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198 records · Page 11

A curated benchmark for cofolding models on kinase conformational states

Abstract Protein kinases are critical drug targets, requiring therapeutics that can modulate their active and inactive conformational states. While cofolding models can generate global folds directly from kinase sequences and ligand SMILES strings, these models have not yet been tested on their ability to recover ligand-induced-fit conformational states of the kinase proteins. Here, we introduce KinConfBench, a curated benchmark of 2225 high-quality human kinase chains to evaluate the ability of four state-of-the-art cofolding models—Boltz-2, Chai-1, Protenix, and RoseTTAFold-All-Atom—to recover both canonical and rare conformational states. We show that geometric success metrics of a ligand pose in the active site do not correlate strongly with the correct kinase conformational state, motivating a new set of dynamical benchmarks for assessing cofolding models. While all four cofolding models achieve ~60–80% prediction accuracy for kinase conformational classification, they exhibit severe mode collapse when performing multiple inferences, show negligible structural diversity in sampling induced-fit motions, and display a prevalent “apo-drift” in which most cofolding models predominantly predict the kinase to be in its ligand-free state. Our results highlight that capturing ligand-induced protein conformational diversity, not just geometric fit, is critical for next-generation structure-based drug discovery.

Sun, Kunyang↗

Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)

The Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria, known primarily for clinical relevance and for chemolithotrophy in various terrestrial and marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded and protein marker analysis become more common, the phylogenetic placement of this class has become less certain. A number of recent analyses of the bacterial tree of life using both 16S rRNA and concatenated marker gene analyses have failed to recover the Epsilonproteobacteria as monophyletic with all other classes of Proteobacteria. In order to address this issue, we investigated the phylogenetic placement of this class in the bacterial domain using 16S and 23S rRNA genes, as well as 120 single-copy marker proteins. Singleand concatenated-marker trees were created using a data set of 4,170 bacterial representatives, including 98 Epsilonproteobacteria. Phylogenies were inferred under a variety of tree building methods, with sequential jackknifing of outgroup phyla to ensure robustness of phylogenetic affiliations under differing combinations of bacterial genomes. Based on the assessment of nearly 300 phylogenetic tree topologies, we conclude that the continued inclusion of Epsilonproteobacteria within the Proteobacteria is not warranted, and that this group should be reassigned to a novel phylum for which we propose the name Epsilonbacteraeota (phyl. nov.). We further recommend the reclassification of the order Desulfurellales (Deltaproteobacteria) to a novel class within this phylum and a number of subordinate changes to ensure consistency with the genome-based phylogeny. Phylogenomic analysis of 658 genomes belonging to the newly proposed Epsilonbacteraeota suggests that the ancestor of this phylum was an autotrophic, motile, thermophilic chemolithotroph that likely assimilated nitrogen from ammonium taken up from the environment or generated from environmental nitrate and nitrite by employing a variety of functional redox modules. The emergence of chemoorganoheterotrophic lifestyles in several Epsilonbacteraeota families is the result of multiple independent losses of various ancestral chemolithoautotrophic pathways. Our proposed reclassification of this group resolves an important anomaly in bacterial systematics and ensures that the taxonomy of Proteobacteria remains robust, specifically as genome-based taxonomies become more common.

evolution↗

HarDWR - Harmonized Water Rights Records

A dataset within the Harmonized Database of Western U.S. Water Rights (HarDWR). For a detailed description of the database, please see the meta-record v2.0. Changelog v2.0 - Recalculated based on data sourced from WestDAAT - Changed using a Site ID column to identify unique records to using aa combination of Site ID and Allocation ID - Removed the Water Management Area (WMA) column from the harmonized records. The replacement is a separate file which stores the relationship between allocations and WMAs. This allows for allocations to contribute to water right amounts to multiple WMAs during the subsequent cumulative process. - Added a column describing a water rights legal status - Added "Unspecified" was a water source category - Added an acre-foot (AF) column - Added a column for the classification of the right's owner v1.02 - Added a .RData file to the dataset as a convenience for anyone exploring our code. This is an internal file, and the one referenced in analysis scripts as the data objects are already in R data objects. v1.01 - Updated the names of each file with an ID number less than 3 digits to include leading 0s v1.0 - Initial public release Description Here we present an updated database of Western U.S. water right records. This database provides consistent unique identifiers for each water right record, and a consistent categorization scheme that puts each water right record into one of seven broad use categories. These data were instrumental in conducting a study of the multi-sector dynamics of inter-sectoral water allocation changes though water markets (Grogan et al., *in review*). Specifically, the data were formatted for use as input to a process-based hydrologic model, Water Balance Model (WBM), with a water rights module (Grogan et al., *in review*). While this specific study motivated the development of the database presented here, water management in the U.S. West is a rich area of study (e.g., Anderson and Woosly, 2005; Tidwell, 2014; Null and Prudencio, 2016; Carney et al., 2021) so releasing this database publicly with documentation and usage notes will enable other researchers to do further work on water management in the U.S. West. We produced the water rights database presented here in four main steps: (1) data collection, (2) data quality control, (3) data harmonization, and (4) generation of cumulative water rights curves. Each of steps (1)-(3) had to be completed in order to produce (4), the final product that was used in the modeling exercise in Grogan et al. (*in review*). All data in each step is associated with a spatial unit called a Water Management Area (WMA), which is the unit of water right administration utilized by the state in which the right came from. Steps (2) and (3) required use to make assumptions and interpretation, and to remove records from the raw data collection. We describe each of these assumptions and interpretations below so that other researchers can choose to implement alternative assumptions an interpretation as fits their research aims. Motivation for Changing Data Sources The most significant change has been a switch from collecting the raw water rights directly from each state to using the water rights records presented in WestDAAT, a product of the Water Data Exchange (WaDE) Program under the Western States Water Council (WSWC). One of the main reasons for this is that each state of interest is a member of the WSWC, meaning that WaDE is partially funded by these states, as well as many universities. As WestDAAT is also a database with consistent categorization, it has allowed us to spend less time on data collection and quality control and more time on answering research questions. This has included records from water right sources we had previously not known about when creating v1.0 of this database. The only major downside to utilizing the WestDAAT records as our raw data is that further updates are tied to when WestDAAT is updated, as some states update their public water right records daily. However, as our focus is on cumulative water amounts at the regional scale, it is unlikely most records updates would have a significant effect on our results. The structure of WestDAAT led to several important changes to how HarWR is formatted. The most significant change is that WaDE has calculated a field known as `SiteUUID`, which is a unique identifier for the Point of Diversion (POD), or where the water is drawn from. This separate from `AllocationNativeID`, which is the identifier for the allocation of water, or the amount of water associated with the water right. It should be noted that it is possible for a single site to have multiple allocations associated with it and for an allocation to be able to be extracted from multiple sites. The site-allocation structure has allowed us to adapt a more consistent, and hopefully more realistic, approach in organizing the water right records than we had with HarDWR v1.0. This was incredibly helpful as the raw data from many states had multiple water uses within a single field within a single row of their raw data, and it was not always clear if the first water use was the most important, or simply first alphabetically. WestDAAT has already addressed this data quality issue. Furthermore, with v1.0, when there were multiple records with the same water right ID, we selected the largest volume or flow amount and disregarded the rest. As WestDAAT was already a common structure for disparate data formats, we were better able to identify sites with multiple allocations and, perhaps more importantly, allocations with multiple sites. This is particularly helpful when an allocation has sites which cross WMA boundaries, instead of just assigning the full water amount to a single WMA we are now able to divide the amount of water between the number of relevant WMAs. As it is now possible to identify allocations with water used in multiple WMAs, it is no longer practical to store this information within a single column. Instead the stAllocationToWMATab.csv file was created, which is an allocation by WMA matrix containing the percent Place of Use area overlap with each WMA. We then use this percentage to divide the allocation's flow amount between the given WMAs during the cumulation process to hopefully provide more realistic totals of water use in each area. However, not every state provides areas of water use, so like HarDWR v1.0, a hierarchical decision tree was used to assign each allocation to a WMA. First, if a WMA could be identified based on the allocation ID, then that WMA was used; typically, when available, this applied to the entire state and no further steps were needed. Second was the spatial analysis of Place of Use to WMAs. Third was a spatial analysis of the POD locations to WMAs, with the assumption that allocation's POD is within the WMA it should belong to; if an allocation still had multiple WMAs based on its POD locations, then the allocation's flow amount would be divided equally between all WMAs. The fourth, and final, process was to include water allocations which spatially fell outside of the state WMA boundaries. This could be due to several reasons, such as coordinate errors / imprecision in the POD location, imprecision in the WMA boundaries, or rights attached with features, such as a reservoir, which crosses state boundaries. To include these records, we decided for any POD which was within one kilometer of the state's edge would be assigned to the nearest WMA. Other Changes WestDAAT has Allowed In addition to a more nuanced and consistent method of assigning water right's data to WMAs, there are other benefits gained from using the WestDAAT dataset. Among those is a consistent categorization of a water right's legal status. In HarDWR v1.0, legal status was effectively ignored, which led to many valid concerns about the quality of the database related to the amounts of water the rights allowed to be claimed. The main issue was that rights with legal status' such as "application withdrawn", "non-active", or "cancelled" were included within HarDWR v1.0. These, and other water rights status' which were deemed to not be in use have been removed from this version of the database. Another major change has been the addition of the "unspecified water source category. This is water that can come from either surface water or groundwater, or the source of which is unknown. The addition of this source category brings the total number of categories to three. Due to reviewer feedback, we decided to add the acre-foot (AF) column so that the data may be more applicable to a wider audience. We added the ownerClassification column so that the data may be more applicable to a wider audience. File Descriptions The dataset is a series of various files organized by state sub-directories. In addition, each file begins with the state's name, in case the file is separate from its sub-directory for some reason. After the state name is the text which describes the contents of the file. Here is each file described in detail. Note that st is a placeholder for the state's name. stFullRecords_HarmonizedRights.csv: A file of the complete water records for each state. The column headers for each of this type of file are: state - The name of the state to which the allocations belong to. FIPS - The two digit numeric state ID code. siteID - The site location ID for POD locations. A site may have multiple allocations, which are the actual amount of water which can be drawn. In a simplified hypothetical, a farm stead may have an allocation for "irrigation" and an allocation for "domestic" water use, but the water is drawn from the same pumping equipment. It should be noted that many of the site ID appear to have been added by WaDE, and therefore may not be recognized by a given state's water rights database. allocationID - The allocation ID for the water right. For most states this is the water right ID, and what is recommended to use should a right be looked up on a given state's water rights database. The water amounts associated with these IDs tend to be finer scaled than those associated with siteID. It should be noted that some allocations may be extracted from multiple sites, particularly for larger Places of Use. ownerClassification - A classification of the types of owners for water rights. The most common is `Private` which incorporates a wide range of entities. Several classifications would be grouped into a government category, most of which are for the U.S. Federal Government. These allocations could be listed as "Federal", "United States of America", or as the names of any number of federal agencies. The last major grouping of entities is for "Native American"s. priorityDate - The date we use as the water right priority date for our modeling analysis. This is the legal priority date when it is available. However, for some rights, specifically from California and New Mexico, we used a pseudo priority date (e.g. well completion date or start of well drilling date) when a legal priority date was not available. The most questionable dates come from New Mexico, where the only date associated with certain water right records was the date the allocation was recorded in the database. As the allocation record creation tended to be within a few months of the filing of the application of the water right, from manually double checking the water rights, and our analysis focuses on aggregating water rights on the timescale of years, we determined it was acceptable to use such dates to include as many records as possible. primaryBeneficialUse - From the numerous state water use categories, WaDE categorized them into 21 categories WestDAAT. This column is the original WaDE category for the primary water use at the PoD site. allocationBeneficialUse - From the numerous state water use categories, WaDE categorized them into 21 categories for WestDAAT. This column is the original WaDE category

Economics↗

Diversification of the Salmonella Fimbriae: A Model of Macro- and Microevolution

Bacteria of the genus Salmonella comprise a large and evolutionary related population of zoonotic pathogens that can infect mammals, including humans and domestic animals, birds, reptiles and amphibians. Salmonella carries a plethora of virulence genes, including fimbrial adhesins, some of them known to participate in mammalian or avian host colonization. Each type of fimbria has its structural subunit and biogenesis genes encoded by one fimbrial gene cluster (FGC). The accumulation of new genomic information offered a timely opportunity to better evaluate the number and types of FGCs in the Salmonella pangenome, to test the use of current classifications based on phylogeny, and to infer potential correlations between FGC evolution in various Salmonella serovars and host niches. This study focused on the FGCs of the currently deciphered 90 genomes and 60 plasmids of Salmonella. The analysis highlighted a fimbriome consisting of 35 different FGCs, of which 16 were new, each strain carrying between 5 and 14 FGCs. The Salmonella fimbriome was extremely diverse with FGC representatives in 8 out of 9 previously categorized fimbrial clades and subclades. Phylogenetic analysis of Salmonella suggested macroevolutionary shifts detectable by extensive FGC deletion and acquisition. In addition, microevolutionary drifts were best depicted by the high level of allelic variation in predicted or known adhesins, such as the type 1 fimbrial adhesin FimH for which 67 different natural alleles were identified in S. enterica subsp. I. Together with strain specific collections of FGCs, allelic variation among adhesins attested to the pathoadaptive evolution of Salmonella towards specific hosts and tissues, potentially modulating host range, strain virulence, disease progression, and transmission efficiency. Further understanding of how each Salmonella strain utilizes its panel of FGCs and specific adhesin alleles for survival and infection will support the development of new approaches for the control of Salmonellosis.

59 BASIC BIOLOGICAL SCIENCES↗

How do supernova remnants cool? – I. Morphology, optical emission lines, and shocks

ABSTRACT Supernovae (SNe) inject ∼1051 erg in the interstellar medium, thereby shocking and heating the gas. A substantial fraction of this energy is later lost via radiative cooling. We present a post-processing module for the flash code to calculate the cooling radiation from shock-heated gas using collisional excitation data from mappings v. When applying this tool to a simulated SN remnant (SNR), we find that most energy is emitted in the EUV. However, optical emission lines ([O iii], [N ii], [S ii], H α, H β) are usually best observable. Our shock detection scheme shows that [S ii] and [N ii] emissions arise from the thin shell surrounding the SNR, while [O iii], H $\rm \alpha$, and H $\rm \beta$ originate from the volume-filling hot gas inside the SNR bubble. We find that the optical emission lines are affected by the SNR’s complex structure and its projection on to the plane of the sky because the escaping line luminosity can be reduced by 10–80 per cent due to absorption along the line of sight. Additionally, the subtraction of contaminating background radiation is required for the correct classification of an SNR on the oxygen or sulphur BPT diagrams. The electron temperature and density obtained from our synthetic observations match well with the simulation but are very sensitive to the assumed metallicity.

Astronomy & Astrophysics↗

Quantifying Parameter Sensitivity, Interaction and Transferability in Hydrologically Enhanced Versions of Noah-LSM over Transition Zones

We use sensitivity analysis to identify the parameters that are most responsible for shaping land surface model (LSM) simulations and to understand the complex interactions in three versions of the Noah LSM: the standard version (STD), a version enhanced with a simple groundwater module (GW), and version augmented by a dynamic phenology module (DV). We use warm season, high-frequency, near-surface states and turbulent fluxes collected over nine sites in the US Southern Great Plains. We quantify changes in the pattern of sensitive parameters, the amount and nature of the interaction between parameters, and the covariance structure of the distribution of behavioral parameter sets. Using Sobol s total and first-order sensitivity indexes, we show that very few parameters directly control the variance of the model output. Significant parameter interaction occurs so that not only the optimal parameter values differ between models, but the relationships between parameters change. GW decreases parameter interaction and appears to improve model realism, especially at wetter sites. DV increases parameter interaction and decreases identifiability, implying it is overparameterized and/or underconstrained. A case study at a wet site shows GW has two functional modes: one that mimics STD and a second in which GW improves model function by decoupling direct evaporation and baseflow. Unsupervised classification of the posterior distributions of behavioral parameter sets cannot group similar sites based solely on soil or vegetation type, helping to explain why transferability between sites and models is not straightforward. This evidence suggests a priori assignment of parameters should also consider climatic differences.

Rosero, Enrique↗

Issues in knowledge representation to support maintainability: A case study in scientific data preparation

Scientific data preparation is the process of extracting usable scientific data from raw instrument data. This task involves noise detection (and subsequent noise classification and flagging or removal), extracting data from compressed forms, and construction of derivative or aggregate data (e.g. spectral densities or running averages). A software system called PIPE provides intelligent assistance to users developing scientific data preparation plans using a programming language called Master Plumber. PIPE provides this assistance capability by using a process description to create a dependency model of the scientific data preparation plan. This dependency model can then be used to verify syntactic and semantic constraints on processing steps to perform limited plan validation. PIPE also provides capabilities for using this model to assist in debugging faulty data preparation plans. In this case, the process model is used to focus the developer's attention upon those processing steps and data elements that were used in computing the faulty output values. Finally, the dependency model of a plan can be used to perform plan optimization and runtime estimation. These capabilities allow scientists to spend less time developing data preparation procedures and more time on scientific analysis tasks. Because the scientific data processing modules (called fittings) evolve to match scientists' needs, issues regarding maintainability are of prime importance in PIPE. This paper describes the PIPE system and describes how issues in maintainability affected the knowledge representation used in PIPE to capture knowledge about the behavior of fittings.

Chien, Steve↗

Characterization of 3D Cirrus Cloud and Radiation Fields Using ARS/AIRS/MODIS data and its Application to Climate Model

During the report period, we have made the following research accomplishments. First, we performed analysis for a number of MODIS scenes comprising of heavy dust events and ice clouds, covering regions of frequent dust outbreaks in East Asia, Middle East, and West Africa, as well as areas associated with long-range dust transports over the Equatorial Tropical Atlantic Ocean. These scenes contain both dust/aerosols and clouds. We collected suitable aerosol/ice-cloud data, correlated ice cloud and aerosol parameters by means of statistical analysis, and interpreted resulting correlation trends based on the physical principles governing cloud microphysics. Aerosol and cloud optical depths and cloud effective particle size inferred from MODIS for selected domains were analyzed from which the parameters including dust aerosol number concentration, ice cloud water path, and ice particle number concentration were subsequently derived. We illustrated that the Twomey (solar albedo) effect can be statistically quantified based on the slope of best-fit straight lines in the correlation study. Analysis of aerosol and cloud retrieval products revealed that for all cases, the region with a larger dust aerosol optical depth is always characterized by a smaller cloud particle size, consistent with the Twomey hypothesis for aerosol-cloud interactions. Second, we developed mean correlation curves with uncertainties associated with small ice-crystal concentration observations for the mean effective ice crystal size (De) and ice water content (IWC) by dividing the atmosphere into three characteristic regions: Tropics cirrus, Midlatitude cirrus, including a temperature classification to improve correlation, and Arctic ice clouds. We illustrated that De has a high correlation with IWC based on theoretical consideration and analysis of thousands of observed ice crystal data obtained from a number of ARM-DOE field campaigns and other experiments. The correlation has the form: ln(De) = a + b ln(IWC) + c ((ln(IWC))2, where a, b, and c are fitting coefficients and are functions of three regions. We demonstrated that this correlation can be effectively incorporated in GCMs and climate models that predict IWC - a significant advance in ice microphysics parameterization for interactive cloud-radiation analysis and feedback. Substantial July mean differences are shown in the OLR (W/m2) and precipitation (mm/day) patterns between UCLA GCM simulations based on Des determined from the De-IWC correlations and the control run using a fixed ice crystal size. Third, in order to improve the computation of spectral radiative transfer processes in the WRF model, we developed a consistent and efficient radiation scheme that can better resolve the spectral bands, determine the cloud optical properties, and provide more reliable and accurate radiative heating fields. In the newly developed radiation module, we have implemented in WRF a modified and improved version referred to as the Fu-Liou-Gu scheme, which includes a combination of delta-four-stream and delta-two-stream approximations for solar and IR flux calculations, respectively. This combination has been proven to be computationally efficient and at the same time to produce a high degree of accuracy. The incorporation of nongray gaseous absorption in multiple scattering atmospheres was based on the correlated k-distribution method. The solar and IR spectra are divided into 6 and 12 bands, respectively, according to the location of absorption bands of H2O, CO2, O3, CH4, N2O, and CFCs. We further included absorption by the water vapor continuum and a number of minor absorbers in the solar spectrum leading to an additional absorption of solar flux in a clear atmosphere on the order of 1-3 W/m2. Additionally, we incorporated the ice microphysics parameterization that includes an interactive mean effective ice crystal size in association with radiation parameterizations. The Fu-Liou-Gu scheme is an ideal tool for the simulation of radiative transfer and ice microphysics within the domain of WRF. It is particularly useful for studying direct and indirect aerosol radiative effects associated with ice cloud formation. The newly implemented radiation module has been demonstrated to work well in WRF and can be effectively used for studies related to cirrus cloud formation and evolution as well as aerosol-cloud-radiation interactions. With the newly implemented radiation scheme, the simulations of cloud cover and ice water path have been improved for cirrus clouds, with a more consistent comparison with the corresponding MODIS observations, especially for optically thin cirrus with an improvement of about 20% in the simulated mean ice water path.

97 MATHEMATICS AND COMPUTING↗

PV Reliability and Resilience in Challenging Climates

Challenging climates for Photovoltaics are usually based on climate classification. However, extreme weather events such as high wind, flooding, large hail, extreme snow etc. have become more ubiquitous globally. To study the impact of extraordinary weather events on PV reliability we used two of the largest databases in the USA. First, the National Oceanic and Atmospheric Administration (NOAA) database on extreme weather and secondly, the PV Fleet Data Initiative where we have collected high-resolution PV performance data of more than 8 gigawatts or about 6-7% of all commercial and utility systems in the USA. We analyzed almost 200 systems between 2008-20022 that were immediately impacted by these weather events. The immediate impact (outages) was determined to be about 1% of or a median of approximately 3 days of annual lost production. However, the risk these events pose is exemplified by a long tail where 0.4 % of all systems lost more than 2 weeks annual production. We also found a threshold for high wind (90 km/hr) and hail (25mm), above which we observed significantly higher degradation implying long-term damage to the systems. In addition, we are using satellite imagery to quantify visible damage to PV plants. Finally, we share module, design and installation lessons from some observed case studies to improve extreme weather resilience for PV power systems.

degradation↗

Improved Characterization of PSC Processes Derived from a Third-Generation CALIOP and MLS Detection and Composition Classification Algorithm

The new 3-year CloudSat and CALIPSO Science Team project described in this poster will use a unique combination of data from the Cloud-Aerosol LIdar with Orthogonal Polarization (CALIOP) instrument on CALIPSO and the Microwave Limb Sounder (MLS) on Aura, in conjunction with supporting meteorological information and detailed modeling studies, to advance our understanding of polar stratospheric cloud (PSC) processes and their role in ozone depletion. We will develop a third-generation (Gen3) PSC detection and composition algorithm that incorporates a new, more robust two-dimensional, multi-channel CALIOP feature detection scheme (2D-McDA). We will also devise and implement an improved two-dimensional PSC composition classification scheme that utilizes multiple parameters (e.g., CALIOP 532-nm parallel and perpendicular scattering ratios, CALIOP 1064-nm total scattering ratio, MLS HNO3 and H2O, ambient temperature, and temperature histories) in a Bayesian approach to determine the most likely PSC composition and help constrain solid PSC particle number density and size/shape. The combined CALIOP/MLS analyses will allow us to study in detail the full life cycle of PSCs and their resulting impact on gas-phase HNO3 and H2O, which should lead to improved parameterizations of PSC microphysics in global CCMs where detailed particle information is not available. The Gen3 CALIOP PSC algorithm will be a natural stepping-stone toward the analysis of data collected during future spaceborne lidar missions, such as NASA’s Atmosphere Observation System (AtmOS) mission currently scheduled for launch late in this decade. We will also investigate possible trends in PSC occurrence and composition over the entire CALIOP data record and through further comparisons with the Stratospheric Aerosol Measurement (SAM) II solar occultation PSC record from 1979-1989. Finally, we will validate the mountain-wave parameterization and PSC schemes used in the UM-UKCA (Unified Model coupled to the United Kingdom Chemistry and Aerosol module) chemistry-climate model through detailed comparisons with earlier CALIOP PSC data products and those developed under this proposal.

CALIPSO↗

Improved Characterization of PSC Processes Derived from a Third-Generation CALIOP and MLS Detection and Composition Classification Algorithm

The new 3-year CloudSat and CALIPSO Science Team project described in this poster will use a unique combination of data from the Cloud-Aerosol LIdar with Orthogonal Polarization (CALIOP) instrument on CALIPSO and the Microwave Limb Sounder (MLS) on Aura, in conjunction with supporting meteorological information and detailed modeling studies, to advance our understanding of polar stratospheric cloud (PSC) processes and their role in ozone depletion. We will develop a third-generation (Gen3) PSC detection and composition algorithm that incorporates a new, more robust two-dimensional, multi-channel CALIOP feature detection scheme (2D-McDA). We will also devise and implement an improved two-dimensional PSC composition classification scheme that utilizes multiple parameters (e.g., CALIOP 532-nm parallel and perpendicular scattering ratios, CALIOP 1064-nm total scattering ratio, MLS HNO3 and H2O, ambient temperature, and temperature histories) in a Bayesian approach to determine the most likely PSC composition and help constrain solid PSC particle number density and size/shape. The combined CALIOP/MLS analyses will allow us to study in detail the full life cycle of PSCs and their resulting impact on gas-phase HNO3 and H2O, which should lead to improved parameterizations of PSC microphysics in global chemistry-climate models (CCMs) where detailed particle information is not available. The Gen3 CALIOP PSC algorithm will be a natural stepping-stone toward the analysis of data collected during future spaceborne lidar missions, such as NASA’s Atmosphere Observation System (AOS) mission currently scheduled for launch late in this decade. We will also investigate possible trends in PSC occurrence and composition over the entire CALIOP data record and through further comparisons with the Stratospheric Aerosol Measurement (SAM) II solar occultation PSC record from 1979-1989. Finally, we will validate the mountain-wave parameterization and PSC schemes used in the UM-UKCA (Unified Model coupled to the United Kingdom Chemistry and Aerosol module) CCM through detailed comparisons with earlier CALIOP PSC data products and those developed under this proposal.

CALIPSO↗

Field validation of data-driven BSDF and peak extraction models for light-scattering fabric shades

Shading and daylighting systems affect cooling, heating, and lighting energy use by modulating solar radiation through the building façade. Characterizing shading systems holistically and accurately helps designers and engineers evaluate shading systems to achieve energy and non-energy performance goals. These complex fenestration systems can be modeled using Bidirectional Scattering Distribution Functions (BSDF), which map incident radiation to hemispherical distributions of outgoing radiation. Data-driven, tabulated BSDFs are derived from interpolated goniophotometer measured data, then sampled during the raytracing calculation. A peak extraction (PE) algorithm was developed to circumvent limits in BSDF angular resolution, where the specular peak is extracted during simulation by evaluating the BSDF in the through direction and surrounding region. The objective of this study was to validate this measurement and modeling workflow using field monitored data from a full scale testbed with eleven installed fabrics of different weaves, openness factors, and colors and assess the accuracy of the workflow under different adaptation and contrast conditions. Test conditions were limited to clear sky conditions with the sun in the field of view. Results showed that, for tensor tree datasets, vertical illuminance, solar luminance (2.5° apex), and daylight glare probability (DGP) were predicted to within a mean bias error (MBE) error of -456 lx (-12.3%), -3.46e5 (-38.4%), and -0.042 (-7.8%) when full PE occurred. With a binary classification of glare/ no glare, DGP was predicted accurately with a true positive rate of 0.98 and true negative rate of 1.0 using tensor tree data and less accurately with Klems BSDF data, particularly for cases of no glare. The workflow may be of insufficient accuracy to distinguish borderline performance between fabrics using the four-point glare scale, particularly under low adaptation, high contrast daylit conditions. Errors were due to reductions in peak shape and intensity across the BSDF interpolation and data reduction workflow. Future work is needed to better preserve measurement fidelity during interpolation and sampling, which in turn will improve PE performance.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

A Proposal to Develop Interactive Classification Technology

Research for the first year was oriented towards: 1) the design of an interactive classification tool (ICT); and 2) the development of an appropriate theory of inference for use in ICT technology. The general objective was to develop a theory of classification that could accommodate a diverse array of objects, including events and their constituent objects. Throughout this report, the term "object" is to be interpreted in a broad sense to cover any kind of object, including living beings, non-living physical things, events, even ideas and concepts. The idea was to produce a theory that could serve as the uniting fabric of a base technology capable of being implemented in a variety of automated systems. The decision was made to employ two technologies under development by the principal investigator, namely, SMS (Symbolic Manipulation System) and SL (Symbolic Language) [see debessonet, 1991, for detailed descriptions of SMS and SL]. The plan was to enhance and modify these technologies for use in an ICT environment. As a means of giving focus and direction to the proposed research, the investigators decided to design an interactive, classificatory tool for use in building accessible knowledge bases for selected domains. Accordingly, the proposed research was divisible into tasks that included: 1) the design of technology for classifying domain objects and for building knowledge bases from the results automatically; 2) the development of a scheme of inference capable of drawing upon previously processed classificatory schemes and knowledge bases; and 3) the design of a query/ search module for accessing the knowledge bases built by the inclusive system. The interactive tool for classifying domain objects was to be designed initially for textual corpora with a view to having the technology eventually be used in robots to build sentential knowledge bases that would be supported by inference engines specially designed for the natural or man-made environments in which the robots would be called upon to operate.

deBessonet, Cary↗

Auto-segmentation of normal and target structures in head and neck CT images: A feature-driven model-based approach

Purpose: Intensity modulated radiation therapy (IMRT) allows greater control over dose distribution, which leads to a decrease in radiation related toxicity. IMRT, however, requires precise and accurate delineation of the organs at risk and target volumes. Manual delineation is tedious and suffers from both interobserver and intraobserver variability. State of the art auto-segmentation methods are either atlas-based, model-based or hybrid however, robust fully automated segmentation is often difficult due to the insufficient discriminative information provided by standard medical imaging modalities for certain tissue types. In this paper, the authors present a fully automated hybrid approach which combines deformable registration with the model-based approach to accurately segment normal and target tissues from head and neck CT images. Methods: The segmentation process starts by using an average atlas to reliably identify salient landmarks in the patient image. The relationship between these landmarks and the reference dataset serves to guide a deformable registration algorithm, which allows for a close initialization of a set of organ-specific deformable models in the patient image, ensuring their robust adaptation to the boundaries of the structures. Finally, the models are automatically fine adjusted by our boundary refinement approach which attempts to model the uncertainty in model adaptation using a probabilistic mask. This uncertainty is subsequently resolved by voxel classification based on local low-level organ-specific features. Results: To quantitatively evaluate the method, they auto-segment several organs at risk and target tissues from 10 head and neck CT images. They compare the segmentations to the manual delineations outlined by the expert. The evaluation is carried out by estimating two common quantitative measures on 10 datasets: volume overlap fraction or the Dice similarity coefficient (DSC), and a geometrical metric, the median symmetric Hausdorff distance (HD), which is evaluated slice-wise. They achieve an average overlap of 93% for the mandible, 91% for the brainstem, 83% for the parotids, 83% for the submandibular glands, and 74% for the lymph node levels. Conclusions: Our automated segmentation framework is able to segment anatomy in the head and neck region with high accuracy within a clinically-acceptable segmentation time.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Prognostic Value of Prevertebral Space Involvement in Nasopharyngeal Carcinoma Based on Intensity-Modulated Radiotherapy

Purpose: To investigate the prognostic significance of prevertebral space involvement (PSI) in patients with nasopharyngeal carcinoma (NPC) treated with intensity-modulated radiotherapy (IMRT). Methods and Materials: A retrospective review of data from 506 biopsy-proven, nonmetastatic NPCs was performed. Patients underwent magnetic resonance imaging examinations and received IMRT as their primary treatment. Results: In this series, 161 NPC patients (31.8%) had PSI. Parapharyngeal space (p < 0.001), skull base (p < 0.001), and paranasal sinuses (p = 0.009) were associated with PSI after multivariate analysis. The 4-year overall survival (OS), local relapse-free survival (LRFS), distant metastasis-free survival (DMFS) for NPC patients with and without PSI was 69.1% and 89.2% (p < 0.0001), 83.9% and 96.4% (p < 0.0001), and 71.6% and 89.6% (p < 0.0001), respectively. Multivariate analysis identified PSI as an independent negative prognostic factor for both OS (HR = 1.478-4.380; p = 0.001) and DMFS (HR = 1.389-4.174; p = 0.002). Patients with PSI had similar survival rates in OS and DMFS (p = 0.241 and p = 0.493, respectively) to that of T4 disease, while the differences between PSI and T3 disease in both OS and DMFS were distinctly significant (p = 0.029 and p = 0.029, respectively). Conclusions: For NPC patients treated with IMRT, PSI was found to be an independent prognostic factor for both OS and DMFS. It seems reasonable that PSI should be classified as a T4 disease on the basis of the current American Joint Committee on Cancer staging classification criteria.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Intensity-Modulated Radiation Therapy in the Salvage of Locally Recurrent Nasopharyngeal Carcinoma

Purpose: Local recurrences of nasopharyngeal carcinoma (NPC) may be salvaged by reirradiation with conventional techniques, but with significant morbidity. Intensity-modulated radiation therapy (IMRT) may improve the therapeutic ratio by reducing doses to normal tissue. The aim of this study was to address the efficacy and toxicity profile of IMRT for a cohort of patients with locally recurrent NPC. Methods and Materials: Between August 2003 and June 2009, 70 patients with radiologic or pathologically proven locally recurrent NPC were treated with IMRT. The median time to recurrence was 30 months after the completion of conventional radiation to definitive dose. Fifty-seven percent of the tumors were classified asrT3-4. The minimum planned doses were 59.4 to 60 Gy in 1.8- to 2-Gy fractions per day to the gross disease with margins, with or without chemotherapy. Results: The median dose to the recurrent tumor was 70 Gy (range, 50-77.4 Gy). Sixty-five patients received the planned radiation therapy; 5 patients received between 50 and 60 Gy because of acute side effects. With a median follow-up time of 25 months, the rates of 2-year locoregional recurrence-free survival, disease-free survival, and overall survival were 65.8%, 65.8%, and 67.4%, respectively. Moderate to severe late toxicities were noted in 25 patients (35.7%). Eleven patients (15.7%) had posterior nasal space ulceration, 17 (24.3%) experienced cranial nerve palsies, 12 (17.1%) had trismus, and 12 (17.1%) experienced deafness. Extended disease-free interval (relative risk 2.049) and advanced T classification (relative risk 3.895) at presentation were adverse prognostic factors. Conclusion: Reirradiation with IMRT provides reasonable long-term control in patients with locally recurrent NPC.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Wintertime synoptic patterns of midlatitude boundary layer clouds over the western North Atlantic: Climatology and insights from in-situ ACTIVATE observations

The winter synoptic evolution of the western North Atlantic and its influence on the atmospheric boundary layer is described by means of a regime classification based on Self Organizing Maps applied to 12 year of data (2009-2020). The regimes are classified into categories according to daily 600-hPa geopotential height: dominant ridge, trough to ridge eastward transition (trough-ridge), dominant trough, and ridge to trough eastward transition (ridge-trough). A fifth synoptic regime resembles the winter climatological mean. Coherent changes in sea-level pressure and large-scale winds are in concert with the synoptic regimes: 1) the ridge regime is associated with a well-developed anticyclone; 2) the trough-ridge gives rise to a low pressure center over the ocean, ascents, and northerly winds over the coastal zone; 3) trough is associated with the eastward displacement of a cyclone, coastal subsidence, and northerly winds, all representative characteristics of cold-air outbreaks; 4) the ridge-trough regime features the development of an anticyclone and weak coastal winds. Low clouds are characteristic of the trough regime, with both trough and trough-ridge featuring synoptic maxima in cloud droplet number concentration (N d ). The N d increase is primarily observed near the coast, concomitant with strong surface heat fluxes exceeding by more than 400 W m -2 compared to fluxes further east. Five consecutive days of aircraft observations collected during the ACTIVATE campaign corroborates the climatological characterization, confirming the occurrence of high N d for days identified as trough. This study emphasizes the role of boundary-layer dynamics and aerosol activation and their roles in modulating cloud microphysics.

54 ENVIRONMENTAL SCIENCES↗

A Machine Learning Approach to Improve Air Traffic Management Initiatives

Collaborating closely with commercial air carriers and related organizations, the Federal Aviation Administration(FAA) regulates air traffic and ensures the safety and efficiency of air operations. Air traffic controllers make strategic decisions, such as delaying, rerouting, or canceling flights, partly based on guidance provided by the FAA’s Air TrafficControl System Command Center (ATCSCC). The guidance includes, among other things, control measures known asTraffic Management Initiatives (TMIs) designed to enhance safety and improve operational efficiency. TMIs play a crucial role in managing the demand and capacity within the U.S. National Airspace System (NAS). Two major TMIs that are routinely used (primarily to mitigate the adverse effects of bad weather) are Ground Delay Programs (GDPs) andGround Stops (GSs). In a GDP, flights destined for airports facing thunderstorm activity experience delays at their origin airports. This proactive approach minimizes the risk of routing aircraft through hazardous weather conditions and also replaces (fuel burning) airborne delays with ground delays. In a GS, a temporary restriction is imposed on the departure or arrival of aircraft at a specific airport or within a designated airspace. Although other TMIs (e.g., miles-in-trail) are also implemented as part of (air) traffic flow management in the NAS, the focus of this work is on GDPs and GSs. Since TMIs, by design, lead to flight delays or cancellations, it is crucial to put in place the right set of parameters(e.g., scope and duration of the GDP). For example, when the end time of a GDP extends beyond what is necessary, it imposes unnecessary delays on departing flights. This situation could occur as a result of inaccurate prediction of the(required) duration of the GDP based on the weather forecast. On the other hand, if a GDP ends prematurely before the underlying capacity constraints are resolved at the destination airport, it may result in airborne holding. The delicate balance lies in matching the termination of the GDP precisely with the resolution of capacity constraints, avoiding both the imposition of unnecessary ground delays and the need for airborne holding due to premature program termination.Failing to specify the right parameters for TMIs also leads to flight delays, creating a significant obstacle in managing the increasing traffic volumes causing increased work load for the controllers. To address this issue, we propose the integration of Machine Learning (ML) models in the traffic flow management(TFM) pipeline. In current operations, decisions are made by human experts based on extensive training, historical patterns, available traffic and weather data. Since we have an abundance of data from past events that tell us the likely impact of various TMIs, by ingesting historical data, properly trained ML models can offer valuable insights and aid human decision-making. With the FAA increasingly exploring advanced analytics, ML emerges as a focal point for enhancing TFM within the National Airspace System (NAS). As a first step, this study aims to provide traffic controllers with decision-making support for the issuance and adjustment of TMIs. Data analytics and machine learning have been previously employed to address some of the challenges associated with TMIs. Numerous studies have concentrated on various facets of TMI issuance, exploring factors influencing TMI parameters, including arrival rate, airport capacity, and delay prediction. For example, using weather forecasts, several statistical methods were used to produce probabilistic capacity profiles which in conjunction with deterministic models provided insights into the GDP planning process [1–4]. The downside of using deterministic models is that they rely on fixed inputs and predetermined rules, which lack the ability to account for the inherent uncertainty and variability present in real-world scenarios. In a separate series of studies, researchers aimed to predict the occurrences of GDPs and GSs. The majority of these studies utilized various supervised learning methods, including Decision Trees, Naive Bayes, Support VectorMachines, and Random Forests to analyze the influence of weather conditions and arrival demand on TMI incidents[5–8]. However, these studies primarily focused on predicting the incidence of TMIs without explicitly addressing the scope of TMIs, including their duration and their geographical coverage. Furthermore, the emphasis of these studies was largely on GDPs, given their higher frequency and longer duration when compared to GSs. A limited number of studies focused on predicting the parameters of TMIs, specifically addressing their duration and extent. In one such study focusing on optimizing the TMI parameters at San Francisco International Airport (SFO),the authors utilized a probabilistic forecast of fog [9]. They simulated various capacity scenarios based on the (fog)burn-off forecasts, selecting GDP parameters that minimized airborne and overall ground delays. However, this approach exclusively emphasizes stratus (fog) burn-off as the primary determinant of GDP and GS, neglecting other influential factors like severe weather events, runway closures, lower capacity than traffic demand, and other important variables. Given the complexity of predicting the TMI and determining its scope, we seek a more holistic approach. We aim to consider all significant factors that could impact TMIs and their parameters. What sets this research apart is the fusion of all data sources relevant to the issuance and adjustment of TMIs and it represents the first comprehensive attempt to optimize TMIs in this manner. Since this comprehensive solution involves various aspects, we break down the problem into smaller components and input all parameters into a unified model called the “TMI Adjuster”. Figure 1 shows the overall framework and the list of datasets used in each model. The objective of the TMI Adjuster module is to deliver reliable, consistent and expedited recommendations for the progression, adjustment, and termination of TMIs. The ML solution entails developing a pipeline capable of predicting the necessity of a TMI (e.g., GS or GDP) along with its various parameters. For example, in the case of a GS, this includes the scope of the GS either in terms of distance from the destination airport or based on pre-defined airspace sectors. Here, scope refers to those regions and departing airports that are subject to the GS. In this paper, we concentrate on the issuance of GSs in the three major airports in the New York area — LaGuardia(LGA), John F. Kennedy International (JFK), and Newark Liberty International (EWR). We fuse traffic, weather and other relevant aviation data from years 2017 to 2019 to train and validate the ML models. In particular, we use the following datasets: •Terminal Aerodrome Forecast (TAF): meteorological forecasts specific to each airport, issued four times a day, covering predefined time periods. •TMI data: includes all GSs and GDPs along with their respective parameters. •Aviation System Performance Metrics (ASPM): includes traffic related data such as aircraft delays, arrival, and departure rates. •Notices to Airmen (NOTAMs): utilized to extract runway closure data and manage interdependencies between terminals in close proximity. •Flight cancellation data •Airspace Flow Programs (AFP): includes information on flight airborne holdings caused by TMIs. The data preprocessing entails transforming ASPM, TMI, AFP, NOTAMs, and weather data into an hourly format and consolidating all datasets by merging them based on date and time as the primary key. The TMI Adjuster framework comprises two parallel models: one dedicated to GS and a second model focused on GDP. As previously mentioned, our specific focus is on the GS model as a multi-classification problem. In this framework, each data point of the GS model input summarizes ten hours of data. Specifically, the data loader for the GS model generates the input and output of the model as follows: at a given time step, the input includes the actual traffic, weather, and TMI data from the two-hour window before the time step, alongside the weather forecast and scheduled traffic for the next 8 hours starting from the time step. Based on this information, the output of the GS model for each time interval consists of three dimensions. The first dimension represents a binary decision on whether there should be a GS in place for the next hour or not. The second dimension is related to the scope of the GS in the United States, and the third dimension is related to the scope of the GS in Canada (i.e., to determine if the GS impacts airports in Canada).One of the challenges with TMI modeling is the sparsity of TMI events, particularly regarding its scope. To address this challenge in the scope of the GS model output, we implement grouping. The GS scope for the US region is defined based on a list of centers that should be included when the GS is in place. With 20 centers in the US, we utilized historical data to group them into 4 categories. In particular, we summarized our historical data in a graph format where nodes represent centers, and link weights are defined based on the co-occurrence of centers in the scope parameter ofTMIs. By identified strongly connected components in this graph, we were able to partition the centers into four groups. We consider two model structures for the GS Model. Firstly, a hierarchical classification model [10], where the human decision-making for a GS is of hierarchical nature. The decision-maker first decides whether there is a need fora GS, and if the answer is yes, determines the scope. A hierarchical classification model organizes the problem into a class hierarchy, typically a tree or a Directed Acyclic Graph (DAG) structure, and considers the dependency of the decision in the previous step to the next component [10]. Here, we employ the local classifier per level approach, which involves training one multi-class classifier for each level of the class hierarchy. The second structure is the independent structure. In this setting, as the name suggests, we do not consider the dependency of the decisions in the different dimensions of the output of the model. Instead, for each dimension, we train a multi-class classifier independently. Table 1 summarizes GS model statistics for training, validation and testing. The table documents the effect of limiting data to the time steps when there was actually a TMI in place or when a TMI had just terminated. This resulted in a more balanced distribution of the GS class(GS positive class)versus “No GS”(GS negative class), which might help the training process. While JFK and LGA follow very similar distributions, with 40% and 42% GS positive class respectively, EWR has proportionally fewer GS incidents at 28%. Our subsequent phase involves evaluating the performance of both hierarchical structure and independent structure using different state-of-the-art multi-class classifier models such as Random Forest, Decision Trees, K-nearest Neighbors, and Logistic Regression and forecast the duration and scope of the GSs.

Farzan Masrour Shalmani↗