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At least 73 records · Page 4

Identification and selection of optimal reference genes for qPCR-based gene expression analysis in Fucus distichus under various abiotic stresses

Quantitative gene expression analysis is an important tool in the scientist’s belt. The identification of evenly expressed reference genes is necessary for accurate quantitative gene expression analysis, whether by traditional RT-PCR (reverse-transcription polymerase chain reaction) or by qRT-PCR (quantitative real-time PCR; qPCR). In the Stramenopiles (the major line of eukaryotes that includes brown algae) there is a noted lack of known reference genes for such studies, largely due to the absence of available molecular tools. Here we present a set of nine reference genes (Elongation Factor 1 alpha (EF1A), Elongation Factor 2 alpha (EF2A), Elongation Factor 1 beta (EF1B), 14-3-3 Protein, Ubiquitin Conjugating Enzyme (UBCE2), Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH), Actin Related Protein Complex (ARP2/3), Ribosomal Protein (40s; S23), and Actin) for the brown alga Fucus distichus . These reference genes were tested on adult sporophytes across six abiotic stress conditions (desiccation, light and temperature modification, hormone addition, pollutant exposure, nutrient addition, and wounding). Suitability of these genes as reference genes was quantitatively evaluated across conditions using standard methods and the majority of the tested genes were evaluated favorably. However, we show that normalization genes should be chosen on a condition-by-condition basis. We provide a recommendation that at least two reference genes be used per experiment, a list of recommended pairs for the conditions tested here, and a procedure for identifying a suitable set for an experimenter’s unique design. With the recent expansion of interest in brown algal biology and accompanied molecular tools development, the variety of experimental conditions tested here makes this study a valuable resource for future work in basic biology and understanding stress responses in the brown algal lineage.

59 BASIC BIOLOGICAL SCIENCES↗

Demonstration of Optimal Benchmark Selection Website and Validation of the q c Coverage Metric Using HEU-SOL-THERM-013-003 Experiment

In the work documented in this interim report, the experiment selection toolkit web site was demonstrated and q C coverage metric methodology was validated for IEU-MET-FAST-002-001, MIX-COMP-THERM 004-004, and HEU-SOL-THERM-013-003 experiments. 𝑞 𝐶 is an information-theoretic measure based on mutual information that quantifies the ability of candidate benchmark experiments to reduce the bias and uncertainty of a target criticality safety application. The metric and an accompanying open-source Python toolkit with a web-based interface were tested against a benchmark set of 425 experiments drawn from the International Criticality Safety Benchmark Evaluation Project Handbook. The interface is hosted at https://edim.covdef.com. It accepts sensitivity data files produced by the TSUNAMI-IP module of the SCALE code system and supports both (i) deterministic analysis using the ENDF/B-VII.0 covariance library and (ii) stochastic analysis based on user-supplied keff samples. Demonstrations on representative applications across a range of material composition, spectrum, and form show that q C -guided benchmark selection achieves greater uncertainty reduction with fewer experiments and yields more stable posterior bias and uncertainty estimates than traditional similarity coefficient ( c k )–based selection, while also capturing valuable low-ck experiments that one-to-one metrics overlook.

Abdel-khalik, Hany S. [Indiana Univ.-Purdue Univ. ↗

Optimal vocabulary selection approaches for privacy-preserving deep NLP model training for information extraction and cancer epidemiology

With the use of artificial intelligence and machine learning techniques for biomedical informatics, security and privacy concerns over the data and subject identities have also become an important issue and essential research topic. Without intentional safeguards, machine learning models may find patterns and features to improve task performance that are associated with private personal information. The privacy vulnerability of deep learning models for information extraction from medical textural contents needs to be quantified since the models are exposed to private health information and personally identifiable information. The objective of the study is to quantify the privacy vulnerability of the deep learning models for natural language processing and explore a proper way of securing patients’ information to mitigate confidentiality breaches. The target model is the multitask convolutional neural network for information extraction from cancer pathology reports, where the data for training the model are from multiple state population-based cancer registries. This study proposes the following schemes to collect vocabularies from the cancer pathology reports; (a) words appearing in multiple registries, and (b) words that have higher mutual information. We performed membership inference attacks on the models in high-performance computing environments. The comparison outcomes suggest that the proposed vocabulary selection methods resulted in lower privacy vulnerability while maintaining the same level of clinical task performance.

59 BASIC BIOLOGICAL SCIENCES↗

NO-LESS: Near optimal curtailment strategy selection for net load balancing in micro grids

The integration of renewable energy sources such as solar PVs into micro grids has increased in recent years. However, the intermittent and unpredictable nature of renewable energy generation makes supply uncertain, in turn requiring continuous net load balancing to ensure grid stability. One technique to achieve net load balancing is curtailment, however, selection of the optimal set of curtailment strategies to achieve a targeted curtailment is NP-hard. State-of-the-art curtailment selection techniques approach this problem by either developing computationally expensive optimal curtailment strategies or reduce accuracy to generate sub-optimal solutions quickly. In this work, we develop NO-LESS: a Near OptimaL CurtailmEnt Strategy Selection algorithm. NO-LESS is a novel Fully Polynomial Time Approximation Scheme (FPTAS) which determines bounded (near optimal) curtailment strategies in a small amount of time while simultaneously satisfying practical constraints on strategy switching overhead and curtailment fairness. We perform both theoretical analysis and practical evaluation to show that NO-LESS is a scalable solution for performing net load balancing through curtailment strategy selection in Micro Grids.

14 SOLAR ENERGY↗

Multiobjective Optimal Controlled Variable Selection for a Gas Turbine–Solid Oxide Fuel Cell System Using a Multiagent Optimization Platform

Hybrid gas turbine–fuel cell systems have immense potential for high efficiency in electrical power generation with cleaner emissions compared with fossil-fueled power generation. We report a systematic controlled variable (CV) selection method is deployed for a hybrid gas turbine–fuel cell system in the HyPer (hybrid performance) facility at the U.S. Department of Energy’s National Energy Technology Laboratory (NETL) for maximizing its economic and control performance. A three-stage approach is used for the CV selection comprising a priori analysis, multiobjective optimization, and a posteriori analysis. The a priori analysis helps to screen off several candidate CVs, thus reducing the size of the combinatorial optimization problem for multiobjective CV selection. For optimal CV selection, a transfer function model of the HyPer facility is identified. By considering several candidate models, the final transfer function model is selected using Akaike’s Final Prediction Error criterion. Experimental data from the HyPer facility are used to estimate the noise in the measurement data. For solving the combinatorial multiobjective optimization problem for CV selection, a multiagent optimization platform comprising simulated annealing, genetic algorithm, and efficient ant colony optimization algorithms is used. Pareto-optimal CV sets exhibit a high trade-off between the economic and control objective. The a posteriori analysis is undertaken for several top Pareto-optimal CV sets. An optimal CV set is selected that shows the best compromise between process economics and controllability under both nominal and off-design conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Optimal Wavelengths for Light Absorption Spectroscopy Measurements Based on Genetic Algorithm–Particle Swarm Optimization

To select the optimal wavelengths in the light extinction spectroscopy measurement, genetic algorithm–particle swarm optimization (GAPSO) based on genetic algorithm (GA) and particle swarm optimization (PSO) is adopted. The change of the optimal wavelength positions in different feature size parameters and distribution parameters is evaluated. Moreover, the Monte Carlo method based on random probability is used to identify the number of optimal wavelengths, and good inversion effects of the particle size distribution are obtained. The method proved to have the advantage of resisting noise. In order to verify the feasibility of the algorithm, spectra with bands ranging from 200 to 1000 nm are computed. Based on this, the measured data of standard particles are used to verify the algorithm.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Partial Least Squares, Experimental Design, and Near-Infrared Spectrophotometry for the Remote Quantification of Nitric Acid Concentration and Temperature

Near-infrared spectrophotometry and partial least squares regression (PLSR) were evaluated to create a pleasantly simple yet effective approach for measuring HNO3 concentration with varying temperature levels. A training set, which covered HNO3 concentrations (0.1–8 M) and temperature (10–40 °C), was selected using a D-optimal design to minimize the number of samples required in the calibration set for PLSR analysis. The top D-optimal-selected PLSR models had root mean squared error of prediction values of 1.4% for HNO 3 and 4.0% for temperature. The PLSR models built from spectra collected on static samples were validated against flow tests including HNO 3 concentration and temperature gradients to test abnormal conditions (e.g., bubbles) and the model performance between sample points in the factor space. Based on cross-validation and prediction modeling statistics, the designed near-infrared absorption approach can provide remote, quantitative analysis of HNO 3 concentration and temperature for production-oriented applications in facilities where laser safety challenges would inhibit the implementation of other optical techniques (e.g., Raman spectroscopy) and in which space, time, and/or resources are constrained. The experimental design approach effectively minimized the number of samples in the training set and maintained or improved PLSR model performance, which makes the described chemometric approach more amenable to nuclear field applications.

07 ISOTOPE AND RADIATION SOURCES↗

Particle Swarm Optimisation for group structure optimization for radiotherapy shielding

Neutron transport simulations are ubiquitous in nuclear engineering because they allow one to model experimental systems and render a model platform for easy perturbation of experimental designs. In addition, simulations allow one to gain experimental insight without actually having to go through the trouble of building a physical experiment. Neutron transport simulations can be stochastic or deterministic based. Stochastic neutron transport simulations are typically simulated using the Monte Carlo method and yield very accurate solutions but are computationally expensive, while deterministic methods are typically faster but can be less accurate. Here we focus on optimizing the accuracy of deterministic neutron transport simulations for radiotherapy simulations. Deterministic neutron transport requires discretization of angle, energy, and space to appropriately analyze the system one is trying to model. Discretization of energy is challenging because of the highly variable neutron flux at certain neutron energies. Improper discretization of energy in the transport model can lead to erroneous results and therefore inaccurate interpretations of the solution. In this study, we evaluate Particle Swarm Optimization (PSO) as a mechanism for selecting optimal group structures for radiotherapy shielding. We tested the particle swarm optimization algorithm on radiotherapy shielding problems using Los Alamos National Laboratory's (LANL) main deterministic transport code PARTISN. Results show that the optimized energy group structures generated from the optimization algorithm outperformed LANL's standard energy group structures, and therefore demonstrate utility in using PSO to expedite computation times due to the increased accuracy obtained with a smaller but optimized group structure. (authors)

43 PARTICLE ACCELERATORS↗

Smart culture medium optimization for recombinant protein production: Experimental, modeling, and AI/ML-driven strategies

Recombinant protein production (RPP) is central to biotechnology, where recombinant proteins are used as either end products or catalysts in the synthesis of chemicals, fuels, and materials. Among the major cost drivers, culture medium plays a pivotal role in determining protein yield and quality. This review presents a comprehensive perspective on the critical stages of “smart” culture medium optimization: planning, screening, modeling, optimization, and validation. In the planning stage, we examine the nutritional and energetic roles of medium components, including carbon, nitrogen, amino acids, salts, and trace metals, and their impacts on culture parameters such as pH, oxidative state, and osmolality. We highlight the variability in trace metal content due to water sources, culture vessels, and raw materials, which can substantially influence RPP. The screening stage covers Design of Experiments (DoE) approaches, assessing their theoretical basis, implementation, and limitations. For modeling, we describe methods that integrate experimental data to develop predictive models for smart medium formulation. Model-based optimization strategies can then be employed to select optimal media compositions for a given application. The validation stage aims to evaluate model predictions and provide feedback for model training and refinement. Finally, we survey mechanistic and artificial intelligence/machine learning (AI/ML)-driven models as integrated, transformational tools for predictive modeling of bioprocess conditions, nutrient availability, cellular metabolism, and protein quality, with the goal of optimizing culture media to enhance protein yields while reducing costs and environmental impact. We conclude by addressing the challenges of translating laboratory-scale medium optimization to industrial-scale settings and exploring future AI/ML-driven approaches that may overcome current bottlenecks and accelerate medium design for RPP. Overall, this review provides a unified framework for advancing smart medium design in RPP.

Artificial Intelligence/Machine Learning (AI/ML)↗

Optimizing Solar PV Deployment in Manufacturing: A Morphological Matrix and Fuzzy TOPSIS Approach

The growing energy demand of the industrial sector and the need for sustainable solutions highlight the importance of efficient decision making in solar photovoltaic (PV) implementation. Selecting optimal PV configuration is complex due to the interdependent technical, economic, environmental, and social factors involved. This study introduces an integrated decision-making method combining a morphological matrix and fuzzy TOPSIS to systematically select and rank optimal PV system configurations for manufacturing firms. While the morphological matrix exhaustively examines possible design solutions based on sensing, smart, sustainable, and social (S4) attributes, the fuzzy TOPSIS method ranks the alternatives by handling uncertainty in decision making. A case study conducted in a Mexican manufacturing company validates the methodology’s effectiveness. The optimal PV configuration identified comprehensively addresses operational and sustainability criteria, covering all lifecycle stages. This approach demonstrates quantitative superiority and greater robustness compared to existing fuzzy TOPSIS-based methods for solar PV applications. The findings highlight the practical value of data-driven, multi-criteria decision making for industrial solar energy adoption, enhancing project feasibility, cost efficiency, and environmental compliance. Future research will incorporate discrete event simulation (DES) to further refine energy consumption strategies in manufacturing.

Briceño, Citlaly Pérez↗

Structure Based Design of a Grp94-Selective Inhibitor: Exploiting a Key Residue in Grp94 To Optimize Paralog-Selective Binding

Grp94 and Hsp90, the ER and cytoplasmic hsp90 paralogs, share a conserved ATP-binding pocket that has been targeted for therapeutics. Paralog-selective inhibitors may lead to drugs with fewer side effects. In this work, we analyzed 1 (BnIm), a benzyl imidazole resorcinylic inhibitor, for its mode of binding. The structures of 1 bound to Hsp90 and Grp94 reveal large conformational changes in Grp94 but not Hsp90 that expose site 2, a binding pocket adjacent to the central ATP cavity that is ordinarily blocked. The Grp94:1 structure reveals a flipped pose of the resorcinylic scaffold that inserts into the exposed site 2. We exploited this flipped binding pose to develop a Grp94-selective derivative of 1. Our structural analysis shows that the ability of the ligand to insert its benzyl imidazole substituent into site 1, a different side pocket off the ATP binding cavity, is the key to exposing site 2 in Grp94.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Calculations of theoretical efficiencies for electrochemically-mediated tandem solar water splitting as a function of bandgap energies and redox shuttle potential

Tandem Z-scheme solar water splitting devices composed of two light-absorbers that are connected electrochemically by a soluble redox shuttle constitute a promising technology for cost-effective solar hydrogen production. In this work, efficiency limits of these devices are modeled by combining the detailed-balance model of the light-absorbers with Butler–Volmer electron-transfer kinetics. The impacts of the redox shuttle thermodynamic potential, light-absorber bandgaps, and electrocatalytic parameters on the solar-to-hydrogen conversion (STH) efficiency are modeled. We report that the thermodynamic potential of the redox shuttle with respect to the hydrogen and oxygen evolution potentials has a direct effect on both the STH efficiency and the optimal tandem light-absorber bandgaps needed to achieve the maximum possible STH efficiency. At 1 sun illumination and assuming ideal and optimally selective electrocatalytic parameters, the STH efficiency varies from a minimum of 21%, for a redox shuttle potential of 0 V vs. the reversible hydrogen electrode (RHE), to a maximum of 34%, for a redox shuttle potential of either 0.36 V or 1.06 V vs. RHE. To attain the maximum possible STH efficiency of 34%, the light-absorber bandgaps must be 1.53 eV and 0.75 eV, yet the optimal redox shuttle potential depends on whether the hydrogen-evolving or oxygen-evolving light-absorber has the larger bandgap. Results also underscore the importance of optimizing the absorptance of the top light-absorber, which enables large STH efficiencies to be achieved with a wider range of bandgap combinations. Moreover, given the large overpotentials for the oxygen evolution reaction and reasonably low overpotentials for most redox shuttle reactions, the tandem design is more efficient than a single light-absorber design even when the potential of the redox shuttle exceeds 1.23 V vs. RHE. When the exchange current density of the redox shuttle reactions is as low as 10 -5 mA cm -2 , STH efficiencies as large as 22% are still achievable as long as selective catalysis and optimal redox shuttle potential are assumed, suggesting that even slow redox shuttle reactions may not limit the practicality of these devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

TaO x electron transport layers for CO 2 reduction Si photocathodes

Electron transport layers (ETLs) used as components of photocathodes for light-driven CO 2 reduction (CO 2 R) in aqueous media should have good electronic transport, be stable under CO 2 R conditions, and, ideally, be catalytically inert for the competing hydrogen evolution reaction (HER). Here, using planar p-Si (100) as the absorbing material, we show that TaO x satisfies all three of the above criteria. TaO x films were synthesized by both pulsed laser deposition (PLD) and radio-frequency (RF) sputtering. In both cases, careful control of the oxygen partial pressure during growth was required to produce ETLs with acceptable electron conductivity. p-Si/TaO x photocathodes were interfaced with ca. 10 nm of a CO 2 R catalyst: Cu or Au. Under front illumination with simulated AM 1.5G in CO 2 -saturated bicarbonate buffer, we observed, for both metals, faradaic efficiencies for CO 2 R products of ~50% and ~30% for PLD TaO x and RF sputtered TaO x , respectively, at photocurrent densities up to 8 mA cm -2 . p-Si/TiO 2 /Cu photocathodes were also evaluated but produced mostly H 2 (>97%) due to reduction of the TiO 2 to Ti metal under CO 2 R conditions. In contrast, a dual ETL photocathode (p-Si/TiO 2 /TaO x /Cu) was selective for CO 2 R, which suggests a strategy for separately optimizing selective charge collection and the stability of the ETL/water interface. The maximum photovoltage obtained with p-Si/TaO x /Cu devices was 300 mV which was increased to 430–460 mV by employing ion implantation to make pn + -Si/TaO x /Cu structures. Photocathodes with RF sputtered TaO x ETLs are stable for CO 2 R for at least 300 min. In conclusion, techno-economic analysis shows that the reported system, if scaled, could allow for an economically viable production of feedstocks for chemical synthesis under the adoption of specific CO 2 credit schemes, thus becoming a significant component of carbon-neutral manufacturing.

36 MATERIALS SCIENCE↗

Optimization of Adjustable Drivetrain Assistance Mechanisms for Efficient Robotic Bipeds

Legged robots promise radical mobility for challenging environments, but must be made more energy efficient to be practical. Historically, legged robot design has required efficiency to be traded against versatility. Much energy is lost in actuators and transmissions because few actuation systems are capable of operating efficiently across the wide range of operating conditions (e.g. different joint speeds and torques) required for legged locomotion. We describe a drivetrain topology that overcomes many of these limitations. Our approach combines high-torque electromagnetic motors and low-loss transmissions with a tailored and adjustable set of joint-specific passive mechanisms called support elements, which modulate the energy flow between motors and joints to minimize the electrical energy consumed. We present an optimization-based design method that draws on available bipedal gait data to select optimal support element configurations and parameters. Simple adjustments may be made to support elements at certain joints to enable a wide variety of locomotion with high efficiency. We present results, specific to the 3D humanoid bipedal STEPPR robot, in which support elements are co-optimized across a library of several gaits, converging on a set of designs that predict an average reduction of electrical energy of more than 50% across a set of 15 gaits, with energy savings reaching as much as 85% for some gaits. Concepts were prototyped and tested on a bench testbed, validating the predicted energy savings. Support elements were implemented on STEPPR, and energy savings of more than 35% were demonstrated.

42 ENGINEERING↗