cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.1594/pangaea.831831
title: Phenotypic plasticity of coralline algae in a High CO2 world

description: It is important to understand how marine calcifying organisms may acclimatize to ocean acidification to assess their survival over the coming century. We cultured the cold water coralline algae, Lithothamnion glaciale, under elevated pCO2 (408, 566, 770, and 1024 µatm) for 10 months. The results show that the cell (inter and intra) wall thickness is maintained, but there is a reduction in growth rate (linear extension) at all elevated pCO2. Furthermore a decrease in Mg content at the two highest CO2 treatments was observed. Comparison between our data and that at 3 months from the same long-term experiment shows that the acclimation differs over time since at 3 months, the samples cultured under high pCO2 showed a reduction in the cell (inter and intra) wall thickness but a maintained growth rate. This suggests a reallocation of the energy budget between 3 and 10 months and highlights the high degree plasticity that is present. This might provide a selective advantage in future high CO2 world.
description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Lavigne and Gattuso, 2011) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2014-04-15.
description: Supplement to: Ragazzola, Federica; Foster, Laura C; Form, Armin; Büscher, Janina Vanessa; Hansteen, Thor H; Fietzke, Jan (2013): Phenotypic plasticity of coralline algae in a High CO2 world. Ecology and Evolution, 3, 3436-3446
DOI: 10.1594/pangaea.855309
title: (Table 1) Temperature and foraminiferal Mg/Ca ratios of samples off Japan

description: We studied Mg/Ca in high-Mg, shallow-water benthic foraminifera in culture and in samples from natural environments, in order to evaluate the expression of latitudinal and seasonal temperature variability in Mg/Ca in their tests. We cultured Planoglabratella opercularis (d'Orbigny) and Quinqueloculina yabei Asano under controlled temperature (10°-25°C) and salinity (30-38) conditions. Both species show a linear correlation between Mg/Ca and temperature, but they differ in temperature sensitivity. Salinity does not significantly influence Mg/Ca. In the samples collected in nature, Mg/Ca and seawater temperatures are positively correlated, but there are more complexities than in the records for cultured specimens due to such factors as seasonal fluctuations in temperature. We conclude that Mg/Ca ratios in monospecific benthic foraminiferal samples may be used as a reliable temperature proxy, if the lifetime of the species is taken into account.
description: Supplement to: Toyofuku, Takashi; Kitazato, Hiroshi; Kawahata, Hodaka; Tsuchiya, Masashi; Nohara, Masato (2000): Evaluation of Mg/Ca thermometry in foraminifera: Comparison of experimental results and measurements in nature. Paleoceanography, 15(4), 456-464
DOI: 10.1594/pangaea.926074
title: Abundance of zooplankton during POLARSTERN cruise ARK-IV/3 (PS11)

description: Abundances of zooplankton taxa were calculated in the Arctic Ocean during Polarstern cruise ARK-IV/3. Samples were taken with the Multinet midi (Hydrobios, Kiel), which is equipped with nine nets (mesh size: 150 µm).
DOI: 10.1594/pangaea.926078
title: Abundance of the life stages of two Calanus species during POLARSTERN cruise ARK-IX/1b (PS24)

description: Abundances of the life stages of the Calanus species Calanus finmarchicusand Calanus hyperboreus were calculated in the Arctic Ocean during Polarstern cruise ARK-IX/1b. Samples were taken with the Multinet midi (Hydrobios, Kiel), which is equipped with nine nets (mesh size: 150 µm), and Bongo nets (Mesh size 200/300 µm)
DOI: 10.1594/pangaea.926079
title: Abundance of zooplankton during POLARSTERN cruise ARK-XI/1 (PS36)

description: Abundances of zooplankton taxa were calculated in the Arctic Ocean during Polarstern cruise ARK-XI/1. Samples were taken with the Multinet midi (Hydrobios, Kiel), which is equipped with nine nets (mesh size: 150 µm).
DOI: 10.5061/dryad.rjdfn2zr3
title: Data and code from: Wildlife temporal behaviors in response to human activity changes during and following COVID-19 park closures

description: With urbanization reducing the amount of available wildlife habitat and
 outdoor recreation increasing the human activity within wildlife habitats,
 it is important to understand the effects of human activity on animal
 behavior. This study examined how the reduction in human presence in urban
 parks in Gainesville, Florida affected the temporal behaviors of medium-
 and large-bodied mammals and ground birds. Camera-trap surveys were
 conducted during (2020) and following (2023) the closure of urban parks
 that are typically open to human recreation due to Coronavirus 2019
 (COVID-19), with the shutdown providing a unique opportunity to study
 wildlife under reduced human activity. We detected biologically
 significant shifts in activity patterns that were consistent with
 avoidance of increased presence of predators (bobcat, coyote, fox) and
 with avoidance of human activity (white-tailed deer) when the parks were
 re-opened. Temporal behavior pattern shifts can have significant effects
 on foraging/hunting, reproduction, and socialization as time of day is an
 important aspect to an animal’s niche and can ultimately affect population
 dynamics at a species and community level. These data may inform
 regulations on public recreation and wildlife population management within
 urban parks and the Florida Wildlife Corridor—the state’s best effort to
 offset the negative impacts of increasing population and development.
description: # Data and code from: Wildlife temporal behaviors in response to human
 activity changes during and following COVID-19 park closures Dataset DOI:
 [10.5061/dryad.rjdfn2zr3](https://doi.org/10.5061/dryad.rjdfn2zr3) ##
 Description of the data and file structure Camera trap data was organized
 using Agouti software and downloaded into an Excel file, for which the
 code is attached. This data was then analyzed using R, for which the file
 is also attached. ### Files and variables #### File: COVID.data_code.R
 **Description:** Code for original camera trap data analysis. #### File:
 time_transformation_standardization_code.R **Description:** Updated code
 that accounts for seasonality following reviewer feedback. #### File:
 CTdata_all_9.4.25.xlsx **Description:** Compiled camera trap observations
 from Agouti. ##### Variables * Site, stage (peak covid or post covid),
 name (observation ID), date, time, species, count ## Code/software Excel
 or any spreadsheet viewer for the camera trap data, and any document
 viewer for the R code. The camera trap data was used in the R analysis.
 The code provides details for which analysis it describes (following the
 "##") and includes the code for downloading any packages needed
 for the data analysis (like the 'overlap' package). ## Access
 information Camera trap R code source: Ridout, M. S., & Linkie, M.
 (2009). Estimating overlap of daily activity patterns from camera trap
 data. *Journal of Agricultural, Biological, and Environmental Statistics*,
 *14*, 322-337.
DOI: 10.1594/pangaea.926080
title: Abundance of zooplankton during POLARSTERN cruise ARK-XII/1 (PS41)

description: Abundances of zooplankton taxa were calculated in the Arctic Ocean during Polarstern cruise ARK-XII/1. Samples were taken with the Multinet midi (Hydrobios, Kiel), which is equipped with nine nets (mesh size: 150 µm).
DOI: 10.15468/dl.gk4u4p
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Perca fluviatilis",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1810",
 "Year is less than or equal to 1814"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004488-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.926081
title: Abundance of zooplankton during POLARSTERN cruise ARK-XIV/1a (PS51)

description: Abundances of zooplankton taxa were calculated in the Arctic Ocean during Polarstern cruise ARK-XIV/1a. Samples were taken with the Multinet midi (Hydrobios, Kiel), which is equipped with nine nets (mesh size: 150 µm). This dataset completes the copepod dataset of Kosobokova (2018).
DOI: 10.1594/pangaea.926082
title: Abundance of life stages of three Calanus species during POLARSTERN cruise ARK-XXII/2 (PS70)

description: Abundances of the life stages of the three Calanus species (Calanus finmarchicus, Calanus glacialis and Calanus hyperboreus) was calculated in the Arctic Ocean during Polarstern cruise ARK-XXII/2. Samples were taken with the Multinet maxi (Hydrobios, Kiel), which is equipped with nine nets (mesh size: 150 µm).
DOI: 10.1594/pangaea.926083
title: Abundance of the life stages of two Calanus species during VALDIVIA cruise VAL136

description: Abundances of the life stages of the Calanus species Calanus finmarchicus and Calanus hyperboreus were calculated in the Arctic Ocean during Valdivia cruise VAL136. Samples were taken with the Multinet midi (Hydrobios, Kiel), which is equipped with nine nets (mesh size: 150 µm), and Bongo nets (Mesh size 200/300 µm).
DOI: 10.1594/pangaea.982944
title: CT raw data (DICOM format) of sediment core GeoB25206-2, MARIA S. MERIAN cruise MSM111

description: Sediment core GeoB25206-2 was scanned using a Toshiba Aquilion 64™ computer tomograph (CT) at the hospital Klinikum Bremen-Mitte, with an Xray source voltage of 120 kV and a current of 600 mA. The CT image stacks have a resolution of 0.35 mm in the x and y directions and 0.5 mm resolution in the z direction (0.3 mm reconstruction unit). Images were reconstructed using Toshiba's patented helical cone beam reconstruction technique.
DOI: 10.1594/pangaea.988344
title: Seawater carbonate chemistry and larval shell growth and shell protein content of the Hong Kong oyster (Magallana hongkongensis)

description: To elucidate how bivalve larvae can overcome the physicochemical barriers imposed by adverse carbonate chemistry through biologically controlled biomineralization, we exposed Hong Kong oyster (Magallana hongkongensis) embryos to favorable carbonate chemistry (control, nominal pH 8.1) and adverse carbonate chemistry (treatment, nominal pH 7.4) conditions until prodissoconch I completion.This dataset is included in the OA-ICC data compilation maintained in the framework of the IAEA Ocean Acidification International Coordination Centre (see https://oa-icc.ipsl.fr). Original data were downloaded from figshare (see Source) by the OA-ICC data curator. In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2024) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2025-12-31.
DOI: 10.5061/dryad.tdz08kqbr
title: Ocean current, temperature, salinity and turbulence collected from the R/V Walton Smith, R/V Pelican, and R/V Pt. Sur during two summer seasons of intensive field campaigns in the Coastal Waters of Gulf of Mexico and the Gulf of Mexico from 20210620 to 20220707

description: Recently, theories for ocean dynamics posit that submesoscale flows
 interacting with near-inertial motions are important for understanding the
 dynamics of both phenomena. These data provide a basis to test theories of
 energy exchange at the submesoscale by studying circulation patterns in
 the Mississippi-Atchafalaya river plume in the northern Gulf of Mexico.
 Observations from ship, moorings, and autonomous platforms made during two
 field campaigns are complemented by hydrostatic ROMS modeling and
 non-hydrostatic Large Eddy Simulations (LES). By combining data and
 models, we characterize, quantify, and understand the energy exchanges
 between balanced and unbalanced motions and the turbulent cascade that can
 result from the interaction. Wave-mean flow interactions in the
 Mississippi-Atchafalaya river plume system could enhance mixing and
 vertical exchange, which are important for understanding coastal hypoxia
 and the dispersal of pollutants in the northern Gulf of Mexico. The data
 archived here are field observations from multiple ships that capture
 circulation patterns, stratification variability and turbulence intensity
 in the Mississippi-Atchafalaya River plume in the northern Gulf of Mexico.
 The region is characterized by a strong sea breeze which leads to the flow
 and wave variations on relatively small spatial scales of less than 1 km.
 Observations were obtained during two intensive field campaigns that
 included ship, moored, and autonomous platforms. The project is a
 collaboration between the US and the United Kingdom (UK) with the UK
 component being supported by the UK National Environmental Research
 Council (NERC) through an agreement with NSF.
description: # Ocean current, temperature, salinity, and turbulence collected from the
 R/V Walton Smith, R/V Pelican, and R/V Pt. Sur during two summer seasons
 of intensive field campaigns in the Coastal Waters of the Gulf of Mexico
 and the Gulf of Mexico from 20210620 to 20220707 Dataset DOI:
 [10.5061/dryad.tdz08kqbr](https://doi.org/10.5061/dryad.tdz08kqbr) ##
 Description of the data and file structure Data is from a Vertical
 Microstructure profiler. There is a readme in each subfile with details on
 the variables. Data that is listed as "NaN" has been removed by
 our quality control algorithms.  ### Files and variables #### File:
 VMP.zip **Description:** Each of these zip files contains 2 directories,
 one for the 2021 field season and one for the 2022 field season. Within
 each there are data files (netcdf) and metadata files (text, with
 corresponding filenames) ## Code/software Data is in standard netcdf
 format. Each file is accompanied by a readme with additional information.
DOI: 10.5061/dryad.ns1rn8q5p
title: Electrophysiology of neurons adjacent and away from microglia in control and TBI conditions

description: Aim: We investigated whether neurons adjacent to satellite microglia
 (microglia juxtaposed to neurons with their soma and processes entwining
 around the neuronal soma) have differences in intrinsic excitability and
 how this relationship might change after traumatic brain injury (TBI) or
 with antagonism of the P2Y12 receptor. Methods: Whole cell patch clamp
 experiments were performed on in vitro slices of the orbitofrontal cortex
 (OFC) in sham or TBI conditions or incubation with a P2Y12 receptor
 antagonist (PSB 0739 1microM) and a series of current steps was used to
 invoke action potentials. Tmem119 mice (Jackson Laboratory 031823) were
 utilized to identify GFP+ microglia and determine whether a neuron was
 adjacent to a satellite microglia or away. TBI was induced with a
 controlled cortical impact ~1-2 months before testing. Full details are
 provided in Feichtenbiner et al. (J Neuroinflammation. 2025. 22:9.)
 Results: Satellite microglial association reduced the intrinsic
 excitability of neurons, but this effect was lost after TBI and with
 antagonism of the P2Y12 receptor. Main Conclusion: Loss of regulation of
 neuronal activity by satellite microglia, perhaps through changes in P2Y12
 receptors, may be a maladaptive circuit change that occurs and contributes
 to impairment in chronic TBI.
description: # Electrophysiology of neurons adjacent and away from microglia in control
 and TBI conditions Dataset DOI:
 [10.5061/dryad.ns1rn8q5p](https://doi.org/10.5061/dryad.ns1rn8q5p) ##
 Description of the data and file structure The response to a series of
 current steps was recorded with pClamp software (Molecular Devices) for
 every cell. Files are stored in the .abf format. The Metadata file
 provides the filename associated with each cell and the associated sham,
 TBI or drug condition as well as the sex of the mouse. ## Code/software
 Abf files can be opened in pClamp software such as Clampfit which is free
 to download as well as other programs such a Matlab with easily accessible
 conversion scripts available online. ## Access information Data was
 derived from the following sources: * Feichtenbiner AB, Sytsma K,
 O'Boyle RP, Mittenzwei R, Maioli H, Scherpelz KP, Child DD, Li N,
 Ariza Torres J, Keene L, Kirkland A, Howard K, Latimer C, Keene CD, Ransom
 C, Nolan AL. Satellite microglia: marker of traumatic brain injury and
 regulator of neuronal excitability. J Neuroinflammation. 2025 Jan
 16;22(1):9. doi: 10.1186/s12974-024-03328-9. PMID: 39819341; PMCID:
 PMC11740464.
DOI: 10.5061/dryad.qbzkh18x9
title: Is an ecosystem perspective sufficient to understand meta-ecosystem processes? A critical reflection

description: Meta-ecosystems are the largest and probably most complex structures
 investigated in ecology. Because of their complexity, they are often
 separated into their respective sub-systems and then studied in isolation.
 This is often done without analysing whether an understanding of the
 individual ecosystems can lead to a proper understanding of the
 meta-ecosystem, likely because we lack clear guidelines as to when such a
 separation is sufficient. In the accompanying study (DOI:
 10.1002/oik.11127), we propose four conceptual models for which a
 separation may approximate the full dynamics. For one of those methods, we
 provide a new theoretical framework to assess how strongly two ecosystems
 are linked and test this new method on virtual data. We show that the new
 method is a good approximation of the coupling strength between two
 ecosystems. Here we provide the computer code to compute this method.
description: # Is an ecosystem perspective sufficient to understand meta-ecosystem
 processes? A critical reflection Dataset DOI:
 [10.5061/dryad.qbzkh18x9](https://doi.org/10.5061/dryad.qbzkh18x9) ##
 Description of the data and file structure Computing Ecosystem Coupling in
 R ### Overview This repository contains two R scripts and two equivalent
 Python scripts that demonstrate how to compute **ecosystem coupling** in
 dynamical systems modeled with differential equations. The provided
 functions integrate the system forward in time, check for equilibrium,
 compute the Jacobian at equilibrium, and derive a **coupling strength**
 between two ecosystems. ### Files #### 1. `ecosystem_example.R` This
 script provides a **worked example** using a **Lotka–Volterra model** with
 two coupled ecosystems: \- Defines species intrinsic growth rates (`mu`)
 and interaction matrices (`A`). \- Simulates species dynamics starting
 from random initial densities. \- Calls the function
 `run_to_equilibrium_and_jacobian` (from the second script). \- Produces
 plots of community dynamics and prints: \- whether equilibrium was
 reached, \- equilibrium densities, \- the Jacobian matrix at equilibrium,
 \- the coupling strength between ecosystems. This file can be used as a
 teaching or demonstration example. #### 2. `get_coupling.R` This script
 defines the core function: \```r
 run_to_equilibrium_and_jacobian(community_model, y0, ecosystem_bool,
 params, ``` t_step = 1.0, tol = 1e-4, max_steps = 20, plot = FALSE) ```
 The corresponding Python scripts are equivalent. ## Code/software Python
 or R ## Access information NA
DOI: 10.5061/dryad.dncjsxmc8
title: R code from: Diagnosing common sources of lack of fit to composition data in fisheries stock assessment models using One-Step-Ahead (OSA) residuals

description: Fisheries stock assessments often include age- and size-composition data
 to estimate recruitment strengths, mortality rates and management
 quantities. Compositions inherently have correlation among the categories,
 and therefore residuals are not independent. One-Step-Ahead (OSA)
 residuals have been proposed as a replacement for the commonly used (but
 incorrectly interpreted) Pearson residuals; however, there is no clear
 best practice for diagnosing model fit when using OSA residuals. We use a
 simple example to illustrate common sources of model-misspecification and
 impacts on statistical and visual diagnostics. We find that visual
 inspection of model fit aggregated across all observations reliably
 identifies many types of misspecification, visual inspection of Pearson
 residuals can reveal further lack of fit, and statistical analysis of OSA
 residuals provides for objective evaluation of both lack-of-fit and
 overall data weighting. The power to detect model misspecification depends
 on the sample size, the number of age bins, and the number of years of
 data. By illustrating common problems when the correct answer is known,
 this work provides a guideline for model diagnostics using OSA residuals
 in more complex settings. This R code will reproduce the simulated data
 and analysis; each of the figures in the paper are also created.
description: # R code from: Diagnosing common sources of lack of fit to composition
 data in fisheries stock assessment models using One-Step-Ahead (OSA)
 residuals Dataset DOI:
 [10.5061/dryad.dncjsxmc8](https://doi.org/10.5061/dryad.dncjsxmc8) ##
 Description of the data and file structure This R code creates the
 simulated data and analysis in "Diagnosing common sources of lack of
 fit to composition data in fisheries stock assessment models using
 One-Step-Ahead (OSA) residuals" ### Files and variables #### File:
 OSA_code_final.R **Description:** This script defines the R packages
 needed to recreate the entire analysis. It creates several functions and
 the produces the simulated data, analyzes each case described in the paper
 and produces the figures in the publication and the supplementary
 material. ## Code/software This code runs in R version 4.5.1. R Core Team.
 2025. R: A language and environment for statistical computing. R
 Foundation for Statistical Computing. Vienna, Austria.
 [https://www.R-project.org](https://www.R-project.org). It requires the
 following packages: compResidual: Trijoulet, V., and Nielsen, A. 2022.
 compResidual: Residual calculation for compositional observations. R
 package version 0.0.1.
 [https://github.com/fishfollower/compResidual](https://github.com/fishfollower/compResidual). TMB: Template Model Builder: A General Random Effect Tool Inspired by 'ADMB'. https://cran.r-project.org/web/packages/available_packages_by_name.html#available-packages-T
DOI: 10.25346/s6/lvrrae/sgign6
title: visualize.m

description: Matlab spectrogram visualization script
DOI: 10.25346/s6/lvrrae/9hfzjl
title: drone_4000_00.mat

description: File uploaded via API
DOI: 10.25346/s6/lvrrae/z7zcwi
title: drone_0400_05.mat

description: File uploaded via API
DOI: 10.25346/s6/lvrrae/ofxkhc
title: drone_0300_02.mat

description: File uploaded via API