cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0cfxpnw0w
title: Simulated distribution of the fluid salinity, Cu and temperature in a sub-volcanic region

description: The files brinelens.00.vtu, brinelens.01.vtu,... contain the
 simulated distributions of the fluid bulk salinity (a), the Cu
 concentration in fluid for the 'no sulfur' case (b), the Cu
 concenration in fluid for the 'sulfur unlimited' case (c), the
 Cu deposition for the 'sulfur unlimited' case (d), and the
 temperature (e) at t=0 yr, 10000 yr, 20000 yr,..., respectively. The
 distributions shown in Fig. 6a-e are in brinelens.10.vtu. The
 file brinelens.csv contains the simulated time evolution of the
 total mass of dissolved and precipitated Cu. These data are plotted in
 Fig. 7.
description: These data were obtained by numerical modelling of the Cu
 transport and deposition for a given distributions of fluid velocity,
 temperature and salinity previously published in Afanasyev et al.
 (2018).
description: The files brinelens.00.vtu, brinelens.01.vtu, ... can be opened
 and processed in ParaView (http://paraview.org). The file brinelens.csv
 can be opened and processed in any software that can read csv files (e.g.
 Microsoft Excel).
DOI: 10.5061/dryad.b2rbnzsd2
title: Data from: Predicting bird-window collisions with weather radar

description: This is the data archive for all recorded bird species and
 carcass counts used to predict bird window collisions using weather
 radar in Stillwater, Oklahoma.
description: Data was collected by morning (0700-0900 cst) bird carcass
 surveys around 17 buildings in Stillwater, Oklahoma during spring
 (April-May) 2015-2017 and fall (September-October) 2015-2016 migration
 seasons. Survey effort and monitoring schedule were accounted for in
 carcass removal estimates. Total, migrant, and non-migrant fatalities were
 summed for all buildings for each date. Migrants were designated based on
 migratory status for individual birds based on date of collision
 occurrence in the study area, bird age, seasonal occurrence for species,
 and species-specific arrival, migration, and departure dates for our study
 area. Experimental carcass removal and surveyor detection trials conducted
 at the same buildings and time were also used incorporated to generate
 adjusted nightly estimates of migratory bird collisions that account for
 these biases.
DOI: 10.5061/dryad.rjdfn2z91
title: Simulation codes and data from: Efficient Flocking: metric versus topological interactions

description: Flocking is a fascinating phenomenon observed across a wide range of
 living organisms. We investigate, based on a simple theoretical particle
 model, how the emergence of ordered motion in a collectively moving group
 is influenced by the local rules of interactions among the individuals,
 namely, metric versus topological interactions as debated over in the
 current literature.
description: This is a theoretical research work. The equation of motion is
 solved numerically using a standard way of solving an ordinary
 differential equation.
description: 1. Simulation codes are provided to generate data for all figures
 in the paper and supplementary materials. One has to just run the
 "run.sh" file to generate data for all the figures. 
 2. The data files for metric interaction and topological
 interaction with lower flock speed (V0=0.01) are also provided, to
 generate the plots one need to run "*.m" file.
DOI: 10.5061/dryad.hx3ffbgcs
title: Supporting data for: Post-fire early successional vegetation buffers surface microclimate and increases survival of planted conifer seedlings in the southwestern United States

description: Climate change and fire-exclusion have increased the flammability of
 western US forests, leading to forest cover loss when wildfires occur
 under severe weather conditions. Increasingly large high-severity burn
 patches are a limitation to natural regeneration because of dispersal
 distance, increasing the chance that these areas are converted to
 non-forest. Post-fire planting can overcome dispersal limitations, yet
 warmer and drier post-fire conditions can still limit survival. Early
 successional vegetation can alter surface microclimate; however, it is
 unclear whether this is enough to increase planted seedling survival in
 southwestern US forests. Here we examined how two shrub species of
 different canopy density would affect survival rates of planted tree
 seedlings following a high-severity fire in northern New Mexico. We
 expected that shrubs with a higher density canopy (Gambel oak) would have
 a greater effect on buffering below-shrub climate than shrubs with a lower
 density canopy (New Mexico locust) and seedlings planted under Gambel oak
 would have higher survival rates. We found that seedlings planted under
 Gambel oak had survival rates approximately 10% to 35% greater than those
 planted under New Mexico locust.  The higher light availability
 beneath New Mexico locust corresponded to higher temperatures, lower
 humidity, and higher VPD, which impacted the mortality of planted tree
 seedlings. These results suggest that by waiting for post-fire shrub
 establishment, shrubs can be leveraged to buffer microclimate and increase
 post-fire planting success in the southwestern US.
description: These data are from an experiment to quantify the effects of two
 common post-fire shrub species (Quercus gambelii and Robinia neomexicana)
 alter survival rates of planted conifer seedlings by modifying
 microclimate.  We planted 64 individuals each of four tree species
 (Douglas-fir, ponderosa pine, southwestern white pine, and piñon pine) in
 a 2km long zone between 2400m and 2750m asl in the footprint of the 2011
 Las Conchas Fire in the Jemez Mountains of northern New Mexico. Seedlings
 were planted under Q. gambelii and R. neomexicana during winter 2018. We
 instrumented five Gambel oak and five New Mexico locust planting locations
 with upward facing game cameras (Moultrie D-80) and iButton®
 temperature/humidity logger (Model number DS1923; Temperature accuracy
 ±0.5°C; humidity resolution 0.6%;
 https://www.maximintegrated.com/en/products/ibutton-one-wire/data-loggers/DS1923.html). Camera and microclimate data were used to quantify the relationship between shrub canopy gap fraction and microclimate variables.  Planted seedlings were surveyed throughout the 2018 growing season.
DOI: 10.15468/dl.b29ye9
title: Occurrence Download

description: A dataset containing 780 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Vatica mangachapoi"
 ]
}

 The dataset includes 780 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002690-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5tb2rbp35
title: Experimental evidence that social information affects habitat selection in Marbled Murrelets

description: Habitat selection decisions can impact individual fitness and ultimately
 scale up to mediate population dynamics. Understanding how birds select
 habitat is thus critical for discerning the biological processes
 structuring populations and developing conservation strategies,
 particularly for species in decline. Marbled Murrelet (Brachyramphus
 marmoratus; hereafter murrelet) populations have declined in recent
 decades due to loss of late-successional forest nesting habitat and
 changing ocean conditions that impact foraging success. Most other
 seabirds in the family Alcidae nest colonially and evidence suggests
 nesting murrelets may aggregate in stands, yet no studies have examined
 murrelet use of social information in nest site selection. In 2016 we
 experimentally simulated presence of murrelets at 14 randomly chosen
 potential breeding sites by broadcasting murrelet calls throughout the
 breeding period. Between broadcasting bouts, we recorded calls of wild
 murrelets and compared call rates with those recorded at 14 control sites
 (no broadcast). One year after playbacks ceased (2017) we conducted
 breeding season surveys to document behaviors indicative of murrelet
 breeding activity. Broadcasting murrelet calls in 2016 increased daily
 odds of wild murrelets vocalizing during the treatment period by up to
 15.4× (95% CI = 2.3, 125.4) relative to control sites. During the 2017
 breeding season, the odds of occupancy were 10.0× (CI = 1.2, 81.4) greater
 at treatment sites than control sites. These results indicate that social
 information influences murrelet breeding site selection because simulated
 conspecific presence in potential nesting habitat appeared to attract
 prospectors in 2016 that continued occupying treatment sites the following
 year. This conspecific attraction implies murrelet nesting sites are
 likely to remain occupied over time and that large tracts of nesting
 habitat may be important for supporting murrelet populations. Murrelets
 may also be susceptible to information-mediated Allee effects whereby a
 lack of conspecific information about nesting habitat could exacerbate
 long-term population declines.
description: This dataset has been formatted using Tidy data principles
 (Wickham 2014).  That is, each observational unit is stored in its own
 table, each observation is a row, and each variable is a column.  There is
 a meta-data tab included in the Excel workbook that explains all variables
 in each table.  We have also included the R code required to import these
 data and perform all analyses in the manuscript.
 Wickham, H. (2014). Tidy data. Journal of Statistical Software
 59:10.
DOI: 10.5061/dryad.05qfttf1w
title: Primordial GATA6 macrophages function as extravascular platelets in sterile injury

description: Most multicellular organisms have a major body cavity that harbors immune
 cells. In primordial species like purple sea urchins, these cells perform
 phagocytic functions but are also crucial in repairing injuries. In
 mammals, the peritoneal cavity contains large numbers of resident GATA6+
 macrophages, which may play a similar role. It is unclear how cavity
 macrophages suspended in the fluid phase (peritoneal fluid) identify and
 migrate towards injuries, however. Here, we show that cavity macrophages
 in fluid rapidly form thrombus-like structures in response to injury using
 primordial scavenger receptor (SRCR) domains. Aggregates of cavity
 macrophages physically sealed injuries and promoted rapid repair of focal
 lesions. In iatrogenic surgical situations, these cavity macrophages
 formed extensive aggregates that promoted the growth of intra-abdominal
 scar tissue termed peritoneal adhesions.
description: This data package contains a copy of the main data files exactly
 as used for the figures in this paper. Please refer to the Material and
 Methods section of our manuscript for a detailed description of how this
 dataset was collected and processed. In addition to the data shown in our
 figures, we provide the raw tif files used for the cell tracking and the
 respective R-Scripts used to visualize these tracking results. Data files
 are comma-separated values (csv) files except for flow cytometry data
 which are stored in a multi-sheet Excel file.
description: Please start by reading the readme.txt file which contains all
 necessary information to use this data set.
DOI: 10.7291/d1k968
title: UVS Occultation Altimetry Code and Synthetic Data

description: This contains the code used to produce the figures in our UVS Occultation
 Altimetry manuscript, as well as the observation locations and synthetic
 data required to run the code. There are 9 .txt files, one is our nominal
 shape model, one is the set of chord ingress and egress points, three of
 them contain the locations of radar altimetric measurements for different
 truncation altitudes, and four of them contain precomputed lengths
 corresponding to our nominal shape model for each of the radar location
 files and the chord location file. In addition, there are two .py files,
 one containing all the functions required by the code, and one containing
 all the plotting routines to make the figures in the associated
 manuscript. To use this repository, open and run
 OccultationAltimetryPlotting.py and then you can run each of the plotting
 functions individually to make the figures in the paper. Each of those
 plotting functions is also meant to work as a demonstration of how to use
 the code to fit shape models using the provided datasets, so that a reader
 can explore other aspects of this problem as they see fit.
DOI: 10.5061/dryad.m63xsj410
title: Sympatry drives colour and song divergence in wood-warblers (Parulidae)

description: Closely related species often exhibit similarities in appearance and
 behaviour, yet when related species exist in sympatry, signals may diverge
 to enhance species recognition. Prior comparative studies provided mixed
 support for this hypothesis, but the relationship between sympatry and
 signal divergence is likely non-linear. Constraints on signal diversity
 may limit signal divergence, especially when large numbers of species are
 sympatric. We tested the effect of sympatric overlap on plumage colour and
 song divergence in wood-warblers (Parulidae), a speciose group with
 diverse visual and vocal signals. We also tested how number of sympatric
 species influences signal divergence. Allopatric species pairs had overall
 greater plumage and song divergence compared to sympatric species pairs.
 However, among sympatric species pairs, plumage divergence positively
 related to degree of sympatric overlap in males and females, while male
 song bandwidth and syllable rate divergence negatively related to
 sympatric overlap. In addition, as the number of species in sympatry
 increased, average signal divergence among sympatric species decreased,
 which likely due to constraints on warbler perceptual space and signal
 diversity. Our findings reveal that sympatry influences signal evolution
 in warblers, though not always as predicted, and that number of sympatric
 species can limit sympatry’s influence on signal evolution.
DOI: 10.5061/dryad.ns1rn8prf
title: Data from: Amphibious mudskipper populations are genetically connected along coastlines, but differentiated across water

description: Aim: Many mudskippers in the family Gobiidae are obligately amphibious,
 requiring both aquatic and terrestrial portions of their life cycle. The
 terrestrial phase involves restrictions to mudflat habitats during
 breeding, when adults build burrows in the mud to lay eggs. The effects of
 this restricted out-of-water phase might be reflected in the population
 structure of the species. However, dispersal during the aquatic larval
 phase could connect distant populations. We examine one such mudskipper,
 Periophthalmus modestus, to test whether populations separated by water
 are more differentiated than those connected along a coastline. Location:
 South and East China Sea Taxon: Periophthalmus modestus (family: Gobiidae,
 subfamily: Oxudercinae) (Cantor 1842) Methods: We collected 236
 individuals from ten locations around the East and South China Seas. We
 used a targeted capture sequencing method, RADcap, to call SNPs from 365
 loci. We used multiple spatial and population genetics analyses and
 coalescent models to address the contemporary and historic biogeography of
 the species. Results: Based on observed levels of genetic variation and
 population structure, populations of Ps. modestus are connected across
 large distances of continuous coastline and small spans of water.
 Restricted long-distance dispersal across deep water has resulted in
 fragmentation of populations. We recovered no signal of isolation by
 distance, but instead, found genetic differentiation associated with
 regional groupings separated by large expanses of water. Main conclusions:
 These results are consistent with the hypothesis that a limited dispersal
 phase significantly affects population structure in fishes. The
 restrictive amphibious life history may be a key factor in the present-day
 distribution and population structure of Ps. modestus. Interactions
 between organismal life history and geography are critical for explaining
 the population genetic structure of a species.
DOI: 10.5061/dryad.bk3j9kd9j
title: Comprehensive investigation of circulating biomarkers and their causal role in atherosclerosis-related risk factors and clinical events

description: Background: Circulating biomarkers have been previously associated with
 atherosclerosis-related risk factors, but the nature of these associations
 is incompletely understood. Methods: We performed multivariable-adjusted
 regressions and 2-sample Mendelian randomization analyses to assess
 observational and causal associations of 27 circulating biomarkers with 7
 cardiovascular traits in up to 451 933 participants of the UK Biobank.
 Results: After multiple-testing correction (alpha=1.3Å~10−4), we found a
 total of 15, 9, 21, 22, 26, 24, and 26 biomarkers strongly associated with
 coronary artery disease, ischemic stroke, atrial fibrillation, type 2
 diabetes, systolic blood pressure, body mass index, and waist-to-hip
 ratio; respectively. The Mendelian randomization analyses confirmed strong
 evidence of previously suggested causal associations for several glucose-
 and lipid-related biomarkers with type 2 diabetes and coronary artery
 disease. Particularly interesting findings included a protective role of
 IGF-1 (insulin-like growth factor 1) in systolic blood pressure, and the
 strong causal association of lipoprotein(a) in coronary artery disease
 development (β, −0.13; per SD change in exposure and outcome and odds
 ratio, 1.28; P=2.6Å~10−4 and P=7.4Å~10−35, respectively). In addition, our
 results indicated a causal role of increased ALT (alanine
 aminotransferase) in the development of type 2 diabetes and hypertension
 (odds ratio, 1.59 and β, 0.06, per SD change in exposure and outcome;
 P=4.8Å~10−11 and P=6.0Å~10−5). Our results suggest that it is unlikely
 that CRP (C-reactive protein) and vitamin D play causal roles of any
 meaningful magnitude in development of cardiometabolic disease.
 Conclusions: We confirmed and extended known associations and reported
 several novel causal associations providing important insights about the
 cause of these diseases, which can help accelerate new prevention
 strategies.
DOI: 10.5061/dryad.jsxksn080
title: Data from: Large frugivores matter more on an island: insights from island-mainland comparison of plant-frugivore communities

description: Endozoochory, a mutualistic interaction between plants and frugivores, is
 one of the key processes responsible for maintenance of tropical
 biodiversity. Islands, which have a smaller subset of plants and
 frugivores when compared with mainland communities, offer an interesting
 setting to understand the organization of plant-frugivore communities
 vis-a-vis the mainland sites.  We examined the
 relative influence of functional traits and phylogenetic relationships on
 the plant-seed disperser interactions on an island and a mainland site.
 The island site allowed us to investigate the organization of the
 plant-seed disperser community in the natural absence of key frugivore
 groups (bulbuls and barbets) of Asian tropics. The endemic
 Narcondam Hornbill, was the most abundant frugivore on the island and
 played a central role in the community. Species strength of frugivores (a
 measure of relevance of frugivores for plants) was positively associated
 with their abundance. Among plants, figs had the highest species strength
 and played a central role in the community. Island-mainland comparison
 revealed that the island plant-seed disperser community was more
 asymmetric, connected and nested as compared to the mainland community.
 Neither phylogenetic relationships or functional traits (after controlling
 for phylogenetic relationships) were able to explain the patterns of
 interactions between plants and frugivores on the island or the mainland
 pointing towards the diffused nature of plant-frugivore interactions. The
 diffused nature is a likely consequence of plasticity in foraging behavior
 and trait convergence that contribute to governing the interactions
 between plants and frugivores. This is one of the few studies to compare
 the plant-seed disperser communities between a tropical island and
 mainland and demonstrates key role played by a point-endemic frugivore in
 seed dispersal on island.
DOI: 10.5061/dryad.47d7wm3c3
title: Semi-Siamese U-Net for separation of lung and heart bioimpedance images: a simulation study of thorax EIT

description: Electrical impedance tomography (EIT) is widely used for bedside
 monitoring of lung ventilation status. Its goal is to reflect the internal
 conductivity changes and estimate the electrical properties of the tissues
 in the thorax. However, poor spatial resolution affects EIT image
 reconstruction to the extent that the heart and lung-related impedance
 images are barely distinguishable. Several studies have attempted to
 tackle this problem, and approaches based on decomposition of EIT images
 using linear transformations have been developed, and recently, U-Net has
 become a prominent architecture for semantic segmentation. In this paper,
 we propose a novel semi-Siamese U-Net specifically tailored for EIT
 application. It is based on the state-of-the-art U-Net, whose structure is
 modified and extended, forming shared encoder with parallel decoders and
 has multi-task weighted losses added to adapt to the individual separation
 tasks. The trained semi-Siamese U-Net model was evaluated with a test
 dataset, and the results were compared with those of the classical U-Net
 in terms of Dice similarity coefficient and mean absolute error. Results
 showed that compared with the classical U-Net, semi-Siamese U-Net
 exhibited performance improvements of 11.37% and 3.2% in Dice similarity
 coefficient, and 3.16% and 5.54% in mean absolute error, in terms of heart
 and lung-impedance image separation, respectively.
description: See manuscript for details of thorax EIT simulation
 data. The experimental design of the FEM phantom comprises varying combinations of three spheres. The combinations represent the interactions between the contractions and expansions of the heart and lungs as shown in Fig 4. Fig 4(a) represents the simulation of the thorax with both of the lungs and heart, whereas Figs 4(b) and (c) represent the lungs and heart in the thorax, respectively. Fig 5 flowchart illustrates the experimental design used for generating FEM phantom and obtaining the reconstructed images for training data.
DOI: 10.5061/dryad.vq83bk3rg
title: Cellular electrical properties of specific membrane capacitance and cytoplasmic conductivity

description: The submitted datasets contain the original data of the
 cell's electronic characteristic parameters of specific
 membrane capacitance and cytoplasmic conductivity. The cell types include
 H1299 cells treated with DMSO and 4-Mu,  95C cells treated with
 DMSO and 4-Mu, A549 control cells and A549 sg-RNA3 cells. The scatter
 plots and bar graphs demonstrated the differences of electroninc
 properties  were according to these datasets.