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13,621 results for “Biologics”
Precision Agriculture Yield Monitoring in Row Crop Agriculture at the Kellogg Biological Station, Hickory Corners, MI (1996 to 2013)
Dataset Abstract The LTER annual crops (corn, soy and wheat), treatments 1-4, are harvested annually using a combine equipped with a GPS and precision agriculture software to allow detailed yield measurements with coincident GPS latitude and longitude data.. original data source http://lter.kbs.msu.edu/datasets/40
KBS LTER Global Positioning System Data at the Kellogg Biological Station, Hickory Corners, MI (1988 to 2014)
Dataset Abstract The KBS LTER uses submeter accuracy GPS to record many locations such as plot corners, gas flux chamber, leaf litter trap locations, soil water samplers (lysimeter), etc. original data source http://lter.kbs.msu.edu/datasets/42
Living Field Laboratory at the Kellogg Biological Station, Hickory Corners, MI (1992 to 2012)
Dataset Abstract The Living Field Laboratory is a long-term rotation study established in 1993 under the direction of Emeritus Professor Dr. Richard Harwood to evaluate the benefits of cover crops (as green manure) and/or the addition of composted dairy manure in two integrated systems compared to a conventional and an organic system. The LFL accommodates every entry point of the crop rotation each year and has a factorial design that allows for the comparison of a number of interactions. These interactions include: differences in N management, rotation effects, and cover crops. From 1993 through 2005, the rotation consisted of corn (Zea mays L.)/corn/soybean (Glycine max)/wheat (Triticum aestivum) vs. continuous corn. During this period, crimson clover (Trifolium incarnatum L.) was seeded to 1st yr. corn, 2nd yr corn was in rye grass (Lolium multiflorum), soybean had no cover, and red clover (Trifolium pretense L.) was frost-seeded into wheat. In 2006, under the direction of Dr. Sieglinde Snapp and through consultation with a farmer advisory group, the rotation was shortened to a 3 yr rotation of corn/soybean/wheat vs. continuous corn. The remaining plot in each management system was converted to a 2 yr rotation of corn/soybean. Cereal rye (Secale cereale) is now planted after corn regardless of crop rotation. Cereal rye follows soybean in the 2-yr rotation. Red clover is frost-seeded into wheat. The management systems are: Conventional, Integrated Fertilizer and Integrated Compost. Weed management is identical across systems, and nitrogen fertilizer management adjusted to take into account soil N availability and balance nitrogen inputs across treatments. The cover crop is present as a split plot (plus minus) within each system. The split-plot cover crop treatment was established in 1993 in Integrated Fertilizer and in Integrated Compost, while the split-plot cover crop treatment was established 14 years later in 2007 in the Conventional treatment, to allow a comp
Soil Carbon and Nitrogen Deep Core Surveys at the Kellogg Biological Station, Hickory Corners, MI (2001 to 2013)
Dataset Abstract An LTER project goal is to periodically collect and analyze deep soil cores for the main site treatments and successional and forest sites. Soil is sampled to a depth of one meter, and analyzed for horizon depths, texture, moisture, and carbon and nitrogen content. original data source http://lter.kbs.msu.edu/datasets/47
Water Chemistry in Streams, Lakes Wetlands and Groundwater near the KBS LTER at the Kellogg Biological Station, Hickory Corners, MI (1996 to 2017)
Dataset Abstract Water chemistry is measured in diverse surface waters and in two water supply wells in the vicinity of the KBS LTER. This dataset includes sites sampled over time (streams, wells, some wetlands) as well as wetland sites sampled once or a few times. A separate dataset includes soil water chemistry sampled from the LTER treatments. original data source http://lter.kbs.msu.edu/datasets/50
Distribution and Composition of the Seed Bank at the Kellogg Biological Station, Hickory Corners, MI (1990 to 2008)
Dataset Abstract The distribution and composition of the weed seed bank in treatments 1-7 of the LTER main site is periodically (every 3-6 years) evaluated using elutriation and seed counting methods. The goal is to determine: how well the seed bank predicts weed abundances and composition in subsequent years, and how changes in disturbance (tillage) and plant species (cropping systems) affect the bank. Composite soil samples to two depths are periodically elutriated to determine seed densities, species composition, and viabilities of seven target species which are dominant on the site. original data source http://lter.kbs.msu.edu/datasets/9
Soil Moisture in the Biodiversity Gradient Experiment at the Kellogg Biological Station, Hickory Corners, MI (2001 to 2001)
Dataset Abstract Soil moisture measurements from the Fall of 2001 original data source http://lter.kbs.msu.edu/datasets/70
Dataset for the manuscript "Barium stable isotopes as a fingerprint of biological cycling in the Amazon River Basin" submitted to Biogeosciences Discussions
<p>This file contains the dataset of the manuscript submitted to Biogeosciences Discussions entitled "Barium stable isotopes as a fingerprint of biological cycling in the Amazon River Basin" by Charbonnier et al. It consists in three spreadsheets: (1) dissolved species concentration and dissolved Ba isotope data on river dissolved load; (2) main characteristics and Ba isotope data of river sediments; (3) compilation of major element and Ba and Li concentration in rocks (compilation made from the GEOROC database) and in the dissolved load of river draining single rock types (compilation made from previously published data and new data).</p>
Fig. 2 in New data on distribution and biology of the invasive species Hydrotaea aenescens (Wiedemann, 1830) (Diptera, Muscidae)
Fig. 2. Copulating pair of H. aenescens attacked by another male.
Fig. 5 in New data on distribution and biology of the invasive species Hydrotaea aenescens (Wiedemann, 1830) (Diptera, Muscidae)
Fig. 5. Copulating pair of H. aenescens
Supporting data files for "Binding of Biologically Relevant Divalent Cations to Aqueous Carboxylates: Molecular Simulations Guided by Raman Spectroscopy"
<p>Parameter files and typical simulation input files that allow replication of the computational work presented in the paper "Binding of Biologically Relevant Divalent Cations to Aqueous Carboxylates: Molecular Simulations Guided by Raman Spectroscopy", authored by Denilson Mendes de Oliveira, Samual R. Zukowski, Vladimir Palivec, Jérôme Hénin, Hector Martinez Seara, Dor Ben Amotz, Pavel Jungwirth and Elise Duboué-Dijon</p>
Mass spectrometry output SILAC labelled (F/Y) biological replicate 2 - anti-HLA-A29 antibody DK1G8
<p>Mass spectrometry output from SILAC labelled (F/Y) ERAP2 WT versus (CRISPR Cas9-mediated) ERAP2-KO lymphoblastoid cell line from a Birdshot Uveitis patient (ERAP1 hap10/10 ERAP2 hapA/A). Peptides were eluted from immuno-purifications with anti-HLA-A29 antibody DK1G8. The dataset was used for subsequent filtering and differential expression analysis by <em>limma</em>. </p>
Mass spectrometry output SILAC labelled (F/Y) biological replicate 2 - anti-HLA-ABC antibody W6/32
<p>Mass spectrometry output from SILAC labelled (F/Y) ERAP2 WT versus (CRISPR Cas9-mediated) ERAP2-KO lymphoblastoid cell line from a Birdshot Uveitis patient (ERAP1 hap10/10 ERAP2 hapA/A). Peptides were eluted from immuno-purifications from HLA-A29-negative (DK1G8-negatively selected) fractions with anti-HLA-ABC antibody W6/32. The dataset was used for subsequent filtering and differential expression analysis by <em>limma</em>. </p>
Fig. 1 in A new species of Ocyale (Araneae, Lycosidae) from Madagascar, with first observations on the biology of a representative in the genus
Fig. 1. Type locality of Ocyale ghost Jocque M. & Jocqué R. sp. nov.
Index and biological spectrum of accessible DNA elements in the human genome
<p>Data associated with the manuscript titled<br> "Index and biological spectrum of accessible DNA elements in the human genome"<br> <a href="https://doi.org/10.1101/822510">https://doi.org/10.1101/822510</a></p> <p>Code repositories for these data are available here:</p> <ul> <li>https://github.com/Altius/Index</li> <li>https://github.com/Altius/Vocabulary</li> </ul> <p><br> Tab-separated file with DNase I Hypersensitive Site (DHS) coordinates,<br> including DHS summits and core regions and assignments to regulatory components.<br> A separate legend file describes the contents of each column in more detail.</p> <ul> <li>DHS_Index_and_Vocabulary_hg38_WM20190703.txt.gz</li> <li>DHS_Index_and_Vocabulary_hg19_WM20190703.txt.gz (mapped using liftOver, not ideal)</li> <li>DHS_Index_and_Vocabulary_legend.txt</li> </ul> <p> </p> <p>Metadata files describing biosample characteristics and annotations,<br> provided in HTML, PDF, TSV and Excel formats:</p> <ul> <li>DHS_Index_and_Vocabulary_metadata.html</li> <li>DHS_Index_and_Vocabulary_metadata.pdf</li> <li>DHS_Index_and_Vocabulary_metadata.tsv</li> <li>DHS_Index_and_Vocabulary_metadata.xlsx</li> </ul> <p> </p> <p>Presence/absence matrix of DHSs (rows) versus biosamples (columns),<br> provided in RData, MatrixMarket and raw formats:</p> <ul> <li>dat_bin_FDR01_hg38.RData</li> <li>dat_bin_FDR01_hg38.mtx.gz</li> <li>dat_bin_FDR01_hg38.txt.gz</li> <li>dat_bin_FDR01_hg19.RData (mapped using liftOver, not ideal)</li> <li>dat_bin_FDR01_hg19.txt.gz (mapped using liftOver, not ideal)</li> </ul> <p> </p> <p>Normalized DNase-seq signal matrix of DHSs (rows) versus biosamples (columns),<br> provided in RData and raw formats:</p> <ul> <li>dat_FDR01_hg38.RData</li> <li>dat_FDR01_hg38.txt.gz</li> </ul> <p>The order of DHSs (rows) is the same as in the DHS Index file(s) above,<br> and the order of biosamples (columns) is the same as in the metadata files.</p> <p> </p> <p>Non-negative Matrix Factorization (NMF) results, decomposing the presence/absence matrix (hg38) into 16 components:</p> <ul> <li>2018-06-08NC16_NNDSVD_Mixture.npy.gz</li> <li>2018-06-08NC16_NNDSVD_Basis.npy.gz</li> </ul> <p> </p> <p>Putative transcription factor-specific regulatory elements,<br> identified using DHS Vocabulary components, TF motif databases and biosample-specific footprinting data:</p> <ul> <li>TF_associated_DHSs_hg38.tar.gz</li> </ul>
Data from: Miniaturization, genome size, and biological size in a diverse clade of salamanders
Genome size (C-value) can affect organismal traits across levels of biological organization, from tissue complexity to metabolism. Neotropical salamanders show wide variation in genome and body sizes, including several clades with miniature species. Because miniaturization imposes strong constraints on morphology and development, and genome size is strongly correlated with cell size, we hypothesize that body size has played an important role in the evolution of genome size in bolitoglossine salamanders. If this hypothesis is correct, then genome size and body size should be correlated in this group. Using Feulgen Image Analysis Densitometry (FIAD), we estimated genome sizes for 60 species of neotropical salamanders. We also estimated the "biological size" of species by comparing genome size and physical body sizes in a phylogenetic context. We found a significant correlation between C-value and physical body size using optimal regression with an Ornstein-Uhlenbeck model, and report the smallest salamander genome found to date. Our index of biological size showed that some salamanders with large physical body size have smaller biological body size than some miniature species, and that several clades showed patterns of increased or decreased biological size compared to their physical size. Our results suggest a causal relationship between physical body size and genome size and show the importance of considering the impact of both on the biological size of organisms. Indeed, biological size may be a more appropriate measure than physical size when considering phenotypic consequences of genome size evolution in many groups.
Isotopic and GDGTs analysis of methane-related biological processes (methane production and oxidation) in a Miocene sedimentary pool
<p>Methane is one of the most important greenhouse gases. A substantial proportion of this gas originates from marine environments where both its biological formation and oxidation occur. Variations in seawater properties due to climatic perturbations are likely to be reflected in the living conditions of both methanotrophic and methanogenic microbiota. The debate about the fate of the marine methane cycle facing global change may benefit from the inclusion of data concerning marine palaeoenvironments, especially salt-bearing sediments, which are a relic of the evaporitic sea. The study presents a GDGT-derived palaeorecord of methane-related biological processes in Miocene Wieliczka Formation sediments (a remnant of the Paratethys sea) as well as a description of present-day microbial communities subsisting in evaporates using activity measurements and high throughput sequencing. The results revealed that GDGT-based indices corresponded with the reconstructed sedimentary conditions and microbial ecophysiology which confirms their applicability of reconstruction for biological methane formation and oxidation in saline environments.</p>
How biological invasions affect animal behaviour: a global, cross-taxonomic analysis
<p>1. In the Anthropocene, species are faced with drastic challenges due to rapid, human-induced changes, such as habitat destruction, pollution and biological invasions. In the case of invasions, native species may change their behaviour to minimise the impacts they sustain from invasive species, and invaders may also adapt to the conditions in their new environment in order to survive and establish self-sustaining populations. 2. We aimed at giving an overview of which changes in behaviour are studied in invasions, and what is known about the types of behaviour that change, the underlying mechanisms and the speed of behavioural changes. 3. Based on a review of the literature, we identified 191 studies and 360 records (some studies reported multiple records) documenting behavioural changes caused by biological invasions in native (236 records from 148 species) or invasive (124 records from 50 species) animal species. This global dataset, which we make openly available, is not restricted to particular taxonomic groups. 4. We found a mild taxonomic bias in the literature towards mammals, birds and insects. In line with the enemy release hypothesis, native species changed their anti-predator behaviour more frequently than invasive species. Rates of behavioural change were evenly distributed across taxa, but not across types of behaviour. 5. Our findings may help to better understand the role of behaviour in biological invasions as well as temporal changes in both population densities and traits of invasive species, and of native species affected by them.</p>
Data and R code for The Finer Points of Urban Adaptation: Intraspecific Variation in Lizard Claw Morphology (2020; Biological Journal of the Linnean Society)
<p>This zip file contains all data (tps files, Rdata, csv) and annotated R script to conduct all analyses presented in Falvey et al. (2020, BJLS), which examines claw morphology in 5 species of anole lizards using geometric morphometrics.</p>
Collision between biological process and statistical analysis revealed by mean-centering
<p>Animal ecologists often collect hierarchically-structured data and analyze these with linear mixed-effects models. Specific complications arise when the effect sizes of covariates vary on multiple levels (e.g., within vs among subjects). Mean-centering of covariates within subjects offers a useful approach in such situations, but is not without problems.</p> <p>A statistical model represents a hypothesis about the underlying biological process. Mean-centering within clusters assumes that the lower level responses (e.g. within subjects) depend on the deviation from the subject mean (relative) rather than on absolute values of the covariate. This may or may not be biologically realistic. We show that mismatch between the nature of the generating (i.e., biological) process and the form of the statistical analysis produce major conceptual and operational challenges for empiricists.</p> <p>We explored the consequences of mismatches by simulating data with three response-generating processes differing in the source of correlation between a covariate and the response. These data were then analyzed by three different analysis equations. We asked how robustly different analysis equations estimate key parameters of interest and under which circumstances biases arise. </p> <p>Mismatches between generating and analytical equations created several intractable problems for estimating key parameters. The most widely misestimated parameter was the among-subject variance in response. We found that no single analysis equation was robust in estimating all parameters generated by all equations. Importantly, even when response-generating and analysis equations matched mathematically, bias in some parameters arose when sampling across the range of the covariate was limited.</p> <p>Our results have general implications for how we collect and analyze data. They also remind us more generally that conclusions from statistical analysis of data are conditional on a hypothesis, sometimes implicit, for the process(es) that generated the attributes we measure. We discuss strategies for real data analysis in face of uncertainty about the underlying biological process.</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.
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.