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At least 55 records · Page 3

Improving Traditional Registrational Trial End Points: Development and Application of a Desirability of Outcome Ranking End Point for Complicated Urinary Tract Infection Clinical Trials

Abstract Background Traditional end points used in registrational randomized, controlled trials (RCTs) often do not allow for complete interpretation of the full range of potential clinical outcomes. Desirability of outcome ranking (DOOR) is an approach to the design and analysis of clinical trials that incorporates benefits and risks of novel treatment strategies and provides a global assessment of patient experience. Methods Through a multidisciplinary committee of experts in infectious diseases, clinical trial design, drug regulation, and patient experience, we developed a DOOR end point for infectious disease syndromes and demonstrated how this could be applied to 3 registrational drug trials (ZEUS, APEKS-cUTI, and DORI-05) for complicated urinary tract infections (cUTIs). ZEUS compared fosfomycin to piperacillin/tazobactam, APEKS-cUTI compared cefiderocol to imipenem, and DORI-05 compared doripenem to levofloxacin. Using DOOR, we estimated the probability of a more desirable outcome with each investigational antibacterial drug. Results In each RCT, the DOOR distribution was similar and the probability that a patient in the investigational arm would have a more desirable outcome than a patient in the control arm had a 95% confidence interval containing 50%, indicating no significant difference between treatment arms. DOOR facilitated improved understanding of potential trade-offs between clinical efficacy and safety. Partial credit and subgroup analyses also highlight unique attributes of DOOR. Conclusions DOOR can effectively be used in registrational cUTI trials. The DOOR end point presented here can be adapted for other infectious disease syndromes and prospectively incorporated into future clinical trials.

Immunology↗

Improved quasiparticle self-consistent electronic band structure and excitons in β – LiGaO 2

The band structure of β–LiGaO 2 is calculated using the quasiparticle self-consistent QSGWˆ method where the screened Coulomb interaction Wˆ is evaluated including electron-hole interaction ladder diagrams and G is the one-electron Green's function. Improved convergence compared to previous calculations leads to a significantly larger band gap of about 7.0 eV. However, exciton binding energies are found to be large and lead to an exciton gap of about 6.0 eV if also a zero-point-motion correction of about –0.4 eV is included. Furthermore, these results are in excellent agreement with recent experimental results on the onset of absorption. Besides the excitons observed thus far, the calculations indicate the existence of a Rydberg-like series of exciton excited states, which is however modified from the classical Wannier exciton model by the anisotropies of the material and the more complex mixing of Bloch states in the excitons resulting from the Bethe-Salpeter equation. The exciton fine structure and the exciton wave functions are visualized and analyzed in various ways.

36 MATERIALS SCIENCE↗

Improving Resiliency for Electric Vehicle Charging

Electric vehicles are seeing growing adoption. However, challenges with range anxiety persists. While charging infrastructure is anticipated to expand, EV charger systems have not been as robust to challenges. This paper discusses potential outage conditions associated with EV charging and presents new technology in development to improve EV charging resilience.

Electric vehicle charging, electric vehicle chargi↗

Integrating 5G Technology for Improved Process Monitoring and Network Slicing in ICS

Industrial Control Systems (ICS) are crucial for monitoring physical processes that support essential cyber-enabled services like power generation. The use of proprietary communication and lack of effective intrusion detection mechanisms pose constraints for efficient operation. Therefore, there is a need to modernize these systems with decentralized technologies like Edge Computing and 5G. However, integrating 5G and Edge Computing into large-scale ICS networks presents implementation and performance challenges. To address these challenges, this paper proposes an integrated ICS architecture that combines 5G and Edge Computing technologies with traditional ICS protocols. The objective is to minimize implementation and operational difficulties while improving the monitoring of physical processes and enabling robust intrusion detection. The proposed architecture outlines the necessary components, services, and communication protocols required for the integration of 5G and Edge Computing.

Aguayo, Jared M.↗

An improved representation of the relationship between photosynthesis and stomatal conductance leads to more stable estimation of conductance parameters and improves the goodness-of-fit across diverse data sets

Stomata play a central role in surface-atmosphere exchange by controlling the flux of water and CO 2 between the leaf and the atmosphere. Representation of stomatal conductance (g sw ) is therefore an essential component of models that seek to simulate water and CO 2 exchange in plants and ecosystems. For given environmental conditions at the leaf surface (CO 2 concentration and vapor pressure deficit or relative humidity), models typically assume a linear relationship between g sw and photosynthetic CO 2 assimilation (A). However, measurement of leaf-level g sw response curves to changes in A are rare, particularly in the tropics, resulting in only limited data to evaluate this key assumption. Here, we measured the response of g sw and A to irradiance in six tropical species at different leaf phenological stages. We showed that the relationship between g sw and A was not linear, challenging the key assumption upon which optimality theory is based-that the marginal cost of water gain is constant. Our data showed that increasing A resulted in a small increase in g sw at low irradiance, but a much larger increase at high irradiance. We reformulated the popular Unified Stomatal Optimization (USO) model to account for this phenomenon and to enable consistent estimation of the key conductance parameters g 0 and g 1 . Our modification of the USO model improved the goodness-of-fit and reduced bias, enabling robust estimation of conductance parameters at any irradiance. In addition, our modification revealed previously undetectable relationships between the stomatal slope parameter g 1 and other leaf traits. We also observed nonlinear behavior between A and g sw in independent datasets that included data collected from attached and detached leaves, and from plants grown at elevated CO 2 concentration. We propose that this empirical modification of the USO model can improve the measurement of g sw parameters and the estimation of plant and ecosystem-scale water and CO 2 fluxes.

54 ENVIRONMENTAL SCIENCES↗

Improving Process Level Understanding of Boundary Layer Winds over the Northeast U.S. Shelf: The Third Wind Forecast Improvement Project (WFIP3)

The third Wind Forecast Improvement Project (WFIP3), a U.S. Department of Energy and National Oceanic and Atmospheric Administration sponsored investigation, sought to improve understanding of the physical phenomena in the atmosphere and ocean that dictate the structure and variability of wind and thermodynamic fields within the marine atmospheric boundary layer. WFIP3 focused on mesoscale and submesoscale flows -- including sea breezes, low-level jets, low-level clouds, and coastal storms -- and the ability of advanced numerical model parameterizations to represent them within fully coupled oceanic and atmospheric modeling systems and foundational weather forecast models. WFIP3 conducted a comprehensive 18-month observational study over the Northeast U.S. outer continental shelf, a high-use coastal zone, using a 3D multiscale sensor array to highly resolve the temporal, vertical, and horizontal structure of the coupled atmospheric and oceanic boundary layers. Multiple land-based study sites adjacent to the coastal ocean observed surface meteorology and vertical profiles of atmospheric properties via passive infrared and microwave radiometers, active lidars and radars, and radiosondes. At sea, an array of surface flux buoys and two vertical profiling lidar buoys observed both atmospheric and oceanic properties, augmented by land-based oceanographic radar systems and routine ship-based surveys. Intensive observations of the marine atmospheric boundary layer over the ocean was done from an air-sea interaction flux tower and extended deployments of a large autonomous barge platform. Numerous critical forecasting phenomena were observed that are being evaluated within regional coupled and uncoupled modeling systems, including the National Oceanic and Atmospheric Administration's foundational High-Resolution Rapid Refresh forecast model.

Kirincich, Anthony↗

Improved Diagnosis of Precipitation Type with LightGBM Machine Learning

Abstract Existing precipitation-type algorithms have difficulty discerning the occurrence of freezing rain and ice pellets. These inherent biases are not only problematic in operational forecasting but also complicate the development of model-based precipitation-type climatologies. To address these issues, this paper introduces a novel light gradient-boosting machine (LightGBM)-based machine learning precipitation-type algorithm that utilizes reanalysis and surface observations. By comparing it with the Bourgouin precipitation-type algorithm as a baseline, we demonstrate that our algorithm improves the critical success index (CSI) for all examined precipitation types. Moreover, when compared with the precipitation-type diagnosis in reanalysis, our algorithm exhibits increased F1 scores for snow, freezing rain, and ice pellets. Subsequently, we utilize the algorithm to compute a freezing-rain climatology over the eastern United States. The resulting climatology pattern aligns well with observations; however, a significant mean bias is observed. We interpret this bias to be influenced by both the algorithm itself and assumptions regarding precipitation processes, which include biases associated with freezing drizzle, precipitation occurrence, and regional synoptic weather patterns. To mitigate the overall bias, we propose increasing the precipitation cutoff from 0.04 to 0.25 mm h −1 , as it better reflects the precision of precipitation observations. This adjustment yields a substantial reduction in the overall bias. Finally, given the strong performance of LightGBM in predicting mixed precipitation episodes, we anticipate that the algorithm can be effectively utilized in operational settings and for diagnosing precipitation types in climate model outputs. Significance Statement Freezing rain can have significant impacts on transportation and infrastructure, making accurate prediction of precipitation types crucial. In this study, we use a machine learning method known as LightGBM to predict precipitation types. We show that the new algorithm performs better than the existing methods for all precipitation types examined. Additionally, we compute a freezing-rain climatology over the eastern United States. Although the resulting climatology pattern corresponds well to observations, the algorithm overpredicts freezing-rain occurrence. We argue that this bias can be substantially reduced by increasing the precipitation cutoff from 0.04 to 0.25 mm h −1 . Overall, this work highlights the potential of the LightGBM algorithm for both weather forecasting and diagnosing precipitation types in climate models.

Meteorology & Atmospheric Sciences↗

Non-target RNA depletion strategy to improve sensitivity of next-generation sequencing for the detection of RNA viruses in poultry

PCR-based assays have become the benchmark for detecting pathogens of poultry and other livestock; however, these techniques are limited in their ability to detect multiple infecting agents, provide limited genetic information on the pathogen, and, for RNA viruses, must be reviewed frequently to assure high sensitivity and specificity. In contrast, untargeted, high-throughput sequencing can rapidly detect all infecting agents in a sample while providing genomic sequence information to allow more in-depth characterization of viruses. Although next-generation sequencing (NGS) offers many advantages, one of its primary limitations is low sensitivity to pathogens given the abundance of host and other non-target sequences in sequencing libraries. We explored methods for improving the sensitivity of NGS to detect respiratory and enteric viruses in poultry from RNA extracts of swab samples. We employed commercial and custom-designed negative enrichment strategies to selectively deplete the most abundant rRNA reads from the host and non-target bacteria; host RNA was diminished from up to 40% of total reads to as low as 3%, and the total number of reads assigned to abundant bacterial classes were reduced greatly. Our treatment resulted in up to a 700-fold increase in the number of viral reads, detection of a greater number of viral agents, and higher average genome coverage for pathogens. Depletion assays added only 2 h to the NGS library preparation workflow. Custom depletion probe design offered significant cost savings (US$7–12 per sample) compared to commercial kits (US$30–50 per sample).

Parris, D. Joshua↗

NGEE Arctic Integrated Modeling (IM3): Improved snow-vegetation interaction

This data product represents the integration of new code capability for arctic tundra snow-vegetation-terrain interactions into the Energy Exascale Earth System Model (E3SM), through the E3SM Land Model (ELM) component. This code integration is the result of collaborative effort between the NGEE Arctic project and the E3SM project. The NGEE Arctic project developed a total of six Integrated Modeling (IM) modules informed by observations and experiments. New ELM capability represented by this data product (IM3) falls into three categories: 1) Downscaling from gridcell to topographic unit level when working through the existing coupler bypass code. 2) Four new parameters (taper, stocking, bendresist, and vegshape) have been added to ELM to allow for flexible definition of snow-vegetation interactions. 3) Vegshape and bendresist parameters are used to calculate the fraction of leaf area and/or stem area buried by snow for a given snow depth. This data record consists of a single document (pdf format) that describes the theoretical basis for the snow-vegetation-terrain interactions added to ELM, and describes the modifications made to the ELM code. The Methods section of this metadata record includes a link to the public E3SM code repository where the exact code modifications as integrated in E3SM can be accessed. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

Thornton, Peter E [ORNL] (ORCID:0000000247595158)↗

Improved Fuel Particle and Compact Matrix Fission Product Release Prediction with Improved Mass Transfer Model

This study was motivated by the need to incorporate more physics-based mass transfer models in BISON in order to improve fuel particle and compact matrix fission product release prediction. This document details the integration of new modeling capabilities in BISON, including (1) development of sorption mass transfer models; improvement of thermal contact model by adding neon to the gas gap inventory, (3) implementation of PCEA and IG-110 graphite thermal models, (4) validation using Advanced Gas Reactor (AGR)-3/4 compact and capsule rings data. These new capabilities have been shown to enforce the desired physics with satisfactory accuracy. BISON’s predictions of fission product release of AGR-3/4 compacts compare favorably with PARFUME and the concentration profiles across capsule rings show reasonable trend to the experiment measurement.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Additively Reinforced Thermoformable PETG Composite Sheets for Improved Structural Efficiency

Thermoforming of short-fiber reinforced thermoplastic sheets offers a viable pathway for producing lightweight composite components; however, inherent anisotropy in fiber-reinforced sheets can limit structural performance under multidirectional loading. In this work, short carbon fiber, glass fiber, and hybrid fiber–reinforced PETG sheets were evaluated as candidate feedstock materials for thermoforming, with flexural and tensile testing performed both along the primary fiber direction and in the off-axis orientation to establish baseline stiffness, strength, and anisotropy. As expected, short carbon fiber PETG exhibited the highest stiffness and strength in the primary fiber direction, while all systems showed reduced performance in the off-axis direction. This off-axis performance reduction provides clear justification for the use of additive reinforcement when such thermoformed sheets are intended for structural applications. The intended manufacturing sequence involves thermoforming the reinforced sheet first, followed by the application of additively manufactured lattice reinforcement; therefore, the reinforcement strategy does not impose limitations on sheet formability during thermoforming. Post-forming lattice reinforcement significantly reduced load-normalized displacement by approximately 95–99% relative to non-reinforced sheets and improved weight-normalized stiffness by ~70%. These findings demonstrate that geometry-driven additive reinforcement can effectively compensate for off-axis property reductions in thermoformed PETG composites, enabling enhanced multidirectional structural performance without compromising manufacturability.

Talabi, Isaac [ORNL] (ORCID:0000000340215594)↗

Integration of proteomics and metabolomics into the Design, Build, Test, Learn cycle to improve 3-hydroxypropionic acid production in Aspergillus pseudoterreus

Biological engineering of microorganisms to produce value-added chemicals is a promising route to sustainable manufacturing. However, overproduction of metabolic intermediates at high titer, rate, and yield from inexpensive substrates is challenging in non-model systems where limited information is available regarding metabolic flux and its control in production conditions. Integrated multi-omic analyses of engineered strains offers an in-depth look at metabolites and proteins directly involved in growth and production of target and non-target bioproducts. Here we applied multi-omic analyses to overproduction of the polymer precursor 3-hydroxypropionic acid (3HP) in the filamentous fungus Aspergillus pseudoterreus. A synthetic pathway consisting of aspartate decarboxylase, beta-alanine pyruvate transaminase, and 3HP dehydrogenase was designed and built for A. pseudoterreus. Strains with single- and multi-copy integration events were isolated and multi-omics analysis consisting of intracellular and extracellular metabolomics and targeted and global proteomics was used to interrogate the strains in shake-flask and bioreactor conditions. Production of a variety of co-products (organic acids and glycerol) and oxidative degradation of 3HP were identified as metabolic pathways competing with 3HP production. Intracellular accumulation of nitrogen as 2,4-diaminobutanoate was identified as an off-target nitrogen sink that may also limit flux through the engineered 3HP pathway. Elimination of the high-expression oxidative 3HP degradation pathway by deletion of a putative malonate semialdehyde dehydrogenase improved the yield of 3HP by 3.4× after 10 days in shake-flask culture. This is the first report of 3HP production in a filamentous fungus amenable to industrial scale biomanufacturing of organic acids at high titer and low pH.

Pomraning, Kyle R.↗

Reducing Sample Size While Improving Equity in Vaccine Clinical Trials: A Machine Learning-Based Recruitment Methodology with Application to Improving Trials of Hepatitis C Virus Vaccines in People Who Inject Drugs

Despite the availability of direct-acting antivirals that cure individuals infected with the hepatitis C virus (HCV), developing a vaccine is critically needed in achieving HCV elimination. HCV vaccine trials have been performed in populations with high incidence of new HCV infection such as people who inject drugs (PWID). Developing strategies of optimal recruitment of PWID for HCV vaccine trials could reduce sample size, follow-up costs and disparities in enrollment. We investigate trial recruitment informed by machine learning and evaluate a strategy for HCV vaccine trials termed PREDICTEE—Predictive Recruitment and Enrichment method balancing Demographics and Incidence for Clinical Trial Equity and Efficiency. PREDICTEE utilizes a survival analysis model applied to trial candidates, considering their demographic and injection characteristics to predict the candidate’s probability of HCV infection during the trial. The decision to recruit considers both the candidate’s predicted incidence and demographic characteristics such as age, sex, and race. We evaluated PREDICTEE using in silico methods, in which we first generated a synthetic candidate pool and their respective HCV infection events using HepCEP, a validated agent-based simulation model of HCV transmission among PWID in metropolitan Chicago. We then compared PREDICTEE to conventional recruitment of high-risk PWID who share drugs or injection equipment in terms of sample size and recruitment equity, with the latter measured by participation-to-prevalence ratio (PPR) across age, sex, and race. Comparing conventional recruitment to PREDICTEE found a reduction in sample size from 802 (95%: 642–1010) to 278 (95%: 264–294) with PREDICTEE, while also reducing screening requirements by 30%. Simultaneously, PPR increased from 0.475 (95%: 0.356–0.568) to 0.754 (95%: 0.685–0.834). Even when targeting a dissimilar maximally balanced population in which achieving recruitment equity would be more difficult, PREDICTEE is able to reduce sample size from 802 (95%: 642–1010) to 304 (95%: 288–322) while improving PPR to 0.807 (95%: 0.792–0.821). PREDICTEE presents a promising strategy for HCV clinical trial recruitment, achieving sample size reduction while improving recruitment equity.

60 APPLIED LIFE SCIENCES↗

Improved Architectures and Training Algorithms for Deep Operator Networks

Operator learning techniques have recently emerged as a powerful tool for learning maps between infinite-dimensional Banach spaces. Trained under appropriate constraints, they can also be effective in learning the solution operator of partial differential equations (PDEs) in an entirely self-supervised manner. In this work we analyze the training dynamics of deep operator networks (DeepONets) through the lens of Neural Tangent Kernel theory, and reveal a bias that favors the approximation of functions with larger magnitudes. To correct this bias we propose to adaptively re-weight the importance of each training example, and demonstrate how this procedure can effectively balance the magnitude of back-propagated gradients during training via gradient descent. We also propose a novel network architecture that is more resilient to vanishing gradient pathologies. Taken together, our developments provide new insights into the training of DeepONets and consistently improve their predictive accuracy by a factor of 10-50x, demonstrated in the challenging setting of learning PDE solution operators in the absence of paired input-output observations.

97 MATHEMATICS AND COMPUTING↗