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At least 1,531 records · Page 85

GRIP: Constraint-based Explanation of Missing Answers for Graph Queries

Abstract: A useful feature in graph query engines is to clarify “Why certain entities (nodes, attribute values or edges) are missing” in query answers. This task is even more challenging when the relevant data is already missing in the underlying data source. Missing data, on the other hand, can be inferred by enforcing data constraints for graphs. We demonstrate GRIP, a system that exploits data constraints to clarify missing answers for graph queries. (1) Constraint-based ex- planation. Given a desired yet missing entity in the query answer, GRIP ensures to generate finite and minimal sequences of data con- strains (an “explanation”) that should be consecutively enforced to ?? to ensure its occurrence for the same query. (2) Answering “why” and“how” questions. Users can query GRIP with both“Why”(“Why” the element is missing) and “How” questions (“How” to refine the graph to include the missing answer). GRIP engine supports run- time generation of explanations by incrementally maintaining a set of bi-directional search trees. (3) Interactive exploration. GRIP provides a user-friendly GUI to support interactive ad visual exploration of explanations, including both automated generation and step-by-step inspection of graph manipulations.

graphs↗

Specific features of the ferroelectric state in two-layer barium strontium titanate-based heterostructures

The structural properties of one- and two-layer heterostructures based on the barium–strontium titanate of various compositions deposited by the Frank–Van der Merve on a magnesium oxide substrate have been studied. The heterostructures have been prepared by the rf sputtering of the stoichiometric ceramic targets in a Plazma 50 SE deposition system. The principal difference of this method of deposition from known analogs is that the growth of single-crystal films occurs from a disperse oxide phase formed in the plasma of a high-current rf discharge during the ceramic target sputtering at the cluster level. The peculiarities of the manifestation of the ferroelectric state in the two-layer heterostructures when changing the sequence order of the films with various compositions of barium–strontium titanate.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

P-wave velocity anisotropy related to sealed fractures reactivation tracing the structural diagenesis in carbonates

Fracture properties are important in carbonate reservoir characterization, as they are responsible for a large part of the fluid transfer properties at all scales. It is especially true in tight rocks where the matrix transfer properties only slightly contribute to the fluid flow. Open fractures are known to strongly affect seismic velocities, amplitudes and anisotropy. Here, we explore the impact of fracture evolution on the geophysical signature and directional V p anisotropy of fractured carbonates through diagenesis. For that purpose, we studied a meter-scale, parallelepiped quarry block of limestone using a detailed structural and diagenetic characterization, and numerous V p measurements. The block is affected by two en-échelon fracture clusters, both being formed in opening mode (mode 1) and cemented, but only one being reactivated in shear. We compared the diagenetic evolution of the fractures, which are almost all 100% filled with successive calcite cements, with the P-wave velocities measured across this meter-scale block of carbonate, which recorded the tectonic and diagenetic changes of a South Provence sedimentary basin. We found that a directional V p anisotropy magnitude as high as 8–16% correlates with the reactivated fractures’ cluster dip angle, which is explained by the complex filling sequence and softer material present inside the fractures that have been reactivated during the basin's tectonic inversion. We show that although a late karstification phase preferentially affected these reactivated fractures, it only amplified the pre-existing anisotropy due to tectonic shear. We conclude that V p anisotropy measurements may help to identify the fracture sealing/opening processes associated with polyphased tectonic history, the anisotropy being independent of the current stress-state. Finally, this case shows that velocity anisotropies induced by fractures resulted here from a cause that is different from how these features have often been interpreted: selective reactivation of sealed fractures clusters rather than direction of currently open ones.

58 GEOSCIENCES↗

A phenomenological rate of injection model for predicting fuel injection with application to mixture formation in light-duty diesel engines

Fuel injection rate laws are one of the most important pieces of information needed when modeling engine combustion with computational fluid dynamics. In this study, a simple phenomenological model of a common-rail injector was developed and calibrated for the Bosch CRI2.2 platform. The model requires three tunable parameter fits, making it relatively easy to calibrate and suitable for injector modeling when high-fidelity information about the internal injector’s geometry and electrical circuit details are not available. Each injection pulse is modeled as a sequence of up to four stages: an injection needle mechanical opening transient, a full-lift viscous flow inertial transient, a Bernoulli steady-state stage, and a needle descent transient. Parameters for each stage are obtained as polynomial fits from measured injection rate properties. The model enforces total injected mass, and the intermediate stages are only introduced if the injection pulse duration is long enough. Experimental rates of injection from two separate campaigns on the same injector were used to calibrate the model. The model was first validated against measured injection rate laws featuring pilot injections, short partially premixed combustion pulses, and conventional diesel combustion injection strategies. Then, it was employed as an input to engine computational fluid dynamics simulations, which were run to simulate experiments of mixture formation in an optically accessible light-duty diesel engine. It was found that, though simple, this model is capable of predicting both pilot and main injection pulse mass flow rates well: the simulations yielded accurate predictions of in-cylinder equivalence ratio distributions from injection strategies for both partially premixed combustion and pilot injections. Also, once calibrated, the model produced appropriate results for a wide range of injected mass and rail pressure values. Finally, it was observed that usage of such a relatively simple model can be a good choice when high-fidelity injection rate input and highly detailed information of the injector’s geometry and operation are not available, particularly as noticeable discrepancies can be present also among different experimental campaigns on similar hardware.

42 ENGINEERING↗

TX$^2$: Transformer eXplainability and eXploration

The Transformer eXplainability and eXploration (Martindale & Stewart, 2021), or TX 2 software package, is a library designed for artificial intelligence researchers to better understand the performance of transformer models (Vaswani et al., 2017) used for sequence classification. The tool is capable of integrating with a trained transformer model and a dataset split into training and testing populations to produce an ipywidget (Project Jupyter Contributors, 2021) dashboard with a number of visualizations to understand model performance with an emphasis on explainability and interpretability. The TX 2 package is primarily intended to integrate into a workflow centered around Jupyter Notebooks (Kluyver et al., 2016), and currently assumes the use of PyTorch (Paszke et al., 2019) and Hugging Face transformers library (Wolf et al., 2020). The dashboard includes visualization and data exploration features to aid researchers, including an interactive UMAP embedding graph (McInnes et al., 2018) to understand classification clusters, a word salience map that can be updated as researchers alter textual entries in near real time, a set of tools to understand word frequency and importance based on the clusters in the UMAP embedding graph, and a set of traditional confusion matrix analysis tools.

97 MATHEMATICS AND COMPUTING↗

Characteristics of arachnoids from Magellan data

Current high resolution Magellan data enables more detailed geological study of arachnoids, first identified by Barsukov et al. as features characterized by a combination of radar-bright, concentric rings and radiating lineations, named 'arachnoids' on the basis of their spider and web-like appearance. Identification of arachnoids in Magellan data has been based on SAR images, in keeping with the original definition. However, there is some overlap by other workers in identification of arachnoids, corona (predominantly bright rings), and novae (predominantly radiating lineations), as all of these features share some common characteristics. Features used in this survey were chosen based on their classification as arachnoids in Head et al.'s catalog and on SAR characteristics matching Barsukov et al.'s original definition. The 259 arachnoids have been currently identified on Venus, all of which were considered in this study. Fifteen arachnoids from different regions, chosen for their 'type' characteristics and lack of deformation by other regional processes, were studied in depth, using SAR and altimetric data to map and profile these arachnoids in an attempt to better determine their geologic and altimetric characteristics and possible formation sequences.

Dawson, C. B.↗

Transparent Object Tracking Benchmark

Visual tracking has achieved considerable progress in recent years. However, current research in the field mainly focuses on tracking of opaque objects, while little attention is paid to transparent object tracking. In this paper, we make the first attempt in exploring this problem by proposing a Transparent Object Tracking Benchmark (TOTB). Specifically, TOTB consists of 225 videos (86K frames) from 15 diverse transparent object categories. Each sequence is manually labeled with axis-aligned bounding boxes. To the best of our knowledge, TOTB is the first benchmark dedicated to transparent object tracking. In order to understand how existing trackers perform and to provide comparison for future research on TOTB, we extensively evaluate 25 state-of-the-art tracking algorithms. The evaluation results exhibit that more efforts are needed to improve transparent object tracking. Besides, we observe some nontrivial findings from the evaluation that are discrepant with some common beliefs in opaque object tracking. For example, we find that deeper features are not always good for improvements. Moreover, to encourage future research, we introduce a novel tracker, named TransATOM, which leverages transparency features for tracking and surpasses all 25 evaluated approaches by a large margin. By releasing TOTB, we expect to facilitate future research and application of transparent object tracking in both the academia and industry.

97 MATHEMATICS AND COMPUTING↗

Genome Features and Biochemical Characteristics of a Robust, Fast Growing and Naturally Transformable Cyanobacterium Synechococcus elongatus PCC 11801 Isolated from India

Cyanobacteria provide an interesting platform for biotechnological applications due to their efficient photoautotrophic growth, amenability to genetic engineering and the ability to grow on non-arable land. An ideal industrial strain of cyanobacteria would need to be fast growing and tolerant to high levels of temperature, light, carbon dioxide, salt and be naturally transformable. In this study, we report Synechococcus elongatus PCC 11801, a strain isolated from India that fulfills these requirements. The physiological and biochemical characteristics of PCC 11801 under carbon and light-limiting conditions were investigated. PCC 11801 shows a doubling time of 2.3h, that is the fastest growth for any cyanobacteria reported so far under ambient CO2 conditions. Genome sequence of PCC 11801 shows genome identity of ~83% with its closest neighbors Synechococcus elongatus PCC 7942 and Synechococcus elongatus UTEX 2973. The unique attributes of PCC 11801 genome are discussed in light of the physiological characteristics that are needed in an industrial strain. The genome of PCC 11801 shows several genes that do not have homologs in neighbor strains PCC 7942 and UTEX 2973, some of which may be responsible for adaptation to various abiotic stresses. The remarkably fast growth rate of PCC 11801 coupled with its robustness and ease of genetic transformation makes it an ideal candidate for the photosynthetic production of fuels and chemicals.

54 ENVIRONMENTAL SCIENCES↗

Synthesis of Speaker Facial Movement to Match Selected Speech Sequences

A system is described which allows for the synthesis of a video sequence of a realistic-appearing talking human head. A phonic based approach is used to describe facial motion; image processing rather than physical modeling techniques are used to create video frames.

phonics speech synthesis imaging image processing ↗

AGFormer: Adaptive Spatiotemporal graph informed transformer for multi-reservoir inflow forecasting

Accurate reservoir inflow forecasting is crucial for effective water resource management, yet most machine learning models focus on single-reservoir prediction and overlook spatial dependencies among hydrologically connected reservoirs. Here, we propose AGFormer (Adaptive Graph-Informed Transformer), an end-to-end framework that integrates adaptive graph learning with temporal sequence modeling for multi-reservoir inflow forecasting. A shared encoder and graph attention mechanism generate reservoir-specific embeddings, which are then processed by the Transformer-based encoder–decoder for multi-step inflow forecasting. We also introduce a pretraining paradigm to learn robust temporal embeddings from misaligned historical records. Evaluated on 30 reservoirs in the Upper Colorado River Basin, AGFormer achieves superior seven-day-ahead forecasts, with NSE > 0.75 for 20 reservoirs—outperforming Encoder–Decoder LSTM, GCN+LSTM, and Transformer baselines. Adaptive graph learning captures dynamic inter-reservoir dependencies, and feature attribution aligns with snowmelt-driven hydrology. Incorporating forecasted meteorological inputs further enhances accuracy, demonstrating AGFormer’s potential to support reservoir management under dynamic hydrological conditions.

Adaptive graph learning↗

Structure of the Regulator of G Protein Signaling 8 (RGS8)-Gα q Complex: Molecular Basis for Gα Selectivity

Regulator of G protein signaling (RGS) proteins interact with activated Gα subunits via their RGS domains and accelerate the hydrolysis of GTP. Although the R4 subfamily of RGS proteins generally accepts both Gα i/o and Gα q/11 subunits as substrates, the R7 and R12 subfamilies select against Gα q/11 . In contrast, only one RGS protein, RGS2, is known to be selective for Gαq/11. The molecular basis for this selectivity is not clear. Previously, the crystal structure of RGS2 in complex with Gα q revealed a non-canonical interaction that could be due to interfacial differences imposed by RGS2, the Gα subunit, or both. To resolve this ambiguity, the 2.6 Å crystal structure of RGS8, an R4 subfamily member, was determined in complex with Gα q . RGS8 adopts the same pose on Gα q as it does when bound to Gα i3 , indicating that the non-canonical interaction of RGS2 with Gα q is due to unique features of RGS2. Here, based on the RGS8-Gα q structure, residues in RGS8 that contact a unique α-helical domain loop of Gα q were converted to those typically found in R12 subfamily members, and the reverse substitutions were introduced into RGS10, an R12 subfamily member. Although these substitutions perturbed their ability to stimulate GTP hydrolysis, they did not reverse selectivity. Instead, selectivity for Gα q seems more likely determined by whether strong contacts can be maintained between α6 of the RGS domain and Switch III of Gα q , regions of high sequence and conformational diversity in both protein families.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DNA methylation and gene expression regulation associated with vascularization in Sorghum bicolor

Plant secondary cell walls constitute the majority of plant biomass. They are predominantly found in xylem cells, which are derived from vascular initials during vascularization. Little is known about these processes in grass species despite their emerging importance as biomass feedstocks. The targeted biofuel crop Sorghum bicolor has a sequenced and well-annotated genome, making it an ideal monocot model for addressing vascularization and biomass deposition. Here we generated tissue-specific transcriptome and DNA methylome data from sorghum shoots, roots and developing root vascular and nonvascular tissues. Many genes associated with vascular development in other species show enriched expression in developing vasculature. However, several transcription factor families varied in vascular expression in sorghum compared with Arabidopsis and maize. Furthermore, differential expression of genes associated with DNA methylation were identified between vascular and nonvascular tissues, implying that changes in DNA methylation are a feature of sorghum root vascularization, which we confirmed using tissue-specific DNA methylome data. Roots treated with a DNA methylation inhibitor also showed a significant decrease in root length. Tissues and organs can be discriminated based on their genomic methylation patterns and methylation context. Consequently, tissue-specific changes in DNA methylation are part of the normal developmental process.

59 BASIC BIOLOGICAL SCIENCES↗

Light Energy Transduction in Green Sulfur Bacteria

Green sulfur bacteria (GSB) are exquisitely adapted for growth at extraordinarily low light intensities. They are important primary producers of biomass in many anoxic environments, and they contribute significantly to the biogeochemical cycling of carbon, nitrogen, and sulfur on Earth. Green bacteria more generally share the property of using chlorosomes for light-harvesting, and these unusual organelles have many unique features. These include the presence of a monolayer lipid-protein envelope, self-assembling bacteriochlorophylls (BChl) in which pigment-pigment interactions predominate, and the presence of redox components ([2Fe-2S] ferredoxins and quinones) that play a role in regulating excitation energy transfer to the type-1 homodimeric reaction centers. The reaction centers of GSB are related to Photosystem I of cyanobacteria and higher plants but also exhibit several unique structural and functional features. The long-term objectives of this research program are to understand the structure, functions, and biogenesis of the chlorosomes, reaction centers, and electron transport chains that carry out the photochemical transduction of light energy into chemical energy in the model green sulfur bacterium, Chlorobaculum (formerly Chlorobium) tepidum. Over a period of 26 years, we characterized chlorosomes in detail. We identified the proteins in the chlorosome envelopes of diverse organisms, identified the nearest neighbors of those proteins, and characterized the chlorosomes of mutant strains lacking one to five of these proteins. After the genome sequence of Cba. tepidum became available, we identified all genes encoding enzymes for BChl a , BChl c/d/e/ƒ , and Chl a biosynthesis Cba. tepidum . We additionally identified all genes encoding enzymes for carotenoid biosynthesis. By constructing a bchQRU mutant strain that produces [Et, Me]-BChl d , together with collaborators who are specialists in solid-state NMR and cryo-electron microscopy, we solved the structure of the BChls in chlorosomes. Using similar methods and chlorosomes containing [Et, Me]-BChl c , we then showed that alternative structures were possible using the same syn-anti BChl dimer. The structures were refined by introducing spectroscopic data from single-chlorosome measurements. Over the course of this project, we sequenced the genomes of approximately twenty GSB strains, which provided important information for comparative analyses. Through analyses of metagenomic data from Mushroom and Octopus Springs in Yellowstone National Park, we identified a novel chlorophototroph belonging to the phylum Acidobacteriota. We successfully isolated an axenic culture of this organism. We characterized the photosynthetic apparatus of this bacterium, named Chloracidobacterium thermophilum, in significant detail, in particular its type-1, homodimeric reaction centers. Surprisingly, these reaction centers contain three types of Chls, BChl a , Chl a , and Zn-BChl a' . We showed that a dimer of Zn-BChl a' is the primary donor and Chl a the primary acceptor of electrons in this reaction center by using advanced spectroscopic techniques. We isolated eight additional strains of Chloracidobacterium spp. from Mushroom Spring and Rupite hot springs in Bulgaria. Comparative genomes showed that these represent three species, Cab. thermophilum , Cab. aggregatum , and Cab. validum . By applying comparative genomics, genetic, biochemical biophysical and physiological approaches to study green bacteria, we produced a wealth of new information about the remarkable light-harvesting and energy transduction capabilities of these poorly characterized microorganisms.

59 BASIC BIOLOGICAL SCIENCES↗

Photogrammetry and photo interpretation applied to analyses of cloud cover, cloud type, and cloud motion

A determination was made of the areal extent of terrain obscured by clouds and cloud shadows on a portion of an Apollo 9 photograph at the instant of exposure. This photogrammetrically determined area was then compared to the cloud coverage reported by surface weather observers at approximately the same time and location, as a check on result quality. Stereograms prepared from Apollo 9 vertical photographs, illustrating various percentages of cloud coverage, are presented to help provide a quantitative appreciation of the degradation of terrain photography by clouds and their attendant shadows. A scheme, developed for the U.S. Navy, utilizing pattern recognition techniques for determining cloud motion from sequences of satellite photographs, is summarized. Clouds, turbulence, haze, and solar altitude, four elements of our natural environment which affect aerial photographic missions, are each discussed in terms of their effects on imagery obtained by aerial photography. Data of a type useful to aerial photographic mission planners, expressing photographic ground coverage in terms of flying height above terrain and camera focal length, for a standard aerial photograph format, are provided. Two oblique orbital photographs taken during the Apollo 9 flight are shown, and photo-interpretations, discussing the cloud types imaged and certain visible geographical features, are provided.

Larsen, P. A.↗

RISK MONITORING CAPABILITES FROM DYNAMIC PRA DATA

Risk Monitors (RMs) are software tools that are employed in nuclear power plants to monitor the safety properties of the plant itself during operation. These safety properties are generated using classical PRA methods which are typically based on static Boolean structures such as Fault-Trees (FTs) and Event-Trees (ETs). The outcomes of these methods are Core Damage Frequency (CDF) and risk importance values of plant components (e.g., valves and pumps). Examples of Risk Importance Measures (RIMs) commonly used are: Risk Achievement Worth (RAW), Risk Reduction Worth (RRW), Birnbaum (B) and Fussell-Vesely (FV) [1,2]. In a RM these values are updated in real time once plant components status is updated (e.g., under maintenance, off-line, testing). In addition, RMs can be used to optimize maintenance schedules so those safety features of the plant are below plant standard values. This paper presents an approach to create temporal profiles of RIMs (i.e., RM capabilities) given a temporal change of the plant configuration. Instead of employing data generated by ETs and FTs, the proposed approach will employ data generated by Dynamic PRA methods. In contrast to classical PRA methods, Dynamic PRA methods couple stochastic methods with safety analysis codes to determine risk associate to complex systems such as nuclear plants. Compared to classical PRA methods, they can evaluate with higher resolution the safety impact of timing and sequencing of events on the accident progression. We will describe how classical RIMs can be generated by Dynamic PRA data and then we will show how the temporal profiles of the RIMs can be generated given a temporal profile of the system configuration.

97 MATHEMATICS AND COMPUTING↗

Time sequence analysis of flickering auroras. I - Application of Fourier analysis

Using a technique that enables one to digitize the brightness of auroral displays from individual fields of a video signal, we have analyzed the frequency content of flickering aurora. Through the application of Fourier analysis to our data, we have found that flickering aurora contains a wide range of enhanced frequencies, although the dominant frequency enhancement generally occurs in the range 6-12 Hz. Each incidence of flickering that we observed was associated with increased radio wave absorption. Furthermore, we have found that flickering occurs in bright auroral surges, the occurrence of which is not limited to the 'breakup' phase of auroral substorms. Our results are interpreted in terms of a recently proposed theory of fluctuating double layers that accounts for a number of the observational features.

Berkey, F. T.↗

Value of long-term streamflow forecast to reservoir operations for water supply in snow-dominated catchments

In this study, we develop a forecast-based adaptive control framework for Oroville reservoir, California, to assess the value of seasonal and inter-annual forecasts for reservoir operation.We use an Ensemble Streamflow Prediction (ESP) approach to generate retrospective, one-year-long streamflow forecasts based on the Variable Infiltration Capacity hydrology model. The optimal sequence of daily release decisions from the reservoir is then determined by Model Predictive Control, a flexible and adaptive optimization scheme.We assess the forecast value by comparing system performance based on the ESP forecasts with that based on climatology and a perfect forecast. In addition, we evaluate system performance based on a synthetic forecast, which is designed to isolate the contribution of seasonal and inter-annual forecast skill to the overall value of the ESP forecasts.Using the same ESP forecasts, we generalize our results by evaluating forecast value as a function of forecast skill, reservoir features, and demand. Our results show that perfect forecasts are valuable when the water demand is high and the reservoir is sufficiently large to allow for annual carry-over. Conversely, ESP forecast value is highest when the reservoir can shift water on a seasonal basis.On average, for the system evaluated here, the overall ESP value is 35% less than the perfect forecast value. The inter-annual component of the ESP forecast contributes 20-60% of the total forecast value. Improvements in the seasonal component of the ESP forecast would increase the overall ESP forecast value between 15 and 20%.

adaptive model control↗

Increased acid resistance of the archaeon, Metallosphaera sedula by adaptive laboratory evolution

Abstract Extremely thermoacidophilic members of the Archaea such as the lithoautotroph, Metallosphaera sedula, are among the most acid resistant forms of life and are of great relevance in bioleaching. Here, adaptive laboratory evolution was used to enhance the acid resistance of this organism while genomics and transcriptomics were used in an effort to understand the molecular basis for this trait. Unlike the parental strain, the evolved derivative, M. sedula SARC-M1, grew well at pH of 0.90. Enargite (Cu3AsS4) bioleaching conducted at pH 1.20 demonstrated SARC-M1 leached 23.78 % more copper relative to the parental strain. Genome re-sequencing identified two mutations in SARC-M1 including a nonsynonymous mutation in Msed_0408 (an amino acid permease) and a deletion in pseudogene Msed_1517. Transcriptomic studies by RNA-seq of wild type and evolved strains at various low pH values demonstrated there was enhanced expression of genes in M. sedula SARC-M1 encoding membrane complexes and enzymes that extrude protons or that catalyze proton-consuming reactions. In addition, M. sedula SARC-M1 exhibited reduced expression of genes encoding enzymes that catalyze proton-generating reactions. These unique genomic and transcriptomic features support a model for increased acid resistance arising from enhanced control over cytoplasmic pH.

Ai, Chenbing↗