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13,621 results for “Biologics”
Data from: Settling dynamics of nanoparticles in simple and biological media
<p>The biological response of organisms exposed to nanoparticles is often studied in vitro using adherent monolayers of cultured cells. In order to derive accurate concentration-response relationships, it is important to determine the local concentration of nanoparticles to which the cells are actually exposed rather than the nominal concentration of nanoparticles in the cell-culture medium. In this study, the sedimentation–diffusion process of different sized and charged gold nanoparticles has been investigated in vitro by evaluating their settling dynamics and by developing a theoretical model to predict the concentration depth-profile of nanoparticles in solution over time. Experiments were carried out in water and in cell-culture media at a range of controlled temperatures. The optical phenomenon of caustics was exploited to track nanoparticles in real-time in a conventional optical microscope without any requirement for fluorescent labelling that potentially affects the dynamics of the nanoparticles. The results obtained demonstrate that size, temperature and the stability of the nanoparticles play a pivotal role in regulating settling dynamics of nanoparticles. For gold nanoparticles larger than 60 nm in diameter, the initial nominal concentration did not accurately represent the concentration of nanoparticles local to the cells.</p>
Human tissue gene expression TPM values for the advanced forensic biology course
<p><strong>Gene expression per tissue</strong></p> <p>This dataset comes from the <a href="https://www.gtexportal.org/home/">Genotype-Tissue Expression (GTEx)</a> database that gathers gene expression data from various human tissues. Specifically, the <strong>GTEx Analysis v7</strong> version was used.</p> <p>The file is called "<a href="https://zenodo.org/api/files/9f872792-6c96-4226-b659-ce0807da66e8/GTEx_Analysis_2016-01-15_v7_RNASeQCv1.1.8_gene_median_tpm.tsv">GTEx_Analysis_2016-01-15_v7_RNASeQCv1.1.8_gene_tpm.tsv</a>" and contains tabulated-separated values of median TPM gene expression by tissue (TPM: transcript per million).</p> <p> </p> <p><strong>Genes with a favored sucutaneous-adipose expression profile</strong></p> <p>This file contains 195 genes that have a statistically (p < 0.01) favored expression profile in subcutaneous adipose tissue compared to other tissues. </p> <p>https://zenodo.org/api/files/7342bbfa-0e4d-49e7-b916-5eff5b638c33/genes_with_a_subcutaneous_adipose_favored_expression.tsv</p>
Data from: Biological controls over the abundances of terrestrial ammonia oxidizers
<blockquote> <p>Aim: Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are the primary agents for nitrification, converting ammonia (NH4+) into nitrate (NO3-) and modulating plant nitrogen (N) utilization and terrestrial N retention. However, there is still lack of a unifying framework describing the patterns of global AOA and AOB distribution. In particular, biotic interactions are rarely integrated into any of the conceptual models.<br> Location: World-wide.<br> Time period: 2005-2016.<br> Major taxa studied: Ammonia-oxidizing archaea and ammonia-oxidizing bacteria. <br> Methods: A meta-analysis and synthesis was conducted to obtain a general picture of global AOA and AOB distribution and identify the primary driving factors. A microcosm experiment was then conducted to assess effects of relative carbon to nitrogen availability for heterotrophic microbes on AOA and AOB in two distinct soils. A mesocosm experiment was further carried out to characterize the effects of plant roots and their arbuscular mycorrhizal fungi (AMF) on AOA and AOB abundances using hyphae- or root-ingrowth techniques. <br> Results: Our meta-analysis showed that soil carbon to nitrogen (C/N) ratios explained the most variance in AOA and AOB abundances, although soil pH had a significant effect. Experimental results demonstrated that high cellulose and mineral N inputs increased total microbial biomass and microbial activities, but inhibited AOA and AOB, suggesting microbial inhibition of AOA and AOB. Also, AMF and roots suppressed AOA and AOB, respectively. <br> Main conclusions: Our study provided convincing evidence illustrating that relative carbon to nitrogen availability can dominate the abundances of AOA and AOB. Our experimental results further validated that biotic competitions among plants, heterotrophic microbes and ammonia oxidizers for substrate N predominantly control AOA and AOB abundances. Together, these findings provide new insights into the role of abiotic and biotic factors in modulating terrestrial AOA and AOB abundances and their potential applications for management of nitrification in an increasing reactive N world.</p> </blockquote>
Learned predators enhance biological control via organizational upward and trophic top‐down cascades
<p>Learning is a behavioral change based on memory of previous experiences and a ubiquitous phenomenon in animals. Learning effects are commonly life stage- and age-specific. In many animals, early life experiences lead to pervasive and persistent behavioral changes.</p> <p>There is broad consensus that learning has far-reaching implications to biological control. Proximate and ultimate factors of individual learning by parasitoids and true predators are relatively well understood, yet the consequences of learning to higher organizational levels, populations and communities, and top-down trophic cascades are unexplored.</p> <p>We addressed this issue using a tri-trophic system consisting of predatory mites <em>Amblyseius swirskii</em>, Western flower thrips <em>Frankliniella occidentalis</em> and whole common bean plants, <em>Phaseolus vulgaris</em>. <em>F. occidentalis</em> are notorious horticultural pests that are difficult to control. Therefore, practitioners have much to gain by optimizing biological control of thrips.</p> <p>Previous studies have shown that early life experience of thrips by <em>A. swirskii</em> improves foraging on thrips later in life due to decreased prey recognition times and increased predation rates, together enhancing predator fecundity. Here, we hypothesized that early learning by<em> A. swirskii </em>enhances biological control of thrips via immediate and cascading effects. We predicted that release of thrips-experienced predators enhances predator population growth and thrips suppression and reduces plant damage as compared to release of thrips-naïve predators.</p> <p>The behavioral changes brought about by early learning cascaded up to the population and community levels. Thrips-experienced predators caused favorable immediate and cascading effects that could not be compensated for in populations founded by thrips-naïve predators. Populations founded by thrips-experienced predators grew faster, reached higher abundances, were more efficacious in suppressing an emerging thrips population and kept plant damage at lower levels than populations founded by thrips-naïve predators. Plant fecundity correlated negatively with thrips abundance and positively with predatory mite abundance. Improved biological control was mainly due to thrips-experienced founders providing for a head-start in predator population growth and thrips suppression.</p> <p>Synthesis and applications: Our study suggests that learned natural enemies have high potential to optimize augmentative biological control on a larger scale due to favorably modulating organizational upward and trophic top-down cascades.</p>
Predicting Nanoparticle Uptake by Biological Membranes: Theory and Simulation - data
<p>Simulation data described in paper entitled "Predicting Nanoparticle Uptake by Biological Membranes: Theory and Simulation"</p>
Kruia rediscovered: phylogenetic implications, larval morphology, and biology of an enigmatic hydrophilid beetle from western Africa (Coleoptera: Hydrophilidae)
<p>This is the dataset for the paper to be published in Arthropod Systematics and Phylogeny, containing original unedited original photos and SEM micrographs, and the moleclar dataset used for the phylogenetic analyses.</p>
easyMF: A Web Platform for Matrix Factorization-based Biological Discovery from Large-scale Transcriptome Data
<p>With the development of high-throughput experimental technologies, large-scale RNA sequencing (RNA-Seq) data have been and continue to be produced, but have led to challenges in extracting relevant biological knowledge hidden in the produced high-dimensional gene expression matrices. Here, we present easyMF, a user-friendly web platform that aims to facilitate biological discovery from large-scale transcriptome data through matrix factorization (MF). The easyMF platform enables users with little bioinformatics experience to streamline transcriptome analysis from raw reads to gene expression and to decompose expression matrix from thousands of genes to a handful of metagenes. easyMF also offers a series of functional modules for metagene-based exploratory analysis with an emphasis on functional gene discovery. As a modular, containerized and open-source platform, easyMF can be customized to satisfy users’ specific demands and deployed as a web server for broad applications. easyMF is freely available at https://github.com/cma2015/easyMF. We demonstrated the application of easyMF with four case studies using 940 RNA sequencing datasets from maize (<em>Zea mays </em>L<em>.</em>).</p>
FIG. 30 in Phalangopsidae crickets (Orthoptera, Grylloidea) from the Mitaraka biological survey, French Guiana
FIG. 30. — Predation of phalangopsid crickets by spiders in the Mitaraka. Photos: Sylvain Hugel.
FIG. 1 in Phalangopsidae crickets (Orthoptera, Grylloidea) from the Mitaraka biological survey, French Guiana
FIG. 1. — Location of 'Our Planet Revisited' Mitaraka survey (white circle). Map by L. Wilmé.
Introductory gestures before songbird vocal displays are shaped by learning and biological predispositions
<p>Numerous animal displays begin with introductory gestures. For example, lizards start their head-bobbing displays with introductory push-ups and many songbirds begin their vocal displays by repeating introductory notes (INs) before producing their learned song. Among songbirds, the acoustic structure and the number of INs produced before song vary considerably between individuals in a species. While similar variation in songs between individuals is a result of learning, whether variation in INs are also due to learning remains poorly understood. Here, using natural and experimental tutoring with male zebra finches, we show that mean IN number and IN acoustic structure are learned from a tutor. Interestingly, IN properties and how well INs were learned, was not correlated with the accuracy of song imitation and only weakly correlated with some features of songs that followed. Finally, birds artificially tutored with songs lacking INs still repeated vocalizations that resembled INs, before their songs, suggesting biological predispositions in IN production. These results demonstrate that INs, just like song elements, are shaped both by learning and biological predispositions. More generally, our results suggest mechanisms for generating variation in introductory gestures between individuals while still maintaining the species-specific structure of complex displays like birdsong.</p>
Data for the manuscript 'Biological response to the interaction of a mesoscale eddy and the river plume in the northern South China Sea'
<p>Satellite data includes daily sea-level anomaly from AVISO, daily surface chlorophyll a data from OC-CCI and sea surface salinity obtained from SMAP. Model simulated daily current, temperature, salinity, chlorophyll and nitrate concentration for three experiments (control, case1 and case2) from our coupled physical-biological model of the South China Sea . For chlorophyll and nitrate concentration, the dataset also includes the 16-day averaged budget terms along section S1. The modeled lagrangian particl tracking data is also avaiable. And all data and matlab scripts used to draw Fig. 1 to Fig. 10 are in Figure_data.rar file.</p>
Prioritization of cell types responsive to biological perturbations in single-cell data with Augur
<p>Processed and analysis-ready input data discussed in our Augur procedures.</p>
FIG. 1 in Catching tuna in the Aegean: biological background of tuna fisheries and the archaeological implications
FIG. 1. — Map of the Aegean Sea with sites mentioned in the text noted on it. Credits: V. Triggas.
Appendix 4 to "The Status of Biological Invasions and their Management in South Africa in 2019"—Species list change tracker
<p>For more details see: http://iasreport.sanbi.org.za</p> <p>SANBI and CIB 2020. Appendix 4 to "The Status of Biological Invasions and their Management in South Africa in 2019"—Species list change tracker. South African National Biodiversity Institute, Kirstenbosch and DSI-NRF Centre of Excellence for Invasion Biology, Stellenbosch. http://dx.doi.org/10.5281/zenodo.3947778</p>
Appendix 5 to "The Status of Biological Invasions and their Management in South Africa in 2019"—Pathways change tracker
<p>For more details see: http://iasreport.sanbi.org.za</p> <p>SANBI and CIB 2020. Appendix 5 to "The Status of Biological Invasions and their Management in South Africa in 2019"—Pathways change tracker. South African National Biodiversity Institute, Kirstenbosch and DSI-NRF Centre of Excellence for Invasion Biology, Stellenbosch. http://dx.doi.org/10.5281/zenodo.3947799</p>
Fig. 5 in Reproductive biology of Poecilia sphenops Valenciennes, 1846 (Cyprinidontiformes: Poeciliidae) at the Emiliano Zapata Reservoir in Morelos, Mexico
Fig. 5. Seasonal variation of development maturity ovary stages for Poecilia sphenops.
Fig. 4 in Reproductive biology of Poecilia sphenops Valenciennes, 1846 (Cyprinidontiformes: Poeciliidae) at the Emiliano Zapata Reservoir in Morelos, Mexico
Fig. 4. Length-weight relationship for females (a) and males (b) of Poecilia sphenops.
Data from: Does biological intimacy shape ecological network structure? A test using a brood pollination mutualism on continental and oceanic islands
Biological intimacy—the degree of physical proximity or integration of partner taxa during their life cycles—is thought to promote the evolution of reciprocal specialization and modularity in the networks formed by co‐occurring mutualistic species, but this hypothesis has rarely been tested. Here, we test this "biological intimacy hypothesis" by comparing the network architecture of brood pollination mutualisms, in which specialized insects are simultaneously parasites (as larvae) and pollinators (as adults) of their host plants to that of other mutualisms which vary in their biological intimacy (including ant‐myrmecophyte, ant‐extrafloral nectary, plant‐pollinator and plant‐seed disperser assemblages). We use a novel dataset sampled from leafflower trees (Phyllanthaceae: Phyllanthus s. l. [Glochidion]) and their pollinating leafflower moths (Lepidoptera: Epicephala) on three oceanic islands (French Polynesia) and compare it to equivalent published data from congeners on continental islands (Japan). We infer taxonomic diversity of leafflower moths using multilocus molecular phylogenetic analysis and examine several network structural properties: modularity (compartmentalization), reciprocality (symmetry) of specialization and algebraic connectivity. We find that most leafflower‐moth networks are reciprocally specialized and modular, as hypothesized. However, we also find that two oceanic island networks differ in their modularity and reciprocal specialization from the others, as a result of a supergeneralist moth taxon which interacts with nine of 10 available hosts. Our results generally support the biological intimacy hypothesis, finding that leafflower‐moth networks (usually) share a reciprocally specialized and modular structure with other intimate mutualisms such as ant‐myrmecophyte symbioses, but unlike nonintimate mutualisms such as seed dispersal and nonintimate pollination. Additionally, we show that generalists—common in nonintimate mutualisms—can also evolve in intimate mutualisms, and that their effect is similar in both types of assemblages: once generalists emerge they reshape the network organization by connecting otherwise isolated modules.
Data from: Offspring telomere length in the long lived Alpine swift is negatively related to the age of their biological father and foster mother
A growing body of studies is showing that offspring telomere length (TL) can be influenced by the age of their parents. Such a relationship might be explained by variation in TL at conception (gamete effect) and/or by alteration of early growth conditions in species providing parental care. In a long-lived bird with bi-parental care, the Alpine swift (Apus melba), we exchanged an uneven number of 2 to 4-day-old nestlings between pairs as part of a brood size manipulation. Nestling TL was measured at 50 days after hatching, which allowed investigation of the influence of the age of both their biological and foster parents on offspring TL, after controlling for the manipulation. Nestling TL was negatively related to the age of their biological father and foster mother. Nestling TL did not differ between enlarged and reduced broods. These findings suggest that offspring from older males were fertilized by gametes with shorter telomeres, presumably due to a greater cell division history or a longer accumulation of damage, and that older females may have provided poorer parental care to their offspring.
Image 1 in Breeding biology of the Small Bee-eater Merops orientalis (Latham, 1801) in Nagapattinam District, Tamil Nadu, India
Image 1. Typical nest of the Small Bee-eater
ScienceDex guides
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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.