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31 records · Page 2

Structure–activity relationship-based chemical classification of highly imbalanced Tox21 datasets

Abstract The specificity of toxicant-target biomolecule interactions lends to the very imbalanced nature of many toxicity datasets, causing poor performance in Structure–Activity Relationship (SAR)-based chemical classification. Undersampling and oversampling are representative techniques for handling such an imbalance challenge. However, removing inactive chemical compound instances from the majority class using an undersampling technique can result in information loss, whereas increasing active toxicant instances in the minority class by interpolation tends to introduce artificial minority instances that often cross into the majority class space, giving rise to class overlapping and a higher false prediction rate. In this study, in order to improve the prediction accuracy of imbalanced learning, we employed SMOTEENN, a combination of Synthetic Minority Over-sampling Technique (SMOTE) and Edited Nearest Neighbor (ENN) algorithms, to oversample the minority class by creating synthetic samples, followed by cleaning the mislabeled instances. We chose the highly imbalanced Tox21 dataset, which consisted of 12 in vitro bioassays for > 10,000 chemicals that were distributed unevenly between binary classes. With Random Forest (RF) as the base classifier and bagging as the ensemble strategy, we applied four hybrid learning methods, i.e., RF without imbalance handling (RF), RF with Random Undersampling (RUS), RF with SMOTE (SMO), and RF with SMOTEENN (SMN). The performance of the four learning methods was compared using nine evaluation metrics, among which F 1 score, Matthews correlation coefficient and Brier score provided a more consistent assessment of the overall performance across the 12 datasets. The Friedman’s aligned ranks test and the subsequent Bergmann-Hommel post hoc test showed that SMN significantly outperformed the other three methods. We also found that a strong negative correlation existed between the prediction accuracy and the imbalance ratio (IR), which is defined as the number of inactive compounds divided by the number of active compounds. SMN became less effective when IR exceeded a certain threshold (e.g., > 28). The ability to separate the few active compounds from the vast amounts of inactive ones is of great importance in computational toxicology. This work demonstrates that the performance of SAR-based, imbalanced chemical toxicity classification can be significantly improved through the use of data rebalancing.

Idakwo, Gabriel↗

Materials Data on SmHO2 by Materials Project

SmO(OH) crystallizes in the orthorhombic Pnma space group. The structure is three-dimensional. Sm3+ is bonded to six O2- atoms to form a mixture of distorted corner and edge-sharing SmO6 octahedra. The corner-sharing octahedral tilt angles are 60°. There are a spread of Sm–O bond distances ranging from 2.27–2.50 Å. H1+ is bonded in a single-bond geometry to one O2- atom. The H–O bond length is 0.99 Å. There are two inequivalent O2- sites. In the first O2- site, O2- is bonded in a distorted single-bond geometry to three equivalent Sm3+ and one H1+ atom. In the second O2- site, O2- is bonded in a trigonal planar geometry to three equivalent Sm3+ atoms.

36 MATERIALS SCIENCE↗

Predictive performance of multi-model ensemble forecasts of COVID-19 across European nations

Background: Short-term forecasts of infectious disease burden can contribute to situational awareness and aid capacity planning. Based on best practice in other fields and recent insights in infectious disease epidemiology, one can maximise the predictive performance of such forecasts if multiple models are combined into an ensemble. Here, we report on the performance of ensembles in predicting COVID-19 cases and deaths across Europe between 08 March 2021 and 07 March 2022. Methods: We used open-source tools to develop a public European COVID-19 Forecast Hub. We invited groups globally to contribute weekly forecasts for COVID-19 cases and deaths reported by a standardised source for 32 countries over the next 1–4 weeks. Teams submitted forecasts from March 2021 using standardised quantiles of the predictive distribution. Each week we created an ensemble forecast, where each predictive quantile was calculated as the equally-weighted average (initially the mean and then from 26th July the median) of all individual models’ predictive quantiles. We measured the performance of each model using the relative Weighted Interval Score (WIS), comparing models’ forecast accuracy relative to all other models. We retrospectively explored alternative methods for ensemble forecasts, including weighted averages based on models’ past predictive performance. Results: Over 52 weeks, we collected forecasts from 48 unique models. We evaluated 29 models’ forecast scores in comparison to the ensemble model. We found a weekly ensemble had a consistently strong performance across countries over time. Across all horizons and locations, the ensemble performed better on relative WIS than 83% of participating models’ forecasts of incident cases (with a total N=886 predictions from 23 unique models), and 91% of participating models’ forecasts of deaths (N=763 predictions from 20 models). Across a 1–4 week time horizon, ensemble performance declined with longer forecast periods when forecasting cases, but remained stable over 4 weeks for incident death forecasts. In every forecast across 32 countries, the ensemble outperformed most contributing models when forecasting either cases or deaths, frequently outperforming all of its individual component models. Among several choices of ensemble methods we found that the most influential and best choice was to use a median average of models instead of using the mean, regardless of methods of weighting component forecast models. Conclusions: Our results support the use of combining forecasts from individual models into an ensemble in order to improve predictive performance across epidemiological targets and populations during infectious disease epidemics. Our findings further suggest that median ensemble methods yield better predictive performance more than ones based on means. Our findings also highlight that forecast consumers should place more weight on incident death forecasts than incident case forecasts at forecast horizons greater than 2 weeks. Funding: AA, BH, BL, LWa, MMa, PP, SV funded by National Institutes of Health (NIH) Grant 1R01GM109718, NSF BIG DATA Grant IIS-1633028, NSF Grant No.: OAC-1916805, NSF Expeditions in Computing Grant CCF-1918656, CCF-1917819, NSF RAPID CNS-2028004, NSF RAPID OAC-2027541, US Centers for Disease Control and Prevention 75D30119C05935, a grant from Google, University of Virginia Strategic Investment Fund award number SIF160, Defense Threat Reduction Agency (DTRA) under Contract No. HDTRA1-19-D-0007, and respectively Virginia Dept of Health Grant VDH-21-501-0141, VDH-21-501-0143, VDH-21-501-0147, VDH-21-501-0145, VDH-21-501-0146, VDH-21-501-0142, VDH-21-501-0148. AF, AMa, GL funded by SMIGE - Modelli statistici inferenziali per governare l'epidemia, FISR 2020-Covid-19 I Fase, FISR2020IP-00156, Codice Progetto: PRJ-0695. AM, BK, FD, FR, JK, JN, JZ, KN, MG, MR, MS, RB funded by Ministry of Science and Higher Education of Poland with grant 28/WFSN/2021 to the University of Warsaw. BRe, CPe, JLAz funded by Ministerio de Sanidad/ISCIII. BT, PG funded by PERISCOPE European H2020 project, contract number 101016233. CP, DL, EA, MC, SA funded by European Commission - Directorate-General for Communications Networks, Content and Technology through the contract LC-01485746, and Ministerio de Ciencia, Innovacion y Universidades and FEDER, with the project PGC2018-095456-B-I00. DE., MGu funded by Spanish Ministry of Health / REACT-UE (FEDER). DO, GF, IMi, LC funded by Laboratory Directed Research and Development program of Los Alamos National Laboratory (LANL) under project number 20200700ER. DS, ELR, GG, NGR, NW, YW funded by National Institutes of General Medical Sciences (R35GM119582; the content is solely the responsibility of the authors and does not necessarily represent the official views of NIGMS or the National Institutes of Health). FB, FP funded by InPresa, Lombardy Region, Italy. HG, KS funded by European Centre for Disease Prevention and Control. IV funded by Agencia de Qualitat i Avaluacio Sanitaries de Catalunya (AQuAS) through contract 2021-021OE. JDe, SMo, VP funded by Netzwerk Universitatsmedizin (NUM) project egePan (01KX2021). JPB, SH, TH funded by Federal Ministry of Education and Research (BMBF; grant 05M18SIA). KH, MSc, YKh funded by Project SaxoCOV, funded by the German Free State of Saxony. Presentation of data, model results and simulations also funded by the NFDI4Health Task Force COVID-19 ( https://www.nfdi4health.de/task-force-covid-19-2 ) within the framework of a DFG-project (LO-342/17-1). LP, VE funded by Mathematical and Statistical modelling project (MUNI/A/1615/2020), Online platform for real-time monitoring, analysis and management of epidemic situations (MUNI/11/02202001/2020); VE also supported by RECETOX research infrastructure (Ministry of Education, Youth and Sports of the Czech Republic: LM2018121), the CETOCOEN EXCELLENCE (CZ.02.1.01/0.0/0.0/17-043/0009632), RECETOX RI project (CZ.02.1.01/0.0/0.0/16-013/0001761). NIB funded by Health Protection Research Unit (grant code NIHR200908). SAb, SF funded by Wellcome Trust (210758/Z/18/Z).

60 APPLIED LIFE SCIENCES↗

Program and Project Management Framework

The primary objective of this project was to develop a framework and system architecture for integrating program and project management tools that may be applied consistently throughout Kennedy Space Center (KSC) to optimize planning, cost estimating, risk management, and project control. Project management methodology used in building interactive systems to accommodate the needs of the project managers is applied as a key component in assessing the usefulness and applicability of the framework and tools developed. Research for the project included investigation and analysis of industrial practices, KSC standards, policies, and techniques, Systems Management Office (SMO) personnel, and other documented experiences of project management experts. In addition, this project documents best practices derived from the literature as well as new or developing project management models, practices, and techniques.

Butler, Cassandra D.↗

Validation of Procedures for Monitoring Crewmember Immune Function

There is ample evidence to suggest that space flight leads to immune system dysregulation, however the nature of the phenomenon as it equilibrates over longer flights has not been determined. This dysregulation may be a result of microgravity, confinement, physiological stress, radiation, environment or other mission-associated factors. The clinical risk (if any) for exploration-class space flight is unknown, but may include increased incidence of infection, allergy, hypersensitivity, hematological malignancy or altered wound healing. The objective of this Supplemental Medical Objective (SMO) is to determine the status of the immune system, physiological stress and latent viral reactivation (a clinical outcome that can be measured) during both short and long-duration spaceflight. In addition, this study will develop and validate an immune monitoring strategy consistent with operational flight requirements and constraints. Pre-mission, in-flight and post-flight blood and saliva samples will be obtained from participating crewmembers. Assays included peripheral immunophenotype, T cell function, cytokine profiles (RNA, intracellular, secreted), viral-specific immunity, latent viral reactivation (EBV, CMV, VZV), and stress hormone measurements. This study is currently ongoing. To date, 10 short duration and 5 long-duration crewmembers have completed the study. Technically, the study is progressing well. In-flight blood samples are being collected, and returned for analysis, including functional assays that require live cells. For all in-flight samples to date, sample viability has been acceptable. Preliminary data (n = 4/7; long/short duration, respectively) indicate that distribution of most peripheral leukocyte subsets is largely unaltered during flight. Exceptions include elevated T cells, reduced B/NK cells, increased memory T cells and increased central memory CD8+ T cells. General T cell function, early blastogenesis response to mitogenic stimulation, is markedly reduced in-flight. In-vivo cytokine production profiles are altered, with in-flight dysregulation observed in the Th1/Th2/Treg equilibrium. EBV specific T cell levels are increased during flight, whereas their function is reduced. VZV reactivation was observed inflight and several days post flight with highest levels measured later during long-duration flight. The shedding of CMV in the urine was detected of 4/5 long duration and 4/7 short duration crewmembers. Plasma cortisol was not elevated during flight. Further data will be required to validate the initial observations.

Crucian, Brian↗

Biosensors for EVA: Improved Instrumentation for Ground-based Studies

During lunar excursions in the EVA suit, real-time measurement of metabolic rate is required to manage consumables and guide activities to ensure safe return to the base. Metabolic rate, or oxygen consumption (VO2), is normally measured from pulmonary parameters but cannot be determined with standard techniques in the oxygen-rich environment of a spacesuit. Our group has developed novel near infrared spectroscopic (NIRS) methods to calculate muscle oxygen saturation (SmO 2), hematocrit, and pH, and we recently demonstrated that we can use our NIRS sensor to measure VO 2 on the leg during cycling. Our NSBRI project has 4 objectives: (1) increase the accuracy of the metabolic rate calculation through improved prediction of stroke volume; (2) investigate the relative contributions of calf and thigh oxygen consumption to metabolic rate calculation for walking and running; (3) demonstrate that the NIRS-based noninvasive metabolic rate methodology is sensitive enough to detect decrement in VO 2 in a space analog; and (4) improve instrumentation to allow testing within a spacesuit. Over the past year we have made progress on all four objectives, but the most significant progress was made in improving the instrumentation. The NIRS system currently in use at JSC is based on fiber optics technology. Optical fiber bundles are used to deliver light from a light source in the monitor to the patient, and light reflected back from the patient s muscle to the monitor for spectroscopic analysis. The fiber optic cables are large and fragile, and there is no way to get them in and out of the test spacesuit used for ground-based studies. With complimentary funding from the US Army, we undertook a complete redesign of the sensor and control electronics to build a novel system small enough to be used within the spacesuit and portable enough to be used by a combat medic. In the new system the filament lamp used in the fiber optic system was replaced with a novel broadband near infrared LED light source. The compact grating spectrometer was replaced with a chip-scale spectrometer. With this new design, the sensor is 4 in 2 in 0.5 in, weighs 60 g, and no fiber optic cables are needed. The sensor, which contains the light source and the spectrometer, is adhered directly to the skin with medical grade adhesive. The sensor can be powered via the USB port of the laptop computer that controls the sensor operation. Alternatively, for studies in the spacesuit, the sensor can be powered by a small battery pack and operated by an ultra-portable hand-held computer. Both the handheld computer and battery pack will easily fit within the PLSS of the test spacesuit. System automation was significantly improved, to add features suggested by our colleagues in the Cardiovascular Laboratory and the NASA JSC Exercise Physiology and Countermeasures Project. The functionality and portability of this system were demonstrated in our UMass laboratory.

Soller, B.↗

Validation of Procedures for Monitoring Crewmember Immune Function

The objective of this Supplemental Medical Objective (SMO) is to determine the status of the immune system, physiological stress and latent viral reactivation (a clinical outcome that can be measured) during both short and long-duration spaceflight. In addition, this study will develop and validate an immune monitoring strategy consistent with operational flight requirements and constraints. Pre-mission, in-flight and post-flight blood and saliva samples will be obtained from participating crewmembers. Assays included peripheral immunophenotype, T cell function, cytokine profiles, viral-specific immunity, latent viral reactivation (EBV, CMV, VZV), and stress hormone measurements. To date, 18 short duration (now completed) and 8 long-duration crewmembers have completed the study. The long-duration phase of this study is ongoing. For this presentation, the final data set for the short duration subjects will be discussed.

Pierson, Duane↗

Human Research Program Human Health Countermeasures Element Cardiovascular Risks Standing Review Panel (SRP)

The Cardiovascular Risk Standing Review Panel (SRP) evaluated several cardiovascular risks associated with space flight along with the ongoing and emerging plans to study these issues and potentially propose and/or develop countermeasures. The areas of focus included: 1) The risk of cardiac rhythm problems during prolonged space flight, and 2) Issues related to the risk of orthostatic intolerance during re-exposure to gravity. An emerging area of concern is radiation associated vascular injury. The risk of cardiac rhythm disturbances has emerged based on case reports only. No systematic study of this risk has been published. However, concerns about this risk are heightened by the age range of astronauts, the structural changes in the heart that occur during space flight, and the potential shifts in fluids and electrolytes. The current plan is to use prolonged Holter monitor EKG records made as part of the "Integrated Cardiovascular SMO" in space to determine more about the frequency and magnitude of this problem and to link this data to complementary data from the nutrition group on electrolytes. The SRP was supportive of this approach. The SRP also felt that any data related to cardiovascular risk in space should be better coordinated with the medical screening data that all astronauts undergo at regular intervals. Additionally, while there are potential privacy issues related to this suggestion, many of the current barriers to better coordination of experimental and clinical data appear to reflect longstanding cultural traditions at NASA that need rethinking. The risk of orthostatic intolerance during re-exposure to gravity was seen by the SRP as an area supported by a wealth of published physiological evidence. The SRP also felt that moving forward with the planned approach to countermeasures was reasonable and that extensive additional hypothesis testing on the physiology of orthostatic intolerance was not needed at this time. There was support for developing ground based models of limited (e.g. 1/6 th) G environments on Earth that generated a number of ideas for consideration by NASA investigators.

Joyner, Michael↗

Corrosion Performance of Stainless Steels in a Simulated Launch Environment

At the Kennedy Space Center, NASA relies on stainless steel (SS) tubing to supply the gases and fluids required to launch the Space Shuttle. 300 series SS tubing has been used for decades but the highly corrosive environment at the launch pad has proven to be detrimental to these alloys. An upgrade with higher alloy content materials has become necessary in order to provide a safer and long lasting launch facility. In the effort to find the most suitable material to replace the existing AISI 304L SS ([iNS S30403) and AISI 316L SS (UNS S31603) shuttle tubing, a study involving atmospheric exposure at the corrosion test site near the launch pads and electrochemical measurements is being conducted. This paper presents the results of an investigation in which stainless steels of the 300 series, 304L, 316L, and AISI 317L SS (UNS S31703) as well as highly alloyed stainless steels 254-SMO (UNS S32154), AL-6XN (N08367) and AL29-4C ([iNS S44735) were evaluated using direct current (DC) electrochemical techniques under conditions designed to simulate those found at the Space Shuttle Launch pad. The electrochemical results were compared to the atmospheric exposure data and evaluated for their ability to predict the long-term corrosion performance of the alloys.

Calle, Luz Marina↗

Fibroblast Growth Factor-23 in Bed Rest and Spaceflight

Many nutritional factors influence bone, from the basics of calcium and vitamin D, to factors which influence bone through acid/base balance, including protein, sodium, and more. Fibroblast growth factor 23 (FGF23) is a recently identified factor, secreted from osteocytes, which is involved in classic (albeit complex) feedback loops controlling phosphorus homeostasis through both vitamin D and parathyroid hormone (PTH) (1, 2). As osteocytes are gravity sensing cells, it is important to determine if there are changes in FGF23 during spaceflight. In extreme cases, such as chronic kidney disease, FGF23 levels are highly elevated. FGF23 imbalances, secondary to dietary influences, may contribute to skeletal demineralization and kidney stone risk during spaceflight. Presented with an imbalanced dietary phosphorus to calcium ratio, increased secretion of FGF23 will inhibit renal phosphorus reabsorption, resulting in increased excretion and reduced circulating phosphorus. Increased intake and excretion of phosphorus is associated with increased kidney stone risk in both the terrestrial and microgravity environments. Highly processed foods and carbonated beverages are associated with higher phosphorus content. Ideally, the dietary calcium to phosphorus ratio should be at minimum 1:1. Nutritional requirements for spaceflight suggest that this ratio not be less than 0.67 (3), while the International Space Station (ISS) menu provides 1020 mg Ca and 1856 mg P, for a ratio of 0.55 (3). Subjects in NASA's bed rest studies, by design, have consumed intake ratios much closer to 1.0 (4). FGF23 also has an inhibitory influence on PTH secretion and 1(alpha)-hydroxylase, both of which are required for activating vitamin D with the conversion of 25-hydroxyvitamin D to 1,25-dihydroxyvitamin D. Decreased 1,25-dihydroxyvitamin D will result in decreased intestinal phosphorus absorption, and increased urinary phosphorus excretion (via decreased renal reabsorption). Should a decrease in 1,25- dihydroxyvitamin D be necessary to reduce intestinal phosphorus absorption, calcium absorption will also proportionally be reduced, potentially leading to skeletal demineralization. Demineralization of bone can increase kidney stone risk, a medical issue that could prove detrimental to mission success. Given the interrelationships described above, we sought to determine circulating FGF23 concentrations in spaceflight and ground analog studies to better understand the potential effects of dietary phosphorus on bone and calcium metabolism. We analyzed serum from ISS astronauts participating in studies of bone biochemistry, including the Nutrition SMO and Pro K experiments, and we also evaluated FGF23 during extended-duration bed rest. Serum intact FGF23 levels were determined using an ELISA kit from Kainos laboratories in Japan. While initial evaluation of the data showed no changes over time during flight or bed rest, evaluation continues of FGF23 data in light of dietary factors, PTH, vitamin D status, and other biochemical and endocrine factors.

Bokhari, R.↗

Risk of Oxidative Damage to Bone from Increased Iron Stores During Space Flight

Iron stores are increased secondary to neocytolysis of red blood cells and a high dietary intake of iron during space flight. This raises concerns about the risk of excess iron causing oxidative damage in many tissues, including bone. Biomarkers of iron status, oxidative damage, and bone resorption during space flight were analyzed for 23 (16 M/7 F) International Space Station crewmembers as part of the Nutrition SMO project. Up to 5 in-flight blood samples and 24-h urine pools were collected over the course of the 4-6 month missions. Serum iron increased slightly during space flight and was decreased at landing (P < 0.0004). An increase in serum ferritin early in flight (217% in women and 68% in men, P < 0.0004), returning to preflight concentrations at landing, and a decrease in transferrin and transferrin receptors during flight indicated that a transient increase in iron stores occurred. No inflammatory response was observed during flight. The oxidative damage markers 8-hydroxy-2'-deoxyguanosine and prostaglandin F(sub 2(alpha)) were positively correlated (both P < 0.001) with serum ferritin. A greater area under the curve for ferritin during flight was correlated with greater changes in bone mineral density of several bone regions after flight (1). In a separate study (2), a ground-based investigation was conducted that examined the combined effects of radiation exposure and iron overload on sensitivity to radiation injury in several physiological systems in 12-wk male Sprague-Dawley rats. The rats were acclimated to an adequate iron diet (45 mg iron (ferric citrate)/kg diet) for 3 wk and then assigned to one of four groups: adequate iron (Fe) diet/no radiation, adequate Fe diet/ radiation, moderately high Fe diet (650 mg Fe (ferric citrate)/kg diet)/no radiation, and moderately high Fe diet/radiation. Animals remained on the assigned diet for 4 wk. Starting on day 14 of experimental diet treatment, animals were exposed to a fractionated dose (0.375 Gy) of Cs-137 every other day (3 Gy total dose). On day 29 (24 h after last radiation exposure), animals were euthanized. Oxidative stress markers in the liver, bone, eyes, and serum were assessed. There was evidence that the iron diet contributed to DNA damage as well as radiation exposure in the liver, eyes, and bone. Together, the results suggest that increased iron stores do constitute a risk factor for oxidative damage and bone resorption, during space flight and on Earth. Funded by the Human Health and Countermeasures Element of the NASA Human Research Program.

Zwart, S. R.↗

The Silicon Meta-shell X-ray Mirror Technology Development Roadmap for the Lynx Mission

This document presents a roadmap for advancing the silicon meta-shell optics (SMO). It describes an overall strategy and key technical elements to be developed to meet the four-fold Lynx requirements: (1) angular resolution, (2) effective area, (3) mass, and (4) production schedule and cost. It also describes the building and testing of an engineering unit whose successful completion will retire all risks, technical, logistical, schedule, and cost, associated with building and delivering a mirror assembly for the Lynx mission. All of this work, designed to advance this technology to TRL 6, will be completed by Preliminary Design Review (PDR) to ensure that the flight mirror assembly production process will be but a repetition of a set of well-defined and mature steps, leading to on-time and on-budget delivery of a mirror assembly for the Lynx mission.

Zhang, William W.↗

Joint Assimilation of SMOS Brightness Temperature and GRACE Terrestrial Water Storage Observations for Improved Soil Moisture Estimation

Observations from recent soil moisture missions (e.g. SMOS) have been used in innovative data assimilation studies to provide global high spatial (i.e. 40 km) and temporal resolution (i.e. 3-days) soil moisture profile estimates from microwave brightness temperature observations. In contrast with microwave-based satellite missions that are only sensitive to near-surface soil moisture (0 - 5 cm), the Gravity Recovery and Climate Experiment (GRACE) mission provides accurate measurements of the entire vertically integrated terrestrial water storage column but, it is characterized by low spatial (i.e. 150,000 km2) and temporal (i.e. monthly) resolutions. Data assimilation studies have shown that GRACE-TWS primarily affects (in absolute terms) deeper moisture storages (i.e., groundwater). This work hypothesizes that unprecedented soil water profile accuracy can be obtained through the joint assimilation of GRACE terrestrial water storage and SMOS brightness temperature observations. A particular challenge of the joint assimilation is the use of the two different types of measurements that are relevant for hydrologic processes representing different temporal and spatial scales. The performance of the joint assimilation strongly depends on the chosen assimilation methods, measurement and model error spatial structures. The optimization of the assimilation technique constitutes a fundamental step toward a multi-variate multi-resolution integrative assimilation system aiming to improve our understanding of the global terrestrial water cycle.

Soil Moisture↗