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230 results for “structure determination”
Physical processes determine spatial structure in water temperature and residence time on a wide reef flat
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Chemical shift-based methods in NMR structure determination
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Flightlessness in insects enhances diversification and determines assemblage structure across whole communities
<p><span><span><span>Dispersal limitation has been recurrently suggested to shape both macroecological patterns and microevolutionary processes within invertebrates. However, because of potential interactions among biological, environmental, temporal, and spatial variables, causal links among flight-related traits, diversification and spatial patterns of community assembly remain elusive. Integrating genetic variation within species across whole insect assemblages, within a simplified spatial and environmental framework, can be used to reduce the impact of these potentially confounding variables. Here we used standardised sampling and mtDNA sequencing for a whole-community characterisation of the beetle fauna inhabiting a singular forested-habitat (laurel forest) within an oceanic archipelago setting (Canary Islands). The spatial structure of species assemblages together with species-level genetic diversity was compared at the archipelago and island scales for 104 winged and 110 wingless beetle lineages. We found that wingless beetle lineages have (i) smaller range sizes at the archipelago scale, (ii) lower representation in younger island communities, (iii) stronger population genetic structure, and (iv) greater spatial structuring of species assemblages between and within islands. Our results reveal that dispersal limitation is a fundamental trait driving diversity patterns at multiple hierarchical levels by promoting spatial diversification and affecting the spatial configuration of entire assemblages at both island and archipelago scales.</span></span></span></p>
Data from: Population structure leads to male-biased population sex ratios under environmental sex determination
Spatial structure has been shown to favor female-biased sex allocation, but current theory fails to explain male biases seen in many taxa, particularly those with environmental sex determination (ESD). We present a theory and accompanying individual-based simulation model that demonstrates how population structure leads to male-biased population sex ratios under ESD. Our simulations agree with earlier work showing that the high productivity of female-producing habitats creates a net influx of sex-determining alleles into male-producing habitats, causing larger sex ratio biases and lower productivity in male-producing environments (Harts et al. 2014). In contrast to previous findings, we show that male-biasing habitats disproportionately impact the global sex ratio, resulting in stable male-biased population sex ratios under ESD. The failure to detect a male bias in earlier work can be attributed to small subpopulation sizes leading to local mate competition, a condition unlikely to be met in most ESD systems. Simulations revealed that consistent male biases are expected over a wide range of population structures, environmental conditions, and genetic architectures of sex determination, with male excesses as large as 30 percent under some conditions. Given the ubiquity of genetic structure in natural populations, we predict that modest, enduring male biased allocation should be common in ESD species, a pattern consistent with reviews of ESD sex ratios.
Data from: Diet is the primary determinant of bacterial community structure in the guts of higher termites
The gut microbiota of termites plays critical roles in the symbiotic digestion of lignocellulose. While phylogenetically 'lower termites' are characterized by a unique association with cellulolytic flagellates, higher termites (family Termitidae) harbour exclusively prokaryotic communities in their dilated hindguts. Unlike the more primitive termite families, which primarily feed on wood, they have adapted to a variety of lignocellulosic food sources in different stages of humification, ranging from sound wood to soil organic matter. In this study, we comparatively analysed representatives of different taxonomic lineages and feeding groups of higher termites to identify the major drivers of bacterial community structure in the termite gut, using amplicon libraries of 16S rRNA genes from 18 species of higher termites. In all analyses, the wood-feeding species were clearly separated from humus and soil feeders, irrespective of their taxonomic affiliation, offering compelling evidence that diet is the primary determinant of bacterial community structure. Within each diet group, however, gut communities of termites from the same subfamily were more similar than those of distantly related species. A highly resolved classification using a curated reference database revealed only few genus-level taxa whose distribution patterns indicated specificity for certain host lineages, limiting any possible cospeciation between the gut microbiota and host to short evolutionary timescales. Rather, the observed patterns in the host-specific distribution of the bacterial lineages in termite guts are best explained by diet-related differences in the availability of microhabitats and functional niches.
Data from: Rearing group size determines social competence and brain structure in a cooperatively breeding cichlid
Social animals can greatly benefit from well-developed social skills. Because the frequency and diversity of social interactions often increase with the size of social groups, the benefits of advanced social skills can be expected to increase with group size. Variation in social skills often arises during ontogeny, depending on early social experience. Whether variation of social-group sizes affects development of social skills and related changes in brain structures remains unexplored. We investigated whether, in a cooperatively breeding cichlid, early group size (1) shapes social behavior and social skills and (2) induces lasting plastic changes in gross brain structures and (3) whether the development of social skills is confined to a sensitive ontogenetic period. Rearing-group size and the time juveniles spent in these groups interactively influenced the development of social skills and the relative sizes of four main brain regions. We did not detect a sensitive developmental period for the shaping of social behavior within the 2-month experience phase. Instead, our results suggest continuous plastic behavioral changes over time. We discuss how developmental effects on social behavior and brain architecture may adaptively tune phenotypes to their current or future environments.
Data from: The making of winners (and losers): how early dominance interactions determine adult social structure in a clonal fish
Across a wide range of animal taxa, winners of previous fights are more likely to keep winning future contests, just as losers are more likely to keep losing. At present, such winner and loser effects are considered to be fairly transient. However, repeated experiences with winning and/or losing might increase the persistence of these effects generating long-lasting consequences for social structure. To test this, we exposed genetically identical individuals of a clonal fish, the Amazon molly (Poecilia formosa), to repeated winning and/or losing dominance interactions during the first two months of their life. We subsequently investigated whether these experiences affected the fish's ability to achieve dominance in a hierarchy five months later during adulthood. Individuals that had only winning interactions early in life consistently ranked at the top of the hierarchy. Interestingly, individuals with only losing experience tended to achieve the middle dominance rank, whereas individuals with both winning and losing experiences generally ended up at the bottom of the hierarchy. In addition to demonstrating that early social interactions can have dramatic and long-lasting consequences for adult social behaviour and social structure, our work also shows that higher cumulative winning experience early in life can counter-intuitively give rise to lower social rank later in life.
J-dimers of phthalocyanine analogues: structural characterization and their use for determination of association constants between ligands and central cation
<p>Dataset for manuscript: J-dimers of phthalocyanine analogues: structural characterization and their use for determination of association constants between ligands and central cation.</p>
Application of health belief model for the assessment of COVID-19 preventive behavior and its determinants among students: A structural equation modeling analysis
<p><strong>Background:</strong> COVID-19 is a new pandemic that poses a threat to people globally. In Ethiopia, where classrooms are limited, students are at higher risk for COVID-19 unless they take consistent preventative actions. However, there is a lack of evidence in the study area regarding student compliance with COVID-19 preventive behavior (CPB) and its predictors.</p> <p><strong>Objective:</strong> This study aimed to assess CPB and its predictors among students based on the perspective of the Health Belief Model (HBM).</p> <p><strong>Method and materials:</strong> A school-based cross-sectional survey was conducted from November to December 2020 to evaluate the determinants of CPB among high school students using a self-administered structured questionnaire. 370 participants were selected using stratified simple random sampling. Descriptive statistics were used to summarize data, and partial least squares structural equation modeling (PLS-SEM) analyses to evaluate the measurement and structural models proposed by the HBM and to identify associations between HBM variables. A T-value of > 1.96 with 95% CI and a P-value of < 0.05 were used to declare the statistical significance of path coefficients.</p> <p><strong> Result:</strong> A total of 370 students participated with a response rate of 92%. The median (interquartile range) age of the participants (51.9% females) was 18 (2) years. Only 97 (26.2%), 121 (32.7%), and 108 (29.2%) of the students had good practice in keeping physical distance, frequent hand washing, and facemask use respectively. The HBM explained 43% of the variance in CPB. Perceived barrier (β= - 0.15, p < 0.001) and self-efficacy (β= 0.51, p <0.001) were significant predictors of student compliance to CPB. Moreover, the measurement model demonstrated that the instrument had acceptable reliability and validity.</p> <p><strong>Conclusion and recommendations:</strong> COVID-19 prevention practice is quite low among students. HBM demonstrated adequate predictive utility in predicting CPBs among students, where perceived barriers and self-efficacy emerged as significant predictors of CPBs. According to the findings of this study, theory-based behavioral change interventions are urgently required for students to improve their prevention practice. Furthermore, these interventions will be effective if they are designed to remove barriers to CPBs and improve students' self-efficacy in taking preventive measures.</p>
Age-specific habitat preference, carrying capacity, and landscape structure determine the response of population spatial variability to fishing-driven age truncation
<p>1. Understanding the mechanisms underlying spatial variability of exploited fish is critical for the sustainable management of fish stocks. Empirical studies suggest that size-selective fishing can elevate fish population spatial variability (i.e., more heterogeneous distribution) through age truncation, making the population less resilient to changing environment. However, species differ in how their spatial variability respond to age truncation and the underlying mechanisms remain unclear.</p> <p>2. We hypothesize that age-specific habitat preference, together with environmental carrying capacity and landscape structure, determines the response of population spatial variability to fishing-induced age truncation. To test these hypotheses, we design an individual-based model of an age-structured fish population on a two-dimensional landscape under size-selective fishing. Individual fish reproduces and survives, and moves between habitats according to age-specific habitat preference and density-dependent habitat selection.</p> <p>3. Population spatial variability elevates with increasing age truncation and the response is stronger for populations with stronger age-specific habitat preference. On a gradient landscape, reducing carrying capacity elevates the relative importance of density-dependence in habitat selection, which weakens the response of spatial variability to age truncation for populations with strong age-specific habitat preference. On a fragmented landscape, both populations with strong and weak age-specific habitat preferences are restricted at local optimal habitats, and reducing carrying capacity weakens the responses of spatial variability to age truncation for both populations.</p> <p>4. Synthesis and applications. We demonstrate that to track and predict the changes in population spatial variability under exploitation, it is essential to consider the interactive effects of age-specific habitat preference, carrying capacity, and landscape structure. To improve spatial management in fisheries, it is crucial to enhance empirical and theoretical developments in the methodology to quantify age-specific habitat preference of marine fish, and to understand how climatic change influences carrying capacity and landscape continuity.</p>
Original 3D ED datasets of Co DHG and the integrated merged dataset used for structure determination with molecular replacement.
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Linked collectors and determiners for: Unique extrication structure in a new megaspilid, Dendrocerus scutellaris Trietsch & Mikó (Hymenoptera: Megaspilidae).
Natural history specimen data linked to collectors and determiners held within, "Unique extrication structure in a new megaspilid, Dendrocerus scutellaris Trietsch & Mikó (Hymenoptera: Megaspilidae)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/d7068326-e029-48e7-a0e6-b13e06d18d8b">https://bionomia.net/dataset/d7068326-e029-48e7-a0e6-b13e06d18d8b</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/d7068326-e029-48e7-a0e6-b13e06d18d8b">https://gbif.org/dataset/d7068326-e029-48e7-a0e6-b13e06d18d8b</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Checklist of pioneer benthic taxa found on Autonomous Reef Monitoring Structures (ARMS) in Terra Nova Bay (Ross Sea, Antarctica).
Natural history specimen data linked to collectors and determiners held within, "Checklist of pioneer benthic taxa found on Autonomous Reef Monitoring Structures (ARMS) in Terra Nova Bay (Ross Sea, Antarctica)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/f024a3d3-7bb2-4985-be57-d890936769ff">https://bionomia.net/dataset/f024a3d3-7bb2-4985-be57-d890936769ff</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/f024a3d3-7bb2-4985-be57-d890936769ff">https://gbif.org/dataset/f024a3d3-7bb2-4985-be57-d890936769ff</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: The morphological diversity of Mymaridae (Hymenoptera): an atlas of scanning electron micrographs. Part 1. General overview and structure of the head.
Natural history specimen data linked to collectors and determiners held within, "The morphological diversity of Mymaridae (Hymenoptera): an atlas of scanning electron micrographs. Part 1. General overview and structure of the head". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/1d5719a4-b5f9-46ff-8d27-4010f0eed663">https://bionomia.net/dataset/1d5719a4-b5f9-46ff-8d27-4010f0eed663</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/1d5719a4-b5f9-46ff-8d27-4010f0eed663">https://gbif.org/dataset/1d5719a4-b5f9-46ff-8d27-4010f0eed663</a>. Formatted as a Frictionless Data package.
Data from: Protein structure determination using metagenome sequence data
Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families and that metagenome sequence data more than triple the number of protein families with sufficient sequences for accurate modeling. We then integrate metagenome data, contact-based structure matching, and Rosetta structure calculations to generate models for 614 protein families with currently unknown structures; 206 are membrane proteins and 137 have folds not represented in the Protein Data Bank. This approach provides the representative models for large protein families originally envisioned as the goal of the Protein Structure Initiative at a fraction of the cost.
Data from: Song structure, not high-frequency song content, determines high-frequency auditory sensitivity in nine species of New World sparrows (Passeriformes: Emberizidae)
1. The evolution of vocal signals can be constrained by a host of factors including habitat effects on sound propagation, morphology of sound-producing structures, and phylogenetic relationships among species. Here, we asked whether auditory sensitivity over a broad range of frequencies correlates with the spectral content of conspecific vocalizations, or whether it is constrained by the overall structure of vocalizations, habitat effects on sound propagation, or relatedness among species. 2. We studied nine New World sparrows (Passeriformes: Emberizidae) including three open-habitat species, three scrub-like habitat species, and three forest species. For each habitat, one species had pure trilled songs, another had tonal songs, and another had complex songs with tones, trills, and amplitude-modulated buzzes. 3. As predicted by the acoustic adaptation hypothesis, song spectral properties (specifically frequency and entropy) had the highest values in open-habitat species and the lowest values in forest species. 4. Based on our results from song analyses, and the sender-receiver matching hypothesis, we predicted that open-habitat species would be more sensitive to high-frequency sounds compared to forest species. Contrary to this prediction, habitat and high-frequency song content had little effect on audiogram shape. Song type, however, had a strong effect, with species that produce complex songs showing higher sensitivity to high-frequency sounds than all other species. 5. Our results suggest that the use of song frequency by receivers depends on song structure and not necessarily on song spectral content. Therefore, our current understanding of how signal-processing mechanisms should match signal properties appears to be too simple. When thinking about the evolution of signal-processing mechanisms, the multidimensionality of signals, and how the different dimensions can interact, should be considered.
FIGURE 4 in CCDC 696447: Experimental Crystal Structure Determination
FIGURE 4. Map of Brazil with indication of the number of species recorded in each state.
single-molecule tertiary structure determination reveals RNA folding landscape
<p>Initial release of the 6HB RNA origami 3D density maps, fitting models and EMDB validation reports.</p>
Fig. 3 in Structure elucidation and absolute configuration determination of C , C and C tirucallane triterpenoids from the leaves of Picrasma quassioides (D. Don) Benn
Fig. 3. Key NOESY correlations of compounds 1–7.
Fig. 2. Key 1H–1H in Structure elucidation and absolute configuration determination of C , C and C tirucallane triterpenoids from the leaves of Picrasma quassioides (D. Don) Benn
Fig. 2. Key 1H–1H COSY and HMBC correlations of compounds 1–7.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.