cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57770/5uncjf
title: Replication Data for: Predicting breast cancer metastasis by using serum biomarkers and clinicopathological data with machine learning technologies

description: Approximately 10%–15% of patients with breast cancer die of cancer metastasis or recurrence, and early diagnosis of it can improve prognosis. Breast cancer outcomes may be prognosticated on the basis of surface markers of tumor cells and serum tests. However, evaluation of a combination of clinicopathological features may offer a more comprehensive overview of breast cancer prognosis. We evaluated serum human epidermal growth factor receptor 2 (sHER2) as part of a combination of clinicopathological features used to predict breast cancer metastasis using machine learning algorithms, namely random forest, support vector machine, logistic regression, and Bayesian classification algorithms. The sample cohort comprised 302 patients who were diagnosed with and treated for breast cancer and received at least one sHER2 test at Chang Gung Memorial Hospital at Linkou between 2003 and 2016. The random-forest-based model was determined to be the optimal model to predict breast cancer metastasis at least 3 months in advance; the corresponding area under the receiver operating characteristic curve value was 0. 75 (p &lt; 0. 001).
DOI: 10.5683/sp2/k1inbl
title: Data from: Automatic segmentation of multiple cardiovascular structures from cardiac computed tomography angiography images using deep learning

description: AbstractObjectives: 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: 10.5683/sp2/sx9d6y
title: Data from: Basal metabolism in tropical birds: latitude, altitude, and the “pace of life”

description: Abstract1. Life history varies across latitudes, with the ‘pace of life’ being ‘slower’ in tropical regions. Because life history is coupled to energy metabolism via allocation tradeoffs and links between performance capacity and energy use, low metabolic intensity is expected in tropical animals. Low metabolism has been reported for lowland tropical birds, but it is unclear if this is due to ‘slow’ life history or to a warm, stable environment. 2. We measured Basal Metabolic Rates (BMR) of 253 bird species across a 2.6 km altitude gradient in Peru. We predicted higher BMR at high altitude due to lower temperatures leading to elevated thermoregulatory costs. We also tested for BMR differences between widely separated tropical regions (Peru and Panama), and between tropical- and temperate-breeding birds. 3. We found no effect of altitude on BMR in Peruvian species and no difference in BMR between Peruvian and Panamanian birds, suggesting that BMR in Neotropical birds is consistent and independent of environmental temperature. In a dataset encompassing more than 500 species, tropical birds had significantly lower BMR than temperate-breeding birds. 4. In contrast to several recent analyses, we found higher BMR in passerine birds than in non-passerines, independent of breeding latitude. 5. Breeding latitude affects BMR, but diversity in avian life history within and between temperate and tropical regions may explain some of the residual variation in BMR after accounting for body mass and breeding latitude. Future studies of links between life history, metabolism, and environmental factors might benefit from examining these variables within individual species as well as across broad geographic contrasts.
DOI: 10.5683/sp2/pytcqz
title: Data from: Being in a “green” building elicits “greener” recycling, but not necessarily “better” recycling

description: AbstractPrevious observational work revealed that transient populations in a sustainable building disposed of waste more accurately when compared to patrons in a non-sustainable building. The current study uses an experimental design to replicate this observed effect and to investigate whether or not the built environment influences motivational factors to impact behavior. We find support that a building designed and built to communicate an atmosphere of sustainability can influence waste disposal behavior. Participants in the sustainable building used the garbage receptacle significantly less and compensated by tending to select the containers and organics receptacle more, which actually resulted in more errors overall. Our findings suggest that building atmospherics can motivate people to recycle more. However, atmospherics alone do not appear to be sufficient to elicit the desired performance outcome.
DOI: 10.5683/sp2/nhvahl
title: Data from: Beyond a single patch: local and regional processes explain diversity patterns in a seagrass epifaunal metacommunity

description: AbstractEcological communities are jointly structured by dispersal, density-independent responses to environmental conditions and density-dependent biotic interactions. Metacommunity ecology provides a framework for understanding how these processes combine to determine community seagrass meadows along the British Columbia coast, we tested the hypothesis that eelgrass (Zostera marina L.) epifaunal invertebrate assemblages are influenced by local environmental conditions, but that high dispersal rates at larger spatial scales dampen effects of environmental differences. We used hierarchical joint species distribution modelling to understand the contribution of environmental conditions, spatial distance between meadows, and species co-occurrences to epifaunal invertebrate abundance and distribution across the region. We found that patterns of taxonomic compositional similarity among meadows were inconsistent with dispersal limitation, and meadows in the same region were often no more similar to each other than meadows over 1000 km away. Abiotic environmental conditions (temperature, dissolved oxygen) explained a small fraction of variation in taxonomic abundances patterns across the region. We found novel co-occurrence patterns among taxa that could not be explained by shared responses to environmental gradients, suggesting the possibility that interspecific interactions influence seagrass invertebrate abundance and distribution. Our results suggest that biodiversity and ecosystem functions provided by seagrass meadows reflect ecological processes occurring both within meadows and across seascapes, and that management of eelgrass habitat for biodiversity may be most effective when both local and regional processes are considered.
DOI: 10.5683/sp2/fpl9f0
title: Data from Beyond MAP: A guide to dimensions of rainfall variability for tropical ecology

description: AbstractTropical ecologists have long recognized rainfall as the key climate filter shaping tropical ecosystem structure and function across space and time. Still, tropical ecologists have historically had a limited toolkit for characterizing rainfall, largely relying on simple metrics like mean annual precipitation (MAP) and dry season length to characterize rainfall regimes that vary along many more dimensions. Here, we review methods for quantifying dimensions of rainfall variability on multiple time scales, with a focus on ecological applications of these methods. We also discuss key considerations for tropical ecologists looking to use rainfall metrics that better align with hypothesized biological or ecological mechanisms or that more effectively describe rainfall variability in the systems we study, and provide a toolkit (R scripts and gridded datasets) to do so. We argue that incorporating more sophisticated approaches to quantify rainfall variability into study design and statistical analyses will enhance our understanding of past, ongoing, and future changes in tropical ecosystems.
DOI: 10.5683/sp2/0bazjm
title: Data from: Biocontrol insect impacts population growth of its target plant species but not an incidentally used nontarget

description: AbstractUnderstanding the impact of herbivory on plant populations is a fundamental goal of ecology. Damage to individual plants can be visually striking and affect the fates of individuals, but these impacts do not necessarily translate into population-level differences in vital rates (survival, growth, or fecundity) or population growth rates. In biological control of weeds, quantitative assessments of population-level impacts of released agents on both target invasive plants and native, nontarget plants are needed to inform evaluations of the benefits and risks of releasing agents into new regions. Here we present a 3-yr experimental demographic field study using the European root-feeding biocontrol weevil, Mogulones crucifer, first released in Canada in 1997 to control the invasive weed Cynoglossum officinale (Boraginaceae). Mogulones crucifer is an effective “search and destroy” agent in Canada, but sporadically feeds, oviposits, and develops on native nontarget Boraginaceae. We investigated the population-level impacts of this biocontrol insect on its target weed and a native nontarget plant, Hackelia micrantha (Boraginaceae), by releasing large numbers of weevils into naturally occurring patches of H. micrantha growing isolated from or interspersed with C. officinale. We followed the fates of individual plants on release and nonrelease (control) sites for two transition years, developed matrix models to project population growth rates (λ) for each plant species, and examined the contributions from differences in vital rates to changes in λ using life table response experiments (LTRE). In contrast to studies of the insect–plant interaction in its native range, as a biocontrol agent, M. crucifer increased mortality of C. officinale rosettes in the year immediately following release, depressing the weed's λ to below the population replacement level. However, λ for H. micrantha was never depressed below the replacement level, and any differences between release and nonrelease sites in the nontarget could not be explained by significant contributions from vital rates in the LTRE. This study is the first to simultaneously and experimentally examine target and nontarget population-level impacts of a weed biocontrol insect in the field, and supports the theoretical prediction that plant life history characteristics and uneven herbivore host preferences can interact to produce differences in population-level impacts between target and nontarget plant species.
DOI: 10.5683/sp2/aktjfv
title: Data from: Bottom time does not always predict prey encounter rate in Antarctic fur seals

description: AbstractOptimal foraging models applied to breath-holding divers predict that diving predators should optimize the time spent foraging at the bottom of dives depending on prey encounter rate, distance to prey patch (depth) and physiological constraints. We tested this hypothesis on a free-ranging diving marine predator, the Antarctic fur seal Arctocephalus gazella, equipped with accelerometers or Hall sensors (n = 11) that recorded mouth-opening events, a proxy for prey capture attempts and thus feeding events. Over the 5896 dives analysed (&gt;15 m depth), the mean number of mouth-opening events per dive was 1·21 ± 1·69 (mean ± SD). Overall, 82% of mouth-openings occurred at the bottom of dives. As predicted, fur seals increased their inferred foraging time at the bottom of dives with increasing patch distance (depth), irrespective of the number of mouth-openings. For dives shallower than 55 m, the mean bottom duration of dives without mouth-openings was shorter than for dives with mouth-opening events. However, this difference was only due to the occurrence of V-shaped dives with short bottom durations (0 or 1 s). When removing those V-shaped dives, bottom duration was not related to the presence of mouth-openings anymore. Thus, the decision to abandon foraging is likely related to other information about prey availability than prey capture attempts (i.e. sensory cues) that seals collect during the descent phase. We did not observe V-shaped dives for dives deeper than 55 m, threshold beyond which the mean dive duration exceeded the apparent aerobic dive limit. For dives deeper than 55 m, seals kept on foraging at bottom irrespective of the number of mouth-openings performed. Most dives occurred at shallower depths (30–55 m) than the 60 m depth of highest foraging efficiency (i.e. of greatest number of mouth-opening events per dive). This is likely related to physiological constraints during deeper dives. We suggest that foraging decisions are more complex than predicted by current theory and highlight the importance of the information collected by the predator during the descent as well as its physiological constraints. Ultimately, this will help establishing reliable predictive foraging models for marine predators based on diving patterns only.
DOI: 10.5683/sp2/tl2j30
title: Data from: Burst muscle performance predicts the speed, acceleration, and turning performance of Anna's hummingbirds

description: AbstractDespite recent advances in the study of animal flight, the biomechanical determinants of maneuverability are poorly understood. It is thought that maneuverability may be influenced by intrinsic body mass and wing morphology, and by physiological muscle capacity, but this hypothesis has not yet been evaluated because it requires tracking a large number of free flight maneuvers from known individuals. We used an automated tracking system to record flight sequences from 20 Anna's hummingbirds flying solo and in competition in a large chamber. We found that burst muscle capacity predicted most performance metrics. Hummingbirds with higher burst capacity flew with faster velocities, accelerations, and rotations, and they used more demanding complex turns. In contrast, body mass did not predict variation in maneuvering performance, and wing morphology predicted only the use of arcing turns and high centripetal accelerations. Collectively, our results indicate that burst muscle capacity is a key predictor of maneuverability.
DOI: 10.5683/sp2/jrfbnt
title: Data from: Calculating the ecological impacts of animal-borne instruments on aquatic organisms

description: Abstract1. Animal-borne instruments provide researchers with valuable data to address important questions on wildlife ecology and conservation. However, these devices have known impacts on animal behaviour and energetics. Tags deployed on migrating animals may reduce reproductive output through increased energy demands or cause phenological mismatches of foraging and nesting events. For marine organisms, the only tagging guidelines that exist are based on lift and thrust impacts on birds – concepts that do not translate well to aquatic animals. Herein, we provide guidelines on assessing drag from animal-borne instruments and discuss the ecological impacts on marine organisms. Of particular concern is the effect of drag from instruments to the welfare of the animals and for the applicability of collected data to wild populations. 2. To help understand how drag from electronic tags affects marine animals in the wild, we used marine turtles as model aquatic organisms and conducted wind tunnel experiments to measure the fluid drag of various marine turtle body types with and without commercially available electronic tags (e.g. satellite, TDR, video cameras). We quantified the drag associated with carrying biotelemetry devices of varying frontal area and design (squared or tear drop shaped) and generated contour plots depicting percentage drag increase as a framework for evaluating tag drag by scientists and wildlife managers. Then, using concepts of fluid dynamics, we derived a universal equation estimating drag impacts from instruments across marine taxa. 3. The drag of the marine turtle casts was measured in wind speeds from 2 to 30 m s−1 (Re 3·0 × 104–1·9 × 106), equivalent to 0·1–1·9 m s−1 in seawater. The drag coefficient (CD) of the marine turtles ranged from 0·11 to 0·22, which is typical of other large, air-breathing, marine vertebrates (0·08–0·26). The CD of tags in reference to the turtle casts was 0·91 ± 0·18 and most tags caused minimal additional drag (&lt;5%) to adult animals, but the same devices increased the drag for juveniles significantly (&gt;100%). The sensitivity of aquatic animals to instrument drag is a dynamic relationship between the fluid flow patterns, or CD, and the frontal area ratio of the animal and tag. 4. In this paper, we have outlined methods for quantifying the drag costs from animal-borne instrumentation considering the instrument retention time (time to release from the animal) and the activity of the instrumented animal. With this valuable tool, researchers can quantify the drag costs from animal-borne instrumentation and choose appropriate tags for their intended study organism and question. Reducing drag will ultimately reduce the impact on the instrumented animals and lead to greater biological realism in the collected data.
DOI: 10.5683/sp2/atohjs
title: Data from: Calorespirometry reveals that goldfish prioritize aerobic metabolism over metabolic rate depression in all but near-anoxic environments

description: AbstractMetabolic rate depression (MRD) has long been proposed as the key metabolic strategy of hypoxic survival, but surprisingly the effects of changes in hypoxic O2 tensions (PwO2) on MRD are largely unexplored. We simultaneously measured the O2 consumption rate (ṀO2) and metabolic heat of goldfish using calorespirometry to test the hypothesis that MRD is employed at hypoxic PwO2s and initiated just below Pcrit, the PwO2 below which ṀO2 is forced to progressively decline as the fish oxyconforms to decreasing PwO2. Specifically, we used closed-chamber and flow-through calorespirometry together with terminal sampling experiments to examine the effects of PwO2 and time on ṀO2, metabolic heat and anaerobic metabolism (lactate and ethanol production). The closed-chamber and flow-through experiments yielded slightly different results. Under closed-chamber conditions with a continually decreasing PwO2, goldfish showed a Pcrit of 3.0±0.3 kPa and metabolic heat production was only depressed at PwO2 between 0 and 0.67 kPa. Under flow-through conditions with PwO2 held at a variety of oxygen tensions for 1 and 4 h, goldfish also initiated MRD between 0 and 0.67 kPa but maintained ṀO2 to 0.67 kPa, indicating that Pcrit is at or below this PwO2. Anaerobic metabolism was strongly activated at PwO2 ≤1.3 kPa, but only used within the first hour at 1.3 and 0.67 kPa as anaerobic end-products did not accumulate between 1 and 4 h exposure. Taken together, it appears that goldfish reserve MRD for near-anoxia, supporting routine metabolic rate at sub-Pcrit PwO2s with the help of anaerobic glycolysis in the closed-chamber experiments, and aerobically after an initial (&lt;1 h) activation of anaerobic metabolism in the flow-through experiments, even at 0.67 kPa PwO2.
DOI: 10.5683/sp2/8mdhjq
title: Data from: Can avian functional traits predict cultural ecosystem services?

description: Abstract The functional trait diversity of species assemblages can predict the provision of ecosystem services such as pollination and carbon sequestration, but it is unclear whether the same trait-based framework can be applied to identify the factors that underpin cultural ecosystem services and disservices. To explore the relationship between traits and the contribution of species to cultural ecosystem services and disservices, we conducted 404 questionnaire surveys with birdwatchers and local residents in Guanacaste, Costa Rica. We used an information-theoretic approach to identify which of 20 functional traits for 199 Costa Rican bird species best predicted their cultural ecosystem service scores related to birdwatching, acoustic aesthetics, education and local identity, as well as disservices (e.g., harm to crops). We found that diet was the most important variable explaining perceptions of cultural ecosystem service and disservice providers. Aesthetic traits such as plumage colour and pattern were important in explaining birdwatching scores. We also found people have a high affinity for forest-affiliated birds. The insight that functional traits can explain variation among cultural perspectives on values derived from birds offers a first step towards a trait-based system for understanding the species attributes that underpin cultural ecosystem services and disservices.
DOI: 10.5683/sp2/3zbzy7
title: Data from: Can clone size serve as a proxy for clone age? An exploration using microsatellite divergence in Populus tremuloides

description: AbstractIn long-lived clonal plant species, the overall size of a clone has previously been used to estimate clone age. The size of a clone, however, might be largely determined by physical or biotic interactions, obscuring the relationship between clone size and age. Here, we use the accumulation of mutations at 14 microsatellite loci to estimate clone age in trembling aspen, Populus tremuloides, from southwestern Canada. We show that the observed patterns of genetic divergence are consistent with a model of clonal growth, allowing us to use pairwise genetic divergence as an estimator of clone age. In the populations studied, clone size did not exhibit a significant relationship with microsatellite divergence, indicating that clone size is not a good proxy for clone age.