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  1. Image formation by Fresnel diffraction utilizes both absorption and phase-contrast to measure electron density profiles. The low spatial and spectral coherence requirements allow the technique to be performed with a laser-produced x-ray source coupled with a narrow slit. This makes it an excellent candidate for probing interfaces between materials at extreme conditions, which can only be generated at large-scale laser or pulsed power facilities. Here, we present the results from a proof-of-principle experiment demonstrating an effective ∼2 μm laser-generated source at the OMEGA Laser Facility. This was achieved using slits of 1 × 30  μm 2 and 2 × 40  μm 2 geometry, which were milled into 30 μm thick Ta plates. Combining these slits with a vanadium He-like 5.2 keV source created a 1D imaging system capable of micrometer-scale resolution. The principal obstacles to achieving an effective 1 μm source are the slit tilt and taper—where the use of a tapered slit is necessary to increase the alignment tolerance. We demonstrate an effective source size by imaging a 2 ± 0.2 μm radius tungsten wire.
    Free, publicly-accessible full text available September 1, 2023
  2. Volkert, Michael R. (Ed.)
    A protein roadblock forms when a protein binds DNA and hinders translocation of other DNA binding proteins. These roadblocks can have significant effects on gene expression and regulation as well as DNA binding. Experimental methods for studying the effects of such roadblocks often target endogenous sites or introduce non-variable specific sites into DNAs to create binding sites for artificially introduced protein roadblocks. In this work, we describe a method to create programmable roadblocks using dCas9, a cleavage deficient mutant of the CRISPR effector nuclease Cas9. The programmability allows us to custom design target sites in a synthetic gene intended for in vitro studies. These target sites can be coded with multivalency—in our case, internal restriction sites which can be used in validation studies to verify complete binding of the roadblock. We provide full protocols and sequences and demonstrate how to use the internal restriction sites to verify complete binding of the roadblock. We also provide example results of the effect of DNA roadblocks on the translocation of the restriction endonuclease NdeI, which searches for its cognate site using one dimensional diffusion along DNA.
    Free, publicly-accessible full text available May 6, 2023
  3. Optimistic initialization underpins many theoretically sound exploration schemes in tabular domains; however, in the deep function approximation setting, optimism can quickly disappear if initialized naively. We propose a framework for more effectively incorporating optimistic initialization into reinforcement learning for continuous control. Our approach uses metric information about the state-action space to estimate which transitions are still unexplored, and explicitly maintains the initial Q-value optimism for the corresponding state-action pairs. We also develop methods for efficiently approximating these training objectives, and for incorporating domain knowledge into the optimistic envelope to improve sample efficiency. We empirically evaluate these approaches on a variety of hard exploration problems in continuous control, where our method outperforms existing exploration techniques.
  4. A fundamental assumption of reinforcement learning in Markov decision processes (MDPs) is that the relevant decision process is, in fact, Markov. However, when MDPs have rich observations, agents typically learn by way of an abstract state representation, and such representations are not guaranteed to preserve the Markov property. We introduce a novel set of conditions and prove that they are sufficient for learning a Markov abstract state representation. We then describe a practical training procedure that combines inverse model estimation and temporal contrastive learning to learn an abstraction that approximately satisfies these conditions. Our novel training objective is compatible with both online and offline training: it does not require a reward signal, but agents can capitalize on reward information when available. We empirically evaluate our approach on a visual gridworld domain and a set of continuous control benchmarks. Our approach learns representations that capture the underlying structure of the domain and lead to improved sample efficiency over state-of-the-art deep reinforcement learning with visual features—often matching or exceeding the performance achieved with hand-designed compact state information.
  5. Beavers have established themselves as a key component of low arctic ecosystems over the past several decades. Beavers are widely recognized as ecosystem engineers, but their effects on permafrost-dominated landscapes in the Arctic remain unclear. In this study, we document the occurrence, reconstruct the timing, and highlight the effects of beaver activity on a small creek valley confined by ice-rich permafrost on the Seward Peninsula, Alaska using multi-dimensional remote sensing analysis of satellite (Landsat-8, Sentinel-2, Planet CubeSat, and DigitalGlobe Inc./MAXAR) and unmanned aircraft systems (UAS) imagery. Beaver activity along the study reach of Swan Lake Creek appeared between 2006 and 2011 with the construction of three dams. Between 2011 and 2017, beaver dam numbers increased, with the peak occurring in 2017 (n = 9). Between 2017 and 2019, the number of dams decreased (n = 6), while the average length of the dams increased from 20 to 33 m. Between 4 and 20 August 2019, following a nine-day period of record rainfall (>125 mm), the well-established dam system failed, triggering the formation of a beaver-induced permafrost degradation feature. During the decade of beaver occupation between 2011 and 2021, the creek valley widened from 33 to 180 m (~450% increase) andmore »the length of the stream channel network increased from ~0.6 km to more than 1.9 km (220% increase) as a result of beaver engineering and beaver-induced permafrost degradation. Comparing vegetation (NDVI) and snow (NDSI) derived indices from Sentinel-2 time-series data acquired between 2017 and 2021 for the beaver-induced permafrost degradation feature and a nearby unaffected control site, showed that peak growing season NDVI was lowered by 23% and that it extended the length of the snow-cover period by 19 days following the permafrost disturbance. Our analysis of multi-dimensional remote sensing data highlights several unique aspects of beaver engineering impacts on ice-rich permafrost landscapes. Our detailed reconstruction of the beaver-induced permafrost degradation event may also prove useful for identifying degradation of ice-rich permafrost in optical time-series datasets across regional scales. Future field- and remote sensing-based observations of this site, and others like it, will provide valuable information for the NSF-funded Arctic Beaver Observation Network (A-BON) and the third phase of the NASA Arctic-Boreal Vulnerability Experiment (ABoVE) Field Campaign.« less
  6. Understanding the adaptive capacity of ecosystems to cope with change is crucial to management. However, unclear and often confusing definitions of adaptive capacity make application of this concept difficult. In this paper, we revisit definitions of adaptive capacity and operationalize the concept. We define adaptive capacity as the latent potential of an ecosystem to alter resilience in response to change. We present testable hypotheses to evaluate complementary attributes of adaptive capacity that may help further clarify the components and relevance of the concept. Adaptive sampling, inference and modeling can reduce key uncertainties incrementally over time and increase learning about adaptive capacity. Such improvements are needed because uncertainty about global change and its effect on the capacity of ecosystems to adapt to social and ecological change is high.