cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zs7h44j98
title: Data for spatial and temporal refugia for an insect population declining due to climate change

description: Insect declines have been reported worldwide, although the particular
 causes of the declines may be complex and are poorly understood. Meadow
 spittlebugs were one of the most abundant insects in the coastal prairie
 along the California coast 40 years ago but have largely disappeared.
 Evidence links this decline to changing climatic conditions, which have
 reduced survival of eggs and neonates. We identified several refugia where
 meadow spittlebug populations have persisted amidst unfavorable
 conditions. Protection from desiccating winds was the common attribute of
 these refugia. Following a wet year, adult meadow spittlebugs were able to
 disperse from one refuge that we studied to recolonize coastal prairie
 habitats, although populations declined over the next two drier years.
 Because of their previous high abundance, loss of meadow spittlebugs is
 likely to affect the functioning of this widespread habitat, including
 energy transfer, their host plants, and their predators. In addition,
 meadow spittlebugs are unusual in having been the subject of extensive
 physiological and long-term ecological data, so they can serve as a
 bellwether species, indicating the effects of climate change.
description: These data indicate the number of meadow spittlebug nymphs that
 were observed on cow parsnip plants at various distances away from the
 edge of Owl Canyon. Owl Canyon served as a refugium for this species.
 Surveys were conducted during the summer in 2019 (wet year), 2020 (dry
 year), and 2021 (dry year). During late summer 2020 we collected sweep net
 samples of adult meadow spittlebugs at various distances away from the
 edge of Owl Canyon.
description: The distance in m from the edge of the canyon is shown in column
 A for 2019. Similarly, distance from the canyon is shown in column D for
 2020 and in column G for 2021. The number of meadow spittlebug nymphs per
 plant in 2019, 2020, and 2021 are in column B (Fig 2A), column E (Fig. 2B)
 and column H (Fig 2C) respectively. The number of adult
 meadow spittlebugs in sweep samples is shown in column K at various
 distances (shown in column J) from the edge of the canyon. This
 corresponds to Fig. 3.
DOI: 10.15468/dl.kxtb57
title: Occurrence Download

description: A dataset containing 2332 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cassia javanica"
 ]
}

 The dataset includes 2332 records from 201 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002897-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.63xsj3v2v
title: Imaging dataset for positron emission microscopy of patient-derived tumor organoids

description: Here, we present a microscopy method to
 image 18F-fluorodeoxyglucose and other radiotracers in
 patient-derived tumor organoids with spatial resolution up to 100-fold
 better than that of clinical positron emission tomography (PET). When
 combined with brightfield imaging, this metabolic imaging approach
 functionally mirrors clinical PET/CT scans and provides a quantitative
 readout of cell glycolysis other metabolic processes. 
description: The dataset was collected in a custom-built radioluminescence
 microscope setup. The images are collected by an EMCCD (Hamamatsu). The
 images are raw and unprocessed. 
description: Each image file is accompanied by a metafile that documents all
 the settings used for EMCCD acquisition. The name of the folders describes
 the experiment or specific modality used for imaging. The readme file
 summarizes the abbreviations used in the folder names.
DOI: 10.5061/dryad.zkh1893b5
title: Dataset used in the article: Evaluation of goal recognition systems on unreliable data and uninspectable agents

description: Goal or intent recognition, where one agent recognizes the goals or
 intentions of another, can be a powerful tool for effective teamwork and
 improving interaction between agents. Such reasoning can be challenging to
 perform, however, because observations of an agent can be unreliable and,
 often, an agent does not have access to the reasoning processes and mental
 models of the other agent. Despite this difficulty, recent work has made
 great strides in addressing these challenges. In particular, two
 Artificial Intelligence (AI)-based approaches to goal recognition have
 recently been shown to perform well: goal recognition as planning, which
 reduces a goal recognition problem to the problem of plan generation; and
 Combinatory Categorical Grammars (CCGs), which treat goal recognition as a
 parsing problem. Additionally, new advances in cognitive science with
 respect to Theory of Mind reasoning have yielded an approach to goal
 recognition that leverages analogy in its decision making. However, there
 is still much unknown about the potential and limitations of these
 approaches, especially with respect to one another. Here, we explore this
 space and compare three state-of-the-art approaches to goal recognition
 along two different axes: reliability of observations and inspectability
 of the other agent’s mental model. Overall, we show that no approach
 dominates across all cases and discuss the relative strengths and
 weaknesses of these approaches. Scientists interested in goal recognition
 problems can use this knowledge as a guide to select the correct starting
 point for their specific domains and tasks.  Research Topic:
 Advances in Goal, Plan and Activity Recognition
DOI: 10.5061/dryad.jwstqjq94
title: Strong non-growing season N uptake by deciduous trees in a temperate forest: A 15N isotopic experiment

description: Nitrogen (N) is a critical element for vegetation growth and subsequent
 carbon (C) and nutrient cycling in terrestrial ecosystems. Plant N uptake,
 the only pathway for plants to directly obtain N from soils, is a
 bottleneck process for ecosystem C and N cycling. Ecological theories
 predict that deciduous trees remain dormant and do not take up N during
 winters as no growth occurs during this season. In this study, we adopted
 a 15N isotopic experiment to trace N processes throughout the non-growing
 season in a temperate forest in northern China. The 15N-labeled inorganic
 N (NH4+ and NO3−) and 13C15N-labeled organic N (glycine and
 tyrosine) (equivalent to 150 mg 15N m-2) were applied to soils at
 mid-fall, and the 15N recovery in various components of dominant
 evergreen and deciduous species was analyzed. We found that soil
 N transformation remained active in the winter and microbial N
 immobilization reached its peak in late winter. Surprisingly, deciduous
 species maintained a high N uptake that was comparable with the evergreen
 species throughout the non-growing season. Perennial herbs did not take up
 N until the next spring. All plant species acquired inorganic N and simple
 amino acids, while only the tree species utilized complex amino acids.
 Throughout the non-growing season, evergreen and deciduous trees showed
 higher uptake rates for NH4+ and glycine than NO3− and
 tyrosine, while deciduous shrubs and herbs showed a stronger
 preference for NO3− over other N forms. Synthesis: The finding
 that deciduous trees have strong N uptake in the non-growing season
 challenges the conventional viewpoint that deciduous trees remain dormant
 during non-growing seasons. This mechanism might supplement the algorithm
 in the model representation of N-limited temperate forest ecosystems.
DOI: 10.5061/dryad.0k6djhb13
title: Natural disturbance impacts on trade-offs and co-benefits of forest biodiversity and carbon

description: With accelerating environmental change, understanding the influence of
 forest disturbances and trade-offs between biodiversity and carbon
 dynamics is of high socio-economic importance. Most studies, however, have
 assessed immediate or short-term effects of disturbance, while long-term
 impacts remain poorly understood. Here, using a tree-ring-based approach,
 we modelled the effect of 250 years of disturbances on present-day
 biodiversity indicators and carbon dynamics in well-preserved European
 temperate primary forests. Our results indicated that disturbance legacies
 spanning centuries shaped contemporary forest co-benefits and trade-offs,
 with contrasting, local-scale effects. In the short-term, disturbances
 enhanced carbon sequestration, reaching maximum rates within a
 comparatively narrow post-disturbance window (up to 50 years).
 Concurrently, disturbance diminished aboveground carbon storage, which
 gradually returned to peak levels over centuries. Temporal patterns in
 biodiversity potential were bimodal; the first maximum coincided with the
 short-term post-disturbance carbon sequestration peak, and the second
 occurred during periods of maximum carbon storage in complex old growth.
 However, despite fluctuating local-scale trade-offs, forest biodiversity
 and carbon storage remained stable across the broader study region. These
 findings underscore the dynamic interdependencies of forest processes, and
 highlight the necessity of large-scale conservation programs to
 effectively promote both biodiversity and long-term carbon storage,
 particularly given the accelerating global biodiversity and climate
 crises.
description: The readme file contains an explanation of each of the variables
 in the dataset, its type, and measurement units. Information on how the
 measurements were done can be found in the associated
 manuscript.
DOI: 10.5061/dryad.sn02v6x4d
title: Different DNA methylome, transcriptome and histological features in uterine fibroids with and without MED12 mutations

description: Somatic mutations in Mediator complex subunit 12 (MED12m) have been
 reported as a biomarker of uterine fibroids
 (UFs).  However, the role of MED12m is still unclear in
 the pathogenesis of UFs.  Therefore, we investigated the
 differences in DNA methylome, transcriptome, and histological features
 between MED12m-positive and -negative UFs.  DNA methylomes and
 transcriptomes were obtained from MED12m-positive and -negative UFs and
 myometrium, and hierarchically
 clustered.  Differentially expressed genes in comparison
 with the myometrium and co-expressed genes detected by weighted gene
 co-expression network analysis were subjected to gene ontology enrichment
 analyses.  The amounts of collagen fibers and the number
 of blood vessels and smooth muscle cells were histologically
 evaluated. Hierarchical clustering based on DNA methylation
 clearly separated the myometrium, MED12m-positive, and MED12m-negative
 UFs.  MED12m-positive UFs showed the increased
 activities of extracellular matrix formation, whereas MED12m-negative UFs
 had the increased angiogenic activities and smooth muscle cell
 proliferation. The MED12m-positive and -negative UFs had
 different DNA methylation, gene expression, and histological
 features.  The MED12m-positive UFs form the tumor with a
 rich extracellular matrix and poor blood vessels and smooth muscle cells
 compared to the MED12m-negative UFs, suggesting MED12 mutations affect the
 tissue composition of UFs.
DOI: 10.5061/dryad.t76hdr81n
title: Managing biotic interactions during early seagrass life-stages to improve seed-based restoration

description: 1. Seagrasses are declining globally, and effective restoration actions to
 promote the recovery of degraded meadows are urgently needed. Harnessing
 positive plant interactions during early life stages is considered a
 valuable strategy to improve terrestrial and coastal habitat restoration.
 Yet, its application to seagrass restoration is still in infancy, and very
 little is known on the role played by biotic interactions in shaping newly
 established populations. 2. We assessed the feasibility of manipulating
 intra- and interspecific plant interactions to enhance seed-based
 restoration success using the seagrass Posidonia oceanica as a model.
 Specifically, we investigated in mesocosm whether seed germination
 increased with increasing seed density and whether increasing seedling
 density and planting a pioneer seagrass promoted facilitation among
 seedlings. To do this, seedlings were grown either as a single individual
 or in clumps of medium and high density, with and without Cymodocea
 nodosa, for two years encompassing their most critical growth stage. 3.
 Germination of P. oceanica seeds was not affected by seed density.
 Posidonia oceanica seedlings planted at medium and high density showed
 higher survival than those planted individually but only in the presence
 of C. nodosa. Seedlings planted at medium and at high density with C.
 nodosa performed better than those grown at low density or without C.
 nodosa due to a positive joint effect of intra- and interspecific
 interaction. Cymodocea nodosa plants grown with P. oceanica seedlings at
 high density were larger than those grown alone, indicating a mutualistic
 relationship. 4. Synthesis and applications: Our results show that in
 seagrasses positive interactions during early life stages can be promoted
 by planting seedlings in dense clumps in association with an early
 successional species. The incorporation of this novel nature-based
 approach in seed-based restoration could accelerate the recolonization of
 degraded seagrass habitats. In planning future seed-based restoration
 interventions, managers should assess both intra- and interspecific
 interactions established by seedlings of target species for identifying
 proper planting density/spatial configuration and potential benefactor
 species promoting facilitative mechanisms to maximize seedling planting
 success.
DOI: 10.5061/dryad.r2280gbdd
title: Autism Spectrum Disorder and screen time during lockdown

description: Abstract: this dataset contain data from a research conducted during the
 Italian lockdown due to COVID-19 (March-May 2020). Lockdown due to
 Covid-19 pandemic brought deep changes to the daily lives of children with
 Autism Spectrum Disorder (ASD), greatly increasing their amount of time
 spent at home. Parents of children with ASD filled an online survey. A
 cohort of 243 parents of children with ASD (2-15 years old) completed an
 original online survey regarding the child’s screen time and the
 modification of the ASD symptomatology during lockdown to investigate the
 relationship between them. This data investigated the relation between ASD
 symptoms modification during lockdown and the amount of time spent with
 the screen by the children. Methods: The data were analyzed with Pycharm
 (Python language). Descriptive and Spearman correlation statistics were
 computed on the original survey data. The variables expressed on a Likert
 scale were transformed into dichotomous variable in order to depict and
 highlight the effect of any improvements or worsen of child’s
 symptomatology, weakening the negative impact of a relatively low sample
 size on model accuracy; the time spent in the screen time activity done
 during lockdown were reparametrized as a percentage of time spent in a
 specific screen time activity over the total time spent in all screetime.
DOI: 10.5061/dryad.5x69p8d3k
title: The effects of ENSO and the North American monsoon on mast seeding in two Rocky Mountain conifer species

description: We aimed to disentangle the patterns of synchronous and variable cone
 production (i.e., masting) and its relationship to climate in two conifer
 species native to dry forests of western North America. We used cone
 abscission scars to reconstruct ca. 15 years of recent cone production in
 Pinus edulis and Pinus ponderosa, and used redundancy analysis to relate
 time series of annual cone production to climate indices describing the
 North American monsoon and the El Niño Southern Oscillation (ENSO). We
 show that the sensitivity to climate and resulting synchrony in cone
 production varies substantially between species. Cone production among
 populations of P. edulis was much more spatially synchronous and more
 closely related to large-scale modes of climate variability than were
 populations of P. ponderosa. Large-scale synchrony in P. edulis cone
 production was associated with the North American monsoon and we
 identified a dipole pattern of regional cone production associated with
 ENSO phase. In P. ponderosa, these climate indices were not strongly
 associated with cone production, resulting in asynchronous masting
 patterns among populations. This study helps frame our understanding of
 mast seeding as a life history strategy and has implications for our
 ability to forecast mast years in these species.
description: Data includes R code and datasets to reproduce figures and
 results from the paper entitled "The effects of ENSO and the North
 American monsoon on mast seeding in two Rocky Mountain conifer
 species"     Data are counts of
 annual cone production from two Rocky Mountain conifer species, Pinus
 ponderosa and Pinus edulis, from 470 trees and 76 sites, reconstructed
 using cone scars, from the time period 2003-2018.  Data also include
 rasters of monthly and seasonal climate, range maps of the two species,
 and several other files needed to recreate the analyses and figures. See
 the readme file for full description of files.
DOI: 10.5061/dryad.bzkh18994
title: Seasonal NDVI data for a biodiversity and consumer removal experiment at the University of Minnesota's Cedar Creek Ecosystem Science Reserve (2009 - 2016)

description: Plant biodiversity and consumers (herbivores, pathogens, and mutualists)
 are important mediators of energy and carbon fluxes in grassland
 ecosystems. Although the role of consumers and plant diversity in
 controlling peak-season biomass production has been characterized,
 knowledge of their roles in within-season variation of energy and carbon
 flux remains poorly understood. Here we measure variation in consumer and
 plant diversity control of plant biomass production throughout the growing
 season and their impact on plant biomass phenology (timing of maximum
 biomass). To do this, we analyzed 5 years of biweekly, non-destructive
 biomass measures in an experiment manipulating plant species richness and
 three consumer groups (foliar fungi, soil fungi, arthropods, or all groups
 via pesticides). We found that plant biomass differences between high
 diversity plots and monocultures were greatest early in the growing
 season, whereas the foliar fungicide and insecticide treatments increased
 biomass most late in the season. The impact of foliar fungi and arthropods
 on biomass production also varied with plant diversity, with the greatest
 effects of foliar fungicide in high diversity plots whereas insecticide
 impacts were greatest in monocultures. Finally, more diverse plots and
 plots containing foliar fungi reached maximum biomass earlier than
 monocultures and plots treated with foliar fungicide. Taken together,
 these results highlight the significant and interactive roles that
 biodiversity and consumers play in dynamically regulating the production
 of plant biomass through the growing season, controlling the flow of
 energy and carbon to support the microbial and animal communities that
 rely on grassland productivity.
description: For 8 years (2009 to 2016), we used a MSR5 multispectral radiometer (Cropscan, Inc., Rochester, MN, USA) to measure reflected radiation (reflectance) in all experimental plots. Measurements were taken every two weeks from April to August in a 2m<sup>2</sup>area above the vegetation canopy in the center of each plot. Normalized Difference Vegetation Index (NDVI) was derived from the red: near-infrared reflectance ratio (Running 1990)using 830mm (near-infrared) and 660mm (red) reflectance readings. NDVI values were calculated for each plot on each day of measurement resulting in 20,135 NDVI estimates across the entire study.
DOI: 10.5061/dryad.d2547d83c
title: Macroevolutionary foundations of a recently-evolved innate immune defense (data)

description: Antagonistic interactions between hosts and parasites may drive the
 evolution of novel host defenses, or new parasite strategies. Host
 immunity is therefore one of the fastest evolving traits. But where do the
 novel immune traits come from? Here, we test for phylogenetic conservation
 in a rapidly evolving immune trait – peritoneal fibrosis. Peritoneal
 fibrosis is a costly defense against a specialist tapeworm,
 Schistocephalus solidus (Cestoda), expressed in some freshwater
 populations of threespine stickleback fish (Gasterosteus aculeatus,
 Perciformes). We asked whether stickleback fibrosis is a derived
 species-specific trait or an ancestral immune response that was widely
 distributed across ray-finned fish (Actinopterygii) only to be employed by
 threespine stickleback against the specialist parasite. We combined
 literature review on peritoneal fibrosis with a comparative experiment
 using either parasite-specific, or non-specific, immune challenge in
 deliberately selected species across fish tree of life. We show that
 ray-finned fish are broadly, but not universally, able to induce
 peritoneal fibrosis when challenged with a generic stimulus (Alum
 adjuvant). The experimental species were, however, largely indifferent to
 the tapeworm antigen homogenate. Peritoneal fibrosis, thus, appears to be
 a common and deeply conserved fish immune response that was co-opted by
 stickleback to adapt to a new selective challenge.
description: There are two datasets used to generate the results of our
 article, the first is a database of published articles that form the basis
 of the literature review, and then the other file contains data from an
 experimental study of phylogenetic conservation of peritoneal fibrosis in
 17 species of ray-finned fish. A detailed description of the methodology
 can be found in the article (https://doi.org/10.1101/2020.07.08.191601).
 The accompanying code is available at FigShare
 (https://doi.org/10.6084/m9.figshare.12619367) and Zenodo
 (https://doi.org/10.5281/zenodo.5137001).
description: All the necessary information can be found in the README.txt file
 in the data folder.