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  1. ; ; ; ; ; ; ; ; ; ; et al ( , Communications Biology)
    Abstract Different intensities of high temperatures affect the growth of photosynthetic cells in nature. To elucidate the underlying mechanisms, we cultivated the unicellular green alga Chlamydomonas reinhardtii under highly controlled photobioreactor conditions and revealed systems-wide shared and unique responses to 24-hour moderate (35°C) and acute (40°C) high temperatures and subsequent recovery at 25°C. We identified previously overlooked unique elements in response to moderate high temperature. Heat at 35°C transiently arrested the cell cycle followed by partial synchronization, up-regulated transcripts/proteins involved in gluconeogenesis/glyoxylate-cycle for carbon uptake and promoted growth. But 40°C disrupted cell division and growth. Both high temperatures induced photoprotection,more »while 40°C distorted thylakoid/pyrenoid ultrastructure, affected the carbon concentrating mechanism, and decreased photosynthetic efficiency. We demonstrated increased transcript/protein correlation during both heat treatments and hypothesize reduced post-transcriptional regulation during heat may help efficiently coordinate thermotolerance mechanisms. During recovery after both heat treatments, especially 40°C, transcripts/proteins related to DNA synthesis increased while those involved in photosynthetic light reactions decreased. We propose down-regulating photosynthetic light reactions during DNA replication benefits cell cycle resumption by reducing ROS production. Our results provide potential targets to increase thermotolerance in algae and crops.« less
    Free, publicly-accessible full text available December 1, 2023
  2. ; ; ; ; ; ( , Plant Physiology)
    Abstract Plant cells communicate information for the regulation of development and responses to external stresses. A key form of this communication is transcriptional regulation, accomplished via complex gene networks operating both locally and systemically. To fully understand how genes are regulated across plant tissues and organs, high resolution, multi-dimensional spatial transcriptional data must be acquired and placed within a cellular and organismal context. Spatial transcriptomics (ST) typically provides a two-dimensional spatial analysis of gene expression of tissue sections that can be stacked to render three-dimensional data. For example, X-ray and light-sheet microscopy provide sub-micron scale volumetric imaging of cellular morphologymore »of tissues, organs, or potentially entire organisms. Linking these technologies could substantially advance transcriptomics in plant biology and other fields. Here, we review advances in ST and 3D microscopy approaches and describe how these technologies could be combined to provide high resolution, spatially organized plant tissue transcript mapping.« less
    Free, publicly-accessible full text available November 2, 2022
  3. ; ; ; ( , Emerging Topics in Life Sciences)
    Jez, Joseph M. ; Topp, Christopher N. (Ed.)
    Single-cell RNA-seq is a tool that generates a high resolution of transcriptional data that can be used to understand regulatory networks in biological systems. In plants, several methods have been established for transcriptional analysis in tissue sections, cell types, and/or single cells. These methods typically require cell sorting, transgenic plants, protoplasting, or other damaging or laborious processes. Additionally, the majority of these technologies lose most or all spatial resolution during implementation. Those that offer a high spatial resolution for RNA lack breadth in the number of transcripts characterized. Here, we briefly review the evolution of spatial transcriptomics methods and wemore »highlight recent advances and current challenges in sequencing, imaging, and computational aspects toward achieving 3D spatial transcriptomics of plant tissues with a resolution approaching single cells. We also provide a perspective on the potential opportunities to advance this novel methodology in plants.« less
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  4. ; ; ; ; ; ; ; ; ; ; et al ( , Earth and Planetary Science Letters)
    Full Text Available 
  5. ; ; ; ; ; ; ; ; ; ; et al ( , Computing and Software for Big Science)
    Abstract The accurate simulation of additional interactions at the ATLAS experiment for the analysis of proton–proton collisions delivered by the Large Hadron Collider presents a significant challenge to the computing resources. During the LHC Run 2 (2015–2018), there were up to 70 inelastic interactions per bunch crossing, which need to be accounted for in Monte Carlo (MC) production. In this document, a new method to account for these additional interactions in the simulation chain is described. Instead of sampling the inelastic interactions and adding their energy deposits to a hard-scatter interaction one-by-one, the inelastic interactions are presampled, independent of the hardmore »scatter, and stored as combined events. Consequently, for each hard-scatter interaction, only one such presampled event needs to be added as part of the simulation chain. For the Run 2 simulation chain, with an average of 35 interactions per bunch crossing, this new method provides a substantial reduction in MC production CPU needs of around 20%, while reproducing the properties of the reconstructed quantities relevant for physics analyses with good accuracy.« less
    Free, publicly-accessible full text available December 1, 2023
  6. ; ; ; ; ; ; ; ; ; ; et al ( , Computing and Software for Big Science)
    Abstract The ATLAS experiment at the Large Hadron Collider has a broad physics programme ranging from precision measurements to direct searches for new particles and new interactions, requiring ever larger and ever more accurate datasets of simulated Monte Carlo events. Detector simulation with Geant4 is accurate but requires significant CPU resources. Over the past decade, ATLAS has developed and utilized tools that replace the most CPU-intensive component of the simulation—the calorimeter shower simulation—with faster simulation methods. Here, AtlFast3, the next generation of high-accuracy fast simulation in ATLAS, is introduced. AtlFast3 combines parameterized approaches with machine-learning techniques and is deployed tomore »meet current and future computing challenges, and simulation needs of the ATLAS experiment. With highly accurate performance and significantly improved modelling of substructure within jets, AtlFast3 can simulate large numbers of events for a wide range of physics processes.« less
    Free, publicly-accessible full text available December 1, 2023
  7. ; ; ; ; ; ; ( , Nanotechnology)
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  8. ; ; ; ; ; ; ; ; ; ; et al ( , Physical Review D)
    Free, publicly-accessible full text available May 1, 2023
  9. ; ; ; ; ; ; ; ; ; ; et al ( , Physical Review D)
    Free, publicly-accessible full text available May 1, 2023
  10. ; ; ; ; ; ; ; ; ; ; et al ( , The European Physical Journal C)
    Abstract The energy response of the ATLAS calorimeter is measured for single charged pions with transverse momentum in the range $$10more »situ single-particle measurements. The calorimeter response to single-pions is observed to be overestimated by $${\sim }2\%$$ ∼ 2 % across a large part of the $$p_{\text {T}}$$ p T spectrum in the central region and underestimated by $${\sim }4\%$$ ∼ 4 % in the endcaps in the ATLAS simulation. The uncertainties in the measurements are $${\lesssim }1\%$$ ≲ 1 % for $$15« less
    Free, publicly-accessible full text available March 1, 2023