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In order to diagnose the cause of some defects in the category of canonical hypergroups, we investigate several categories of hyperstructures that generalize hypergroups. By allowing hyperoperations with possibly empty products, one obtains categories with desirable features such as completeness and cocompleteness, free functors, regularity, and closed monoidal structures. We show by counterexamples that such constructions cannot be carried out within the category of canonical hypergroups. This suggests that (commutative) unital, reversible hypermagmas—which we call mosaics—form a worthwhile generalization of (canonical) hypergroups from the categorical perspective. Notably, mosaics contain pointed simple matroids as a subcategory, and projective geometries as a full subcategory. 

We develop a Stockmayer fluid model for molecular dynamics simulations of ionic liquids that captures molecular polarization, ionic conductivity, viscosity, and glass transition temperature, using ethylammonium nitrate (EAN) as an example. The ions in EAN are treated as spheres interacting via the Lennard-Jones potential with an embedded point charge and a permanent dipole moment. We show that our simulation results for EAN are consistent with experimental data and then explore the effects of the molecular parameters on the viscosity of ionic liquids. Our results indicate that viscosity monotonically increases with ionic charge and dipole moment but non-monotonically changes with ionic diameter (or molar volume). This non-monotonic trend arises from the competition among the electrostatic interactions, molecular packing, and size asymmetry between the cation and anion. Our model also shows that long-lived ion pairs result in higher viscosities. 

Abstract Atmospheric blocking entails a persistent, anomalous meandering of the jet stream that disrupts the eastward migration of transient eddies in the midlatitudes. Here we analyze a large number of blocking (and blocking-like) events in the Northern Hemisphere winter with the ERA5 reanalysis through the lens of vertically-averaged wave-activity budget. By applying a feature tracking algorithm, large-valued wave-activity anomalies that persist for 4 days or longer at a given location are identified as blocks, and block-centered composites are constructed for the wave-activity budget through the lifecycle of blocks. The identified events share commonly recognized features of blocking. The majority of the persistent events occur in clusters collocated with the quasi-stationary ridge associated with the Atlantic and the Pacific storm track. Frequency of persistent blocks is higher (lower) in regions where the ‘carrying capacity’ of the jet stream is lower (higher). A very low carrying capacity for the transient waves leads to a large population of blocks over Europe. The composite lifecycle of persistent blocks shows that convergence (divergence) of the zonal flux of wave-activity dominates the budget during the onset (decay) phase of the block, while the eddy-induced wind plays a crucial role of suppressing the zonal flux during the maturation period. Our finding broadly supports the ‘traffic jam’ hypothesis of Nakamura and Huang as a common mechanism of block formation, although there is vast diversity in the actual manifestation of individual blocks. It is argued that carrying capacity is suited for estimating blocking probability rather than for making deterministic forecasts of blocking events. 

Abstract Synoptic eddies embedded in a westerly flow undergo downstream developments due to their dispersive nature. This paper examines the finite-amplitude aspects of downstream development with the budget of local wave activity (LWA), including explicit contributions from diabatic heating. LWA captures well individual troughs/ridges and the wave packet, and its column budget affords simplified interpretations. In the LWA framework, (linear) downstream development demonstrated in previous analyses is represented by the LWA advection by the zonal reference flow plus LWA flux induced by the radiation of Rossby waves. In addition, convergence of nonlinear advective LWA flux, baroclinic sources at the lower boundary, meridional redistribution by eddy momentum flux, and diabatic sources and sinks complete the column budget of LWA. When applied to the life cycles of troughs within coherent wave packets in the Southern Hemisphere, the LWA budget reveals that individual troughs grow mainly through downstream development, convergence of nonlinear advective flux by eddies, and diabatic heating. Downstream development and divergence of nonlinear flux also dominate trough decay. Contributions from nonlinear advective eddy flux are large in the presence of a strong ridge either immediately upstream or downstream of the trough. Furthermore, anticyclonic components of advective LWA fluxes associated with the upstream or downstream ridge transfer LWA into or out of the trough. Diabatic contributions are significant when the heating exhibits a tilted vertical structure that gives rise to enhanced vertical gradient in heating. 

ABSTRACT Weather at the mid‐latitudes is governed by cyclones and anticyclones mostly migrating eastward. These weather systems cause the jet streams to undulate; the meandering patterns are known as the Rossby waves. Occasionally, Rossby waves bring forth localised extreme weather phenomena. An example of a finite‐amplitude wave phenomenon is atmospheric blocking, which is often associated with heat waves and droughts. Recent development of a finite‐amplitude local wave activity (FALWA) theory by Nakamura and collaborators enables comprehensive analysis of the dynamics of finite‐amplitude Rossby waves observed in climate data, which helps to understand the drivers of their life cycles. Despite the simplicity of interpretation it brings about, to apply the FALWA diagnostic to climate data requires more involved calculations than the traditional Eulerian framework. This article introduces the open‐source Python packagefalwa,which encapsulates the FALWA diagnostics implemented on gridded climate data presented in the authors' previous publications. It reviews the essence of the FALWA theory, the corresponding components in the package that implement the calculations, and where users can find sample notebooks to start with. It aims to serve as a road map for new users to easily navigate through this package. The latter half of this article documents the practices of the developers, which include the documentation tools, continuous integration practice, and repository maintenance using automated GitHub functionalities. The authors also discuss existing numerical issues and future improvement plans. This open‐source project aims to promote the broader application of FALWA diagnostics on climate data and model outputs by streamlining complex numerical computations. 

Abstract Magnetic reconnection is a ubiquitous plasma process that transforms magnetic energy into particle energy during eruptive events throughout the universe. Reconnection not only converts energy during solar flares and geomagnetic substorms that drive space weather near Earth, but it may also play critical roles in the high energy emissions from the magnetospheres of neutron stars and black holes. In this review article, we focus on collisionless plasmas that are most relevant to reconnection in many space and astrophysical plasmas. Guided by first-principles kinetic simulations and spaceborne in-situ observations, we highlight the most recent progress in understanding this fundamental plasma process. We start by discussing the non-ideal electric field in the generalized Ohm’s law that breaks the frozen-in flux condition in ideal magnetohydrodynamics and allows magnetic reconnection to occur. We point out that this same reconnection electric field also plays an important role in sustaining the current and pressure in the current sheet and then discuss the determination of its magnitude (i.e., the reconnection rate), based on force balance and energy conservation. This approach to determining the reconnection rate is applied to kinetic current sheets with a wide variety of magnetic geometries, parameters, and background conditions. We also briefly review the key diagnostics and modeling of energy conversion around the reconnection diffusion region, seeking insights from recently developed theories. Finally, future prospects and open questions are discussed. 

ABSTRACT Retrons are bacterial immune systems that protect a bacterial population against phages by killing infected hosts. Retrons typically comprise a reverse transcriptase, a template noncoding RNA that is partially reverse transcribed into RT-DNA, and a toxic effector. The reverse transcriptase, noncoding RNA, and RT-DNA complex sequester the toxic effector until triggered by phage infection, at which point the toxin is released to induce cell death. Due to their ability to produce single-stranded DNA in vivo, retrons have also been engineered to produce donor templates for genome editing in both prokaryotes and eukaryotes. However, the current repertoire of experimentally characterized retrons is limited, with most retrons sourced from clinical and laboratory strains of bacteria. To better understand retron biology and natural diversity, and to expand the current toolbox of retron-based genome editors, we developed a pipeline to isolate retrons and their bacterial hosts from a variety of environmental samples. Here, we present six of these novel retrons, each isolated from a different host bacterium. We characterize the full operon of these retrons and test their ability to defend against a panel ofE. coliphages. For two of these retrons, we further unravel their mechanism of defense by identifying the phage genes responsible for triggering abortive infection. Finally, we engineer these retrons for genome editing inE. coli, demonstrating their potential use in a biotechnological application. 

Incoherent feedforward networks exhibit the ability to generate temporal pulse behavior. However, exerting control over specific dynamic properties, such as amplitude and rise time, poses a challenge and is intricately tied to the network’s implementation. In this study, we focus on analyzing sequestration-based networks capable of exhibiting pulse behavior. By employing time-scale separation in the fast sequestration regime, we approximate the temporal dynamics of these networks. This approach allows us to establish a mapping that elucidates the impact of varying the kinetic rates and pulse specifications, including amplitude and rise time. Furthermore, we introduce a positive feedback mechanism to regulate the amplitude of the pulsing response. 

The morphological transformation of the pectoral/shoulder girdle is fundamental to the water-to-land transition in vertebrate evolution. Although previous studies have resolved the embryonic origins of tetrapod shoulder girdles, those of fish pectoral girdles remain uncharacterized, creating a gap in the understanding of girdle transformation mechanisms from fish to tetrapods. Here, we identify the embryonic origins of the zebrafish pectoral girdle, including the cleithrum as an ancestral girdle element lost in extant tetrapods. Our combinatorial approach of photoconversion and genetic lineage tracing demonstrates that cleithrum development combines four adjoining embryonic populations. A comparison of these pectoral girdle progenitors with extinct and extant vertebrates highlights that cleithrum loss, indispensable for neck evolution, is associated with the disappearance of its unique developmental environment at the head/trunk interface. Overall, our study establishes an embryological framework for pectoral/shoulder girdle formation and provides evolutionary trajectories from their origin in water to diversification on land.