cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.1594/pangaea.831499
title: Spatially explicit estimates of North Atlantic albacore tuna (Thunnus alalunga) biomass in the North Atlantic for the period 1956-2010 - Gridded data product (NetCDF)

description: The development of the ecosystem approach and models for the management of ocean marine resources requires easy access to standard validated datasets of historical catch data for the main exploited species, together with the model estimates achieved from these data, allowing models inter-comparison and evaluation of model skills. North Atlantic albacore tuna is exploited all year round by longline and in summer and autumn by surface fisheries and fishery statistics compiled by the International Commission for the Conservation of Atlantic Tunas (ICCAT). Catch and effort with geographical coordinates at monthly spatial resolution of 1° or 5° squares were extracted for this species with a careful definition of fisheries and data screening. Length frequencies of catch were also extracted according to the definition of fisheries for the period 1956-2010. Using these data, an application of the spatial ecosystem and population dynamics model (SEAPODYM) was developed for the North Atlantic albacore population and fisheries and provided the first spatially explicit estimate of albacore density in the North Atlantic by life stage. These densities by life stage (larval recruits, young immature fish adult mature fish and total biomass) are provided in gridded file (Netcdf) at resolution of 2° x 2° x month.
description: This work was funded in part by the European project EURO-BASIN, funded by Framework Programme 7 (Contract 264933). Special thanks to ICCAT for the access to its public fishing database and Carlos Palma (ICCAT) and Alain Fonteneau (IRD) for their helpful advice on these data.
DOI: 10.1594/pangaea.914912
title: Ocean bottom seismometer and ocean bottom hydrophone seismic refraction and wide angle data from profile P01 of Maria S. Merian cruise MSM69 with links to sgy data files

description: During MSM69, in November and December of 2017, an 1100-km-long transect in the equatorial Atlantic Ocean aboard the German research vessel MARIA S. MERIAN. The profiles runs from 12.8°W/2.8°S,for 75 km on the South American plate, crosses the Mid-Atlantic Ridge and terminates at 3.2°W/0.7°S, roughly covering zero-age to approximately 50 Myr old lithosphere of the African plate. The seismic refraction and wide-angle transect was covered with 71 Ocean-Bottom-Seismometers and hydrophones spaced at 10 to 20 km intervals. The profile was shot at an increased interval of 210 s to decrease the shot-induced-level, improving signal-noise-ratio and providing an average shot spacing of 410 m. Seismic data in SEGY format are reduced with 8 km/s and the origin of the time series is at -1 sec.
DOI: 10.1594/pangaea.833155
title: Model results of sensitivity experiments for marine nitrogen cycle in four NetCDF files

description: The marine nitrogen (N) inventory is thought to be stabilized by negative feedback mechanisms that reduce N inventory excursions relative to the more slowly overturning phosphorus inventory. Using a global biogeochemical ocean circulation model we show that negative feedbacks stabilizing the N inventory cannot persist if a close spatial association of N2 fixation and denitrification occurs. In our idealized model experiments, nitrogen deficient waters, generated by denitrification, stimulate local N2 fixation activity. But, because of stoichiometric constraints, the denitrification of newly fixed nitrogen leads to a net loss of N. This can enhance the N deficit, thereby triggering additional fixation in a vicious cycle, ultimately leading to a runaway N loss. To break this vicious cycle, and allow for stabilizing negative feedbacks to occur, inputs of new N need to be spatially decoupled from denitrification. Our idealized model experiments suggest that factors such as iron limitation or dissolved organic matter cycling can promote such decoupling and allow for negative feedbacks that stabilize the N inventory. Conversely, close spatial co-location of N2 fixation and denitrification could lead to net N loss.
description: Supplement to: Landolfi, Angela; Dietze, Heiner; Koeve, Wolfgang; Oschlies, Andreas (2013): Overlooked runaway feedback in the marine nitrogen cycle: the vicious cycle. Biogeosciences, 10(3), 1351-1363
DOI: 10.1594/pangaea.910973
title: Model simulations of satellite data products from OC-CCI, SynSenPFT, OC-PFT and PhytoDOAS assimilated in to MITgcm-REcoM, links to simulation results in NetCDF format

description: Satellite data products are assimilated to MITgcm-REcoM coupled model for the year 2008 and 2009 in a global configuration. The model simulation uses PDAF an assimilation framework for data assimilation in a five day forecast-analysis cycle. Small Phytoplankton and diatoms were assimilated from SynsenPFT, OC-PFT and PhytoDOAS data while total chlorophyll from OC-CCI was assimilated into the coupled model. Simulation data without assimilation called as “Free run” is also available here.
DOI: 10.1594/pangaea.911007
title: Valvometry measurements of the giant clam Tridacna maxima to different levels of irradiance

description: Metabolic and physiological responses of Red Sea Tridacna maxima clams, including net calcification and primary production, as well as valvometry (i.e. shell gaping behavior) were assessed when exposed to simulated high radiation levels received at 3 and 5 m underwater. The two levels of radiation included exposure treatments to photosynthetically active radiation (PAR; 400-700 nm) alone and to both, PAR and ultraviolet-B radiation (UV-B; 280-315 nm).
DOI: 10.1594/pangaea.909707
title: Morphological and genetic data from Cnemidocarpa verrucosa sensu lato

description: The Southern Ocean is one of the most isolated marine ecosystems, characterized by high levels of endemism, diversity and biomass. Ascidians are among the dominant groups in the Antarctic benthic communities, thus recording the evolutionary patterns of this group is crucial to improve our current understanding on the assembly of this polar ocean. In this study, we studied the genetic variation within Cnemidocarpa verrucosa sensu lato, one of the most widely distributed and abundant ascidians in Antarctica. Using a mitochondrial and a nuclear gene (mtCOI and 18S), the phylogeography of fifteen populations distributed along the Antarctic Peninsula and South America (Burdwood Bank/MPA Namuncurá) was characterized, where the bimodal distribution of the genetic distance suggested the existence of two species within the nominal C. verrucosa. When re-evaluating morphological traits to distinguish between genetically defined species, the presence of basal disc in one of the genotypes allowed to differentiate the species.
description: (1) Both siphons are terminals, on the same line on the distal part (1) or one of them, oriented towards the one side (2).(2) Counts are made from the endostyle on the right side of the body (RE) to the dorsal lamina (DL) and from the DL to the endostyle on the left side (EL).(3) In general there are two gonadas to each side, but there are specimens with one gonad in each side, or two gonads in one side and one in other side of the body.
description: Supplement to: Ruiz, Micaela Belen; Taverna, Anabela; Servetto, Natalia; Sahade, Ricardo José; Held, Christoph (2020): Hidden diversity in Antarctica: Molecular and morphological evidence of two different species within one of the most conspicuous ascidian species. Ecology and Evolution
DOI: 10.1594/pangaea.909113
title: Estimation of reference evapotranspiration by Penman-Monteith (PM) method using meteorological data from fifteen CLIMWAT stations located in the Pannonian Basin

description: The Penman-Monteith (PM) method for estimation of reference evapotranspiration (ET0) uses numerous input data that are often missing in many regions. In such circumstances, temperature-based equations can be used for estimating ET0. The primary objective of this note was to compare the calibrated temperature-based ET0 approaches with the PM equation using meteorological data from fifteen CLIMWAT stations located in the Pannonian Basin. The most of these locations are classified as humid. Twelve temperature-based PM, Hargreaves and Thornthwaite equations were evaluated according to the standard PM method. The regionally calibrated Hargreaves equation (HT) gave the lowest RMSE at seven sites and the second lowest RMSE at three sites. New regionally calibrated Thornthwaite approach (TT) yielded the lowest RMSE three times and the second lowest RMSE seven times. These approaches resulted in the lowest average RMSE for all fifteen locations (0.28 and 0.30 mm day−1, respectively). The other temperature-based approaches significantly fall behind the HT and TT equations at most stations. The overall results show the advantage of the HT approach except for a few southeast stations where the TT approach is dominant. It can be concluded that the regionally calibrated temperature-based approaches (HT and TT) are the most suitable to estimate ET0 in the Pannonian Basin.
description: Supplement to: Trajkovic, Slavisa; Gocic, Milan; Pongracz, Rita; Bartholy, Judit; Milanovic, Mladen (2020): Assessment of Reference Evapotranspiration by Regionally Calibrated Temperature-Based Equations. KSCE Journal of Civil Engineering, 24(3), 1020-1027
DOI: 10.1594/pangaea.915932
title: Spectral reflectance of Jamtalferner ablation zone, September 4 2019

description: Spectral reflectance of glacier ice was measured on September 4, 2019, in the ablation zone of Jamtalferner, Austria, using an ASD Field Spec 2 handheld spectrometer. The instrument has an operating range of 325 to 1075nm. A new SRT-- 99-020 Spectralon (serial number 99AA08-0918-1593) manufactured by Lab Sphere was used to calibrate the instrument. Initial processing of the raw ASD data files was carried out using the “specdal” Python package. In total, 246 reflectance spectra were collected.12 spectra were measured at point locations and 234 were measured along 16 profile lines throughout the ablation zone of the glacier. The field of view for each measurement is a circle of approximately 30cm diameter. The surface characteristics of the ice varies between measurement sites and the data set contains spectra e.g. of dry ice, wet ice, and ice containing impurities such as mineral dust or debris, showing the spatial variability of spectral reflectance in the ablation zone. The data set also includes photographs of the ice surface at each measurement point to illustrate the different surface types.
DOI: 10.1594/pangaea.494683
title: Physical oceanography during cruise K9004XXXXXC
DOI: 10.1594/pangaea.915585
title: Back Trajectories for "Atmospheric Dust Deposition Varies by Season and Elevation in the Colorado Front Range, USA"

description: Back trajectory runs to accompany analysis of dust at sites near Boulder, CO, USA using the Stochastic Time-Inverted Lagrangian Trajectory model (STILT) run with High Resolution Rapid Refresh reanalysis data. This analysis was performed on the University of Utah's High Performance Computer 'lonepeak'. This modeling data may be used with scripts available at https://github.com/putmanannie/FrontRange-Dust; to produce the figures presented in the manuscript and supplemental information.
description: The zip files (view dataset as html and download via link instead of tab delimited) are named for the site and season of the back trajectory experiment. The files include the full output from the STILT model using the R interface (https://uataq.github.io/stilt/docs/), which also includes metadata about the model initialization. The initializing file is called 'run_stilt.r' and is found in the 'r' subdirectory. The results are a series of folders which include of r serialized data files (*.rds) found in the '/out/by-id' subdirectory. The folders are named with the convention 'YYYYMMDDHH_longitude_latitude_elev' where: YYYY = 4 digit year MM = 2 digit month number DD = 2 digit day HH = 2 digit hour. (Dates and times are in UTC) longitude = decimal degree longitude of back trajectory initialization site (projection = +proj=longlat) latitude = decimal degree latitude of back trajectory initialization site. (projection = +proj=longlat) elev = elevation of back trajectory initialization site in meters the *.rds files within each folder share the folder naming convention with '_traj.rds' appended. Intermediary summary files for site trajectory distances and season land use categories are included, as well as tables of the summary stats that were included in the manuscript.
DOI: 10.1594/pangaea.913422
title: Tryapanosoma prevalence in tsetse proboscis (Glossina sp.) collected in protected and tsetse invested areas in Nigeria

description: This data set includes the results of nested PCR-analysis of tsetse (Glossina sp.) proboscis samples with primers described by Adams et.al. (2006) and Hamilton et al (2004) from a tsetse (Glossina sp.) collection carried out in Nigeria between 2014 and 2016. Traps were employed for one to three days in four different National Parks, one Game Reserve and two tsetse invested areas. Each tsetse was identified morphologically and dissected in the field. DNA was crudely extracted from the proboscis by Proteinase K digest. Presence of trypanosomes was investigated by amplification of Internal Transcribed Spacer-1 (ITS1). Identification of the respective trypanosome species was done based on lengths polymorphism of the ITS1 region by estimating the approximate size of the DNA amplicon based on electrophoretic separation in agarose gels, as well as sequencing of selected ITS1 amplicons and additional glycosomal Glyceraldehyde-3-phosohate dehydrogenase.
DOI: 10.1594/pangaea.871085
title: Faunal abundances of the biodiversity integration study of seep associated benthic biota (unformated data collection)

description: These files contain in total 15 individual data sets related to various projects for instance HERMES, HERMIONE or LusoMarBoL. Detailed information (including Abstract, Authors etc.) to each of the datasets are found in the corresponding word files but the data themselves are grouped the uploaded excel-file (DBUA-data). The data are already assigned to the corresponding PANGAEA EvenLabel and list EvenLabel list provided by the author just as information. These data are also part of the HERMIONE seep biodiversity integration approach.2 tables (xlsx) and 14 text files (docx) representing results from various publications.
DOI: 10.1594/pangaea.734804
title: (Table 11) Uranium isotopic composition (234U/238U) in sediments from DSDP Leg 42 holes
DOI: 10.1594/pangaea.826305
title: Point measurements of magnetic susceptibility from IODP Hole 330-U1373A

description: Geocode = Depth CSF-A (m)
DOI: 10.1594/pangaea.810493
title: Distribution of sulphide and its oxidation intermediates in seep sediments of the Dvurechenskii mud volcano at station M72/2_279
DOI: 10.1594/pangaea.898027
title: CICE output from Global Ocean Forecast System (GOFS) 3.1 for 2019012712

description: INITIALIZATION: 2019012712FORECASTS:12-hrly out to 7.5 days (t180)GRIDS:ARCu0.08 -- poleward of 40NANTu0.08 -- poleward of 49.52SPARAMETERS:hi:standard_name = "sea_ice_thickness" ;hs:standard_name = "surface_snow_thickness" ;Tsfc:standard_name = "surface_temperature_where_sea_ice" ;aice:standard_name = "sea_ice_area_fraction" ;uvel:standard_name = "eastward_sea_ice_velocity" ;vvel:standard_name = "northward_sea_ice_velocity" ;sst:standard_name = "sea_water_temperature" ;uocn:standard_name = "eastward_sea_water_velocity" ;vocn:standard_name = "northward_sea_water_velocity" ;Tair:standard_name = "air_temperature" ;strength:standard_name = "compressive_strength_of_sea_ice" ;
DOI: 10.1594/pangaea.826306
title: Natural gamma radiation from IODP Hole 330-U1373A

description: Geocode = Depth CSF-A (m)
DOI: 10.1594/pangaea.783122
title: (Table 1) Age and U and Th isotopes in bottom sediments from Core VER-99-1-St2, Baikal Lake

description: Relative errors are shown for 1 sigma based on 10 measurements. Extracts have been recovered by 8% (0.7 M) water solution of NH4HCO3.
DOI: 10.1594/pangaea.783124
title: (Table 2) Isotopic ratio 234U/238U in bottom sediments from Core VER-99-1-St2, Baikal Lake
DOI: 10.1594/pangaea.912178
title: High resolution bathymetry of the Red Sea Rift from PELAGIA cruise 64PE445, SALTAX

description: Gridded multibeam bathymetry from Pelagia cruise 64PE445, Project SALTAX in 2018. The raw-data were post-processed and gridded at a resolution of 30 m with QPS Qimera. Small gaps are interpolated. TFW and PRJ files included. For RAW data please contact the authors.
description: DESCRIPTION=64PE445_RedSea_30m_IP_WGS84.tifUL CORNER LONGITUDE=37° 30' 27.2196" EUL CORNER LATITUDE=21° 54' 10.0332" NUR CORNER LONGITUDE=38° 35' 37.5756" EUR CORNER LATITUDE=21° 54' 10.0332" NLR CORNER LONGITUDE=38° 35' 37.5756" ELR CORNER LATITUDE=19° 53' 32.5212" NLL CORNER LONGITUDE=37° 30' 27.2196" ELL CORNER LATITUDE=19° 53' 32.5212" NPROJ_DESC=Geographic (Latitude/Longitude) / WGS84 / arc degreesPROJ_DATUM=WGS84PROJ_UNITS=arc degreesEPSG_CODE=EPSG:4326BBOX AREA=25279 sq kmPIXEL WIDTH=0.00027 arc degreesPIXEL HEIGHT=0.00027 arc degreesMIN ELEVATION=-2803.49 mMAX ELEVATION=-555.89 mELEVATION UNITS=METERSThese data should not be used for navigational purposes.
DOI: 10.1594/pangaea.909406
title: Synthetic Splitting Parameters and Synthetic Lattice Preferred Orientation (LPO) derived from Edge Driven Convection and Mantle Wind Models in Madagascar

description: We provide model outputs from "Numerical Modeling of Mantle Flow beneath Madagascar to Constrain Upper Mantle Rheology Beneath Continental Regions" submitted to Journal of Geophysical Research, Solid-Earth. The model outputs are 6 spreadsheets which contain calculated splitting parameters and TI axes or synthetic Lattice Preferred Orientations (LPO) derived from 3 regional mantle flow models in Madagascar: Edge Driven Convection (EDC) model, lithosphere-mantle wind model from Behn et al. (2004), and lithosphere-mantle wind model from Forte et al. (2010):1. model1_splitting parameters.xlsx: calculated splitting parameters derived from Edge Driven Convection (EDC) at individual stations formatted as: Stations name, longitude [◦], latitude[◦], calculated fast azimuth φcalc[◦], calculated fast azimuth standard deviation [◦], and delay time δt [sec].2. model2_splitting parameters.xlsx: calculated splitting parameters derived from lithosphere-mantle wind of Behn et al. (2004) at individual stations formatted as: Stations name, longitude [◦], latitude[◦], calculated fast azimuth φcalc[◦], calculated fast azimuth standard deviation [◦], and delay time δt [sec].3. model3_splitting parameters.xlsx: calculated splitting parameters derived from lithosphere-mantle wind of Forte et al. (2010) at individual stations formatted as: Stations name, longitude [◦], latitude[◦], calculated fast azimuth φcalc[◦], calculated fast azimuth standard deviation [◦], and delay time δt [sec].4. model1_TI axis.xlsx: calculated EDC-derived TI axes at individual seismic stations and at regular grids of 0.5◦×0.5◦. The file is formatted as longitude [◦], latitude[◦], depth [km], azimuth [◦], and percentage anisotropy [%].5. "model2_TI axis.xlsx": calculated TI axes derived from lithosphere-mantle wind of Behn et al. (2004) at individual seismic stations and at regular grids of 0.5◦×0.5◦. The file is formatted as longitude [◦], latitude[◦], depth [km], azimuth [◦] , and percentage anisotropy [%].6. "model3_TI axis.xlsx": calculated TI axes derived from lithosphere-mantle wind of Forte et al. (2010) at individual seismic stations and at regular grids of 0.5◦×0.5◦. The file is formatted as longitude [◦], latitude[◦], depth [km], azimuth [◦], and percentage anisotropy [%].
description: Supplement to: Rajaonarison, Tahiry A; Stamps, D Sarah; Fishwick, Stewart; Brune, Sascha; Glerum, Anne; Hu, Jingwen (2020): Numerical Modeling of Mantle Flow Beneath Madagascar to Constrain Upper Mantle Rheology Beneath Continental Regions. Journal of Geophysical Research: Solid Earth, 125(2), e2019JB018560
DOI: 10.1594/pangaea.908137
title: Supplementary material on the effects of elevated pCO2 levels on the extracellular polymer metabolism of Phaeodactylum tricornutum

description: Supplementary Table S1. Seawater dissolved inorganic carbon characteristics in the LC and HC treatments, before and after partial renewal of the medium in semi-continuous cultures. Total inorganic carbon (DIC), pH, salinity, nutrient concentrations, and temperature were used to derive all other parameters using a CO2 system analyzing software (CO2SYS).DIC, total dissolved inorganic carbon; TA, total alkalinity. Data are shown as the means ± SD (n=3).Supplementary Table S2. Sequencing data quality and sequence read alignment analysis.Raw_reads, original reads; Raw_bases, number of bases in the original sequencing data; Clean_reads, the number of clean reads obtained after filtering; Clean_bases, the number of bases in clean reads after filtering; valid_base, valid base percentage; Q30, the percentage of bases with a Qphred value &gt; 30 as a percentage of the total number of bases; GC, total G + C content in the clean bases as a percentage of the total number of bases. For read mapping analyses: Total reads, the number of reads after sequence filtering (e.g., the clean reads); Total mapped, the number of sequences mapped to the genome; Multiple mapped, the number of sequences with multiple alignment positions on the reference genome; Uniquely mapped, the number of sequences with unique alignment positions on the reference genome; Splice reads: uniquely mapped reads that were segmentally aligned two exons (also known as Junction reads) where non-splice reads show the sequences aligned to the exon with reads mapped in proper pairs and the number of sequences on the double-ended alignment.Supplementary Table S3. RT-qPCR primers and amplification results.Supplementary Table S4. Gene identifiers, abbreviations, and annotations for 115 EPS metabolism-related genes.Supplementary Figure 1. Hierarchical clustering of expression values (mean fragments per kilobase of transcript per million mapped reads; FPKM) among samples for 194 genes encoding carbohydrate-active enzymes in the Phaeodactylum tricornutum genome (http://protists.ensembl.org/Phaeodactylum_tricornutum/Info/Index). The enzymes were identified based on the CArbohydrate-Active enZYmes (CAZy) database. The color scale ranges from saturated red indicating highly expressed genes to saturated blue indicating weakly expressed genes, while white indicates relatively moderate expression. The heatmap was generated using the ComplexHeatmap program (Gu et al., 2016) using k-means clustering with a one minus Pearson correlation distance metric and average linkage method to cluster genes into a dendrogram.