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357 results for “supplementary information”
Supplementary Information: Effects of cryo-EM cooling on structural ensembles
<p>This data set contains a pdb file with the ribosome-EF-Tu complex atoms used for analysis. The trajectories (xtc files) contain the ensembles of structures before cooling and after cooling with various cooling time spans.</p> <p>model3_training.zip contains the code to train and and analyse kinetic model3 as well as the rmsf quantiles obtained from MD simulations, and the temperature drop estimates used for the model.</p>
Supplementary data and information for 'Electron-Beam-Induced Carbon Contamination in STEM-in-SEM: Quantification and Mitigation'
<p>This repository contains supplementary data and information for the journal article "Electron-beam-induced carbon contamination in STEM-in-SEM: Quantification and mitigation" (https://doi.org/10.1093/micmic/ozac003).</p> <p>It provides comprehensive documentation of the thickness evaluation procedure based on STEM images. The thickness evaluation procedure is packed into a PYTHON library that can run using the provided exemplary images. It can also be adapted and applied to other images and individual settings, as described in the documentation file PythonTDL_Documentation.pdf. K. Adrion prepared the library based on the scripts written by her and M. Hugenschmidt, which were used for evaluating contamination thicknesses in the before-mentioned publication and on a conference poster: https://doi.org/10.5445/IR/1000135526.</p>
Supplementary information, datasets and fluorescence images related to the article "The role of NSP6 in the biogenesis of the SARS-CoV-2 replication organelle"
<p>Supplementary information, datasets and fluorescence images related to the article "The role of NSP6 in the biogenesis of the SARS-CoV-2 replication organelle".<br> The PDF file entitled "Supplementary material" contains the uncropped original western blots and autoradiographs published in the article.<br> The PDF files entitled "Extended Data Fig.2,6,7,9,10 all panels" and "Figure 1,4 all panels" contain the original full-size confocal immunofluorescence images from which specific ROIs are published in the article.<br> The Excel files "Source Data Principal Figures" and "Source Data Extended Figures" contain all the original datasets used for calculation and graphical representation of data published in the article.</p>
Supplementary information for: A continuous-score occupancy modeling framework for incorporating uncertain machine learning output in autonomous biodiversity surveys
<p><span>Ecologists often study biodiversity by evaluating species occupancy and the relationship between occupancy and other covariates. Occupancy models are now widely used to account for false absences in field surveys and to reduce bias in estimates of covariate relationships. Existing occupancy models take as inputs binary detection/non-detection observations of species at each visit to each site. However, autonomous sensing devices and machine learning models are increasingly used to survey biodiversity, generating a new type of observation record (i.e., continuous-score data) that reflects the model's confidence a species is present in each autonomously sensed file, instead of binary detection/non-detection data. These data are not directly compatible with traditional binary occupancy modeling methods.</span></p> <p><span>Here, we develop a new occupancy model that models continuous scores on a visit level as a Gaussian mixture, combining a distribution of scores for files that do contain the species of interest and a distribution of scores for files that do not. The model takes as input continuous scores for each autonomously sensed and classified file, along with an optional small number of binary, manually verified detection and non-detection annotations.</span></p> <p><span>We present a simulation study that shows that over a range of empirically realistic parameters, our model outperforms traditional occupancy models that are based on binary annotation alone. We also apply this new model to an empirical case study using data generated from five machine learning classifiers applied to autonomous acoustic recordings gathered in the eastern United States.</span></p> <p><span>Because our occupancy model generalizes allowable input data beyond binary observations, it is particularly well-suited to the increasing volume of machine learning classified data in ecology and conservation.</span></p>
Data, scripts and supplementary information for analysis of the functioning of a three-species microcosm under cadmium pressure
<p>Data files of different experiments conducted with a three-species microcosm + Rscript for infering paremeters from a mechanistic EDO based model describing the functioning of the microcosm and the effect of cadmium + JAGS script of the model + supplementary information</p>
Wallacean and Melanesian islands promote higher rates of diversification within the global passerine radiation Corvides: Supplementary information
<p class="MsoNormal"><span>The complex island archipelagoes of Wallacea and Melanesia have provided empirical data behind integral theories in evolutionary biology, including allopatric speciation and island biogeography. Yet, questions regarding the relative impact of the layered biogeographic barriers, such as deep-water trenches and isolated island systems, on faunal diversification remain underexplored. One such barrier is Wallace's Line, a significant biogeographic boundary that largely separates Australian and Asian biodiversity. To assess the relative roles of biogeographic barriers—specifically isolated island systems and Wallace's Line—we investigated the tempo and mode of diversification in a diverse avian radiation, Corvides (Crows and Jays, Birds-of-paradise, Vangas, and allies). We combined a genus-level dataset of thousands of ultraconserved elements (UCEs) and a species-level, 12-gene Sanger sequence matrix to produce a well-resolved supermatrix tree that we leveraged to explore the group's historical biogeography and effects of biogeographic barriers on their macroevolutionary dynamics. The tree is well-resolved and differs substantially from what has been used extensively for past comparative analyses within this group. We confirmed that Corvides, and its major constituent clades, arose in Australia and a burst of dispersal west across Wallace's Line occurred after the uplift of Wallacea during the mid-Miocene. We found that dispersal across this biogeographic barrier were generally rare, though westward dispersals were two times more frequent than eastward dispersals. Wallacea's central position between Sundaland and Sahul no doubt acted as a bridge for island-hopping dispersal out of Australia, across Wallace's Line, to colonize the rest of Earth. In addition, we found that the complex island archipelagos east of Wallace's Line harbor the highest rates of net diversification and are a substantial source of colonists to continental systems on both sides of this biogeographic barrier. Our results support emerging evidence that island systems, particularly the geologically complex archipelagoes of the Indo-pacific, are drivers of species diversification.<br></span></p>
Electronic Supplementary Information: Impact of a suspension drop onto a hot substrate: diminution of splash and prevention of film boiling
<p>This database includes Electronic Supplementary Information for <em>Soft Matter </em>manuscript: Impact of a suspension drop onto a hot substrate: diminution of splash and prevention of film boiling. </p> <p>The supplementary videos to Fig. 4: </p> <ul> <li>supplementary_video_fig_4_a-d.mp4</li> <li>supplementary_video_fig_4_e-h.mp4</li> <li>supplementary_video_fig_4_i-l.mp4</li> </ul> <p> </p> <p>and the supplementary videos to Fig. 12 (please do not regard to the file name)</p> <ul> <li>supplementary_video_fig_11_a-d.mp4</li> <li>supplementary_video_fig_11_e-h.mp4</li> <li>supplementary_video_fig_11_i-l.mp4</li> </ul>
Supplementary Material for "Joint Inversion Based on Variation of Information - A Crustal Model of Wilkes Land, East Antarctica"
<p>Inversion_Results_Cluster.nc - contains geographical and vertical information of clusters</p> <p>Inversion_Results_RealData_Run1.nc - contains inverted susceptibilities and densities after the first inversion run with high coupling</p> <p>Inversion_Results_RealData_Run2.nc - contains inverted susceptibilities and densities after the second continuous inversion run with low coupling</p> <p>Plot.ipynb - python script for visualization</p>
Supplementary materials for ""Who makes corporates tell more about CSR?"-Research on the influencing factors of environmental information disclosure"
<p>These are supplementary materials and primary data for article“Who makes corporates tell more about CSR?”-Research on the influencing factors of environmental information disclosure.</p>
Supplementary informations of endogenous starter culture and cheese metagenomes
<p>The first description of the virome composition in Brazilian artisanal Canastra cheese and the phage-bacterial interactions in this food system. Here you can access supplemental methods and results (docx) and supplemental data (MAGs contigs, novel 987 group phage contigs, and MAGs spacers).</p>
Characterising the stone artefact raw materials at Liang Bua, Indonesia - Supplementary Information
<p>Supplementary Information, including data and R code, for the paper titled "Characterising the stone artefact raw materials at Liang Bua, Indonesia" by Sam Lin, Lloyd White, Jatmiko, I Made Agus Julianto, Matthew Tocheri and Thomas Sutikna.</p>
Supplementary information for: Monitoring cheese ripening by single-sided NMR
<p>Supplementary information for: Monitoring cheese ripening by single-sided NMR</p> <p>Raw experimental data used to create the manuscript.</p> <p>Data structure:</p> <p>Each folder contains the date of acquisition. Inside folders are CPMG, DT2, and T1T2 experiments with suffix showing the position of the acquired region in micrometers.</p> <p> </p>
Supplementary information for: Redundancy analysis, genome-wide association studies, and the pigmentation of brown trout (Salmo trutta L.)
<p><span>The association of molecular variants to phenotypic variation is a main issue in biology, often tackled with genome-wide association studies (GWAS). GWAS are challenging, with increasing, but still limited use in evolutionary biology. We used redundancy analysis (RDA) as a complimentary ordination approach to single- and multi-trait GWAS to explore the molecular basis of pigmentation variation in brown trout (<em>Salmo</em> <em>trutta</em>) belonging to wild populations impacted by hatchery fish. Based on 75,684 single nucleotide polymorphic (SNP) markers, RDA, single- and multi-trait GWAS allowed us to extract 337 independent "colour patterning loci" (CPLs) associated with trout pigmentation traits, such as the number of red and black spots on flanks. Collectively, these CPLs (<em>i</em>) mapped onto 35 out of 40 brown trout linkage groups indicating a polygenic genomic architecture of pigmentation, (<em>ii</em>) were found associated with</span><span> 218 </span><span>candidate genes, including 197 genes </span><span>formerly mentioned in the literature dealing with skin pigmentation, skin patterning, differentiation or structure notably in a close relative, the rainbow trout (<em>Onchorhynchus</em> <em>mykiss</em>)</span><span>, and (<em>iii</em>) related to functions relevant to pigmentation variation (e.g., calcium- and ion-binding, cell adhesion). Annotated CPLs include genes with well-known pigmentation effects (e.g., PMEL, SLC45A2, SOX10), but also markers associated with genes formerly found expressed in rainbow or brown trout skins. RDA was also shown useful to investigate management issues, especially the dynamics of trout pigmentation submitted to several generations of hatchery introgression.</span></p>
Supplementary information for: Macrophage- and CD4+ T cell-derived SIV differ in glycosylation, infectivity, and neutralization sensitivity
<p>The human immunodeficiency virus (HIV) envelope protein (Env) mediates viral entry into host cells and is the primary target for the humoral immune response. Env is extensively glycosylated, and these glycans shield underlying epitopes from neutralizing antibodies. The glycosylation of Env is influenced by the type of host cell in which the virus is produced. Thus, HIV is distinctly glycosylated by CD4<sup>+</sup> T cells, the major target cells, and macrophages. However, the specific differences in glycosylation between viruses produced in these cell types have not been explored at the molecular level. Moreover, it remains unclear whether the production of HIV in CD4<sup>+</sup> T cells or macrophages affects the efficiency of viral spread and resistance to neutralization. To address these questions, we employed the simian immunodeficiency virus (SIV) model. Glycan analysis implied higher relative levels of oligomannose-type <em>N</em>-glycans in SIV from CD4<sup>+</sup> T cells (T-SIV) compared to SIV from macrophages (M-SIV), and the complex-type <em>N</em>-glycans profiles seem to differ between the two viruses. Notably, M-SIV demonstrated greater infectivity than T-SIV, even when accounting for Env incorporation, suggesting that host cell-dependent factors influence infectivity. Further, M-SIV was more efficiently disseminated by HIV-binding cellular lectins. We also evaluated the influence of cell type-dependent differences on SIV's vulnerability to carbohydrate-binding agents (CBAs) and neutralizing antibodies. T-SIV demonstrated greater susceptibility to mannose-specific CBAs, possibly due to its elevated expression of oligomannose-type <em>N</em>-glycans. In contrast, M-SIV exhibited higher susceptibility to neutralizing sera in comparison to T-SIV. These findings underscore the importance of host cell-dependent attributes of SIV, such as glycosylation, in shaping both infectivity and the potential effectiveness of intervention strategies.</p>
Supplementary Material - Systematic Mapping Study - Information and Software Technology
<p>Supplementary material - Article title: "Constructing the graphical structure of expert-based Bayesian networks in the context of software engineering: A systematic mapping study" - Information and Software Technology. This file contains the detailed procedure employed in the systematic mapping.</p>
Supplementary information from: A systematic review of trace elements in the tissues of bats (Chiroptera)
<p>Bats constitute about 22% of known mammal species; they have various ecological roles and provide many ecosystem services. Bats suffer from several threats caused by anthropization, including exposure to toxic metals and metalloids. In our systematic review, we analyzed 75 papers to investigate how species, diet, and tissue type impact bioaccumulation in bat species all over the world. Most studies documented element accumulation in fur, liver, and kidney; at least 36 metals and metalloids have been measured in bat tissues, among the most studied were mercury and zinc. Comparisons with known toxicological thresholds for other mammals showed concerning values for mercury and zinc in bat hair, lead and some essential metals in liver, and iron and calcium in kidneys. Moreover, accumulation patterns in tissues differed depending on bat diet: insectivorous bats showed higher metal concentrations in fur than in liver and kidney while frugivorous species showed higher values in liver and kidney than in fur. This review points out several information gaps in the understanding of metal contamination in bats, including a lack of measured toxicity thresholds specific for bat tissues. Data on trace element bioaccumulation and its associated health effects on bats is important for conservation of bat species, many of which are threatened.</p>
Data and supplementary information from: Sequential bayesian phylogenetic inference
<p>The ideal approach to Bayesian phylogenetic inference is to estimate all parameters of interest jointly in a single hierarchical model. However, this is often not feasible in practice due to the high computational cost. Instead, phylogenetic pipelines generally consist of sequential analyses, whereby a single point estimate from a given analysis is used as input for the next analysis (e.g., a single multiple sequence alignment is used to estimate a gene tree). In this framework, uncertainty is not propagated from step to step, which can lead to inaccurate or spuriously certain results. Here, we formally develop and test the sequential approach for Bayesian phylogenetic inference, which uses importance sampling to generate observations for the next step of an analysis pipeline from the posterior produced in the previous step. The sequential approach presented here not only accounts for uncertainty between analysis steps, but also allows for greater flexibility in software choice (and hence model availability) and can be more efficient computationally than the traditional joint approach when multiple models are being tested. We show that the sequential approach is identical in practice to the joint approach only if sufficient information in the data is present (a narrow posterior distribution) and/or sufficiently many importance samples are used. Conversely, we show that the common practice of using a single point estimate can be biased, e.g., a single phylogeny estimate to transform an unrooted phylogeny into time-calibrate phylogeny. We demonstrate the theory of sequential Bayesian inference using both a toy example and an empirical case study of insect divergence times estimation using a relaxed clock model from transcriptome data. In the empirical example, we estimate three posterior distributions of branch lengths from the same data (DNA character matrix with a GTR+Gamma+I substitution model, an amino acid data matrix with empirical substitution models, and an amino acid data matrix with the PhyloBayes CAT-GTR model). Finally, we apply three different-node calibration strategies and show that both, the data source and underlying substitution process to estimate branch lengths as well as the node-calibration strategies, impact divergence time estimates. Thus, our new sequential Bayesian phylogenetic inference provides the opportunity to efficiently test different approach for divergence time estimation, including branch lengths estimation from other software.</p>
Supplementary Information for "Biocatalytic Ether Lipid Synthesis by an Archaeal Glycerolprenylase" - Computational Data
<p>This is part of the external Supplementary Information covering the molecular dynamics simulations section for our publication "Biocatalytic Ether Lipid Synthesis by an Archaeal Glycerolprenylase" by Felix Kaspar et al., freely available as a preprint from ChemRxiv ( ).</p> <p>The .zip file contains raw data, processed data and metadata for the <strong>computational results</strong>. This includes files for the MD simulations and the preparations of the structures. </p> <p>Raw data regarding the experimental results are stored in a separate zenodo entry (<a href="../doi/10.5281/zenodo.10559443">https://zenodo.org/doi/10.5281/zenodo.10559443</a>) by Felix Kaspar. This includes UV, flourescence, NMR data, as well as data results of crystallization screens and reports on MPLC runs. </p>
Supplementary information to "Rainbow in the dark. The identification of diagnostic projectile impact features on rock crystal"
<p>Images of the experimental projectiles (pre-hafting, hafted before and after shooting), Hirox (Low magnification) pictures of pre-hafting and post-shooting projectiles and selection of fractures smoked with magnesium.</p>
Supplementary information for samples and data used in Salazar et al. (2019)
<p>Supplementary information for samples and data used in Salazar et al. (2019). <em>Gene expression changes and community turnover differentially shape the global ocean metatranscriptome</em>. https://doi.org/10.1016/j.cell.2019.10.014</p>
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.