A short note on rank-2 relaxation for waveform inversion

This note is a first attempt to perform waveform inversion by utilizing recent developments in semidefinite relaxations for polynomial equations to mitigate non-convexity. The approach consists in reformulating the inverse problem as a set of constraints on a low-rank moment matrix in a higher-dimensional space. While this idea has mostly been a theoretical curiosity so far, the novelty of this note is the suggestion that a modified adjoint-state method enables algorithmic scalability of the relaxed formulation to standard 2D community models in geophysical imaging. Numerical experiments show that the new formulation leads to a modest increase in the basin of attraction of least-squares waveform inversion.TOTAL (Firm)Belgian National Foundation for Scientific ResearchMIT International Science and Technology InitiativesUnited States. Air Force. Office of Scientific ResearchUnited States. Office of Naval ResearchNational Science Foundation (U.S.

Characterization of deep-sea benthic invertebrate megafauna of the Galapagos Islands

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Salinas-de-León, P., Martí-Puig, P., Buglass, S., Arnés-Urgellés, C., Rastoin-Laplane, E., Creemers, M., Cairns, S., Fisher, C., O'Hara, T., Ott, B., Raineault, N. A., Reiswig, H., Rouse, G., Rowley, S., Shank, T. M., Suarez, J., Watling, L., Wicksten, M. K., & Marsh, L. Characterization of deep-sea benthic invertebrate megafauna of the Galapagos Islands. Scientific Reports, 10(1), (2020): 13894, doi:10.1038/s41598-020-70744-1.The deep sea represents the largest and least explored biome on the planet. Despite the iconic status of the Galapagos Islands and being considered one of the most pristine locations on earth, the deep-sea benthic ecosystems of the archipelago are virtually unexplored in comparison to their shallow-water counterparts. In 2015, we embarked on a multi-disciplinary scientific expedition to conduct the first systematic characterization of deep-sea benthic invertebrate communities of the Galapagos, across a range of habitats. We explored seven sites to depths of over 3,300 m using a two-part Remotely Operated Vehicle (ROV) system aboard the E/V Nautilus, and collected 90 biological specimens that were preserved and sent to experts around the world for analysis. Of those, 30 taxa were determined to be undescribed and new to science, including members of five new genera (2 sponges and 3 cnidarians). We also systematically analysed image frame grabs from over 85 h of ROV footage to investigate patterns of species diversity and document the presence of a range of underwater communities between depths of 290 and 3,373 m, including cold-water coral communities, extensive glass sponge and octocoral gardens, and soft-sediment faunal communities. This characterization of Galapagos deep-sea benthic invertebrate megafauna across a range of ecosystems represents a first step to study future changes that may result from anthropogenic impacts to the planet’s climate and oceans, and informed the creation of fully protected deep-water areas in the Galapagos Marine Reserve that may help preserve these unique communities in our changing planet.We are thankful to the Ocean Exploration Trust as well as the pilots and crew aboard the E/V Nautilus during cruise NA064 for their assistance in sample collection and exploration using the Hercules ROV. Thank you to the NOAA Office of Exploration and Research for funding the E/V Nautilus Exploration Program (NA15OAR0110220). Further acknowledgements and thanks go out to the Charles Darwin Foundation and the Galapagos National Park Directorate for their collaboration and assistance in the exploration of the Galapagos Platform conducted under research permits PC-26–15 & PC-45-15. We also gratefully recognize the Government of Ecuador via the Ecuadorian Navy for permission to operate in their territorial waters. This research was supported by a grant from the Helmsley Charitable Trust and the Gordon and Betty Moore Foundation. This publication is contribution number 2354 of the Charles Darwin Foundation for the Galapagos Islands

Genetic diversity and demographic instability in Riftia pachyptila tubeworms from eastern Pacific hydrothermal vents

<p>Abstract</p> <p>Background</p> <p>Deep-sea hydrothermal vent animals occupy patchy and ephemeral habitats supported by chemosynthetic primary production. Volcanic and tectonic activities controlling the turnover of these habitats contribute to demographic instability that erodes genetic variation within and among colonies of these animals. We examined DNA sequences from one mitochondrial and three nuclear gene loci to assess genetic diversity in the siboglinid tubeworm, <it>Riftia pachyptila</it>, a widely distributed constituent of vents along the East Pacific Rise and Galápagos Rift.</p> <p>Results</p> <p>Genetic differentiation (<it>F</it>_<it>ST</it>) among populations increased with geographical distances, as expected under a linear stepping-stone model of dispersal. Low levels of DNA sequence diversity occurred at all four loci, allowing us to exclude the hypothesis that an idiosyncratic selective sweep eliminated mitochondrial diversity alone. Total gene diversity declined with tectonic spreading rates. The southernmost populations, which are subjected to superfast spreading rates and high probabilities of extinction, are relatively homogenous genetically.</p> <p>Conclusions</p> <p>Compared to other vent species, DNA sequence diversity is extremely low in <it>R. pachyptila</it>. Though its dispersal abilities appear to be effective, the low diversity, particularly in southern hemisphere populations, is consistent with frequent local extinction and (re)colonization events.</p

The Earth BioGenome Project 2020: Starting the clock

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The Earth BioGenome Project 2020: Starting the clock.

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lewin, H. A., Richards, S., Lieberman Aiden, E., Allende, M. L., Archibald, J. M., Bálint, M., Barker, K. B., Baumgartner, B., Belov, K., Bertorelle, G., Blaxter, Mark L., Cai, J., Caperello, N. D., Carlson, K., Castilla-Rubio, J. C., Chaw, S-M., Chen, L., Childers, A. K., Coddington, J. A., Conde, D. A., Corominas, M., Crandall, K. A., Crawford, A. J., DiPalma, F., Durbin, R., Ebenezer, T. E., Edwards, S. V., Fedrigo, O., Flicek, P., Formenti, G., Gibbs, R. A., Gilbert, M. Thomas P., Goldstein, M. M., Graves, J. M., Greely, H. T., Grigoriev, I. V., Hackett, K. J., Hall, N., Haussler, D., Helgen, K. M., Hogg, C. J., Isobe, S., Jakobsen, K. S., Janke, A., Jarvis, E. D., Johnson, W. E., Jones, S. J. M., Karlsson, E. K., Kersey, P. J., Kim, J-H., Kress, W. J., Kuraku, S., Lawniczak, M. K. N., Leebens-Mack, J. H., Li, X., Lindblad-Toh, K., Liu, X., Lopez, J. V., Marques-Bonet, T., Mazard, S., Mazet, J. A. K., Mazzoni, C. J., Myers, E. W., O’Neill, R. J., Paez, S., Park, H., Robinson, G. E., Roquet, C., Ryder, O. A., Sabir, J. S. M., Shaffer, H. B., Shank, T. M., Sherkow, J. S., Soltis, P. S., Tang, B., Tedersoo, L., Uliano-Silva, M., Wang, K., Wei, X., Wetzer, R., Wilson, J. L., Xu, X., Yang, H., Yoder, A. D., Zhang, G. The Earth BioGenome Project 2020: starting the clock. Proceedings of the National Academy of Sciences of the United States of America, 119(4), (2022): e2115635118, https://doi.org/10.1073/pnas.2115635118.November 2020 marked 2 y since the launch of the Earth BioGenome Project (EBP), which aims to sequence all known eukaryotic species in a 10-y timeframe. Since then, significant progress has been made across all aspects of the EBP roadmap, as outlined in the 2018 article describing the project’s goals, strategies, and challenges (1). The launch phase has ended and the clock has started on reaching the EBP’s major milestones. This Special Feature explores the many facets of the EBP, including a review of progress, a description of major scientific goals, exemplar projects, ethical legal and social issues, and applications of biodiversity genomics. In this Introduction, we summarize the current status of the EBP, held virtually October 5 to 9, 2020, including recent updates through February 2021. References to the nine Perspective articles included in this Special Feature are cited to guide the reader toward deeper understanding of the goals and challenges facing the EBP

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements

Measurement of inclusive jet and dijet cross-sections in proton-proton collisions at s √ =13 TeV with the ATLAS detector

Inclusive jet and dijet cross-sections are measured in proton-proton collisions at a centre-of-mass energy of 13 TeV. The measurement uses a dataset with an integrated luminosity of 3.2 fb−1 recorded in 2015 with the ATLAS detector at the Large Hadron Collider. Jets are identified using the anti-kt algorithm with a radius parameter value of R = 0.4. The inclusive jet cross-sections are measured double-differentially as a function of the jet transverse momentum, covering the range from 100 GeV to 3.5 TeV, and the absolute jet rapidity up to |y| = 3. The double-differential dijet production cross-sections are presented as a function of the dijet mass, covering the range from 300 GeV to 9 TeV, and the half absolute rapidity separation between the two leading jets within |y| < 3, y∗, up to y∗ = 3. Next-to-leading-order, and next-to-next-to-leading-order for the inclusive jet measurement, perturbative QCD calculations corrected for non-perturbative and electroweak effects are compared to the measured cross-sections