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At least 721 records · Page 40

Correct Interpretations of ENDF-102 Definitions for Resonance Effects

My Uncle Willie circa 1600 wrote “What’s in a name; a rose by any other name would smell as sweet.” I fear in this case we have a somewhat similar problem in that we may be using the same word but are not using the same definition; specifically, the word Unresolved. The simplest physics definition as it applies to neutron resonances, is the energy point where we can no longer see/measure ALL – let me repeat that – ALL - of the individual resonances. That seems simple and clear, but the question is: how to represent resonances beyond this point in order to accurately reproduce the effects we have seen in measurements and expect/need to reproduce in our applications. We know there are more, unseen resonances, otherwise we wouldn’t say Unresolved. The ENDF approach is well defined in ENDF-102 and simple: for ENDF data the only way to represent Unresolved data is by using a theoretical model to define the distribution of resonances, including those that are too narrow to measure (i.e., are unresolved). It is important to note that in ENDF this is the one and only Unresolved model, e.g., there is no provision in ENDF to accurately define individually ALL resonances above the Resolved energy range – by ALL here I mean both those that we can measure and those that we cannot individually measure, but that theory and integral measurements tells us are present. An alternative approach, which would appear to be equally valid, would be to include the latest measured data as tabulated energy expendent data extending upwards in energy above the Resolved energy range. In this approach the evaluation would not include an ENDF style Unresolved energy range; it would only include a Resolved resonance region, followed by tabulated higher energy points, representing the resonances that could be measured beyond the Resolved range. But an important point to note: By listing these resonances above the resolved energy one admits that at least some resonances in this energy range are missing as Unresolved; i.e., they are too narrow or overlapping to measure. The purpose of this paper is to illustrate that the later approach, while done with good intentions, and appearing to be valid/adequate in plots, does not meet the need of our engineering applications. Why? As we will see below, of these two possible approaches, only the ENDF use of a model to statistically include the missing, i.e., unresolved, resonances, can meet our engineering needs to reproduce the integral effects we have measured and understand. Only with this statistical model can we predict and include in our calculated results the important effects of temperature (Doppler broadening), and energy integrals (self-shielding). Below I will first present results using two ENDF/B-VIII.1 evaluations, U235 and U238, that use the correct ENDF-102 definition of an Unresolved resonance region, using a statistical model to include the effects of resonances that theory predicts are present, but are too narrow to measure. These two evaluations reproduce the expected temperature (Doppler) and energy integral (self-shielding) effects that we expect. Next I will present results using one ENDF/B-VIII.1 evaluation, 26-Fe-56, that does not use an ENDF-102 Unresolved resonance region; instead above its Resolved energy range it lists many tabulated energy points, that look like measured data, but by definition, since they are included above the ENDF Resolved energy range there are missing Unresolved resonances, i.e., there are missing the resonances that are too narrow to resolve, i.e., are unresolved. My conclusion, and I hope yours, is that the below figures illustrate that this approach does not reproduce the temperature and energy integrals that we expect and need to accurately calculate results for our fission reactor calculations. As such this approach should not be used in ENDF formatted evaluations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

AmeriFlux FLUXNET-1F US-UMd UMBS Disturbance

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-UMd UMBS Disturbance. This is the FLUXNET version of the carbon flux data for the site US-UMd UMBS Disturbance produced by applying the standard ONEFlux (1F) software. Site Description - The UMBS Disturbance site is an artificial disturbance site that has recently been created as part of the Forest Accelerate Succession ExperimenT (FASET). In Spring 2008, every aspen and birch tree (>6,700, ~35% canopy LAI), the dominant early successional trees, were girdled over 39 ha of the FASET treatment plot to stimulate a disturbance that will move the forest into a later successional stage, dominated by maples, oaks, and white pine. This treatment caused aspen and birch mortality within 2 - 3 years. As a result of the changed canopy structure, there is a divergence in net ecosystem exchange between the control plot (enhanced carbon uptake) and the treatment plot (reduced carbon uptake).

Classen, Aimee↗

Unitary Bethe-Salpeter Methods in Two- and Three-Body Systems

The study of resonances, unstable particles formed in particle scattering, is motivated by the questions about the strong interaction and the composition of hadrons. In order to advance this study in the intermediate energy region, a variety of techniques are used. In this thesis, we present work done on two different analyses that use the principle of unitarity and the Bethe-Salpeter equation to study the resonances Lambda(1405), Sigma(1385), and a1(1260). Firstly, we perform a simultaneous analysis of Sand P-waves of the Strangeness = -1 two-body meson-baryon scattering amplitude using all low-energy data. For the first time, differential cross section data are included for chiral unitary coupled-channel models. From this model, S- and P-wave amplitudes are extracted and we observe both well-known I(JP)=0(1/2^-) S-wave states as well as a new I(JP)=1(1/2^+) state absent in quark models and lattice QCD results. Multiple statistical and phenomenological tests suggest that, while the data clearly require an I =1 P-wave resonance, the new state just accounts for the absence of the decuplet Sigma(1385)3/2+ in the model which is subsequently included in the parameterization. Secondly, we formulate the final state interaction of the a1(1260) resonance decay in a manifestly three-body-unitary parameterization and fit it to the a1(1260) lineshape measured by the ALEPH experiment. Dalitz plots calculated from this fit are presented. The work demonstrates the feasibility to numerically solve a previously derived amplitude and its generalization to isobars with spin and coupled channels. The model is a good test case because it can also be applied to other meson decays including exotic states and modified for the finite-volume problem as it arises in lattice QCD due to its manifest unitarity. The understanding of the resonances being analyzed in both the two-body work and the three-body work gives a better understanding of intermediate energy QCD.

Sadasivan, Daniel↗

Data for Soil Fertility Management for Sustainable Miscanthus × giganteus Production: Increased Tiller Weight from Nitrogen Management Explains Yield Gains in Aged Miscanthus

Aging-related yield decline in Miscanthus × giganteus (miscanthus) remains a major constraint to sustainable biomass production. This study evaluated how nitrogen (N) management and soil fertility influence yield-component traits and productivity in aging miscanthus. Trials were conducted at two sites established in 2008 at the University of Illinois Energy Farm, Urbana, IL. (i) The Sun Grant trial received 0, 60, and 120 kg N ha−1 annually until 2015. Starting 2021, half of each plot received 60 or 120 kg N ha−1, resulting in six legacy-contemporary treatments: 0N–0N, 0N–120N, 60N–0N, 60N–60N, 120N–0N, 120N–120N. (ii) The Energy Farm trial remained unfertilized until 2014, when one half of each plot received 56 kg N ha−1, forming two treatments: 0N–0N, 0N–56N. Sun Grant trial results showed N fertilization increased tiller density (tillers m−2) and tiller weight (g tiller−1) in juvenile to early-mature miscanthus (2011–2015). After N withdrawal, both traits declined (20 % and 40 %), though legacy effects persisted in tiller weight in the aging stands (2020–2023). Contemporary N had little effect on tiller density but increased tiller weight by 34 %–77 %, resulting in 23 %–106 % higher machine-harvested biomass yield in 0–120N, 60-60N, and 120-120N plots. At the Energy Farm trial, 0N–56N plots yielded 59 %–108 % more biomass than 0N–0N. Soil total N increased (Sun Grant: 47 % by 2020; Energy Farm: 58 % by 2023), while Mehlich-3 P (42 %–44 %) and K (21 %–46 %) declined. These findings identify tiller weight as a key determinant of biomass yield in aging miscanthus and highlight the need for P and K management for long-term productivity.

miscanthus↗

Bootstrapping a stress-tensor form factor through eight loops

We bootstrap the three-point form factor of the chiral stress-tensor multiplet in planar $\mathcal{N}$ = 4 supersymmetric Yang-Mills theory at six, seven, and eight loops, using boundary data from the form factor operator product expansion. This may represent the highest perturbative order to which multi-variate quantities in a unitary four-dimensional quantum field theory have been computed. In computing this form factor, we observe and employ new restrictions on pairs and triples of adjacent letters in the symbol. We provide details about the function space required to describe the form factor through eight loops. Plotting the results on various lines provides striking numerical evidence for a finite radius of convergence of perturbation theory. By the principle of maximal transcendentality, our results are expected to give the highest weight part of the gg → Hg and H → ggg amplitudes in the heavy-top limit of QCD through eight loops. These results were also recently used to discover a new antipodal duality between this form factor and a six-point amplitude in the same theory.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Distances to Prompt Effects for a Nuclear Device

In 2010, nuclear weapon effects experts at Sandia National Laboratories (SNL) were asked to provide a quick reference document containing estimated prompt nuclear effects. This report is an update to the 2010 document that includes updated model assumptions. This report addresses only the prompt effects associated with a nuclear detonation (e.g., blast, thermal fluence, and prompt ionizing radiation). The potential medium- and longer-term health effects associated with nuclear fallout are not considered in this report because, in part, of the impracticality of making generic estimates given the high dependency of fallout predictions on the local meteorological conditions at the time of the event. The results included in this report also do not consider the urban environment (e.g., shielding by or collapse of structures) which may affect the extent of prompt effects. It is important to note that any operational recommendations made using the estimates in this report are limited by the generic assumptions considered in the analysis and should not replace analyses made for a specific scenario/device. Furthermore, nuclear effects experts (John Hogan, SNL, and Byron Ristvet, Defense Threat Reduction Agency (DTRA)) have indicated that the accuracy of effects predictions below 0.5 kilotons (kT) or 500 tons nuclear yield have greater uncertainty because of the limited data available for the prompt effects in this regime. The Specialized Hazard Assessment Response Capability (SHARC) effects prediction tool was used for these analyses. Specifically, the NUKE model within SHARC 2021 Version 10.2 was used. NUKE models only the prompt effects following a nuclear detonation. The algorithms for predicting range-to-output data contained within the NUKE model are primarily based on nuclear test effects data. Probits have been derived from nuclear test data and the U.S. Environmental Protection Agency (EPA) protective action guides. Probits relate the probability of a hazard (e.g., fatality or injury) caused by a given insult (e.g., overpressure, thermal fluence, dose level). Several probits have been built into SHARC to determine the fatality and injury associated with a given level of insult. Some of these probits differ with varying yield. Such probits were used to develop the tables and plots in this report.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

A nomogram for prediction of stage III/IV gastric cancer outcome after surgery: A multicenter population‐based study

Abstract Most patients with gastric cancer (GC) are first diagnosed at stage III‐IV and surgery resection remains the primary therapeutic modality for these patients. However, clinical staging used for prediction of those patients provides limited information. We collected clinicopathological data and disease‐progression information from 508 patients with stage III‐IV GC at three Chinese hospitals and 1298 patients from the Surveillance, Epidemiology, and End Results database. Based on the stepwise multivariate regression model, we constructed a novel nomogram to predict overall survival (OS). The performance of discrimination for this model was measured using Harrell's concordance index (C‐index) and receiver‐operating characteristic curve (ROC), and was validated using calibration plots. Multivariate Cox regression analyses showed that tumor size, age at diagnosis, N stage, tumor grade, and distant metastases were outstanding independent prognostic factors of stage III‐IV GC. We developed a nomogram based on these five prognostic predictors. In the training set, the C‐index of the nomogram was 0.645 (95% CI: 0.611‐0.679), which was higher than that of the American Joint Committee on Cancer TNM system alone (sixth TNM: 0.544; seventh TNM: 0.575; eighth TNM: 0.568). Similar results were observed in validation cohort. Moreover, calibration blots demonstrated good consistency between the actual and predicted OS probabilities. According to the nomogram, GC individuals could be classified into three groups (low‐, middle‐, and high‐risk) ( P < .001). Our nomogram complements the current staging system for prediction of individual prognosis with stage III‐IV GC, and may be helpful for making individualized treatment decisions.

Gao, Zhiying↗

AI-powered topic modeling: comparing LDA and BERTopic in analyzing opioid-related cardiovascular risks in women

Topic modeling is a crucial technique in natural language processing (NLP), enabling the extraction of latent themes from large text corpora. Traditional topic modeling, such as Latent Dirichlet Allocation (LDA), faces limitations in capturing the semantic relationships in the text document although it has been widely applied in text mining. BERTopic, created in 2022, leveraged advances in deep learning and can capture the contextual relationships between words. In this work, we integrated Artificial Intelligence (AI) modules to LDA and BERTopic and provided a comprehensive comparison on the analysis of prescription opioid-related cardiovascular risks in women. Opioid use can increase the risk of cardiovascular problems in women such as arrhythmia, hypotension etc. 1,837 abstracts were retrieved and downloaded from PubMed as of April 2024 using three Medical Subject Headings (MeSH) words: “opioid,” “cardiovascular,” and “women.” Machine Learning of Language Toolkit (MALLET) was employed for the implementation of LDA. BioBERT was used for document embedding in BERTopic. Eighteen was selected as the optimal topic number for MALLET and 23 for BERTopic. ChatGPT-4-Turbo was integrated to interpret and compare the results. The short descriptions created by ChatGPT for each topic from LDA and BERTopic were highly correlated, and the performance accuracies of LDA and BERTopic were similar as determined by expert manual reviews of the abstracts grouped by their predominant topics. The results of the t-SNE (t-distributed Stochastic Neighbor Embedding) plots showed that the clusters created from BERTopic were more compact and well-separated, representing improved coherence and distinctiveness between the topics. Our findings indicated that AI algorithms could augment both traditional and contemporary topic modeling techniques. In addition, BERTopic has the connection port for ChatGPT-4-Turbo or other large language models in its algorithm for automatic interpretation, while with LDA interpretation must be manually, and needs special procedures for data pre-processing and stop words exclusion. Therefore, while LDA remains valuable for large-scale text analysis with resource constraints, AI-assisted BERTopic offers significant advantages in providing the enhanced interpretability and the improved semantic coherence for extracting valuable insights from textual data.

Research & Experimental Medicine↗

Neurosensory and Sinus Evolution as Tyrannosauroid Dinosaurs Developed Giant Size: Insight from the Endocranial Anatomy of Bistahieversor sealeyi

Tyrannosaurus rex and other tyrannosaurid dinosaurs were apex predators during the latest Cretaceous, which combined giant size and advanced neurosensory systems. Computed tomography (CT) data have shown that tyrannosaurids had a trademark system of a large brain, large olfactory bulbs, elongate cochlear ducts, and expansive endocranial sinuses surrounding the brain and sense organs. Older, smaller tyrannosauroid relatives of tyrannosaurids developed some, but not all, of these features, raising the hypothesis that tyrannosaurid-style brains evolved before the enlarged tyrannosaurid-style sinuses, which might have developed only with large body size. This has been difficult to test, however, because little is known about the brains and sinuses of the first large-bodied tyrannosauroids, which evolved prior to Tyrannosauridae. Here we present the first CT data for one of these species, Bistahieversor sealeyi from New Mexico. Bistahieversor had a nearly identical brain and sinus system as tyrannosaurids like Tyrannosaurus, including a large brain, large olfactory bulbs, reduced cerebral hemispheres, and optic lobes, a small tab-like flocculus, long and straight cochlear ducts, and voluminous sinuses that include a supraocciptal recess, subcondyar sinus, and an anterior tympanic recess that exits the braincase via a prootic fossa. When characters are plotted onto tyrannosauroid phylogeny, there is a two-stage sequence in which features of the tyrannosaurid-style brain evolved first (in smaller, nontyrannosaurid species like Timurlengia), followed by features of the tyrannosaurid-style sinuses (in the first large-bodied nontyrannosaurid tyrannosauroids like Bistahieversor). This suggests that the signature tyrannosaurid sinus system evolved in concert with large size, whereas the brain did not.

59 BASIC BIOLOGICAL SCIENCES↗

Aragonite saturation horizon variability along North Pacific seamounts and implications for deep-sea coral reefs

The 2014 discovery of living deep-sea coral reefs along the Northwest Hawaiian Islands (NWHI) and lower Emperor Seamount Chain (ESC), despite the North Pacific’s shallow aragonite saturation horizon (ASH) and high CaCO3 dissolution rates, underscores the need to understand the local seawater chemistry that allows these reefs to persist. We investigated seawater carbonate chemistry using discrete samples along the NWHI and ESC from two cruises ~1 year apart (08/26/21 – 09/26/21, 09/09/22 – 10/24/22). Across the two cruises, ASH depth difference ranged from 15 to 77 m. Since the Pacific ASH shoals by 1–2 m yr?¹, this long-term trend cannot explain the magnitude of ASH change observed between cruises. Temperature-salinity plots similarly indicate no major shifts in intermediate water masses that could account for these changes. Instead, ASH depth variability was primarily governed by localized biogeochemical processes, namely changes in intermediate water respiration and CaCO3 dissolution. Indicators for dissolution (TA*) and respiration (AOU) suggest changes in ASH depth were driven by changes in dissolution at the northern- and southern-most sites, whereas respiration exerted stronger control at central sites. Combining 2021 and 2022 data with data from 2014 – 2019 (excluding 2018) revealed high interannual ASH variability, by as much as >200 m at one site. Deep-sea coral reefs across the NWHI and ESC currently reside close to the ASH depth and likely experience seasonal and interannual shifts between under- and supersaturation. As ocean acidification progresses however, persistent exposure to undersaturated seawater could further threaten these critical deep-sea ecosystems.

coral reefs↗

16S and ITS Amplicon Sequencing Fastq files and metadata from PARCHED Panama Tropical Forest soils, 2019-2020,

Model projections predict tropical forests will experience longer periods of drought and more intense precipitation cycles under a changing climate. Such transitions have implications for structure-function relationships within microbial communities. We examine how chronic drying might reshape prokaryotic and fungal communities across four lowland forests in Panama with a wide variation in mean annual precipitation and soil fertility. Four sites were established across a 1000 mm span in mean annual precipitation (2335 to 3300 mm). We expected microbial communities at sites with lower MAP to be less sensitive to chronic drying than sites with higher MAP; while fungal communities to be more resistant to disturbance than prokaryotes. At each location, partial throughfall exclusion structures were established over 10 x 10 m plots to reduce direct precipitation input. Raw demultiplexed sequences (bacteria, archaea, fungal) from soil samples taken from PARCHED Panama Tropical Forest throughfall exclusion experiments. Files that contain 16S are sequences from prokaryotes, ITS indicates sequences from fungi. Compressed fastq files are contained in Field_PARCHED_ITS_fastq_2020.zip, Field_PARCHED_ITS_fastq_2019.zip, Field_PARCHED_16S_fastq_2020.zip, Field_PARCHED_16S_fastq_2019.zip.There are four sites across the isthmus of Panama, each with 4 control and 4 exclusion plots. Throughfall exclusion shelters were built to intercept 50% of throughfall precipitation that hits the soil. Samples were taken on May 2019 and Jan 2020 from 0-10 cm and 10-20 cm depth approximately 9 and 18 months after shelter installation. Metadata and sample IDs for fastq files for 2019 sampling are within Field_PARCHED_Metadata_2019_ITS.csv and Field_PARCHED_Metadata_2019_16S.csv. The metadata for both 16S and ITS fastq files for January 2020 is included in Field_PARCHED_Metadata_2020.csv. No data processing or QA/QC was done on the raw data. Data processing example provided in R notebook file.

54 ENVIRONMENTAL SCIENCES↗

Data from: No‐till establishment improves the climate benefit of bioenergy crops on marginal grasslands

Expanding biofuel production is expected to accelerate the conversion of unmanaged marginal lands to meet biomass feedstock needs. Greenhouse gas production during conversion jeopardizes ensuing climate benefits, but most research to date has focused only on conversion to annual crops and only following tillage. Here we report the global warming impact of converting USDA Conservation Reserve Program (CRP) grasslands to three types of bioenergy crops using no-till (NT) versus conventional tillage (CT). In three CRP fields planted to continuous corn, switchgrass, or restored prairie we established replicated NT and CT plots. For the two years following an initial soybean year in all fields, we found that, on average, NT conversion reduced nitrous oxide (N2O) emissions by 50% and carbon dioxide (CO2) emissions by 20% compared to CT conversion. Differences were higher in year 1 than in year 2 in the continuous corn field, and in the two perennial systems the differences disappeared after year 1. In all fields net CO2 emissions (as measured by eddy covariance) were positive for the first two years following CT establishment, but following NT establishment net CO2 emissions were close to zero or negative, indicating net C sequestration. Overall, NT improved the global warming impact of biofuel crop establishment following CRP conversion by over 20-fold compared to CT (-6.01 Mg CO2e ha-1 yr-1 for NT vs. -0.25 Mg CO2e ha-1 yr-1 for CT, on average). We also found that IPCC estimates of N2O emissions (as measured by static chambers) greatly underestimated actual emissions for converted fields regardless of tillage. Policies should encourage adoption of NT for converting marginal grasslands to perennial bioenergy crops in order to reduce carbon debt and maximize climate benefits.

09 BIOMASS FUELS↗

Ion Mobility – Mass Spectrometry Rapid Imaging of Special Nuclear Materials

Robot Nose will use new fast data throughput methods and experience with laser microfocus to dramatically improve the speed and spatial resolution of an established instrument, making it a useful tool for imaging special nuclear materials (SNM). Mass spectrometry imaging instruments have traditionally been too slow and mass alone is generally an insufficient measurement for organic analyses. This situation was markedly improved by Ionwerks Inc., who pioneered the combination of ion mobility with mass spectrometry imaging. In 2D mobility-mass plots, clearly identifiable trend lines can be selected and reduced to 1D mass spectra without isobaric interferences. This is a major advantage over other imaging mass spectrometers that generally cannot distinguish isobars without custom-built lasers or high voltage accelerators. Special nuclear material (SNM) contains substantial fissile isotopes, particularly 233U, 235U, and 239Pu. A complete forensic analysis of SNM therefore requires quantitative isotopic measurement – often through some form of mass spectrometry. SNM contaminated with inclusions such as pollen grains can help identify its prior locations. The project team is presently working on an approach to allow rapid screening of 1-3 cm diameter thin samples of such material.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Interdependence in active mobility adoption: Joint modeling and motivational spillover in walking, cycling and bike-sharing

Active mobility offers an array of physical, emotional, and social well-being benefits. However, with the proliferation of the sharing economy, new nonmotorized means of transport are entering the fold, complementing some existing mobility options while competing with others. The purpose of this research study is to investigate the adoption of three active travel modes—namely walking, cycling, and bikesharing—in a joint modeling framework. Here, the analysis is based on an adaptation of the stages of change framework, which originates from the health behavior sciences. Multivariate ordered probit modeling drawing on U.S. survey data provides well-needed insights into individuals’ preparedness to adopt multiple active modes as a function of personal, neighborhood, and psychosocial factors. The research suggests three important findings. (1) The joint model structure confirms interdependence among different active mobility choices. The strongest complementarity is found for walking and cycling adoption. (2) Each mode has a distinctive adoption path with either three or four separate stages. We discuss the implications of derived stage-thresholds and plot adoption contours for selected scenarios. (3) Psychological and neighborhood variables generate more coupling among active modes than individual and household factors. Specifically, identifying strongly with active mobility aspirations, experiences with multimodal travel, possessing better navigational skills, along with supportive local community norms are the factors that appear to drive the joint adoption decisions. This study contributes to the understanding of how decisions within the same functional domain are related and help to design policies that promote active mobility by identifying positive spillovers and joint determinants.

42 ENGINEERING↗

SPRUCE: Shrub Leaf and Stem Functional Traits from 10-year Shrub Layer Biomass Harvests (August 2025)

This data set contains Leaf Mass Area (LMA), Specific Leaf Area (SLA), Leaf Area Index (LAI), and Huber value (Hv) measurements from the 10-year Shrub-layer Biomass harvests in the Spruce and Peatland Responses Under Environmental Change (SPRUCE) experiment in August 2025. The total ground-level cross-sectional sapwood area of Chamaedaphne calyculata (CHCA), Rhododendron groenlandicum (RHGR), and Vaccinium angustifolium (VAAN) were calculated for each of the three shrub-layer community survey plots located in each experimental enclosure. Representative current-year leaves were removed, scanned, dried, and weighed to derive SLA. Grab-samples for VAAN were used to calculate SLA when no biomass was harvested in the shrub-layer community plots. These SLA values were used to infer total one-sided leave surface area from the total species lead dry mass for calculation of LAI and Hv.

Birkebak, Joshua [ORNL] (ORCID:0009000955611494)↗

Deep learning methods for drug response prediction in cancer: Predominant and emerging trends

Cancer claims millions of lives yearly worldwide. While many therapies have been made available in recent years, by in large cancer remains unsolved. Exploiting computational predictive models to study and treat cancer holds great promise in improving drug development and personalized design of treatment plans, ultimately suppressing tumors, alleviating suffering, and prolonging lives of patients. A wave of recent papers demonstrates promising results in predicting cancer response to drug treatments while utilizing deep learning methods. These papers investigate diverse data representations, neural network architectures, learning methodologies, and evaluations schemes. However, deciphering promising predominant and emerging trends is difficult due to the variety of explored methods and lack of standardized framework for comparing drug response prediction models. To obtain a comprehensive landscape of deep learning methods, we conducted an extensive search and analysis of deep learning models that predict the response to single drug treatments. A total of 61 deep learning-based models have been curated, and summary plots were generated. Based on the analysis, observable patterns and prevalence of methods have been revealed. This review allows to better understand the current state of the field and identify major challenges and promising solution paths.

60 APPLIED LIFE SCIENCES↗

Vegetation Warming Experiment: Chamber and ambient plot digital camera imagery for vegetation phenology, Utqiagvik (Barrow), Alaska, 2021

Time lapse photography of experimental plots within five warming chambers (ZPWs) and paired control plots located on the Barrow Environmental Observatory (BEO), Utqiagvik, Alaska. Images were recorded from 17 June to 19 September, 2021 to capture vegetation dynamics during the growing season. Vegetation phenology, including green up and senescence were captured. Images were recorded daily at 30 minute intervals, from 09:00 - 16:30 Alaska daylight time (AKDT, UTC-8), using Wingscapes TimelapseCam Pro cameras. The target species was Carex aquatilis. Individual jpg images from each camera have been combined in zip format. The data package includes a metadata document with example fields of view from each camera (*.pdf). 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).

54 ENVIRONMENTAL SCIENCES↗

HIResist: a database of HIV-1 resistance to broadly neutralizing antibodies

Changing the course of the human immunodeficiency virus type I (HIV-1) pandemic is a high public health priority with approximately 39 million people currently living with HIV-1 (PLWH) and about 1.5 million new infections annually worldwide. Broadly neutralizing antibodies (bnAbs) typically target highly conserved sites on the HIV-1 envelope glycoproteins (Envs), which mediate viral entry, and block the infection of diverse HIV-1 strains. But different mechanisms of HIV-1 resistance to bnAbs prevent robust application of bnAbs for therapeutic and preventive interventions. Here we report the development of a new database that provides data and computational tools to aid the discovery of resistant features and may assist in analysis of HIV-1 resistance to bnAbs. Bioinformatic tools allow identification of specific patterns in Env sequences of resistant strains and development of strategies to elucidate the mechanisms of HIV-1 escape; comparison of resistant and sensitive HIV-1 strains for each bnAb; identification of resistance and sensitivity signatures associated with specific bnAbs or groups of bnAbs; and visualization of antibody pairs on cross-sensitivity plots. The database has been designed with a particular focus on user-friendly and interactive interface. Our database is a valuable resource for the scientific community and provides opportunities to investigate patterns of HIV-1 resistance and to develop new approaches aimed to overcome HIV-1 resistance to bnAbs.

60 APPLIED LIFE SCIENCES↗