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799 results for “abundance data”
Data for: Engineering tRNA abundances for synthetic cellular systems
<p>Data for publication:<strong> Engineering tRNA abundances for synthetic cellular systems</strong></p> <p><strong>Abstract</strong></p> <p>Routinizing the engineering of synthetic cells requires specifying determining beforehand how many of each molecule are needed. First-principles tools for specifying molecular abundances enabling whole-cell synthetic biology are missing. We use a colloidal dynamics simulator to make predictions for how tRNA abundances impact protein synthesis rates. We use rational design and direct RNA synthesis to make 21 synthetic tRNA surrogates from scratch. We use evolutionary algorithms within a computer aided design framework to design engineer translation systems predicted to work faster or slower depending on tRNA abundance differences. We build and test the so-specified synthetic systems and find that qualitative agreement between expected and observed systems performance matchqualitatively match. First-principles modeling combined with bottom-up experiments can help molecular-to-cellular scale synthetic biology realize “design, build, work” frameworks that transcend tinker-and-test.</p> <p><strong>Data description</strong></p> <p>The data here consists of (1) All Colloidal Smoldyn & CD-CAD simulation input parameter and output files & (2) experimental data used for the associated publication. Simulation data was produced using Colloidal Dynamics modeling and Colloidal Dyamics-CAD (CD-CAD) as described in the associated manuscript. Data folders should be used directly with modeling and analysis code provided on Github: https://github.com/EndyLab/tRNACAD.</p>
Abundance and size data of Elysia crispata from coral reefs of Southern Gulf of Mexico and Mexican Caribbean
<p>Three populations of the solar-powered sea slug <em>Elysia crispata</em> on coral reefs from the southern Gulf of Mexico and the Mexican Caribbean were analyzed. This data contains information regarding the number of organisms and sizes found in Cayo Arcas, Verde (Sistema Arrecifal Veracruzano), and Puerto Morelos at different depths and five times of the day (sunrise, morning, zenith, evening, and night).</p>
Isotope and faunal abundance and TOC data from eastern Arabian sea during last 25 kiloyear by Majumder et al., 2023
<p>We present multiproxy data spanning between ~25000 and 3500 calibrated years before the present (cal yr BP) from the eastern Arabian sea (EAS). This is possibly the first record of stable isotope record in pteropods from the EAS. Based on this dataset, we found that the Indian summer monsoon (ISM) was weak during the Last Glacial Maximum (LGM). Moreover, upwelling intensity was high during the early Holocene, which was followed by a significant weakening of ISM during the 4.2 ka event.</p>
Data for: Waterbird abundance in aquaculture ponds: the significance of day and night and pond type
<p><span>The loss of coastal wetlands represents a grave threat to waterbirds, prompting the use of artificial wetlands, such as aquaculture ponds, as a means of conservation. Aquaculture ponds are common in coastal areas and provide production value and ecological function as waterbird habitats. However, certain piscivorous birds may cause economic losses to the aquaculture industry. Different types of ponds provide habitat for various bird assemblages, and waterbirds exhibit nocturnal feeding behavior and utilize habitats distinct from those used during the day. Most waterbird surveys were conducted during the daytime, limiting our understanding of their nocturnal habitat utilization. This study conducted diurnal and nocturnal surveys on shorebirds, waterfowl, and Black-crowned Night Heron (<em>Nycticorax</em> <em>nycticorax</em>) ten times in three aquaculture ponds situated in the Cigu District of Tainan, namely fish/shrimp, hard clam, and abandoned ponds between October 2021 and November 2022. The results showed no significant difference in shorebird density between day and night. However, shorebird density in fish/shrimp ponds was the highest and significantly higher than in abandoned ponds. Conversely, waterfowl density exhibits a significant increase in abandoned ponds compared to the other two pond types, irrespective of diurnal or nocturnal conditions. Furthermore, waterfowl density in abandoned ponds is significantly higher during daylight hours compared to the nocturnal period. In the daytime, the density of night herons was significantly higher in abandoned ponds than in the other two ponds. Nevertheless, during nighttime hours, fish/shrimp ponds exhibit the highest density of Black-crowned Night Herons, significantly surpassing that found in hard clam ponds. Notably, water coverage also influences the density of both shorebirds and waterfowl. The foraging frequency of waterfowl and night herons was greater during nocturnal hours, while shorebirds did not exhibit significant variations between day and night. Consequently, this study underscores the significance of considering both diurnal and nocturnal habitats in formulating strategies for waterbird conservation.</span></p>
Data from: Optimising trait and source selection for explaining occurrence and abundance changes: a case study using British Butterflies
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Data from: Comparison of fish detections, community diversity, and relative abundance using environmental DNA metabarcoding and traditional gears
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Data on bird abundance in urban woodlands in 32 Swedish cities
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Cannot see the diversity for all the species: evaluating inclusion criteria for local species lists when using abundant citizen science data
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Data from: Prevalence and abundance of bees visiting major conventionally-managed agricultural crops in Brazil
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Data from: Social behavior in bees influences the abundance of Sodalis (Enterobacteriaceae) symbionts
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Data from: Genotypic diversity and spatial-temporal distribution of Symbiodinium clones in an abundant reef coral
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Data from: Predicting the effects of increasing temporal scale on species composition, diversity, and rank-abundance distributions
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Data from: A new composite abundance metric detects stream fish declines and community homogenization during six decades of invasions
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Data from: Honey bees are the most abundant visitors to Australian watermelon but native stingless bees are equally effective as pollinators
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Data from: Accounting for the effects of biological variability and temporal autocorrelation in assessing the preservation of species abundance
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Data from: Species-habitat relationships and ecological correlates of butterfly abundance in a transformed tropical landscape
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Data from: Supportive breeding boosts natural population abundance with minimal negative impacts on fitness of a wild population of Chinook salmon
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Data from: Reduced hornbill abundance associated with low seed arrival and altered recruitment in a hunted and logged tropical forest
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Data from: Climate and local abundance in freshwater fishes
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Data from: Wide prevalence of hybridization in two sympatric grasshopper species may be shaped by their relative abundances
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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.
International Brain Laboratory public data
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.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.