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1. Multiple compensatory mutations contribute to the de‐domestication of Iberian weedy rice

   https://doi.org/10.1002/ppp3.10286  

   Li, Xiang ; Zhang, Shulin ; Amaro‐Blanco, Ignacio ; Perera, Sherin ; Khandekar, Nikhil Shirish ; Lowey, Daniel ; Osuna, Maria Dolores ; Caicedo, Ana L. ( July 2022 , PLANTS, PEOPLE, PLANET)

   Weedy plants are a major constraint on agricultural productivity. Weedy rice is a weed that invades rice fields worldwide and is responsible for reductions in rice yields. Studies to date have detected multiple independent weedy rice origins in different parts of the world. We investigated the origin of weedy rice in Spain and Portugal and found that it has evolved from a cultivated rice variety group grown locally. Iberian weeds carry mutations that reverse domesticated pericarp color to its ancestral red color. Our results imply that management strategies are needed to prevent the evolution of troublesome weeds from cultivated ancestors.

   Weedy rice, a damaging conspecific weed of cultivated rice, has arisen multiple times independently around the world. Understanding all weedy rice origins is necessary to create more effective weed management strategies. The origins of weedy rice in Spain and Portugal, where there are no nativeOryzaspecies, are unknown. In this study, we try to identify the likely ancestors of Iberian weedy rice and the mechanisms involved in the evolution of two weedy traits, seed shattering, and red pericarps.

   We used genotyping by sequencing to understand the origin of Iberian weedy rice and its relationship to other weedy, wild, and cultivated rice groups worldwide. We also genotyped candidate genes for shattering and pericarp color.

   We find that weedy rice in the Iberian Peninsula has primarily evolved through de‐domestication oftemperate japonicacultivars, with minor origins from exotic weedy rice. Iberian weeds have evolved the capacity to shatter seeds via novel loci and have acquired red pericarps via compensatory mutations in theRcdomestication gene. Our results suggest the Iberian weeds have experienced selection at multiple locations in the genome to establish as weeds, likely targeting male fertility genes among other functions.

   Our characterization of Iberian weedy rice adds to the growing evidence that de‐domestication of cultivated rice varieties is the main source of weedy rice worldwide. Their evolutionary versatility explains why weedy rice continues to be one of the most problematic weeds of cultivated rice.

    

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2. Multi‐level convergence of complex traits and the evolution of bioluminescence

   https://doi.org/10.1111/brv.12672  

   Lau, Emily S. ; Oakley, Todd H. ( December 2020 , Biological Reviews)

   Evolutionary convergence provides natural opportunities to investigate how, when, and why novel traits evolve. Many convergent traits are complex, highlighting the importance of explicitly considering convergence at different levels of biological organization, or ‘multi‐level convergent evolution’. To investigate multi‐level convergent evolution, we propose a holistic and hierarchical framework that emphasizes breaking down traits into several functional modules. We begin by identifying long‐standing questions on the origins of complexity and the diverse evolutionary processes underlying phenotypic convergence to discuss how they can be addressed by examining convergent systems. We argue that bioluminescence, a complex trait that evolved dozens of times through either novel mechanisms or conserved toolkits, is particularly well suited for these studies. We present an updated estimate of at least 94 independent origins of bioluminescence across the tree of life, which we calculated by reviewing and summarizing all estimates of independent origins. Then, we use our framework to review the biology, chemistry, and evolution of bioluminescence, and for each biological level identify questions that arise from our systematic review. We focus on luminous organisms that use the shared luciferin substrates coelenterazine or vargulin to produce light because these organisms convergently evolved bioluminescent proteins that use the same luciferins to produce bioluminescence. Evolutionary convergence does not necessarily extend across biological levels, as exemplified by cases of conservation and disparity in biological functions, organs, cells, and molecules associated with bioluminescence systems. Investigating differences across bioluminescent organisms will address fundamental questions on predictability and contingency in convergent evolution. Lastly, we highlight unexplored areas of bioluminescence research and advances in sequencing and chemical techniques useful for developing bioluminescence as a model system for studying multi‐level convergent evolution.

    

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3. On the Detection of Sharp Upper Mantle Discontinuities with Radon-Transformed Ps Receiver Functions (CRISP-RF)

   Tolulope Olugboji, Ziqi Zhang ( June 2023 , Geophysical journal international)

   Seismic interrogation of the upper mantle from the base of the crust to the top of the mantle transition zone has revealed discontinuities that are variable in space, depth, lateral extent, amplitude and lack a unified explanation for their origin. Improved constraints on the detectability and properties of mantle discontinuities (depth, amplitude, sharpness) can be obtained with Ps receiver functions where energy scatters from P to S as seismic waves propagate across discontinuities of interest. However, due to the interference of crustal multiples, uppermost mantle discontinuities are more commonly imaged with lower-resolution Sp-RFs which are not affected by these multiples. Here, we present a novel method for obtaining ‘Clean Receiver-function Imaging using SParse Radon Filters’ (CRISP-RF). The central idea involves the transformation of Ps-RF-data into a Radon-transformed Ps-RF. This approach results in the decomposition of the signal into its underlying wavefield contributions: direct conversions, multiple reflections, and noise. A selective filter is then applied to create multiple-free, denoised, source-deconvolved seismograms. The Radon transform is implemented using a sparsity-promoting regularization, common in disciplines such as compressive sensing and model-based image reconstruction, e.g., optical and microscopic imaging, magnetic resonance imaging, and radar astronomy. We review different algorithms for solving this optimization problem and, based on synthetic and real data, show that our approach outperforms the conventional Tikhonov-regularized least-squares methods. The application of CRISP-RF to global datasets will advance our understanding of the enigmatic origins of the upper mantle discontinuities like the ubiquitous Mid-Lithospheric Discontinuity (MLD), and the elusive X-discontinuity. 

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4. Automated patient-robot assignment for a robotic rehabilitation gym: a simplified simulation model

   https://doi.org/10.1186/s12984-022-01105-4  

   Miller, Benjamin A. ; Adhikari, Bikranta ; Jiang, Chao ; Novak, Vesna D. ( November 2022 , Journal of NeuroEngineering and Rehabilitation)

   A robotic rehabilitation gym can be defined as multiple patients training with multiple robots or passive sensorized devices in a group setting. Recent work with such gyms has shown positive rehabilitation outcomes; furthermore, such gyms allow a single therapist to supervise more than one patient, increasing cost-effectiveness. To allow more effective multipatient supervision in future robotic rehabilitation gyms, we propose an automated system that could dynamically assign patients to different robots within a session in order to optimize rehabilitation outcome.

   As a first step toward implementing a practical patient-robot assignment system, we present a simplified mathematical model of a robotic rehabilitation gym. Mixed-integer nonlinear programming algorithms are used to find effective assignment and training solutions for multiple evaluation scenarios involving different numbers of patients and robots (5 patients and 5 robots, 6 patients and 5 robots, 5 patients and 7 robots), different training durations (7 or 12 time steps) and different complexity levels (whether different patients have different skill acquisition curves, whether robots have exit times associated with them). In all cases, the goal is to maximize total skill gain across all patients and skills within a session.

   Analyses of variance across different scenarios show that disjunctive and time-indexed optimization models significantly outperform two baseline schedules: staying on one robot throughout a session and switching robots halfway through a session. The disjunctive model results in higher skill gain than the time-indexed model in the given scenarios, and the optimization duration increases as the number of patients, robots and time steps increases. Additionally, we discuss how different model simplifications (e.g., perfectly known and predictable patient skill level) could be addressed in the future and how such software may eventually be used in practice.

   Though it involves unrealistically simple scenarios, our study shows that intelligently moving patients between different rehabilitation robots can improve overall skill acquisition in a multi-patient multi-robot environment. While robotic rehabilitation gyms are not yet commonplace in clinical practice, prototypes of them already exist, and our study presents a way to use intelligent decision support to potentially enable more efficient delivery of technologically aided rehabilitation.

    

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5. Plant periderm as a continuum in structural organisation: a tracheophyte‐wide survey and hypotheses on evolution

   https://doi.org/10.1111/brv.13064  

   Lalica, Madison A. K. ; Tomescu, Alexandru M. F. ( February 2024 , Biological Reviews)

   Periderm is a well‐known structural feature with vital roles in protection of inner plant tissues and wound healing. Despite its importance to plant survival, knowledge of periderm occurrences outside the seed plants is limited and the evolutionary origins of periderm remain poorly explored. Here, we review the current knowledge of the taxonomic distribution of periderm in its two main forms – canonical periderm (periderm formed as a typical ontogenetic stage) and wound periderm (periderm produced as a self‐repair mechanism) – with a focus on major plant lineages, living and extinct. We supplement the published occurrences with data based on our own observations and experiments. This updated body of data reveals that the distribution of wound periderm is more widespread taxonomically than previously recognized and some living and extinct groups are capable of producing wound periderm, despite canonical periderm being absent from their normal developmental program. A critical review of canonical and wound periderms in extant and fossil lineages indicates that not all periderms are created equal. Their organisation is widely variable and the differences can be characterised in terms of variations in three structural features: (i) the consistency in orientation of periclinal walls within individual files of periderm cells; (ii) the lateral coordination of periclinal walls between adjacent cell files; and (iii) whether a cambial layer and conspicuous layering of inward and outward derivatives can be distinguished. Using a new system of scoring periderm structure based on these criteria, we characterise the level of organisation of canonical and wound periderms in different lineages. Looking at periderms through the lens provided by their level of organisation reveals that the traditional image of periderm as a single generalised feature, is best viewed as a continuum of structural configurations that are all predicated by the same basic process (periclinal divisions), but can fall anywhere between very loosely organized (diffuse periclinal growth) to very tightly coordinated (organized periclinal growth). Overall, wound periderms in both seed plants and seed‐free plants have lower degrees of organisation than canonical periderms, which may be due to their initiation in response to inherently disruptive traumatic events. Wound and canonical periderms of seed plants have higher degrees of organisation than those of seed‐free plants, possibly due to co‐option of the programs responsible for organizing their vascular cambial growth. Given the importance of wound periderm to plant survival, its widespread taxonomic distribution, and its early occurrence in the fossil record, we hypothesise that wound periderm may have had a single origin in euphyllophytes and canonical periderm may have originated separately in different lineages by co‐option of the basic regulatory toolkit of wound periderm formation. In one evolutionary scenario, wound periderm regulators activated initially by tissue tearing due to tensional stresses elicited by woody growth underwent heterochronic change that switched their activation trigger from tissue tearing to the tensional stresses that precede it, with corresponding changes in the signalling that triggered the regulatory cascade of periderm development from tearing‐induced signals to signalling induced by tension in cells.

    

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