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Supplementary Data for "Tuning the Redox Activity of Metal–Organic Frameworks for Enhanced, Selective O2 Binding: Design Rules and Ambient Temperature O2 Chemisorption in a Cobalt–Triazolate Framework"
<p>Supplementary dataset to support "Tuning the Redox Activity of Metal–Organic Frameworks for Enhanced, Selective O<sub>2</sub> Binding: Design Rules and Ambient Temperature O<sub>2</sub> Chemisorption in a Cobalt–Triazolate Framework"</p>
Supplementary Data for Multiform: Multi-objective Evolution of Requirements Models Constrained by Formal Verification Results
<p>This data set provides supplementary material for the article "<em>Multiform: Multi-objective Evolution of Requirements Models Constrained by Formal Verification Results</em>" (to appear). It contains the following files:</p> <ul> <li><strong>experiment-input-models.zip</strong> which contains the SML input models for the EBEAS and production cell examples that were used to conduct the experiment</li> <li><strong>experiment-results.tar</strong> which contains the computed candidate SML models as well as H2 database files that contain measurements.</li> <li><strong>experiment-results.pdf</strong> which summarizes the conducted controlled experiment and results.</li> </ul> <p> </p> <p><strong>Input models</strong> (example for EBEAS)</p> <ul> <li><strong>ebeas.sml</strong> contains the actual SML input model to be evolved</li> <li><strong>ebeas.ecore</strong> contains the metamodel of the EBEAS example</li> <li><strong>ebeas.xmi</strong> contains the object system of the EBEAS example that is used for the SML realizability check</li> <li><strong>ebeas.runconfig</strong> contains the runtime configuration for ScenarioTools that binds the SML input model with the object system</li> <li><strong>ebeas.cspec</strong> contains the solution space model used by Multiform.</li> </ul> <p> </p> <p><strong>Measurements</strong> are stored in an <a href="http://h2database.com/html/main.html">H2 database</a> file. To open one of the database files for the EBEAS or production cell examples extract the appropriate zip file to a local folder, navigate to the folder in a terminal, and start H2 with the appropriate database file as follows:</p> <pre><code>java -jar h2-1.4.199.jar -url jdbc:h2:./Statistics</code></pre> <p>A web-based SQL client will open in your browser. H2 cann be obtained free of charge from their homepage.</p> <p> </p> <p>The <strong>database schema</strong> consists of three simple tables:</p> <p><strong>SMLCANDIDATESTATISTICS</strong> contains measurements for each evolved candidate SML model and consists of the following columns:<br> <strong>ALGORITHM </strong>- one of 'Random', 'NSGA2', 'tabu-75-intensify'<br> <strong>SEED </strong>- seed id for which the measurement was taken<br> <strong>ITERATION </strong>- iteration id during whch the measurement was taken<br> <strong>CANDIDATE </strong>- unique id of the evaludated candidate SML model<br> <strong>SYNTHESISTIME </strong>- synthesis time of the evaludated candidate SML model<br> <strong>O1_SCENARIOS </strong>- objective value for o1<br> <strong>O2_FRAGMENTSRATIO </strong>- objective value for o2<br> <strong>O3_ENVFRAGMENTSRATIO </strong>- objective value for o3<br> <strong>C1_REALIZABILITY </strong>- constraint value for c1<br> <strong>C2_REACHABILITY </strong>- constraint value for c1</p> <p><strong>SMLITERATIONSTATISTICS </strong>contains aggregated statistical data for each iteration and consists of the following columns:<br> <strong>ALGORITHM </strong>- one of 'Random', 'NSGA2', 'tabu-75-intensify'<br> <strong>SEED </strong>- seed id for which the data was aggregated<br> <strong>ITERATION </strong>- unique id of this aggregated iteration data<br> <strong>ITERATIONSUCCESSRATE </strong>- achieved success rate in this iteration<br> <strong>ACCUMULATEDSUCCESSRATE </strong>- achieved aggregated success reate until this iteration<br> <strong>ACCUMULATEDHYPERVOLUMEINDICATOR </strong>- achieved hypervolume until this iteration<br> <strong>NUMITERATIONPARETOEQUIVALENTCANDIDATES </strong>- number of pareto-equivalent candidate SML models in this iteration<br> <strong>NUMACCUMULATEDPARETOEQUIVALENTCANDIDATES </strong>- number of pareto-equivalent candidate SML models until this iteration<br> <strong>NUMITERATIONPARETODOMINANTCANDIDATES </strong>- number of pareto-dominant candidate SML models in this iteration<br> <strong>NUMACCUMULATEDPARETODOMINANTCANDIDATES </strong>- number of pareto-dominant candidate SML models until this iteration<br> <strong>ITERATIONSYNTHESISTIME </strong>- total synthesis time of this iteration<br> <strong>ACCUMULATEDSYNTHESISTIME </strong>- accumulated total synthesis time until this iteration</p> <p><strong>SMLSEEDSTATISTICS</strong> contains aggregated statistical data for each seed and consists of the following columns:<br> <strong>ALGORITHM </strong>- one of 'Random', 'NSGA2', 'tabu-75-intensify'<br> <strong>SEED </strong>- unique id of this aggregated seed data<br> <strong>SUCCESSRATE</strong>- achieved success rate in this seed<br> <strong>HYPERVOLUMEINDICATOR </strong>- achieved hypervolume in this seed<br> <strong>NUMPARETOEQUIVALENTCANDIDATES </strong>- number of pareto-equivalent candidate SML models in this seed<br> <strong>NUMPARETODOMINANTCANDIDATES </strong>- number of pareto-dominant candidate SML models in this seed<br> <strong>TOTALSYNTHESISTIME </strong>- total synthesis time of this seed</p> <p> </p> <p><strong>Please note</strong>: the database files contain data for algorithms 'tabu-50-intensify' and 'tabu-25-intensify' representing evaluation runs with different Tabu search configurations. However, these still need to be analyzed and <strong>experiment-results.pdf</strong> refers to '<strong>tabu-75-intensify</strong>' only.</p>
Supplementary data
<p>Figures supplementary: Effects of Elastic Tape on Thoracoabdominal mechanics, Dyspnea, Exercise Capacity and Activity Level in non-Obese Male Subjects with COPD<strong>.</strong></p>
Supplementary material 3 from: Petersen M, Pramann B, Toepfer R, Neumann J, Enke H, Hoffmann J, Mauer R (2020) Research Data Management - Current status and future challenges for German non-university research institutions. Research Ideas and Outcomes 6: e55141. https://doi.org/10.3897/rio.6.e55141
Praxisbericht: Entwicklung eines Maßnahmenkatalogs zur Verbesserung des Forschungsdatenmanagements am Herder-Institut für historische Ostmitteleuropaforschung
Supplementary material 1 from: Datta A, Schweiger O, Kühn I (2020) Origin of climatic data can determine the transferability of species distribution models. NeoBiota 59: 61-76. https://doi.org/10.3897/neobiota.59.36299
Variable selection using cluster analsys based on Spearman's rank corellation and UPGMA method for agglomeration
Supplementary material 2 from: Nugent CM, Adamowicz SJ (2020) Alignment-free classification of COI DNA barcode data with the Python package Alfie. Metabarcoding and Metagenomics 4: e55815. https://doi.org/10.3897/mbmg.4.55815
File S2 – Python script for custom grid search of hyperparameters for optimization of the neural network
Supplementary material 3 from: Nugent CM, Adamowicz SJ (2020) Alignment-free classification of COI DNA barcode data with the Python package Alfie. Metabarcoding and Metagenomics 4: e55815. https://doi.org/10.3897/mbmg.4.55815
File S3 – The parameters utilized in the grid search for each of the five machine learning algorithms tested in the design of the Alfie package
Supplementary material 4 from: Nugent CM, Adamowicz SJ (2020) Alignment-free classification of COI DNA barcode data with the Python package Alfie. Metabarcoding and Metagenomics 4: e55815. https://doi.org/10.3897/mbmg.4.55815
File S4 – Jupyter notebook with tutorial demonstrating how to apply the Alfie classifier in the Python programming language, and how to train custom alignment-free classifiers using the Alfie training module
Supplementary data for "Reducing the risk of rostral bending failure"
<pre>Supplementary data for "Reducing the risk of rostral bending failure" <strong>Author summary:</strong> Weevils are among the most diverse and evolutionarily successful animal lineages on Earth. Their success is driven in part by a structure called the rostrum, which gives weevil heads a characteristic "snout-like" appearance. Nut weevils in the genus <em>Curculio</em> use the rostrum to drill holes into developing fruits and nuts, into which they deposit their eggs. During oviposition this exceedingly slender structure is bent into a straightened configuration - in some species up to 90° - but does not suffer any damage during this process. Using finite element models of the rostra of three morphologically distinct species, we show that the <em>Curculio</em> rostrum is only able to withstand repeated, extreme bending because of modifications to the composite structure of the cuticle in the rostral apex. This is the first time that the laminate profile, orthotropic behavior, and functional gradation of the cuticle have been incorporated into a three-dimensional finite element model of an insect cuticular structure. Our models highlight the significance of biomechanical constraint - i.e., avoidance of catastrophic structural failure - on the evolution of insect morphology. <strong>Finite element models of <em>Curculio</em> rostra</strong>. FE model databases, job files, and output databases containing imported part geometries, meshes, and fully-specified material models of the head and rostrum for each species; full dataset available here. File names indicate species, mesh size (s02 is the finest model scale), load condition (either in mg for validation models or bending for prescribed displacement models), and which modifications have been <em>removed</em> from the layup (i.e., layer thicknesses or orientation angles - or both - are set equal to those of the head capsule). Files for a single species should all be placed into a single folder after unzipping. The abaqus plugins folder (with material definitions) and the .cae/.jnl files (.cae is used to open all the models in Abaqus CAE) should be in the same folder with the rest of the model files. The sulcatulus folder shows this organization, the models for other species had to be separated due to file size constraints. <strong>X-ray tomography data</strong>. JPEG image stack and 3D reconstruction from µ-CT scan of female <em>Curculio caryae</em>; full dataset available here.</pre>
Supplementary data for "Visual cues of predation risk outweigh acoustic cues: a field experiment in black-capped chickadees"
<p>All data required for the analyses, including R code, presented in the paper "Visual cues of predation risk outweigh acoustic cues: a field experiment in black-capped chickadees" DOI: 10.1098/rspb.2020.2002</p>
Supplementary material (individual data set): Egeler, G.-A. & Baur, P. (2020). Menüwahl in der Hochschulmensa: Fleisch oder Vegi? Ergebnisse eines 12-wöchigen Feldexperiments (NOVANIMAL Working Paper No. 5). ZHAW. https://doi.org/10.21256/zhaw-1405
<p><strong>Meal choice at two university canteens in a field experiment during 12 weeks: anonymised individual menu sales data</strong></p> <p>How do canteen visitors respond to a revised offer of meat-based and plant-based meals? Selected innovations were simultaneously implemented and tested in a trans­disciplinary field experiment in two university canteens over a 12-week period in the autumn semester 2017. Throughout this time, the meat dishes and ‘veg-meals’ (ovo-lacto-vegetarian and vegan meals) were randomly distributed among the three menu lines, the veg-meals were not marketed and advertised as such and the previous vegetarian menu line was abolished. Weeks where the usual number of meat dishes were on offer (the ‘base weeks’) alternated with weeks where the share of veg-meals was increased (the ‘intervention weeks’). </p> <p>The field experiment did not have a negative impact on the number of meals sold or the turnover compared to the two previous years. Women choose meat dishes less often than men. This connection applies in the base weeks and intervention weeks, in all age groups, among both students and among staff. Remarkably, the share of (non-labelled) vegan dishes is comparable for women and men over all age groups, independent of university affiliation (student, staff). Authentic vegan dishes were particularly welcome. Veg-meals could also be sold on the more expensive menu line. There was a better correlation between meal choice, eating habits and attitudes (health, environment, animal welfare, social aspects) than expected. </p> <p><strong>The dataset the dataset contains over <em>21'000</em> anonymised individual menu sales. The analyses and results are summarized in the working paper No. 5 <a href="https://doi.org/10.21256/zhaw-1405">https://doi.org/10.21256/zhaw-1405</a></strong></p> <p>The corresponding scripts are: </p> <p>- <a href="http://doi.org/10.5281/zenodo.4034686">10.5281/zenodo.4034686</a></p> <p>- <a href="http://doi.org/10.5281/zenodo.4034698">10.5281/zenodo.4034698</a></p> <p>- <a href="http://doi.org/10.5281/zenodo.4244258">10.5281/zenodo.4244258</a> (newer Version)</p> <p>For more information visit the <a href="http://novanimal.ch">novanimal.ch</a> website.</p>
Supplementary data for: Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression
<p>Our understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time. To address this and other phylogenetic questions, here we present new reference genome assemblies for three Old World Monkey species: <i>Colobus angolensis ssp. palliatus </i>(the black and white colobus), <i>Macaca nemestrina </i>(southern pig-tailed macaque), and <i>Mandrillus leucophaeus </i>(the drill). We combine these data with 23 additional primate genomes to estimate both the species tree and individual gene trees using thousands of loci. While our species tree is largely consistent with previous phylogenetic hypotheses, the gene trees reveal high levels of genealogical discordance associated with multiple primate radiations. We use strongly asymmetric patterns of gene tree discordance around specific branches to identify multiple instances of introgression between ancestral primate lineages. In addition, we exploit recent fossil evidence to perform fossil-calibrated molecular dating analyses across the tree. Taken together, our genome-wide data help to resolve multiple contentious sets of relationships among primates, while also providing insight into the biological processes and technical artifacts that led to the disagreements in the first place.</p>
Supplementary data from: Decoupling of morphological disparity and taxonomic diversity during the end-Permian mass extinction
<p>An increasing number of unexpectedly diverse benthic communities are being reported from microbially-precipitated carbonate facies in shallow-marine platform settings after the end-Permian mass extinction. Ostracoda, which was one of the most diverse and abundant metazoan groups during this interval, recorded their greatest diversity and abundance associated with these facies. Previous studies, however, focused mainly on their taxonomic diversity and, therefore, left room for discussion of paleoecological significance. Here, we apply a morphometric method (semi-landmarks) to investigate morphological variance through time to better understand the ecological consequences of the end-Permian mass extinction, and to examine the hypothesis that microbial mats played a key role in ostracod survival. Our results show that taxonomic diversity and morphological disparity were decoupled during the end-Permian extinction, and that morphological disparity declined rapidly at the onset of the end-Permian extinction, even though the high diversity of ostracods initially survived in some places. The decoupled changes in taxonomic diversity and morphological disparity suggest that the latter is a more robust proxy for understanding the ecological impact of the extinction event, and the low morphological disparity of ostracod faunas is a consequence of sustained environmental stress or a delayed post-Permian radiation. Furthermore, the similar morphological disparity of ostracods between microbialite and non-microbialite facies indicates that microbial mats most likely represent a taphonomic window rather than a biological refuge during the end-Permian extinction interval.</p>
Supplementary data to accompany "Abundant metabolite-matrix adducts illuminate the dark metabolome of MALDI-mass-spectrometry imaging datasets"
<p>This dataset accompanies the publication "Abundant metabolite-matrix adducts illuminate the dark metabolome of MALDI-mass-spectrometry imaging datasets". The dataset includes all files, scripts and results that are included in the associated publication.</p> <p>Spatial metabolomics using mass spectrometry imaging (MSI) is a powerful tool to map hundreds or thousands of metabolites across biological systems. One major challenge is the complexity of the data, which includes signals from experimental artifacts. Formation of adducts (<em>e.g. </em>with Na+or K+) or abundant matrix-cluster, in the case of matrix-assisted laser desorption ionization (MALDI)-MSI, strongly increase peak counts. We developed <em>mass2adduct</em>, a universally applicable tool for adduct abundance estimations in high-mass-resolution spatial metabolomics datasets. Our study illustrates that MALDI-MSI data density is remarkably driven by adduct formation and revealed a major influence of so far unrecognized metabolite-matrix adducts on total peak counts. Current data analyses neglect those matrix adducts and therefore overestimate total metabolite numbers, thereby inflating the dark metabolome size.</p> <p>mass2adduct zenodo doi (10.5281/zenodo.1405088)</p> <p>mass2adduct gihub: https://github.com/kbseah/mass2adduct</p>
Blue-Action D5.13 Supplementary data, documentation and figures
<p>This archives supplementary information for D5.13 Evaluation of the polar lows forecast system (related to Case Study 3: <a href="https://doi.org/10.5281/zenodo.4294460">https://doi.org/10.5281/zenodo.4294460</a>). The data produced are uploaded. Descriptions of methods and scripts are given in:</p> <p>To_create_Marine_Cold_Air_Outbreaks_MCAO_data_from_ERA_Interim.pdf</p> <p>Analysing_anomalies_of_a_few_weather_variables_associated_with_MCAO_event_durations.pdf</p> <p>Further analyses that are not presented in D5.13 are also provided:</p> <p>kingetal_2020_weatherpatternsassociatedwithmcaos.pdf</p> <p>king_2019jul_slidesforwp1group.pdf</p>
Supplementary data - cl. difficile
<p>Supplementary data</p> <p><strong>Table S1.</strong> Categorization of the active principles into the corresponding antimicrobial classes.</p> <p><strong>Table S2: </strong>Distribution of antimicrobial classes prescribed on farm and association to <em>C. difficile</em> positive farms<strong><em>. </em></strong>Data on associations of different antimicrobial classes are not shown because they were not significant.</p> <p><strong>Table S3: </strong>Descriptive statistics relating to the average number of treated animals for each antibiotic class. Data on associations are not shown.</p> <p><strong>Table S4. </strong>Molecular characterization of 39 <em>C. difficile</em> isolates from human.</p>
Supplementary material for: Exploring the impact of unstable terminals on branch support values in paleontological data
<p>The dataset consists of a PDF file and two plain-text TNT scripts (*.run files). The PDF includes supporting Figures for the additional analyses conducted by Flores et al. on paleontological datasets. The TNT scripts conduct two complementary sets of analyses: (a) evaluation of taxon instability relative to the incompleteness ("mc.run"), and (b) changes in branch support values after pruning unstable taxa ("avmc.run"). To properly run these files in TNT, the name of the matrix files should be given as arguments (see the TNT documentation webpage for details on the usage of script files). The scripts generate CSV-formatted output for being subsequently read into any other software. Script files are provided as "ready-for-use", and are freely distributable and modifiable. We request that you cite the respective paper and dataset.</p>
Supplementary Data for "Convergent organization of aberrant MYB complexes controls oncogenic gene expression in acute myeloid leukemia"
<p>These files contain the computational analysis of sequencing data and mass spectrometry data for "Convergent organization of aberrant MYB complexes controls oncogenic gene expression in acute myeloid leukemia" by Takao, Forbes, Uni, and Kentsis et al.</p>
SUPPLEMENTARY TABLE 3 in Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919 (Anura: Dicroglossidae)
SUPPLEMENTARY TABLE 3. Call properties measurements of Minervarya species A and Minervarya species B in the present study.
SUPPLEMENTARY TABLE 2 in Importance of genetic data in resolving cryptic species: A century old problem of understanding the distribution of Minervarya syhadrensis Annandale 1919 (Anura: Dicroglossidae)
SUPPLEMENTARY TABLE 2. Morphometric data (in mm) of type specimens of Minervarya caperata deposited at BNHS and described by Kuramoto et al. (2007).
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.