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Genome Sequence of the Chestnut Blight Fungus Cryphonectria parasitica EP155: A Fundamental Resource for an Archetypical Invasive Plant Pathogen
Cryphonectria parasitica is the causal agent of chestnut blight, a fungal disease that almost entirely eliminated mature American chestnut from North America over a 50-year period. Here, we formally report the genome of C. parasitica EP155 using a Sanger shotgun sequencing approach. After finishing and integration with simple-sequence repeat markers, the assembly was 43.8 Mb in 26 scaffolds (L 50 = 5; N 50 = 4.0Mb). Eight chromosomes are predicted: five scaffolds have two telomeres and six scaffolds have one telomere sequence. In total, 11,609 gene models were predicted, of which 85% show similarities to other proteins. Finally, this genome resource has already increased the utility of a fundamental plant pathogen experimental system through new understanding of the fungal vegetative incompatibility system, with significant implications for enhancing mycovirus-based biological control.
Unstable Invasion of Sedimenting Granular Suspensions
Here we investigate the development of mobility inversion and fingering when a granular suspension is injected radially between horizontal parallel plates of a cell filled with a miscible fluid. While the suspension spreads uniformly when the suspension and the displaced fluid densities are exactly matched, even a small density difference is found to result in a dense granular front which develops fingers with angular spacing that increase with granular volume fraction and decrease with injection rate. We show that the timescale over which the instability develops is given by the volume fraction dependent settling timescale of the grains in the cell. We then show that the mobility inversion and the nonequilibrium Korteweg surface tension due to granular volume fraction gradients determine the number of fingers at the onset of the instability in these miscible suspensions.
Vacant niches help predict invasion risk by birds
Abstract Aim If communities have a ceiling determining the number of species that can coexist, then the ability of alien species to establish at any given location should be related to the quantity of vacant niches available. We developed a new approach to estimate the extent to which niches are vacant and then explored the relationship between vacant niches and alien species. Location Global with focal tests in Europe and North America. Taxon Birds. Methods Drawing on a global classification of trophic structures for birds, we calculated a ‘vacant niche ratio’ metric to quantify the expected level of saturation (i.e. number of vacant niches) for each 1° × 1° grid cell globally, based on the difference between expected and observed numbers of bird species for all trophic guilds. Next, we used random forests to examine if the presence of plant‐invertivore (whose food source represents plants, seeds, fruits and invertebrates) and granivore alien bird species was associated with the vacant niche ratio across well‐sampled regions. Results In Europe, we found a significant relationship between alien species and vacant niches, with greater numbers of alien species being found in communities that offered greater numbers of vacant niches overall, and across habitat types. In North America, we found no significant relationship between plant‐invertivores and vacant niches, while for granivores, we found that areas with fewer vacant niches had greater numbers of alien species, especially in forests. However, vacant niches alone correctly predict 69% of the presence of alien bird species when combining both regions and trophic guilds. Main Conclusions Most regions of the world have unsaturated bird communities, with the level of saturation in communities varying within regions and trophic guilds. We found that although often‐neglected, vacant niches are likely to be, at least partially, related with the successful establishment of alien bird species.
A mummy?s secrets: serendipity, computed tomography, and non-invasive x-ray diffraction
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Digital holography for real-time non-invasive monitoring of larval fish at power plant intakes
Effective evaluation of technological and operational approaches to reduce entrainment of marine organisms at cooling water intake structures (CWIS) requires accurate organism-sensing systems. Current detection methods lead to large temporal data gaps, require tedious manual analysis, and are fatal to organisms. In this report we describe integrating deep learning with a non-lethal, non-intrusive imaging method—digital holography—to rapidly detect fish larvae. Laboratory experiments demonstrated that the instrument could successfully image fish larvae at flow rates exceeding ranges seen in CWIS. Holograms of two fish larvae species, in the presence of bubbles and detritus, were collected to build a large database for training a lightweight convolutional neural network. The model achieves 97% extraction accuracy in quantifying larvae, and distinguishing them from other particles, including detritus and bubbles, when applied to a dataset of manually classified images, exceeding previous metrics for non-lethal, accurate, and real-time detection. These results demonstrate the potential of in situ holographic imaging for monitoring endangered larval fish species at power plant intake structures, and for high-fidelity, real-time applications in monitoring aquatic ichthyoplankton.
Active sampling of volatile chemicals for non-invasive classification of chicken eggs by sex early in incubation
According to industry estimates, approximately 7 billion day-old male chicks are disposed of annually worldwide because they are not of use to the layer industry. A practical process to identify the sex of the egg early in incubation without penetrating the egg would improve animal welfare, reduce food waste and mitigate environmental impact. We implemented a moderate vacuum pressure system through commercial egg-handling suction cups to collect volatile organic compounds (VOCs). Three separate experiments were set up to determine optimal conditions to collect eggs VOCs to discriminate male from female embryos. Optimal extraction time (2 min), storage conditions (short period of incubation during egg storage (SPIDES) at days 8–10 of incubation), and sampling temperature (37.5°C) were determined. Our VOC-based method could correctly differentiate male from female embryos with more than 80% accuracy. These specifications are compatible with the design of specialized automation equipment capable of high-throughput, in-ovo sexing based on chemical sensor microchips.
Well Logs: A Non-Invasive Approach for Elucidating the Spatial Distribution of In-Situ Stress in Deep Subsurface Geologic Formations Considered for CO2 Storage
Routine and geomechanical well logs for 3 wells— State Otsego Lake 8-15A, Lawnichak 9-33, Chester 8-16.
Topological Data Analysis as a Descriptive Tool for Structural Similarity in Non-Invasive Inspection.
Abstract not provided.
A Non-Invasive Approach for Elucidating the Spatial Distribution of In Situ Stress in Deep Subsurface Geologic Formations Considered for CO 2 Storage (Task 2 Report Extracting Stress Data from Seismic Data)
This report describes research accomplishments achieved with funding provided through Department of Energy (DOE) Contract DE-FE0031686. The purpose of this DOE funding is to develop methods that can provide key information about stress fields that act on deep rocks without invading the earth to acquire that information. The research objective was to demonstrate methods that extract the azimuth directions of SHmax and SHmin stress in deep rocks from traditional seismic reflection data like the data that are used to explore for deep oil and gas reservoirs. Battelle performed two seismic investigations and achieved estimates of SHmax and SHmin azimuths in both efforts that agreed with local, non-seismic, ground-truth measurements of SHmax orientation. The first procedure utilized vertical seismic profiling (VSP) data; the second effort utilized three-dimensional (3D) seismic data.
Data Assimilation using Non-invasive Monte Carlo Sensitivity Analysis of Reactor Kinetics Parameters [Slides]
Sensitivity coefficients of prompt neutron decay constant (α) and effective delayed neutron fraction (β eff ) to Pu-239 nuclear data were calculated using a newly available tool (ACEtk). Uncertainty calculations showed the following trends: (1) The prompt neutron decay constant can be used to reduce nuclear data-induced uncertainty in Pu-239(n,f) and (2) the effective delayed neutron fraction can be used to effectively reduce nuclear data-induced uncertainty in Pu-239 total fission $\tilde{v}$. Sensitivity/uncertainty analysis can be used to determine optimal experiment/detector setup to identify compensating errors in nuclear data. Upcoming work includes investigating other nuclide-reaction pairs and response sensitivities, such as Δ$\rho$, neutron leakage spectra, and reaction rate measurements to constrain nuclear data of interest.
First LIA measurements of a gated non-invasive beam spot size diagnostic
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Using Non-invasive Scanning for Envelope Assessments with LiDAR Enhanced Diagnostics and Air Infiltration Results (UNSEALED-AIR) (CRADA Final Report)
Abstract not provided.