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At least 1,063 records · Page 59

Automating cell detection and classification in human brain fluorescent microscopy images using dictionary learning and sparse coding

Background Immunofluorescence (IF) plays a major role in quantifying protein expression in situ and understanding cell function. It is widely applied in assessing disease mechanisms and in drug discovery research. Automation of IF analysis can transform studies using experimental cell models. However, IF analysis of postmortem human tissue relies mostly on manual interaction, often subjected to low-throughput and prone to error, leading to low inter and intra-observer reproducibility. Human postmortem brain samples challenges neuroscientists because of the high level of autofluorescence caused by accumulation of lipofuscin pigment during aging, hindering systematic analyses. We propose a method for automating cell counting and classification in IF microscopy of human postmortem brains. Our algorithm speeds up the quantification task while improving reproducibility. New method Dictionary learning and sparse coding allow for constructing improved cell representations using IF images. These models are input for detection and segmentation methods. Classification occurs by means of color distances between cells and a learned set. Results Our method successfully detected and classified cells in 49 human brain images. We evaluated our results regarding true positive, false positive, false negative, precision, recall, false positive rate and F1 score metrics. We also measured user-experience and time saved compared to manual countings. Comparison with existing methods We compared our results to four open-access IF-based cell-counting tools available in the literature. Lastly, our method showed improved accuracy for all data samples. Conclusion The proposed method satisfactorily detects and classifies cells from human postmortem brain IF images, with potential to be generalized for applications in other counting tasks.

59 BASIC BIOLOGICAL SCIENCES↗

Solvent selection for biphasic extraction of 5-hydroxymethylfurfural via multiscale modeling and experiments

We introduce a comprehensive conceptual framework for selecting solvents for reactive extraction in biphasic organic-water systems and demonstrate it for the separation of HMF (5-hydroxylmethylfurfural), a platform chemical produced in the acid-catalyzed dehydration of hexoses. We first perform in silico screening of ~2500 solvents, from the ADFCRS-2018 database using the ADF COSMO-RS implementation, and classification, based on the solvent partition coefficient. We then determine experimentally the partition coefficients for HMF, fructose, and products of HMF rehydration (levulinic acid (LA), and formic acid (FA)), the mutual water-organic solvent solubilities, and the separation factors in >50 select solvents spanning multiple homologous series at room temperature and a typical reaction temperature with in situ sampling. We find that COSMO-RS is excellent for screening purposes (typical error in most cases within a factor of ~2). Increased temperatures lead to significant reduction in partitioning, and room temperature measurements are clearly inadequate for solvent selection. Upon down selecting classes of solvents based on separation performance, we perform experimental thermal stability and reaction compatibility studies of a small set of solvents at relevant reactive-extraction temperatures. We discover that many substituted phenols exhibit an order-of-magnitude increase in partitioning compared to conventional solvents due chiefly to hydrogen bond interactions and show the necessary stability but retain a significant fraction of water and LA, factors that need to be considered in technoeconomic analysis. In contrast, anilines, aldehydes, and acids are good to excellent regarding separation but incompatible with this specific reaction medium. Furthermore, this multifaceted framework can be extended to other biomass-derived products and processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The enhancement in dielectric and magnetic property in Na and Mn co substituted lanthanum ferrite

Nanocrystalline solid solutions of La{sub 1-x}Na{sub x}Fe{sub 1-y}Mn{sub y}O{sub 3} (x=y=0.00 and 0.25) were prepared via modified Pechini route. No evidence of secondary or impurity phase has been detected up to the detection of error limit of high power X-ray diffractometer. Dielectric property of the samples has been investigated in the frequency range 100 Hz-4MHz at temperature ranging 300–450K. The value of relative permittivity (ε{sub r}) increases drastically and shows colossal dielectric response (∼10{sup 4}) by cosubstitution of Na and Mn as compared to pure LaFeO{sub 3}. Dielectric relaxation peak in loss tangent in both samples have been found and shift towards higher frequency region as temperature increases. Magnetization-Field (M-H) loop of the calcined sample have been recorded at room temperature (300K) at field ±60kOe. Magnetic property also enhanced by co substitution of Na and Mn. The change in Fe/Mn-O-Fe/Mn angle by co-substitution of Na and Mn in LaFeO{sub 3} and indirect exchange interaction between two different magnetic sub lattices Fe and Mn might be responsible for drastic change. Saturation/maximum magnetic moment increase ∼four times in LNFM25 (5.335emu/g) as compared to pure LaFeO{sub 3} (1.302emu/g).

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Influence of defects on the thermal conductivity of compressed LiF

We report defect formation in LiF, which is used as an observation window in ramp and shock experiments, has significant effects on its transmission properties. Given the extreme conditions of the experiments it is hard to measure the change in transmission directly. Using molecular dynamics, we estimate the change in conductivity as a function of the concentration of likely point and extended defects using a Green-Kubo technique with careful treatment of size effects. With this data, we form a model of the mean behavior and its estimated error; then, we use this model to predict the conductivity of a large sample of defective LiF resulting from a direct simulation of ramp compression as a demonstration of the accuracy of its predictions. Given estimates of defect densities in a LiF window used in an experiment, the model can be used to correct the observations of thermal energy through the window. Also, the methodology we develop is extensible to modeling, with quantified uncertainty, the effects of a variety of defects on the thermal conductivity of solid materials.

36 MATERIALS SCIENCE↗

Beta Radiation Hardness of GYGAG(Ce) Transparent Ceramic Scintillators

GYGAG(Ce) transparent ceramic garnet scintillators were irradiated with electrons from 0.5 to 2 MeV with fluences from 10 16 e – /cm 2 to 10 19 e – /cm 2 , corresponding to doses from 0.3 to 310 Gigarad. Absorption spectra were measured before and after irradiations. Light yields from alpha, beta, and gamma excitations were measured before and after irradiation and compared to preirradiation values to gain a deeper understanding of how electron irradiations can affect light yield, as well as defects generated in both the surface and bulk. Within experimental error, no degradation in light yield was observed for the electron-irradiated samples, as measured via beta or gamma excitation, with minimal degradation observed via alpha excitation. A small increase in optical absorption near the wavelength of emission was observed following the largest dose irradiation. These results suggest that GYGAG(Ce) is radiation hard to electron irradiation up to 10 19 e – /cm 2 and doses up to 310 Gigarad. Furthermore, this robustness to irradiation indicates that transparent ceramic garnets may prove useful for applications such as scintillation-based nuclear batteries by allowing for higher energy beta emitters, increased power densities, and enabling long service lifetimes.

36 MATERIALS SCIENCE↗

Smoothing Motion Estimates for Radar Motion Compensation.

Simple motion models for complex motion environments are often not adequate for keeping radar data coherent. Eve n perfect motion samples appli ed to imperfect models may lead to interim calculations e xhibiting errors that lead to degraded processing results. Herein we discuss a specific i ssue involving calculating motion for groups of pulses, with measurements only available at pulse-group boundaries. - 4 - Acknowledgements This report was funded by General A tomics Aeronautical Systems, Inc. (GA-ASI) Mission Systems under Cooperative Re search and Development Agre ement (CRADA) SC08/01749 between Sandia National Laboratories and GA-ASI. General Atomics Aeronautical Systems, Inc. (GA-ASI), an affilia te of privately-held General Atomics, is a leading manufacturer of Remotely Piloted Aircraft (RPA) systems, radars, and electro-optic and rel ated mission systems, includin g the Predator(r)/Gray Eagle(r)-series and Lynx(r) Multi-mode Radar.

47 OTHER INSTRUMENTATION↗

Coastal Acoustic Buoy for Offshore Wind: Project Synthesis

The population of North Atlantic right whales is critically endangered and their habitat overlaps with offshore windfarm leases. It is therefore imperative that effective mitigation strategies be used to avoid impacts on right whales during the construction of offshore windfarms. The Department of Energy issued FOA Number DE-FOA-0001924 to encourage the development of technology that could monitor large exclusion zones for right whales in order to mitigate potential impact of construction noise on right whales. This report summarizes the past two years of the development and evaluation of the Coastal Acoustic Buoy for Offshore Wind (CABOW) project which aimed to develop technology to monitor large exclusion zones for North Atlantic right whales. Over the course of the project SMRU Consulting have implemented a rigorous design process including comparison of different approaches (e.g., single sensor vs multiple sensors), as well as consideration of placement and timing of acoustic monitoring. We have evaluated critical components of the CABOW system including, reliability, detection range, and bearing accuracy in areas adjacent to offshore windfarm leases in Maryland by conducting 3,536 playbacks of simulated right whale upcalls. The maximum call detection range was 7.5 km when noise was 99 dB re 1µPa rms (50-225 Hz), but this reduced to < 1 km when ambient noise levels were high. Our detection probability in the field was measured as a function of range as well as the source-to-noise level ratio allowing us to build a model to predict the probability of detection under various scenarios (sample size: 3,536 calls x 5 buoys = 17,680). The median bearing error was -0.25° but this is likely an underestimate of error due to experimental design. Using the published recall and precision of the two detectors we implemented in the CABOW system, we estimate that at a recall of 80%, our precision was > 80%, within the range of what we were aiming for in this project. To estimate our exclusion zone false negative and false positive rates, we built a simulation model using the empirical data from our field trial. We modelled three to nine CABOW units placed on the 10 km exclusion zone and estimated our false negative rate to be 1% or less (which was our project goal) and our false positive rate to be between seven and nine percent, slightly above our goal of 5%. However, we also modelled an equivalent PAM system that does not have bearing capabilities and found the false positive rates for that system to be six to eight times higher than the CABOW rate. This higher false positive rate of PAM systems with low spatial information could have significant cost repercussions for offshore wind developers by adding work shutdowns or delays without providing additional protection for right whales. The model we built allows us to explore the placement of PAM systems under various scenarios and will thus help facilitate planning of PAM mitigation systems to meet NOAA Incidental Harassment Authorizations for specific windfarms. We achieved an average system uptime of 98.3%, just below our goal of 99%. The issues that caused these short losses of data have been identified and fixed. Right whale detections and audio clips were typically transferred via radio from the buoys to the base station in two to four seconds. We therefore believe we have developed a highly robust real-time PAM system. Based on the above, we feel we have achieved the stated funding goal of developing a cost-effective and robust real-time PAM system that enables the monitoring of large exclusion zones for right whales during the constructions of offshore windfarms. This should lead to decreased costs and risks for the offshore wind sector while providing robust mitigation for right whales. It is important to state that PAM mitigation will need to be implemented with other mitigation strategies (e.g., visual observers) to provide a complete mitigation strategy to ensure that any effects on right whales from offshore windfarm construction is minimized.

17 WIND ENERGY↗

Improvements of Nuclear Data Evaluations for Lead Isotopes in Support of Next Generation Lead-Cooled Fast Systems

The neutron evaluation of the isotopes that comprise natural lead were undertaken as a part of DOE-NEUP Project #19-16739. The goal of the project was to update the neutron cross sections to account for new differential measurements and incorporate the most up-to-date physics. Shortcomings in the lead cross sections was made known by several independent reports. The work performed here repeated the simulation of all the “benchmark” validation systems and concluded that the major issue is the scattering cross sections in the major lead isotopes above 100 keV. Re-evaluation of 206,207,208 Pb included both the resolved resonance region and fast region evaluations of the cross sections. Combined these regions cover energies from thermal to 20 MeV. The most drastic improvement is the resolved resonance region evaluation of 208 Pb which is now extended from 1.0 to 1.5 MeV. Parameterization of these resonances in the R-matrix provides a superior reconstruction of not only the experimental cross section but also the scattering distributions via the Blatt-Biedenharn formalism. Fast region evaluations of the three major isotopes were done to include new inelastic experimental data from the neutron Time-of-Flight facility at CERN. The culmination of all the changes to the cross section is a drastic improvement in the scattering kernel as shown in Rensselaer Polytechnic Institute (RPI) Quasi-Differential scattering measurements and improved prediction of keff for fast integral experiments. Alongside the new cross sections, new nuclear data covariance (uncertainties) have been computed and are included in the evaluation. Little is changed in the magnitude of the uncertainties but the correlations within the covariance display non-trivial changes. The new evaluations of 206,207,208 Pb have been submitted to the National Nuclear Data Center to be included in the ENDF/B-VIII.1 library. While the cross sections have been updated extensively, knowledge and modeling of the cross sections between 1.0 and 3.0 MeV for the isotopes remain a challenge. Most notably is the double differential elastic cross section for 208 Pb and 206 Pb. New quasi-differential measurements for pure samples of these two nuclei would go a long way in reducing compensating errors in the evaluations. Qualitatively, the project has produced a prosperous collaboration between the nuclear data group at RPI with staff scientists at Brookhaven National Laboratory, Naval Nuclear Laboratory, Oak Ridge National Laboratory, Los Alamos National Laboratory, Lawrence Livermore National Laboratory, and Sandia National Laboratories. Quantitatively this is reflected in seven conference presentations, at least one journal submission, and one doctoral thesis.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Can Agricultural Management Induced Changes in Soil Organic Carbon Be Detected Using Mid-Infrared Spectroscopy?

A major limitation to building credible soil carbon sequestration programs is the cost of measuring soil carbon change. Diffuse reflectance spectroscopy (DRS) is considered a viable low-cost alternative to traditional laboratory analysis of soil organic carbon (SOC). While numerous studies have shown that DRS can produce accurate and precise estimates of SOC across landscapes, whether DRS can detect subtle management induced changes in SOC at a given site has not been resolved. Here, we leverage archived soil samples from seven long-term research trials in the U.S. to test this question using mid infrared (MIR) spectroscopy coupled with the USDA-NRCS Kellogg Soil Survey Laboratory MIR spectral library. Overall, MIR-based estimates of SOC%, with samples scanned on a secondary instrument, were excellent with the root mean square error ranging from 0.10 to 0.33% across the seven sites. In all but two instances, the same statistically significant (p < 0.10) management effect was found using both the lab-based SOC% and MIR estimated SOC% data. Despite some additional uncertainty, primarily in the form of bias, these results suggest that large existing MIR spectral libraries can be operationalized in other laboratories for successful carbon monitoring.

54 ENVIRONMENTAL SCIENCES↗

Digital simulation error curves for a spring-mass-damper system

Plotting digital simulation errors for a spring-mass-damper system and using these error curves to select type of integration, feedback update method, and number of samples per cycle at resonance reduces excessive number of samples per cycle and unnecessary iterations.

Knox, L. A.↗

A three stage sampling model for remote sensing applications

A conceptual model and an empirical application of the relationship between the manner of selecting observations and its effect on the precision of estimates from remote sensing are reported. This three stage sampling scheme considers flightlines, segments within flightlines, and units within these segments. The error of estimate is dependent on the number of observations in each of the stages.

Eisgruber, L. M.↗

Development and modification of a digital program for final approach to landing

The development and implementation of a dynamic digital computer simulator which may be used to evaluate aircraft performance when operating under the control and guidance of various navigation, landing, and flight control systems are discussed. The digital computer program may be used to simulate and evaluate the relationships and interactions between various factors such as the microwave landing system, avionics receivers and onboard processors, aircraft aerodynamics, aircraft automatic control systems, control surfaces, and wind and other external effects. The models used to represent aircraft aerodynamics, control system and control surfaces; weather and wind effects; and the microwave landing system are described. Example results are presented for a simulation of a Boeing 737 using two sample control systems while subjected to various atmospheric conditions and microwave landing system errors. The limitations and performance capabilities of these control systems are discussed in terms of their ability to utilize the microwave landing system signal.

Duff, W. G.↗

Image stretching on a curved surface to improve satellite gridding

A method for substantially reducing gridding errors due to satellite roll, pitch and yaw is given. A gimbal-mounted curved screen, scaled to 1:7,500,000, is used to stretch the satellite image whereby visible landmarks coincide with a projected map outline. The resulting rms position errors averaged 10.7 km as compared with 25.6 and 34.9 km for two samples of satellite imagery upon which image stretching was not performed.

Ormsby, J. P.↗

Comparison of video fields and frames for transform compression

Because of the interlaced television scan, the two fields that form an interlaced video frame are generated 1/60 of a second apart. If the two fields are compressed independently, the correlation between adjacent lines is unused. The transmission rate can be reduced by using a field memory to form an interlaced frame. Four test images were processed as fields and as interlaced frames, using both theoretical and experimental compression designs. For comparable mean-square error and subjective appearance, field compression requires about one-half bit per sample more than frame compression. However, the overall transmission rate - the number of bits per image times the number of images per second - is more meaningful than the number of bits per sample. When transform compression at low transmission rates merges the adjacent lines, frame compression becomes similar to field repeating, and the memory can be reduced.

Jones, H. W., Jr.↗

Spectroscopic observations of winds on Venus. I - Technique and data reduction

Methods of measurement and reduction of high-dispersion photographic spectra of Venus are presented. Preliminary results are consistent with slow direct or no rotation at the level sample, and disagree strongly with a 4-day retrograde rotation. A serious systematic error, which affects much published work, is due to blending of solar lines in the sky with those reflected from the planet. This always tends to produce a spurious retrograde 'rotation'. Only data obtained in a dark sky, or daytime observations from which the sky lines have been accurately subtracted, can be relied upon. All such data give low wind speeds.

Young, A. T.↗

The effect of abnormal cell proportion on specimen classifier performance

An analysis is presented of the results obtained from a cell classifier which is confronted with an abnormal/normal cell ratio which is different from the ratio assumed in the calibration of the classifier. False negative and false positive error rates are determined in advance for classifier operation, along with the necessary sample size in order to validate the predicted distributions. Changes are demonstrated to happen only regarding the false negative rate, where reductions in the abnormal cell rate below the expected rates would cause totally unreliable data. Substantial overproduction of abnormal cells would be quickly noticeable, while production rates beyond, but close to, the expected rates would only require more extensive sampling. Classifier systems for 10% proportions of abnormal cells are concluded to be possible, but difficulties are present with much lower rates

Castleman, K. R.↗

Investigation, development and application of optimal output feedback theory. Volume 2: Development of an optimal, limited state feedback outer-loop digital flight control system for 3-D terminal area operation

This report contains the development of a digital outer-loop three dimensional radio navigation (3-D RNAV) flight control system for a small commercial jet transport. The outer-loop control system is designed using optimal stochastic limited state feedback techniques. Options investigated using the optimal limited state feedback approach include integrated versus hierarchical control loop designs, 20 samples per second versus 5 samples per second outer-loop operation and alternative Type 1 integration command errors. Command generator tracking techniques used in the digital control design enable the jet transport to automatically track arbitrary curved flight paths generated by waypoints. The performance of the design is demonstrated using detailed nonlinear aircraft simulations in the terminal area, frequency domain multi-input sigma plots, frequency domain single-input Bode plots and closed-loop poles. The response of the system to a severe wind shear during a landing approach is also presented.

Broussard, J. R.↗

Quaternions for Galileo scan platform control

The application of quaternions for the articulation control of the Galileo scan platform is presented in this paper. The purpose of selecting quaternions is to minimize onboard computation time and program size. Attention has been focused on performing inertial pointing while the spacecraft is in a dual spin configuration. Target quaternion and relative target quaternion are introduced and used to specify the target position of the scan platform for point-to-point absolute slews and mosaic relative slews, respectively. The pointing error of the platform is represented by an error quaternion which is converted into gimbal angular errors defining the attitude change. For path control, a moving target quaternion is generated; the corresponding tracking error quaternion and the related spacecraft motion compensation capability are also addressed. A sample slew case is used to demonstrate the implementation of these concepts.

Breckenridge, W. G.↗