cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gf1vhhmqx
title: Data from: Tree species and genetic diversity increase productivity via functional diversity and trophic feedbacks

description: This data was collected in the species × genetic diversity experiment of
 the Biodiversity–Ecosystem Functioning Experiment China Platform
 (BEF-China, www.bef-china.com). This data set includes four species
 (Alniphyllum fortunei, Cinnamanum camphora, Daphniphyllum oldhamii, and
 Idesia polycarpa) with the mother trees of all tree individuals known, and
 the offspring from the same mother tree was defined as a seed family. In
 total, 92 subplots with 4 tree diversity levels were included: species
 diversity (1 or 4 species) and genetic diversity (1 or 4 seed families per
 species) which resulted in four tree diversity levels: one species with
 one seed family (1.1), one species with four seed families (1.4), four
 species with one seed family per species (4.1) and four species with four
 seed families per species (4.4). For tree functional traits, five leaf
 functional traits were measured in 2017 and 2018, including leaf area
 (LA), specific leaf area (SLA), chlorophyll content (CHL), leaf nitrogen
 content (LN), and leaf carbon content (LC). Herbivory was visually
 recorded as leaf damage in 2017. Soil fungal diversity was used as proxies
 for unspecified trophic interactions. Soil samples were taken on subplot
 level for the 1.1 and 1.4 diversity treatments, but on plot level for the
 4.1 and 4.4 diversity treatments in 2017. Tree community productivity was
 summed by the biomass of individual trees in each subplot and individual
 tree biomass (kg) was calculated using the biomass equation (H × BA × CV)
 of the BEF-China experiment, where CV is a correction factor for stem
 shape and wood density.
DOI: 10.5061/dryad.d7wm37q2h
title: American black duck PTT data from Atlantic Canada

description: American black ducks, native to eastern North America, have been the focus
 of significant international conservation and management programs. The
 combined USA and Canadian population has traditionally been managed as a
 single population; however black duck demographics may vary by region. To
 help understand potential regional differences in black ducks, we used
 satellite telemetry to assess migratory chronology and movements of black
 ducks wintering near Windsor, Nova Scotia, Canada, near the northern
 limits of their wintering range where numbers are increasing. Wintering
 black ducks from Nova Scotia did not leave the Atlantic Flyway and
 included both longer-distance migrants (~ 1 500 km north) and
 locally-breeding individuals. None of our tracked ducks travelled south of
 Nova Scotia during any part of the annual cycle, indicating a population
 segment that never leaves Canada and is subject solely to Canadian harvest
 pressures. Band recovery data revealed that a small portion (2.4%) of
 black ducks originally banded during winter in Nova Scotia were recovered
 south along the east coast of the USA, indicating that some of these black
 ducks are subject to international harvest pressures. Our results show
 that there are differences in annual black duck movements even within a
 small part of their range, adding to the growing evidence that black duck
 populations show fine-scale temporal and spatial structure. This structure
 will need to be considered in future interprovincial and international
 harvest management plans of this important species.
description: Collected through 11 PTTs; processed using the Douglas 'Best
 of Day' filter.
DOI: 10.5061/dryad.sn02v6x51
title: Herbivore grazing mitigates the negative effects of nitrogen deposition on soil organic carbon in low-diversity grassland

description: 1. Changes in soil carbon (C) sequestration in grassland ecosystems have
 important impacts on the global C cycle. As such, it is important that
 researchers better understand the underlying mechanisms affecting soil C.
 Increasing evidence has shown that atmospheric nitrogen (N) deposition can
 cause dramatic changes in grassland soil C. It remains unclear whether
 herbivore grazing, a primary means to manage and utilize grassland
 resources, can regulate the effects of N deposition on soil C, and whether
 these effects are dependent on plant community diversity. 2. Here, we
 examined the joint effects of herbivore grazing and N-addition on soil
 organic C (SOC) stocks in two types of communities with low and high plant
 diversity, respectively. 3. Our results showed that the effects of
 N-addition and its combination with herbivore grazing on grassland SOC
 were inconsistent in the two types of communities. In the low-diversity
 community, N-addition greatly decreased SOC stocks, while grazing
 significantly increased it. Additionally, the grazing-induced increase in
 soil C stocks in presence of N-addition was so great that it completely
 counteracted the significant decline in SOC induced by N-addition.
 However, in the high-diversity community, we observed no effects of
 N-addition on SOC and grazing increased SOC only in the absence of
 N-addition and had no significant effect in presence of N-addition. 4.
 Synthesis and applications. Our study suggests that increased N deposition
 can trigger a remarkable reduction in soil C sequestration in grasslands
 with low plant diversity, but that herbivore grazing can offset this
 decline, which may help to mitigate greenhouse gas emissions caused by
 atmospheric N deposition. As a result, we suggest that moderate herbivore
 grazing should be considered as an effective grassland management measure
 for maintaining and improving grassland soil C sequestration as the
 increasing global change such as elevated atmospheric carbon dioxide, N
 deposition, and biodiversity losses threat.
DOI: 10.15468/dl.x33yz7
title: Occurrence Download

description: A dataset containing 243 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Silene wilfordii"
 ]
}

 The dataset includes 243 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002962-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jsxksn0b3
title: Experimental disturbance and productivity gradients drive community diversity in aquatic mesocosms

description: Combined effects of disturbance and productivity on ecological diversity
 have been considered for decades as the dynamic equilibrium model (DEM)
 but are rarely tested together. Instead, most studies focus on either the
 intermediate disturbance hypothesis or sometimes the intermediate
 productivity hypothesis. In addition, most analyses of disturbance and
 productivity effects have relied on nonexperimental patterns, limited
 sample sizes, inaccurate proxies for productivity, and/or simple measures
 of diversity. The DEM operates at regional and local scales; here, we
 conducted a year‐long experiment at local scales using submersed aquatic
 vegetation in outdoor mesocosms with a factorial combination of physical
 disturbance and productivity treatments. We evaluated diversity in several
 ways, directly measured productivity, and compared alternative hypotheses
 using model selection. The DEM was supported for effective diversity; both
 productivity and disturbance effects were clear, though productivity
 effects were stronger. Other diversity measures for the simple communities
 in the mesocosms did not clearly reflect treatments. The DEM is a valuable
 general framework for understanding disturbance and productivity effects
 on ecological systems and is made more general by minor conceptual
 adjustments here.
DOI: 10.5061/dryad.1g1jwstxq
title: Does sexual experience affect the strength of male mate choice for high-quality females in Drosophila melanogaster?

description: Although females are traditionally thought of as the choosy sex, there is
 increasing evidence in many species that males will preferentially court
 or mate with certain females over others when given a choice. In
 the fruit fly, Drosophila melanogaster, males discriminate
 between potential mating partners based on a number of
 female traits, including species, mating history, age, and
 condition. Interestingly, many of these male preferences are
 affected by the male’s previous sexual experiences, such that males
 increase courtship toward types of females that they have previously mated
 with and decrease courtship toward types of females that have previously
 rejected them. D. melanogaster males also show courtship
 and mating preferences for larger females over smaller females,
 likely because larger females have higher fecundity. It is unknown,
 however, whether this preference shows behavioral plasticity based on the
 male’s sexual history as we see for other male preferences. Here, we
 manipulate the sexual experience of D.
 melanogaster males and test whether this manipulation has any
 effect on the strength of male mate choice for large females. We find that
 sexually inexperienced males have a robust courtship preference for large
 females that is unaffected by previous experience mating with, or being
 rejected by, females of differing sizes. Given that female body
 size is one of the most common targets of male mate choice across insect
 species, our experiments with D. melanogaster may
 provide insight into how these preferences develop and evolve.
DOI: 10.5061/dryad.7d7wm37wc
title: A hierarchical dependent double-observer method for estimating waterfowl breeding pairs abundance from helicopters

description: We applied a dependent double-observer method for helicopter surveys and
 developed a hierarchical Bayesian model as a means to adjust counts of
 waterfowl for incomplete detection. We conducted our study using 52 plots
 in Labrador, Canada. A designated pair of primary observers reported
 counts and location of all waterfowl flocks that they detected to a pair
 of secondary observers, including details regarding the species, age and
 sex of observed birds. Secondary observers then reported any additional
 flocks observed by them but missed by the primary observers. The pairs of
 observers alternated between primary and secondary roles during the course
 of the survey, as well as position (front or back) within the helicopter.
 We used hierarchical Bayesian models to estimate detection probabilities
 of waterfowl flocks, as well as derive species-specific
 detection-corrected abundance and sex composition estimates of flocks. The
 hierarchical model output allowed us to derive estimates of indicated
 breeding pairs for each species in the survey area corrected for
 incomplete detection. Observers seated in the back of the helicopter had
 higher detection probabilities (0.89; 90% Bayesian Credible Intervals
 [BCI] = 0.82 – 0.95) than those in the front (0.74; 90% BCI = 0.66 –
 0.83), and observer experience had a limited effect on detection. Total
 crew detection probabilities ranged between 0.99 (90% BCI = 0.97 – 1.00)
 and 0.97(90% BCI = 0.94 – 0.99), depending on the individual observers’
 position and role in the helicopter. Detection probabilities were higher
 for sea ducks and diving ducks and lower for dabbling ducks. Observers
 generally missed less than 5% of the total indicated pairs for all
 species. We recommend that detection in helicopter surveys be measured to
 control for observer turnover, observer experience, and aircraft-related
 differences in visibility.
description: Data was collected during a waterfowl helicopter survey.  The
 flock composition file contains all the individuals obervations while the
 total flock file contain the totla number of flock of each species
 observer in each plot that was surveyed. Also included
 are a R file that contains all the previous data manipulations to put the
 data in a structure that is ready for analysis with JAGS, a R-script to
 run the analysis in JAGS, and the JAGS model to carry out the
 analysis.
description: There are no obervations in plots:
 "P61","S09", "S24", "S32",
 "S58",  and "S60" so these plots are not included in
 the flock composition file. The code to manipulate teh data and run the
 analysis in R format are also provided in the article supplementary
 material.
DOI: 10.5061/dryad.00000004p
title: Data for: Carnivore niche partitioning in a human landscape

description: To minimize competitive overlap, carnivores modify one of their critical
 niche axes: space, time, or resources. However, we currently lack rules
 for how carnivore communities operate in human-dominated landscapes. We
 simultaneously quantified overlap in the critical niche axes of a simple
 carnivore community – an apex carnivore (Puma concolor), a dominant
 meso-carnivore (Lycalopex culpaeus), and a subordinate meso-carnivore (L.
 griseus) – in a human-landscape featuring pastoralists and semi-domestic
 carnivores (i.e., dogs Canis familiaris). We found that dominant species
 had strong negative effects on the space-use of subordinate ones, which
 ultimately created space for subordinate small-carnivores. Humans and dogs
 were strictly diurnal, whereas the native carnivore community was
 nocturnal and exhibited high temporal overlap. Dietary overlap was high
 among the native carnivores, but dogs were trophically decoupled, largely
 because of human food subsidies. Our results show that in landscapes with
 evident human presence, temporal and dietary partitioning among native
 carnivores can be limited, leaving space as the most important axis to be
 partitioned among carnivores. We believe that these findings – the first
 to simultaneously assess all three critical niche axes among competing
 carnivores and humans and their associated species (i.e., domesticated
 carnivores) – are transferable to other carnivore communities in human
 modified landscapes.
DOI: 10.5061/dryad.9kd51c5j6
title: COVID-19 evidence syntheses with artificial intelligence: an empirical study of systematic reviews

description: Objectives: A rapidly developing scenario like a pandemic requires the
 prompt production of high-quality systematic reviews, which can be
 automated using artificial intelligence (AI) techniques. We evaluated the
 application of AI tools in COVID-19 evidence syntheses. Study design:
 After prospective registration of the review protocol, we automated the
 download of all open-access COVID-19 systematic reviews in the COVID-19
 Living Overview of Evidence database, indexed them for AI-related
 keywords, and located those that used AI tools. We compared their
 journals’ JCR Impact Factor, citations per month, screening workloads,
 completion times (from pre-registration to preprint or submission to a
 journal) and AMSTAR-2 methodology assessments (maximum score 13 points)
 with a set of publication date matched control reviews without AI.
 Results: Of the 3999 COVID-19 reviews, 28 (0.7%, 95% CI 0.47-1.03%) made
 use of AI. On average, compared to controls (n=64), AI reviews were
 published in journals with higher Impact Factors (median 8.9 vs 3.5,
 P&lt;0.001), and screened more abstracts per author (302.2 vs 140.3,
 P=0.009) and per included study (189.0 vs 365.8, P&lt;0.001) while
 inspecting less full texts per author (5.3 vs 14.0, P=0.005). No
 differences were found in citation counts (0.5 vs 0.6, P=0.600), inspected
 full texts per included study (3.8 vs 3.4, P=0.481), completion times
 (74.0 vs 123.0, P=0.205) or AMSTAR-2 (7.5 vs 6.3, P=0.119). Conclusion: AI
 was an underutilized tool in COVID-19 systematic reviews. Its usage,
 compared to reviews without AI, was associated with more efficient
 screening of literature and higher publication impact. There is scope for
 the application of AI in automating systematic reviews.
description: Dataset produced from bibliographic references to COVID-19
 systematic reviews obtained from the COVID-19 Living Overview of Evidence
 database. We obtained accessibility information and download links from
 the Unpaywall database, and indexed the resulting downloaded files with
 the OpenSemanticSearch search engine.
description: Please read README.txt for usage notes. Shasums for all included
 files (and downloaded reviews) are provided in SHASUMS.asc (signed by PGP
 key 0x39DB6ED67D52F190). Re-running the commands with a different (more
 recent) "References.ris" file might result in different shasums
 due to changes in the hosting servers; for this reason, all intermediary
 files are provided.
DOI: 10.5061/dryad.g4f4qrfrc
title: CODEX multiplexed imaging cell datasets used for using STELLAR to transfer cell type annotations to other tissues and donors

description: We performed CODEX (co-detection by indexing) multiplexed imaging
 on 24 sections of the human intestine from 3 donors (B004, B005, B006)
 using a panel of 47 oligonucleotide-barcoded antibodies. We also
 performed CODEX imaging on both human tonsil and Barrett's
 esophagus (BE) using a panel of 57 oligonucleotide-barcoded
 antibodies.  Subsequently images underwent standard CODEX image
 processing (tile stitching, drift compensation, cycle concatenation,
 background subtraction, deconvolution, and determination of best focal
 plane), single cell segmentation, and column marker z-normalization by
 tissue. Output of this process were dataframes of 870,000 cells and
 220,000 cells respectively with fluorescence values quantified from each
 marker.
description: See README file.
description: This dataset could be used to test machine learning algorithms
 for cell type label transfer accuracy methods. It could also be used to
 look at cell type relationships in tonsil, intestine, and Barrett's
 esophagus tissues. The overall structure of the
 datasets are individual cells segmented out in each row. Then there are
 columns for the X, Y position in pixels in the overall montage image of
 the dataset. There are also columns to indicate which region the data came
 from. There are also cell type labels generated from expert annotations.
 The other columns are the values of the antibody staining the target
 protein within the tissue quantified at the single-cell level. This value
 is the per cell/area averaged fluorescent intensity that has subsequently
 been z normalized along each column as described above. 
 For the B004_training_dryad.csv dataset, data from donor B004 was
 expert annotated for cell types within the small intestine and colon
 (~250,000 cells) and contains cell type labels in addition to protein
 marker expressions and x, y positions. Each donor has 4 regions from the
 colon and 4 regions from the small intestine. For the intra-region
 comparisons we looked at B004 regions in the colon with training 3 regions
 and then predicting on the fourth. For the
 B0056_unnanotated_dryad.csv dataset, data from donors B005 and B006 were
 unnanotated samples we transferred cell type labels to from the B004
 training dataset. This means that B0056 has the quantified and
 preprocessed single-cell quantified protein expression with x, y positions
 from CODEX imaging, but no cell type annotation labels associated
 yet. The TonsilBE_processed_0.5 pkl is the
 preconstructed graph for the tonsil and BE datasets so that running a demo
 example of STELLAR found on our github (https://github.com/snap-stanford/stellar) runs faster and is included as supplementary data.
DOI: 10.5061/dryad.sj3tx965v
title: Data from: Exploring trophic role similarity and phylogenetic relatedness between species in food webs

description: Understanding the mechanism shaping species assemblage is a fundamental
 goal in ecology. In the past two hypotheses have been suggested. One is
 the filtering hypothesis where environmental factors select for species of
 similar traits such that they co-occurring in similar niches. The other is
 the competitive exclusion hypothesis where related species are driven far
 apart by competition such that they over-disperse across different niches.
 Here, we investigate the relationship between species assemblage and their
 phylogenetic relatedness from the network perspective by using five
 different ecosystems ranging from oceans to an inland lake. We quantified
 the similarity in species’network positions in a food web and cluster them
 into different trophic role groups; and from an on-line database we
 quantified their phylogenetic distances. We then investigated whether
 related species tend to under or overdisperse across different trophic
 role groups. In general, our result suggests the environmental filtering
 process is the dominant force shaping the species assemblage of those
 ecosystems. However, there are some possible cases where related species
 are driven by competition such that they evolve to adopt different trophic
 roles in relatively closed ecosystems.
DOI: 10.5061/dryad.0zpc866z8
title: Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection

description: In the last decade, High-Throughput Sequencing (HTS) has revolutionized
 biology and medicine. This technology allows the sequencing of huge amount
 of DNA and RNA fragments at a very low price. In medicine, HTS tests for
 disease diagnostics are already brought into routine practice. However,
 the adoption in plant health diagnostics is still limited. One of the main
 bottlenecks is the lack of expertise and consensus on the standardization
 of the data analysis. The Plant Health Bioinformatic Network (PHBN) is an
 Euphresco project aiming to build a community network of
 bioinformaticians/computational biologists working in plant health. One of
 the main goals of the project is to develop reference datasets that can be
 used for validation of bioinformatics pipelines and for standardization
 purposes. Semi-artificial datasets have been created for this purpose
 (Datasets 1 to 10). They are composed of a “real” HTS dataset spiked with
 artificial viral reads. It will allow researchers to adjust their
 pipeline/parameters as good as possible to approximate the actual viral
 composition of the semi-artificial datasets. Each semi-artificial dataset
 allows to test one or several limitations that could prevent virus
 detection or a correct virus identification from HTS data (i.e. low viral
 concentration, new viral species, non-complete genome). Eight artificial
 datasets only composed of viral reads (no background data) have also been
 created (Datasets 11 to 18). Each dataset consists of a mix of several
 isolates from the same viral species showing different frequencies. The
 viral species were selected to be as divergent as possible. These datasets
 can be used to test haplotype reconstruction software, the goal being to
 reconstruct all the isolates present in a dataset. A GitLab repository
 (https://gitlab.com/ilvo/VIROMOCKchallenge) is available and provides a
 complete description of the composition of each dataset, the methods used
 to create them and their goals.
description: <strong>Dataset_x.fastq.gz</strong>
 These are the fastq files of the 18 datasets.
 <strong>Description of the
 datasets</strong> This is a word document
 describing each dataset.