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At least 91 records · Page 5

The State of the Art in Visualizing Dynamic Multivariate Networks

Abstract Most real‐world networks are both dynamic and multivariate in nature, meaning that the network is associated with various attributes and both the network structure and attributes evolve over time. Visualizing dynamic multivariate networks is of great significance to the visualization community because of their wide applications across multiple domains. However, it remains challenging because the techniques should focus on representing the network structure, attributes and their evolution concurrently. Many real‐world network analysis tasks require the concurrent usage of the three aspects of the dynamic multivariate networks. In this paper, we analyze current techniques and present a taxonomy to classify the existing visualization techniques based on three aspects: temporal encoding, topology encoding, and attribute encoding. Finally, we survey application areas and evaluation methods; and discuss challenges for future research.

Kale, Bharat↗

Techno-economic analysis and network design for CO 2 conversion to jet fuels in the United States

The conversion of carbon dioxide (CO 2 ) into jet fuel holds significant potential for reducing CO 2 emissions, providing an alternative to carbon-based resources, and offering a renewable means of energy storage. The objective of this study is to conduct a techno-economic analysis and optimize the supply chain network for converting CO 2 to jet fuel in the United States, aiming to minimize total costs while assessing the environmental and economic feasibility of two CO 2 conversion pathways. This first pathway is based on Fischer-Tropsch synthesis (FTS), and the other one is based on the valorization and upgrading of light methanol (MeOH). Incorporating spatial and techno-economic data, a mixed-integer linear programming model was developed to select source plants and conversion pathways, locations of conversion refinery sites, and the amount of captured CO 2 across the United States. The optimal results indicate that the FTS pathway is adopted at all selected refineries when the hydrogen price is 1000 dollars/t and the operating cost, mainly electricity used in conversion, is reduced to 5 % of its current level. Under this scenario, the total annual profit is 8 billion dollars, and the net carbon emissions are -88,783,284 tons. The sensitivity analyses reveal that the prices of electricity and hydrogen significantly contribute to total production costs. The CO 2 recycle percentage of the FTS pathway influences the choice of applied pathways at refineries. Additionally, a higher conversion rate holds a substantial promise for reducing the total production cost and can make the MeOH pathway a viable choice.

10 SYNTHETIC FUELS↗

An ODE-Enabled Distributed Transient Stability Analysis for Networked Microgrids

Networked microgrid (NMG) exhibits noteworthy resiliency and flexibility benefits for the mutual support from neighboring microgrids. With high penetration of distributed energy resources (DERs) and the associated controls, the transient stability analysis of NMGs is of critical significance. To address the issues of computation burdens and privacy in the centralized transient analysis, this paper devises an ordinary differential equation (ODE)-enabled distributed transient stability (DTS) methodology for NMGs. First, an ODE-based microgrid model is established to capture the dynamics in the droop control of DERs as well as network and load. Further, a distributed DTS is devised for the ODE representation of an NMG, allowing a privacy-preserving transient analysis of each microgrid while accurately reconstructing the frequency dynamics under droop controls in all DERs. In conclusion, extensive tests are performed to verify the validity of the ODE-based microgrid model through both dynamic response and eigenvalue analysis, and the efficacy of the DTS algorithm in simulating the large signal responses and the frequent fluctuations in NMG.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Network performance analysis for HPC datacenters (net_perf) v1.0

The software has two main features: (1) identify data movement trends in HPC data centers that use network flow monitoring (2) analyze the performance of individual data flows under the existing data movement management strategy and identify performance bottlenecks that impede timely data availability for science workflows. Its main advantage is that it is tailored for HPC network traffic by considering HPC data movement management intricacies.

Giannakou, Anna↗

Disrupting the ArcA Regulatory Network Amplifies the Fitness Cost of Tetracycline Resistance in Escherichia coli

There is an urgent need for strategies to discover secondary drugs to prevent or disrupt antimicrobial resistance (AMR), which is causing >700,000 deaths annually. Here, we demonstrate that tetracycline-resistant (Tet R ) Escherichia coli undergoes global transcriptional and metabolic remodeling, including downregulation of tricarboxylic acid cycle and disruption of redox homeostasis, to support consumption of the proton motive force for tetracycline efflux. Using a pooled genome-wide library of single-gene deletion strains, at least 308 genes, including four transcriptional regulators identified by our network analysis, were confirmed as essential for restoring the fitness of Tet R E. coli during treatment with tetracycline. Targeted knockout of ArcA, identified by network analysis as a master regulator of this new compensatory physiological state, significantly compromised fitness of Tet R E. coli during tetracycline treatment. A drug, sertraline, which generated a similar metabolome profile as the arcA knockout strain, also resensitized Tet R E. coli to tetracycline. We discovered that the potentiating effect of sertraline was eliminated upon knocking out arcA, demonstrating that the mechanism of potential synergy was through action of sertraline on the tetracycline-induced ArcA network in the Tet R strain. Our findings demonstrate that therapies that target mechanistic drivers of compensatory physiological states could resensitize AMR pathogens to lost antibiotics.

59 BASIC BIOLOGICAL SCIENCES↗

Knowledge Spillovers and Cost Reductions in Solar Soft Costs

Despite the commonly acknowledged importance of knowledge spillovers in reducing solar soft costs, we are only beginning to answer a fundamental question: who learns what (knowledge acquisition), from whom (knowledge production), and how (spillover mechanisms)? Until recently, this important topic has been largely unexplored in the case of solar soft costs. Thus, this project set out to identify how knowledge spillovers affect soft costs in the U.S. photovoltaic (PV) installation industry, specifically how important spillovers are, what types of knowledge are most likely to spillover, and how networks of actors affect spillovers. Our findings offer insights for designing solutions that address problems associated with knowledge spillovers and that leverage spillovers to reduce solar soft costs. Recognizing the ambiguity in the definition of soft costs, i.e., “non-hardware costs,” and variability in soft cost categories, we developed the Solar Soft Cost Ontology (SSCO) to systematically identify key concepts related to soft costs, network actors, learning processes, and the relationships between them. This ontology served as a foundational organizational structure for the methodology of the remaining tasks: case studies, surveys, pricing analysis, patent analysis, network analysis, and project integration across tasks. While there is substantial learning among installers that is reducing the soft costs for PV installations, most of that learning is retained by firms rather than spread across the industry. The positive relationship between experience accumulation and cost reductions is typically explained as learning by doing (LBD), but we find that LBD effects are mediated by other learning mechanisms, including learning by searching and learning by interacting. Knowledge spillovers have significant potential to reduce solar PV soft costs, but successful knowledge spillover pathways are complex and non-trivial. There are a wide variety of ways to construct an installation business, thus categories of firms that can effectively cross-learn directly are small and what knowledge is relevant to whom is challenging and costly for firms to assess. This fragmentation limits the critical mass needed for spillover related soft cost reductions. Knowledge does not flow directly between installers. Indirect knowledge transfer pathways are critical: distributors, software providers, collaboratives, and hiring. Furthermore, diverse, more integrated knowledge networks tend to promote successful learning by organizations and across the system as a whole. Accordingly, we find the need to supporting the whole ecosystem using an integrated policy and programmatic approach to support installers, distributors, complementary sector, and facilitators. Overall, a deliberate policy-mix design is needed to reduce the solar PV deployment barrier in terms of installation cost reductions, because deployment policies could potentially interact with policies that facilitate network-building and technological innovation. A combination of deployment policies, innovation-support policies, and network-facilitating policies could potentially lead to a more desired market outcome through achieving higher joint learning rates from firms’ cumulative experiences developed in a more integrated production and deployment ecosystem.

14 SOLAR ENERGY↗

GPS Spoofing Mitigation and Timing Risk Analysis in Networked Phasor Measurement Units via Stochastic Reachability

To address phasor measurement unit (PMU) vulnerability to spoofing, we propose the use of a set-valued state estimation technique known as stochastic reachability (SR)-based distributed Kalman filter (DKF) that computes secure global positioning system (GPS) timing across a network of receivers. Utilizing SR, we estimate not only GPS time but also its stochastic reachable set, which is parameterized by probabilistic zonotope (p-Zonotope). While requiring known measurement error bounds in only non-spoofed conditions, we designed a two-tiered approach. We first performed measurement-level spoofing mitigation via deviation of a measurement innovation from its expected p-Zonotope. We then performed state-level timing risk analysis via a determination of the intersection probability of the estimated p-Zonotope with an unsafe set that violates IEEE C37.118.1a-2014 standards. Finally, we validated our SR-DKF algorithm by subjecting it to a simulated receiver network to coordinate signal-level spoofing. We demonstrate improved timing accuracy and successful spoofing mitigation via the use of our SR-DKF algorithm. We also validated the robustness of the estimated timing risk as the number of receivers were varied.

47 OTHER INSTRUMENTATION↗

Hypothesis-Agnostic Network-Based Analysis of Real-World Data Suggests Ondansetron is Associated with Lower COVID-19 Any Cause Mortality

Background: The COVID-19 pandemic generated a massive amount of clinical data, which potentially hold yet undiscovered answers related to COVID-19 morbidity, mortality, long-term effects, and therapeutic solutions.Objectives: The objectives of this study were (1) to identify novel predictors of COVID-19 any cause mortality by employing artificial intelligence analytics on real-world data through a hypothesis-agnostic approach and (2) to determine if these effects are maintained after adjusting for potential confounders and to what degree they are moderated by other variables.Methods: A Bayesian statistics-based artificial intelligence data analytics tool (bAIcis®) within the Interrogative Biology® platform was used for Bayesian network learning and hypothesis generation to analyze 16,277 PCR+ patients from a database of 279,281 inpatients and outpatients tested for SARS-CoV-2 infection by antigen, antibody, or PCR methods during the first pandemic year in Central Florida. This approach generated Bayesian networks that enabled unbiased identification of significant predictors of any cause mortality for specific COVID-19 patient populations. These findings were further analyzed by logistic regression, regression by least absolute shrinkage and selection operator, and bootstrapping.Results: We found that in the COVID-19 PCR+ patient cohort, early use of the antiemetic agent ondansetron was associated with decreased any cause mortality 30 days post-PCR+ testing in mechanically ventilated patients.Conclusions: The results demonstrate how a real-world COVID-19-focused data analysis using artificial intelligence can generate unexpected yet valid insights that could possibly support clinical decision making and minimize the future loss of lives and resources.

60 APPLIED LIFE SCIENCES↗

Fluid dynamic simulation and analysis of water-cooling systems for the Electron-Ion Collider

The Electron-Ion Collider is the newest large-scale project at Brookhaven National Laboratory. The collider’s purpose is to provide further advancements in the knowledge of the universe’s origin by accelerating particles near the speed of light. Our project for this 3.8 km ring was to create a thermal hydraulic steady-state simulation design of the water-cooling system to be cost-effective and energy efficient, as envisioned by Charlie Foltz, the EIC Infrastructure Division Director. The system would include a supply and return header, which cools several thousand components of the ring. The water would then be returned and cooled down using a system of cooling towers and plate and frame heat exchangers. Due to the size of the system and the complexity of the network analysis, a fluid dynamic simulation software, AFT Fathom, was used. Since previous methods of maintaining systems relied on building upon smaller real-life models and implementing empirical data, this flow model was unique and first of a kind in the domain of accelerator design, construction and operation. Therefore, our hydraulic team piloted a new method to perform network analysis on a large scale cooling system. We successfully created several test scenarios for system behavior in a shorter time compared to the method of performing hand calculations. Cooling specifications for heat rejection, pressure drop, flow rate, and pipe sizing were changed based on the individual systems of the vacuum, radio frequency (RF), magnet and power supply, and cryogenics sections. Finally, we used DOE guidelines to perform life-cycle cost analysis with net present value and carbon saving analysis on the systems where pipe size could be optimized.

43 PARTICLE ACCELERATORS↗

Molecular and Epidemiological Investigation of Fluconazole-resistant Candida parapsilosis —Georgia, United States, 2021

Abstract Background Reports of fluconazole-resistant Candida parapsilosis bloodstream infections are increasing. We describe a cluster of fluconazole-resistant C parapsilosis bloodstream infections identified in 2021 on routine surveillance by the Georgia Emerging Infections Program in conjunction with the Centers for Disease Control and Prevention. Methods Whole-genome sequencing was used to analyze C parapsilosis bloodstream infections isolates. Epidemiological data were obtained from medical records. A social network analysis was conducted using Georgia Hospital Discharge Data. Results Twenty fluconazole-resistant isolates were identified in 2021, representing the largest proportion (34%) of fluconazole-resistant C parapsilosis bloodstream infections identified in Georgia since surveillance began in 2008. All resistant isolates were closely genetically related and contained the Y132F mutation in the ERG11 gene. Patients with fluconazole-resistant isolates were more likely to have resided at long-term acute care hospitals compared with patients with susceptible isolates (P = .01). There was a trend toward increased mechanical ventilation and prior azole use in patients with fluconazole-resistant isolates. Social network analysis revealed that patients with fluconazole-resistant isolates interfaced with a distinct set of healthcare facilities centered around 2 long-term acute care hospitals compared with patients with susceptible isolates. Conclusions Whole-genome sequencing results showing that fluconazole-resistant C parapsilosis isolates from Georgia surveillance demonstrated low genetic diversity compared with susceptible isolates and their association with a facility network centered around 2 long-term acute care hospitals suggests clonal spread of fluconazole-resistant C parapsilosis. Further studies are needed to better understand the sudden emergence and transmission of fluconazole-resistant C parapsilosis.

Misas, Elizabeth (ORCID:0000000162437716)↗

Neural network based analysis of multimodal bond distributions using extended x-ray absorption fine structure spectra

Knowledge of the local coordination environment around atomic species in functional materials is critical for understanding their mechanisms of operation. Heterogeneous mixtures of metal complexes are ubiquitous in catalysts, ionic liquids, molten salts, biological enzymes, and geochemical systems, among many others. Extracting information from ensemble-average measurements about the structural and compositional descriptors of each type of coordination complex comprising the mixture is not generally possible, especially when they possess multimodal bond-length distributions. Here, we developed a method that enables the mapping of an x-ray absorption spectrum on the radial distribution function describing the average environment of the metal ions. The supervised neural network based method utilizes an objective training set, for which the choice of the local structural motifs is completely agnostic to the theoretically expected structure and dynamics of the modeled system. The method was validated using first-principles modeling of structural dynamics of nickel complexation in molten salts, and it applies to a large class of heterogeneous systems, including those studied under in situ and operando conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multi-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in Rhodosporidium toruloides

An oleaginous yeast Rhodosporidium toruloides is a promising host for converting lignocellulosic biomass to bioproducts and biofuels. In this work, we performed multi-omics analysis of lignocellulosic carbon utilization in R. toruloides and reconstructed the genome-scale metabolic network of R. toruloides . High-quality metabolic network models for model organisms and orthologous protein mapping were used to build a draft metabolic network reconstruction. The reconstruction was manually curated to build a metabolic model using functional annotation and multi-omics data including transcriptomics, proteomics, metabolomics, and RB-TDNA sequencing. The multi-omics data and metabolic model were used to investigate R. toruloides metabolism including lipid accumulation and lignocellulosic carbon utilization. The developed metabolic model was validated against high-throughput growth phenotyping and gene fitness data, and further refined to resolve the inconsistencies between prediction and data. We believe that this is the most complete and accurate metabolic network model available for R. toruloides to date.

09 BIOMASS FUELS↗

Concentration-response gene expression analysis in zebrafish reveals phenotypically-anchored transcriptional responses to retene

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental contaminants and are associated with human disease. Canonically, many PAHs induce toxicity via activation of the aryl hydrocarbon receptor (AHR) pathway. While the interaction between PAHs and the AHR is well-established, understanding which AHR-regulated transcriptional effects directly result in observable phenotypes and which are adaptive or benign is important to better understand PAH toxicity. Retene is a frequently detected PAH in environmental sampling and has been associated with AHR2-dependent developmental toxicity in zebrafish, though its mechanism of toxicity has not been fully elucidated. To interrogate transcriptional changes causally associated with retene toxicity, we conducted whole-animal RNA sequencing at 48 hours post-fertilization after exposure to eight retene concentrations. The concentrations were selected to produce effects ranging from no phenotype to mortality and malformations in 100% of animals at 5 days post-fertilization. We identified a concentration-response relationship between retene teratogenicity and differential gene expression in both number of DEGs and magnitude of expression change. Elevated expression of cyp1a at retene concentrations below the threshold for teratogenicity suggested that while cyp1a expression is a sensitive biomarker of AHR activation, it may be too sensitive to serve as a biomarker of AHR-dependent teratogenicity. Genes differentially expressed at only non-teratogenic concentrations were enriched for transforming growth factor-ß (TGF-ß) signaling pathway disruption while DEGs identified at only teratogenic concentrations were significantly enriched for response to xenobiotic stimulus and reduction-oxidation reaction activity. DEGs which spanned both non-teratogenic and teratogenic concentrations showed similar disrupted biological processes to those unique to teratogenic concentrations, indicating these processes were disrupted at low exposure concentrations. Gene co-expression network analysis identified several gene modules, including those associated with PAHs and AHR2 activation. One, Module 7, was strongly enriched for AHR2-associated genes and contained the strongest responses to retene. Benchmark concentration (BMC) of Module 7 genes identified a median BMC of 7.5 µM, nearly the highest retene concentration with no associated teratogenicity, supporting the hypothesis that Module 7 genes are largely responsible for retene toxicity.

Toxin, Zebrafish, Retene, Transcriptomics, network↗

Hydraulic architecture explains species moisture dependency but not mortality rates across a tropical rainfall gradient

Aim Intensified droughts are affecting tropical forests across the globe. However, the underlying mechanisms of tree drought response and mortality are poorly understood. Hydraulic traits and especially hydraulic safety margins (HSMs), i.e. the extent to which plants buffer themselves from thresholds of water stress, provide insights into species-specific drought vulnerability. Methods We investigated hydraulic traits during an intense drought triggered by the 2015-2016 El Niño on 27 canopy trees across three tropical forest sites with differing precipitation. We capitalized on the drought event as a time when plant water status might approach or exceed thresholds of water stress. We investigated the degree to which these traits varied across the rainfall gradient, as well as relationships amongst hydraulic traits and species-specific optimal moisture and mortality rates. Results There were no differences among sites for any measured trait. There was strong coordination among traits, with a network analysis revealing two major groups of coordinated traits. In one group there were water potentials, turgor loss point, sapwood capacitance and density, HSMs, and mortality rate. In the second group there was leaf mass per area, leaf dry matter content, hydraulic architecture (leaf area to sapwood area ratio), and species-specific optimal moisture. Conclusion These results demonstrated that while species with greater safety from turgor loss had lower mortality rates, hydraulic architecture was the only trait that explained species’ moisture dependency. Species with a greater leaf area to sapwood area ratio were associated with drier sites and reduced their transpirational demand during the dry season via deciduousness.

Hydraulic Saftey Margins, drought, tropical forest↗

Current and future directions in network biology

Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field has been around for two decades, it remains nascent. It has witnessed rapid evolution, accompanied by emerging challenges. These stem from various factors, notably the growing complexity and volume of data together with the increased diversity of data types describing different tiers of biological organization. We discuss prevailing research directions in network biology, focusing on molecular/cellular networks but also on other biological network types such as biomedical knowledge graphs, patient similarity networks, brain networks, and social/contact networks relevant to disease spread. In more detail, we highlight areas of inference and comparison of biological networks, multimodal data integration and heterogeneous networks, higher-order network analysis, machine learning on networks, and network-based personalized medicine. Following the overview of recent breakthroughs across these five areas, we offer a perspective on future directions of network biology. Additionally, we discuss scientific communities, educational initiatives, and the importance of fostering diversity within the field. This article establishes a roadmap for an immediate and long-term vision for network biology.

59 BASIC BIOLOGICAL SCIENCES↗

Machine Learning Downscaling of SoilMERGE in the United States Southern Great Plains

SoilMERGE (SMERGE) is a root-zone soil moisture (RZSM) product that covers the entire continental United States and spans 1978 to 2019. Machine learning techniques, Random Forest (RF), eXtreme Gradient Boosting (XGBoost), and Gradient Boost (GBoost) downscaled SMERGE to spatial resolutions straddling the field scale domain (100 to 3000 m). Study area was northern Oklahoma and southern Kansas. The coarse resolution of SMERGE (0.125 degree) limits this product’s utility. To validate downscaled results in situ data from four sources were used that included: United States Department of Energy Atmospheric Radiation Measurement (ARM) observatory, United States Climate Reference Network (USCRN), Soil Climate Analysis Network (SCAN), and Soil moisture Sensing Controller and oPtimal Estimator (SoilSCAPE). In addition, RZSM retrievals from NASA’s Airborne Microwave Observatory of Subcanopy and Surface (AirMOSS) campaign provided a nearly spatially continuous comparison. Three periods were examined: era 1 (2016 to 2019), era 2 (2012 to 2015), and era 3 (2003 to 2007). During eras 1 and 2, RF outperformed XGBoost and GBoost, whereas during era 3 no model dominated. Performance was better during eras 1 and 2 as opposed to the pre-L band era 3. Improvements across all eras, regions, and models realized from downscaling included an increase in correlation from 0.03 to 0.42 and a decrease in ub RMSE from -0.0005 to -0.0118 m 3 /m 3 . This study demonstrates the feasibility of SMERGE downscaling opening the prospect for the development of a long-term RZSM dataset at a more desirable field-scale resolution with the potential to support diverse hydrometeorological and agricultural applications.

54 ENVIRONMENTAL SCIENCES↗