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At least 415 records · Page 23

The impact of kidney function on Alzheimer’s disease blood biomarkers: implications for predicting amyloid-β positivity

Impaired kidney function has a potential confounding effect on blood biomarker levels, including biomarkers for Alzheimer’s disease (AD). Given the imminent use of certain blood biomarkers in the routine diagnostic work-up of patients with suspected AD, knowledge on the potential impact of comorbidities on the utility of blood biomarkers is important. We aimed to evaluate the association between kidney function, assessed through estimated glomerular filtration rate (eGFR) calculated from plasma creatinine and AD blood biomarkers, as well as their influence over predicting Aβ-positivity. We included 242 participants from the Translational Biomarkers in Aging and Dementia (TRIAD) cohort, comprising cognitively unimpaired individuals (CU; n = 124), mild cognitive impairment (MCI; n = 58), AD dementia (n = 34), and non-AD dementia (n = 26) patients all characterized by [ 18 F] AZD-4694. Plasma samples were analyzed for Aβ42, Aβ40, glial fibrillary acidic protein (GFAP), neurofilament light chain (NfL), tau phosphorylated at threonine 181 (p-tau181), 217 (p-tau217), 231 (p-tau231) and N-terminal containing tau fragments (NTA-tau) using Simoa technology. Kidney function was assessed by eGFR in mL/min/1.73 m 2 , based on plasma creatinine levels, age, and sex. Participants were also stratified according to their eGFR-indexed stages of chronic kidney disease (CKD). We evaluated the association between eGFR and blood biomarker levels with linear models and assessed whether eGFR provided added predictive value to determine Aβ-positivity with logistic regression models. Biomarker concentrations were highest in individuals with CKD stage 3, followed by stages 2 and 1, but differences were only significant for NfL, Aβ42, and Aβ40 (not Aβ42/Aβ40). All investigated biomarkers showed significant associations with eGFR except plasma NTA-tau, with stronger relationships observed for Aβ40 and NfL. However, after adjusting for either age, sex or Aβ-PET SUVr, the association with eGFR was no longer significant for all biomarkers except Aβ40, Aβ42, NfL, and GFAP. When evaluating whether accounting for kidney function could lead to improved prediction of Aβ-positivity, we observed no improvements in model fit (Akaike Information Criterion, AIC) or in discriminative performance (AUC) by adding eGFR to a base model including each plasma biomarker, age, and sex. While covariates like age and sex improved model fit, eGFR contributed minimally, and there were no significant differences in clinical discrimination based on AUC values. We found that kidney function seems to be associated with AD blood biomarker concentrations. However, these associations did not remain significant after adjusting for age and sex, except for Aβ40, Aβ42, NfL, and GFAP. While covariates such as age and sex improved prediction of Aβ-positivity, including eGFR in the models did not lead to improved prediction for any biomarker. Our findings indicate that renal function, within the normal to mild impairment range, does not seem to have a clinically relevant impact when using highly accurate blood biomarkers, such as p-tau217, in a biomarker-supported diagnosis.

60 APPLIED LIFE SCIENCES↗

Nanobodies as potential tools for microbiological testing of live biotherapeutic products

Nanobodies are highly specific binding domains derived from naturally occurring single chain camelid antibodies. Live biotherapeutic products (LBPs) are biological products containing preparations of live organisms, such as Lactobacillus, that are intended for use as drugs, i.e. to address a specific disease or condition. Demonstrating potency of multi-strain LBPs can be challenging. The approach investigated here is to use strain-specific nanobody reagents in LBP potency assays. Llamas were immunized with radiation-killed Lactobacillus jensenii or L. crispatus whole cell preparations. A nanobody phage-display library was constructed and panned against bacterial preparations to identify nanobodies specific for each species. Nanobody-encoding DNA sequences were subcloned and the nanobodies were expressed, purified, and characterized. Colony immunoblots and flow cytometry showed that binding by Lj75 and Lj94 nanobodies were limited to a subset of L. jensenii strains while binding by Lc38 and Lc58 nanobodies were limited to L. crispatus strains. Mass spectrometry was used to demonstrate that Lj75 specifically bound a peptidase of L. jensenii, and that Lc58 bound an S-layer protein of L. crispatus. The utility of fluorescent nanobodies in evaluating multi-strain LBP potency assays was assessed by evaluating a L. crispatus and L. jensenii mixture by fluorescence microscopy, flow cytometry, and colony immunoblots. Our results showed that the fluorescent nanobody labelling enabled differentiation and quantitation of the strains in mixture by these methods. Development of these nanobody reagents represents a potential advance in LBP testing, informing the advancement of future LBP potency assays and, thereby, facilitation of clinical investigation of LBPs.

60 APPLIED LIFE 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↗

Multiplexing of frequency-modulation spectroscopy by spread-spectrum codes, demonstrated in continuous-wave LIDAR

Frequency-modulation spectroscopy (FMS) is generally suited to code-division multiplexing, and we demonstrate that capacity in a form of continuous-wave LIDAR, utilizing a sharp CO 2 absorption transition at 1.6 µm in simple ranging setups. The approach retains the advantages of FMS, including coherent detection and good rejection of broad absorption backgrounds. Extensions of this multiplexed approach to the continuous, simultaneous detection of several transitions would come by transmitting an encoded combination of frequency-modulated carriers, each tuned to detect a unique absorption transition. Signal analysis at the receiver involves a simple process of de-multiplexing that, in a general application, reveals targets at various distances and the absorption-related FMS signals in between.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Enhanced biochemical sensing with high- Q transmission resonances in free-standing membrane metasurfaces

Optical metasurfaces provide solutions to label-free biochemical sensing by localizing light resonantly beyond the diffraction limit, thereby selectively enhancing light–matter interactions for improved analytical performance. However, high-Q resonances in metasurfaces are usually achieved in the reflection mode, which impedes metasurface integration into compact imaging systems. Here, we demonstrate a metasurface platform for advanced biochemical sensing based on the physics of the bound states in the continuum (BIC) and electromagnetically induced transparency (EIT) modes, which arise when two interfering resonances from a periodic pattern of tilted elliptic holes overlap both spectrally and spatially, creating a narrow transparency window in the mid-infrared spectrum. We experimentally measure these resonant peaks observed in transmission mode (Q ~ 734 at λ ~ 8.8 µm) in free-standing silicon membranes and confirm their tunability through geometric scaling. We also demonstrate the strong coupling of the BIC-EIT modes with a thinly coated PMMA film on the metasurface, characterized by a large Rabi splitting (32 cm -1 ) and biosensing of protein monolayers in transmission mode. Our new photonic platform can facilitate the integration of metasurface biochemical sensors into compact and monolithic optical systems while being compatible with scalable manufacturing, thereby clearing the way for on-site biochemical sensing in everyday applications.

Rosas, Samir [Univ. of Wisconsin, Madison, WI (Uni↗

HighDimMixedModels.jl: Robust high-dimensional mixed-effects models across omics data

High-dimensional mixed-effects models are an increasingly important form of regression in which the number of covariates rivals or exceeds the number of samples, which are collected in groups or clusters. The penalized likelihood approach to fitting these models relies on a coordinate descent algorithm that lacks guarantees of convergence to a global optimum. Here, we empirically study the behavior of this algorithm on simulated and real examples of three types of data that are common in modern biology: transcriptome, genome-wide association, and microbiome data. Our simulations provide new insights into the algorithm’s behavior in these settings, and, comparing the performance of two popular penalties, we demonstrate that the smoothly clipped absolute deviation (SCAD) penalty consistently outperforms the least absolute shrinkage and selection operator (LASSO) penalty in terms of both variable selection and estimation accuracy across omics data. To empower researchers in biology and other fields to fit models with the SCAD penalty, we implement the algorithm in a Julia package, HighDimMixedModels.jl .

Gorstein, Evan↗

Age-specific case data reveal varying dengue transmission intensity in US states and territories

Dengue viruses (DENV) are endemic in the US territories of Puerto Rico, American Samoa, and the US Virgin Islands, with focal outbreaks also reported in the states of Florida and Hawaii. However, little is known about the intensity of dengue virus transmission over time and how dengue viruses have shaped the level of immunity in these populations, despite the importance of understanding how and why levels of immunity against dengue may change over time. These changes need to be considered when responding to future outbreaks and enacting dengue management strategies, such as guiding vaccine deployment. We used catalytic models fitted to case surveillance data stratified by age from the ArboNET national arboviral surveillance system to reconstruct the history of recent dengue virus transmission in Puerto Rico, American Samoa, US Virgin Islands, Florida, Hawaii, and Guam. We estimated average annual transmission intensity (i.e., force of infection) of DENV between 2010 and 2019 and the level of seroprevalence by age group in each population. We compared models and found that assuming all reported cases are secondary infections generally fit the surveillance data better than assuming all cases are primary infections. Using the secondary case model, we found that force of infection was highly heterogeneous between jurisdictions and over time within jurisdictions, ranging from 0.00008 (95% CrI: 0.00002–0.0004) in Florida to 0.08 (95% CrI: 0.044–0.14) in American Samoa during the 2010–2019 period. For early 2020, we estimated that seropositivity in 10 year-olds ranged from 0.09% (0.02%–0.54%) in Florida to 56.3% (43.7%–69.3%) in American Samoa. In the absence of serological data, age-specific case notification data collected through routine surveillance combined with mathematical modeling are powerful tools to monitor arbovirus circulation, estimate the level of population immunity, and design dengue management strategies.

60 APPLIED LIFE SCIENCES↗

Cbp1, a fungal virulence factor under positive selection, forms an effector complex that drives macrophage lysis

Intracellular pathogens secrete effectors to manipulate their host cells. Histoplasma capsulatum (Hc) is a fungal intracellular pathogen of humans that grows in a yeast form in the host. Hc yeasts are phagocytosed by macrophages, where fungal intracellular replication precedes macrophage lysis. The most abundant virulence factor secreted by Hc yeast cells is Calcium Binding Protein 1 (Cbp1), which is absolutely required for macrophage lysis. Here we take an evolutionary, structural, and cell biological approach to understand Cbp1 function. We find that Cbp1 is present only in the genomes of closely related dimorphic fungal species of the Ajellomycetaceae family that lead primarily intracellular lifestyles in their mammalian hosts (Histoplasma, Paracoccidioides, and Emergomyces), but not conserved in the extracellular fungal pathogen Blastomyces dermatitidis. We observe a high rate of fixation of non-synonymous substitutions in the Cbp1 coding sequences, indicating that Cbp1 is under positive selection. We determine the de novo structures of Hc H88 Cbp1 and the Paracoccidioides americana (Pb03) Cbp1, revealing a novel “binocular” fold consisting of a helical dimer arrangement wherein two helices from each monomer contribute to a four-helix bundle. In contrast to Pb03 Cbp1, we show that Emergomyces Cbp1 orthologs are unable to stimulate macrophage lysis when expressed in the Hc cbp1 mutant. Consistent with this result, we find that wild-type Emergomyces africanus yeast are able to grow within primary macrophages but are incapable of lysing them. Finally, we use subcellular fractionation of infected macrophages and indirect immunofluorescence to show that Cbp1 localizes to the macrophage cytosol during Hc infection, making this the first instance of a phagosomal human fungal pathogen directing an effector into the cytosol of the host cell. We additionally show that Cbp1 forms a complex with Yps-3, another known Hc virulence factor that accesses the cytosol. Taken together, these data imply that Cbp1 is a fungal virulence factor under positive selection that localizes to the cytosol to trigger host cell lysis.

59 BASIC BIOLOGICAL SCIENCES↗

Electrodynamics of photo-carriers in multiferroic Eu 0.75 Y 0.25 MnO 3

Understanding and controlling the antiferromagnetic order in multiferroic materials on an ultrafast time scale is a long standing area of interest, due to their potential applications in spintronics and ultrafast magnetoelectric switching. We present an optical pump-terahertz (THz) probe study on multiferroic Eu 0.75 Y 0.25 MnO 3 . The optical pump predominantly excites the d-d transitions of the Mn 3+ ions, and the temporal evolution of the pump-induced transient conductivity is measured with a subsequent THz pulse. Two distinct, temperature-dependent decay times are revealed. The shorter relaxation time corresponds to spin-lattice thermalization, while the longer one is ascribed to electron-hole recombination. A spin-selection rule in the relaxation process is proposed in the magnetic phase. Slight suppression of the electromagnons was observed after the optical pump pulse within the spin-lattice thermalization time scale. These observed fundamental magnetic processes can shed light on ultrafast control of magnetism and photoinduced phase transitions in multiferroics.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Leaf gas exchange raw data, 2015 - 2017, at Manaus, Brazil

This data package contains raw leaf gas exchange data from the NGEE Tropics K34 tower site on a plateau near Manaus, Brazil. Data was collected using sensor and leaf sample measurements. Leaves on a target tree were chosen by accessing a branch near the tower. In some cases, the branch was naturally positioned near the tower and in other cases, a small rope was used to pull the branch closer to the tower for better access to leaves. Mature leaves were targeted in nearly all cases. The gas exchange system was hauled with a climbing rope to the level of the branch on the tower and the sensor head/leaf enclosure was installed near the branch of interest using a magic arm. We measured leaf gas exchange from 5:00 AM to 5:00 PM, randomly cycling through the approximately 20 leaves in the targeted branch(es). Data were collected over two time periods, detailed within the files. The attached data files contain raw data, sensor manuals, and PDFs with detailed methods and procedures separated into multiple folders. Data is in Excel file format. See data references for data package containing related metadata. This dataset replaces the leaf gas exchange data of two retired packages, NGT0019 and NGT0040.

54 ENVIRONMENTAL SCIENCES↗

Leaf isoprene and monoterpene emission data-set across hyperdominant tree genera in the Amazon basin

This data package contains the analyzed data used to support the publication "Leaf isoprene and monoterpene emission distribution across hyperdominant tree genera in the Amazon basin," Phytochemistry, in-press. Data was collected from 162 trees across four sites in the Amazon. For all leaf samples studied for volatile isoprenoid emissions, branch cuttings were conducted in the upper canopy with sun exposed leaves with the assistance of a tree climber utilizing a pole pruner or directly accessed from flux towers. Large branches were removed from the upper canopy (up to 0.5-1.0 meter in length) and rapidly recut on the ground under water to maintain the transpiration stream. Net photosynthesis and isoprene and monoterpene emission rates were quantified from leaves during controlled changes in photosynthetically active radiation (PAR) using a commercial leaf photosynthesis system (LI-6400XT, LI-COR Inc., USA) interfaced with a gas chromatograph-mass spectrometer (GC-MS, 5975C series, Agilent Technologies, USA). For detailed methods and raw data, refer to the publication and related material cited in Dataset References.

54 ENVIRONMENTAL SCIENCES↗

Raw leaf gas exchange data in the Amazon basin, 2014-2016

This data package contains raw leaf gas exchange data used to support the publication "Leaf isoprene and monoterpene emission distribution across hyperdominant tree genera in the Amazon basin," Phytochemistry, in-press. Data was collected from 162 individuals, distributed among 25 botanical families and 113 species, from four sites in the Amazon. The data was collected using a modified portable photosynthesis system for environmental control coupled to a thermal desorption tube for volatile isoprenoid collections. Collected TD tube samples were analysed in Manaus, Brazil, using thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS). The dataset includes both photosynthesis and isoprene/monoterpene emission rates from leaves under standard environmental conditions as well as controlled light response curves. For detailed methods and raw data, refer to the publication and related material cited in Dataset References.

54 ENVIRONMENTAL SCIENCES↗

Raw leaf isoprene and monoterpene emission GC-MS chromatograms/calibrations for MassHunter software, Brazil, 2014-2016

This data package contains raw gas chromatography–mass spectrometry (GC-MS) data for isoprene/monoterpene emission rates used to support the publication "Leaf isoprene and monoterpene emission distribution across hyperdominant tree genera in the Amazon basin," Phytochemistry, in-press. The attached data files require use of the Agilent MassHunter software. Alternatively, data has been exported into Excel files and can be accessed at [DOI]. For further information on how to Raw isoprene and monoterpene emission rates data

54 ENVIRONMENTAL SCIENCES↗

MiNAA: Microbiome Network Alignment Algorithm

A microbial network is a mathematical representation of a microbial community where nodes represent microbes and edges represent interactions. It is well-recognized that microbes are among the main drivers of biological phenotypes in soil, plants, and animals alike, and thus, their study has vast implications for soil, plant and human health. In particular, recognizing the microbial, environmental, and agricultural factors that drive plant and soil phenotypes is crucial to comprehend processes connected to plant and soil health, to identify global practices of sustainable agriculture, as well as to predict plant and soil responses to environmental perturbations such as climate change. The adaptability of microbes to thrive in every environment poses challenges for scientists who try to understand their communities. Indeed, two microbial communities with the exact same players can interact differently depending on the environmental conditions. It is thus desirable to identify commonalities and differences on two microbial networks, hence the need for computational tools that can match (or align) them.

97 MATHEMATICS AND COMPUTING↗

Oxygen diffusion in garnet: Experimental calibration and implications for timescales of metamorphic processes and retention of primary O isotopic signatures

Knowledge of oxygen diffusion in garnet is crucial for a correct interpretation of oxygen isotope signatures in natural samples. A series of experiments was undertaken to determine the diffusivity of oxygen in garnet, which remains poorly constrained. The first suite included high-pressure (HP), nominally dry experiments performed in piston-cylinder apparatus at: (1) T = 1050–1600 °C and P = 1.5 GPa and (2) T = 1500 °C and P = 2.5 GPa using yttrium aluminum garnet (YAG; Y3Al5O12) cubes. Second, HP H2O-saturated experiments were conducted at T = 900 °C and P = 1.0–1.5 GPa, wherein YAG crystals were packed into a YAG + Corundum powder, along with 18O-enriched H2O. Third, 1 atm experiments with YAG cubes were performed in a gas-mixing furnace at T = 1500–1600 °C under Ar flux. Finally, an experiment at T = 900 °C and P = 1.0 GPa was done using a pyrope cube embedded into pyrope powder and 18O-enriched H2O. Experiments using grossular were not successful. Profiles of 18O/(18O+16O) in the experimental charges were analyzed with three different secondary ion mass spectrometers (SIMS): sensitive high-resolution ion microprobe (SHRIMP II and SI), CAMECA IMS-1280, and NanoSIMS. Considering only the measured length of 18O diffusion profiles, similar results were obtained for YAG and pyrope annealed at 900 °C, suggesting limited effects of chemical composition on oxygen diffusivity. However, in both garnet types, several profiles deviate from the error function geometry, suggesting that the behavior of O in garnet cannot be fully described as simple concentration-independent diffusion, certainly in YAG and likely in natural pyrope as well. The experimental results are better described by invoking O diffusion via two distinct pathways with an inter-site reaction allowing O to move between these pathways. Modeling this process yields two diffusion coefficients (D values) for O, one of which is approximately two orders of magnitude higher than the other. Taken together, Arrhenius relationships are:logDm2s-1=-7.2(±1.3)+(-321(±32)kJmol-12.303RT) for the slow pathway, andlogDm2s-1=-5.4(±0.7)+(-321(±20)kJmol-12.303RT) for the fast pathway. We interpret the two pathways as representing diffusion following vacancy and inter-stitial mechanisms, respectively. Regardless, our new data suggest that the slow mechanism is prevalent in garnet with natural compositions, and thus is likely to control the retentivity of oxygen isotopic signatures in natural samples. The diffusivity of oxygen is similar to Fe-Mn diffusivity in garnet at 1000–1100 °C and Ca diffusivity at 850 °C. However, the activation energy for O diffusion is larger, leading to lower diffusivities at P-T conditions characterizing crustal metamorphism. Therefore, original O isotopic signatures can be retained in garnets showing major element zoning partially re-equilibrated by diffusion, with the uncertainty caveat of extrapolating the experimental data to lower temperature conditions.

Geochemistry & Geophysics↗

Model and Standard Operating Procedures Supporting Signal Variation Flow Graph Analysis

This document will describe the principles of the Signal Variation Flow Technique, and the uncertainty models generated using it. We focus on the capture of the variation between the ideal signal and the measured signal. The ideal signal is defined to represent the signal output of a system whose full state behavior is known, with no variation in environment or during operation, and whose photons trajectories are not modified by the object. A CT uncertainty analysis is the result of two main steps. First, the radiography regime extends from the source to the collected image, which is 2D in the case of standard CT. This maps all upstream uncertainties into the variation observed on the radiograph and captures all variation in the physical domain. Second, the reconstruction regime extends from the captured images to the reconstructed 3D image. This regime is purely in the mathematical domain and corrects reconstruction algorithm artifacts/anomalies. The present work focuses on building the model through the radiography regime. The reconstruction regime is expected to be largely a study of algorithmic sensitivity, requiring the definition of a range of standardized tests through which the algorithms would be run. Radiographic variation would then be mapped through reconstruction sensitivities to predict the signal variation in the final image. An incomplete list for the reconstructed image variation output basis includes voxel density, edge blur and length variation, in analogous fashion to the basis functions presented in this work. The signal variation occurs in several forms at the radiograph. These forms are gathered into a complete basis set of functions describing all variation on the radiograph. The scale of each basis function is calculated independently via a specific SVFG. This includes 0D pixel noise (0DI), 0D energy noise (0DE), 1D blur (1DB), 1D length (1DL) or 2D position (2DP). These models are orthogonal in that they each explore a space in the signal variation domain that cannot be reached by the other basis functions. The variation basis functions, and associated SVFG models are split by output dimensionality, a term loosely used for categorization, and explained further below.

42 ENGINEERING↗

Emerging Threats and Technology Investigation: Industrial Internet of Things - Risk and Mitigation for Nuclear Infrastructure

Industries supporting the global nuclear infrastructure striving for cost savings, expansions in efficiency, and convenience are likely to adopt components (e.g., hardware, software) that comprise the Internet of Things (IoT) and Industrial Internet of Things (IIoT). These devices offer potential improvements along with security challenges. Modern conveniences achieved through application of technology have propagated through society in the form of interconnected devices, from doorbells to microwave ovens, commonly referred to as IoT. IoT devices are often Internet-connected devices that are designed to send data back to a cloud-based server, where a smart phone application then presents device status and control options. Home-based IoT applications carry a different set of risks when compared to a business or security environment, where there is also a history of convenience and interconnection. Industrial settings have long relied on specifically designed Supervisory Control and Data Acquisition (SCADA) systems for process control where IIoT devices are intended to inform business decisions and augment traditional processes. A recent National Institute of Standards and Technology (NIST) report provides a distinction between process control and IIoT in that traditional process control is not replaced by IIoT, but rather IIoT devices are intended to enhance industrial processes through additional monitoring of various sensors and application of data analytics models using artificial intelligence (AI) and machine learning (ML) (Fagan, Marron, et al. 2021) (Ross, et al. 2021).

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗