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At least 451 records · Page 25

Genomic Diversity Evaluation of Populus trichocarpa Germplasm for Rare Variant Genetic Association Studies

Genome-wide association studies are powerful tools to elucidate the genome-to-phenome relationship. In order to explain most of the observed heritability of a phenotypic trait, a sufficient number of individuals and a large set of genetic variants must be examined. The development of high-throughput technologies and cost-efficient resequencing of complete genomes have enabled the genome-wide identification of genetic variation at large scale. As such, almost all existing genetic variation becomes available, and it is now possible to identify rare genetic variants in a population sample. Rare genetic variants that were usually filtered out in most genetic association studies are the most numerous genetic variations across genomes and hold great potential to explain a significant part of the missing heritability observed in association studies. Rare genetic variants must be identified with high confidence, as they can easily be confounded with sequencing errors. In this study, we used a pre-filtered data set of 1,014 pure Populus trichocarpa entire genomes to identify rare and common small genetic variants across individual genomes. We compared variant calls between Platypus and HaplotypeCaller pipelines, and we further applied strict quality filters for improved genetic variant identification. Finally, we only retained genetic variants that were identified by both variant callers increasing calling confidence. Based on these shared variants and after stringent quality filtering, we found high genomic diversity in P. trichocarpa germplasm, with 7.4 million small genetic variants. Importantly, 377k non-synonymous variants (5% of the total) were uncovered. We highlight the importance of genomic diversity and the potential of rare defective genetic variants in explaining a significant portion of P. trichocarpa's phenotypic variability in association genetics. The ultimate goal is to associate both rare and common alleles with poplar's wood quality traits to support selective breeding for an improved bioenergy feedstock.

Genetics & Heredity↗

Formulation of a strategy for monitoring control integrity in critical digital control systems

Advanced aircraft will require flight critical computer systems for stability augmentation as well as guidance and control that must perform reliably in adverse, as well as nominal, operating environments. Digital system upset is a functional error mode that can occur in electromagnetically harsh environments, involves no component damage, can occur simultaneously in all channels of a redundant control computer, and is software dependent. A strategy is presented for dynamic upset detection to be used in the evaluation of critical digital controllers during the design and/or validation phases of development. Critical controllers must be able to be used in adverse environments that result from disturbances caused by an electromagnetic source such as lightning, high intensity radiated field (HIRF), and nuclear electromagnetic pulses (NEMP). The upset detection strategy presented provides dynamic monitoring of a given control computer for degraded functional integrity that can result from redundancy management errors and control command calculation error that could occur in an electromagnetically harsh operating environment. The use is discussed of Kalman filtering, data fusion, and decision theory in monitoring a given digital controller for control calculation errors, redundancy management errors, and control effectiveness.

Belcastro, Celeste M.↗

Pulsed radio frequency interference effects on data communications via satellite transponder

Power-limited communication links may be susceptible to significant degradation if intentional or unintentional pulsed high level radio frequency interference (RFI) is present. Pulsed RFI is, in fact, of current interest to NASA in studies relating to its Tracking and Data Relay Satellite System (TDRSS). The present paper examines the impact of pulsed RFI on the error probability performance of a power-limited satellite communication link: the assumed modulation scheme is PN coded binary PSK. The composite effects of thermal noise, pulsed CW and pulsed Gaussian noise are analyzed, where RFI arrivals are assumed to follow Poisson statistics. Under the assumption that the satellite repeater is ideal and that integrate and dump filtering is employed at the ground receiver, an exact error probability expression and associated approximations are derived. Computed results are generated using an arbitrarily specified RFI model.

Weinberg, A.↗

Qubit control noise spectroscopy with optimal suppression of dephasing

Here, we extend quantum noise spectroscopy (QNS) of amplitude control noise to settings where dephasing noise or detuning errors make significant contributions to qubit dynamics. Previous approaches to characterize amplitude noise are limited by their vulnerability to low-frequency dephasing noise and static detuning errors, which can overwhelm the target control noise signal and introduce bias into estimates of the amplitude noise spectrum. To overcome this problem, we leverage optimal control to identify a family of amplitude control waveforms that optimally suppress low-frequency dephasing noise and detuning errors, while maintaining the spectral concentration in the amplitude filter essential for spectral estimation. The waveforms found via numerical optimization have surprisingly simple analytic forms, consisting of oscillating sine waves obeying particular amplitude and frequency constraints. In numerically simulated QNS experiments, these waveforms demonstrate superior robustness, enabling accurate estimation of the amplitude noise spectrum in regimes where existing approaches are biased by low-frequency dephasing noise and detuning errors.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Extending the impulse response in order to reduce errors due to impulse noise and signal fading

A finite impulse response (FIR) digital smearing filter was designed to produce maximum intersymbol interference and maximum extension of the impulse response of the signal in a noiseless binary channel. A matched FIR desmearing filter at the receiver then reduced the intersymbol interference to zero. Signal fades were simulated by means of 100 percent signal blockage in the channel. Smearing and desmearing filters of length 256, 512, and 1024 were used for these simulations. Results indicate that impulse response extension by means of bit smearing appears to be a useful technique for correcting errors due to impulse noise or signal fading in a binary channel.

Webb, Joseph A.↗

Stitching-error reduction in gratings by shot-shifted electron-beam lithography

Calculations of the grating spatial-frequency spectrum and the filtering properties of multiple-pass electron-beam writing demonstrate a tradeoff between stitching-error suppression and minimum pitch separation. High-resolution measurements of optical-diffraction patterns show a 25-dB reduction in stitching-error side modes.

Integrated optics semiconductor lasersgratings↗

Multi-star processing and gyro filtering for the video inertial pointing system

The video inertial pointing (VIP) system is being developed to satisfy the acquisition and pointing requirements of astronomical telescopes. The VIP system uses a single video sensor to provide star position information that can be used to generate three-axis pointing error signals (multi-star processing) and for input to a cathode ray tube (CRT) display of the star field. The pointing error signals are used to update the telescope's gyro stabilization system (gyro filtering). The CRT display facilitates target acquisition and positioning of the telescope by a remote operator. Linearized small angle equations are used for the multistar processing and a consideration of error performance and singularities lead to star pair location restrictions and equation selection criteria. A discrete steady-state Kalman filter which uses the integration of the gyros is developed and analyzed. The filter includes unit time delays representing asynchronous operations of the VIP microprocessor and video sensor. A digital simulation of a typical gyro stabilized gimbal is developed and used to validate the approach to the gyro filtering.

Murphy, J. P.↗

Advances in Serial MSK modems

Lumped element as well as distributed element networks are used in the Serial MSK (SMSK) modems, for 20-1000 Mbps data rate range applications, whose design and performance characteristics are described. It is noted that the use of baseband conversion filters for the modulator yields good performance in many applications, with typical matched filter designs (structurally simple to implement) causing less than 0.5 dB bit error rate performance degradation. The SMSK modem technique begins with the use of a biphased shift-keyed modulator, and then employs passive filters to obtain the MSK signal.

Ryan, C. R.↗

A Reduced Dimension Static, Linearized Kalman Filter and Smoother

An approximate Kalman filter and smoother, based on approximations of the state estimation error covariance matrix, is described. Approximations include a reduction of the effective state dimension, use of a static asymptotic error limit, and a time-invariant linearization of the dynamic model for error integration. The approximations lead to dramatic computational savings in applying estimation theory to large complex systems. Examples of use come from TOPEX/POSEIDON.

Kalman filter smoother modeling ocean simulation↗

Digital image gathering and minimum mean-square error restoration

Most digital image restoration algorithms are inherently incomplete because they are conditioned on a discrete-input, discrete-output model which only accounts for blurring during image gathering and additive noise. For those restoration applications where sampling and reconstruction are important, the restoration algorithm should be based on a more comprehensive end-to-end model which also accounts for the potentially important noiselike effects of aliasing and the low-pass filtering effects of interpolative reconstruction. It is demonstrated that although the mathematics of this more comprehensive model is more complex, the increase in complexity is not so great as to prevent a complete development and analysis of the associated minimum mean-square error (Wiener) restoration filter.

Park, Stephen K.↗

Z-Sequence: photometric redshift predictions for galaxy clusters with sequential random k-nearest neighbours

ABSTRACT We introduce Z-Sequence, a novel empirical model that utilizes photometric measurements of observed galaxies within a specified search radius to estimate the photometric redshift of galaxy clusters. Z-Sequence itself is composed of a machine learning ensemble based on the k-nearest neighbours algorithm. We implement an automated feature selection strategy that iteratively determines appropriate combinations of filters and colours to minimize photometric redshift prediction error. We intend for Z-Sequence to be a standalone technique but it can be combined with cluster finders that do not intrinsically predict redshift, such as our own DEEP-CEE. In this proof-of-concept study, we train, fine-tune, and test Z-Sequence on publicly available cluster catalogues derived from the Sloan Digital Sky Survey. We determine the photometric redshift prediction error of Z-Sequence via the median value of |Δ$z$|/(1 + $z$) (across a photometric redshift range of 0.05 ≤ $z$ ≤ 0.6) to be ∼0.01 when applying a small search radius. The photometric redshift prediction error for test samples increases by 30–50 per cent when the search radius is enlarged, likely due to line-of-sight interloping galaxies. Eventually, we aim to apply Z-Sequence to upcoming imaging surveys such as the Legacy Survey of Space and Time to provide photometric redshift estimates for large samples of as yet undiscovered and distant clusters.

Chan, Matthew C.↗

Convex Q-Learning in Continuous Time with Application to Dispatch of Distributed Energy Resources

Convex Q-learning is a recent approach to reinforcement learning, motivated by the possibility of a firmer theory for convergence, and the possibility of making use of greater a priori knowledge regarding policy or value function structure. This paper explores algorithm design in the continuous time domain, with a finite-horizon optimal control objective. The main contributions are (i) The new Q-ODE: a model-free characterization of the Hamilton-Jacobi-Bellman equation. (ii) A formulation of Convex Q-learning that avoids approximations appearing in prior work. The Bellman error used in the algorithm is defined by filtered measurements, which is necessary in the presence of measurement noise. (iii) Convex Q-learning with linear function approximation is a convex program. It is shown that the constraint region is bounded, subject to an exploration condition on the training input. (iv) The theory is illustrated in application to resource allocation for distributed energy resources, for which the theory is ideally suited.

Lu, Fan↗

BLOC Site - ASSIST Thermodynamic retrievals TROPoe / Derived Data

This dataset contains daily files with thermodynamic profiles retrieved with the optimal estimation physical retrieval TROPoe (Turner and Löhnert 2014; Turner and Blumberg 2019; Turner and Löhnert 2021). The profiles are retrieved every 10 minutes from instantaneous radiances observed with an Atmospheric Sounder Spectrometer by Infrared Spectral Technology (ASSIST, Rochette et al. 2009) operated by NOAA Physical Sciences Laboratory on Block Island for WFIP3. The spectral bands used in the retrieval are in the wavenumber range from 612 - 905.4 cm-1 and are specified in Turner and Löhnert (2021). Radiances are noise-filtered but not averaged in time to minimize errors due to non-uniform clouds. Additional input data in TROPoe are cloud base height from a collocated ceilometer operated by NOAA GML and temperature, water vapor mixing ratio, and pressure from a sensor attached to the ASSIST housing. In addition to these temporally resolved input data, TROPoe requires an a priori dataset (prior) that provides mean climatological estimates of thermodynamic profiles and specifies how temperature and humidity covary with height as an input (for details see, e.g., Djalalova et al. 2022). The prior is a key component of the retrieval and provides a constraint on the ill-posed inversion problem. A monthly prior was computed from operational radiosonde launches at Upton, NY.

17 WIND ENERGY↗

NWTC Site 4.0 - NREL ASSIST (SN10) / Thermodynamic retrievals TROPoe

This dataset contains daily files with thermodynamic profiles retrieved with the optimal estimation physical retrieval TROPoe v0.12 (Turner and Löhnert 2014; Turner and Blumberg 2019; Turner and Löhnert 2021). The profiles are retrieved every 10 minutes from instantaneous observations from the NREL ASSIST-II (SN 10) infrared spectrometer. Observations are noise-filtered but not averaged in time to minimize errors due to non-uniform clouds. Additional input data in TROPoe are cloud base height from a Vaisala CL51 ceilometer. The full pipeline for running the retrieval is available at https://github.com/StefanoWind/TROPoe_processor. Met data were not ingested. In addition to these temporally resolved input data, TROPoe requires an a priori dataset (prior) that provides mean climatological estimates of thermodynamic profiles and specifies how temperature and humidity covary with height as an input (for details see, e.g., Djalalova et al. 2022). The prior is a key component of the retrieval and provides a constraint on the ill-posed inversion problem. A monthly prior was computed from operational radiosonde launches at Denver, CO.

17 WIND ENERGY↗

NWTC Site 3.2 - NREL ASSIST (SN12) / Thermodynamic retrievals TROPoe

This dataset contains daily files with thermodynamic profiles retrieved with the optimal estimation physical retrieval TROPoe v0.12 (Turner and Löhnert 2014; Turner and Blumberg 2019; Turner and Löhnert 2021). The profiles are retrieved every 10 minutes from instantaneous observations from the NREL ASSIST-II (SN 12) infrared spectrometer. Observations are noise-filtered but not averaged in time to minimize errors due to non-uniform clouds. Additional input data in TROPoe are cloud base height from a Vaisala CL51 ceilometer. The full pipeline for running the retrieval is available at https://github.com/StefanoWind/TROPoe_processor. Met data were not ingested. In addition to these temporally resolved input data, TROPoe requires an a priori dataset (prior) that provides mean climatological estimates of thermodynamic profiles and specifies how temperature and humidity covary with height as an input (for details see, e.g., Djalalova et al. 2022). The prior is a key component of the retrieval and provides a constraint on the ill-posed inversion problem. A monthly prior was computed from operational radiosonde launches at Denver, CO.

17 WIND ENERGY↗

Title NWTC Site 3.2 - NREL ASSIST (SN11) / Thermodynamic retrievals TROPoe

This dataset contains daily files with thermodynamic profiles retrieved with the optimal estimation physical retrieval TROPoe v0.12 (Turner and Löhnert 2014; Turner and Blumberg 2019; Turner and Löhnert 2021). The profiles are retrieved every 10 minutes from instantaneous observations from the NREL ASSIST-II (SN 11) infrared spectrometer. Observations are noise-filtered but not averaged in time to minimize errors due to non-uniform clouds. Additional input data in TROPoe are cloud base height from a Vaisala CL51 ceilometer. The full pipeline for running the retrieval is available at https://github.com/StefanoWind/TROPoe_processor. Met data were not ingested. In addition to these temporally resolved input data, TROPoe requires an a priori dataset (prior) that provides mean climatological estimates of thermodynamic profiles and specifies how temperature and humidity covary with height as an input (for details see, e.g., Djalalova et al. 2022). The prior is a key component of the retrieval and provides a constraint on the ill-posed inversion problem. A monthly prior was computed from operational radiosonde launches at Denver, CO.

17 WIND ENERGY↗

NREL ASSIST Barge / Thermodynamic retrievals TROPoe v0.19

This dataset contains daily files with thermodynamic profiles retrieved with the optimal estimation physical retrieval TROPoe v0.19 (Turner and Löhnert, 2014; Turner and Blumberg, 2019; Turner and Löhnert, 2021). The profiles are retrieved every 10 minutes from instantaneous observations from the NREL ASSIST-II (SN 12) infrared spectrometer. Observations are noise-filtered but not averaged in time to minimize errors due to non-uniform clouds. Additional input data in TROPoe are cloud base height from a collocated NREL Vaisala CL51 ceilometer (when available) or vertically staring Halo XR lidar, and surface temperature, relative humidity, and pressure from the collocated Oregon State University met tower. The full pipeline to run the retrieval is available at https://github.com/StefanoWind/TROPoe_processor. In addition to these temporally resolved input data, TROPoe requires an a priori dataset (prior) that provides mean climatological estimates of thermodynamic profiles and specifies how temperature and humidity covary with height as an input (for details see, e.g., Djalalova et al., 2022). The prior is a key component of the retrieval and provides a constraint on the ill-posed inversion problem. A monthly prior was computed from operational radiosonde launches at Upton, NY.

17 WIND ENERGY↗

Site B - NREL ASSIST (SN11) Thermodynamic Retrievals TROPoe / Derived Data

This dataset contains daily files with thermodynamic profiles retrieved with the optimal estimation physical retrieval TROPoe v0.12 (Turner and Löhnert 2014; Turner and Blumberg 2019; Turner and Löhnert 2021). The profiles are retrieved every 10 minutes from instantaneous observations from the NREL ASSIST-II (SN 11) infrared spectrometer. Observations are noise-filtered but not averaged in time to minimize errors due to non-uniform clouds. Additional input data in TROPoe are cloud base height (CBH), which is a combined data product that uses data from ceilometers at sites A1 and H and scanning lidars from ARM sites C1 and E37. The CBH is weighted inversely proportionally to the distance to the respective site to take into account the spatial variability of clouds (see https://github.com/StefanoWind/ASSIST_analysis/blob/main/awaken_processing/combine_cbh.py). The full pipeline for running the retrieval is available at https://github.com/StefanoWind/TROPoe_processor. Met data was not ingested. In addition to these temporally resolved input data, TROPoe requires an a priori dataset (prior) that provides mean climatological estimates of thermodynamic profiles and specifies how temperature and humidity covary with height as an input (for details see, e.g., Djalalova et al. 2022). The prior is a key component of the retrieval and provides a constraint on the ill-posed inversion problem. A monthly prior was computed from operational radiosonde launches at ARM SGP, OK.

17 WIND ENERGY↗