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At least 145 records · Page 8

Impact of COVID-19 Restrictions on Atmospheric Concentrations of O3 and NO2 Across the Globe

We use a machine learning algorithm combining information from the NASA GEOS composition forecast (GEOS-CF) model and surface observations of nitrogen dioxide (NO2) and ozone (O3) at more than 5,000 observation sites to assess the impact of COVID-19 restrictions on surface air quality in 46 countries. Our methodology removes the compounding impacts of meteorology, seasonality and atmospheric chemistry on air pollution, thus allowing for a quantitative estimate of the change in surface air quality following COVID-19 containment measures. Compared to GEOS-CF model predictions that do not include emission reductions related to COVID-19 restrictions, surface observations show a drop in surface NO2 of up to 60% after the implementation of lockdowns. Average NO2 concentrations between February 2020 to June 2020 were 18% lower than business as usual. The earliest and strongest declines are observed over China, followed by Europe and the US. While NO2 concentrations over China recovered within 2 months, the recovery has been slower over Europe and the US. The impact of COVID-19 restrictions on O3 is complicated by non-linear atmospheric chemistry. Locally, O3 can show a short-term increase of up to 50% as a result of the decrease in NO2, which leads to a reduction in night time titration. However, this effect is offset by a decrease in photochemical production during the day. Our results indicate that these two competing processes resulted in a net zero change in average surface ozone during the first 5 months of the pandemic. The results also indicate that the reduced photochemical production becomes increasingly important over time. Our analysis is based on surface observations and model simulations available in near real-time, and we will present an up-to-date view of the short and medium-term impacts of COVID-19 restrictions on air quality around the world.

COVID-19↗

IMPECCABLE: Integrated Modeling Pipeline for COVID Cure by Assessing Better Leads

ABSTRACT The drug discovery process currently employed in the pharmaceutical industry typically requires about 10 years and $2-3 billion to deliver one new drug. This is both too expensive and too slow, especially in emergencies like the COVID-19 pandemic. In silico methodologies need to be improved both to select better lead compounds, so as to improve the efficiency of later stages in the drug discovery protocol, and to identify those lead compounds more quickly. No known methodological approach can deliver this combination of higher quality and speed. Here, we describe an Integrated Modeling PipEline for COVID Cure by Assessing Better LEads (IMPECCABLE) that employs multiple methodological innovations to overcome this fundamental limitation. We also describe the computational framework that we have developed to support these innovations at scale, and characterize the performance of this framework in terms of throughput, peak performance, and scientific results. We show that individual workflow components deliver 100× to 1000× improvement over traditional methods, and that the integration of methods, supported by scalable infrastructure, speeds up drug discovery by orders of magnitudes. IMPECCABLE has screened ~10 11 ligands and has been used to discover a promising drug candidate. These capabilities have been used by the US DOE National Virtual Biotechnology Laboratory and the EU Centre of Excellence in Computational Biomedicine.

97 MATHEMATICS AND COMPUTING↗

Functional Volume Assessment of an Early Version of the Mars Transit Habitat

During the summer of 2020, the NASA Mars Architecture Team (MAT) conducted a functional volume assessment of the Transit Habitat (TH). The TH has evolved substantially since that time and the current TH does not share the same internal configuration, but the insights gained from the assessment remain relevant. In virtually all architectures involving chemical, electric, or nuclear propulsion, the majority of the crew mission is spent aboard the TH. The Earth to Mars transit durations may vary from architecture to architecture, but all are on the order of hundreds of days, regardless of whether an opposition or conjunction class trajectory is selected, and regardless of whether the propulsion system is chemical, electric, or nuclear. Thus, the TH must provide capabilities appropriate to a very long duration. So, despite significant changes in the current Mars architecture over the past few years, this evaluation still provides useful recommendations in the form of habitability guidance that can be applied to current and future TH concepts. This assessment had six primary objectives: provide a sanity check to the BOC-derived TH layout; understand if we can fit the hardware and functional tasks in the volume; provide a high-level assessment of how aggressive the layout is; generate a list of challenges or assumptions necessary to make it work; generate a list of future work to refine understanding; and identify proposed requirements. All of this information is critical to drive habitat sizing studies and key architecture decisions. It was clear that a human-in-the-loop (HITL) evaluation of some kind would be necessary, but several challenges were immediately identified. The most information could be gleaned from a Desert Research and Technology Studies (DRATS) type of mission operations test (MOT), but the TH concept was too low fidelity to construct the type of prototype necessary to conduct a MOT, nor were their financial resources to do so. The next best option – and really the one most appropriate for the BOC’s stage of maturity – is a Virtual Reality (VR) walk-through evaluation. However, NASA was in a shutdown state due to the COVID-19 pandemic and the VR labs were inaccessible. As a result, a tabletop evaluation was created, using .jpg imagery from the ECM CAD model along with Excel-based datasheets. High-level crew living and working functions within the habitat were identified for evaluation. Questionnaires using Likert scales assessed acceptability of habitat functions and sim quality – the degree to which the function was represented in CAD. This enabled the evaluation to be conducted by personnel working remotely. Each function was evaluated individually along with several overarching habitability parameters and vehicle subsystems. The results of this evaluation are discussed, including methodological challenges and rating challenges. Acceptability results are discussed for functions that the participants were able to rate and participant comments for functions that could not be related are also described. Final conclusions are described, including challenges or assumptions needed to make the TH design acceptable, future work needed to refine understanding of the TH, and proposed habitat requirements based on test data.

Transit Habitat↗

Identifiability and predictability of integer- and fractional-order epidemiological models using physics-informed neural networks

Here we analyze a plurality of epidemiological models through the lens of physics-informed neural networks (PINNs) that enable us to identify time-dependent parameters and data-driven fractional differential operators. In particular, we consider several variations of the classical susceptible-infectious-removed (SIR) model by introducing more compartments and fractional-order and time-delay models. We report the results for the spread of COVID-19 in New York City, Rhode Island and Michigan states and Italy, by simultaneously inferring the unknown parameters and the unobserved dynamics. For integer-order and time-delay models, we fit the available data by identifying time-dependent parameters, which are represented by neural networks. In contrast, for fractional differential models, we fit the data by determining different time-dependent derivative orders for each compartment, which we represent by neural networks. We investigate the structural and practical identifiability of these unknown functions for different datasets, and quantify the uncertainty associated with neural networks and with control measures in forecasting the pandemic.

60 APPLIED LIFE SCIENCES↗

Graph-Based Modeling for the Detection and Tracking of Sarin-Surrogate-Induced Neurotoxicity Using a Human-Relevant, In-Vitro Brain Model

Organophosphorus (OP) nerve agents are a chemical threat to the United States, to the civilian population (e.g., pesticides) and historically weaponized (e.g., sarin) as chemical warfare agents. The unprecedented, accelerated process from “bench-to-bedside” during the SARSCov2 pandemic has made it clear that technology and tools need to be readily available for immediate response. Advances in human organ tissue mimetic systems are a promising technology to evaluate the human-relevant response in vitro for basic and applied research and drug screening. In particular, current brain microphysiological systems (MPS) have the capability to monitor and detect changes in engineered human neural circuit activity. However, current data analytics approaches for these systems lack the granularity to functionally detect and distinguish the different mechanisms that occur in the brain following neurotoxicity, injury, and disease. The goal of this project was to advance the computational analytical capabilities of the brain MPS to detect functional changes in neural circuit structure at different stages of Sarin surrogate-induced neurotoxicity. We developed graph-based models to (1) identify the composition of the neural circuit structure; (2) detect and monitor how this structure changes following sarin-induced neurotoxicity; and (3) evaluate the analytical pipeline using known/promising oxime reactivators. Through experiments on the bMPS where in vitro neuronal cultures were exposed to a sarin surrogate, we demonstrated the capabilities of our computational pipeline to identify different responses in the functional networks of brain cells exposed to low and high concentrations of the nerve agent. We identified a biphasic response of human neural network activity following exposure to a sarin-surrogate that had not been reported in the literature before. The graph-based models and software developed in this project can be used for future studies that leverage the brain MPS technology, such as treatment efficacy assessment.

59 BASIC BIOLOGICAL SCIENCES↗

Sneezing and asymptomatic virus transmission

The novel coronavirus disease (COVID-19) spread pattern continues to show that geographical barriers alone cannot contain a virus. Asymptomatic carriers play a critical role in the nature of this virus quickly escalating into a global pandemic. Asymptomatic carriers may transmit the virus unintentionally through sporadic sneezing. A novel Computational Fluid Dynamics (CFD) approach has been proposed with a realistic modeling of a human sneeze achieved by the combination of state-of-the-art experimental and numerical methods. This modeling approach may be suitable for future engineering analyses aimed at reshaping public spaces and common areas, with the main objective to accurately predict the spread of aerosol and droplets that may contain pathogens. This study shows that the biomechanics of a human sneeze, including complex muscle contractions and relaxations, can be accurately modeled by the angular head motion and the dynamic pressure response during sneezing. These have been considered as the human factors and were implemented in the CFD simulation by imposing a momentum source term to the coupled Eulerian–Lagrangian momentum equations. The momentum source was modeled by the measured dynamic pressure response in conjunction with the angular head motion. This approach eliminated the need to create an ad hoc set of inlet boundary conditions. With this proposed technique, it is easier to add multiple fixed and/or moving sources of sneezes in complex computational domains. Additionally, extensive sensitivity analyses based on different environmental conditions were performed, and their impact was described in terms of potential virus spread.

42 ENGINEERING↗

Battery-powered bargains? Assessing electric vehicle resale value in the United States

Abstract The resale market will play a critical role in expanding plug-in electric vehicle (PEV) adoption to middle- and lower-income households. Understanding PEV depreciation trends in comparison to those of conventional gasoline vehicles (CVs) is critical for assessing PEV affordability and informing relevant policy, such as subsidies for used PEVs. We deliver comprehensive, high-resolution estimates of value retention rates at the make-model level in the United States for battery electric vehicles (BEVs), plug-in hybrid electric vehicles (PHEVs), hybrid electric vehicles (HEVs), and CVs using a database of 9 million used cars listed online between 2016 and 2022. While BEVs and PHEVs have depreciated at faster rates than CVs, this trend is changing, with newer model year BEVs and those with larger ranges have significantly higher retention rates than older model years with smaller ranges. Tesla BEVs are a notable exception following the opposite trend, with earlier model years holding their value better than newer model years. Subsidized BEVs in the new market are associated with lower prices for the same model in the resale market, with the $7500 federal subsidy translating to a 3% lower resale price on average. Finally, disruptions from the COVID-19 pandemic have affected affordability across all vehicles, with mean listing prices rising 37% and 39% for CVs and BEVs, respectively, from January 2020 to March 2022 in inflation-adjusted 2019 dollars.

Environmental Sciences & Ecology↗

Synthetic method of analogues for emerging infectious disease forecasting

The Method of Analogues (MOA) has gained popularity in the past decade for infectious disease forecasting due to its non-parametric nature. In MOA, the local behavior observed in a time series is matched to the local behaviors of several historical time series. The known values that directly follow the historical time series that best match the observed time series are used to calculate a forecast. This non-parametric approach leverages historical trends to produce forecasts without extensive parameterization, making it highly adaptable. However, MOA is limited in scenarios where historical data is sparse. This limitation was particularly evident during the early stages of the COVID-19 pandemic, where the emerging global epidemic had little-to-no historical data. In this work, we propose a new method inspired by MOA, called the Synthetic Method of Analogues (sMOA). sMOA replaces historical disease data with a library of synthetic data that describe a broad range of possible disease trends. This model circumvents the need to estimate explicit parameter values by instead matching segments of ongoing time series data to a comprehensive library of synthetically generated segments of time series data. We demonstrate that sMOA has competitive performance with state-of-the-art infectious disease forecasting models, out-performing 78% of models from the COVID-19 Forecasting Hub in terms of averaged Mean Absolute Error and 76% of models from the COVID-19 Forecasting Hub in terms of averaged Weighted Interval Score. Additionally, we introduce a novel uncertainty quantification methodology designed for the onset of emerging epidemics. Developing versatile approaches that do not rely on historical data and can maintain high accuracy in the face of novel pandemics is critical for enhancing public health decision-making and strengthening preparedness for future outbreaks.

97 MATHEMATICS AND COMPUTING↗

Impacts of COVID-19 related stay-at-home restrictions on residential electricity use and implications for future grid stability

“Stay-at-home” orders and other health precautions enacted during the COVID-19 pandemic have led to substantial changes in residential electricity usage. Here, we conduct a case study to analyze data from 390 apartments in New York City (NYC) to examine the impacts of two key drivers of residential electricity usage: COVID-19 case-loads and the outdoor temperature. We develop a series of regression models to predict two characteristics of residential electricity usage on weekdays: The average occupied apartment’s consumption (kWh) over a 9am-5pm window and the hourly peak demand (Watt) over a 12pm-5pm window. Via a Monte Carlo simulation, we forecast the two usage characteristics under a possible scenario in which stay-at-home orders in NYC, or a similar metropolitan region, coincide with warm summer weather. Under the scenario, the 9am-5pm residential electricity usage on weekdays is predicted to be 15% – 24% higher than under prior, pre-pandemic conditions. This could lead to substantially higher utility costs for residents. Additionally, we predict that the residential hourly peak demand between 12pm and 5pm on weekdays could be 35% – 53% higher than that under pre-pandemic conditions. We conclude that the projected increase in peak demand - which might arise if stay-at-home guidelines coincided with hot weather conditions - could pose grid management challenges, especially for residential feeders. We also note that, if there is a longer lasting shift towards work and study-from-home, utilities will have to rethink load profile considerations. The applications of our predictive models to managing future smart-grid technology are also highlighted.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Aerosol transport pathways and source attribution in China during the COVID-19 outbreak

Abstract. Due to the coronavirus disease 2019 (COVID-19) pandemic, human activities and industrial productions were strictly restricted during January–March 2020 in China. Despite the fact that anthropogenic aerosol emissions largely decreased, haze events still occurred. Characterization of aerosol transport pathways and attribution of aerosol sources from specific regions are beneficial to air quality and pandemic control strategies. This study establishes source–receptor relationships in various regions covering all of China during the COVID-19 outbreak based on the Community Atmosphere Model version 5 with Explicit Aerosol Source Tagging (CAM5-EAST). Our analysis shows that PM2.5 burden over the North China Plain between 30 January and 19 February is mostly contributed by local emissions (40 %–66 %). For other regions in China, PM2.5 burden is largely contributed from nonlocal sources. During the most polluted days of the COVID-19 outbreak, local emissions within the North China Plain and eastern China contributed 66 % and 87 % to the increase in surface PM2.5 concentrations, respectively. This is associated with the anomalous mid-tropospheric high pressure at the location of the climatological East Asia trough and the consequently weakened winds in the lower troposphere, leading to the local aerosol accumulation. The emissions outside China, especially those from South Asia and Southeast Asia, contribute over 50 % to the increase in PM2.5 concentration in southwestern China through transboundary transport during the most polluted day. As the reduction in emissions in the near future is desirable, aerosols from long-range transport and unfavorable meteorological conditions are increasingly important to regional air quality and need to be taken into account in clean-air plans.

54 ENVIRONMENTAL SCIENCES↗

Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong

Abstract Analysis of phylogenetic trees has become an essential tool in epidemiology. Likelihood-based methods fit models to phylogenies to draw inferences about the phylodynamics and history of viral transmission. However, these methods are often computationally expensive, which limits the complexity and realism of phylodynamic models and makes them ill-suited for informing policy decisions in real-time during rapidly developing outbreaks. Likelihood-free methods using deep learning are pushing the boundaries of inference beyond these constraints. In this paper, we extend, compare, and contrast a recently developed deep learning method for likelihood-free inference from trees. We trained multiple deep neural networks using phylogenies from simulated outbreaks that spread among 5 locations and found they achieve close to the same levels of accuracy as Bayesian inference under the true simulation model. We compared robustness to model misspecification of a trained neural network to that of a Bayesian method. We found that both models had comparable performance, converging on similar biases. We also implemented a method of uncertainty quantification called conformalized quantile regression that we demonstrate has similar patterns of sensitivity to model misspecification as Bayesian highest posterior density (HPD) and greatly overlap with HPDs, but have lower precision (more conservative). Finally, we trained and tested a neural network against phylogeographic data from a recent study of the SARS-Cov-2 pandemic in Europe and obtained similar estimates of region-specific epidemiological parameters and the location of the common ancestor in Europe. Along with being as accurate and robust as likelihood-based methods, our trained neural networks are on average over 3 orders of magnitude faster after training. Our results support the notion that neural networks can be trained with simulated data to accurately mimic the good and bad statistical properties of the likelihood functions of generative phylogenetic models.

Evolutionary Biology↗

Human Mobility to Parks Under the COVID-19 Pandemic and Wildfire Seasons in the Western and Central United States

In 2020, people's health suffered a great crisis under the dual effects of the COVID-19 pandemic and the extensive, severe wildfires in the western and central United States. Parks, including city, national, and cultural parks, offer a unique opportunity for people to maintain their recreation behaviors following the social distancing protocols during the pandemic. However, massive forest wildfires in western and central US, producing harmful toxic gases and smoke, pose significant threats to human health and affect their recreation behaviors and mobility to parks. In this study, we employed the geographically and temporally weighted regression (GTWR) Models to investigate how COVID-19 and wildfires jointly shaped human mobility to parks, regarding the number of visits per capita, dwell time, and travel distance to parks, during June - September 2020. We detected strong correlations between visitations and COVID-19 incidence in southern Montana, western Wyoming, Colorado, and Utah before August. However, the pattern was weakened over time, indicating the decreasing trend of the degree of concern regarding the pandemic. Moreover, more park visits and lower dwell time were found in parks further away from wildfires and less air pollution in Washington, Oregon, California, Colorado, and New Mexico, during the wildfire season, suggesting the potential avoidance of wildfires when visiting parks. This study provides important insights on people's responses in recreation and social behaviors when facing multiple severe crises that impact their health and wellbeing, which could support the preparation and mitigation of the health impacts from future pandemics and natural hazards.

54 ENVIRONMENTAL SCIENCES↗

Sandia's Research in Support of COVID-19 Pandemic Response: Computing and Information Sciences

This report summarizes the goals and findings of eight research projects conducted under the Computing and Information Sciences (CIS) Research Foundation and related to the COVID- 19 pandemic. The projects were all formulated in response to Sandia's call for proposals for rapid-response research with the potential to have a positive impact on the global health emergency. Six of the projects in the CIS portfolio focused on modeling various facets of disease spread, resource requirements, testing programs, and economic impact. The two remaining projects examined the use of web-crawlers and text analytics to allow rapid identification of articles relevant to specific technical questions, and categorization of the reliability of content. The portfolio has collectively produced methods and findings that are being applied by a range of state, regional, and national entities to support enhanced understanding and prediction of the pandemic's spread and its impacts.

59 BASIC BIOLOGICAL SCIENCES↗

Dynamical model for social distancing in the U.S. during the COVID-19 epidemic

Social distancing has led to a “flattening of the curve” in many states across the U.S. This is part of a novel, massive, global social experiment which has served to mitigate the COVID-19 pandemic in the absence of a vaccine or effective anti-viral drugs. Hence it is important to be able to forecast hospitalizations reasonably accurately. We propose on phenomenological grounds a random walk/generalized diffusion equation which incorporates the effect of social distancing to describe the temporal evolution of the probability of having a given number of hospitalizations. The probability density function is log-normal in the number of hospitalizations, which is useful in describing pandemics where the number of hospitalizations is very high. We used this insight and data to make forecasts for states using Monte Carlo methods. Back testing validates our approach, which yields good results about a week into the future. States are beginning to reopen at the time of submission of this paper and our forecasts indicate possible precursors of increased hospitalizations. However, the trends we forecast for hospitalizations as well as infections thus far show moderate growth. Additionally we studied the reproducibility in New York (Italian strain) and California (Wuhan strain). We find that even if there is a difference in the transmission of the two strains, social distancing has been able to control the progression of COVID 19.

97 MATHEMATICS AND COMPUTING↗

Resource distribution under spatiotemporal uncertainty of disease spread: Stochastic versus robust approaches

We consider the problem of optimizing locations of distribution centers (DCs) and plans for distributing resources such as test kits and vaccines, under spatiotemporal uncertainties of disease spread and demand for the resources. We aim to balance the operational cost (including costs of deploying facilities, shipping, and storage) and quality of service (reflected by demand coverage), while ensuring equity and fairness of resource distribution across multiple populations. We compare a sample-based stochastic programming (SP) approach with a distributionally robust optimization (DRO) approach using a moment-based ambiguity set. Numerical studies are conducted on instances of distributing COVID-19 vaccines in the United States and test kits, to compare SP and DRO models with a deterministic formulation using estimated demand and with the current resource distribution plans implemented in the US. We demonstrate the results over distinct phases of the pandemic to estimate the cost and speed of resource distribution depending on scale and coverage, and show the “demand-driven” properties of the SP and DRO solutions. Furthermore, our results further indicate that if the worst-case unmet demand is prioritized, then the DRO approach is preferred despite of its higher overall cost. Nevertheless, the SP approach can provide an intermediate plan under budgetary restrictions without significant compromises in demand coverage.

97 MATHEMATICS AND COMPUTING↗

Quantitative methods and modeling to assess COVID–19–interrupted in vivo pharmacokinetic bioequivalence studies with two reference batches

The coronavirus disease 2019 (COVID-19) has presented unprecedented challenges to the generic drug development, including interruptions in bioequivalence (BE) studies. Per guidance published by the US Food and Drug Administration (FDA) during the COVID-19 public health emergency, any protocol changes or alternative statistical analysis plan for COVID-19-interrupted BE study should be accompanied with adequate justifications and not lead to biased equivalence determination. In this study, we used a modeling and simulation approach to assess the potential impact of study outcomes when two different batches of a Reference Standard (RS) were to be used in an in vivo pharmacokinetic BE study due to the RS expiration during the COVID-19 pandemic. Simulations were performed with hypothetical drugs under two scenarios: (1) uninterrupted study using a single batch of an RS, and (2) interrupted study using two batches of an RS. The acceptability of BE outcomes was evaluated by comparing the results obtained from interrupted studies with those from uninterrupted studies. The simulation results demonstrated that using a conventional statistical approach to evaluate BE for COVID-19-interrupted studies may be acceptable based on the pooled data from two batches. An alternative statistical method which includes a “batch” effect to the mixed effects model may be used when a significant “batch” effect was found in interrupted four-way crossover studies. However, such alternative method is not applicable for interrupted two-way crossover studies. Overall, the simulated scenarios are only for demonstration purpose, the acceptability of BE outcomes for the COVID19-interrupted studies could be case-specific.

60 APPLIED LIFE SCIENCES↗

A new Software Training Model at Belle II

The physics output of modern experimental HEP collaborations hinges not only on the quality of its software but also on the ability of the collaborators to make the best possible use of it. With the COVID-19 pandemic making in-person training impossible, the training paradigm at Belle II was shifted from periodic workshops towards guided self-study. To that end, the study material was rebuilt from scratch as a series of modular and hands-on lessons tightly integrated with the software documentation using Sphinx. Each lesson contains multiple exercises that are supplemented with hints and complete solutions. Rather than duplicating information, students are systematically taught to work with the technical reference documentation to find the important sections for themselves. Unit tests ensure that all examples work with different software versions, and feedback buttons make it easy to submit comments for improvements.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

UrbanPop: A spatial microsimulation framework for exploring demographic influences on human dynamics

Ensuring the social equity of planning measures in social systems requires an understanding of human dynamics, particularly how individual relationships, activities, and interactions intersect with individual needs. Spatial microsimulation models (SMSMs) support planning for human security goals by representing human dynamics through realistic, georeferenced synthetic populations, that a) provide a complete representation of social systems while b) also protecting individual privacy. In this paper, we present UrbanPop, an open and reproducible SMSM framework for analysis of human dynamics with high spatial, temporal, and demographic resolution. UrbanPop creates synthetic populations of demographically detailed worker and student agents, positioning them first at probable nighttime locations (home), then moving them to probable daytime locations (work/school). Summary aggregations of these populations match the granular detail available at the census block group level in the American Community Survey Summary File (SF), providing realistic approximations of the actual population. UrbanPop users can select particular demographic traits important in their application, resulting in a highly tailored agent population. We first lay out UrbanPop's baseline methodology, including population synthesis, activity modeling, and diagnostics, then demonstrate these capabilities by developing case studies of shifting population distributions and high-risk populations in Knox County, TN during the global COVID-19 pandemic.

60 APPLIED LIFE SCIENCES↗