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391 results for “mismatch”
Supplementary data for Willemsen et al., 2024 "Novel high-quality amoeba genomes reveal widespread codon usage mismatch between giant viruses and their hosts".
<p>Supplementary data for Willemsen et al., 2024 "Novel high-quality amoeba genomes reveal widespread codon usage mismatch between giant viruses and their hosts". The data set consists of five folders: “Codon_usage_amoebae_and_viruses”, "Genome_annotations_amoebae", "Phylogenetic_trees_18S_amoebae", “Phylogenomic_trees_amoebae”, and "Viral_integration_detection_amoebae". The “Codon_usage_amoebae_and_viruses” folder contains for each amoeba host the calculated codon usage tables in the subfolder "codon_usage_table_host", the calculated codon usage preferences using different scores in the subfolder "codon_usage_scores_host", and the calculated codon usage preferences of giant viruses versus each host in the subfolder "codon_usage_scores_viruses_vs_host". The giant viruses in the subfolder "codon_usage_scores_viruses_vs_host" are organised by viral family and genus in separate sub-subfolders. The "Genome_annotations_amoebae" folder contains the generated genome annotations in different formats and the manually curated mitochondrial genome annotations for each amoeba host. The "Phylogenetic_trees_18S_amoebae" contains for the eukaryotic phyla <em>Discosea</em>, <em>Heterolobosea</em>, and <em>Tubulinea, </em>the 18S rRNA nucleotide alignments, distance matrices, and computed phylogenetic trees. The folder "Phylogenomic_trees_amoebae" contains for the eukaryotic clades <em>Amoebozoa</em> and <em>Discoba, </em>the protein alignment matrices and computed phylogenomic trees. The folder "Viral_integration_detection_amoebae" contains the MCP databases used (fasta file, alignment file, HMM profile and DIAMOND BLASTX database) and the MCP sequences detected in this study and the blast results of these. </p>
How to choose a task? Mismatches in perspectives of newcomers and existing contributors
<p>Dataset for the paper: How to choose a task? Mismatches in perspectives of newcomers and existing contributors</p>
Seasonal trajectories of plant-pollinator interaction networks differ following phenological mismatches along an urbanization gradient - Data and code
<p>Dataset and code used in the article "Seasonal trajectories of plant-pollinator interaction networks differ following phenological mismatches along an urbanization gradient", by A. Fisogni et al., published in Landscape and Urban Planning (2022, 226:104512, <a href="https://www.sciencedirect.com/science/article/pii/S016920462200161X?via%3Dihub">https://doi.org/10.1016/j.landurbplan.2022.104512</a>)</p>
Raw data from: "Thermal mismatches explain consumer-resource dynamics in response to environmental warming".
<p>Data from:</p> <p>Álvarez-Codesal, S, Faillace CA, Garreau, A, Bestion, E, Synodinos, AD, & Montoya, JM. 2023. Thermal mismatches explain consumer-resource dynamics in response to environmental warming. Ecology and Evolution.<br> </p> <p>Composed of seven associated datasets:</p> <p>- Algae_Net_Photosynthesis.csv</p> <p>- Daphnia_Ingestion.csv</p> <p>- Algae_Respiration.csv</p> <p>- Daphnia_Ingestion.csv</p> <p>- Daphnia_respiration.csv</p> <p>- Interaction_Strength.csv</p> <p>- Energy_Balance_Ratios_dataset.csv</p> <p> </p> <p>A detailed explanation of the methods is provided in the related Alvarez-Codesal et al. 2023 article, please refer to it for a full understanding of the methods and results.</p> <p>Briefly: our aim was to quantify the impact of warming on consumer-resource interactions, using as consumer <em>Daphnia pulex</em>, and as resources two algae species, <em>Chlamydomonas reinhardtii</em> and <em>Desmodesmus</em> sp.</p> <p>First, we measured thermal dependencies of physiological rates related to energy gain (i.e., ingestion, net photosynthesis) and loss (i.e., respiration) for <em>Daphnia</em> and the algae in basal conditions at eight temperatures. From these, we calculated species energetic balances as net photosynthesis-to-respiration ratio (P/R<sub>r</sub>) for resources, or as ingestion-to-respiration ratio (I/R<sub>c</sub>) for consumers, using predicted values of each (per capita) rate from the models. We used energetic balances as an indicator of how species respond to increasing temperatures, defining intraspecific energetic mismatches when the energetic balance decreases.</p> <p>Second, we inferred interspecific thermal mismatches (inter-TM) by comparing individual energetic balances for both consumer-resource pairs, and identified the thermal mismatch regions, where: 1) trends of energetic balances contrast between the interacting species; and 2) both species reduce their energetic balance with increasing temperature. The inter-TMs were used to increase our qualitative understanding on the outcomes of thermal dependencies of interaction strength.</p> <p>Third, we calculated the natural logarithm of the consumer-resource energetic balance for each interacting pair as the ratio between consumer energetic balance and the resource energetic balance to get qualitative predictions on the trends of interaction strength with temperature.</p> <p>Finally, we measured experimentally thermal dependencies of interaction strength for each consumer-resource pair and verified if our predictions using the thermal mismatches fitted the trends of interaction strengths across temperatures.</p>
Lake browning generates a spatiotemporal mismatch between DOC and limiting nutrients, 2018 spatial survey, modeled light limitation and whole-lake productivity changes in long-term Adirondack lake survey 1994-2012
This data set contains information on a spatial survey of dissolved organic matter (DOM) across lakes and wetlands in the Northeast and Midwest, USA and modeled long-term changes in light limitation and whole-lake productivity in a suite of lakes in the Adirondack State Park, New York, USA. Widespread long-term increases in DOM have been observed in many lakes in a process known as browning. This data set enables the assessment of potential changes in dissolved absorbance and dissolved organic nutrients associated with browning. This data set accompanies a manuscript in review at Limnology and Oceanography: Letters.
Virulence mismatches in index hosts shape the outcomes of cross-species transmission
<p>Supplemental data and code for the paper <em>Virulence mismatches in index hosts shape the outcomes of cross-species transmission</em>.</p> <ul> <li>Dataset 1 is an R Shiny app allowing the estimation of rabies disease progression parameters for all observed combinations of virus source (reservoir) and recipient species, including within-species inoculations.</li> <li>Dataset 2 contains the original data and the analysis code used in this study.</li> </ul> <p>See the README files in each dataset folder for further information and usage instructions.</p>
Data Set for the Journal Article "Automated Preparation of Nanoscopic Structures: Graph-Based Sequence Analysis, Mismatch Detection, and pH-Consistent Protonation with Uncertainty Estimates"
<p>This repository containes the data generated by ASAP and discussed in the journal article [Csizi, K.-S. and Reiher, M., 2023, arXiv:2307.16344], including Cartesian coordinates of training and test set molecules, and MD trajectories. </p>
Different currencies for calculating resource phenology result in opposite inferences about trophic mismatches
<p>Shifts in phenology are among the key responses of organisms to climate change. When rates of phenological change differ between interacting species they may result in phenological asynchrony. Studies have found conflicting patterns concerning the direction and magnitude of changes in synchrony, which have been attributed to biological factors. A hitherto overlooked additional explanation is differences in the currency used to quantify resource phenology, such as abundance and biomass. Studying an insectivorous bird, Sanderling, and its prey, we show that the median date of cumulative arthropod biomass occurred, on average, 6.9 days after the median date of cumulative arthropod abundance. In some years this difference could be as large as 21 days. For 23 years, hatch dates of Sanderlings became less synchronized with the median date of arthropod abundance, but more synchronized with the median date of arthropod biomass. The currency-specific trends can be explained by our finding that mean biomass per arthropod specimen increased with date. Using a conceptual simulation, we show that estimated rates of phenological change for abundance and biomass can differ depending on temporal shifts in the size distribution of resources. We conclude that studies of trophic mismatch based on different currencies for resource phenology can be incompatible with each other.</p>
Energetic mismatch induced by warming decreases leaf litter decomposition by aquatic detritivores
<p>1. The balance of energetic losses and gains is of paramount importance for understanding and predicting the persistence of populations and ecosystem processes in a rapidly changing world. Previous studies suggested that metabolic rate often increases faster with warming than resource ingestion rate, leading to an energetic mismatch at high temperature. However, little is known about the ecological consequences of this energetic mismatch for population demography and ecosystem functions.</p> <p>2. Here, we combined laboratory experiments and modeling to investigate the energetic balance of a stream detritivore (Gammarus fossarum) along a temperature gradient and the consequences for detritivore populations and organic matter decomposition.</p> <p>3. We experimentally measured the energetic losses (metabolic rate) and supplies (ingestion rate) of Gammarus and we modeled the impact of rising temperatures and changes in Gammarus body size induced by warming on population dynamics and benthic organic matter dynamics in freshwater systems.</p> <p>4. Our experimental results indicated an energetic mismatch in a Gammarus population where losses via metabolic rate increase faster than supplies via food ingestion with warming, which translated in a decrease of energetic efficiency with temperature rising from 5 to 20 °C. Moreover, our consumer-resource model predicts a decrease in the biomass of Gammarus population with warming, associated with lower maximum abundances and steeper abundance decreases after biomass annual peaks. These changes resulted in a decrease of leaf litter decomposition rate and thus longer persistence of leaf litter standing stock over years in the simulations. In addition, Gammarus body size reductions led to shorter persistence for both leaf litter and Gammarus biomasses at low temperature and the opposite trend at high temperature, revealing that body size reduction was weakening the effect of temperature on resource and consumer persistence.</p> <p>5. Our model contributes to identifying the mechanisms that explain how thermal effects at the level of individuals may cascade through trophic interactions and influence important ecosystem processes. Considering the balance of physiological processes is crucial to improve our ability to predict the impact of climate change on carbon stocks and ecosystem functions.</p>
Data collection for article "Regional scale mapping of ecosystem services supply, demand, flow and mismatches in Southern Myanmar"
<p>This dataset contains supply, demand, and flow maps from nine ecosystem service models (as layer files in .tif format) underlying the publication "Regional scale mapping of ecosystem services supply, demand, flow and mismatches in Southern Myanmar". </p>
Data and code from: Functional rarity of plants in German hay meadows - patterns on the species level and mismatches with community species richness
<p>Functional rarity (FR) - a feature combining a species' rarity with the distinctiveness of its traits - represents a promising tool to better understand the ecological importance of rare species and consequently to protect functional diversity more efficiently. Yet, we lack a systematic understanding of FR on both the species level (which species are functionally rare and why) and the community level (how is FR associated with biodiversity and environmental conditions). Here, we quantify FR for 218 plant species from German hay meadows on a local, regional, and national scale by combining data from 6500 vegetation relevés and 15 ecologically relevant traits. We investigate the association between rarity and trait distinctiveness on different spatial scales via correlation measures and show which traits lead to low or high trait distinctiveness via distance-based redundancy analysis. We test how species richness and FR are correlated and use boosted regression trees to determine environmental conditions driving species richness and FR. On the local scale, only rare species showed high trait distinctiveness while on larger spatial scales rare and common species showed high trait distinctiveness. As infrequent trait attributes (e.g., legumes, low clonality) led to higher trait distinctiveness, we argue that functionally rare species are either specialists or transients. While specialists occupy a particular niche in hay meadows leading to lower rarity on larger spatial scales, transients display distinct but maladaptive traits resulting in high rarity across all spatial scales. More functionally rare species than expected by chance occurred in species-poor communities indicating that they prefer environmental conditions differing from characteristic conditions of species-rich hay meadows. Finally, we argue that functionally rare species are not necessarily relevant for nature conservation, since many were transients from surrounding habitats. Yet, FR can facilitate our understanding of why species are rare in a habitat and under which conditions these species occur.</p>
figure 3 Mismatch distributions within the G in Unraveling goitered gazelle (Gazella subgutturosa) diversification: insights from phylogeography and species distribution modeling
figure 3 Mismatch distributions within the G. subgutturosa. The expected line (green color) compared with the observed frequencies under the sudden expansion model using cytb. (A) the mmd diagram for the Asiatic population shows a recent expansion. (B) the mmd diagram for the Middle Eastern population and (C) the mmd diagram for the Central Iranian population.
Fig. 6. Mismatch distribution for X. formosensis determined using Arlequin 3.5.2.2 in Tuerkayana rotundum
Fig. 6. Mismatch distribution for X. formosensis determined using Arlequin 3.5.2.2 and based on mitochondrial DNA cytochrome oxidase subunit I (COI) data. Blue-colored bars represent the observed frequency and the red-colored curve represents the expected frequencies under a sudden expansion model.
Supported data for manuscript: 'Future hydrogen economies imply environmental trade-offs and a supply-demand mismatch' (DOI: 10.1038/s41467-024-51251-7)
<p>After unpacking the ZIP file, this repository contains the following files:</p> <p><strong>results_lcoh_ecoinvent_391_reference.tif:</strong> grid-specific hydrogen production cost (euro/kg H2) for the reference scenario.</p> <p><strong>results_lcoh_SSP2-Base_2050_base.tif:</strong> grid-specific hydrogen production cost (euro/kg H2) for the baseline scenario in 2050.</p> <p><strong>results_lcoh_SSP2-PkBudg1150_2050_base.tif:</strong> grid-specific hydrogen production cost (euro/kg H2) for the 2°C scenario in 2050.</p> <p><strong>results_lcoh_SSP2-PkBudg500_2050_base.tif:</strong> grid-specific hydrogen production cost (euro/kg H2) for the 1.5°C scenario in 2050.</p> <p><strong>results_ghg_kg_h2_ecoinvent_391_reference.tif:</strong> grid-specific GHG emissions (kg CO2-eq./kg H2) from hydrogen production for the reference scenario.</p> <p><strong>results_ghg_kg_h2_SSP2-Base_2050_base.tif:</strong> grid-specific GHG emissions (kg CO2-eq./kg H2) from hydrogen production for the baseline scenario in 2050.</p> <p><strong>results_ghg_kg_h2_SSP2-PkBudg1150_2050_base.tif:</strong> grid-specific GHG emissions (kg CO2-eq./kg H2) from hydrogen production for the 2°C scenario in 2050.</p> <p><strong>results_ghg_kg_h2_SSP2-PkBudg500_2050_base.tif:</strong> grid-specific GHG emissions (kg CO2-eq./kg H2) from hydrogen production for the 1.5°C scenario in 2050.</p> <p><strong>main_gen_figures.ipynb: </strong>Jupyter Notebook script used to generate the main figures of the manuscript.</p>
Data from: Hurry Up and Wait: Managing the Inherent Mismatches in Timescales in Natural and Artificial Photosynthetic Systems
<p>Houle, Frances A.; Yano, Junko; Ager, Joel W.;<br> Hurry Up and Wait: Managing the Inherent Mismatches in Timescales in<br> Natural and Artificial Photosynthetic Systems</p> <p><strong>Files</strong><br> Supplementary data coupled reaction-transport and cascades.xlxs<br> Input parameters for Kinetiscope calculations and associated figure data</p> <p>CO2R microkinetic model-DRC.ipynb<br> CO2R microkinetic model-DRC.pdf<br> Jupyter notebook and pdf for degree of rate control in CO2 reduction<br> Packages used:<br> Python: 3.7.7<br> Numpy: 1.21.5<br> SciPy: 1.7.3<br> Matplotlib: 3.5.1</p> <p>Wang 2018 Pathway 1 only DRC.ipynb<br> Wang 2018 Pathway 1 only DRC.pdf<br> Jupyter notebook and pdf for degree of rate control photoelectrocatalytic water oxidation<br> Python: 3.7.7<br> Numpy: 1.21.5<br> SciPy: 1.7.3<br> mpmath: 1.2.1<br> Matplotlib: 3.5.1</p>
Phenological mismatch affects individual fitness and population growth in the winter moth
<p>Climate change can severely impact species that depend on temporary resources by inducing phenological mismatches between consumer and resource seasonal timing. In the winter moth, warmer winters caused eggs to hatch before their food source, young oak leaves, became available. This phenological mismatch changed the selection on the temperature sensitivity of egg development rate. However, we know little about the fine-scale fitness consequences of phenological mismatch at the individual level and how this mismatch affects population dynamics in the winter moth. To determine the fitness consequences of mistimed egg hatching relative to timing of oak budburst, we quantified survival and pupation weight in a feeding experiment. We found that mismatch greatly increased mortality rates of freshly hatched caterpillars, as well as affecting caterpillar growth and development time. We then investigated whether these individual fitness consequences have population-level impacts by estimating the effect of phenological mismatch on population dynamics, using our long-term data (1994–2021) on relative winter moth population densities at four locations in the Netherlands. We found a significant effect of mismatch on population density with higher population growth rates in years with a smaller phenological mismatch. Our results indicate that climate change-induced phenological mismatch can incur severe individual fitness consequences that can impact population density in the wild.</p>
Host species differences in the thermal mismatch of host–parasitoid interactions
<p>Extreme high temperatures associated with climate change can affect species directly, and indirectly through temperature-mediated species interactions. In most host–parasitoid systems, parasitization inevitably kills the host, but differences in heat tolerance between host and parasitoid, and between different hosts, may alter their interactions. Here, we explored the effects of extreme high temperatures on the ecological outcomes – including, in some rare cases, escape from the developmental disruption of parasitism – of the parasitoid wasp, Cotesia congregata, and two co-occurring congeneric larval hosts, Manduca sexta and M. quinquemaculata. Both host species had higher thermal tolerance than C. congregata, resulting in a thermal mismatch characterized by parasitoid (but not host) mortality under extreme high temperatures. Despite parasitoid death at high temperatures, hosts typically remain developmentally disrupted from parasitism. However, high temperatures resulted in a partial developmental recovery from parasitism (reaching the wandering stage at the end of host larval development) in some host individuals, with a significantly higher frequency of this partial developmental recovery in M. quinquemaculata than in M. sexta. Hosts species also differed in their growth and development in the absence of parasitoids, with M. quinquemaculata developing faster and larger at high temperatures relative to M. sexta. Our results demonstrate that co-occurring congeneric species, despite shared environments and phylogenetic histories, can vary in their responses to temperature, parasitism and their interaction, resulting in altered ecological outcomes.</p>
Different currencies for calculating resource phenology result in opposite inferences about trophic mismatches
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Demand-resource mismatch explains body shrinkage in a migratory shorebird
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Phenology-informed decline risk of estuarine fishes and their prey suggests potential for future trophic mismatches
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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