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357 results for “supplementary information”
Supplementary Information: The Late Lutetian Thermal Maximum: first record of the deep-sea benthic foraminiferal response in the Tasman Sea (IODP Site U1508)
<div> <div> <div> <div> <div> <div> <div> <div> <p>Here, we provide supplementary information including inorganic and organic geochemistry data, magnetostratigraphy data, foraminifera data, and the age model derived from sediment samples taken from IODP Hole U1508C.</p> </div> </div> </div> </div> <p>At this IODP Hole, from the Tasman Sea, we have documented the Late Lutetian Thermal Maximum (LLTM), a brief warming event in the middle Eocene (41.52 Ma). This is the first record of deep-sea benthic foraminifera changes during the LLTM in the SW Pacific. The event coincides with negative δ13C excursions in bulk sediment (0.47‰) and benthic foraminifera (0.36‰), as well as shifts in foraminiferal species and organic geochemistry. Reduced diversity in benthic foraminiferal assemblages during the event indicates environmental stress, likely due to low oxygen conditions, as suggested by dysoxic taxa. Despite the dominance of calcareous taxa, corrosion-resistant species point to slightly CaCO3-corrosive waters without evident dissolution. We infer a shallower thermocline and increased stratification during the LLTM.</p> <div> <div> <div> <div> </div> </div> </div> </div> <div> <div> </div> </div> </div> </div> </div> </div> <div> <div> <div> <p> </p> </div> </div> </div>
Supplementary Information for Decoding Segregation
<pre>This is the Supplementary Information to the paper "Decoding Segregation: Navigating a century of segregation research across disciplines and introducing a bottom-up taxonomy."</pre>
Supplementary information for phylogenetic benchmarking study
<p>This dataset comprises the following files:</p> <p>- A tarball containing all alignments per run, used to infer phylogenies from (gzipped)</p> <p>- A tarball containing all assemblies (where applicable) per run (gzipped)</p> <p>- Several files with final results of the analyses. These can be read directly into SuperPlotsOfData to obtain the plots in our paper. RF = Robinson Foulds distance, KC = Kendall Colijn metric. L_0, L_0.5 and L_1 indicate lambda values of 0, 0.5 and 1 respectively in the calculation of the Kendall Colijn metric. full_data.csv contains all data. full_data_nomlst.csv contains all data, excluding the runs employing MLST alignment. run_differences_absolute.csv contains absolute differences between identical runs.</p>
Supplementary Information for Phylogenetic analyses of ray-finned fishes (Actinopterygii) using collagen type I protein sequences
<p>Ray-finned fishes (Actinopterygii) are the largest and most diverse group of vertebrates, comprising over half of all living vertebrate species. Phylogenetic relationships between ray-finned fishes have historically pivoted on the study of morphology, which has notoriously failed to resolve higher-order relationships, such as within the percomorphs. More recently, comprehensive genomic analyses have provided further resolution of actinopterygian phylogeny, including higher-order relationships. Such analyses are rightfully regarded as the 'gold standard' for phylogenetics. However, DNA retrieval requires modern or well-preserved tissue and is less likely to be preserved in archaeological or fossil specimens. In contrast some proteins, such as collagen, are phylogenetically informative and can survive into deep time. Here, we test the utility of collagen type I amino acid sequences for phylogenetic estimation of ray-finned fishes. We estimate topology using Bayesian approaches and compare the congruence of our estimated trees with published genomic phylogenies. Furthermore, we apply a Bayesian molecular clock approach and compare estimated divergence dates with previously published genomic clock analyses. Our collagen-derived trees exhibit 77% of node positions as congruent with recent genomic-derived trees, with the majority of discrepancies occurring in higher-order node positions, almost exclusively within the Percomorpha. Our molecular clock trees present divergence times that are fairly comparable with genomic-based phylogenetic analyses. We estimate the mean node age of Actinopteri at ~293 million years (Ma), the base of Teleostei at ~211 Ma and the radiation of percomorphs beginning at ~141 Ma (~350 Ma, ~250–283 Ma and ~120–133 Ma in genomic trees, respectively). Finally, we show that the average rate of collagen (I) sequence evolution is 0.9 amino acid substitutions for every million years of divergence, with the α3 (I) sequence evolving the fastest, followed by the α2 (I) chain. This is the quickest rate known for any vertebrate group. We demonstrate that phylogenetic analyses using collagen type I amino acid sequences generate tangible signals for actinopterygians that are highly congruent with recent genomic-level studies. However, there is limited congruence within percomorphs, perhaps due to clade-specific functional constraints acting upon collagen sequences. Our results provide important insights for future phylogenetic analyses incorporating extinct actinopterygian species via collagen (I) sequencing.</p>
Supplementary Information for Consonance-emerging Hebbian Learning neural network model predicts discreteness of musical scales and the Natural Just Intonation scale
<p><strong>The following phenomena and features are apparent in music and auditory perception in general: the discreteness of the tones in musical scales</strong> [1]<strong>, the prevalence of the tonal frequency span of one semitone (100 cents) in musical scales across cultures </strong>[1]<strong>, the list of tonal intervals ordered by consonance [2], and the musical performers’ preference of the Natural Just-Intonation scale [3] (A). However, researchers still have no agreement about the causes and the emergence of said phenomena (A). Here we show that the consonance-pattern emerging neural network model introduced in our previous study [4], predicts and yields all the said phenomena (A) with a precision of 1/100<sup>th</sup> of a semitone (1 cent). This precision is beyond the resolution of human hearing </strong>[5], [6], [7]. <strong>Since the Hebbian learning paradigm and harmonicity are the main features of our model, we propose that they are sufficient conditions for any system to yield the said phenomena (A). Therefore, they have a crucial role in processing pitch, consonance, and music perception in general. As a consequence, we additionally propose that the mentioned phenomena (A) are a balanced result of the joint workings of the Hebbian paradigm (nurture and cultural exposure) and harmonicity (auditory physics and biology).</strong></p>
Supplementary Information for "Semi-automated high-throughput substrate screening assay for nucleoside kinases
<p>This is the external Supplementary Information for our publication "Semi-automated high-throughput substrate screening assay for nucleoside kinases". Files are to follow soon. We apologize for the delay. Thank you for your patience.</p> <p> </p> <p>The preprint and the Supporting Information are available at ChemRxiv (https://doi.org/10.33774/chemrxiv-2021-k0w7q).</p>
Supplementary information for: NUMT PARSER: Automated identification and removal of nuclear mitochondrial pseudogenes (numts) for accurate mitochondrial genome reconstruction in Panthera
<p>Nuclear mitochondrial pseudogenes (numts) may hinder the reconstruction of mtDNA genomes and affect the reliability of mtDNA datasets for phylogenetic and population genetic comparisons. Here, we present the program Numt Parser, which allows for the identification of DNA sequences that likely originate from numt pseudogene DNA. Sequencing reads are classified as originating from either numt or true cytoplasmic mitochondrial (cymt) DNA by direct comparison against cymt and numt reference sequences. Classified reads can then be parsed into cymt or numt datasets. We tested this program using whole genome shotgun-sequenced data from two ancient Cape lions (<em>Panthera</em> <em>leo</em>) because mtDNA is often the marker of choice for ancient DNA studies, and the genus <em>Panthera</em> is known to have numt pseudogenes. Numt Parser decreased sequence disagreements that were likely due to numt pseudogene contamination and equalized read coverage across the mitogenome by removing reads that likely originated from numts. We compared the efficacy of Numt Parser to two other bioinformatic approaches that can be used to account for numt contamination. We found that Numt Parser outperformed approaches that rely only on read alignment or Basic Local Alignment Search Tool (BLAST) properties, and was effective at identifying sequences that likely originated from numts while having minimal impacts on the recovery of cymt reads. Numt Parser therefore improves the reconstruction of true mitogenomes, allowing for more accurate and robust biological inferences.</p>
Supplementary Information for "Modeling the circular economy in environmentally extended input–output: A web application"
<p>Supplementary Information for "Modeling the circular economy in environmentally extended input–output: A web application"</p> <p>Annex I: This supporting information provides the software review for native and web-based tools that could be used for Circular Economy and environmental analysis.</p> <p>Annex II: This supporting information provides the use-case result analysis.</p>
Exercise training prior to manifestation of hypertrophic cardiomyopathy in mice attenuates expression of pro-fibrotic genes - supplementary information
<p>Supplementary data for research article titled "Exercise training prior to manifestation of hypertrophic cardiomyopathy in mice attenuates expression of pro-fibrotic genes"</p>
Supplementary Information Materials for the G-Cubed submission by Zakharov et al.
<p>The supporting information is provided for the publication <a href="https://doi.org/10.1029/2022GC010741">https://doi.org/10.1029/2022GC010741</a><em>. </em>The upload contains identification of MGL opal-CT as well as the results of the SIMS and EMPA measurements in cherts. This file also features δD values plotted against the triple O-isotope values of cherts. The Secondary Ion Probe Mass Spectrometry (SIMS) measurements are included as the .xslx table (Data Set S1) with analytical conditions, raw measurements and VSMOW-calibrated values. The Electron Microprobe (EMPA) analyses are provided in the .xslx file (Data Set S2). The Data Set S2 is separated by tabs for individual sample. Images feature the analyzed areas, including petrographic image, reflected light and the SIMS points.</p>
Supplementary Information for "Mapping potential conflicts between global agriculture and terrestrial conservation"
<p>This archive contains supplementary figures from mapping potential conflicts between global agriculture and terrestrial conservation in 2010 and 2070. Please see the captions of these figures below.</p> <p><strong>Supplementary Figure 3.</strong> Distribution of regional land use by agricultural commodity and conservation priority (CP) index intervals (48 x 3 sub-figures).<br> <strong>Supplementary Figure 4.</strong> Distribution of regional land use (left) and global land use (right) of 48 agricultural commodities (48 x 3 sub-figures). The x-axis is the land use as a proportion of the total global production area.<br> <strong>Supplementary Figure 5.</strong> Comparison of the distribution of regional land use for 48 agricultural commodities between 2010 and 2070 scenarios (48 x 7 x 2 sub-figures).<br> <strong>Supplementary Figure 6.</strong> Comparison of land use and conservation conflict between national and global levels. The y-axis refers to the land use as a proportion of the total global production area. There are 48 agricultural commodities for 197 countries (197 x 48 x 3 sub-figures).<br> <strong>Supplementary Figure 7.</strong> Comparison of the land use distribution of top producers for 48 agricultural commodities between 2010 and 2070 scenarios (48 x 10 x 2 sub-figures).<br> <strong>Supplementary Figure 8.</strong> Spatial distribution maps of production areas for 48 agricultural commodities (48 x 3 maps).<br> <strong>Supplementary Figure 9.</strong> Conflict between conservation priority sites and (non-)domestic land use for 42 agricultural commodities associated with consumption in 197 countries (197 x 42 x 3 sub-figures).<br> <strong>Supplementary Figure 10.</strong> Land use maps of 42 agricultural commodities linked to consumption in 197 countries (197 x 42 x 3 maps).<br> <strong>Supplementary Figure 11.</strong> Conservation priority index and export rate of selected agricultural commodity for primary production cells (land use of each agricultural commodity > 10% of cell area). <strong>a</strong>) Current status in 2010. <strong>b</strong>) Shifts of conservation priority in 2070 (RCP 8.5). Triangles point-up and point-down to indicate increased and decreased CP, respectively. Density plots on top and right show cell densities corresponding to export rate and CP index, respectively.<br> <strong>Supplementary Figure 12.</strong> Maps of global conservation priority index in 2010 and 2070.<br> <strong>Supplementary Figure 13. a</strong>, Performance curves for prioritization per scenario 2010, 2070-RCP2.6, and 2070-RCP8.5). Curves show the average fraction of species' range covered in each scenario weighted by each species weight, divided by the total weight of species (y-axis), by a given fraction of the landscape (x-axis). <strong>b</strong>, Histograms and boxplots of all CP map pixels. Each jittered point in boxplots represents a map pixel.</p>
Field margins as substitute habitat for the conservation of birds in agricultural wetlands; Supplementary information
<p>Supplementary material, dataset and script links to the research paper submit for recommendation by PCI Ecology.</p>
Probe Ranking Information - Supplementary Table 2
<p>List of the 1096 genomic loci (ordered by the lowest corrected q-values) investigated in the study "<strong>Validation of differentially methylated DNA regions in precancerous colorectal lesions"</strong>. Genome coordinates are based on the GRCh37/hg19 genome assembly. </p>
Supplementary Online Content to "Alterity marking and enhancing accessibility in lexical borrowing: Meta-information techniques in the use of incipient anglicisms in French and Italian"
<ul> <li>Overview of newspaper articles analysed in Sections 4 and 5</li> <li>Sources of the newspaper articles</li> <li>Sample analyses of the use of meta-information techniques in F2 and I3</li> </ul>
Supplementary material for 'The MAP metric in Information Retrieval Fault Localization'
<pre># map_bench4bl This is the supplementary material, data, and evaluation source code for the paper "The MAP metric in Information Retrieval Fault Localization" by Thomas Hirsch and Birgit Hofer. ## Preliminaries ### Python environment - Python 3.8 - pandas - numpy - matplotlib ## Datasets The [Bench4BL](<em>https://github.com/exatoa/Bench4BL</em>) dataset has been used in this evaluation, with the addition of intermediate files taken from the [SABL](<em>http://dx.doi.org/10.5281/zenodo.4681242</em>) experiment performed on this Bench4BL dataset. All data used in our evaluation is included in this repository. However, if the data is to be re-imported directly from these benchmark and datasets they have to be downloaded first and their local paths have to be set in [paths.py](<em>paths.py</em>). ### Bench4BL The Bench4BL dataset was published with the paper "Bench4BL: Reproducibility study on the performance of IR-based bug localization" by Lee, J., Kim, D., Bissyandé, T.F., Jung, W. and Le Traon, Y.. The dataset can be obtained [here](<em>https://github.com/exatoa/Bench4BL</em>). Follow the steps described in the corresponding [README](<em>https://github.com/exatoa/Bench4BL/blob/master/README.md</em>) to set up the dataset. The Bench4BL dataset contains the _old subjects_ subdataset, containing 558 bugs from AspectJ, JDT, PDE, SWT, and ZXing that have been widely used in older IRFL studies. This _old subjects_ subdataset was used in answering our RQ1, as discussed below, the corresponding scripts use _old subjects_ in their name to highlight this. #### SABL The SABL dataset is the online appendix of the paper "An Extensive Study of Smell-Aware Bug Localization" by TTakahashi, A., Sae-Lim, N., Hayashi, S. and Saeki, M.. The dataset can be downloaded [here](<em>http://dx.doi.org/10.5281/zenodo.4681242</em>). The experiments in this dataset build on top of Bench4BL and intermediate files are provided in the datapackage. #### Rankings Rankings for BLIA, BRTracer, and BugLocator were produced by running these tools on Bench4BL locally. Rankings for AmaLgam and BLUiR were taken from the SABL experiment dataset. ## Structure ### Folders Bench4BL ground truths: - bench4bl_old_subjects_summary - bench4bl_summary Localization results of the included tools in Bench4BL: - bench4bl_localization_results - bench4bl_localization_results_sabl Target projects size metrics: - cloc_results - cloc_results_old_subjects Utility functions: - utils Output folders containing results, generated figures and tables: - results - results_old_subjects ### Scripts Scripts for re-importing data from Bench4BL and SABL datasets: - data_preparation_step_1_cloc_bench4bl.py - data_preparation_step_1_cloc_old_subjects_bench4bl.py - data_preparation_step_2_import_ground_truth_from_bench4bl.py - data_preparation_step_2_import_ground_truth_from_old_subjects_bench4bl.py - data_preparation_step_3_import_bench4bl_ranking_results.py - data_preparation_step_3_import_sabl_ranking_results.py Utilities: - paths.py - utils/bench4bl_utils.py - utils/Logger.py ### Evaluation scripts for the corresponding research questions: **Dataset analysis:** - rq_0_dataset_analysis_bench4bl_issues.py **RQ1: How big is the average ground truth in Bench4BL datasets, and what proportion of bugs have a ground truth containing multiple files?** - rq_1_bench4bl_ground_truth_size.py - rq_1_old_subjects_bench4bl_ground_truth_size.py RQ2: Do the IRFL tools included in Bench4BL truncate their results? - rq_2_ranking_lengths.py **RQ3: How strong is $AP_{asrd}$ overestimating $AP_{mb}$ for truncated BugLocator retrieval results on the Bench4BL dataset? RQ3a: How strong is $AP_{asrd}$ overestimating $AP_{mb}$ for truncated BugLocator retrieval results when considering the bloated ground truth issue found in Bench4BL?** - rq_3_truncating_BugLocator_rankings_bench4bl.py **RQ3b: How strong is $AP_{asrd}$ overestimating $AP_{mb}$ for truncated BugLocator retrieval results when undefined $AP$ values are simply ignored?** - rq_3b_undefined_ap_BugLocator_rankings_bench4bl.py ## Licence All code and results are licensed under [CCA v4](<em>https://creativecommons.org/licenses/by/4.0/</em>), according to LICENSE file. Other licences may apply for some tools and datasets contained in this repo: [cloc-1.92.pl](<em>https://github.com/AlDanial/cloc</em>) under GPL v2, [Bench4BL](<em>https://github.com/exatoa/Bench4BL</em>) and [SABL](<em>http://dx.doi.org/10.5281/zenodo.4681242</em>) under CCA 4.0.</pre>
Supplementary materials for Education and Information Technologies
<p>Anonymized supplementary materials for publication 'Using Data Clustering to Reveal Trainees’ Behavior \\in Cybersecurity Education' in the journal Education and Information Technologies</p> <p> </p>
Data and supplementary information: Effects of lithium on locomotor activity and circadian rhythm of honey bees
<p>Data and supplementary files for publication:</p><p>Erdem, B., Arslan, O.C., Sevin, S. Gozen, A. G., Agosto-Rivera, J. L., Tugrul, G., & Alemdar, H. (2023). Effects of lithium on locomotor activity and circadian rhythm of honey bees. <i>Scientific Reports</i>, <i>13,</i> 19861. https://doi.org/10.1038/s41598-023-46777-7</p><p> </p><p>AcuteExp_Dark_ActivityData.xlsx - Total LMA counts of acute experiment in dark condition.</p><p>AcuteExp_Light_ActivityData.xlsx - Total LMA counts of acute experiment in light condition.</p><p>ChronicExp_ActivityData.xlsx - Total LMA counts of the chronic experiment.</p><p>ChronicExp_MortalityData.xlsx - Mortality data of the chronic experiment.</p><p>ChronicExp_PeriodRhytmData.xlsx - Defines rhythmic and arrhythmic individuals and the circadian periods (h) of the rhythmic individuals in chronic experiment.</p><p>LD_doubleplots.pdf - Double-plotted actograms of the individuals in the chronic experiment in the 12 h light / 12 h dark condition.</p><p>DD_doubleplots.pdf - Double-plotted actograms of the individuals in the chronic experiment in the constant dark condition.</p><p>LL_doubleplots.pdf - Double-plotted actograms of the individuals in the chronic experiment in the constant light condition.<br>In the double-plotted actograms, NR indicates "non-rhythmic" individuals.</p>
Supplementary information to Bjørn et al. (2023)
<p>This spreadsheet contains the data behind all figures displayed in the following paper:</p> <p> </p> <p>Title: Differentiation of greenhouse gases in corporate science-based targets improves alignment with Paris temperature goal</p> <p>Authors: Anders Bjørn<sup>1-3</sup>*, Shannon Lloyd<sup>4</sup>, Urs Schenker<sup>5</sup>, Manuele Margni<sup>6,7</sup>, Annie Levasseur<sup>8</sup>, Maxime Agez<sup>6</sup> and Damon Matthews<sup>2</sup></p> <p><sup>1</sup> Section for Quantitative Sustainability Assessment, Department of Environmental and Resource Engineering, Technical University of Denmark, Kgs. Lyngby, Denmark.</p> <p><sup>2 </sup>Department of Geography, Planning and Environment, Concordia University, Montréal, Canada.</p> <p><sup>3 </sup>Centre for Absolute Sustainability, Technical University of Denmark, Kongens Lyngby, Denmark.</p> <p><sup>4 </sup>Department of Management, Concordia University, Montréal, Quebec, Canada.</p> <p><sup>5</sup> Nestlé Research, Vers-chez-les-Blanc, 1010 Lausanne 26, Switzerland</p> <p><sup>6</sup> Department of Mathematical and Industrial Engineering, Polytechnique Montréal, Montréal, Canada</p> <p><sup>7</sup> Institute of Sustainable Energy, School of Engineering, University of Applied Sciences and Arts Western Switzerland, Switzerland</p> <p><sup>8</sup> Department of Construction Engineering, École de technologie supérieure, Montréal, Canada.</p> <p>*Corresponding author: <a href="mailto:anbjo@dtu.dk">anbjo@dtu.dk</a>.</p> <p> </p> <p>The paper is currently (June 11th, 2023) under review with Environmental Research Letters </p>
Deep decarbonisation pathways of the energy system in times of unprecedented uncertainty in the energy sector. Energy Policy (2023). Supplementary Information on Assumptions and Results
<p>This dataset supplements the article with the title "Deep decarbonisation pathways of the energy system in times of unprecedented uncertainty in the energy sector", published in Energy Policy. </p> <p>The dataset contains the following:</p> <ul> <li>The Latin Hypercube Sample of the multipliers that are applied to the key input parameters of ETSAP-TIAM in order to generate 1000 different states of the world regarding economic and demographic growth, energy resources potentials, energy technology costs, climate sensitivity and radiative forcing, LULUCF CO<sub>2</sub> sink potential, CO<sub>2</sub> sequestration potential, and decoupling between energy consumption and economic development. The multipliers are sampled from the underlying probability distributions described in the article. </li> <li>The results (at the global scale) from four scenario families for each one of the 1000 wofld states. These scenario families are: <ul> <li>BASE_SSP2: Describes the development of the global energy system consistent with recent trends and policies.</li> <li>2C_SSP2: Introduces to the BASE_SSP2 scenario a global constraint of 2 °C as the maximum post-industrial temperature change from 2020 to 2100.</li> <li>2C_SSP2_DA30: Delayed climate action. The climate change mitigation policies of 2C_SSP2 start in 2030. </li> <li>1p5c_OS_SSP2: Introduces to the BASE_SSP2 scenario a global constraint of 1.5 °C as the maximum post-industrial temperature change from 2020 onwards to 2100</li> </ul> </li> </ul> <p>Key results included in the dataset are: Temperature change, Radiative Forcing, GHG concentrations, CO2 emissions, Marginal abatement cost, Electricity Supply Primary Energy Consumption, and Annual Total Global Energy System Cost.</p> <p>The dataset also includes sectoral results regarding energy consumption and use, such as shares of different electric uses, shares of hydrogen consumption in end-use sectors, hydrogen supply, Demand electrification by sector, Renewable energy consumption by sector, Alternative fuels consumption in transport, and Total final energy consumption by sector. </p>
Supplementary information for the manuscript 'GFViz: A tutorial on creating interactive visualization of genomic features using R Tidyverse and plotly'
<p>This is the supplementary information of the manuscript 'GFViz: A tutorial on creating interactive visualization of genomic features using R Tidyverse and plotly' published as a part of the thesis 'Annotating and making use of the <em>Avena sativa</em> cv. Sang reference genome' by Nikos Tsardakas Renhuldt.</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.