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357 results for “supplementary information”
Supplementary Information for Biogeography a key influence on distal forelimb variation in horses through the Cenozoic
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Supplementary Information for Heterogeneous Parallelization and Acceleration of Molecular Dynamics Simulations in GROMACS
<p>Supplementary information for<br> Páll, S., Zhmurov, A., Bauer, P., Abraham, M., Lundborg, M., Gray, A., Hess, B, & Lindahl, E.. (2020). Heterogeneous Parallelization and Acceleration of Molecular Dynamics Simulations in GROMACS. The Journal of Chemical Physics, 2020</p> <p>Contains benchmark methodology description as well as all inputs used in the application performance benchmarks included the paper.</p>
Supplementary materials for Arzi et al 2012: Humans can learn new information during sleep
<p>Supplementary materials for Arzi et al 2012: Humans can learn new information during sleep:</p> <p> </p> <p>Arzi, A., Shedlesky, L., Ben-Shaul, M. <em>et al.</em> Humans can learn new information during sleep. <em>Nat Neurosci</em> <strong>15, </strong>1460–1465 (2012). https://doi.org/10.1038/nn.3193</p>
Supplementary information to the article by van Beijnum et al. "Integrating phenotypic search and phosphoproteomic profiling of active kinases for optimization of drug mixtures for RCC treatment"
<p>Supplementary information to the article "Integrating phenotypic search and phosphoproteomic profiling of active kinases for optimization of drug mixtures for RCC treatment".</p> <p><strong>Judy R. van Beijnum<sup>1</sup>, Andrea Weiss<sup>2, 3</sup>, Robert H. Berndsen<sup>1,2 </sup>, Tse J. Wong<sup>1</sup>, Louise C. Reckman<sup>1</sup>, Sander R. Piersma<sup>4,5</sup>, Marloes Zoetemelk<sup>2,3</sup>, Richard de Haas<sup>1,4,5</sup>, Olivier Dormond<sup>6</sup>, Axel Bex<sup>7,8</sup>, Alexander A. Henneman<sup>4,5</sup>, Connie R. Jimenez<sup>4,5</sup>, Arjan W. Griffioen<sup>1</sup>, Patrycja Nowak-Sliwinska<sup>2,3,9</sup>*</strong></p> <p> </p> <p><sup>1</sup> Angiogenesis Laboratory, Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands;</p> <p><sup>2</sup> Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland*;</p> <p><sup>3 </sup>Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland</p> <p><sup>4 </sup>Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands</p> <p><sup>5</sup> OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands</p> <p><sup>6</sup> Department of Visceral surgery, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland<sup> </sup> </p> <p><sup>7</sup> Royal Free London NHS Foundation Trust, Renal Cancer Centre, UCL Division of Surgical and Interventional Science, London, UK</p> <p><sup>8</sup> Netherlands Cancer Institute, Amsterdam, The Netherlands</p> <p><sup>9 </sup> Translational Research Centre in Oncohaematology, Geneva, Switzerland</p> <p> Correspondence: <a href="mailto:Patrycja.Nowak-Sliwinska@unige.ch">Patrycja.Nowak-Sliwinska@unige.ch</a></p>
Supplementary information for: The effects of geographic range size and abundance on extinction during a time of 'sluggish' evolution
<p>Geographic range size and abundance are important determinants of extinction risk in fossil and extant taxa. However, the relationship between these variables and extinction risk has not been tested extensively during evolutionarily 'quiescent' times of low extinction and speciation in the fossil record. Here we examine the influence of geographic range size and abundance on extinction risk during the late Paleozoic (Mississippian–Permian), a time of 'sluggish' evolution when global rates of origination and extinction were roughly half those of other Paleozoic intervals. Analyses used spatio-temporal occurrences for 164 brachiopod species from the North American midcontinent. We found abundance to be a better predictor of extinction risk than measures of geographic range size. Moreover, species exhibited reductions in abundance prior to their extinction, but did not display contractions in geographic range size. The weak relationship between geographic range size and extinction in this time and place may reflect the relative preponderance of larger-ranged taxa, combined with the physiographic conditions of the region that allowed for easy habitat tracking that dampened both extinction and speciation. These conditions led to a prolonged period (19 – 25 Myr) during which standard macroevolutionary rules did not apply.</p>
Supplementary materials for article focused on traffic information enrichment: Animation and complete overview of all road segments on which basis summary test results were calculated
<p><strong>Supplementary materials </strong>(Appendix A and B) for the article:</p> <p>Traffic Information Enrichment: Creating Long-Term Traffic Speed Prediction Ensemble Model for Better Navigation through Waypoints</p> <p><em>Abstract: </em>Traffic speed prediction for a selected road segment from a short-term and long-term perspective is among the fundamental issues of intelligent transportation systems (ITS). During the course of the past two decades, many artefacts (e.g., models) have been designed dealing with traffic speed prediction. However, no satisfactory solution has been found for the issue of a long-term prediction for days and weeks using the vast spatial and temporal data. This article aims to introduce a long-term traffic speed prediction ensemble model using country-scale historic traffic data from 37,002 km of roads, which constitutes 66% of all roads in the Czech Republic. The designed model comprises three submodels and combines parametric and nonparametric approaches in order to acquire a good-quality prediction that can enrich available real-time traffic information. Furthermore, the model is set into a conceptual design which expects its usage for the improvement of navigation through waypoints (e.g., delivery service, goods distribution, police patrol) and the estimated arrival time. The model validation is carried out using the same network of roads, and the model predicts traffic speed in the period of 1 week. According to the performed validation of average speed prediction at a given hour, it can be stated that the designed model achieves good results, with mean absolute error of 4.67 km/h. The achieved results indicate that the designed solution can effectively predict the long-term speed information using large-scale spatial and temporal data, and that this solution is suitable for use in ITS.</p> <p>Simunek, M., & Smutny, Z. (2021). Traffic Information Enrichment: Creating Long-Term Traffic Speed Prediction Ensemble Model for Better Navigation through Waypoints. <em>Applied Sciences</em>, 11(1), 315. <a href="https://doi.org/10.3390/app11010315">https://doi.org/10.3390/app11010315</a></p> <p> </p> <p><strong>Appendix A</strong><br> Examples of the deviation between the average speed and the FreeFlowSpeed for selected hours.</p> <p> </p> <p><strong>Appendix B</strong><br> The text file provides a complete overview of all road segments on which basis summary test results were calculated in Section 6 of the article.</p>
Supplementary Information for "Resolution and the Detection of Cultural Dispersals: development and application of spatiotemporal methods in Lowland South America"
<p>Data and code to reproduce the analyses in "Resolution and the Detection of Cultural Dispersals: development and application of spatiotemporal methods in Lowland South America"</p> <p> </p> <p><strong>Abstract</strong></p> <p>Inferring episodes of expansion, admixture, diffusion, and/or migration in prehistory is at present undergoing a resurgence in macro-scale archaeological interpretation. In parallel to this renewed popularity, expanding access to computational tools and datasets has seen the use of aggregated radiocarbon datasets for the study of dispersals also increasing. This paper advocates for developing reflexive practice in the application of radiocarbon dates to prehistoric dispersals, by reflecting on the quality and qualities of the underlying data, particularly chronometric uncertainty, and framing dispersals explicitly in terms of hypothesis testing. This paper draws on cultural expansions within South America and employs two emblematic examples, the Arauquinoid and Tupiguarani traditions, to develop an analytical solution that not only incorporates chronometric uncertainty in bivariate regression but, importantly, tests whether the datasets provide statistically significant evidence for a dispersal process. The analysis, which the paper provides the means to replicate, identifies fundamental issues with resolution and data quality that impede identification of pre-Columbian cultural dispersals through simple spatial gradients of radiocarbon data. The results suggest that reflexivity must be fed back into theoretical frameworks of prehistoric mobility for the study of dispersals, in turn informing the construction of more critical statistical null models. As a first step, alternative models of cultural expansion should be formally considered alongside demographic models.Inferring episodes of expansion, admixture, diffusion, and/or migration in prehistory is at present undergoing a resurgence in macro-scale archaeological interpretation. In parallel to this renewed popularity, expanding access to computational tools and datasets has seen the use of aggregated radiocarbon datasets for the study of dispersals also increasing. This paper advocates for developing reflexive practice in the application of radiocarbon dates to prehistoric dispersals, by reflecting on the quality and qualities of the underlying data, particularly chronometric uncertainty, and framing dispersals explicitly in terms of hypothesis testing. This paper draws on cultural expansions within South America and employs two emblematic examples, the Arauquinoid and Tupiguarani traditions, to develop an analytical solution that not only incorporates chronometric uncertainty in bivariate regression but, importantly, tests whether the datasets provide statistically significant evidence for a dispersal process. The analysis, which the paper provides the means to replicate, identifies fundamental issues with resolution and data quality that impede identification of pre-Columbian cultural dispersals through simple spatial gradients of radiocarbon data. The results suggest that reflexivity must be fed back into theoretical frameworks of prehistoric mobility for the study of dispersals, in turn informing the construction of more critical statistical null models. As a first step, alternative models of cultural expansion should be formally considered alongside demographic models.</p>
Informing antenna design for Global 21-cm experiments using a simulated Bayesian data analysis pipeline (supplementary data)
<p>These are the posterior files, foreground simulation data sets and chromaticity factor values used to produce the results for <a href="https://arxiv.org/abs/2106.10193">arXiv:2106.10193</a>.</p> <p>Plots of the fitted signal and residuals for each case are included, as is a plotting function to reproduce key figures.</p> <p>Naming conventions:</p> <ul> <li>f0: Centre frequency of the 21cm signal present in the simulated data</li> <li>A: Amplitude of the simulated 21cm signal present in the simulated data</li> <li>M_sig: Model being fit to the data includes a 21cm signal</li> <li>M_nosig: Model being fit to the data is a foreground only</li> </ul> <p>Software used:</p> <ul> <li><a href="https://github.com/PolyChord/PolyChordLite/tree/839292290a7747dbee82933bb9f7f955ac45c3ca">PolyChord</a></li> </ul> <p> </p>
On the calculation of second-order magnetic properties using subsystem approaches in the relativistic framework - supplementary information
<p>Supplementary information to the publication "On the calculation of second-order magnetic properties using subsystem approaches in the relativistic framework"</p> <p>The attached 'supplementary_info_fde_mag.zip' unpacks to three directories:</p> <ul> <li>'optimized_structures' directory contains optimized molecular structures in xyz format</li> <li>'results' directory contains all the results obtained in this work, collected in <ul> <li>gnumeric and xlsx spreadsheets with complete results from DIRAC and from ADF</li> <li>csv files (data involving heavy atoms, X, and hydrogen-bonded H atoms, Hb)</li> <li>'supplementary_tables' latex and pdf files</li> </ul> </li> <li>'visualization' directory contains the data for plotting the NMR shielding density and prepared plots; for the explanation of files in this directory open the 'visualization/visualization.html' document in your browser or read the corresponding jupyter notebook (visualization/visualization.ipynb')</li> </ul>
Supplementary information for: "A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling".
<p>This is supplementary data for F1000Research article: A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling.</p> <p>Here are files for modeling archaerhodopsin-3 with I-TASSER, Medeller and RosettaCM algorithms, structure postprocessing and spectra calculations.</p>
On the calculation of second-order magnetic properties using subsystem approaches in the relativistic framework - supplementary information
<p>Supplementary information to the publication "On the calculation of second-order magnetic properties using subsystem approaches in the relativistic framework"</p> <p>The attached 'supplementary_info_fde_mag.tar.gz' unpacks to three directories:</p> <ul> <li>'optimized_structures' directory contains optimized molecular structures in xyz format</li> <li>'results' directory contains all the results obtained in this work, collected in <ul> <li>spreadsheets with complete results from DIRAC and from ADF (in *xlsx and *gnumeric format)</li> <li>csv files (data involving heavy atoms, X, and hydrogen-bonded H atoms, Hb obtained with DC and ZORA Hamiltonians and TZ-type basis sets)</li> <li>'supplementary_tables' latex and pdf files</li> </ul> </li> <li>'visualization' directory contains the data for plotting the NMR shielding density and prepared plots; for the explanation of files in this directory open the 'visualization/visualization.html' document in your browser or read the corresponding jupyter notebook (visualization/visualization.ipynb')</li> </ul>
Supplementary information associated with a "Whole-Organism Integrated DNA Methylation and Transcriptomics Analysis of Butterfly Metamorphosis".
<p>Supplementary information, annotation and code related to the manuscript studying <em>Bicyclus anynana</em> development entitled "Whole-Organism Integrated DNA Methylation and Transcriptomics Analysis of Butterfly Metamorphosis".</p>
Supplementary information: Specific versus Nonspecific Solvent Interactions of a Biomolecule in Water [Dataset]
<p><strong>Data availability</strong><strong> to the manuscript </strong><em>"</em>Specific versus Nonspecific Solvent Interactions of a Biomolecule in Water<em>"</em> by <strong>Lanhai He, Lukáš Tomaník, Sebastian Malerz, Florian Trinter, Sebastian Trippel, Michal Belina, Petr Slavíček, Bernd Winter, and Jochen Küpper</strong>, pubulished at<em> JPCL </em></p> <p>The dataset contains the complete x-ray photoelectron-emission spectra of indole<sub>aq</sub> in a liquid microjet. The uploaded files include:</p> <ul> <li>Valence band PES data (<a href="../api/files/eec96d6e-1972-463a-bc54-ee320bb2280e/May02_0053VB.ibw">May02_0053VB.ibw</a>, <a href="../api/files/eec96d6e-1972-463a-bc54-ee320bb2280e/May02_0058VB_background.ibw">May02_0058VB_background.ibw</a>),</li> <li>core level PES data (<a href="../api/files/eec96d6e-1972-463a-bc54-ee320bb2280e/May02_0045C1s.ibw">May02_0045C1s.ibw</a>, <a href="../api/files/eec96d6e-1972-463a-bc54-ee320bb2280e/May02_0049N1s.ibw">May02_0049N1s.ibw</a>),</li> <li>Auger PES pectra (<a href="../api/files/eec96d6e-1972-463a-bc54-ee320bb2280e/May02_0052CAuger.ibw">May02_0052CAuger.ibw</a>, <a href="../api/files/eec96d6e-1972-463a-bc54-ee320bb2280e/May02_0057CAuger.ibw">May02_0057CAuger.ibw</a>, <a href="../api/files/eec96d6e-1972-463a-bc54-ee320bb2280e/May02_0056NAuger.ibw">May02_0056NAuger.ibw</a>)</li> <li>rough-scanned full spectra (<a href="../api/files/eec96d6e-1972-463a-bc54-ee320bb2280e/May02_0046Full.ibw">May02_0046Full.ibw</a>, <a href="../api/files/eec96d6e-1972-463a-bc54-ee320bb2280e/May02_0047Full.ibw">May02_0047Full.ibw</a>).</li> </ul> <p>In addition, a python script (Read_ibw_file.py) has been uploaded, which can be used to read raw PES data files in .ibw format and export the intergraded PES data as a .txt file.</p>
Supplementary information for: The artefactual branch effect and phylogenetic conflict: Species delimitation with gene flow in mangrove pit vipers (Trimeresurus purpureomaculatus-erythrurus complex)
<p>Mangrove pit vipers of the <em>Trimeresurus</em> <em>purpureomaculatus</em>-<em>erythrurus</em> complex are the only species of viper known to naturally inhabit mangroves. Despite serving integral ecological functions in mangrove ecosystems, the evolutionary history, distribution, and species boundaries of mangrove pit vipers remain poorly understood, partly due to overlapping distributions, confusing phenotypic variations, and the lack of focused studies. Here, we present the first genomic study on mangrove pit vipers and introduce a robust hypothesis-driven species delimitation framework that considers gene flow and phylogenetic uncertainty in conjunction with a novel application of a new class of speciation-based delimitation model implemented through the program Delineate. Our results showed that gene flow produced phylogenetic conflict in our focal species and substantiated the artefactual branch effect where highly admixed populations appear as divergent nonmonophyletic lineages arranged in a stepwise manner at the basal position of clades. Despite the confounding effects of gene flow, we were able to obtain unequivocal support for the recognition of a new species based on the intersection and congruence of multiple lines of evidence. This study demonstrates that an integrative hypothesis-driven approach predicated on the consideration of multiple plausible evolutionary histories, population structure/ differentiation, gene flow, and the implementation of a speciation-based delimitation model can effectively delimit species in the presence of gene flow and phylogenetic conflict.</p>
Code and supplementary information for the speed of neutral evolution on graphs
<p>The speed of evolution on structured populations is crucial for biological and social systems. The likelihood of invasion is key for evolutionary stability, but it makes little sense if it takes long. It is far from known what population structure slows down evolution. We investigate the absorption time of a single neutral mutant for all the 112 non-isomorphic undirected graphs of size 6. We find that about three-quarters of the graphs have an absorption time close to that of the complete graph, less than one-third are accelerators, and more than two-thirds are decelerators. Surprisingly, determining whether a graph has a long absorption time is too complicated to be captured by the joint degree distribution. Via the largest sojourn time, we find that echo-chamber-like graphs, which consist of two homogeneous graphs connected by few sparse links, are likely to slow down absorption. These results are robust for large graphs, mutation patterns as well as evolutionary processes. This work serves as a benchmark for timing evolution with complex interactions and fosters the understanding of polarization in opinion formation.</p>
Supplementary information for the report "Fracture Mapping on the Reykjanes Peninsula"
<p>Supplementary material for the University of Iceland's Institute of Earth Sciences (Jarðvísindastofnun Háskólans) research report RH-06-24: "Fracture Mapping on the Reykjanes Peninsula". These are fractures mapped with TerraSAR-X data following the methods of Ducrocq et al. (2024), published in Bulletin of Volcanology (<a href="https://doi.org/10.1007/s00445-023-01699-0" target="_blank" rel="noopener">https://doi.org/10.1007/s00445-023-01699-0</a>), for September 2021 to July 2024. </p>
Electronic supplementary information: Independent and adaptive evolution of phenotypic novelties is driven by coral symbiosis in barnacle larvae
<p class="Standard">The invasion of novel habitats is recognized as a major promotor of adaptive trait evolution in animals. We tested whether similar ecological niches entail independent and adaptive evolution of key phenotypic structures related to larval host invasion in distantly related taxa. We use disparately related clades of coral barnacles as our model system (Acrothoracica: <i>Berndtia</i> and Thoracica: Pyrgomatidae). We analyze the larval antennular phenotypes and functional morphologies facilitating host invasion. Extensive video recordings show that coral host invasion is carried out exclusively by cypris larvae with spear-shaped antennules. These first exercise a series of complex probing behaviors followed by repeated antennular penetration of the soft host tissues, which subsequently facilitates permanent invasion. Phylogenetic mapping of larval form and function related to niche invasion in 99 species of barnacles (Thecostraca) compellingly shows that the spear-phenotype is uniquely associated with corals and penetrative behaviors. These features evolved independently in the two coral barnacle clades and from ancestors with fundamentally different antennular phenotypes. The larval host invasion system in coral barnacles likely evolved adaptively across millions of years for overcoming challenges associated with invading and entering demanding coral hosts.</p> <p class="Standard"> </p> <p class="Standard"><i>Key words: </i>adaptive host invasion, larval phenotypes, coral barnacle, barnacle phylogeny</p>
Supplementary Information – HyDRA challenge
<p>Related Output files for the geometry optimizations (wB97xD/def2-TZVP) of train and blind set of Hydra Challenge.</p>
Synthesis, Herbicidal Activity, Crop Safety and Soil Degradation of Pyrimidine- and Triazine-Substituted Chlorsulfuron Derivatives Supplementary Information
<p>The content include SI1-Melting points, 1H-NMR, 13C-NMR and HRMS of W103-W111, SI2-Crystal data of compound W110(CCDC number 2142702), SI3-Biological assay and crop safety, SI4-Soil degradation assay, SI5-Report of soil analysis in Chinese, and SI6-Report of soil analysis in English.</p>
Evaluating refugia in recent human evolution in Africa: Supplementary information
<p><em>Homo sapiens</em> have adapted to an incredible diversity of habitats around the globe. This capacity to adapt to different landscapes is clearly expressed within Africa, with Late Pleistocene <em>Homo sapiens</em> populations occupying savannahs, woodlands, coastlines and mountainous terrain. As the only area of the world where <em>Homo sapiens</em> have clearly persisted through multiple glacial-interglacial cycles, Africa is the only continent where classic refugia models can be formulated and tested to examine and describe changing patterns of past distributions and human phylogeographies. The potential role of refugia has frequently been acknowledged in the Late Pleistocene palaeoanthropological literature, yet explicit identification of potential refugia has been limited by the patchy nature of palaeoenvironmental and archaeological records, and the low temporal resolution of climate or ecological models. Here, we apply potential climatic thresholds on human habitation, rooted in ethnographic studies, in combination with high resolution model datasets for precipitation and biome distributions to identify persistent refugia spanning the Late Pleistocene (130-10 thousand years ago). We present two alternate models suggesting that between 27-66% of Africa may have provided refugia to Late Pleistocene human populations, and examine variability in precipitation, biome, and ecotone distributions within these refugial zones.</p>
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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.