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At least 19 records

Microgravity simulations with human lymphocytes in the free fall machine and in the random positioning machine

The purpose of this paper is to present the results obtained in our laboratory with both instruments, the FFM [free fall machine] and the RPM [random positioning machine], to compare them with the data from earlier experiments with human lymphocytes conducted in the FRC [fast rotating clinostat] and in space. Furthermore, the suitability of the FFM and RPM for research in gravitational cell biology is discussed.

Rotation↗

Simulated Microgravity Regulates Gene Transcript Profiles of 2T3 Preosteoblasts: Comparison of the Random Positioning Machine and the Rotating Wall Vessel Bioreactor

Microgravity of spaceflight induces bone loss due in part to decreased bone formation by osteoblasts. We have previously examined the microgravity-induced changes in gene expression profiles in 2T3 preosteoblasts using the Random Positioning Machine (RPM) to simulate microgravity conditions. Here, we hypothesized that exposure of preosteoblasts to an independent microgravity simulator, the Rotating Wall Vessel (RWV), induces similar changes in differentiation and gene transcript profiles, resulting in a more confined list of gravi-sensitive genes that may play a role in bone formation. In comparison to static 1g controls, exposure of 2T3 cells to RWV for 3 days inhibited alkaline phosphatase activity, a marker of differentiation, and downregulated 61 genes and upregulated 45 genes by more than two-fold as shown by microarray analysis. The microarray results were confirmed with real time PCR for downregulated genes osteomodulin, bone morphogenic protein 4 (BMP4), runx2, and parathyroid hormone receptor 1. Western blot analysis validated the expression of three downregulated genes, BMP4, peroxiredoxin IV, and osteoglycin, and one upregulated gene peroxiredoxin I. Comparison of the microarrays from the RPM and the RWV studies identified 14 gravi-sensitive genes that changed in the same direction in both systems. Further comparison of our results to a published database showing gene transcript profiles of mechanically loaded mouse tibiae revealed 16 genes upregulated by the loading that were shown to be downregulated by RWV and RPM. These mechanosensitive genes identified by the comparative studies may provide novel insights into understanding the mechanisms regulating bone formation and potential targets of countermeasure against decreased bone formation both in astronauts and in general patients with musculoskeletal disorders.

Patel, Mamta J.↗

Plastid position in Arabidopsis columella cells is similar in microgravity and on a random-positioning machine

In order to study gravity effects on plant structure and function, it may become necessary to remove the g-stimulus. On Earth, various instruments such as clinostats have been used by biologists in an attempt to neutralize the effects of gravity. In this study, the position of amyloplasts was assayed in columella cells in the roots of Arabidopsis thaliana (L.) Heynh. seedlings grown in the following conditions: on Earth, on a two-dimensional clinostat at 1 rpm, on a three-dimensional clinostat (also called a random-positioning machine, or an RPM), and in space (true microgravity). In addition, the effects of these gravity treatments on columella cell area and plastid area also were measured. In terms of the parameters measured, only amyloplast position was affected by the gravity treatments. Plastid position was not significantly different between spaceflight and RPM conditions but was significantly different between spaceflight and the classical two-dimensional clinostat treatments. Flanking columella cells showed a greater susceptibility to changes in gravity compared to the central columella cells. In addition, columella cells of seedlings that were grown on the RPM did not exhibit deleterious effects in terms of their ultrastructure as has been reported previously for seedlings grown on a two-dimensional clinostat. This study supports the hypothesis that the RPM provides a useful simulation of weightlessness.

Non-NASA Center↗

Design and Development of Modules to Support Live Microscopic Imaging on Ground-Based Microgravity Simulators

In space, astronauts are exposed to environmental stressors that often result in physiological changes. One prominent stressor in spaceflight is microgravity, and research has shown that long term microgravity exposure causes muscle atrophy, bone loss, cardiovascular concerns, and vision impairment. It is critical to understand how altered gravity affects physiology on the cellular, molecular, and gene level in order to accurately assess health risks and to develop effective countermeasures. Ground-based microgravity simulators such as random positioning machines (RPMs) are used to produce some of the biological effects of altered gravity on different cell types and organisms. Real-time imaging during simulations are of particular interest as we can study how basic cell functions such as cell division, cell migration, and proliferation progress under microgravity conditions. However, design limitations of present microgravity simulators such as susceptibility to parasitic vibration and displacement of the sample from the center of rotation challenge the accuracy of experiment results and live images. We have developed a cell culture sample holder module suitable for live microscopic imaging on an RPM. CAD modeling and 3D printing technology were used to implement modifications to the sample holder and to install a digital microscope to perform live bright-field and fluorescent imaging. Vibration damping materials were also investigated to allow for stable imaging while the microgravity simulator was within a cell culture incubator. Novel methods and hardware modifications for improving live cell imaging on ground-based microgravity simulators were proposed and discussed.

3D printing↗

Molecular Basis of Mechano-Signal Transduction in Vascular Endothelial Cells

Simulated microgravity studies using a random positioning machine (RPM). One RPM machine has been built for us by Fokker Science in Netherland. Using the device, we have developed an in vitro system to examine the effect of simulated microgravity on osteoblastic bone cells. Using this system, we have carried out gene chip studies to determine the gene expression profiles of osteoblasts cultured under simulated microgravity conditions in comparison to static controls. From this study, we have identified numerous genes, some of which are expected ones inducing bone loss, but many of which are unexpected and unknown. These findings are being prepared for publications.

Jo, Hanjoong↗

Root Growth Response of Arabidopsis Thaliana Seeds Exposed to Simulated Solar Particle Event Radiation and Microgravity

As NASA manned missions are planned to go past earth’s orbit, the effects of microgravity and radiation on plants will be essential to know as plants will be a part of the crew’s diet. APPROACH: Imbibed Arabidopsis thaliana seeds were exposed to simulated solar particle event (SPE) radiation, experiencing up to 80 cGy of radiation. After the radiation exposure, they were grown under simulated microgravity using a Random Positioning Machine. Images of the plants were taken after six to seven days of growth and the root length, top angle, tip angle were analyzed.

Karen Perkins↗

Customized Science Carrier Modules and Accessories Developed for Microgravity Simulation Devices

Because the access to the true weightless environment of the ISS and other Low Earth Orbit (LEO) vehicles is limited and cost prohibitive, the need for ground-based microgravity simulation analogs to bridge the gravity continuum gap between 1g gravity and costly space flight studies with true weightlessness was realized. As such, the Microgravity Simulation Support Facility (MSSF) was established at NASA John F. Kennedy Space Center (KSC) to fulfill the need of the scientific community. Our facility provides the US science community with a focal point in the field of gravitational research by granting access to an array of two-dimensional(2D) and three-dimensional (3D)clinostats, and Random Positioning Machine (RPM) platforms developed by teams throughout the world. The availability of these capabilities will allow further understanding the role of altered gravity vectors from “functional weightlessness”, partial gravity conditions (1 x 10-3to 0.9g, and Moon and Mars ‘g vectors), to hypergravity (up to3g) on biological processes. We have designed and 3D printed a variety of specialized attachments(and associated “static control” hardware)to allow researchers to mount their samples onto these microgravity simulation devices to meet their unique science requirements. A summary of each attachment module will be presented below. Note: All software or code information should be requested to the author Ye Zhang, Kennedy Space Center ye.zhang-1@nasa.gov

Ye Zhang↗

NASA’s Ground-Based Microgravity Simulation Facility

Since opportunities to conduct experiments in space are scarce, various microgravity simulators and analogs have been widely used in space biology ground studies. Even though microgravity simulators do not produce all of the biological effects observed in the true microgravity environment, they provide alternative test platforms that are effective, affordable, and readily available to facilitate microgravity research. The Microgravity Simulation Support Facility (MSSF) at the National Aeronautics and Space Administration (NASA) John F. Kennedy Space Center (KSC) has been established for conducting short duration experiments, typically less than 1 month, utilizing a variety of microgravity simulation devices for research at different gravity levels. The simulators include, but are not limited to, 2D Clinostats, 3D Clinostats, Random Positioning Machines, and Rotating Wall Vessels. In this presentation, we will provide an overview of current MSSF capabilities, research conducted in MSSF, new technology developments, customized sample holder designs, and the physical characteristics of these microgravity simulators.

Ye Zhang↗

Investigation into Stimulated Microgravity Techniques used to Study Biofilm Growth

Bacterial growth in liquid media in microgravity conditions is not well understood. Trends such as a shortened lag phase, longer log phase, slower growth rate, and a higher final population concentration have been noted but the underlying cause remains unclear. At the single cell level, it is predicted that bacteria are less gravity-sensitive than larger species. The effects on their immediate environment, including the lack of cell settlement and slower mass transfer of nutrients due to lack of density driven convection, could help explain the trends. Ground-based spaceflight analogs, or simulated microgravity devices, are often employed to achieve different attributes of weightlessness to study effects on bacterial growth. Though these technologies could isolate gravity’s role in various biological processes, they cannot replicate all its effects and underlying mechanisms. Hence, interpretation of results could be misleading, even if similar to spaceflight. In this study two common simulated microgravity devices were investigated to determine whether they could simulate relevant microgravity conditions for bacterial growth. A bioreactor, the high aspect ratio vessel (HARV), was used with dyes of different density mounted on a random positioning machine (RP machine) or a rotating wall vessel (RWV). The RP machine displayed higher mixing rates than the RWV. The RWV was further tested at different rotations per minute (RPM). The range to minimize effects of density driven convection (low speeds) or centrifugal forces (high speeds) was between a range of 15-20 RPM. These results will help inform the selection of simulated microgravity device as well as interpretation of subsequent biofilm growth results.

Angie M. Diaz↗

NASA's Ground-Based Microgravity Simulation Facility

Since opportunities to conduct experiments in space are scarce, various microgravity simulators and analogs have been widely used in space biology ground studies. Even though microgravity simulators do not produce all of the biological effects observed in the true microgravity environment, they provide alternative test platforms that are effective, affordable, and readily available to facilitate microgravity research. The Microgravity Simulation Support Facility (MSSF) at the National Aeronautics and Space Administration (NASA) John F. Kennedy Space Center (KSC) has been established for conducting short duration experiments, typically less than 1 month, utilizing a variety of microgravity simulation devices for research at different gravity levels. The simulators include, but are not limited to, 2D Clinostats, 3D Clinostats, Random Positioning Machines, and Rotating Wall Vessels. In this chapter, we will discuss current MSSF capabilities, development concepts, customized sample holder designs, and the physical characteristics of these microgravity simulators.

Ye Zhang↗

Impact of Simulated Microgravity on Mesenchymal Stem Cell Proliferation

Background Long term exposure to microgravity has adverse effects on human body such as bone loss. Due to the vital role of mesenchymal stem cell (MSC) in bone regeneration, studying MSC under microgravity conditions has been of interest during the past decade. However, high cost and limited access to space flight can dampen enthusiasm of researchers. Microgravity simulators provide a way to investigate the effects of microgravity in human physiology. Methods In this study, we compared MSC cultures under simulated microgravity using random positioning machine (RPM) and Gravite 3D simulators. Two culture durations, 1 week and 2 weeks, were selected for MSC cultures without media change. To evaluate impact of simulated microgravity on cell proliferation, cell counting was performed using trypan blue exclusion assay. Additionally, RNA samples and conditioned media were collected for further analysis. Results After 1 week and 2 weeks, no cell morphology change was observed from RPM and Gravite cultures compared to control. Notably, distinct lower cell confluence at the edge of the flasks on the RPM was observed, which could be caused by fluid sheer forces. MSCs cultured on both microgravity simulators showed decreased cell proliferation after 1-week culture. After 2-week culture, cells grown on the RPM showed no significant difference in cell proliferation compared with control while cells cultured on the Gravite bioreactor showed significantly enhanced MSC proliferation. Conclusion Type of microgravity simulator and duration of culture significantly affect MSC proliferation. Further investigation into how simulated microgravity influences MSC gene expression and cytokine secretion related to bone loss is currently on going in our lab.

Cuiping Zhang↗

Vehicle Position Detection Based on Machine Learning Algorithms in Dynamic Wireless Charging

Dynamic wireless charging (DWC) has emerged as a viable approach to mitigate range anxiety by ensuring continuous and uninterrupted charging for electric vehicles in motion. DWC systems rely on the length of the transmitter, which can be categorized into long-track transmitters and segmented coil arrays. The segmented coil array, favored for its heightened efficiency and reduced electromagnetic interference, stands out as the preferred option. However, in such DWC systems, the need arises to detect the vehicle’s position, specifically to activate the transmitter coils aligned with the receiver pad and de-energize uncoupled transmitter coils. This paper introduces various machine learning algorithms for precise vehicle position determination, accommodating diverse ground clearances of electric vehicles and various speeds. Through testing eight different machine learning algorithms and comparing the results, the random forest algorithm emerged as superior, displaying the lowest error in predicting the actual position.

47 OTHER INSTRUMENTATION↗

Node-degree aware edge sampling mitigates inflated classification performance in biomedical random walk-based graph representation learning

Motivation: Graph representation learning is a family of related approaches that learn low-dimensional vector representations of nodes and other graph elements called embeddings. Embeddings approximate characteristics of the graph and can be used for a variety of machine-learning tasks such as novel edge prediction. For many biomedical applications, partial knowledge exists about positive edges that represent relationships between pairs of entities, but little to no knowledge is available about negative edges that represent the explicit lack of a relationship between two nodes. For this reason, classification procedures are forced to assume that the vast majority of unlabeled edges are negative. Existing approaches to sampling negative edges for training and evaluating classifiers do so by uniformly sampling pairs of nodes. Results: We show here that this sampling strategy typically leads to sets of positive and negative examples with imbalanced node degree distributions. Using representative heterogeneous biomedical knowledge graph and random walk-based graph machine learning, we show that this strategy substantially impacts classification performance. If users of graph machine-learning models apply the models to prioritize examples that are drawn from approximately the same distribution as the positive examples are, then performance of models as estimated in the validation phase may be artificially inflated. We present a degree-aware node sampling approach that mitigates this effect and is simple to implement. Availability and implementation: Our code and data are publicly available at https://github.com/monarch-initiative/negativeExampleSelection.

59 BASIC BIOLOGICAL SCIENCES↗

Automatic Calibration Of Manual Machine Tools

Modified scheme uses data from multiple positions and eliminates tedious positioning. Modification of computer program adapts calibration system for convenient use with manually-controlled machine tools. Developed for use on computer-controlled tools. Option added to calibration program allows data on random tool-axis positions to be entered manually into computer for reduction. Instead of setting axis to predetermined positions, operator merely sets it at variety of arbitrary positions.

Gurney, Rex D.↗

Graph-based featurization methods for classifying small molecule compounds

For over a decade, drug-induced liver injury (DILI) has posed significant drawbacks in the synthesis and development of drugs and remains a consequential concern. With finite success within the existing preclinical models, DILI is one of the main causes of drug withdrawal or termination from the market. Particularly, this withdrawal occurs during the late stages of drug development (Kullak-Ublick, 2017). Since DILI is difficult to diagnose and treat, it has become an obstacle in the drug production market that in turn affects clinicians, pharmaceutical companies, and consumers. We propose a method for learning features of DILI-positive drugs based on the graphical relationships and patterns they possess within a network of biological databases. We also train various statistical and machine learning models on these learned features in order to classify the drugs as DILI-positive or negative. Our methods include Random Forest, Neural networks, and logistic regression classification. We utilize labeled DILI-positive and DILI-negative datasets, which were developed by the FDA and the National center for toxicological research, as well as additional literature datasets (Thakkar, 2020) in order to validate our results and assess our featurization and model accuracy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Classifying Agnostic Biosignatures using Raman, VNIR, and Elemental Data

How can we use our current wealth of terrestrial data, encompassing biogenic and abiogenic systems, to determine the distinguishing properties of life? SCOBI (Statistical Classification of Biosignature Information) uses machine learning techniques to algorithmically identify combinations of measurements that are “indicative of life”. A set of ~1000 observations, comprising elemental abundance, isotopic fractionation, VNIR reflectance, and (in progress) Raman spectra, have been assembled from existing literature and databases. The observations cover systems classified as “indicative alive” (e.g., cells, vegetation), “indicative non-alive” (e.g., fossils, teeth), “mixed indicative” (e.g., soil, pond water), or “non-indicative” (e.g., rocks, meteorites). VNIR data was preprocessed by linear interpolation from 400-2100 nm and smoothed with a Savitzky-Golay filter. To limit the amount of Earth-biochemistry-specific (non-agnostic) information included, the first five spectral features extracted were number of peaks, number of troughs, mean reflectance, mean peak width, and broadest peak width. To help further emphasize agnostic biosignatures, Earth-specific features such as chlorophylls have been manually flagged so that feature importance with and without them can be compared. Classifiers including k-nearest neighbors (KNN), Gaussian Naïve Bayes (GNB), logistic regression (LR), random forest (RF), and support vector machine (SVM) were implemented, as was a combination voting classifier. Performance metrics included false positive rates, false negative rates, and AUC with 50-50 test/train splits (Monte Carlo simulations). Key takeaways from this stage, prior to the inclusion of Raman spectra, are (1) the overall success rate of 0.933 AUC was most heavily influenced by the elemental abundance data; and (2) VNIR reflectance had the lowest classification performance with 0.52 AUC (58% of objects correctly classified). The next steps are to complete integration of Raman spectral data and to improve the approach to pre-processing and feature extraction for both types of spectral data, such as automated baseline removal, whole spectrum matching, and dimensionality reduction.

Biosignatures↗

Autonomous fabrication of tailored defect structures in 2D materials using machine learning-enabled scanning transmission electron microscopy

Materials with tailored quantum properties can be engineered from atomic-scale assembly techniques, but existing methods often lack the agility and accuracy to precisely and intelligently control the manufacturing process. Here, we demonstrate a fully autonomous approach for fabricating atomic-level defects using electron beams in scanning transmission electron microscopy (STEM) that combines advanced machine learning and automated beam control. As a proof of concept, we achieved controlled fabrication of MoS-nanowire (MoS-NW) edge structures by iterative and targeted exposure of MoS 2 monolayer to a focused electron beam to selectively eject sulfur atoms, utilizing high-angle annular dark-field (HAADF) imaging for feedback-controlled monitoring of structural evolution of defects. A machine learning framework combining a random forest model and a convolutional neural network (CNN) was developed to decode the HAADF image and accurately identify atomic positions and species. This atomic-level information was then integrated into an autonomous decision-making platform, which applied predefined fabrication strategies to instruct beam control about atomic sites to be ejected. The selected sites were subsequently exposed to a localized electron beam using an FPGA-controlled scan routine with precise control over beam positioning and duration. While the MoS-NW edge structures produced exhibit promising mechanical and electronic properties, the proposed methods to build the autonomous fabrication framework is material-agnostic and can be extended to other 2D materials for the creation of diverse defect structures and heterostructures beyond Mo S2 .

Engineering↗

A bi-level data-driven framework for fault-detection and diagnosis of HVAC systems

Long-term operation of heating, ventilation, and air conditioning (HVAC) systems will eventually lead to a range of HVAC system failures, resulting in excessive energy consumption and maintenance costs. Here, to avoid HVAC malfunctioning, fault detection diagnostic (FDD) is utilized as a common practice. Machine learning methods have lately received considerable interest for FDD analysis of HVAC systems due to their high detection accuracy. Meanwhile, HVAC malfunctions are regarded as rare occurrences, hence normal operating data samples are much more accessible than data samples in faulty and malfunctioning conditions. The dominating frequency of normal operation in HVAC datasets has also led to heavily biased classification algorithms within the literature. Moreover, the focus of previous literature has been on increasing the accuracy of the models which leads to a high number of false positives (misleading alarms) in the system. In order to enhance the performance of diagnostic procedures and fill the mentioned gaps, this study proposes a novel data-driven framework. A bi-level machine learning framework is developed for diagnosing faults in air handling units (AHUs) and rooftop units (RTUs) based on principal component analysis (PCA), time series anomaly detection, and random forest (RF). It is shown that PCA can reduce the dataset dimension with one principal component accounting for 95% of data variance. Also, the random forest could classify the faults with 89% precision for single-zone AHU, 85% precision for RTU, and 79% for multi-zone AHU. By proposing this framework, three persistent challenges are addressed: (I) minimizing false positives; (II) accounting for data imbalance; and (III) normal condition monitoring of equipment.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗