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1,773 results for “Supplementary data,”
MAgNET: A Graph U-Net Architecture for Mesh-Based Simulations [Supplementary data]
<p>Supplementary data for '<a href="https://arxiv.org/abs/2211.00713">MAgNET: A Graph U-Net Architecture for Mesh-Based Simulations</a>'. </p>
Supplementary data and code to "An assessment of quaternary structure functionality in homomer protein complexes" by G. Abrusan and C. Foguet, https://doi.org/10.1093/molbev/msad070
<p>Scripts and high-level data to reproduce the figures and supplementary figures of "An assessment of quaternary structure functionality in homomer protein complexes" by G. Abrusan and C. Foguet, https://doi.org/10.1093/molbev/msad070</p>
Supplementary data PhD of Lisa Joos
<p>Here you can find the following supplementary material of my Phd:</p> <p>- Chapter 2 - Table S2.1</p> <p>- Supplementary excel of Chapter 2</p> <p>- Supplementary excel of Chapter 5</p>
Supplementary Data for the publication "High economic costs of reduced carbon sinks and declining biome stability in Central American forests"
<p>Supplementary data from the DGVM simulations underlying the main figures presented in the publication.</p> <p>Naming convention: {variable}_{aggregation period}-{comparison period [only relevant for bsprob]}_{climate model}-{climate scenario}.tif</p> <p>Variables are:</p> <ul> <li>bsprob-Snell2013ed = biome shift probability (biomization adjusted from Snell et al. 2013) [%]</li> <li>nee = net ecosystem exchange [kgC/m2/year]</li> </ul> <p>Global climate models include GFDL = GFDL-ESM4 and IPSL= IPSL-CM6A-LR. Climate scenarios refer to the shared socioeconomic pathways (SSP) SSP126= SSP1-2.6 and SSP370= SSP3-7.0.</p>
Supplementary data to publication "Abomasal infusion of essential fatty acids and conjugated linoleic acid during late pregnancy and early lactation affects immunohematological and oxidative stress markers in dairy cows"
<p>Supplementary data to publication "Abomasal infusion of essential fatty acids and conjugated linoleic acid during late pregnancy and early lactation affects immunohematological and oxidative stress markers in dairy cows" in Journal of Dairy Science; DOI: <a href="https://doi.org/10.3168/jds.2022-22514">https://doi.org/10.3168/jds.2022-22514</a></p>
Supplementary data for: Tackling hysteresis in conformational sampling --- how to be forgetful with MEMENTO
<p>This is the supplementary data for our publication entitled: "Tackling hysteresis in conformational sampling --- how to be forgetful with MEMENTO". This version corresponds to the first revision of our paper in response to reviewer feedback.</p> <p>Abstract:</p> <p><<<</p> <p>The structure of proteins has long been recognised to hold the key to understanding and engineering their function, and rapid advances in structural biology and protein structure prediction are now supplying researchers with an ever-increasing wealth of structural information. Most of the time, however, structures can only be determined in free energy minima, one at a time. While conformational flexibility may thus be inferred from static end-state structures, their interconversion mechanisms --- a central ambition of structural biology --- are often beyond the scope of direct experimentation. Given the dynamical nature of the processes in question, many studies have attempted to explore conformational transitions using molecular dynamics (MD). However, ensuring proper convergence and reversibility in the predicted transitions is extremely challenging. In particular, a commonly used technique to map out a path from a starting to a target conformation called steered MD (SMD) can suffer from starting-state dependence (hysteresis) when combined with techniques such as umbrella sampling (US) to compute the free energy profile of a transition. \\</p> <p> </p> <p>Here, we study this problem in detail on conformational changes of increasing complexity. We also present a new, history-independent approach that we term “MEMENTO” (Morphing End states by Modelling Ensembles with iNdependent TOpologies) to generate paths that alleviate hysteresis in the construction of conformational free energy profiles. MEMENTO utilises template-based structure modelling to restore physically reasonable protein conformations based on coordinate interpolation (morphing) as an ensemble of plausible intermediates, from which a smooth path is picked. We compare SMD and MEMENTO on well-characterized test cases (the toy peptide deca-alanine and the enzyme adenylate kinase) before discussing its use in more complicated systems (the kinase P38α and the bacterial leucine transporter LeuT). Our work shows that for all but the simplest systems SMD paths should not in general be used to seed umbrella sampling or related techniques, unless the paths are validated by consistent results from biased runs in opposite directions. MEMENTO, on the other hand performs well as a flexible tool to generate intermediate structures for umbrella sampling. We also demonstrate that extended end-state sampling combined with MEMENTO can aid the discovery of collective variables on a case-by-case basis.</p> <p>>>></p> <p>There are 4 folders in this dataset for the 4 simulation systems studied in the paper. Deca-alanine, ADK, P38a and LEUT. Each folder contains key coordinate files used to initialise MEMENTO and SMD runs, and data produced in the course of simulations (as labelled in the folders). In the simulation folders, 'raw_data' corresponds to the outputs produced by PLUMED during REUS or SMD, 'convergence' contains WHAM outputs taken at a certain percentage of the data included, and 'pointsfile' are the metadata files required by the Grossfield WHAM implementation.</p>
Supplementary data S1 associated with the manuscript "Limited climatic space for alternative ecosystem states in Africa"
<p>Site locations and meta-data used in this study. The original sources of the data and how they were filtered for this study are described in the methods section of the manuscript.</p>
Supplementary data for "WebQUAST: online evaluation of genome assemblies"
<p>Supplementary data for A. Mikheenko, V. Saveliev, P. Hirsch, A. Gurevich. WebQUAST: online evaluation of genome assemblies.</p> <p><br> Reference genomes of two <em>Escherichia coli</em> K-12 substrains (MG1655 and W3110) and genome annotation of MG1655.</p> <p><em>De novo</em> assemblies of the <em>Escherichia coli</em> K-12 MG1655 short-read Illumina dataset (<a href="https://trace.ncbi.nlm.nih.gov/Traces/index.html?view=run_browser&acc=ERR008613&display=metadata">ERR008613</a>) with ABySS, MEGAHIT, SPAdes, and Velvet.</p> <p>WebQUAST reports in three evaluation modes: <br> * Use Case 1: reference-free evaluation (<em>sample_data_no_ref</em>)<br> * Use Case 2: reference-based evaluation (<em>sample_data_true_ref</em>) <br> * Use Case 3: evaluation based on a close reference (<em>sample_data_close_ref</em>)</p> <p>The snapshot (<a href="https://github.com/ablab/quast/commit/2bd50600bcf63ee826965c10f6ca4cdc2aa046e5">commit 2bd5060</a>) of the QUAST command-line version used by WebQUAST for generating the reports.</p>
Supplementary data for: Selection on visual opsin genes in diurnal Neotropical frogs and loss of the SWS2 opsin in poison frogs
<p><span></span></p> <p><span></span></p> <p>Amphibians are ideal for studying visual system evolution because their biphasic (aquatic and terrestrial) life history and ecological diversity expose them to a broad range of visual conditions. Here we evaluate signatures of selection on visual opsin genes across Neotropical anurans and focus on three diurnal clades that are well-known for the concurrence of conspicuous colors and chemical defense (i.e., aposematism): poison frogs (Dendrobatidae), Harlequin toads (Bufonidae: <em>Atelopus</em>), and pumpkin toadlets (Brachycephalidae: <em>Brachycephalus</em>). We found evidence of positive selection on 44 amino acid sites in LWS, SWS1, SWS2, and RH1 opsin genes, of which one in LWS and two in RH1 have been previously identified as spectral tuning sites in other vertebrates. Given that anurans have mostly nocturnal habits, the patterns of selection revealed new sites that might be important in spectral tuning for frogs, potentially for adaptation to diurnal habits and for color-based intraspecific communication. Furthermore, we provide evidence that SWS2, normally expressed in rod cells in frogs and some salamanders, has likely been lost in the ancestor of Dendrobatidae, suggesting that under low-light levels, dendrobatids have inferior wavelength discrimination compared to other frogs. This loss might follow the origin of diurnal activity in dendrobatids and could have implications for their chemical ecology, biodiversity, and behavior. Our analyses show that assessments of opsin diversification in understudied groups could expand our understanding of the role of sensory system evolution in ecological adaptation.</p>
Supplementary code and data for the paper: 'The fall of genres that did not happen: formalising history of the "universal" semantics of Russian iambic tetrameter'
<p>The dataset provides preprocessed data and the full code used in the paper 'The fall of genres that did not happen: formalising history of the "universal" semantics of Russian iambic tetrameter'. The code can be also be accessed as rendered notebooks on Github.</p><p>The dataset is structured as follows:</p><ul><li><i>data/ </i>: This folder contains preprocessed data,including a sampled corpus of periodicals and a document-term matrix used for topic modelling; </li><li><i>scr/</i> : The code used for the analysis, with separate scripts for figures; </li><li><i>plots/</i> : The figures used in the paper, which correspond to the aforementioned code.</li></ul>
Supplementary data for: Chromosome-level genome assembly and circadian gene repertoire of the Patagonia blennie Eleginops maclovinus
<p>This dataset contains the genome assembly and associated annotation of the Patagonian Blennie (<em>Eleginops maclovinus</em>), the closest extant taxon to the Antarctic notothenioid radiation. In addition to the characterization of the <em>E. maclovinus </em>genome, the dataset includes a description of circadian rhythm orthologs for <em>E. maclovinus</em>, other notothenenioid taxa, and teleost outgroups, as well as a copy of the bioinformatic scripts used for the assembly, annotation, and other downstream analysis.</p>
Supplementary data for a systematic literature review on source code similarity measurement and clone detection: techniques, applications, and challenges
<p>The Microsoft Excel files containing the supplementary data and diagrams for the paper:</p> <p><strong>A systematic literature review on source code similarity measurement and clone detection: techniques, applications, and challenges</strong></p> <p>The article is under review in the Journal of Systems and Software.</p> <p>In this version, the literature search has been performed between April and May 2023, and studies published until that date has been mentioned in the attached Excel files.</p> <p>This version (v3.4.0) corresponds to the third revision (R3) of the manuscript.</p> <p> </p>
Supplementary data and videos for "'Freezing' in Pachyoliva semistriata (Caenogastropoda: Olividae) is induced olfactorily by its main predator and differs from unspecific avoidance behaviour"
<p> </p><p>The eight supplementary video and data files available below accompany my article, "'Freezing' in <i>Pachyoliva semistriata</i> (Caenogastropoda: Olividae) is induced olfactorily by its main predator and differs from unspecific avoidance behaviour", published in <i>Archiv für Molluskenkunde</i> <strong>152:</strong> 25-33 (2023), https://doi.org/10.1127/arch.moll/152/025-033.</p><p> </p><p><strong>Supplementary Data 1.</strong> Numerical data used in creating Figure 3.</p><p><strong>Supplementary Video 1.</strong> Two examples of <i>P. semistriata</i> freezing upon encountering tracks of <i>Agaronia propatula</i>.</p><p><strong>Supplementary Video 2.</strong> Three examples of <i>P. semistriata</i> showing no response to stimulation.</p><p><strong>Supplementary Video 3.</strong> Three examples of <i>P. semistriata</i> showing irritation responses.</p><p><strong>Supplementary Video 4.</strong> Three examples of <i>P. semistriata</i> turning when stimulated.</p><p><strong>Supplementary Video 5.</strong> Three examples of <i>P. semistriata</i> burrowing when stimulated.</p><p><strong>Supplementary Video 6.</strong> Three examples of <i>P. semistriata</i> showing the freeze response.</p><p><strong>Supplementary Video 7.</strong> Three examples of <i>P. semistriata</i> showing active flight responses.</p>
Supplementary data for Long-term trends in functional diversity of exploited marine fish in the Azores archipelago: past and present
<p>Supplementary infromation for the manuscript entitled "<strong>Long-term trends in functional diversity of exploited marine fish in the Azores’ archipelago: past and present</strong>"</p>
Supplementary data for "Evolution of magmas during late-stage rhyolitic magmatism in the Altiplano-Puna Volcanic Complex as inferred by melt inclusion geochemistry at Cerro La Torta lava dome"
<p>This repository contains the supplementary data for the publication submitted to the Journal of Volcanology and Geothermal Research entitled "Evolution of magmas during late-stage rhyolitic magmatism in the Altiplano-Puna Volcanic Complex as inferred by melt inclusion geochemistry at Cerro La Torta lava dome".</p> <p>The excel file contains the complete dataset with major, minor and trace elements composition from melt inclusions, their host minerals (plagioclase and amphibole), accessory minerals (Fe-Ti oxides, apatites, pyroxene and zircon) and groundmass glass from Cerro La Torta lava dome.</p> <p>Instructions about how to read the dataset are included in the first sheet of the Excel file.</p>
Supplementary data for wave current scour prediction
<p>This CSV file has data obtained, which is obtained from various works of literature containing Normalized scour depth around monopile foundations due to waves and currents.</p>
Analysis of gaps in rapeseed (Brassica napus L.) collections in European genebanks - supplementary data
<p>Species distribution modelling (or ecological niche modelling) was used to predict the effects of climate change on the future distribution of the wild relatives of Brassica napus L. in Europe and countries bordering the Mediterranean Sea. Modelling procedures followed the methods described by Aguirre-Gutierrez et al. 2017 (10.1111/ddi.12573) and van Treuren et al. 2017+2020 (10.1016/j.biocon.2017.10.003; 10.1016/j.gecco.2020.e01054).</p>
Data and supplementary materials in support of "Development and Preliminary Validation of an Open Access, Open Data and Open Outreach Indicator"
<p>Data and supplementary materials in support of "Evgenios Vlachos, Regine Ejstrup, Thea Marie Drachen, Bertil Fabricius Dorch (2023) Development and Preliminary Validation of an Open Access, Open Data and Open Outreach Indicator, Frontiers in Research Metrics and Analytics, doi: 10.3389/frma.2023.1218213" </p> <p>It includes the anonymized dataset with the OADO values for all researchers from 10 departments (2 per faculty), the R code to perform the analysis and the graphs, the Scopus search string for the background search on Open Access and metrics, and the documentation for pulling data out from Pure.</p>
Supplementary data and scripts for "New insights into the relationship between mass eruption rate and volcanic column height based on the IVESPA dataset"
<p>Supplementary tables and MATLAB scripts associated with the manuscript "New insights into the relationship between mass eruption rate and volcanic column height based on the IVESPA dataset".</p>
Supplementary data for: DNA sequences are as useful as protein sequences for inferring deep phylogenies
<p>Inference of deep phylogenies has almost exclusively used protein rather than DNA sequences, based on the perception that protein sequences are less prone to homoplasy and saturation or to issues of compositional heterogeneity than DNA sequences. Here we analyze a model of codon evolution under an idealized genetic code and demonstrate that those perceptions may be misconceptions. We conduct a simulation study to assess the utility of protein versus DNA sequences for inferring deep phylogenies, with protein-coding data generated under models of heterogeneous substitution processes across sites in the sequence and among lineages on the tree, and then analyzed using nucleotide, amino acid, and codon models. Analysis of DNA sequences under nucleotide-substitution models (possibly with the third codon positions excluded) recovered the correct tree at least as often as analysis of the corresponding protein sequences under modern amino acid models. We also applied the different data-analysis strategies to an empirical dataset to infer the metazoan phylogeny. Our results from both simulated and real data suggest that DNA sequences may be as useful as proteins for inferring deep phylogenies and should not be excluded from such analyses. Analysis of DNA data under nucleotide models has a major computational advantage over protein-data analysis, potentially making it feasible to use advanced models that account for among-site and among-lineage heterogeneity in the nucleotide-substitution process in inference of deep phylogenies.</p>
ScienceDex guides
Understand access before you commit
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.