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At least 181 records · Page 10

Inferring the shape of data: a probabilistic framework for analysing experiments in the natural sciences

A critical step in data analysis for many different types of experiments is the identification of features with theoretically defined shapes in N -dimensional datasets; examples of this process include finding peaks in multi-dimensional molecular spectra or emitters in fluorescence microscopy images. Identifying such features involves determining if the overall shape of the data is consistent with an expected shape; however, it is generally unclear how to quantitatively make this determination. In practice, many analysis methods employ subjective, heuristic approaches, which complicates the validation of any ensuing results—especially as the amount and dimensionality of the data increase. Here, we present a probabilistic solution to this problem by using Bayes’ rule to calculate the probability that the data have any one of several potential shapes. This probabilistic approach may be used to objectively compare how well different theories describe a dataset, identify changes between datasets and detect features within data using a corollary method called Bayesian Inference-based Template Search; several proof-of-principle examples are provided. Altogether, this mathematical framework serves as an automated ‘engine’ capable of computationally executing analysis decisions currently made by visual inspection across the sciences.

Science & Technology - Other Topics↗

Congruity of genomic and epidemiological data in modelling of local cholera outbreaks

Cholera continues to be a global health threat. Understanding how cholera spreads between locations is fundamental to the rational, evidence-based design of intervention and control efforts. Traditionally, cholera transmission models have used cholera case-count data. More recently, whole-genome sequence data have qualitatively described cholera transmission. Integrating these data streams may provide much more accurate models of cholera spread; however, no systematic analyses have been performed so far to compare traditional case-count models to the phylodynamic models from genomic data for cholera transmission. Here, we use high-fidelity case-count and whole-genome sequencing data from the 1991 to 1998 cholera epidemic in Argentina to directly compare the epidemiological model parameters estimated from these two data sources. We find that phylodynamic methods applied to cholera genomics data provide comparable estimates that are in line with established methods. Our methodology represents a critical step in building a framework for integrating case-count and genomic data sources for cholera epidemiology and other bacterial pathogens.

59 BASIC BIOLOGICAL SCIENCES↗

Measuring the growth of Alfvén wave parametric decay instability using counter-propagating waves: Theory and simulations

The parametric decay instability (PDI) of Alfvén waves—where a pump Alfvén wave decays into a backward-propagating child Alfvén wave and a forward ion acoustic wave—is a fundamental nonlinear wave-wave interaction and holds significant implications for space and laboratory plasmas. However, to date there has been no direct experimental measurement of PDI. Here, we propose a novel and experimentally viable scheme to quantify the growth of Alfvén wave PDI on a linear device using a large pump Alfvén wave and a small counter-propagating seed Alfvén wave, with the seed-wave frequency tuned to match the backward Alfvén wave generated by standard PDI. Using hybrid simulations, we show that energy transfer from the pump to the seed reduces the latter's spatial damping. By comparing seed-wave amplitudes with and without the pump wave, this damping reduction can be used as a direct and reliable proxy for PDI growth. The method is validated in our simulations across a range of plasma and wave parameters and agrees well with theoretical predictions. Notably, the scheme exhibits no threshold for PDI excitation and is, in principle, readily implementable under current laboratory conditions. Finally, this scheme is a critical step toward solving the challenge of experimentally accessing Alfvén wave PDI and provides an elegant method that may be used to validate fundamental theories of parametric instabilities in controlled laboratory settings.

heliosphere↗

Gaps in topological magnon spectra: Intrinsic versus extrinsic effects

Determining and explaining the presence of a gap at a magnon crossing point is a critical step to characterize the topological properties of a material. An inelastic neutron scattering study of a single crystal is a powerful experimental technique to probe the magnetic excitation spectra of topological materials. Here, we show that when the scattering intensity rapidly disperses in the vicinity of a crossing point, such as a Dirac point, the apparent topological gap size is extremely sensitive to experimental conditions including sample mosaic, resolution, and momentum integration range. In this work, we demonstrate these effects using comprehensive neutron scattering measurements of CrCl 3 . Our measurements confirm the gapless nature of the Dirac magnon in CrCl 3 , but also reveal an artificial, i.e., extrinsic, magnon gap unless the momentum integration range is carefully controlled. Our study provides an explanation of the discrepancies between spectroscopic and first-principles estimates of Dirac magnon gap sizes and provides guidelines for accurate measurement of topological magnon gaps.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Moment extraction using an unfolding protocol without binning

Deconvolving (“unfolding”) detector distortions is a critical step in the comparison of cross-section measurements with theoretical predictions in particle and nuclear physics. However, most existing approaches require histogram binning while many theoretical predictions are at the level of statistical moments. We develop a new approach to directly unfold distribution moments as a function of another observable without having to first discretize the data. Our moment unfolding technique uses machine learning and is inspired by Boltzmann weight factors and generative adversarial networks (GANs). We demonstrate the performance of this approach using jet substructure measurements in collider physics. With this illustrative example, we find that our moment unfolding protocol is more precise than bin-based approaches and is as or more precise than completely unbinned methods.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Femtosecond Compression Dynamics and Timing Jitter Suppression in a THz-driven Electron Bunch Compressor

Herein we present the first demonstration of THz driven bunch compression and timing stabilization of a relativistic electron beam. Quasi-single-cycle strong field THz radiation is used in a shorted parallel-plate structure to compress a few-fC beam with 2.5 MeV kinetic energy by a factor of 2.7, producing a 39 fs rms bunch length and a reduction in timing jitter by more than a factor of 2 to 31 fs rms. This THz driven technique offers a significant improvement to beam performance for applications like ultrafast electron diffraction, providing a critical step towards unprecedented timing resolution in ultrafast sciences, and other accelerator applications using femtosecond-scale electron beams.

43 PARTICLE ACCELERATORS↗

Window Observables for Benchmarking Parton Distribution Functions

Global analysis of collider and fixed-target experimental data and calculations from lattice quantum chromodynamics (QCD) are used to gain complementary information on the structure of hadrons. We propose novel “window observables” that allow for higher precision cross-validation between the different approaches, a critical step for studies that wish to combine the datasets. Global analyses are limited by the kinematic regions accessible to experiment, particularly in a range of Bjorken-𝑥, and lattice QCD calculations also have limitations requiring extrapolations to obtain the parton distributions. We provide two different window observables that can be defined within a region of 𝑥 where extrapolations and interpolations in global analyses remain reliable and where lattice QCD results retain sensitivity and precision.

lattice QCD↗

A simple technique to classify diffraction data from dynamic proteins according to individual polymorphs

One often observes small but measurable differences in the diffraction data measured from different crystals of a single protein. These differences might reflect structural differences in the protein and may reveal the natural dynamism of the molecule in solution. Partitioning these mixed-state data into single-state clusters is a critical step that could extract information about the dynamic behavior of proteins from hundreds or thousands of single-crystal data sets. Mixed-state data can be obtained deliberately (through intentional perturbation) or inadvertently (while attempting to measure highly redundant single-crystal data). To the extent that different states adopt different molecular structures, one expects to observe differences in the crystals; each of the polystates will create a polymorph of the crystals. After mixed-state diffraction data have been measured, deliberately or inadvertently, the challenge is to sort the data into clusters that may represent relevant biological polystates. Here, this problem is addressed using a simple multi-factor clustering approach that classifies each data set using independent observables, thereby assigning each data set to the correct location in conformational space. This procedure is illustrated using two independent observables, unit-cell parameters and intensities, to cluster mixed-state data from chymotrypsinogen (ChTg) crystals. It is observed that the data populate an arc of the reaction trajectory as ChTg is converted into chymotrypsin.

36 MATERIALS SCIENCE↗

ADAPTIVE GROUP TESTING WITH MISMATCHED MODELS

Accurate detection of infected individuals is one of the critical steps in stopping any pandemic. When the underlying infection rate of the disease is low, testing people in groups, instead of testing each individual in the population, can be more efficient. In this work, we consider noisy adaptive group testing design with specific test sensitivity and specificity that select the optimal group given previous test results based on pre-selected utility function. As in prior studies on group testing, we model this problem as a sequential Bayesian Optimal Experimental Design (BOED) to adaptively design the groups for each test. We analyze the required number of group tests when using the updated posterior on the infection status and the corresponding Mutual Information (MI) as our utility function for selecting new groups. More importantly, we study how the potential bias on the ground-truth noise of group tests may affect the group testing sample complexity.

97 MATHEMATICS AND COMPUTING↗

Advancements in NbTiN based circuits for Superconducting Digital Logic

Superconducting (SC) electronics have emerged as a promising platform for high-speed, energy-efficient computing and quantum information processing. This work, centered on NbTiN, presents recent advances in material science and fabrication methods leading to significant improvements in performance, scalability and vertical integration. We specifically report on fabrication and characterization of key components, including Josephson junctions (JJs), flux trapping structures and SC interconnects. Together, these efforts represent critical steps towards realizing practical, complex, dense and large-scale SC integrated circuits.

Pokhrel, A. [Imec,Heverlee,Belgium]↗

Generalized and Mechanistic PV Module Performance Prediction From Computer Vision and Machine Learning on Electroluminescence Images

Electroluminescence (EL) imaging of photovoltiac (PV) modules offers high-speed, high-resolution information about device performance, affording opportunities for greater insight and efficiency in module characterization across manufacturing, research and development, and power plant operations and management. Predicting module electrical properties from EL image features is a critical step toward these applications. In this article, we demonstrate quantification of both generalized and performance mechanism-specific EL image features, using pixel intensity-based and machine learning classification algorithms. From EL image features, we build predictive models for PV module power and series resistance, using time-series current-voltage (I-V) and EL data obtained stepwise on five brands of modules spanning three Si cell types through two accelerated exposures: damp heat (DH) (85°C/85% RH) and thermal cycling (TC) (IEC 61215). Overall, 195 pairs of EL images and I-V characteristics were analyzed, yielding 11700 individual PV cell images. A convolutional neural network was built to classify cells by the severity of busbar corrosion with high accuracy (95%). Generalized power predictive models estimated the maximum power of PV modules from EL images with high confidence and an adjusted-R 2 of 0.88, across all module brands and cell types in extended DH and TC exposures. Mechanistic degradation prediction was demonstrated by quantification of busbar corrosion in EL images of three module brands in DH, and subsequent modeling of series resistance using these mechanism-specific EL image features. For modules exhibiting busbar corrosion, we demonstrated series resistance predictive models with adjusted-R 2 of up to 0.73.

14 SOLAR ENERGY↗

The Path to Autonomous Cyberdefense

Defenders are overwhelmed by attacks against their networks, which will only be exacerbated as attackers leverage artificial intelligence to automate workflows. Here, we propose a path to autonomous cyberagents able to augment defenders by automating critical steps in the cyberdefense lifecycle.

Oesch, Sean↗

Assembly of the MOLLER Toroidal Magnets at Jefferson Lab

The MOLLER experiment at the Thomas Jefferson National Accelerator Facility (JLab) aims to precisely measure the weak interaction between electrons. This experiment leverages the 12 GeV electron beam and will run for three years. A crucial component of MOLLER is a system of five uniquely shaped water-cooled toroidal magnets. These magnets, possessing seven-fold symmetry, are designed to focus particles by separating electrons scattered off hydrogen in a liquid hydrogen target. The five magnets separate electrons scattered off electrons (Møller scattering) and protons (elastic e-p scattering) within target into approximately circular rings at the detector. Here, this paper presents the assembly process for these five toroidal magnets, detailing critical steps including epoxy application, pin insertion, soldering and brazing, coil assembly, and alignment, all performed to meet stringent magnet specifications. Additionally, it discusses challenges encountered during construction and highlights lessons learned, offering insights for future magnet development projects.

Lamont, Joseph [Thomas Jefferson National Accelera↗

Seeing the forest for all the trees: Mycorrhizal‐associated nutrient economies are modulated by stem density and the synchrony between overstorey and understorey communities

1. Identifying relationships between plant communities and soil characteristics is a critical step in understanding the consequences of species gains and losses in ecosystems. The mycorrhizal associated nutrient economy (MANE) hypothesis predicts that the degree to which tree species and their mycorrhizal associates affect soil properties is driven by the relative dominance of different mycorrhizal types (often measured by relative basal area). While this approach emphasizes the importance of canopy trees, it does not account for how other factors (e.g. the density and composition of understorey trees) may alter tree–soil relationships. 2. We analysed tree–soil data from an eastern deciduous forest in southern Indiana, USA that contains >29,000 georeferenced stems, including 21 species that associate with arbuscular mycorrhizal (AM) fungi and 14 that associate with ectomycorrhizal (ECM) fungi. We sampled soils (upper 5 cm) from across the plot and modelled soil characteristics to tree communities. Given differences in soil characteristics among AM-dominated and ECM-dominated neighbourhoods, we hypothesized that relationships between tree-mycorrhizal dominance and soils would be affected by both the density of stems in the plot (owing to ‘Zinke’ individual plant effects) and composition of the understorey trees (owing to ‘trait divergence effects’) 3. In support of our Zinke hypothesis, we found that the relationships between tree-mycorrhizal dominance and soil variables (soil pH, nitrification rates and carbon to nitrogen ratio) were strengthened as stand density increased. In support of the trait divergence hypothesis, we found that as the mismatch between overstorey and understorey composition increased (e.g. AM-dominated understories beneath ECM-dominated overstories and vice versa), the relationship between tree dominance and soil variables weakened. We were able to use these insights to create mycorrhizal metrics to predict soil variables that were sensitive to the structural composition of neighbourhoods. 4. Synthesis. Our results indicate that relationships between plants and soils in forests are not only shaped by dominant overstorey trees but also the density and composition of understorey trees. Thus, efforts to predict the ecosystem consequences of species gains and losses may benefit from considering these elements of forest structure and not only the basal area of the dominant trees.

MANE framework↗

Solving the sample size problem for resource selection functions

Abstract Sample size sufficiency is a critical consideration for estimating resource selection functions (RSFs) from GPS‐based animal telemetry. Cited thresholds for sufficiency include a number of captured animals and as many relocations per animal N as possible. These thresholds render many RSF‐based studies misleading if large sample sizes were truly insufficient, or unpublishable if small sample sizes were sufficient but failed to meet reviewer expectations. We provide the first comprehensive solution for RSF sample size by deriving closed‐form mathematical expressions for the number of animals M and the number of relocations per animal N required for model outputs to a given degree of precision. The sample sizes needed depend on just 3 biologically meaningful quantities: habitat selection strength, variation in individual selection and a novel measure of landscape complexity, which we define rigorously. The mathematical expressions are calculable for any environmental dataset at any spatial scale and are applicable to any study involving resource selection (including sessile organisms). We validate our analytical solutions using globally relevant empirical data including 5,678,623 GPS locations from 511 animals from 10 species (omnivores, carnivores and herbivores living in boreal, temperate and tropical forests, montane woodlands, swamps and Arctic tundra). Our analytic expressions show that the required M and N must decline with increasing selection strength and increasing landscape complexity, and this decline is insensitive to the definition of availability used in the analysis. Our results demonstrate that the most biologically relevant effects on the utilization distribution (i.e. those landscape conditions with the greatest absolute magnitude of resource selection) can often be estimated with much fewer than animals. We identify several critical steps in implementing these equations, including (a) a priori selection of expected model coefficients and (b) regular sampling of background (pseudoabsence) data within a given definition of availability. We discuss possible methods to identify a priori expectations for habitat selection coefficients, effects of scale on RSF estimation and caveats for rare species applications. We argue that these equations should be a mandatory component for all future RSF studies.

Street, Garrett M.↗

Predicting initial dissolution rates using structural features from molecular dynamics simulations

Predicting chemical durability of glass materials is important for various applications from daily life such as drink glass and kitchen ware to advanced technologies such as nuclear waste disposal and biomedicine. In this work, we explored prediction of initial dissolution rate through structural features from molecular dynamics (MD) simulations for a wide range of glass compositions (total 28) including borosilicate and aluminosilicate glasses, ZrO 2 -containing and V 2 O 5 -containing boroaluminosilicate glasses. The initial dissolution rates (r 0 ) measured experimentally at 90 °C with varying solution conditions were correlated with structural features (e.g., polyhedral linkages and non-bridging oxygen species) obtained from MD simulations, either from this study or from literature. Since hydrolysis of the glass network through breaking of the network former linkages (e.g., Si-O-Si, Si-O-Al, etc.) is a critical step of network glass dissolution, the statistics of these linkages obtained from MD were correlated to r0 through linear regression, where the coefficient of determination (R 2 ) and root mean square error are found to be 0.949 and 0.681, respectively. This model was compared and discussed with existing models developed by various approaches including machine learning, the kinetic rate equation, topological constraint theory, and other descriptors from MD simulations. The discussion provides insights on future model improvements to predict glass dissolution. In addition, the impact of V 2 O 5 on the glass dissolution was examined in detail, implicating that the impact is not the same across all glass compositions and test conditions.

36 MATERIALS SCIENCE↗

Viral‐mediated delivery of morphogenic regulators enables leaf transformation in Sorghum bicolor (L.)

Recent advancements in monocot transformation, using leaf tissue as explant material, have expanded the number of grass species capable of transgenesis. However, the complexity of vectors and reliance on inducible excision of essential morphogenic regulators have so far limited widespread application. Plant RNA viruses, such as Foxtail Mosaic Virus (FoMV), present a unique opportunity to express morphogenic regulator genes, such as Babyboom (Bbm), Wuschel2 (Wus2), Wuschel-like homeobox protein 2a (Wox2a) and the GROWTH-REGULATING FACTOR 4 (GRF4) GRF-INTERACTING FACTOR 1 (GIF1) fusion protein transiently in leaf explant tissues. Furthermore, altruistic delivery of conventional and viral vectors could provide opportunities to simplify vectors used for leaf transformation—facilitating vector optimization and reducing reliance on morphogenic regulator gene integration. In this study, both viral and conventional T-DNA vectors were tested for their ability to promote the formation of embryonic calli, a critical step in leaf transformation protocols, using Sorghum bicolor leaf explants. Although conventional leaf transformation vectors yielded viable embryonic calli (43.2 ± 2.9%: GRF4-GIF1, 50.2 ± 3%: Bbm/Wus2), altruistic conventional vectors employing the GRF4-GIF1 morphogenic regulator resulted in improved efficiencies (61.3 ± 4.7%). Altruistic delivery was further enhanced with the use of viral vectors employing both GRF4-GIF1 and Bbm/Wus2 regulators, resulting in 75.1 ± 2.3% and 79.2 ± 2.5% embryonic calli formation, respectively. Embryonic calli generated from both conventional and viral vectors produced shoots expressing fluorescent reporters, which were confirmed using molecular analysis. This work provides an important proof-of-concept for the use of both altruistic vectors and viral-expressed morphogenic regulators for improving plant transformation.

59 BASIC BIOLOGICAL SCIENCES↗

Acquisition and Processing Considerations for Infrared Images of Rotating Turbine Blades

Abstract As designers aim to increase efficiency in gas turbines for aircraft propulsion and power generation, spatially resolved experimental measurements are needed to validate computational models and compare improvement gains of new cooling designs. Infrared (IR) thermography is one such method for obtaining spatially resolved temperature measurements. As technological advances in thermal detectors enable faster integration times, surface temperature measurements of rotating turbine blades become possible to capture including the smallest features. This paper outlines opportunities enabled by the latest IR detector technologies for capturing spatially resolved rotating blade temperatures, while also addressing some of the challenges of implementing IR for turbine rigs such as the one in the Steady Thermal Aero Research Turbine (START) Laboratory. This paper documents critical steps in achieving accurate measurements including calibration, integration times, spatial noise, and motion blur. From these results, recommendations are provided for achieving accurate IR measurements collected in a rotating turbine facility to study film cooling.

Engineering↗