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  • Blackwell Publishing Ltd  (37,208)
  • National Academy of Sciences  (12,450)
  • American Chemical Society (ACS)
  • 2020-2023  (40)
  • 1990-1994  (49,618)
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  • 1
    Publication Date: 2022-04-01
    Description: We present a workflow to estimate geostatistical aquifer parameters from pumping test data using the Python package welltestpy. The procedure of pumping test analysis is exemplified for two data sets from the Horkheimer Insel site and from the Lauswiesen site, Germany. The analysis is based on a semi‐analytical drawdown solution from the upscaling approach Radial Coarse Graining, which enables to infer log‐transmissivity variance and horizontal correlation length, beside mean transmissivity, and storativity, from pumping test data. We estimate these parameters of aquifer heterogeneity from type‐curve analysis and determine their sensitivity. This procedure, implemented in welltestpy, is a template for analyzing any pumping test. It goes beyond the possibilities of standard methods, for example, based on Theis' equation, which are limited to mean transmissivity and storativity. A sensitivity study showed the impact of observation well positions on the parameter estimation quality. The insights of this study help to optimize future test setups for geostatistical aquifer analysis and provides guidance for investigating pumping tests with regard to aquifer statistics using the open‐source software package welltestpy.
    Description: Article impact statement: We present a workflow to infer parameters of subsurface heterogeneity from pumping test data exemplified at two sites using welltestpy.
    Description: German Federal Environmental Foundation (DBU) http://dx.doi.org/10.13039/100007636
    Keywords: ddc:551.49
    Language: English
    Type: doc-type:article
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  • 2
    Publication Date: 2022-04-01
    Description: In designed experiments, different sources of variability and an adequate scale of measurement need to be considered, but not all approaches in common usage are equally valid. In order to elucidate the importance of sources of variability and choice of scale, we conducted an experiment where the effects of biochar and slurry applications on soil properties related to soil fertility were studied for different designs: (a) for a field‐scale sampling design with either a model soil (without natural variability) as an internal control or with composited soils, (b) for a design with a focus on amendment variabilities, and (c) for three individual field‐scale designs with true field replication and a combined analysis representative of the population of loess‐derived soils. Three silty loam sites in Germany were sampled and the soil macroaggregates were crushed. For each design, six treatments (0, 0.15 and 0.30 g slurry‐N kg−1 with and without 30 g biochar kg−1) were applied before incubating the units under constant soil moisture conditions for 78 days. CO2 fluxes were monitored and soils were analysed for macroaggregate yields and associated organic carbon (C). Mixed‐effects models were used to describe the effects. For all soil properties, results for the loess sites differed with respect to significant contributions of fixed effects for at least one site, suggesting the need for a general inclusion of different sites. Analysis using a multilevel model allowed generalizations for loess soils to be made and showed that site:slurry:biochar and site:slurry interactions were not negligible for macroaggregate yields. The use of a model soil as an internal control enabled observation of variabilities other than those related to soils or amendments. Experiments incorporating natural variability in soils or amendments resulted in partially different outcomes, indicating the need to include all important sources of variability. Highlights Effects of biochar and slurry applications were studied for different designs and mixed‐effects models were used to describe the effects. Including an internal control allowed observation of, e.g., methodological and analytical variabilities. The results suggested the need for a general inclusion of different sites. Analysis using a multilevel model allowed generalizations for loess soils. The results indicated the need to include all important sources of variability.
    Keywords: ddc:631.4
    Language: English
    Type: doc-type:article
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  • 3
    Publication Date: 2022-04-01
    Description: Temperate forest soils are often considered as an important sink for atmospheric carbon (C), thereby buffering anthropogenic CO2 emissions. However, the effect of tree species composition on the magnitude of this sink is unclear. We resampled a tree species common garden experiment (six sites) a decade after initial sampling to evaluate whether forest floor (FF) and topsoil organic carbon (Corg) and total nitrogen (Nt) stocks changed in dependence of tree species (Norway spruce—Picea abies L., European beech—Fagus sylvatica L., pedunculate oak—Quercus robur L., sycamore maple—Acer pseudoplatanus L., European ash—Fraxinus excelsior L. and small‐leaved lime—Tilia cordata L.). Two groups of species were identified in terms of Corg and Nt distribution: (1) Spruce with high Corg and Nt stocks in the FF developed as a mor humus layer which tended to have smaller Corg and Nt stocks and a wider Corg:Nt ratio in the mineral topsoil, and (2) the broadleaved species, of which ash and maple distinguished most clearly from spruce by very low Corg and Nt stocks in the FF developed as mull humus layer, had greater Corg and Nt stocks, and narrow Corg:Nt ratios in the mineral topsoil. Over 11 years, FF Corg and Nt stocks increased most under spruce, while small decreases in bulk mineral soil (esp. in 0–15 cm and 0–30 cm depth) Corg and Nt stocks dominated irrespective of species. Observed decadal changes were associated with site‐related and tree species‐mediated soil properties in a way that hinted towards short‐term accumulation and mineralisation dynamics of easily available organic substances. We found no indication for Corg stabilisation. However, results indicated increasing Nt stabilisation with increasing biomass of burrowing earthworms, which were highest under ash, lime and maple and lowest under spruce. Highlights We studied if tree species differences in topsoil Corg and Nt stocks substantiate after a decade. The study is unique in its repeated soil sampling in a multisite common garden experiment. Forest floors increased under spruce, but topsoil stocks decreased irrespective of species. Changes were of short‐term nature. Nitrogen was most stable under arbuscular mycorrhizal species.
    Description: Deutsche Forschungsgemeinschaff (DFG)
    Keywords: ddc:551.9 ; ddc:631.41
    Language: English
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  • 4
    Publication Date: 2022-10-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Peredo, E. L., & Cardon, Z. G. Shared up-regulation and contrasting down-regulation of gene expression distinguish desiccation-tolerant from intolerant green algae. Proceedings of the National Academy of Sciences of the United States of America, 117(29), 1(2020): 7438-17445, doi:10.1073/pnas.1906904117.
    Description: Among green plants, desiccation tolerance is common in seeds and spores but rare in leaves and other vegetative green tissues. Over the last two decades, genes have been identified whose expression is induced by desiccation in diverse, desiccation-tolerant (DT) taxa, including, e.g., late embryogenesis abundant proteins (LEA) and reactive oxygen species scavengers. This up-regulation is observed in DT resurrection plants, mosses, and green algae most closely related to these Embryophytes. Here we test whether this same suite of protective genes is up-regulated during desiccation in even more distantly related DT green algae, and, importantly, whether that up-regulation is unique to DT algae or also occurs in a desiccation-intolerant relative. We used three closely related aquatic and desert-derived green microalgae in the family Scenedesmaceae and capitalized on extraordinary desiccation tolerance in two of the species, contrasting with desiccation intolerance in the third. We found that during desiccation, all three species increased expression of common protective genes. The feature distinguishing gene expression in DT algae, however, was extensive down-regulation of gene expression associated with diverse metabolic processes during the desiccation time course, suggesting a switch from active growth to energy-saving metabolism. This widespread downshift did not occur in the desiccation-intolerant taxon. These results show that desiccation-induced up-regulation of expression of protective genes may be necessary but is not sufficient to confer desiccation tolerance. The data also suggest that desiccation tolerance may require induced protective mechanisms operating in concert with massive down-regulation of gene expression controlling numerous other aspects of metabolism.
    Description: Dr. Louise Lewis (University of Connecticut) provided F. rotunda and A. deserticola. Suzanne Thomas and Jordan Stark provided expert technical assistance. This work was supported by the NSF, Division of Integrative Organismal Systems (1355085 to Z.G.C.), and an anonymous donor (to Z.G.C.).
    Keywords: Aquatic green algae ; Desert-evolved green algae ; Extremophiles ; Microbiotic ; Crusts ; Scenedesmaceae
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 5
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Criswell, K. E., Roberts, L. E., Koo, E. T., Head, J. J., & Gillis, J. A. Hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea. Proceedings of the National Academy of Sciences of the United States of America, 118(51), (2021): e2114563118, https://doi.org/10.1073/pnas.2114563118.
    Description: The axial skeleton of tetrapods is organized into distinct anteroposterior regions of the vertebral column (cervical, trunk, sacral, and caudal), and transitions between these regions are determined by colinear anterior expression boundaries of Hox5/6, -9, -10, and -11 paralogy group genes within embryonic paraxial mesoderm. Fishes, conversely, exhibit little in the way of discrete axial regionalization, and this has led to scenarios of an origin of Hox-mediated axial skeletal complexity with the evolutionary transition to land in tetrapods. Here, combining geometric morphometric analysis of vertebral column morphology with cell lineage tracing of hox gene expression boundaries in developing embryos, we recover evidence of at least five distinct regions in the vertebral skeleton of a cartilaginous fish, the little skate (Leucoraja erinacea). We find that skate embryos exhibit tetrapod-like anteroposterior nesting of hox gene expression in their paraxial mesoderm, and we show that anterior expression boundaries of hox5/6, hox9, hox10, and hox11 paralogy group genes predict regional transitions in the differentiated skate axial skeleton. Our findings suggest that hox-based axial skeletal regionalization did not originate with tetrapods but rather has a much deeper evolutionary history than was previously appreciated.
    Description: This research was funded by a Natural Environment Research Council Grant (to J.J.H., J.A.G., and K.E.C.: NE/S000739/1) and a Royal Society University Research Fellowship (UF130182 and URF\R\191007), Royal Society Research Grant (RG140377), and University of Cambridge Sir Isaac Newton Trust Grant (14.23z) (to J.A.G.).
    Keywords: Hox genes ; Regionalization ; Chondrichthyan ; Vertebral column
    Repository Name: Woods Hole Open Access Server
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  • 6
    Publication Date: 2022-10-31
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Northcutt, A. J., Kick, D. R., Otopalik, A. G., Goetz, B. M., Harris, R. M., Santin, J. M., Hofmann, H. A., Marder, E., & Schulz, D. J. Molecular profiling of single neurons of known identity in two ganglia from the crab Cancer borealis. Proceedings of the National Academy of Sciences of the United States of America, 116 (52) (2019): 26980-26990, doi: 10.1073/pnas.1911413116.
    Description: Understanding circuit organization depends on identification of cell types. Recent advances in transcriptional profiling methods have enabled classification of cell types by their gene expression. While exceptionally powerful and high throughput, the ground-truth validation of these methods is difficult: If cell type is unknown, how does one assess whether a given analysis accurately captures neuronal identity? To shed light on the capabilities and limitations of solely using transcriptional profiling for cell-type classification, we performed 2 forms of transcriptional profiling—RNA-seq and quantitative RT-PCR, in single, unambiguously identified neurons from 2 small crustacean neuronal networks: The stomatogastric and cardiac ganglia. We then combined our knowledge of cell type with unbiased clustering analyses and supervised machine learning to determine how accurately functionally defined neuron types can be classified by expression profile alone. The results demonstrate that expression profile is able to capture neuronal identity most accurately when combined with multimodal information that allows for post hoc grouping, so analysis can proceed from a supervised perspective. Solely unsupervised clustering can lead to misidentification and an inability to distinguish between 2 or more cell types. Therefore, this study supports the general utility of cell identification by transcriptional profiling, but adds a caution: It is difficult or impossible to know under what conditions transcriptional profiling alone is capable of assigning cell identity. Only by combining multiple modalities of information such as physiology, morphology, or innervation target can neuronal identity be unambiguously determined.
    Description: We thank members of the D.J.S., H.A.H., and E.M. laboratories for helpful discussions. We thank the Genomic Sequencing and Analysis Facility (The University of Texas [UT] at Austin) for library preparation and sequencing and the bioinformatics consulting team at the UT Austin Center for Computational Biology and Bioinformatics for helpful advice. This work was supported by National Institutes of Health grant R01MH046742-29 (to E.M. and D.J.S.) and the National Institute of General Medical Sciences T32GM008396 (support for A.J.N.) and National Institute of Mental Health grant 5R25MH059472-18 and the Grass Foundation (support for Neural Systems and Behavior Course at the Marine Biological Laboratory).
    Keywords: qPCR ; RNA-seq ; Stomatogastric ; Expression profiling
    Repository Name: Woods Hole Open Access Server
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  • 7
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lebrato, M., Garbe-Schönberg, D., Müller, M. N., Blanco-Ameijeiras, S., Feely, R. A., Lorenzoni, L., Molinero, J. C., Bremer, K., Jones, D. O. B., Iglesias-Rodriguez, D., Greeley, D., Lamare, M. D., Paulmier, A., Graco, M., Cartes, J., Barcelos E Ramos, J., de Lara, A., Sanchez-Leal, R., Jimenez, P., Paparazzo, F. E., Hartman, S. E., Westernströer, U., Küter, M., Benavides, R., da Silva, A. F., Bell, S., Payne, C., Olafsdottir, S., Robinson, K., Jantunen, L. M., Korablev, A., Webster, R. J., Jones, E. M., Gilg, O., Bailly du Bois, P., Beldowski, J., Ashjian, C., Yahia, N. D., Twining, B., Chen, X. G., Tseng, L. C., Hwang, J. S., Dahms, H. U., & Oschlies, A. Global variability in seawater Mg:Ca and Sr:Ca ratios in the modern ocean. Proceedings of the National Academy of Sciences of the United States of America, 117(36), (2020): 22281-22292, doi:10.1073/pnas.1918943117.
    Description: Seawater Mg:Ca and Sr:Ca ratios are biogeochemical parameters reflecting the Earth–ocean–atmosphere dynamic exchange of elements. The ratios’ dependence on the environment and organisms' biology facilitates their application in marine sciences. Here, we present a measured single-laboratory dataset, combined with previous data, to test the assumption of limited seawater Mg:Ca and Sr:Ca variability across marine environments globally. High variability was found in open-ocean upwelling and polar regions, shelves/neritic and river-influenced areas, where seawater Mg:Ca and Sr:Ca ratios range from ∼4.40 to 6.40 mmol:mol and ∼6.95 to 9.80 mmol:mol, respectively. Open-ocean seawater Mg:Ca is semiconservative (∼4.90 to 5.30 mol:mol), while Sr:Ca is more variable and nonconservative (∼7.70 to 8.80 mmol:mol); both ratios are nonconservative in coastal seas. Further, the Ca, Mg, and Sr elemental fluxes are connected to large total alkalinity deviations from International Association for the Physical Sciences of the Oceans (IAPSO) standard values. Because there is significant modern seawater Mg:Ca and Sr:Ca ratios variability across marine environments we cannot absolutely assume that fossil archives using taxa-specific proxies reflect true global seawater chemistry but rather taxa- and process-specific ecosystem variations, reflecting regional conditions. This variability could reconcile secular seawater Mg:Ca and Sr:Ca ratio reconstructions using different taxa and techniques by assuming an error of 1 to 1.50 mol:mol, and 1 to 1.90 mmol:mol, respectively. The modern ratios’ variability is similar to the reconstructed rise over 20 Ma (Neogene Period), nurturing the question of seminonconservative behavior of Ca, Mg, and Sr over modern Earth geological history with an overlooked environmental effect.
    Description: We thank the researchers, staff, students, and volunteers in all the expeditions around the world for their contributions. One anonymous referee and Bernhard Peucker-Ehenbrink, Woods Hole Oceanographic Institution, contributed significantly to the final version of the manuscript. This study was developed under a grant from the Federal Ministry of Education and Research to D.G.-S. under contract 03F0722A, by the Kiel Cluster of Excellence “The Future Ocean” (D1067/87) to A.O. and M.L., and by the “European project on Ocean Acidification” (European Community’s Seventh Framework Programme FP7/2007-2013, grant agreement 211384) to A.O. and M.L. Additional funding was provided from project DOSMARES CTM2010-21810-C03-02, by the UK Natural Environment Research Council, to the National Oceanography Centre. This is Pacific Marine Environmental Laboratory contribution number 5046.
    Keywords: global ; seawater ; Mg:Ca ; Sr:Ca ; biogeochemistry
    Repository Name: Woods Hole Open Access Server
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  • 8
    Publication Date: 2022-10-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Chakraborty, A., Ruff, S. E., Dong, X., Ellefson, E. D., Li, C., Brooks, J. M., McBee, J., Bernard, B. B., & Hubert, C. R. J. Hydrocarbon seepage in the deep seabed links subsurface and seafloor biospheres. Proceedings of the National Academy of Sciences of the United States of America, 117(20), (2020): 11029-11037, doi: 10.1073/pnas.2002289117.
    Description: Marine cold seeps transmit fluids between the subseafloor and seafloor biospheres through upward migration of hydrocarbons that originate in deep sediment layers. It remains unclear how geofluids influence the composition of the seabed microbiome and if they transport deep subsurface life up to the surface. Here we analyzed 172 marine surficial sediments from the deep-water Eastern Gulf of Mexico to assess whether hydrocarbon fluid migration is a mechanism for upward microbial dispersal. While 132 of these sediments contained migrated liquid hydrocarbons, evidence of continuous advective transport of thermogenic alkane gases was observed in 11 sediments. Gas seeps harbored distinct microbial communities featuring bacteria and archaea that are well-known inhabitants of deep biosphere sediments. Specifically, 25 distinct sequence variants within the uncultivated bacterial phyla Atribacteria and Aminicenantes and the archaeal order Thermoprofundales occurred in significantly greater relative sequence abundance along with well-known seep-colonizing members of the bacterial genus Sulfurovum, in the gas-positive sediments. Metabolic predictions guided by metagenome-assembled genomes suggested these organisms are anaerobic heterotrophs capable of nonrespiratory breakdown of organic matter, likely enabling them to inhabit energy-limited deep subseafloor ecosystems. These results point to petroleum geofluids as a vector for the advection-assisted upward dispersal of deep biosphere microbes from subsurface to surface environments, shaping the microbiome of cold seep sediments and providing a general mechanism for the maintenance of microbial diversity in the deep sea.
    Description: We wish to thank Jody Sandel as well as the crew of R/V GeoExplorer for collection of piston cores, onboard core processing, sample preservation, and shipment. Cynthia Kwan and Oliver Horanszky are thanked for assistance with amplicon library preparation. We also wish to thank Jayne Rattray, Daniel Gittins, and Marc Strous for valuable discussions and suggestions, and Rhonda Clark for research support. Collaborations with Andy Mort from the Geological Survey of Canada, and Richard Hatton from Geoscience Wales are also gratefully acknowledged. This work was financially supported by a Mitacs Elevate Postdoctoral Fellowship awarded to A.C.; an Alberta Innovates-Technology Futures/Eyes High Postdoctoral Fellowship to S.E.R.; and a Natural Sciences and Engineering Research Council Strategic Project Grant, a Genome Canada Genomics Applications Partnership Program grant, a Canada Foundation for Innovation grant (CFI-JELF 33752) for instrumentation, and Campus Alberta Innovates Program Chair funding to C.R.J.H.
    Keywords: Deep biosphere ; Microbiome ; Dispersal
    Repository Name: Woods Hole Open Access Server
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  • 9
    Publication Date: 2022-10-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in MBL Hernandez, C. M., van Daalen, S. F., Caswell, H., Neubert, M. G., & Gribble, K. E. A demographic and evolutionary analysis of maternal effect senescence. Proceedings of the National Academy of Sciences of the United States of America, 17(28), (2020):16431-16437, doi: 10.1073/pnas.1919988117.
    Description: Maternal effect senescence—a decline in offspring survival or fertility with maternal age—has been demonstrated in many taxa, including humans. Despite decades of phenotypic studies, questions remain about how maternal effect senescence impacts evolutionary fitness. To understand the influence of maternal effect senescence on population dynamics, fitness, and selection, we developed matrix population models in which individuals are jointly classified by age and maternal age. We fit these models to data from individual-based culture experiments on the aquatic invertebrate, Brachionus manjavacas (Rotifera). By comparing models with and without maternal effects, we found that maternal effect senescence significantly reduces fitness for B. manjavacas and that this decrease arises primarily through reduced fertility, particularly at maternal ages corresponding to peak reproductive output. We also used the models to estimate selection gradients, which measure the strength of selection, in both high growth rate (laboratory) and two simulated low growth rate environments. In all environments, selection gradients on survival and fertility decrease with increasing age. They also decrease with increasing maternal age for late maternal ages, implying that maternal effect senescence can evolve through the same process as in Hamilton’s theory of the evolution of age-related senescence. The models we developed are widely applicable to evaluate the fitness consequences of maternal effect senescence across species with diverse aging and fertility schedule phenotypes.
    Description: K.E.G. was supported by Grant 5K01AG049049 from the National Institute on Aging and by the Bay and Paul Foundations. H.C. and S.F.v.D. were supported by the European Research Council through Advanced Grants 322829 and 788195 and by the Dutch Research Council through Grant ALWOP.2015.100. C.M.H. was supported by a National Science Foundation Graduate Research Fellowship. M.G.N. received funding from The Paul MacDonald Fye Chair for Excellence in Oceanography at the Woods Hole Oceanographic Institution.
    Keywords: Aging ; Demography ; Fitness ; Maternal effects ; Selection gradients
    Repository Name: Woods Hole Open Access Server
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  • 10
    Publication Date: 2022-10-27
    Description: Author Posting. © National Academy of Sciences, 2021. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 118(11), (2021): e2020025118, https://doi.org/10.1073/pnas.2020025118.
    Description: For organisms to have robust locomotion, their neuromuscular organization must adapt to constantly changing environments. In jellyfish, swimming robustness emerges when marginal pacemakers fire action potentials throughout the bell’s motor nerve net, which signals the musculature to contract. The speed of the muscle activation wave is dictated by the passage times of the action potentials. However, passive elastic material properties also influence the emergent kinematics, with time scales independent of neuromuscular organization. In this multimodal study, we examine the interplay between these two time scales during turning. A three-dimensional computational fluid–structure interaction model of a jellyfish was developed to determine the resulting emergent kinematics, using bidirectional muscular activation waves to actuate the bell rim. Activation wave speeds near the material wave speed yielded successful turns, with a 76-fold difference in turning rate between the best and worst performers. Hyperextension of the margin occurred only at activation wave speeds near the material wave speed, suggesting resonance. This hyperextension resulted in a 34-fold asymmetry in the circulation of the vortex ring between the inside and outside of the turn. Experimental recording of the activation speed confirmed that jellyfish actuate within this range, and flow visualization using particle image velocimetry validated the corresponding fluid dynamics of the numerical model. This suggests that neuromechanical wave resonance plays an important role in the robustness of an organism’s locomotory system and presents an undiscovered constraint on the evolution of flexible organisms. Understanding these dynamics is essential for developing actuators in soft body robotics and bioengineered pumps.
    Description: This research was funded by the NSF Division of Mathematical Sciences, under Faculty Early Career Development Program Grant 1151478 (to L.A.M.).
    Description: 2021-09-16
    Keywords: Jellyfish ; Propulsion ; Neuromechanics ; Fluid-structure interaction ; Maneuverability
    Repository Name: Woods Hole Open Access Server
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