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At least 415 records · Page 23

Murine hematopoietic stem cell dormancy controlled by induction of a novel short form of PSF1 by histone deacetylase inhibitors

Hematopoietic stem cells (HSCs) can survive long-term in a state of dormancy. Little is known about how histone deacetylase inhibitors (HDACi) affect HSC kinetics. Here, we use trichostatin A (TSA), a histone deacetylase inhibitor, to enforce histone acetylation and show that this suppresses cell cycle entry by dormant HSCs. Previously, we found that haploinsufficiency of PSF1, a DNA replication factor, led to attenuation of the bone marrow (BM) HSC pool size and lack of acute proliferation after 5-FU ablation. Because PSF1 protein is present in CD34{sup +} transiently amplifying HSCs but not in CD34{sup −} long-term reconstituting-HSCs which are resting in a dormant state, we analyzed the relationship between dormancy and PSF1 expression, and how a histone deacetylase inhibitor affects this. We found that CD34{sup +} HSCs produce long functional PSF1 (PSF1a) but CD34{sup −} HSCs produce a shorter possibly non-functional PSF1 (PSF1b, c, dominantly PSF1c). Using PSF1a-overexpressing NIH-3T3 cells in which the endogenous PSF1 promoter is suppressed, we found that TSA treatment promotes production of the shorter form of PSF1 possibly by inducing recruitment of E2F family factors upstream of the PSF1 transcription start site. Our data document one mechanism by which histone deacetylase inhibitors affect the dormancy of HSCs by regulating the DNA replication factor PSF1. - Highlights: • Hematopoetic stem cell dormancy is controlled by histone deacetylation inhibitors. • Dormancy of HSCs is associated with a shorter form of non-functional PSF1. • Histone deacetylase inhibitors suppress PSF1 promoter activity.

60 APPLIED LIFE SCIENCES↗

Equilibrated Gas and Carbonate Standard‐Derived Dual (Δ 47 and Δ 48 ) Clumped Isotope Values

Abstract Carbonate clumped isotope geochemistry has primarily focused on mass spectrometric determination of m/z 47 CO 2 for geothermometry, but theoretical calculations and recent experiments indicate paired analysis of the m/z 47 ( 13 C 18 O 16 O) and m/z 48 ( 12 C 18 O 18 O) isotopologues (referred to as Δ 47 and Δ 48 ) can be used to study non‐equilibrium isotope fractionations and refine temperature estimates. We utilize 5,448 Δ 47 and 3,400 Δ 48 replicate measurements of carbonate samples and standards, and 183 Δ 47 and 195 Δ 48 replicate measurements of gas standards from 2015 to 2021 from a multi‐year and multi‐instrument data set to constrain Δ 47 and Δ 48 values for 27 samples and standards, including Devils Hole cave calcite, and study equilibrium Δ 47 ‐Δ 48 , Δ 47 ‐temperature, and Δ 48 ‐temperature relationships. We compare results to previously published findings and calculate equilibrium regressions based on data from multiple laboratories. We report acid digestion fractionation factors, Δ* 63‐47 and Δ* 64‐48 , and account for their dependence on the initial clumped isotope values of the mineral.

58 GEOSCIENCES↗

Genetic control of photoprotection and photosystem II operating efficiency in plants

Summary Photoprotection against excess light via nonphotochemical quenching (NPQ) is indispensable for plant survival. However, slow NPQ relaxation under low light conditions can decrease yield of field‐grown crops up to 40%. Using semi‐high‐throughput assay, we quantified the kinetics of NPQ and photosystem II operating efficiency (ΦPSII) in a replicated field trial of more than 700 maize ( Zea mays ) genotypes across 2 yr. Parametrized kinetics data were used to conduct genome‐wide association studies. For six candidate genes involved in NPQ and ΦPSII kinetics in maize the loss of function alleles of orthologous genes in Arabidopsis ( Arabidopsis thaliana ) were characterized: two thioredoxin genes, and genes encoding a transporter in the chloroplast envelope, an initiator of chloroplast movement, a putative regulator of cell elongation and stomatal patterning, and a protein involved in plant energy homeostasis. Since maize and Arabidopsis are distantly related, we propose that genes involved in photoprotection and PSII function are conserved across vascular plants. The genes and naturally occurring functional alleles identified here considerably expand the toolbox to achieving a sustainable increase in crop productivity.

59 BASIC BIOLOGICAL SCIENCES↗

Scalable Linked Dynamic Equilibrium (SLiDE)

SLiDE (Scalable Linked Dynamic Equilibrium) replicates the blueNOTE (National Open source Tools for general Equilibrium analysis) datastream from the Wisconsin National Data Consortium. From there, it produces a recursive dynamic computable general equilibrium model of the US states and eventually the global/national economies. The datastream operations have been set up to allow for scalability of both regions and sectors represented. The model has the capability to flexibly define functional forms similar to other general equilibrium model construction software.

Hughes, Caroline↗

KBase Narrative - Supplemental Data for "Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes"

Here we provide the complete set of circular elements produced by SCAPP from metagenomic data that may represent mobile genetic elements (MGEs). For the publication, these sequences were de-replicated within the high [U] and low [U] sample sets. Additionally, 98 of the circular elements were removed for downstream analysis due to high suspicion of being (1) chloroplast or mitochondrial sequences or (2) erroneously circularized long repeat regions. The complete list of circular elements used for the analysis along with metadata can be found in Tables S5 and S6.

Goff, Jennifer↗

Utilization of GIS technology to support development of flow and contaminant fate and transport models at US DOE sites - 15457

U.S. Department of Energy (DOE) sites have accumulated years of data and millions of spatial and temporal records related to the hydrological cycle, contaminant transport, and parameters of remediation technologies. In addition, numerical models which use field monitoring data to help understand flow and transport produce gigabytes of computed spatial and temporal data for each computation node. There is a need therefore for an advanced spatial data structure that can be used to address the management, processing, and analysis of spatial and temporal numerical modeling data derived from multiple sources. This can be accomplished using a geo-database. The development of an ArcSDE geo-database facilitates the centralized storage, backup, accessibility, organization, and management of model configuration and computed simulation data, putting it into a structured, coherent, and logical computer-supported system. GIS data processing and automation would enable faster and hence more complex analyses of field test data. The Applied Research Center (ARC) at Florida International University (FIU) has provided analysis of flow and transport for several watersheds at DOE's Oak Ridge Reservation (ORR), including East Fork Poplar Creek (EFPC), Upper EFPC in the Y-12 National Security Complex area (Y-12 NSC) and White Oak Creek (WOC). Integrated surface and subsurface flow, fate and transport models were developed to provide analysis of contaminant patterns within each watershed. In addition, digital monitoring data available from the Oak Ridge Environmental Information System (OREIS) related to mercury (Hg) contamination and remediation within these watersheds was used for calibration and verification of the model. Experimental studies were also carried out which provided kinetic and equilibrium data about important parameters related to Hg transport, speciation and methylation/demethylation kinetics within the watershed. Geographic Information Systems (GIS) technology was employed to support the modeling work through storage and geo-processing of spatial and temporal data required by the models and to produce hydrogeological maps for visualization. An ArcGIS geo-database was developed for centralized storage and management of experimental and computed model data and its capabilities were extended over the years using tools such as ModelBuilder combined with Python scripting to automate repetitive tasks, perform statistical analyses and generate maps and reports. The hydrologic geo-database model developed possesses a structure that enables linkage with scalable hydrologic modeling tools/applications to model hydrologic systems, and in this case, enables the testing of the potential impacts of various remediation scenarios on the ORR watersheds. The ArcSDE geo-database can also be used to automate and simplify the process of calling stored GIS and time series data. This geo-database can serve as a tool for contaminant flow and transport analyses which require large amounts of high-quality spatial and temporal data in order to ensure reliability and validity of modeling results. The existing geo-database structure developed for the hydrological modeling at ORR was designed to be replicable for application at other DOE sites. An investigation of downloadable free/open source GIS software along with required security protocols to facilitate online querying of the database was also conducted to determine methods by which project-derived data can be more easily shared with other project stakeholders such as DOE personnel and site contractors. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Improved recovery of cell-cycle gene expression in Saccharomyces cerevisiae from regulatory interactions in multiple omics data

Gene expression is regulated by DNA-binding transcription factors (TFs). Together with their target genes, these factors and their interactions collectively form a gene regulatory network (GRN), which is responsible for producing patterns of transcription, including cyclical processes such as genome replication and cell division. However, identifying how this network regulates the timing of these patterns, including important interactions and regulatory motifs, remains a challenging task. Results We employed four in vivo and in vitro regulatory data sets to investigate the regulatory basis of expression timing and phase-specific patterns cell-cycle expression in Saccharomyces cerevisiae . Specifically, we considered interactions based on direct binding between TF and target gene, indirect effects of TF deletion on gene expression, and computational inference. We found that the source of regulatory information significantly impacts the accuracy and completeness of recovering known cell-cycle expressed genes. The best approach involved combining TF-target and TF-TF interactions features from multiple datasets in a single model. In addition, TFs important to multiple phases of cell-cycle expression also have the greatest impact on individual phases. Important TFs regulating a cell-cycle phase also tend to form modules in the GRN, including two sub-modules composed entirely of unannotated cell-cycle regulators ( STE12-TEC1 and RAP1-HAP1-MSN4 ). Conclusion Our findings illustrate the importance of integrating both multiple omics data and regulatory motifs in order to understand the significance regulatory interactions involved in timing gene expression. This integrated approached allowed us to recover both known cell-cycles interactions and the overall pattern of phase-specific expression across the cell-cycle better than any single data set. Likewise, by looking at regulatory motifs in the form of TF-TF interactions, we identified sets of TFs whose co-regulation of target genes was important for cell-cycle expression, even when regulation by individual TFs was not. Overall, this demonstrates the power of integrating multiple data sets and models of interaction in order to understand the regulatory basis of established biological processes and their associated gene regulatory networks.

59 BASIC BIOLOGICAL SCIENCES↗

Enhancing Streamflow Reanalysis Across the Conterminous US Leveraging Multiple Gridded Precipitation Data Sets

Streamflow observations, essential for various water resource applications, are often unavailable at critical locations in need. Although different models have been proposed to enhance streamflow predictability at ungauged locations, the challenge extends beyond model fidelity. Differences in meteorologic forcing data sets, precipitation in particular, can significantly affect the accuracy of hydrologic predictions. This challenge intensifies across regions characterized by diverse hydro-climatological and geographical conditions, such as in the conterminous US (CONUS) where a single precipitation product struggles to consistently replicate observed hydrographs, particularly peak flow dynamics. To enhance streamflow predictions, we utilize a VIC-RAPID hydrologic modeling framework driven by multiple commonly used meteorological forcing data sets, such as Daymet, PRISM, ST4, AORC, and their hybrids and create multiple sets of 40-year (1980–2019) hourly, daily, and monthly streamflow reanalysis, Dayflow Version 2, for 2.7 million river reaches across the CONUS. Most forcings lead to skillful streamflow performance, except for ST4 in the mountainous west, where severe radar blockage adversely affects the accuracy. The evaluation using over 6,000 hourly stream gauges shows that hourly AORC and ST4 lead to improved annual peak flow performance over Daymet—driven streamflow (Dayflow V1), particularly in smaller basins, highlighting the value of high temporal resolution forcings in hydrologic predictions. Compared with other benchmark data sets like National Water Model V3.0, AORC-driven VIC-RAPID exhibits improved regional streamflow performance, with comparable peak flow representation. We envision that multi-forcing streamflow reanalysis data can inform regions in need of forcing data enhancement, diagnose hydrologic model performance, and benefit diverse water resource applications.

54 ENVIRONMENTAL SCIENCES↗

Dry in-pile fracture test (DRIFT) for separate-effects validation of ceramic fuel fracture models

Fracture is an important component of nuclear fuel behavior, and significant efforts have been invested into developing fuel performance models that are capable of accurately representing fracture. Usable data on the process of fracture propagation in nuclear fuel under realistic service conditions are very limited. To address this need, a series of separate-effects experiments were developed and performed at Idaho National Laboratory's Transient Reactor Test (TREAT) facility. These experiments employ a heat sink to radially remove heat from the fuel in a manner that approximates the effect of coolant in an operating light-water reactor (LWR). The test holder for these experiments is known as the Dry In-pile Fracture Test (DRIFT). A series of experiments employing DRIFT and TREAT were performed to provide data on the extent and nature of fracture in fresh fuel at various points during a ramp to full power. Novel aspects of these experiments include the way they employ a heat sink to replicate steady-state LWR conditions, as well as the use of fiber optic sensors for in-reactor thermal instrumentation. Details on the development of this experiment, experimental conditions, and resulting data (including in situ thermal measurements and post-irradiation imaging of fracture) are provided in this work. LWR-equivalent powers ranging from 10 to 25 kW/m were tested using this apparatus. Cracking was visible at all power levels, with increasing cracking extent as the power level increased, although there was little difference in the cracking between the two highest-power tests, which had LWR-equivalent powers of 20 and 25 kW/m.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

COMPASS-FME Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments (TEMPEST) Experiment Level 2 Sensor Data v2-1

This is the version v2-1 Level 2 (L2) data release for COMPASS-FME environmental sensors located at our Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments (TEMPEST) experimental site. This manipulative, ecosystem-scale TEMPEST experiment addresses the potential for freshwater and estuarine-water disturbance events to alter tree function, species composition, and ecosystem processes in a deciduous coastal forest in MD, USA. The experiment uses a large-unit (2000 m2), un-replicated experimental design, with three 50 m × 40 m plots serving as control, freshwater, and estuarine-water treatments. Level 2 (L2) data consist of sensor observations from the COMPASS-FME synoptic sites, TEMPEST, and DELUGE. Compared to the L1 data, these are more consistent (always 15-minute timestamps for the entire year); better QA/QC’d (out of bounds, out of service, and extreme outlier values are removed); and more complete, with a gap-filled time series available alongside the main observations, and additional derived (calculated) variables. L2 data are intended to be rapidly and easily usable in analyses and simulations. However, algorithmic outlier identification always carries the risk of removing valid data, and Level 1 data may be more suitable for analyses that focus on variability or extreme events. This dataset includes: - An overall dataset README file that describes the current version, gives citation and contact information, etc. - Site- and year-specific folders, each holding variable-specific Parquet (a high performance, space efficient format; see https://parquet.apache.org) data files for each site and plot in that year. - Metadata files within each site-year folder provide full information on data units, expected ranges, contact information, detailed flood times, as well as a general description of the site. - Environmental sensor types that appear in the data files include weather (ClimaVUE50, CS, RM Young, and LI instruments in the graphs below); soil conditions (TEROS12); soil redox state (Redox); groundwater variables (AquaTROLL200 and AquaTROLL600); open water sondes (Exo); tree sap velocity (Sapflow); and system voltage and state (Datalogger). Data are reported every 15 minutes. Please see v2-1 TEMPEST L2 Sensor Package Quick Start.pdf for detailed information on data package structure, temporal coverage, and versioning. Data files are in Apache Parquet, a high performance, space efficient format for tabular data. These files can be read using R's `arrow` package (https://arrow.apache.org/docs/r/), with similar tools available in other languages. The TEMPEST flood events occurred on the following dates. They lasted for ~10 hours each day and delivered ~80,000 gallons to each plot; many data streams are available at 1 or 5 minute frequency during these periods. * Tests: Aug 25 (fresh plot) and Sep 9 (salt plot), 2021 * TEMPEST 1: June 22, 2022 * TEMPEST 2: June 6-7, 2023 * TEMPEST 3: June 11-13, 2024

EARTH SCIENCE > ATMOSPHERE > ATMOSPHERIC TEMPERATU↗

Phosphorylation cascade regulates the formation and maturation of rotaviral replication factories

The rotavirus (RV) genome is replicated and packaged into virus progeny in cytoplasmic inclusions called viroplasms, which require interactions between RV nonstructural proteins NSP2 and NSP5. How viroplasms form remains unknown. We previously found two forms of NSP2 in RV-infected cells: a cytoplasmically dispersed dNSP2, which interacts with hypophosphorylated NSP5; and a viroplasm-specific vNSP2, which interacts with hyperphosphorylated NSP5. Other studies report that CK1α, a ubiquitous cellular kinase, hyperphosphorylates NSP5, but requires NSP2 for reasons that are unclear. Here we show that silencing CK1α in cells before RV infection resulted in ( i ) >90% decrease in RV replication, ( ii ) disrupted vNSP2 and NSP5 interaction, ( iii ) dispersion of vNSP2 throughout the cytoplasm, and ( iv ) reduced vNSP2 protein levels. Together, these data indicate that CK1α directly affects NSP2. Accordingly, an in vitro kinase assay showed that CK1α phosphorylates serine 313 of NSP2 and triggers NSP2 octamers to form a lattice structure as demonstrated by crystallographic analysis. Additionally, a dual-specificity autokinase activity for NSP2 was identified and confirmed by mass spectrometry. Together, our studies show that phosphorylation of NSP2 involving CK1α controls viroplasm assembly. Considering that CK1α plays a role in the replication of other RNA viruses, similar phosphorylation-dependent mechanisms may exist for other virus pathogens that require cytoplasmic virus factories for replication.

59 BASIC BIOLOGICAL SCIENCES↗

Climate data, analysis and models for the study of natural variability and anthropogenic change

Gridded Temperature Under prior/current support, we completed and published (Jones et al., 2012) the fourth major update to our global land dataset of near-surface air temperatures, CRUTEM4. This is one of the most widely used records of the climate system, having been updated, maintained and further developed with DoE support since the 1980s. We have continued to update the CRUTEM4 (Jones et al., 2012) database that is combined with marine data to produce HadCRUT4 (Morice et al., 2012). The emphasis in our use of station temperature data is to access as many land series that have been homogenized by National Meteorological Services (NMSs, including NCDC/NOAA, Asheville, NC). Unlike the three US groups monitoring surface temperatures in a similar way, we do not infill areas that have no or missing data. We can only infill such regions in CRUTEM4 by accessing more station temperature series. During early 2014, we have begun the extensive task of updating as many of these series as possible using data provided by some NMSs and also through a number of research projects and programs around the world. All the station data used in CRUTEM4 have been available since 2009, but in Osborn and Jones (2014) we have made this more usable using a Google Earth interface (http://www.cru.uea.ac.uk/cru/data/crutem/ge/ ). We have recently completed the update of our infilled land multi-variable dataset (CRU TS 3.10, Harris et al., 2014). This additionally produces complete land fields (except for the Antarctic) for temperature, precipitation, diurnal temperature range, vapour pressure and sunshine/cloud. Using this dataset we have calculated sc-PDSI (self-calibrating Palmer Drought Severity Index) data and compared with other PDSI datasets (Trenberth et al., 2014). Also using CRU TS 3.10 and Reanalysis datasets, we showed no overall increase in global temperature variability despite changing regional patterns (Huntingford et al., 2013). Harris et al. (2014) is an update of an earlier dataset (Mitchell and Jones, 2005) which also had earlier DoE support. The earlier dataset has been cited over 1700 times according to ResearcherID on 31/July/2014 and the recent paper has already been cited 22 times. Analyses of Temperature Data Using the ERA-Interim estimate of the absolute surface air temperature of the Earth (instead of in the more normal form of anomalies) we compared the result against estimates we produced in 1999 with earlier DoE support. The two estimates are surprisingly close (differing by a couple of tenths of a degree Celsius), with the average temperature of the world (for 1981-2010) being very close to 14°C (Jones and Harpham, 2013). We have assessed ERA-Interim against station temperatures from manned and automatic weather station measurements across the Antarctic (Jones and Lister, 2014). Agreement is generally excellent across the Antarctic Peninsula and the sparsely sampled western parts of Antarctica. Differences tend to occur over eastern Antarctica where ERA-Interim is biased warm (up to 6°C) in the interior of the continent and biased cool (up to 6°C) for some of the coastal locations. Opportunities presented themselves during 2012 for collaborative work with a couple of Chinese groups. Three papers develop new temperature series for China as a whole and also for the eastern third of China (Wang et al., 2014, Cao et al., 2013 and Zhao et al., 2014). A dataset of ~400 daily Chinese temperature stations has been added to the CRU datasets. The latter paper finds that urban effects are generally about 10% of the long-term warming trend across eastern China. A fourth paper (Wang et al., 2013) illustrates issues with comparisons between reanalyses and surface temperatures across China, a method that has been widely used by some to suggest urban heating effects are much larger in the region. ERA-Interim can be used but NCEP/NCAR comparisons are very dependent on the period analysed. Earlier a new temperature dataset of homogenized records was developed for China (Li et al., 2009). Urbanization has also been addressed for London (Jones and Lister, 2009) where two rural sites have not warmed more than a city centre site since 1900. Additionally, in Ethymiadis and Jones (2010) we show that land air temperatures agree with marine data around coastal areas, further illustrating that urbanization is not a major component of large-scale surface air temperature change. Early instrumental data (before the development of modern thermometer screens) have always been suspected of being biased warm in summer, due to possible direct exposure to the sun. Two studies (Böhm et al., 2010 and Brunet et al., 2010) show this for the Greater Alpine Region (GAR) and for mainland Spain respectively. The issue is important before about 1870 in the GAR and before about 1900 in Spain. After correction for the problems, summer temperature estimates before these dates are cooler by about 0.4°C. In Jones and Wigley (2010), we discussed the importance of the biases in global temperature estimation. Exposure and to a lesser extent urbanization are the most important biases for the land areas, but both are dwarfed by the necessary adjustments for bucket SST measurements before about 1950. Individual station homogeneity is only important at the local scale. This was additionally illustrated by Hawkins and Jones (2013) where we replicated the temperature record developed by Guy Stewart Callendar in papers in 1938 and 1961. Analyses of Daily Climate Data Work here indicates that ERA-Interim (at least in Europe, Cornes and Jones, 2013, discussed in more detail in this proposal) can be used to monitor extremes (using the ETCCDI software – see Zhang et al., 2011). Additionally, also as a result of Chinese collaboration, a new method of daily temperature homogenization has been developed (Li et al., 2014). In Cornes and Jones (2011) we assessed storm activity in the northeast Atlantic region using daily gridded data. Even though the grid resolution is coarse (5° by 5° lat/long) the changes in storm activity are similar to those developed from the pressure triangle approach with station data. Analyses of humidity and pressure data In Simmons et al. (2010) we showed a reduction in relative humidity over low-latitude and mid-latitude land areas for the 10 years to 2008, based on monthly anomalies of surface air temperature and humidity from ECMWF reanalyses (ERA-40 and ERA-Interim) and our earlier land-only dataset (CRUTEM3) and synoptic humidity observations (HadCRUH). Updates of this station-based humidity dataset (now called HadISDH) extend the record, showing continued reductions (Willett et al., 2013). Analyses of Proxy Temperature Data In Vinther et al. (2010), relationships between the seasonal stable isotope data from Greenland Ice Cores and Greenland and Icelandic instrumental temperatures were investigated for the past 150-200 years. The winter season stable isotope data are found to be influenced by the North Atlantic Oscillation (NAO) and very closely related to SW Greenland temperatures. The summer season stable isotope data display higher correlations with Icelandic summer temperatures and North Atlantic SST conditions than with local SW Greenland temperatures. In Jones et al. (2014) we use these winter isotope reconstructions to show the expected inverse correlation (due to the NAO) with winter-season documentary reconstructions from the Netherlands and Sweden over the last 800 years. Finally, in this section Jones et al. (2013) shows the agreement between tree-ring width measurements from Northern Sweden and Finland and an assessment of the link to explosive volcanic eruptions. An instrumental record for the region in the early 19th century indicates that the summer of 1816 was only slightly below normal, explaining why this year has normal growth for both ring width and density. GCM/RCM/Reanalysis Evaluation In this section we have intercompared daily temperature extremes across Europe in Cornes and Jones (2013) using station data, E-OBS and ERA-Interim. We have additionally considered the impact of the urban issue on the global scale using the results of the Compo et al. (2011) Reanalyses, 20CR. These only make use of SST and station pressure data. Across the world’s land areas, they indicate similar warming since 1900 to that which has occurred (Compo et al., 2013), again illustrating that urbanization is not the cause of the long-term warming. Changes in HadCRUH global land surface specific humidity and CRUTEM3 surface temperatures from 1973 to 1999 were compared to the CMIP3 archive of climate model simulations with 20th Century forcings (Willett et al., 2010). The models reproduce the magnitude of observed interannual variance over all large regions. Observed and modelled trends and temperature-humidity relationships are comparable with the exception of the extra-tropical Southern Hemisphere where observations exhibit no trend but models exhibit moistening.

54 ENVIRONMENTAL SCIENCES↗

Numerical analysis of experimental studies of methane hydrate formation in a sandy porous medium

Here we analyse numerically an earlier experimental study that involved the formation of methane hydrates by the excess water method in a small reactor filled with a sandy porous medium, and seek to address questions about the type of the hydration reaction and the phase heterogeneity in the resulting hydrate-bearing sand. Using a fine discretization describing the reactor assembly, the experimental process is faithfully replicated numerically. The multi-stage process of hydrate formation is subdivided in 7 steps. The experimental data from the continuously-monitored pressure and temperature during each step are used for comparison against the numerical predictions, the identification of the dominant processes and the determination of the associated parameters through a history-matching process that minimizes deviations between observations and simulation results. The results of this first-ever study on this subject demonstrate unequivocally that the hydration reaction is a kinetic (as opposed to an equilibrium) process, and that the spatial distributions of the various phases (aqueous, gas and hydrate) at the end of the formation process are strongly heterogeneous. This has serious implications in simulation studies of hydrate dissociation that assume uniform initial phase saturation distributions. Finally, the history-matching process indicates that (a) the system behaviour is sensitive to some flow parameters (porosity and irreducible water saturation) only during the first water injection, (b) it is insensitive to the sand intrinsic permeability during all steps of the study, and (c) thermal processes dominate after the first water injection, yielding estimates of the thermal properties of the sand and of time-variable key parameters of the kinetic reaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Zika virus mutation enhances transmission potential and confers escape from protective dengue virus immunity

Zika virus (ZIKV) and dengue virus (DENV) are arthropod-borne pathogenic flaviviruses that co-circulate in many countries. To understand some of the pressures that influence ZIKV evolution, we mimic the natural transmission cycle by repeating serial passaging of ZIKV through cultured mosquito cells and either DENV-naive or DENV-immune mice. Compared with wild-type ZIKV, the strains passaged under both conditions exhibit increased pathogenesis in DENV-immune mice. Application of reverse genetics identifies an isoleucine-to-valine mutation (I39V) in the NS2B proteins of both passaged strains that confers enhanced fitness and escape from pre-existing DENV immunity. Introduction of I39V or I39T, a naturally occurring homologous mutation detected in recent ZIKV isolates, increases the replication of wild-type ZIKV in human neuronal precursor cells and laboratory-raised mosquitoes. Our data indicate that ZIKV strains with enhanced transmissibility and pathogenicity can emerge in DENV-naive or -immune settings, and that NS2B-I39 mutants may represent ZIKV variants of interest.

59 BASIC BIOLOGICAL SCIENCES↗

Establishing coherent momentum-space electronic states in locally ordered materials

Rich momentum-dependent electronic structure naturally arises in solids with long-range crystalline symmetry. Reliable and scalable quantum technologies rely on materials that are either not perfect crystals or non-crystalline, breaking translational symmetry. This poses the fundamental questions of whether coherent momentum-dependent electronic states can arise without long-range order, and how they can be characterized. Here we investigate Bi 2 Se 3 , which exists in crystalline, nanocrystalline, and amorphous forms, allowing direct comparisons between varying degrees of spatial ordering. Through angle-resolved photoemission spectroscopy, we show for the first time momentum-dependent band structure with Fermi surface repetitions in an amorphous solid. The experimental data is complemented by a model that accurately reproduces the vertical, dispersive features as well as the replication at higher momenta in the amorphous form. These results reveal that well-defined real-space length scales are sufficient to produce dispersive band structures, and that photoemission can expose the imprint of these length scales on the electronic structure.

36 MATERIALS SCIENCE↗

Design and Implementation of Papyrus: Parallel Aggregate Persistent Storage

A surprising development in recently announced HPC platforms is the addition of, sometimes massive amounts of, persistent (nonvolatile) memory (NVM) in order to increase memory capacity and compensate for plateauing I/O capabilities. However, there are no portable and scalable programming interfaces using aggregate NVM effectively. This paper introduces Papyrus: a new software system built to exploit emerging capability of NVM in HPC architectures. Papyrus (or Parallel Aggregate Persistent -YRU- Storage) is a novel programming system that provides features for scalable, aggregate, persistent memory in an extreme-scale system for typical HPC usage scenarios. Papyrus mainly consists of Papyrus Virtual File System (VFS) and Papyrus Template Container Library (TCL). Papyrus VFS provides a uniform aggregate NVM storage image across diverse NVM architectures. It enables Papyrus TCL to provide a portable and scalable high-level container programming interface whose data elements are distributed across multiple NVM nodes without requiring the user to handle complex communication, synchronization, replication, and consistency model. We evaluate Papyrus on two HPC systems, including UTK Beacon and NERSC Cori, using real NVM storage devices.

Kim, Jungwon↗

Experimental Combustion and Flame Characterization of a Chemical Looping-Based Oxidative Dehydrogenation Byproduct Fuel Mixture Containing High CO2 Dilution

Abstract This study investigates the combustion performance of a CO2-rich fuel mixture containing ethane and methane as active species using a constant volume combustion chamber. This fuel is obtained as a byproduct of a chemical looping-based oxidative dehydrogenation (Cl-ODH) process ethylene production. The byproduct gas mixture has 40.79% CO2, 39.49% ethane, and 4.88% methane by weight with other minor compounds. Using this fuel for energy extraction would improve the process efficiency of the ethane to ethylene conversion. After initial combustion modeling, the gas fuel mixture was reduced to just the major species: CO2, ethane, and methane. The mixture was then tested for flammability limits and combustion performance under spark-ignition conditions. Effects of ambient conditions like temperatures between 300 and 400 K with initial pressures from 1 to 10 bar were tested. The effects of stoichiometry were tested to understand flame velocities and heat release. The fuel mixture showed an overall reduced flame velocity compared to gasoline. Instability in combustion was believed to be caused by the dissociation of ethane under elevated conditions. At higher pressures, the flame produces lower cumulative heat release. Simulations were also performed using a model tuned to replicate the operations of the combustion chamber used in the experiments. Heat release and unburnt fuel mass data were calculated to identify the discrepancies in the combustion completeness at elevated pressures. The effects of CO2 quenching the flame coupled with the increased dissociation of the fuel species can lead to up to more than 75% of the fuel mixture being unburnt. Data from this study were used to modify a small-scale spark-ignition engine to use this fuel and produce usable energy.

Energy & Fuels↗

SU-F-T-49: Dosimetry Parameters and TPS Commissioning for the CivaSheet Directional Pd-103 Brachytherapy Source

Purpose: The CivaSheet is a new LDR Pd-103 brachytherapy device offering directional-radiation for preferentially irradiating malignancies with healthy-tissue sparing. Observations are presented on dosimetric characterization, TPS commissioning, and evaluation of the dosesuperposition- principle for summing individual elements comprising a planar CivaSheet Methods: The CivaSheet comprises individual sources (CivaDots, 0.05cm thick and 0.25cm diam.) inside a flexible bioabsorbable substrate with a 0.8cm center-to-center rectangular array. All non-radioactive components were measured to ensure accuracy of manufacturer-provided dimensional information. The Pd spatial distribution was gleaned from radioactive and inert samples, then modeled with the MCNP6 radiation-transport-code. A 6×6 array CivaSheet was modeled to evaluate the dose superposition principle for treatment planning. Air-kerma-strength was estimated using the NIST WAFAC geometry. Absorbed dose was estimated in water with polar sampling covering 0.05≤r≤15cm in 0.05cm increments and 0°≤θ≤180° in 1° increments. These data were entered into VariSeed9.0 and tested for the dose-superposition-principle. Results: The dose-rate-constant was 0.579 cGy/h/U with g(r) determined along the rotational-axis of symmetry (0°) instead of 90°. gP(r) values at 0.1, 0.5, 2, 5, and 10cm were 1.884, 1.344, 0.558, 0.088, and 0.0046. F(r,θ) decreased between 0° and 180° by factors of 270, 23, and 5.1 at 0.1, 1, and 10cm. The highest dose-gradient was at 92°, changing by a factor of 3 within 1° due to Au-foil shielding. TPS commissioning from 0.1≤r≤11cm and 0°≤θ≤180° demonstrated 2% reproducibility of input data except at the high-dose-gradient where interpolations caused 3% differences. Dose superposition of CivaDots replicated a multi-source CivaSheet array within 2% except where another CivaDot was present. Following implantation, the device is not perfectly planar. TPS accuracy utilizing the dose-superposition-principle through geometric repositioning of CivaDots supersedes TPS limitations of intersource shielding effects Conclusion: Dosimetric characterization, source commissioning, and evaluation of the dose-superposition-principle with VariSeed9.0 permits treatment planning for the CivaSheet brachytherapy device. Research supported in part by CivaTech Oncology, Inc.

60 APPLIED LIFE SCIENCES↗