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At least 253 records · Page 14

UV–Visible reflectance of common light reflectors and their degradation after an ionization dose up to 100 Mrad

We report light reflectors are widely used to enhance scintillation light collection. Their enhancement level depends on the reflector’s reflectance at the scintillator’s emission wavelength. We report UV–Visible reflectance spectra, relative to BaSO 4 , for several common reflectors. Also reported is their radiation hardness against an ionization dose up to 100 Mrad. The results of this investigation provide a reference for applications of these reflectors in a severe radiation environment.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Seismic Diffusivity and the Influence of Heterogeneity on Injection‐Induced Seismicity

Abstract The spatiotemporal patterns of injection‐induced seismicity (IIS) are commonly interpreted with the concept of a triggering front, which propagates in a diffusion‐like manner with an associated diffusivity parameter. Here, we refer to this diffusivity as the “seismic diffusivity.” Several previous studies implicitly assume that seismic diffusivity is equivalent to the effective hydraulic diffusivity of the subsurface, which describes the behavior of the mean pressure field in heterogeneous porous media. Seismicity‐based approaches for hydraulic characterization or simulations of IIS using domains of homogeneous equivalent porous media are implicitly based on this assumed equivalence. However, seismicity is expected to propagate with the threshold triggering pressure, and thus not be controlled by the evolution of the mean pressure field. We present numerical simulations of fluid injection to compare the seismic and effective hydraulic diffusivities in heterogeneous formations (including fractured rock). The numerical model combines uncoupled, linear pressure diffusion with the Mohr‐Coulomb failure criterion to simulate IIS. We demonstrate that connected pathways of relatively high hydraulic diffusivity in heterogeneous media (particularly in fractured rock domains) allow the threshold triggering pressure to propagate more rapidly than predicted by the effective hydraulic diffusivity. As a result, the seismic diffusivity is greater than the effective hydraulic diffusivity in heterogeneous porous media, possibly by an order of magnitude or more. Additionally, we present a case study of IIS near Soultz‐sous‐Forêts where seismic diffusivity is found to be at least one order of magnitude larger than the effective hydraulic diffusivity.

Haagenson, Ryan↗

Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein

The ARTIC Network provides a common resource of PCR primer sequences and recommendations for amplifying SARS-CoV-2 genomes. The initial tiling strategy was developed with the reference genome Wuhan-01, and subsequent iterations have addressed areas of low amplification and sequence drop out. Recently, a new version (V4) was released, based on new variant genome sequences, in response to the realization that some V3 primers were located in regions with key mutations. Herein, we compare the performance of the ARTIC V3 and V4 primer sets with a matched set of 663 SARS-CoV-2 clinical samples sequenced with an Illumina NovaSeq 6000 instrument. We observe general improvements in sequencing depth and quality, and improved resolution of the SNP causing the D950N variation in the spike protein. Importantly, we also find nearly universal presence of spike protein substitution G142D in Delta-lineage samples. Due to the prior release and widespread use of the ARTIC V3 primers during the initial surge of the Delta variant, it is likely that the G142D amino acid substitution is substantially underrepresented among early Delta variant genomes deposited in public repositories. In addition to the improved performance of the ARTIC V4 primer set, this study also illustrates the importance of the primer scheme in downstream analyses.

59 BASIC BIOLOGICAL SCIENCES↗

Comparative Genomics Applied to Systematically Assess Pathogenicity Potential in Shiga Toxin-Producing Escherichia coli O145:H28

Shiga toxin-producing Escherichia coli (STEC) O145:H28 can cause severe disease in humans and is a predominant serotype in STEC O145 environmental isolates. Here, comparative genomics was applied to a set of clinical and environmental strains to systematically evaluate the pathogenicity potential in environmental strains. While the core genes-based tree separated all O145:H28 strains from the non O145:H28 reference strains, it failed to segregate environmental strains from the clinical. In contrast, the accessory genes-based tree placed all clinical strains in the same clade regardless of their genotypes or serotypes, apart from the environmental strains. Loss-of-function mutations were common in the virulence genes examined, with a high frequency in genes related to adherence, autotransporters, and the type three secretion system. Distinct differences in pathogenicity islands LEE, OI-122, and OI-57, the acid fitness island, and the tellurite resistance island were detected between the O145:H28 and reference strains. A great amount of genetic variation was detected in O145:H28, which was mainly attributed to deletions, insertions, and gene acquisition at several chromosomal “hot spots”. Finally, our study demonstrated a distinct virulence gene repertoire among the STEC O145:H28 strains originating from the same geographical region and revealed unforeseen contributions of loss-of-function mutations to virulence evolution and genetic diversification in STEC.

59 BASIC BIOLOGICAL SCIENCES↗

Role of the junction voltage on the overflow current in light-emitting diodes

Quantum-well (QW)-based light emitters, such as light-emitting diodes (LEDs) and lasers, of various semiconductor materials experience a reduction in their efficiency when operating at higher temperatures, a phenomenon referred to as “thermal droop.” Among the various claims on the origins of thermal droop, an increased overflow current with increasing temperatures is a common contender. Since overflow of carriers can only occur when the junction voltage 𝑉 Junction approaches the built-in voltage 𝑉 BI of any diodes, we develop a simple method relating the difference between 𝑉 Junction and 𝑉 BI to approximate the upper limit of overflow occurring in QW-based light-emitting diodes. The measured difference between 𝑉 Junction and 𝑉 BI of state-of-the-art commercial blue and green In⁢Ga⁢N-based LEDs at temperatures up to ∼450 K suggests negligible overflow. To further experimentally verify the absence of overflow, we perform temperature-dependent electron emission spectroscopy on the same commercial blue and green LEDs and find no evidence of thermally enhanced overflow carriers up to ∼450 K. In agreement with our claims that 𝑉 Junction must approach 𝑉 BI for overflow to occur, two-dimensional temperature-dependent electrical simulations of violet, blue, and green LEDs including alloy disorder and V-defects demonstrate that overflow can be significant in violet LEDs, where the small band offset between the In⁢Ga⁢N QW and Ga⁢N cladding layers due to the larger QW bandgap requires larger 𝑉 Junction to reach standard operating current densities, thereby approaching 𝑉 BI . By contrast, simulations indicate that overflow is negligible in blue and green LEDs, whose smaller QW bandgaps result in smaller quasi-Fermi levels difference to reach significant carrier injection, resulting in a 𝑉 Junction much smaller than 𝑉 BI up to large operating current densities. Considering that overflow is negligible in blue and longer-wavelength LEDs, and our observations of the large thermal droop occurring at low current densities, where Shockley-Read-Hall (SRH) recombination dominates, we conclude that thermally enhanced SRH processes are the most significant contributor to thermal droop. Finally, we also simulate the carrier densities in the different QWs of a multiple-QW LED and observe a reduction in the total carrier density at a given operating current density, which results in a decrease in the total Auger-Meitner current of the LED from just the thermally enhanced carrier redistribution among QWs without taking any possible additional temperature dependence of their recombination coefficients. Taking all this into account, minimizing thermal droop effects in LEDs can be achieved by a reduction in defect density, using wider band gap p-n junction-defining cladding layers, and operating at higher currents.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Single-element balanced detector giving 65 dB CMRR at 30 MHz

We present a simple design for a single-element balanced detector (BD) that utilizes optical fibers in the sensing and reference channels with path length differences set to detect the differential signal at a desired frequency. With this approach, we easily achieve a common-mode rejection ratio of 65 dB, corresponding to the shot-noise limit of our setup. The CMRR demonstration is made in the MHz frequency range but could be extended to the kHz or GHz range. Using a single detector, the BD achieves stable CMRR over extended periods and does not require careful matching of detectors and amplification electronics. We demonstrate the single-element balanced detector design using the optical Kerr effect induced by a 30 MHz pulsed laser, showing a significant improvement over similar experiments using a commercial balanced detector.

Badilla-Nunez, Kelly [Georgia Institute of Technol↗

Adaptive gene loss in the common bean pan-genome during range expansion and domestication

The common bean ( Phaseolus vulgaris L.) is a crucial legume crop and an ideal evolutionary model to study adaptive diversity in wild and domesticated populations. Here, we present a common bean pan-genome based on five high-quality genomes and whole-genome reads representing 339 genotypes. It reveals ~234 Mb of additional sequences containing 6,905 protein-coding genes missing from the reference, constituting 49% of all presence/absence variants (PAVs). More non-synonymous mutations are found in PAVs than core genes, probably reflecting the lower effective population size of PAVs and fitness advantages due to the purging effect of gene loss. Our results suggest pan-genome shrinkage occurred during wild range expansion. Selection signatures provide evidence that partial or complete gene loss was a key adaptive genetic change in common bean populations with major implications for plant adaptation. The pan-genome is a valuable resource for food legume research and breeding for climate change mitigation and sustainable agriculture.

59 BASIC BIOLOGICAL SCIENCES↗

Colloid-Facilitated Actinide Transport in a Cementitious-Impacted SRS Groundwater

The objective of this report is to provide a literature review relevant to the question of whether colloid facilitated transport of plutonium is enhanced in a cementitious groundwater system on the Savannah River Site (SRS). Contaminant transport is commonly described as taking place in a system with a mobile aqueous phase and an immobile solid phase. There has been an increasing awareness of a third phase, a mobile solid phase, also referred to as a mobile colloidal phase. Mobile colloids consist of organic and/or inorganic submicron-particles that move with groundwater flow. When radionuclides are associated with the mobile colloids, the net effect is that radionuclides can move faster through the subsurface system than would be predicted by transport models that do not include mobile colloids. It is important to distinguish between subsurface colloids and subsurface mobile colloids. The subsurface environment includes an enormous reservoir of colloids, but only a tiny fraction, if any, are mobile. Mobile colloid formation is commonly described as involving a three-step process: genesis, stabilization, and transport. It was concluded that there is a strong likelihood that submicron colloids of plutonium exist near the source term, (i.e., the genesis step is likely completed). While such particles have not been directly detected, it is highly likely that plutonium could either attach to submicron particles in the sediment or that submicron plutonium fragments exist at the source. However, the tendency for these plutonium colloids to move in the SRS subsurface is extremely low, especially in engineered cementitious environments where the ionic strength of the solution and the elevated concentrations of divalent cations greatly curtails colloid suspension stability (i.e., the stabilization step is likely not completed). Together these data strongly indicate that plutonium-bearing colloids would likely exist in the near field of a tank closure facility, but the colloids would be unlikely to be mobile, thereby providing a vector for enhanced transport. Under cementitious leachate impacted groundwater conditions, it is reasonable to assume plutonium transport occurs primarily as a two-phase system, a mobile aqueous phase and an immobile solid phase.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Development of a Reference Design for a Cyber-Physical System

The purpose of this thesis is to develop a reference design to assist in the selection of security practices in power electronics design. A prototype will be developed from this reference design for evaluation. This evaluation will include a brief cost/benefit analysis to gauge the efficacy of implementing each layer of security throughout the power electronics design process. This thesis will also describe the obstacles and effectiveness of integrating a Trusted Platform Module (TPM) into a cyber-hardened grid-connected device. The TPM device is a secured crypto processor that assists in generating, storing, and restricting the use of cryptographic keys. The emphasis of this research is to establish integrity, authenticity, and confidentiality within a system by providing a baseline of security concerns for segments of the system. This research considers communication, control, and hardware level securities. The scope of this thesis will review the necessary security methods as well as consider the effects these methods have on the embedded system, to assess the desired security to responsiveness trade off. Applying this approach to a design process will alleviate various unknowns of appending security to a power electronics design. This thesis describes the specific vulnerabilities introduced within this grid-edge environment, and how the liabilities within the system can be mitigated. Initially, common security techniques will be considered to establish a guideline to benchmark performance and resource costs of the system. The foundation will be a non-hardened power electronic system platform with industry standard communication protocols. Several security techniques and attack vectors will then be evaluated to contribute to the base level platform. Other fail-safe features take place to gauge progress of the selected approach, non-inclusive to the TPM. Collectively, this investigation will determine a valid experiment by appraising and categorizing resource allocation, performance overhead, and monetary cost analysis results into a reference design. The prototype will then demonstrate methods to relieve common threats that are purposefully implemented into the design.

Blair, Nicholas Paul↗

Comparative Study of Nonlinear Black-Box Modeling for Power Electronics Converters

With the increasing penetration level of renewable sources and power electronics loads in modern power systems, accurate and computationally efficient models are needed. Black-box model (BBM) could be a useful method in such systems. However, not very extensive research efforts have been made for power electronics BBM so far, and existing works mostly focus on steady-state operation, neglecting the important transient behaviors such as load transients, voltage transients, and faults. This paper presents a comparative study of three commonly used nonlinear BBM approaches for transient behaviors of power electronics converters. Comparison methods are proposed, and the evaluations are conducted under different transients using a grid-connected single-phase photovoltaic inverter. The findings of this study provide valuable references for further feasibility investigations on implementing BBMs in large-scale power electronics-rich power systems.

Qiao, Liang↗

Generalizing Microbial Parameters in Soil Biogeochemical Models: Insights From a Multi‐Site Incubation Experiment

Abstract Incorporating microbial processes into soil biogeochemical models has received growing interest. However, determining the parameters that govern microbially driven biogeochemical processes typically requires case‐specific model calibration in various soil and ecosystem types. Here each case refers to an independent and individual experimental unit subjected to repeated measurements. Using the Microbial‐ENzyme Decomposition model, this study aimed to test whether a common set of microbially‐relevant parameters (i.e., generalized parameters) could be obtained across multiple cases based on a two‐year incubation experiment in which soil samples of four distinct soil series (i.e., Coland, Kesswick, Westmoreland, and Etowah) collected from forest and grassland were subjected to cellulose or no cellulose amendment. Results showed that a common set of parameters controlling microbial growth and maintenance as well as extracellular enzyme production and turnover could be generalized at the soil series level but not land cover type. This indicates that microbial model developments need to prioritize soil series type over plant functional types when implemented across various sites. This study also suggests that, in addition to heterotrophic respiration and microbial biomass data, extracellular enzyme data sets are needed to achieve reliable microbial‐relevant parameters for large‐scale soil model projections.

58 GEOSCIENCES↗

Neural Network Analysis of Nuclear Magnetic Resonance and Infrared Spectra

Nuclear magnetic resonance (NMR) spectroscopy and infrared (IR) spectroscopy are powerful chemical characterization techniques with broad general usage. However, the manual evaluation of the resulting spectra is time-consuming and requires significant expertise, preventing insights from being used in real-time applications. With recent advances in computation and artificial intelligence (AI), new tools are available for automating spectral interpretation. In this work, machine learning (ML) algorithms using 1-dimensional convolutional neural networks (CNNs) were applied to identify common functional groups from spectral information. Raw spectra were collected virtually from the Human Metabolome Database (HMDB) and National Institute of Standards and Technology (NIST) Chemistry WebBook and processed into a suitable standard. Algorithm design was tailored to best fit the nature of the problem, with built-in flexibility to accommodate relevant parameters beyond the raw spectral input, specifically solvent identity and magnetic frequency for NMR. The predictive capability of the algorithm in identifying functional groups is displayed in several examples. This methodology has been compiled into a code repository and could easily be modified to adapt alternative data sources, including other spectrum types. To mitigate overfitting, a common problem in mathematical modeling where overfamiliarity with training data produces trends that are not representative of the general data, a novel metric was developed, referred to as Accufit. Accufit includes a parameter that penalizes substantial differences in the training accuracy and the accuracy of an independent validation set. Examples are presented showing the effectiveness of Accufit in maintaining the model’s predictive capability while controlling the overfitting when used as a custom metric for hyperparameter tuning.

Sturgill, James↗

Detailed space–time variations of the seismic response of the shallow crust to small earthquakes from analysis of dense array data

SUMMARY We compute high-resolution space–time variations of subsurface seismic properties from autocorrelation functions (ACF’s) of noise and local earthquakes, recorded by the Sage Brush Flat dense array deployed around the Clark branch of the San Jacinto fault. The resolved temporal changes are referred to as apparent velocity changes because they reflect both nonlinear response and variations of material properties such as cracking and damage. Apparent velocity changes are estimated at four frequency bands (10–15, 10–20, 15–30 and 20–40 Hz) for two local earthquake data sets. In one analysis, ACF’s from P- and S-wave windows of 31 small events with magnitudes below 3.1 are used to compute the apparent velocity variations with respect to the mean ACF of each phase, and we also use the mean ACF of noise data as reference to estimate the changes. In a further analysis, the temporal evolution of properties is computed using moving time windows in continuous waveform over one-hour long data with noise and earthquake signals. The apparent velocity changes and recovery times are frequency dependent and present a strong spatial variability across the array. The resolved changes are larger and recovery time shorter with data associated with higher frequencies. At frequencies larger than 15 Hz, and using the mean ACF of noise data as a reference, the apparent average velocity changes across the array during the passage of the P and S waves from the small local events are 2.5 per cent and 6 per cent, respectively. The apparent velocity changes decrease by one order of magnitude when the earthquake data are used as a reference. The relatively large changes in response to very low ground motion have important implications on nonlinear processes involving degradation and healing of the subsurface material during common earthquake shaking.

Geochemistry & Geophysics↗

Functional Principal Component Analysis of Radio–Optical Reference Frame Tie

The Gaia optical reference frame is intrinsically undefined with respect to global orientation and spin, so it needs to be anchored in the radio-based International Celestial Reference Frame (ICRF) to provide a referenced and quasi-inertial celestial coordinate system. The link between the two fundamental frames is realized through two samples of distant extragalactic sources, mostly active galactic nuclei and quasars, but only the smaller sample of radio-loud ICRF sources with optical counterparts is available to determine the mutual orientation. The robustness of this link can be mathematically formulated in the framework of functional principal component analysis using a set of vector spherical harmonics to represent the differences in celestial positions of the common objects. The weakest eigenvectors are computed, which describe the greatest deficiency of the link. The deficient or poorly determined terms are specific vector fields on the sphere that carry the largest errors of absolute astrometry using Gaia in reference to the ICRF. This analysis provides guidelines for the future development of the ICRF maximizing the accuracy of the link over the entire celestial sphere. A measure of the robustness of a least-squares solution, which can be applied to any linear model fitting problem, is introduced to help discriminate between reference frame tie models of different degrees.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics

Background Candida parapsilosis is a common cause of invasive candidiasis, especially in newborn infants, and infections have been increasing over the past two decades. C. parapsilosis has been primarily studied in pure culture, leaving gaps in understanding of its function in a microbiome context. Results. Here, we compare five unique C. parapsilosis genomes assembled from premature infant fecal samples, three of which are newly reconstructed, and analyze their genome structure, population diversity, and in situ activity relative to reference strains in pure culture. All five genomes contain hotspots of single nucleotide variants, some of which are shared by strains from multiple hospitals. A subset of environmental and hospital-derived genomes share variants within these hotspots suggesting derivation of that region from a common ancestor. Four of the newly reconstructed C. parapsilosis genomes have 4 to 16 copies of the gene RTA3, which encodes a lipid translocase and is implicated in antifungal resistance, potentially indicating adaptation to hospital antifungal use. Time course metatranscriptomics and metaproteomics on fecal samples from a premature infant with a C. parapsilosis blood infection revealed highly variable in situ expression patterns that are distinct from those of similar strains in pure cultures. For example, biofilm formation genes were relatively less expressed in situ, whereas genes linked to oxygen utilization were more highly expressed, indicative of growth in a relatively aerobic environment. In gut microbiome samples, C. parapsilosis co-existed with Enterococcus faecalis that shifted in relative abundance over time, accompanied by changes in bacterial and fungal gene expression and proteome composition. Conclusions The results reveal potentially medically relevant differences in Candida function in gut vs. laboratory environments, and constrain evolutionary processes that could contribute to hospital strain persistence and transfer into premature infant microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗

Nomenclatural issues concerning cultured yeasts and other fungi: why it is important to avoid unneeded name changes

The unambiguous application of fungal names is important to communicate scientific findings. Names are critical for (clinical) diagnostics, legal compliance, and regulatory controls, such as biosafety, food security, quarantine regulations, and industrial applications. Consequently, the stability of the taxonomic system and the traceability of nomenclatural changes is crucial for a broad range of users and taxonomists. The unambiguous application of names is assured by the preservation of nomenclatural history and the physical organisms representing a name. Fungi are extremely diverse in terms of ecology, lifestyle, and methods of study. Predominantly unicellular fungi known as yeasts are usually investigated as living cultures. Methods to characterize yeasts include physiological (growth) tests and experiments to induce a sexual morph; both methods require viable cultures. Thus, the preservation and availability of viable reference cultures are important, and cultures representing reference material are cited in species descriptions. Historical surveys revealed drawbacks and inconsistencies between past practices and modern requirements as stated in the International Code of Nomenclature for Algae, Fungi, and Plants (ICNafp). Improper typification of yeasts is a common problem, resulting in a large number invalid yeast species names. With this opinion letter, we address the problem that culturable microorganisms, notably some fungi and algae, require specific provisions under the ICNafp. We use yeasts as a prominent example of fungi known from cultures. But viable type material is important not only for yeasts, but also for other cultivable Fungi that are characterized by particular morphological structures (a specific type of spores), growth properties, and secondary metabolites. We summarize potential proposals which, in our opinion, will improve the stability of fungal names, in particular by protecting those names for which the reference material can be traced back to the original isolate.

59 BASIC BIOLOGICAL SCIENCES↗

Dominance of Particulate Mercury in Stream Transport and Rapid Watershed Recovery from Wildfires in Northern California, USA

Frequency and intensity of wildfires are expected to increase due to climate change, especially in areas with a long summer drought. Forests are a major sink for the global pollutant mercury (Hg), and fluvial transport of Hg from recently burned watersheds has not been widely investigated. Here, we examined two years of fluvial transport of Hg and its speciation (total Hg, methyl-Hg, particulate, and dissolved forms) under storm events and baseflow in two recently burned watersheds with different burned proportions and one nonburned reference watershed in the Coastal Ranges of northern California. We examined postfire storm-event transport of Hg and its methylated form (methyl-Hg), addressed the importance of the “initial runoff pulse” to postfire Hg fluvial transport and its predominant association with suspended solids, and elucidated potential sources of Hg exports from the burned landscapes using geochemical indicators, which suggested that ash materials were likely the significant sources of particulates in the first high-flow season postfire but not subsequently. The maximum total suspended solid and total Hg levels in the “first pulse” at the severely burned watershed were 442 and 46 times higher, respectively, than those at the reference watershed. Stream suspended solid and Hg levels declined substantially in the burned watersheds after just a few months of rainfall likely due to the rapid regrowth of vegetation commonly observed in postfire landscapes, implying that the wildfire effects on immediate Hg inputs from the burned landscape are at most transient in nature.

54 ENVIRONMENTAL SCIENCES↗

Query relaxation for portable brick-based applications

Semantic metadata standards pave the way for interoperability by providing building operators and application developers with common schemes to describe building resources. Applications can query building metadata models to retrieve the set of entities and relationships they need to operate, instead of hard-coding references to specific points and objects from the underlying data sources. Currently, querying such models requires the developer to be very specific when formulating queries in order to obtain meaningful answers (or any answer). The developer is inevitably expected to be familiar with the systems and components of the buildings being queried, as well as the schema used to represent them. The variety of buildings - both in the composition of their subsystems and in how they happen to be modeled - means that the developer will need to use multiple queries in order to retrieve necessary results. This is complex, time-consuming and error-prone. To address this limitation, we investigate query relaxation as a technique to facilitate discovery of meaningful building resources in a collection of ontology-based buildings data. We evaluate our query relaxation approach over a set of Brick models and demonstrate its use in the context of real-world building applications.

Brick↗