almost entirely the landscape of nuclear data in this mass region, as also indicated by a number of recent review articles: 2017Og01, 2016Ho09, 2016Ho06 (for fission barriers), 2015Og05, 2015Og07, 2015Mo25, 2015OgZX, 2013Th02, and 2011Og07. See 2016Ka49 for IUPAC technical discussions for the discovery of Z=117 (Ts), Z=115 (Mc), Z=113 (Nh), 2001Ka70 and 2003Ka71 for Z=110-112, 2011Ba54 for Z≥113, 2009Ba62 for Z=112, and 2016Ka50 for Z=118 (Og). A special issue of Nuclear Physics A444 (2015) is devoted to research on superheavy elements (SHE) with 27 articles. In particular, see article by 2015Ko20 on mass spectrometric searches for superheavy elements in terrestrial matter. See also Proceedings of Nobel Symposium NS160 ‘Chemistry and Physics of Heavy and Superheavy Elements’ published in Eur. Phys. Jour. Web of Conferences 131 (2016), in particular 2016UtZZ, 2016DmZZ and 2016HoZY. See also 2016DuZX for future prospects of discovery of elements beyond Z=118 A=266: {sup 266}Db, {sup 266}Sg, {sup 266}Bh, {sup 266}Hs and {sup 266}Mt are the experimentally identified nuclides with A=266. Identification of {sup 266}Lr from α decay of {sup 270}Db has been proposed by 2014Kh04 from experiments at GSI, but complete details and analyses of all the four decay chains reported in this experiment have not yet been published, and discussion in 2015Og05 review article considering their work from Dubna (2013Og04, 2011Og04) and from GSI (2014Kh04) still concluded that {sup 270}Db decayed dominantly by SF mode, in contrast with dominant α decay mode proposed by 2014Kh04. Experiments carried out at FLNR-JINR-Dubna in collaboration with LLNL and ORNL, GSI-SHIP facility, RIKEN, and LBNL facilities: {sup 266}Db from the α-decay of {sup 282}Nh in two correlated decay chains at Dubna; {sup 266}Sg as α-daughter of {sup 270}Hs in 12 correlated decay chains at Dubna and GSI; {sup 266}Bh in α decay of {sup 278}Nh in three correlated decay chains observed at RIKEN, and also directly with one event in {sup 249}Bk({sup 22}Ne,5n) at LBNL, and with four events in {sup 243}Am({sup 26}Mg,3n) at HIRFL-Lanzhou; {sup 266}Hs as α-daughter of {sup 270}Ds at GSI in two different experiments, six correlated decays in the first, and 25 decay chains in the second experiment, the analysis of which has not been fully reported as yet; and {sup 266}Mt directly in {sup 209}Bi({sup 58}Fe,n) reaction at GSI in two different experiments, observing three events in the first experiment and 12 events in the second, also produced in {sup 208}Pb({sup 59}Co,n) reaction at LBNL, observing five correlated decay chains. See also 2000Ho27 for discussion on {sup 266}Sg and {sup 266}Mt. A=270: {sup 270}Db, {sup 270}Bh, {sup 270}Hs, {sup 270}Mt and {sup 270}Ds are the experimentally identified nuclides with A=270 are presented. Experiments carried out at FLNR-JINR-Dubna in collaboration with LLNL and ORNL, GSI-SHIP facility, and RIKEN: {sup 270}Db from the decay of {sup 294}Ts in six correlated decay chains at Dubna and GSI; {sup 270}Bh as α great-granddaughter of {sup 282}Nh in two correlated decay chains observed at Dubna; {sup 270}Hs directly in {sup 248}Cm({sup 26}Mg,4n) reaction at GSI, and in {sup 226}Ra({sup 48}Ca,4n) reaction at Dubna; {sup 270}Mt as granddaughter of {sup 278}Ts in three correlated decay chains at RIKEN; and {sup 270}Ds directly in {sup 207}Pb({sup 64}Ni,n) at GSI in 33 correlated decay chains. A=274: {sup 274}Bh, {sup 274}Mt and {sup 274}Rg are the experimentally identified nuclides with A=274. Search for {sup 274}Ds in {sup 238}U({sup 40}Ar, 4n),E=5.7 MeV/nucleon reaction and subsequent α decays at GSI (1990Sc11) proved negative. Experiments carried out at FLNR-JINR-Dubna in collaboration with LLNL and ORNL, GSI-SHIP facility, and RIKEN: {sup 274}Bh from the decay of {sup 294}Ts in six correlated decay chains at Dubna and GSI, {sup 274}Mt produced as α daughter of {sup 282}Nh in two correlated decay chains observed at Dubna, and {sup 274}Rg as α daughter of {sup 278}Nh produced in three correlated decay chains at RIKEN. A=278: {sup 278}Mt, {sup 278}Rg and {sup 278}Nh are the experimentally identified nuclides with A=278. A very tentative evidence is provided for {sup 278}Bh and {sup 278}Hs from a chain originally observed and assigned to {sup 289}Fl by 1999Og10, but later reassigned by 2004Og10 to {sup 290}Fl, and further discussed in detail by 2016Ho09, where, based on systematics of α decays and SF half-lives, {sup 290}Fl is proposed to decay via ε mode to {sup 290}Nh, which then decays by an α chain, ending in {sup 278}Bh that decays by SF mode. Experiments carried out at FLNR-JINR-Dubna in collaboration with LLNL and ORNL labs in the USA, GSI-SHIP facility, and RIKEN: {sup 278}Mt from the decay of {sup 294}Ts in six correlated decay chains at Dubna and GSI, {sup 278}Rg produced as α daughter of {sup 282}Nh in two correlated decay chains observed at Dubna, and {sup 278}Nh produced directly in three correlated decay chains at RIKEN. A=282: {sup 282}Rg, {sup 282}Cn and {sup 282}Nh are the experimentally identified nuclides with A=282. A very tentative evidence is provided for {sup 282}Mt and {sup 282}Ds from a chain originally observed and assigned to {sup 289}Fl by 1999Og10, but later reassigned by 2004Og10 to {sup 290}Fl, and further discussed in detail by 2016Ho09, where, based on systematics of α decays and SF half-lives, {sup 290}Fl is proposed to decay via ε mode to {sup 290}Nh, which then decays by an α chain, ending in {sup 278}Bh that decays by SF mode. Experiments carried out at FLNR-Dubna, in collaboration with LLNL and ORNL labs in the USA, and at GSI-SHIP facility confirm the identification of these isotopes, {sup 282}Rg in α decay chain of {sup 294}Ts in six correlated decay chains at Dubna and GSI, {sup 282}Cn produced in four ways at Dubna: independently in one correlated decay chain, as α daughter of {sup 286}Lv in 11 correlated decay chains, as α grand-daughter of {sup 290}Lv in 12 correlated decay chains, as α great-grand daughter of {sup 294}Og in four correlated decay chains, and {sup 282}Nh produced at Dubna directly in two correlated decay chains. A=286: {sup 286}Nh and {sup 286}Fl are the only experimentally identified nuclides with A=286. A very tentative evidence is provided for {sup 286}Rg and {sup 286}Cn from a chain originally observed and assigned to {sup 289}Fl by 1999Og10, but later reassigned by 2004Og10 to {sup 290}Fl, and further discussed in detail by 2016Ho09, where, based on systematics of α decays and SF half-lives, {sup 290}Fl is proposed to decay via ε mode to {sup 290}Nh, which then decays by an α chain, ending in {sup 278}Bh that decays by SF mode. 2017Ka66 in experiments at RIKEN using GARIS separator interpret one correlated decay chain in three different ways, one involving possible production of {sup 294}Lv in {sup 248}Cm({sup 48}Ca,2n),E=261.6 MeV, and α decay to {sup 290}Fl which further decays to {sup 286}Cn. Experiments carried out at FLNR-Dubna, in collaboration with LLNL and ORNL labs in the USA, and at GSI-SHIP facility confirm the identification of these isotopes, {sup 286}Nh as α grand-daughter of {sup 294}Ts in six correlated decay chains, and {sup 286}Fl produced in three ways: independently in 11 correlated decay chains, as α daughter of {sup 290}Lv in 12 correlated decay chains, and as α grand-daughter of {sup 294}Og in four correlated decay chains. A=290: {sup 290}Mc and {sup 290}Lv are the only experimentally identified nuclides with A=290. A tentative evidence is provided for {sup 290}Nh and {sup 290}Fl from a chain originally observed and assigned to {sup 289}Fl by 1999Og10, but later reassigned by 2004Og10 to {sup 290}Fl, and further discussed in detail by 2016Ho09, where, based on systematics of α decays and SF half-lives, {sup 290}Fl is proposed to decay via ε mode to {sup 290}Nh, which then decays by an α chain, ending in {sup 278}Bh that decays by SF mode. 2017Ka66 in experiments at RIKEN using GARIS separator interpret one correlated decay chain in three different ways, one involving possible production of {sup 294}Lv in {sup 248}Cm({sup 48}Ca,2n),E=261.6 MeV, and α decay to {sup 290}Fl. Experiments carried out at FLNR-Dubna, in collaboration with LLNL and ORNL labs in the USA, and at GSI-SHIP facility confirm the identification of these isotopes, {sup 290}Mc as α daughter of {sup 294}Ts in six correlated decay chains, and {sup 290}Lv produced in two ways, independently in 14 correlated decay chains, and as α daughter of {sup 294}Og in four correlated decay chains. A=294: {sup 294}Ts and {sup 294}Og are the only experimentally identified nuclides with A=294. Experiments carried out at FLNR-Dubna, in collaboration with LLNL and ORNL labs in the USA, and at GSI-SHIP facility confirm the identification of these isotopes, with a total of six EVR-α-SF correlated decay chains observed for {sup 294}Ts and four for {sup 294}Og. Tentative identification of {sup 294}Lv is provided by 2017Ka66 from the observation one correlated event using GARIS-RIKEN facility, where this event is interpreted in three possible ways, two interpretations lead to production of {sup 293}Lv and successive odd-A nuclides of {sup 289}Fl, {sup 285}Cn and {sup 281}Ds, whereas the third prediction starts with the production of {sup 294}Lv and successive {sup 290}Fl and {sup 286}Cn nuclides. Search for {sup 294}Rg in natural gold materials (2011De03), and for {sup 294}Ds, {sup 294}Fl and {sup 294}Mc in natural Pt, Pb and Bi samples (2011De21) using accelerator mass spectroscopy (AMS) proved negative, with extremely low upper limits established. Also 1980St05 did not see any evidence for {sup 294}Ds in natural Pt sample using AMS. A=298: Search for {sup 298}120 through fusion-evaporation reaction at Dubna, and for {sup 298}Fl and {sup 298}Mc in natural Pt, Pb and Bi samples using accelerator mass spectroscopy (AMS) proved negative. Tentative assignment of three α-α-α decay chains by 2016Ho09 to {sup 299}120 in {sup 248}Cm({sup 54}Cr,3n){sup 299}120 at GSI was refuted by 2017He11, assigning these correlations to random events, instead. A=302: Fluorescent x rays from Z=120 element were observed by 2012Fr03 from compound nucleus {sup 302}120 produced in {sup 238}U({sup 64}Ni,X),E=6.6 MeV/nucleon at GANIL, and x-ray yields were measured, together with minimum average time deduced from x-ray multiplicity. The compound nucleus could decay by 3n- or 4n-channels to produce {sup 299}120 or {sup 298}120. 2012He05 and 2016Ho09 also produced {sup 302}120 compound nucleus in {sup 248}Cm({sup 54}Cr, xn){sup 302}120{sup *},E=6.035 MeV/nucleon; and {sup 238}U({sup 64}Ni,xn){sup 302}120{sup *},E=5.53 MeV/nucleon reactions using UNILAC at GSI. Three α-α-α correlated decays from {sup 248}Cm({sup 54}Cr,xn){sup 302}120{sup *} reaction were tentatively assigned by 2016Ho09 to {sup 299}120 decay, however, a detailed analysis by 2017He11 refuted this claim, ascribing these events to random sequences. There are no data tables for A=302.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

RNA language models predict mutations that improve RNA function

Structured RNA lies at the heart of many central biological processes, from gene expression to catalysis. RNA structure prediction is not yet possible due to a lack of high-quality reference data associated with organismal phenotypes that could inform RNA function. We present GARNET (Gtdb Acquired RNa with Environmental Temperatures), a new database for RNA structural and functional analysis anchored to the Genome Taxonomy Database (GTDB). GARNET links RNA sequences to experimental and predicted optimal growth temperatures of GTDB reference organisms. Using GARNET, we develop sequence- and structure-aware RNA generative models, with overlapping triplet tokenization providing optimal encoding for a GPT-like model. Leveraging hyperthermophilic RNAs in GARNET and these RNA generative models, we identify mutations in ribosomal RNA that confer increased thermostability to the Escherichia coli ribosome. The GTDB-derived data and deep learning models presented here provide a foundation for understanding the connections between RNA sequence, structure, and function.

59 BASIC BIOLOGICAL SCIENCES↗

Integral constraints in the study of Richtmyer-Meshkov turbulent mixing

An experimental study of the temporal evolution of the shock-induced Richtmyer-Meshkov instability in the turbulent regime with three-dimensional random interfacial perturbations is carried out. The primary interest is the growth rate of the turbulent mixing layer that develops after an impulsive acceleration of the perturbed interface between two gases (air/SF6) by a weak Ma = 1.2 incident shock wave. Planar Mie scattering is used to visualize the flow, and image sequences are captured using a high-speed video camera. The analysis of the total mixing width has been extended to study the growth behaviors of the bubbles and spikes, separately. A novel definition of the bubble and spike widths is introduced using the mass and linear momentum conservation laws. For the planar incident shock wave the newly defined bubble and spike widths increase in time as hb.s ∝ tθ, with a growth exponent θ = 1/2 that does not depend on either the initial conditions or the physical properties of the gases composing the interface.

Likhachev, Oleg A.↗

Dynamics of implosion, bounce, and re-implosion of a shell directly driven by a time-shaped laser pulse

Gas-filled plastic spherical shells have been imploded using the 60-beam OMEGA laser. The same laser pulse was used as in a previous experiment, which demonstrated the dynamic formation of a shell by irradiating a homogeneous plastic foam sphere. In the present experiment, the shell initially implodes, bounces, and expands; a new shell then forms and undergoes a second implosion. Analysis of x-ray self-emission-streaked images and sequences of 2D x-ray self-emission framing camera images show shell evolution that is in reasonable agreement with 1D simulations. Shell integrity and symmetry are well maintained until the formation of the new shell. The final implosion, instead, is affected by substantial asymmetries.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Recent Studies on the Asymptotic Convergence of the Spatial Discretization for Two-Dimensional Discrete Ordinates Solutions

In this paper, four types of quadrature schemes are used to define discrete directions in the solution of a two-dimensional fixed-source discrete ordinates problem in Cartesian geometry. Such schemes enable generating numerical results for averaged scalar fluxes over specified regions of the domain with high number (up to 105) of directions per octant. Two different nodal approaches, the ADO and AHOT-N0 methods, are utilized to obtain the numerical results of interest. The AHOT-N0 solutions on a sequence of refined meshes are then used to develop an asymptotic analysis of the spatial discretization error in order to derive a reference solution. It was more clearly observed that the spatial discretization error converges asymptotically with second order for the source region with all four quadratures employed, while for the other regions refined meshes along with tighter convergence criterion must be applied to evidence the same behavior. Although, in that case, some differences among the four quadrature schemes results were found.

97 MATHEMATICS AND COMPUTING↗

Model-based data center cooling controls comparative co-design

This article presents a comparative simulation-based control logic design process. It uses the Control Description Language (CDL) and the ASHRAE Guideline 36 high-performing building control sequences with the Modelica Buildings Library (MBL) to demonstrate a comparative analysis of two control designs for a data center chilled water plant. Details include a description of the closed-loop plant and control design methodology, including sizing and parameterization, base and alternative (Guideline 36) control logic with software implementation structure, and outline of the simulation experimentation process. The selected control designs are paired with comparable chilled water plant configurations. The models include a chiller, a water-side economizer, and an evaporative cooling tower. The plant provides cooling at 27ºC zone supply air temperature to a data center in Sacramento, CA. The comparative simulation results examined the impacts of a selected control logic detail, and present an example model-based design application. Overall, the simulation results showed a 25% annual and a 18% summer energy use reduction for alternative controls. This shows that simulation-based control logic design performance evaluation can improve energy efficiency and resilience aspects of system controls at large.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Characterization and Improvement of RNA-Seq Precision in Quantitative Transcript Expression Profiling

Measurement precision determines the power of any analysis to reliably identify significant signals, such as in screens for differential expression, independent of whether the experimental design incorporates replicates or not. With the compilation of large scale RNA-Seq data sets with technical replicate samples, however, we can now, for the first time, perform a systematic analysis of the precision of expression level estimates from massively parallel sequencing technology. This then allows considerations for its improvement by computational or experimental means. Results: We report on a comprehensive study of target coverage and measurement precision, including their dependence on transcript expression levels, read depth and other parameters. In particular, an impressive target coverage of 84% of the estimated true transcript population could be achieved with 331 million 50 bp reads, with diminishing returns from longer read lengths and even less gains from increased sequencing depths. Most of the measurement power (75%) is spent on only 7% of the known transcriptome, however, making less strongly expressed transcripts harder to measure. Consequently, less than 30% of all transcripts could be quantified reliably with a relative error < 20%. Based on established tools, we then introduce a new approach for mapping and analyzing sequencing reads that yields substantially improved performance in gene expression profiling, increasing the number of transcripts that can reliably be quantified to over 40%. Extrapolations to higher sequencing depths highlight the need for efficient complementary steps. In discussion we outline possible experimental and computational strategies for further improvements in quantification precision.

59 BASIC BIOLOGICAL SCIENCES↗

Ebolavirus comparative genomics

The 2014 Ebola outbreak in West Africa is the largest documented for this virus. We examine the dynamics of this genome, comparing more than one hundred currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms a distinct group from all other sequenced viral genomes. All filovirus genomes sequenced to date encode proteins with similar functions and gene order, although there is considerable divergence in sequences between the three genera Ebolavirus, Cuevavirus, and Marburgvirus within the family Filoviridae. Whereas all ebolavirus genomes are quite similar (multiple sequences of the same strain are often identical), variation is most common in the intergenic regions and within specific areas of the genes encoding the glycoprotein (GP), nucleoprotein (NP), and polymerase (L). We predict regions that could contain epitope-binding sites, which might be good vaccine targets. In conclusion, this information, combined with glycosylation sites and experimentally determined epitopes, can identify the most promising regions for the development of therapeutic strategies.

59 BASIC BIOLOGICAL SCIENCES↗

Annotated genome sequence of a fast-growing diploid clone of red alder ( Alnus rubra Bong.)

Abstract Red alder (Alnus rubra Bong.) is an ecologically significant and important fast-growing commercial tree species native to western coastal and riparian regions of North America, having highly desirable wood, pigment, and medicinal properties. We have sequenced the genome of a rapidly growing clone. The assembly is nearly complete, containing the full complement of expected genes. This supports our objectives of identifying and studying genes and pathways involved in nitrogen-fixing symbiosis and those related to secondary metabolites that underlie red alder's many interesting defense, pigmentation, and wood quality traits. We established that this clone is most likely diploid and identified a set of SNPs that will have utility in future breeding and selection endeavors, as well as in ongoing population studies. We have added a well-characterized genome to others from the order Fagales. In particular, it improves significantly upon the only other published alder genome sequence, that of Alnus glutinosa. Our work initiated a detailed comparative analysis of members of the order Fagales and established some similarities with previous reports in this clade, suggesting a biased retention of certain gene functions in the vestiges of an ancient genome duplication when compared with more recent tandem duplications.

59 BASIC BIOLOGICAL SCIENCES↗