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9 results for “seaports”

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zenodo48/100

Data for "Rapid seaward expansion of seaport footprints worldwide"

[updated November 2023]This dataset comprises data and code used in "Rapid seaward expansion of seaport footprints worldwide" (Sengupta & Lazarus, 2023; <a href="https://doi.org/10.1038/s43247-023-01110-y">https://doi.org/10.1038/s43247-023-01110-y</a>).This repository includes three .csv files, one .xlsx file, and a .ipynb file:'Sengupta_Lazarus_REC_1990_2020_v05.csv' – annual time series of seaward expansion (km^2) between 1990–2020 through coastal reclamation for 65 of the world's top 100 container seaports in 2020, as ranked by reported container throughput (<a href="https://lloydslist.maritimeintelligence.informa.com/-/media/lloyds-list/images/top-100-ports-2021/top-100-ports-2021-digital-edition.pdf">Lloyd's List, 2021</a>). Dataset includes Year, Seaport, Country, Region, and Reclaimed area (km^2) [raw measurement]. 'Sengupta_Lazarus_REC_TEU_2011_2020_v03.csv' – annual time series of seaward expansion (km^2) and reported container throughput (millions TEU) between 2011–2020 for 43 of the world's top 100 container seaports in 2020, as ranked by reported container throughput (<a href="https://lloydslist.maritimeintelligence.informa.com/-/media/lloyds-list/images/top-100-ports-2021/top-100-ports-2021-digital-edition.pdf">Lloyd's List, 2021</a>). Dataset includes Year, Seaport, Country, Region, Reclaimed area (km^2) [raw measurement], and TEU (millions), collated from archived Lloyd's List reports.'Sengupta_Lazarus_REC_TEU_totals_v04.csv' – Simplified dataset listing total seaward expansion (km^2) and container throughput in 2020 for 65 of the world's top 100 container seaports in 2020, as ranked by reported container throughput (<a href="https://lloydslist.maritimeintelligence.informa.com/-/media/lloyds-list/images/top-100-ports-2021/top-100-ports-2021-digital-edition.pdf">Lloyd's List, 2021</a>). Dataset includes Seaport, Country, Region, Reclaimed area (km^2) [raw measurement], ranked list of seaports by expansion extent, and TEU (millions) handled in 2020, and Lloyd's List rank in 2020 (<a href="https://lloydslist.maritimeintelligence.informa.com/-/media/lloyds-list/images/top-100-ports-2021/top-100-ports-2021-digital-edition.pdf">Lloyd's List, 2021</a>).'Sengupta_Lazarus_2023_ports_excluded_v2.xlsx' – contains list of 35 ports excluded from thus analysis because they are either not on an open coastline (e.g. estuarine, riverine) or expanded less than 1 km^2 seaward between 1990–2020.'RECLAIM_port_trajectories_v11.ipynb' – Jupyter notebook for data wrangling and plotting figures presented in Sengupta & Lazarus (2023). (Note that this notebook does not produce the map-based figures presented in that work.)The method for calculating reclaimed area over time in Google Earth Engine (GEE) is described in Sengupta et al. (<a href="https://doi.org/10.1029/2022EF002927">2023</a>), and the GEE code is available here: <a href="https://github.com/dhritirajsen/Mapping_Coastal_land_reclamation">https://github.com/dhritirajsen/Seaport_reclamation</a>These data and code are also available here: <a href="https://github.com/edlazarus/Seaports">https://github.com/edlazarus/Seaports</a>

opencc-by-4.0Feb 2023View details →

zenodo36/100

The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves (metazoa data)

This dataset is associated to the following publication: Macé, B., Mouillot, D., Dalongeville, A., Bruno, M., Deter, J., Varenne, A., Gudefin, A., Boissery, P., & Manel, S. (2024). The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves. Molecular Ecology, e17373. <a href="https://doi.org/10.1111/mec.17373">https://doi.org/10.1111/mec.17373</a> It contains the data obtained with the metazoa marker: <ul> <li>fastq files are the raw NGS eDNA sequencing outputs</li> <li>dat file records the adapters names and oligos used for sequencing</li> </ul> Metadata associated to each eDNA sample are also provided.   Methods <blockquote> eDNA extractions were performed in a BSL-2 lab dedicated for eDNA samples following the protocol described in Polanco Fernández et al. (2021). Four PCR amplifications were conducted with different assays covering the whole tree of life. The teleo primer pair (Valentini et al., 2016) targets a 12S mitochondrial DNA marker from teleosts and elasmobranchs; the metazoa primer pair (Kelly et al., 2016) targets a 16S mitochondrial DNA marker from metazoans; the euka2 primer pair (Guardiola et al., 2015) targets a marker from eukaryotes located on the V7 region of the 18S ribosomal RNA; and the bact2 primer pair (Taberlet et al., 2018) targets a marker from prokaryotes located on the V4 region of the 16S ribosomal RNA. The idea of this experimental design is to give a holistic overview of communities, with a nested hierarchy euka2-metazoa-teleo to obtain a finer taxonomic resolution over animal communities, and particularly fish. Twelve PCR replicates per sample were run, with negative extractions and PCR positive and negative controls analyzed in parallel. Unique tags were used for each PCR replicate amplified with the teleo primers only, allowing to differentiate them in the bioinformatic analysis (see after). NGS library preparation and MiSeq paired-end sequencing (2 × 150 bp) were performed at DNA Gensee (Le Bourget-du-Lac, France). </blockquote>   References Guardiola, M., Uriz, M. J., Taberlet, P., Coissac, E., Wangensteen, O. S., & Turon, X. (2015). Deep-Sea, Deep-Sequencing: Metabarcoding Extracellular DNA from Sediments of Marine Canyons. PLOS ONE, 10(10), e0139633. https://doi.org/10.1371/journal.pone.0139633 Kelly, R. P., O’Donnell, J. L., Lowell, N. C., Shelton, A. O., Samhouri, J. F., Hennessey, S. M., Feist, B. E., & Williams, G. D. (2016). Genetic signatures of ecological diversity along an urbanization gradient. PeerJ, 4, e2444. https://doi.org/10.7717/peerj.2444 Polanco Fernández, A., Marques, V., Fopp, F., Juhel, J.-B., Borrero-Pérez, G. H., Cheutin, M.-C., Dejean, T., González Corredor, J. D., Acosta-Chaparro, A., Hocdé, R., Eme, D., Maire, E., Spescha, M., Valentini, A., Manel, S., Mouillot, D., Albouy, C., & Pellissier, L. (2021). Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes. Environmental DNA, 3(1), 142–156. https://doi.org/10.1002/edn3.140 Taberlet, P., Bonin, A., Zinger, L., & Coissac, E. (2018). Environmental DNA: For Biodiversity Research and Monitoring. Oxford University Press. Valentini, A., Taberlet, P., Miaud, C., Civade, R., Herder, J., Thomsen, P. F., Bellemain, E., Besnard, A., Coissac, E., Boyer, F., Gaboriaud, C., Jean, P., Poulet, N., Roset, N., Copp, G. H., Geniez, P., Pont, D., Argillier, C., Baudoin, J.-M., … Dejean, T. (2016). Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology, 25(4), 929–942. https://doi.org/10.1111/mec.13428

opencc-by-nc-4.0Mar 2024View details →

zenodo36/100

The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves (bact2 data)

This dataset is associated to the following publication: Macé, B., Mouillot, D., Dalongeville, A., Bruno, M., Deter, J., Varenne, A., Gudefin, A., Boissery, P., & Manel, S. (2024). The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves. Molecular Ecology, e17373. <a href="https://doi.org/10.1111/mec.17373">https://doi.org/10.1111/mec.17373</a> It contains the data obtained with the bact2 marker: <ul> <li>fastq files are the raw NGS eDNA sequencing outputs</li> <li>dat file records the adapters names and oligos used for sequencing</li> </ul> Metadata associated to each eDNA sample are also provided.   Methods <blockquote> eDNA extractions were performed in a BSL-2 lab dedicated for eDNA samples following the protocol described in Polanco Fernández et al. (2021). Four PCR amplifications were conducted with different assays covering the whole tree of life. The teleo primer pair (Valentini et al., 2016) targets a 12S mitochondrial DNA marker from teleosts and elasmobranchs; the metazoa primer pair (Kelly et al., 2016) targets a 16S mitochondrial DNA marker from metazoans; the euka2 primer pair (Guardiola et al., 2015) targets a marker from eukaryotes located on the V7 region of the 18S ribosomal RNA; and the bact2 primer pair (Taberlet et al., 2018) targets a marker from prokaryotes located on the V4 region of the 16S ribosomal RNA. The idea of this experimental design is to give a holistic overview of communities, with a nested hierarchy euka2-metazoa-teleo to obtain a finer taxonomic resolution over animal communities, and particularly fish. Twelve PCR replicates per sample were run, with negative extractions and PCR positive and negative controls analyzed in parallel. Unique tags were used for each PCR replicate amplified with the teleo primers only, allowing to differentiate them in the bioinformatic analysis (see after). NGS library preparation and MiSeq paired-end sequencing (2 × 150 bp) were performed at DNA Gensee (Le Bourget-du-Lac, France). </blockquote>   References Guardiola, M., Uriz, M. J., Taberlet, P., Coissac, E., Wangensteen, O. S., & Turon, X. (2015). Deep-Sea, Deep-Sequencing: Metabarcoding Extracellular DNA from Sediments of Marine Canyons. PLOS ONE, 10(10), e0139633. https://doi.org/10.1371/journal.pone.0139633 Kelly, R. P., O’Donnell, J. L., Lowell, N. C., Shelton, A. O., Samhouri, J. F., Hennessey, S. M., Feist, B. E., & Williams, G. D. (2016). Genetic signatures of ecological diversity along an urbanization gradient. PeerJ, 4, e2444. https://doi.org/10.7717/peerj.2444 Polanco Fernández, A., Marques, V., Fopp, F., Juhel, J.-B., Borrero-Pérez, G. H., Cheutin, M.-C., Dejean, T., González Corredor, J. D., Acosta-Chaparro, A., Hocdé, R., Eme, D., Maire, E., Spescha, M., Valentini, A., Manel, S., Mouillot, D., Albouy, C., & Pellissier, L. (2021). Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes. Environmental DNA, 3(1), 142–156. https://doi.org/10.1002/edn3.140 Taberlet, P., Bonin, A., Zinger, L., & Coissac, E. (2018). Environmental DNA: For Biodiversity Research and Monitoring. Oxford University Press. Valentini, A., Taberlet, P., Miaud, C., Civade, R., Herder, J., Thomsen, P. F., Bellemain, E., Besnard, A., Coissac, E., Boyer, F., Gaboriaud, C., Jean, P., Poulet, N., Roset, N., Copp, G. H., Geniez, P., Pont, D., Argillier, C., Baudoin, J.-M., … Dejean, T. (2016). Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology, 25(4), 929–942. https://doi.org/10.1111/mec.13428

opencc-by-nc-4.0Mar 2024View details →

zenodo36/100

The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves (euka2 data)

This dataset is associated to the following publication: Macé, B., Mouillot, D., Dalongeville, A., Bruno, M., Deter, J., Varenne, A., Gudefin, A., Boissery, P., & Manel, S. (2024). The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves. Molecular Ecology, e17373. <a href="https://doi.org/10.1111/mec.17373">https://doi.org/10.1111/mec.17373</a> It contains the data obtained with the euka2 marker: <ul> <li>fastq files are the raw NGS eDNA sequencing outputs</li> <li>dat file records the adapters names and oligos used for sequencing</li> </ul> Metadata associated to each eDNA sample are also provided.   Methods <blockquote> eDNA extractions were performed in a BSL-2 lab dedicated for eDNA samples following the protocol described in Polanco Fernández et al. (2021). Four PCR amplifications were conducted with different assays covering the whole tree of life. The teleo primer pair (Valentini et al., 2016) targets a 12S mitochondrial DNA marker from teleosts and elasmobranchs; the metazoa primer pair (Kelly et al., 2016) targets a 16S mitochondrial DNA marker from metazoans; the euka2 primer pair (Guardiola et al., 2015) targets a marker from eukaryotes located on the V7 region of the 18S ribosomal RNA; and the bact2 primer pair (Taberlet et al., 2018) targets a marker from prokaryotes located on the V4 region of the 16S ribosomal RNA. The idea of this experimental design is to give a holistic overview of communities, with a nested hierarchy euka2-metazoa-teleo to obtain a finer taxonomic resolution over animal communities, and particularly fish. Twelve PCR replicates per sample were run, with negative extractions and PCR positive and negative controls analyzed in parallel. Unique tags were used for each PCR replicate amplified with the teleo primers only, allowing to differentiate them in the bioinformatic analysis (see after). NGS library preparation and MiSeq paired-end sequencing (2 × 150 bp) were performed at DNA Gensee (Le Bourget-du-Lac, France). </blockquote>   References Guardiola, M., Uriz, M. J., Taberlet, P., Coissac, E., Wangensteen, O. S., & Turon, X. (2015). Deep-Sea, Deep-Sequencing: Metabarcoding Extracellular DNA from Sediments of Marine Canyons. PLOS ONE, 10(10), e0139633. https://doi.org/10.1371/journal.pone.0139633 Kelly, R. P., O’Donnell, J. L., Lowell, N. C., Shelton, A. O., Samhouri, J. F., Hennessey, S. M., Feist, B. E., & Williams, G. D. (2016). Genetic signatures of ecological diversity along an urbanization gradient. PeerJ, 4, e2444. https://doi.org/10.7717/peerj.2444 Polanco Fernández, A., Marques, V., Fopp, F., Juhel, J.-B., Borrero-Pérez, G. H., Cheutin, M.-C., Dejean, T., González Corredor, J. D., Acosta-Chaparro, A., Hocdé, R., Eme, D., Maire, E., Spescha, M., Valentini, A., Manel, S., Mouillot, D., Albouy, C., & Pellissier, L. (2021). Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes. Environmental DNA, 3(1), 142–156. https://doi.org/10.1002/edn3.140 Taberlet, P., Bonin, A., Zinger, L., & Coissac, E. (2018). Environmental DNA: For Biodiversity Research and Monitoring. Oxford University Press. Valentini, A., Taberlet, P., Miaud, C., Civade, R., Herder, J., Thomsen, P. F., Bellemain, E., Besnard, A., Coissac, E., Boyer, F., Gaboriaud, C., Jean, P., Poulet, N., Roset, N., Copp, G. H., Geniez, P., Pont, D., Argillier, C., Baudoin, J.-M., … Dejean, T. (2016). Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology, 25(4), 929–942. https://doi.org/10.1111/mec.13428

opencc-by-nc-4.0Mar 2024View details →

zenodo36/100

The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves (teleo data)

This dataset is associated to the following publication: Macé, B., Mouillot, D., Dalongeville, A., Bruno, M., Deter, J., Varenne, A., Gudefin, A., Boissery, P., & Manel, S. (2024). The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves. Molecular Ecology, e17373. <a href="https://doi.org/10.1111/mec.17373">https://doi.org/10.1111/mec.17373</a> It contains the data obtained with the teleo marker: <ul> <li>fastq files are the raw NGS eDNA sequencing outputs</li> <li>dat file records the adapters names and oligos used for sequencing</li> </ul> Metadata associated to each eDNA sample are also provided.   Methods <blockquote> eDNA extractions were performed in a BSL-2 lab dedicated for eDNA samples following the protocol described in Polanco Fernández et al. (2021). Four PCR amplifications were conducted with different assays covering the whole tree of life. The teleo primer pair (Valentini et al., 2016) targets a 12S mitochondrial DNA marker from teleosts and elasmobranchs; the metazoa primer pair (Kelly et al., 2016) targets a 16S mitochondrial DNA marker from metazoans; the euka2 primer pair (Guardiola et al., 2015) targets a marker from eukaryotes located on the V7 region of the 18S ribosomal RNA; and the bact2 primer pair (Taberlet et al., 2018) targets a marker from prokaryotes located on the V4 region of the 16S ribosomal RNA. The idea of this experimental design is to give a holistic overview of communities, with a nested hierarchy euka2-metazoa-teleo to obtain a finer taxonomic resolution over animal communities, and particularly fish. Twelve PCR replicates per sample were run, with negative extractions and PCR positive and negative controls analyzed in parallel. Unique tags were used for each PCR replicate amplified with the teleo primers only, allowing to differentiate them in the bioinformatic analysis (see after). NGS library preparation and MiSeq paired-end sequencing (2 × 150 bp) were performed at DNA Gensee (Le Bourget-du-Lac, France). </blockquote>   References Guardiola, M., Uriz, M. J., Taberlet, P., Coissac, E., Wangensteen, O. S., & Turon, X. (2015). Deep-Sea, Deep-Sequencing: Metabarcoding Extracellular DNA from Sediments of Marine Canyons. PLOS ONE, 10(10), e0139633. https://doi.org/10.1371/journal.pone.0139633 Kelly, R. P., O’Donnell, J. L., Lowell, N. C., Shelton, A. O., Samhouri, J. F., Hennessey, S. M., Feist, B. E., & Williams, G. D. (2016). Genetic signatures of ecological diversity along an urbanization gradient. PeerJ, 4, e2444. https://doi.org/10.7717/peerj.2444 Polanco Fernández, A., Marques, V., Fopp, F., Juhel, J.-B., Borrero-Pérez, G. H., Cheutin, M.-C., Dejean, T., González Corredor, J. D., Acosta-Chaparro, A., Hocdé, R., Eme, D., Maire, E., Spescha, M., Valentini, A., Manel, S., Mouillot, D., Albouy, C., & Pellissier, L. (2021). Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes. Environmental DNA, 3(1), 142–156. https://doi.org/10.1002/edn3.140 Taberlet, P., Bonin, A., Zinger, L., & Coissac, E. (2018). Environmental DNA: For Biodiversity Research and Monitoring. Oxford University Press. Valentini, A., Taberlet, P., Miaud, C., Civade, R., Herder, J., Thomsen, P. F., Bellemain, E., Besnard, A., Coissac, E., Boyer, F., Gaboriaud, C., Jean, P., Poulet, N., Roset, N., Copp, G. H., Geniez, P., Pont, D., Argillier, C., Baudoin, J.-M., … Dejean, T. (2016). Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology, 25(4), 929–942. https://doi.org/10.1111/mec.13428

opencc-by-nc-4.0Mar 2024View details →

zenodo32/100

Distribution. Originally distributed throughout the Indo-Malayan Region and S China, including Taiwan, Hainan, and Sri Lanka (only original range shaded in the map). Possible human-mediate introduced range in Maldives, islands of Malaysia, Indonesia, Brunei, Philippines, Japan (Kyushu and Ryukyu Is), Guam, Palau, and New Guinea. Introduced in historical times into East Africa (Egypt, Sudan, Eritrea, Djibouti, Kenya, Rwanda, and Tanzania), Pemba and Zanzibar (Unguja) Is, Madagascar, Comoro Is, Mauritius, Réunion I, and into coastal Arabia (in the vicinity of seaports in Iraq, Kuwait, Bahrain, Saudi Arabia, Yemen, and Oman). in Soricidae

Distribution. Originally distributed throughout the Indo-Malayan Region and S China, including Taiwan, Hainan, and Sri Lanka (only original range shaded in the map). Possible human-mediate introduced range in Maldives, islands of Malaysia, Indonesia, Brunei, Philippines, Japan (Kyushu and Ryukyu Is), Guam, Palau, and New Guinea. Introduced in historical times into East Africa (Egypt, Sudan, Eritrea, Djibouti, Kenya, Rwanda, and Tanzania), Pemba and Zanzibar (Unguja) Is, Madagascar, Comoro Is, Mauritius, Réunion I, and into coastal Arabia (in the vicinity of seaports in Iraq, Kuwait, Bahrain, Saudi Arabia, Yemen, and Oman).

opennotspecifiedJul 2018View details →

dryad32/100

Data from: Common bottlenose dolphin (Tursiops truncatus) behavior in an active narrow seaport

Open the record for dataset details and reuse information.

publicFeb 2019View details →

zenodo24/100

Seaport Shipwreck Futtock

In May 2016, construction crews excavating the foundations at the building site of 121 Seaport Boulevard discovered the hull of a large ship preserved in the clay of the former South Boston Flats. This model represents one of the futtocks of the 19th-century schooner, which was transporting lime. Photogrammetry by Joe Bagley and Nadia Kline. For more information, please visit: https://www.boston.gov/departments/archaeology/seaport-shipwreck Source: Objaverse 1.0 / Sketchfab

opencc-byJan 2020View details →

ClinicalTrials.gov24/100

The SEAPORT 1 Study: Evaluation of the Safety and Tolerability of INZ-701 in Adults With End-Stage Kidney Disease Undergoing Hemodialysis

ClinicalTrials.gov study NCT06283589. IPD Sharing: Not stated. Countries: 1. Publications: 0.

restrictedIPD-UNDECIDEDFeb 2026View details →

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Allen Brain Atlas

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Last verified 2026-04-30Open record

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dandi-nwb

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Last verified 2026-04-30Open record

International Brain Laboratory public data

The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.

ibl

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Last verified 2026-04-29Open record

OpenNeuro

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Last verified 2026-04-29Open record