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Creators/Authors contains: "Thomas, F"

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  1. Free, publicly-accessible full text available December 1, 2026
  2. Free, publicly-accessible full text available December 1, 2026
  3. ABSTRACT Neuromesodermal progenitors (NMPs) are a vertebrate cell type that contribute descendants to both the spinal cord and the mesoderm. The undifferentiated bipotential NMP state is maintained when both Wnt signaling is active and Sox2 is present. We used transgenic zebrafish reporter lines to live-image both Wnt activity and Sox2 levels in NMPs and observed a unique cellular ratio in NMPs compared to NMP-derived mesoderm or neural tissue. We used this unique signature to identify the previously unknown anatomical position of a progenitor population that gives rise to midline tissues of the floor plate of the spinal cord and the mesodermal notochord. Thus, quantification of the active Wnt signaling to Sox2 ratio can be used to predict and identify cells with neuromesodermal potential. We also developed the auxin-inducible 2 degron system for use in zebrafish to test the temporal role that Sox2 plays during midline formation. We found that ectopic Sox2 in the presence of Wnt activity holds cells in the undifferentiated floor plate/notochord progenitor state, and that degradation of the ectopic Sox2 is required for cells to adopt a notochord fate. 
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    Free, publicly-accessible full text available November 15, 2026
  4. Free, publicly-accessible full text available July 1, 2026
  5. Abstract Co‐production is becoming an increasingly important approach to facilitating integrated climate, environmental, social and earth systems research to achieve societal impact. Across the research and science‐policy ecosystem, there are multiple indicators of its growing prominence as means to engage the public and generate research that is more likely to address real‐world problems and community priorities. Power plays a key role in co‐production, as power imbalances can affect participation, decision‐making, and the distribution of benefits. Addressing power imbalances, through a focus on equity in co‐production, helps to ensure past harms are addressed and participants have the resources and opportunities to contribute effectively. This special issue includes articles that explore equity in co‐production. Articles describe the results of projects that used co‐production approaches, social scientific findings that can inform equitable co‐production, and some that do both. Across the submissions, inclusive decision‐making, strengthening capacity at multiple levels, and fostering trust and respect were key themes. The collection provides practical lessons and future directions to advance equity in co‐production processes, meeting the urgent demand for more inclusive and impactful environmental science practices. 
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    Free, publicly-accessible full text available December 1, 2026
  6. Channel incision degrades ecosystems by lowering water tables and disconnecting floodplains. Stream restoration often aims to reverse these impacts. However, projects typically receive minimal monitoring, and treatment effectiveness has not been validated. We used trait‐based analysis to evaluate whether two stream restoration techniques—beaver dam analogs (BDAs) and plug‐and‐ponds—raised water tables and increased overbank flooding, whether these altered environmental filters facilitated recovery of riparian plant communities, and how reassembly impacted the representation of traits that influence ecosystem function. We report on a before‐after‐control‐impact study and Bayesian analysis that estimated the probability that treatments affected riparian plant functional diversity and composition. We found a high probability (0.99 and 0.97, respectively) that BDAs decreased functional dispersion by ≥50% and plug‐and‐ponds decreased dispersion by ≥30%. Both treatments increased the relative abundance of high moisture use plants, wetland plants, and plants with high anaerobic tolerance. For example, BDAs increased the relative abundance of obligate wetland plants by 100%, and plug‐and‐ponds increased the relative abundance of facultative wetland plants by 105%, on average. These results suggest treatments modified environmental filters and recovered riparian plant communities. Ecosystem function was likely altered as the streamside plant community reassembled. Small increases in functional divergence suggest both treatments increased resource use efficiency, and we found a high probability of small treatment effect sizes (<20%) related to changes in community‐level C:N and nitrogen fixation. Our results demonstrate trait‐based analysis can detect a rapid response to restoration and offer a cost‐effective monitoring approach to compare treatments across space and time. 
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    Free, publicly-accessible full text available April 4, 2026
  7. Free, publicly-accessible full text available November 1, 2026
  8. Mechanical forces play a critical role in tendon development and function, influencing cell behavior through mechanotransduction signaling pathways and subsequent extracellular matrix (ECM) remodeling. Here, we investigate the molecular mechanisms by which tenocytes in developing zebrafish embryos respond to muscle contraction forces during the onset of swimming and cranial muscle activity. Using genome-wide bulk RNA sequencing of FAC-sorted tenocytes we identify novel tenocyte markers and genes involved in tendon mechanotransduction. Embryonic tendons show dramatic changes in expression ofmatrix remodeling associated 5b(mxra5b),matrilin 1(matn1), and the transcription factorkruppel-like factor 2a(klf2a), as muscles start to contract. Using embryos paralyzed either by loss of muscle contractility or neuromuscular stimulation we confirm that muscle contractile forces influence the spatial and temporal expression patterns of all three genes. Quantification of these gene expression changes across tenocytes at multiple tendon entheses and myotendinous junctions reveals that their responses depend on force intensity, duration, and tissue stiffness. These force-dependent feedback mechanisms in tendons, particularly in the ECM, have important implications for improved treatments of tendon injuries and atrophy. 
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    Free, publicly-accessible full text available March 27, 2026
  9. Geology logline: How a catastrophic series of floods were recognized by J Harlen Bretz and Joseph Pardee to have formed the Channeled Scablands of eastern Washington State, USA. Cognitive science logline: Runnable mental models, mental simulations of geological processes applied to spe- cific events, 
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