Find research datasets worth reusing

opencc-by-4.0Dec 2016View details →

Contrasting Effects of Heat Pulses of Different Trophic Levels

Data used for publication of "Contrasting Effects of Heat Pulses of Different Trophic Levels, an Experiment with a Herbivore-Parasitoid Model System". Data in sheet "Data", metadata in sheet "Legend".

opencc-by-4.0Jul 2024View details →

Data from: Seeing the Invisible: On Aortic Valve Reconstruction in Non-Contrast CT

Abstract In this dataset, we present supplementary material from the paper by Bujny et al. (2024). The material includes STL models of aorta segmented in contrast Computed Tomography (CT) scans by a medical expert and using the Machine Learning (ML) model described in the paper. A gallery of ML-based segmentations of the aortic root in non-contrast CT, with the corresponding scans and aortic valve meshes registered from contrast CT using the Iterative Closest Point (ICP) algorithm is provided, as well. Finally, we include the source code of the ICP-based accuracy evaluation method proposed in the paper, with an example in Jupyter Notebook. All of the data included in the dataset has been generated based on the CT scans from the openly available orCaScore dataset (Wolterink et al. 2016).   Dataset organization The root folder contains 3 catalogs: <ul> <li>contrast_aorta_stls – set of 19 Ground Truth (GT) segmentations of aorta in contrast CT, with the corresponding inferences of the contrast ML model described in the paper, for the scans from the open-source orCaScore dataset (Wolterink et al. 2016).</li> <li>icp_code – Python code of the ICP-based accuracy evaluation method proposed in the paper.</li> <li>icp_gallery – HTML gallery of aorta segmentations based on the non-contrast ML model described in the paper, with the corresponding CT scans and meshes of the aortic valves segmented in contrast CT, which were rigidly registered to the non-contrast scans using the proposed ICP-based approach. In the CT scans, blue and red contours were used to depict non-contrast-based and registered contrast-based ML segmentations, respectively.</li> </ul>   References M. Bujny, K. Jesionek, J. Nalepa, T. Bartczak, K. Miszalski-Jamka, M. Kostur, “Seeing the Invisible: On Aortic Valve Reconstruction in Non-Contrast CT,” 27th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Marrakesh, Morocco, 2024 [accepted]. J. M. Wolterink et al., “An evaluation of automatic coronary artery calcium scoring methods with cardiac CT using the orCaScore framework: Evaluation of cardiac CT-based automatic coronary calcium scoring,” Med. Phys., vol. 43, no. 5, pp. 2361–2373, 2016.

opencc-zeroOct 2023View details →

Contrasting effects of indigenous arbuscular mycorrhizal fungi on nitrogen absorption of C3 and C4 grasses: Evidence from microcosm and 15N labeling experiments

Background and aims Nitrogen (N) captured by arbuscular mycorrhizal (AM) symbiosis is a major pathway in the N uptake of host plants. However, the relative contribution of arbuscular mycorrhizal fungi (AMF) to N uptake in different plant functional types has not been well assessed. Methods Two dominant plant species in semiarid steppe ecosystems on the Mongolian plateau, i.e. Leymus chinensis (C3 grass) and Cleistogenes squarrosa (C4 grass), were selected in this study. We conducted a greenhouse manipulation experiment using novel microcosms combined with 15N labeling techniques and investigated the effect of indigenous AMF on plant growth and quantified their relative contribution to N uptake under high and low levels of available soil N. Results Indigenous AMF contribute more to N uptake in C3 grass than that in C4 grass, and mycorrhizal partners act as parasites for C4 plant growth. For L. chinensis, indigenous AM symbiosis suppressed plant growth under low soil N but improved plant growth under high soil N conditions. AMF contributed to c. 23% and 20% of the total plant N uptake under low and high soil N conditions, respectively. For C. squarrosa, indigenous AM symbiosis consistently inhibited plant growth under both low and high soil N conditions, and the percent contributions of AMF to N uptake were only c. 9% and 7%, respectively. Conclusions Our results demonstrate that indigenous AM symbiosis plays a vital role in N uptake by host plants, even in the absence of a positive growth response. AMF can modify the fitness of C3 and C4 grasses and thereby alter plant community composition and ecosystem N cycling, particularly under high N conditions. Our study has important implications for improving global N cycling models in the face of increasing global N deposition.

opencc-by-4.0Nov 2023View details →

Contrasting Activation Characteristics of Biomass Burning and Fossil Fuel Combustion Aerosols in Fogs and Clouds: Implications for Regional Air Quality and Climate

The key 'jul' in data use 2021-01-01 as the referece day, for example,  2021-01-02 12:00:00 corresponding to jul of 2.5.

opencc-by-4.0May 2023View details →

Phase-contrast time-lapse recordings of four bacterial species growing in microfluidic microtraps

This dataset and software accompany the article <a href="https://doi.org/10.1371/journal.pcbi.1011181">"Label-free deep learning based species classification of bacteria imaged by phase-contrast microscopy"</a>  for reproducing the results. The study applies deep-learning based image and video models for species classification of the bacteria Enterococcus faecalis, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa growing in microfluidic chip traps.

opencc-by-4.0Nov 2023View details →

Replication Data for "Inverse-designed low-index-contrast structures on silicon photonics platform for vector-matrix multiplication"

COMSOL files and Python post-processing code.

opencc-zeroNov 2023View details →

Data from: Warming had contrasting effects on the importance of facilitative interactions with a cushion nurse species on native and non-native species in the high-Andes of central Chile

Alpine habitats are regarded as particularly vulnerable to the effects of climate change. On one hand, global warming is supposed to contributes to alpine environments becoming less stressful. On the other hand, altered snowpack due to warmer temperatures can intensify the stress in these habitats. The presence of non-native plants on some of these habitats is due to the facilitative effects exerted by native nurse plants, becoming an additional threat. According to the stress gradient hypothesis the importance of facilitative interactions with nurse species is expected to diminish as environmental harshness decreases due to climate change, yet remains important if climate change heightens the stress in alpine habitats. However, the responses also depend on climate change's impact on the nurse species. We conducted an experimental warming experiment in the Andes of the central Chile to assess the effects of warmer temperatures on the growth, reproduction and photochemical efficiency of the cushion nurse plant Azorella madreporica. Further we performed a cushion removal experiment involving three native species (Gamocarpha ventosa, Nocaccea magellanica and Rytidosperma pictum) and two non-native species (Cerastium arvense and Taraxacum officinale) to assess whether facilitative interactions changed with warming. We expected that under warmer conditions facilitation continued be important for the native species but decreased for the non-natives as the latter are abundant at warmer low elevations. We found that warmer conditions increased the photochemical efficiency and growth of the nurse cushions. Removal of cushions resulted in high mortality rates for all species. However, under warmer conditions, native species exhibited lower survival rates, whereas non-natives showed no significant changes compared to control groups. In summary, warmer temperatures were beneficial for the nurses maintaining the importance of facilitative interactions for native species, but not for the non-natives.

opencc-zeroDec 2023View details →

Data from: Continuous variation in an aposematic pattern affects background contrast, but is not associated with differences in microhabitat use

Variation in aposematic signals was once predicted to be rare, yet in recent years it has become increasingly well-documented. Despite increases in the frequency with which polytypism and polymorphism have been suggested to occur, population-wide variance is rarely quantified. We comprehensively sampled a subpopulation of the poison frog Oophaga sylvatica, a species which is polytypic across its distribution and also shows considerable within-population polymorphism. On one hand, color pattern polymorphism could be the result of multifarious selection acting to balance different signaling functions and leading to the evolution of discrete sub-morphs which occupy different fitness peaks. Alternatively, variance could simply be due to relaxed selection, where variation would be predicted to be continuous. We used visual modeling of conspecific and heterospecific observers to quantify the extent of within-population phenotypic variation and assess whether this variation produced distinct signals. We found that, despite considerable color pattern variation, variance could not be partitioned into distinct groups, but rather all viewers would be likely to perceive variation as continuous. Similarly, we found no evidence that frog color pattern contrast was either enhanced or diminished in the frogs' chosen microhabitats compared to alternative patches in which conspecifics were observed. Within population phenotypic variance therefore does not seem to be indicative of strong selection towards multiple signaling strategies, but rather pattern divergence has likely arisen due to weak purifying selection, or neutral processes, on a signal that is highly salient to both conspecifics and predators.

opencc-by-4.0Jul 2023View details →

Data for the paper: Critical role of radiative cooling vertical contrast in triggering episodic deluges in small-domain hothouse climates

Data for the paper: Critical role of radiative cooling vertical contrast in triggering episodic deluges in small-domain hothouse climates. The paper has just been submitted, which means this dataset might change before the final publication.

opencc-zeroDec 2023View details →

Contrasting responses of fine root biomass and traits to large-scale nitrogen and phosphorus addition in tropical forests in the Guiana shield

Fine roots mediate plant nutrient acquisition and growth. Depending on soil nutrient availability, plants can regulate fine root biomass and morphological traits to optimise nutrient acquisition. Little is known, however, about the importance of these parameters influencing forest functioning. In this study, we measured root responses to nutrient additions to gain a mechanistic understanding of plant adaptations to nutrient limitation in two tropical forests in French Guiana, differing two-fold in their soil nutrient statuses. We analysed the responses of root biomass, mean root diameter (RD), specific root length (SRL), specific root area (SRA), root tissue density (RTD) and carbon (C), nitrogen (N) and phosphorus (P) concentrations in roots down to 15 cm soil depth after three years of N and P additions. At the lower-fertility site Paracou, no changes in root biomass or morphological traits were detected with either N or P addition, although P concentrations in roots increased with P addition. In the higher fertility site, Nouragues, root biomass and P concentrations in roots increased with P addition, with no changes in morphological traits. In contrast, N addition shifted root traits from acquisitive to more conservative by increasing RTD. A significant interaction between N and P in Nouragues pointed to stronger responses to P addition in the absence of N. Our results suggest that the magnitude and direction of root biomass and trait expression were regulated by soil fertility, corroborated by the response to N or P additions. At low fertility sites, we found lower plasticity in root trait expression compared to more fertile conditions, where N and P additions caused stronger and antagonistic responses. Identifying the exact role of mechanisms affecting root nutrient uptake in Amazon forests growing in different soils will be crucial to foresee if and how rapid global changes can affect their carbon allocation.

opencc-zeroDec 2023View details →

Data from: Seasonal variability drives differences in the structure of the calanoid copepod community in two contrasting regions of the Gulf of Mexico

Calanoid copepods (CC) are key contributors to the biological carbon pump and pelagic trophic dynamics. The deep-water regions of Perdido and the Bay of Campeche in the western and southern Gulf of Mexico (GM), respectively, differ in hydrography and productivity, leading to potential differences in copepod biomass and community structure. Zooplankton (0-200 m) were collected from the shelf edge to the deep-water region during the winter and summer autumn 2016. Calanoids contributed 38-60% of total zooplankton biomass and 55-70% of overall copepod abundance. The Bay of Campeche had the highest total zooplankton biovolume (287±120 ml 1000 m-3) and total mean copepod abundance (CC and non-calanoids ~146,000 ind. 1000 m-3) during summer-autumn, likely resulting from cross-shelf nutrient transport fueling local productivity. Adult females dominated calanoid numerical abundance (43-50%), thus suggesting a high reproductive potential. Cluster analysis showed differences between seasons (~40% dissimilarity) but not regions. Environmental conditions explained 22% of the variability in community composition; the winter assemblage was significantly related to oxygen concentrations, whereas the summer-autumn community was related to warmer conditions and higher integrated chlorophyll-a concentrations. The CC community responded to seasonal changes more than regionally related hydrographic differences, with likely implications for organic matter cycling and export.

Data from: Contrasting the form and strength of pre- and postcopulatory sexual selection in a flatworm

Sexual traits may be selected during multiple consecutive episodes of selection, occurring before, during, or after copulation. In the research article entitled "Contrasting the form and strength of pre- and postcopulatory sexual selection in a flatworm", published in Evolution, we measured pre- and postcopulatory phenotypic traits alongside variation in fitness components at different episodes. Namely, we assessed the mating success, sperm-transfer efficiency, and sperm fertilising efficiency of focal worms in which we measured 13 morphological traits, and performed multivariate selection analyses assessing the form and strength of selection. We archived the datasets and R scripts necessary to reproduce all analyses performed in this paper.

Data from: Contrasting patterns of female house mouse spatial organisation among outbreaking and stable populations

The size and distribution of home ranges reflects how individuals within a population use, defend, and share space and resources, and may thus be an important predictor of population-level dynamics. In eruptive species like the house mouse in Australian grain growing regions, contrasting space use between stable and outbreaking populations allows us to test predictions regarding social or life history strategies that may contribute to an outbreak. In this study we use spatially explicit capture-recapture models to compare home range overlap (as a proxy for territoriality) in female mice from populations showing different outbreak trajectories. We found that female space use in spring varied between outbreaking and stable populations. Our analysis indicated greater home range overlap in populations with stable trajectories compared to those that would later experience an outbreak, suggesting females in these stable populations may have had greater potential for cooperative group formation as indicated by shared space use. We discuss the results with respect to intrinsic factors, such as kin structure, with potential implications for better predicting mouse outbreaks at a microgeographic scale.

Phylogeny and climate explain contrasting hydraulic traits in different life forms of 150 woody Fabaceae species

<ol> <li>The contrasting hydraulic traits observed among different plant life forms are shaped by entangled environmental and evolutionary processes. However, we lack an understanding of the relative importance of life form, climate and phylogeny in explaining the variance of hydraulic traits.</li> <li>We analyzed seven hydraulic traits and eleven climatic variables of 150 Fabaceae species representing three life forms from 62 sites worldwide, using phylogenetic comparative analyses and variance partitioning.</li> <li>The phylogenetic signal found in most traits disappeared after considering life form, indicating that phylogenetic conservatism in traits originated from the divergence among life forms. The trait-climate relationships were also phylogenetically dependent, implying that trait responses are driven by climate and phylogeny together. Variance partitioning showed that phylogeny and climate explained greater trait variation than life form did.</li> <li> Synthesis. The climate-driven hydraulic trait responses in Fabaceae still existed with phylogeny being considered, suggesting that this large family may be particularly sensitive to climate change. Our results emphasize the need to include phylogeny in plant hydraulic adaptation studies under future climate change.</li> </ol>

Data from: Born in heterogenous landscapes: birth timing, body mass and growth of roe deer (Capreolus capreolus) fawns in contrasting habitats

Although the widespread effects of global change impact almost all ecosystems, we lack a detailed understanding of how wildlife that thrive in human-dominated environments are able to adjust their life history to modifications in land use of their natural habitat. In particular, spatial variation in environmental conditions is predicted to influence development during the crucial early life phase, with marked impacts on individual performance and population dynamics for long-lived species. Large herbivores such as roe deer (Capreolus capreolus), a synanthropic species, have increased substantially in number and distribution over the last half century across Europe. Roe deer have been particularly successful, gradually colonizing agricultural landscapes to cope with a global warming-driven phenological mismatch in their natural forest habitat. However, to date, little is known about how habitat heterogeneity impacts their demographic performance in this heavily human-impacted environment. Specifically, we predicted that fawns born in predominantly cultivated local habitats would achieve faster early development due to the food subsidies obtained by their mothers from agricultural crops. Contrary to our expectations, fawns in semi-natural forest habitats were around 10% heavier at birth than those born in more mixed (by 0.163 ± 0.058 kg) and open (by 0.169 ± 0.006 kg) agricultural habitats. However, all fawns subsequently grew at a similar average rate (0.148 ± 0.058 kg/day), irrespective of their habitat. This habitat-dependent variation in birth mass appeared to be driven by reproductive phenology, as i) early-born fawns were heavier than late-born fawns, and ii) mothers living in the forest gave birth around 10 days earlier than those living in the mixed and open habitats. As natural habitats become increasingly scarce and fragmented due to the activities of humans, the prospects for many wild populations will depend on their ability to subsist in the heavily modified habitats of anthropogenic landscapes.

Regional and fine-scale local adaptation in salinity tolerance in Daphnia inhabiting contrasting clusters of inland saline waters

Freshwater salinisation is an important threat to biodiversity, ecosystem functioning, and the provision of ecosystem services. Therefore, understanding the capacity of species to adapt to salinity gradients is crucial. Clusters of naturally saline habitats represent ideal test cases to study the extent and scale of local adaptation to salinisation. We studied local genetic adaptation of the water flea Daphnia magna, a key component of pond food webs, to salinity in two contrasting landscapes - a dense cluster of sodic bomb crater ponds and a larger-scale cluster of soda pans. We show regional differentiation in salinity tolerance reflecting the higher salinity levels of soda pans versus bomb crater ponds. We found local adaptation to differences in salinity levels at the scale of tens of metres among bomb crater pond populations but not among geographically more distant soda pan populations. The population-level salinity tolerance range was reduced in more saline bomb crater ponds through an upward shift of the minimum salt tolerance observed across clones and a consequent gradual loss of less tolerant clones in a nested pattern. Our results show genetic adaptation to salinity gradients at different spatial scales and fine-tuned local adaptation in neighbouring habitat patches in a natural landscape.

Data from: Contrasting drivers of aboveground woody biomass and aboveground woody productivity in lowland forests of Colombia

The relative importance of abiotic and biotic factors in shaping forest biomass stocks and fluxes remains a controversial issue. Here, using data gathered from 39 1-ha plots located in flooded and terra firme mature tropical lowland forests of the Amazon and Orinoquia regions of Colombia, we evaluated the importance of climate, soil fertility, flooding as well as tree taxonomic/phylogenetic diversity and forest structural properties, in determining the aboveground biomass stocks (AGB; Mg ha-1) and aboveground woody productivity (AWP; Mg ha-1 y-1). Using information-theoretic multimodel inference and variance partitioning we found that forest structural features, such as the number of trees with diameter at breast height ≥ 70 cm and wood density, are the main drivers of variation in AGB. However, taxonomic diversity also contributes to AGB because it is associated with more large trees in these forests. In contrast, the key drivers of AWP in these forests were soil P and Mg concentration, with no significant effects of diversity indices. These findings emphasize the need to include other major soil cations than N and P (e.g., Mg) in experimental studies to improve our understanding about the extent to which soil fertility can modulate increases in forest AWP due to climate change. Terra firme forests had higher AGB stocks than flooded forests, but both had similar AWP; and we found similar results for the drivers of AGB and AWP between flooded and terra firme forests. Our results provide limited evidence for strong effects of plant diversity on AGB or AWP. Therefore, we call for caution on generalizations of nature-based initiatives aiming to preserve diversity based on maximizing carbon stocks and productivity due to the complex nature of the processes controlling carbon accumulation and carbon fluxes in tropical forests.

opencc-by-4.0Jan 2024View details →

Datasets for "Peatland evaporation across hemispheres: contrasting controls and sensitivity to climate warming driven by plant functional types" - Version 2

Version 2 of datasets used for analyses in the paper titled "Peatland evaporation across hemispheres: contrasting controls and sensitivity to climate warming driven by plant functional types" submitted to Biogeosciences. There are two datasets - one from Kopuatai bog, Aotearoa New Zealand, and one from Mer Bleue bog, Canada - which contain gap-filled and filtered data that were used to produce the results of our study. Due to improvements made to our methodology following the paper peer review process, the data in this version slightly differs from that of the previous version. Information on these revisions can be found in the README file below or the Discussion/Peer Review tab of our paper.

opencc-zeroFeb 2024View details →

Contrasting patterns of sequence variation in steelhead populations reflect distinct evolutionary processes

Multiple evolutionary processes influence genome‐wide allele frequencies and quantifying effects of genetic drift, and multiple forms of selection remain challenging in natural populations. Here, we investigate variation at major effect loci in contrast to patterns of neutral drift across a wide collection of steelhead (Oncorhynchus mykiss) populations that have declined in abundance due to anthropogenic impacts. Whole‐genome resequencing of 74 populations of steelhead revealed genome‐wide patterns (~8 million SNPs) consistent with expected neutral population structure. However, allelic variation at major effect loci associated with adult migration timing (chromosome 28: GREB1L/ROCK1) and age at maturity (chromosome 25: SIX6) reflected how selection has acted on phenotypic variation in contrast with neutral structure. Variation at major effect loci was influenced by evolutionary processes with differing signals between the strongly divergent Coastal and Inland lineages, while allele frequencies within and among populations within the Inland lineage have been driven by local natural selection as well as recent anthropogenic influences. Recent anthropogenic effects appeared to have influenced the frequency of major effect alleles including artificial selection for specific traits in hatchery stocks with subsequent gene flow into natural populations. Selection from environmental factors at various scales has also likely influenced variation for major effect alleles. These results reveal evolutionary mechanisms that influence allele frequencies at major effect loci that are critical for conservation of phenotypic traits and life history variation of this protected species.