GEM Workshop Closing Remarks
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Heliospheric and Magnetospheric Physics↗
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GEM 2022 Summer Workshop: Closing Remarks
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Heliospheric and Magnetospheric Physics↗
Application of GEM (Geologic Element Motion) to Heave Modeling of Cast Blasting, Mineral and Iron Ore Blasting.
Abstract not provided.
Preece, Dale -ext↗
Synergistic Use of Hyperspectral UV-Visible OMI and Broadband Meteorological Imager MODIS Data for a Merged Aerosol Product
The retrieval of optimal aerosol datasets by the synergistic use of hyperspectral ultraviolet(UV)–visible and broadband meteorological imager (MI) techniques was investigated. The Aura Ozone Monitoring Instrument (OMI) Level 1B (L1B) was used as a proxy for hyperspectral UV–visible instrument data to which the Geostationary Environment Monitoring Spectrometer (GEMS) aerosol algorithm was applied. Moderate-Resolution Imaging Spectroradiometer (MODIS) L1B and dark target aerosol Level 2 (L2) data were used with a broadband MI to take advantage of the consistent time gap between the MODIS and the OMI. First, the use of cloud mask information from the MI infrared (IR) channel was tested for synergy. High-spatial-resolution and IR channels of the MI helped mask cirrus and sub-pixel cloud contamination of GEMS aerosol, as clearly seen in aerosol optical depth (AOD) validation with Aerosol Robotic Network (AERONET) data. Second, dust aerosols were distinguished in the GEMS aerosol-type classification algorithm by calculating the total dust confidence index (TDCI) from MODIS L1B IR channels. Statistical analysis indicates that the Probability of Correct Detection (POCD) between the forward and inversion aerosol dust models (DS) was increased from 72% to 94% by use of the TDCI for GEMS aerosol-type classification, and updated aerosol types were then applied to the GEMS algorithm. Use of the TDCI for DS type classification in the GEMS retrieval procedure gave improved single-scattering albedo (SSA) values for absorbing fine pollution particles (BC) and DS aerosols. Aerosol layer height (ALH) retrieved from GEMS was compared with Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) data, which provides high-resolution vertical aerosol profile information. The CALIOP ALH was calculated from total attenuated backscatter data at 1064 nm, which is identical to the definition of GEMS ALH. Application of the TDCI value reduced the median bias of GEMS ALH data slightly. The GEMS ALH bias approximates zero, especially for GEMS AOD values of>~0.4 and GEMS SSA values of<~0.95.Finally, the AOD products from the GEMS algorithm and MI were used in aerosol merging with the maximum-likelihood estimation method, based on a weighting factor derived from the standard deviation of the original AOD products. With the advantage of the UV–visible channel in retrieving aerosol properties over bright surfaces, the combined AOD products demonstrated better spatial data availability than the original AOD products, with comparable accuracy. Furthermore, pixel-level error analysis of GEMS AOD data indicates improvement through MI synergy.
aerosol↗
The accuracy of geopotential models
The accuracy of two recent geopotential models, GEM 7 and GEM 8, is evaluated and is found to be about 4.3 m with respect to the global geoid surface for GEM 7 and 3.9 m for GEM 8. The accuracies are root mean square values obtained by the use of 400 coefficients for GEM 7 and 706 coefficients for GEM 8. Independent observations used in the evaluation include 159 lumped coefficients from 35 resonant orbits, two sets of fields derived from optical-only and laser-only data, sets of zonal and resonant coefficients, and geoid undulations. The ratio of estimated commission to formal error in GEM 7 and GEM 8 ranges from 2 to 5. Several other recent geopotential models are examined.
Wagner, C. A.↗
Knowledge-matching based computational framework for genome-scale metabolic model refinement
Genome-scale metabolic models (GEMs) are mathematically structured knowledge base reconstructed from annotated genome of different organisms. With the advancement of next-generation sequencing technology, many organisms have had their genomes sequenced. However, obtaining a high-quality GEM is highly time-consuming, even with the introduction of several genome-scale reconstruction tools that offer automated draft network generation and gap filling. It has been recognized that the iterative process of manual curation and refinement is the limiting step of GEM development, and how to expedite the GEM refinement is still an open question. As cellular metabolism is a complex system with very high degree of freedom and redundancy, the principles and techniques developed in process systems engineering can be adapted to expedite GEM refinement. In this paper we present a knowledge-matching based computation framework for GEM refinement, and demonstrate the effectiveness of the proposed solution using the refinement of a GEM for Clostridium tyrobutyricum.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Previously unaccounted atmospheric mercury deposition in a midlatitude deciduous forest
Significance Direct measurements of atmospheric deposition of gaseous elemental mercury (GEM) over a temperate forest showed a pronounced annual deposition of 25.1 µg ⋅ m −2 , which dominated as a source of mercury. GEM deposition was five times greater than wet deposition and three times greater than litterfall deposition, which has been used as a proxy for GEM deposition until now. Measured GEM deposition is driven by combined plant GEM uptake and underlying forest floor GEM uptake. Global forests may be a much larger global GEM sink than currently assumed, which may explain high mercury levels in soils across forests. Forest mercury mobilizes via watershed runoff and bioaccumulates in aquatic biota, ultimately leading to mercury exposures in wildlife and humans.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Improvement in the geopotential derived from satellite and surface data /Gem 7 and 8/
A refinement has been obtained in the earth's gravitational field by using satellite and surface data. In addition to a more complete treatment of data previously employed on 27 satellites, the new satellite solution Gem 7 (Goddard Earth Model 7) includes 64,000 laser measurements taken on seven satellites. Gem 7, containing 400 harmonic terms, is complete through degree and order 16. The companion solution Gem 8 combines the same satellite data as Gem 7 with surface gravimetry over 39% of the earth. Gem 8 is complete to degree and order 25. Extensive tests on data independent of the solution show that the undulations of the geoidal surface computed by Gem 7 have an accuracy of about 2.5 m (rms). The overall accuracy of the geoid calculated by Gem 8 is estimated to be about 4 m (rms). The new combination solution is the first to show signs of 'convection rolls' in the upper mantle below the Pacific Ocean.
Wagner, C. A.↗
Evaluation of a High-Resolution Numerical Weather Prediction Model’s Simulated Clouds Using Observations from CloudSat, GOES-13 and in Situ Aircraft
This study aimed to assess tropical cloud properties predicted by Environment and Climate Change Canada’s Global Environmental Multiscale (GEM)modelwhen run with the Milbrandt–Yau double-moment cloud microphysical scheme and one-way nesting that culminated at a (∼300 km)2 inner domain with 0.25 km horizontal grid spacing. The assessment utilized satellite and in situ data collected during the High Ice Water Content (HIWC) and High Altitude Ice Crystals (HAIC) projects for a mesoscale convective system on 16May 2015 over French Guiana.Data fromCloud- Sat’s cloud-profiling radar and GOES-13’s imager were compared to data either simulated directly by GEM or produced by operating on GEM’s cloud data with both the CFMIP (Cloud Feedback Model Intercomparison Project) Observation Simulator Package (COSP) instrument simulator and a three-dimensional Monte Carlo solar radiative transfer model. In situ observations were made from research aircraft – Canada’s National Research Council Convair-580 and the French SAFIRE Falcon-20 – whose flight paths were aligned with CloudSat’s ground-track. Spatial and temporal shifts of clouds simulated by GEM compared well to GOES-13 imagery. There are, however, differences between simulated and observed amounts of high and low cloud. While GEM did well at predicting ranges of ice-water content (IWC) near 11 km altitude (Falcon-20), it produces too much graupel and snow near 7 km (Convair-580). This produced large differences between CloudSat’s and COSP-generated radar reflectivities and two-way attenuations. On the other hand, CloudSat’s inferred values of IWC agree well with in situ samples at both altitudes. Generally, GEM’s visible reflectances exceeded GOES-13’s on account of having produced too much low-level liquid cloud. It is expected that GEM’s disproportioning of cloud hydrometeors will improve once it includes a better representation of secondary ice production.
Qu, Zhipeng↗
Analysis of Coronado State Historic Site artifacts using X‐rays
Abstract Two historic‐period metal artifacts were provided by the New Mexico Historic Sites to Los Alamos National Laboratory for non‐destructive analysis. The artifacts were a crossbow quarrel (or bolthead) and a reliquary pendant recovered from Kuaua Pueblo (also known as the Coronado Historic Site) in Bernalillo, NM. The quarrel is a heavily patinated metal that had been flattened due to compressive forces. The pendant consisted of a metal casing that had previously surrounded two center gemstones on the front and rear face of the pendant. The gemstone in the rear setting had fractured and was displaced from the setting, leaving only a small, loose fragment within the pendant for study. The front gem appeared to be very dark, near‐black in color, and the fragment of the rear gem was a bright red color. The artifacts were analyzed to ascertain their composition and glean insight into their provenance using the following X‐ray techniques: X‐ray computed tomography, confocal micro X‐ray fluorescence, and X‐ray diffraction. Infrared spectroscopy and electron microscopy were used on selected areas. Ultraviolet Raman spectra were collected on the two gems and the pendant. The metal material of the artifacts was found to be primarily composed of copper. The gems in the pendant were composed of manganese (front gem) and calcium (side gem).
36 MATERIALS SCIENCE↗
Advances in genome-scale metabolic models of industrially important fungi
Many fungal species have been used in industrial production for biofuels and bioproducts. Developing strains with better performance in biomanufacturing requires systematic understanding of cellular metabolism. Genome-scale metabolic models (GEMs) offer a comprehensive view of interconnected pathways and a mathematical framework for downstream analysis. Recently, GEMs have been developed or updated in several industrially important fungi. Some of them incorporate enzyme constraints, enabling improved predictions of cell states and proteome allocation. In this report we provide an overview of these newly developed GEMs and computational methods that facilitate construction of enzyme-constrained GEMs and utilize flux predictions from GEMs. Furthermore, we highlight the pivotal roles of these GEMs in iterative design-build-test- learn cycles, ultimately advancing the field of fungal biomanufacturing.
59 BASIC BIOLOGICAL SCIENCES↗
In vitro assessment of a synergistic combination of gemcitabine and zebularine in pancreatic cancer cells
Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers with an extremely poor prognosis. Gemcitabine (Gem) is still the mainstay drug for the treatment of PDAC. However, rapid inactivation by cytidine deaminase (CDA) present in pancreatic cancer cells severely limits anticancer efficacy of Gem. In this study, we investigated the effect of a CDA inhibitor - Zebularine (Zeb) on anticancer activity of Gem in pancreatic cancer cell lines MiaPaCa-2, BxPC-3, and Panc-1. Zeb treatment synergistically increased Gem-induced cytotoxicity in all three pancreatic cancer cell lines. The strongest synergistic activity was found at 1:10 M ratio of Gem/Zeb (combination index 0.04–0.4). Additionally, Gem + Zeb treated cells showed marked decreased in the expressions of anti-apoptotic protein including Bcl-2 and survivin while significantly increased the cleaved caspase-3, and loss of mitochondrial membrane potential was observed. Multicellular 3D spheroids of MiaPaCa-2 cells treated with combination showed significant reduction (25–60%) in spheroid size, weight compared to single drug and control group. Live/dead cell imaging showed that Gem + Zeb treated spheroids exhibited a highly distorted surface with significantly higher number of dead cells (red). The results of the present study confirm that this synergistic combination is worthy of future investigations as a potential approach for the treatment of PDAC.
60 APPLIED LIFE SCIENCES↗
Probing interspecies metabolic interactions within a synthetic binary microbiome using genome-scale modeling
Metabolic interactions within a microbial community play a key role in determining the structure, function, and composition of the community. However, due to the complexity and intractability of natural microbiomes, limited knowledge is available on interspecies interactions within a community. In this work, using a binary synthetic microbiome, a methanotroph-photoautotroph (M-P) coculture, as the model system, we examined different genome-scale metabolic modeling (GEM) approaches to gain a better understanding of the metabolic interactions within the coculture, how they contribute to the enhanced growth observed in the coculture, and how they evolve over time. Using batch growth data of the model M-P coculture, we compared three GEM approaches for microbial communities. Two of the methods are existing approaches: SteadyCom, a steady state GEM, and dynamic flux balance analysis (DFBA) Lab, a dynamic GEM. We also proposed an improved dynamic GEM approach, DynamiCom, for the M-P coculture. SteadyCom can predict the metabolic interactions within the coculture but not their dynamic evolutions; DFBA Lab can predict the dynamics of the coculture but cannot identify interspecies interactions. DynamiCom was able to identify the cross-fed metabolite within the coculture, as well as predict the evolution of the interspecies interactions over time. A new dynamic GEM approach, DynamiCom, was developed for a model M-P coculture. Constrained by the predictions from a validated kinetic model, DynamiCom consistently predicted the top metabolites being exchanged in the M-P coculture, as well as the establishment of the mutualistic N-exchange between the methanotroph and cyanobacteria. The interspecies interactions and their dynamic evolution predicted by DynamiCom are supported by ample evidence in the literature on methanotroph, cyanobacteria, and other cyanobacteria-heterotroph cocultures.
59 BASIC BIOLOGICAL SCIENCES↗
Analysis of Coronado State Historic Site artifacts using X-rays
Two historic-period metal artifacts were provided by the New Mexico Historic Sites to Los Alamos National Laboratory for non-destructive analysis. The artifacts were a crossbow quarrel (or bolthead) and a reliquary pendant recovered from Kuaua Pueblo (also known as the Coronado Historic Site) in Bernalillo, NM. The quarrel is a heavily patinated metal that had been flattened due to compressive forces. The pendant consisted of a metal casing that had previously surrounded two center gemstones on the front and rear face of the pendant. The gemstone in the rear setting had fractured and was displaced from the setting, leaving only a small, loose fragment within the pendant for study. The front gem appeared to be very dark, near-black in color, and the fragment of the rear gem was a bright red color. The artifacts were analyzed to ascertain their composition and glean insight into their provenance using the following X-ray techniques: X-ray computed tomography, confocal micro X-ray fluorescence, and X-ray diffraction. Infrared spectroscopy and electron microscopy were used on selected areas. Ultraviolet Raman spectra were collected on the two gems and the pendant. The metal material of the artifacts was found to be primarily composed of copper. The gems in the pendant were composed of manganese (front gem) and calcium (side gem).
36 MATERIALS SCIENCE↗
Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data
Genome-scale metabolic models (GEMs) enable the mathematical simulation of the metabolism of archaea, bacteria, and eukaryotic organisms. GEMs quantitatively define a relationship between genotype and phenotype by contextualizing different types of Big Data (e.g., genomics, metabolomics, and transcriptomics). In this review, we analyze the available Big Data useful for metabolic modeling and compile the available GEM reconstruction tools that integrate Big Data. We also discuss recent applications in industry and research that include predicting phenotypes, elucidating metabolic pathways, producing industry-relevant chemicals, identifying drug targets, and generating knowledge to better understand host-associated diseases. In addition to the up-to-date review of GEMs currently available, we assessed a plethora of tools for developing new GEMs that include macromolecular expression and dynamic resolution. Finally, we provide a perspective in emerging areas, such as annotation, data managing, and machine learning, in which GEMs will play a key role in the further utilization of Big Data.
59 BASIC BIOLOGICAL SCIENCES↗
Formation and Processing of Amorphous Silicates in Primitive Carbonaceous Chondrites and Cometary Dust
Chondritic-porous interplanetary dust particles (CP IDPs) exhibit strongly heterogeneous and unequilibrated mineralogy at sub-micron scales, are enriched in carbon, nitrogen and volatile trace elements, and contain abundant presolar materials [1-4]. These observations suggest that CP IDPs have largely escaped the thermal processing and water-rock interactions that have severely modified or destroyed the original mineralogy of primitive meteorites. CP IDPs are believed to represent direct samples of the building blocks of the Solar System - a complex mixture of nebular and presolar materials largely unperturbed by secondary processing. The chemical and isotopic properties of CP IDPs and their atmospheric entry velocities are also consistent with cometary origins. GEMS (glass with embedded metal and sulfides) grains are a major silicate component of CP IDPs. GEMS grains are < 0.5 microns in diameter objects that consist of numerous 10 to 50 nm-sized Fe-Ni metal and Fe-Ni sulfide grains dispersed in a Mg-Si-Al-Fe amorphous silicate matrix [2, 5]. Based on their chemistry and isotopic compositions, most GEMS appear to be non-equilibrium condensates from the early solar nebula [2]. If GEMS grains are a common nebular product, then they should also be abundant in the matrices of the most physically primitive chondritic meteorites. Although amorphous silicates are common in the most primitive meteorites [6-9], their relationship to GEMS grains and the extent to which their compositions and microstructure have been affected by parent body processing (oxidation and aqueous alteration) is poorly constrained. Here we compare and contrast the chemical, microstructural and isotopic properties of amorphous silicates in primitive carbonaceous chondrites to GEMS grains in IDPs.
Keller, Lindsay P.↗
Heterogeneity of Bulk Oxygen Isotopic Compositions in Anhydrous Interplanetary Dust Particles
Introduction: Anhydrous interplanetary dust particles are one of the least altered ancient solar systemmaterials. Their bulk chemical compositions match those of CI chondrites within a factor of 2-3, except for carbonwhich is enriched in both anhydrous and hydrated IDPs by ~4x CI [1]. Hydrous IDPs often show 16O-poor isotopiccompositions, likely due to the interaction with isotopically heavy H2O [2]. Anhydrous IDPs are interpreted tooriginate from comets from the outer solar system [3]. Oxygen isotopic data for these materials is scarce, but resultspoint to a wider range of compositions [4]. This heterogeneity might be a result of mixing between a 16O-rich and a16O-poor reservoir formed via self-shielding and photodissociation of CO [5]. Here, we report bulk oxygen isotopiccompositions of three anhydrous IDPs in context of their mineralogical composition and discuss possible origins ofisotopic heterogeneity. Experimental: Bulk chemical composition and mineralogy of 70 nm thin ultramicrotomed sections of threeanhydrous IDPs (L2099A7, L2099A8, and L2071AB1) were analyzed using a Thermo Scientific Titan Themis G360-300 TEM equipped with a four-quadrant energy-dispersive X-ray detector (Super-X G2) at University ofMünster. Bulk oxygen isotopic compositions were measured using a NanoSIMS 50 at the Max-Planck-Institut fürChemie in Mainz. A focused Cs+ ion beam (~1 pA, ~100 nm) was rastered over a field of view varying from 5 x 5 to6 x 6 μm2, depending on particle size for 15 layers. Negative secondary ions of 16O, 17O, 18O, 12C14N, and 28Si werecollected on electron multipliers. The 16OH contribution to the 17O peak was 1-2 ‰. As a standard, a matrix regionof meteorite CR2 Queen Alexandra Range (QUE) 99177 was used, whose oxygen isotopic composition wasmeasured by [6]. Results and Discussion: Particles A7 and A8 are both fine-grained, consisting mostly of small, 100 nm-sizedequilibrated aggregates (EA). Both particles exhibit discontinuous magnetite rims with thicknesses up to 50 nm inA7 and 100 nm in A8 on the outsides. In Particle AB1, the upper part of the particle consists of a few EAs, while thelower part contains lots of small GEMS grains with 100-200 nm diameter clustered together. Magnetite rims arenearly absent, the rare rims reaching maximum 20 nm thickness, indicating that AB1 is of more primitive naturethan the other two IDPs [1]. Furthermore, it contains several diffuse GEMS-like areas, identified by an amorphoussilicate groundmass with small nano-inclusions of Fe,Ni-metal and Fe-sulfides. All three particles are subsolar forall major element/Si ratios. Mean S/Si of particles A7 and A8 is 0.046 and 0.048, respectively, while it is an order ofmagnitude higher in AB1 (0.184). This reflects the higher degree of thermal alteration in A7 and A8, resulting in theloss of volatile S and oxidation of Fe-sulfides and FeNi-metal to magnetite as present in particle rims. A8 is rather16O-poor with δ17OSMOW = 7.8 ± 3.4 ‰ and δ18OSMOW = 9.5 ± 3.1 ‰ (1σ), followed by A7 with δ17OSMOW = − 0.8 ±4.6 ‰ and δ18OSMOW = −2.2 ± 3.4 ‰. In contrast to that, AB1 has the most 16O-rich bulk composition with δ17OSMOW= −24.2 ± 5.4 ‰ and δ18OSMOW = −25.3 ± 3.6 ‰. All investigated IDPs plot slightly above the CCAM line aspreviously reported for other anhydrous IDPs [4], maybe due to a contribution from circumstellar dust from AGBstars enriched in 17O [7]. The 16O-rich composition of AB1 is similar to the most 16O-rich anhydrous IDP U2015D21measured by [8] which is dominated by GEMS [9] and the GEMS-rich IDP GM4-2 reported by [10]. Nevertheless,it is unlikely that GEMS are the carrier for the 16O-rich composition of AB1 because most GEMS have O isotopiccompositions indistinguishable from terrestrial values, although errors on these analyses are large [11]. The isotopicheterogeneity is best explained by contribution of grains from different regions in the protoplanetary disk, samplingdifferent O isotope reservoirs, created by self-shielding and photodissociation of CO. This process resulted in 16O-rich CO gas and 16O-poor H2O that froze as ice-mantles onto dust grains [12]. Alternatively, the higher degree ofheating in A7 and A8 could have influenced isotopic fractionation, because higher δ17,18O values are reported fromthe regions of the atmosphere where small particles are heated and oxidized, as observed for the thermal alteration ofcosmic spherules [13]. Acknowledgements: We would like to thank NASA Astromaterials Acquisition & Curation Office for providing IDPsamples and DFG for funding this project (VO1816/5-1)
B Schulz↗
Redesigned Nylon 6 Variants with Enhanced Recyclability, Ductility, and Transparency
Abstract Geminal ( gem −) disubstitution in heterocyclic monomers is an effective strategy to enhance polymer chemical recyclability by lowering their ceiling temperatures. However, the effects of specific substitution patterns on the monomer's reactivity and the resulting polymer's properties are largely unexplored. Here we show that, by systematically installing gem ‐dimethyl groups onto ϵ‐caprolactam (monomer of nylon 6) from the α to ϵ positions, both the redesigned lactam monomer's reactivity and the resulting gem ‐nylon 6’s properties are highly sensitive to the substitution position, with the monomers ranging from non‐polymerizable to polymerizable and the gem ‐nylon properties ranging from inferior to far superior to the parent nylon 6. Remarkably, the nylon 6 with the gem ‐dimethyls substituted at the γ position is amorphous and optically transparent, with a higher T g (by 30 °C), yield stress (by 1.5 MPa), ductility (by 3×), and lower depolymerization temperature (by 60 °C) than conventional nylon 6.
Tian, Jun‐Jie↗