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1,221 results for “Aggregators”
Fig. 3 in The sperm aggregation in a whirligig beetle (Coleoptera, Gyrinidae): structure, functions, and comparison with related taxa
Fig. 3 Spermatozoa and first sperm bundle of Gyretes sp. extracted from the efferent ducts. Photographs under LM. A. Individualized spermatozoid. The arrow indicates the transition between the nucleus (n) and flagellum (f). B–D. Nuclei stained with DAPI. B. Observe the lateral extension of the n in the posterior extremity (arrow). C. Mag-
Fig. 1 in The sperm aggregation in a whirligig beetle (Coleoptera, Gyrinidae): structure, functions, and comparison with related taxa
Fig. 1 Spermatogenesis of Gyretes sp. Histological sections under LM. A. Spermatogonia. B–J. testicular cysts at different stages of development. B. Spermatocytes. C, D. Younger spermatids. E–I. Elongation of the cytoplasm and then of the nucleus (n) of the spermatids. Note in (E) the young spermatids with nebenkern (nb), which will give rise to mitochondrial derivatives. J. Cyst at the end of sper-
Fig. 2 in The sperm aggregation in a whirligig beetle (Coleoptera, Gyrinidae): structure, functions, and comparison with related taxa
Fig. 2 Male reproductive tract of Gyretes sp. A. General view of the reproductive structures: part of a testis (t), efferent duct (ed), vasa deferentia (vd), and accessory glands (ag) (one testis, efferent and ejaculatory ducts (ed) were removed). The yellow dotted lines indicate the approximate region shown in the histological sections. Longitudinal (B–D) and transversal (E) sections under LM. B, C. Sper-
Fig. 4 in The sperm aggregation in a whirligig beetle (Coleoptera, Gyrinidae): structure, functions, and comparison with related taxa
Fig. 4 Secondary aggregation of the spermatozoa of Gyretes sp. extracted from the second portion of the vasa deferentia. Photographs under LM (A–C) and SEM (D–F). A. A complete sperm aggregate showing the spermatostyle (sp) and the spermatozoa. B, E, F. The
FIGURE 1. Box-plots regarding A in Agrimonia eupatoria subsp. major stat. nov. (Rosaceae) and notes on the Agrimonia eupatoria aggregate
FIGURE 1. Box-plots regarding A) angle hypanthium/lowest bristles (measure in degree, axis y), and B) length of hypanthium + crown (measures in mm, axis y).
Supplementary Data for Bayesian material flow analysis of the construction aggregate cycle in England (2019)
<p>Supplementary Data for Bayesian material flow analysis of the construction aggregate cycle in England (2019) by </p> <p><span>Adam R. Mason <sup>1,a</sup>, Tom Bide <sup>2,b</sup>, Junyang Wang <sup>3,c</sup>, John Morley <sup>4,d</sup>, Mohit Arora <sup>5,e</sup>, Alperen Yayla<sup>1,f</sup>, Julia A. Stegemann <sup>5,g</sup>, Rupert J. Myers <sup>1,h,*</sup></span></p> <p><span> </span></p> <p><sup><span>1</span></sup><span> Department of Civil and Environmental Engineering, Imperial College London, UK</span></p> <p><sup><span>2</span></sup><span> British Geological Survey, UK</span></p> <p><sup><span>3 </span></sup><span>Department of Mathematics, Imperial College London, UK</span></p> <p><sup><span>4</span></sup><sub><span> </span></sub><span>Department of Earth Science and Engineering, Imperial College London, UK</span></p> <p><sup><span>5</span></sup><span> School of Engineering, King’s College London, UK</span></p> <p><sup><span>6</span></sup><span> Department of Civil, Environmental and Geomatic Engineering, University College London, UK</span></p> <p><span> </span></p> <p><span>Author e-mails: <sup>a </sup></span><a href="mailto:a.mason19@imperial.ac.uk"><span>a.mason19@imperial.ac.uk</span></a><span>,<sup> b </sup></span><a href="mailto:tode@bgs.ac.uk"><span>tode@bgs.ac.uk</span></a><span>,<sup> c </sup></span><a href="mailto:junyang.wang21@imperial.ac.uk"><span>junyang.wang21@imperial.ac.uk</span></a><span>,<sup> d </sup></span><a href="mailto:john.morley18@imperial.ac.uk"><span>john.morley18@imperial.ac.uk</span></a><span>,<sup> e </sup></span><a href="mailto:mohit.arora@kcl.ac.uk"><span>mohit.arora@kcl.ac.uk</span></a><span>,<sup> f </sup></span><a href="mailto:a.yayla22@imperial.ac.uk"><span>a.yayla22@imperial.ac.uk</span></a><span>,<sup> g </sup></span><a href="mailto:j.stegemann@ucl.ac.uk"><span>j.stegemann@ucl.ac.uk</span></a><span>; *corresponding author:<sup> h</sup> </span><a href="mailto:r.myers@imperial.ac.uk"><span>r.myers@imperial.ac.uk</span></a></p> <p> </p>
raw data for "Elucidating ATP's Role as Solubilizer of Biomolecular Aggregate"
<p>It contains 4 raw trajectories corresponding to the two proteins Trp-cage (prod_trpcage_ATP0M_REMD_303K_a99SBdisp.xtc and prod_trpcage_ATP0M_REMD_303K_a99SBdisp.xtc) and A<span><span>β40 (prod_trpcage_ATP0M_REMD_303K_a99SBdisp.xtc) proteins in absence and in presence of ATP (0.5 M). The replica exchange molecular dynamics trajectories corresponding to 303 K temperature have been included for each cases. The trajectory (.xtc) and topology (.tpr) files are labeled as "prod_protein-name_ATP-concentration_simulation_temperature_forcefield".<br></span></span></p> <p><span><span>The raw data employed in constructing each of the plots provided in manuscript are included in the respective zip files.The data corresponding to the experimental results are included in the associated zip file, named according to the specific figure referenced in the manuscript. Also some GROAMCS command lines are also provided in the respective data files. For any further inquiries or requests for additional data, please contact <a rel="noopener">jmondal@tifrh.res.in</a>.</span></span></p>
Supplementary tables for the paper: "Comprehensive computational analysis via Adverse Outcome Pathways and Aggregate Exposure Pathways in exploring synergistic effects from radon and tobacco smoke on lung cancer."
<p><strong>Authors</strong>:<br>Thomas Jaylet, Vinita Chauhan, Laura Mezquita, <em>Nadia Boroumand</em><em>, </em>Olivier Laurent, <em>Karine Elihn</em><em>, Lovisa Lundholm</em><em>, </em>Olivier Armant, Karine Audouze</p>
Temperature data collected in turf aggregations, seaweed patches and the water masses in mesocosm in the Oslofjord, Norway
<p><span>Temperature data collected in turf aggregations, seaweed patches and the water masses in the NIVA mesocosm basins at Solbergstrand, in the Oslofjord, Norway</span></p>
Temperature data collected in the surface turf aggregations and the water masses below, in the Varildsfjorden in the Oslofjord, Norway
<p>Temperature data collected in the surface turf aggregations and the water masses just below the turf, in the Varildsfjorden in the Oslofjord, Norway</p>
Exploring the Impact of Physiological C-Terminal Truncation on α-Synuclein Conformations to Unveil Mechanisms Regulating Pathological Aggregation
<p><span>Emerging evidence suggests that <a name="_Hlk179101300"></a>physiological C-terminal truncation of α-synuclein (αS) plays a critical role in regulating <a name="_Hlk178755669"></a>liquid–liquid phase separation and promoting amyloid aggregation, processes implicated in neurodegenerative diseases such as Parkinson’s disease (PD). However, the molecular mechanisms through which C-terminal truncation influences αS conformation and modulates its aggregation remain poorly understood. In this study, we investigated the impact of C-terminal truncation on αS conformational dynamics by comparing full-length αS<sub>1-140</sub> with truncated αS<sub>1-103</sub> monomers using atomistic discrete molecular dynamics (DMD) simulations. Our findings revealed that both αS<sub>1-140</sub> and αS<sub>1-103</sub> primarily adopted helical conformations around residues 7–32, while residues 35-95, located in the second half of the N-terminal and NAC domains, predominantly formed a dynamic β-sheet core. The C-terminus of αS<sub>1-140</sub> was largely unstructured and dynamically wrapped around the β-sheet core. While residues 1-95 exhibited similar secondary structure propensities in both αS<sub>1-140</sub> and αS<sub>1-103</sub>, the dynamic capping by the C-terminus in αS<sub>1-140</sub> slightly enhanced β-sheet formation around residues 35-95. In contrast, key aggregation-driving regions (residues 2-9, 36-42, 45-57, and 68-78) were dynamically shielded by the C-terminus in αS<sub>1-140</sub>, reducing their exposure and potentially preventing inter-peptide interactions that drive aggregation. C-terminal truncation, on the other hand, increased the exposed surface area of these aggregation-prone regions, thereby enhancing inter-peptide interactions, phase separation, and amyloid aggregation. Overall, our simulations provide valuable insights into the conformational effects of C-terminal truncation on αS and its role in promoting pathological aggregation.</span></p>
Experimental Study on Concrete Strength for Rigid Pavement with Marginal Aggregate
Open the record for dataset details and reuse information.
Data from: Number of neighbors instead of group size significantly affects individual vigilance levels in large animal aggregations
The group size effect states that animals living in groups gain anti-predator benefits through reducing vigilance levels as group size increases. A basic assumption of group size effect is that all individuals are equally important for a focal individual, who may adjust its vigilance levels according to social information acquired from them. However, some studies have indicated that neighbors pose greater influences on an individual's vigilance decisions than other group members, especially in large aggregations. Vigilance has also been found to be directed to both predators (anti-predation vigilance) and conspecifics (social vigilance). Central individuals might rely more on social vigilance than peripheral individuals. To test these hypotheses, we examined the effects of flock size, number of neighbors and position within a flock on vigilance and competition of greater white-fronted goose (Anser albifrons) that form large foraging flocks in winter, controlling the effects of other variables (group identity, winter period, and site). We found that individual vigilance levels were significantly affected by number of neighbors and position within a flock, whereas flock size showed no effect. Individuals devoted a large component of vigilance to nearby flock mates. Central individuals directed a relatively larger proportion of vigilance to monitor neighbors than peripheral ones, indicating that central individuals more relied on social information acquired from neighbors, possibly caused by the more blocked visual field of central individuals. Moreover, some social vigilance may function as conducting or preventing agonistic interactions since competition intensity was positively correlated with number of neighbors. Our study therefore demonstrate that the number of neighbors is more important than group size in determining individual vigilance in large animal groups. Further studies are still needed to unravel which neighbors pose greater influence on individual vigilance, and the factors that influence individuals to acquire information from their neighbors to adjust vigilance behaviors.
Data from: Free-living bacterial communities associated with tubeworm (Ridgeia piscesae) aggregations in contrasting diffuse flow hydrothermal vent habitats at the Main Endeavour Field, Juan de Fuca Ridge
We systematically studied free-living bacterial diversity within aggregations of the vestimentiferan tubeworm Ridgeia piscesae sampled from two contrasting flow regimes (High Flow and Low Flow) in the Endeavour Hydrothermal Vents Marine Protected Area (MPA) on the Juan de Fuca Ridge (Northeast Pacific). Eight samples of particulate detritus were recovered from paired tubeworm grabs from four vent sites. Most sequences (454 tag and Sanger methods) were affiliated to the Epsilonproteobacteria, and the sulfur-oxidizing genus Sulfurovum was dominant in all samples. Gammaproteobacteria were also detected, mainly in Low Flow sequence libraries, and were affiliated with known methanotrophs and decomposers. The cooccurrence of sulfur reducers from the Deltaproteobac- teria and the Epsilonproteobacteria suggests internal sulfur cycling within these habitats. Other phyla detected included Bacteroidetes, Actinobacteria, Chloroflexi, Firmicutes, Planctomycetes, Verrucomicrobia, and Deinococcus–Thermus. Statisti- cally significant relationships between sequence library composition and habitat type suggest a predictable pattern for High Flow and Low Flow environments. Most sequences significantly more represented in High Flow libraries were related to sulfur and hydrogen oxidizers, while mainly heterotrophic groups were more represented in Low Flow libraries. Differences in temperature, avail- able energy for metabolism, and stability between High Flow and Low Flow habitats potentially explain their distinct bacterial communities.
Data from: Genotyping-by-sequencing reveals genomic homogeneity among overwintering Pacific Dunlin (Calidris alpina pacifica) aggregations along the Pacific coast of North America
Information on how migratory populations are genetically structured during the overwintering season of the annual cycle can improve our understanding of the strength of migratory connectivity and help identify populations as units for management. Here, we use a genotype-by-sequencing approach to investigate whether population genetic structure exists among overwintering aggregations of the Pacific Dunlin subspecies (Calidris alpina pacifica) sampled at two spatial scales (i.e. within and among overwintering sites) in the eastern Pacific Flyway. Genome-wide analyses of 874 single nucleotide polymorphisms across 80 sampled individuals revealed no evidence for genetic differentiation among aggregations overwintering at three locations within the Fraser River Estuary (FRE) of British Columbia. Similarly, comparisons of aggregations in the FRE and those overwintering in southern sites in California and Mexico indicated no genetic segregation between northern and southern overwintering areas. These results suggest that Pacific Dunlin residing within the FRE, Sacramento Valley (California) and Guerrero Negro (Mexico) are genetically homogeneous, with no evident genetic structure between sampled sites or regions across the overwintering range. Despite no evidence for differentiation among aggregations, we identified a significant effect of geographical distance between sites on the distribution of individual genotypes in a redundancy analysis; however, a small proportion of the total genotypic variance (R2 = 0.036, P = 0.011) was explained by the combined effect of latitude and longitude, suggesting weak genomic patterns of isolation-by-distance that are consistent with chain-like migratory connectivity between breeding and overwintering areas. Our study represents the first genome-scale investigation of population structure for a Dunlin subspecies and provides essential baseline estimates of genomic diversity and differentiation within the Pacific Dunlin.
Data from: High-molecular-weight polymers from dietary fiber drive aggregation of particulates in the murine small intestine
The lumen of the small intestine (SI) is filled with particulates: microbes, therapeutic particles, and food granules. The structure of this particulate suspension could impact uptake of drugs and nutrients and the function of microorganisms; however, little is understood about how this suspension is re-structured as it transits the gut. Here, we demonstrate that particles spontaneously aggregate in SI luminal fluid ex vivo. We find that mucins and immunoglobulins are not required for aggregation. Instead, aggregation can be controlled using polymers from dietary fiber in a manner that is qualitatively consistent with polymer-induced depletion interactions, which do not require specific chemical interactions. Furthermore, we find that aggregation is tunable; by feeding mice dietary fibers of different molecular weights, we can control aggregation in SI luminal fluid. This work suggests that the molecular weight and concentration of dietary polymers play an underappreciated role in shaping the physicochemical environment of the gut.
Data from: Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA
Population genetics is essential for understanding and managing marine ecosystems, but sampling remains challenging. We demonstrate that high-throughput sequencing of seawater environmental DNA can provide useful estimates of genetic diversity in a whale shark (Rhincodon typus) aggregation. We recover similar mitochondrial haplotype frequencies in seawater compared to tissue samples, reliably placing the studied aggregation in a global genetic context and expanding the applications of environmental DNA to encompass population genetics of aquatic organisms.
FIGURE 1 in Amaranthus bengalense (Amaranthaceae) a new species from India, with taxonomical notes on A. blitum aggregate
FIGURE 1. Box plot for the diagnostic measurable characters (measurements are in mm): A) Seed dimeter; B) Ratio length bracts/tepals. Abbreviations: bli = A. blitum. var. blitum, ole = A. blitum. var. oleraceus, ben = A. bengalense, ema = A. emarginatus. var. emarginatus, pse = A. emarginatus. var. pseudogracilis.
FIGURE 2. Amaranthus bengalense Das & Iamonico. A in Amaranthus bengalense (Amaranthaceae) a new species from India, with taxonomical notes on A. blitum aggregate
FIGURE 2. Amaranthus bengalense Das & Iamonico. A. Habit; B. Synflorescence (part); C. Bract; D. Bracteole; E. Tepal of male flower; F. Tepal of female flower; G. Male flower; H. Female flower.
Insights into the aggregation mechanism of RRM domains in TDP-43: A theoretical exploration
<p>The transactive response DNA-binding protein 43 (TDP-43) is associated with several diseases such as Amyotrophic lateral sclerosis (ALS) and Frontotemporal lobar degeneration (FTLD) due to pathogenic aggregations. In this work, we examined the dimer, tetramer and hexamer models built from the RRM domains of TDP-43 using molecular dynamics simulations in combination with the protein-protein docking. Our results showed that the formations of the dimer models are mainly achieved by the interactions of the RRM1 domains. The parallel β-sheet layers between the RRM1 domains in these oligomer models, which provide the potential binding sites in the aggregation process, are formed energetically favorable. The approaching of the parallel β-sheet layers from small oligomer models gradually expand to large ones through the allosteric communication between the α1/α2 helices of the RRM1 domains, which maintains the binding affinities and interactions in the larger oligomer models. Using the repeatable-superimposing method based on the tetramer models, we proposed a new aggregation mechanism of RRM domains in TDP-43, which could well characterize the formation of the large aggregation models with the repeated, helical and rope-like structures. These new insights help to understand the amyloid-like aggregation phenomena of TDP-43 protein in ALS and FTLD diseases.</p>
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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)
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.
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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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