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"Li, Peggy"
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Multiscale Simulation, Data Assimilation, and Forecasting in Support of the SPURS-2 Field Campaign
A multiscale simulation, data assimilation, forecasting system was developed in support of the SPURS-2 (Salinity Processes in the Upper-ocean Regional Study 2) field campaign. Before the field campaign, a multiyear simulation was produced for characterizing variabilities in upper-ocean salinity, eddy activity, and other parameters and for illustrating major processes that control the region’s upper-ocean salinity at different spatial and temporal scales. This simulation assisted in formulating sampling plans. During the field experiment, the system integrated SPURS-2 measurements with those from routine operational observing networks, including Argo floats and satellite surface temperatures, salinities, and heights, and provided real-time skillful daily forecasts of ocean conditions. Forecast reports were prepared to summarize oceanic conditions and multiscale features and were delivered to the SPURS-2 chief scientist and other SPURS-2 investigators through the SPURS-2 Information System. After the field experiment, the data assimilation system was used to produce a reanalysis product to help quantify contributions of different processes to salinity variability in the region.
Journal Article
A Novel Digital PCR Assay for Accurate Detection and Differentiation of Focal and Non-Focal Subtypes of Mesenchymal–Epithelial Transition (MET) Gene Amplification in Lung Cancer
Background/Objectives: Mesenchymal–epithelial transition (MET) gene amplification is a critical biomarker in non-small cell lung cancer (NSCLC), significantly influencing treatment decisions and prognostic evaluations. However, current detection methods such as fluorescence in situ hybridization (FISH) and next-generation sequencing (NGS) have limitations in speed, cost, and specificity, particularly when distinguishing between focal MET amplification and MET polysomy. Methods: This study introduces a novel digital PCR (dPCR) assay designed not only to detect MET amplification but also to differentiate between its focal and non-focal subtypes. The assay was evaluated against established FISH and targeted NGS panels using 55 NSCLC samples with known MET amplification statuses (26 positive and 29 negative) confirmed by FISH and NGS. Results The dPCR assay demonstrated high sensitivity (96.0%) and specificity (96.7%), achieving 100% concordance with FISH in differentiating focal MET amplification from MET polysomy. Additionally, the assay exhibited excellent precision, accuracy, and linearity (R2 = 1.00) in MET copy number quantification, surpassing NGS in diagnostic performance. Offering a robust, cost-effective, and efficient alternative to FISH, the dPCR assay significantly reduces the turnaround time (3 h versus 2 days) and provides a quantitative and objective method for MET amplification detection and subtype differentiation. This makes it suitable for clinical laboratories with limited molecular expertise. Conclusions: This study highlights the potential of the dPCR assay to complement existing molecular diagnostic techniques, delivering reliable and actionable results for MET-targeted therapy selection in NSCLC patients and thereby advancing precision oncology.
Journal Article
An Eye on the Storm: Integrating a Wealth of Data for Quickly Advancing the Physical Understanding and Forecasting of Tropical Cyclones
Tropical cyclones (TCs) are among the most destructive natural phenomena with huge societal and economic impact. They form and evolve as the result of complex multiscale processes and nonlinear interactions. Even today the understanding and modeling of these processes is still lacking. A major goal of NASA is to bring the wealth of satellite and airborne observations to bear on addressing the unresolved scientific questions and improving our forecast models. Despite their significant amount, these observations are still underutilized in hurricane research and operations due to the complexity associated with finding and bringing together semicoincident and semicontemporaneous multiparameter data that are needed to describe the multiscale TC processes. Such data are traditionally archived in different formats, with different spatiotemporal resolution, across multiple databases, and hosted by various agencies. To address this shortcoming, NASA supported the development of the Jet Propulsion Laboratory (JPL) Tropical Cyclone Information System (TCIS)—a data analytic framework that integrates model forecasts with multiparameter satellite and airborne observations, providing interactive visualization and online analysis tools. TCIS supports interrogation of a large number of atmospheric and ocean variables, allowing for quick investigation of the structure of the tropical storms and their environments. This paper provides an overview of the TCIS’s components and features. It also summarizes recent pilot studies, providing examples of how the TCIS has inspired new research, helping to increase our understanding of TCs. The goal is to encourage more users to take full advantage of the novel capabilities. TCIS allows atmospheric scientists to focus on new ideas and concepts rather than painstakingly gathering data scattered over several agencies.
Journal Article
Active learning enables generation of molecules that advance the known Pareto front
Although generative models hold promise for discovering molecules with optimized desired properties, they often fail to suggest synthesizable molecules that improve upon the properties of the structures represented in the training distribution. We find that this limitation arises not only from the molecule generation process itself, but also from the poor generalization capabilities of molecular property predictors. We address this challenge by creating a closed-loop molecule generation pipeline with iterative retraining on new quantum chemical simulation data. Compared against static, single-pass generative modeling approaches, only our closed-loop iterative workflow generates molecules with properties extending beyond the training distribution (up to 0.44 standard deviations beyond the original range) and achieves a 79% improvement in out-of-distribution molecule classification accuracy. Furthermore, by conditioning molecular generation on thermodynamic stability data obtained during the iterative loop, the proportion of stable and hence potentially synthesizable molecules generated is 3.5x higher than the next-best model.
Journal Article
Impact of Microphysical Parameterizations on Simulated Hurricanes—Using Multi-Parameter Satellite Data to Determine the Particle Size Distributions that Produce Most Realistic Storms
Understanding and forecasting hurricanes remains a challenge for the operational and research communities. To accurately predict the Tropical Cyclone (TC) evolution requires properly reflecting the storm’s inner core dynamics by using: (i) high-resolution models; (ii) realistic physical parameterizations. The microphysical processes and their representation in cloud-permitting models are of crucial importance. In particular, the assumed Particle Size Distribution (PSD) functions affect nearly all formulated microphysical processes and are among the most fundamental assumptions in the bulk microphysics schemes. This paper analyzes the impact of the PSD assumptions on simulated hurricanes and their synthetic radiometric signatures. It determines the most realistic, among the available set of assumptions, based on comparison to multi-parameter satellite observations. Here we simulated 2005′s category-5 Hurricane Rita using the cloud-permitting community Weather Research and Forecasting model (WRF) with two different microphysical schemes and with seven different modifications of the parametrized hydrometeor properties within one of the two schemes. We then used instrument simulators to produce satellite-like observations. The study consisted in evaluating the structure of the different simulated storms by comparing, for each storm, the calculated microwave signatures with actual satellite observations made by (a) the passive microwave radiometer that was carried by the Tropical Rainfall Measuring Mission (TRMM) satellite—the TRMM microwave imager TMI, (b) TRMM’s precipitation radar (PR) and (c) the ocean-wind-vector scatterometer carried by the QuikSCAT satellite. The analysis reveals that the different choices of microphysical parameters do produce significantly different microwave signatures, allowing an objective determination of a “best” parameter combination whose resulting signatures are collectively most consistent with the wind and precipitation observations obtained from the satellites. In particular, we find that assuming PSDs with larger number of smaller hydrometeors produces storms that compare best to observations.
Journal Article
Data Management Support for the SPURS Atlantic Field Campaign
We developed the data management system for the US National Aeronautics and Space Administration-sponsored Salinity Processes in the Upperocean Regional Study (SPURS) Atlantic field campaign (SPURS-1). Data management support means more than simply collecting and archiving static data sets. It involves a complex mixture of data visualization, interaction with principal investigators, Web development, public outreach, quality assurance, and archiving for posterity.
Journal Article
Formation of Transitory Intrachain and Interchain Disulfide Bonds Accompanies the Folding and Oligomerization of Simian Virus 40 Vp1 in the Cytoplasm
Pentamer formation by Vp1, the major capsid protein of simian virus 40, requires an interdigitation of structural elements from the Vp1 monomers [Liddington, R. C., Yan, Y., Moulai, J., Sahli, R., Benjamin, T. L. & Harrison, S. C. (1991) Nature (London) 354, 278-284]. Our analyses reveal that disulfide-linked Vp1 homooligomers are present in the simian virus 40-infected cytoplasm and that they are derived from a 41-kDa monomeric intermediate containing an intrachain disulfide bond(s). The 41-kDa species, emerging within 5 min of pulse labeling with [35S]methionine, is converted into a 45-kDa, disulfide-free Vp1 monomer and disulfide-bonded dimers through pentamers. The covalent oligomer formation is blocked in the presence of a sulfhydryl-modifying reagent. We propose that there are two stages in this Vp1 disulfide bonding. First, the newly synthesized Vp1 monomers acquire intrachain bonds as they fold and begin to interact. Next, these bonds are replaced with intermolecular bonds as the monomers assemble into pentamers. This sequential appearance of transitory disulfide bonds is consistent with a role for sulfhydryl-disulfide redox reactions in the coordinate folding of Vp1 chains into pentamers. The cytoplasmic Vp1 does not colocalize with marker proteins of the endoplasmic reticulum. This paper demonstrates in vivo disulfide formations and exchanges coupled to the folding and oligomerization of a mammalian protein in the cytoplasm, outside the secretory pathway. Such disulfide dynamics may be a general phenomenon for other cysteine-bearing mammalian proteins that fold in the cytoplasm.
Journal Article