Find research datasets worth reusing

opencc-by-4.0Nov 2020View details →

Monthly SPEI dataset at 3-, 6-, and 12-month time scales in the Amazon River Basin

SPEI datasets derived from the Global SPEI database webpage and developed by Vicente-Serrano et al. (2010). This product is disseminated by the Spanish National Research Council (CSIC) for the period from January 1901 to December 2018 (118 years, version 2.6). The SPEI datasets at 3-, 6-, and 12-month time scales are gridded over a 0.50-degree grid on the Amazon River Basin. A total of 1416 GeoTIFF files in Geographic Tagged Image File Format (GeoTIFF) format, one per month, are provided.

opencc-by-4.0Jan 2024View details →

Water surface occurrence and recurrence from the article "Amazon's 2023 Drought: Sentinel-1 Reveals Extreme Rio Negro River Contraction"

This data package contains the 10 m spatial resolution occurrence and recurrence water surface masks from the article "Amazon's 2023 Drought: Sentinel-1 Reveals Extreme Rio Negro River Contraction" . These maps have been produced with Sentinel-1 images (10 m) and a Deep Learning method for image segmentation called U-net, methods and data are fully described in the article. Water surface occurrence is computed for the period 2022-2023 and indicates the percentage of time that a pixel is classified as water (100%: always water, 0%: never water, and values between 0 and 100 indicate seasonality). Water surface recurrence is computed for the period 2022-2023 and indicates the number of times that a pixel was classified as a water surface, i.e., 35 indicates that the pixel was classified 35 times as a water surface during the 2022-2023 period. The total size of the dataset is 158 Mo and is distributed in two Geotiffs, one for the water surface occurence and one for the water surface. When using this dataset, please cite the original article <a href="https://doi.org/10.3390/rs16061056">https://doi.org/10.3390/rs16061056</a>

opencc-by-4.0Apr 2022View details →

Maps of the Sustainable Development Goal (SDG) indicator 15.3.1 with its sub-indicators for the entire Amazon River Basin

Maps of the SDG indicator 15.3.1 adopted by the United Nations Convention to Combat Desertification (UNCCD) together with its sub-indicators for the Amazon River Basin for the period 2001-2020. The sub-indicators are trajectory (or trend), state, and performance. The SDG indicator 15.3.1 was calculated using the procedures described in the second version of the Good Practice Guidance for SDG Indicator 15.3.1. The annual LCLU maps from the MapBiomas project at 30 m spatial resolution and the 16-day MOD13Q1 NDVI and SoilGrids dataset were used as inputs. In addition, annualized maps of drought severity derived from SPI12, SPEI12, and scPDSI are added.      A total of seven GeoTIFF files in Geographic Tagged Image File Format (GeoTIFF) format are provided at 250 m spatial resolution. Coding for the SDG indicator 15.3.1, trajectory, state, and performance. -32768   is ‘No data’ -1 is ‘Degraded’ 0 is ‘Stable’’ 1 is ‘Improvement’ Coding for the drought severity. From 0 (minimum drought severity) to 1 (maximum drought severity).

opencc-by-4.0Nov 2018View details →

Annotation of metagenome-assembled genomes retrieved from Amazon river basin metagenomes

Annotation of metagenome-assembled genomes retrieved from Amazon river basin metagenomes                       RELEASE MAG-2018/01                      --------------------------------------   1. INTRODUCTION Here is deposited the genes and proteins annotation from metagenome-assembled genomes (MAGs) retrieved from Amazon river basin metaganomes (SRP044326, PRJEB25171 and SRP039390) were deposited under European Nucleotide Archive - ENA project PRJEB25176. Briefly, metagenomes were coassembled in groups by geographical location with Megahit v.1.0 and the contigs were used to a reads mapping and binning with BWA-MEM (version 0.7.12-r1039), SamTools (version 1.3.1) and Metabat (v2.12.1). MAGs with overall quality greater than 50, calculated with CheckM (version 1.0.11), were selected for refining precedures. Contigs outliers were eliminated by using RefineM (version 0.0.23). Finished MAGs were then annotated by Prokka (version 1.11) pipeline, and with the other most completes databases up to date (KEGG, UniProtKB, dbCAN, PFAM, eggNOG and COG).   2. LOCATION      MAGs sequences are available under ENA project PRJEB25176.        ENA_accession   Isolate     --------------------    --------------     ERZ494218    AM_0118     ERZ494219    AM_0219     ERZ494220    AM_0226     ERZ494221    AM_0228     ERZ494222    AM_0233     ERZ494223    AM_0240     ERZ494224    AM_0244     ERZ494225    AM_0256     ERZ494226    AM_0268     ERZ494227    AM_0275     ERZ494228    AM_0466     ERZ494229    AM_0507     ERZ494230    AM_0510     ERZ494231    AM_0519     ERZ494232    AM_0528     ERZ494233    AM_0546     ERZ494234    AM_0608     ERZ494235    AM_0615     ERZ494236    AM_0616     ERZ494237    AM_0619     ERZ494238    AM_0621     ERZ494239    AM_0630     ERZ494240    AM_0643     ERZ494241    AM_0729     ERZ494242    AM_0764     ERZ494243    AM_0832     ERZ494244    AM_0849     ERZ494245    AM_0854     ERZ494246    AM_0876     ERZ494247    AM_0902     ERZ494248    AM_0936     ERZ494249    AM_1003     ERZ494250    AM_1104     ERZ494251    AM_1111     ERZ494252    AM_1205     ERZ494253    AM_1312     ERZ494254    AM_1409     ERZ494255    AM_1503     ERZ494256    AM_1603     ERZ494257    AM_1606     ERZ494258    AM_1801     ERZ494259    AM_1811     ERZ494260    AM_2104     ERZ494261    AM_2116     ERZ494262    AM_2124     ERZ494263    AM_2202     ERZ494264    AM_2207     ERZ494265    AM_2208     ERZ494266    AM_2324     ERZ494267    AM_2502     ERZ494268    AM_2804     3. ACKNOWLEDGEMENTS     This work is a joint effort of Laboratory of molecular biology from Federal University of São Carlos, São Paulo, Brazil (LBM/UFSCAR) and Protists group of Institut del Ciencias del Mar, Barcelone, Spain (ICM). We are grateful to Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), as well as,                     the spanish funding organ Consejo Superior de Investigaciones Científicas (CSIC). This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) - Finance Code 001.   4. CONTACT INFORMATION    Current curators:    - Célio Dias Santos Júnior (celio.diasjunior@gmail.com)    - Flavio Henrique-Silva (dfhs@ufscar.br)    - Ramiro R. Logares (ramiro.logares@icm.csic.es)   5. COPYRIGHT NOTICE    Amazon River Basin Metagenome-Assembled Genomes Annotation - AM/MAGs    Copyright (C) 2018 The AMnrGC consortium.    This database is provided “as is” and without any warranty of any kind,    of openly available. You can redistribute and/or modify it    as you wish, under the terms of Creative Commons CC BY 4.0:     https://creativecommons.org/licenses/by/4.0/ ___________________ Barcelone, Feb/2018

opencc-by-4.0Sep 2024View details →

River Sediment Database-Amazon (RivSed-Amazon)

The River Sediment Database-Amazon (RivSed-Amazon) database contains surface suspended sediment concentrations (SSC) derived from Landsat 5, 7, and 8 Level 1 Collection 1 surface reflectance from all rivers in the Amazon River Basin that are ~60 meters wide or greater. SSC represent spatially integrated "reach" median concentrations over the footprint of SWOT River Database (SWORD, Altenau et al., 2021) centerlines (median reach length = 10 km) where high quality river water pixels were detected within each Landsat image from 1984-2018.  The methods used to produce this database were initially developed in the following publications: <ul> <li>Gardner, J., Pavelsky, T. M., Topp, S., Yang, X., Ross, M. R., & Cohen, S. (2023). Human activities change suspended sediment concentration along rivers. Environmental Research Letters. <a href="https://iopscience.iop.org/article/10.1088/1748-9326/acd8d8">https://iopscience.iop.org/article/10.1088/1748-9326/acd8d8</a> and </li> <li>Gardner et al. (2020). The color of rivers. Geophysical Research Letters.  <a href="https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2020GL088946">https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2020GL088946</a></li> </ul> The publication associated with RivSed-Amazon is in review. Files: 1) Metadata (rivSed_Amazon_metadata_v1.01.pdf): Description key data files associated with this repository.  2) RiverSed (RiverSed_Amazon_v1.1.txt). Table of  SSC  and associated data that is joinable to SWORD based on the ""reach_id". 3) Shapefile of river centerlines over South America to which the reflectance data can be attached (SWORD_SA.shp). 4) Shapefile of the reach polygons associated with SWORD_SA over the Amazon Basin. (reach_polygons_amazon.shp). 5) SSC-Landsat matchup database with extended metadata on locations and in-situ data (train_full_v1.1.csv). 6) The final training data used to build the xgboost machine learning model (train_v1.1.csv). 7) The xgboost model that can make SSC predictions over inland waters in USA using Landsat bands/band combinations (tssAmazon_model_v1.1.rds and .rda). The model can only be loaded and used in R at this time. 8) The correction coefficients applied to Landsat 5 and 8 to harmonized surface reflectance across Landsat 5,7,8 and over all bands to enable time series analysis.

opencc-by-4.0May 2018View details →

Figures 1–13 in New records and diagnostic notes on large carpenter bees (Hymenoptera: Apidae: genus Xylocopa Latreille), from the Amazon River basin of South America

Figures 1–13. Dorsal habitus photographs of pinned, preserved specimens of females of Xylocopa (Neoxylocopa) species from the Amazon River basin, from the USNM collection. 1) X. (N.) aeneipennis. 2) X. (N.) amazonica. 3) X. (N.) aurulenta. 4) X. (N.) carbonaria. 5) X. (N.) cearensis. 6) X. (N.) fimbriata. 7) X. (N.) frontalis. 8) X. (N.) grisescens. 9) X. (N.) hirsutissima. 10) X. (N.) orthogonaspis. 11) X. (N.) similis. 12) X. (N.) suspecta. 13) X. (N.) tegulata.

opencc-by-4.0Oct 2018View details →

Fig. 7 in The changing course of the Amazon River in the Neogene: center stage for Neotropical diversification

Fig. 7. Growth of mega-wetlands in northern South America. Geological time scale at top. Eustatic sea-level estimates from Zachos et al. (2001). Area estimates of for Atlantic and Caribbean draining mega-wetlands from paleogeographic reconstructions in Wesselingh, Hoorn (2010) and Hoorn et al. (2017), and for the Orinoco basin by Jaramillo et al. (2017). Caribbeandraining Andean foreland basins in orange; Atlantic-draining basins contributing to transcontinental Amazon in yellow. Areas estimated using ImageJ (Abràmoff et al., 2004). Curves smoothed using a third-order Bezier Spline.

opencc-by-4.0Nov 2020View details →

Fig. 2 in Integrative taxonomy reveals two new cryptic species of Hyphessobrycon Durbin, 1908 (Teleostei: Characidae) from the Maracaçumé and middle Tocantins River basins, Eastern Amazon region

Fig. 2. Hyphessobrycon frickei Guimarães, Brito, Bragança, Katz & Ottoni sp. nov. (CICCAA 02388), 17.7 mm SL; jaw suspensory. A. Premaxillary. B. Maxilla. C. Dentary. Scale bar: 1 mm

opencc-by-4.0Nov 2020View details →

Fig. 8 in Integrative taxonomy reveals two new cryptic species of Hyphessobrycon Durbin, 1908 (Teleostei: Characidae) from the Maracaçumé and middle Tocantins River basins, Eastern Amazon region

Fig. 8. Topology of the ultrametric tree performed in BEAST ver. 1.8.4 including unique haplotypes summarizing the results of GMYC, bPTP and ABGD. Numbers above and below branches are posterior probability values. The star indicates the Hyphessobrycon copelandi clade.

Fig. 2 in Patterns of growth and natural mortality in Lysapsus bolivianus (Anura, Hylidae, Pseudae) in an environmental protection area in the estuary of the Amazon River

Fig. 2. Weight-length relationships in adult male and female Lysapsus bolivianus from the Rio Curiaú EPA on the estuary of the Amazon River, in northern Brazil.

Fig. 4 in Patterns of growth and natural mortality in Lysapsus bolivianus (Anura, Hylidae, Pseudae) in an environmental protection area in the estuary of the Amazon River

Fig. 4. Von Bertalanffy's growth curves for (A) male and (B) female Lysapsus bolivianus from the Rio Curiaú EPA in Amapá, Brazil.

Fig. 3 in Patterns of growth and natural mortality in Lysapsus bolivianus (Anura, Hylidae, Pseudae) in an environmental protection area in the estuary of the Amazon River

Fig. 3. Plot of the Ford-Walford estimates of growth parameters (SVL, k) of adult (A) male and (B) female Lysapsus bolivianus ∞ from the Rio Curiaú EPA in Amapá, Brazil. The values were estimated by the linear regressions between SVL and SVL+1 for each gender, as SVL ∞ = (a/1-b) and K = -loge b.

Fig. 1 in Patterns of growth and natural mortality in Lysapsus bolivianus (Anura, Hylidae, Pseudae) in an environmental protection area in the estuary of the Amazon River

Fig. 1. Relative frequency of the body size classes (SVL, snout–vent length; mm) recorded in the (A) adult males and females and (B) juveniles of the Lysapsus bolivianus population from the Rio Curiaú EPA on the estuary of the Amazon River, in northern Brazil.

Fig. 2 in Molecular diagnosis of the arowanas Osteoglossum ferreirai Kanazawa, 1966 and O. bicirrhossum (Cuvier, 1829) from the Orinoco and Amazon River basins

Fig. 2. Maximum likelihood phylogenetic hypothesis of relationships of Osteoglossum individuals representing the species O. bicirrhossum and O. ferreirai.

Fig. 1 in Molecular diagnosis of the arowanas Osteoglossum ferreirai Kanazawa, 1966 and O. bicirrhossum (Cuvier, 1829) from the Orinoco and Amazon River basins

Fig. 1. Sampling localities in the Amazon and Orinoco basins of O. bicirrhossum and O. ferreirai. Base map was obtained from Online Map Creation (Geomar) currently available as Planiglobe (http://www.planiglobe.com/).

Fig. 3 in Cytogenetic and DNA barcoding reveals high divergence within the trahira, Hoplias malabaricus (Characiformes: Erythrinidae) from the lower Amazon River

Fig. 3. Phylogenetic trees of Hoplias malabaricus haplotypes based on COI mitochondrial gene sequences. a) Neighbor-Joining; b) Maximum likelihood and c) Maximum Parsimony. Values in the nodes indicate the statistical support from bootstrap test.

Fig. 2. C in Cytogenetic and DNA barcoding reveals high divergence within the trahira, Hoplias malabaricus (Characiformes: Erythrinidae) from the lower Amazon River

Fig. 2. C-banded karyotype of karyomorph C of Hoplias malabaricus, from lower Amazonas River. M - metacentric, SM - submetacentric. Bar = 10µm.

Fig. 1 in Cytogenetic and DNA barcoding reveals high divergence within the trahira, Hoplias malabaricus (Characiformes: Erythrinidae) from the lower Amazon River

Fig. 1. Map of collection sites of Hoplias malabaricus in the lower Amazonas River. Localities: 1 - Sapucuá lake; 2 - Óbidos; 3 - Juá lake; 4 - Urumari stream; 5 - Maicá lake; 6 - Almeirim. A map of Brazil (box on left corner) with the Pará State shaded in gray indicates the studied area by a white rectangle.