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2,904 results for “Solute”
Data and code for "A Linear Time Solution to the Labeled Robinson-Foulds Distance Problem"
<p><strong>Data and code for "A Linear Time Solution to the Labeled Robinson-Foulds Distance Problem"</strong></p> <p>Samuel Briand, Christophe Dessimoz, Nadia El-Mabrouk, Yannis Nevers</p> <p> </p> <p><strong>Experimental data</strong></p> <p>The __ALF\_Output__ directory contains the results obtained from ALF with parameters specified in the paper, as well as additional files generated in the downstream analysis (see below)</p> <p>The __Partitions__ directory contains one directory by partitioning of the 100 species from ALF in nested sets. Each contains three folder and a file.</p> <p> The summary.txt directory report which family are part of the nested set.</p> <p> The Allfamily directory contains the FASTA file of the 100 gene families generated with ALF, with only the species selected in the partition.</p> <p> The Aln directory contains the MSA for each gene family as generated with MAFFT with the selected species set</p> <p> The FTree directory contains the gene tree for each family as generated with FastTree with the selected species set</p> <p>The __Script__ directory containst the files used to generated the data from the ALF directory, as well as downstream analysis</p> <p> </p> <p> </p> <p>To reproduce the results start by runing __rewriteSeq.py__ , which is used for generating the Partitions. It takes as parameter the ALF directory, the directory in which you wish to generate the partitions, and the path to ALF's genomes FASTA files. If the partition file already exist, you can use the -r option to redo the random selection, otherwise it will generate file for the previous random selection. </p> <p>Example command :</p> <p>python rewriteSeq.py -i ../ALF\_output -o ../Partitions -g ../ALF\_output/DB</p> <p> </p> <p>Then, by runing __rewriteTree.py__ you will generated the reference trees used for the RF comparisons, as well as species tree used for each partitions. It takes as parameters the ALF directory , the Partitions directory and the species file of the partitions used to create the reference tree (smallest of all partitions)</p> <p>Example command :</p> <p>python rewriteTree.py -i ../ALF\_output/ -p ../Partitions/ -s ../Partitions/Part10/summary.txt</p> <p> </p> <p>Then, the script __launchFastTree.sh__ will, by partitions, generate a MSA using MAFFT and a phylogenetic tree using FastTree. It takes as parameter the Partitions directory and the number of the identifier of the partition for which you wish tu run it. Notes that the afforementionned software need to be installed before hand.</p> <p>Example command:</p> <p>bash launchFastTree.sh ../Partitions 10</p> <p> </p> <p>Finally, the __LRFAnalysis.ipynb__ file is a Jupyer Notebook used to run downstream analysis of RF and LRF on the different Partitions, including figure generation. Path to the data directory can be set in the 4th block of the Notebook.</p> <p> </p> <p><strong>Comparison of RF, LRF, and ELRF</strong></p> <p> </p> <p>The code to compare is provided as a Jupyter notebook in the directory "Comparison with RF and ELRF". The input NOX4 family from Ensembl version 99 is provided. The output figures are provided as PDF but they can be regenerated by running the notebook.</p> <p> </p>
Experiment results and codes for: A novel systems solution for accurate colorimetric measurement through smartphone-based augmented reality
<p>This dataset includes the images, codes and Excel files of the results of 2 synthetic and 2 real experiments in the Section "Experiment". This dataset also includes anonymous pH human reading records. In addtion, two new experiments for comments from reviewers are added.</p>
Emergent Solutions on Requirement Engineering for Agile Software Development: A tertiary study (Auxiliary Documentation in PDF)
<p><strong>[Context and motivation]</strong> Agile Software Development (ASD) is a new trend in software development and has become popular. Its advocates claim that ASD is well suited to solving traditional software development problems by valuing human factors over technical ones. However, one of the most critical phases in software development, Requirements Engineering (RE), can be overwhelming for ASD values.<br> <strong>[Question/problem]</strong> Trying to work with RE in a traditional way for ASD can limit ASD's potential. Therefore, it is necessary to investigate what academia and industry have done in RE to exploit all of the capabilities of ASD beyond traditional RE. <br> <strong>[Principal ideas/results]</strong> This work presents an overview of the state-of-the-art Requirement Engineering (RE) for Agile Software Development (ASD). We conducted a Tertiary Study in secondary studies published from 1st January 2015 to 30th June 2021, looking for solutions for RE-ASD using the Systematic Literature Review (SLR) protocol described by Kitchenham and Charters (2007). After executing the SLR protocol, we accepted 37 out of 169 studies and encountered 136 solutions used by academia and industry for RE-ASD. We considered only a few solutions that could be classified as emergent for RE-ASD, 24 out of 106. Furthermore, we cataloged the challenges presented by the emergent solutions (e.g., a steep learning curve due to the lack of experience, process, or culture) that should be addressed. Finally, we identified a possible gap between academia and industry regarding these emerging solutions that need further investigation. <br> <strong>[Contribution]</strong> By highlighting emerging Requirements Engineering (RE) solutions for Agile Software Development (ASD), we made our contribution to help researchers who need to propose new solutions to some of the problems that remain unsolved by pointing out the recent trends for RE for ASD.</p> <p>The repository contains the following:</p> <ul> <li>Auxiliary Documentation in PDF;</li> <li>Dataset from the Tertiary Study - compressed file (refsq2023Complement.zip): <ul> <li> <p><strong>REFSQ2023-ALL-ARTICLES.csv:</strong> is a comma-separated file with all 198 (including the duplicates) found in our search in the digital libraries with their respective status (accepted, rejected, or duplicated).</p> </li> <li> <p><strong>REFSQ2023-DISTINCT-SOLUTIONS.csv:</strong> is a comma-separated file with all the distinct solutions we found in our research. They are classified according to our classification method, explained in the article.</p> </li> <li> <p><strong>REFSQ2023-GOOGLE-TRENDS-RESULTS.csv:</strong> is a comma-separated file with all results of our query in the Google Trends tool. It also brings the used search terms and the code and classification of each solution.</p> </li> </ul> </li> </ul>
Data set for: "Model atmospheric aerosols convert to vesicles upon entry into aqueous solution"
<p>This document compiles raw data used in the aerosol to vesicle transformation study carried out by <strong>Serge Nader <em>et al.</em></strong><br> For detailed information and context, refer to the main article and its supplementary material published in ACS Earth and Space Chemistry.</p> <p>The Excel file contains data relevant to each figure in the main article and supporting information. The additional compressed file contains raw Transmission Electron Microscopy (TEM) photographs.</p>
Solution of convection equation with compact scheme different sub-domain closures.
<p>Solution of convection equation with CFL number, Nc = 0.001. Computational domain extends from -1 to 19 and from -1 to +1 in x- and y- directions; 2001\times201 equidistant points are sub divided into 10x2 processors. The solid black lines indicate the processor boundary. RK4-OUCS3 scheme is used with CD8 sub-domain closure in the top frame and NOHAP closure is used in the bottom frame</p>
Circumbinary Periodic Solutions in the CR3BP
<p>HDF5 files containing initial conditions, periods, Jacobi constant, and Floquet stability of circumbinary periodic trajectories in the Circular Restricted Three-body Problem. </p>
Data: Thermodiffusion of aqueous solutions of various potassium salts
<p>Data, which are presented in the following publication: Mohanakumar, Shilpa; Luettmer-Strathmann, Jutta; Wiegand, Simone (2021): Thermodiffusion of aqueous solutions of various potassium salts. In: J Chem Phys 154 (8), S. 84506. DOI: 10.1063/5.0038039.</p>
A Model Instability Issue in the NCEP Global Forecast System Version 16 and Potential Solutions
<p>This dataset includes the GFSv16 model source code and the scripts and data to plot the figures for the manuscript</p> <p>" A Model Instability Issue in the NCEP Global Forecast System Version 16 and Potential Solutions" submitted to GMD</p>
Supplementary Materials for "Temperature field, flow field and temporal fluctuations thereof 2 in ammonothermal growth of bulk GaN – transition from dis-3 solution stage to growth stage conditions"
<p>Video S1: dissolution stage (upper part of nutrient and above), Video S2: 630 dissolution stage (baffle region), Video S3: dissolution stage (top seed), Video S4: dissolution stage 631 (middle seed), Video S5: dissolution stage (bottom seed), Video S6: growth stage (upper part of 632 nutrient and above), Video S7: growth stage (baffle region), Video S8: growth stage (top seed), Video 633 S9: growth stage (middle seed), Video S10: growth stage (bottom seed).</p>
Modeling water flow and solute transport in unsaturated soils using physics-informed neural networks trained with geoelectrical data
<p>Numerical codes and results for the article: Modeling water flow and solute transport in unsaturated soils using physics-informed neural networks trained with geoelectrical data</p>
Data for Sleep cycle-dependent vascular dynamics and the predicted effects on perivascular cerebrospinal fluid flow and solute transport
<p>Datasets containing derived data and results used by code in: https://github.com/AlexandraVallet/PVSflow for "Sleep cycle-dependent vascular dynamics and the predicted effects on perivascular cerebrospinal fluid flow and solute transport", Bojarskaite et al. 2023. Please see github for instructions. </p>
Electronic Structure and Optical Properties of Tin Iodide Solution Complexes
<p>(TD)DFT+PCM study on the structural, electronic, and optical properties of 14 tin-iodide-solution complexes with the chemical formula SnI<sub>2</sub>M<sub>4</sub>, with M one of 14 common solvent molecules.</p>
FIGURE 2 in Ecology determines appearance: a new taxonomic solution for the soft bottom dwelling spider crab Pisoides bidentatus (A. Milne-Edwards, 1873) from the Sea of Japan, with remarks on Pisoides ortmanni (Balss, 1924) and the northwestern Pacific Pugettia Dana, 1851 (Majoidea: Epialtidae)
FIGURE 2. Scyra bidentata (A. Milne-Edwards, 1873) comb. nov., ZMMU Ma-6228, coloration and camouflage (dorsal view) of living specimens, Vostok Bay of the Sea of Japan. Scale 10 mm.
FIGURE 6 in Ecology determines appearance: a new taxonomic solution for the soft bottom dwelling spider crab Pisoides bidentatus (A. Milne-Edwards, 1873) from the Sea of Japan, with remarks on Pisoides ortmanni (Balss, 1924) and the northwestern Pacific Pugettia Dana, 1851 (Majoidea: Epialtidae)
FIGURE 6. Scyra bidentata (A. Milne-Edwards, 1873) comb. nov., ZMMU Ma-6226, ♁, gonopod I (a–f) and gonopod II (g–j): a—gonopod I, general view; b–f—tip of gonopod I, different views; g,h—gonopod II, different views; i, j—tip of gonopod II, different views. Scale 1 mm.
FIGURE 1 in Ecology determines appearance: a new taxonomic solution for the soft bottom dwelling spider crab Pisoides bidentatus (A. Milne-Edwards, 1873) from the Sea of Japan, with remarks on Pisoides ortmanni (Balss, 1924) and the northwestern Pacific Pugettia Dana, 1851 (Majoidea: Epialtidae)
FIGURE 1. Bayesian and Maximum Likelihood phylogenetic trees of the family Epialtidae for combined molecular data (concatenated sequences from COI, 16S rRNA and 18S rRNA gene fragments). Number above or under the brunches are Bayesian posterior probabilities and bootstrap values for ML analysis.
FIGURE 4 in Ecology determines appearance: a new taxonomic solution for the soft bottom dwelling spider crab Pisoides bidentatus (A. Milne-Edwards, 1873) from the Sea of Japan, with remarks on Pisoides ortmanni (Balss, 1924) and the northwestern Pacific Pugettia Dana, 1851 (Majoidea: Epialtidae)
FIGURE 4. Scyra bidentata (A. Milne-Edwards, 1873) comb. nov., ZMMU Ma XXXX, ♁ (a, c, e–g), ♀ (b, d), fixed specimens, Vostok Bay of the Sea of Japan: a, b—carapace (lateral view); c, d—front of carapace, ventral view; e—front of carapace, lateral view; f—front of carapace, dorsal view; g—carapace and sternites, ventral view. Scale 5 mm.
FIGURE 5 in Ecology determines appearance: a new taxonomic solution for the soft bottom dwelling spider crab Pisoides bidentatus (A. Milne-Edwards, 1873) from the Sea of Japan, with remarks on Pisoides ortmanni (Balss, 1924) and the northwestern Pacific Pugettia Dana, 1851 (Majoidea: Epialtidae)
FIGURE 5. Scyra bidentata (A. Milne-Edwards, 1873) comb. nov., ♁, ZMMU Ma-6226 (a, b), ♀, ZMMU Ma-6227 (c), fixed specimens, Vostok Bay of the Sea of Japan: a—chela of pereiopod I (chelipeds), outer view; b—pereiopod II; c—sterno-pleonal cavity. Scale 5 mm.
FIGURE 3 in Ecology determines appearance: a new taxonomic solution for the soft bottom dwelling spider crab Pisoides bidentatus (A. Milne-Edwards, 1873) from the Sea of Japan, with remarks on Pisoides ortmanni (Balss, 1924) and the northwestern Pacific Pugettia Dana, 1851 (Majoidea: Epialtidae)
FIGURE 3. Scyra bidentata (A. Milne-Edwards, 1873) comb. nov., ZMMU Ma-6226 (♁) and Ma-6227 (♀), fixed specimens (dorsal view), Vostok Bay of the Sea of Japan. Scale 10 mm.
A numerical exploration of hyporheic zone solute transport behavior estimated from electrical resistivity inversions
<p>1). We run the Comsol model (ER3D_cs300ws6ds20_Zxl1.m) with an electrical push-pull loop, and then the voltage at every electrode of each time is printed to model_name.out and resistivity to model_name.ro. </p> <p>2). superposition.m is used to create final voltage results for later use in R2 inversions.</p> <p>3). postproc_c_dual.m is used to create the pixel breakthrough curves of the simulated results.</p> <p>4). plot_c_comsol.m read the resistivity result from step (1), convert the resistivity to bulk EC, and plot the bulk EC contour map. </p> <p>5). protocal_pc.m is used to take the voltages, add some random noise, and make the input files and batch scripts for R2.</p> <p>6). runr2.bat and runr2_TL.bat are used to generate inverted bulk EC.</p> <p>7). plot_C_r2_dual.m is used to plot the inversed bulk EC.</p>
Data created in a stakeholder analysis of selected cases of Nature-Based Solutions in Scotland
<p>These data represent the results of a stakeholder analysis of selected cases of catchment-related 'Nature-Based Solutions' (NbS) in Scotland. This arose from a desk-based study to examine publicly-accessible website content and associated reports to assess the actors involved in Nature-Based Solutions (NbS), their attributes, and relationship to six NbS related initiatives in Scotland. These data were collected and analysed November 2022-March 2023. Please see the first tab for more information about the study, and the content on each of the tabs of the spreadsheet.</p> <p>This was carried out as part of investigation into Scaling and Mainstreaming Nature-based Solutions: WP4 of Project JHI-D2-2 in the 2022-2027 Strategic Research Programme funded by the Scottish Government. Please visit https://www.hutton.ac.uk/research/projects/scaling-and-mainstreaming-nature-based-solutions for more information about this project and a report which accompanies and used these data.</p>
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