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At least 145 records · Page 8

Methods and Devices for Micro-Isolation, Extraction, and/or Analysis of Microscale Components

Provided herein are devices and methods for the micro-isolation of biological cellular material. A micro-isolation apparatus described can comprise a photomask that protects regions of interest against DNA-destroying illumination. The micro-isolation apparatus can further comprise photosensitive material defining access wells following illumination and subsequent developing of the photosensitive material. The micro-isolation apparatus can further comprise a chambered microfluidic device comprising channels providing access to wells defined in photosensitive material. The micro-isolation apparatus can comprise a chambered microfluidic device without access wells defined in photosensitive material where valves control the flow of gases or liquids through the channels of the microfluidic device. Also included are methods for selectively isolating cellular material using the apparatuses described herein, as are methods for biochemical analysis of individual regions of interest of cellular material using the devices described herein. Further included are methods of making masking arrays useful for the methods described herein.

Kartalov, Emil P.↗

Single reader between-cases AUC estimator with nested data

The area under the receiver operating characteristic curve (AUC) is widely used in evaluating diagnostic performance for many clinical tasks. It is still challenging to evaluate the reading performance of distinguishing between positive and negative regions of interest (ROIs) in the nested-data problem, where multiple ROIs are nested within the cases. To address this issue, we identify two kinds of AUC estimators, within-cases AUC and between-cases AUC. We focus on the between-cases AUC estimator, since our main research interest is in patient-level diagnostic performance rather than location-level performance (the ability to separate ROIs with and without disease within each patient). Another reason is that as the case number increases, the number of between-cases paired ROIs is much larger than the number of within-cases ROIs. We provide estimators for the variance of the between-cases AUC and for the covariance when there are two readers. We derive and prove the above estimators’ theoretical values based on a simulation model and characterize their behavior using Monte Carlo simulation results. We also provide a real-data example. Moreover, we connect the distribution-based simulation model with the simulation model based on the linear mixed-effect model, which helps better understand the sources of variation in the simulated dataset.

Health Care Sciences & Services↗

Bragg edge imaging (BEI) of B12W and M8N socket sections of the Arecibo telescope

From neutron user principal investigator: We kindly request the public release of three neutron imaging datasets through ONCat. All datasets were collected from two forensic specimens, B12W and M8N, sectioned from zinc-filled steel-wire sockets recovered from the collapsed Arecibo Telescope. The dataset titled “Neutron radiographs of B12W and M8N socket sections of the Arecibo telescope” contains normalized two-dimensional (2D) neutron radiographs of the specimens, showing the geometry and spatial distribution of the steel wires embedded within the zinc matrix, as well as internal features such as voids and cracks. The dataset titled “Neutron computed tomography of B12W and M8N socket sections of the Arecibo telescope” contains normalized 2D neutron projection images acquired over a range of specimen rotation angles for one selected region of each specimen. These projection images were used to reconstruct three-dimensional (3D) tomographic volumes that reveal the embedded-wire geometry and internal defects. The dataset titled “Bragg edge imaging (BEI) of B12W and M8N socket sections of the Arecibo telescope” contains six time-of-flight (TOF) neutron imaging datasets, three from each specimen, acquired at regions of interest selected based on the radiographs. The spatially resolved 2D TOF images show the zinc matrix and embedded steel wires, and the wavelength-dependent neutron transmission data were used to characterize crystallographic texture within the zinc. All components and their condition are in the public domain as they are the property of the National Science Foundation (NSF). The neutron imaging data, part geometries, and detailed forensic information have been widely published in the Arecibo Telescope Collapse Forensic Report by Thornton Tomasetti Engineers and others (NASA report and NASEM report).

Bilheux, Hassina↗

A Moving Embedded Boundary Approach for the Compressible Navier-Stokes Equations in a Block-Structured Adaptive Refinement Framework

A computational technique has been developed to perform compressible flow simulations involving moving boundaries using an embedded boundary approach within the block-structured adaptive mesh refinement (SAMR) framework of AMReX [1], [91], [92]. We leverage the SAMR capability to obtain quantitatively accurate results whilst using robust, second-order finite volume schemes. A conservative, unsplit, cut-cell approach is utilized and a ghost-cell approach is developed for computing the flux on the moving, embedded boundary faces. A third-order least-squares formulation has been developed to compute the wall velocity gradients, and was found to significantly improve the performance of the solver in terms of the quantitative comparison of surface quantities such as the skin friction coefficient. Various test cases are performed to validate the method, and compared with analytical, experimental, and other numerical results in literature. Inviscid and viscous test cases are performed that span a wide regime of flow speeds - acoustic (harmonically pulsating sphere), smooth flows (expansion fan created by a receding piston) and flows with shocks (shock-cylinder interaction, shock-wedge interaction, pitching NACA 0012 airfoil and shock-cone interaction). A closed system with moving boundaries - an oscillating piston in a cylinder, showed that the percentage error in mass within the system decreases with refinement, demonstrating that the numerical scheme is conservative with grid refinement, but is not discretely conservative. Viscous test cases involve that of a horizontally moving cylinder at Re = 40, an inline oscillating cylinder at Re = 100, and a transversely oscillating cylinder at Re = 185. The judicious use of adaptive mesh refinement with appropriate refinement criteria to capture the regions of interest leads to well-resolved flow features, and good quantitative comparison is observed with the results available in literature.

adaptive refinement↗

Nonuniform visual pattern image sequence coding

Visual Pattern Image Sequence Coding (VPISC) is a pyramidal image coding scheme which utilizes human visual system (HVS) properties to achieve low bit rates while maintaining a good perceived image quality, all with extremely low computational cost. This paper describes extensions of VPISC, termed Foveal VPISC (FVPISC) and Adaptive VPISC (AVPISC). Both algorithms produce decreased bit rates by selectively allowing some image regions to be coded at low resolution. In FVPISC, a foveation criterion is used to select a region of interest. In AVPISC, the algorithm adaptively determines which regions require high-resolution coding in order to maintain uniform image quality over the entire image.

Silsbee, Peter L.↗

Analysis of fractal dimensions of rat bones from film and digital images

OBJECTIVES: (1) To compare the effect of two different intra-oral image receptors on estimates of fractal dimension; and (2) to determine the variations in fractal dimensions between the femur, tibia and humerus of the rat and between their proximal, middle and distal regions. METHODS: The left femur, tibia and humerus from 24 4-6-month-old Sprague-Dawley rats were radiographed using intra-oral film and a charge-coupled device (CCD). Films were digitized at a pixel density comparable to the CCD using a flat-bed scanner. Square regions of interest were selected from proximal, middle, and distal regions of each bone. Fractal dimensions were estimated from the slope of regression lines fitted to plots of log power against log spatial frequency. RESULTS: The fractal dimensions estimates from digitized films were significantly greater than those produced from the CCD (P=0.0008). Estimated fractal dimensions of three types of bone were not significantly different (P=0.0544); however, the three regions of bones were significantly different (P=0.0239). The fractal dimensions estimated from radiographs of the proximal and distal regions of the bones were lower than comparable estimates obtained from the middle region. CONCLUSIONS: Different types of image receptors significantly affect estimates of fractal dimension. There was no difference in the fractal dimensions of the different bones but the three regions differed significantly.

NASA Discipline Musculoskeletal↗

INR-TEM: Robust cavity detection in multifocus TEM images via implicit neural representations

When characterizing materials using transmission electron microscopy (TEM) images, detecting and quantifying small features in microstructures, such as cavities, pose significant challenges. Off-the-shelf object detection models, including YOLOv8, show considerable performance degradation, particularly when images vary in resolution and the objects of interest possess a low percentage of the total image region of interest. In this study, we introduce a novel detection pipeline that incorporates an implicit neural representation (INR)-based detection method, INR-TEM, and two-modality imaging (e.g., under-focused and over-focused images typically acquired during materials characterization) to improve object detection performance. The INR-TEM method incorporates a pixel-wise prediction principle inspired by pixel-wise centerness weighting. INR-TEM demonstrates superior robustness to resolution variability, maintaining high detection accuracy even at low image resolutions compared to YOLOv8. To leverage INR-TEM effectively in real-world two-modality characterization applications, we further integrate a two-stage motion correction pipeline designed explicitly for aligning multifocus TEM images. The alignment process, comprising keypoint (based on scale-invariant feature transform, SIFT) and intensity matching, significantly mitigates the adverse effects of perceived motion-induced image degradation during through-focal TEM imaging, directly enhancing INR-TEM’s detection capability over conventional single-focus images. Our integrated INR-TEM cavity detection framework notably improves performance across various cavity sizes, outperforming off-the-shelf YOLOv8 detections that rely on a single image modality.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

ARM Mobile Facility Leaving Alaska for U.S. Southeast

The Atmospheric Radiation Measurement (ARM) user facility will soon begin the process of moving its third mobile facility (AMF3) from Alaska to the Southeastern United States. A workshop in August 2018 identified the Southeast as a priority region of interest for further study by ARM. The Southeast is a region with abundant atmospheric convection, yet the land surface, boundary layer, vegetation, and aerosol properties are markedly different from those seen at ARM’s fixed observatory in Oklahoma, allowing opportunities to explore new research questions. To maximize the scientific value of the new site, DOE’s Biological and Environmental Research program selected a site science team that will help guide the move of AMF3. Brookhaven National Laboratory (BNL) in New York will lead the AMF3 relocation effort. Supported by ARM and DOE’s Atmospheric System Research (ASR), the multi-institutional team is responsible for developing a science plan and initial research project for the Southeastern U.S. deployment.

54 ENVIRONMENTAL SCIENCES↗

More Efficient Precipitation Rate Data Acquisition with the STORM Swath-Based Analysis Tool

A multitude of locations exist for acquiring satellite-derived precipitation rate data. Because the volume of data exceeds what can reasonably be analyzed manually, online tools have been developed to help researchers make more informed data acquisition decisions. Some interfaces provide sample images generated from prioritized variables to enable efficient visual inspection, while others include the ability to subset geographically to reduce the volume of the data to the area of interest. Building upon such value-added services is the STORM (the NASA Precipitation Processing System (PPS) data product ordering system) Swath-Based Analysis Tool (https://storm.pps.eosdis.nasa.gov/storm/Analysis.jsp). With it, users can compare overflights of multiple precipitation satellites simultaneously and from this make determinations about which swaths will best serve their research. They can preview these overflights with two distinct visualization tools. Finally, they can then download geographically subset swaths that have precipitation rate characteristics matching their research needs. A user starts by making up to six selections. They then select their date range of interest going back to 1997. Finally, they select a geographical region either by inputting latitude-longitude corners of a rectangle or drawing that rectangle on an interactive map. The system processes each file, determining aggregate statistics about the precipitation rates within the selected region as observed by each instrument. These statistical values are added to a time series graph as a "time remaining" counter is continuously updated. The chart is fully interactive, with detailed values displayed upon mouseover, and numerous options available upon clicking each point. Since the user is likely to need the relevant files for their own research, they can generate an order from their request. All files are geographically subset to the region of interest, and the user can use the statistical values to limit which files are added to the order. This flexibility helps to ensure researchers are only downloading the files they need for their work, making for a more efficient process both from a time-consumption and a storage perspective. This paper will introduce the Swath-Based Analysis Tool and explore its numerous features. It will discuss several use cases for precipitation scientists.

remote sensing↗

A technique for studying (n,p) reactions of astrophysical interest using radioactive beams with SECAR

The formation of nuclei in slightly proton-rich regions of the neutrino-driven wind of core-collapse supernovae could be attributed to the neutrino-p process (νp-process). As it proceeds via a sequence of (p,γ) and (n,p) reactions, it may produce elements in the range of Ni and Sn, considering adequate conditions. Recent studies identify a number of decisive (n,p) reactions that control the efficiency of the νp-process. The study of one such (n,p) reaction via the measurement of the reverse (p,n) in inverse kinematics was performed with SECAR at NSCL/FRIB. Proton-induced reaction measurements, especially at the mass region of interest, are notably difficult since the recoils have nearly identical masses as the unreacted projectiles. Such measurements are feasible with the adequate separation level achieved with SECAR, and the in-coincidence neutron detection. Adjustments of the SECAR system for the first (p,n) reaction measurement included the development of new ion beam optics, and the installation of the neutron detection system. The aforementioned developments along with a discussion on the preliminary results of the p(58Fe,n)58Co reaction measurement are presented.

Tsintari, P↗

Adaptive grid methods for RLV environment assessment and nozzle analysis

Rapid access to highly accurate data about complex configurations is needed for multi-disciplinary optimization and design. In order to efficiently meet these requirements a closer coupling between the analysis algorithms and the discretization process is needed. In some cases, such as free surface, temporally varying geometries, and fluid structure interaction, the need is unavoidable. In other cases the need is to rapidly generate and modify high quality grids. Techniques such as unstructured and/or solution-adaptive methods can be used to speed the grid generation process and to automatically cluster mesh points in regions of interest. Global features of the flow can be significantly affected by isolated regions of inadequately resolved flow. These regions may not exhibit high gradients and can be difficult to detect. Thus excessive resolution in certain regions does not necessarily increase the accuracy of the overall solution. Several approaches have been employed for both structured and unstructured grid adaption. The most widely used involve grid point redistribution, local grid point enrichment/derefinement or local modification of the actual flow solver. However, the success of any one of these methods ultimately depends on the feature detection algorithm used to determine solution domain regions which require a fine mesh for their accurate representation. Typically, weight functions are constructed to mimic the local truncation error and may require substantial user input. Most problems of engineering interest involve multi-block grids and widely disparate length scales. Hence, it is desirable that the adaptive grid feature detection algorithm be developed to recognize flow structures of different type as well as differing intensity, and adequately address scaling and normalization across blocks. These weight functions can then be used to construct blending functions for algebraic redistribution, interpolation functions for unstructured grid generation, forcing functions to attract/repel points in an elliptic system, or to trigger local refinement, based upon application of an equidistribution principle. The popularity of solution-adaptive techniques is growing in tandem with unstructured methods. The difficultly of precisely controlling mesh densities and orientations with current unstructured grid generation systems has driven the use of solution-adaptive meshing. Use of derivatives of density or pressure are widely used for construction of such weight functions, and have been proven very successful for inviscid flows with shocks. However, less success has been realized for flowfields with viscous layers, vortices or shocks of disparate strength. It is difficult to maintain the appropriate mesh point spacing in the various regions which require a fine spacing for adequate resolution. Mesh points often migrate from important regions due to refinement of dominant features. An example of this is the well know tendency of adaptive methods to increase the resolution of shocks in the flowfield around airfoils, but in the incorrect location due to inadequate resolution of the stagnation region. This problem has been the motivation for this research.

Thornburg, Hugh J.↗

Search for new non-resonant phenomena in high-mass dilepton final states with the ATLAS detector

A search for new physics with non-resonant signals in dielectron and dimuon final states in the mass range above 2 TeV is presented. This is the first search for non-resonant signals in dilepton final states at the LHC to use a background estimate from the data. The data, corresponding to an integrated luminosity of 139 fb –1 , were recorded by the ATLAS experiment in proton-proton collisions at a center-of-mass energy of √s = 13 TeV during Run 2 of the Large Hadron Collider. The benchmark signal signature is a two-quark and two-lepton contact interaction, which would enhance the dilepton event rate at the TeV mass scale. To model the contribution from background processes a functional form is fit to the dilepton invariant-mass spectra in data in a mass region below the region of interest. It is then extrapolated to a high-mass signal region to obtain the expected background there. No significant deviation from the expected background is observed in the data. Upper limits at 95% CL on the number of events and the visible cross-section times branching fraction for processes involving new physics are provided. Observed (expected) 95% CL lower limits on the contact interaction energy scale reach 35.8 (37.6) TeV.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Machine Learning Models for Binary Molecular Classification using VUV Absorption Spectra

Machine learning methods were combined with differential absorption spectroscopy measurements in the vacuum-ultraviolet region (5.167 – 9.920 eV) in order to develop predictive capabilities for inferring molecular structure from the spectra. Several types of species were analyzed and, for modeling purposes, were defined using a single classification: (1) alkane, (2) conjugation with oxygen (e.g. diacetyl, ethyl vinyl ether), (3) non-conjugated alkene (e.g. 1-butene, 1,4-cyclohexadiene), (4) oxygen-containing (e.g. 1-butanol, tetrahydrofuran), or (5) cyclic (e.g. cyclopentane, cyclohexanone). The latter molecular classification excluded cyclic ethers. Several modeling methods were employed in the analysis of 102 absorption spectra, 24 of which were measured for the first time. The primary objective was to identify suitable methods that enable accurate predictions of molecular structure classifications with minimized statistical uncertainties. Rather than identifying a single, unifying method to reliably predict molecular structure contributions to VUV absorption spectra, coordination is required among a particular method, the type of molecular structure detail (e.g. conjugation), and absorption region of interest. The latter is accomplished using a binning approach, wherein absorption regions of ~0.5 eV were utilized rather than the entire ~4.8 eV range. Photon energy binning enabled analysis of region-specific predictions of accuracy, precision, and recall. The outcome from the binning approach is that, rather than utilizing the entire spectrum, optimal determination of molecular structure using machine learning methods depends on the absorption region. Furthermore, the present work provides separate machine learning models for each molecular classification, which enables the identification of multi-functional species relevant to atmospheric chemistry and combustion chemistry, where isomer-resolved speciation is critical to understanding complex reaction networks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Optimal observing strategies for velocity-suppressed dark matter annihilation

Numerous particle models for the cosmological dark matter feature a pair-annihilation rate that scales with powers of the relative velocity between the annihilating particles. As a result, the annihilation rate in the central regions of a dark matter halo can be significantly lower than at the halo’s periphery for particular ambient gravitational potentials. While this might be offset by an increasing dark matter pair number density in the inner halo, it raises the question; what angular region for dark matter models with velocity-suppressed annihilation rates optimizes the signal to noise ratio? We consider simplified background models for galactic and extragalactic targets and demonstrate that the optimal observing strategy varies greatly case by case. Generally, a bright central source warrants an annular region of interest, while a flatter background warrants as large as possible an angular region, possibly including the central regions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Fabrication

What aspects of optical fabrication technology need to be developed so as to facilitate existing planned missions, or enable new ones? Throughout the submillimeter to UV wavelengths, the common goal is to push technology to the limits to make the largest possible apertures that are diffraction limited. At any one wavelength, the accuracy of the surface must be better than lambda/30 (rms error). The wavelength range is huge, covering four orders of magnitude from 1 mm to 100 nm. At the longer wavelengths, diffraction limited surfaces can be shaped with relatively crude techniques. The challenge in their fabrication is to make as large as possible a reflector, given the weight and volume constraints of the launch vehicle. The limited cargo diameter of the shuttle has led in the past to emphasis on deployable or erectable concepts such as the Large Deployable Reflector (LDR), which was studied by NASA for a submillimeter astrophysics mission. Replication techniques that can be used to produce light, low-cost reflecting panels are of great interest for this class of mission. At shorter wavelengths, in the optical and ultraviolet, optical fabrication will tax to the limit the most refined polishing methods. Methods of mechanical and thermal stabilization of the substrate will be severely stressed. In the thermal infrared, the need for large aperture is tempered by the even stronger need to control the telescope's thermal emission by cooled or cryogenic operation. Thus, the SIRTF mirror at 1 meter is not large and does not require unusually high accuracy, but the fabrication process must produce a mirror that is the right shape at a temperature of 4 K. Future large cooled mirrors will present more severe problems, especially if they must also be accurate enough to work at optical wavelengths. At the very shortest wavelengths accessible to reflecting optics, in the x-ray domain, the very low count fluxes of high energy photons place a premium on the collecting area. It is not necessary to reach or even approach the diffraction limit, which would demand subnanometer fabrication and figure control. Replication techniques that produce large very lightweight surfaces are of interest for x-ray optics just as they are for the submillimeter region. Optical fabrication requirements are examined in more detail for missions in each of the three spectral regions of interest in astrophysics.

Angel, Roger↗

Photonics: From target recognition to lesion detection

Since 1989, Martin Marietta has invested in the development of an innovative concept for robust real-time pattern recognition for any two-dimensioanal sensor. This concept has been tested in simulation, and in laboratory and field hardware, for a number of DOD and commercial uses from automatic target recognition to manufacturing inspection. We have now joined Rose Health Care Systems in developing its use for medical diagnostics. The concept is based on determining regions of interest by using optical Fourier bandpassing as a scene segmentation technique, enhancing those regions using wavelet filters, passing the enhanced regions to a neural network for analysis and initial pattern identification, and following this initial identification with confirmation by optical correlation. The optical scene segmentation and pattern confirmation are performed by the same optical module. The neural network is a recursive error minimization network with a small number of connections and nodes that rapidly converges to a global minimum.

Henry, E. Michael↗

A Deconvolution Approach for the Mapping of Acoustic Sources (DAMAS) Determined from Phased Microphone Arrays

Current processing of acoustic array data is burdened with considerable uncertainty. This study reports an original methodology that serves to demystify array results, reduce misinterpretation, and accurately quantify position and strength of acoustic sources. Traditional array results represent noise sources that are convolved with array beamform response functions, which depend on array geometry, size (with respect to source position and distributions), and frequency. The Deconvolution Approach for the Mapping of Acoustic Sources (DAMAS) method removes beamforming characteristics from output presentations. A unique linear system of equations accounts for reciprocal influence at different locations over the array survey region. It makes no assumption beyond the traditional processing assumption of statistically independent noise sources. The full rank equations are solved with a new robust iterative method. DAMAS is quantitatively validated using archival data from a variety of prior high-lift airframe component noise studies, including flap edge/cove, trailing edge, leading edge, slat, and calibration sources. Presentations are explicit and straightforward, as the noise radiated from a region of interest is determined by simply summing the mean-squared values over that region. DAMAS can fully replace existing array processing and presentations methodology in most applications. It appears to dramatically increase the value of arrays to the field of experimental acoustics.

Brooks, Thomas F.↗