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At least 649 records · Page 36

Technology Assessment of High Capacity Data Storage Systems: Can We Avoid a Data Survivability Crisis?

In a recent address at the California Science Center in Los Angeles, Vice President Al Gore articulated a Digital Earth Vision. That vision spoke to developing a multi-resolution, three-dimensional visual representation of the planet into which we can roam and zoom into vast quantities of embedded geo-referenced data. The vision was not limited to moving through space, but also allowing travel over a time-line, which can be set for days, years, centuries, or even geological epochs. A working group of Federal Agencies, developing a coordinated program to implement the Vice President's vision, developed the definition of the Digital Earth as a visual representation of our planet that enables a person to explore and interact with the vast amounts of natural and cultural geo-referenced information gathered about the Earth. One of the challenges identified by the agencies was whether the technology existed that would be available to permanently store and deliver all the digital data that enterprises might want to save for decades and centuries. Satellite digital data is growing by Moore's Law as is the growth of computer generated data. Similarly, the density of digital storage media in our information-intensive society is also increasing by a factor of four every three years. The technological bottleneck is that the bandwidth for transferring data is only growing at a factor of four every nine years. This implies that the migration of data to viable long-term storage is growing more slowly. The implication is that older data stored on increasingly obsolete media are at considerable risk if they cannot be continuously migrated to media with longer life times. Another problem occurs when the software and hardware systems for which the media were designed are no longer serviced by their manufacturers. Many instances exist where support for these systems are phased out after mergers or even in going out of business. In addition, survivability of older media can suffer from physical breakdown of components (e.g. tapes simply lose their magnetic properties after a long time in storage). As a result, a potential data survivability crisis is emerging. The scale of the crisis is comparable to that facing the Social Security System. Sometime in one or two decades, the exponential growth of data will become so great that many enterprises will not be able to migrate through their data to more permanent media during the lifetime of the media on which it resides. This will result in significant losses of data and their resultant impacts. To avoid this crisis, we need to plan and devote greater financial and intellectual resources are needed for the development and refinement of new storage media and migration technologies in order to preserve all data any organization determines worth saving permanently. This talk will explore technological solutions and suggested recommendations to address this technological data crisis.

Halem, Milton↗

NPCC4: New York City Climate Risk Information 2022—Observations and Projections

New York City (NYC) faces many challenges in the coming decades due to climate change and its interactions with social vulnerabilities and uneven urban development patterns and processes. This New York City Panel on Climate Change (NPCC) report contributes to the Panel’s mandate to advise the city on climate change and provide timely climate risk information that can inform flexible and equitable adaptation pathways that enhance resilience to climate change. This report presents up-to-date scientific information as well as updated sea level rise projections of record. We also present a new methodology related to climate extremes and describe new methods for developing the next generation of climate projections for the New York metropolitan region. Future work by the Panel should compare the temperature and precipitation projections presented in this report with a subset of models to determine the potential impact and relevance of the “hot model” problem. NPCC4 expects to establish new projections-of-record for precipitation and temperature in 2024 based on this comparison and additional analysis. Nevertheless, the temperature and precipitation projections presented in this report may be useful for NYC stakeholders in the interim as they rely on the newest generation of global climate models.

NPCC4↗

DOE BSSD Performance Management Metrics Report Q2

The vision of the National Microbiome Data Collaborative (NMDC) centers on the concept of connecting data, people, and ideas to advance microbiome innovation and discovery. Building data infrastructure, while key to NMDC’s ability to execute on our vision, can only go so far in creating scientific impact. By fostering strong community partnerships and developing a set of robust community outreach and training programs, we are able to turn our products – the Submission Portal, NMDC EDGE, and the Data Portal – into tools that empower the scientific community. Our multi-pronged community building approach spans individual researchers, research teams, consortia and scientific societies, and institutions and federal agencies. To foster a collaborative and inclusive community-centered environment, we have identified three strategic objectives to promote an inclusive and connected community: (1) recognize and support the diverse research needs and perspectives of the microbiome research community; (2) promote best practices across the microbiome community, from researchers to funders, through community-driven practices (FAIR, CARE, and TRUST); and (3) build a microbiome ecosystem that enables scientific discovery and innovation across stakeholders. These strategic objectives allow our team to focus on impact across a diverse range of activities, from launching the American Society for Microbiology (ASM) Microbiome Data Prize to supporting the Ambassador and Champions programs fostering learning and building a collaborative network. We broadly communicate our work through social media (X/Twitter, LinkedIn, and Instagram), The Microbiome Standard (our quarterly newsletter), and Annual Reports. All our work is underpinned by a strong commitment to diversity, equity, and inclusion as articulated in our Action Plan that tracks progress towards key metrics. A core component of our engagement strategy is user research. User research ensures the Submission Portal, NMDC EDGE, Data Portal, and the new Field Notes mobile app are designed with and for the scientific community. Our user research efforts consist of asking researchers exploratory questions to collect information on researcher priorities, methodologies, and perceptions to ensure that we are aware of the current state of microbiome research. Our usability testing provides researchers with prototypes or test environments of the NMDC products, and we capture valuable information on how users interact with the products to make improvements. Given the diverse nature of microbiome work, we acknowledge that we are not aware of all pressing data challenges and thus rely on the research community to help us identify the most important issues to prioritize. To date, we have conducted 24 interviews and one beta-testing call with 10 participants across all NMDC products, which have generated 321 insights and 120 action items. Herein, we describe the ways we engage with the microbiome research community to advance the NMDC mission.

59 BASIC BIOLOGICAL SCIENCES↗

A holistic platform for accelerating sorbent-based carbon capture

Abstract Reducing carbon dioxide (CO 2 ) emissions urgently requires the large-scale deployment of carbon-capture technologies. These technologies must separate CO 2 from various sources and deliver it to different sinks 1,2 . The quest for optimal solutions for specific source–sink pairs is a complex, multi-objective challenge involving multiple stakeholders and depends on social, economic and regional contexts. Currently, research follows a sequential approach: chemists focus on materials design 3 and engineers on optimizing processes 4,5 , which are then operated at a scale that impacts the economy and the environment. Assessing these impacts, such as the greenhouse gas emissions over the plant’s lifetime, is typically one of the final steps 6 . Here we introduce the PrISMa (Process-Informed design of tailor-made Sorbent Materials) platform, which integrates materials, process design, techno-economics and life-cycle assessment. We compare more than 60 case studies capturing CO 2 from various sources in 5 global regions using different technologies. The platform simultaneously informs various stakeholders about the cost-effectiveness of technologies, process configurations and locations, reveals the molecular characteristics of the top-performing sorbents, and provides insights on environmental impacts, co-benefits and trade-offs. By uniting stakeholders at an early research stage, PrISMa accelerates carbon-capture technology development during this critical period as we aim for a net-zero world.

Science & Technology - Other Topics↗

CpG ODN D35 improves the response to abbreviated low-dose pentavalent antimonial treatment in non-human primate model of cutaneous leishmaniasis

Cutaneous leishmaniasis (CL) affects the lives of 0.7–1 million people every year causing lesions that take months to heal. These lesions can result in disfiguring scars with psychological, social and economic consequences. Antimonials are the first line of therapy for CL, however the treatment is lengthy and linked to significant toxicities; further, its efficacy is variable and resistant parasites are emerging. Shorter or lower dose antimonial treatment regimens, which would decrease the risk of adverse events and improve patient compliance, have shown reduced efficacy and further increase the risk emergence of antimonial-resistant strains. The progression of lesions in CL is partly determined by the immune response it elicits, and previous studies showed that administration of immunomodulatory type D CpG ODNs, magnifies the immune response to Leishmania and reduces lesion severity in nonhuman primates (NHP) challenged with Leishmania major or Leishmania amazonensis. Here we explored whether the addition of a single dose of immunomodulating CpG ODN D35 augments the efficacy of a short-course, low-dose pentavalent antimonial treatment regimen. Results show that macaques treated with D35 plus 5mg/kg sodium stibogluconate (SbV ) for 10 days had smaller lesions and reduced time to re-epithelization after infection with Leishmania major. No toxicities were evident during the studies, even at doses of D35 10 times higher than those used in treatment. Critically, pentavalent antimonial treatment did not modify the ability of D35 to induce type I IFNs. The findings support the efficacy of D35 as adjuvant therapy for shorter, low dose pentavalent antimonial treatment.

59 BASIC BIOLOGICAL SCIENCES↗

Fire as a fundamental ecological process: Research advances and frontiers

Fire is a powerful ecological and evolutionary force that regulates organismal traits, population sizes, species interactions, community composition, carbon and nutrient cycling and ecosystem function. It also presents a rapidly growing societal challenge, due to both increasingly destructive wildfires and fire exclusion in fire–dependent ecosystems. As an ecological process, fire integrates complex feedbacks among biological, social and geophysical processes, requiring coordination across several fields and scales of study. Here, we describe the diversity of ways in which fire operates as a fundamental ecological and evolutionary process on Earth. We explore research priorities in six categories of fire ecology: (a) characteristics of fire regimes, (b) changing fire regimes, (c) fire effects on above–ground ecology, (d) fire effects on below–ground ecology, (e) fire behaviour and (f) fire ecology modelling. We identify three emergent themes: the need to study fire across temporal scales, to assess the mechanisms underlying a variety of ecological feedbacks involving fire and to improve representation of fire in a range of modelling contexts. As fire regimes and our relationships with fire continue to change, prioritizing these research areas will facilitate understanding of the ecological causes and consequences of future fires and rethinking fire management alternatives.

54 ENVIRONMENTAL SCIENCES↗

Informing climate adaptation strategies using ecological simulation models and spatial decision support tools

Introduction: Forest landscapes offer resources and ecosystem services that are vital to the social, economic, and cultural well-being of human communities, but managing for these provisions can require socially and ecologically relevant trade-offs. We designed a spatial decision support model to reveal trade-offs and synergies between ecosystem services in a large eastern Cascade Mountain landscape in Washington State, USA. Methods: We used process-based forest landscape (LANDIS-II) and hydrology (DHSVM) models to compare outcomes associated with 100 years of simulated forest and wildfire dynamics for two management scenarios, Wildfire only and Wildfire + Treatments. We then examined the strength and spatial distribution of potential treatment effects and trends in a set of resources and ecosystem services over the simulation period. Results: We found that wildfire area burned increased over time, but some impacts could be mitigated by adaptation treatments. Treatment benefits were not limited to treated areas. Interestingly, we observed neighborhood benefits where fire spread and severity were reduced not only in treated patches but in adjacent patches and landscapes as well, creating potential synergies among some resource benefits and services. Ordinations provided further evidence for two main kinds of outcomes. Positive ecological effects of treatments were greatest in upper elevation moist and cold forests, while positive benefits to human communities were aligned with drier, low- and mid-elevation forests closer to the wildland urban interface. Discussion: Our results contribute to improved understanding of synergies and tradeoffs linked to adaptation and restoration efforts in fire-prone forests and can be used to inform management aimed at rebuilding resilient, climate-adapted landscapes.

54 ENVIRONMENTAL SCIENCES↗

Ultra-large-scale ab initio quantum chemical computation of bio-molecular systems: The case of spike protein of SARS-CoV-2 virus

The COVID-19 pandemic poses a severe threat to human health with an unprecedented social and economic disruption. Spike (S) glycoprotein of the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the first contact with the ACE2 receptor in the human cell. We report results of ab initio computation of the spike protein, the largest ab initio quantum chemical computation to date on any bio-molecular system, using a divide and conquer strategy by focusing on individual structural domains. In this approach we divided the S-protein into seven structural domains: N-terminal domain (NTD), receptor binding domain (RBD), subdomain 1 (SD1), subdomain 2 (SD2), fusion peptide (FP), heptad repeat 1 with central helix (HR1-CH) and connector domain (CD). The entire Chain A has 14,488 atoms including the hydrogen atoms but excluding the amino acids with missing coordinates based on the PDB data (ID: 6VSB). The results include structural refinement, ab initio calculation of intramolecular bonding mechanism, 3- dimensional non-local inter-amino acid interaction with implications for the inter-domain interaction. Details of the electronic structure, interatomic bonding, partial charge distribution and the role played by hydrogen bond network are discussed. In the interaction among structural domains, we present new insights for crucial hinge-like movement and fusion process. Extension of such calculation to the interface between the S-protein binding domain and ACE2 receptor can provide a pathway for computational understanding of mutations and the design of therapeutic drugs to combat the COVID-19 pandemic.

59 BASIC BIOLOGICAL SCIENCES↗

Baltimore Social-Environmental Collaborative (BSEC) Doppler Lidar & Derived Products

This repository contains all processed Doppler‐lidar outputs from the PSU lidar deployed for the Baltimore Social‐Environmental Collaborative (BSEC) project. Vertical Stare Scans (fixed‐beam, vertical profiling): 1 Hz backscatter intensity (m⁻¹ sr⁻¹), signal‐to‐noise ratio (unitless), and Doppler vertical‐velocity (m s⁻¹) on ~30 m range gates, stored as CF-compliant NetCDF. Wind Profiles (horizontal‐wind retrieval): daily NetCDF outputs of retrieved horizontal wind speed (m s⁻¹) and direction (degrees), computed from the angled‐scan returns. Profile Statistics (summary statistics on the vertical velocity): 15 min windows (default) of mean, variance, skewness, kurtosis, high-frequency variance, etc., as a function of height; saved as CF-compliant NetCDF files. Boundary Layer Height (BLH) (fuzzy-logic output): 15 min BLH estimates (m), with lower/upper fuzzy bounds (m) and a quality flag (0–4) indicating data status (e.g., no data, good, below range, ran out of signal, cloud-topped). Cloud Base Height (Haar-gradient detection): 15 min estimates of cloud-base height (m) with a cloud-detection quality flag (0–3: none, low, moderate, high). All five product streams are organized by year and date under their own top-level folders (01_Vertical_Stare_Scans/ through 05_Cloud_Height/). Each folder contains a data_ /YYYY/ subdirectory with daily CF-compliant NetCDF outputs (96 windows per day at 15 min intervals). Global attributes in each file include creation history, version (2.0.0), institution, and source. Instrument & MeasurementsThe PSU Doppler Lidar samples aerosol backscatter (m⁻¹ sr⁻¹), signal-to-noise ratio, and radial velocity at ~1 Hz. Vertical stare scans point the beam straight up; after collecting angled scans through multiple elevation angles, the "Wind Profiles" product contains the fully retrieved horizontal wind speed and direction. Data were collected continuously at ~30 m range resolution, with a typical height ceiling of ~12 km. How to Use Open any NetCDF with Python's xarray, MATLAB, or similar CF-compliant tools. Stare scans and angled-scan retrievals (Wind Profiles) are CF-compliant daily NetCDF files. Profile-Statistics, BLH, and Cloud Height files are daily 15 min summaries (96 time steps per file). Inspect the included variables (e.g., vertical_velocity_variance, wind_speed, BLH, cloud_base_height) for your analyses. Use the quality flags (BLH_flag, cloud_flag) to filter out poor-quality retrievals. For more information or questions about processing methods, please contact:Nicholas E. Prince ⟨nec5299@psu.edu⟩Penn State Department of Meteorology & Atmospheric Science

Air Quality↗

Urban relatives ameliorate survival disparities for genitourinary cancer in rural patients

Patients living in rural areas have worse cancer-specific outcomes. This study examines the effect of family-based social capital on genitourinary cancer survival. We hypothesized that rural patients with urban relatives have improved survival relative to rural patients without urban family. We examined rural and urban based Utah individuals diagnosed with genitourinary cancers between 1968 and 2018. Familial networks were determined using the Utah Population Database. Patients and relatives were classified as rural or urban based on 2010 rural–urban commuting area codes. Overall survival was analyzed using Cox proportional hazards models. We identified 24,746 patients with genitourinary cancer with a median follow-up of 8.72 years. Rural cancer patients without an urban relative had the worst outcomes with cancer-specific survival hazard ratios (HRs) at 5 and 10 years of 1.33 (95% CI 1.10–1.62) and 1.46 (95% CI 1.24–1.73), respectively relative to urban patients. Rural patients with urban first-degree relatives had improved survival with 5- and 10-year survival HRs of 1.21 (95% CI 1.06–1.40) and 1.16 (95% CI 1.03–1.31), respectively. Our findings suggest rural patients who have been diagnosed with a genitourinary cancer have improved survival when having relatives in urban centers relative to rural patients without urban relatives. Further research is needed to better understand the mechanisms through which having an urban family member contributes to improved cancer outcomes for rural patients. Better characterization of this affect may help inform policies to reduce urban–rural cancer disparities.

60 APPLIED LIFE SCIENCES↗

Baltimore Social-Environmental Collaborative (BSEC) Doppler Lidar & Derived Products

This repository contains all processed Doppler‐lidar outputs from the PSU lidar deployed for the Baltimore Social‐Environmental Collaborative (BSEC) project. Vertical Stare Scans (fixed‐beam, vertical profiling): 1 Hz backscatter intensity (m⁻¹ sr⁻¹), signal‐to‐noise ratio (unitless), and Doppler vertical‐velocity (m s⁻¹) on 30 m range gates (and 3 m range gates), stored as CF-compliant NetCDF. Wind Profiles (horizontal‐wind retrieval): daily NetCDF outputs of retrieved horizontal wind speed (m s⁻¹) and direction (degrees), computed from the angled‐scan returns. Profile Statistics (summary statistics on the vertical velocity): 15 min windows (default) of mean, variance, skewness, kurtosis, high-frequency variance, etc., as a function of height; saved as CF-compliant NetCDF files. Boundary Layer Height (BLH) (fuzzy-logic output): 15 min BLH estimates (m), with lower/upper fuzzy bounds (m) and a quality flag (0–4) indicating data status (e.g., no data, good, ran out of signal, below range, cloud-topped). Cloud Base Height (Haar-gradient detection): 10 min estimates of cloud-base height (m). All five product streams are organized by year and date under their own top-level folders (01_Vertical_Stare_Scans/ through 05_Cloud_Height/). Each folder contains a data_ /YYYY/ subdirectory with daily CF-compliant NetCDF outputs (96 windows per day at 15 min intervals). Global attributes in each file include creation history, version (3.0.0), institution, and source. Instrument & MeasurementsThe PSU Doppler Lidar samples aerosol backscatter (m⁻¹ sr⁻¹), signal-to-noise ratio, and radial velocity at ~1 Hz. Vertical stare scans point the beam straight up; after collecting angled scans through multiple elevation angles, the "Wind Profiles" product contains the fully retrieved horizontal wind speed and direction. Data were collected continuously at ~30 m range resolution (and 3 m for the year of 2025), with a typical height ceiling of ~12 km. How to Use Open any NetCDF with Python's xarray, MATLAB, or similar CF-compliant tools. Stare scans and angled-scan retrievals (Wind Profiles) are CF-compliant daily NetCDF files. Profile-Statistics, BLH, and Cloud Height files are daily 15 min (10 min for Cloud Heights) summaries (96 time steps per file). Inspect the included variables (e.g., vertical_velocity_variance, wind_speed, BLH, cloud_base_height) for your analyses. Use the quality flags (BLH_flag, cloud_flag) to filter out poor-quality retrievals. For more information or questions about processing methods, please contact:Nicholas E. Prince ⟨nec5299@psu.edu⟩Penn State Department of Meteorology & Atmospheric Science

Air Quality↗

Baltimore Social-Environmental Collaborative (BSEC) Doppler Lidar & Derived Products

This repository contains all processed Doppler‐lidar outputs from the PSU lidar deployed for the Baltimore Social‐Environmental Collaborative (BSEC) project. Vertical Stare Scans (fixed‐beam, vertical profiling): 1 Hz backscatter intensity (m⁻¹ sr⁻¹), signal‐to‐noise ratio (unitless), and Doppler vertical‐velocity (m s⁻¹) on 30 m range gates (and 3 m range gates), stored as CF-compliant NetCDF. Wind Profiles (horizontal‐wind retrieval): daily NetCDF outputs of retrieved horizontal wind speed (m s⁻¹) and direction (degrees), computed from the angled‐scan returns. Profile Statistics (summary statistics on the vertical velocity): 15 min windows (default) of mean, variance, skewness, kurtosis, high-frequency variance, etc., as a function of height; saved as CF-compliant NetCDF files. Boundary Layer Height (BLH) (fuzzy-logic output): 15 min BLH estimates (m), with lower/upper fuzzy bounds (m) and a quality flag (0–4) indicating data status (e.g., no data, good, ran out of signal, below range, cloud-topped). Cloud Base Height (Haar-gradient detection): 10 min estimates of cloud-base height (m). All five product streams are organized by year and date under their own top-level folders (01_Vertical_Stare_Scans/ through 05_Cloud_Height/). Each folder contains a data_ /YYYY/ subdirectory with daily CF-compliant NetCDF outputs (96 windows per day at 15 min intervals). Global attributes in each file include creation history, version (3.0.1), institution, and source. Instrument & MeasurementsThe PSU Doppler Lidar samples aerosol backscatter (m⁻¹ sr⁻¹), signal-to-noise ratio, and radial velocity at ~1 Hz. Vertical stare scans point the beam straight up; after collecting angled scans through multiple elevation angles, the "Wind Profiles" product contains the fully retrieved horizontal wind speed and direction. Data were collected continuously at ~30 m range resolution (and 3 m for the year of 2025), with a typical height ceiling of ~12 km. How to Use Open any NetCDF with Python's xarray, MATLAB, or similar CF-compliant tools. Stare scans and angled-scan retrievals (Wind Profiles) are CF-compliant daily NetCDF files. Profile-Statistics, BLH, and Cloud Height files are daily 15 min (10 min for Cloud Heights) summaries (96 time steps per file). Inspect the included variables (e.g., vertical_velocity_variance, wind_speed, BLH, cloud_base_height) for your analyses. Use the quality flags (BLH_flag, cloud_flag) to filter out poor-quality retrievals. For more information or questions about processing methods, please contact:Nicholas E. Prince ⟨nec5299@psu.edu⟩Penn State Department of Meteorology & Atmospheric Science

Air Quality↗

Decoding substance use disorder severity from clinical notes using a large language model

Substance use disorder (SUD) poses a major concern due to its detrimental effects on health and society. SUD identification and treatment depend on a variety of factors such as severity, co-determinants (e.g., withdrawal symptoms), and social determinants of health. Existing diagnostic coding systems used by insurance providers, like the International Classification of Diseases (ICD-10), lack granularity for certain diagnoses, but American clinicians will add this granularity (as that found within the Diagnostic and Statistical Manual of Mental Disorders classification or DSM-5) as supplemental unstructured text in clinical notes. Traditional natural language processing (NLP) methods face limitations in accurately parsing such diverse clinical language. Large language models (LLMs) offer promise in overcoming these challenges by adapting to diverse language patterns. This study investigates the application of LLMs for extracting severity-related information for various SUD diagnoses from clinical notes. We propose a workflow employing zero-shot learning of LLMs with carefully crafted prompts and post-processing techniques. Through experimentation with Flan-T5, an open-source LLM, we demonstrate its superior recall compared to the rule-based approach. Focusing on 11 categories of SUD diagnoses, we show the effectiveness of LLMs in extracting severity information, contributing to improved risk assessment and treatment planning for SUD patients.

60 APPLIED LIFE SCIENCES↗

Sustainability of soil organic carbon in consolidated gully land in China’s Loess Plateau

Massive gully land consolidation projects, launched in China’s Loess Plateau, aim to restore 2667 km 2 agricultural lands in total by consolidating 2026 highly eroded gullies. This effort represents a social engineering project where the economic development and livelihood of the farming families are closely tied to the ability of these emergent landscapes to provide agricultural services. Whether these ‘time zero’ landscapes have the resilience to provide a sustainable soil condition such as soil organic carbon (SOC) content remains unknown. By studying two watersheds, one of which is a control site, we show that the consolidated gully serves as an enhanced carbon sink, where the magnitude of SOC increase rate (1.0 gC/m 2 /year) is about twice that of the SOC decrease rate (-0.5 gC/m 2 /year) in the surrounding natural watershed. Over a 50-year co-evolution of landscape and SOC turnover, we find that the dominant mechanisms that determine the carbon cycling are different between the consolidated gully and natural watersheds. In natural watersheds, the flux of SOC transformation is mainly driven by the flux of SOC transport; but in the consolidated gully, the transport has little impact on the transformation. Furthermore, we find that extending the surface carbon residence time has the potential to efficiently enhance carbon sequestration from the atmosphere with a rate as high as 8 gC/m 2 /year compared to the current 0.4 gC/m 2 /year. The success for the completion of all gully consolidation would lead to as high as 26.67 GgC/year sequestrated into soils. This work, therefore, not only provides an assessment and guidance of the long-term sustainability of the ‘time zero’ landscapes but also a solution for sequestration CO 2 into soils.

54 ENVIRONMENTAL SCIENCES↗

Development of a Genome-Scale Metabolic Model of Clostridium thermocellum and Its Applications for Integration of Multi-Omics Datasets and Computational Strain Design

Solving environmental and social challenges such as climate change requires a shift from our current non-renewable manufacturing model to a sustainable bioeconomy. To lower carbon emissions in the production of fuels and chemicals, plant biomass feedstocks can replace petroleum using microorganisms as biocatalysts. The anaerobic thermophile Clostridium thermocellum is a promising bacterium for bioconversion due to its capability to efficiently degrade lignocellulosic biomass. However, the complex metabolism of C. thermocellum is not fully understood, hindering metabolic engineering to achieve high titers, rates, and yields of targeted molecules. In this study, we developed an updated genome-scale metabolic model of C. thermocellum that accounts for recent metabolic findings, has improved prediction accuracy, and is standard-conformant to ensure easy reproducibility. We illustrated two applications of the developed model. We first formulated a multi-omics integration protocol and used it to understand redox metabolism and potential bottlenecks in biofuel (e.g., ethanol) production in C. thermocellum. Second, we used the metabolic model to design modular cells for efficient production of alcohols and esters with broad applications as flavors, fragrances, solvents, and fuels. The proposed designs not only feature intuitive push-and-pull metabolic engineering strategies, but also present novel manipulations around important central metabolic branch-points. We anticipate the developed genome-scale metabolic model will provide a useful tool for system analysis of C. thermocellum metabolism to fundamentally understand its physiology and guide metabolic engineering strategies to rapidly generate modular production strains for effective biosynthesis of biofuels and biochemicals from lignocellulosic biomass.

59 BASIC BIOLOGICAL SCIENCES↗

Impact of changes in protective behaviors and out-of-household activities by age on COVID-19 transmission and hospitalization in Chicago, Illinois

Even with an efficacious vaccine, protective behaviors (social distancing, masking) are essential for preventing COVID-19 transmission and could become even more important if current or future variants evade immunity from vaccines or prior infection. Here we created an agent-based model representing the Chicago population and conducted experiments to determine the effects of varying adult out-of-household activities (OOHA), school reopening, and protective behaviors across age groups on COVID-19 transmission and hospitalizations. From September-November 2020, decreasing adult protective behaviors and increasing adult OOHA both substantially impacted COVID-19 outcomes; school reopening had relatively little impact when adult protective behaviors and OOHA were maintained. As of November 1, 2020, a 50% reduction in young adult (age 18-40) protective behaviors resulted in increased latent infection prevalence per 100,000 from 15.93 (IQR 6.18, 36.23) to 40.06 (IQR 14.65, 85.21)and 19.87 (IQR 6.83, 46.83) to 47.74 (IQR 18.89, 118.77) with 15% and 45% school reopening. Increasing adult (age ≥18) OOHA from 65% to 80% of pre-pandemic levels resulted in increased latent infection prevalence per 100,000 from 35.18 (IQR 13.59, 75.00) to 69.84 (IQR 33.27, 145.89) and 38.17 (IQR 15.84, 91.16) to 80.02 (IQR 30.91, 186.63) with 15% and 45% school reopening. Similar patterns were observed for hospitalizations. In areas without widespread vaccination coverage, interventions to maintain adherence to protective behaviors, particularly among younger adults and in out-of-household settings, remain a priority for preventing COVID-19 transmission.

60 APPLIED LIFE SCIENCES↗

A review of water valuation metrics: Supporting sustainable water use in manufacturing

In the manufacturing sector, water has been often considered too cheap to conserve. Such thinking relies on water valuations that limit the value of water to the price paid. Using such simple methods, the share of water cost to total manufacturing cost is significantly small, <3%. As a result, conserving water and enabling technology uptake is difficult to justify economically and slow to advance, hindering progress toward sustainable water use. However, the value of water to a manufacturer is far greater than the price paid. Valuations such as the true cost of water consider the additional in-plant treatment and energy costs and have been gaining greater traction in the manufacturing sector. However, true cost alone still undervalues water by not accounting for economic and social costs related to scarcity and environmental externalities. This paper makes the case and presents a framework for valuing manufacturing water beyond the price paid and the true cost. The proposed fuller valuation of manufacturing water takes into account the internal and opportunity costs associated with the realization of water risks. The paper follows with a review of a wide range of water valuation metrics, both at the specific industry level and regional/economy-wide level. The use of various valuation metrics incorporating the relationship between the change in value with change in water use, such as marginal value of water, shadow price, and elasticity at the specific industry level, has been limited in the U.S. manufacturing sector. Further, a limited number of studies exist on data-intensive subjective evaluation techniques such as computable general equilibrium modeling and input-output modeling for regional water valuation. After reviewing water value metrics, several recent case studies from manufacturers from the literature are presented to illustrate both the promise and challenges of a fuller valuation of water as proposed here. Some large multinational corporations have moved toward assessing the value of water via supply chain sustainability initiatives, environmental profit and loss accounting, estimating risk-adjusted values of water, hydro-economic modeling, natural capital asset valuation, and developing value chain indices. This paper provides policymakers and technology developers a framework for monetizing water value beyond its true cost and current metrics. If adopted, such fuller water valuations can help make the business case for the development and deployment of cost-effective water-conserving technologies, thereby improving the sustainability of the manufacturing sector with respect to water.

54 ENVIRONMENTAL SCIENCES↗

US wildfire potential: a historical view and future projection using high-resolution climate data

Abstract Recent wildfires in the western United States have led to substantial economic losses and social stresses. There is a great concern that the new climatic state may further increase the intensity, duration, and frequency of wildfires. To examine temporal and spatial features of historical wildfire trends and future changes, a common fire index, the Keetch–Byram Drought Index (KBDI), is calculated over the contiguous United States (CONUS) and Alaska. We introduce an efficient initialization method and calculate 36 years (1982–2017) of historical KBDI at 4 km using a high-quality observational dataset. KBDIs are also calculated at 12 km using regional climate models and extended into the mid- and late-21st century. Based on the observational data, annual mean (and 95th percentile) KBDI over forested regions in the southwestern and northwestern CONUS has risen since 1982 at a rate of 5.2 (4.0) and 2.9 (3.3) per year, respectively, indicating a persistent drying trend fostering fire activities; the number of days exceeding the top 5% historical KBDI has increased by 16 and 25 d in the 36 years. Multiple regional climate model simulations project increasing wildfire potential and longer fire seasons over broader areas based on the estimated KBDI for the mid- and late-21st century. By the end of the century, most of the CONUS would experience about 90–189 more days per year exceeding the historical local maximum KBDI; areas with high KBDI (>600), whose occurrence correlates with large burned area, are projected to broaden by nearly 60 times in the southern CONUS. While both temperature and precipitation contribute to future KBDI changes, warming is the main driver of more frequent, intense and wide-spread extreme wildfires indicated by high KBDIs in future projections.

54 ENVIRONMENTAL SCIENCES↗