Progress on Multielement Spectroscopic Temperature and Impurity Studies on a High Flow Velocity Z-Pinch
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70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
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Inferring plant–plant interactions using remote sensing
Rapid technological advancements and increasing data availability have improved the capacity to monitor and evaluate Earth's ecology via remote sensing. However, remote sensing is notoriously ‘blind’ to fine-scale ecological processes such as interactions among plants, which encompass a central topic in ecology. Here, we discuss how remote sensing technologies can help infer plant–plant interactions and their roles in shaping plant-based systems at individual, community and landscape levels. At each of these levels, we outline the key attributes of ecosystems that emerge as a product of plant–plant interactions and could possibly be detected by remote sensing data. We review the theoretical bases, approaches and prospects of how inference of plant–plant interactions can be assessed remotely. At the individual level, we illustrate how close-range remote sensing tools can help to infer plant–plant interactions, especially in experimental settings. At the community level, we use forests to illustrate how remotely sensed community structure can be used to infer dominant interactions as a fundamental force in shaping plant communities. At the landscape level, we highlight how remotely sensed attributes of vegetation states and spatial vegetation patterns can be used to assess the role of local plant–plant interactions in shaping landscape ecological systems. Synthesis . Remote sensing extends the domain of plant ecology to broader and finer spatial scales, assisting to scale ecological patterns and search for generic rules. Robust remote sensing approaches are likely to extend our understanding of how plant–plant interactions shape ecological processes across scales—from individuals to landscapes. Combining these approaches with theories, models, experiments, data-driven approaches and data analysis algorithms will firmly embed remote sensing techniques into ecological context and open new pathways to better understand biotic interactions.
59 BASIC BIOLOGICAL SCIENCES↗
The protein structurome of Orthornavirae and its dark matter
Metatranscriptomics is uncovering more and more diverse families of viruses with RNA genomes comprising the viral kingdom Orthornavirae in the realm Riboviria. Thorough protein annotation and comparison are essential to get insights into the functions of viral proteins and virus evolution. In addition to sequence- and hmm profile-based methods, protein structure comparison adds a powerful tool to uncover protein functions and relationships. We constructed an Orthornavirae “structurome” consisting of already annotated as well as unannotated (“dark matter”) proteins and domains encoded in viral genomes. We used protein structure modeling and similarity searches to illuminate the remaining dark matter in hundreds of thousands of orthornavirus genomes. The vast majority of the dark matter domains showed either “generic” folds, such as single α-helices, or no high confidence structure predictions. Nevertheless, a variety of lineage-specific globular domains that were new either to orthornaviruses in general or to particular virus families were identified within the proteomic dark matter of orthornaviruses, including several predicted nucleic acid-binding domains and nucleases. In addition, we identified a case of exaptation of a cellular nucleoside monophosphate kinase as an RNA-binding protein in several virus families. Notwithstanding the continuing discovery of numerous orthornaviruses, it appears that all the protein domains conserved in large groups of viruses have already been identified. The rest of the viral proteome seems to be dominated by poorly structured domains including intrinsically disordered ones that likely mediate specific virus-host interactions.
59 BASIC BIOLOGICAL SCIENCES↗
RolyPoly (rp) v0.1.0
The Rolypoly pipeline is designed to process raw RNA-seq data and identify potential RNA viral sequences. It is split into several self contained steps: 1. input data filtering and QC, 2. Genome assembly and refinement, 3. Assembly filtering, 4. Mapping to known RNA viral genomes, 5. Searching for RNA viral marker genes. 6. Genome functional and structural annotation. 6. Report preparation and potential downstream analysis The last module, may include taxonomic assignment, host range estimation, and phenotypic prediction. There are many similar software, but they focus on human related viruses, and lack the downstream applications or differ in their sensitivity. The initial user base are non-computational microbial ecologists who wish to better understand the potential RNA viruses in their own generated samples.
Neri, Uri↗
polars-dovmed (dovmed) v0.1.0
polars-dovmed is a python package for text search and extraction from NCBI's PubMed Central Open Access subset. It is powered by the polars dataframe library and leverages modern file formats (parquet) to efficiently scan public literature.
Roux, Simon [Lawrence Berkeley National Laboratory↗
SpacerExtractor v0.9
The SpacerExtractor tool is meant to robustly identify and extract CRISPR spacers from metagenome short reads. Working from a database of known CRISPR repeats, SpacerExtractor quickly scans short reads for the corresponding repeat sequences, extract the potential spacer between two repeats, apply several quality control, denoising, and clustering steps, and provides a full non-redundant complement of spacers for each detected repeat. Because of the high variability observed at CRISPR loci, this read mining approach typically recovers a much larger diversity of spacers than can be found in assembled contigs. SpacerExtractor also includes commands to run CRISPR-Cas Typer on a new set of genomes or MAGs, and add newly predicted repeats to the repeat database.
Bushnell, Brian↗
Fellowship of the Resolved [Slides]
There are new evaluation methods being explored for combined RRR + URR. Simple example demonstrated in SAMMY code using. Potential to be applied to future LoFi, Medium-Fi covariance efforts. Much more work needs to be done to fully correlate regions.
Nuclear Criticality Safety Program (NCSP)↗
Instant Folded Strings, Dark Energy and a Cyclic Bouncing Universe
We present a wholly self-consistent, complete cyclic bouncing cosmology based on components drawn from string theory and constructed in a way that is under perturbative control throughout (e.g., with temperature much less than the string scale and string coupling $g_s \ll 1$ at all times). The cyclic evolution is governed by standard dilaton-gravity in $(3+1)$-dimensions with a perturbatively generated potential and a coupling between the dilaton and a second field that becomes massless at $ϕ= ϕ_{ESP}$, resulting in an enhanced symmetry point (ESP) that prevents the dilaton from running all the way to zero coupling. A central role is played by instant folded strings (IFSs) - fundamental strings with the unusual property of being much lighter than the string mass while extending far beyond the string length, and violating the Null Energy Condition (NEC). IFSs are produced classically when the string coupling grows with time, which occurs at two critical points in each cycle. In turn, they fulfill a dual function: enabling cosmological bounces and initiating transient epochs of dark-energy domination that naturally transition into slow contraction. The resulting cosmology eliminates the cosmic singularity and multiverse problems of big bang inflationary models and robustly predicts time-varying IFS-induced dark energy and the absence of primordial B-mode polarization in the cosmic microwave background.
Cosmology and Nongalactic Astrophysics (astro-ph.C↗
Plasma confinement system with outer electrode having liquifiable material and methods for use
An example plasma confinement system includes an inner electrode having a rounded first end that is disposed on a longitudinal axis of the plasma confinement system and an outer electrode that at least partially surrounds the inner electrode. The outer electrode includes a solid conductive shell and an electrically conductive material disposed on the solid conductive shell and on the longitudinal axis of the plasma confinement system. The electrically conductive material has a melting point within a range of 170° C. to 800° C. at 1 atmosphere of pressure. Related plasma confinement systems and methods are also disclosed herein.
Shumlak, Uri↗
Z-pinch plasma confinement system having intermediate electrode and methods for use
An example method includes directing gas, via one or more first valves, from within an inner electrode to an acceleration region between the inner electrode and an outer electrode that substantially surrounds the inner electrode, directing gas, via two or more second valves, from outside the outer electrode to the acceleration region, and applying, via a power supply, a voltage between the inner electrode and the outer electrode, thereby converting at least a portion of the directed gas into a plasma saving a substantially annular cross section, the plasma flowing axially within the acceleration region toward a first end of the inner electrode and a first end of the outer electrode and, thereafter, establishing a Z-pinch plasma that flows between the first end of the outer electrode and the first end of the inner electrode. Related plasma confinement systems and methods are also disclosed herein.
Shumlak, Uri↗
Electrode configuration for extended plasma confinement
Methods and systems are provided for plasma confinement utilizing various electrode and valve configurations. In one example, a device includes a first electrode positioned to define an outer boundary of an acceleration volume, a second electrode arranged coaxially with respect to the first electrode and positioned to define an inner boundary of the acceleration volume, at least one power supply to drive an electric current along a Z-pinch plasma column between the first second electrodes, and a set of valves to provide gas to the acceleration volume to fuel the Z-pinch plasma column, wherein an electron flow of the electric current is in a first direction from the second electrode to the first electrode. In additional or alternative examples, a shaping part is conductively connected to the second electrode to, in a presence of the gas, cause a gas breakdown of the gas to generate a sheared flow velocity profile.
Meier, Eric T.↗
Apparatus and method for extended plasma confinement
Methods and systems are provided for plasma confinement utilizing various electrode and valve configurations. In one example, a device includes a first electrode positioned to define an outer boundary of an acceleration volume, a second electrode arranged coaxially with respect to the first electrode and positioned to define an inner boundary of the acceleration volume, at least one power supply to drive an electric current along a Z-pinch plasma column between the first second electrodes, and a set of valves to provide gas to the acceleration volume to fuel the Z-pinch plasma column, wherein an electron flow of the electric current is in a first direction from the second electrode to the first electrode. In additional or alternative examples, a shaping part is conductively connected to the second electrode to, in a presence of the gas, cause a gas breakdown of the gas to generate a sheared flow velocity profile.
Shumlak, Uri↗
"Traffic Control via Connected and Automated Vehicles: An Open-Road Field Experiment with 100 CAVs"
The CIRCLES project aims to reduce instabilities in traffic flow, which are naturally occurring phenomena due to human driving behavior. These "phantom jams" or "stop-and-go waves,"are a significant source of wasted energy. Toward this goal, the CIRCLES project designed a control system referred to as the MegaController by the CIRCLES team, that could be deployed in real traffic. Our field experiment leveraged a heterogeneous fleet of 100 longitudinally-controlled vehicles as Lagrangian traffic actuators, each of which ran a controller with the architecture described in this paper. The MegaController is a hierarchical control architecture, which consists of two main layers. The upper layer is called Speed Planner, and is a centralized optimal control algorithm. It assigns speed targets to the vehicles, conveyed through the LTE cellular network. The lower layer is a control layer, running on each vehicle. It performs local actuation by overriding the stock adaptive cruise controller, using the stock on-board sensors. The Speed Planner ingests live data feeds provided by third parties, as well as data from our own control vehicles, and uses both to perform the speed assignment. The architecture of the speed planner allows for modular use of standard control techniques, such as optimal control, model predictive control, kernel methods and others, including Deep RL, model predictive control and explicit controllers. Depending on the vehicle architecture, all onboard sensing data can be accessed by the local controllers, or only some. Control inputs vary across different automakers, with inputs ranging from torque or acceleration requests for some cars, and electronic selection of ACC set points in others. The proposed architecture allows for the combination of all possible settings proposed above. Most configurations were tested throughout the ramp up to the MegaVandertest.
Lee, Jonathan↗
"Hierarchical Speed Planner for Automated Vehicles: A Framework for Lagrangian Variable Speed Limit in Mixed Autonomy Traffic"
This paper introduces a novel control framework for Lagrangian variable speed limits in hybrid traffic flow environments utilizing automated vehicles (AVs). The framework was validated using a fleet of 100 connected automated vehicles as part of the largest coordinated open-road test designed to smooth traffic flow. The framework includes two main components: a high-level controller deployed on the server side, named Speed Planner, and low-level controllers called vehicle controllers deployed on the vehicle side. The Speed Planner designs and updates target speeds for the vehicle controllers based on real-time Traffic State Estimation (TSE) [1]. The Speed Planner comprises two modules: a TSE enhancement module and a target speed design module. The TSE enhancement module is designed to minimize the effects of inherent latency in the received traffic information and to improve the spatial and temporal resolution of the input traffic data. The target speed design module generates target speed profiles with the goal of improving traffic flow. The vehicle controllers are designed to track the target speed meanwhile responding to the surrounding situation. The numerical simulation indicates the performance of the proposed method: the bottleneck throughput has increased by 5.01%, and the speed standard deviation has been reduced by a significant 34.36%. We further showcase an operational study with a description of how the controller was implemented on a field-test with 100 AVs and its comprehensive effects on the traffic flow.
Wang, Han↗