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At least 37 records · Page 2

Evaluation of the radiometric quality of the TM data using clustering and multispectral distance measures

Radiometrically and geometrically corrected TM data from three different geographic locations were examined. Histograms were inspected for each band to determine the dynamic range of the data, the shape of the distributions, and to verify whether empty bins were introduced by the radiometric correction process. The effect of geometric correction on the radiometry of the resampled pixels was determined. The information content between TM and MSS data sets were compared and the TM data were used to map the thermal effluent discharge into a river ecosystem from a nuclear thermal power plant, and application only possible previously only possible through the acquisition of thermal infrared scanner data from aircraft altitudes.

Bartolucci, L. A.↗

Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes

Microbiomes are constrained by physicochemical conditions, nutrient regimes, and community interactions across diverse environments, yet genomic signatures of this adaptation remain unclear. Metagenome sequencing is a powerful technique to analyze genomic content in the context of natural environments, establishing concepts of microbial ecological trends. Here, we developed a data discovery tool-a tetranucleotide-informed metagenome stability diagram-that is publicly available in the integrated microbial genomes and microbiomes (IMG/M) platform for metagenome ecosystem analyses. We analyzed the tetranucleotide frequencies from quality-filtered and unassembled sequence data of over 12,000 metagenomes to assess ecosystem-specific microbial community composition and function. We found that tetranucleotide frequencies can differentiate communities across various natural environments and that specific functional and metabolic trends can be observed in this structuring. Our tool places metagenomes sampled from diverse environments into clusters and along gradients of tetranucleotide frequency similarity, suggesting microbiome community compositions specific to gradient conditions. Within the resulting metagenome clusters, we identify protein-coding gene identifiers that are most differentiated between ecosystem classifications. We plan for annual updates to the metagenome stability diagram in IMG/M with new data, allowing for refinement of the ecosystem classifications delineated here. This framework has the potential to inform future studies on microbiome engineering, bioremediation, and the prediction of microbial community responses to environmental change. IMPORTANCE: Microbes adapt to diverse environments influenced by factors like temperature, acidity, and nutrient availability. We developed a new tool to analyze and visualize the genetic makeup of over 12,000 microbial communities, revealing patterns linked to specific functions and metabolic processes. This tool groups similar microbial communities and identifies characteristic genes within environments. By continually updating this tool, we aim to advance our understanding of microbial ecology, enabling applications like microbial engineering, bioremediation, and predicting responses to environmental change.

Kellom, Matthew↗

Landsat-4 MSS and Thematic Mapper data quality and information content analysis

Landsat-4 Thematic Mapper and Multispectral Scanner data were analyzed to obtain information on data quality and information content. Geometric evaluations were performed to test band-to-band registration accuracy. Thematic Mapper overall system resolution was evaluated using scene objects which demonstrated sharp high contrast edge responses. Radiometric evaluation included detector relative calibration, effects of resampling, and coherent noise effects. Information content evaluation was carried out using clustering, principal components, transformed divergence separability measure, and numerous supervised classifiers on data from Iowa and Illinois. A detailed spectral class analysis (multispectral classification) was carried out on data from the Des Moines, IA area to compare the information content of the MSS and TM for a large number of scene classes.

Anuta, P. E.↗

EMPDF : inferring the Milky Way mass with data-driven distribution function in phase space

We introduce the emPDF (empirical distribution function), a novel dynamical modelling method that infers the gravitational potential from kinematic tracers with optimal statistical efficiency under the minimal assumption of steady state. emPDF determines the best-fitting potential by maximizing the similarity between instantaneous kinematics and the time-averaged phase-space distribution function (DF), which is empirically constructed from observation upon the theoretical foundation of oPDF (Han et al. 2016). This approach eliminates the need for presumed functional forms of DFs or orbit libraries required by conventional DF- or orbit-based methods. emPDF stands out for its flexibility, efficiency, and capability in handling observational effects, making it preferable to the popular Jeans equation or other minimal assumption methods, especially for the Milky Way (MW) outer halo where tracers often have limited sample size and poor data quality. We apply emPDF to infer the MW mass profile using Gaia DR3 data of satellite galaxies and globular clusters, obtaining enclosed masses of M (,r) = 26±8, 46±8, 90±13⁠, and 149±40 x 10 10 M ⊙ at r = 30, 50, 100⁠, and 200 kpc, respectively. These are consistent with the updated constraints from simulation-informed DF fitting (Li et al. 2020). While the simulation-informed DF offers superior precision owing to the additional information extracted from simulations, emPDF is independent of such supplementary knowledge and applicable to general tracer populations. emPDF is currently implemented for tracers with complete 6D kinematics within spherical potentials, but it can potentially be extended to address more general problems.

Astrophysics of Galaxies (astro-ph.GA)↗

A study of the feasibility of using sea and wind information from the ERS-1 satellite. Part 1: Wind scatterometer data

The use of scatterometer and altimeter data in wind and wave assimilation, and the benefits this offers for quality assurance and validation of ERS-1 data were examined. Real time use of ERS-1 data was simulated through assimilation of Seasat scatterometer data. The potential for quality assurance and validation is demonstrated by documenting a series of substantial problems with the scatterometer data, which are known but took years to establish, or are new. A data impact study, and an analysis of the performance of ambiguity removal algorithms on real and simulated data were conducted. The impact of the data on analyses and forecasts is large in the Southern Hemisphere, generally small in the Northern Hemisphere, and occasionally large in the Tropics. Tests with simulated data give more optimistic results than tests with real data. Errors in ambiguity removal results occur in clusters. The probabilities which can be calculated for the ambiguous wind directions on ERS-1 contain more information than is given by a simple ranking of the directions.

Anderson, D.↗

Validation of TRMM Multi-Satellite Precipitation Analysis (TMPA) Products in the Peruvian Andes

The relevance of accurate and timely rainfall estimates cannot be overstated. The rainfall gauge network is still insufficient across significant areas worldwide. Rainfall estimates fromspaceborne sensors present an opportunity to supplement the existing network and enable the development of critical, near real time applications. However, the societal benefits of such systems can only be realized if the estimates are properly validated and the performance of existing products accurately described. In this study, two products generated by the Tropical Rainfall Measuring Mission (TRMM) Multisatellite Precipitation Analysis (TMPA) are validated for the Peruvian Andes. This is a region of complex topography that poses significant challenges to the retrieval of rainfall values fromspace. The TMPA products, both research grade (3B42V7) and near real time (3B42RT), are compared against in situ data. Different observation lengths are studied and the results are analyzed in light of geographic, topographic and climatic constraints. The Time Series of the science grade product were also studied under Dynamic TimeWarping and Hierarchical Clustering to streamline intertile comparisons. The TMPA products showa good agreementwith the gauge values, especially formore prolonged observation periods (over 8 days). The validation results display a strong regional dependence as a consequence of differences in the climate and topography. This region-specific performance calls for additional, detailed case studies and localized validation efforts. Overall the TMPAwas found to performadequately and provide quality information for a number of applications requiring timely estimates in convenient formats.

satellites↗

An interactive machine learning platform for analyzing multi-particle coincidence data from cold target recoil ion momentum spectroscopy

We present SCULPT (Supervised Clustering and Uncovering Latent Patterns with Training), a comprehensive software platform for analyzing tabulated high-dimensional multi-particle coincidence data from Cold Target Recoil Ion Momentum Spectroscopy (COLTRIMS) experiments. The software addresses critical challenges in modern momentum spectroscopy by integrating advanced machine learning techniques with physics-informed analysis in an interactive web-based environment. SCULPT implements uniform manifold approximation and projection for non-linear dimensionality reduction to reveal correlations in high-dimensional data. We also discuss potential extensions to deep autoencoders for feature learning and genetic programming for automated discovery of physically meaningful observables. A novel adaptive confidence scoring system provides quantitative reliability assessments by evaluating user-selected clustering quality metrics with predefined weights that reflect each metric’s robustness. The platform features configurable molecular profiles for different experimental systems, interactive visualization with selection tools, and comprehensive data filtering capabilities. Utilizing a subset of SCULPT’s capabilities, we analyze photo-double-ionization data measured using the COLTRIMS method for three-body dissociation of the D 2 O molecule, revealing distinct fragmentation channels and their correlations with physics parameters. The software’s modular architecture and web-based implementation make it accessible to the broader atomic and molecular physics community, significantly reducing the time required for complex multi-dimensional analyses. This opens the door to finding and isolating rare events exhibiting non-linear correlations on the fly during experimental measurements, which can help steer exploration and improve the efficiency of experiments.

Artificial neural networks↗

Reuniting crystallography with real space: Ab initio structure elucidation with 4D-STEM

Structure elucidation via single-crystal methods has historically lacked experimental access to real-space information, instead relying exclusively on diffraction-space measurements of Bragg reflections. Here we exploit the dual-space imaging power of 4D scanning transmission electron microscopy to meaningfully integrate real-space information into the crystallographic workflow. We show that virtual apertures assembled by segmentation of high-angle annular dark-field images enable i) pixel-by-pixel separation of coherent Bragg signal from clusters of closely spaced nanocrystals and ii) selective extraction of integrated intensities from thinner subregions of individual specimens, facilitating retroactive tuning of multiple scattering artifacts. This strategy empowers us to simply pick and choose whichever nanoscale regions of interest generate the highest-quality diffraction patterns, allowing us to solve several independent structures of the metal-organic framework UiO-66 from specimens whose agglomerated morphology proved intractable for conventional microcrystal electron diffraction. Our method is compatible with both rotational and serial approaches to data processing, ultimately divulging the first scanning nanobeam electron diffraction structures determined by direct methods at subangstrom resolution.

Saha, Ambarneil↗

Coordinated Science Campaign Scheduling for Sensor Webs

Future Earth observing missions will study different aspects and interacting pieces of the Earth's eco-system. Scientists are designing increasingly complex, interdisciplinary campaigns to exploit the diverse capabilities of multiple Earth sensing assets. In addition, spacecraft platforms are being configured into clusters, trains, or other distributed organizations in order to improve either the quality or the coverage of observations. These simultaneous advances in the design of science campaigns and in the missions that will provide the sensing resources to support them offer new challenges in the coordination of data and operations that are not addressed by current practice. For example, the scheduling of scientific observations for satellites in low Earth orbit is currently conducted independently by each mission operations center. An absence of an information infrastructure to enable the scheduling of coordinated observations involving multiple sensors makes it difficult to execute campaigns involving multiple assets. This paper proposes a software architecture and describes a prototype system called DESOPS (Distributed Earth Science Observation Planning and Scheduling) that will address this deficiency.

Edgington, Will↗

Replacing non-biomedical concepts improves embedding of biomedical concepts

Embeddings are semantically meaningful representations of words in a vector space, commonly used to enhance downstream machine learning applications. Traditional biomedical embedding techniques often replace all synonymous words representing biological or medical concepts with a unique token, ensuring consistent representation and improving embedding quality. However, the potential impact of replacing non-biomedical concept synonyms has received less attention. Embedding approaches often employ concept replacement to replace concepts that span multiple words, such as non-small-cell lung carcinoma, with a single concept identifier (e.g., D002289). Also, all synonyms of each concept are merged into the same identifier. Here, we additionally leveraged WordNet to identify and replace sets of non-biomedical synonyms with their most common representatives. This combined approach aimed to reduce embedding noise from non-biomedical terms while preserving the integrity of biomedical concept representations. We applied this method to 1,055 biomedical concept sets representing molecular signatures or medical categories and assessed the mean pairwise distance of embeddings with and without non-biomedical synonym replacement. A smaller mean pairwise distance was interpreted as greater intra-cluster coherence and higher embedding quality. Embeddings were generated using the Word2Vec algorithm applied to a corpus of 10 million PubMed abstracts. Our results demonstrate that the addition of non-biomedical synonym replacement reduced the mean intra-cluster distance by an average of 8%, suggesting that this complementary approach enhances embedding quality. Future work will assess its applicability to other embedding techniques and downstream tasks. Python code implementing this method is provided under an open-source license.

algorithms↗

Exploiting a Shortcoming of Coupled-Cluster Theory: The Extent of Non-Hermiticity as a Diagnostic Indicator of Computational Accuracy

The fundamental non-Hermitian nature of the forms of the coupled-cluster (CC) theory widely used in quantum chemistry has usually been viewed as a negative, but the present paper shows how this can be used to an advantage. Specifically, the non-symmetric nature of the reduced one-particle density matrix (in the molecular orbital basis) is advocated as a diagnostic indicator of computational quality. In the limit of the full coupled-cluster theory [which is equivalent to full configuration interaction (FCI)], the electronic wave function and correlation energy are exact within a given one-particle basis set, and the symmetric character of the exact density matrix is recovered. The extent of the density matrix asymmetry is shown to provide a measure of “how difficult the problem is” (like the well-known T 1 diagnostic), but its variation with the level of theory also gives information about “how well this particular method works”, irrespective of the difficulty of the problem at hand. The proposed diagnostic is described and applied to a select group of small molecules, and an example of its overall utility for the practicing quantum chemist is illustrated through its application to the beryllium dimer (Be 2 ). Future application of this idea to excited states, open-shell systems, and symmetry-breaking problems and an extension of the method to the two-particle density are then proposed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Development of Two Science Investigator-led Processing Systems (SIPS) for NASA's Earth Observation System (EOS)

In 2001, NASA Goddard Space Flight Center's Laboratory for Terrestrial Physics started the construction of a science Investigator-led Processing System (SIPS) for processing data from the Ozone Monitoring Instrument (OMI) which will launch on the Aura platform in mid 2004. The Ozone Monitoring Instrument (OMI) is a contribution of the Netherlands Agency for Aerospace Programs (NIVR) in collaboration with the Finnish Meteorological Institute (FMI) to the Earth Observing System (EOS) Aura mission. It will continue the Total Ozone Monitoring System (TOMS) record for total ozone and other atmospheric parameters related to ozone chemistry and climate. OMI measurements will be highly synergistic with the other instruments on the EOS Aura platform. The LTP previously developed the Moderate Resolution Imaging Spectrometer (MODIS) Data Processing System (MODAPS), which has been in full operations since the launches of the Terra and Aqua spacecrafts in December, 1999 and May, 2002 respectively. During that time, it has continually evolved to better support the needs of the MODIS team. We now run multiple instances of the system managing faster than real time reprocessings of the data as well as continuing forward processing. The new OMI Data Processing System (OMIDAPS) was adapted from the MODAPS. It will ingest raw data from the satellite ground station and process it to produce calibrated, geolocated higher level data products. These data products will be transmitted to the Goddard Distributed Active Archive Center (GDAAC) instance of the Earth Observing System (EOS) Data and Information System (EOSDIS) for long term archive and distribution to the public. The OMIDAPS will also provide data distribution to the OMI Science Team for quality assessment, algorithm improvement, calibration, etc. We have taken advantage of lessons learned from the MODIS experience and software already developed for MODIS. We made some changes in the hardware system organization, database and software to adapt the system for OMI. We replaced the fundamental database system, Sybase, with an Open Source RDBMS called PostgreSQL, and based the entire OMIDAPS on a cluster of Linux based commodity computers rather than the large SGI servers that MODAPS uses. Rather than relying on a central I/O server host, the new system distributes its data archive among multiple server hosts in the cluster. OMI is also customizing the graphical user interfaces and reporting structure to more closely meet the needs of the OMI Science Team. Prior to 2003, simulated OMI data and the science algorithms were not ready for production testing. We initially constructed a prototype system and tested using a 25 year dataset of Total Ozone Mapping Spectrometer (TOMS) and Solar Backscatter Ultraviolet Instrument (SBUV) data. This prototype system provided a platform to support the adaptation of the algorithms for OMI, and provided reprocessing of the historical data aiding in its analysis. In a recent reanalysis of the TOMS data, the OMIDAPS processed 108,000 full orbits of data through 4 processing steps per orbit, producing about 800,000 files (400 GiB) of level 2 and greater data files. More recently we have installed two instances of the OMIDAPS for integration and testing of OM1 science processes as they get delivered from the Science Team. A Test instance of the OMIDAPS has also supported a series of "Interface Confidence Tests" (ICTs) and End-to-End Ground System tests to ensure the launch readiness of the system. This paper will discuss the high-level hardware, software, and database organization of the OMIDAPS and how it builds on the MODAPS heritage system. It will also provide an overview of the testing and implementation of the production OMIDAPS.

Tilmes, Curt↗

Large field-of-view event-mode camera for high-precision epithermal neutron resonance imaging

A large-area event-mode camera system coupled with a 6 LiF-ZnS:Ag scintillator is applied for neutron resonance imaging (NRI) on the energy-resolved neutron imaging (ERNI) flight path, also known as Flight Path 5 (FP5), at the Los Alamos Neutron Science Center (LANSCE). This novel neutron imaging system, featuring a 120 x 120 mm 2 field of view, efficiently captures resonance information across the entire image in a single acquisition, significantly reducing beam time requirements compared to conventional energy-resolved neutron imaging systems. High-quality neutron radiographs with enhanced spatial resolution are achieved through the reconstruction of neutron events based on observations of individual photons emitted from the scintillator. The system demonstrates reduced background through neutron/gamma discrimination capabilities while maintaining sharpness across a large fields of view. In the measurements presented here, a spatial resolution of approximately 340 μm was achieved using center-of-gravity photon cluster centroiding. We demonstrate the system’s capability for quantitatively determining isotopic distributions in various thin samples, as well as automatically reconstructing complex scenes with overlapping resonances from diverse samples. These results are obtained using standard data analysis tools, despite the relatively slow 6 LiF-ZnS:Ag scintillator, which may not be optimal for absorption resonance detection. The capabilities demonstrated here offer a valuable, versatile, and cost-effective solution for high spatial and temporal resolution, large field-of-view energy-resolved neutron imaging, with potential applications across various scientific and industrial domains.

36 MATERIALS SCIENCE↗

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.

59 BASIC BIOLOGICAL SCIENCES↗

Unsupervised Segmentation and Clustering Workflow for Efficient Processing of 4D-STEM and 5D-STEM Data

Four-dimensional scanning transmission electron microscopy (4D-STEM) enables mapping of diffraction information with nanometer-scale spatial resolution, offering detailed insight into local structure, orientation, and strain. However, as data dimensionality and sampling density increase, particularly for in situ scanning diffraction experiments (5D-STEM), robust segmentation of structurally consistent behavior across sequential measurements becomes essential for efficient and physically meaningful analysis. Here, we introduce a clustering framework that identifies crystallographically distinct domains from 4D-STEM datasets. By using local diffraction-pattern similarity as a metric, the method extracts closed contours delineating spatially contiguous regions. This approach produces cluster-averaged diffraction patterns that improve signal quality while reducing data volume by orders of magnitude, enabling rapid and accurate orientation, phase, and strain mapping. We demonstrate the applicability of this approach to in situ liquid-cell 4D-STEM data of gold nanoparticle growth. Our method provides a scalable and generalizable route for spatially coherent segmentation, data compression, and quantitative structure–strain mapping across diverse 4D-STEM modalities. The full analysis code and example workflows are publicly available to support reproducibility and reuse.

4D-STEM↗

SZ–X-Ray Surface Brightness Fluctuations in the SPT-XMM Clusters

The hot plasma in galaxy clusters, the intracluster medium, is expected to be shaped by subsonic turbulent motions, which are key for heating, cooling, and transport mechanisms. The turbulent motions contribute to the nonthermal pressure, which, if not accounted for, consequently imparts a hydrostatic mass bias. Accessing information about turbulent motions is thus of major astrophysical and cosmological interest. Characteristics of turbulent motions can be indirectly accessed through surface brightness fluctuations. This study expands on our pilot investigations of surface brightness fluctuations in the Sunyaev–Zel’dovich and in X-ray data by examining, for the first time, a large sample of 60 clusters using both SPT-SZ and XMM-Newton data and spans the redshift range 0.2 < z < 1.5, thus constraining the respective pressure and density fluctuations within 0.6 R $_{500}$. We deem density fluctuations to be of sufficient quality for 32 clusters, finding mild correlations between the peak of the amplitude spectra of density fluctuations and various dynamical parameters. We infer turbulent velocities from density fluctuations with an average Mach number $\mathcal{M}$ 3D = 0.52 ± 0.14, in agreement with numerical simulations. For clusters with inferred turbulent Mach numbers from fluctuations in both pressure, $\mathcal{M}$ P , and density, $\mathcal{M}$ ρ , we find broad agreement between $\mathcal{M}$ P and $\mathcal{M}$ ρ . Our results suggest either a bimodal or a skewed unimodal Mach number distribution, with the majority of clusters being turbulence-dominated (subsonic) while the remainder are shock-dominated (supersonic).

79 ASTRONOMY AND ASTROPHYSICS↗

Identification of characteristic oligonucleotides in the bacterial 16S ribosomal RNA sequence dataset

MOTIVATION: The phylogenetic structure of the bacterial world has been intensively studied by comparing sequences of 16S ribosomal RNA (16S rRNA). This database of sequences is now widely used to design probes for the detection of specific bacteria or groups of bacteria one at a time. The success of such methods reflects the fact that there are local sequence segments that are highly characteristic of particular organisms or groups of organisms. It is not clear, however, the extent to which such signature sequences exist in the 16S rRNA dataset. A better understanding of the numbers and distribution of highly informative oligonucleotide sequences may facilitate the design of hybridization arrays that can characterize the phylogenetic position of an unknown organism or serve as the basis for the development of novel approaches for use in bacterial identification. RESULTS: A computer-based algorithm that characterizes the extent to which any individual oligonucleotide sequence in 16S rRNA is characteristic of any particular bacterial grouping was developed. A measure of signature quality, Q(s), was formulated and subsequently calculated for every individual oligonucleotide sequence in the size range of 5-11 nucleotides and for 15mers with reference to each cluster and subcluster in a 929 organism representative phylogenetic tree. Subsequently, the perfect signature sequences were compared to the full set of 7322 sequences to see how common false positives were. The work completed here establishes beyond any doubt that highly characteristic oligonucleotides exist in the bacterial 16S rRNA sequence dataset in large numbers. Over 16,000 15mers were identified that might be useful as signatures. Signature oligonucleotides are available for over 80% of the nodes in the representative tree.

NASA Discipline Life Sciences Technologies↗

Retrieve Methane from IR sounder measurements Using Machine Learning-Enhanced Physical Inversion

The sensitivity of IR sounder measurements to atmospheric CH 4 is often limited due to interferences from signals of other trace gases, insufficient thermal contrast, and cloud blockage. In order to resolve the geographical and vertical distribution of atmospheric CH 4 profiles, accurate scene-dependent a priori information is critically needed to support an optimal estimation method-based physical inversion scheme. Following the principles of indexing, representation, and retrieval, a spectral fingerprinting methodology is developed to address the needs for both accuracy and computational efficiency in sounder-based CH 4 retrieval. Within this framework, a clustering method based on machine learning is first employed to stratify and identify the a priori state within the pre-constructed database, using optimized spectral radiances as predictors. The corresponding radiative kernel is then used to establish the physical inversion scheme for finding the solution. High-quality data from CH 4 data assimilation systems like the Carbon-Tracker and the Copernicus Atmosphere Monitoring Service (CAMS) reanalysis, as well as the state-of-art sounder products are used to build the training database, including radiative kernels. We will demonstrate the results retrieved from CrIS observations and the associated validation work.

Wan Wu↗