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At least 865 records · Page 48

PNNL DataHub Project: Omics Lethal Human Viruses Project Profiling of the Host Response to West Nile Virus Infection, Processed Experimental Dataset Catalog

West Nile virus (WNV) is classified as a Category B priority pathogen (mosquito-borne Flavivirus) by the National Institute of Allergy and Infectious Diseases (NIAID), and are known to cause severe infections in humans where lethal host-associated mechanisms are not clearly defined. The NIAID Modeling Host Responses to Understand Severe Human Virus Infections Research Program project (2013 - 2018) aimed to develop an improved comprehensive understanding of the host response to a suite of viruses causing lethal infections leveraging a systems biology approach. The NIAID Modeling Host Responses to Understand Severe Human Virus Infections Research Program project (2013-2018) aimed to develop an improved comprehensive understanding of the host response to a suite of viruses causing lethal infections leveraging a systems biology approach. Herein, PNNL sub-projects provide a never before released comprehensive infectious disease collection of primary and secondary transformation multi-Omics data profiling a series of priority pathogen primary experimental studies for enhanced open-access to viral Omics datasets and project lifecycle metadata. Secondary host-pathogen viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Leveraging unique high-resolution Omics capabilities for proteomics (P), metabolomics (M), lipidomics (L), and transcriptomics (T) dataset downloads each have a direct relationship to a primary sample submission corresponding a specific West Nile virus [NCBITAXON:11082] (WNV-NY99 382) experimental infection study. Host sample types include cerebellum ["CB", BTO:0000232], cortical neurons ["CN", BTO:0004102], cortex ["CT", BTO:0000233], dendritic cells ["DC", BTO:0002042], granule cell neurons ["GCN", BTO:0003393], lymph node ["LN", BTO:0000784], and serum ["SE", BTO:0001239] from mouse (Mus musculus) tissue collections.

59 BASIC BIOLOGICAL SCIENCES↗

Diffuse Bands 9577 and 9633: Relations to Other Interstellar Features

We study, for the first time, the relations of two strong diffuse bands (DIBs) at 9633 and 9577 Å, commonly attributed to C{sub 60}{sup +}, to other interstellar features seen in optical and UV spectra including H i, Ca i, Fe ii, Na i, Ti ii, CN, CH, CH{sup +}, and C{sub 2} and DIBs 5780, 5797, 6196, 6269, 6284, and 6614. We analyzed 62 lines of sight where the stellar contamination by Mg ii was corrected or found negligible for DIB 9633. Equivalent widths of DIB 9577 were measured in 62 lines of sight. Poor mutual correlation between the strengths of the above features and the major diffuse bands (5780 and 5797) as well as with other DIBs (with some exceptions) were revealed. The considered DIBs are also poorly correlated with the features of neutral hydrogen, molecular carbon, and those of simple interstellar radicals. Perhaps this phenomenon can be explained if the diffuse band 9577 is an unresolved blend of two or more interstellar features. There are indications that 9633 and 9577 diffuse bands are stronger in σ-type clouds, i.e., these features resemble the behavior of reasonably broad DIBs, which are strong in the lines of sight where the UV flux from the very hot nearby stars plays an important role.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Radial-velocity Search for Binary RR Lyrae Variables

We report 272 radial velocities for 19 RR Lyrae variables. For most of the stars we have radial velocities for the complete pulsation cycle. These data are used to determine robust center-of-mass radial velocities that have been compared to values from the literature in a search for evidence of binary systems. Center-of-mass velocities were determined for each star using Fourier Series and template fits to the radial velocities. Our center-of-mass velocities have uncertainties from ±0.16 km s{sup −1} to ±2.5 km s{sup −1}, with a mean uncertainty of ±0.92 km s{sup −1}. We combined our center-of-mass velocities with values from the literature to look for deviations from the mean center-of-mass velocity of each star. Fifteen RR Lyrae show no evidence of binary motion (BK And, CI And, Z CVn, DM Cyg, BK Dra, RR Gem, XX Hya, SZ Leo, BX Leo, TT Lyn, CN Lyr, TU Per, U Tri, RV UMa, and AV Vir). In most cases this conclusion is reached due to the sporadic sampling of the center-of-mass velocities over time. Three RR Lyrae show suspicious variation in the center-of-mass velocities that may indicate binary motion but do not prove it (SS Leo, ST Leo, and AO Peg). TU UMa was observed by us near a predicted periastron passage (at 0.14 in orbital phase) but the absence of additional center-of-mass velocities near periastron makes the binary detection, based on radial velocities alone, uncertain. Two stars in our sample show Hγ emission in phases 0.9–1.0: SS Leo and TU UMa.

47 OTHER INSTRUMENTATION↗

New Clues to the Evolution of Dwarf Carbon Stars From Their Variability and X-Ray Emission

As main-sequence stars with C > O, dwarf carbon (dC) stars are never born alone but inherit carbon-enriched material from a former asymptotic giant branch (AGB) companion. In contrast to M dwarfs in post-mass-transfer binaries, C 2 and/or CN molecular bands allow dCs to be identified with modest-resolution optical spectroscopy, even after the AGB remnant has cooled beyond detectability. Accretion of substantial material from the AGB stars should spin up the dCs, potentially causing a rejuvenation of activity detectable in X-rays. Indeed, a few dozen dCs have recently been found to have photometric variability with periods under a day. However, most of those are likely post-common-envelope binaries, spin–orbit locked by tidal forces, rather than solely spun-up by accretion. Here, we study the X-ray properties of a sample of the five nearest-known dCs with Chandra. Two are detected in X-rays, the only two for which we also detected short-period photometric variability. We suggest that the coronal activity detected so far in dCs is attributable to rapid rotation due to tidal locking in short binary orbits after a common-envelope phase, late in the thermally pulsing (TP) phase of the former C-AGB primary (TP-AGB).

79 ASTRONOMY AND ASTROPHYSICS↗

The Rest-frame Submillimeter Spectrum of High-redshift, Dusty, Star-forming Galaxies from the SPT-SZ Survey

We present the average rest-frame spectrum of the final catalog of dusty star-forming galaxies (DSFGs) selected from the South Pole Telescope's SPT-SZ survey and measured with Band 3 of the Atacama Large Millimeter/submillimeter Array. This work builds on the previous average rest-frame spectrum, given in Spilker et al. (2014) for the first 22 sources, and is comprised of a total of 78 sources, normalized by their respective apparent dust masses. The spectrum spans 1.9 < z < 6.9 and covers rest-frame frequencies of 240–800 GHz. Combining this data with low-J CO observations from the Australia Telescope Compact Array, we detect multiple bright line features from 12 CO, [Ci], and H 2 O, as well as fainter molecular transitions from 13 CO, HCN, HCO + , HNC, CN, H 2 O + , and CH. We use these detections, along with limits from other molecules, to characterize the typical properties of the interstellar medium (ISM) for these high-redshift DSFGs. We are able to divide the large sample into subsets in order to explore how the average spectrum changes with various galaxy properties, such as effective dust temperature. We find that systems with hotter dust temperatures exhibit differences in the bright 12 CO emission lines, and contain either warmer and more excited dense gas tracers or larger dense gas reservoirs. These observations will serve as a reference point to studies of the ISM in distant luminous DSFGs (L IR > 10 12 L ⊙ ), and will inform studies of chemical evolution before the peak epoch of star formation at z = 2–3.

79 ASTRONOMY AND ASTROPHYSICS↗

Investigating the contribution of grown new particles to cloud condensation nuclei with largely varying preexisting particles – Part 1: Observational data analysis

This study employed multiple techniques to investigate the contribution of grown new particles to the number concentration of cloud condensation nuclei (CCN) at various supersaturation (SS) levels at a rural mountain site in the North China Plain from 29 June to 14 July 2019. On 8 new particle formation (NPF) days, the total particle number concentrations (N cn ) were 8.4 ± 6.1×10 3 cm -3 , which was substantially higher compared to 4.7 ± 2.6×10 3 cm -3 on non-NPF days. However, the CCN concentration (Nccn) at 0.2 % SS and 0.4 % SS on the NPF days was significantly lower than those observed on non-NPF days (p<0.05). This was due to the lower cloud activation efficiency of preexisting particles resulting from organic vapor condensation and smaller number concentrations of preexisting particles on NPF days. A case-by-case examination showed that the grown new particles only yielded a detectable contribution to N ccn at 0.4 % SS and 1.0 % SS during the NPF event on 1 July 2019, accounting for 12 % ± 11 % and 23 % ± 12 % of N ccn , respectively. The increased N ccn during two other NPF events and at 0.2 % SS on 1 July 2019 were detectable but determined mainly by varying preexisting particles rather than grown new particles. In addition, the hygroscopicity parameter values, concentrations of inorganic and organic particulate components, and surface chemical composition of different sized particles were analyzed in terms of chemical drivers to grow new particles. The results showed that the grown new particles via organic vapor condensation generally had no detectable contribution to N ccn but incidentally did. However, this conclusion was drawn from a small size of observational data, leaving more observations, particularly long-term observations and the growth of preexisting particles to the CCN required size, needed for further investigation.

54 ENVIRONMENTAL SCIENCES↗

FUN-BioCROP model with litter decomposition parameters derived from the LIDET dataset

This repository contains the code and data necessary to run the FUN-BioCROP (Fixation and Uptake of Nitrogen-Bioenergy Carbon, Rhizosphere, Organisms, and Protection) model with litter decomposition parameters derived from a modified Monte Carlo simulation that used the Long-term Intersite Decomposition Experiment Team dataset. Related publication:Juice, S.M., Ridgeway, J.R., Hartman, M.D., Parton, W.J., Berardi, D.M., Sulman, B.N., Allen, K.E., & Brzostek, E.R. Reparameterizing litter decomposition using a simplified Monte Carlo method improves litter decay simulated by a microbial model and alters bioenergy soil carbon estimates. Description of Files: FUNBioCROP_LIDET Study.Rmd R code with FUN-BioCROP model that can be run with 10 different sets of parameters for litter decomposition (Baseline, LIDET, or eight other best parameter sets identified in the modified Monte Carlo simulation. CORPSE Functions_Bioenergy_V2.R Code with CORPSE model functions, called by FUNBioCROP_LIDET Study.Rmd Model Input Data: bulk.csv, bulk_till.csv, rhizo.csv, rhizo_till.csv, litter.csv Initial C and N (kg C or N/m2) pool values for each soil compartment, final values from spin up. All five files have the same columns: (Column - Description - Units) uFastC - Unprotected fast decomposing carbon - kg carbon/m2 uSlowC - Unprotected slow decomposing carbon - kg carbon/m2 uNecroC - Unprotected necromass carbon - kg carbon/m2 pFastC - Protected fast decomposing carbon - kg carbon/m2 pSlowC - Protected slow decomposing carbon - kg carbon/m2 pNecroC - Protected necromass carbon - kg carbon/m2 livingMicrobeC - Carbon in living microbial biomass - kg carbon/m2 uFastN - Unprotected fast decomposing nitrogen - kg nitrogen/m2 uSlowN - Unprotected slow decomposing nitrogen - kg nitrogen/m2 uNecroN - Unprotected necromass nitrogen - kg nitrogen/m2 pFastN - Protected fast decomposing nitrogen - kg nitrogen/m2 pSlowN - Protected slow decomposing nitrogen - kg nitrogen/m2 pNecroN - Protected necromass nitrogen - kg nitrogen/m2 inorganicN - Inorganic nitrogen - kg nitrogen/m2 CO2 - Carbon in carbon dioxide - kg carbon/m2 livingMicrobeN - Nitrogen in living microbial biomass - kg nitrogen/m2 Model Input Data: FluxTower_AvgSoilT.csv: Average daily soil temperature (oC) at 10 cm depth at University of Illinois Urbana-Champaign (UIUC) Energy Farm flux tower from 7/2008-3/2016. (One year of averaged data) Model Input Data: FluxTower_AvgSoilVWC.csv: Average daily soil volumetric water content (VWC) at 10 cm depth at UIUC Energy Farm flux tower from 7/2008-3/2016. (One year of averaged data) Model Input Data: input_CCS_LIDET Study.csv: This file has daily data to run FUN-BioCROP (Column - Description - Units): yr - calendar year - year doy - day of year (1 to 365) (no leap year) - day anpp - aboveground NPP (DayCent) - kg C/m2/day bnpp - belowground NPP (DayCent) - kg C/m2/day aglivc - live aboveground biomass carbon (DayCent) - kg C/m2 bglivcj - live juvenile fine root biomass carbon (DayCent) - kg C/m2 bglivcm - live mature fine root biomass carbon (DayCent) - kg C/m2 aglivn - live aboveground biomass nitrogen (DayCent) - kg N/m2 bglivnj - live juvenile fine root biomass nitrogen (DayCent) - kg N/m2 bglivnm - live mature fine root biomass nitrogen (DayCent) - kg N/m2 nyr - simulation year - year cult - indicates a cultivation event (0 or 1) crop - indicates a new crop (0 or 1) fert - indicates a fertilizer event (0 or 1) frst - indicates the first day of the growing season (0 or 1) harv - indicates a harvest event (0 or 1) last - indicates the end of the growing season (0 or 1) croptype - crop type (0=none; 1=alfalfa; 2=corn; 3=grass clover pasture; 4=soybean; 5=wheat) cropsrl - crop specific root length - mm/g root cultrhizmix - fraction of rhizosphere mixed with bulk soil during cultivation (0.0-1.0) - fraction cultlitmix - fraction of litter mixed with bulk soil during cultivation (0.0-1.0) - fraction harvremov - fraction of above ground biomass removed during harvest (0.0-1.0) - fraction fertamt - fertilization amount - g N/m2 lifehist - plant life history (0 = annual, 1 = perennial) froot_turnover_c - amount of C in fine root turnover - kg C/m2 froot_turnover_n - amount of N in fine root turnover - kg N/m2 agrd_turnover_c - amount of C in aboveground biomass turnover - kg C/m2 agrd_turnover_n - amount of N in aboveground biomass turnover - kg N/m2 leaf_litter_fastfrac - Fast decomposing fraction of leaf litter (0.0-1.0) - fraction root_litter_fastfrac - Fast decomposing fraction of root litter (0.0-1.0) - fraction root_diameter - root diameter - mm root_length - root length - mm root/m2 rhizo_frac - fraction of total soil volume that is rhizosphere (0.0 - 1.0) - fraction date - date in format YYYY-MM-DD Instructions: Save the model code ("FUN-BioCROP_LIDET Study.Rmd") and accompanything files (data streams and CORPSE function code) in the same folder. In model code "Chunk 3: Load CORPSE Data Streams" set the working directory (setwd) to the folder with the files saved in step #1. In "Chunk 5: Define LIDET parameter sets" select the litter decomposition parameter set to be used in the run, and comment out all other sets. If changing any parameter values, edit them in "Chunk 6: Load parameters." Run all chunks up to and including "Chunk 10: Prepare Data for Export." In "Chunk 11: Export Output Data" edit data frames for export and filenames, as necessary. "Chunk 12: Graph Total Soil C" makes a figure of C remaining over the model run period. Description of each model chunk (in file FUN-BioCROP_LIDET Study.Rmd): Chunk 1: Remove all functions, clear memory. Removes all functions from R environment, clears the memory. Chunk 2: Load Packages. Loads packages necessary to run the code. Chunk 3: Load CORPSE Data Streams. Sets the working directory and loads the data files necessary to run CORPSE. Chunk 4: Load CORPSE Functions. Loads the R script with CORPSE functions from the working directory, "CORPSE Functions_Bioenergy_V2.R". Chunk 5: Define LIDET parameter sets. Has ten different parameter sets for litter decomposition tested in this study: Baseline parameters, LIDET parameters, and the other 8 best performing parameter sets identified in the modified Monte Carlo. To run the model, all but one parameter set must be commented out. Chunk 6: Load Parameters. Loads all fixed parameters to run the model. Data frame with definitions of parameters is in the CORPSE function script "CORPSE Functions_Bioenergy_V2.R" Chunk 7: Prepare Data Streams. Takes data streams loaded in Chunk 3 and puts them in the format necessary to run the model. The model is coded to run at least two sites at a time, so if only one site is being run it must be run in duplicate. Individual data tables of daily values are created in this chunk from the input data file. Chunk 8: Set Initial Conditions. Creates data tables of soil C and N pools for each soil compartment (rhizo_till, rhizo, bulk_till, bulk, litter) and loads initial values into the data tables. Creates lists for each soil compartment to hold model output. Chunk 9: Load FUN Data and Set Up Matrices. Uses DayCent data to calculate FUN input data: root and leaf N demand, total N demand, plant CN, leaf N available for retranslocation, and litter production. Creates matrices for FUN model outputs. Chunk 10: Run Model. Runs the model. Chunk 11: Prepare Data for Export. Combines data from each day saved as lists into data frames for each soil compartment. Adds values from all soil compartments together to calculate total soil values, creates separate data frames for each soil C and N pool (e.g., protected slow C) for the total soil value. Adds different C and N pools together to calculate total soil C and N for all layers. Creates data frame of ratio of protected to unprotected SOC. Organizes FUN data for export. Chunk 12: Export Results. Exports CSV files of model results to the working directory. Chunk 13: Graph Total Soil C. Makes figure of C remaining over time. Related Links: Original FUN-BioCROP model: https://github.com/BrzostekEcologyLab/FUN-BioCROP LIDET dataset: https://andlter.forestry.oregonstate.edu/data/abstract.aspx?dbcode=TD023

Juice, Stephanie↗

Mercury Methylation and Soil Organic Matter Degradation in Incubations with Added Acetate, Isotope-Labeled Mercury, and Selective Microbial Inhibitors, Teller and Council Sites, Seward Peninsula, 2018-2019

This dataset provides the results of laboratory soil microcosm incubation experiments conducted under anaerobic conditions with added acetate, isotope-labeled mercury, and selective microbial inhibitors (2-bromoethanesulfonate and sodium molybdate). The microcosms contained soil collected in August 2018 from the NGEE Arctic Teller Road Site at mile marker 27 (TL_MM27) near Intensive Site 9 (TL_IS_9) and from the Council Road Site (CN_MM71). Incubations were conducted at 8°C for 180 days (Teller incubations) or 60 days (Council incubations). The microcosm headspace was sampled at designated intervals for greenhouse gas concentrations, then destructively harvested and extracted using ultrapure water and 0.1 M KCl for analysis of the porewater geochemistry. This dataset contains one pdf, two csv data files, and one zipped file with raw data.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

Surface and Active Layer Water Chemistry, Teller Road Mile Marker 27, Seward Peninsula, Alaska, 2016-2018

This dataset provides the results of spatial surveys of aqueous geochemistry conducted at Teller Road Site, Seward Peninsula, Alaska. Surface water and soil pore water samples were collected from multiple depth within the active layer at designated Intensive Stations 2 through 9 at the Teller Road MM 27 Site (TL_MM27). Reported analytes include dissolved methane and carbon dioxide, dissolved organic and inorganic carbon, major inorganic anions, and major and minor cations. Samples and measurements were collected from 2016-2018. Specifically, samples were collected in September of 2016, August and September of 2017, and August of 2018. Most of the samples were collected from piezometers installed at various depths within the active layer (70 cm max). A few are surface water grab samples. Data are provided in a single comma separated (.xlsx / .csv) file. One supplemental file is also included. It provides the results of a limited set of analyses (dissolved methane and carbon dioxide and Fe(II)) on surface and soil pore water samples collected at Teller (TL_MM27) and Council (CN_MM71) locations in September 2019. The metadata and data are draft with outstanding clarifications and additions to come. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a 10-year research effort (2012-2022) to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy?s Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy?s Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

Shrub Seedling Experiment: Environmental Conditions, Vegetation Composition, and Seedling Recruitment, Seward Peninsula, Alaska, 2018-2019

In June 2018, a manipulative seed-addition experiment was established at the Council Mile Marker 71 (CN_MM71), Quartz Creek Burn Area (Kougarok Mile Marker 86), and Quartz Creek Unburned (Kougarok Mile Marker 80) sites on the Seward Peninsula, Alaska. At each site, 5 replicate blocks were established in disturbed and intact upland tussock tundra (a total of 40 plots). Disturbed plots at Council were located on thermo-erosional (thermokarst) slopes, while disturbed plots in Quartz Creek were in burned areas affected by the Mingvk Lake fire in 2015. Using a split-plot design, an additional manual disturbance treatment (scraping to remove the surface bryophyte layer) was implemented across all blocks in June 2018. Seeds of five erect, deciduous shrubs were broadcast seeded into each plot in June 2018, and seedlings were censused in August 2018 and August 2019. The dataset includes ancillary measurements of plot-level environmental conditions (soil temperature, moisture, chemistry, thaw depth, microtopography, substrate thickness) and vegetation composition (NDVI and estimated percent cover by species and plant functional type). Dataset contains 10 csv data files (five data files with corresponding data dictionaries and one file-level metadata file) and one pdf user guide. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

Prediction of electron density in the boundary layer on entry vehicles with ablation

A rather general computer code has been developed for the numerical solution of the laminar boundary layer and thin shock layer (stagnation point only) equations for a multi-component gas mixture with finite reaction rates. The purpose of this paper is to indicate the capabilities of this computer program by presenting solutions for pure air flows and flows with carbon ablation. At the body surface the effects of oxidation and sublimation of carbon are taken into account with the following species included in the gas model: 0 2 , N 2 , O, N, NO, NO + , C 1 , C 2 , C 3 , CN, CO, and CO 2 . Results for the boundary layer along a 10° half-angle hyperboloid with ablation of carbon are compared to pure air results. Shock layer results for several wall temperatures and altitudes are presented and compared to pure air results. Other types of problems that can be solved with this computer code are indicated.

F. G. Blottner↗