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1,392 results for “accumulation”
Mercury accumulation in leaves of different plant types – the significance of tissue age and specific leaf area
<p></p><p>Mercury, Hg, is one of the most problematic metals from an environmental perspective. To assess the problems caused by Hg in the environment it is crucial to understand the processes of Hg biogeochemistry, but the exchange of Hg between the atmosphere and vegetation is not sufficiently well characterised. We explored the mercury concentration, [Hg], in foliage from a diverse set of plant types, locations and sampling periods to study whether there is a continuous accumulation of Hg in leaves/needles over time. Measurements of [Hg] were made in deciduous and conifer trees in Gothenburg, Sweden (Botanical Garden and city area) as well as of evergreen trees in Rwanda. In addition, data for wheat from an ozone experiment conducted at Östad, Sweden, were included. Conifer data were quantitatively compared with literature data. In every case where older foliage was directly compared with younger, [Hg] was higher in older tissue. Covering the range of current year up to four-year old needles, there was no sign of Hg saturation in conifer needles with age. Thus, over time scales of approximately one month to several years, the Hg uptake in foliage from the atmosphere always dominated over Hg evasion. Rwandan broadleaved trees had generally older leaves due to lack of seasonal abscission and higher [Hg] than Swedish broadleaved trees. The significance of atmospheric Hg uptake in plants was shown in a wheat experiment where charcoal filtrated air lead to significantly lower leaf [Hg]. To search for general patterns, the accumulation rates of Hg in the diverse set of tree species in the Gothenburg area were related to the specific leaf area (SLA). Leaf area based [Hg] was strongly negatively and non-linearly correlated with SLA, while mass-based [Hg] had a somewhat weaker positive relationship with SLA (both relationships with p < 0.001). An elaborated understanding of the relationship behind [Hg] and SLA would support large-scale modelling of Hg uptake by vegetation and Hg circulation in general. </p><p></p>
MicroED datasets of peptide crystals (AVAAGA) at different accumulated electron exposures
<p>Continuous rotation data sets in SMV format were collected on a Tecnai F30 (300 kv) equipped with a TVIPS TEM CAM XF416 detector. Datasets were collected from 3 different crystals. To simulate increasing dose each crystal had 4 datasets collected from it with an approximate fluence of 3 e<sup>- </sup>Å<sup>2</sup> per dataset (12 e<sup>- </sup>Å<sup>2 </sup>total accumulated exposure per crystal). Datasets at each exposure were indexed with XDS and merged with XSCALE to produce a final set of intensities at each total exposure. Experimental parameters are as follows:<br> <br> Accelerating voltage: 300 kV<br> Wavelength: 0.019687<br> Cameralength: 1320 mm<br> Exposure time: 3 s<br> Rotation speed: 0.3 degrees s<sup>-1</sup><br> Rotation: +/- 45 degrees <br> Detector area: 2048 x 2048 (Bin 2)<br> Pixel size: 0.031 mm<br> Spot size: 11<br> C2 aperture: 20 µm<br> SA aperture: 1 µm</p> <p>Datasets are grouped as follows: Crystal 1 = mov1-4, Crystal 2 = mov5-8, Crystal 3 = mov9-12. An example XDS and XSCALE file are provided. Note: It has been brought to our attention that the zip file does not always unpack in a linux environment. The following workaround was found by T. Nakane using OpenJDK (17.0.1)</p> <p><code>jar -xvf</code> AVAAGA_dose_series.zip</p>
A new approach to simulate peat accumulation, degradation and stability in a global land surface scheme (JULES vn5.8_accumulate_soil) for northern and temperate peatlands
<p>This is the data (model output from JULES and observational data) used in the paper "A new approach to simulate peat accumulation, degradation and stability in a global land surface scheme (JULES vn5.8_accumulate_soil) for northern and temperate peatlands" for the resubmitted version after review of the discussion paper in Geoscientific Model Development Discussions (2021) https://doi.org/10.5194/gmd-2021-263. R code is provided that will recreate all of the plots in the paper using the data provided. These data include outputs from the JULES model including developments to represent peat accumulation, and observational data of peat properties (most are taken from other sources: references provided therein).</p>
Fitness effects of mutations: An assessment of PROVEAN predictions using mutation accumulation data
<p><span><span><span><span>Predicting fitness in natural populations is a major challenge in biology. It may be possible to leverage fast-accumulating genomic datasets to infer the fitness effects of mutant alleles, allowing evolutionary questions to be addressed in any organism. In this paper, we investigate the utility of one such tool, called PROVEAN. This program compares a query sequence with existing data to provide an alignment-based score for any protein variant, with scores categorized as neutral or deleterious based on a preset threshold. PROVEAN has been used widely in evolutionary studies, e.g., to estimate mutation load in natural populations, but has not been formally tested as a predictor of aggregate mutational effects on fitness. Using three large, published datasets on the genome sequences of laboratory mutation accumulation lines, we assessed how well PROVEAN predicted the actual fitness patterns observed, relative to other metrics. In most cases, we find that a simple count of the total number of mutant proteins is a better predictor of fitness than the number of variants scored as deleterious by PROVEAN. We also find that the sum of all mutant protein scores explains variation in fitness better than the number of mutant proteins in one of the datasets. We discuss the implications of these results for studies of populations in the wild.</span></span></span></span></p>
Artifact for "Accumulation Analysis"
<p>The artifact for the paper "Accumulation Analysis", published at ECOOP 2022. It contains the data for our literature survey of papers that use typestate specifications, as well as supporting evidence for miscellaneous claims. See the file `README.md` for details.</p>
Ocean-atmosphere changes in the midlatitude North Pacific over the last 330 ka: Dust, biogenic sediment and authigenic uranium accumulation at Shatsky Rise — Dataset
<p><strong>Title</strong>: Ocean-atmosphere changes in the midlatitude North Pacific over the last 330 ka: Dust, biogenic sediment and authigenic uranium accumulation at Shatsky Rise — Dataset</p> <p><strong>Version</strong>: 1.0</p> <p><strong>Date of Release</strong>: July 03, 2022</p> <p><strong>Last Update</strong>: July 03, 2022</p> <p><strong>Identifier</strong>: 10.5281/zenodo.6791726</p> <p><strong>Permalink</strong>: <a href="https://doi.org/10.5281/zenodo.6791725">https://doi.org/10.5281/zenodo.6791725</a></p> <p><strong>Associated publication</strong>: </p> <p><strong>Link to publication preprint</strong>: </p> <p><strong>Suggested citation</strong>: Please reference the associated publication above when using any datasets or materials in this repository.</p> <p><strong>Contact information</strong>: Christopher W. Kinsley, ckinsley@mit.edu OR cwkinsley@gmail.com</p> <p><strong>Dates of data collection and generation</strong>: </p> <p>---------------</p> <p><strong>DESCRIPTION OF DATA</strong></p> <p>This data repository contains the following dataset. We refer the user to the original manuscript (see above) and the text of the Supporting Information published alongside this manuscript for additional general information regarding the collection and generation of these data.</p> <p>DATA TABLES FOR ALL CORE SITES</p> <ul> <li> <p><strong>Kinsley et al. (2022) P&P - Data Tables for ODP 198-1208A</strong><strong> core - v1</strong>: This Excel workbook contains all data used in the study for the ODP 198-1208A core site, taken by the R/V JOIDES Resolution close to the center of the Central High of Shatsky Rise in the western North Pacific Ocean during Ocean Drilling Program Leg 198. This includes the age control and age model, biogenic %s, U-Th isotopic measurements, and <sup>230</sup>Th-normalized flux data. All previously published data is noted as such and referenced.</p> </li> </ul>
Evidence accumulation occurs locally in the parietal cortex
<p>We uploaded electrophysiological data collected from the lateral intraparietal area (LIP) of two macaque monkeys when they performed a probabilistic reasoning task. The relevant paper (Evidence accumulation occurs locally in the parietal cortex, <a href="https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1038%2Fs41467-022-32210-6&data=05%7C01%7C%7Cd48eee4c9d4f47238f7a08da720be1af%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637947692608533539%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=IfRirBDis37vOCpejmH8jTORoybd%2BV7%2Fcz2ieFmD%2Bhc%3D&reserved=0">https://doi.org/10.1038/s41467-022-32210-6</a>) is published in Nature Communications. </p> <p>The description of the data and codes for reproducing results in the paper can be found at https://github.com/zwzhangi36/sensory-evidence_transformation_in_LIP .</p>
A computational method for predicting the most likely evolutionary trajectories in the stepwise accumulation of resistance mutations
<p>Supporting information dataset for <em>A computational method for predicting the most likely evolutionary trajectories in the stepwise accumulation of resistance mutations, </em>including Flex ddG binding free energy predictions, epistasis calculations, pathway probabilities, Rosetta files and structural files. </p>
Accumulation of gene copy number variations during the early phase of free-spawning abalone speciation
<p><span>The g</span><span>enetic basis of speciation in free-spawning marine invertebrates is poorly understood. Although gene copy number variations (GCNVs) as well as nucleotide variations possibly trigger the speciation of these organisms, empirical evidence for such </span><span>a hypothesis</span><span> is limited. In this study, we searched for genomic signatures of GCNVs that may contribute to the speciation of Western Pacific abalone species. Whole-genome sequencing data suggested the existence of significant amounts of GCNVs in closely related abalones, <em>Haliotis discus</em> and <em>H. madaka</em>, in the early phase of speciation. In addition, the degree of interspecies genetic differentiation in the genes where GCNVs were estimated was higher than </span><span>that </span><span>in other genes, suggesting that nucleotide divergence also accumulate</span><span>s in the genes with GCNVs.</span><span> GCNVs in some genes were also detected in other related abalone species, suggesting that these GCNVs are derived from both ancestral and <em>de novo</em> mutations.</span> <span>Our findings </span><span>suggest that GCNVs have been accumulated in </span><span>the early phase</span><span> of free-spawning abalone speciation.</span></p>
Contrasting Responses of Particulate and Mineral-Associated Organic Carbon to Afforestation Potentially Obscure Soil Carbon Accumulation [Dataset]
<p><span>This is the data repository for the manuscript “Contrasting Responses of Particulate and Mineral-Associated Organic Carbon to Afforestation Potentially Obscure Soil Carbon Accumulation” submitted to <em>Global Biogeochemical Cycles</em>.</span></p>
Heat Stress and Microbial Stress Induced Defensive Phenol Accumulation in Medicinal Plant Sparganium stoloniferum
Open the record for dataset details and reuse information.
Data supporting "Seasonal dynamics and punctuated carbon sink reduction suggest photosynthetic capacity of boreal silver birch is reduced by the accumulation of hexose"
<p>Data supporting our New Phytologist publication: "Seasonal dynamics and punctuated carbon sink reduction suggest photosynthetic capacity of boreal silver birch is reduced by the accumulation of hexose". The file present the data produced during long-term (three consecutive years 2019-2021) field observations and short-term girdling manipulation of top-crown shoots in three mature <em>Betula pendula</em> trees as details of our manuscript. Values of leaf gas-exchange, environmental variables, leaf water and nitrogen status, and concentrations of sucrose, hexoses (glucose and fructose), starch, total sugar, and total non-structural carbohydrate in leaves are listed. </p>
Data from: Caenorhabditis elegans germ granules accumulate hundreds of low translation mRNAs with no systematic preference for germ cell fate regulators
<p>In animals with germ plasm, embryonic germline precursors inherit germ granules, condensates proposed to regulate mRNAs coding for germ cell fate determinants. In <em>C. elegans</em>, mRNAs are recruited to germ granules by MEG-3, a sequence non-specific RNA-binding protein that forms stabilizing interfacial clusters on germ granules. Using fluorescent <em>in situ </em>hybridization, we confirmed that 441 MEG-3-bound transcripts distribute in a pattern consistent with enrichment in germ granules. 13 are related to transcripts reported in germ granules in <em>Drosophila</em> or <em>Nasonia</em>. The majority, however, are low-translation maternal transcripts required for embryogenesis that are not maintained preferentially in the nascent germline. Granule enrichment raises the concentration of certain transcripts in germ plasm but is not essential to regulate mRNA translation or stability. Our findings suggest that only a minority of germ granule-associated transcripts contribute to germ cell fate in <em>C. elegans</em> and that the vast majority function as non-specific scaffolds for MEG-3.</p>
Fig. 4 in Species Accumulation Curves And Similarity Traits Of A Species-Rich Fly (Diptera) Community
Fig. 4. Jackknifed NESS indices relating to the first and kth group of 50, k = 1,2,…, 20
Fig. 3 in Species Accumulation Curves And Similarity Traits Of A Species-Rich Fly (Diptera) Community
Fig. 3. Quasi individual-based species accumulation curves after normalisation
Fig. 1 in Species Accumulation Curves And Similarity Traits Of A Species-Rich Fly (Diptera) Community
Fig. 1. Sample-based species accumulation curves without normalisation
Data used in manuscript "High-resolution geophysical monitoring of moisture accumulation preceding slope movement – a path to improved early warning"
<p>Data used in the study titled "High-resolution geophysical monitoring of moisture accumulation preceding slope movement – a path to improved early warning" published in Environmental Research Letters</p>
Effects of the Invasive Freshwater Mussel Limnoperna fortunei on Sediment Properties and Accumulation Rates
<p>Environmental data and results of an experiment conducted in the vicinity of the Río de la Plata Estuary (Argentina), aimed at assessing the influence of the invasive mussel <em>Limnoperna fortunei</em> on sediment properties and accumulation rates. In the experiment, eighteen 20 L flow-through experimental units with and without mussels were used monitoring where changes in the mass and characteristics of the sediments accumulated throughout a yearly cycle in monthly, biannual and annual intervals.</p>
In situ clamped beam bending of accumulative roll bonded Cu/Nb with 16 nm individual layer thickness
<p>In situ scanning electron microscope (SEM) videos of clamped beam bending of Cu/Nb ARB nanolaminates with 16 nm layer thickness. Each video contains the video captured with SEM and the corresponding measured load vs. displacement curve.</p> <p>The beams were fabricated using focused ion beam (FIB) milling from bulk Cu/Nb sample produced in Los Alamos National Lab, USA. The sample was made using accumulative roll bonding (ARB) process, described in ref. [1]. </p> <p>All the beam lengths are aligned with rolling direction (RD) of the sample. Each beam has a rectangular notch located in the center of the beam length. Each notch spans through the beam width. Owing to limited accuracy of FIB, the notch depth was not always same at the front and rear sides of the beam (typically, smaller at the rear sides)</p> <p>Beam geometries:</p> <p>Id | Length, µm | Width, µm | Thickness, µm | Notch depth (front), nm | Notch width (front), nm</p> <p>ARBRD1 | 40 | 4.9 | 4.2 | 800 | 180</p> <p>ARBRD2 | 40 | 5.1 | 2.4 | 350 | 160</p> <p>All the beams were loaded using Hysitron PI85 picoindenter with truncated cone shape (5 µm diameter). The indenter tip was aligned with the notch location and the middle of beam width. </p> <p>All the beams were loaded under displacement control with displacement rates between 2nm/s to 10nm/s until failure.</p> <p>The SEM videos were captured using JEOL JSM-7600F SEM. </p> <p>[1] Irene J Beyerlein et al. “Interface-driven microstructure development and ultra high strength of bulk nanostructured Cu-Nb multilayers fabricated by severe plastic deformation”. In: Journal of materials research 28.13 (2013), pp. 1799–1812</p>
Accumulated tidal heating of stars over multiple pericentre passages near SgrA*
<p>MESA inlist and run_star_extras associated with <a href="https://ui.adsabs.harvard.edu/?#abs/2013MNRAS.429.3040L">Li & Loeb (2013)</a>. MESA version 4298.</p> <p>Publication DOI: <a href="https://doi.org/10.1093/mnras/sts567">10.1093/mnras/sts567</a></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.
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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.
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.