cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n2z34tn10
title: Data for: Triose phosphate utilization stress during photosynthesis addressed with dynamic assimilation measurements

description: Oscillations in CO2 assimilation rate and associated fluorescence
 parameters have been observed alongside the triose phosphate utilization
 (TPU) limitation of photosynthesis for nearly 50 years. However, the
 mechanics of these oscillations are poorly understood. Here we utilize the
 recently developed Dynamic Assimilation Techniques (DAT) for measuring the
 rate of CO2 assimilation to increase our understanding of what
 physiological condition is required to cause oscillations. We found that
 TPU limiting conditions alone were insufficient, and that plants must
 enter TPU limitation quickly to cause oscillations. We found that ramps of
 CO2 caused oscillations proportional in strength to the speed of the ramp,
 and that ramps induce oscillations with worse outcomes than oscillations
 induced by step change of CO2 concentration. An initial overshoot is
 caused due to a temporary excess of available phosphate. During the
 overshoot, the plant out-performs steady state TPU and ribulose
 1,5-bisphosphate regeneration limitations of photosynthesis but cannot
 exceed the rubisco limitation. We performed additional optical
 measurements which support the role of photosystem I reduction and
 oscillations in availability of NADP+ and ATP in supporting oscillations.
description: This data was collected in laboratory in East Lansing MI using
 LI-COR LI-6800 instruments capable of dynamic assimilation measurements
 and modified to be able to take optical and fluorescent measurements. Data
 was processed using R scripts and collated into tables that are presented
 in this dataset.
description: All data is presented in comma delimited tabular text.
DOI: 10.5061/dryad.1vhhmgqx1
title: Simulated cannabis days-of-use data

description: Background: The numbers of days that people consume alcohol and other
 drugs over a fixed time interval, such as 28 days, are often collected in
 surveys for research in the addictions field. The presence of an upper
 bound on these variables can result in response distributions with
 "ceiling effects". Also, if some peoples’ substance use
 behaviors are characterized by various weekly patterns of use, summaries
 of substance days-of-use over longer periods can exhibit multiple modes.
 Multiple modes can also result from "heaping" of responses when
 respondents are unsure about the precise value. These characteristics of
 substance days-of-use data mean that models assuming common parametric
 response distributions will not always provide a good fit. Repository
 contents: Simulate longitudinal cannabis days-of-use over 28-day intervals
 intended to reproduce characteristics of data reported by respondents to
 an Australian survey of illicit drug users run over 4 waves during the
 COVID-19 pandemic in Australia in 2020–21. The dataset includes generated
 subject_id and survey_wave and iso explanatory variables, where iso is a
 dummy variable indicating subjects that were in quarantine or isolation at
 the time of the 28-day interval. R-code to fit proportional-odds and
 continuation-ratio ordinal models as well as binomial, beta-binomial,
 negative binomial and hurdle negative binomial models to these data are
 available at a linked companion website.
description: We fitted a Bayesian multinomial model to reported cannabis
 days-of-use over four 28-day intervals (four survey waves) during the
 COVID-19 pandemic in Australia. Cannabis days-of-use was modeled as a
 nominal categorical variable with 29 levels, one for each possible
 response (0 days, 1 day, ..., 28 days). The model,
 fitted to responses by 443 illicit drug users across four survey waves,
 included only survey wave and isolation status (in isolation or quarantine
 yes/no) as explanatory variables with subject_id as a random
 intercept. A simulated sample of 600 participants was
 generated by twice subsampling 300 subject_ids without replacement from
 the full set of 443. Most participants will have been selected in both
 subsamples. A single cannabis days-of-use was simulated
 for 2 subsamples x 300 subject_ids x 4 survey waves = 2400 28-day
 intervals. The cannabis days of use simulated response was generated by a
 single draw from the posterior predictive distribution for each
 subsample. The survey wave and isolation explanatory
 variables and subject_id are included in the supplied dataset. Survey
 participants are not identifiable.
description: The data are provided in an R dataset,
 synthetic_cannabis_use.RData. In order to run R code
 accompanying the dataset, the Rstan software package https://mc-stan.org/users/interfaces/rstan also needs to be installed.
DOI: 10.5061/dryad.h18931zqj
title: Spatial controls on eco-evolutionary processes in microbial communities

description: Microorganisms are the most biodiverse life forms on our planet, yet we
 know little about the spatial processes underlying their ecology and
 evolution. Here, we highlight the importance of two spatial processes that
 act on individual cells – spatial intermixing of different populations and
 mechanical cell shoving during growth – to improve our understanding of
 microbial eco-evolutionary dynamics. Using an individual-based model, we
 show that the coexistence between slow- and fast-growing populations
 becomes highly constrained under two conditions: when the slow- and
 fast-growing populations are highly spatially intermixed and when the
 ability to shove other cells (both conspecific and heterospecific) is
 weak. The potential for evolution through plasmid-mediated horizontal gene
 transfer between slow- and fast- growing populations also becomes
 restricted in the same scenario. Our modeling highlights that ecological
 constraints can dampen evolutionary opportunities within microbial
 communities due to variation in spatial intermixing and mechanical shoving
 at the cellular scale.
description: Data are all generated using Cellmodeller.
DOI: 10.5061/dryad.qv9s4mwjn
title: Community biomass is driven by dominants and their characteristics –the insight from a field biodiversity experiment with realistic species loss scenario

description: 1. Revealing the role of biodiversity in ecosystem functioning (BEF) has
 been a major focus of ecological research over recent decades. In general,
 results from artificially assembled communities point to the important
 role of biodiversity showing that the loss of species has a negative
 effect on various ecosystem functions (mostly assessed by aboveground peak
 biomass). However, the evidence from manipulations of natural communities
 is scarce and results are often contradictory between these two
 approaches. In particular, the importance of species dominance for
 ecosystem functioning remains poorly understood. 2. We created a gradient
 of plant species richness in a meadow community following a realistic
 species loss scenario (removal of less abundant species) to test the
 effect of diversity on community biomass and assess the importance of
 subordinate species compared to dominants in a five-year experiment. 3.
 Contrasting with the results of BEF experiments with artificial assembly,
 we did not find any relationship between plant species diversity and
 aboveground biomass across the timeframe of the experiment. We provide
 evidence that dominant species’ identity and traits are the main drivers
 of community biomass, because dominant species were able to maintain
 biomass production after substantial species loss. Further, dominants
 prevented community biomass from declining and biomass was indirectly
 influenced not by species richness but through differences in functional
 diversity. Our results support the mass ratio hypothesis, showing a much
 bigger effect of dominant species on community biomass production and
 hints at the rather minor importance of the complementarity effect between
 species. We emphasize that BEF research should more focus on the role of
 dominant species in maintaining various ecosystem functions. 4. Synthesis.
 Species diversity is a poor predictor of community aboveground biomass
 production and dominant species can effectively compensate the total
 production after substantial loss of other species in a grassland
 community.
DOI: 10.5061/dryad.vx0k6djwf
title: Amacrine cells differentially balance zebrafish colour circuits in the central and peripheral retina

description: In vertebrate vision, the feature-extracting circuits of the inner retina
 are driven by photoreceptors whose outputs are already pre-processed. In
 zebrafish, for example, outer retinal circuits split “colour” from
 “greyscale” information across all four cone-photoreceptor types. How does
 the inner retina process this incoming spectral information while also
 combining cone signals to shape new greyscale functions? We address this
 question by imaging the light-driven responses of amacrine cells (ACs) and
 bipolar cells (BCs) in larval zebrafish, in the presence and
 pharmacological absence of inner retinal inhibition. We find that amacrine
 cells exert distinct effects on greyscale processing depending on retinal
 region, as well as contributing to the generation of colour opponency in
 the central retina. However, in the peripheral retina amacrine cells
 enhanced opponency in some bipolar cells while at the same time
 suppressing pre-existing opponency in others, such that the net change in
 the number of colour-opponent units was essentially zero. To achieve this
 ‘dynamic balance’ ACs counteracted intrinsic colour opponency of BCs via
 the On-channel. Consistent with these observations, Off-stratifying ACs
 were exclusively achromatic, while all colour opponent ACs stratified in
 the On-sublamina. This study reveals that the central and peripheral
 retina of larval zebrafish employ fundamentally distinct inhibitory
 circuits to control the interaction between greyscale- and
 colour-processing. Differential actions on the On- and Off-channels
 control the transmission of colour-opponent signals in the periphery.
description: All the imaging data was collected under two-photon microscope,
 the data was then further processed using ImageJ or custom-written script
 in Igor Pro.
description: the *.h5 files can be opened by any software support HDF5
 format.
DOI: 10.5061/dryad.x3ffbg7p2
title: Functional interactions among neurons within single columns of macaque V1

description: Recent developments in high-density neurophysiological tools now make it
 possible to record from hundreds of single neurons within local, highly
 interconnected neural networks. Among the many advantages of such
 recordings is that they dramatically increase the quantity of
 identifiable, functional interactions between neurons
 thereby providing an unprecedented view of local circuits. Using
 high-density, Neuropixels recordings from single neocortical columns of
 primary visual cortex in nonhuman primates, we identified 1000s of
 functionally interacting neuronal pairs using
 established crosscorrelation approaches. Our results reveal clear and
 systematic variations in the synchrony and strength of
 functional interactions within single cortical columns.
 Despite neurons residing within the same column, both measures
 of interactions depended heavily on the vertical
 distance separating neuronal pairs, as well as on the similarity of
 stimulus tuning. In addition, we leveraged the statistical power afforded
 by the large numbers of functionally interacting pairs
 to categorize interactions between neurons based on
 their crosscorrelation functions. These analyses identified distinct,
 putative classes of functional interactions within the
 full population. These classes of
 functional interactions were corroborated by their
 unique distributions across defined laminar compartments and were
 consistent with known properties of V1 cortical circuitry, such as the
 lead-lag relationship between simple and complex cells. Our results
 provide a clear proof-of-principle for the use of high-density
 neurophysiological recordings to assess circuit-level interactions within
 local neuronal networks.
description: The activity of V1 neurons was recorded in two anesthetized
 macaque monkeys (M1, M2) using high-density, multi-contact Neuropixel
 probes (version 3A; IMEC Inc, Belgium). Probes were inserted into the
 lateral operculum of V1 with the aid of a surgical microscope at angles
 nearly perpendicular to the cortical surface. In each of the 5
 experimental sessions (3 in M1, 2 in M2), we measured the visual responses
 of 115–221 simultaneously recorded neurons to drifting gratings presented
 at varying orientations (total = 802 neurons). To estimate the
 functional interactions between pairs of neurons recorded simultaneously
 within columns of V1, we computed cross-correlograms (CCGs) using the 802
 visually responsive neurons recorded across sessions. CCGs were computed
 from the spike trains of 68,579 pairs of simultaneously recorded neurons
 (6,555–24,310 pairs/session).
description: Software of MATLAB (The MathWorks Inc.) is required to open the
 data files. Users may register and download the software at https://www.mathworks.com.
DOI: 10.15468/dl.zze6gf
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Etmopterus lailae"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003341-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2z34tmpqh
title: Rapid and transient evolution of local adaptation to seasonal host fruits in an invasive pest fly

description: Both local adaptation and adaptive phenotypic plasticity can influence the
 match between phenotypic traits and local environmental conditions. Theory
 predicts that environments stable for multiple generations promote local
 adaptation, while highly heterogeneous environments favor adaptive
 phenotypic plasticity. However, when environments have periods of
 stability mixed with heterogeneity, the relative importance of local
 adaptation and adaptive phenotypic plasticity is unclear. Here, we used
 Drosophila suzukii as a model system to evaluate the relative influence of
 genetic and plastic effects on the match of populations to environments
 with periods of stability from three to four generations. This invasive
 pest insect can develop within different fruits, and persists throughout
 the year in a given location on a succession of distinct host fruits, each
 one being available for only a few generations. Using reciprocal common
 environment experiments of natural D. suzukii populations
 collected from cherry, strawberry and blackberry, we found that both
 oviposition preference and offspring performance were higher on medium
 made with the fruit from which the population originated, than on media
 made with alternative fruits. This pattern, which remained after two
 generations in the laboratory, was analyzed using a statistical method we
 developed to quantify the contributions of local adaptation and adaptive
 plasticity in determining fitness. Altogether, we found that genetic
 effects (local adaptation) dominate over plastic effects (adaptive
 phenotypic plasticity). Our study demonstrates that spatially and
 temporally variable selection does not prevent the rapid evolution of
 local adaptation in natural populations. The speed and strength of
 adaptation may be facilitated by several mechanisms including a large
 effective population size and strong selective pressures imposed by host
 plants.
DOI: 10.5061/dryad.b8gtht7gq
title: Data for: Using a demographic model to project the long-term effects of fire management on tree biomass in Australian savannas

description: Tropical savannas are characterised by high primary productivity and high
 fire frequency, such that much of the carbon captured by vegetation is
 rapidly returned to the atmosphere. Hence, there have been suggestions
 that management-driven reductions in savanna fire frequency and/or
 severity could significantly reduce greenhouse gas emissions and sequester
 carbon in tree biomass. However, a key knowledge gap is the extent to
 which savanna tree biomass will respond to modest shifts in fire regimes
 due to plausible, large-scale management interventions. Here, we: (1)
 characterise relationships between the frequency and severity of fires and
 key demographic rates of savanna trees, based on long-term observations in
 vegetation monitoring plots across northern Australia; (2) use these
 relationships to develop a process-explicit demographic model describing
 the effects of fire on savanna tree populations; and (3) use the
 demographic model to address the question: to what extent is it feasible,
 through the strategic application of prescribed burning, to increase tree
 biomass in Australian tropical savannas? Our long-term tree monitoring
 dataset included observations of 12,344 tagged trees in 236 plots,
 monitored for between 3 and 24 years. Analysis of this dataset showed that
 frequent high-severity fires significantly reduced savanna tree
 recruitment, survival and growth. Our demographic model suggested that:
 (1) despite the negative effects of frequent high-severity fires on
 demographic rates, savanna tree biomass appears to be suppressed by only a
 relatively small amount by contemporary fire regimes, characterised by a
 mix of low- to high-severity fires; and (2) plausible, management-driven
 reductions in the frequency of high-severity fires are likely to lead to
 increases in tree biomass of about 11.0 t DM ha–1 (95% confidence
 interval: -1.2–20.8) over a century. Accounting for this increase in
 carbon storage could generate significant carbon credits, worth on average
 three times those generated annually by current greenhouse gas (methane
 and nitrous oxide) abatement projects, and has the potential to
 significantly increase the economic viability of fire/carbon projects,
 thereby promoting ecologically sustainable management of tropical savannas
 in Australia and elsewhere. This growing industry has the potential to
 bring much-needed economic activity to savanna landscapes, without
 compromising important natural and cultural values.
description: Data files are in comma separated text file format.
DOI: 10.7280/d1v11s
title: Monthly mean temperature and salinity outputs from the Southern Ocean high-resolution (SOhi) simulation

description: The Southern Ocean high-resolution (SOhi) is a MITgcm simulation developed
 to understand ocean-ice interactions along the margin of Antarctica and
 better quantify ocean thermal forcing on the ice shelves. SOhi is a
 high-resolution extension of SOSE with a longitudinal resolution of 1/24
 degrees (~1.2 km at 75S) from 85.5S and telescopes to 1/12 between 40S and
 30S. It has a northern boundary at the equator forced by ECCOv4r4, uses a
 locally improved bathymetric model from GEBCO 2020, atmospheric forcing
 from ERA-5, and contains thermodynamically active ice shelves. SOhi is
 used to understand the mechanisms of heat transport around Antarctica in
 order to best constrain ocean thermal forcing on the Antarctic Ice Sheet.
description: Monthly mean potential temperature (C) and practical salinity
 (psu) outputs for 12 months of SOhi simulations spanning October 2005 to
 September 2006 - including the ice draft and modified GEBCO 2020
 bathymetry used in the SOhi simulation.
description: # Southern Ocean high-resolution (SOhi) simulation outputs --- Monthly
 mean potential temperature (C) and practical salinity (psu) outputs for 12
 months of SOhi simulations spanning October 2005 to September 2006. ##
 Description of the data and file structure Each monthly SOhi outputs are
 store in a zipped - .zarr format. Unzip the provide data and the zarr
 store can be accessed with python using: ```python import zarr dataset =
 zarr.open('path/to/SOhi_outputs.zarr', mode='r')
 var_data = dataset['var_name'] ``` **Replace
 "var_name" with variable name.** **Available variables in
 monthly mean outputs are:** `lat` dim = (2344) Latitude dimension at
 cell's center `lon` dim = (8640) Longitude dimension (0 - 360) at
 cell's center `depth` dim = (225) Depth dimension at cell's
 center `date` dim = (1) Date of data in 'yyyy_mm' string `theta`
 dim = (225, 2344, 8640) SOhi's temperature field in potential
 temperature (C). Dimensions are (depth, lat, lon). No data is replaced
 with np.nan. `salt` dim = (225, 2344, 8640) SOhi's salinity field in
 practical salinty (psu). Dimensions are (depth, lat, lon). No data is
 replaced with np.nan. **Bathymetry and Icedraft area available in
 misc.zarr** `icedraft` dim = (2344, 8640) Depth of the ice draft (in
 meter) from the surface `bathymetry` dim = (2344, 8640) Depth of the sea
 floor (in meters) from the surface
DOI: 10.5061/dryad.1g1jwsv11
title: Seasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation (Part 1/2)

description: Long-term field monitoring of leaf pigment content is informative for
 understanding plant responses to environments distinct from regulated
 chambers but is impractical by conventional destructive measurements. We
 developed PlantServation, a method incorporating robust image-acquisition
 hardware and deep learning-based software that extracts leaf color by
 detecting plant individuals automatically. As a case study, we applied
 PlantServation to examine environmental and genotypic effects on the
 pigment anthocyanin content estimated from leaf color. We analyzed
 &gt;4 million images of small individuals of four Arabidopsis species
 in the field, where the plant shape, color, and background vary over
 months. Past radiation, coldness, and precipitation significantly affected
 the anthocyanin content. The synthetic allopolyploid A. kamchatica
 recapitulated the fluctuations of natural polyploids by integrating
 diploid responses. The data support a long-standing hypothesis stating
 that allopolyploids can inherit and combine the traits of progenitors.
 PlantServation facilitates the study of plant responses to complex
 environments termed “in natura”.
description: Top-view images of <em>Arabidopsis</em> were
 collected multiple times per day using commercial RGB cameras in a common
 garden in Switzerland for three seasons.