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At least 37 records · Page 2

The 38 th Annual Interdisciplinary Plant Group Symposium: Enhancing the Resilience of Plant Systems to Climate Change (Meeting Summary)

The University of Missouri’s Interdisciplinary Plant Group held its 38th annual symposium on May 25–27. In short, it was a resounding success! The air was almost electric because of a confluence of events that were particular to this symposium. Not only was there great enthusiasm from students attending their first ever scientific meeting, but this was coupled with excitement and delight exuded by many of our senior invited speakers, who were attending their first in-person meeting since the Covid pandemic began. After a long planning period, and with the ongoing pandemic injecting uncertainty, it was gratifying to see the symposium unfold with such excitement and engagement among participants. The symposium was organized to address the grand challenge of “Enhancing the Resilience of Plant System to Climate Change”, by bringing together experts at the intersections of multiple disciplines to educate our community on the opportunities to develop innovative mitigation strategies and to adapt plants to climate change.

54 ENVIRONMENTAL SCIENCES↗

Comprehensive compartmental model and calibration algorithm for the study of clinical implications of the population-level spread of COVID-19: a study protocol

The complex dynamics of the coronavirus disease 2019 (COVID-19) pandemic has made obtaining reliable long-term forecasts of the disease progression difficult. Simple mechanistic models with deterministic parameters are useful for short-term predictions but have ultimately been unsuccessful in extrapolating the trajectory of the pandemic because of unmodelled dynamics and the unrealistic level of certainty that is assumed in the predictions. We propose a 22-compartment epidemiological model that includes compartments not previously considered concurrently, to account for the effects of vaccination, asymptomatic individuals, inadequate access to hospital care, post-acute COVID-19 and recovery with long-term health complications. Additionally, new connections between compartments introduce new dynamics to the system and provide a framework to study the sensitivity of model outputs to several concurrent effects, including temporary immunity, vaccination rate and vaccine effectiveness. Subject to data availability for a given region, we discuss a means by which population demographics (age, comorbidity, socioeconomic status, sex and geographical location) and clinically relevant information (different variants, different vaccines) can be incorporated within the 22-compartment framework. Considering a probabilistic interpretation of the parameters allows the model's predictions to reflect the current state of uncertainty about the model parameters and model states. We propose the use of a sparse Bayesian learning algorithm for parameter calibration and model selection. This methodology considers a combination of prescribed parameter prior distributions for parameters that are known to be essential to the modelled dynamics and automatic relevance determination priors for parameters whose relevance is questionable. This is useful as it helps prevent overfitting the available epidemiological data when calibrating the parameters of the proposed model. Population-level administrative health data will serve as partial observations of the model states.

59 BASIC BIOLOGICAL SCIENCES↗

The novel Mechanical Ventilator Milano for the COVID-19 pandemic

This paper presents the Mechanical Ventilator Milano (MVM), a novel intensive therapy mechanical ventilator designed for rapid, large-scale, low-cost production for the COVID-19 pandemic. Free of moving mechanical parts and requiring only a source of compressed oxygen and medical air to operate, the MVM is designed to support the long-term invasive ventilation often required for COVID-19 patients and operates in pressure-regulated ventilation modes, which minimize the risk of furthering lung trauma. The MVM was extensively tested against ISO standards in the laboratory using a breathing simulator, with good agreement between input and measured breathing parameters and performing correctly in response to fault conditions and stability tests. The MVM has obtained Emergency Use Authorization by U.S. Food and Drug Administration (FDA) for use in healthcare settings during the COVID-19 pandemic and Health Canada Medical Device Authorization for Importation or Sale, under Interim Order for Use in Relation to COVID-19. Furthermore, following these certifications, mass production is ongoing and distribution is under way in several countries. The MVM was designed, tested, prepared for certification, and mass produced in the space of a few months by a unique collaboration of respiratory healthcare professionals and experimental physicists, working with industrial partners, and is an excellent ventilator candidate for this pandemic anywhere in the world

60 APPLIED LIFE SCIENCES↗

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.

59 BASIC BIOLOGICAL SCIENCES↗

Rapid, Sensitive, Label-Free Electrical Detection of SARS-CoV-2 in Nasal Swab Samples

Rapid diagnosis of coronavirus disease 2019 (COVID-19) is key for the long-term control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) amid renewed threats of mutated SARS-CoV-2 around the world. Here, we report on an electrical label-free detection of SARS-CoV-2 in nasopharyngeal swab samples directly collected from outpatients or in saliva-relevant conditions by using a remote floating-gate field-effect transistor (RFGFET) with a 2-dimensional reduced graphene oxide (rGO) sensing membrane. RFGFET sensors demonstrate rapid detection (<5 min), a 90.6% accuracy from 8 nasal swab samples measured by 4 different devices for each sample, and a coefficient of variation (CV) < 6%. Also, RFGFET sensors display a limit of detection (LOD) of pseudo-SARS-CoV-2 that is 10 000-fold lower than enzyme-linked immunosorbent assays, with a comparable LOD to that of reverse transcriptionpolymerase chain reaction (RT-PCR) for patient samples. To achieve this, comprehensive systematic studies were performed regarding interactions between SARS-CoV-2 and spike proteins, neutralizing antibodies, and angiotensin-converting enzyme 2, as either a biomarker (detection target) or a sensing probe (receptor) functionalized on the rGO sensing membrane. Finally, taken together, this work may have an immense effect on positioning FET bioelectronics for rapid SARS-CoV-2 diagnostics.

60 APPLIED LIFE SCIENCES↗

The 2020 Nonlinear Mechanics and Dynamics Research Institute

The 2020 Nonlinear Mechanics and Dynamics (NOMAD) Research Institute was successfully held from June 15 to July 30, 2020. NOMAD brings together participants with diverse technical backgrounds to work in small teams to cultivate new ideas and approaches in engineering mechanics and dynamics research. NOMAD provides an opportunity for researchers – especially early career researchers - to develop lasting collaborations that go beyond what can be established from the limited interactions at their institutions or at annual conferences. A total of 11 students participated in the seven-week long program held virtually due to the COVID-19 health pandemic. The students collaborated on one of four research projects that were developed by various mentors from Sandia National Laboratories, the University of New Mexico, and other academic and research institutions. In addition to the research activities, the students attended weekly technical seminars, various virtual tours, and socialized at virtual gatherings. At the end of the summer, the students gave a final technical presentation on their research findings. Many of the research discoveries made at NOMAD 2020 are published as proceedings at technical conferences and have direct alignment with the critical mission work performed at Sandia.

42 ENGINEERING↗

Scenarios of a Sustainable Energy Transition: Perspectives from the U.S.

The energy sector has been undergoing a significant transition over the past decade, which was accelerated in 2020 during the COVD-19 pandemic. This presentation provides an overview of energy trends in the U.S., including electricity, oil and gas, coal, and renewables, the impact of the pandemic in 2020, and forecasts for recovery. Scenarios of energy use and future integrated technologies are outlined as near and mid-term approaches. The presentation concludes with potential U.S. policy priorities focused on energy and economic recovery, as well as perspectives on energy planning from the disruptions of 2020. The presentation is part of day-long series of presentations covering post-COVID-19 energy responses in Asia, Australia, Europe, and the United States.

COVID-19↗

Semi-Analytical Hierarchical Bayesian Inference of Nonlinear Model Structure in Stochastic Dynamics: Applied to Compartmental Models of Infectious Diseases

A Bayesian computational framework for parsimonious inference in stochastic nonlinear dynamical systems is presented. This framework enables the concurrent estimation of system states, time-varying parameters, time-invariant parameters, and the optimal sparsity structure of the model parameters. Because differential equation-based models are often simplified mechanistic or phenomenological representations, robust inference from noisy measurement data requires explicit treatment of model error and uncertainty. Model error and time-varying parameters can be represented as random processes, enabling inference while making minimal assumptions about the underlying sources of discrepancy and variability. Adopting stochastic differential equation representations affords the model significant flexibility, but can also render it susceptible to overfitting during statistical inversion, where the inferred model may track noise rather than the underlying signal. To alleviate the effects of overfitting and to enable the discovery of the optimal sparse representation of the time-invariant parameters, a Bayesian sparse learning algorithm is embedded within the framework. This sparse learning framework adopts an approximate hierarchical Bayesian setting defined by a series of semi-analytical expressions. The model structure inference framework is validated using a stochastic compartmental model for tracking and forecasting active cases of an infectious disease. Compartmental models describe population-level infectious disease dynamics through interactions among population fractions grouped by disease state. Mathematically, such models consist of a system of coupled ordinary differential equations. This example adopts an expressive compartmental model that includes multiple possible interactions between disease states, motivated by early uncertainty surrounding COVID-19 reinfection dynamics and their implications for long-term epidemic forecasting. The sparse learning exercise permits the inference of a priori unknown epidemiological dynamics from simulated public health data, discovering the nested compartmental model that optimizes the trade-off between average data-fit and model complexity. It is shown that inducing sparsity among the model parameters eliminates redundant interactions between compartments, equivalently revealing the optimal coupling structure between differential equations.

97 MATHEMATICS AND COMPUTING↗

How New Mexico Leveraged a COVID-19 Case Forecasting Model to Preemptively Address the Healthcare Needs of the State: Quantitative Analysis

Prior to the COVID-19 pandemic, US hospitals relied on static projections of future trends for long-term planning and were only beginning to consider forecasting methods for short-term planning of staffing and other resources. With the overwhelming burden imposed by COVID-19 on the health care system, an emergent need exists to accurately forecast hospitalization needs within an actionable timeframe. Our goal was to leverage an existing COVID-19 case and death forecasting tool to generate the expected number of concurrent hospitalizations, occupied intensive care unit (ICU) beds, and in-use ventilators 1 day to 4 weeks in the future for New Mexico and each of its five health regions. We developed a probabilistic model that took as input the number of new COVID-19 cases for New Mexico from Los Alamos National Laboratory’s COVID-19 Forecasts Using Fast Evaluations and Estimation tool, and we used the model to estimate the number of new daily hospital admissions 4 weeks into the future based on current statewide hospitalization rates. The model estimated the number of new admissions that would require an ICU bed or use of a ventilator and then projected the individual lengths of hospital stays based on the resource need. By tracking the lengths of stay through time, we captured the projected simultaneous need for inpatient beds, ICU beds, and ventilators. We used a postprocessing method to adjust the forecasts based on the differences between prior forecasts and the subsequent observed data. Thus, we ensured that our forecasts could reflect a dynamically changing situation on the ground. Forecasts made between September 1 and December 9, 2020, showed variable accuracy across time, health care resource needs, and forecast horizon. Forecasts made in October, when new COVID-19 cases were steadily increasing, had an average accuracy error of 20.0%, while the error in forecasts made in September, a month with low COVID-19 activity, was 39.7%. Across health care use categories, state-level forecasts were more accurate than those at the regional level. Although the accuracy declined as the forecast was projected further into the future, the stated uncertainty of the prediction improved. Forecasts were within 5% of their stated uncertainty at the 50% and 90% prediction intervals at the 3- to 4-week forecast horizon for state-level inpatient and ICU needs. However, uncertainty intervals were too narrow for forecasts of state-level ventilator need and all regional health care resource needs. Real-time forecasting of the burden imposed by a spreading infectious disease is a crucial component of decision support during a public health emergency. Our proposed methodology demonstrated utility in providing near-term forecasts, particularly at the state level. This tool can aid other stakeholders as they face COVID-19 population impacts now and in the future.

60 APPLIED LIFE SCIENCES↗

Earth's record-high greenness and its attributions in 2020

Terrestrial vegetation is a crucial component of Earth's biosphere, regulating global carbon and water cycles and contributing to human welfare. Despite an overall greening trend, terrestrial vegetation exhibits a significant inter-annual variability. The mechanisms driving this variability, particularly those related to climatic and anthropogenic factors, remain poorly understood, which hampers our ability to project the long-term sustainability of ecosystem services. Here, in this work, by leveraging diverse remote sensing measurements, we pinpointed 2020 as a historic landmark, registering as the greenest year in modern satellite records from 2001 to 2020. Using ensemble machine learning and Earth system models, we found this exceptional greening primarily stemmed from consistent growth in boreal and temperate vegetation, attributed to rising CO 2 levels, climate warming, and reforestation efforts, alongside a transient tropical green-up linked to the enhanced rainfall. Contrary to expectations, the COVID-19 pandemic lockdowns had a limited impact on this global greening anomaly. Our findings highlight the resilience and dynamic nature of global vegetation in response to diverse climatic and anthropogenic influences, offering valuable insights for optimizing ecosystem management and informing climate mitigation strategies.

54 ENVIRONMENTAL SCIENCES↗

Bayesian Inference of State-Level COVID-19 Basic Reproduction Numbers across the United States

Although many persons in the United States have acquired immunity to COVID-19, either through vaccination or infection with SARS-CoV-2, COVID-19 will pose an ongoing threat to non-immune persons so long as disease transmission continues. We can estimate when sustained disease transmission will end in a population by calculating the population-specific basic reproduction number ℛ0, the expected number of secondary cases generated by an infected person in the absence of any interventions. The value of ℛ0 relates to a herd immunity threshold (HIT), which is given by 1−1/ℛ0. When the immune fraction of a population exceeds this threshold, sustained disease transmission becomes exponentially unlikely (barring mutations allowing SARS-CoV-2 to escape immunity). Here, we report state-level ℛ0 estimates obtained using Bayesian inference. Maximum a posteriori estimates range from 7.1 for New Jersey to 2.3 for Wyoming, indicating that disease transmission varies considerably across states and that reaching herd immunity will be more difficult in some states than others. ℛ0 estimates were obtained from compartmental models via the next-generation matrix approach after each model was parameterized using regional daily confirmed case reports of COVID-19 from 21 January 2020 to 21 June 2020. Our ℛ0 estimates characterize the infectiousness of ancestral strains, but they can be used to determine HITs for a distinct, currently dominant circulating strain, such as SARS-CoV-2 variant Delta (lineage B.1.617.2), if the relative infectiousness of the strain can be ascertained. On the basis of Delta-adjusted HITs, vaccination data, and seroprevalence survey data, we found that no state had achieved herd immunity as of 20 September 2021.

60 APPLIED LIFE SCIENCES↗

A Quick Route to Multiple Highly Potent SARS-CoV-2 Main Protease Inhibitors**

The COVID-19 pathogen, SARS-CoV-2, requires its main protease (SC2M Pro ) to digest two of its translated long polypeptides to form a number of mature proteins that are essential for viral replication and pathogenesis. Inhibition of this vital proteolytic process is effective in preventing the virus from replicating in infected cells and therefore provides a potential COVID-19 treatment option. Guided by previous medicinal chemistry studies about SARS-CoV-1 main protease (SC1M Pro ), we have designed and synthesized a series of SC2M Pro inhibitors that contain β-(S-2-oxopyrrolidin-3-yl)-alaninal (Opal) for the formation of a reversible covalent bond with the SC2M Pro active-site cysteine C145. All inhibitors display high potency with K i values at or below 100 nM. The most potent compound, MPI3, has as a K i value of 8.3 nM. Crystallographic analyses of SC2M Pro bound to seven inhibitors indicated both formation of a covalent bond with C145 and structural rearrangement from the apoenzyme to accommodate the inhibitors. Virus inhibition assays revealed that several inhibitors have high potency in inhibiting the SARS-CoV-2-induced cytopathogenic effect in both Vero E6 and A549/ACE2 cells. Two inhibitors, MPI5 and MPI8, completely prevented the SARS-CoV-2-induced cytopathogenic effect in Vero E6 cells at 2.5-5 μM and A549/ACE2 cells at 0.16-0.31 μM. Their virus inhibition potency is much higher than that of some existing molecules that are under preclinical and clinical investigations for the treatment of COVID-19. Our study indicates that there is a large chemical space that needs to be explored for the development of SC2M Pro inhibitors with ultra-high antiviral potency.

3C-like protease↗

Mining and Validating Social Media Data for COVID-19–Related Human Behaviors Between January and July 2020: Infodemiology Study

Background: Health authorities can minimize the impact of an emergent infectious disease outbreak through effective and timely risk communication, which can build trust and adherence to subsequent behavioral messaging. Monitoring the psychological impacts of an outbreak, as well as public adherence to such messaging, is also important for minimizing long-term effects of an outbreak. Objective: We used social media data from Twitter to identify human behaviors relevant to COVID-19 transmission, as well as the perceived impacts of COVID-19 on individuals, as a first step toward real-time monitoring of public perceptions to inform public health communications. Methods: We developed a coding schema for 6 categories and 11 subcategories, which included both a wide number of behaviors as well codes focused on the impacts of the pandemic (eg, economic and mental health impacts). We used this to develop training data and develop supervised learning classifiers for classes with sufficient labels. Classifiers that performed adequately were applied to our remaining corpus, and temporal and geospatial trends were assessed. We compared the classified patterns to ground truth mobility data and actual COVID-19 confirmed cases to assess the signal achieved here. Results: We applied our labeling schema to approximately 7200 tweets. The worst-performing classifiers had F1 scores of only 0.18 to 0.28 when trying to identify tweets about monitoring symptoms and testing. Classifiers about social distancing, however, were much stronger, with F1 scores of 0.64 to 0.66. We applied the social distancing classifiers to over 228 million tweets. We showed temporal patterns consistent with real-world events, and we showed correlations of up to –0.5 between social distancing signals on Twitter and ground truth mobility throughout the United States. Conclusions: Behaviors discussed on Twitter are exceptionally varied. Twitter can provide useful information for parameterizing models that incorporate human behavior, as well as for informing public health communication strategies by describing awareness of and compliance with suggested behaviors.

60 APPLIED LIFE SCIENCES↗

Lung Cancer and Heart Disease Risks Associated With Low-Dose Pulmonary Radiotherapy to COVID-19 Patients With Different Background Risks

The respiratory disease COVID-19 reached global pandemic status in 2020. Excessive inflammation is believed to result in the most severe symptoms and death from this disease. Because treatment options for patients with severe COVID-19 related pulmonary symptoms remain limited, whole-lung low-dose radiation therapy is being evaluated as an anti-inflammatory modality. However, there is concern about the long-term risks associated with low-dose pulmonary irradiation. To help quantify the benefit-risk balance of low-dose radiation therapy for COVID-19, we estimated radiation-induced lifetime risks of both lung cancer and heart disease (major coronary events) for patients of different sexes, treated at ages 50 to 85, with and without other relevant risk factors (cigarette smoking and baseline heart disease risk).

62 RADIOLOGY AND NUCLEAR MEDICINE↗

New Norms or Old Habits: Evaluating Interlinked Trajectories of Online Shopping and Work Commute Post-Pandemic

The COVID-19 pandemic has significantly shifted travel behaviors, with major changes observed in online shopping and travel to work. Despite considerable research into pandemic-induced changes in travel behavior, it remains uncertain whether these new patterns have persisted or reverted to pre-pandemic norms. This study addresses this uncertainty by evaluating whether shifts in online shopping and work travel during the pandemic have become permanently ingrained in individuals' daily routine. Leveraging data from the 2022 National Household Travel Survey, a bivariate ordered probit model is employed to analyze changes in online shopping and work travel - whether they have increased, decreased, or remained stable compared to pre-pandemic levels across different population segments. The analysis finds that the pandemic did not significantly alter online shopping for home delivery and travel to work for the majority of society. However, a substantial portion of respondents reported increased online shopping for home delivery and reduced travel to work compared to pre-pandemic levels, with online shopping trends appearing more permanent. Segment-wise analysis and model results indicate heterogeneity in behavioral shifts with females engaging more in online shopping, while zero-vehicle households are traveling less to work, compared to pre-pandemic levels. Additionally, increase in online shopping frequency is significantly and negatively correlated with decrease in traveling to work. These findings highlight the need for improved digital infrastructure, flexible work policies, and integrated transportation solutions tailored to evolving demographic and socioeconomic needs in the post-pandemic era. Additionally, the study calls for integrating passenger and freight movement in a single framework rather than treating them in silos.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Stochastic social behavior coupled to COVID-19 dynamics leads to waves, plateaus, and an endemic state

It is well recognized that population heterogeneity plays an important role in the spread of epidemics. While individual variations in social activity are often assumed to be persistent, that is, constant in time, here we discuss the consequences of dynamic heterogeneity. By integrating the stochastic dynamics of social activity into traditional epidemiological models, we demonstrate the emergence of a new long timescale governing the epidemic, in broad agreement with empirical data. Our stochastic social activity model captures multiple features of real-life epidemics such as COVID-19, including prolonged plateaus and multiple waves, which are transiently suppressed due to the dynamic nature of social activity. The existence of a long timescale due to the interplay between epidemic and social dynamics provides a unifying picture of how a fast-paced epidemic typically will transition to an endemic state.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Melting and Re-Freezing Leads to Irreversible Changes in the Morphology and Molecular-Level Dynamics of Pfizer-BioNTech COVID-19 Vaccine

As an mRNA-based vaccine, the Pfizer-BioNTech COVID-19 vaccine has stringent cold storage requirements to preserve functionality of the mRNA active ingredient. To this end, lipid components of the vaccine formulation play an important role in stabilizing and protecting the mRNA molecule for long-term storage. The purpose of the current study was to measure molecular-level dynamics as a function of temperature in the Pfizer-BioNTech COVID-19 vaccine to gain microscopic insight into its thermal stability. Materials and Methods: We used quasielastic and inelastic neutron scattering to probe (1) the vaccine extracted from the manufacturer-supplied vials and (2) unperturbed vaccine in the original manufacturer-supplied vials. The latter measurement was possible due to the high penetrative power of neutrons. Upon warming from the low-temperature frozen state, the vaccine in its original form exhibits two-step melting, indicative of a two-phase morphology. Once the melting is completed (above 0 °C), vaccine re-freezing cannot restore its original two-phase state. This observation is corroborated by the changes in the molecular vibrational spectra. The molecular-level mobility measured in the resulting single-phase state of the re-frozen vaccine greatly exceeds the mobility measured in the original vaccine. Even a brief melting (above 0 °C) leads to an irreversible alteration of the two-phase morphology of the original vaccine formulation. Re-freezing of the vaccine results in a one-phase morphology with much increased molecular-level mobility compared to that in the original vaccine, suggesting irreversible deterioration of the vaccine’s in-storage stability. Neutron scattering can be used to distinguish between the vibrational spectra characteristic of the original and deteriorated vaccines contained in the unperturbed original manufacturer-supplied vials.

60 APPLIED LIFE SCIENCES↗

Black carbon-climate interactions regulate dust burdens over India revealed during COVID-19

India as a hotspot for air pollution has heavy black carbon (BC) and dust (DU) loadings. BC has been identified to significantly impact the Indian climate. However, whether BC-climate interactions regulate Indian DU during the premonsoon season is unclear. Here, using long-term Reanalysis data, we show that Indian DU is positively correlated to northern Indian BC while negatively correlated to southern Indian BC. We further identify the mechanism of BC-dust-climate interactions revealed during COVID-19. BC reduction in northern India due to lockdown decreases solar heating in the atmosphere and increases surface albedo of the Tibetan Plateau (TP), inducing a descending atmospheric motion. Colder air from the TP together with warmer southern Indian air heated by biomass burning BC results in easterly wind anomalies, which reduces dust transport from the Middle East and Sahara and local dust emissions. The premonsoon aerosol-climate interactions delay the outbreak of the subsequent Indian summer monsoon.

54 ENVIRONMENTAL SCIENCES↗