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The present disclosure relates to methods, apparatuses, and systems to measure one or more electrical signals from a cultured cell layer. In some embodiments, such electrical signals can be indicative of transport or lack of transport of an agent through the cell layer.
We reported that, for a 21FC task with multiple Gabor patches in each interval, thresholds for speed discrimination decreased with the number of patches, while simply increasing the area of a single patch produced no such effect. This result could be explained by multiple patches reducing spatial uncertainty. However, the fact that thresholds decrease with number even when the patches are in fixed positions argues against this explanation. We therefore performed additional experiments to explore the lack of an area effect. Three observers did a 21FC speed discrimination task with 6 Gabor patches in each interval, and were asked to pick the interval in which the gratings moved faster. The 50% contrast patches were placed on a circle at 4 deg. eccentricity, either equally spaced and maximally separated (hexagonal array), or closely-spaced, in consecutive positions (string of pearls). For the string-of-pearls condition, the grating phases were either random, or consistent with a full-field grating viewed through multiple Gaussian windows. When grating phases were random, the thresholds for the hexagonal and string-of-pearls layouts were indistinguishable. For the string-of-pearls layout, thresholds in the consistent-phase condition were higher by 15 +/- 6% than in the random-phase condition. (Thresholds increased by 57 +/- 7% in going from 6 patches to a single patch of equivalent area.). For random-phase patches, the lower thresholds for 6 patches does not depend on a specific spacing or spatial layout. Multiple, closely-spaced, consistent-phase patches that can be interpreted as a single grating, result in thresholds closer to that produced by a single patch. Together, our results suggest that object segmentation may play a role in the integration of speed information.
As the National Aeronautics and Space Association (NASA) begins to pursue long-duration space flights, they will need to be able to provide astronauts with a nutritious and reliable food source. To meet the administration’s goal of traveling to the Moon and Mars, astronauts will need to begin to grow their own food in space. To protect their food source, extensive monitoring will occur to test for the effects of a space flight environment (e.g., radiation) as well as for early pathogen and disease detection. Genomic sequencing allows for both concerns to be tested on a regular basis. However, NASA’s current sequencer is unable to process plant tissues. Therefore, a novel method for plant DNA extraction using microneedle (MN) patches that will be able to feed into NASA’s existing system, but also require minimal human input is proposed. To support this, the design was broken down into four components (1) MN patch fabrication (2) MN patch extraction, (3) automated sampling motion control, and (4) a processing module. The MN patch is fabricated using a custom mold with conically shaped needles. The mold is filled with Polyvinyl alcohol (PVA) solution and placed in a vacuum desiccator. The mold is left in the vacuum overnight until the patch is dry and ready for use. The protocol was tested with varying pressures, drying times, volume amounts, and preparation methods to determine if highquality needles can be produced. A MN is a method of DNA extraction where the patch is applied to a leaf, the needles penetrate the leaf, breaking the rigid plant cell wall to isolate the DNA. A protocol for this method of extraction was tested to ensure the patch could produce the needed yield and purity. The tests varied by the number of patches, number of applications, and plant type. To automate the MN extraction method, motion control will utilize two separate axis tables which move in the x and y directions. The y-axis table will have an end effector that fits a MN patch and will have the ability to apply the patch to the leaf sample. This end effector will also act as a lid for a downstream processing module. The other axis will position the leaf sample and processing container so that the patch can be applied accurately. The Joint Comprehensive Sequencing System (JCSS) module integrates all the components together. The output of this module feeds into the NASA Charged Information-Storage Polymer Preparation System (CHIPPS) for genomic sequencing. The extraction module operates using a series of syringes and tubing to pump the varying reagents needed for the extraction protocol. The results of the study proved that MN patches are a viable method of DNA extraction. While fabrication of high-quality needles was unsuccessful, the protocol was able to be further developed using centrifugation. The integrated design between the motion control and the JCSS enabled the potential for automation with a complete conceptual design and prototype. Future research and development for this study would include (1) further testing for fabrication (2) expanding the range of plant species compatible with the MN patch, and (3) building a working prototype for the integrated system.
We address a surprising result in a previous study of speed discrimination with multiple moving gratings: discrimination thresholds decreased when the number of stimuli was increased, but remained unchanged when the area of a single stimulus was increased [Verghese & Stone (1995). Vision Research, 35, 2811-2823]. In this study, we manipulated the spatial- and phase relationship between multiple grating patches to determine their effect on speed discrimination thresholds. In a fusion experiment, we merged multiple stimulus patches, in stages, into a single patch. Thresholds increased as the patches were brought closer and their phase relationship was adjusted to be consistent with a single patch. Thresholds increased further still as these patches were fused into a single patch. In a fission experiment, we divided a single large patch into multiple patches by superimposing a cross with luminance equal to that of the background. Thresholds decreased as the large patch was divided into quadrants and decreased further as the quadrants were maximally separated. However, when the cross luminance was darker than the background, it was perceived as an occluder and thresholds, on average, were unchanged from that for the single large patch. A control experiment shows that the observed trend in discrimination thresholds is not due to the differences in perceived speed of the stimuli. These results suggest that the parsing of the visual image into entities affects the combination of speed information across space, and that each discrete entity effectively provides a single independent estimate of speed.
The purpose is to describe a recently developed technique aimed at providing a universal interface between surface types. In brief, a software package was developed which functions a common denominator of CAD/CAM surface types. This software enable one to convert from any given surface representation to any other target representation. The tiles maintain the same slope continuity as the target surface gram, bicubic patches are used since they allow one to match point, slope, and twist vectors to the target surface. Thus, slopes can be continuous or discontinuous as they are on the target surface. The patches can be of lower order if desired. For example, if only point information is available, the patches produced will be bilinear; however, the number of patches required is likely to increase correspondingly. The patches can be of higher order although many systems will not accept patches of more than order four. The final result of the program is a rectangular grid of bicubic patches. The patches fit the target surface exactly at their corners. Also, the patch corners have the same tangent and twist vectors. Adjacent patches will have slope continuity, unless a discontinuity was indicated by the target surface.
The Unsteady Pressure-Sensitive Paint (uPSP) is widely used to measure the surface pressure of scaled models in wind tunnel tests. Compared to the conventional pressure transducers, uPSP has the advantage of high spatial resolution. With multiple high-speed Complementary Metal Oxide Superconductor (CMOS) cameras, the uPSP data collected with the camera pixels are mapped to the surface grid of the scaled model and converted to pressure. The shot noise is the dominant component of the noise in the uPSP measurement. The integrated pressure is usually computed on the grid nodes of a user-defined patch. The effect of shot noise is reduced in the integrated pressure on the patch; however, the measurement of the aerodynamic pressure may also be attenuated by the decorrelation of the flow pressure field being measured. This paper discusses the Joint Acceptance Attenuation Factor (JAAF) of the integrated pressure with uPSP measurements. The JAAF, a function of frequency, is defined as the ratio of the Power Spectral Density (PSD) of the integrated aerodynamic pressure on the patch to the average PSD of the aerodynamic pressure on the grid nodes of the patch. In this paper, the JAAF is investigated for the integrated pressure on rectangular patches, whose edges are defined in the direction along the streamline or across the streamline. Based on the assumption that the surface pressure field can be described by the Corcos model, the closed-form formulas to compute the JAAFs of the integrated pressure on the discrete grid nodes of a rectangular patch and over the continuous area of a rectangular patch are derived respectively. It is shown that the JAAF of the integrated pressure over the continuous area of a rectangular patch is the limit of that on discrete nodes of the rectangular patch when the number of nodes in each row or column goes to infinity. The closed-form formulas of the JAAF derived in this paper, with estimated parameters of the model, are verified with the measurements of the uPSP and the conventional pressure transducer collected in the Space Launch System Ascent Unsteady Aerodynamics Test at NASA Ames Research Center in November 2017. The closed-form formulas of the JAAF of the integrated pressure on the rectangular patches, based on the Corcos model, provide an efficient method to estimate the attenuation of integration by the decorrelation of the flow pressure field and set references for the comparison of the spectrum of the integrated uPSP measurements and the conventional pressure transducer measurements. The work described in this paper is a part of NASA’s development of a new state-of-the-art uPSP capability in production wind tunnels. Funding was provided by the NASA Aerosciences Evaluation and Test Capabilities Portfolio Office.
The Unsteady Pressure-Sensitive Paint (uPSP) is widely used to measure the surface pressure of scaled models in wind tunnel tests. Compared to the conventional pressure transducers, uPSP has the advantage of high spatial resolution. With multiple high-speed Complementary Metal Oxide Superconductor (CMOS) cameras, the uPSP data collected with the camera pixels are mapped to the surface grid of the scaled model and converted to pressure. The shot noise is the dominant component of the noise in the uPSP measurement. The integrated pressure is usually computed on the grid nodes of a user-defined patch. The effect of shot noise is reduced in the integrated pressure on the patch; however, the measurement of the aerodynamic pressure may also be attenuated by the decorrelation of the flow pressure field being measured. This paper discusses the Joint Acceptance Attenuation Factor (JAAF) of the integrated pressure with uPSP measurements. The JAAF, a function of frequency, is defined as the ratio of the Power Spectral Density (PSD) of the integrated aerodynamic pressure on the patch to the average PSD of the aerodynamic pressure on the grid nodes of the patch. In this paper, the JAAF is investigated for the integrated pressure on rectangular patches, whose edges are defined in the direction along the streamline or across the streamline. Based on the assumption that the surface pressure field can be described by the Corcos model, the closed-form formulas to compute the JAAFs of the integrated pressure on the discrete grid nodes of a rectangular patch and over the continuous area of a rectangular patch are derived respectively. It is shown that the JAAF of the integrated pressure over the continuous area of a rectangular patch is the limit of that on discrete nodes of the rectangular patch when the number of nodes in each row or column goes to infinity. The closed-form formulas of the JAAF derived in this paper, with estimated parameters of the model, are verified with the measurements of the uPSP and the conventional pressure transducer collected in the Space Launch System Ascent Unsteady Aerodynamics Test at NASA Ames Research Center in November 2017. The closed-form formulas of the JAAF of the integrated pressure on the rectangular patches, based on the Corcos model, provide an efficient method to estimate the attenuation of integration by the decorrelation of the flow pressure field and set references for the comparison of the spectrum of the integrated uPSP measurements and the conventional pressure transducer measurements. The work described in this paper is a part of NASA’s development of a new state-of-the-art uPSP capability in production wind tunnels. Funding was provided by the NASA Aerosciences Evaluation and Test Capabilities Portfolio Office.
Patch-based relaxation refers to a family of methods for solving linear systems which partitions the matrix into smaller pieces often corresponding to groups of adjacent degrees of freedom residing within patches of the computational domain. The two most common families of patch-based methods are block-Jacobi and Schwarz methods, where the former typically corresponds to non-overlapping domains and the later implies some overlap. We focus on cases where each patch consists of the degrees of freedom on a finite element method mesh cell. Patch methods often capture complex local physics much more effectively than simpler point-smoothers such as Jacobi; however, forming, inverting, and applying each patch can be prohibitively expensive in terms of both storage and computation time. To this end, we propose several approaches for performing analysis on these patches and constructing a reduced representation. The compression techniques rely on either matrix norm comparisons or unsupervised learning via a clustering approach. We illustrate how it is frequently possible to retain/factor less than 5% of all patches and still develop a method that converges only a little slower than when all patches are stored/factored.
Abstract Soil microorganisms play outsized roles in nutrient cycling, plant health, and climate regulation. Despite their importance, we have a limited understanding of how soil microbes are affected by habitat fragmentation, including their responses to conditions at fragment edges, or “edge effects.” To understand the responses of soil communities to edge effects, we analyzed the distributions of soil bacteria, archaea, and fungi in an experimentally fragmented system of open patches embedded within a forest matrix. In addition, we identified taxa that consistently differed among patch, edge, or matrix habitats (“specialists”) and taxa that showed no habitat preference (“nonspecialists”). We hypothesized that microbial community turnover would be most pronounced at the edge between habitats. We also hypothesized that specialist fungi would be more likely to be mycorrhizal than nonspecialist fungi because mycorrhizae should be affected more by different plant hosts among habitats, whereas specialist prokaryotes would have smaller genomes (indicating reduced metabolic versatility) and be less likely to be able to sporulate than nonspecialist prokaryotes. Across all replicate sites, the matrix and patch soils harbored distinct microbial communities. However, sites where the contrasts in vegetation and pH between the patch and matrix were most pronounced exhibited larger differences between patch and matrix communities and tended to have edge communities that differed from those in the patch and forest. There were similar numbers of patch and matrix specialists, but very few edge specialist taxa. Acidobacteria and ectomycorrhizae were more likely to be forest specialists, while Chloroflexi, Ascomycota, and Glomeromycota (i.e., arbuscular mycorrhizae) were more likely to be patch specialists. Contrary to our hypotheses, nonspecialist bacteria were not more likely than specialist bacteria to have larger genomes or to be spore‐formers. We found partial support for our mycorrhizal hypothesis: arbuscular mycorrhizae, but not ectomycorrhizae, were more likely to be specialists. Overall, our results indicate that soil microbial communities are sensitive to edges, but not all taxa are equally affected, with arbuscular mycorrhizae in particular showing a strong response to habitat edges. In the context of increasing habitat fragmentation worldwide, our results can help inform efforts to maintain the structure and functioning of the soil microbiome.
Whole Slide Imaging (WSI) captures microscopic details of a patient's histopathological features at multiple res-olutions organized across different levels. Images produced by WSI are gigapixel-sized, and saving a single image in memory requires a few gigabytes which is scarce since a complicated model occupies tens of gigabytes. Performing a simple met-ric operation on these large images is also expensive. High-performance computing (HPC) can help us quickly analyze such large images using distributed training of complex deep learning models. One popular approach in analyzing these images is to divide a WSI image into smaller tiles (patches) and then train a simpler model with these reduced-sized but large numbers of patches. However, we need to solve three pre-processing challenges efficiently for pursuing this patch-based approach. 1) Creating small patches from a high-resolution image can result in a high number (hundreds of thousands per image) of patches. Storing and processing these images can be challenging due to a large number of I/O and arithmetic operations. To reduce I/Oand memory accesses, an optimal balance between the size and number of patches must exist to reduce I/O and memory accesses. 2) WSI images may have tiny annotated regions for cancer tissue and a significant portion with normal and fatty tissues; correct patch sampling should avoid dataset imbalance. 3) storing and retrieving many patches to and from disk storage might incur I/O latency while training a deep learning model. An efficient distributed data loader should reduce I/O latency during the training and inference steps. This paper explores these three challenges and provides empirical and algorithmic solutions deployed on the Summit supercomputer hosted at the Oak Ridge Leadership Computing Facility.
Natural wetlands are intrinsically heterogeneous and typically composed of a mosaic of ecosystem patches with different vegetation types. Hydrological and biogeochemical processes in wetlands vary strongly among these ecosystem patches. To date, most remote sensing classification approaches for wetland vegetation either rely on coarse images that cannot capture the spatial variability of wetland vegetation or rely on very-high-resolution multi-spectral images that are detailed but very sporadic in time (less than once per year). This study aimed to use NDVI time series, generated from NASA’s HLS dataset, to classify vegetation patches. We demonstrate our approach at a temperate, coastal lake, estuarine marsh. To classify vegetation patches, a standard time series library of the four land-cover patch types was built from referencing specific locations that were identified as “pure” pixels. These were identified using a single-time high-resolution image. We calculated the distance between the HLS-NDVI time series at each pixel and the “pure”-pixel standards for each land-cover type. The resulting true-positive classified rate was >73% for all patch types other than water lily. The classification accuracy was higher in pixels of a more uniform composition. A set of vegetation maps was created for the years 2016 to 2020 at our research site to identify the vegetation changes at the site as it is affected by rapid water elevation increases in Lake Erie. Our results reveal how changes in water elevation have changed the patch distribution in significant ways, leading to the local extinction of cattail by 2019 and a continuous increase in the area cover of water lily patches.
The characteristics of a parasitic microstrip antenna array with a center-fed patch are experimentally investigated. The parasitic array is composed of identical parasitic patches which are symmetrically arranged and electromagnetically coupled to a center-fed patch. The shape and dimensions of the parasitic patches and their positions relative to the center-fed patch are parameters in the study. To show mutual coupling effects between radiating and nonradiating edges of adjacent patches, the impedance and radiation characteristics of a three-element parasitic array excited with (0.1) mode are examined, and compared to that of a single patch. Experimental data indicate that the presence of parasitic patches has significant effects upon the gain, resonant frequency, and impedance bandwidth of the array.
We reported that for a 21FC task with multiple moving grating patches (Gabors) in each interval, thresholds for speed discrimination decreased with the number of patches, while increasing the area of a single grating produced no such effect. Furthermore, this decrease occurred regardless of the spacing of the patches about a circle of eccentricity 4 degrees, i.e., whether they were maximally separated or almost touching. These results suggest that it is the multiple, discrete grating patches that cause thresholds to decrease, rather than the spatial arrangement. To test this hypothesis, we measured the effect of dividing a large grating into four quadrants, by superimposing a mean-luminance cross on it. The mean speed discrimination thresholds (Weber Fractions) for four observers were 19, 15, and 11 plus or minus 2%, for the single large grating, the grating with cross, and the 4 maximally-separated, small gratings, respectively. Thus, breaking up a single large grating into multiple parts caused thresholds to improve, despite the fact that less of the original patch was visible. To investigate the possible contribution of total bounding contour length, we measured the effect of coalescing three small grating patches into a single banana-shaped patch, while keeping the total contour length constant. These two conditions were compared to a single, circular Gabor patch of equivalent area that had (necessarily) a smaller contour length. Preliminary data from 3 of 4 observers were similar for the small-grating and banana configurations, but increased for the single, large grating, suggesting that contour length might play a role. We are also investigating the role of low-level factors pertinent to the large grating, such as the pooling of signals from motion units at different eccentricities, and the stimulation of extended inhibitory motion surrounds, as well as the possible contribution of topdown influences that segment the stimulus into distinct objects.
This compact, lightweight, dual-frequency antenna feed developed for future soil moisture and sea surface salinity (SSS) missions can benefit future soil and ocean studies by lowering mass, volume, and cost of the antenna system. It also allows for airborne soil moisture and salinity remote sensors operating on small aircraft. While microstrip antenna technology has been developed for radio communications, it has yet to be applied to combined radar and radiometer for Earth remote sensing. The antenna feed provides a key instrument element enabling high-resolution radiometric observations with large, deployable antennas. The design is based on the microstrip stacked-patch array (MSPA) used to feed a large, lightweight, deployable, rotating mesh antenna for spaceborne L-band (approximately equal to 1 GHz) passive and active sensing systems. The array consists of stacked patches to provide dual-frequency capability and suitable radiation patterns. The stacked-patch microstrip element was designed to cover the required L-band center frequencies at 1.26 GHz (lower patch) and 1.413 GHz (upper patch), with dual-linear polarization capabilities. The dimension of patches produces the required frequencies. To achieve excellent polarization isolation and control of antenna sidelobes for the MSPA, the orientation of each stacked-patch element within the array is optimized to reduce the cross-polarization. A specialized feed-distribution network was designed to achieve the required excitation amplitude and phase for each stacked-patch element.
Microstrip-patch-style antennas that generate monopole radiation patterns similar to those of quarter-wave whip antennas can be designed to have dimensions smaller than those needed heretofore for this purpose, by taking advantage of a feed configuration different from the conventional one. The large sizes necessitated by the conventional feed configuration have, until now, made such antennas impractical for frequencies below about 800 MHz: for example, at 200 MHz, the conventional feed configuration necessitates a patch diameter of about 8 ft (.2.4 m) . too large, for example, for mounting on the roof of an automobile or on a small or medium-size aircraft. By making it possible to reduce diameters to between a tenth and a third of that necessitated by the conventional feed configuration, the modified configuration makes it possible to install such antennas in places where they could not previously be installed and thereby helps to realize the potential advantages (concealment and/or reduction of aerodynamic drag) of microstrip versus whip antennas. In both the conventional approach and the innovative approach, a microstrip-patch (or microstrip-patch-style) antenna for generating a monopole radiation pattern includes an electrically conductive patch or plate separated from an electrically conductive ground plane by a layer of electrically insulating material. In the conventional approach, the electrically insulating layer is typically a printed-circuit board about 1/16 in. (.1.6 mm) thick. Ordinarily, a coaxial cable from a transmitter, receiver, or transceiver is attached at the center on the ground-plane side, the shield of the cable being electrically connected to the ground plane. In the conventional approach, the coaxial cable is mated with a connector mounted on the ground plane. The center pin of this connector connects to the center of the coaxial cable and passes through a hole in the ground plane and a small hole in the insulating layer and then connects with the patch above one-third of the radial distance from the center. The modified feed configuration of the innovative approach is an inductive-short-circuit configuration that provides impedance matching and that has been used for many years on other antennas but not on microstrip-style monopole antennas. In this configuration, the pin is connected to both the conductive patch and the ground plane. As before, the shield of the coaxial cable is connected to the ground plane, but now the central conductor is connected to a point on the pin between the ground plane and the conductive plate (see figure). The location of the connection point on the pin is chosen so that together, the inductive short circuit and the conductive plate or patch act as components of a lumped-element resonant circuit that radiates efficiently at the resonance frequency and, at the resonance frequency, has an impedance that matches that of the coaxial cable. It should be noted that the innovative design entails two significant disadvantages. One disadvantage is that the frequency bandwidth for efficient operation is only about 1/20 to 1/15 that of a whip antenna designed for the same nominal frequency. The other disadvantage is that the estimated gain is between 3-1/2 and 4-1/2 dB below that of the whip antenna. However, if an affected radio-communication system used only a few adjacent frequency channels and the design of the components of the system other than the antenna provided adequate power or gain margin, then these disadvantages could be overcome.
We investigate the structural and thermodynamic properties of a model of particles with 2 patches of type A and 10 patches of type B. Particles are placed on the sites of a face centered cubic lattice with the patches oriented along the nearest neighbor directions. The competition between the self-assembly of chains, rings, and networks on the phase diagram is investigated by carrying out a systematic investigation of this class of models, using an extension of Wertheim's theory for associating fluids and Monte Carlo numerical simulations. We varied the ratio r ≡ ε{sub AB}/ε{sub AA} of the interaction between patches A and B, ε{sub AB}, and between A patches, ε{sub AA} (ε{sub BB} is set to 0) as well as the relative position of the A patches, i.e., the angle θ between the (lattice) directions of the A patches. We found that both r and θ (60°, 90°, or 120°) have a profound effect on the phase diagram. In the empty fluid regime (r < 1/2) the phase diagram is reentrant with a closed miscibility loop. The region around the lower critical point exhibits unusual structural and thermodynamic behavior determined by the presence of relatively short rings. The agreement between the results of theory and simulation is excellent for θ = 120° but deteriorates as θ decreases, revealing the need for new theoretical approaches to describe the structure and thermodynamics of systems dominated by small rings.
Purpose: It is an intriguing problem to generate an instantaneous volumetric image based on the corresponding x-ray projection. The purpose of this study is to develop a new method to achieve this goal via a sparse learning approach. Methods: To extract motion information hidden in projection images, the authors partitioned a projection image into small rectangular patches. The authors utilized a sparse learning method to automatically select patches that have a high correlation with principal component analysis (PCA) coefficients of a lung motion model. A model that maps the patch intensity to the PCA coefficients was built along with the patch selection process. Based on this model, a measured projection can be used to predict the PCA coefficients, which are then further used to generate a motion vector field and hence a volumetric image. The authors have also proposed an intensity baseline correction method based on the partitioned projection, in which the first and the second moments of pixel intensities at a patch in a simulated projection image are matched with those in a measured one via a linear transformation. The proposed method has been validated in both simulated data and real phantom data. Results: The algorithm is able to identify patches that contain relevant motion information such as the diaphragm region. It is found that an intensity baseline correction step is important to remove the systematic error in the motion prediction. For the simulation case, the sparse learning model reduced the prediction error for the first PCA coefficient to 5%, compared to the 10% error when sparse learning was not used, and the 95th percentile error for the predicted motion vector was reduced from 2.40 to 0.92 mm. In the phantom case with a regular tumor motion, the predicted tumor trajectory was successfully reconstructed with a 0.82 mm error for tumor center localization compared to a 1.66 mm error without using the sparse learning method. When the tumor motion was driven by a real patient breathing signal with irregular periods and amplitudes, the average tumor center error was 0.6 mm. The algorithm robustness with respect to sparsity level, patch size, and presence or absence of diaphragm, as well as computation time, has also been studied. Conclusions: The authors have developed a new method that automatically identifies motion information from an x-ray projection, based on which a volumetric image is generated.