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2,682 results for “implementation”
theoretical and experimental study of the deposition of dielectric stacks on twin-hole silica fibers for implementation of compact all-fiber resonators
<p>This dataset includes the Matlab code to engineer theoretically a Bragg stack made of different dielectric layers. By changing the number of alternating stacks, their thickness and the refractive index of each layer it is possible to obtain the transmission curve of the Bragg stack versus the wavelength of the light in a certain range of values. The dataset includes also the experimental measurements of the resonances related to one of the fabricated compact resonators (based on the twin-hole fiber not poled) and obtained sweeping the wavelength of the input light injected through one of the two Bragg stacks and collecting the power at the exit of the other Bragg stack. </p>
Data for common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline
<p>This upload contains the HZV029 Plasma and HZV029 Two-Phase dataset for reviewers of the "Data for common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline" submission. </p> <p>Both datasets will be uploaded to metabolomics workbench and the upload completed before final publication of the manuscript. For the he HZV029 Plasma datasets only the final run is included for any sample (i.e., failed injections or other samples with data quality issues that were reran during acquisition were omitted).</p> <p>Also included in the upload is the source code for the MetDataModel and the pcpfm at the time of manuscript re-submission and the pcpfm itself. If you find this upload in the future, please check out the github repos for more updated versions:</p> <p>https://github.com/shuzhao-li-lab/PythonCentricPipelineForMetabolomics</p> <p>https://github.com/shuzhao-li-lab/metDataModel</p> <p>The github repo does not store the input the data for space reasons, they only have the notebooks. However, the .zip here has both the notebooks by themselves in the notebook subdirectory and a separate directory with the notebooks and the data used to generate all the figures and results in the manuscript.</p> <p><strong>Some information that is needed to rerun this analysis:</strong></p> <p>Sequence files are critical to the functioning of the pipeline. The sequence files for all analyses are provided under sequence_files.zip. These can be used to recapitulate the analysis by eitehr changing the filepath to each acquisition to where you put it on your sytem or by placing the sequence file in the same directory as the mzml or raw. In the latter case, the pipeline will search for filenames matching the sample names. The sequence files also store some sample metadata such as the type of sample a given acquisition is (unknown, pooled, qc, etc...)</p> <p>.raw to .mzML conversion works well on MacOS but may not work well on other systems. You will need to use the ability to specify your own conversion command or convert files outside of the pipeline. </p> <p>To replicate the results, you do need to have the annotation sources downloaded which can be done using the pipeline. MS2 annotation requires the files in the AcquireX directory which is MS2 acquisitions on pooled HZV029 plasma samples.</p> <p>For the comparison between MetaboAnalystR and the pcpfm, subsets of the datasets were used. These subsets and the sequence files are in Subsets_for_performance_testing.zip. The sequences are also in the sequence_files directory as well</p> <p>The notebooks reference data in the analysis folders. Copies of these files are located with the notebooks to ease reproduction of the exact results in the paper; however, to do so, you will need to change paths to this data in the notebook. This lets the notebooks be ran during a rerun without copying intermediates back and forth and it keeps the github repo clean.</p> <p><strong>Version History:</strong></p> <p>This version is after reviewer comments and is for resubmission.</p> <p> </p> <p><strong>Contributions:</strong></p> <p>Joshua M Mitchell implemented the pipeline and was first author on the manuscript. Shuzhao Li is the corresponding author on the manuscript. </p> <p>Maheshwor Thapa performed the experiments to collect the HZV029 data. Yuanye Chi helped with testing and documenting the pipeline. </p> <p>Jiangou (Jeff) Xia and Zhiqiang Pang provided the R portion of the analysis. </p>
Multiscale analysis of triglycerides with X-ray scattering: Implementing a shape-dependent model for CNP characterization - Supporting Dataset
<p>This dataset contains the files used to substantiate the outcomes of the publication "<em>Multiscale analysis of triglycerides with X-ray scattering: Implementing a shape-dependent model for CNP characterization</em> <em>" </em></p> <p>The dataset includes:</p> <ul> <li>X-ray scattering profiles - in absolute units</li> <li>Images used to measure CNP distributions</li> </ul> <p>Relevant abbreviations: </p> <ul> <li>SSS - Tristearin</li> <li>OOO - Triolein</li> <li>FHRO - Fully Hydrogenated Rapeseed Oil</li> <li>HOSO - High Oleic Sunflower Oil</li> </ul>
Evaluation Data of the Implementation of the Approach for Automatic Test Generation for Information-Flow Properties
<p>This data set contains the programs for which the automatic test generation approach of the KeY theorem prover was used to automatically generate noninterference tests.</p> <p>The approach is described in <a href="http://dx.doi.org/10.1145/3297280.3297500 ">http://dx.doi.org/10.1145/3297280.3297500 </a></p> <p>DATA<br> ---------<br> The data folder contains the secure and insecure programs which were evaluated and the tests which were generated for them.</p> <p>Each program is in the folder "program" and is written in Java and specified in an extended version of the JML specification language. Check out <a href="http://dx.doi.org/10.5445/IR/1000046878">http://dx.doi.org/10.5445/IR/1000046878</a> for a reference on the used specification language.</p> <p>For each example we provide the tests that were generated. For the insecure examples we provide the tests generated with each of the two options of our approach. The tests generated with the option for searching for counterexamples is in the folder "WithPost" of each insecure example.</p> <p> </p>
Fed4Fire/CDN-X-ALL M3AP, M2AP reference points implementation pcap datatsets for the 3GPP MBMS profile
<p>Following datasets were generated at VICOMTECH (https://www.vicomtech.org) under project/experiment CDN-X-ALL: "CDN edge-cloud computing for efficient cache and reliable streaming aCROSS Aggregated unicast-multicast LinkS".</p> <p>Project funded by Fed4FIRE+ OC5 (<a href="https://www.fed4fire.eu/">https://www.fed4fire.eu</a>) under grant 732638.</p> <p>The following data provide reference pcap captures that include relevant traces with standardized 3GPP interfaces for the 3GPP MBMS (Multimedia Broadcast Multicast Services) profile.</p> <p>Among others, traces include E-UTRAN and Evolved Packet Core pcap captures with standardized 3GPP M2AP and M3AP interfaces and UE MBMS end to end MAC layer PDUs:</p> <p>1- MBMS_OAI_M3AP_M2AP.pcap</p> <p>- OAI eNB LTE; Evolved Universal Terrestrial Radio Access Network (E-UTRAN); M3 Application Protocol (M3AP) in between an MME (Mobility Management Entity) and MCE (Multicast Control Entity) (3GPP TS 36.444 version 14.1.0 Release 14)</p> <p>- OAI eNB LTE; Evolved Universal Terrestrial Radio Access Network (E-UTRAN); M2 Application Protocol (M2AP) in between an MCE (Multicast Control Entity) and eNB (Evolved NodeB) (3GPP TS 36.443 version 14.0.1 Release 14)</p> <p>2- oai_opt_ue_mbms_SIB13_MTCH_MCCH.pcap</p> <p>- OAI UE side LTE MAC and RRC messages</p> <p>Moreover, the above data can be self-re-generated by downloading and building the original open source code pushed (as part of CDN-X-ALL project) to OpenAirInteface5G gitlab open repository. At the time of publishing these data, the original source code falls under branch (https://gitlab.eurecom.fr/oai/openairinterface5g/tree/fed4fire_fec5_cdn-x-all) and is part of ongoing merge request (https://gitlab.eurecom.fr/oai/openairinterface5g/merge_requests/673)</p>
Qualitative dataset - Socially just urban food policy implementation: a case study in Groningen (NL)
<p>This qualitative dataset contains the transcripts of 43 interviews that have been conducted with members of social food initiatives (e.g. community gardens and orchards, food assistance, social restaurants, food education projects, social employment trajectories, fair trade campaigns, and so on) in the city of Groningen, as well as the interview guide and the information sheet and consent form that have been used during data collection. In addition, the upload includes the interview guide, posters, assessment table, information sheet and consent form that have been used in a two-part focus group with 3 food policy coordinators of the municipality of Groningen. The data was collected from November 2019 till March 2020. The transcripts have been analysed in NVivo (qualitative data analysis software).The link to and abstract of the paper based on this dataset will be provided when our manuscript gets published.</p> <p><em>This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 765389. </em></p> <p>Project webpage: <a href="https://recoms.eu/">https://recoms.eu/</a></p>
Dataset for "Implementing a Functional Precision Medicine Tumor Board for Acute Myeloid Leukemia"
<p><strong>Article: Implementing a Functional Precision Medicine Tumor Board for Acute Myeloid Leukemia</strong></p> <p><em>Cancer Discovery</em>, <strong>DOI:</strong> 10.1158/2159-8290.CD-21-0410</p> <p> </p> <p>Data Types:</p> <p>1. Clinical summary</p> <p>2. Drug response data</p> <p>3. Exome-sequencing data</p> <p>4. RNA-sequencing data</p> <p> </p> <p><strong>Updates:</strong></p> <p>- <strong>FILE</strong>: File_3.2. <strong>DATE</strong>: 28.11.2022.</p> <p> </p> <p><strong>1. Clinical summary</strong></p> <p><strong>File_0: </strong>Common sample annotation including patient and sample IDs, stage of the disease, tissue type and availability of different data types.</p> <p><strong>File_1.1: </strong>Clinical data for 186 AML patients including clinical diagnosis, disease classification, gender, age at diagnosis, treatments, cytogenetic and molecular details. The description of the variables/column titles is given below the clinical data.</p> <p><strong>File_1.2</strong>: Description of the clinical variables in File_1.1.</p> <p> </p> <p><strong>2. Drug response data for 164 AML patient samples and 17 healthy samples</strong></p> <p><strong>File_2: </strong>Drug library details for 515 chemical compounds. The compound collection includes drugs names, drug class defined by molecular targets or mode of action, concentration range used for drug testing, supplier information, solvent information and vendor information.</p> <p><strong>File_3.1.: </strong>Drug response data including selective drug sensitivity scores (sDSS) for 515 compounds across 181 samples (164 AML patient samples and 17 healthy control samples). The DSS is modified area under the curve values and are calculated as shown in Yadav et al publication (1). The selective drug sensitivity scores (sDSS) is healthy control normalized DSS that gives estimated cancer-selective drug responses. The higher the sDSS values indicate drug sensitivities and negative sDSS values represent drug resistance.</p> <p><strong>File_3.2.: </strong>Drug response data including drug sensitivity scores (DSS) and selective drug sensitivity scores (sDSS) for 515 compounds across 181 samples (164 AML patient samples and 17 healthy control samples). The data is identical to the Supplementary Table 7 in the manuscript.</p> <p><em>Note: We recommend using selective DSS values instead of raw values (% inhibition, IC50, DSS). </em></p> <p><em>Note: If the value is missing, </em><em>the drug was not tested for </em><em>that</em><em> given sample</em><em>.</em></p> <p><strong>File_4: </strong>Drug sensitivity and resistance testing (DSRT) assay details for 181 samples (164 AML patient samples and 17 healthy control samples). The information includes medium (MCM or CM) used for the drug testing, % cell viability after 72 h without drug testing and blast cell percentage of each sample.</p> <p><em>Note: Column E is </em><em>the ratio of luminescence values at 72 h and 0 h. The fold change in the cell viability without drug treatment was calculated as % cell viability. That is why the value could be more than 100% e.g. 70% cell viability meaning that 30% cells died during 72 h and 300% cell viability meaning that cells grew 3 times in 72 h incubation period.</em></p> <p> </p> <p><strong>3. Exome-sequencing data for 225 AML patient samples</strong></p> <p><em>Note: The number of samples in the manuscript is 226. The correct number used in the analyses is 225.</em></p> <p>Mutation data. The cancer specific gene list was prepared by combining AML related genes from TCGA(2) (n=23), InToGen(3) (n=32), Papaemmanuil et al.(4) (n=111) and Census database(5) (n=616). Out of these genes, we found 340 genes as mutated across 225 AML patient samples. The mutation was called with P-values less than 0.05.</p> <p><strong>File_5: </strong>VAF (variant allele frequency) of 340 cancer-specific genes across 225 AML patient samples. The VAF was calculated using paired skin samples as a control from the same AML patient.</p> <p><strong>File_6:</strong> Binary data for 57 cancer specific genes frequently mutated (a given mutation detected in 5 or more samples) across 225 AML patient samples.</p> <p> </p> <p><strong>4. RNA-sequencing data for 163 AML patient samples and 4 healthy</strong></p> <p>CPM (count per million) data: The CPM values are batch corrected values used for direct comparison of gene expression.</p> <p><strong>File_7:</strong> Log2CPM values for 18,202 protein coding genes across 167 samples (163 AML patient samples and 4 healthy CD34+ samples).</p> <p><strong>File_8: </strong>Raw read count data RNA-seq library information for all 60,619 genes across 167 samples (163 AML patient samples and 4 healthy CD34+ samples). The raw read count data was used to calculate differential gene expression.</p> <p><strong>File_9: </strong>RNA-seq library information including RNA extraction method and sequencing library preparation information for 167 samples (163 AML patient samples and 4 healthy CD34+ samples).</p> <p> </p> <p><strong>References</strong></p> <p>1. Yadav B, Pemovska T, Szwajda A, Kulesskiy E, Kontro M, Karjalainen R<em>, et al.</em> Quantitative scoring of differential drug sensitivity for individually optimized anticancer therapies. Scientific Reports <strong>2014</strong>;4:5193.</p> <p>2. Ley TJ, Miller C, Ding L, Raphael BJ, Mungall AJ, Robertson A<em>, et al.</em> Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med <strong>2013</strong>;368(22):2059-74.</p> <p>3. Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Tamborero D, Schroeder MP, Jene-Sanz A<em>, et al.</em> IntOGen-mutations identifies cancer drivers across tumor types. Nature Methods <strong>2013</strong>;10(11):1081-2.</p> <p>4. Papaemmanuil E, Gerstung M, Bullinger L, Gaidzik VI, Paschka P, Roberts ND<em>, et al.</em> Genomic classification and prognosis in acute myeloid leukemia. New England Journal of Medicine <strong>2016</strong>;374(23):2209-21.</p> <p>5. Tate JG, Bamford S, Jubb HC, Sondka Z, Beare DM, Bindal N<em>, et al.</em> COSMIC: the Catalogue Of Somatic Mutations In Cancer. Nucleic Acids Research <strong>2019</strong>;47(D1):D941-D7.</p> <p> </p>
Dataset: Health worker compliance with severe malaria treatment guidelines in the context of implementing pre-referral rectal artesunate in the Democratic Republic of the Congo, Nigeria and Uganda: an operational study
<p>Dataset underlying the publication "<strong>Health worker compliance with severe malaria treatment guidelines in the context of implementing pre-referral rectal artesunate in the Democratic Republic of the Congo, Nigeria and Uganda: an operational study</strong>" (Plos Medicine)</p> <p>Data originating from the Community Access to Rectal Artesunate for Malaria (CARAMAL) Project, 2018-2021.</p> <p>Analysis of health workers' compliance with the treatment guidelines for severe malaria in the context of rolling out pre-referral rectal artesunate (RAS) in the Democratic Republic of the Congo, Nigeria and Uganda. Details provided in the publication.</p>
Datasets for figures in Implementation and evaluation of Wet Bulb Globe Temperature within non-urban environments in the Community Land Model version 5
<p>The files contain 4 scripts and 6 netcdf files. </p> <p>"laborCap_200400.ncl" uses "Lancet_LRF.nc" to create Figure 1.</p> <p>Script "world_plot_ensemble_Avg.I2000.csh", drives a NCL script, "plot_modern.I2000.WBGT.ncl" to make figures 3 and 4, using the netcdf files, "I2000_PR_22_x1_60_5.exceed.WBGT.20yrs.75_99.nc," "I2000_PR_22_x1_60_5.exceed.WBGT_BG_R.20yrs.75_99.nc," "I2000_PR_22_x1_60_5.exceed.WBGT_BC_R.20yrs.75_99.nc," and "I2000_PR_22_x1_60_5.exceed.WBGT_AC_R.20yrs.75_99.nc."</p> <p>"heatmap.wbgt.v4.org.ncl" uses netcdf "I2000_PR_23_Chicago_x1_60_1.11-17.Chicago.allvars.nc" to create figures 5-7. </p>
Data, code and software to reproduce the article entitled "Modeling soil-plant functioning of intercrops using comprehensive and generic formalisms implemented in the STICS model"
<p>This is the data, code and software to reproduce the article entitled " Modeling soil-plant functioning of intercrops using comprehensive and generic formalisms implemented in the STICS model". Here is a summary of the paper:</p> <p>The growing demand for sustainable agriculture is raising interest in intercropping for its multiple potential benefits to avoid or limit the use of chemical inputs or increase the production per surface unit. Predicting the existence and magnitude of those benefits remains a challenge given the numerous interactions between interspecific plant-plant relationships, their environment and the agricultural practices. Soil-crop models are critical in understanding these interactions in dynamics during the whole growing season, but few models are capable of accurately simulating intercropping systems.</p> <p>In this study, we propose a set of simple and generic formalisms for simulating key interactions in intercropping systems that can be readily included into existing dynamic crop models. This requires simulating important processes such as development, light interception, plant growth, N and water balance, and yield formation in response to management practices, soil conditions, and climate. These formalisms were integrated into the STICS soil-crop model and evaluated using observed data of intercropping systems of cereal and legumes mixtures, including Faba bean-Wheat, Pea-Barley, Sunflower-Soybean, and Wheat-Pea mixtures. We demonstrate that the proposed formalisms provide a comprehensive simulation of soil-plant interactions in various types of bispecific intercrops. The model was found consistent and generic under a range of spring and winter intercrops (nRMSE = 25% for maximum leaf area index, 23% for shoot biomass at harvest, and 18% for yield).</p> <p>This is the first time a complete set of formalisms has been developed and published for simulating intercropping systems and integrated into a soil-crop model. With its emphasis on being generic, sufficiently accurate, simple, and easy to parameterize, STICS is well-suited to help researchers designing <em>in silico</em> the agroecological transition by virtually pre-screening sustainable, manageable intercrop systems adapted to local conditions.</p> <p> </p> <p> </p> <p> </p>
Implementation of GR hydrological models in 95 near-natural catchments across Chile
<p>All the files included here contain the data and calibration results produced for the paper "Exploring parameter (dis)agreement due to calibration metric selection in conceptual rainfall-runoff models" accepted for publication in Hydrological Sciences Journal (HSJ). This database summarizes the calibrated parameter sets for the GR4J, GR5J and GR6J conceptual rainfall-runoff models, all coupled to the CemaNeige snow module (i.e., GRXJ + CemaNeige = GRXJCN), using 12 objective functions. The models are configured for 95 near-natural catchments located in Continental Chile. Each basin is identified by a unique code registered in the National Water Bank (BNA by its acronym in Spanish) by the Chilean Water Bureau (DGA; https://dga.mop.gob.cl/). Meteorological forcings and hypsometric curves for each basin studied are also included.</p> <p>The information is organized as follows:</p> <p>- "01 Forcings" : It includes a "Comma-separated value" file (".csv") per basin (according to the notation "BNA code.csv") which contains daily time series of precipitation (P; mm/d), temperature (°C) and potential evapotranspiration (E; mm/d) for the period 1980-01-01 to 2017-12-31. The daily runoff observations (Q; mm/d) and snow water equivalent (SWE; mm) from Cortés et al. (2017) are included. P and T are estimated from the basin-scale average of the CR2Met v2.0 gridded product, while E was calculated using Oudin's formula.<br> - "02 Hypsometry" : It includes a "Comma-separated value" file (".csv") per basin with elevation (in m a.s.l.) vs. area below elevation (in percentage) in the format required by GR models ("BNA code.csv" notation), and the full hypsometric curve ("BNA code_original.csv" notation) retrieved from the SRTM DEM clipped to the basin of interest.<br> - "03 Calibrated parameters": It includes one sub-directory per basin, containing a summary of the calibrated parameters for each combination of model structure (GR4JCN, GR5JCN and GR6JCN) and objective function.</p> <p>Additionally, we include the following "Comma-separated value" (i.e., ".csv") files:</p> <p>- "BNA_select.csv": list of case study basins (BNA code and name).<br> - "Catchment_attributes_CAMELS-CL.csv": catchments attributes directly obtained from CAMELS-CL.<br> - "Catchment_attributes.csv": catchments attributes used for this study. Note that this file contains re-calculated values for climatic attributes. </p>
Data for "Detection of large-scale cloud microphysical changes within a major shipping corridor after implementation of the IMO 2020 fuel sulfur regulations"
<p>Processed data used for the manuscript "Detection of large-scale cloud microphysical changes within a major shipping corridor after implementation of the IMO 2020 fuel sulfur regulations".</p> <p>Includes input data for kriging algorithm as "SSF1deg_shipkrige_Terra.nc" and output data files as "Data_Terra_[VAR]_[YEAR]_C_M[MONTH].nc" for [VAR] Acld (overcast albedo) or cer (cloud droplet effective radius), [YEAR] the starting year of a three-year period starting with 2002 and ending at 2020 or "clim" for the 2002-2019 climatology, and [MONTH] 1to12 (annual mean) or 9to11 (austral spring).</p> <p>For the output data, "Obs" is the original data, "Est" is the mean counterfactual field obtained via kriging, "lowEst" and "highEst" are the 2.5th and 97.5th percentiles of the kriged fields for each grid box, "krSims" stores the results of the 5,000 simulated kriged fields, "Semivariance" is the binned empirical variogram values, "pVal" is the raw field significance (not adjusted for multiple testing), "nOut" is the number of individually significant grid boxes, "tran" is the transform applied (none for cer, logit for Acld), "iniPhi" and "iniSigma2" are the initial values for the fitted variogram, "Phi" and "Sigma2" are the fitted values using weighted least squares, and "parSel" is the list of selected regressors for the mean function that minimize the Bayesian information criterion.</p>
Background optimization of powder electron diffraction to implement e-PDF technique and study the local structure of iron oxide nanocrystals
<p>The local structural characterization of iron oxide nanoparticles is explored using a total scattering analysis method known as Pair Distribution Function (PDF) (also known as Reduced Density Function) profiles derived from background corrected powder electron diffraction patterns. Due to the strong coulombic interaction between the electron beam and the sample, electron diffraction generally leads to multiple scattering, causing redistribution of intensities towards higher scattering angles and an increased background in the diffraction profile. In addition to this, the electron-specimen interaction gives rise to an undesirable inelastic scattering signal that contributes primarily to the background. The present work demonstrates the efficacy of a pre-treatment of the underlying complex background function, which is a combination of both incoherent multiple and inelastic scatterings that cannot be identical for different electron beam energies. Therefore, two different background subtraction approaches are proposed for the electron diffraction patterns acquired at 80 kV and 300 kV beam energies. From the least square refinement (small-box modelling), both approaches are found to be very promising, leading to a successful implementation of the e-PDF technique to study the local structure of the considered nanomaterial.</p>
Reproduction package for the paper "The effects of surface fossil magnetic fields on massive star evolution - II. Implementation of magnetic braking in MESA and implications for the evolution of surface rotation in OB stars "
<p>This is a reproduction package for the paper "The effects of surface fossil magnetic fields on massive star evolution - II. Implementation of magnetic braking in MESA and implications for the evolution of surface rotation in OB stars" by Keszthelyi et al. (2020), https://doi.org/10.1093/mnras/staa237</p>
Cluster randomized controlled trial evaluating the impact on children's linear growth of an unconditional cash transfer program implemented in rural areas of North Togo
<p>A parallel cluster randomized controlled trial was implemented in North Togo. 162 rural landlocked villages were randomized into either an intervention arm (cash transfers + package of community activities, <em>n</em>=82) or a control arm (package of community activities only, <em>n</em>=80). </p> <p>Two different representative samples of children aged 6-29 months and their mothers were surveyed, one before the intervention (2014, <em>n</em>=2,658), the other two years afterwards (2016, <em>n</em>=2,031).</p> <p>You will found here:</p> <ul> <li>Two datasets, fully anonymized (French, CSV files): one for observations on households and the other for observations on mother-child pairs</li> <li>Two dictionaries of variables (French, Excel files): one for the household database and the other for the mother-child pairs database</li> <li>The study protocol as submitted to the Ministry of Health of Togo (French, PDF)</li> <li>The technical and financial proposal (to evaluate the CT program) as submitted to funders (English, PDF)</li> </ul> <p> </p>
Computational Implementation of "Uncoupling electrokinetic flow solutions", published in Mathematical Geosciences
<p>This dataset includes Python and Mathematica scripts used to generate figures, and images used in the Mathematical Geosciences (MG) manuscript "Uncoupling Electrokinetic Flow Solutions" by Kuhlman and Malama (2020).</p> <p>Python scripts implementing eigenvalue uncoupling approach for differential equations governing 1D cylindrically symmetric electrokinetic flow problem (i.e., flow to a pumping well).</p> <ol> <li>mpmath python script (recombine-expint.py) implementing Theis "type curve" solution for an infinite domain (Figures 1-3 in MG manuscript)</li> <li>fipy python script (compare-via-fipy.py) and plotting script (plot_fipy_results.py) showing a finite-volume fully coupled solution for a similar finite domain for comparison against eigenvalue uncoupling approach (Figure 4 in MG manuscript). Also includes two shell scripts for driving python scripts for a variety of inputs.</li> </ol> <p>mathematica script (periodic-1D-steady-state-type-1.nb) for solving the algebra associated with the governing equations and plotting figures for analytical solution of periodically driven 1D solution (i.e., laboratory sinusoidal streaming potential and electroosmosis; Figures 4-9 in MG manuscript).</p> <p> </p>
Implementation of a 4Pi-SMS super-resolution microscope - Example data II
<p>4Pi-SMS image of Nup96-SNAP labelled with BG-Alexa 647 in the lower nuclear envelope of a U2OS cell in TDE-based index-matching imaging buffer</p>
Technical Debt: A Clean Architecture Implementation
<p>Technical Debt (TD) and Technical Debt Management (TDM) are terms that are receiving increasing attention from practitioners and researchers. They reflect a concern on how shortcuts taken during the software development process can incur negative impacts on software maintainability and how practitioners may use tools and techniques to mitigate the effects of the debt over time. A widely used tool to manage TD on an implementation level is SonarQube with the SQALE method, as it allows developers and managers to track debt over time. However, even SonarQube has its weaknesses since it only provides a set of architecture agnostic rules for TD, and the implementation of new rules can prove to be a challenging job. In this paper, we discuss how, during a real industrial project on a Brazilian software house, we developed a set of rules based on the Clean Architecture model, created a plug-in for SonarQube, and integrated it into our development cycle. At last, the preliminary results show that using a rigorous set of rules allows keeping track of TD on an implementation level.</p>
A standardized method for the construction of tracer specific PET and SPECT rat brain templates: validation and implementation of a toolbox
<p>Data set used in "A standardized method for the construction of tracer specific PET and SPECT rat brain templates: validation and implementation of a toolbox"</p>
RPL: a domain-specific language for designing and implementing parallel C++ applications
<p>Parallelising sequential applications is usually a very hard job, due to many different ways in which an application can be parallelised and a large number of programming models (each with its own advantages and disadvantages) that can be used. In this paper, we describe a method to semi-automatically generate and evaluate different parallelisations of the same application, allowing programmers to find the best parallelisation without significant manual reengineering of the code. We describe a novel, high-level domain-specific language, Refactoring Pattern Language (RPL), that is used to represent the parallel structure of an application and to capture its extra-functional properties (such as service time). We then describe a set of RPL rewrite rules that can be used to generate alternative, but semantically equivalent, parallel structures (parallelisations) of the same application. We also describe the RPL Shell that can be used to evaluate these parallelisations, in terms of the desired extra-functional properties. Finally, we describe a set of C++ refactorings, targeting OpenMP, Intel TBB and FastFlow parallel programming models, that semi-automatically apply the desired parallelisation to the application's source code, therefore giving a parallel version of the code. We demonstrate how the RPL and the refactoring rules can be used to derive efficient parallelisations of two realistic C++ use cases (Image Convolution and Ant Colony Optimisation).</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.