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At least 1,207 records · Page 67

Phase noise limited frequency shift impulsive Raman spectroscopy

We introduce a method to enable optical amplification of a coherent Raman spectroscopy signal, which we call radio frequency (RF) Doppler Raman spectroscopy. In this article, we consider the perturbation of a probe pulse in a sample due to an excited Raman vibrational coherence as a generalized Doppler shift, which connects a time-varying optical path length (the product of the propagation length and refractive index, OPL = n ℓ) with an optical frequency shift. Amplification of a Raman signal outside of the focused interaction is enabled by converting the Doppler frequency shift experienced by a laser probe pulse into a periodic timing jitter. This transit time perturbation is detected through the phase of a RF electronic signal measured at a harmonic of the probe pulse train with a method adapted from precision metrology techniques used to measure laser pulse train timing jitter. Measurement of a timing jitter allows access to much lower noise floors than other coherent Raman techniques, and by exploiting the new capability to scale the signal of a coherent Raman spectroscopic signal, this method opens the potential to detect very weak Raman signals that are currently not observable due to limits of illumination intensity imposed by laser damage to the specimen and noise.

47 OTHER INSTRUMENTATION↗

Sci—Thur AM: YIS - 03: irtGPUMCD: a new GPU-calculated dosimetry code for {sup 177}Lu-octreotate radionuclide therapy of neuroendocrine tumors

In peptide receptor radionuclide therapy (PRRT), huge inter-patient variability in absorbed radiation doses per administered activity mandates the utilization of individualized dosimetry to evaluate therapeutic efficacy and toxicity. We created a reliable GPU-calculated dosimetry code (irtGPUMCD) and assessed {sup 177}Lu-octreotate renal dosimetry in eight patients (4 cycles of approximately 7.4 GBq). irtGPUMCD was derived from a brachytherapy dosimetry code (bGPUMCD), which was adapted to {sup 177}Lu PRRT dosimetry. Serial quantitative single-photon emission computed tomography (SPECT) images were obtained from three SPECT/CT acquisitions performed at 4, 24 and 72 hours after {sup 177}Lu-octreotate administration, and registered with non-rigid deformation of CT volumes, to obtain {sup 177}Lu-octreotate 4D quantitative biodistribution. Local energy deposition from the β disintegrations was assumed. Using Monte Carlo gamma photon transportation, irtGPUMCD computed dose rate at each time point. Average kidney absorbed dose was obtained from 1-cm{sup 3} VOI dose rate samples on each cortex, subjected to a biexponential curve fit. Integration of the latter time-dose rate curve yielded the renal absorbed dose. The mean renal dose per administered activity was 0.48 ± 0.13 Gy/GBq (range: 0.30–0.71 Gy/GBq). Comparison to another PRRT dosimetry code (VRAK: Voxelized Registration and Kinetics) showed fair accordance with irtGPUMCD (11.4 ± 6.8 %, range: 3.3–26.2%). These results suggest the possibility to use the irtGPUMCD code in order to personalize administered activity in PRRT. This could allow improving clinical outcomes by maximizing per-cycle tumor doses, without exceeding the tolerable renal dose.

60 APPLIED LIFE SCIENCES↗

Bacterial Biogeography across the Amazon River-Ocean Continuum

Spatial and temporal patterns in microbial biodiversity across the Amazon river-ocean continuum were investigated along ~675 km of the lower Amazon River mainstem, in the Tapajos River tributary, and in the plume and coastal ocean during low and high river discharge using amplicon sequencing of 16S rRNA genes in whole water and size-fractionated samples (0.2-2.0 μm and >2.0 μm). River communities varied among tributaries, but mainstem communities were spatially homogeneous and tracked seasonal changes in river discharge and co-varying factors. Co-occurrence network analysis identified strongly interconnected river assemblages during high (May) and low (December) discharge periods, and weakly interconnected transitional assemblages in September, suggesting that this system supports two seasonal microbial communities linked to river discharge. In contrast, plume communities showed little seasonal differences and instead varied spatially tracking salinity. However, salinity explained only a small fraction of community variability, and plume communities in blooms of diatom-diazotroph assemblages were strikingly different than those in other high salinity plume samples. This suggests that while salinity physically structures plumes through buoyancy and mixing, the composition of plume-specific communities is controlled by other factors including nutrients, phytoplankton community composition, and dissolved organic matter chemistry. Co-occurrence networks identified interconnected assemblages associated with the highly productive low salinity nearshore region, diatom-diazotroph blooms, and the plume edge region, and weakly interconnected assemblages in high salinity regions. This suggests that the plume supports a transitional community influenced by immigration of ocean bacteria from the plume edge, and by species sorting as these communities adapt to local environmental conditions. Few studies have explored patterns of microbial diversity in tropical rivers and coastal oceans. Comparison of Amazon continuum microbial communities to those from temperate and arctic systems suggest that river discharge and salinity are master variables structuring a range of environmental conditions that control bacterial communities across the river-ocean continuum.

58 GEOSCIENCES↗

A new cw-NMR Q-meter for dynamically polarized targets for particle physics

Polarized solid targets produced via Dynamic Nuclear Polarization rely on Continuous-Wave Nuclear Magnetism Resonance measurements to accurately determine the degree of polarization of bulk samples polarized to nearly 100%. Since the late 1970's phase sensitive detection methods have been utilized to observe the magnetization of a sample as a small change in inductance under RF excitation near the Larmor frequency of the nuclear species of interest, using a device known as a Q-meter. Liverpool Q-meters, produced in the UK in the 80's and 90's, have been the workhorse devices for these targets for decades, however their age and scarcity has meant new systems are needed. In conclusion, we describe a Q-meter system designed and built at Jefferson Lab in the Liverpool style to have comparable electronic performance with several improvements to update and adapt the devices for modern use.

Dynamic nuclear polarization↗

Probing subwavelength in-plane anisotropy with antenna-assisted infrared nano-spectroscopy

Infrared nano-spectroscopy based on scattering-type scanning near-field optical microscopy (s-SNOM) is commonly employed to probe the vibrational fingerprints of materials at the nanometer length scale. However, due to the elongated and axisymmetric tip shank, s-SNOM is less sensitive to the in-plane sample anisotropy in general. In this article, we report an easy-to-implement method to probe the in-plane dielectric responses of materials with the assistance of a metallic disk micro-antenna. As a proof-of-concept demonstration, we investigate here the in-plane phonon responses of two prototypical samples, i.e. in (100) sapphire and x-cut lithium niobate (LiNbO 3 ). In particular, the sapphire in-plane vibrations between 350 cm–1 to 800 cm–1 that correspond to LO phonon modes along the crystal b- and c-axis are determined with a spatial resolution of < λ/10, without needing any fitting parameters. In LiNbO 3 , we identify the in-plane orientation of its optical axis via the phonon modes, demonstrating that our method can be applied without prior knowledge of the crystal orientation. Furthermore, our method can be elegantly adapted to retrieve the in-plane anisotropic response of a broad range of materials, i.e. subwavelength microcrystals, van-der-Waals materials, or topological insulators.

36 MATERIALS SCIENCE↗

Gaming the beamlines—employing reinforcement learning to maximize scientific outcomes at large-scale user facilities

Abstract Beamline experiments at central facilities are increasingly demanding of remote, high-throughput, and adaptive operation conditions. To accommodate such needs, new approaches must be developed that enable on-the-fly decision making for data intensive challenges. Reinforcement learning (RL) is a domain of AI that holds the potential to enable autonomous operations in a feedback loop between beamline experiments and trained agents. Here, we outline the advanced data acquisition and control software of the Bluesky suite, and demonstrate its functionality with a canonical RL problem: cartpole. We then extend these methods to efficient use of beamline resources by using RL to develop an optimal measurement strategy for samples with different scattering characteristics. The RL agents converge on the empirically optimal policy when under-constrained with time. When resource limited, the agents outperform a naive or sequential measurement strategy, often by a factor of 100%. We interface these methods directly with the data storage and provenance technologies at the National Synchrotron Light Source II, thus demonstrating the potential for RL to increase the scientific output of beamlines, and layout the framework for how to achieve this impact.

36 MATERIALS SCIENCE↗

Virus-Host and CRISPR Dynamics in Archaea-Dominated Hypersaline Lake Tyrrell, Victoria, Australia

The study of natural archaeal assemblages requires community context, namely, a concurrent assessment of the dynamics of archaeal, bacterial, and viral populations. Here, we use filter size-resolved metagenomic analyses to report the dynamics of 101 archaeal and bacterial OTUs and 140 viral populations across 17 samples collected over different timescales from 2007–2010 from Australian hypersaline Lake Tyrrell (LT). All samples were dominated by Archaea (75–95%). Archaeal, bacterial, and viral populations were found to be dynamic on timescales of months to years, and different viral assemblages were present in planktonic, relative to host-associated (active and provirus) size fractions. Analyses of clustered regularly interspaced short palindromic repeat (CRISPR) regions indicate that both rare and abundant viruses were targeted, primarily by lower abundance hosts. Although very few spacers had hits to the NCBI nr database or to the 140 LT viral populations, 21% had hits to unassembled LT viral concentrate reads. This suggests local adaptation to LT-specific viruses and/or undersampling of haloviral assemblages in public databases, along with successful CRISPR-mediated maintenance of viral populations at abundances low enough to preclude genomic assembly. This is the first metagenomic report evaluating widespread archaeal dynamics at the population level on short timescales in a hypersaline system.

59 BASIC BIOLOGICAL SCIENCES↗

Adaptive center determination for effective suppression of ring artifacts in tomography images

Ring artifacts on tomogram slices hinder image interpretation. They are caused by minor variation in the response from individual elements in a two dimensional (2D) X-ray detector. Polar space decreases the suppression complexity by transforming the rings on the tomogram slice to linear stripes. However, it requires that the center of rings lie at the origin of polar transformation. If this is not the case, all methods employing polar space become ineffective. We developed a method based on Gaussian localization of the ring center in Hough parameter space to assign the origin for the polar transformation. Thus, obtained linear stripes can be effectively suppressed by already existing methods. This effectively suppresses ring artifacts in the data from a variety of experimental setups, sample types and also handles tomograms that are previously cropped. This approach functions automatically, avoids the need for assumptions and preserves fine details, all critical for synchrotron based nanometer resolution tomography.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Measuring the Error in Approximating the Sub-Level Set Topology of Sampled Scalar Data

This paper studies here the influence of the definition of neighborhoods and methods used for creating point connectivity on topological analysis of scalar functions. It is assumed that a scalar function is known only at a finite set of points with associated function values. In order to utilize topological approaches to analyze the scalar-valued point set, it is necessary to choose point neighborhoods and, usually, point connectivity to meaningfully determine critical-point behavior for the point set. Two distances are used to measure the difference in topology when different point neighborhoods and means to define connectivity are used: (i) the bottleneck distance for persistence diagrams and (ii) the distance between merge trees. Usually, these distances define how different scalar functions are with respect to their topology. These measures, when properly adapted to point sets coupled with a definition of neighborhood and connectivity, make it possible to understand how topological characteristics depend on connectivity. Noise is another aspect considered. Five types of neighborhoods and connectivity are discussed: (i) the Delaunay triangulation; (ii) the relative neighborhood graph; (iii) the Gabriel graph; (iv) the k-nearest-neighbor (KNN) neighborhood; and (v) the Vietoris–Rips complex. It is discussed in detail how topological characterizations depend on the chosen connectivity.

97 MATHEMATICS AND COMPUTING↗

Automated Crystal Orientation Mapping in py4DSTEM using Sparse Correlation Matching

Crystalline materials used in technological applications are often complex assemblies composed of multiple phases and differently oriented grains. Robust identification of the phases and orientation relationships from these samples is crucial, but the information extracted from the diffraction condition probed by an electron beam is often incomplete. We have developed an automated crystal orientation mapping (ACOM) procedure which uses a converged electron probe to collect diffraction patterns from multiple locations across a complex sample. We provide an algorithm to determine the orientation of each diffraction pattern based on a fast sparse correlation method. We demonstrate the speed and accuracy of our method by indexing diffraction patterns generated using both kinematical and dynamical simulations. We have also measured orientation maps from an experimental dataset consisting of a complex polycrystalline twisted helical AuAgPd nanowire. From these maps we identify twin planes between adjacent grains, which may be responsible for the twisted helical structure. All of our methods are made freely available as open source code, including tutorials which can be easily adapted to perform ACOM measurements on diffraction pattern datasets.

36 MATERIALS SCIENCE↗

Uncertainty Analysis on the Design of Thermal Conductivity Measurement by a Guarded Cut-Bar Technique

A technique adapted from the guarded-comparative-longitudinal heat flow method was selected for the measurement of the thermal conductivity of a nuclear fuel compact over a temperature range characteristic of its usage. This technique fulfills the requirement for non-destructive measurement of the composite compact. Although numerous measurement systems have been created based on the guarded comparative method, comprehensive systematic (bias) and measurement (precision) uncertainty associated with this technique have not been fully analyzed. Using finite element modeling, this paper presents the study of two types of error sources in the thermal conductivity measurement process: sample and system geometries and working conditions. The results and conclusions provide valuable reference for designing and operating an experimental measurement system using this technique.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Morphological biomarkers in Prochilodus lineatus (pisces, prochilodontidae) for environmental impact assessment in the region of the Baixada Maranhense, Brazil

This study aimed to identify the types of histopathological lesions found in gills of Prochilodus lineatus of the Environmental Protection Area of the Baixada Maranhense region (Brazil). Fish were collected in Mearim river. Sampling took place in October, November and December 2014. We have purchased 30 samples of fish from local fishermen. In the laboratory fish gills were removed, and then fixed in 10% formalin solution and kept into alcohol 70% to the usual histological processing. The tissue was performed by light microscopy and findings were photomicrographed in light microscope - ZEIS. The following lesions were identified: epithelial displacement, the marginal channel shift a start vascular congestion, hyperplasia and merging multiple slides; epithelial disruption, edema, vascular congestion, total fusion of lamellae and disorganization of secondary lamellae. These changes express a response of the body to some xenobiontes. Morphological changes in the gills may represent adaptive strategies for conservation of some biological functions when animals are facing changes in the water quality.

54 ENVIRONMENTAL SCIENCES↗

The evolution of analytical techniques for multiplex analysis of protein biomarkers

Introduction: The landscape of biomarker development has evolved with advanced analytical technologies, particularly affinity- and mass spectrometry-based techniques. These advancements have deepened our understanding of disease mechanisms, enabling the development of precise diagnostic tools and personalized medicine. Protein biomarkers, which play pivotal roles in biological processes, have become invaluable in diagnosing and monitoring diseases, aided by their presence in various biological samples and the availability of established detection methods. Areas covered: This review covers the role of protein biomarkers in clinical practice, the development and dimensionality of protein biomarkers, advancements in detection technologies, a comparison of these technologies, and future directions in biomarker discovery and disease mechanism elucidation. Expert opinion: Advances in biomarker technologies have the potential to transform diagnostics and personalized treatment but face challenges such as high costs and technical complexity. Enhancing reproducibility and integrating multi-omics approaches may offer better insights. In conclusion, the field should evolve toward high-throughput, automated methods, continuously adapting research, and clinical practices.

59 BASIC BIOLOGICAL SCIENCES↗

Investigation of soil properties using different techniques of mid‐infrared spectroscopy

Summary Diffuse reflectance spectroscopy (DRF), attenuated total reflectance spectroscopy (ATR) and Fourier transform infrared photoacoustic spectroscopy (PAS) are useful techniques that are commonly used to characterize soil properties. Here, these techniques were used to evaluate individual properties of 1456 paddy soil samples from Nanjing, China, to explore their features in the mid‐infrared range. The diffuse reflectance spectroscopy showed broad and shouldered peaks that ranged from 4000 to 500 cm −1 . Attenuated total reflectance spectroscopy produced main peaks around 1000 cm −1 . Fourier transform infrared photoacoustic spectroscopy spectra showed several moderate intensity peaks in the regions of 4000–2600 and 2500–500 cm −1 . The effective variables (wavenumbers) were selected using an uninformative variable elimination (UVE) algorithm to predict soil pH, and soil organic matter (SOM), total nitrogen (TN) and available phosphorus (AP) contents; it used a self‐adaptive partial least squares model (SAM–PLS). The results showed that selected wavenumbers improved the accuracy of prediction for pH, and SOM, TN and AP contents. For the prediction of pH, ATR spectra showed marginally better performance than the other spectra. The DRF spectroscopy was the optimal method for SOM and TN prediction. Available phosphorus contents were predicted poorly by all three spectra. Furthermore, mid‐infrared incident light paths, absorption modes, sensing styles, as well as peak interference and the prediction model, were the main factors that affected the assessment of soil properties in the three types of spectroscopy. Highlights Soil spectra data were measured with DRF, ATR and PAS spectrometers over the range 4000–500 cm −1 . A UVE algorithm was used to select effective wavenumbers from the full spectrum. The pH, SOM, TN and AP were estimated using three techniques based on a SAM–PLS model. Mid‐infrared incident light paths and absorption modes affected prediction performance of the three techniques.

Ma, F.↗

Three-Dimensional Single-Molecule Localization Microscopy in Whole-Cell and Tissue Specimens

Super-resolution microscopy techniques are versatile and powerful tools for visualizing organelle structures, interactions, and protein functions in biomedical research. However, whole-cell and tissue specimens challenge the achievable resolution and depth of nanoscopy methods. We focus on three-dimensional single-molecule localization microscopy and review some of the major roadblocks and developing solutions to resolving thick volumes of cells and tissues at the nanoscale in three dimensions. These challenges include background fluorescence, system- and sample-induced aberrations, and information carried by photons, as well as drift correction, volume reconstruction, and photobleaching mitigation. We also highlight examples of innovations that have demonstrated significant breakthroughs in addressing the abovementioned challenges together with their core concepts as well as their trade-offs.

59 BASIC BIOLOGICAL SCIENCES↗

Predictive Factor Analysis of Response-Adapted Radiation Therapy for Chemotherapy-Sensitive Pediatric Hodgkin Lymphoma: Analysis of the Children's Oncology Group AHOD 0031 Trial

Purpose: To evaluate whether clinical risk factors could further distinguish children with intermediate-risk Hodgkin lymphoma (HL) with rapid early and complete anatomic response (RER/CR) who benefit significantly from involved-field RT (IFRT) from those who do not, and thereby aid refinement of treatment selection. Methods and Materials: Children with intermediate-risk HL treated on the Children's Oncology Group AHOD 0031 trial who achieved RER/CR with 4 cycles of chemotherapy, and who were randomized to 21-Gy IFRT or no additional therapy (n=716) were the subject of this study. Recursive partitioning analysis was used to identify factors associated with clinically and statistically significant improvement in event-free survival (EFS) after randomization to IFRT. Bootstrap sampling was used to evaluate the robustness of the findings. Result: Although most RER/CR patients did not benefit significantly from IFRT, those with a combination of anemia and bulky limited-stage disease (n=190) had significantly better 4-year EFS with the addition of IFRT (89.3% vs 77.9% without IFRT; P=.019); this benefit was consistently reproduced in bootstrap analyses and after adjusting for other prognostic factors. Conclusion: Although most patients achieving RER/CR had favorable outcomes with 4 cycles of chemotherapy alone, those children with initial bulky stage I/II disease and anemia had significantly better EFS with the addition of IFRT as part of combined-modality therapy. Further work evaluating the interaction of clinical and biologic factors and imaging response is needed to further optimize and refine treatment selection.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

A green sulfur bacterium from epsomitic Hot Lake, Washington, USA

Hot Lake is a small heliothermal and hypersaline lake in far north–central Washington State (USA) and is limnologically unusual because MgSO 4 rather than NaCl is the dominant salt. In late summer, the Hot Lake metalimnion becomes distinctly green from blooms of planktonic phototrophs. In a study undertaken over 60 years ago, these blooms were predicted to include green sulfur bacteria, but no cultures were obtained. We sampled Hot Lake and established enrichment cultures for phototrophic sulfur bacteria in MgSO 4 -rich sulfidic media. Most enrichments turned green or red within 2 weeks, and from green-colored enrichments, pure cultures of a lobed green sulfur bacterium (phylum Chlorobi) were isolated. Phylogenetic analyses showed the organism to be a species of the prosthecate green sulfur bacterium Prosthecochloris. Cultures of this Hot Lake phototroph were halophilic and tolerated high levels of sulfide and MgSO 4 . In addition, unlike all recognized species of Prosthecochloris, the Hot Lake isolates grew at temperatures up to 45°C, indicating an adaptation to the warm summer temperatures of the lake. Photoautotrophy by Hot Lake green sulfur bacteria may contribute dissolved organic matter to anoxic zones of the lake, and their diazotrophic capacity may provide a key source of bioavailable nitrogen, as well.

59 BASIC BIOLOGICAL SCIENCES↗

mosartwmpy sample input data; 1980 - 1985

Sample input data spanning the years 1980-1985 for running the `mosartwmpy` water routing and management model: https://github.com/IMMM-SFA/mosartwmpy. More information is available in the README.md. Changelog: v0.0.7: new reservoir files with corrected locations based on an exhaustive review by Dan Broman for the 9505 project; corresponding long term mean demand and flow files updated based on VIC4 simulations using Daymet forcing. v0.0.6: updates reservoir parameters to indicate which reservoirs should follow generic operating rules and which should follow ISTARF data-driven operating rules. v0.0.5: adds supporting files for running the Farmer Agent Based Model of adaptive water demand.

Rexer, Emily↗