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At least 1,351 records · Page 75

A single genomic region controls primocane fruiting in tetraploid blackberry

The fresh-market blackberry ( Rubus subgenus Rubus ) industry has expanded dramatically in the past 2 decades, driven in part by improved cultivars. Introgression of the primocane-fruiting (PF; annual flowering) trait into elite germplasm has enabled dual cropping in a single year, season extension, and cultivation in tropical and subtropical regions. Despite its economic performance, the genetic basis of PF is not well understood. It has been proposed that the PF trait is controlled by a major recessive locus, but its genomic location is unclear. Here, a genome-wide association study (GWAS) of 365 tetraploid blackberry genotypes identified a single genomic region on chromosome Ra03 (∼33 Mb) strongly associated with PF. Genetic linkage analysis in a biparental population confirmed that the same interval (32–35 Mb) was linked to the PF phenotype. Ten putative candidate genes were identified in this region. Allele mining using whole-genome resequencing of 17 genotypes highlighted 2 high-priority candidates: a CCCH-type zinc finger gene and an ubiquitin-specific protease gene. Use of an improved Rubus argutus “Hillquist” genome annotation (v1.2) enabled refined variant interpretation, including identification of regulatory 3′ UTR polymorphisms in the zinc finger homolog. Two diagnostic KASP markers (PF1 and PF2), designed from the most significant GWAS SNPs, predicted the PF phenotype with over 96% accuracy in a validation panel of 494 tetraploid blackberries from multiple breeding programs. Together, these results provide the first high-resolution mapping of the PF locus in blackberry, identify candidate genes for flowering regulation in Rubus , and deliver diagnostic markers that can be immediately deployed in breeding programs.

GWAS↗

Generalizable, fast, and accurate DeepQSPR with fastprop

Abstract Quantitative Structure–Property Relationship studies (QSPR), often referred to interchangeably as QSAR, seek to establish a mapping between molecular structure and an arbitrary target property. Historically this was done on a target-by-target basis with new descriptors being devised to specifically map to a given target. Today software packages exist that calculate thousands of these descriptors, enabling general modeling typically with classical and machine learning methods. Also present today are learned representation methods in which deep learning models generate a target-specific representation during training. The former requires less training data and offers improved speed and interpretability while the latter offers excellent generality, while the intersection of the two remains under-explored. This paper introduces , a software package and general Deep-QSPR framework that combines a cogent set of molecular descriptors with deep learning to achieve state-of-the-art performance on datasets ranging from tens to tens of thousands of molecules. provides both a user-friendly Command Line Interface and highly interoperable set of Python modules for the training and deployment of feedforward neural networks for property prediction. This approach yields improvements in speed and interpretability over existing methods while statistically equaling or exceeding their performance across most of the tested benchmarks. is designed with Research Software Engineering best practices and is free and open source, hosted at github.com/jacksonburns/fastprop.

Burns, Jackson W. (ORCID:0000000206579426)↗

AN INVESTIGATION OF TIME LAG MAPS USING THREE-DIMENSIONAL SIMULATIONS OF HIGHLY STRATIFIED HEATING

The location and frequency of coronal energy release provide a significant constraint on the coronal heating mechanism. The evolution of the intensity observed in coronal structures found from time lag analysis of Atmospheric Imaging Assembly (AIA) data has been used to argue that heating must occur sporadically. Recently, we have demonstrated that quasi-steady, highly stratified (footpoint) heating can produce results qualitatively consistent with the evolution of observed coronal structures. The goals of this paper are to demonstrate that time lag analysis of 3D simulations of footpoint heating are qualitatively consistent with time lag analysis of observations and to use the 3D simulations to further understand whether time lag analysis is a useful tool in defining the evolution of coronal structures. We find the time lag maps generated from simulated data are consistent with the observed time lag maps. We next investigate several example points. In some cases, the calculated time lag reflects the evolution of a unique loop along the line of sight, though there may be additional evolving structures along the line of sight. We confirm that using the multi-peak AIA channels can produce time lags that are difficult to interpret. We suggest using a different high temperature channel, such as an X-ray channel. Finally, we find that multiple evolving structures along the line of sight can produce time lags that do not represent the physical properties of any structure along the line of sight, although the cross-correlation coefficient of the lightcurves is high. Considering the projected geometry of the loops may reduce some of the line-of-sight confusion.

79 ASTRONOMY AND ASTROPHYSICS↗

An evaluation of EREP (Skylab) and ERTS imagery for integrated natural resources survey

The author has identified the following significant results. An experimental procedure has been devised and is being tested for natural resource surveys to cope with the problems of interpreting and processing the large quantities of data provided by Skylab and ERTS. Some basic aspects of orbital imagery such as scale, the role of repetitive coverage, and types of sensors are being examined in relation to integrated surveys of natural resources and regional development planning. Extrapolation away from known ground conditions, a fundamental technique for mapping resources, becomes very effective when used on orbital imagery supported by field mapping. Meaningful boundary delimitations can be made on orbital images using various image enhancement techniques. To meet the needs of many developing countries, this investigation into the use of satellite imagery for integrated resource surveys involves the analysis of the images by means of standard visual photointerpretation methods.

Vangenderen, J. L.↗

Evaluation of ERTS-1 imagery for land use/resource inventory information

This investigation was to develop a low cost, manual technique for enhancing ERTS-1 imagery and preparing it in suitable format for use by users with wide and varied interests related to land use and natural resources information. The goals were: to develop enhancement techniques based on concepts and practices extant in photographic sciences, to provide a means of allowing productive interpretation of the imagery by manual means, to produce a product at low cost, to provide a product that would have wide applications, and one compatible with existing information systems. Cost of preparation of the photographically enhanced, enlarged negatives and positives and the diazo materials is about 1 cent per square mile. Cost of creating and mapping a land use classification of twelve use types at a scale of 1:250,000 is only $1 per square mile. The product is understood by users, is economical, and is compatible with existing information systems.

Hardy, E. E.↗

Electrically scanning microwave radiometers

The electrically scanning microwave radiometer (ESMR) developed for and currently used onboard the Nimbus 5 meteorological satellite is described, along with the ESMR developed for the Nimbus F satellite. They serve for synoptic mapping of microwave emissions from the earth's surface, the instrument on Nimbus 5 measuring these emissions at a wavelength of 1.55 cm (19.35 GHz) and the instrument on Nimbus F, at a wavelength of 0.81 cm (37 GHz). Radiative transfer characteristics measured at these wavelengths are sufficiently different from IR measurements to permit derivation and interpretation of unique meteorological, geomorphological, and oceanographic data.

Mix, R. F.↗

Geologic and mineral and water resources investigations in western Colorado using ERTS-1 data

The author has identified the following significant results. Most of the geologic information in ERTS-1 imagery can be extracted from bulk processed black and white transparencies by a skilled interpreter using standard photogeologic techniques. In central and western Colorado, the detectability of lithologic contacts on ERTS-1 imagery is closely related to the time of year the imagery was acquired. Geologic structures are the most readily extractable type of geologic information contained in ERTS images. Major tectonic features and associated minor structures can be rapidly mapped, allowing the geologic setting of a large region to be quickly accessed. Trends of geologic structures in younger sedimentary appear to strongly parallel linear trends in older metamorphic and igneous basement terrain. Linears and color anomalies mapped from ERTS imagery are closely related to loci of known mineralization in the Colorado mineral belt.

Knepper, D. H.↗

Analysis of tectonic features in US southwest from Skylab photographs

The author has identified the following significant results. Skylab photographs were utilized to study faults and tectonic lines in selected areas of the U.S. Southwest. Emphasis was on elements of the Texas Zone in the Mojave Desert and the tectonic intersection in southern Nevada. Transverse faults believed to represent the continuation of the Texas Zone were found to be anomalous in strike. This suggests that the Mojave Desert block was rotated counterclockwise as a unit with the Sierra Nevada. Left-lateral strike-slip faults in Lake Mead area are interpreted as elements of the Wasatch tectonic zone; their anomalous trend indicates that the Lake Mead area has rotated clockwise with the Colorado Plateau. A tectonic model relating major fault zones to fragmentation and rotation of crustal blocks was developed. Detailed correlation of the high resolution S190B metric camera photographs with U-2 photographs and geologic maps demonstrates the feasibility of utilizing S190B photographs for the identification of geomorphic features associated with recent and active faults and for the assessment of seismic hazards.

Abdel-Gawad, M.↗

Natural resources inventory and land evaluation in Switzerland

The author has identified the following significant results. Using MSS channels 5 and 7 and a supervised classification system with a PPD classification algorithm, it was possible to map the exact areal extent of the snow cover and of the transition zone with melting snow patches and snow free parts of various sizes over a large area under different aspects such as relief, exposure, shadows etc. A correlation of the data from ground control, areal underflights and earth resources satellites provided a very accurate interpretation of the melting procedure of snow in high mountains.

Haefner, H.↗

Geologic interpretation of texture in Seasat and SIR-A radar images

Geological information in radar images of heavily vegetated areas is contained mainly in the depiction of topography as image texture. This paper describes three techniques for the analysis of texture in radar images: the split-spectrum technique, Fourier transforms of subareas, and spatial frequency bandpass classification. These techniques were applied to a heavily vegetated area of Belize in Central America in order to evaluate their utility for geological mapping; Seasat and Shuttle Imaging Radar (SIR-A) images were considered.

Farr, T. G.↗

Anaysis of the quality of image data required by the LANDSAT-4 Thematic Mapper and Multispectral Scanner

The spatial, geometric, and radiometric qualities of LANDSAT 4 thematic mapper (TM) and multispectral scanner (MSS) data were evaluated by interpreting, through visual and computer means, film and digital products for selected agricultural and forest cover types in California. Multispectral analyses employing Bayesian maximum likelihood, discrete relaxation, and unsupervised clustering algorithms were used to compare the usefulness of TM and MSS data for discriminating individual cover types. Some of the significant results are as follows: (1) for maximizing the interpretability of agricultural and forest resources, TM color composites should contain spectral bands in the visible, near-reflectance infrared, and middle-reflectance infrared regions, namely TM 4 and TM % and must contain TM 4 in all cases even at the expense of excluding TM 5; (2) using enlarged TM film products, planimetric accuracy of mapped poins was within 91 meters (RMSE east) and 117 meters (RMSE north); (3) using TM digital products, planimetric accuracy of mapped points was within 12.0 meters (RMSE east) and 13.7 meters (RMSE north); and (4) applying a contextual classification algorithm to TM data provided classification accuracies competitive with Bayesian maximum likelihood.

Colwell, R. N.↗

Numerical simulation of upstream disturbance on flows around a slender body

Numerical solutions of the thin-layer approximation of the compressible Navier-Stokes equations have been obtained for flows around an ogive-cylinder body with and without a small fixed disturbance placed upstream of the body tip. Locating the disturbance at positions in the flow field upstream of the tip provokes the same range of behavior of the asymmetric flow that was numerically produced earlier by use of a geometrical disturbance on the body tip. Results remain consistent with the presence of a convective instability mechanism, and demonstrate the potential for a precise mapping of the body's receptivity to fixed disturbances in the flow field. Numerical solutions were also obtained for the flow-field responses to impulsive upstream disturbances to determine whether there is a growing response to an asymmetric impulsive disturbance that is consistent with presence of a convective instability mechanism. Results for surface pressure are interpreted with the aid of a mathematical model. The model suggests that the observed growth of surface pressure gradient with time and distance along a ray in response to an asymmetnc impulsive disturbance is in accord with the solution of a Ginzberg-Landau equation, with distinguishing features of the solution being consistent with the convective instability mode of behavior.

Degani, David↗

H II regions and the abundance properties of spiral galaxies

We investigate the relationships between the characteristic oxygen abundance, the radial abundance gradient, and the macroscopic properties of spiral galaxies by examining the properties of individual H II regions within those galaxies. Our observations of the line flux ratio (O II) lambda lambda 3726, 3729 + (O III) lambda lambda 4959, 5007)/H beta for 159 H II regions in 14 spiral galaxies are combined with published data to provide a sample of 39 disk galaxies for which (O II) + (O III)/H beta has been measured for at least five H II regions. We find that the characteristic gas-phase abundances and luminosities of spiral galaxies are strongly correlated. This relationship maps almost directly onto the luminosity-metallicity relationship of irregular galaxies and is also quite similar to that found for elliptical and dwarf spheroidal galaxies. Within our sample of spirals, a strong correlation between characteristic abundance and Hubble type also exists. The correlation between luminosity and Hubble type complicates the issue, but we discuss several interpretations of the correlations. The relationship between circular velocity and characteristic abundance is also discussed. We find that the slopes of the radial abundance gradients, when expressed in units of dex/isophotal radius, do not significantly correlate with either luminosity or Hubble type. However, the hypothesis that both early and very late type spirals have shallower gradients than intermediate spirals is consistent with the data. We find suggestive evidence that the presence of a bar induces a flatter gradient and also briefly discuss whether abundance gradients are exponential, as is usually assumed. We investigate the properties of individual H II regions in a subset of 42 regions for which we have spectra that cover almost the entire spectral range from 3500 to 9800 A. We use those data to estimate the densitites and ionizing spectra within the H II regions. We confirm that the ionizing spectrum hardens with increasing radius and decreasing abundance. We find no correlation between the ionization parameter and either radius or abundance, but this may be due to significant scatter introduced by the simple conversion of line ratios to ionization parameter.

Zaritsky, Dennis↗

Citrus Inventory

An aerial color infrared (CIR) mapping system developed by Kennedy Space Center enables Florida's Charlotte County to accurately appraise its citrus groves while reducing appraisal costs. The technology was further advanced by development of a dual video system making it possible to simultaneously view images of the same area and detect changes. An image analysis system automatically surveys and photo interprets grove images as well as automatically counts trees and reports totals. The system, which saves both time and money, has potential beyond citrus grove valuation.

Source record↗

MAPX: A FULL-FIELD X-RAY FLUORESCENCE IMAGER FOR IN-SITU HABITABILITY AND BIOSIGNATURE INVESTIGATIONS

The Mapping X-ray Spectrometer (MapX)is an arm-deployed, in-situ contact instrument. MapX produces 2.5 X 2.5 cm2 elemental images and compositional Regions of Interest(ROI) with ~100 μm lateral spatial resolution, yielding elemental chemistry at a scale where many relict physical, chemical, or bio-logical features can be imaged and interpreted. The instrument has no moving parts and a depth of field of ±5 mm with minimal loss of resolution(so that regolith surfaces can be imaged without sample preparation). MapX can utilize 244Cm radioisotope fluorescence sources in place of X-ray tubes, reducing instrument complexity, mass and risk.

R C Walroth↗

Machine-learning error models for approximate solutions to parameterized systems of nonlinear equations

Here, this work proposes a machine-learning framework for constructing statistical models of errors incurred by approximate solutions to parameterized systems of nonlinear equations. These approximate solutions may arise from early termination of an iterative method, a lower-fidelity model, or a projection-based reduced-order model, for example. The proposed statistical model comprises the sum of a deterministic regression-function model and a stochastic noise model. The method constructs the regression-function model by applying regression techniques from machine learning (e.g., support vector regression, artificial neural networks) to map features (i.e., error indicators such as sampled elements of the residual) to a prediction of the approximate-solution error. The method constructs the noise model as a mean-zero Gaussian random variable whose variance is computed as the sample variance of the approximate-solution error on a test set; this variance can be interpreted as the epistemic uncertainty introduced by the approximate solution. This work considers a wide range of feature-engineering methods, data-set-construction techniques, and regression techniques that aim to ensure that (1) the features are cheaply computable, (2) the noise model exhibits low variance (i.e., low epistemic uncertainty introduced), and (3) the regression model generalizes to independent test data. Finally, numerical experiments performed on several computational-mechanics problems and types of approximate solutions demonstrate the ability of the method to generate statistical models of the error that satisfy these criteria and significantly outperform more commonly adopted approaches for error modeling.

97 MATHEMATICS AND COMPUTING↗

A data-driven CO 2 leakage detection using seismic data and spatial–temporal densely connected convolutional neural networks

In carbon capture and sequestration (also known as carbon capture and storage, or CCS), developing effective monitoring methods is needed to detect and respond to CO 2 leakage. CO 2 leakage detection methods rely on geophysical observations and monitoring sensor network. However, traditional methods usually require the development of site-specific physical models and expert interpretation, and the effectiveness of these methods can be limited to different application locations, operational scenarios, and conditions. Here, we developed a novel data-driven leakage detection method based on densely connected convolutional neural networks. Our method is an end-to-end detection approach, that differs from conventional leakage monitoring methods by directly learning a mapping relationship between seismic data and the CO 2 leakage mass. To account for the spatial and temporal characteristics of seismic data, our novel networks architecture combines 1D and 2D convolutional neural networks. To overcome the computational expense of solving optimization problems, we apply a densely-connecting strategy in our network architecture that reduces the number of network parameters. Based on the features generated by our convolutional neural networks, we further incorporate a long short-term memory network to utilize time-sequential information, which further improves the detection accuracy. Lastly, we employ our detection method to synthetic seismic datasets generated based on flow simulations of a hypothetical CO 2 storage scenario with injection into a partially compartmentalized sandstone storage reservoir. To evaluate method performance, we conducted multiple experiments including a random leakage test, a sequential test, and a robustness test. Numerical results show that our CO 2 leakage detection method successfully detects the leakage and accurately predicts the leakage mass, suggesting that it has the potential for application in monitoring of real CO 2 storage sites.

58 GEOSCIENCES↗

Ensuring thermodynamic consistency with invertible coarse-graining

Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insights by isolating the essential degrees of freedom that dictate the thermodynamic properties of a complex, condensed-phase system. The reduced complexity of the model typically leads to lower computational costs and more efficient sampling compared with atomistic models. Designing “good” coarse-grained models is an art. Generally, the mapping from fine-grained configurations to coarse-grained configurations itself is not optimized in any way; instead, the energy function associated with the mapped configurations is. In this work, we explore the consequences of optimizing the coarse-grained representation alongside its potential energy function. We use a graph machine learning framework to embed atomic configurations into a low-dimensional space to produce efficient representations of the original molecular system. Because the representation we obtain is no longer directly interpretable as a real-space representation of the atomic coordinates, we also introduce an inversion process and an associated thermodynamic consistency relation that allows us to rigorously sample fine-grained configurations conditioned on the coarse-grained sampling. We illustrate that this technique is robust, recovering the first two moments of the distribution of several observables in proteins such as chignolin and alanine dipeptide.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗