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At least 199 records · Page 11

Production of alternate realizations of DESI fiber assignment for unbiased clustering measurement in data and simulations

A critical requirement of spectroscopic large scale structure analyses is correcting for selection of which galaxies to observe from an isotropic target list. This selection is often limited by the hardware used to perform the survey which will impose angular constraints of simultaneously observable targets, requiring multiple passes to observe all of them. In SDSS this manifested solely as the collision of physical fibers and plugs placed in plates. In DESI, there is the additional constraint of the robotic positioner which controls each fiber being limited to a finite patrol radius. A number of approximate methods have previously been proposed to correct the galaxy clustering statistics for these effects, but these generally fail on small scales. To accurately correct the clustering we need to upweight pairs of galaxies based on the inverse probability that those pairs would be observed (Bianchi & Percival 2017). This paper details an implementation of that method to correct the Dark Energy Spectroscopic Instrument (DESI) survey for incompleteness. To calculate the required probabilities, we need a set of alternate realizations of DESI where we vary the relative priority of otherwise identical targets. These realizations take the form of alternate Merged Target Ledgers (AMTL), the files that link DESI observations and targets. We present the method used to generate these alternate realizations and how they are tracked forward in time using the real observational record and hardware status, propagating the survey as though the alternate orderings had been adopted. We detail the first applications of this method to the DESI One-Percent Survey (SV3) and the DESI year 1 data. We include evaluations of the pipeline outputs, estimation of survey completeness from this and other methods, and validation of the method using mock galaxy catalogs.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Hydrogen separation with a graphenylene monolayer: Diffusion Monte Carlo study

Here, we performed fixed-node diffusion Monte Carlo (DMC) calculations to investigate structural and energetic properties of graphenylene (GPNL), a two-dimensional network of sp 2 -bonded carbon atoms with large near-circular pores, and its H 2 separation performance for gas mixtures. We have found that the energetic stability of a GPNL monolayer is comparable to that of γ-graphyne, as evidenced by its large cohesive energy of 6.755(3) eV/atom. Diffusion barriers of several gas molecules, including hydrogen, through a GPNL membrane were determined from the analysis of their adsorption energies depending on the adsorption distance, which led to our estimation for hydrogen selectivity with respect to other target molecules. DMC hydrogen selectivity of a GPNL monolayer was found to be exceptionally high at 300 K, as high as 10 10 –10 11 against CO and N 2 gases. This, along with high hydrogen permeance due to its generic pore structure, leads us to conclude that GPNL is a promising membrane to be used as a high-performance hydrogen separator from gas mixtures. We find that when compared to our DMC results, DFT calculations tend to overestimate H 2 selectivity, which is mostly due to their inaccurate description of short-range repulsive interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Encapsulation in a Bacterial Microcompartment Shell Improves Thermal Stability of a Glycolytic Enzyme

Selective encapsulation of target enzymes is an increasingly well-studied field, with a host of potential applications for biotechnology. Natively, many bacteria utilize bacterial microcompartments (BMCs) for enzyme encapsulation to enhance catalysis. BMCs are protein shells that enable selective localization of targeted metabolic enzymes and may improve catalytic rates by colocalizing pathway enzymes and/or serve to sequester toxic or volatile intermediates. The microcompartment shell of Haliangium ochraceum (HO) is a notable BMC chassis because of its modularity and versatility; it is easily expressed and assembled outside its native host and can accept a wide array of cargo. Recently, it was demonstrated that assembly of HO BMC shells can be easily achieved in vitro. Following up on our previous work on in vivo assembly of HO-BMCs with triose phosphate isomerase (TPI) as a model enzyme cargo, here we have demonstrated the advantages of in vitro assembly (IVA) for targeted enzyme encapsulation. We achieved variable loading of BMC shells with targeted amounts of TPI and demonstrated enhanced thermal stability of encapsulated TPI versus free TPI up to 62 °C.

assays↗

Selection of a Pair of Experiments to Optimally Reduce Uncertainty in Targeted Nuclear Data

We propose a novel process to select a pair of differential and integral experiments that best reduce uncertainties in targeted 239 ⁢Pu nuclear data while compressing the current nuclear data pipeline from 20 to 3 years. 239⁢ Pu nuclear data are poorly understood for neutrons in the intermediate energy range due to sparsity and uncertainty in historical experiments. New experiments targeting this range will enable better understanding of these nuclear data, but choosing the ideal experiments to conduct is challenging. Beginning with a prior distribution represented by samples of nuclear data generated from theory, generalized least squares adjustments are made to incorporate data from historical experiments. To quantify potential uncertainty reduction obtainable from a pair of candidate experiments, we compute the D-optimality criterion of the posterior covariance of intermediate energy range nuclear data compared to the equivalent covariance after additional adjustment to the pair of candidate experiments. Repeating the process for each of many candidate pairs facilitates the final selection. Results support 63⁢ Cu total cross section measurements for differential experiments and alumina and alumina/graphite configurations for integral experiments. This analysis enables choosing differential and integral experiments to be executed concurrently while shortening decision times relative to the current nuclear data pipeline.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Validation of a Proteomic Signature of Lung Cancer Risk from Bronchial Specimens of Risk-Stratified Individuals

A major challenge in lung cancer prevention and cure hinges on identifying the at-risk population that ultimately develops lung cancer. Previously, we reported proteomic alterations in the cytologically normal bronchial epithelial cells collected from the bronchial brushings of individuals at risk for lung cancer. The purpose of this study is to validate, in an independent cohort, a selected list of 55 candidate proteins associated with risk for lung cancer with sensitive targeted proteomics using selected reaction monitoring (SRM). Bronchial brushings collected from individuals at low and high risk for developing lung cancer as well as patients with lung cancer, from both a subset of the original cohort (batch 1: n = 10 per group) and an independent cohort of 149 individuals (batch 2: low risk (n = 32), high risk (n = 34), and lung cancer (n = 83)), were analyzed using multiplexed SRM assays. ALDH3A1 and AKR1B10 were found to be consistently overexpressed in the high-risk group in both batch 1 and batch 2 brushing specimens as well as in the biopsies of batch 1. Validation of highly discriminatory proteins and metabolic enzymes by SRM in a larger independent cohort supported their use to identify patients at high risk for developing lung cancer.

60 APPLIED LIFE SCIENCES↗

The impact of spectroscopic incompleteness in direct calibration of redshift distributions for weak lensing surveys

ABSTRACT Obtaining accurate distributions of galaxy redshifts is a critical aspect of weak lensing cosmology experiments. One of the methods used to estimate and validate redshift distributions is to apply weights to a spectroscopic sample, so that their weighted photometry distribution matches the target sample. In this work, we estimate the selection bias in redshift that is introduced in this procedure. We do so by simulating the process of assembling a spectroscopic sample (including observer-assigned confidence flags) and highlight the impacts of spectroscopic target selection and redshift failures. We use the first year (Y1) weak lensing analysis in Dark Energy Survey (DES) as an example data set but the implications generalize to all similar weak lensing surveys. We find that using colour cuts that are not available to the weak lensing galaxies can introduce biases of up to Δz ∼ 0.04 in the weighted mean redshift of different redshift intervals (Δz ∼ 0.015 in the case most relevant to DES). To assess the impact of incompleteness in spectroscopic samples, we select only objects with high observer-defined confidence flags and compare the weighted mean redshift with the true mean. We find that the mean redshift of the DES Y1 weak lensing sample is typically biased at the Δz = 0.005−0.05 level after the weighting is applied. The bias we uncover can have either sign, depending on the samples and redshift interval considered. For the highest redshift bin, the bias is larger than the uncertainties in the other DES Y1 redshift calibration methods, justifying the decision of not using this method for the redshift estimations. We discuss several methods to mitigate this bias.

79 ASTRONOMY AND ASTROPHYSICS↗

A striking relationship between dust extinction and radio detection in DESI QSOs: evidence for a dusty blow-out phase in red QSOs

ABSTRACT We present the first eight months of data from our secondary target programme within the ongoing Dark Energy Spectroscopic Instrument (DESI) survey. Our programme uses a mid-infrared and optical colour selection to preferentially target dust-reddened quasi-stellar objects (QSOs) that would have otherwise been missed by the nominal DESI QSO selection. So far, we have obtained optical spectra for 3038 candidates, of which ∼70 per cent of the high-quality objects (those with robust redshifts) are visually confirmed to be Type 1 QSOs, consistent with the expected fraction from the main DESI QSO survey. By fitting a dust-reddened blue QSO composite to the QSO spectra, we find they are well-fitted by a normal QSO with up to AV ∼ 4 mag of line-of-sight dust extinction. Utilizing radio data from the LOFAR Two-metre Sky Survey (LoTSS) DR2, we identify a striking positive relationship between the amount of line-of-sight dust extinction towards a QSO and the radio detection fraction, that is not driven by radio-loud systems, redshift and/or luminosity effects. This demonstrates an intrinsic connection between dust reddening and the production of radio emission in QSOs, whereby the radio emission is most likely due to low-powered jets or winds/outflows causing shocks in a dusty environment. On the basis of this evidence, we suggest that red QSOs may represent a transitional ‘blow-out’ phase in the evolution of QSOs, where winds and outflows evacuate the dust and gas to reveal an unobscured blue QSO.

79 ASTRONOMY AND ASTROPHYSICS↗

An obscured quasar census with the 4MOST IR AGN survey: design, predicted properties, and scientific goals

ABSTRACT We present the 4MOST (4-metre Multi-Object Spectroscopic Telescope) infrared (IR) AGN survey, the first large-scale optical spectroscopic survey characterizing mid-infrared (MIR) selected obscured active galactic nuclei (AGNs). The survey targets $\approx 212\,000$ obscured IR AGN candidates over $\approx 10\,000 \rm \: deg^2$ down to a magnitude limit of $r_{\rm AB}=22.8 \, \rm mag$ and will be $\approx 100 \times$ larger than any existing obscured IR AGN spectroscopic sample. We select the targets using an MIR colour criterion applied to the unWISE catalogue from the WISE (Wide-field Infrared Survey Explorer) all-sky survey, and then apply a $r-W2\ge 5.9 \rm \: mag$ cut; we demonstrate that this selection will mostly identify sources obscured by $N_{\rm H}>10^{22} \rm \: cm^{-2}$. The survey complements the 4MOST X-ray survey, which will follow up $\sim 1\,\rm M$ eROSITA (extended ROentgen Survey with an Imaging Telescope Array)-selected (typically unobscured) AGN. We perform simulations to predict the quality of the spectra that we will obtain and validate our MIR–optical colour-selection method using X-ray spectral constraints and UV-to-far-IR spectral energy distribution (SED) modelling in four well-observed deep-sky fields. We find that: (1) $\approx 80-87{{\ \rm per\ cent}}$ of the WISE-selected targets are AGN down to $r_{\rm AB}=22.1-22.8 \: \rm mag$ of which $\approx 70{{\ \rm per\ cent}}$ are obscured by $N_{\rm H}>10^{22} \: \rm cm^{-2}$, and (2) $\approx 80{{\ \rm per\ cent}}$ of the 4MOST IR AGN sample will remain undetected by the deepest eROSITA observations due to extreme absorption. Our SED-fitting results show that the 4MOST IR AGN survey will primarily identify obscured AGN and quasars ($\approx 55{{\ \rm per\ cent}}$ of the sample is expected to have $L_{\rm AGN,IR}>10^{45} \rm \: erg \: s^{-1}$) residing in massive galaxies ($M_{\star }\approx 10^{10}-10^{12} \rm \: M_{\odot }$) at $z\approx 0.5-3.5$ with $\approx 33{{\ \rm per\ cent}}$ expected to be hosted by starburst galaxies.

Andonie, Carolina (ORCID:0000000255804298)↗

To image, or not to image: class-specific diffractive cameras with all-optical erasure of undesired objects

Abstract Privacy protection is a growing concern in the digital era, with machine vision techniques widely used throughout public and private settings. Existing methods address this growing problem by, e.g., encrypting camera images or obscuring/blurring the imaged information through digital algorithms. Here, we demonstrate a camera design that performs class-specific imaging of target objects with instantaneous all-optical erasure of other classes of objects. This diffractive camera consists of transmissive surfaces structured using deep learning to perform selective imaging of target classes of objects positioned at its input field-of-view. After their fabrication, the thin diffractive layers collectively perform optical mode filtering to accurately form images of the objects that belong to a target data class or group of classes, while instantaneously erasing objects of the other data classes at the output field-of-view. Using the same framework, we also demonstrate the design of class-specific permutation and class-specific linear transformation cameras, where the objects of a target data class are pixel-wise permuted or linearly transformed following an arbitrarily selected transformation matrix for all-optical class-specific encryption, while the other classes of objects are irreversibly erased from the output image. The success of class-specific diffractive cameras was experimentally demonstrated using terahertz (THz) waves and 3D-printed diffractive layers that selectively imaged only one class of the MNIST handwritten digit dataset, all-optically erasing the other handwritten digits. This diffractive camera design can be scaled to different parts of the electromagnetic spectrum, including, e.g., the visible and infrared wavelengths, to provide transformative opportunities for privacy-preserving digital cameras and task-specific data-efficient imaging.

47 OTHER INSTRUMENTATION↗

Target Affinity and Structural Analysis for a Selection of Norovirus Aptamers

Aptamers, single-stranded oligonucleotides that specifically bind a molecule with high affinity, are used as ligands in analytical and therapeutic applications. For the foodborne pathogen norovirus, multiple aptamers exist but have not been thoroughly characterized. Consequently, there is little research on aptamer-mediated assay development. This study characterized seven previously described norovirus aptamers for target affinity, structure, and potential use in extraction and detection assays. Norovirus-aptamer affinities were determined by filter retention assays using norovirus genotype (G) I.1, GI.7, GII.3, GII.4 New Orleans and GII.4 Sydney virus-like particles. Of the seven aptamers characterized, equilibrium dissociation constants for GI.7, GII.3, GII.4 New Orleans and GII.4 Sydney ranged from 71 ± 38 to 1777 ± 1021 nM. Four aptamers exhibited affinity to norovirus GII.4 strains; three aptamers additionally exhibited affinity toward GII.3 and GI.7. Aptamer affinity towards GI.1 was not observed. Aptamer structure analysis by circular dichroism (CD) spectroscopy showed that six aptamers exhibit B-DNA structure, and one aptamer displays parallel/antiparallel G-quadruplex hybrid structure. CD studies also showed that biotinylated aptamer structures were unchanged from non-biotinylated aptamers. Finally, norovirus aptamer assay feasibility was demonstrated in dot-blot and pull-down assays. This characterization of existing aptamers provides a knowledge base for future aptamer-based norovirus detection and extraction assay development and aptamer modification.

59 BASIC BIOLOGICAL SCIENCES↗

Comparison of model predictions with measured proton-induced production of nickel and iridium isotopes

Calculations were performed to support method development for simultaneous production of Ni and Ir isotopes. Here, the work scope included development of the physical target, irradiation configuration, and post-irradiation radiochemical separations. The assumptions of predictive models previously developed were refined based upon the precise experimental configuration selected, including Os target material and a set of stacked targets for concurrent production of Ni and Ir isotopes. Model predictions of the reaction cross sections with EMPIRE 3.21 and implied isotopic yields are compared with proton beam irradiation measurements to refine model parameters and guide future experiments.

Isotope Production↗

CRISPRi-ART enables functional genomics of diverse bacteriophages using RNA-binding dCas13d

Bacteriophages constitute one of the largest reservoirs of genes of unknown function in the biosphere. Even in well-characterized phages, the functions of most genes remain unknown. Experimental approaches to study phage gene fitness and function at genome scale are lacking, partly because phages subvert many modern functional genomics tools. Here we leverage RNA-targeting dCas13d to selectively interfere with protein translation and to measure phage gene fitness at a transcriptome-wide scale. We find CRISPR Interference through Antisense RNA-Targeting (CRISPRi-ART) to be effective across phage phylogeny, from model ssRNA, ssDNA and dsDNA phages to nucleus-forming jumbo phages. Using CRISPRi-ART, we determine a conserved role of diverse rII homologues in subverting phage Lambda RexAB-mediated immunity to superinfection and identify genes critical for phage fitness. CRISPRi-ART establishes a broad-spectrum phage functional genomics platform, revealing more than 90 previously unknown genes important for phage fitness.

59 BASIC BIOLOGICAL SCIENCES↗

Biological Upcycling of Plastics Waste

Plastic wastes accumulate in the environment, impacting wildlife and human health and representing a significant pool of inexpensive waste carbon that could form feedstock for the sustainable production of commodity chemicals, monomers, and specialty chemicals. Current mechanical recycling technologies are not economically attractive due to the lower-quality plastics that are produced in each iteration. Thus, the development of a plastics economy requires a solution that can deconstruct plastics and generate value from the deconstruction products. Biological systems can provide such value by allowing for the processing of mixed plastics waste streams via enzymatic specificity and using engineered metabolic pathways to produce upcycling targets. We focus on the use of biological systems for waste plastics deconstruction and upcycling. We highlight documented and predicted mechanisms through which plastics are biologically deconstructed and assimilated and provide examples of upcycled products from biological systems. Additionally, we detail current challenges in the field, including the discovery and development of microorganisms and enzymes for deconstructing non–polyethylene terephthalate plastics, the selection of appropriate target molecules to incentivize development of a plastic bioeconomy, and the selection of microbial chassis for the valorization of deconstruction products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Wettability variation and its impact on CO 2 storage capacity at the Wyoming CarbonSAFE storage hub: An experimental approach

Meeting global and national net zero carbon emission targets will require geologic carbon disposal. The U.S. Department of Energy (DOE) has accordingly funded significant research in this area, including the Wyoming CarbonSAFE project at Dry Fork Station (DFS) in Campbell County, Wyoming. This work studied wettability on micro- and macro-scales, CO 2 storage potential, and the correlation between the two to support the Wyoming CarbonSAFE project’s subsurface assessment. During the study, a target formation’s wettability was found to affect how much CO 2 can be stored in a given formation. Here, in this study, representative rock samples were selected from the target storage formations— Lakota, Hulett, and Minnelusa—based on the heterogeneity of the lithology, permeability, and porosity of the respective formations. The rock samples are all fine-grained sandstone with variable cementation and bedding structure, including different scales of laminated bedding. The porosity and permeability vary within the range of 9.0–14.3% and 0.1–28.9 mD, respectively. These rock samples were prepared for the micro-scale wettability (contact angle measurement), macro-scale wettability (wettability index derived from unsteady-state flow characterization for the core plugs), and CO 2 storage evaluation. The macro-scale experiments suggested that wettability appeared to dominate the CO 2 storage potential performance during the drainage process, where less water-wet behavior promoted higher CO 2 storage potential. The micro-scale wettability tests showed that the rock samples at the studied reservoir conditions behaved water-wet and became more water-wet as pressure increased. This kind of wettability change discourages further CO 2 storage potential yet benefits the CO 2 residual trapping as the CO 2 injection proceeds for the studied area. The results allow the recommendation of the best reservoir candidate for storage based on wettability that affects CO 2 storage. The work presented in this study provides valuable insights into wettability’s effect on the CO 2 storage capacity and wettability’s importance when identifying the optimal CO 2 storage formation to meet the project’s goals.

58 GEOSCIENCES↗

Structures of drug-specific monoclonal antibodies bound to opioids and nicotine reveal a common mode of binding

Opioid-related fatal overdoses have reached epidemic proportions. Because existing treatments for opioid use disorders offer limited long-term protection, accelerating the development of newer approaches is critical. Monoclonal antibodies (mAbs) are an emerging treatment strategy that targets and sequesters selected opioids in the bloodstream, reducing drug distribution across the blood-brain barrier, thus preventing or reversing opioid toxicity. We previously identified a series of murine mAbs with high affinity and selectivity for oxycodone, morphine, fentanyl, and nicotine. To determine their binding mechanism, we used X-ray crystallography to solve the structures of mAbs bound to their respective targets, to 2.2 Å resolution or higher. Structural analysis showed a critical convergent hydrogen bonding mode that is dependent on a glutamic acid residue in the mAbs’ heavy chain and a tertiary amine of the ligand. Further, characterizing drug-mAb complexes represents a significant step toward rational antibody engineering and future manufacturing activities to support clinical evaluation.

60 APPLIED LIFE SCIENCES↗

Substituted polynorbornene membranes: a modular template for targeted gas separations

Polynorbornenes are ideal materials for systematic structure–property investigations designed to correlate gas-transport properties to polymer structure. The modular nature of norbornene-based systems provides a facile route towards the synthesis of diverse polymeric materials. Though many valuable correlations between gas-permeability and polynorbornene structure have been summarized in a prior review (2017), many of these efforts focused heavily on the design of materials with high permeabilities. More recently, the design of next-generation polynorbornene membranes has shifted toward the development of materials that are highly selective for multiple targeted gas separations. Since 2017, tremendous progress has been realized in the preparation of stable and highly selective polynorbornenes for membrane-based gas separations. Examples include polynorbornene derivatives that exhibit very high selectivity for CO 2 /N 2 and light hydrocarbon (e.g., C 3 +/C 1 ) separations, some of which exhibit gas separation performances that approach or exceed the 2008 upper bound. In this work, we summarize prior findings, present recent developments in the field of advanced polynorbornene membrane materials for targeted gas separations, and provide an outlook for the future of this field of research.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spin-selective photocatalysis and quantum transport using ab initio density-matrix dynamics

The overarching goal of this research program is to quantitatively predict out-of-equilibrium quantum dynamics and transport with electrons and spin degrees of freedom coupled to phonons, photons, defects and liquid environments, specifically targeting spin-selective chemistry. Spin polarized carriers, which can be generated at room temperature by circularly-polarized light, provide unique opportunities for creating new reaction pathways and increasing selectivity towards specific pathways. If realized, this can substantially increase the level of reaction control possible in the field of heterogeneous catalysis. Spin, a quantum mechanical entity without a classical counterpart, requires quantum dynamics. Capturing both coherent and incoherent dynamics and accurate correlation of spins, electrons and phonon environments are essential to quantitative description of generation, relaxation and transport, as well as chemical reaction of spin-polarized carriers in molecules and materials promising for spin-photocatalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Rational Design of Lanmodulin Variants for Size-Based Selectivity of Individual Rare Earth Elements

Rare earth elements (REEs) are essential to modern technologies, yet their high physical and chemical similarity makes separation of individual REEs difficult and environmentally taxing. Metalloproteins offer a promising alternative for selective REE binding, as they tend to have high metal ion affinity and specificity. Lanmodulin (LanM), in particular, has arisen as a potential candidate for REE separation as it exhibits picomolar affinity for elements in the REE family. Prior work has shown that the single point mutation D9N can shift LanM’s preference away from lanthanides toward actinides, motivating efforts to tune selectivity of LanM through targeted mutagenesis. Here, we tested the hypothesis that introducing selective aspartic acid to glutamic acid substitutions in the metal coordinating EF hands of LanM would impose steric constraints that would drive LanM affinity away from larger ions, such as La3+, to smaller ions, such as Y3+. To test this hypothesis, a combination of computational and experimental approaches were employed to evaluate the signal mutations LanM D5E and LanM D3E and the double mutants LanM D1ED5E and LanM D3ED9E. Surprisingly, increasing the number of mutations within the metal center did not enhance affinity for smaller REEs, or decrease affinity for larger ions. Only the single point mutation LanM D5E weakened La3+ binding by one order of magnitude relative to LanM wild type (WT), and pairing it with a second mutation to produce LanM D1ED5E drove La3+ affinity to be stronger than that seen for LanM WT. The D3E mutation alone prevented proper expression and folding, but paring it with D9E to produce LanM D3ED9E rescued expression and yielded La3+ affinities comparable to LanM WT. All variants that expressed (LanM D5E, LanM D1ED5E, LanM D3ED9E) displayed Y3+ affinities comparable to LanM WT. Overall, these results highlight the tunability of LanM’s metal-binding environment but also expose current limitations in predicting structural responses to point mutations within a protein sequence. This work establishes a foundation that can be used for refining computational and experimental strategies to engineer metalloproteins with tailored REE selectivity.

Close, Emily [Pacific Northwest National Laborator↗