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  • 1
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    Quantifying the parameter dependent basin of the unsafe regime of asymmetric Lévy-noise-induced critical transitions (2021)
    In:  Applied Mathematics and Mechanics
    Details
    Publication Date: 2022-03-21
    Description: In real systems, the unpredictable jump changes of the random environment can induce the critical transitions (CTs) between two non-adjacent states, which are more catastrophic. Taking an asymmetric Lévy-noise-induced tri-stable model with desirable, sub-desirable, and undesirable states as a prototype class of real systems, a prediction of the noise-induced CTs from the desirable state directly to the undesirable one is carried out. We first calculate the region that the current state of the given model is absorbed into the undesirable state based on the escape probability, which is named as the absorbed region. Then, a new concept of the parameter dependent basin of the unsafe regime (PDBUR) under the asymmetric Lévy noise is introduced. It is an efficient tool for approximately quantifying the ranges of the parameters, where the noise-induced CTs from the desirable state directly to the undesirable one may occur. More importantly, it may provide theoretical guidance for us to adopt some measures to avert a noise-induced catastrophic CT.
    Type: info:eu-repo/semantics/article
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  • 2
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    Suppression of noise-induced critical transitions: a linear augmentation method (2021)
    In:  European Physical Journal - Special Topics
    Details
    Publication Date: 2022-03-21
    Description: In stochastic complex systems, some sudden critical transitions (CTs) from one desirable state to another contrasting one can take place because of noise, which may even lead to catastrophic consequences. To keep a certain system in one desirable state of performance, methods that suppress these catastrophic CTs in the presence of noise need to be developed. In this paper, the ability of an external linear augmentation method to suppress Gaussian white noise-induced CTs away from a desirable state is investigated from a new perspective. This control is designed in such a way that, as a noise-induced CT is impending, the desirable state of performance in a stochastic complex system can be stabilized using a specific type of coupling with a linear dynamical system. Then, the contrasting state is annihilated with increasing coupling strength. Taking a bi-stable system with one CT (from the desirable state to the undesirable one) and a tri-stable system with two CTs (from the desirable state to the sub-desirable one and from the sub-desirable state to the undesirable one) as the prototype class of real complex systems, the potential of our technique is demonstrated.
    Language: English
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  • 3
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    Role of C4 carbon fixation in Ulva prolifera, the macroalga responsible for the world's largest green tides (2020)
    Nature Research
    Details
    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 Liu, D., Ma, Q., Valiela, I., Anderson, D. M., Keesing, J. K., Gao, K., Zhen, Y., Sun, X., & Wang, Y. Role of C4 carbon fixation in Ulva prolifera, the macroalga responsible for the world's largest green tides. Communications Biology, 3(1), (2020): 494, doi:10.1038/s42003-020-01225-4.
    Description: Most marine algae preferentially assimilate CO2 via the Calvin-Benson Cycle (C3) and catalyze HCO3− dehydration via carbonic anhydrase (CA) as a CO2-compensatory mechanism, but certain species utilize the Hatch-Slack Cycle (C4) to enhance photosynthesis. The occurrence and importance of the C4 pathway remains uncertain, however. Here, we demonstrate that carbon fixation in Ulva prolifera, a species responsible for massive green tides, involves a combination of C3 and C4 pathways, and a CA-supported HCO3− mechanism. Analysis of CA and key C3 and C4 enzymes, and subsequent analysis of δ13C photosynthetic products showed that the species assimilates CO2 predominately via the C3 pathway, uses HCO3− via the CA mechanism at low CO2 levels, and takes advantage of high irradiance using the C4 pathway. This active and multi-faceted carbon acquisition strategy is advantageous for the formation of massive blooms, as thick floating mats are subject to intense surface irradiance and CO2 limitation.
    Description: This work was supported by the State Key Project of Research and Development Plan, Ministry of Science and Technology of the Peopleʼs Republic of China (2016YFC1402106). Support for D.M.A. provided by the Woods Hole Oceanographic Institution—Ocean University of China Cooperative Research Initiative. We thank Dr. Juntian Xu, Jing Ma, Ying Li, and Chenglong Ji for assisting culture experiments and sample analysis.
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  • 4
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    A draft genome sequence of the elusive giant squid, Architeuthis dux (2020)
    Oxford University Press
    Details
    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 da Fonseca, R. R., Couto, A., Machado, A. M., Brejova, B., Albertin, C. B., Silva, F., Gardner, P., Baril, T., Hayward, A., Campos, A., Ribeiro, A. M., Barrio-Hernandez, I., Hoving, H. J., Tafur-Jimenez, R., Chu, C., Frazao, B., Petersen, B., Penaloza, F., Musacchia, F., Alexander, G. C., Osorio, H., Winkelmann, I., Simakov, O., Rasmussen, S., Rahman, M. Z., Pisani, D., Vinther, J., Jarvis, E., Zhang, G., Strugnell, J. M., Castro, L. F. C., Fedrigo, O., Patricio, M., Li, Q., Rocha, S., Antunes, A., Wu, Y., Ma, B., Sanges, R., Vinar, T., Blagoev, B., Sicheritz-Ponten, T., Nielsen, R., & Gilbert, M. T. P. A draft genome sequence of the elusive giant squid, Architeuthis dux. Gigascience, 9(1), (2020): giz152. doi: 10.1093/gigascience/giz152.
    Description: Background: The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea–dwelling species will allow several pending evolutionary questions to be unlocked. Findings: We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. Conclusions: This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.
    Description: R.R.F. thanks the Villum Fonden for grant VKR023446 (Villum Fonden Young Investigator Grant), the Portuguese Science Foundation (FCT) for grant PTDC/MAR/115347/2009; COMPETE-FCOMP-01-012; FEDER-015453, Marie Curie Actions (FP7-PEOPLE-2010-IEF, Proposal 272927), and the Danish National Research Foundation (DNRF96) for its funding of the Center for Macroecology, Evolution, and Climate. H.O. thanks the Rede Nacional de Espectrometria de Massa, ROTEIRO/0028/2013, ref. LISBOA-01-0145-FEDER-022125, supported by COMPETE and North Portugal Regional Operational Programme (Norte2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). A.C. thanks FCT for project UID/Multi/04423/2019. M.P. acknowledges the support from the Wellcome Trust (grant number WT108749/Z/15/Z) and the European Molecular Biology Laboratory. M.P.T.G. thanks the Danish National Research Foundation for its funding of the Center for GeoGenetics (grant DNRF94) and Lundbeck Foundation for grant R52–5062 on Pathogen Palaeogenomics. S.R. was supported by the Novo Nordisk Foundation grant NNF14CC0001. A.H. is supported by a Biotechnology and Biological Sciences Research Council David Phillips Fellowship (fellowship reference: BB/N020146/1). T.B. is supported by the Biotechnology and Biological Sciences Research Council-funded South West Biosciences Doctoral Training Partnership (training grant reference BB/M009122/1). This work was partially funded by the Lundbeck Foundation (R52-A4895 to B.B.). H.J.T.H. was supported by the David and Lucile Packard Foundation, the Netherlands Organization for Scientific Research (#825.09.016), and currently by the Deutsche Forschungsgemeinschaft (DFG) under grant HO 5569/2-1 (Emmy Noether Junior Research Group). T.V. and B. Brejova were supported by grants from the Slovak grant agency VEGA (1/0684/16, 1/0458/18). F.S. was supported by a PhD grant (SFRH/BD/126560/2016) from FCT. A.A. was partly supported by the FCT project PTDC/CTA-AMB/31774/2017. C.C. and Y.W. are partly supported by grant IIS-1526415 from the US National Science Foundation. Computation for the work described in this article was partially supported by the DeiC National Life Science Supercomputer at DTU.
    Keywords: Cephalopod ; Invertebrate ; Genome assembly
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Silica-rich vein formation in an evolving stress field, Atlantis Bank Oceanic Core Complex (2020)
    American Geophysical Union
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ma, Q., Dick, H. J. B., Urann, B., & Zhou, H. Silica-rich vein formation in an evolving stress field, Atlantis Bank Oceanic Core Complex. Geochemistry Geophysics Geosystems, 21(7), (2020): e2019GC008795, doi:10.1029/2019GC008795.
    Description: Drilling 809‐m Hole U1473A in the gabbro batholith at the Atlantis Bank Oceanic Core Complex (OCC) found two felsic vein generations: late magmatic fractionates, rich in deuteric water, hosted by oxide gabbros, and anatectic veins associated with dike intrusion and introduction of seawater‐derived volatiles. Microtextures show a change from compressional to tensional stress during vein formation. Temperatures and oxidation state were obtained from amphibole‐plagioclase and oxide pairs in the adjacent gabbros. Type I veins generally have reverse shear‐sense, with restricted ΔFMQ, high Mt/Ilm ratios, and low‐amphibole Cl/F indicating deuteric fluids. They formed during percolation and fractionation of Fe‐Ti‐rich melts into the primary olivine gabbro. Type II veins are usually hosted by olivine gabbro, occur at dike contacts and the margins of normal‐sense shear zones. They are undeformed or weakly deformed, with highly variable ΔFMQ, low Mt/Ilm ratios, and high‐amphibole Cl/F, indicating seawater‐derived fluids. The detachment fault on which the gabbro massif was emplaced rooted near the base of the dike‐gabbro transition beneath the rift valley. The ingress of seawater volatiles began at 〉800°C and penetrated at least ~590 m into the lower crust during extensional faulting in the rift valley and adjacent rift mountains. The sequence of the felsic vein formation likely reflects asymmetric diapiric flow, with a reversal of the stress regime, and a transition from juvenile to seawater‐derived volatiles. This, in turn, is consistent with fault capture leading to the large asymmetries in spreading rates during OCC formations and heat flow beneath the rift mountains.
    Description: This study was supported by the Chinese National Key Basic Research Program (Grant 2012CB417300). H. Dick and B. Urann were supported by U.S. National Science Foundation (Grant OCE‐MG&G 8371300). Emmanuel Codillo provided numerous useful comments and moral support. We thank N. Chatterjee for assistance in analyzing major element mineral composition in the MIT Electron Microprobe Laboratory. The great contributions of 360 Scientific Party for their initial shipboard description and interpretations of the Hole U1473A cores made this work possible. Special thanks go to C. J. MacLeod, Expedition cochief scientist, and Peter Blum, staff scientist, Stephen Midgley, IODP operations superintendent, and Siem Offshore James Samuel McLelland, offshore installation manager, ship's master Terry Skinner, and the crew and drillers on the JOIDES Resolution.
    Keywords: Felsic veins ; Magma chambers ; Ocean ridge ; Geothermometry ; Flourine‐chlorine ; Dynamics
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  • 6
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    Pathways, volume transport, and seasonal variability of the lower deep limb of the Pacific Meridional Overturning Circulation at the Yap-Mariana Junction (2021)
    Frontiers Media
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wang, J., Wang, F., Lu, Y., Ma, Q., Pratt, L. J., & Zhang, Z. Pathways, volume transport, and seasonal variability of the lower deep limb of the Pacific Meridional Overturning Circulation at the Yap-Mariana Junction. Frontiers in Marine Science, 8, (2021): 672199, https://doi.org/10.3389/fmars.2021.672199.
    Description: The lower deep branch of the Pacific Meridional Overturning Circulation (L-PMOC) is responsible for the deep-water transport from Antarctic to the North Pacific and is a key ingredient in the regulation of global climate through its influence on the storage and residence time of heat and carbon. At the Pacific Yap-Mariana Junction (YMJ), a major gateway for deep-water flowing into the Western Pacific Ocean, we deployed five moorings from 2018 to 2019 in the Eastern, Southern, and Northern Channels in order to explore the pathways and variability of L-PMOC. We have identified three main patterns for L-PMOC pathways. In Pattern 1, the L-PMOC intrudes into the YMJ from the East Mariana Basin (EMB) through the Eastern Channel and then flows northward into the West Mariana Basin (WMB) through the Northern Channel and southward into the West Caroline Basin (WCB) through the Southern Channel. In Pattern 2, the L-PMOC intrudes into the YMJ from both the WCB and the EMB and then flows into the WMB. In Pattern 3, the L-PMOC comes from the WCB and then flows into the EMB and WMB. The volume transports of L-PMOC through the Eastern, Southern, and Northern Channels all exhibit seasonality. During November–April (May–October), the flow pathway conforms to Pattern 1 (Patterns 2 and 3), and the mean and standard deviation of L-PMOC transports are −4.44 ± 1.26 (−0.30 ± 1.47), −0.96 ± 1.13 (1.75 ± 1.49), and 1.49 ± 1.31 (1.07 ± 1.10) Sv in the Eastern, Southern, and Northern Channels, respectively. Further analysis of numerical ocean modeling results demonstrates that L-PMOC transport at the YMJ is forced by a deep pressure gradient between two adjacent basins, which is mainly determined by the sea surface height (SSH) and water masses in the upper 2,000-m layer. The seasonal variability of L-PMOC transport is attributed to local Ekman pumping and westward-propagating Rossby waves. The L-PMOC transport greater than 3,500 m is closely linked to the wind forcing and the upper ocean processes.
    Description: This study was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (grant XDA22000000), the National Natural Science Foundation of China (grants 91958204 and 41776022), the Key Research Program of Frontier Sciences, CAS (grant QYZDB-SSW-SYS034), and the International Partnership Program of CAS (grant 133137KYSB20180056). FW thanks the support from the National Natural Science Foundation of China (grants 41730534 and 41421005). QM thanks the support by the National Natural Science Foundation of China (grant 42006003).
    Keywords: PMOC ; Mooring observations ; Seasonal variability ; Pathways ; Transport ; Yap-Mariana Junction ; Ekman pumping ; Rossby waves
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  • 7
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    Dynamic accretion beneath a slow-spreading ridge segment: IODP hole 1473A and the Atlantis Bank oceanic core complex (2020)
    American Geophysical Union
    Details
    Publication Date: 2022-10-26
    Description: Author Posting. © American Geophysical Union, 2019. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research-Solid Earth 124(12), (2019): 12631-12659, doi:10.1029/2018JB016858.
    Description: 809 deep IODP Hole U1473A at Atlantis Bank, SWIR, is 2.2 km from 1,508‐m Hole 735B and 1.4 from 158‐m Hole 1105A. With mapping, it provides the first 3‐D view of the upper levels of a 660‐km2 lower crustal batholith. It is laterally and vertically zoned, representing a complex interplay of cyclic intrusion, and ongoing deformation, with kilometer‐scale upward and lateral migration of interstial melt. Transform wall dives over the gabbro‐peridotite contact found only evolved gabbro intruded directly into the mantle near the transform. There was no high‐level melt lens, rather the gabbros crystallized at depth, and then emplaced into the zone of diking by diapiric rise of a crystal mush followed by crystal‐plastic deformation and faulting. The residues to mass balance the crust to a parent melt composition lie at depth below the center of the massif—likely near the crust‐mantle boundary. Thus, basalts erupted to the seafloor from 〉1,550 mbsf. By contrast, the Mid‐Atlantic Ridge lower crust drilled at 23°N and at Atlantis Massif experienced little high‐temperature deformation and limited late‐stage melt transport. They contain primitive cumulates and represent direct intrusion, storage, and crystallization of parental MORB in thinner crust below the dike‐gabbro transition. The strong asymmetric spreading of the SWIR to the south was due to fault capture, with the northern rift valley wall faults cutoff by a detachment fault that extended across most of the zone of intrusion. This caused rapid migration of the plate boundary to the north, while the large majority of the lower crust to spread south unroofing Atlantis Bank and uplifting it into the rift mountains.
    Description: The first author wishes to also recognize grants OCE1434452 and OCE1637130 from The National Science Foundation (NSF) for synthesis of the Atlantis Bank site survey data and post‐cruise rock analysis and for analysis of Expedition 360 and 362T cores and data. Additional support was also gratefully received from The Investment in Science Fund at WHOI.
    Description: 2020-05-07
    Keywords: Lower ocean crust ; Crustal accretion ; SW Indian Ridge ; Crust‐mantle boundary ; Ocean core complex ; Ocean drilling
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  • 8
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    Towards an end-to-end analysis and prediction system for weather, climate, and marine applications in the Red Sea (2021)
    American Meteorological Society
    Details
    Publication Date: 2022-05-27
    Description: Author Posting. © American Meteorological Society, 2021. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Bulletin of the American Meteorological Society 102(1), (2021): E99-E122, https://doi.org/10.1175/BAMS-D-19-0005.1.
    Description: The Red Sea, home to the second-longest coral reef system in the world, is a vital resource for the Kingdom of Saudi Arabia. The Red Sea provides 90% of the Kingdom’s potable water by desalinization, supporting tourism, shipping, aquaculture, and fishing industries, which together contribute about 10%–20% of the country’s GDP. All these activities, and those elsewhere in the Red Sea region, critically depend on oceanic and atmospheric conditions. At a time of mega-development projects along the Red Sea coast, and global warming, authorities are working on optimizing the harnessing of environmental resources, including renewable energy and rainwater harvesting. All these require high-resolution weather and climate information. Toward this end, we have undertaken a multipronged research and development activity in which we are developing an integrated data-driven regional coupled modeling system. The telescopically nested components include 5-km- to 600-m-resolution atmospheric models to address weather and climate challenges, 4-km- to 50-m-resolution ocean models with regional and coastal configurations to simulate and predict the general and mesoscale circulation, 4-km- to 100-m-resolution ecosystem models to simulate the biogeochemistry, and 1-km- to 50-m-resolution wave models. In addition, a complementary probabilistic transport modeling system predicts dispersion of contaminant plumes, oil spill, and marine ecosystem connectivity. Advanced ensemble data assimilation capabilities have also been implemented for accurate forecasting. Resulting achievements include significant advancement in our understanding of the regional circulation and its connection to the global climate, development, and validation of long-term Red Sea regional atmospheric–oceanic–wave reanalyses and forecasting capacities. These products are being extensively used by academia, government, and industry in various weather and marine studies and operations, environmental policies, renewable energy applications, impact assessment, flood forecasting, and more.
    Description: The development of the Red Sea modeling system is being supported by the Virtual Red Sea Initiative and the Competitive Research Grants (CRG) program from the Office of Sponsored Research at KAUST, Saudi Aramco Company through the Saudi ARAMCO Marine Environmental Center at KAUST, and by funds from KAEC, NEOM, and RSP through Beacon Development Company at KAUST.
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  • 9
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    16S V4 rRNA gene tag sequences from reef seawater samples collected in the Florida Keys and the U.S. Virgin Islands in 2019-2020 (2021)
    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Details
    Publication Date: 2022-05-27
    Description: Dataset: 16S V4 rRNA gene tag sequences from reef seawater
    Description: This dataset describes 16S V4 rRNA gene tag sequences from reef seawater. Samples were collected from three reefs in U.S. Virgin Islands and three reefs in Florida Reef tract. Sequence data can be found in the NCBI SRA database under the bioproject PRJNA733652. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/858459
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1938147
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  • 10
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    Reassessing evidence of Moon–Earth dynamics from tidal bundles at 3.2 Ga (Moodies Group, Barberton Greenstone Belt, South Africa) (2022)
    Details
    Publication Date: 2022-10-04
    Description: Past orbital parameters of the Moon are difficult to reconstruct from geological records because relevant data sets of tidal strata are scarce or incomplete. The sole Archean data point is from the Moodies Group (ca 3.22 Ga) of the Barberton Greenstone Belt, South Africa. From the time‐series analysis of tidal bundles from a well‐exposed subaqueous sand wave of this unit, Eriksson and Simpson (Geology, 28, 831) suggested that the Moon’s anomalistic month at 3.2 Ga was closer to 20 days than the present 27.5 days. This is in apparent accordance with models of orbital mechanics which place the Archean Moon in a closer orbit with a shorter period, resulting in stronger tidal action. Although this study’s detailed geological mapping and section measuring of the site confirmed that the sandstone bed in question is likely a migrating dune, the presence of angular mud clasts, channel‐margin slumps, laterally aggrading channel fills and bidirectional paleocurrents in overlying and underlying beds suggests that this bedform was likely located in a nearshore channel near lower‐intertidal flats and subtidal estuarine bars; it thus carries risk of incomplete preservation. Repeated measurements of foreset thicknesses along the published traverse, measured perpendicular to bedding, failed to show consistent spectral peaks. Larger data sets acquired along traverses measured parallel to bedding along the 20.5 m wide exposure are affected by minor faulting, uneven outcrop weathering, changing illumination, weather, observer bias and show a low reproducibility. The most robust measurements herein confirm the periodicity peak of approximately 14 in the original data of Eriksson and Simpson (Geology, 28, 831). Because laminae may have been eroded, the measurements may represent a lower bound of about 28 lunar days per synodic month. This estimate agrees well with Earth–Moon dynamic models which consider the conservation of angular momentum and place the Archaean Moon in a lower orbit around a faster‐spinning Earth.
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:551.3 ; ddc:556
    Language: English
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