cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vx0k6djv5
title: Belowground ecosystem engineers enhance biodiversity and function in a polluted ecosystem

description: Many important ecosystem functions are underpinned by belowground
 biodiversity and processes. Marine sediments, one of the most abundant
 habitats on earth, are essential to the mineralisation of organic matter.
 However, they are increasingly polluted by urban activities leading to the
 loss of biodiversity and the functions they provide. While traditional
 sediment remediation strategies are focussed on microbial and engineering
 solutions, we propose that the reintroduction of belowground ecosystem
 engineers (bioturbators) is important to rehabilitate polluted sediments
 and drive recovery of their functions in urban coastal ecosystems. We
 tested this notion by introducing bioturbators to nutrient polluted
 sediments to assess their survival, as well as their capacity to drive
 biodiversity and oxygenation and their potential to remediate nutrient
 pollution. Polychaete worms Diopatra aciculata and clams Katelysia sp.
 were added to mesocosms (ex-situ), and the worms also added to
 experimental plots in-situ. Potential for remediation was assessed with
 measures of nutrient content. All animals survived when introduced to
 polluted sediments and showed no evidence of sub-lethal effects. Worms
 oxygenated sediments and reduced organic matter content by up to 50%
 in-situ. The worms also drove shifts in the receiving communities at all
 locations and increased the number of taxa at one location. On the other
 hand, the effects of clams were variable, showing opposite effects in
 organic matter content at different sites and levels of pollution.
 Synthesis and applications. Global seafloor habitats are becoming
 increasingly degraded and novel strategies that combine biodiversity
 restoration with remediation are urgently needed to return function.
 Tube-building bioturbators can stimulate nutrient processing in sediments
 proving multiple functional outcomes, but these effects are dependent on
 the receiving environment. In areas with medium levels of pollution, they
 can kick-start recovery in a feedback loop whereby bioturbation increases
 oxygenation and nutrient remediation, shifting sediment biodiversity and
 contributing to further recovery. This can drive long-term changes in
 sediment communities, particularly in urban areas where unvegetated
 sediments are conspicuous.
description: As specied in article.
DOI: 10.5061/dryad.j3tx95xhc
title: Data from: Estimating maize harvest index and nitrogen concentrations in grain and residue using globally available data

description: Estimates of crop nitrogen (N) uptake and offtake are critical in
 estimating N balances, N use efficiencies and potential losses to the
 environment. Calculation of crop N uptake and offtake requires estimates
 of crop product yield (e.g. grain or beans) and crop residue yield (e.g.
 straw or stover) and the N concentration of both components. Yields of
 crop products are often reasonably well known, but those of crop residues
 are not. While the harvest index (HI) can be used to interpolate the
 quantity of crop residue from available data on crop product yields,
 harvest indices are known to vary across locations, as do N concentrations
 of residues and crop products. The increasing availability of crop data
 and advanced statistical and machine learning methods present us with an
 opportunity to move towards more locally relevant estimates of crop
 harvest index and N concentrations using more readily available data. This
 dataset includes maize field experiment data. It is a culmination of
 summary statistic data collected from the literature as well as raw data
 requested from various researchers and organisations from around the
 world. These data will enable more locally relevant estimates of crop
 nutrient offtake, nutrient balances and nutrient use efficiency at
 national, regional or global levels, as part of strategies towards more
 sustainable nutrient management.
description: Maize field experiment data were collected from a search across
 the world using two main sources. One source was from summary statistics
 gleaned from the peer reviewed literature and the other source was for raw
 datasets obtained through requests of various researchers and
 organisations. Further details of how these two sources of data were
 collected and processed are described by Ludemann et al. (2022).
 Reference Ludemann CI, Hijbeek R, van Loon MP,
 Murrell ST, Dobermann A, van Ittersum MK, 2022 Estimating maize harvest
 index and nitrogen concentrations in grain and residue using globally
 available data <em>Field Crops Research</em> 284:108578
 https://doi.org/10.1016/j.fcr.2022.108578
DOI: 10.5061/dryad.rn8pk0pdb
title: Genotype data for: Population genetics reveals divergent lineages and ongoing hybridization in a declining migratory fish species complex

description: Deciphering the effects of historical and recent demographic processes
 responsible for the spatial patterns of genetic diversity and structure is
 a key objective in evolutionary and conservation biology. Using population
 genetic analyses, we investigated the demographic history, the
 contemporary genetic diversity and structure, and the occurrence of
 hybridization and introgression of two species of anadromous fish with
 contrasting life history strategies and which have undergone recent
 demographic declines, the allis shad (Alosa alosa) and the twaite shad
 (Alosa fallax). We genotyped 706 individuals from 20 rivers and 5 sites at
 sea in Southern Europe at thirteen microsatellite markers. Genetic
 structure between populations was lower for the nearly semelparous species
 A. alosa, which disperses greater distances compared to the iteroparous
 species, A. fallax. Individuals caught at sea were assigned at the river
 level for A. fallax and at the region level for A. alosa. Using an
 approximate Bayesian computation framework, we inferred that the most
 likely long term historical divergence scenario between both species and
 lineages involved historical separation followed by secondary contact
 accompanied by strong population size decline. Accordingly, we found
 evidence for contemporary hybridization and bidirectional introgression
 due to gene flow between both species and lineages. Moreover, our results
 support the existence of at least one distinct species in the
 Mediterrannean sea: A. agone in Golfe du Lion area, and another divergent
 lineage in Corsica. Overall, our results shed light on the interplay
 between historical and recent demographic processes and life history
 strategies in shaping population genetic diversity and structure of
 closely related species. The recent demographic decline of these species’
 populations and their hybridization should be carefully considered while
 implementing conservation programs.
DOI: 10.5061/dryad.rr4xgxdbj
title: Single-cell phenotypic characteristics of tolerance under recurring antibiotic exposure in Escherichia coli

description: Non-heritable drug resistance, such as tolerance and persistence towards
 antibiotics, is little characterized compared to genetic resistance.
 Tolerance and persistence allow cells to survive application of
 antibiotics that are bactericidal to non-tolerant cells. Non-heritable
 drug resistance challenges antibiotic treatment, particularly of recurrent
 infections, and have implications towards heritable resistance evolution.
 Tolerant cells have commonly been characterized as growth arrested cells
 prior and during antibiotic application that quickly resume growth
 post-application. Here, we explore characteristic of tolerant and
 susceptible E. coli single bacteria cells to different levels of recurrent
 antibiotic exposure and quantify their occurrence. In using a high
 throughput single-cell microfluidic device, we find that tolerant cells
 reduce their growth rate by about 50%, but contrary to previous findings
 do not go into growth arrest or near growth arrest. The growth reduction
 is induced by antibiotic exposure and not caused by a stochastic switch or
 predetermined state as previously described. Cells exhibiting constant
 intermediate growth survived best under antibiotic exposure and selection
 did not primarily act on fast growing cells, as expected for a β-lactam
 antibiotic. Control experiments on population cultures confirmed and
 challenged scaling of single cell findings to population level processes.
 Our findings suggest a prevalent type of tolerance that differs from
 previously described tolerance and persister characteristics. Our
 described characteristics and its high frequency of occurrence supports
 acclaims of an underappreciated role of tolerant cells towards resistance
 evolution.
description: Single-cell bacteria data on survival, size, growth/cell
 elongation, division, under recurring exposure to eight different
 concentrations of ampicillin. Data was collected using a mircofluidic
 device, a mother machine. Original images were processed using a custom
 software for cell segmentation and tracking. A parallel
 experiment at the cell culture level with recurent exposure of antibiotics
 at different concentrations has been performed counting colony forming
 units, as well as a control experiment under constant antibiotic
 concentrations measuring optical density (OD_600).
DOI: 10.5061/dryad.jm63xsjdd
title: Histological stacks for: Vestigial structures and variation in the evolution of the marsupial mammal dental development: A study of the Woolly Opossum Caluromys philander

description: The pattern of dental replacement in marsupial mammals has received much
 attention for its derived nature and potential relationship to the life
 history of the group. However, few species have been studied thoroughly
 and little is known about the embryonic structures and their use in
 addressing issues of homology and dental evolution in general. We studied
 a developmental series of ten individuals of pouch young Caluromys
 philander to thoroughly document dental development with histological
 sections and 3D models of dental series. This dataset contains the raw
 TIFF stacks for the above histological sections. These may be used for
 direct histological analysis, or to generate 3D-reconstructions using
 software such as Fiji and TrakEM2.
description: Histological specimens were imaged using a Leica DM2500M
 microscope and DFC 240 C camera (0.55x mount) and imported using Leica
 IM50 image manager. The deposited images are raw, unedited TIFF files of
 the specimens, alongside periodic duplicates which also contain a scale
 bar.
description: Beyond using software to unzip the files, no additional software
 is required. Note: † Deceased.
DOI: 10.57707/fmi-b2share.xsy2e-4bc68
title: Data for the manuscript "Evaluating the potential of acoustic data for avian migration analyses  in comparison with citizen science and weather radar observations" by Weisshaupt et al. submitted to J AppEcol

description: Tables and figures of the supporting information of the manuscript "Evaluating the potential of acoustic data for avian migration analyses in comparison with citizen science and weather radar observations" submitted to J App Ecol by Nadja Weisshaupt
DOI: 10.5061/dryad.5dv41ns7z
title: Correlative 3D SBFSEM data from: Intermittent bulk release of human cytomegalovirus

description: Human Cytomegalovirus (HCMV) can infect a variety of cell types by using
 virions of varying glycoprotein compositions. It is still unclear how this
 diversity is generated, but spatio-temporally separated envelopment and
 egress pathways might play a role. So far, one egress pathway has been
 described in which HCMV particles are individually enveloped into small
 vesicles and are subsequently exocytosed continuously. However, some
 studies have also found enveloped virus particles inside multivesicular
 structures but could not link them to productive egress or degradation
 pathways.We used a novel 3D-CLEM workflow allowing us to investigate these
 structures in HCMV morphogenesis and egress at high spatio-temporal
 resolution. We found that multiple envelopment events occurred at
 individual vesicles leading to multiviral bodies (MViBs), which
 subsequently traversed the cytoplasm to release virions as intermittent
 bulk pulses at the plasma membrane to form extracellular virus
 accumulations (EVAs). Our data support the existence of a novel bona fide
 HCMV egress pathway, which opens the gate to evaluate divergent egress
 pathways in generating virion diversity.
description: Details on data acquisition and processing can be found in the
 original publication. The uploaded here are the unprocessed raw
 data.
description: The data are in the proprietary dm4 format as saved by the
 acquisition software. However, they can be easily opened and converted in
 Fiji/ImageJ with the Bioformats importer. We recommend alignment of the
 stack and binning of 2x2 for working with the data.
DOI: 10.5061/dryad.1c59zw3xv
title: Cortical adaptation to sound reverberation

description: In almost every natural environment, sounds are reflected by nearby
 objects, producing many delayed and distorted copies of the original
 sound, known as reverberation. Our brains usually cope well with
 reverberation, allowing us to recognize sound sources regardless of their
 environments. In contrast, reverberation can cause severe difficulties for
 speech recognition algorithms and hearing-impaired people. The present
 study examines how the auditory system copes with reverberation. We
 trained a linear model to recover a rich set of natural, anechoic sounds
 from their simulated reverberant counterparts. The model neurons achieved
 this by extending the inhibitory component of their receptive filters for
 more reverberant spaces, and did so in a frequency-dependent manner. These
 predicted effects were observed in the responses of auditory cortical
 neurons of ferrets in the same simulated reverberant environments.
 Together, these results suggest that auditory cortical neurons adapt to
 reverberation by adjusting their filtering properties in a manner
 consistent with dereverberation.
description: Spike data were recorded using Neuropixels electrodes in the
 auditory cortex of anaesthetised ferrets.
description: We have provided our Matlab scripts for generating our figures on
 Github: https://github.com/PhantomSpike/DeReverb
DOI: 10.5061/dryad.b5mkkwhg7
title: Information integration for nutritional decision-making in desert locusts

description: Swarms of the migratory desert locust can extend over several hundred
 square kilometres, and starvation compels this ancient pest to devour
 everything in its path. Theory suggests that gregarious behaviour benefits
 foraging efficiency over a wide range of spatial food distributions.
 However, despite the importance of identifying the processes by which
 swarms locate and select feeding sites to predict their progression, the
 role of social cohesion during foraging remains elusive. We investigated
 the evidence accumulation and information integration processes that
 underlie locusts' nutritional decision-making by employing a Bayesian
 formalism on high-resolution tracking data from foraging locusts. We
 tested individual gregarious animals and groups of different sizes in a
 2-choice behavioural assay in which food patch qualities were either
 different or similar. We then predicted the decisions of individual
 locusts based on personally acquired and socially derived evidence by
 disentangling the relative contributions of each information class. Our
 study suggests that locusts balance incongruent evidence but reinforce
 congruent ones, resulting in more confident assessments when evidence
 aligns. We provide new insights into the interplay between personal
 experience and social context in locust foraging decisions which
 constitute a powerful empirical system to study local individual decisions
 and their consequent collective dynamics.
DOI: 10.5061/dryad.hmgqnk9kf
title: Ecological data on evergreen forest types of central plains Cambodia

description: Four different lowland evergreen forest types, each with a unique species
 composition and ecological characteristics is described from the central
 plains, Cambodia. Through six botanical expeditions, we collected data on
 the forest types using 50x10 = 500 sqm strip sample plots (n=119); i)
 riverine forest dominated by Dipterocarpus costatus (Dipterocarpaceae):
 ii) tall dipterocarp forest dominated by Anisoptera costata
 (Dipterocarpaceae); iii) swamp forest dominated by Macaranga triloba
 (Euphorbiaceae); and iv) “Sralao” forest with a monodominance of
 Lagerstroemia cochinchinensis (Lythraceae). This dataset includes i) a
 matrix showing the occurrence of different species within the 119 sample
 plots, ii) a summary of forest structure and diversity index values for
 the 119 individual sample plots, iii) a summary for individual species
 within forest types of mean, standard error and coefficient of variation
 of the mean for diameter, density, basal area and frequency, as well as
 relative density, dominance and frequency and importance value index
 (IVI), iv) a summary of forest structure variables for diameter classes
 and forest types. The dataset was analyzed and used to characterize and
 compare the four evergreen forest types in the publication: Theilade et
 al. 2022. Evergreen forest types of the central plains in Cambodia:
 floristic composition and ecological characteristics; published in Nordic
 Journal of Botany. https://doi.org/10.1111/njb.03494
description: Botanical expeditions in 2007, 2008, 2009, 2011, 2012 and 2013. A
 total of 119 Gentry plots were surveyed and all trees above 10 cm DBH was
 identified. Herbarium specimens were collected and species identifications
 checked at Bangkok Forest Herbarium and the herbarium at Chiang Mai
 University.
DOI: 10.5061/dryad.nk98sf7w7
title: An open-access database of infectious disease transmission trees to explore superspreader epidemiology

description: Historically, emerging and reemerging infectious diseases have caused
 large, deadly, and expensive multinational outbreaks. Often outbreak
 investigations aim to identify who infected whom by reconstructing the
 outbreak transmission tree, which visualizes transmission between
 individuals as a network with nodes representing individuals and branches
 representing transmission from person to person. We compiled a database,
 called OutbreakTrees, of 382 published, standardized transmission trees
 consisting of 16 directly transmitted diseases ranging in size from 2 to
 286 cases. For each tree and disease, we calculated several key
 statistics, such as tree size, average number of secondary infections, the
 dispersion parameter, and the proportion of cases considered
 superspreaders, and examined how these statistics varied over the course
 of each outbreak and under different assumptions about the completeness of
 outbreak investigations. We demonstrated the potential utility of the
 database through 2 short analyses addressing questions about superspreader
 epidemiology for a variety of diseases, including Coronavirus Disease 2019
 (COVID-19). First, we found that our transmission trees were consistent
 with theory predicting that intermediate dispersion parameters give rise
 to the highest proportion of cases causing superspreading events.
 Additionally, we investigated patterns in how superspreaders are infected.
 Across trees with more than 1 superspreader, we found preliminary support
 for the theory that superspreaders generate other superspreaders. In sum,
 our findings put the role of superspreading in COVID-19 transmission in
 perspective with that of other diseases and suggest an approach to further
 research regarding the generation of superspreaders. These data have been
 made openly available to encourage reuse and further scientific inquiry.
description: The code using these data to reproduce the figures in Taube et
 al. "An open-access database of infectious disease transmission trees
 enables exploration of superspreader epidemiology" can be found on
 Github at https://github.com/DrakeLab/taube-transmission-trees. OutbreakTrees, the database of transmission trees underlying these data, can be found at https://outbreaktrees.ecology.uga.edu/.
DOI: 10.5061/dryad.n8pk0p2xw
title: Quantifying phenology and migratory behaviours of hummingbirds using single-site dynamics and mark-detection analyses

description: Nuanced understanding of seasonal movements of partially migratory birds
 is paramount to species and habitat conservation. Using nascent
 statistical methods, we identified migratory strategies of birds outfitted
 with radio-frequency identification (RFID) tags detected at RFID feeders
 in two sites in California, USA. We quantified proportions of migrants and
 residents and the seasonal phenology for each movement strategy in Allen’s
 and Anna’s hummingbirds; we also validated our methodology by fitting our
 model to obligate migratory black-chinned hummingbirds. Allen’s and Anna’s
 hummingbirds exhibited characteristics of facultative migratory behaviour.
 We also quantified apparent annual survival for each migratory strategy
 and found that residents had significantly higher probabilities of
 apparent survival. Low survival estimates for migrants suggest that a high
 proportion of birds in the migrant group permanently emigrated from our
 study sites. Considered together, our analyses suggest that hummingbirds
 in both northern and southern California sites partake in diverse and
 highly plastic migratory behaviours. Our assessment elucidates the
 dynamics underlying idiosyncratic migratory behaviours of two species of
 hummingbirds, in addition to describing a framework for similar
 assessments of migratory behaviours using the multi-state open robust
 design with state uncertainty (MSORD-SU) model and single-site dynamics.
description: The dataset "EnglishEtAl2022_CaptureHistories.csv"
 includes individual monthly detection histories for each tagged bird in
 the study. Each detection history comprises 36 characters corresponding to
 each month from February 2018 to January 2021.
 Detections were encoded with one of three characters: `0` denotes
 no detection within the monthly period, `u` denotes that the bird was
 detected, but detection took place outside of the 3 winter months
 (November to January) and its state is therefore unknown, and lastly `R`
 denotes that a bird was detected during winter and is therefore classified
 as a resident.
description: These data were analysed using Program MARK via RMark version
 2.2.7.
DOI: 10.57707/fmi-b2share.cgxfh-nth88
title: Bird densities from the Vihti radar for the manuscript "Evaluating the potential of acoustic data for avian migration analyses  in comparison with citizen science and weather radar observations" by Weisshaupt et al.

description: Bird densities from April-May and Aug-Oct 2022 obtained from the Vihti weather radar used in the manuscript "Evaluating the potential of acoustic data for avian migration analyses in comparison with citizen science and weather radar observations" submitted by Nadja Weisshaupt
DOI: 10.57707/fmi-b2share.e1pqx-wj234
title: Bird densities from the Vihti radar for the manuscript "Evaluating the potential of acoustic data for avian migration analyses  in comparison with citizen science and weather radar observations" by Weisshaupt et al.

description: Bird densities from April-May and Aug-Oct 2022 obtained from the Vihti weather radar used in the manuscript "Evaluating the potential of acoustic data for avian migration analyses in comparison with citizen science and weather radar observations" submitted by Nadja Weisshaupt