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357 results for “supplementary information”
Supplementary information: How robust is the ligand binding transition state?
<p>We have used the REVO weighted ensemble approach followed by Markov state models to identify the ligand unbinding transition states for five ligands unbinding from the enzyme soluble epoxide hydrolase (sEH). This repo provides the <em><strong>counts matrices, properties and state (cluster) labels</strong></em> of the markov state models. The counts matrices can be converted to conformation space networks using CSNAnalysis software (<a href="https://github.com/ADicksonLab/CSNAnalysis">https://github.com/ADicksonLab/CSNAnalysis</a>). The <em><strong>networks</strong></em> are also provided in the gexf formatted files to be visualized in gephi (<a href="https://github.com/gephi/gephi">https://github.com/gephi/gephi</a>).</p>
Table S3. List of Locustella sound recordings included in bioacoustic analysis surrounding description of the Taliabu Grasshopper-Warbler. The table provides information on sound library sources and sampling localities of recordings as well as raw data on all 11 bioacoustic parameters measured (see Supplementary Materials section SM3 for more details on parameters). Recordings whose source is labeled as "private recording" were obtained by colleagues and are available upon demand from the corresponding author.
<p>supplement to Rheindt, Frank E., Prawiradilaga, Dewi M., Ashari, Hidayat, Suparno, Gwee, Chyi Yin, Lee, Geraldine W. X., Wu, Meng Yue, Ng, Nathaniel S. R. (2020): A lost world in Wallacea: Description of a montane archipelagic avifauna. Science 367: 167-170, DOI: 10.1126/science.aax2146</p>
Figure 9 in Descriptions of Pelodera scrofulata sp. nov. and Pelodera aligarhensis sp. nov. (Nematoda: Rhabditidae) with supplementary information on Pelodera teres (Schneider, 1866).
Figure 9. Pelodera teres (Schneider, 1866). (A–E) Anterior end (A and B, scanning electron micrographs); (F) anterior pharyngeal region (lateral); (G) posterior pharyngeal region (lateral); (H) posterior intestinal region; (I) anterior genital branch; (J, K) uterine region with embryonating eggs; (L) vulval region (lateral); (M) vulval region (Ventral); (N) female posterior region (lateral); (O–Q) male posterior region (lateral) (Q is scanning electron micrograph); (R) male posterior region (ventral) (R is scanning electron micrograph). Scale bars: 10 μm.
Figure 7 in Descriptions of Pelodera scrofulata sp. nov. and Pelodera aligarhensis sp. nov. (Nematoda: Rhabditidae) with supplementary information on Pelodera teres (Schneider, 1866).
Figure 7. Pelodera aligarhensis sp. nov. male. (A–C) Anterior end (A is scanning electron micrograph); (D) anterior pharyngeal region (lateral); (E) posterior pharyngeal region (lateral); (F) male genital tract at level of ejaculatory gland (ventral); (G) posterior region (lateral); (H–J) tail end showing bursa and genital papillae (lateral) (J is scanning electron micrograph); (K–N) Tail end showing bursa and genital papillae (ventral) (K is scanning electron micrograph). Scale bars: 10 μm.
Figure 8 in Descriptions of Pelodera scrofulata sp. nov. and Pelodera aligarhensis sp. nov. (Nematoda: Rhabditidae) with supplementary information on Pelodera teres (Schneider, 1866).
Figure 8. Cluster analysis (complete linkage) showing relationship between species of Pelodera (coarctata-group) based on morphological data.
Figure 4 in Descriptions of Pelodera scrofulata sp. nov. and Pelodera aligarhensis sp. nov. (Nematoda: Rhabditidae) with supplementary information on Pelodera teres (Schneider, 1866).
Figure 4. Cluster analysis (complete linkage) showing relationship between species of Pelodera (strongyloides-group) based on morphological data.
Figure 1 in Descriptions of Pelodera scrofulata sp. nov. and Pelodera aligarhensis sp. nov. (Nematoda: Rhabditidae) with supplementary information on Pelodera teres (Schneider, 1866).
Figure 1. Pelodera scrofulata sp. nov. (all lateral) (A) Entire female; (B) entire male; (C) female anterior end; (D) female pharyngeal region; (E) female reproductive system; (F) female tail region; (G) male tail region.
Mehrabi et al. 2020. The global divide in data-driven farming. Supplementary Information.
<p>This repository contains data, data sources, and code for reproducing the results of the paper Mehrabi et al. 2020. The global divide in data-driven farming. Nature Sustainability. https://doi.org/10.1038/s41893-020-00631-0.</p> <p>There are five directories included here, listed in alphabetical order. Directory SI_A contains the script for reproducing the analysis presented in the main text of the paper. Directories SI_B to SI_E contain the scripts for creating the input data sets used in the analysis.</p> <p>This is a baseline study, that is intended to be built upon and improved as and when new data become available. For issues and suggestions, please contact zia.mehrabi@ubc.ca.</p>
Supplementary Information for "The Peculiar Case of the Hyperthermostable Pyrimidine Nucleoside Phosphorylase from Thermus thermophilus"
<p>This is the external Supplementary Information for our publication "The Peculiar Case of the Hyperthermostable Pyrimidine Nucleoside Phosphorylase from <em>Thermus thermophilus</em>".</p> <p>The .pdf file contains the Supplementary Information: author contributions, experimental procedures and supplementary items.</p> <p>The .zip file contains the raw data and metadata for all items (supplementary and main text) and the calculations.</p> <p>The Python code used for spectral unmixing is available on this platform (10.5281/zenodo.3243376) and has been described in our previous publications (10.3390/mps2030060, 10.5281/zenodo.3333469, 10.1002/cbic.202000204, 10.5281/zenodo.3723806 ). Further applications of this method can be found in our recent article in <em>Adv. Synth. Catal.</em> (10.1002/adsc.201901230) and its supporting material (10.5281/zenodo.3568858).</p>
Supplementary materials for "Relative Information Gain: Shannon entropy-based measure of the relative structural conservation in RNA alignments"
<p>Supplementary materials for "Relative Information Gain: Shannon entropy-based measure of the relative structural conservation in RNA alignments". These include precalculated RNA Blocks, MBRs (Matrix of Bear encoded RNA), sPSSMs (structural Position Specific Scoring Matrix), RIG (Relative Information Gain) scores, and plots calculated for 3016 Rfam 14.1 families. In particular:</p> <ul> <li><strong>alignments.zip:</strong> zipped file containing the structural alignments for each Rfam family.</li> <li><strong>RNA_Blocks.zip</strong>: zipped file containing the RNA blocks used to derive different substitution matrices.</li> <li><strong>MBRs.zip</strong>: zipped file containing the substitution matrices.</li> <li><strong>sPSSMs.zip</strong>: zipped file containing the structural Position Specific Scoring Matrices.</li> <li><strong>RIGs.zip</strong>: zipped file containing the RIG scores.</li> <li><strong>entropy.zip</strong>: zipped file containing the (rescaled) entropy.</li> <li><strong>plots.zip</strong>: zipped file containing the plots. </li> </ul> <p>All the scripts to build all these files are available at <a href="https://github.com/helmercitterich-lab/RIG">https://github.com/helmercitterich-lab/RIG</a>.</p>
Supplementary data: What millimeter-wavelength radar reflectivity reveals about snowfall: An information-centric analysis
<p>This dataset includes supplementary data used in the analyses described in Wood, N. B., and T. S. L'Ecuyer, 2020: What millimeter-wavelength radar reflectivity reveals about snowfall: An information-centric analysis. Atmospheric Measurement Techniques, doi:10.5194/amt-2020-216.</p>
Supplementary Information S1 - Detailed results of the CAPRI N-LCA and S2 - Quantification of the main N budget flows in the EU25 agriculture sector of Leip, A., Billen, G., Garnier, J., Grizzetti, B., Lassaletta, L., Reis, S., Simpson, D., Sutton, M. a, de Vries, W., Weiss, F., Westhoek, H. (2015). Impacts of European livestock production: nitrogen, sulphur, phosphorus and greenhouse gas emissions, land-use, water eutrophication and biodiversity. Environ. Res. Lett. 10, 115004. doi:10.1088/1748-9326/10/11/115004
<p>Table S1-1 Quantification of GHG and Nr flow intensities [kg CO2eq (kg product)<sup>-1</sup> yr<sup>-1</sup>] or [g N (kg product)<sup>-1</sup> yr<sup>-1</sup>] with the CAPRI N-LCA model for six main livestock products (BEEF: beef, PORK: pork, EGGS: eggs, POUM: poultry meat; DAIR: milk and dairy products, SGMP: meat from sheep and goats) and six main vegetable food groups (POTA: potatoes, SUGB: sugar beet before processing, OILP: oil seeds before processing; CERR: cereals, LEGU: leguminous crops) as well as other crops (OCRP) and aggregated livestock (ANIMP) and vegetable (CROPP) food. </p> <p>Table S2-1 Quantification of the main N budget flows in the EU25 agriculture sector</p>
Supplementary material 1: Global Biodiversity Information Facility: Taxa and Records from: Integrating and visualizing primary data from prospective and legacy taxonomic literature - Biodiversity Data Journal 3: e5063 (12 May 2015) https://doi.org/10.3897/BDJ.3.e5063
All records in GBIF with taxonomic ranks (kingdom, phylum, class, order, and species), basis of record (e.g., preserved specimen), and count of records, exported from GBIF on 7 December 2014.
Supplementary information for "Anharmonic origin of large thermal displacements in the metal-organic framework UiO-67"
<p>Supplementary information for DOI: 10.1021/acs.jpcc.7b04757</p> <p>POSCAR-XXX: DFT optimised structures</p> <p>Phonons-XXX.zip: Folders containing the force constants (FORCE_SETS), the resulting phonon frequencies (mesh.yaml), phonon partial density of states (partial_dos.dat), animations of all phonon modes (anime.ascii) e.g. to be visualized in VMD and gifs of selected phonon modes. </p> <p>XDATCAR-XXX: MD trajectories</p>
Supplementary information
<p>Integrative evolutionary analyses that are based upon fossil and extant species provide a unique source of evidence for understanding past diversification events and for assessing the tempo of evolution across the Tree of Life. Herein, we demonstrate the importance of integrating fossil and extant species for inferring patterns of lineage diversification that would otherwise be masked in analyses that examine only one source of evidence. </p>
Supplementary material for "Playback experiments highlight the importance of nearest-neighbor distance and social information for nest site selection in the House Martin (Delichon urbicum)"
<p><strong>Abstract</strong></p> <p>Understanding nest site selection is crucial for species conservation. Bird conservation often involves installing nesting aids to increase nest site availability and induce colonization of unoccupied sites. However, prospecting individuals must find nesting aids, which may be facilitated by social information. Here, we investigated the effectiveness of artificial nests and playback in the declining, migratory House Martin <em>Delichon urbicum</em>. We selected unoccupied sites with artificial nests along a distance gradient to occupied sites and broadcasted conspecific vocalizations during prospection times of House Martins in both the post- and the following pre-breeding periods. Visitation and colonization rates increased considerably in proximity to occupied sites. Playback during the post-breeding and pre-breeding periods enhanced visitation rates, while pre-breeding-only and post-breeding-only playback had smaller positive effects. Colonization rate increased exclusively with pre-breeding-only playback. Colonized playback and non-playback sites had similar breeding success, indicating that playback did not create ecological traps by attracting House Martins to suboptimal sites. Hence, broadcasting conspecific vocalizations informs prospecting birds of nest site availability, thereby increasing visitation, and to some degree, colonization of unoccupied House Martin sites. To boost colonization, we recommend installing artificial House Martin nests within approximately 500 meters of occupied sites and using playback of conspecific vocalizations.</p>
Supplementary information for Yamada et al. (2023): Natural history notes of the rare enigmatic ant Opamyrma hungvuong: A first glimpse of their preying behavior on centipedes (Hymenoptera: Formicidae: Leptanillinae)
<p>Supprementary figure and videos (with original unedited source videos of behavior of <i>Opamyrma hungvuong</i>) for: Aiki Yamada, An Van Dang & Katsuyuki Eguchi (2023). Natural history notes of the rare enigmatic ant <i>Opamyrma hungvuong</i>: A first glimpse of their preying behavior on centipedes (Hymenoptera: Formicidae: Leptanillinae). Asian Myrmecology 16: e016009</p>
Data, code, and supplementary information for Hyracoid locus identification
<p>Serially homologous elements pose an identification problem in fragmentary records, particularly those of vertebrate fossils. Examples include individual vertebrae in the vertebral column and teeth in a tooth row. Until an isolated element can be accurately attributed to a specific position within its series, multiple lines of ecological and evolutionary research cannot be conducted. However, varying levels of differentiability between loci, and varying patterns of differentiation across clades, make it impossible to develop a single set of diagnostic traits for any particular set of serial homologs, particularly mammalian molars. Here, we test the utility of a set of classification criteria for distinguishing molar tooth positions of hyraxes (Mammalia, Afrotheria, Hyracoidea), which have been considered indistinguishable in previous taxonomic studies. As part of the test, we evaluate the degree to which between-locus variation is conservative in this taxon, which would strengthen the predictive power of proposed traits even in cases where species identity is unknown. Suitable tests for hypotheses of conservatism in categorical traits did not exist, to our knowledge, and we, therefore, explored the behavior of previously developed metrics, Borges et al.'s δ, to assess conservatism in contrast to the phylogenetic signal produced by Brownian motion. This metric shows some promise but the nature of resulting distributions makes tests difficult to interpret, indicating a line of potential future methods improvement. We used a linear morphometric characterization of shape to validate the candidate traits. In the case of hyracoid molars, relatively simple ratios of linear measurements have strong discriminatory power despite evolutionary variation in between-locus differences. Overall, new or understudied taxa are likely to have lower molar loci differentiable by their relative length and talonid vs. trigonid width.</p>
Supplementary Information for Chemical Properties of the Southeast Asian Haze from Indonesian Peatland Fires
<p>This repository contains supplementary information (SI-1 and SI-2) related to the article entitled "Chemical Properties of the Southeast Asian Haze from Indonesian Peatland Fires" published in Global Environmental Research (GER, Volume 27, No.1, Pages 37–48, Year 2023, <a href="https://doi.org/10.57466/ger.27.1_37" target="_blank" rel="noopener">https://doi.org/10.57466/ger.27.1_37</a>). SI-1 contains the newly created dataset used in GER and SI-2 contains supplementary documents for Sections 4 and 6 as well as tables and figures referred to but not included in the main article of GER.</p>
Dispilio. Supplementary Information for Maczkowski et al., Absolute dating of the European Neolithic using the 5259 BC rapid 14C excursion
<p>Supplementary Material for the paper "Absolute dating of the European Neolithic using the 5259 BC rapid 14C excursion":</p> <p> </p> <p><strong>Supplementary Information</strong> includes OxCal code, wiggle-matching output, photographs of the Neolithic juniper wood samples analysed, photographs of the tree-ring sampling for annual radiocarbon, photographs of modern tree-ring analogues, supplementary text on the data presented in the article, as well as the tree-ring width measurements in Heidelberg format (.fh).</p> <p><strong>Supplementary Data 1-2 </strong>includes spreadsheets with all the new raw radiocarbon data presented in the article, the associated uncertainties and ring numbers.</p> <p><strong>Supplementary Data 3</strong> includes the R code and the source data used for the generation of Figures 3 and 5 in the main article text, as well as the OxCal code used for the wiggle-matching of annual 14C in OxCal as presented in Fiugre 5</p> <p>The latest version of the Supplementary Material is just an expanded version of the first, files have been renamed according to editorial guidlines, few extra figures, OxCal code, and extra information added after the review process. No changes were made to any of the data published online in the initial version of the Supplementary Material.</p> <p> </p> <p>File renaming from last version:</p> <p>Supplementary Material = Supplementary Information</p> <p>Supplementary Material S1 = Supplementary Note 1</p> <p>Supplementary Material S2 = Supplementary Figures</p> <p>Supplementary Material S3 = Supplementary Note 2</p> <p>Supplementary Table T1 = Supplementary Data 1-2</p> <p>Supplementary Material S4 = Supplementary Data 3</p> <p> </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.