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opencc-zeroJan 2024View details →

Data from: The contribution of carbon budget to masting intervals in Veratrum album populations inhabiting different elevations

Premise: Mast flowering/seeding is often more extreme in lower-resource environments, such as alpine compared to lowland habitats. We studied a masting herb which had less extreme masting at higher elevations, and tested if this difference could be explained by higher photosynthetic productivity and/or lower reproductive investment at the higher elevation sites. Methods: We examined the relationship between flowering intervals and carbon budget (i.e., the balance between reproductive investment and annual carbon fixation) in a masting herb, Veratrum album subsp. oxysepalum, across five lowland and six alpine populations in northern Japan. We evaluated the previous flowering histories of individual plants based on rhizome morphology and analyzed the masting patterns of individual populations. Total mass of the reproductive organs, as a proxy of reproductive investment, was compared between the lowland and alpine populations. Annual carbon fixation was estimated based on photosynthetic capacity, total leaf area per plant, and seasonal transition of light availability. Results: Interval between high-flowering years was shorter and total reproductive investment was smaller in the alpine than in the lowland populations. Owing to its high photosynthetic capacity and continuous bright conditions, annual carbon fixation per plant was 1.5 times greater at the alpine habitat than at the lowland habitat. These results suggest that V. album alpine populations have shorter flowering intervals than lowland populations due to faster recovery from energy loss after reproduction. Conclusions: Our study demonstrated that masting intervals in V. album populations can be explained by habitat-specific carbon budget balances.

opencc-zeroMay 2022View details →

Demographic consequences of heterogeneity in conspecific density dependence among mast fruiting tropical trees

The role of conspecific density dependence (CDD) in the maintenance of species richness is a central focus of tropical forest ecology. However, tests of CDD often ignore the integrated effects of CDD over multiple life-stages and their long-term impacts on population demography. We combined a 10-year time series of seed production, seedling recruitment and sapling and tree demography of three dominant Southeast Asian tree species that adopt a mast fruiting phenology. We used these data to construct individual-based models that examine the effects of CDD on population growth rates (λ) across life-history stages. Recruitment was driven by positive CDD for all species, supporting the predator satiation hypothesis, while negative CDD affected seedling and sapling growth of two species, significantly reducing λ. This negative CDD on juvenile growth overshadowed the positive CDD of recruitment, suggesting the cumulative effects of CDD during seedling and sapling development has greater importance than the positive CDD during infrequent masting events. Overall, CDD varied between positive and negative across life-history stages for all species, suggesting that assessments of CDD on transitions between just two stages (e.g. seeds-seedlings or juveniles-mature trees) likely misrepresents the importance of CDD on population growth and stability.

opencc-zeroJun 2022View details →

Data from: Masting increases seedling recruitment near and far: predator satiation and improved dispersal in a fleshy-fruited tree

The animal dispersal hypothesis predicts that mast seeding can increase dispersal rate of seeds by dispersers and enhance reproductive success of plants. However, in contrast to pollination efficiency and predator satiation hypothesis, the animal dispersal hypothesis has received mixed support. Using 12-year data on fruit production and seedling recruitment of a fleshy-fruited tree rowan (Sorbus aucuparia, Rosaceae), we tested if an increase in the fruit production at the population level results in higher proportion of fruits recruiting into seedlings. Recruitment was recorded near (under rowans) and far (under heterospecifics) from conspecifics. Higher recruitment rates under rowans would support predator satiation hypothesis. Higher recruitment rates under heterospecific trees, where fruits can only arrive with animal assistance, would support animal dispersal hypothesis. High population-level fruit production increased the proportion of fruits recruiting into seedlings both near and far from rowans. In contrast, high individual-level fruit production did not have a positive effect on the proportion of fruits recruiting into seedlings. Synthesis. Population-level synchronization of fruit production is required to generate a more effective plant regeneration. Our findings show that masting enhances seedling recruitment through predator satiation and increased seed dispersal by frugivores. The results provide support for both animal dispersal and predator satiation hypotheses indicating that both mechanisms can operate simultaneously.

opencc-zeroJun 2022View details →

Does mast seeding shape mating time in wild boar? A comparative study

In seasonal environments, the timing of reproduction often matches with the peak of food resources. One well-known effect of global warming is an earlier phenology of resources, leading to a possible mismatch between timing of reproduction for consumers and food peak. However, global warming may also change the dynamics of food resources, such as the intensity and frequency of pulsed mast seeding. How quantitative changes in mast seeding influence the timing of reproduction of seed consumers remains unexplored. Here, we assess how yearly variation in mast seeding influences mating time in wild boar (Sus scrofa), a widespread seed consumer species. We took advantage of the intensive monitoring of both female reproduction (1,636 females) and acorn production over 6 consecutive years across 15 populations of wild boar in the wild. We found that mating time occurs earlier when acorn production increases in most but not all populations. In three out of fifteen populations, heavy females mated earlier than light ones. Our findings demonstrate that mast seeding does shape mating time in wild boar females, but differently across populations. This high plasticity of mating times in wild boar indicates that females locally adapt to environmental conditions.

opencc-zeroOct 2022View details →

Data from: The selective advantage of a mast-flowering behavior in Veratrum album subsp. oxysepalum: Implications of the predator satiation hypothesis

Premise: The synchronous highly variable flower or seed production among years within a population– i.e., masting – has been reported in numerous perennial plants. Although ecological advantages of masting are recognized as the enhancement of pollination efficiency and/or escape from predator attack, little is known about the degree of these advantages and the variation in masting behavior among populations of conspecific plants. Methods: We observed flowering ramet density and reproductive success (fruit-set success and herbivorous damage) of a perennial herb, Veratrum album subsp. oxysepalum, across six lowland and six alpine populations in northern Japan during 2–3 years. We then analyzed the relationship between floral density and reproductive success to clarify the ecological significance of mast flowering. Furthermore, flowering intervals of individual plants were estimated by counting annual scars on rhizomes. Results: Mast flowering was observed in most populations, but flowering intervals of individual plants were shorter in the alpine populations compared with the lowland populations. Floral damage by stem borers (dipteran larvae) and seed predation by lepidopteran larvae were intense in the lowland populations. The seed production of individual ramets increased with higher floral density owing to the effective avoidance of floral-stem damage and seed predation. Although stem borers were absent in alpine habitat, seed predation decreased with higher floral density also in the alpine populations. Pollination success was independent of floral density in both the alpine and lowland populations. Conclusions: These results strongly support the predator satiation hypothesis for the mast flowering behavior in this species.

opencc-zeroMay 2024View details →

Data from: Mast seeding in European beech (Fagus sylvatica L.) is associated with reduced fungal sporocarp production and community diversity

A time series of seed production data from European beech (Fagus sylvatica) was combined with a fungal census (1977 to 2006) from La Chanéaz Fungus Reserve to evaluate the relationship between mast seeding and fungal resource availability. Annual fungal species' counts, traits, contemporaneous weather and seed production data are available here, alongside the code used to complete the analyses.

opencc-zeroJun 2024View details →

Data from: Positive spatial and temporal density-dependence drive early reproductive economy-of-scale effects of masting in a European old-growth forest community

Masting, the spatial synchronization of interannual variation in seed production, can enhance reproductive efficiency through positive density-dependent processes (DD) that result in economies of scale (EOS), such as decreased pollen limitation and predator satiation in years of high reproduction. While the general occurrence of such EOS effects has been documented for masting species, few studies simultaneously investigated how spatial and temporal variation in reproduction affects pollination and predation. Furthermore, it is unclear whether the same mechanisms apply to co-occurring species with different levels of conspecific density, pollen limitation, and seed defenses. Here, we use a long-term data set with high spatial resolution of seed production of European beech (Fagus sylvatica), Norway spruce (Picea abies), and silver fir (Abies alba) in a primeval montane forest to investigate the relationship between reproductive effort, pollination efficiency, and predispersal predation by insects. We found that, along the temporal axis, the proportion of sound (fertilized and unpredated) seeds correlated positively with annual seed production over the 14-year study period in all three species, most strongly in beech and only weakly in silver fir. Moreover, the results show that in beech, spatial seed density interacts with plot-wide annual seed rain to enhance DD effects on seed predation, suggesting additive effects of synchronous reproduction on fitness benefits. Synthesis: For both pollination and predispersal predation in beech and spruce, the strongest DD effects occur at low levels of reproduction and quickly reach asymptotes at higher levels, suggesting the presence of thresholds in different EOS mechanisms. As variability and synchrony in mast-seeding are expected to decline with climate change, EOS effects driven by DD may remain stable until the threshold is reached, at which sudden declines would result in devastating effects on the availability of viable seeds for germination and recruitment.

opencc-zeroJul 2024View details →

MAST: Phylogenetic inference with mixtures across sites and trees (revised)

Hundreds or thousands of loci are now routinely used in modern phylogenomic studies. Concatenation approaches to tree inference assume that there is a single topology for the entire dataset, but different loci may have different evolutionary histories due to incomplete lineage sorting, introgression, and/or horizontal gene transfer; even single loci may not be treelike due to recombination. To overcome this shortcoming, we introduce an implementation of a multi-tree mixture model that we call MAST. This model extends a prior implementation by Boussau et al. (2009) by allowing users to estimate the weight of each of a set of pre-specified bifurcating trees in a single alignment. The MAST model allows each tree to have its own weight, topology, branch lengths, substitution model, nucleotide or amino acid frequencies, and model of rate heterogeneity across sites. We implemented the MAST model in a maximum-likelihood framework in the popular phylogenetic software, IQ-TREE. Simulations show that we can accurately recover the true model parameters, including branch lengths and tree weights for a given set of tree topologies, under a wide range of biologically realistic scenarios. We also show that we can use standard statistical inference approaches to reject a single-tree model when data are simulated under multiple trees (and vice versa). We applied the MAST model to multiple primate datasets and found that it can recover the signal of incomplete lineage sorting in the Great Apes, as well as the asymmetry in minor trees caused by introgression among several macaque species. When applied to a dataset of four Platyrrhine species for which standard concatenated maximum likelihood and gene tree approaches disagree, we observe that MAST gives the highest weight (i.e. the largest proportion of sites) to the tree also supported by gene tree approaches. These results suggest that the MAST model is able to analyse a concatenated alignment using maximum likelihood while avoiding some of the biases that come with assuming there is only a single tree. We discuss how the MAST model can be extended in the future.

opencc-zeroSep 2021View details →

Mast seeding records in North American Pinaceae and summer temperature data (1960-2014)

Mast seeding database compilation for conifer tree reproduction in North America (belonging to genus: Abies, Picea, Pinus, Tsuga). All data included in analyses met the criteria that they: i) had at least 6 years of mast seeding data for a species of coniferous tree in North America, ii) data were collected on a continuous scale (e.g., based on seed traps, visual cone counts, or cone scars), iii) occurred between 1960-2014, and iv) for a taxon to be included in the study, there was a minimum of 10 separate time series at the level of the genus. Data from distinct sites or on different species were included separately. Data are standardized to values between 0-100 for each dataset. Summer temperature data are based on ClimateNA, including mean annual July temperatures from 1960-2014 for each location where there is mast-seeding data, and the difference in consecutive summer mean July temperatures.

opencc-zeroApr 2023View details →

Data from: Density-dependent reproductive success among sympatric dipterocarps during a major mast fruiting event

The files hold the data for the paper entitled "Density-dependent reproductive success among sympatric dipterocarps during a major mast fruiting event", which includes (i) the weight and status of seeds collected with seed traps in a Bornean tropical forest during a mast fruiting event, and (ii) the results of a seed sowing experiment in primary and secondary forests. Study site was the Deramakot and Tangkulap Forest Reserves, Sabah, Malaysia (5°14– 30'N, 117°11–36'E).

zenodo36/100

MAST melody dataset

The Musical Aptitude Standard Test (MAST) melody dataset is designed and shared to facilitate comparison of algorithms in the field of automatic music performance assessment. The dataset includes melodic pattern reproduction performances by students (singing) together with the reference melodic pattern played on piano and assessment results. All recordings are collected during entrance exams (in 2015 and 2016) of Istanbul Technical University (ITU).  The recordings are annotations in 2022 within the context of another research project supported by TUBITAK with grant number 121E198 as a part of the Scientific and Technological Research Projects Funding Program (1001).  Annotations are performed via blind listening of individual performances after listening to a few renditions of  the melodic pattern by the experts. The files were presented in random order (after grouping samples in terms of melodic patterns) (i.e. the expert annotated all samples of a melodic pattern in random order and moved to the next group of samples for the next melodic pattern).  A 4-level grading system was used during the evaluations of the data set;  1-Completely Off, 2-Major Mistakes, 3-Minor Mistakes, and 4-Perfect.  Annotations were carried by 3 experts; a professor of musicology who has taken part as a jury member in entrance  exam auditions, and two music conservatory students of graduate-level programs. The last two annotators re-annotated all collection a few months after the first annotation task. The csv file contains 5 annotations in 5 columns where two of these columns are for the repeated annotations. To facilitate analysis, we also added columns that carry a flag if all annotations match (column: 'fullAgree'), the score/grade all annotations agreed on (column: 'fullAgree_score')  and the majority score. In addition to audio files and annotations, two commonly used features are also included: 1) f0-series extracted using Crepe Pitch Tracker (https://github.com/marl/crepe), 2) chroma features computed using Librosa library's chroma_stft function (https://librosa.org/doc/main/generated/librosa.feature.chroma_stft.html) The directory structure is: <ul> <li>annotations: Contains 5 distinct annotations by 3 experts in a scale 1-4 in a csv file. </li> <li>f0data_crepe: MASTmelody dataset, latest version (f0 series extracted using Crepe Pitch Tracker)</li> <li>audioFiles: Audio files sampled at 8kHz</li> <li>chroma: chroma features computed using Librosa library's chroma_stft function using its default settings except n_chroma which is set to 24. </li> </ul> If you use this dataset, please refer to the following paper which announced its original version: <blockquote> Bozkurt, B., Baysal, O., Yuret, D. A Dataset and Baseline System for Singing Voice Assessment, 13th Int. Symposium on Computer Music Multidisciplinary Research, Porto, Sept. 25-28, 2017. </blockquote> <pre><code>@inproceedings{inproceedings, author={Bozkurt, B., Baysal, O., Yuret, D.}, title={A Dataset and Baseline System for Singing Voice Assessment}, year={2017}, booktitle={13th Int. Symposium on Computer Music Multidisciplinary Research, CMMR 2017} }</code></pre>

opencc-by-4.0Jun 2023View details →

opencc-zeroJun 2023View details →

Landscape of Mast cell populations across organs in mice and humans

Mast cells (MCs) are tissue-resident immune cells which exhibit homeostatic and neuron-associated functions. Here we combined whole-tissue imaging and single-cell RNA sequencing datasets to generate a pan-organ analysis of MCs in mice and humans at steady state. In mice, we identify two mutually exclusive MC populations, MrgprB2+ connective tissue-type MCs and MrgprB2neg mucosal-type MCs, with specific transcriptomic core signatures. While MrgprB2+ MCs develop in-utero independently of the bone marrow, MrgprB2neg MCs develop after birth and are renewed by bone marrow progenitors. In humans, we unbiasedly identify 7 MC subsets (MC1 to 7) distributed across 12 organs with different transcriptomic core signatures. MC1 are preferentially enriched in the bladder, MC2 in the lungs, and MC4, MC6 and MC7 in the skin. Conversely, MC3 and MC5 are shared by most organs, but not skin. This comprehensive analysis offers valuable insights into the natural diversity of MC subtypes in both mice and humans.

MAST Trial: Multi-modal Analgesic Strategies in Trauma

ClinicalTrials.gov study NCT03472469. IPD Sharing: NO. Countries: 1. Publications: 2.

Phase 2 Midostaurin in Aggressive Systemic Mastocytosis and Mast Cell Leukemia

ClinicalTrials.gov study NCT00233454. IPD Sharing: NO. Countries: 1. Publications: 3.

Mast Cell Activation Test in Allergic Disease

ClinicalTrials.gov study NCT03406325. IPD Sharing: NO. Countries: 1. Publications: 1.

Brentuximab Vedotin in Treating Patients With Advanced Systemic Mastocytosis or Mast Cell Leukemia

ClinicalTrials.gov study NCT01807598. IPD Sharing: NO. Countries: 1. Publications: 1.

publicMay 2020View details →

How does increasing mast seeding frequency affect population dynamics of seed consumers? Wild boar as a case study

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publicOct 2022View details →

Data from: The selective advantage of a mast-flowering behavior in Veratrum album subsp. oxysepalum: Implications of the predator satiation hypothesis

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publicFeb 2025View details →

MAST: Phylogenetic inference with mixtures across sites and trees (revised)

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