Find research datasets worth reusing

opencc-by-4.0Aug 2020View details →

Mutual extinction and transparency of multiple incident light waves

The basic publication is: A. Lagendijk, A.P. Mosk, and W.L. Vos Europhys. Lett., 130, 34002 (2020) "Mutual extinction and transparency of multiple incident light waves"   We have uploaded to the Zenodo database all data enabling everyone to reuse our data, and to reproduce all the figures of our paper The upload contains the file "readme.txt" explaining the content of the upload

opencc-by-4.0Nov 2020View details →

Data and R Code for 'Domestication via the commensal pathway in a fish-invertebrate mutualism'

This document contains all data and R code required to replicate the analyses in 'Domestication via the commensal pathway in a fish-invertebrate mechanism' as published in Nature Communications. The R Markdown provided includes descriptions of all variables and the code used for the analysis of the following eight datasets: 1. Transects 2. Census of farms 3. Paired choice experiments 4. Predation experiment 1 5. Predation experiment 2 6. Timed observations 7. Farm algae composition 8. Longfin damselfish body condition In addition, the R Markdown also includes descriptions of all variables for two additional datasets: 9. Estimates of mysid swarm density 10. Mysid waste excretion and nutrient availability A PDF version of the R Markdown with all output is also provided. Please see the methods section of the associated manuscript for further information on data collection and analysis procedures. Author contributions to data collection and analysis: RMB, JMC, ZLC, TLS & WEF collected the data; WEF, RMB, JMC, ZLC & AM implemented the analyses.  Correspond with: rohan.m.brooker@gmail.com

opencc-by-4.0Nov 2023View details →

Mutual Induced Fit Transition Structure Stabilization of Corannulene's Bowl-to-Bowl Inversion in a Perylene Bisimide Cyclophane

Additional data to report <a href="https://doi.org/10.1039/D3SC05341E">https://doi.org/10.1039/D3SC05341E</a>: Corannulene is known to undergo a fast bowl-to-bowl inversion at r.t. via a planar transition structure (TS). Herein we present the catalysis of this process within a perylene bisimide (PBI) cyclophane composed of chirally twisted, non-planar chromophores, linked by para-xylylene spacers. Variable temperature NMR studies reveal that the bowl-to-bowl inversion is significantly accelerated within the cyclophane template despite the structural non-complementarity between the binding site of the host and the TS of the guest. The observed acceleration corresponds to a decrease in the bowl-to-bowl inversion barrier of 11.6 kJ mol−1 compared to the uncatalyzed process. Comparative binding studies for corannulene (20 π-electrons) and other planar polycyclic aromatic hydrocarbons (PAHs) with 14 to 24 π-electrons were applied to rationalize this barrier reduction. They revealed high binding constants that reach, in tetrachloromethane as a solvent, the picomolar range for the largest guest coronene. Computational models corroborate these experimental results and suggest that both TS stabilization and ground state destabilization contribute to the observed catalytic effect. Hereby, we find a “mutual induced fit” between host and guest in the TS complex, such that mutual geometric adaptation of the energetically favored planar TS and curved π-systems of the host results in an unprecedented non-planar TS of corannulene. Concomitant partial planarization of the PBI units optimizes noncovalent TS stabilization by π–π stacking interactions. This observation of a “mutual induced fit” in the TS of a host–guest complex was further validated experimentally by single crystal X-ray analysis of a host–guest complex with coronene as a qualitative transition state analogue.

opencc-by-4.0May 2021View details →

Mutually Beneficial Combination of Molecular Dynamics Computer Simulations and Scattering Experiments - DATA

Specular reflectivities of the SoyPC bilayer stack measured at the vertical reflectometer MARIA  at Heinz Maier-Leibnitz Zentrum (MLZ) in Garching, Germany. Offspecular reflectivity map (log scale) of the multilayer sample as a function of theangle of incidence (θi) and of the reflection angle (θi). Specular reflectivities of the Si/SiO2/DMPC/H2O at 4 different contrasts (H2O, D2O, SMW and 4MW) Small-angle neutron scattering of the unilamellar  SoyPC

opencc-zeroDec 2016View details →

Data from: The acacia ants revisited: convergent evolution and biogeographic context in an iconic ant/plant mutualism

Phylogenetic and biogeographic analyses can enhance our understanding of multispecies interactions by placing the origin and evolution of such interactions in a temporal and geographical context. We use a phylogenomic approach—ultraconserved element sequence capture—to investigate the evolutionary history of an iconic multispecies mutualism: Neotropical acacia ants (Pseudomyrmex ferrugineus group) and their associated Vachellia hostplants. In this system, the ants receive shelter and food from the host plant, and they aggressively defend the plant against herbivores and competing plants. We confirm the existence of two separate lineages of obligate acacia ants that convergently occupied Vachellia and evolved plant-protecting behaviour, from timid ancestors inhabiting dead twigs in rainforest. The more diverse of the two clades is inferred to have arisen in the Late Miocene in northern Mesoamerica, and subsequently expanded its range throughout much of Central America. The other lineage is estimated to have originated in southern Mesoamerica about 3 Myr later, apparently piggy-backing on the pre-existing mutualism. Initiation of the Pseudomyrmex/Vachellia interaction involved a shift in the ants from closed to open habitats, into an environment with more intense plant herbivory. Comparative studies of the two lineages of mutualists should provide insight into the essential features binding this mutualism.

opencc-by-4.0Oct 2023View details →

Supplementary material for "Mutual predictiveness of sound correspondences for reconstruction and language subgrouping: The case of Gyalrongic preinitials"

This is the supplementary material of the paper "Mutual predictiveness of sound correspondences for reconstruction and language subgrouping: The case of Gyalrongic preinitials", to be published in Diachronica. It includes the datasets, codes and images involved in the research. Publication is still several months away, and I am trying to collect and identify more cognates as well as correct mistakes.  Version 2 has included a few more cognates. I have added a file explaning my cognate judgements and annotations, and removed some doubtful forms after verification with native speakers.  <div> <div> <div> <div> Comments, corrections and suggestions about cognate judgement, annotation and bibliographical references are welcome. I will correct and update the data from time to time. </div> </div> </div> </div>

opencc-zeroFeb 2022View details →

Host-symbiont stress response to lack-of-sulfide in the giant ciliate mutualism

The mutualism between the thioautotrophic bacterial ectosymbiont Candidatus Thiobius zoothamnicola and the giant ciliate Zoothamnium niveum thrives in a variety of shallow-water marine environments with highly fluctuating sulfide emissions. To persist over time, both partners must reproduce and ensure the transmission of symbionts before the sulfide stops, which enables carbon fixation of the symbiont and nourishment of the host. We experimentally investigated the response of this mutualism to depletion of sulfide. We found that colonies released some initially present but also newly produced macrozooids until death, but in fewer numbers than when exposed to sulfide. The symbionts on the colonies proliferated less without sulfide, and became larger and more rod-shaped than symbionts from freshly collected colonies that were exposed to sulfide and oxygen. The symbiotic monolayer was severely disturbed by growth of other microbes and loss of symbionts. We conclude that the response of both partners to the termination of sulfide emission was remarkably quick. The development and the release of swarmers continued until host died and thus this behavior contributed to the continuation of the association.

opencc-zeroApr 2022View details →

Negotiating mutualism: a locus for exploitation by rhizobia has a broad effect size distribution and context-dependent effects on legume hosts

In mutualisms, variation at genes determining partner fitness provides the raw material upon which coevolutionary selection acts, setting the dynamics and pace of coevolution. However, we know little about variation in the effects of genes that underlie symbiotic fitness in natural mutualist populations. In some species of legumes that form root nodule symbioses with nitrogen-fixing rhizobial bacteria, hosts secrete nodule-specific cysteine-rich (NCR) peptides that cause rhizobia to differentiate in the nodule environment. However, rhizobia can cleave NCR peptides through the expression of genes like the plasmid-borne Host range restriction peptidase (hrrP), whose product degrades target NCR peptides. Although hrrP activity can confer host exploitation by depressing host fitness and enhancing symbiont fitness, the effects of hrrP on symbiosis phenotypes depend strongly on the genotypes of the interacting partners. However, the effects of hrrP have yet to be characterized in a natural population context, so its contribution to variation in wild mutualist populations is unknown. To understand the distribution of effects of hrrP in wild rhizobia, we measured mutualism phenotypes conferred by hrrP in 12 wild Ensifer medicae strains. To evaluate context dependency of hrrP effects, we compared hrrP effects across two Medicago polymorpha host genotypes and across two experimental years for five E. medicae strains. We show for the first time in a natural population context that hrrP has a wide distribution of effect sizes for many mutualism traits, ranging from strongly positive to strongly negative. Furthermore, we show that hrrP effect size varies across both host genotype and experiment year, suggesting that researchers should be cautious about extrapolating the role of genes in natural populations from controlled laboratory studies of single genetic variants.

opencc-zeroMay 2022View details →

Spatial structure within root systems moderates stability of Arbuscular Mycorrhizal mutualism and plant-soil feedbacks

The persistence of mutualisms is paradoxical, as there are fitness incentives for exploitation. This is particularly true for plant-microbe mutualisms like arbuscular mycorrhizae (AM), which are promiscuously, horizontally-transmitted. Preferential allocation by hosts to the best mutualist can stabilize horizontal mutualisms, however preferential allocation is imperfect, with its fidelity likely depending upon the spatial structure of symbionts in plant roots. In this study, we tested AM mutualisms' dependence on two dimensions of spatial structure: the initial dispersion of fungi and the ease of fungal dispersal, through three complementary experiments. We found that fitness of the beneficial AM fungus increased when fungi were initially separate, while initial spatial mixing benefited the fitness of the non-beneficial fungus. These effects were strongest when dispersal was limited, and hosts could discriminate. Additionally, we found that spatial structure moderated changes in AM fungal composition produced differential feedbacks on plant growth. Our results identify symbiont spatial structure within plant roots as an important modifier of plant preferential allocation and the dynamics of mycorrhizal mutualisms, with cascading effects on plant communities.

opencc-by-4.0Jul 2015View details →

Supplementary material from: Aslan CE, Sikes BA, Gedan KB (2015) Research on mutualisms between native and non-native partners can contribute critical ecological insights. NeoBiota 26: 39-54. https://doi.org/10.3897/neobiota.26.8837

Supplementary material from: Aslan CE, Sikes BA, Gedan KB (2015) Research on mutualisms between native and non-native partners can contribute critical ecological insights. NeoBiota 26: 39-54. https://doi.org/10.3897/neobiota.26.8837

opencc-zeroMay 2024View details →

Data from: Asynchronous life histories generate uneven arms races and impact the maintenance of mutualisms

Mutualisms constitute a diverse class of ecologically important interactions, yet their ecological and evolutionary stability remain topics of debate in coevolutionary theory. Recent theoretical and empirical work has suggested that coevolutionary arms races may be involved in the maintenance of mutualistic interactions, sustaining mutually beneficial outcomes for interacting species while producing exaggerated traits. Here we present an individual-based model that evaluates how asynchronous life histories – i.e., partners with different average lifespans – change the dynamics of trait coevolution, the expected fitness outcomes for species involved, and the dynamics of selection differentials across time for each species. Results indicate that a longer-lived mutualist will consistently 'lose' an otherwise balanced coevolutionary arms race, being outpaced in both the mean trait value and fitness outcome compared to a shorter-lived partner. Furthermore, linear selection differentials on mutualistic traits become increasingly divergent as life histories become increasingly asynchronous, with the longer-lived species experiencing persistent directional selection and the shorter-lived species experiencing weaker, more inconsistent selection. These results suggest that asynchronous life histories can complicate the maintenance of mutualistic interactions via coevolutionary arms-races and that detecting coevolution via selection differentials may be difficult when life histories are sufficiently divergent.

opencc-zeroJun 2024View details →

Dataset: Richmond Mutual Bancorporation, Inc. (RMBI) Stock Performance

This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.

opencc-by-4.0Feb 2024View details →

CLDF dataset accompanying Nieder and List's "Assessment of Mutual Intelligibility" from 2024

Dataset contains cognate sets from Kluge's etymological dictionary used in the following study: <blockquote> Nieder, J. and List, J.-M. (2024): A Computational Model for the Assessment of Mutual Intelligibility Among Closely Related Languages. In: Proceedings of the 6th Workshop on Research in Computational Linguistic Typology and Multilingual NLP (SIGTYP 2024) </blockquote>

opencc-by-4.0Oct 2024View details →

MUTUAL RECOGNITION IN PRISON RULES AND PRE -TRIAL DETENTION AND DETENTION IN EU

The purpose of this study is to highlight the important aspects on the creation of a criminal justice section inside prisons, as well as the creation of minimum requirements for jail and detention settings and a uniform set of rights for all EU inmates. The Council of Europe believes that efforts should be taken to improve mutual trust and to more effectively implement the concept of mutual recognition in custody, as stated in the Stockholm Program, which calls for the Council to address detention and related concerns. Among the instruments of mutual recognition of terms of incarceration that may be affected we mention the European Arrest Warrant issued by the Council, the transfer of prisoners, the mutual recognition of alternative sanctions and judicial proceedings, and the European supervision order. Following the analysis and empirical research, the paper summarizes that without mutual trust in detention, the European Union's mutual recognition instruments affecting detention will not work properly, as one Member State is unwilling to recognize and implement a decision taken by the authorities of another Member State. Without greater efforts to improve detention conditions and promote alternatives to detention, it may be difficult to develop closer judicial cooperation between Member States.

opencc-zeroOct 2021View details →

Cheating in mutualisms

Mutualisms such as those between flowering plants and their pollinators are common in nature. Yet, understanding their persistence in the face of cheaters and identifying the mechanisms behind their stunning diversity provide formidable challenges for evolutionary biologists. To shed light into these questions, we introduce an individual-based model of two coevolving species in which individuals of one species use a Boolean circuit to discriminate between cooperators and cheaters in the other species. This conveys the idea that interactions are often mediated by complex biological processes rather than simple trait matching, as often assumed in models of coevolution. Our results show that cheating promotes diversification and complex discrimination mechanisms at the cost of a higher risk for mutualism to collapse. This result is mediated by an inverse relationship between mutational robustness and organismal complexity.

opencc-by-4.0Oct 2022View details →

Resilient rivers and connected marine systems: a review of mutual sustainability opportunities

Associated data used in the following review paper (under review) - Resilient rivers and connected marine systems: a review of mutual sustainability opportunities. Abstract: The United Nations initiated the sustainable development goals (SDGs) to produce "a shared blueprint for peace and prosperity for people and the planet, now and into the future." Established in 2015, progress of SDGs directed at the aquatic environment is slow despite an encroaching 2030 deadline. The modification of flow regimes combined with other anthropogenic pressures underpin ecological impacts across aquatic ecosystems. Current SDG 14 targets (Life Below Water) do not incorporate the interrelationships of rivers and marine systems systematically, nor do they provide recommendations on how to improve existing management and policy in a comprehensive manner. Therefore, this review aims to illustrate the linkages between rivers and marine ecosystems concerning the SDG 14 targets and to illustrate land to sea based strategies to reach sustainability goals. We provide an applied case study to show how opportunities can be explored. We review three major areas where mutual opportunities are present: 1) rivers contribute to marine and estuary ecosystem resilience (targets 14.1, 14.2, 14.3, 14.5); (2) resilient rivers are part of the global fisheries sustainability concerns (targets  14.4, 14.6, 14.7, 14.B); and (3) enhancing marine policy and research from a river and environmental flows perspective (targets 14.A, 14.C). Associated data used in the review is described below.

opencc-zeroNov 2022View details →

Data from: Which traits optimize plant benefits? Meta-analysis on the effect of partner traits on the outcome of an ant-plant protective mutualism

1. Theoretical models on mutualism dynamics predict that partner traits may influence the outcome of mutualistic interactions. However, most empirical data on this issue is restricted to case studies, limiting our ability to reach a more widespread comprehension of the role of partner traits on the dynamic of mutualisms. 2. We investigated how the outcome of protective mutualisms between ants and plants bearing extrafloral nectaries (EFNs) is influenced by the traits of EFNs and ants feeding on EFNs. We used a meta-analytical approach based on 35 studies investigating the effect of ant attendance on the herbivores and reproductive performance of EFN-bearing plants. We evaluated how variation in the EFN vascularization and location on plants and the ant aggressiveness can modulate the effect of ant attendance on the plants. 3. Both plant and ant traits investigated here drove the outcome of the protective mutualism for EFN-bearing plants. Plants exclusively bearing EFNs near reproductive organs benefited more from ant attendance than plants bearing EFNs on vegetative or vegetative and reproductive organs. Ants had a higher positive impact on the reproductive performance of plants bearing non-vascularized EFNs than plants bearing vascularized EFNs, although their effects on herbivores had been similar in both plant types. Regarding the ant behavior, plants often attended by more aggressive ant species had a higher reproductive performance than plants often attended by less aggressive ones. 4. Synthesis: Our results highlight that the selective pressures and evolutionary routes in ant-plant protective mutualisms may depend on the pool of traits exhibited by partner species. Although some studies have already reported some impact of species traits on the outcome of ant-plant mutualisms, this is the first time that a generalization about the role of species traits on the net balance of ant attendance was proposed. Due to this generalization, it was possible to advance our knowledge about the evolution of facultative mutualisms by showing that the role of species traits on the mutualistic outcome can vary in intricate ways due to a particular trait combination found among partners in communities where the interactions are embedded in.

opencc-zeroNov 2022View details →

When wax wanes: competitors for beeswax stabilize rather than jeopardize the honeyguide-human mutualism

Many mutualisms are exploited by third-party species, which benefit without providing anything in return. Exploitation can either destabilize or promote mutualisms, via mechanisms that are highly dependent on the ecological context. Here we study a remarkable bird–human mutualism, in which wax-eating greater honeyguides (Indicator indicator) guide humans (Homo sapiens) to wild bees' nests, in an exchange of knowledge about the location of nests for access to the wax combs inside. We test whether the depletion of wax by mammalian and avian exploiter species either threatens or stabilizes the mutualism. Using camera traps, we monitored feeding visits to wax comb made available following honey harvests. We found that greater honeyguides face competition for wax from conspecifics and nine exploiter species, five of which were not previously known to consume wax. Our results support the hypothesis that heterospecific exploiters stabilize the mutualism, because wax depletion by these competitors likely limits feeding opportunities for conspecific exploiters, favouring the early-arriving individual that guided humans to the bees' nest. These findings highlight the importance of the ecological context of species interactions and provide further evidence for how mutualisms can persist because of, and not in spite of, exploitation by third-party species.