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  1. ; ; ; ; ( , Accounts of Chemical Research)
    Free, publicly-accessible full text available April 5, 2023
  2. ; ; ; ; ; ( , Journal of Experimental Biology)
    ABSTRACT Ticks are blood-feeding ectoparasites but spend most of their life off-host where they may have to tolerate low winter temperatures. Rapid cold hardening (RCH) is a process commonly used by arthropods, including ticks, to improve survival of acute low temperature exposure. However, little is known about the underlying mechanisms in ticks associated with RCH, cold shock and recovery from these stresses. In the present study, we investigated the extent to which RCH influences gene expression and metabolism during recovery from cold stress in Dermacentor variabilis, the American dog tick, using a combined transcriptomics and metabolomics approach. Following recovery frommore »RCH, 1860 genes were differentially expressed in ticks, whereas only 99 genes responded during recovery to direct cold shock. Recovery from RCH resulted in an upregulation of various pathways associated with ion binding, transport, metabolism and cellular structures seen in the response of other arthropods to cold. The accumulation of various metabolites, including several amino acids and betaine, corresponded to transcriptional shifts in the pathways associated with these molecules, suggesting congruent metabolome and transcriptome changes. Ticks, D. variabilis and Amblyomma maculatum, receiving exogenous betaine and valine demonstrated enhanced cold tolerance, suggesting cryoprotective effects of these metabolites. Overall, many of the responses during recovery from cold shock in ticks were similar to those observed in other arthropods, but several adjustments may be distinct from the responses in other currently examined taxa.« less
    Free, publicly-accessible full text available April 15, 2023
  3. ; ; ; ; ( , IEEE Control Systems Letters)
    Free, publicly-accessible full text available January 1, 2023
  4. ; ; ; ; ; ; ( , Bioinformatics)
    Valencia, Alfonso (Ed.)
    Abstract Motivation This article introduces Vivarium—software born of the idea that it should be as easy as possible for computational biologists to define any imaginable mechanistic model, combine it with existing models and execute them together as an integrated multiscale model. Integrative multiscale modeling confronts the complexity of biology by combining heterogeneous datasets and diverse modeling strategies into unified representations. These integrated models are then run to simulate how the hypothesized mechanisms operate as a whole. But building such models has been a labor-intensive process that requires many contributors, and they are still primarily developed on a case-by-case basis withmore »each project starting anew. New software tools that streamline the integrative modeling effort and facilitate collaboration are therefore essential for future computational biologists. Results Vivarium is a software tool for building integrative multiscale models. It provides an interface that makes individual models into modules that can be wired together in large composite models, parallelized across multiple CPUs and run with Vivarium’s discrete-event simulation engine. Vivarium’s utility is demonstrated by building composite models that combine several modeling frameworks: agent-based models, ordinary differential equations, stochastic reaction systems, constraint-based models, solid-body physics and spatial diffusion. This demonstrates just the beginning of what is possible—Vivarium will be able to support future efforts that integrate many more types of models and at many more biological scales. Availability and implementation The specific models, simulation pipelines and notebooks developed for this article are all available at the vivarium-notebooks repository: https://github.com/vivarium-collective/vivarium-notebooks. Vivarium-core is available at https://github.com/vivarium-collective/vivarium-core, and has been released on Python Package Index. The Vivarium Collective (https://vivarium-collective.github.io) is a repository of freely available Vivarium processes and composites, including the processes used in Section 3. Supplementary Materials provide with an extensive methodology section, with several code listings that demonstrate the basic interfaces. Supplementary information Supplementary data are available at Bioinformatics online.« less
    Free, publicly-accessible full text available February 4, 2023
  5. ; ; ; ; ; ( , IEEE Control Systems Letters)
    Free, publicly-accessible full text available January 1, 2023
  6. ; ; ; ; ; ; ; ; ; ( , bioRxiv)
    Free, publicly-accessible full text available January 21, 2023
  7. ; ; ; ; ( , International Symposium of Medical Robotics)
    Free, publicly-accessible full text available November 17, 2022
  8. ; ; ( , Journal of the American Chemical Society)
    Entangled two-photon absorption (ETPA) is known to create photoinduced transitions with extremely low light intensity, reducing the risk of phototoxicity compared to classical two-photon absorption. Previous works have predicted the ETPA cross-section, σe, to vary inversely with the product of entanglement time (Te) and entanglement area (Ae), i.e., σe ∼ 1/AeTe. The decreasing σe with increasing Te has limited ETPA to fs-scale Te, while ETPA applications for ps-scale spectroscopy have been unexplored. However, we show that spectral−spatial coupling, which reduces Ae as the SPDC bandwidth (σf ) decreases, plays a significant role in determining σe when Te > ∼100 fs.more »We experimentally measured σe for zinc tetraphenylporphyrin at several σf values. For type-I ETPA, σe increases as σf decreases down to 0.1 ps−1 . For type-II SPDC, σe is constant for a wide range of σf . With a theoretical analysis of the data, the maximum type-I σe would occur at σf = 0.1 ps−1 (Te = 10 ps). At this maximum, σe is 1 order of magnitude larger than fs-scale σe and 3 orders of magnitude larger than previous predictions of ps-scale σe. By utilizing this spectral−spatial coupling, narrowband type-I ETPA provides a new opportunity to increase the efficiency of measuring nonlinear optical signals and to control photochemical reactions requiring ps temporal precision.« less
    Free, publicly-accessible full text available October 1, 2022
  9. ; ; ; ( , IEEE Transactions on Robotics)
    Free, publicly-accessible full text available October 8, 2022
  10. ; ; ; ( , 2021 IEEE International Conference on Robotics and Automation (ICRA))
    Full Text Available