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A machine learning approach for identifying variables associated with risk of developing neutralizing antidrug antibodies to factor VIII

A key unmet need in the management of hemophilia A (HA) is the lack of clinically validated markers that are associated with the development of neutralizing antibodies to Factor VIII (FVIII) (commonly referred to as inhibitors). This study aimed to identify relevant biomarkers for FVIII inhibition using Machine Learning (ML) and Explainable AI (XAI) using the My Life Our Future (MLOF) research repository. The dataset includes biologically relevant variables such as age, race, sex, ethnicity, and the variants in the F8 gene. In addition, we previously carried out Human Leukocyte Antigen Class II (HLA-II) typing on samples obtained from the MLOF repository. Using this information, we derived other patient-specific biologically and genetically important variables. These included identifying the number of foreign FVIII derived peptides, based on the alignment of the endogenous FVIII and infused drug sequences, and the foreign-peptide HLA-II molecule binding affinity calculated using NetMHCIIpan. The data were processed and trained with multiple ML classification models to identify the top performing models. The top performing model was then chosen to apply XAI via SHAP, (SHapley Additive exPlanations) to identify the variables critical for the prediction of FVIII inhibitor development in a hemophilia A patient. Using XAI we provide a robust and ranked identification of variables that could be predictive for developing inhibitors to FVIII drugs in hemophilia A patients. These variables could be validated as biomarkers and used in making clinical decisions and during drug development. The top five variables for predicting inhibitor development based on SHAP values are: (i) the baseline activity of the FVIII protein, (ii) mean affinity of all foreign peptides for HLA DRB 3, 4, & 5 alleles, (iii) mean affinity of all foreign peptides for HLA DRB1 alleles), (iv) the minimum affinity among all foreign peptides for HLA DRB1 alleles, and (v) F8 mutation type.

60 APPLIED LIFE SCIENCES↗

UAS remote sensing (Osprey platform): Red-green-blue (RGB) imagery, thermal infrared (TIR) imagery, and canopy reflectance, Seward Peninsula, Alaska, 2017

Airborne remote sensing data collected using the Brookhaven National Laboratory's (BNL) heavy-lift unoccupied aerial system (UAS) octocopter platform - the Osprey - operated by the Terrestrial Ecosystem Science and Technology (TEST) group (https://www.bnl.gov/testgroup). This package includes raw (L0) data from 14 flights flown over the NGEE-Arctic Council Mile Marker 71 (MM71), Kougarok MM64, and Teller MM 27 sites in August, 2017. The Osprey is a multi-sensor UAS platform that simultaneously measures very high spatial resolution optical red/green/blue (RGB) and thermal infrared (TIR) surface "skin" temperature imagery, as well as near-surface surface reflectance at 1 nm intervals in the visible to near-infrared spectral range from ~350-1000 nm measured at regular intervals along each flight path. This package provides the Level 0 (raw, unprocessed) data collected by the Osprey platform. Ancillary aircraft data, flight mission parameters, and general flight conditions provided by the onboard flight and data collection computers are also included. Data and metadata are provided as text (*.txt, *.json), tabular (*.dat, *.csv, *.waypoint), and image (*.jpg) formats. This metadata documents contain flight campaign, platform, sensor, flight and file metadata, along with a description of the L0 data and the file naming scheme. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a 15-year research effort (2012-2027) 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↗

All-Optical Micro Motors Based on Moving Gratings in Photosensitive Media

This research effort was a feasibility study of the concept of an all-optical micro motor with a rotor driven by a traveling wave. The wave was a result of a photo induced surface deformation of a photosensitive material produced by a traveling holographic grating. Two phases modulated coherent optical beams were used to generate the grating in two types of photosensitive materials. The materials that were studied were photorefractive crystals and thin polymer films. Theoretical studies were performed on lithium niobate giving predictions of deformations of the order of nanometers. The experimental deformation size was also on the order of nanometers. The deformations were deep enough to provide conditions for the implementation of the all-optical motor using lithium niobate. We also were able to align micron-size dielectric particles along the holographic gratings by means of the periodic electric forces generated by the grating. These forces can also move the particles along the surface if the grating is moving. We then turned our attention on thin films and obtained a deformation visible on the order of 100 microns. An experimental breadboard demonstration of a prototype was done in the summer of 2001 at Glenn Research Center (GRC). The demonstration included the movement of clocks mechanical workings by an optically driven motor based on a polymer film. The application of this technology can be adapted to government as well as industrial uses. One such project is to make a chemical sensor for the detection of hazardous chemicals. The thin polymer film is highly suited for this purpose since a marker dye could be easily placed on the film in order to detect chemical compounds. This system could be a self-regulating chemical monitoring system used on launches of the space shuttle or locations where hazardous chemicals are present. The project provided support for two black minority graduate students targeting MS and PhD degrees in Applied Optics.

Adamovsky, Gregory↗

ESI-FTICR-MS Analysis of Organic Matter during Incubations with Nitrogen Addition, Teller Road Site, Seward Peninsula, Alaska

This dataset contains the results of the molecular characterization of water-extractable organic matter collected during soil microcosm incubations of tundra soil. The microcosms contained soil collected in April 2017 from the NGEE Arctic Teller Road Site at mile marker 27 (TL_MM27) near Intensive Site 9 (“Toeslope”) and Intensive Site 5 (“Plateau”). The incubations were conducted under an atmosphere of N2 at 8°C for 55 days, with or without addition of ammonium chloride (NH4Cl). Soils were extracted with deionized water and extracted using Bond Elut PPL cartridges prior to analysis. Molecular characterization was performed using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI- FTICR-MS). Two data files are provided with this dataset. The first is the summary, by soil type and treatment, of the mass spectrometry results for formulas (as a % of the total) containing C, H, and O only, and with N, S, and other elements. These formulas were then grouped into nine biochemical classes of compounds based on O:C and H:C ratios. The second file provides soil sample characteristics and the processed high-resolution mass spectrometry results by soil type and treatment.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a 10-year research effort (2012-2022) 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↗

HEMODOSE: A Set of Multi-parameter Biodosimetry Tools

After the events of September 11, 2001 and recent events at the Fukushima reactors in Japan, there is an increasing concern of the occurrence of nuclear and radiological terrorism or accidents that may result in large casualty in densely populated areas. To guide medical personnel in their clinical decisions for effective medical management and treatment of the exposed individuals, biological markers are usually applied to examine the radiation induced changes at different biological levels. Among these the peripheral blood cell counts are widely used to assess the extent of radiation induced injury. This is due to the fact that hematopoietic system is the most vulnerable part of the human body to radiation damage. Particularly, the lymphocyte, granulocyte, and platelet cells are the most radiosensitive of the blood elements, and monitoring their changes after exposure is regarded as the most practical and best laboratory test to estimate radiation dose. The HEMODOSE web tools are built upon solid physiological and pathophysiological understanding of mammalian hematopoietic systems, and rigorous coarse-grained biomathematical modeling and validation. Using single or serial granulocyte, lymphocyte, leukocyte, or platelet counts after exposure, these tools can estimate absorbed doses of adult victims very rapidly and accurately. Some patient data in historical accidents are utilized as examples to demonstrate the capabilities of these tools as a rapid point-of-care diagnostic or centralized high-throughput assay system in a large scale radiological disaster scenario. Unlike previous dose prediction algorithms, the HEMODOSE web tools establish robust correlations between the absorbed doses and victim's various types of blood cell counts not only in the early time window (1 or 2 days), but also in very late phase (up to 4 weeks) after exposure

Hu, Shaowen↗

Digital camera imagery for vegetation phenology, Seward Peninsula, Alaska, 2022-2023

Timelapse camera images from Council Mile Marker (MM) 71, Kougarok MM 64, Kougarok Fire Complex (KFC), and Teller MM 27 NGEE-Arctic field sites on the Seward Peninsula, Alaska, captured from July 2022 to July 2023. Eight Wingscape Timelapse Pro cameras, and thirty-one Power-interval Camera Automation Modules (PiCAMs) designed by Brookhaven National Laboratory?s Terrestrial Ecosystem Science and Technology (TEST) group were deployed targeting patches of low and tall shrubs (including Alnus sp. and Salix sp.) and general vegetation and landscape views. Images from Wingscape cameras were recorded at hourly intervals from 11 AM to 2 PM, and images from PiCAMs were recorded at 5 hourly intervals from 12 AM to 8 PM, continuously for 12 months and capture vegetation phenology, snow accumulation and snow melt events. This data package includes images (*.jpg), organized by site and camera ID, and metadata with details of the cameras used, number of images recorded, start and end dates, GPS locations and example fields of view. 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↗

The cumulative cost of additional wakefulness: dose-response effects on neurobehavioral functions and sleep physiology from chronic sleep restriction and total sleep deprivation

OBJECTIVES: To inform the debate over whether human sleep can be chronically reduced without consequences, we conducted a dose-response chronic sleep restriction experiment in which waking neurobehavioral and sleep physiological functions were monitored and compared to those for total sleep deprivation. DESIGN: The chronic sleep restriction experiment involved randomization to one of three sleep doses (4 h, 6 h, or 8 h time in bed per night), which were maintained for 14 consecutive days. The total sleep deprivation experiment involved 3 nights without sleep (0 h time in bed). Each study also involved 3 baseline (pre-deprivation) days and 3 recovery days. SETTING: Both experiments were conducted under standardized laboratory conditions with continuous behavioral, physiological and medical monitoring. PARTICIPANTS: A total of n = 48 healthy adults (ages 21-38) participated in the experiments. INTERVENTIONS: Noctumal sleep periods were restricted to 8 h, 6 h or 4 h per day for 14 days, or to 0 h for 3 days. All other sleep was prohibited. RESULTS: Chronic restriction of sleep periods to 4 h or 6 h per night over 14 consecutive days resulted in significant cumulative, dose-dependent deficits in cognitive performance on all tasks. Subjective sleepiness ratings showed an acute response to sleep restriction but only small further increases on subsequent days, and did not significantly differentiate the 6 h and 4 h conditions. Polysomnographic variables and delta power in the non-REM sleep EEG-a putative marker of sleep homeostasis--displayed an acute response to sleep restriction with negligible further changes across the 14 restricted nights. Comparison of chronic sleep restriction to total sleep deprivation showed that the latter resulted in disproportionately large waking neurobehavioral and sleep delta power responses relative to how much sleep was lost. A statistical model revealed that, regardless of the mode of sleep deprivation, lapses in behavioral alertness were near-linearly related to the cumulative duration of wakefulness in excess of 15.84 h (s.e. 0.73 h). CONCLUSIONS: Since chronic restriction of sleep to 6 h or less per night produced cognitive performance deficits equivalent to up to 2 nights of total sleep deprivation, it appears that even relatively moderate sleep restriction can seriously impair waking neurobehavioral functions in healthy adults. Sleepiness ratings suggest that subjects were largely unaware of these increasing cognitive deficits, which may explain why the impact of chronic sleep restriction on waking cognitive functions is often assumed to be benign. Physiological sleep responses to chronic restriction did not mirror waking neurobehavioral responses, but cumulative wakefulness in excess of a 15.84 h predicted performance lapses across all four experimental conditions. This suggests that sleep debt is perhaps best understood as resulting in additional wakefulness that has a neurobiological "cost" which accumulates over time.

NASA Discipline Regulatory Physiology↗

Geophysical and Environmental Monitoring Data, Lower Watershed, Teller Road Mile Marker 27, Seward Peninsula, Alaska, 2017-2019

This data set contains geophysical and environmental monitoring data acquired between September 2017 and 2019 at the lower Teller watershed, Seward Peninsula, Alaska. Geophysical data comprises processed resistivity data, acquired daily between Spring and Fall of 2018 and 2019, and a baseline measurement of Fall 2017. The environmental monitoring data comprises depth resolved, distributed soil moisture and soil temperature data. These measurements were obtained used Decagon 5TE sensors placed at 0.1 m, 0.2 m , 0.3 m, and 0.4 m depth. In addition, temperature data at 0.5 m, 1.0 m, and 1.5 m were acquired using Hobo temperature sensors. Data were collected to improve our understanding of the hydrological response of discontinuous permafrost systems, in particular focusing on multi-annual dynamics and short term disturbances, such as snowmelt or precipitation events. The electrical resistivity tomography (ERT) monitoring data are included as processed resistivity models, with model cells x dimension equal to the distance along the profile, and model z dimension being elevation. The start and end point of the transect are (UTM Zone 3N): E 454881.66 m, N 7178949.45 m, and E 454772.60, N 7178885.81. Locations of the soil moisture and temperature sensors are provided in the data package. This dataset is discussed in detail in the Uhlemann, S. et al 2021 paper listed in the references. This dataset includes one *.pdf user guide and 315 *.csv data files included within four zipped files.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↗

An Updated Look at the Pro K Experiment: Urinary Acid Excretion Can Predict Changes in Bone Metabolism During Space Flight

Mitigating space flight-induced bone loss is critical for space exploration, and diet can play a major role in this effort (1). Previous ground-based studies provide evidence that dietary composition can influence bone resorption during bed rest (2). In this study we examined the role of dietary intake patterns as one factor that can influence bone mineral loss in astronauts during space flight. Crew members were asked to consume, for 4 days at a time, prescribed menus with either a low (0.3-0.6 g/mEq) or high (1.0-1.3 g/mEq) ratio of animal protein to potassium (APro:K). Menus were developed for each crewmember, and were designed to meet both crew preferences and study constraints. Intakes of energy, total protein, calcium, and sodium were held relatively constant between the two diets. The order of the menus was randomized, and crews completed each set (low and high) once before and twice during space flight, for a total of 6 controlled diet sessions. One inflight session and three postflight sessions (R+30, R+180, R+365) monitored typical dietary intake. As of this writing, data are available from 14 crew members. Two subject's samples are awaiting return from ISS via Space-X, and the final subject has one more collection session planned in November 2014. On the last day of each of the 4-d controlled diet sessions, 24-h urine samples were collected, along with a fasting blood sample on the morning of the 5th day. Preliminary analyses will show the relationships between diet and flight on markers of bone metabolism. The results from this study, which represent healthy individuals in a unique environment, will be important to better understand diet and bone interrelationships during space flight as well as on Earth. These data will be important as nutritional requirements and food systems are developed for future exploration-class missions. This study was funded by the Human Health Countermeasures Element of NASA Human Research Program.

Zwart, Sara R.↗

Surface elevation, snow depth, vegetation height, and color imagery from multiple UAV surveys from 2018 to 2023 across a watershed near Teller road mile marker 27, Seward Peninsula, Alaska

Multiple photogrammetric surveys using an unoccupied aerial system (UAS) were performed across a watershed along Teller road on the Seward Peninsula (Alaska) to investigate terrain, vegetation and snowpack properties. This work was led by the environmental geophysics team from Lawrence Berkeley National Laboratory as part of the Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic). The multiple photogrammetric surveys used mostly a DJI Matrice 210 UAS with a DJI X5S camera, Ground Control Points (GCPs) surveyed with a Real Time Kinematic (RTK)-GPS, and a structure from motion (SfM) technique for photogrammetric reconstruction. Digital Surface elevation Models (DSMs) were inferred at various times of year, including near peak in plant and leaf density (July 19 2017), close to peak in snow depth (April 1 2019 and April 11 2022), and at low plant and leaf density of tall after the first bare-ground date (June 9 2019). Snow and canopy height were obtained by subtracting DSMs from a Digital Terrain Model (DTM) proxy inferred from the June 9 2019 survey. The derived products include ortho-mosaiced RGB map, DSMs, a DTM proxy, snow depth (April 2019 and 2022) and canopy height (July 2017). Unprocessed and processed data products are included in this package (processing levels 0-2). Data and metadata are provided as text (*.csv), image (*.jpg), and GeoTiff (*.tif) formats. This metadata document contains a description of the survey and processing steps and the inferred products.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic) was a 15-year research effort (2012-2027) 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↗

iButton and Tinytag snow/ground interface temperature measurements at Teller 27 and Kougarok 64 from 2022-2023, Seward Peninsula, Alaska

Snow/ground interface temperature measurements were collected at the NGEE Arctic Teller Road Site at mile marker 27 (TL_MM27) and at the Kougarok Road Site at mile marker 64 (KG_MM64) on the Seward Peninsula, Alaska. Data were collected between October 1, 2022 to September 18, 2023 using iButton Link DS1921G-F5# Thermochron miniature temperature sensors (https://www.ibuttonlink.com/products/ds1921g) and Tinytag TGP-4017 internal sensors (https://www.micronmeters.com/product/tgp-4017-internal-sensor-40-to-85-c-40-f-to-185-f) deployed across the Kougarok and Teller sites. These sensors are a cost-efficient way to collect snowpack temperatures at a higher spatial resolution than what is normally achieved. iButton data were collected every 4 hours, while Tinytag data were collected every 30 minutes. In total, data were collected from 196 iButtons and 26 Tinytags. This dataset contains four *.csv files of near-ground surface temperatures at various locations throughout each study site and two *.kml files of sensor locations. Data were collected throughout the snow cover season so that snowpack characteristics could be derived using the temperature data. Sensors were placed both inside and outside of vegetation to better capture the spatial variability of snow properties across each domain.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic) was a 15-year research effort (2012-2027) 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↗

Shrub Seedling Experiment: Environmental Conditions, Vegetation Composition, and Seedling Recruitment, Seward Peninsula, Alaska, 2018-2019

In June 2018, a manipulative seed-addition experiment was established at the Council Mile Marker 71 (CN_MM71), Quartz Creek Burn Area (Kougarok Mile Marker 86), and Quartz Creek Unburned (Kougarok Mile Marker 80) sites on the Seward Peninsula, Alaska. At each site, 5 replicate blocks were established in disturbed and intact upland tussock tundra (a total of 40 plots). Disturbed plots at Council were located on thermo-erosional (thermokarst) slopes, while disturbed plots in Quartz Creek were in burned areas affected by the Mingvk Lake fire in 2015. Using a split-plot design, an additional manual disturbance treatment (scraping to remove the surface bryophyte layer) was implemented across all blocks in June 2018. Seeds of five erect, deciduous shrubs were broadcast seeded into each plot in June 2018, and seedlings were censused in August 2018 and August 2019. The dataset includes ancillary measurements of plot-level environmental conditions (soil temperature, moisture, chemistry, thaw depth, microtopography, substrate thickness) and vegetation composition (NDVI and estimated percent cover by species and plant functional type). Dataset contains 10 csv data files (five data files with corresponding data dictionaries and one file-level metadata file) and one pdf user guide. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was 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↗

Monitoring Airspace Complexity and Determining Contributing Factors

The national airspace has evolved over many years to accommodate increased traffic demand [1] while simultaneously maintaining one of the safest forms of transportation [2], [3]. One of the reasons for this success is the ability of the system and the operators to adapt and accommodate to situations that routinely disrupt optimal operations. These situations may include: adverse weather, delays, early arrivals, equipment outages, and other factors that are outside the operators ability to control. These factors can lead to states where automation is unable to properly handle these issues and therefore air traffic controllers and pilots have to intervene, ultimately increasing communication between operators resulting in higher workload. As controller workload increases to handle sub-optimal operating conditions this can be viewed as an increase in complexity. The reasoning for this is because humans are now required to make tactical decisions in response to external factors, resulting in a departure from the strategic plan where operations would be more efficiently managed. Human operators control airspace complexity under rigid regulations that are constantly changing. The airspace is divided into sectors and the number of aircraft assigned to each controller is limited for safe handling. There has been past work that devised airspace complexity metrics in commercial aviation and related these metrics to controller workload (e.g., [4],[5]). The upper bounds on the system load are pre-determined. Such bounds on complexity make for a safe system, but the system cannot scale and adapt to autonomous, dense, and heterogeneous traffic, including the many types of Unmanned Aerial Vehicles (UAVs) envisioned to be added to the operations. We hypothesize that, as traffic density and heterogeneity grow, and other key metrics change, there will be phase transitions at which the way traffic should be managed changes significantly [6]. We offer a method for in-time detection of contributing factors that lead to phase transitions, characterized by increased complexity. To the best of our knowledge, there is no tool similar to our proposed effort that identifies such contributing factors or precursor patterns. To define the scope we are proposing to measure complexity from the viewpoint of the Terminal Radar Approach Control Facilities (TRACON) controller’s perspective. In particular we are analyzing arrivals into KSFO. With safety as the top concern for airspace operators, it is important to recognize that as density and heterogeneity grow, the focus of the system will change. Times of the day when the airspace has low density and heterogeneity, the flights will follow more efficient paths where the aircraft move on established routes that are more or less directly to the destination. However, when density and heterogeneity increases, the system will begin changing focus to avoiding conflicts and collisions and route the flights in a more flexible way. Higher flexibility requires more communication and coordination between controllers and pilots which the current automation is unable to handle. This paper proposes a novel approach that monitors airspace complexity at multiple scales, uses a Machine Learning-based tool that predicts when operations will transition to a regime of greater complexity, and identifies actions that can reduce the complexity while still maintaining efficient and safe operations. We demonstrate our proposed approach using data from multiple complementary sources. This includes, but is not limited to: historical aircraft surveillance data from NASA’s Sherlock Data Warehouse [7], METAR weather data, and airport configuration data from Aviation System Performance Metrics (ASPM). The surveillance data flight paths are sampled at a variable sample rate — increasing as the aircraft approaches the airport. This is due to how Sherlock manages flight track stitching between different radar facilities which have different sampling rates. The weather and performance data are logged at defined intervals throughout the day at a courser refresh rate. In addition to the logged data and metrics, we leverage pre-defined Standard Terminal Arrival Routes (STARs) procedures to characterize the path of each flight. Each flight files for one of these routes in the flight plan well before entering the terminal airspace, and approximately follows the route until it leaves the STAR, typically on the final fix of a runway transition. However, most flights do not always fly the full STAR procedure to completion [8], but the majority do adhere to the fixes within the common route of the procedure. Our approach leverages fixes in the common route of each of the STARs to build a reference path to the airport. This allows us to characterize the flight paths in what we are defining as the “maneuvering area” (the airspace between the STAR and before the flight is lined up on the runway’s final approach) to determine how off nominal the flights are to calculate its complexity score. Determining airspace complexity is a concept that does not have a concrete answer. In designing this metric, we consider what increases the workload for the air traffic controllers. Consequently more specialized vectoring maneuvers results in higher workload. Accordingly, we start with a theory: each flight has a direct path it takes from the STAR’s common route to the final approach’s outer marker fix for the flight’s landing runway. It is important to note that the direct path is only used as a reference. If the majority of the flights have a large consistent offset as compared to other routes it does not necessarily mean that those flights have higher complexity. We are merely building a distribution based on this direct path for that particular STAR and runway pair to determine the normal mode of operations for that route. Flights that are in the upper tail of these distributions will result in higher complexity scores and flights that fly in the median will represent the normal mode of operations and therefore will have lower complexity scores. Since flights following each STAR route take different paths to the airport, we have a different distribution for each STAR route and therefore can model these distributions to compute a complexity score from their respective normalized distributions. To evaluate the effectiveness of our proposed airspace complexity metric we will compare against an established approach based on trajectory clustering [9]. This unsupervised learning technique consists of the following steps: (1) identify the general maneuvering areas (waypoints) by performing $\kappa$-means or DBSCAN clustering on locations where aircraft frequently turn based on the surveillance radar track data, (2) map flight trajectories onto sequences of waypoints, and (3) cluster the sequences based on their common subsequences. From a high-level perspective, this baseline model learns nominal operations in the airspace through the sequence of waypoints that are representative of where aircraft change direction and defines deviations from the nominal operations as “complex.” Therefore, more deviations from the nominal operations correspond to higher complexity values. For our validation, we re-implemented this technique and tune model hyper-parameters to correctly detect waypoints for the arrival traffic into the San Francisco bay area. We will compute the complexity measure over a one-year period using our proposed technique as well as the baseline. Our validation will be based on each technique’s ability to detect a set of undesirable outcomes (e.g., go-arounds, holding patterns, average time in the airspace, etc.). Since our current complexity metric is derived from the offset from the direct reference path, it’s important to understand what causes these offsets. In many of the flights with high offset distance, flights performing holding patterns and S turns can be observed. These maneuvering tactics are utilized to add distance between the aircraft and the destination runway to prevent multiple flights from having conflicting arrival times. In order to predict a rise in complexity (or the precursor to complexity), it’s necessary to be able to identify these potential conflicts (which in turn, result in higher offsets). To do this, we define a “representative flight” for each STAR route and runway pair. This flight is approximately the path the flight would take if there was a clear path with no other flights in the airspace — including the time remaining to the airport. We first identify the flights for a given STAR runway pair using the offset to the reference path distributions that fall between the 44-55 percentiles. This yields the flights that conform to the most normal mode of operation. Each of these flights is partitioned based on the percent complete from the entry point into the maneuvering areas from 0\% – 100\% complete. Then for each percent “bin”, we take the median value of the flight’s latitude/longitude coordinates, airspeed, and (non causal) time remaining to the airport to construct a lookup table for each percent complete bin on a given route. As a flight enters the maneuvering area, we can find the estimated arrival time of a flight to the airport by finding the closest point to the representative path’s percent complete bin (relative to the flight’s current position at any snapshot in the airspace) and therefore retrieve the corresponding remaining time left on the “representative path”. We assume that the flight will follow the representative path to completion when deriving these estimates. We can then compare these estimated arrival times against other flights for the same snapshot in time to identify potential conflicts. If more flights are estimated to arrive within a tolerance window than there are runways available, then we have a potential conflict. We can use this derived measure along with other factors expected to add disruption to the operation such as weather and runway configuration changes as an input to machine learning tools to detect precursors that increases in our complexity measure. This novel method will assist in uncovering insights into the contributing factors that lead to increased complexity that may allow for in-time responses to avoid reaching a high complexity state in the airspace.

complexity↗

DEM, DSM, and Cleaned LiDAR Point Cloud Data from the NGEE Arctic UAS Campaigns at the Teller 27 Field Site from 2017 and 2018, Seward Peninsula, Alaska

A Digital Elevation Model (DEM) and Digital Surface Model (DSM) were derived from airborne Light Detection and Ranging (LiDAR) data collected from Los Alamos National Laboratory's (LANL) heavy-lift unoccupied aerial system (UAS) quadcopter and hexacopter platforms operated by Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic) scientists from the EES-14 group at LANL. These data were collected in August 2017 and July 2018 at the NGEE Arctic field site near mile marker 27 of the Bob Blodgett Nome-Teller Memorial Highway between Nome, Alaska and Teller, Alaska. A Vulcan Raven X8 Airframe (Mitcheldean, Gloucestershire, UK), DJI Matrice 600 Pro Airframe (Shenzhen, China), and Routescene UAV LiDARSystem (Edinburgh, Scotland, UK) were used to collect LiDAR data. Following pre-processing in Routescene LidarViewer Pro software, the LiDAR point clouds were cleaned and processed using CloudCompare software to separate ground and off-ground points. A high resolution DEM and DSM were then created using ArcGIS Pro software. This data package contains fully cleaned point clouds of ground and off-ground points (.las), a 25 cm DEM (.tif), and a 25 cm DSM (.tif) for the Teller 27 field site. Ancillary aircraft data, flight mission parameters, weather conditions, and raw lidar data and imagery can be found in the L0 datasets for these campaigns: NGA299 (2017) and NGA297 (2018). Minimally processed point clouds and auxiliary files can be found in the L1 dataset: NGA304 (2017 and 2018).The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a 15-year research effort (2012-2027) 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↗

Subsidence Measurements at the Teller 27 Field Site, Seward Peninsula, Alaska, 2021

In September 2021, differential GPS (dGPS) points were collected in areas of visual subsidence in the Teller watershed near mile marker 27 of the Bob Blodgett Nome-Teller Memorial Highway on the Seward Peninsula of Alaska. This study aimed to understand how structural permafrost loss is affecting meter-scale ground elevation. As ice thaws, heaving and slumping of the landscape creates new microtopographical features on the landscape that may alter surface hydrology and soil moisture and thus plant community composition and biogeochemical cycling. The Teller 27 field site is underlain with discontinuous permafrost, so the landscape features a variety of permafrost features. We collected ground elevations from eight subsidence areas in two forms: 1) Transects were sampled laterally through areas of ground subsidence to capture the high edges and low spots where the earth slumped. 2) The circumference of the subsidence area was sampled in order to measure the ground area affected by subsidence. These data were collected with an Emlid Reach RS2 dGPS and a base station. This dataset includes one *.csv of dGPS locations of the eight subsidence locations and one *.kml of measurement locations.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic) was a 15-year research effort (2012-2027) 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↗

Digital camera imagery for vegetation phenology, Seward Peninsula, Alaska, 2021-2022

Timelapse camera images from Council Mile Marker (MM) 71, Kougarok MM 64, Kougarok Fire Complex (KFC, also referred to as the Garfield Fire Site), and Teller MM 27 NGEE-Arctic field sites on the Seward Peninsula, Alaska, captured from August 2021 to July 2022. Ten Wingscape Timelapse Pro cameras, and twenty seven Power-interval Camera Automation Modules (PiCAMs) designed by Brookhaven National Laboratory's Terrestrial Ecosystem Science and Technology (TEST) group were deployed targeting patches of low and tall shrubs (including Alnus sp. and Salix sp.) and general vegetation and landscape views. Images from Wingscape cameras were recorded at hourly intervals from 11 AM to 2 PM, and images from PiCAMs were recorded at 5 hourly intervals from 12 AM to 8 PM, continuously for 12 months and capture vegetation phenology, snow accumulation and snow melt events. This data package includes images (*.jpg), organized by site and camera ID, and metadata with details of the cameras used, number of images recorded, start and end dates, GPS locations and example fields of view. Additional information available in *.pdf and *.csv files. 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↗

Exploring Endothelial Function Risk Factors and Optic Disc Edema Changes During Strict 6º Head-Down Tilt Bed Rest

Approximately 20% of astronauts on International Space Station missions experience ophthalmic pathologies including optic disc edema, part of what is characterized as Spaceflight Associated Neuro-ocular Syndrome (SANS). While the cause of SANS is unknown, there are likely multiple contributing factors, including genetics, that may affect the response to spaceflight in affected individuals. B-vitamin status and the presence of specific one-carbon pathway single nucleotide polymorphism (SNP) alleles predicted the incidence of SANS pathologies in astronauts and in bed rest subjects. There are several hypotheses for how genetic variants could lead to SANS, specifically related to endothelial function. The biochemical pathway to which these genes are associated is intimately involved in maintaining endothelial function via nitric oxide synthase (eNOS) coupling and nitric oxide (NO) production. Furthermore, eNOS uncoupling can impair the functional status of the endothelial glycocalyx, which lines the entirety of the vascular lumen and affects endothelial function. Vascular distension, stasis and altered shear forces, which are associated with headward fluid shifts, may also contribute to glycocalyx dysfunction and shedding, resulting in endothelial dysfunction and increased vascular permeability and tissue edema, potentially contributing to optic nerve and optic disc edema in affected individuals. Given the findings relating genetics and the risk of optic disc edema in astronauts during flight and subjects during bed rest, further investigation is warranted. In this study, we will assess the same genetic variants in another bed rest study: AGBRESA. Some of the AGBRESA subjects developed optic disc edema, but their genetics have not been studied. Furthermore, we will test available urine samples from prior bed rest studies (VaPER and AGBRESA) for markers of glycocalyx degradation to expand our understanding of factors contributing to SANS.

S R Zwart↗

iButton and Tinytag snow temperature measurements at Teller 27 and Kougarok 64, Seward Peninsula, Alaska, 2021-2022

Snow temperature measurements were collected at the NGEE Arctic Teller Road Site at mile marker 27 (TL_MM27) and at the Kougarok Road Site at mile marker 64 (KG_MM64) on the Seward Peninsula. Data were collected from October 1, 2021 to August 16, 2022 using iButton Link DS1926-F5# Thermochron miniature temperature sensors (https://www.ibuttonlink.com/products/ds1921g) and Tinytag TGP-4017 internal sensors (https://www.micronmeters.com/product/tgp-4017-internal-sensor-40-to-85-c-40-f-to-185-f) deployed across the Kougarok and Teller sites. These sensors are a cost-efficient way to collect snowpack temperatures at a higher spatial resolution than what is normally achieved. iButton data were collected every 4 hours beginning on October 1, 2021. Tinytag data collection began between October 9 and October 12, 2021 depending on sensor installation date. Tinytag data were collected every 30 minutes. In total, data were collected from 236 iButtons and 30 Tinytags. This dataset contains four *.csv files of near-ground surface temperatures at various locations throughout each study site and four *.shp files of sensor locations. Data were collected throughout the snow cover season so that snowpack characteristics could be derived using the temperature data. Sensors were placed both inside and outside of vegetation to better capture the spatial variability of snow properties across each domain. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), 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↗