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At least 793 records · Page 44

Determining protein polarization proteome-wide using physical dissection of individual Stentor coeruleus cells

Cellular components are non-randomly arranged with respect to the shape and polarity of the whole cell. Patterning within cells can extend down to the level of individual proteins and mRNA. But how much of the proteome is actually localized with respect to cell polarity axes? Proteomics combined with cellular fractionation has shown that most proteins localize to one or more organelles but does not tell us how many proteins have a polarized localization with respect to the large-scale polarity axes of the intact cell. Genome-wide localization studies in yeast found that only a few percent of proteins have a localized position relative to the cell polarity axis defined by sites of polarized cell growth. Here, we describe an approach for analyzing protein distribution within a cell with a visibly obvious global patterning - the giant ciliate Stentor coeruleus. Ciliates, including Stentor, have highly polarized cell shapes with visible surface patterning. A Stentor cell is roughly 2mmlong, allowing a ‘‘proteomic dissection’’ in which microsurgery is used to separate cellular fragments along the anterior-posterior axis, followed by comparative proteomic analysis. In our analysis, 25% of the proteome, including signaling proteins, centrin/SFI proteins, and GAS2 orthologs, shows a polarized location along the cell’s anterior-posterior axis. We conclude that a large proportion of all proteins are polarized with respect to global cell polarity axes and that proteomic dissection provides a simple and effective approach for spatial proteomics.

59 BASIC BIOLOGICAL SCIENCES↗

Quantification of Deformation-Induced Concentration Fluctuations in Polymeric Liquids by Small-Angle Neutron Scattering

This study demonstrates how the large concentration fluctuations of polymeric liquids under deformation and flow can be quantitatively studied by applying the spherical harmonic expansion technique to small-angle neutron scattering. Using a series of binary polymer blends, it is shown that the emergence of the so-called butterfly patterns is caused by the change of sign in the leading anisotropic component of the small-angle spectrum, when the scattering is dominated by intermolecular correlation associated with flow-induced demixing. The increasing spatial fluctuations of concentration are evidenced by the enhancement of the isotropic component of the scattering spectrum in the zero-angle limit and peak shift of the leading anisotropic coefficients toward low Q. Additionally, the spherical harmonic expansion framework permits real-space analysis of anisotropic scattering length density correlation in a convenient form. The methodology described in this work provides a concrete venue for quantitative studies of phase behavior of fluids under deformation and flow via small-angle scattering techniques, where mainly qualitative approaches were previously employed.

Chemical structure↗

Modeling the Transmission of Optical Lightning Signals Through Complex 3‐D Cloud Scenes

Abstract Space‐based lightning imagers have shown that complex cloud scenes consisting of multiple tall convective features, anvil clouds, and warm boundary cloud layers are illuminated by lightning in many different ways depending on where the lightning occurs and how energetic it is. Modifications to the optical lightning signals from radiative transfer in the cloud medium can lead to reductions in detection efficiency and location accuracy for these instruments and can also cause some of the optical signals that are detected to have unexpected spatial energy distributions. In this study, we perform Monte Carlo radiative transfer simulations of optical lightning emissions in clouds with complex 3‐D geometries to shed some light on the origins of certain irregular radiance patterns that have been recorded from orbit. We show that diffuse reflections off nearby cloud faces can explain lightning signals in nonelectrified clouds, tall clouds can result in poor optical transmission and suppressed radiances that could lead to missed events and that particularly favorable viewing conditions can cause otherwise normal lightning to produce a superbolt that is orders of magnitude brighter than the same flash seen from a different angle.

54 ENVIRONMENTAL SCIENCES↗

Testing the reliability of interpretable neural networks in geoscience using the Madden–Julian oscillation

Abstract. We test the reliability of two neural network interpretation techniques, backward optimization and layerwise relevance propagation, within geoscientific applications by applying them to a commonly studied geophysical phenomenon, the Madden–Julian oscillation. The Madden–Julian oscillation is a multi-scale pattern within the tropical atmosphere that has been extensively studied over the past decades, which makes it an ideal test case to ensure the interpretability methods can recover the current state of knowledge regarding its spatial structure. The neural networks can, indeed, reproduce the current state of knowledge and can also provide new insights into the seasonality of the Madden–Julian oscillation and its relationships with atmospheric state variables. The neural network identifies the phase of the Madden–Julian oscillation twice as accurately as a linear regression approach, which means that nonlinearities used by the neural network are important to the structure of the Madden–Julian oscillation. Interpretations of the neural network show that it accurately captures the spatial structures of the Madden–Julian oscillation, suggest that the nonlinearities of the Madden–Julian oscillation are manifested through the uniqueness of each event, and offer physically meaningful insights into its relationship with atmospheric state variables. We also use the interpretations to identify the seasonality of the Madden–Julian oscillation and find that the conventionally defined extended seasons should be shifted later by 1 month. More generally, this study suggests that neural networks can be reliably interpreted for geoscientific applications and may thereby serve as a dependable method for testing geoscientific hypotheses.

58 GEOSCIENCES↗

Assessing the Impact of Lightning NOx Emissions in CMAQ Using Lightning Flash Data from WWLLN over the Contiguous United States

Comparison of lightning flash data from the National Lightning Detection Network (NLDN) and from the World Wide Lightning Location Network (WWLLN) over the contiguous United States (CONUS) for the 2016–2018 period reveals temporally and spatially varying flash rates that would influence lightning NO x (LNO x ) production due to known detection efficiency differences especially during summer months over land (versus over ocean). However, the lightning flash density differences between the two networks show persistent seasonal patterns over geographical regions (e.g., land versus ocean). Since the NLDN data are considered to have higher accuracy (lightning detection with >95% efficiency), we developed scaling factors for the WWLLN flash data based on the ratios of WWLLN to NLDN flash data over time (months of year) and space. In this study, sensitivity simulations using the Community Multiscale Air Quality (CMAQ) model are performed utilizing the original data sets (both NLDN and WWLLN) and the scaled WWLLN flash data for LNO x production over the CONUS. The model performance of using the different lightning flash datasets for ambient O 3 and NO x mixing ratios that are directly impacted by LNO x emissions and the wet and dry deposition of oxidized nitrogen species that are indirectly impacted by LNO x emissions is assessed based on comparisons with ground-based observations, vertical profile measurements, and satellite products. During summer months, the original WWLLN data produced less LNO x emissions (due to its lower lightning detection efficiency) compared to the NLDN data, which resulted in less improvement in model performance than the simulation using NLDN data as compared to the simulation without any LNO x emissions. However, the scaled WWLLN data produced LNO x estimates and model performance comparable with the NLDN data, suggesting that scaled WWLLN may be used as a substitute for the NLDN data to provide LNO x estimates in air quality models when the NLDN data are not available (e.g., due to prohibitive cost or lack of spatial coverage).

54 ENVIRONMENTAL SCIENCES↗

Sulfur Species in Zinc-Rich Condylar Zones of a Rat Temporomandibular Joint

We performed synchrotron-based micro-X-ray absorption near-edge spectroscopy (µ-XANES) coupled with micro-X-ray fluorescence (µ-XRF) for the identification of elements that included biometal zinc (Zn) and nonmetal sulfur (S) (and its species) in the condylar zones of a rat temporomandibular joint (TMJ). Zone-specific spatial localization of biometal Zn and nonmetal S from a materials viewpoint when correlated with hypoxia inducible factor-1α (HIF-1α) (a surrogate for tissue oxygenation) can provide insights into Zn-specific redox pathways at the vulnerable subchondral interface. Histologic localization of Zn, HIF-1α, and sulfur-rich proteoglycans (PGs) were mapped using an optical microscope. The µ-XRF maps coupled with site-specific micro-X-ray diffraction (µ-XRD) patterns were used to underline Zn-incorporated biological apatite in the subchondral bone and the bone of a rat TMJ condyle. Results demonstrated an association between Zn, PG, and HIF-1α histologic maps with µ-XRF, µ-XANES, and µ-XRD data and provided insights into plausible biological S species in Zn-enriched zones of a rat TMJ condyle. Spatially localized Zn and S underscore their roles in cell and tissue functions in a zone-specific manner. Elemental Zn with organic and inorganic S species at the cartilage-bone interface and the biomineral phase of Zn-enriched biological apatite from subchondral bone to condylar bone were ascertained using µ-XRF-XANES and µ-XRF-XRD. The coupled µ-XRF-XANES in situ complemented with µ-XRF-XRD in situ and immunohistochemistry provided valuable biological insights into zone-specific biological pathways in rat TMJ condyles. Based on these data, we present a workflow to reliably map and correlate S species within Zn-enriched regions of cartilage, bone, and their interface. We suggest the use of this correlative and complementary microspectroscopic spatial information for zone-specific localization of biometal Zn and nonmetal S to gain insights into plausible microanatomy-specific oxidative stress in the TMJ.

apatites↗

Climatic factors and human population changes in Eurasia between the Last Glacial Maximum and the early Holocene

Archaeological records document a significant expansion of populations from the Last Glacial Maximum (LGM, ~23–19 ka) to the early Holocene (EH, ~9 ka) in Eurasia, which is often attributed to the influence of orbital-scale climate changes. Yet, information remains limited concerning the climatic factor(s) which were responsible for conditioning demographic patterns. Here, in this work, we present results from an improved Minimalist Terrestrial Resource Model (MTRM), forced by a transient climate simulation from the LGM to the EH. Simulated potential hunter-gatherer population densities and spatial distributions across Eurasia are supported by observed archaeological sites in Europe and China. In the low latitudes, potential population size change was predominantly controlled by precipitation and its strong influence on plant and animal resources. In the middle-high latitudes, temperature was the dominant driver in influencing potential population size change and animal resource availability. Different regional responses of potential populations to climate change across Eurasia - owing to variations in available food resources between the LGM and EH - provide a better understanding of human dispersal during the Late Pleistocene.

54 ENVIRONMENTAL SCIENCES↗

Microwave Heating-Induced Temperature Gradients in Liquid–Liquid Biphasic Systems

Microwaves (MWs) can enable the electrification and intensification of chemical manufacturing. They have been applied to various unit separations, such as drying, distillation, and extraction, entailing gas–liquid and solid–liquid systems. However, a limited quantitative understanding of MW-heated liquid–liquid biphasic systems related to extraction exists. This work measures the temporal and spatial temperature difference between an aqueous and an organic phase in batch and continuous microfluidic modes. We demonstrate permanent temperature differences between phases over 35 °C and spatiotemporal periodic and quasiperiodic oscillations modulated by the flow patterns. The temperature differences are primarily driven by the faster absorption rate of MW irradiation by the aqueous phase versus the slower heat transfer from the aqueous phase to the organic phase. These are amplified by low specific interfacial area and modifications of the electromagnetic field. We employ a multiphysics model to predict the temperature difference in a batch system. The model is in good agreement with the experiments. We demonstrate a strong effect of input power, dielectric properties of organic solvents, the volume of solvents, and the volume ratio between phases on the temperature difference. A simple analytical model describes the temperature difference and provides design principles. Furthermore, the combined approach offers new insights into the design and optimization of the MW-heated biphasic systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Assessing reservoir performance for geologic carbon sequestration in offshore saline reservoirs

Carbon capture and storage (CCS) is a technological strategy to reduce CO 2 emissions from hydrocarbon-based energy production and non-energy industrial emitters, like fertilizer and cement production. To expand the geographic opportunities for CCS, offshore geologic settings are increasingly considered for saline CO 2 storage, particularly where legacy oil and gas infrastructure may be repurposed for CO 2 transport and injection. In this context, the Gulf of Mexico (GoM), United States (U.S.), may offer tremendous opportunity for CCS because the surrounding states are among the largest CO 2 producers in the U.S. and there has been extensive oil and gas development over the last half century. Nevertheless, there remains significant uncertainty in how GoM reservoir/seal systems will respond to industrial-scale CO 2 injections, particularly in the context of meso-scale (1–10s of meters) permeability variations that are difficult to identify prior to injection. Such permeability variations can have significant impacts on CO 2 migration and fluid pressure propagation, both of which govern the overall effectiveness of the CCS project. This research uses ensemble simulation methods to quantify the influence of spatially variable and a priori unknown permeability fields on CO 2 plume development and fluid pressure propagation when CO 2 is injected at 1 MMt per year for ten years. Results show a number of characteristic patterns that reveal the substantial influence of both near- and far-field permeability on reservoir performance. By focusing on basin characteristics that are common among offshore basins worldwide, results from this study suggest that offshore CCS may be a feasible carbon management strategy in regions where offshore basins are proximal to industrial CO 2 sources.

42 ENGINEERING↗

On the Impact of Bus Dwelling on Macroscopic Fundamental Diagrams

Network macroscopic fundamental diagrams (MFDs) have recently been shown to exist in real-world urban traffic networks. When present, MFDs can be used to model traffic dynamics within an urban network by dividing the network into a set of spatially compact homogeneous regions and tracking the average level of congestion in each region. Existing analytical methods to estimate MFD mostly focus on the behavior of a single type of vehicle and do not capture the patterns of mixed traffic (e.g., cars and buses). The existence of buses matters since a bus will block the movements of other vehicles when it dwells at the bus stop. This paper proposes an analytical method to estimate the impact of bus dwelling on a network’s MFD based on the network’s geometric features, traffic control strategies, and bus operation parameters, and validates the performance of the proposed method using simulations based on microscopic traffic models. Comparisons of the analytical and simulation results show that the proposed analytical method can generally provide a good estimate of the lower bound and upper bound of the network’s MFD.

Xu, Guanhao↗

Curves, Coriolis, and Cross-Channel Circulation in the Hudson River Estuary

Abstract Despite its relatively small magnitude, cross-channel circulation in estuaries can influence the along-channel momentum balance, dispersion, and transport. We investigate spatial and temporal variation in cross-channel circulation at two contrasting sites in the Hudson River estuary. The two sites differ in the relative strength and direction of Coriolis and curvature forcing. We contrast the patterns and magnitudes of flow at the two sites during varying conditions in stratification driven by tidal amplitude and river discharge. We found well-defined flows during flood tides at both sites, characterized by mainly two-layer structures when the water column was more homogeneous and structures with three or more layers when the water column was more stratified. Ebb tides had generally weaker and less definite flows, except at one site where curvature and Coriolis reinforced each other during spring tide ebbs. Cross-channel currents had similar patterns, but were oppositely directed at the two sites, demonstrating the importance of curvature even in channels with relatively gradual curves. Coriolis and curvature dominated the measured terms in the cross-channel momentum balance. Their combination was generally consistent with driving the observed patterns and directions of flow, but local acceleration and cross-channel advection made some notable contributions. A large residual in the momentum balance indicates that some combination of vertical stress divergence, baroclinic pressure gradients, and along-channel and vertical advection must play an essential role, but data limitations prevented an accurate estimation of these terms. Cross-channel advection affected the along-channel momentum balance at times, with implications for the exchange flow’s strength. Significance Statement Currents that flow across the channel in an estuary move slower than those flowing along the channel, but they can transport materials and change water properties in important ways, affecting human uses of estuaries such as shipping, aquaculture, and recreation. We wanted to better understand cross-channel currents in the Hudson River estuary. We found that larger tides produced the strongest cross-channel currents with a two-layer pattern, compared to weaker currents with three layers during smaller tides. Higher or lower river flow also affected current strength. Comparing two locations, we saw cross-channel currents moving in opposite directions because of differences in the curvature of the river channel. Our results show how channel curvature and Earth’s rotation combine to produce cross-channel currents.

Conley, Margaret M.↗

Recoil imaging for dark matter, neutrinos, and physics beyond the Standard Model

Recoil imaging entails the detection of spatially resolved ionization tracks generated by particle interactions. This is a highly sought-after capability in many classes of detector, with broad applications across particle and astroparticle physics. However, at low energies, where ionization signatures are small in size, recoil imaging only seems to be a practical goal for micro-pattern gas detectors. This white paper outlines the physics case for recoil imaging, and puts forward a decadal plan to advance towards the directional detection of low-energy recoils with sensitivity and resolution close to fundamental performance limits. The science case covered includes: the discovery of dark matter into the neutrino fog, directional detection of sub-MeV solar neutrinos, the precision study of coherent-elastic neutrino-nucleus scattering, the detection of solar axions, the measurement of the Migdal effect, X-ray polarimetry, and several other applied physics goals. We also outline the R&D programs necessary to test concepts that are crucial to advance detector performance towards their fundamental limit: single primary electron sensitivity with full 3D spatial resolution at the $\sim$100 micron-scale. These advancements include: the use of negative ion drift, electron counting with high-definition electronic readout, time projection chambers with optical readout, and the possibility for nuclear recoil tracking in high-density gases such as argon. We also discuss the readout and electronics systems needed to scale-up such detectors to the ton-scale and beyond.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Effect of material composition of diamond field emission array cathodes on quality of transversely shaped beams

Diamond field emitter array field emission cathodes (DFEA FECs) are attractive for the next generation of injectors due to their ability to produce transversely shaped beams without the need for complex masking or laser schemes. However, reliability of this cathode technology remains a challenging issue as principal mechanisms guiding and allowing for output beam shaping remained poorly understood. Here, this paper reports the results of testing two DFEA FECs with the same pattern and emitter tip geometry. Although both cathodes were able to sustain gradients of 44 MV/m and produce maximum output integral charge of 0.5 nC per radio frequency pulse, their emission patterns were different. One cathode did not produce a shaped beam, while the other one did. This difference was explained by the extent of the local variations of the diamond material across the arrays as discovered by spatially resolved Raman spectroscopy. The main practical takeaways were (i) tip sharpness was not a prerequisite for producing a shaped beam and instead (ii) material characteristics resulting in different cathode ballast resistance affected emission spatial uniformity across the array and hence the beam shaping.

36 MATERIALS SCIENCE↗

Performance of plane wavefront Fizeau interferometers in power spectral density measurements with tilted plane optics

Binary pseudo-random array (BPRA) test samples are useful devices for calibrating the instrument transfer function (ITF) of Fizeau interferometers, interferometric microscopes, and other optical and non-optical surface and wavefront metrology instruments. The intrinsic white noise character of the power spectral density (PSD) function of the BPRA pattern simplifies the extraction of the ITF from the measured PSD. The ITF determined in a dedicated calibration experiment can be used to reconstruct the surface height profile from the measured data, effectively enhancing the instrument’s spatial resolution. For a high confidence reconstruction procedure, a reliable analytical model of the IFT is desirable. Usually, the model accounts for the contributions to the ITF related the imperfections of the instrument’s optical and detector systems. Here, we experimentally demonstrate that in the case of surface height metrology with Fizeau interferometers, the PSD measurements and, therefore, the efficacy of the ITF calibration of the tool, are strongly affected by the instrument data acquisition and processing procedures, as well as by the shape of the optic under test and its alignment with respect to the interferometer.

Yashchuk, V V↗

Heterogeneous Multi-Domain Dataset Synthesis to Facilitate Privacy and Risk Assessments in Smart City IoT

The emergence of the Smart Cities paradigm and the rapid expansion and integration of Internet of Things (IoT) technologies within this context have created unprecedented opportunities for high-resolution behavioral analytics, urban optimization, and context-aware services. However, this same proliferation intensifies privacy risks, particularly those arising from cross-modal data linkage across heterogeneous sensing platforms. To address these challenges, this paper introduces a comprehensive, statistically grounded framework for generating synthetic, multimodal IoT datasets tailored to Smart City research. The framework produces behaviorally plausible synthetic data suitable for preliminary privacy risk assessment and as a benchmark for future re-identification studies, as well as for evaluating algorithms in mobility modeling, urban informatics, and privacy-enhancing technologies. As part of our approach, we formalize probabilistic methods for synthesizing three heterogeneous and operationally relevant data streams—cellular mobility traces, payment terminal transaction logs, and Smart Retail nutrition records—capturing the behaviors of a large number of synthetically generated urban residents over a 12-week period. The framework integrates spatially explicit merchant selection using K-Dimensional (KD)-tree nearest-neighbor algorithms, temporally correlated anchor-based mobility simulation reflective of daily urban rhythms, and dietary-constraint filtering to preserve ecological validity in consumption patterns. In total, the system generates approximately 116 million mobility pings, 5.4 million transactions, and 1.9 million itemized purchases, yielding a reproducible benchmark for evaluating multimodal analytics, privacy-preserving computation, and secure IoT data-sharing protocols. To show the validity of this dataset, the underlying distributions of these residents were successfully validated against reported distributions in published research. We present preliminary uniqueness and cross-modal linkage indicators; comprehensive re-identification benchmarking against specific attack algorithms is planned as future work. This framework can be easily adapted to various scenarios of interest in Smart Cities and other IoT applications. By aligning methodological rigor with the operational needs of Smart City ecosystems, this work fills critical gaps in synthetic data generation for privacy-sensitive domains, including intelligent transportation systems, urban health informatics, and next-generation digital commerce infrastructures.

IoT↗

A global gridded dataset for cloud vertical structure from combined CloudSat and CALIPSO observations

Abstract. The vertical structure of clouds has a profound effect on the global energy budget, the global circulation, and the atmospheric hydrological cycle. The CloudSat and Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO) missions have taken complementary, colocated observations of cloud vertical structure for over a decade. However, no globally gridded dataset is available to the public for the full length of this unique combined data record. Here we present the 3S-GEOPROF-COMB product (Bertrand et al. 2023, https://doi.org/10.5281/zenodo.8057791), a globally gridded (level 3S) community data product summarizing geometrical profiles (GEOPROF) of hydrometeor occurrence from combined (COMB) CloudSat and CALIPSO data. Our product is calculated from the latest release (R05) of per-orbit (level-2) combined cloud mask profiles. We process a set of cloud cover, vertical cloud fraction, and sampling variables at 2.5, 5, and 10° spatial resolutions and monthly and seasonal temporal resolutions. We address the 2011 reduction in CloudSat data collection with Daylight-Only Operations (DO-Op) mode by subsampling pre-2011 data to mimic DO-Op collection patterns, thereby allowing users to evaluate the impact of the reduced sampling on their analyses. We evaluate our data product against CloudSat-only and CALIPSO-only global-gridded data products as well as four comparable surface-based sites, underscoring the added value of the combined product. Interest in the product is anticipated for the study of cloud processes, cloud–climate interactions, and as a candidate baseline climate data record for comparison to follow-up satellite missions, among other uses.

Bertrand, Leah (ORCID:0009000001607558)↗

Data-Driven Whole-Genome Clustering to Detect Geospatial, Temporal, and Functional Trends in SARS-CoV-2 Evolution

Current methods for defining SARS-CoV-2 lineages ignore the vast majority of the SARS-CoV-2 genome. We develop and apply an exhaustive vector comparison method that directly compares all known SARS-CoV-2 genome sequences to produce novel lineage classifications. We utilize data-driven models that (i) accurately capture the complex interactions across the set of all known SARS-CoV-2 genomes, (ii) scale to leadership-class computing systems, and (iii) enable tracking how such strains evolve geospatially over time. We show that during the height of the original Omicron surge, countries across Europe, Asia, and the Americas had a spatially asynchronous distribution of Omicron sub-strains. Moreover, neighboring countries were often dominated by either different clusters of the same variant or different variants altogether throughout the pandemic. Analyses of this kind may suggest a different pattern of epidemiological risk than was understood from conventional data, as well as produce actionable insights and transform our ability to prepare for and respond to current and future biological threats.

Jacobson, Daniel↗

Grain size estimation in fluvial gravel bars using uncrewed aerial vehicles: A comparison between methods based on imagery and topography

Abstract Grain size assessments are necessary for understanding the various geomorphological, hydrological and ecological processes that occur within rivers. Recent research has shown that the application of Structure‐from‐Motion (SfM) photogrammetry to imagery from uncrewed aerial vehicles (UAVs) shows promise for rapidly characterising grain sizes along rivers in comparison to traditional field‐based methods. Here, we evaluated the applicability of different methods for estimating grain sizes in gravel bars along a study reach in the Olentangy River in Columbus, Ohio. We collected imagery of these gravel bars with a UAV and processed those images with SfM photogrammetry software to produce three‐dimensional point clouds and orthomosaics. Our evaluation compared statistical models calibrated on topographic roughness, which was computed from the point clouds, and to those based on image texture, which was computed from the orthomosaics. Our results showed that statistical models calibrated on image texture were more accurate than those based on topographic roughness. This might be because of site‐specific patterns of grain size, shape and imbrication. Such patterns would have complicated the detection of topographic signatures associated with individual grains. Our work illustrates that UAV‐SfM approaches show potential to be used as an accessible method for characterising surface grain sizes along rivers at higher spatial and temporal resolutions than those provided by traditional methods.

Wong, Tyler↗