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  • Machine Learning Enabled Traveltime Inversion Based on the Horizontal Source Location Perturbation

    Yildirim, Isa Eren; Alkhalifah, Tariq Ali; Yildirim, Ertugrul Umut (GEOPHYSICS, Society of Exploration Geophysicists, 2021-10-17) [Article]
    Gradient based traveltime tomography, which aims to minimize the difference between modeled and observed first arrival times, is a highly non-linear optimization problem. Stabilization of this inverse problem often requires employing regularization. While regularization helps avoid local minima solutions, it might cause low resolution tomograms because of its inherent smoothing property. On the other hand, although conventional ray-based tomography can be robust in terms of the uniqueness of the solution, it suffers from the limitations inherent in ray tracing, which limits its use in complex media. To mitigate the aforementioned drawbacks of gradient and ray-based tomography, we approach the problem in a completely novel way leveraging data-driven inversion techniques based on training deep convolutional neural networks (DCNN). Since DCNN often face challenges in detecting high level features from the relatively smooth traveltime data, we use this type of network to map horizontal changes in observed first arrival traveltimes caused by a source shift to lateral velocity variations. The relationship between them is explained by a linearized eikonal equation. Construction of the velocity models from this predicted lateral variation requires information from, for example, a vertical well-log in the area. This vertical profile is then used to build a tomogram from the output of the network. Both synthetic and field data results verify that the suggested approach estimates the velocity models reliably. Because of the limited depth penetration of first arrival traveltimes, the method is particularly favorable for near-surface applications.
  • How often should dead-reckoned animal movement paths be corrected for drift?

    Gunner, Richard M.; Holton, Mark D.; Scantlebury, David M.; Hopkins, Phil; Shepard, Emily L. C.; Fell, Adam J.; Garde, Baptiste; Quintana, Flavio; Gómez-Laich, Agustina; Yoda, Ken; Yamamoto, Takashi; English, Holly; Ferreira, Sam; Govender, Danny; Viljoen, Pauli; Bruns, Angela; van Schalkwyk, O. Louis; Cole, Nik C.; Tatayah, Vikash; Börger, Luca; Redcliffe, James; Bell, Stephen H.; Marks, Nikki J.; Bennett, Nigel C.; Tonini, Mariano H.; Williams, Hannah J.; Duarte, Carlos M.; van Rooyen, Martin C.; Bertelsen, Mads F.; Tambling, Craig J.; Wilson, Rory P. (Animal Biotelemetry, Springer Science and Business Media LLC, 2021-10-16) [Article]
    Abstract Background Understanding what animals do in time and space is important for a range of ecological questions, however accurate estimates of how animals use space is challenging. Within the use of animal-attached tags, radio telemetry (including the Global Positioning System, ‘GPS’) is typically used to verify an animal’s location periodically. Straight lines are typically drawn between these ‘Verified Positions’ (‘VPs’) so the interpolation of space-use is limited by the temporal and spatial resolution of the system’s measurement. As such, parameters such as route-taken and distance travelled can be poorly represented when using VP systems alone. Dead-reckoning has been suggested as a technique to improve the accuracy and resolution of reconstructed movement paths, whilst maximising battery life of VP systems. This typically involves deriving travel vectors from motion sensor systems and periodically correcting path dimensions for drift with simultaneously deployed VP systems. How often paths should be corrected for drift, however, has remained unclear. Methods and results Here, we review the utility of dead-reckoning across four contrasting model species using different forms of locomotion (the African lion Panthera leo, the red-tailed tropicbird Phaethon rubricauda, the Magellanic penguin Spheniscus magellanicus, and the imperial cormorant Leucocarbo atriceps). Simulations were performed to examine the extent of dead-reckoning error, relative to VPs, as a function of Verified Position correction (VP correction) rate and the effect of this on estimates of distance moved. Dead-reckoning error was greatest for animals travelling within air and water. We demonstrate how sources of measurement error can arise within VP-corrected dead-reckoned tracks and propose advancements to this procedure to maximise dead-reckoning accuracy. Conclusions We review the utility of VP-corrected dead-reckoning according to movement type and consider a range of ecological questions that would benefit from dead-reckoning, primarily concerning animal–barrier interactions and foraging strategies.
  • The Importance of Larval Stages for Considering Crab Microbiomes as a Paradigm for the Evolution of Terrestrialization

    Wale, Matthew; Daffonchio, Daniele; Fusi, Marco; Marasco, Ramona; Garuglieri, Elisa; Diele, Karen (Frontiers in Microbiology, Frontiers Media SA, 2021-10-15) [Article]
    The transition from an aquatic to a terrestrial lifestyle has evolved multiple times, and in numerous different phyla, in earth’s history. In many crab species, this process is still underway (Bliss and Mantel, 1968), providing a unique opportunity to study the evolution of terrestrialization, as well as the role of associated microbiomes during this process (Cannicci et al., 2020). Recently, Cannicci et al. (2020) reported on the potential importance of microbiomes in the transition of crabs, formally wholly aquatic species, to life, fully or in part, in terrestrial environments. The authors argue that symbiotic bacteria, such as those of gill and gut microbiomes, may play a key role in easing this transition, by helping crabs to overcome physiological and morphological challenges associated with conquering the terrestrial environment, such as impaired respiration and osmotic regulation, and a new, often primary plant-based low nitrogen diet. Here we focus on the microbiomes of crab larvae and their potential role for the evolution of terrestrialization. Crabs that are transitioning to life on land fall into two broad categories: terrestrial species that spend their whole adult life (except for larval release) on land independent of tidal inundation or freshwater bodies, and semi-terrestrial species that spend their adult life on land but are dependent on tidal inundation or freshwater (Burggren and McMahon, 1988; Anger, 1995). Many marine organisms form symbiotic relationships with microorganisms to aid life in extreme environments (Sogin et al., 2020). In line with the hologenome theory, this suggests that host-microbe interactions play an important role in an organism’s evolution, where the genes of both the host and its microbes co-evolve in the collective “holobiont” (Zilber-Rosenberg and Rosenberg, 2008), potentially allowing the colonization of formerly hostile environments (Bang et al., 2018). Microbial symbionts, as individual species or in mixed-species assemblages, are present in many crustaceans, such as the marine isopod Idotea balthica (diet-specific gut microbiomes, Mattila et al., 2014), the intertidal brachyuran crab Eriocheir sinensis (gill and gut microbiomes, Zhang et al., 2016), and the freshwater signal crayfish Pacifastacus leniusculus (intestinal bacteria, Hernández-Pérez et al., 2021). Given that microbial assemblages are often specific to certain organs of their hosts (Chomicki et al., 2020), symbioses have likely evolved in support of a specific function. The microbial assemblages associated with the guts of semi-terrestrial crabs have been proposed to aid in the adaptation of a low nitrogen, herbivorous diet during terrestrialization (Bui and Lee, 2015), like microbial assemblages of other aquatic invertebrates, e.g., isopods, where they enable the digestion of cellulose (Zimmer et al., 2002; O’Connor et al., 2014). The bacteria specifically associated with crab gills (Zhang et al., 2016, 2017) may facilitate ammonia excretion (Weihrauch et al., 2004), utilize gaseous CO2 (Morris, 2001), and buffer exposure to oxygen, which occurs at a concentration 30 times higher (Hsia et al., 2013) in the terrestrial compared to the marine environment where the host organism evolved. The microbiomes of both gut and gills could therefore provide terrestrial and semi-terrestrial crabs (here collectively called semi-/terrestrial) with means to cope with life in marine as well as in terrestrial environments. Whilst the presence of microbiomes and their role in buffering the stresses imposed on crabs by terrestrialization is beginning to be discussed (Bui and Lee, 2015; Cannicci et al., 2020), there are many unknowns. For example, the mode of bacterial acquisition, bacterial diversity, topological association, and the precise functions of their organ-specific microbial assemblages are still poorly understood, both for adult semi-/terrestrial crabs and their early life stages. Most semi-/terrestrial crab species, like their aquatic counterparts, have a biphasic life cycle including fully aquatic larvae, via which they transition to semi-/terrestrial juvenile/adult life (Anger, 1995; Hartnoll etal.,2014).Understanding microbial colonization of the larvae would likely provide critical insights into how these crabs have been able to move from water to land, and whether the bacteria themselves facilitate this transition.
  • Quasi-Newton methods for machine learning: forget the past, just sample

    Berahas, A. S.; Jahani, M.; Richtarik, Peter; Takáč, M. (Optimization Methods and Software, Informa UK Limited, 2021-10-15) [Article]
    We present two sampled quasi-Newton methods (sampled LBFGS and sampled LSR1) for solving empirical risk minimization problems that arise in machine learning. Contrary to the classical variants of these methods that sequentially build Hessian or inverse Hessian approximations as the optimization progresses, our proposed methods sample points randomly around the current iterate at every iteration to produce these approximations. As a result, the approximations constructed make use of more reliable (recent and local) information and do not depend on past iterate information that could be significantly stale. Our proposed algorithms are efficient in terms of accessed data points (epochs) and have enough concurrency to take advantage of parallel/distributed computing environments. We provide convergence guarantees for our proposed methods. Numerical tests on a toy classification problem as well as on popular benchmarking binary classification and neural network training tasks reveal that the methods outperform their classical variants.
  • Nickel-Catalyzed Reductive Cross-Couplings: New Opportunities for Carbon–Carbon Bond Formations through Photochemistry and Electrochemistry

    Yi, Liang; Ji, Tengfei; Chen, Kun-Quan; Chen, Xiang-Yu; Rueping, Magnus (CCS Chemistry, Chinese Chemical Society, 2021-10-15) [Article]
    Metal-catalyzed cross-electrophile couplings have become a valuable tool for carbon–carbon bond formation. This minireview provides a comprehensive overview of the recent developments in the topical field of cross-electrophile couplings, provides explanations of the current state-of-the-art, and highlights new opportunities arising in the emerging fields of photoredox catalysis and electrochemistry.

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