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At least 145 records · Page 8

Considerations for AMI-Based Operations for Distribution Feeders

More than $5 billion in investments in advanced metering infrastructure (AMI) technologies, AMI deployments, as pervasive secondary network voltage monitoring systems, provide opportunities for utility operations and controls. This paper focuses on the considerations for AMI-based tools and techniques as the industry moves toward operationalizing such large data sets. Phase identification is a first such tool. Numerous distribution network analysis, monitoring, and control applications - including volt/volt-ampere reactive control, state estimation, and distribution automation - require accurate phase connectivity information in the system models. The phase connectivity database maintained by utilities is inaccurate because of a significant amount of missing data, restoration activities, and network reconfiguration. Existing phase identification techniques that estimate phase connectivity work well in distribution feeders that have low or no photovoltaic (PV) generation; however, they fail to identify the phases accurately when considerable PV generation is present. This work addresses the phase identification problem in the presence of high PV generation using statistical analysis methods. Further, insights into the AMI data requirements for this application in terms of data window length and resolution are provided using sensitivity analysis performed on an actual distribution feeder model of San Diego Gas & Electric Company. The results of this study show that the phase connectivity, even in the presence of high PV generation, can be accurately identified using statistical analysis of AMI data of 1 day.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Tripogon loliiformis tolerates rapid desiccation after metabolic and transcriptional priming during initial drying

Abstract Crop plants and undomesticated resilient species employ different strategies to regulate their energy resources and growth. Most crop species are sensitive to stress and prioritise rapid growth to maximise yield or biomass production. In contrast, resilient plants grow slowly, are small, and allocate their resources for survival in challenging environments. One small group of plants, termed resurrection plants, survive desiccation of their vegetative tissue and regain full metabolic activity upon watering. However, the precise molecular mechanisms underlying this extreme tolerance remain unknown. In this study, we employed a transcriptomics and metabolomics approach, to investigate the mechanisms of desiccation tolerance in Tripogon loliiformis , a modified desiccation-tolerant plant, that survives gradual but not rapid drying. We show that T. loliiformis can survive rapid desiccation if it is gradually dried to 60% relative water content (RWC). Furthermore, the gene expression data showed that T. loliiformis is genetically predisposed for desiccation in the hydrated state, as evidenced by the accumulation of MYB, NAC, bZIP, WRKY transcription factors along with the phytohormones, abscisic acid, salicylic acid, amino acids (e.g., proline) and TCA cycle sugars during initial drying. Through network analysis of co-expressed genes, we observed differential responses to desiccation between T. loliiformis shoots and roots. Dehydrating shoots displayed global transcriptional changes across broad functional categories, although no enrichment was observed during drying. In contrast, dehydrating roots showed distinct network changes with the most significant differences occurring at 40% RWC. The cumulative effects of the early stress responses may indicate the minimum requirements of desiccation tolerance and enable T. loliiformis to survive rapid drying. These findings potentially hold promise for identifying biotechnological solutions aimed at developing drought-tolerant crops without growth and yield penalties.

59 BASIC BIOLOGICAL SCIENCES↗

Chromosome-level genome assembly of Quercus variabilis provides insights into the molecular mechanism of cork thickness

Quercus variabilis is a deciduous woody species with high ecological and economic value and is a major source of cork in East Asia. Cork from thick softwood sheets have higher commercial value than those from thin sheets. It is extremely difficult to genetically improve Q. variabilis to produce high quality softwood due to the lack of genomic information. Here, we present a high-quality chromosomal genome assembly for Q. variabilis with length of 791,89 Mb and 54,606 predicted genes. Comparative analysis of protein sequences of Q. variabilis with 11 other species revealed that specific and expanded gene families were significantly enriched in the "fatty acid biosynthesis" pathway in Q. variabilis, which may contribute to the formation of its unique cork. Additionally, based on weighted correlation network analysis of time-course (i.e., five important developmental ages) gene expression data in thick-cork versus thin-cork genotypes of Q. variabilis, we identified one co-expression gene module associated with the thick-cork trait. Within this co-expression gene module, 10 hub genes were associated with suberin biosynthesis. Furthermore, we identified a total of 198 suberin biosynthesis-related new candidate genes that were up-regulated in trees with a thick cork layer relative to those with a thin cork layer. Also, we found that some genes related to cell expansion and cell division were highly expressed in trees with a thick cork layer. Collectively, our results revealed that two metabolic pathways (i.e., suberin biosynthesis, fatty acid biosynthesis), along with other genes involved in cell expansion, cell division, and transcriptional regulation, were associated with the thick-cork trait in Q. variabilis, providing insights into the molecular basis of cork development and knowledge for informing genetic improvement of cork thickness in Q. variabilis and closely related species.

59 BASIC BIOLOGICAL SCIENCES↗

Diel dynamics of multi-omics in elkhorn fern provide new insights into weak CAM photosynthesis

Crassulacean acid metabolism (CAM) has high water-use efficiency (WUE) and is widely recognized to have evolved from C 3 photosynthesis. Different plant lineages have convergently evolved CAM, but the molecular mechanism that underlies C 3 -to-CAM evolution remains to be clarified. Platycerium bifurcatum (elkhorn fern) provides an opportunity to study the molecular changes underlying the transition from C 3 to CAM photosynthesis because both modes of photosynthesis occur in this species, with sporotrophophyll leaves (SLs) and cover leaves (CLs) performing C 3 and weak CAM photosynthesis, respectively. Here, we report that the physiological and biochemical attributes of CAM in weak CAM-performing CLs differed from those in strong CAM species. We investigated the diel dynamics of the metabolome, proteome, and transcriptome in these dimorphic leaves within the same genetic background and under identical environmental conditions. We found that multi-omic diel dynamics in P. bifurcatum exhibit both tissue and diel effects. Our analysis revealed temporal rewiring of biochemistry relevant to the energy-producing pathway (TCA cycle), CAM pathway, and stomatal movement in CLs compared with SLs. We also confirmed that PHOSPHOENOLPYRUVATE CARBOXYLASE KINASE (PPCK) exhibits convergence in gene expression among highly divergent CAM lineages. Gene regulatory network analysis identified candidate transcription factors regulating the CAM pathway and stomatal movement. Taken together, our results provide new insights into weak CAM photosynthesis and new avenues for CAM bioengineering.

59 BASIC BIOLOGICAL SCIENCES↗

Insights of Molecular Mechanism of Xylem Development in Five Black Poplar Cultivars

Black poplar (Populus deltoides, P. nigra, and their hybrids) is the main poplar cultivars in China. It offers interesting options of large-scale biomass production for bioenergy due to its rapid growth and high yield. Poplar wood properties were associated with chemical components and physical structures during wood formation. In this study, five poplar cultivars, P. euramericana ‘Zhonglin46’ (Pe1), P. euramericana ‘Guariento’ (Pe2), P. nigra ‘N179’ (Pn1), P. deltoides ‘Danhong’ (Pd1), and P. deltoides ‘Nanyang’ (Pd2), were used to explore the molecular mechanism of xylem development. We analyzed the structural differences of developing xylem in the five cultivars and profiled the transcriptome-wide gene expression patterns through RNA sequencing. The cross sections of the developing xylem showed that the cell wall thickness of developed fiber in Pd1 was thickest and the number of xylem vessels of Pn1 was the least. A total of 10,331 differentially expressed genes were identified among 10 pairwise comparisons of the five cultivars, most of them were related to programmed cell death and secondary cell wall thickening. K-means cluster analysis and Gene Ontology enrichment analysis showed that the genes highly expressed in Pd1 were related to nucleotide decomposition, metabolic process, transferase, and microtubule cytoskeleton; whereas the genes highly expressed in Pn1 were involved in cell wall macromolecule decomposition and polysaccharide binding processes. Based on a weighted gene co-expression network analysis, a large number of candidate regulators for xylem development were identified. And their potential regulatory roles to cell wall biosynthesis genes were validated by a transient overexpression system. This study provides a set of promising candidate regulators for genetic engineering to improve feedstock and enhance biofuel conversion in the bioenergy crop Populus.

59 BASIC BIOLOGICAL SCIENCES↗

AWB-GCN: A Graph Convolutional Network Accelerator with Runtime Workload Rebalancing

The recent development of deep learning has been mostly focusing on Euclidean data, such as images, videos, audios, etc. However, most real-world information and relation are often expressed as graphs. To efficiently learn from graph data, graph convolutional networks (GCNs) emerge as a promising approach, showing advantages in several practical applications such as social network analysis, knowledge discovery, 3D modeling, motion capturing, etc. Real-world graphs are usually extremely large and imbalanced, posting significant performance demand and design challenges on the hardware dedicated for GCN inference. In this paper, we propose an architecture design called UW-GCN to accelerate graph convolutional network inference. To tackle the major performance bottleneck from workload imbalance, we propose dynamic neighborhood stealing and remote chunk shuffling techniques, relying on hardware flexibility to achieve hardware auto-tuning under negligible area or delay overhead. Specifically, UW-GCN is able to smartly profile the sparse graph pattern while continuously adjusting the workload distribution via routing reconfiguration among parallel processing elements (PEs). The ideal configuration is then reused in the remaining iterations. To the best of our knowledge, this is the first accelerator design particularly for GCN and the first work relying on hardware auto-tuning, which is normally based on software, to achieve near-optimal workload balance in processing sparse structures.

Geng, Tong↗

Global droughts connected by linkages between drought hubs

Abstract Quantifying the spatial and interconnected structure of regional to continental scale droughts is one of the unsolved global hydrology problems, which is important for understanding the looming risk of mega-scale droughts and the resulting water and food scarcity and their cascading impact on the worldwide economy. Using a Complex Network analysis, this study explores the topological characteristics of global drought events based on the self-calibrated Palmer Drought Severity Index. Event Synchronization is used to measure the strength of association between the onset of droughts at different spatial locations within the time lag of 1-3 months. The network coefficients derived from the synchronization network indicate a highly heterogeneous connectivity structure underlying global drought events. Drought hotspot regions such as Southern Europe, Northeast Brazil, Australia, and Northwest USA behave as drought hubs that synchronize regionally and with other hubs at inter-continental or even inter-hemispheric scale. This observed affinity among drought hubs is equivalent to the ‘rich-club phenomenon’ in Network Theory, where ‘rich’ nodes (here, drought hubs) are tightly interconnected to form a club, implicating the possibility of simultaneous large-scale droughts over multiple continents.

54 ENVIRONMENTAL SCIENCES↗

Rhythmic Mechanisms Governing CAM Photosynthesis in Kalanchoe fedtschenkoi : High-Resolution Temporal Transcriptomics

Crassulacean acid metabolism (CAM) is a specialized photosynthetic pathway that enhances water-use efficiency by temporally separating nocturnal CO 2 uptake from daytime decarboxylation and carbon fixation. To uncover the regulatory mechanisms coordinating these temporal dynamics, we generated high-resolution, 48 h time-course transcriptomes for the CAM model Kalanchoe fedtschenkoi under both 12 h/12 h light/dark (LD) cycles and continuous light (LL). A rhythmicity analysis revealed that diel light cues are the dominant driver of transcript oscillations: 16,810 genes (54.3% of annotated genes) exhibited rhythmic expression only under LD, whereas just 399 genes (1.3%) remained rhythmic under LL. A smaller set of 3009 genes (9.7%) oscillated in both conditions, indicating that the intrinsic circadian clock sustains rhythmicity for a limited subset of the transcriptome. A gene co-expression network analysis revealed extensive integration between circadian clock components, core CAM pathway enzymes, and stomatal regulators, defining regulatory modules that coordinate metabolic and physiological timing. Notably, key hub genes associated with post-translational and post-transcriptional regulation, including the E3 ubiquitin ligase HUB2 and several pentatricopeptide repeat (PPR) proteins, act as central nodes in CAM-associated networks. This discovery implicates epigenetic and organellar regulation as previously unrecognized critical tiers of control in CAM. Together, our results support a regulatory model in which CAM rhythmicity is governed by both external light/dark cues and the endogenous circadian clock through multi-level control spanning transcriptional and protein-level regulation. To support community exploration, we also provide an interactive eFP (electronic Fluorescent Pictograph) browser for visualizing time-resolved gene expression profiles.

09 BIOMASS FUELS↗

Bacterial hemophilin homologs and their specific type eleven secretor proteins have conserved roles in heme capture and are diversifying as a family

Cellular life relies on enzymes that require metals, which must be acquired from extracellular sources. Bacteria utilize surface and secreted proteins to acquire such valuable nutrients from their environment. These include the cargo proteins of the type eleven secretion system (T11SS), which have been connected to host specificity, metal homeostasis, and nutritional immunity evasion. This Sec-dependent, Gram-negative secretion system is encoded by organisms throughout the phylum Proteobacteria, including human pathogens Neisseria meningitidis, Proteus mirabilis, Acinetobacter baumannii, and Haemophilus influenzae. Experimentally verified T11SS-dependent cargo include transferrin-binding protein B (TbpB), the hemophilin homologs heme receptor protein C (HrpC), hemophilin A (HphA), the immune evasion protein factor-H binding protein (fHbp), and the host symbiosis factor nematode intestinal localization protein C (NilC). Here, we examined the specificity of T11SS systems for their cognate cargo proteins using taxonomically distributed homolog pairs of T11SS and hemophilin cargo and explored the ligand binding ability of those hemophilin cargo homologs. In vivo expression in Escherichia coli of hemophilin homologs revealed that each is secreted in a specific manner by its cognate T11SS protein. Sequence analysis and structural modeling suggest that all hemophilin homologs share an N-terminal ligand-binding domain with the same topology as the ligand-binding domains of the Haemophilus haemolyticus heme binding protein (Hpl) and HphA. We term this signature feature of this group of proteins the hemophilin ligand-binding domain. Network analysis of hemophilin homologs revealed five subclusters and representatives from four of these showed variable heme-binding activities, which, combined with sequence-structure variation, suggests that hemophilins are diversifying in function.

59 BASIC BIOLOGICAL SCIENCES↗

Whole-Genome Sequencing and Bioinformatic Analysis of Environmental, Agricultural, and Human Campylobacter jejuni Isolates From East Tennessee

As a leading cause of bacterial-derived gastroenteritis worldwide, Campylobacter jejuni has a significant impact on human health in both the developed and developing worlds. Despite its prevalence as a human pathogen, the source of these infections remains poorly understood due to the mutation frequency of the organism and past limitations of whole genome analysis. Recent advances in both whole genome sequencing and computational methods have allowed for the high-resolution analysis of intraspecies diversity, leading multiple groups to postulate that these approaches may be used to identify the sources of Campylobacter jejuni infection. To address this hypothesis, our group conducted a regionally and temporally restricted sampling of agricultural and environmental Campylobacter sources and compared isolated C. jejuni genomes to those that caused human infections in the same region during the same time period. Through a network analysis comparing genomes from various sources, we found that human C. jejuni isolates clustered with those isolated from cattle and chickens, indicating these as potential sources of human infection in the region.

59 BASIC BIOLOGICAL SCIENCES↗

Brain phosphoproteomic analysis identifies diabetes‐related substrates in Alzheimer's disease pathology in older adults

INTRODUCTION: Type 2 diabetes increases the risk of Alzheimer's disease (AD) dementia. Insulin signaling dysfunction exacerbates tau protein phosphorylation, a hallmark of AD pathology. However, the comprehensive impact of diabetes on patterns of AD-related phosphoprotein in the human brain remains underexplored. METHODS: We performed tandem mass tag–based phosphoproteome profiling in post mortem human brain prefrontal cortex samples from 191 deceased older adults with and without diabetes and pathologic AD. RESULTS: Among 7874 quantified phosphosites, microtubule-associated protein tau (MAPT) phosphorylated at T529 and T534 (isoform 8 T212 and T217) were more abundant in AD and showed differential associations with diabetes. Network analysis of co-abundance patterns uncovered synergistic interactions between AD and diabetes, with one module exhibiting higher MAPT phosphorylation (15 MAPT phosphosites) and another displaying lower MAP1B phosphorylation (22 MAP1B phosphosites). DISCUSSION: This study offers phosphoproteomics insights into AD in diabetes, shedding light on mechanisms that can inform the development of therapeutics for dementia. Highlights: The risk of Alzheimer's disease (AD) dementia is increased among older adults living with diabetes. The patterns of AD-related phosphoprotein in the human brain in older adults are differential among older adults living with diabetes. Microtubule-associated protein tau phosphorylated at T529 and T534 (isoform 8 T212 and T217) showed differential associations with diabetes. Phosphosite co-abundance networks of synergistic interactions between AD and diabetes were identified.

60 APPLIED LIFE SCIENCES↗

Understanding Discrete Fracture Networks Through Spectral Graph Theory

Discrete Fracture Network models (DFNs) are used to simulate fluid flow and particle transport through fracture networks in low permeability rock. Understanding these processes are essential in many subsurface applications, such as environmental restoration of contaminated fractured media, CO 2 sequestration, detection of low-level nuclear tests, and hydrocarbon extraction. Compared with other models, DFNs allow for incorporation of a wider range of network characteristics but have substantially greater computation cost. These networks can be represented with graphs, allowing the use of graph theory tools to study the networks. I used Python to simulate flow and transport on a range of DFNs and analyzed these networks using methods from network analysis and spectral graph theory. My purpose was to find ways to gain insight about flow and transport on DFNs using these graph representations, bypassing the computationally intensive meshing typically required. My work is still in progress, but I have discovered several interesting trends and patterns that I believe could be useful towards my goal. If I am able to bring these results to fruition, they will aid subsurface geologists in extracting flow and transport information about fracture networks more efficiently.

54 ENVIRONMENTAL SCIENCES↗

Integrating phytoplankton pigment and DNA meta-barcoding observations to determine phytoplankton composition in the coastal ocean

Quantifying phytoplankton composition is critical to predicting marine ecosystem structure and function. DNA meta-barcoding and high-performance liquid chromatography (HPLC) pigment analysis are two widely used methods for assessing phytoplankton composition; however, comparing their performance has been done only rarely. Here, we integrate DNA meta-barcoding and HPLC pigment observations to determine eukaryotic phytoplankton composition in the Santa Barbara Channel, California. We find that both methods identify the same four dominant eukaryotic phytoplankton taxa (diatoms, dinoflagellates, chlorophytes, and prymnesiophytes), but inter- and intra-lineage variability in biomarker pigmentation (associated with both a lack of taxonomic specificity of biomarker pigments and intrinsic differences in accessory pigmentation) drives substantial disagreement between the methods. Covariation network analysis circumvents this disagreement and reveals that diverse assemblages of phytoplankton and other protists covary with distinct suites of biomarker pigments. Our results highlight the strengths and weaknesses of each method in characterizing phytoplankton composition and reveal novel insights into phytoplankton physiology that could only be gained by integrating the two methods. Finally, we suggest a path to monitor eukaryotic plankton communities on unprecedented spatiotemporal scales based on the covariation of unique phytoplankton and protistan assemblages with remotely sensible phytoplankton pigment concentrations.

59 BASIC BIOLOGICAL SCIENCES↗

Generalized Canonical Polyadic Tensor Decomposition

Tensor decomposition is a fundamental unsupervised machine learning method in data science, with applications including network analysis and sensor data processing. This work develops a generalized canonical polyadic (GCP) low-rank tensor decomposition that allows other loss functions besides squared error. For instance, we can use logistic loss or Kullback--Leibler divergence, enabling tensor decomposition for binary or count data. We present a variety of statistically motivated loss functions for various scenarios. We provide a generalized framework for computing gradients and handling missing data that enables the use of standard optimization methods for fitting the model. Furthermore, we demonstrate the flexibility of the GCP decomposition on several real-world examples including interactions in a social network, neural activity in a mouse, and monthly rainfall measurements in India.

97 MATHEMATICS AND COMPUTING↗

Deep Koopman learning of nonlinear time-varying systems

Here this paper presents a data-driven approach to approximate the dynamics of a nonlinear time-varying system (NTVS) by a linear time-varying system (LTVS), which results from the Koopman operator and deep neural networks. Analysis of the approximation error between states of the NTVS and the resulting LTVS is presented. Simulations on a representative NTVS show that the proposed method achieves small approximation errors, even when the system changes rapidly. Furthermore, simulations in an example of quadcopters demonstrate the computational efficiency of the proposed approach.

97 MATHEMATICS AND COMPUTING↗

New Measurements of the Lyα Forest Continuum and Effective Optical Depth with LyCAN and DESI Y1 Data

Abstract We present the Ly α Continuum Analysis Network (LyCAN), a convolutional neural network that predicts the unabsorbed quasar continuum within the rest-frame wavelength range of 1040–1600 Å based on the red side of the Ly α emission line (1216–1600 Å). We developed synthetic spectra based on a Gaussian mixture model representation of nonnegative matrix factorization (NMF) coefficients. These coefficients were derived from high-resolution, low-redshift ( z < 0.2) Hubble Space Telescope/Cosmic Origins Spectrograph (COS) quasar spectra. We supplemented this COS-based synthetic sample with an equal number of DESI Year 5 mock spectra. LyCAN performs extremely well on testing sets, achieving a median error in the forest region of 1.5% on the DESI mock sample, 2.0% on the COS-based synthetic sample, and 4.1% on the original COS spectra. LyCAN outperforms principal component analysis (PCA) and NMF-based prediction methods using the same training set by 40% or more. We predict the intrinsic continua of 83,635 DESI Year 1 spectra in the redshift range of 2.1 ≤ z ≤ 4.2 and perform an absolute measurement of the evolution of the effective optical depth. This is the largest sample employed to measure the optical depth evolution to date. We fit a power law of the form τ ( z ) = τ 0 ( 1 + z ) γ to our measurements and find τ 0 = (2.46 ± 0.14) × 10 −3 and γ = 3.62 ± 0.04. Our results show particular agreement with high-resolution, ground-based observations around z = 2, indicating that LyCAN is able to predict the quasar continuum in the forest region with only spectral information outside the forest.

79 ASTRONOMY AND ASTROPHYSICS↗

Long-term excess nitrogen fertilizer increases sensitivity of soil microbial community to seasonal change revealed by ecological network and metagenome analyses

Nitrogen (N) fertilizer has often been generously applied to increase crop biomass yield. Although the influences of inorganic N fertilizer on soil microbial communities have been widely studied, the effect of N fertilizer on microbial co-occurrence networks and its metagenome is largely unknown. Further, seasonal changes in microbial community responses to N addition have rarely been reported. In this study, three N fertilizer rates (0, 56, 196 kg N/ha) were applied annually in switchgrass (Panicum virgatum L.) grown for bioenergy production in the upper Midwest, USA. The soil microbiome was affected by both fertilizer and low pH in the 7th year of fertilization treatments. The microbial community structures were relatively stable during the growing season for each N fertilizer rate. However, the excess N fertilizer (196N) increased the seasonal variation of bacterial and fungal communities. Network analysis showed that the microbial interactions at the 196N treatment were more intense, with decreased bacteria-fungal interactions compared to 56N and 0N. Furthermore, this suggests that the microbial community became more sensitive to environmental change under the influence of long-term excess N fertilizer. Metagenomic analysis showed that the long-term excess N fertilizer promoted many metabolic processes, especially carbohydrate and amino acid related metabolism and Archaea mediated ammonia oxidation. However, N fertilizer also reduced many other traits, especially N 2 fixation and signal transduction, the latter of which may contribute to the decreased interactions between bacteria and fungi.

54 ENVIRONMENTAL SCIENCES↗

Analysis of Neural Networks as Random Dynamical Systems

In this report we present our findings and outcomes of the NNRDS (analysis of Neural Networks as Random Dynamical Systems) project. The work is largely motivated by the analogy of a large class of neural networks (NNs) with a discretized ordinary differential equation (ODE) schemes. Namely, residual NNs, or ResNets, can be viewed as a discretization of neural ODEs (NODEs) where the NN depth plays the role of the time evolution. We employ several legacy tools from ODE theory, such as stiffness, nonlocality, autonomicity, to enable regularization of ResNets thus improving their generalization capabilities. Furthermore, armed with NN analysis tools borrowed from the ODE theory, we are able to efficiently augment NN predictions with uncertainty overcoming wellknown dimensionality challenges and adding a degree of trust towards NN predictions. Finally, we have developed a Python library QUiNN (Quantification of Uncertainties in Neural Networks) that incorporates improved-architecture ResNets, besides classical feed-forward NNs, and contains wrappers to PyTorch NN models enabling several major classes of uncertainty quantification methods for NNs. Besides synthetic problems, we demonstrate the methods on datasets from climate modeling and materials science.

97 MATHEMATICS AND COMPUTING↗