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13,621 results for “Biologics”
Figure 8 in Breeding biology of Long-tailed Cinclodes Cinclodes pabsti Sick, 1969 (Passeriformes: Furnariidae)
Figure 8. Breeding chronology of Cinclodes pabsti during the breeding season of 2010-2011 based on the monitoring of eight nests in three nesting cavities in Campos de Cima da Serra, southern Brazil. Scheme of phenophases based on Faria et al. (2008), evidencing: 08/15/2011 – Beginning of the 2010-2011 breeding season with the laying of the first egg in the nest of nesting cavity NC09 [Nesting Cavity 09]; 08/18/2010 – Beginning of the incubation phase of three eggs in the nest of the nesting cavity NC09 [Nesting Cavity 09]; and 01/09/2011 – End of the 2010-2011 breeding season with the nestlings fledgling from the nesting cavity NC10 [Nesting Cavity 10].
Data for: (Epi)genomic adaptation driven by fine geographical scale environmental heterogeneity after recent biological invasions
<p><span>Elucidating processes and mechanisms involved in rapid local adaptation to varied environments is a poorly understood but crucial component in management of invasive species. Recent studies have proposed that genetic and epigenetic variation could both contribute to ecological adaptation, yet it remains unclear on the interplay between these two components underpinning rapid adaptation in wild animal populations. To assess their respective contributions to local adaptation, we explored epigenomic and genomic responses to environmental heterogeneity in eight recently colonized ascidian (<em>Ciona intestinalis</em>) populations at a relatively fine geographical scale. Based on MethylRADseq data, we detected strong patterns of local environment-driven DNA methylation divergence among populations, significant epigenetic isolation by environment (IBE), and a large number of local environment-associated epigenetic loci. Meanwhile, multiple genetic analyses based on single nucleotide polymorphisms (SNPs) showed genomic footprints of </span><span>divergent selection</span><span>. </span><span>In addition, for five genetically similar populations, we detected significant methylation divergence and local environment-driven methylation patterns, indicating strong effects of local environments on epigenetic variation. From a functional perspective, a majority of functional genes, gene ontology (GO) terms, and biological pathways were largely specific to one of these two types of variation, suggesting partial independence between epigenetic and genetic adaptation. The methylation quantitative trait loci (mQTL) analysis showed that the genetic variation explained only 18.67% of methylation variation, further confirming the autonomous relationship between these two types of variation. Altogether, we highlight the complementary interplay of genetic and epigenetic variation involved in local adaptation, which may jointly promote populations' rapid adaptive capacity and successful invasions in different environments. The findings here provide valuable insights into interactions between invaders and local environments to allow invasive species to rapidly spread, thus contributing to better prediction of invasion success and development of management strategies.</span></p>
Biological and biogeochemical responses of benthic communities to marine heatwaves - BioHeat
<p>The dataset presents data from a laboratory experiment exploring the effect of heatwaves of different intensities on benhic bioturbation, community excretion and biogeochemical cycling of solutes. <span>We tested the effects of short-term, moderate and strong marine heatwaves on macrofauna bioturbation and associated solute fluxes as examples of ecosystem functioning. We also measured macrofaunal excretion rates to assess effects of temperature on macrofauna metabolism. For this experiment, we used unmanipulated sediment cores with natural animal communities collected from a muddy location at 32 m depth in the northern Baltic Sea. Despite the mechanistic effect of bioturbation remaining unchanged between the treatments, there were significant differences in oxygen consumption, solute fluxes and excretion. Biogeochemical and biological processes were boosted by the moderate heatwave, whereas biogeochemical cycling seemed to decrease under a strong heatwave.</span></p>
Data for: Direct and indirect effects of management and landscape on biological pest control and crop pest infestation in apple orchards
<p>Biological pest control, relying on naturally occurring predator-prey dynamics, is considered a key element to achieve more sustainable farming systems. However, the combined effects of local management and landscape factors on communities of natural enemies as well as the cascading effects on pest infestations are rarely addressed, especially in perennial crops. Here, we used Piecewise Structural Equation Modelling (PSEM) to test direct and indirect effects of landscape composition, landscape configuration and local management practices on natural enemy communities, the pest control services they provide and ultimately on pest infestation and pest-related yield damage in apple crops. To this end, we surveyed 12 organic and 12 Integrated Pest Management (IPM) orchards during three consecutive years, and we also established a semi-natural benchmark to quantify the extent to which predator communities in the orchards were degraded. Natural enemies had a different community composition and were more abundant in organic orchards compared to IPM orchards. This had a small and positive effect on sentinel egg predation rates in organic orchards, but overall had very little impact on actual apple pest infestation. On the contrary, apple pest infestation levels were directly and positively affected by organic management practices and by increasing semi-natural habitat cover and landscape edge density. Compared to a semi-natural benchmark, both agricultural management systems showed degraded predator communities, which translated into an impaired delivery of biological control services. Synthesis and applications. Our results indicate that organic management and habitat conservation can enhance natural enemies and stimulate pest control, but also show that these factors can enhance pest infestations and can even lead to an overall increase in pest-related crop damage. Our study thus highlights the complex interplay of ecosystem services and disservices provided by biodiversity, which should be taken into account when advising farmers, policy makers and land managers on effective and sustainable strategies to control pest species and safeguard crop production.</p>
Dataset of "Tracking Urban Human Activity from Mobile Phone Calling Patterns" PLOS Computational Biology paper
<p>This are the dataset file for "Tracking Urban Human Activity from Mobile Phone Calling Patterns", to be published in PLOS Computational Biology.</p> <p>The files contain probability distributions of finding a first, last, or any call as a function of time, derived from anonymized call detail records for a 12 months period in the year 2007 from a mobile phone service provider in a European country. The first data file contains the data obtained fom 30 different cities. the second for the six most populated cities, splitting the data into different age and gender groups.</p> <p>Details in README files.</p>
SSU rRNA Gene Analysis of the Environmental and Biological Influences on Carbonate Precipitation within Hot Spring Microbial Mats in Little Hot Creek, CA
<p>R Markdown notebook and all data required to recreate the 16S rRNA Gene analysis figures found in Wilmeth et. al (In Submission), including mapping files, BIOM files, and R markdown notebook. </p>
DESIGN, SYNTHESIS AND STUDY OF BIOLOGICAL ACTIVITY OF PEPTIDES WITH NEUROPROTECTIVE PROPERTIES
<p>The main purpose of this project is to search for novel compounds that will protect neurons against oxidative stress (6-hydroxydopamine, 6-OHDA) and glucocorticoids (corticosterone, CORT) in a human neuroblastoma cell line (SH-SY5Y) and elucidate the mechanism by which attenuated the physiological changes induced by these neurotoxins. We will explore whether this protective role of tested compounds will be involved also in the regulation of apoptosis, maintaining oxidoreductive balance, and stabilization of mitochondrial membrane potential. Furthermore, the involvement of the BDNF/TrkB-ERK-CREB/mTOR signalling pathway in neuronal survival will be examined.</p>
Advanced Molecular Dynamics Model for Investigating Biological-Origin Microfibril Structures
<p>This data contains all necessary input file to construct the micro fibril.</p>
Data from: Longevity of hymenopteran parasitoids in natural vs. agricultural habitats and implications for biological control
<p>Agricultural habitats are frequently disturbed, and disturbances could have large effects on species in upper trophic levels such as hymenopteran parasitoids that are important for biological control. A strategy for conservation biological control is to provide a diversified agricultural landscape which increases the availability of resources such as sugar required by parasitoid biological control agents. Here, we ask whether parasitoids occurring in agriculture benefit from sugar resources more or less than parasitoids occurring in natural habitats surrounding agricultural fields. We collected parasitoids from agricultural alfalfa fields, field margins and natural prairies, and in the lab we randomly divided them into two treatments: half were given a constant supply of a sugar source to test their residual lifespan, and half were given neither sugar nor water to test their hardiness. Collected individuals were monitored daily and their day of death recorded. Parasitoids receiving a sugar source lived substantially longer than those without. Parasitoids collected in prairies lived longer than those from alfalfa fields in both the residual lifespan and hardiness treatments, with parasitoids from field margins being intermediate between them. Furthermore, the benefits of a sugar source to increase longevity was lower for parasitoids collected in agriculture than in natural habitats. This suggests that, even though parasitoid biological control agents benefit from sugar resources, their short lifespans make the benefit of sugar resources small compared to parasitoids that occur in natural habitats and have longer lifespans, and are adapted to consistent sugar sources.</p>
Data for: Biological mitigation of soil nitrous oxide emissions by plant metabolites
<p>Plant metabolites significantly affect soil nitrogen (N) cycling, but their influence on nitrous oxide (N<sub>2</sub>O) emissions has not been quantitatively analyzed on a global scale. We conduct a comprehensive meta-analysis of 173 observations from 42 articles to evaluate global patterns of, and principal factors controlling, N<sub>2</sub>O emissions in the presence of root exudates and extracts. Overall, plant metabolites promoted soil N<sub>2</sub>O emissions by about 10%. However, the effects of plant metabolites on N<sub>2</sub>O emissions from soils varied with experimental conditions and properties of both metabolites and soils. Primary metabolites, such as sugars, amino acids, and organic acids, strongly stimulated soil N<sub>2</sub>O emissions, by an average of 79%, while secondary metabolites, such as phenolics, terpenoids, and flavonoids, often characterised as both biological nitrification inhibitors (BNIs) and biological denitrification inhibitors (BDIs), reduced soil N<sub>2</sub>O emissions by an average of 41%. The emission mitigation effects of BNIs/BDIs were closely associated with soil texture and pH, increasing with increasing soil clay content and soil pH on acidic and neutral soils, and with decreasing soil pH on alkaline soils. We furthermore present soil incubation experiments that show that three secondary metabolite types act as BNIs to reduce N<sub>2</sub>O emissions by 32-45% while three primary metabolite classes possess a stimulatory effect of 56-63%, confirming the results of the meta-analysis. Our results highlight the potential role and application range of specific secondary metabolites in bio-mitigation of global N<sub>2</sub>O emissions, and provide new biological parameters for N<sub>2</sub>O emission models that should help improve the accuracy of model predictions.</p>
A Machine Learning Approach for Multiscale Modeling of Biological Tissues, Companion Dataset
<p>This dataset includes the response of a Delaunay fiber network to various deformation gradients. The dataset is in adios2 format and includes stress, strain, strain energy, stiffness, and the applied deformation gradients.</p> <p>This also includes the pytorch implementation of our neural network.</p>
MIVIA Dataset of Biological Graphs
<p>The databases have been structured for the monomorphism problem, so each one is composed of very large graphs, called target, from which have been extracted a set of not induced subgraphs, called pattern, and so grouped by three densities: 1, 0.5 and 0.25. The aim of the authors is to use pattern graphs as queries on the target graph. We do not use all the six databases, but the following tree:</p> <ul> <li><strong>AIDS</strong>: a molecular database containing 40000 graphs, from 4 to 256 nodes, representing the topological structure of a chemical compound tested for evidence of anti-HIV activity. </li> <li><strong>Graemlin:</strong> database contains 10 target graphs having up to 6726 nodes, extracted from 10 microbial networks.</li> <li><strong>Protein-Protein interaction</strong> (<strong>PPI</strong>): a dataset networks contains 10 network graphs, from 5720 to 12575 nodes, describing known protein interactions of 10 organisms. This is composed of more dense and big graphs than those in Graemlin.</li> </ul> <p>The Graemlin and PPI databases have nodes with no labels. Since graph matching algorithms usually employ label information to reduce the computational costs, the matching times on unlabeled graphs are very long. For this reason, we have attached labels to the nodes of the graphs. The labels have been generated using random integer values. We have generated 5 labeled version of each database, varying the number of possible label values (128, 256, 512, 1024 and 2048 values have been used). For graph isomorphism we have generated two new databases, extracting random node-induced subgraphs from the target graphs in Graemlin and PPI; for each graph, 10 random permutations of the nodes have been computed to obtain isomorphic pairs of graphs. In order to test isomorphism algorithms on dense graphs, we have also added extra edges at random. So finally we have two isomorphism databases having 700 pairs, varying from 8 to 512 nodes.</p>
Data from: Phenological mismatches mitigate the ecological impact of a biological invader on amphibian communities
<p>Data and code for the manuscript entitled "Phenological mismatches mitigate the ecological impact of a biological invader on amphibian communities" for Ecological Applications (2024). <br><br><br><br>The raw sequencing data was submitted to NCBI’s Sequence Read Archive (SRA) under BioProject number PRJNA1023717 (https://dataview.ncbi.nlm.nih.gov/object/PRJNA1023717?reviewer=rciv7kme2qq5vpcnqqog4vjioo). </p>
Data and Script used in "Effects of canopy gaps on microclimate, soil biological activity and their relationship in a European mixed floodplain forest"
<p>The R code and data provided in this repository allow to reproduce the data carpentry, analysis and visualization of “Effects of canopy gaps on microclimate, soil biological activity and their relationship in a European mixed floodplain forest” (https://doi.org/10.1016/j.scitotenv.2024.173572).</p> <p> </p> <p>Folder structure</p> <p> </p> <p>Data abstracts:</p> <p>Data_abstract_climate.pdf</p> <p>Data_abstract_soil_biotics.pdf</p> <p>Data_abstract_soil_abiotics_openness.pdf</p> <p> </p> <p>Data:</p> <p>Climate_data.xlsx</p> <p>Soil_biotics.xlsx</p> <p>Soil_abiotics_openness.xlsx</p> <p> </p> <p>R Scripts:</p> <p>00-preamble.R loads all required packages</p> <p>01-data-carpentry.R loads all datasets and prepares the analysis of all experimental periods.</p> <p>02-data-analyses-microclimate.R compares understorey air and soil microclimate between forest types and treatments, presents diurnal and seasonal variations and tests the relationship of under- and overstorey openness on microclimate.</p> <p>03-data-analyses-decomposition.R compares decomposition rates and feeding activity between forest types and treatments and models the dependencies of soil biological activity on microclimate and soil abiotic factors.</p> <p> </p> <p>Information of related software and package versions used in the script:<br>R version 4.3.2 (2023-10-31 ucrt)<br>Platform: x86_64-w64-mingw32/x64 (64-bit)<br>Running under: Windows 10 x64 (build 19045)<br>Matrix products: default</p> <p> </p> <p>Contact</p> <p>Please contact me at annalena.lenk@uni-leipzig.de if you have further questions.</p>
Fig. 1 in New record of blunthead pufferfish, Sphoeroides pachygaster (Muller & Troschel, 1848) (Tetraodontiformes: Tetraodontidae) from Indian water along with DNA barcode and some biological aspects
Fig. 1 — Sphoeroides pachygaster (Müller & Troschel, 1848) 223 mm TL
Data from: The interplay of intercropping, wildflower strips and weeds in conservation biological control and productivity
<p>Diversifying agroecosystems is instrumental to reduce pesticide use in agriculture. While different diversification practices have the potential to reduce pests, their integration at the agroecosystem level and the evaluation of their multifunctional effects remain limited. Through a two-year field experiment conducted in Germany, we tested whether associating intercropping (faba bean-wheat, followed by breadseed poppy-barley) with pluriannual wildflower strips strengthens the biological regulation of aphid pests and weeds, and enhances cropping system productivity. The contribution of flowering weeds to conservation biological control was also analysed. Aphid colonization rates, but also predator colonization and predation rates, on bean and poppy were consistently lower in intercropping compared to sole cropping. Associating wildflower strips to intercropping enhanced aphid predation in bean-wheat intercropping, and further reduced aphid colonization at 10 m distance from the flower strip but not at 20 m in poppy-barley intercropping. Weed biomass was strongly reduced in intercropping compared to sole crop bean and poppy, and did not significantly affect bean and poppy yields in intercropping. The cover of one flowering weed species, <em>Matricaria recutita</em>, was negatively correlated to aphid colonization rate and positively correlated to predation rate in bean-wheat intercropping. In poppy-barley intercropping, <em>M. recutita</em> flowers were visited more often by predatory hoverflies in plots adjacent to wildflower strips. Finally, land equivalent ratio, measuring land-use efficiency, was consistently higher than 1, and the highest in bean-wheat intercropping associated to wildflower strips. The study shows that intercropping is key to control multiple pests and enhance land-use efficiency, and demonstrates that associating wildflower strips to intercropping can strengthen biological control and cropping system productivity. Flowering weeds, maintained at an acceptable level through intercropping, turn out to be relevant functional biodiversity in interacting with wildflower strips to support natural enemies for conservation biological control.</p>
Fig. 1 in Influence of okra (Abelmoschus spp.) accessions on colonization by Aphis gossypii (Hemiptera: Aphididae) and their effects on aphid biological parameters
Fig. 1.:attern of climatic factors for the bimodal warm, humid forest of Yaoundé.
Figure 1 in Population biology of the ghost shrimps, Trypaea australiensis and Biffarius arenosus (Decapoda: Thalassinidea), in Western Port, Victoria.
Figure 1. Map of Australia showing the study sites located in Western Port: Warneet and Crib Point.
Fig. 4 in A Study On The Feeding Biology Of Soil Oribatid Mite Papillacarus (Papillacarus) Elongatus (Acari, Lohmanniidae)
Fig. 4. Mouth parts of P. (P.) elongatus. a — chelicera; b — rutellum. Scale 50μm
Fig. 5 in On the biology of blackbellied angler, Lophius budegassa Spinola, 1807, in the north-western Mediterranean Abstract
Fig. 5: Maturity ogives for females (dark grey) and males (light grey) of L. budegassa.
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.