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1,582 results for “Manuscripts”
SQUID manuscript workflow with outputs
<p>This repository reproduces the analysis performed in for our method <strong>SQUID</strong> (<strong>S</strong>urrogate <strong>Qu</strong>antitative <strong>I</strong>nterpretability for <strong>D</strong>eepnets; Seitz, McCandlish, Kinney and Koo). It contains tools to apply SQUID on several previously-published genomic models, and compare its results to existing attribution methods.</p><p>The scripts contained in this release are a replica of those found in the current release of our GitHub repository (https://github.com/evanseitz/squid-manuscript as of commit 5b47a7d), with the addition that all intermediate and final outputs are provided here.</p>
Source Data for Manuscript "Sodium salicylate improves detection of amplitude-modulated sound in mice"
<p>This repository contains the source data for our papers <strong>Sodium salicylate improves detection of amplitude-modulated sound in mice </strong>(van den Berg*, Wong*, Houtak, Williamson, Borst). The code to generate figure panels can be found in our github repository at https://github.com/aaronbwong/salicylateonam</p>
Dataset for manuscript "During haptic communication, the central nervous system compensates distinctly for delay and noise"
<p>Data relating to the manuscript "Dataset for manuscript "During haptic communication, the central nervous system compensates distinctly for delay and noise". This includes the experiment dataset (in file experiment_dataset.csv) as well as the MATLAB functions used for the development of the simulation model (with main function main_delay.m)</p>
Datasets of the DIMet manuscript
<p>Datasets for reproducing the results of the manuscript "<em>DIMet : An open-source tool for Differential analysis of targeted Isotope-labeled Metabolomics data". </em>DIMet tool is available <a href="https://github.com/cbib/DIMet/">here</a>, and the tool documentation is accessible in the <a href="https://github.com/cbib/DIMet/wiki/">DIMet wiki page </a>and in its Galaxy site.</p> <p><strong> </strong>Users of the <strong>Galaxy version of DIMet:</strong></p> <ul> <li>download and decompress (unzip) the .zip file.</li> <li>within the 'datasets_manuscript_DIMet/' there is a sub-folder <strong><em>data/</em></strong>, preserve.</li> <li>within 'datasets_manuscript_DIMet/' there is a sub-folder <em>config/,</em> the user can delete it as it is not used in the Galaxy version.</li> <li>use the .csv files that are provided in <strong><em>data/</em></strong> . The specific .csv files to be given as input are explained in each 'dimet_' module in Galaxy.</li> <li>check <em> metadata_endo_ldh.csv</em> and <em>metadata_timeseries.csv</em> files: if all the content has quotes (") for delimiting the strings, please edit the file in a plain text editor (e.g. Notepad, Gedit, etc) and delete such quotes (replace all " by no character). These quotes (") in the samples metadata, which are tolerated in the command line version, are not allowed in the galaxy version.</li> </ul> <p> Users of the <strong>command-line</strong> version of <strong>DIMet</strong>:</p> <ul> <li>download, decompress it and follow the instructions of the documentation in the <a href="https://github.com/cbib/DIMet/wiki/">DIMet wiki page</a>.</li> </ul>
Supplementary datasets for manuscript titled: Seasonal tissue-specific gene expression in wild crown-of-thorns starfish reveals reproductive and stress-related transcriptional systems
<p>Supplementary datasets for manuscript titled: Seasonal tissue-specific gene expression in wild crown-of-thorns starfish reveals reproductive and stress-related transcriptional systems</p>
Dataset underlying the manuscript: MAViS: Modular Autonomous Virtualization System for Two-Dimensional Semiconductor Quantum Dot Arrays
<p>Datasets underlying the manuscript. Information on how to run the scripts is detailed in the README file.</p>
Dataset and Input Files for the "Sustainability and Resilience Through Connection: The Economic Metacommunites of the Western USA" Manuscript
<p>Datasets and input files used for the Ecology and Society manusript "Sustainability and Resilience Through Connection: The Economic Metacommunites of the Western USA". </p>
Data for manuscript: A framework for integrating genomics, microbial traits, and ecosystem biogeochemistry
<p>Support manuscript: A framework for integrating genomics, microbial traits, and ecosystem biogeochemistry. </p> <p>Dataset includes 1) model and analysis, and 2) supplemental data. </p> <p>In the "model_analysis" file, we include the ecosys model source code, the modeling runs, and the modeling results. The detailed introduction is in README.md file. </p> <p><strong>Acknowledgments</strong></p> <p>We thank the EMERGE Biology Integration Institute Coordinators (members listed in Supplementary Information) for project guidance and management. This research is a contribution of the EMERGE Biology Integration Institute, funded by the National Science Foundation, Biology Integration Institutes Program, Award # 2022070 (V.I.R., R.K.V., S.R.S., M.B.S., E.L.B., and the EMERGE Coordinators). Additional support for individual contributors included the following. Z.L. was additionally supported by Lawrence Livermore National Laboratory under the auspices of the U.S. Department of Energy under contract DE-AC52-07NA27344. W.J.R. was supported by the Belowground Biogeochemistry Scientific Focus Area and U.K. was supported by the Watershed Function Science Area, both funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under contract no. DE-AC02-05CH11231. G.L.M. was supported by the LLNL "Microbes Persist" Soil Microbiome Scientific Focus Area SCW1632 and an associated KBase award SCW1746. N.J.B. was supported by the US Department of Energy, Office of Science (BER), Early Career Research Program (#FP00005182). B.J.W. was supported by an Australian Research Council Future Fellowship (#FT210100521). J.T. was supported by the Laboratory Directed Research and Development Program of Lawrence Berkeley National Laboratory. </p> <p>We thank the Swedish Polar Research Secretariat and SITES for the support of the work done at the Abisko Scientific Research Station. SITES is supported by the Swedish Research Council’s grant 4.3-2021-00164. This research used resources of the National Energy Research Scientific Computing Center (NERSC) which is a U.S. Department of Energy Office of Science user facility. This research used the Lawrencium computational cluster resource provided by the IT Division at the Lawrence Berkeley National Laboratory (Supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231). </p> <p><strong>Full list of the EMERGE Biology Integration Institute Coordinators and Affiliations</strong></p> <p>Eoin L. Brodie1,2, Sarah C. Bagby3, Jeffrey P. Chanton4, Jessica G. Ernakovich5, Regis Ferriere6,7, Suzanne B. Hodgkins8, William J. Riley1, Virginia I. Rich8,9, Scott R. Saleska6, Matthew B. Sullivan8,9,10, Ruth K. Varner11, Gene W. Tyson12, Malak M. Tfaily13, Ahmed A. Zayed8,9<br> 1Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory; Berkeley, CA 94720, USA.<br>2Department of Environmental Science, Policy and Management, University of California; Berkeley, CA 94720, USA.<br>3Department of Biology, Case Western Reserve University; Cleveland, OH, USA, 44106<br>4Earth Ocean and Atmospheric Sciences, Florida State University; Tallahassee, FL, USA<br>5Department of Natural Resources and the Environment, University of New Hampshire;<br>Durham, NH, USA 03824<br>6Department of Ecology and Evolutionary Biology, University of Arizona; Tucson, AZ,<br>85721, USA<br>7Institut de Biologie de l’ENS, Université Paris Sciences & Lettres; Paris, 75005, France<br>8Department of Microbiology, The Ohio State University; Columbus, OH, USA, 43210<br>9Center of Microbiome Science, The Ohio State University; Columbus, Ohio 43210, USA.<br>10Department of Civil, Environmental and Geodetic engineering, The Ohio State University; Columbus, Ohio 43210, USA.<br>11Department of Earth Sciences and Institute for the Study of Earth, Oceans and Space, University of New Hampshire; Durham, NH 03824, USA.<br>12Centre for Microbiome Research, School of Biomedical Sciences, Queensland University<br>of Technology (QUT), Translational Research Institute; Woolloongabba, QLD, Australia<br>13Department of Environmental Science, University of Arizona; Tucson, AZ, 85721, USA</p>
Dataset for manuscript Tracing Quartz Provenance: A Multi-Disciplinary Investigation of Luminescence Sensitisation Mechanisms of Quartz from Granite Source Rocks and Derived Sediments
<p><span>Quartz optically stimulated luminescence (OSL) sensitivity as well as some electron spin resonance (ESR) and cathodoluminescence (CL) signals have been empirically proposed as provenance indicators. Sensitivity is defined as luminescence emitted in response to a given dose per unit mass. While it is largely believed to be acquired by earth surface processes, recent studies bring evidence that sensitisation processes depend on source geology.</span></p> <p><span>Here we combine OSL and thermoluminescence (TL), ESR and CL analyses to understand the mechanisms of quartz OSL sensitisation. We investigate granites and their derived sediments from catchments draining simple lithologies of known age that display contrasting OSL sensitisation behaviour both in nature and during irradiation and light exposure laboratory experiments. The sample displaying increased OSL sensitisation is characterised by TL emission at intermediate temperatures (150-250 °C), Ti-related signals in CL, and Ti and Ge lithium compensated signals in ESR. <span>The insensitive samples either lack or exhibit very weak such characteristics and contain several times less amount of trace titanium measured by </span></span><span>laser ablation inductively coupled plasma mass spectrometry (</span><span>LA-ICP-MS).</span></p> <p><span>We demonstrate that the OSL sensitisation results as an effect of the existence of certain defects and impurities in the quartz crystal in the parent rock, such as titanium and germanium. However, the degree of sensitisation reached in nature is significantly higher than in the laboratory. <span> </span>As such, the existence of this precursor represents the potential for sensitisation, which can later be amplified by environmental factors during sedimentary history.</span></p>
Data set associated to the manuscript entitled Carbon emissions from inland waters may be underestimated: evidence from European river networks fragmented by drying by López-Rojo et. al
<p>CO2 and CH4 emissions and several associated environmental variables were taken in 6 European drying river networks, in 20 river reaches per river network. The field work was carried across 3 sampling campaigns in 2021, coinciding with 3 hydrological seasons (pre-dry, dry and post-rewetting) to encompass most of the hydrological variability. Each time, measures were taken in the habitats available (flowing water, dry riverbeds, isolated pools).</p>
Raw Data and Scripts for manuscript submitted to Oikos as 'Early Spring Snowmelt and Summer Droughts Strongly Impair the Resilience of Key Microbial Communities in a Subalpine Grassland Ecosystems'
<p>Raw Data and Scripts for manuscript submitted to PCI as 'Early Spring Snowmelt and Summer Droughts Strongly Impair the Resilience of Key Microbial Communities in Subalpine Grassland Ecosystems'</p>
Raw and analyzed data to manuscript "Influence of air plasma pretreatments on mechanical properties in metal-reinforced laminated wood"
<p><strong>Abstract</strong><br> The use of wood-based materials in building and construction is constantly increasing as environmental aspects and sustainability gain importance. For structural applications, however, there are many examples where hybrid material systems are needed to fulfil the specific mechanical requirements of the individual application. In particular, metal reinforcements are a common solution to enhance the mechanical properties of a wooden structural element. Metal-reinforced wood components further help to reduce cross-sectional sizes of load-bearing structures, improve the attachment of masonry or other materials, enhance the seismic safety and tremor dissipation capacity, as well as the durability of the structural elements in highly humid environments and under high permanent mechanical load. A critical factor to achieve these benefits, however, is the mechanical joint between the different material classes, namely the wood and metal parts. Currently, this joint is formed using epoxy or polyurethane (PU) adhesives, the former yielding highest mechanical strengths, whereas the latter presents a compromise between mechanical and economical constraints. Regarding sustainability and economic viability, the utilization of different adhesive systems would be preferable, whereas mechanical stabilities yielded for metal-wood joints do not permit for the use of other common adhesive systems in such structural applications.<br> This study extends previous research on the use of non-thermal air plasma pretreatments for the formation of wood-metal joints. The plasma treatments of Norway spruce (Picea abies (L.) Karst.) wood and anodized (E6/EV1) aluminum AlMgSi0.5 (6060) F22 were optimized, using water contact angle measurements to determine the effect and homogeneity of plasma treatments. The adhesive bond strengths of plasma-pretreated and untreated specimens were tested with commercial 2-component epoxy, PU, melamine-urea formaldehyde (MUF), polyvinyl acetate (PVAc), and construction adhesive glue systems. The influence of plasma treatments on the mechanical performance of the compounds was evaluated for one selected glue system via bending strength tests. The impact of the hybrid interface between metal and wood was isolated for the tests by using five-layer laminates from three wood lamellae enclosing two aluminum plates, thereby excluding the influence of congeneric wood-wood bonds. The effect of the plasma treatments is discussed based on the chemical and physical modifications of the substrates and the respective interaction mechanisms with the glue systems. </p>
Dataset for the manuscript "ExSTED microscopy reveals contrasting functions of dopamine and somatostatin CSF-c neurons along the central canal"
<p>Description: Dataset that supports the expansion-STED and light sheet microscopy methods in spinal cord and support the findings in the manuscript: ExSTED microscopy reveals contrasting functions of dopamine and somatostatin CSF-c neurons along the central canal (Elham Jalalvand, Jonatan Alvelid, Giovanna Coceano, Steven Edwards, Brita Robertson, Sten Grillner, Ilaria Testa).</p> <p>The software used to open the files and perform the analysis: Imspector v0.10_rev8575 and ImageJ 1.52i.</p> <p>The preprint of the manuscript can be found here: https://doi.org/10.1101/2021.08.17.456595</p>
Data used in the manuscript: "Influence of coastal vegetation on the 2004 tsunami wave impact in west Aceh"
<p>The data set presented accompanies the study by Laso Bayas et al. (2011) “Influence of coastal vegetation on the 2004 tsunami wave impact in west Aceh”. The data set contains all the observed (not transformed) variables used in the above mentioned study. The accompanying text file describes each of the variables included. A total of 180 transects were employed for the Laso Bayas et al (2011) study. The variables were further standardized and simplified to use them into the statistical models described in the paper.</p>
Medieval manuscripts and their migrations: Using SPARQL to investigate the research potential of an aggregated Knowledge Graph
<p>This dataset contains the <strong>SPARQL queries</strong> presented and discussed in our article published in <em>Digital Medievalist</em> 2022 (as a PDF file), together with the <strong>results of those queries</strong> as CSV files. The query and step numbering follows that given in the article.</p> <p>The queries can be run against the SPARQL endpoint for the <strong>Mapping Manuscript Migrations</strong> project: <a href="https://ldf.fi/mmm/sparql">https://ldf.fi/mmm/sparql</a></p> <p>The full <strong>Mapping Manuscript Migrations dataset </strong>can also be downloaded from the Zenodo repository and installed in your own triple store: <a href="https://zenodo.org/record/4440464">https://zenodo.org/record/4440464</a></p> <p>When copying and pasting these SPARQL queries into a SPARQL client like <a href="https://yasgui.triply.cc/">YASGUI</a>, please check that the line numbering has been copied over correctly. Copying from a PDF file can sometimes break a single long line into multiple separate lines, which will cause a SPARQL validation error.</p> <p>The CSV files contain the results of the queries when run against the Mapping Manuscript Migrations SPARQL endpoint as of 17 December 2021. Please note that Query 2, Step 2, produces no results, so a CSV file has not been provided.</p> <p>The<strong> Mapping Manuscript Migrations portal </strong>can be found at <a href="https://mappingmanuscriptmigrations.org/en/">https://mappingmanuscriptmigrations.org/en/ </a></p> <p>SPARQL tutorials are included in the project's <strong>GitHub documentation</strong>: <a href="https://mapping-manuscript-migrations.github.io/">https://mapping-manuscript-migrations.github.io/</a></p>
Raw and analyzed data for manuscript "The synergistic effect of microwave drying and plasma surface treatments on the wettability of green wood"
<p><strong>Abstract:</strong></p> <p>In spite of being a one-step solution to several problems associated with woodworking and being energy efficient, the application of microwave (MW) modification in wood research remained very limited and the promising method has practically no use in wood industries across the globe. Research done so far in this field primarily sheds light on its potential in enhancing wood permeability, treatability and uniform wood drying. While MW treatments are mostly used on wet or green wood, another modification technique, plasma, has potential benefits to synergistically enhance effects of MW treatment, but has not been applied on wet or green wood specimens, so far. This study takes a first step to investigate effects of plasma treatments (PT) on green wood specimens as well as combinations of MW and plasma treatments. As a preliminary study, the methodology focuses on water contact angle measurements, since these are most commonly used as indicators for surface modifications in industrial applications. On the investigated samples of Norway spruce (<em>Picea abies</em> Karst.), an exponential time dependence was found for the contact angle. Initial contact angle after droplet deposition increased due to drying and migration of organic molecules during treatments. In comparison to the literature, the effect of plasma was significantly less pronounced on wet wood specimens. The initial contact angle showed lowest statistical variations after MW treatment, whereas plasma increased inhomogeneities. The final contact angle on treated specimens was lowest for PT-only specimens as well as specimens treated with plasma after MW. In contrast to the initial contact angle, the final contact angle showed lowest variations after PT. Wetting rates were insignificantly improved by plasma, with reduced statistical variations after all treatments.</p>
Data and statistical analysis scripts for manuscript on wheat root response to nitrate using X-ray CT and OpenSimRoot
<p>Data and statistical analysis scripts for manuscript on wheat root response to nitrate using X-ray CT and OpenSimRoot</p> <blockquote> <p><strong>X-ray CT reveals 4D root system development and lateral root responses to nitrate in soil </strong>- [<a href="https://doi.org/10.1002/ppj2.20036">https://doi.org/10.1002/ppj2.20036</a>]</p> </blockquote> <p>The ZIP file contains:</p> <ul> <li><code>MCT1_Rcode.R</code> - Statistics script for candidate single-timepoint experiment. Requires all CSV data files in the directory. User needs to set working directory to location of this script and the CSV data files before running.</li> <li><code>MCT1... .csv</code> - 3 CSV data files required by the R script.</li> <li><code>MCT2_Rcode.R</code> - Statistics script for time-series experiment. Requires all CSV data files in the directory. User needs to set working directory to location of this script and the CSV data files before running.</li> <li><code>MCT2... .csv</code> - 3 CSV data files required by the R script.</li> <li><code>R_RooThProcessing.R</code> - R code for aggregating root traits from RooTh software.</li> <li><code>Modelling folder</code> - OpenSimRoot with model parameters and root data used in manuscript.</li> </ul>
Extended data for Manuscript: Identification of potential biological targets of oxindole scaffolds via in silico repositioning strategies
<p>This is the Extended Data for the manuscript "<strong>Identification of potential biological targets of oxindole scaffolds via <em>in silico</em> repositioning strategies" </strong>submitted to F1000 Research.</p> <p>Extended Data include a list of all the accession codes as mentioned in the text, the results of 2D fingerprint-based similarity analyses and ligand-protein complexes predicted by rigid docking and Induced Fit Docking calculations.</p>
Data used to create figures and tables in the ACP manuscript "Two-way coupled meteorology and air quality models in Asia: a systematic review and meta-analysis of impacts of aerosol feedbacks on meteorology and air quality" by Gao et al. (2022)
<p>This dataset contains the original data that extracted from all collected papers refering applications of two-way coupled models in Asia. It is supplied to the review paper, which titled as "Review on two-way coupled meteorology and air quality models in Asia: impacts of aerosol feedbacks on meteorology and air quality". The dataset includes three excel files (in the format of xlsx) as follows:</p> <p>1. Basic information of literatures (Table S1.xlsx)</p> <p>2. Model performance metrics (Table S2.xlsx)</p> <p>3. Quantitative results of aerosol effects on meteorological and air quality variables (Table S3.xlsx)</p> <p>4. Basic information of model setup for two-way coupled model applications in Asia (Table S4.xlsx)</p> <p>5. Summary of aerosol-induced variations of simulated shortwave and longwave radiative forcing at the bottom and top of atmosphere and in the atmosphere in Asia (Table S5.xlsx)</p> <p>.</p>
Supplementary Data for the manuscript 'The Rad9-Rad1-Hus1 DNA repair clamp is found in Microsporidia'
<p>This dataset contains the supplementary data files for the manuscript titled 'The Rad9-Rad1-Hus1 DNA repair clamp is found in Microsporidia'.</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.