cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.c876q2
title: Occurrence Download

description: A dataset containing 622 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-10.59483 26.06882,18.80342 26.06882,18.80342 46.68044,-10.59483 46.68044,-10.59483 26.06882))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Rugulopteryx okamurae"
 ]
}

 The dataset includes 622 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002242-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8sf7m0cj3
title: The effects of age on the demography of a perennial plant depend on interactions with size and environment

description: Age-dependence of the demographic rates survival, fecundity and individual
 growth is a fundamental aspect of population biological theory. Knowledge
 about plant ageing can also be important for conservation and agriculture
 as it will improve the accuracy of population viability assessments and
 long-term performance assessments in perennial crops. Recent studies show
 age effects on demographic rates for several plant species, yet much
 remains to be learned about the patterns and mechanisms of plant ageing,
 particularly about how age effects interact with the environment and with
 plant size. We collected age-and-size-based demographic data, as well as
 individual-based environmental data, for the perennial herb Plantago
 lanceolata in Denmark over three annual transitions (four years). We
 combined frequent field monitoring of carefully mapped individuals with
 the underused technique of root histology to determine age of herbaceous
 plants. We used generalized linear mixed effects models to assess how age,
 soil properties, and year influenced survival, growth, and reproduction.
 Our results show no strong evidence of consistent age declines, rather, we
 found mostly positive effects of age on vital rates. For all vital rates,
 i.e. survival, growth, flowering, and reproductive output, age effects
 also differed significantly among years. Additionally, we detected an
 interactive effect of age and size in the growth model. Size, and temporal
 and spatial environmental variation also affected vital rates
 independently of age. Synthesis: Our study shows that age-dependence of
 demographic rates can depend both on individual size and environmental
 variation. These results suggest that a consideration of potential
 age-interactions may improve the accuracy of comparative studies of ageing
 and population projections. Moreover, this study shows that much is still
 unknown about how plant ageing can be affected by the environment, and
 illustrates how age determination using herb chronology provides an
 opportunity to increase our knowledge about ageing in herbaceous plants.
DOI: 10.5061/dryad.msbcc2fv9
title: Risk factors for cardiovascular disease (CVD) in adults with type 1 diabetes: findings from prospective real-life T1D exchange registry

description: Context Cardiovascular disease (CVD) is a major cause of mortality in
 adults with type 1 diabetes. Objective We prospectively evaluated CVD risk
 factors in a large, contemporary cohort of adults with type 1 diabetes
 living in the United States. Design Observational study of CVD and CVD
 risk factors over a median of 5.3 years. Setting The T1D Exchange clinic
 network. Patients Adults (age ≥18 years) with type 1 diabetes and without
 known CVD diagnosed before or at enrollment. Main Outcome Measure
 Associations between CVD risk factors and incident CVD were assessed by
 multivariable logistic regression. Results The study included 8,727
 participants (53% female, 88% non-Hispanic white, median age 33 years
 [IQR=21, 48], type 1 diabetes duration 16 years [IQR=9, 26]). At
 enrollment, median HbA1c was 7.6% (66 mmol/mol) [IQR=6.9 (52), 8.6 (70)],
 33% used a statin, and 37% used blood pressure medication. Over a mean
 follow-up of 4.6 years, 325 (3.7%) participants developed incident CVD.
 Ischemic heart disease was the most common CVD event. Increasing age, BMI,
 HbA1c, presence of hypertension and dyslipidemia, increasing duration of
 diabetes, and diabetic nephropathy were associated with increased risk for
 CVD. There were no significant gender differences in CVD risk. Conclusion
 HbA1c, hypertension, dyslipidemia and diabetic nephropathy are important
 risk factors for CVD in adults with type 1 diabetes. A longer follow-up is
 likely required to assess the impact of other traditional CVD risk factors
 on incident CVD in the current era.
DOI: 10.5061/dryad.4xgxd2560
title: Data from: Interspecific hybrids show a reduced adaptive potential under DNA damaging conditions

description: The data is framed in a context of experimental evolution. 
 Popular Summary: Hybridization between species can be a dead end or a
 stimulus for adaptation and speciation. This stimulus could be fueled,
 among other things, by the intrinsic elevated rate of evolution of hybrid
 genomes. Whether this serves as an advantage for hybrids when faced with
 extreme stress is largely unknown. Here we tested this by evolving yeast
 species and their hybrids in UV mimetic conditions. We find that hybrids
 adapt slower than parental species in these conditions. We reason that
 this may be caused by the fact that the intrinsic genome instability of
 hybrids is pushed to levels above which it helps adaptive evolution.
description: Among the files you will find a document "README.txt"
 which explains how the data should be analyzed.
DOI: 10.5061/dryad.djh9w0vwq
title: Agouti reintroduction recovers seed dispersal of a large-seeded tropical tree

description: The aim of animal reintroductions has mainly been species recovery; only
 few reintroduction initiatives focus on ecosystem restoration. Therefore,
 reintroduction consequences on ecological interactions are seldom
 assessed. We used the interaction between a reintroduced population of
 agoutis (Dasyprocta leporina) and a vulnerable tropical endemic tree
 (Joannesia princeps) to examine reintroduction effects on seed dispersal
 and seedling establishment. To test the outcomes of this interaction we
 tracked seeds of J. princeps in two adjacent forest areas with and without
 reintroduced agoutis. We also assessed if dispersal distances affected
 seedling survival. To determine seed fate and dispersal distance we used
 spool-and-line tracking, together with camera traps to identify
 dispersers. Agoutis were the only species removing J. princeps seeds, thus
 dispersal only occurred where agoutis had been reintroduced; in the area
 without agoutis, all seeds remained intact on the soil, even one year
 after the experiment’s beginning. At the reintroduction area, most seeds
 were preyed upon by agoutis but 7% remained dispersed and 2% germinated
 after ten months. Only seeds buried by agoutis were able to germinate.
 Most dispersed seeds were disperse 15 m or farther and longer dispersal
 distances benefited J. princeps, since seedlings farther from a
 conspecific adult tree had greater survival probability. Agoutis were also
 seen burying seeds of two other plant species; these mammals have the
 potential to benefit dozens of large-seeded species in our study system.
 Agouti reintroduction thus exemplifies the value of trophic rewilding
 programs to re-establish ecological interactions and restore ecosystem
 functioning.
description: Data and code about seed dispersal of <em>Joannesia
 princeps</em> by agoutis<br>
DOI: 10.5061/dryad.q2bvq83g0
title: Territory acquisition mediates the influence of predators and climate on juvenile red squirrel survival

description: 1) Juvenile survival to first breeding is a key life history stage for all
 taxa. Survival through this period can be particularly challenging when it
 can coincide with harsh environmental conditions such as a winter climate
 or food scarcity, leading to highly variable cohort survival. However, the
 small size and dispersive nature of juveniles generally makes studying
 their survival more difficult. 2) In territorial species, a key life
 history event is the acquisition of a territory. A territory is expected
 to enhance survival, but how it does so is not often identified. We tested
 how the timing of territory acquisition influenced the winter survival of
 juvenile North American red squirrels Tamiasciurus hudsonicus, hereafter
 red squirrels, and how the timing of this event mediated sources of
 mortality. We hypothesized that securing a territory prior to when food
 resources become available would reduce juvenile susceptibility to
 predation and climatic factors over winter. 3) Using 27 years of data on
 the survival of individually-marked juvenile red squirrels, we tested how
 the timing of territory acquisition influenced survival, whether the
 population density of red squirrel predators and mean temperature over
 winter were related to individual survival probability, and if territory
 ownership mediated these effects. 4) Juvenile red squirrel survival was
 lower in years of high predator abundance and in colder winters. Autumn
 territory owners were less susceptible to lynx Lynx canadensis, and
 possibly mustelid Mustela and Martes spp., predation. Autumn territory
 owners had lower survival in colder winters, but surprisingly non-owners
 had higher survival in cold winters. 5) Our results show how the timing of
 a life history event like territory acquisition can directly affect
 survival and also mediate the effects of biotic and abiotic factors later
 in life. This engenders a better understanding of the fitness consequences
 of the timing of key life history events.
description: A population of red squirrels in the southwest Yukon has been
 monitored since 1989. We used reproductive and survival data from this
 population, along with data on predator abundance and weather conditions,
 to measure survival of juveniles that were alive at the end of the summer
 in the year of their birth.
DOI: 10.5061/dryad.tmpg4f4vw
title: The social function of the feeling and expression of guilt

description: Humans are uniquely cooperative and form crucial short-
 and long-term social bonds between individuals that
 ultimately shape human societies. The need for such intense
 cooperation may have provided a particularly powerful selection
 pressure on the emotional and communicative behaviours
 regulating cooperative processes, such as guilt. Guilt is a
 social, other-oriented moral emotion that promotes relationship
 repair and pro-sociality. For example, people can be more
 lenient towards wrongdoers who display guilt than towards
 those who do not. Here, we examined the social consequences
 of guilt in a novel experimental setting with pairs of
 friends differing in relationship quality. Pairs of participants
 took part in a cooperative game with a mutual goal. We then
 induced guilt in one of the participants and informed the
 other participant of their partner’s wrongdoing. We examined
 the outcome using a dictator game to see how they split a
 joint reward. We found that guilty people were motivated to
 repair wrongdoing regardless of friendship. Observing guilt
 in others led to a punishment effect and a victim of
 wrongdoing punished close friends who appeared guilty more so
 than acquaintances. We suggest, therefore, that guilt has a
 stronger function between close friends as the costs of
 relationship breakdown are greater. Relationship context,
 therefore, is crucial to the functional relevance of moral
 emotions.
description: <b>Facial expression. </b>The stimulus videos of
 Player 1 were coded using the Facial Action Coding System
 <b>Dictator game - reward
 split</b> In the dictator game presented to Player 1 (Fig. 1), players were forced to make an uneven split and attribute at least £1 more to themselves or to their partner. Therefore the dependent variable was the overall proportion of coins given to Player 2 (of the 15 available: <i>percentage</i> &lt; 0.5: more money retained for self; <i>percentage</i> &gt; 0.5: more money to Player 2). In conditions 1 and 2, Player 2 was presented with the reward money already split (10 to Player 1, 5 to Player 2). Here, the dependent variable was the magnitude of change from the original split to the final split: <i> </i><i>10-x</i><i>15</i> , with <i>x</i>  being the final number of coins given to Player 1. In condition 3, Player 2 was presented with an un-split reward and the dependent variable was calculated as for Player 1.
DOI: 10.5061/dryad.2fqz612kw
title: Changes in the coordination between respiration and swallowing from suckling through weaning

description: All mammals undergo weaning from milk to solid food. This process requires
 substantial changes to mammalian oropharyngeal function. The coordination
 of swallowing and respiration is a crucial component of maintaining airway
 function throughout feeding and matures over infant development. However,
 how this coordination is affected by weaning is unknown. In this study we
 ask how changes in posture, neural maturation, and food properties
 associated with weaning affect coordination of respiration and swallowing
 in a validated infant pig model. We recorded 7 piglets feeding before and
 during weaning age with liquid milk in a bottle, in a bowl, and solid feed
 in a bowl. Using videofluoroscopy synchronized with respiration we found
 1) the delay in the onset of inspiration after swallowing does not change
 with head position; 2) the delay is different between solid food and bowl
 drinking at the same age; and 3) the delay increases over time when bottle
 feeding, suggesting a maturational effect. Significant changes in
 aerodigestive coordination occur prior to and post weaning, resulting in
 distinctive patterns for liquid and solid food. The interplay of
 maturational timelines of oropharyngeal function at weaning may serve as a
 locus for behavioral and life history plasticity.
DOI: 10.5061/dryad.80gb5mknq
title: Data from: Interaction networks of avian mixed-species flocks along elevation in the tropical Andes

description: Ecological communities are comprised of species that interact with each
 other and those interactions ultimately generate community structure.
 Network theory provides a useful framework to study communities, by
 simultaneously considering species composition and the interactions among
 species. In this study, I use mixed-species flocks as model systems to
 gain insights on community and network structure. Specifically, I use
 co-occurrence network analyses to explore if avian mixed-species flocks
 change in richness and composition and/or in network structure and
 pair-wise associations, across elevations in the tropical Andes of
 Bolivia. Networks of flocking species changed both in composition and in
 the frequency and realization of pair-wise interactions across elevations,
 but changes in pair-wise associations explained most of network turnover
 along elevation. Pair-wise interactions changed rapidly, with shared
 species changing in position and importance within the network. Network
 dissimilarity was mostly explained by changes in the nature of
 associations rather than by differences in composition. Altogether,
 results show that montane mixed-species flocks are composed of loosely
 connected species and that most species have the potential of switching
 associations, often increasing in association strength at high elevations
 (up to 3150m). Networks increased in connectivity and cohesion with
 elevation; flocks in lower elevations had more connections and these were
 less even. Above 3150 m asl, there was rapid decay suggesting that flocks
 above this critical point are less connected and cohesive. This study
 exemplifies how combining community, network and pair-wise analyses can
 provide a more holistic view on the responses of species and assemblages
 to environmental gradients.
description: Flocks were surveyed between May and November 2016 and May and
 August 2017, along an elevational gradient (~1350 – 3500 m asl) in
 Cotapata National Park, a protected area in the Andes of western Bolivia.
 A flock was defined as a gathering of at least two species foraging
 &lt; 10 meters from each other while moving in the same
 direction.Flock data were collected with the “gambit of the group” method,
 where several individuals observed at the same time and place are assumed
 to be associated. Raw data on presence-absence of 164
 bird species participating of 358 mixed-species flocks in the Andes of
 western Bolivia are included in the dataset, with species in columns
 and flocks in rows 
description: Species are presented in columns and flocks in rows.
 Column 1: Flock, includes the flock ID number
 Columns 2 – 165: Species, nomenclature coincides with that of
 Jetz et al. (2012) available in  https://birdtree.org/ Column 166: Elevation band, range of elevation in m asl, where the flock was observed. Column 167: Site, reference elevation (in m asl) used in the manuscript to describe the elevational position of the network.
DOI: 10.15468/dl.8k4fh6
title: Occurrence Download

description: A dataset containing 3252 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Parapercis colias",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 3252 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002244-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.m63xsj3z7
title: Elements of fish metacommunity structure in Neotropical freshwater streams

description: The identification of the mechanisms underlying co-occurrence
 patterns of species is
 a way to identify which processes
 (niche, neutral or both) structure metacommunities. In this
 paper, our goals are to identify patterns of co-occurrence in
 neotropical stream fish and determine which
 processes structure the metacommunity
 and the gradients that underlie this
 structure.  Our results pointed out
 that the metacommunity formed by the total pool of species is
 structured by a nested pattern (Hyperdispersed Species Loss) of
 co-occurrence and the mass effect mechanism. On the other
 hand, a set of core species displays a
 Clementisian pattern and is structured by the species
 sorting mechanism. Both, hyperdispersed species
 loss and the Clementisian patterns point to a discrete
 set of communities in the metacommunity. These communities could be
 isolated by physicochemical conditions, or physical barriers, like dams or
 waterfalls.
description: We used a data set formed by 66 streams , composed by a pool of
 143 species and richness varying from 1 to 27 species. Stream data entered
 the database when meet the following criteria : (i) the collection was
 carried out in a 1<sup>st</sup> – 3<sup>rd</sup>
 order stream; (ii) the stream stretch was georeferenced; (iii) fish
 sampling was carried out by electric fishing, trawl nets, and/or hand
 nets; (iv) a minimum of 50-meter stretch was sampled by stream; (v) a
 single sample site per stream; (vi) there was a stream species list;
 (<i>vii</i>) environmental variables (turbidity, conductivity,
 pH, dissolved oxygen, water velocity, stream channel depth and width) were
 measured <i>in situ</i> at three or more points in each
 stream; (viii) fish sampling, transport and preservation of sampled
 specimens were authorized by the <i>Sistema de Autorização e
 Informação em Biodiversidade</i> (SISBIO),  <i>Instituto Chico
 Mendes de Conservação da Biodiversidade, Ministerio do Meio Ambiente
 </i>and (ix) all streams was located in the Cerrado Biome.
 Constraining the data for streams under the same vegetation condition
 ensure that the features linked to vegetation type, like substrate and
 temperature, are not so different decreasing the amount of
 variability.
DOI: 10.5061/dryad.9s4mw6mc9
title: Data from: Automatic segmentation of multiple cardiovascular structures from cardiac computed tomography angiography images using deep learning

description: Objectives: To develop, demonstrate and evaluate an automated
 deep learning method for multiple cardiovascular structure segmentation.
 Background: Segmentation of cardiovascular images is
 resource-intensive. We design an automated deep learning method for the
 segmentation of multiple structures from Coronary Computed Tomography
 Angiography (CCTA) images. Methods: Images from a multicenter
 registry of patients that underwent clinically-indicated CCTA were used.
 The proximal ascending and descending aorta (PAA, DA), superior and
 inferior vena cavae (SVC, IVC), pulmonary artery (PA), coronary sinus
 (CS), right ventricular wall (RVW) and left atrial wall (LAW) were
 annotated as ground truth. The U-net-derived deep learning model was
 trained, validated and tested in a 70:20:10 split. Results: The
 dataset comprised 206 patients, with 5.130 billion pixels. Mean age was
 59.9 ± 9.4 yrs., and was 42.7% female. An overall median Dice score of
 0.820 (0.782, 0.843) was achieved. Median Dice scores for PAA, DA, SVC,
 IVC, PA, CS, RVW and LAW were 0.969 (0.979, 0.988), 0.953 (0.955, 0.983),
 0.937 (0.934, 0.965), 0.903 (0.897, 0.948), 0.775 (0.724, 0.925), 0.720
 (0.642, 0.809), 0.685 (0.631, 0.761) and 0.625 (0.596, 0.749)
 respectively. Apart from the CS, there were no significant differences in
 performance between sexes or age groups. Conclusions: An
 automated deep learning model demonstrated segmentation of multiple
 cardiovascular structures from CCTA images with reasonable overall
 accuracy when evaluated on a pixel level.
DOI: 10.6086/d1z396
title: Connecting species’ geographical distributions to environmental variables: range maps versus observed points of occurrence

description: Connecting the geographical occurrence of a species with underlying
 environmental variables is fundamental for many analyses of life history
 evolution and for modeling species distributions for both basic and
 practical ends.  However, raw distributional information comes
 principally in two forms:  points of occurrence (specific
 geographical coordinates where a species has been observed), and
 expert-prepared range maps.  Each form has potential
 short-comings:  range maps tend to overestimate the true
 occurrence of a species, whereas occurrence points (because of their
 frequent non-random spatial distribution) tend to underestimate
 it.  Whereas previous comparisons of the two forms have focused
 on how they may differ when estimating species richness, less attention
 has been paid to the extent to which the two forms actually differ in
 their representation of a species’ environmental associations. 
 We assess such differences using the globally distributed avian order
 Galliformes (294 species).  For each species we overlaid range
 maps obtained from IUCN and point-of-occurrence data obtained from GBIF on
 global maps of four climate variables and elevation.  Over all
 species, the median difference in distribution centroids was 234 km, and
 median values of all five environmental variables were highly correlated,
 although there were a few species outliers for each variable.  We
 also acquired species’ elevational distribution mid-points (mid-point
 between minimum and maximum elevational extent) from the literature;
 median elevations from point occurrences and ranges were consistently
 lower (median -420 m) than mid-points.  We concluded that in most
 cases occurrence points were likely to produce better estimates of
 underlying environmental variables than range maps, although differences
 were often slight.  We also concluded that elevational range
 mid-points were biased high, and that elevation distributions based on
 either points or range maps provided better estimates.
description: Details provided in original publication.
description: READ_ME file has been uplodaded