Emulation of Monthly Water Allocations Using LSTM Models: A Case Study of the Colorado River Basin in Texas
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Bonney, Kirk Lane [Sandia National Laboratories (S↗
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Accelerating data acquisition with FPGA-based edge machine learning: a case study with LCLS-II
New scientific experiments and instruments generate vast amounts of data that need to be transferred for storage or further processing, often overwhelming traditional systems. Edge machine learning (EdgeML) addresses this challenge by integrating machine learning (ML) algorithms with edge computing, enabling real-time data processing directly at the point of data generation. EdgeML is particularly beneficial for environments where immediate decisions are required, or where bandwidth and storage are limited. In this paper, we demonstrate a high-speed configurable ML model in a fully customizable EdgeML system using a field programmable gate array (FPGA). Our demonstration focuses on an angular array of electron spectrometers, referred to as the ‘CookieBox,’ developed for the Linac Coherent Light Source II project. The EdgeML system captures 51.2 Gbps from a 6.4 GS s −1 analog to digital converter and is designed to integrate data pre-processing and ML inside an FPGA. Our implementation achieves an inference latency of 0.2 µs for the ML model, and a total latency of 0.4 µs for the complete EdgeML system, which includes pre-processing, data transmission, digitization, and ML inference. The modular design of the system allows it to be adapted for other instrumentation applications requiring low-latency data processing.
97 MATHEMATICS AND COMPUTING↗
Strategies for community-sourced biocuration in bioinformatics: a case study on MIBiG 4.0
Biocuration is essential to transform molecular sequence data into standardized, machine-readable resources. Such curated datasets enable comparative analysis, predictive modeling, and data integration across bioinformatics platforms. While professional biocuration is resource-intensive and usually limited to institutional settings, community-driven approaches can mobilize large-scale annotation of specialized datasets and are more resilient to disruptions in scientific funding. Here, we present a model for community-powered curation applied to the Minimum Information about a Biosynthetic Gene Cluster (MIBiG) repository. Through a framework of workflows for metadata capture, annotation validation, and contributor coordination, the MIBiG 4.0 initiative recruited 267 scientists across 178 institutions from 33 countries, volunteering an estimated 4000 h of work. These efforts expanded the MIBiG repository by 22% and enhanced its usability in downstream molecular data analyses in comparative genomic analyses, natural product discovery, and machine learning applications. We provide strategies and actionable lessons for adopting this model, supporting the sustainability of curated bioinformatics resources central to nucleic acid research and related fields.
biocuration↗
The geometry of signal space: a case study of direct mapping between seismic signals and event distribution
SUMMARY Under favourable circumstances, seismic waveforms corresponding to an ensemble of events related by a common, spatially distributed process collectively exhibit a regular, signal-space geometry. When events in the ensemble have a common, or nearly common, source mechanism, this geometry is a distorted image of the distribution of events in the source region. The signal-space image can be visualized using a relatively simple waveform alignment and projection operation. Ensemble waveform correlation measurements can be inverted to estimate the distribution of the events in the source region, up to an arbitrary rotation, reflection and scaling, with residual distortion. We demonstrate these concepts with synthetic waveforms and with observations of long-wall mining induced seismicity for which substantial ground truth information is available. Our experience with these data has implications for location, correlation detection and machine learning and possible application to studies of repeating events in induced, volcanic and glacial seismicity. Our results place limits on the widely held assumption that waveform correlation is a useful measure of event separation. We suggest that the constraints on event separation need to be evaluated in the context of a population of related events, whose waveforms sample the signal space image of the source region. A better indicator of event separation is the length of the shortest path in signal space along the image.
58 GEOSCIENCES↗
Network analysis of earthquake ground motion spatial correlation: a case study with the San Jacinto seismic nodal array
SUMMARY The spatial correlation of earthquake ground motion intensity can be measured from strong motion data; however, the data used in past studies is sparsely sampled in space, and only the interstation distance was considered as a correlation variable. These limitations mean that we have only weak constraints on the true correlation structure of ground motion and that potentially important aspects of spatial correlation are unconstrained. In this study, we combine a large-N seismic array and graph analytics to explore this issue at a local scale using small local and regional earthquakes. Our result suggests site conditions, and how they interact with the incident seismic wavefield, strongly condition the spatial correlation of ground motion. Future progress in characterizing ground motion spatial variability will require dense wavefield measurements, either through nodal deployments, or perhaps distributed acoustic sensing measurements, of seismic wavefields. Aftershock sequences of major earthquakes would provide particularly data-rich targets of opportunity.
58 GEOSCIENCES↗
Development of Martini 2.2 parameters for N -glycans: a case study of the HIV-1 Env glycoprotein dynamics
N-linked glycans are ubiquitous in nature and play key roles in biology. For example, glycosylation of pathogenic proteins is a common immune evasive mechanism, hampering the development of successful vaccines. Due to their chemical variability and complex dynamics, an accurate molecular understanding of glycans is still limited by the lack of effective resolution of current experimental approaches. Here, we have developed and implemented a reductive model based on the popular Martini 2.2 coarse-grained force field for the computational study of N-glycosylation. We used the HIV-1 Env as a direct applied example of a highly glycosylated protein. Finally, our results indicate that the model not only reproduces many observables in very good agreement with a fully atomistic force field but also can be extended to study large amount of glycosylation variants, a fundamental property that can aid in the development of drugs and vaccines.
59 BASIC BIOLOGICAL SCIENCES↗
Seabird distribution is better predicted by abundance of prey than oceanography. A case study in the Gulf of Cadiz (SW, Iberian Peninsula)
Abstract Quantifying factors that influence marine predator distributions is essential to understanding the current and future change in marine biodiversity. Here, we test whether marine predator distribution relates to prey, or is better predicted by other specific habitat features. We examine the correlation between spatial distribution of three seabird species and their prey, as well as environmental proxies (oceanographic characteristics) in the Gulf of Cadiz, NE Atlantic. We modeled the at-sea distribution of Cory's shearwater, Balearic shearwater and Northern gannet, based on: (i) pelagic fish abundance according to acoustic surveys, and (ii) a forecast-model of remotely sensed environmental variables (productivity, sea surface temperature, and salinity). In general, seabird distributions were better predicted by abundance of fish than by environmental variables at the habitat scale. We obtained consistent correlations between seabird presence and the abundance of medium-sized (10–20 cm) sardines, anchovies and Mediterranean horse mackerel, providing information on their preferred prey. Additionally, oceanographic productivity variables moderately contributed to seabird distribution models, with better predictive value for the critically endangered Balearic shearwater and Northern gannet in the summer, whilst the model for Cory's shearwater's produced poorer predictions. Predator–prey combined studies may represent essential tools for an efficient ecosystem-based management of marine environments.
de la Cruz, Andrés (ORCID:0000000203632498)↗
Machine learning-enabled computer vision for plant phenotyping: a primer on AI/ML and a case study on stomatal patterning
Abstract Artificial intelligence and machine learning (AI/ML) can be used to automatically analyze large image datasets. One valuable application of this approach is estimation of plant trait data contained within images. Here we review 39 papers that describe the development and/or application of such models for estimation of stomatal traits from epidermal micrographs. In doing so, we hope to provide plant biologists with a foundational understanding of AI/ML and summarize the current capabilities and limitations of published tools. While most models show human-level performance for stomatal density (SD) quantification at superhuman speed, they are often likely to be limited in how broadly they can be applied across phenotypic diversity associated with genetic, environmental, or developmental variation. Other models can make predictions across greater phenotypic diversity and/or additional stomatal/epidermal traits, but require significantly greater time investment to generate ground-truth data. We discuss the challenges and opportunities presented by AI/ML-enabled computer vision analysis, and make recommendations for future work to advance accelerated stomatal phenotyping.
Plant Sciences↗
Nanoscale Phase Identification Using Two-Dimensional Pair Correlation Functions: A Case Study on Hafnium Oxide
Accurate identification of local phases in nanocrystalline materials is essential for understanding their functional properties, but it remains a significant challenge for polymorphic materials to locally differentiate them at nanoscale. This challenge is further compounded in polycrystalline materials with randomly oriented grains and the coexistence of multiple phases. In this report, we present a methodology for phase and orientation identification at the nanoscale by leveraging vector pair correlation functions extracted from atomically resolved scanning transmission electron microscopy (STEM) images. We demonstrate the accuracy of the methodology on both simulated and experimental data from HfO 2 -based films, a material that exhibits multiple coexisting phases in films with thicknesses ranging from 5 to 20 nm. While demonstrated on HfO 2 films, the methodology can be extended to other polymorphic nanocrystalline systems with complex phase coexistence.
36 MATERIALS SCIENCE↗
Assessing the sources of reionization: a spectroscopic case study of a 30× lensed galaxy at z ~ 5 with Ly α , C IV, Mg ιι, and [Ne ιιι]
We present a detailed spectroscopic analysis of a galaxy at z ≃ 4.88 that is, by chance, magnified ~30× by gravitational lensing. Only three sources at z ≳ 5 are known with such high magnification. This particular source has been shown to exhibit widespread, high equivalent width ${{\rm C\, \small {IV}}}\ \lambda 1549\, \mathring{\rm A}$ emission, implying it is a unique example of a metal-poor galaxy with a hard radiation field, likely representing the galaxy population responsible for cosmic reionization. Using ultraviolet (UV) nebular line ratio diagnostics, Very Large Telescope (VLT)/X-shooter observations rule out strong active galactic nuclei (AGN) activity, indicating a stellar origin of the hard radiation field instead. We present a new detection of ${[{\rm Ne\, \small {III}}]}\ \lambda 3870\, \mathring{\rm A}$ and use the [${\rm Ne\, \small {III}}$]/[${\rm O\, \small {II}}$] line ratio to constrain the ionization parameter and gas-phase metallicity. Closely related to the commonly used [${\rm O\, \small {III}}$]/[${\rm O\, \small {II}}$] ratio, our [${\rm Ne\, \small {III}}$]/[${\rm O\, \small {II}}$] measurement shows this source is similar to local ‘Green Pea’ galaxies and Lyman-continuum leakers. It furthermore suggests this galaxy is more metal poor than expected from the fundamental metallicity relation, possibly as a consequence of excess gas accretion diluting the metallicity. Finally, we present the highest redshift detection of ${{\rm Mg\, \small {II}}}\ \lambda 2796\, \mathring{\rm A}$, observed at high equivalent width in emission, in contrast to more evolved systems predominantly exhibiting ${\rm Mg\, \small {II}}$ absorption. Strong ${\rm Mg\, \small {II}}$ emission has been observed in most z ~ 0 Lyman-continuum leakers known and has recently been proposed as an indirect tracer of escaping ionizing radiation. In conclusion, this strongly lensed galaxy, observed just $300\, \mathrm{Myr}$ after reionization ends, enables testing of observational diagnostics proposed to constrain the physical properties of distant galaxies in the James Webb Space Telescope (JWST)/Extremely Large Telescope (ELT) era.
79 ASTRONOMY AND ASTROPHYSICS↗
The role of magnetic fields in the stability and fragmentation of filamentary molecular clouds: two case studies at OMC-3 and OMC-4
We present the stability analysis of two regions, OMC-3 and OMC-4, in the massive and long molecular cloud complex of Orion A. We obtained 214 $\mu$m HAWC + /SOFIA polarization data, and we make use of archival data for the column density and C 18 O (1–0) emission line. We find clear depolarization in both observed regions and that the polarization fraction is anticorrelated with the column density and the polarization-angle dispersion function. We find that the filamentary cloud and dense clumps in OMC-3 are magnetically supercritical and strongly subvirial. This region should be in the gravitational collapse phase and is consistent with many young stellar objects (YSOs) forming in the region. Our histogram of relative orientation (HRO) analysis shows that the magnetic field is dynamically sub-dominant in the dense gas structures of OMC-3. We present the first polarization map of OMC-4. We find that the observed region is generally magnetically subcritical except for an elongated dense core, which could be a result of projection effect of a filamentary structure aligned close to the line of sight. The relative large velocity dispersion and the unusual positive shape parameters at high column densities in the HROs analysis suggest that our viewing angle may be close to axes of filamentary substructures in OMC-4. The dominating strong magnetic field in OMC-4 is unfavourable for star formation and is consistent with much fewer YSOs than in OMC-3.
79 ASTRONOMY AND ASTROPHYSICS↗
Search and identification of transient and variable radio sources using MeerKAT observations: a case study on the MAXI J1820+070 field
ABSTRACT Many transient and variable sources detected at multiple wavelengths are also observed to vary at radio frequencies. However, these samples are typically biased towards sources that are initially detected in wide-field optical, X-ray, or gamma-ray surveys. Many sources that are insufficiently bright at higher frequencies are therefore missed, leading to potential gaps in our knowledge of these sources and missing populations that are not detectable in optical, X-rays, or gamma-rays. Taking advantage of new state-of-the-art radio facilities that provide high-quality wide-field images with fast survey speeds, we can now conduct unbiased surveys for transient and variable sources at radio frequencies. In this paper, we present an unbiased survey using observations obtained by MeerKAT, a mid-frequency (∼GHz) radio array in South Africa’s Karoo Desert. The observations used were obtained as part of a weekly monitoring campaign for X-ray binaries (XRBs) and we focus on the field of MAXI J1820+070. We develop methods to efficiently filter transient and variable candidates that can be directly applied to other data sets. In addition to MAXI J1820+070, we identify four likely active galactic nuclei, one source that could be a Galactic source (pulsar or quiescent XRB) or an AGN, and one variable pulsar. No transient sources, defined as being undetected in deep images, were identified leading to a transient surface density of <3.7 × 10−2 deg−2 at a sensitivity of 1 mJy on time-scales of 1 week at 1.4 GHz.
Rowlinson, A. (ORCID:0000000211957022)↗
Dark matter substructure or source model systematics? A case study of cluster lens Abell S1063
Mapping the small-scale structure of the universe through gravitational lensing is a promising tool for probing the particle nature of dark matter. Curved Arc Basis (CAB) has been proposed as a local lensing formalism in galaxy clusters, with the potential to detect low-mass dark matter substructure. In this work, we analyse the cluster lens Abell S1063 in search of dark matter substructure with the CAB formalism, using multiband imaging data from James Webb Space Telescope ( JWST ). We use two different source modelling methods: shapelets and pixel-based source reconstruction based on Delaunay triangulation. We find that source modelling systematics from shapelets result in a disagreement between CAB parameters measured from different filters. Source modelling with Delaunay significantly alleviates this systematic, as seen in the improvement in agreement across filters. We also find that inadequate complexity in source modelling can result in convincing spurious detections of dark matter substructure from strong gravitational lenses, as seen by our $\Delta \text{BIC} > 20$ measurement of a $M \sim 10^{10}$ ${\rm M}_{\odot }$ subhalo with shapelets, a spurious detection that is not reproduced with Delaunay source modelling. We demonstrate that multiband analysis with different JWST filters is key for disentangling source and lens model systematics from dark matter substructure detections.
79 ASTRONOMY AND ASTROPHYSICS↗
The Road to Recovery: Using an integrated approach to restoring rapidly declining bird species, a case study with the Yellow-billed Cuckoo (Coccyzus americanus)
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59 BASIC BIOLOGICAL SCIENCES↗
Back squat mechanics in persons with a unilateral transtibial amputation: A case study
Not provided.
Orthopedics↗
Importance of finite-size corrections for accurate ab initio modeling of carrier capture at semiconductor defects: A case study of substitutional C N in GaN
In ab initio studies of carrier-capture processes in defective semiconductor materials, the single-effective-mode formalism and the static-coupling approximation have become the predominant theoretical approaches for determining carrier-capture coefficients. The single-mode formalism relies on accurate nonequilibrium defect energies obtained from density-functional theory (DFT), where required inputs are a series of configurationally displaced, defect-containing supercells obtained using an interpolative ansatz, and where the DFT outputs are corresponding total energies that have traditionally been postprocessed using a long-established ground-state formulation of finite-size corrections and defect-formation energies. This formulation remains commonly used even though the defects that form a configuration-coordinate (CC) diagram typically exist as structures that are displaced from the ground state. To remedy this inconsistency, Kumagai has recently proposed novel methods for implementing finite-size corrections specifically intended for DFT calculations of the defect energies used to construct CC diagrams and implement the single-mode formalism [Y. Kumagai, Phys. Rev. B 107, L220101 (2023)]. Kumagai's approach builds on the latest finite-size-correction methods introduced to describe vertical charge-state transitions for charge-localizing point defects in semiconductors and insulators [T. Gake et al., Phys. Rev. B 101, 020102 (2020); S. Falletta et al., Phys. Rev. B 102, 041115 (2020)]. The newly identified finite-size artifact treated in these studies is the polarization charge induced on a configurationally frozen defect and its subsequent interaction with a vertical transition in charge state. In this work, we evaluate Kumagai's proposed methodology by applying it in a high-precision DFT study of carrier capture by substitutional C N in GaN, a well-characterized and technologically relevant defect and material. We have rigorously calculated C N defect energies across various supercell sizes for each defect configuration and charge state on the hole-capture CC diagram of C N (𝑞=−1), enabling a direct comparison of the slopes of the defect energies versus inverse cell size with those predicted by Kumagai. The most consequential prediction of Kumagai's method is that these slopes distinctly vary as the square of the linear-interpolation parameter used to construct the nonequilibrium defect configurations. Our results quantitatively support this prediction. Moreover, with these new finite-size corrections and multiple-cell-size DFT calculations in place, we find that the classical energy barrier for hole capture by C N (𝑞=−1) in GaN decreases to 0.092–0.127 eV. This finding confirms the recent ≈ 0.1 eV prediction of Reshchikov based on the weak temperature dependence for hole capture observed in photoluminescence experiments [M. A. Reshchikov, J. Appl. Phys. 129, 121101 (2021)]. These results stand in stark contrast to previously calculated barriers of 0.486 and 0.73 eV, which also used the single-mode formalism but were obtained by instead using ground-state-based finite-size corrections. Our reduced classical barrier for capture increases the temperature-dependent hole-capture coefficient of a C N (𝑞=−1) defect by more than two to four orders of magnitude for temperatures of 100–600 K, compared to the previous 0.486 eV results. While other defects may not be as dramatically affected as here, we suggest that incorporating proper finite-size corrections for the vertical-transition-like states embedded within CC diagrams is an essential, yet previously unrecognized, component of accurate modeling of carrier-capture when using the single-effective-mode formalism.
dielectric properties↗
Close-up view of the interplay between lattice distortions and charge density waves: Case study on rare-earth nickel carbides
Using variable temperature total x-ray scattering and large-scale structure modeling, we study the temperature and composition evolution of lattice distortions and charge density waves (CDWs) in the archetypal strongly correlated system RENi C 2 (RE=Dy, Tb, Gd, and Sm). Joint analysis of reciprocal and real space data reveals the presence of strong lattice distortions that, depending on the RE species and temperature, appear periodic or remain local, forming a complex CDW phase diagram. Apparently, the CDWs in RENi C 2 materials arise from a common to the system lattice instability involving diverse distortion modes that persist when magnetic order also sets in at very low temperature. In conclusion, the results support the notion that intrinsic lattice distortions are important to the emergence of exotic electronic phases in strongly correlated systems and call for their further investigation using the advanced approach adopted here.
36 MATERIALS SCIENCE↗
Ultrafast light-induced shear strain probed by time-resolved x-ray diffraction: Multiferroic BiFeO 3 as a case study
Enabling the light control of complex systems on ultrashort timescales gives rise to rich physics with promising applications. Although crucial, the quantitative determination of both the longitudinal and the shear photoinduced strains still remains challenging. Here, by scrutinizing asymmetric Bragg peaks pairs (±h01) in BiFeO 3 using picosecond time-resolved x-ray diffraction experiments, we simultaneously determine the longitudinal and shear strains. Importantly, we reveal a difference in the dynamical response of the longitudinal strain with respect to the shear one due to an interplay of quasilongitudinal and quasitransverse acoustic modes, well reproduced by our model. Lastly, we show that the relative amplitude of those strains can be explained only if both thermal and nonthermal processes contribute to the acoustic phonon photogeneration process.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗