cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tdz08kq09
title: Threading the needle: how humans influence predator-prey spatiotemporal interactions in a multiple-predator system

description: Perceived predation risk and the resulting antipredator behavior varies
 across space, time, and predator identity. Communities with multiple
 predators that interact and differ in their use of space, time of
 activity, and hunting mode create a complex landscape for prey to avoid
 predation. Anthropogenic presence and disturbance have the potential to
 shift interactions among predators and prey and the where and when
 encounters occur. We examined how spatiotemporal antipredator behavior of
 white-tailed deer fawns (Odocoileus virginianus) differed along an
 anthropogenic disturbance gradient that had black bears (Ursus
 americanus), coyotes (Canis latrans), bobcats (Lynx rufus), and humans
 present. We quantified 1) coarse-scale spatial co-occurrence in species
 distributions, 2) temporal overlap across the diel cycle, and 3)
 fine-scale spatiotemporal associations between humans, bears, coyotes,
 bobcats, adult male deer, and fawns. We also examined how deer vigilance
 behavior changed across the anthropogenic disturbance gradient and survey
 duration. Anthropogenic disturbance influenced spatiotemporal
 co-occurrence across multiple scales, often increasing spatiotemporal
 overlap among species. In general, species’ spatial co-occurrence was
 neutral or positive in anthropogenically disturbed environments. Bears and
 fawns, coyotes and adult male deer, and bobcats and fawns all had higher
 temporal overlap in the agriculture-development matrix sites. In addition,
 factors that influenced deer vigilance (e.g., distance to forest edge and
 predator relative abundance) in the agriculture-development matrix sites
 did not in the forest matrix site. By taking into account the different
 antipredator behaviors that can be detected and the different scales these
 behaviors might occur, we were able to gain a more comprehensive picture
 of how humans reduce available niche space for wildlife, creating the
 neutral and positive spatiotemporal associations between species that
 studies have been seeing in more disturbed areas.
description: Information on each dataset used for each analysis can be found
 in the "covariate information" .xls/x files in each folder. For
 the spatial co-occurrence analysis, for species capture histories (e.g.,
 bobfull.csv), columns are survey occasions and rows are individual camera
 locations.
DOI: 10.5061/dryad.8pk0p2nn9
title: Data from: Data-driven bioregionalization: A seascape-scale study of macrobenthic communities in the Eurasian Arctic

description: Aim: We conduct the first model-based assessment of the biogeographical
 subdivision of Eurasian Arctic seas to (1) delineate spatial distribution
 and boundaries of macrobenthic communities on a seascape level; (2) assess
 the significance of environmental drivers of macrobenthic community
 structures; (3) compare our modelling results to historical
 biogeographical classifications; and (4) couple the model to
 climate-change scenarios of environmental changes to project potential
 shifts in the distribution and composition of macrobenthic communities by
 2100. Location: Eurasian Arctic seas, in particular Barents, Kara, and
 Laptev Seas Taxon: Macrobenthic fauna Methods: We employed the Region of
 Common Profile (RCP) approach to assess the regionalization patterns of
 Eurasian Arctic seafloor communities. Results: Four RCPs were identified
 based on the spatial distribution patterns of 169 macrobenthic species and
 a set of environmental factors, such as sediment composition, sea-ice
 concentration, depth of the euphotic zone, particulate organic carbon
 concentration at the ocean surface, as well as near-bottom water
 temperature and salinity. The identified regions are in strong agreement
 with previous classifications of macrobenthic communities. The projections
 are driven by climate-change scenario “Representative Concentration
 Pathway 6.0” suggested a general eastward shift of the RCPs over the 21st
 century, correlated to retreating sea-ice and increasing sea-bottom
 temperature. Main conclusions: The RCP approach allowed us to identify
 seascape-scale distribution patterns of macrobenthic communities in
 Eurasian Arctic seas by simultaneously considering biotic and
 environmental data within one modelling step. This technique can represent
 biota and ecoregions in a probabilistic form together with assessment of
 uncertainties of the predictions, and assess the significance of a broad
 selection of environmental drivers. This first quantitative assessment of
 potential climate-driven changes in macrobenthic biodiversity will promote
 their inclusion in conservation measures.
description: We employed the Region of Common Profile (RCP) approach to assess
 the regionalization patterns of Eurasian Arctic seafloor communities. The
 entire data analysis was conducted in R using package 'RCPmod'.
DOI: 10.5061/dryad.m905qfv1f
title: Do fine-scale experiments underestimate predator consumption rates?

description: Understanding ecological processes across spatial scales helps link
 observations and predictions from experiments to ecological patterns
 occurring at coarser scales relevant to management and conservation. Using
 fish, we experimentally manipulated the size of arenas to test the spatial
 scaling of predator-prey interactions. We measured variation in predator
 consumption and prey behavior (prey aggregation, spatial overlap with
 predators, and movement) across arena sizes. Variation in prey behavior
 across arena sizes was hypothesized to drive consumption patterns by
 altering prey vigilance and encounter rates with predators. Per capita
 consumption and movement were highest in the largest arena relative to the
 smallest and we observed a mismatch between where bass were present and
 the highest densities of prey across all arena sizes. We hypothesize more
 movement in largest arenas increased encounter rates and drove the
 observed increase in consumption with increasing arena size. 5.
 Consumption estimates obtained in experimental studies may underestimate
 consumption, but understanding the mechanisms driving bias across scales
 helps predict the outcomes of predator-prey interactions in natural
 systems. 
description: This data includes observations of fish in pool units of outdoor
 mesocosms. Locations of fish were tracked at 1-minute intervals using
 Passive Integrated Transponder (PIT) tags and antenna systems. The dataset
 includes unique fish ids, the length of each fish, the time and date of
 observation, the pool identification, the size of the mesocosm unit, and
 the trial and treatment information of the experiment.
description: Some PIT tags were reused across trials.
DOI: 10.5061/dryad.4qrfj6q9n
title: Steering microbiomes by organic amendments towards climate-smart agricultural soils

description: We steered the soil microbiome via applications of organic residues (mix
 of cover crop residues, sewage sludge + compost, and digestate + compost)
 to enhance multiple ecosystem services in line with climate-smart
 agriculture. Our result highlights the potential to reduce greenhouse
 gases (GHG) emissions from agricultural soils by the application of
 specific organic amendments (especially digestate + compost).
 Unexpectedly, also the addition of mineral fertilizer in our mesocosms led
 to similar combined GHG emissions than one of the specific organic
 amendments. However, the application of organic amendments has the
 potential to increase soil C, which is not the case when using mineral
 fertilizer. While GHG emissions from cover crop residues were
 significantly higher compared to mineral fertilizer and the other organic
 amendments, crop growth was promoted. Furthermore, all organic amendments
 induced a shift in the diversity and abundances of key microbial groups.
 We show that organic amendments have the potential to not only lower GHG
 emissions by modifying the microbial community abundance and composition,
 but also favour crop growth-promoting microorganisms. This modulation of
 the microbial community by organic amendments bears the potential to turn
 soils into more climate-smart soils in comparison to the more conventional
 use of mineral fertilizers.
DOI: 10.5061/dryad.95x69p8kq
title: Assessing consistency across functional screening datasets in cancer cells

description: Many high-throughput screening studies have been carried out in cancer
 cell lines to identify therapeutic agents and targets. Existing
 consistency assessment studies only examined two datasets at a time, with
 conclusions based on a subset of carefully selected features rather than
 considering global consistency of all the data. In this study we assembled
 nine compound screening datasets and three functional genomics datasets,
 and derived direct measures of consistency as well as indirect measures of
 consistency based on association between functional data and copy
 number-adjusted gene expression data. These results have been integrated
 into a web application – the Functional Data Consistency Explorer (FDCE),
 to allow users to make queries and generate interactive visualizations so
 that functional data consistency can be assessed for individual features
 of interest.
description: The source and processing methods were briefly described
 in https://lccl.shinyapps.io/FDCE/, dataset section.  The scripts for
 cleaning and processing the data are uploaded as scripts.zip. The source
 script and data for making the shiny app "Functional Data Consistency
 Explorer (FDCE)" is uploaded as app.zip.
DOI: 10.5061/dryad.wwpzgmsk2
title: Phase response analyses support a relaxation oscillator model of locomotor rhythm generation in Caenorhabditis elegans

description: This dataset contains all data and codes that are used in the manuscript
 entitled "Phase response analyses support a relaxation oscillator
 model of locomotor rhythm generation in Caenorhabditis elegans". The
 data include raw videos and intermediate data for optogenetic
 experiments of all strains, experimental conditions (illumination
 duration, illuminated region, fluid viscosity and date). Within the parent
 folder 'Videos', each subfolder represents data of a group
 of experiments using the same strain under the same condition,
 as indicated explicitly by the subfolder name. Within each
 subfolder, there are raw videos of freely moving worms perturbed by
 transient optogenetic perturbations and intermediate data which include
 locomotory information and the corresponding figure plots (kymographs)
 that were generated by analysing the raw videos with the image analysis
 software (also in the dataset) The codes include scripts for
 image data analysis and model simulations. The image data
 analysis codes include scripts specifically for generating phase
 portrait graphs, phase response curves, head oscillation stability plots,
 phase isochron map and vector field. The model simulation codes include
 scripts for model oscillators implementation, paramter
 estimation/optimization and simulations of optogenetic inhibition.
description: Methods for data curation and analysis were described in Methods
 and Appendix sections in the manuscript.
description: README.txt file was attached
DOI: 10.5061/dryad.47d7wm3d4
title: Association between physical activity and mortality among community-dwelling stroke survivors

description: Objective:  To determine the relationship between physical
 activity and mortality in community-dwelling stroke survivors.
 Methods:  The Canadian Community Health Survey was used to obtain
 self-reported physical activity (PA) across four survey years and was
 linked to administrative databases to obtain prior diagnosis of stroke and
 subsequent all-cause mortality.  PA was measured as metabolic
 equivalents (METs) per week and meeting minimal PA guidelines was defined
 as 10 MET-hours/week.  Cox proportional hazard regression models
 and restricted cubic splines were used to determine the relationship
 between PA and all-cause mortality in respondents with prior stroke and
 controls, adjusting for sociodemographic factors, co-morbidities, and
 functional health status. Results:  The cohort included 895
 respondents with prior stroke and 97805 controls.  Adhering to PA
 guidelines was associated with lower hazard of death for those with prior
 stroke (adjusted hazard ratio [aHR] 0.46, 95% CI 0.29-0.73) and controls
 (aHR 0.69, 95% CI 0.62-0.76). There was a strong dose-response
 relationship in both groups, with a steep early slope and the vast
 majority of associated risk reduction occurring between 0 and 20
 MET-hours/week.  In the group of stroke respondents, PA was
 associated with stronger associated risk reduction in those &lt;75
 years of age (aHR 0.21, 95% CI 0.10-0.43) compared to those &gt;75
 years of age (aHR 0.68, 95% CI 0.42-1.12). 
 Conclusions:  PA was associated with lower all-cause mortality in
 a dose-dependent manner among those with prior stroke, particularly in
 younger stroke survivors.  Our findings support efforts towards
 the implementation of PA programs for stroke survivors in the
 community.
DOI: 10.5061/dryad.vt4b8gts4
title: Natural noise affects conspecific signal detection and territorial defense behaviors in songbirds

description: Recent research suggests that anthropogenic noise can substantially alter
 animal behavior. Although there are many sources of natural background
 noise, the relative influence of these sounds on behavior has received
 much less attention. Using landscape-scale playbacks of rushing rivers and
 crashing ocean surf, we investigated how habitat appropriate natural noise
 alters territorial defense behaviors in lazuli buntings (Passerina amoena)
 occupying riparian areas and spotted towhees (Pipilo maculatus) in
 riparian and coastal areas when exposed to simulated intruder song. We
 also incorporated naturally occurring cicada noise as an acoustic source
 influencing lazuli bunting behavior. Both songbird species possess songs
 that share substantial spectral overlap with low-frequency,
 water-generated noise, and lazuli bunting song shares an additional
 high-frequency overlap with cicada calls. Thus, there is potential for
 background acoustic conditions to mask conspecific signals. We found that
 detection and discrimination of conspecific playback occurred more slowly
 for both species as background sound level increased. Lazuli buntings also
 exhibited complex flight behavior in noise, suggesting they respond
 differently depending on the amplitude and type (with versus without
 cicada calls) of background noise. Our results suggest natural noise can
 impair territorial defense behaviors in songbirds, highlighting natural
 soundscapes as an under-appreciated axis of the environment.
DOI: 10.5061/dryad.8931zcrr0
title: Both sexes responded equally to food restriction

description: The collected juveniles were randomly assigned into two groups (Nstarving
 = 161, Ncontrol = 159), the control group was supplied with abundant food
 across the entire experiment process, and the experiment group was
 provided with only half amount of required food resource for the entire
 development process.In order to investigate the effects of food
 restriction on the development duration, adult body length and weight of
 spiders and the differences between female and male spiders, we measured
 the body length of each spider every five days since the experiment
 started until they reached adulthood, then their body weight, sex and the
 development duration were recorded.In order to explore the behavioral
 responses, concerning daily time allocation and hunting, of spiders
 between different food conditions, sexes and growth stages, we randomly
 selected some spiders from “Experiment 1” and carried out the following
 trails. Detailed number of spiders from each sex, each growth stage and
 each food condition are summarized in supplementary materials.
description: Spiders were kept in independent plastic boxes (5.4 × 5.4 × 4.2
 cm), with a temperature of 25 ± 2℃ with a 12:12 hour light: dark cycle
 (light: 8:00 – 20:00) and fed with fruit flies (<i>Drosophila
 melanogaster</i>) <i>Experiment 1:
 Developmental response</i> We measured the body
 length of each spider every five days since the experiment started until
 they reached adulthood, then their body weight, sex and the development
 duration were recorded. During the experiment, mortality of spiders was
 recorded every day.
 <i>E</i><i>xperiment 2: Behavioral
 responses</i> We randomly selected some spiders
 from “Experiment 1” and carried out the following trails.
 1)  The time allocation The status of staying
 inside the nests were thought to be in rest, while staying outside the
 nests were thought to be seeking for food or mates. Every spider was
 checked four times (twice between 9-11 am, and twice between 3-5 pm) on
 the third day after feeding. 2) Concerning hunting
 behavior Randomly chosen juvenile spiders reared for
 two weeks or longer, and adult spiders were tested. During the test, each
 spider was put into a plastic tube (diameter × height: 15 × 80 mm) to get
 accustomed to the arena for 5 min. Then fruit flies were released into the
 tube and the mouth of the tube was plugged with porous cotton (Juvenile
 spiders The hunting behavior was recorded for two hours with video camera
 SONY FDR-AX60. We measured the time spent to notice the prey, the latency
 from noticing to the start of hunting, the time of chasing before subduing
 the prey and the result (successful or not). All tests were conducted on
 the feeding day but before feeding to make sure the spiders were hungry
 and ready to hunt, and the control group was supplemented with sufficient
 prey after the tests were completed to keep the food amount constant
 within each age stage.were provided
 with one fruit fly, while adult spiders were provided with two).
DOI: 10.5061/dryad.rxwdbrv8g
title: Data from: Humus microhabitat affects distributions of soil fungi and bacteria in a temperate mountain forest

description: Humus layer have an important effect on the diversity and spatial
 distribution of microbes. However, the role of partitioning of humus layer
 microhabitats for soil microbial diversity has been poorly documented. In
 this study, 120 soil samples were collected from a 5-ha forest dynamic
 monitoring sample plot in a deciduous broad-leaved forest. Clustering
 analysis was used to delineate microhabitats by humus layer. We explored
 diversity and community composition of soil fungi and bacteria using
 Illumina sequencing of the ITS rRNA gene and 16S rRNA gene region on the
 MiSeq platform. We investigated the diversity, species composition and the
 microhabitat preferences of fungi and bacteria, and then analyzed the
 effects of environmental factors on soil fungi and bacteria. Our results
 showed that the diversity, species composition and the indicator species
 of the fungal and bacterial community varied among different humus layer
 microhabitats. In network analysis, the specialization indexes showed that
 16.20%/22.30% of the fungal/bacterial operational taxonomic units (OTUs)
 had the characteristics of distribution specialization for humus layer
 microhabitats. Mantel test showed that the main environmental drivers of
 fungi and bacteria were not consistent among the four microhabitats. Our
 findings indicated that the distribution of soil microbe among humus layer
 microhabitats is not random, but specialized. We furthermore found that
 there were differences in the relationship between soil microbes and
 environment among microhabitats defined by humus layer. Together these
 findings suggest that the importance of partitioning of humus layer
 microhabitats in maintaining local diversity in a soil microbial
 community.
description: High-throughput sequencing.
DOI: 10.7280/d10h40
title: A study of gene expression, structure, and contractility of iPSC-Derived Cardiac Myocytes from a family with heart disease due to LMNA mutation

description: Genetic mutations to the Lamin A/C gene (LMNA) can cause heart disease,
 but the mechanisms making cardiac tissues uniquely vulnerable to the
 mutations remain largely unknown. Further, patients with LMNA mutations
 have highly variable presentation of heart disease progression and type.
 In vitro patient-specific experiments could provide a powerful platform
 for studying this phenomenon, but the use of induced pluripotent stem
 cell-derived cardiomyocytes (iPSC-CM) introduces heterogeneity in maturity
 and function thus complicating the interpretation of the results of any
 single experiment. We hypothesized that integrating single cell RNA
 sequencing (scRNA-seq) with analysis of the tissue architecture and
 contractile function would elucidate some of the probable mechanisms. To
 test this, we investigated five iPSC-CM lines, three controls and two
 patients with a (c.357-2A&gt;G) mutation. The patient iPSC-CM tissues
 had significantly weaker stress generation potential than control iPSC-CM
 tissues demonstrating the viability of our in vitro approach. Through
 scRNA-seq, differentially expressed genes between control and patient
 lines were identified. Some of these genes, linked to quantitative
 structural and functional changes, were cardiac specific, explaining the
 targeted nature of the disease progression seen in patients. The results
 of this work demonstrate the utility of combining in vitro tools in
 exploring heart disease mechanics.
description: The data set for single cell RNA analyzed by SCTransform utility in Seurat with default parameters to preprocess the two datasets separately. The two datasets then were integrated using Seurat with the top 3000 variable genes. A UMAP coordination shared by the two datasets were generated using the top 20 principal components. All the graphical plots were generated based on the single cell RNA dataset. Other data was collected using tissue engineering experimental methods described in the paper.
description: The
 readme file contains an explanation of each if the supplement files in the
 DRYAD. More information the other methods and statistics can be found in
 the associated manuscript referenced above.