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  1. Free, publicly-accessible full text available October 23, 2024
  2. Abstract

    Mechanical characterization of dynamic DNA nanodevices is essential to facilitate their use in applications like molecular diagnostics, force sensing, and nanorobotics that rely on device reconfiguration and interactions with other materials. A common approach to evaluate the mechanical properties of dynamic DNA nanodevices is by quantifying conformational distributions, where the magnitude of fluctuations correlates to the stiffness. This is generally carried out through manual measurement from experimental images, which is a tedious process and a critical bottleneck in the characterization pipeline. While many tools support the analysis of static molecular structures, there is a need for tools to facilitate the rapid characterization of dynamic DNA devices that undergo large conformational fluctuations. Here, we develop a data processing pipeline based on Deep Neural Networks (DNNs) to address this problem. The YOLOv5 and Resnet50 network architecture were used for the two key subtasks: particle detection and pose (i.e. conformation) estimation. We demonstrate effective network performance (F1 score 0.85 in particle detection) and good agreement with experimental distributions with limited user input and small training sets (~ 5 to 10 images). We also demonstrate this pipeline can be applied to multiple nanodevices, providing a robust approach for the rapid characterization of dynamic DNA devices.

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  3. Cytonuclear disruption may accompany allopolyploid evolution as a consequence of the merger of different nuclear genomes in a cellular environment having only one set of progenitor organellar genomes. One path to reconcile potential cytonuclear mismatch is biased expression for maternal gene duplicates (homoeologs) encoding proteins that target to plastids and/or mitochondria. Assessment of this transcriptional form of cytonuclear coevolution at the level of individual cells or cell types remains unexplored. Using single-cell (sc-) and single-nucleus (sn-) RNAseq data from eight tissues in three allopolyploid species, we characterized cell type–specific variations of cytonuclear coevolutionary homoeologous expression and demonstrated the temporal dynamics of expression patterns across development stages during cotton fiber development. Our results provide unique insights into transcriptional cytonuclear coevolution in plant allopolyploids at the single-cell level.

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    Free, publicly-accessible full text available October 3, 2024
  4. Programmable networks are enabling a new class of applications that leverage the line-rate processing capability and on-chip register memory of the switch data plane. Yet the status quo is focused on developing approaches that share the register memory statically. We present NetVRM, a network management system that supports dynamic register memory sharing between multiple concurrent applications on a programmable network and is readily deployable on commodity programmable switches. NetVRM provides a virtual register memory abstraction that enables applications to share the register memory in the data plane, and abstracts away the underlying details. In principle, NetVRM supports any memory allocation algorithm given the virtual register memory abstraction. It also provides a default memory allocation algorithm that exploits the observation that applications have diminishing returns on additional memory. NetVRM provides an extension of P4, P4VRM, for developing applications with virtual register memory, and a compiler to generate data plane programs and control plane APIs. Testbed experiments show that NetVRM generalizes to a diverse variety of applications, and that its utility-based dynamic allocation policy outperforms static resource allocation. Specifically, it improves the mean satisfaction ratio (i.e., the fraction of a network application’s lifetime that it meets its utility target) by 1.6–2.2× under a range of workloads. 
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  5. Abstract This paper concerns the design and rigorous in silico evaluation of a closed-loop hemorrhage resuscitation algorithm with blood pressure (BP) as controlled variable. A lumped-parameter control design model relating volume resuscitation input to blood volume (BV) and BP responses was developed and experimentally validated. Then, three alternative adaptive control algorithms were developed using the control design model: (i) model reference adaptive control (MRAC) with BP feedback, (ii) composite adaptive control (CAC) with BP feedback, and (iii) CAC with BV and BP feedback. To the best of our knowledge, this is the first work to demonstrate model-based control design for hemorrhage resuscitation with readily available BP as feedback. The efficacy of these closed-loop control algorithms was comparatively evaluated as well as compared with an empiric expert knowledge-based algorithm based on 100 realistic virtual patients created using a well-established physiological model of cardiovascular (CV) hemodynamics. The in silico evaluation results suggested that the adaptive control algorithms outperformed the knowledge-based algorithm in terms of both accuracy and robustness in BP set point tracking: the average median performance error (MDPE) and median absolute performance error (MDAPE) were significantly smaller by >99% and >91%, and as well, their interindividual variability was significantly smaller by >88% and >94%. Pending in vivo evaluation, model-based control design may advance the medical autonomy in closed-loop hemorrhage resuscitation. 
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