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1,782 results for “algorithms”
Benchmark cancer datasets for Clustering algorithms for Omics-based Patient Stratification (COPS)
<p>This repository contains seven multi-omic cancer datasets including several cancer types (breast, kidney, lung, ovary, prostate, and thyroid cancers as well as low grade gliomas) that were used for benchmarking several multi-view clustering algorithms implemented by COPS (https://github.com/UEFBiomedicalInformaticsLab/COPS). The datasets were originally compiled from The Cancer Genoma Atlas (TCGA) and downloaded using the <em>curatedTCGAData</em> R-package. The datasets include copy-number variations, methylomics as well as mRNA and miRNA transcriptomics. The methylomics data was mapped to genes by averaging methylation level of probes associated with the promoter regions of genes. Similarly the miRNA transcriptomics data was mapped to genes by using known and predicted miRNA -> gene interactions. Updated survival data was acquired from the Liu et al. 2018 paper. </p> <p>This repository also includes two sets of cancer associated pathway networks used by pathway-based multi-omic methods benchmarked in our study. NCI-PID pathways were downloaded using the <em>ndexr</em> R-package on December 22 2021. While KEGG pathways were downloaded using the <em>pathview</em> R-package on May 3 2022. </p> <p>More details on the processing can be found on the related publication.</p>
Figure 5. Algorithm A5pseudocode-Efficient Filtering of Noisy Fingerprint Images
<p>A5&apply thresholds globally across the image (Figure 5.);</p>
Figure 2. Flow chart of the CoDOA (Kose & Arslan, 2015).0Cognitive Development Optimization Algorithm Based Support Vector Machines for Determining Diabetes
<p>The related algorithm steps can be visualized with a flow chart as shown in Figure 2 [26].</p>
A Reconfiguration Algorithm for Power-Aware Parallel Applications
<p><strong><em>Abstract: </em></strong><em>In current computing systems, many applications require guarantees on their maximum power consumption to not exceed the available power budget. On the other hand, for some applications, it could be possible to decrease their performance, yet maintaining an acceptable level, in order to reduce their power consumption. To provide such guarantees, a possible solution consists in changing the number of cores assigned to the application, their clock frequency and the placement of application threads over the cores. However, power consumption and performance have different trends depending on the application considered and on its input. Finding a configuration of resources satisfying user requirements is in the general case a challenging task. In this paper we propose Nornir, an algorithm to automatically derive, without relying on historical data about previous executions, performance and power consumption models of an application in different configurations. By using these models, we are able to select a close to optimal configuration for the given user requirement, either performance or power consumption. The configuration of the application will be changed on-the-fly throughout the execution to adapt to workload fluctuations, external interferences and/or application's phase changes. We validate the algorithm by simulating it over the applications of the PARSEC benchmark suite. Then, we implement our algorithm and we analyse its accuracy and overhead over some of these applications on a real execution environment. Eventually, we compare the quality of our proposal with that of the optimal algorithm and of some state of the art solutions.</em></p> <p>This dataset contains the raw data of the experiments and the scripts used to plot them.</p> <p> </p>
Pressure-based algorithm for compressible interfacial flows with acoustically-conservative interface discretisation (Supporting data)
<p>The dataset contains sample numerical results associated with the manuscript under the same title, "Pressure-based algorithm for compressible interfacial flows with acoustically-conservative interface discretisation", published in Journal of Computational Physics (2018), https://doi.org/10.1016/j.jcp.2018.04.028.</p>
Results for Several Simple Algorithms on the W-Model for Black-Box Discrete Optimization Benchmarking
<p>The W-Model follows a layered approach, where each layer can either be omitted or introduce a different characteristic feature such as neutrality via redundancy, ruggedness and deceptiveness, epistasis, and multi-objectivity, in a tunable way. The model problem is defined over bit string representations, which allows for extracting some of its layers and stacking them on top of existing problems that use this representation, such as OneMax, the Maximum Satisfisiability or the Set Covering tasks, and the NK landscape. The ruggedness and deceptiveness layer can be stacked on top of any problem with integer-valued objectives.</p> <p>Here we provide some experimental results with several simple algorithms on the W-Model along with the algorithm and experiment executor implementation. The most recent version of the code can be found at <a href="http://www.github.com/thomasWeise/BBDOB_W_Model">http://www.github.com/thomasWeise/BBDOB_W_Model</a>, while the program used in the experiment are attached to this dataset. The implemented algorithms are</p> <ul> <li>1-flip hill climber with restarts,</li> <li>2-flip hill climber with restarts,</li> <li>μ+λ Evolutionary Algorithms (for different values of μ, λ, and different crossover rates),</li> <li>μ+λ Evolutionary Algorithms with Frequency Fitness Assignment (FFA) (for different values of μ, λ, and different crossover rates),</li> <li>exhaustive enumerate (EE), and</li> <li>random sampling (RS)</li> </ul> <p>These algorithms are applied to a range of different parametric setups of the W-Model for single-objective optimization and fixed-length bit string representations.</p> <p>The experiments are executed on a HP Z640 Work Station with 32 GB DDR4-2400 RAM and Intel Xeon E5-2609v4 CPU under Ubuntu Server Linux 16.04, Kernel 4.4.0-116-generic, and with Java 1.8.0_151. Each run was granted at most 1048576 function evaluations (FEs). The total amount of data collected is about 45 GB, with tar.xz compression down to about 1.2 GB. The text files containing the algorithm traces are fairly self-describing.</p> <p>Publications that describe the W-Model:</p> <ul> <li>Thomas Weise and Zijun Wu. Difficult Features of Combinatorial Optimization Problems and the Tunable W-Model Benchmark Problem for Simulating them. In Black Box Discrete Optimization Benchmarking (<a href="http://iao.hfuu.edu.cn/bbdob-gecco18">BB-DOB</a>) Workshop of <em>Companion Material Proceedings of the Genetic and Evolutionary Computation Conference (<a href="http://gecco-2018.sigevo.org/">GECCO 2018</a>)</em>, July 15th-19th 2018, Kyoto, Japan, ISBN: 978-1-4503-5764-7. ACM. doi:<a href="http://dx.doi.org/10.1145/3205651.3208240">10.1145/3205651.3208240</a> / <a href="http://github.com/thomasWeise/BBDOB_W_Model">source codes</a> [This paper contains some errata for the one below]</li> <li>Thomas Weise, Stefan Niemczyk, Hendrik Skubch, Roland Reichle, and Kurt Geihs. A Tunable Model for Multi-Objective, Epistatic, Rugged, and Neutral Fitness Landscapes. In Maarten Keijzer, Giuliano Antoniol, Clare Bates Congdon, Kalyanmoy Deb, Benjamin Doerr, Nikolaus Hansen, John H. Holmes, Gregory S. Hornby, Daniel Howard, James Kennedy, Sanjeev P. Kumar, Fernando G. Lobo, Julian Francis Miller, Jason H. Moore, Frank Neumann, Martin Pelikan, Jordan B. Pollack, Kumara Sastry, Kenneth Owen Stanley, Adrian Stoica, El-Ghazali, and Ingo Wegener, editors, <em>Proceedings of the 10th Annual Conference on Genetic and Evolutionary Computation Conference (GECCO'08)</em>, pages 795-802, July 12-16, 2008, Renaissance Atlanta Hotel Downtown: Atlanta, GA, USA. ISBN: 978-1-60558-130-9, New York, NY, USA: ACM Press. doi:<a href="http://dx.doi.org/10.1145/1389095.1389252">10.1145/1389095.1389252</a> / <a href="http://iao.hfuu.edu.cn/images/publications/WNSRG2008ATMFMOERANFL.pdf">pdf</a> [This paper has some deficits fixed in the paper above]</li> </ul>
Online Optimization in Cloud Resource Provisioning: Predictions, Regrets, and Algorithms: Virtual Machine ID Dataset
<p>The csv files in this dataset contain the virtual machine IDs used in [1] which correspond to the virtual machine traces in the Azure Public Dataset [2]. The file named "vmtable_lifetime_VMoL_1003.csv" holds the IDs used in Section 5 [1] and the file named "vmtable_lifetime_VMoL_55.csv" holds the IDs used in Section 6 [1]. The first column in both files refers to the ID labels in [1], while the second, third, and fourth columns refer to the Virtual Machine IDs, the Subscription IDs, and the Deployment IDs, respectively.</p> <p> </p> <p>[1] Joshua Comden, Sijie Yao, Niangjun Chen, Haipeng Xing, and Zhenhua Liu. 2019. Online Optimization in<br> Cloud Resource Provisioning: Predictions, Regrets, and Algorithms. Proc. ACM Meas. Anal. Comput. Syst. 3, 1,<br> Article 179 (March 2019).</p> <p>[2] Eli Cortez, Anand Bonde, Alexandre Muzio, Mark Russinovich, Marcus Fontoura, and Ricardo Bianchini. 2017. Resource Central: Understanding and Predicting Workloads for Improved Resource Management in Large Cloud Platforms. In Proceedings of SOSP’17. ACM, New York, NY, USA, 15 pages. https://doi.org/10.1145/3132747.3132772 Dataset access: https://github.com/Azure/AzurePublicDataset (August 2018)</p>
CID2013: A Database for Evaluating No-Reference Image Quality Assessment Algorithms
<p>The CID2013 Camera Image Database consists of real images taken by consumer cameras and mobile phones. It is developed to provide useful tool to allow researchers target more commercially relevant distortions when developing processes of objective image quality assessment algorithms.</p> <p>The CID2013 database consists of 480 evaluated images captured by 79 imaging devices (mobile phones, DSC, DSLR) in six Image Sets. Note that the actual number of images in the database is 474. In Image Set II, Device 6 is evaluated twice as we wanted to test inter-observer reliablity. The scores are later combined into a single MOS value as the two evaluations correlated strongly.</p> <p>If you use this database in your research, we kindly ask that you follow the copyright notice bellow and cite the following paper:</p> <p>Virtanen, T., Nuutinen, M., Vaahteranoksa, M., Oittinen, P. and Häkkinen, J. “CID2013: a database for evaluating no-reference image quality assessment algorithms”, IEEE Transactions on Image Processing, vol. 24, no. 1, pp. 390-402, Jan. 2015. <a href="http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6975172">[pdf]</a></p> <p><strong>Method</strong></p> <p>The images are evaluated by 188 observers using Dynamic Reference (DR-ACR) method (explained below). A separate scale realignment ACR data consisting evaluations from 34 observers is also included that allows to combine the data from the six image sets</p> <p>In other respects the DR-ACR method resembles very much a basic Absolute Category Rating (ACR) method (ITU-R 500-11), except the observers saw a slideshow of all the other images in the test depicting the same scene before every evaluation (See DR_demo.mp4). By seeing the other images in the test setup as reference the observers were more aware of the total variation of quality represented within a single image set. This improved their evaluation as they didn’t need to save the far ends of the scale in case there would be even more better or worse image later on the experiment. The DR-ACR method is explained in detail in:</p> <p>Mikko Nuutinen, Toni Virtanen, Tuomas Leisti, Terhi Mustonen, Jenni Radun, Jukka Häkkinen (2014) A new method for evaluating the subjective image quality of photographs : dynamic reference Multimedia Tools and Applications 75: 4. 2367-2391 Dec.</p> <p>Database contains consumer camera images and their subjective evaluations in mean opinion score (MOS), sharpness, graininess, lightness and color saturation scales. It includes the complete raw data and background information from the naïve observers used to evaluate the images. Subjects’ vision was controlled for the near visual acuity, near contrast vision (near F.A.C.T.) and color vision (Farnsworth D15) before the participation. They received movie tickets as a reward. Outlier removal is made for mean opinion score (MOS) evaluations using ITU-R 500-11 recommendations to ease out the implementation of the database.</p> <p><strong>Material</strong></p> <p>The images in CID2013 are intended to represent typical photographs that consumers might capture with their cameras. The photographed scenes were based partly on the Photospace approach described by I3A (CPIQ Initiative Phase 1 White Paper: Fundamentals and review of considered test methods, I3A, 2007) The I3A CPIQ project has migrated under IEEE.</p> <p><strong>The test environment</strong></p> <p>The room has been covered with medium gray curtains to diffuse the ambient illumination. Fluorescent lights (5800K) were positioned behind the monitors and reflected from the back wall covered with grey curtain to create dim and uniform ambient illumination in the room. The light hitting the monitors measured below 20 lx. The subject’s viewing distance (approximately 80 cm) was controlled by a line hanging from the ceiling, and they were instructed to keep their forehead steady next to the line. Because of the display size, images were scaled to a size of 1600 x 1200 pixels using the bicubic interpolation method. Eizo ColorEdge CG241W, with 1920x1200 pixel resolution, monitors in was calibrated to sRGB having target values of: 80 cd/m2, 6500K and gamma 2.2 using EyeOne Pro calibrator (X-rite co.).</p> <p> </p> <p>-----------COPYRIGHT NOTICE STARTS WITH THIS LINE------------</p> <p>Copyright (c) 2014 The University of Helsinki<br> All rights reserved.</p> <p>Permission is hereby granted, without written agreement and without license or royalty fees, to use, copy, modify, and distribute this database (the videos, the images, the results and the source files) and its documentation for any purpose, provided that the copyright notice in its entirely appear in all copies of this database, and the original source of this database,Visual Cognition research group (www.helsinki.fi/psychology/groups/visualcognition/index.htm) and the Institute of Behavioral Science (www.helsinki.fi/ibs/index.html) at the University Helsinki (www.helsinki.fi/university/), is acknowledged in any publication that reports research using this database. Individual videos and images may not be used outside the scope of this database (e.g. in marketing purposes) without prior permission.</p> <p>The database and our paper are to be cited in the bibliography as:</p> <p>-----------------------------------------------------------------------------<br> Virtanen, T., Nuutinen, M., Vaahteranoksa, M., Oittinen, P. and Häkkinen, J. “CID2013: a database for evaluating no-reference image quality assessment algorithms”, IEEE Transactions on Image Processing, 2014, In press.<br> -----------------------------------------------------------------------------</p> <p>LIMITATION OF LIABILITY</p> <p>UNIVERSITY OF HELSINKI SHALL IN NO CASE BE LIABLE IN CONTRACT, TORT OR OTHERWISE FOR ANY LOSS OF REVENUE, PROFIT, BUSINESS OR GOODWILL OR ANY DIRECT, INDIRECT, SPECIAL, CONSEQUENTIAL, INCIDENTAL OR PUNITIVE COST, DAMAGES OR EXPENSE OF ANY KIND HOWEVER CAUSED OR HOWEVER ARISING UNDER OR IN CONNECTION WITH THE USE OF THIS DATABASE.</p> <p>THE UNIVERSITY OF HELSINKI SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE DATABASE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF HELSINKI HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.</p> <p>THIS AGREEMENT SHALL BE CONSTRUED AND INTERPRETED IN ACCORDANCE WITH THE LAWS OF FINLAND, EXCLUDING ITS RULES FOR CHOICE OF LAW.</p> <p>-----------COPYRIGHT NOTICE ENDS WITH THIS LINE------------</p> <p> </p>
Dataset for: A graph-based algorithm for RNA-seq data normalization
<p>mRNA-seq assays on mouse tissues were downloaded from the ENCODE project and consolidated into matrices of expression</p>
The optimization of a jet turbojet engine by PSO and searching algorithms
<p>The turbojet engine operates on the ideal Brayton cycle (gas turbine) and consists of six main parts: diffusers, compressors, combustion chambers, turbines, afterburners and nozzles. Using computer code writing in MATLAB software environment, exergy analysis on all selected turbojet engine components, exergy analysis on J85-GE-21 turbojet engine for selective height of 10008000 meters above sea level at speeds of 200 m/s and temperatures of 10, 20 and 40 ° C have been provided and then, according to the system functions, the system is optimized based on the PSO method. For the purpose of optimization, variables of Mach number, efficiency of the compressor, turbine, nozzle and compressor pressure ratio are considered in the range of 0.6 to 1.4, 0.8 to 0.95, 0.8 to 0.95 and 7 to 10, respectively. The highest exergy efficiency of different parts of the engine at sea level with an inlet air velocity of 200 m/s corresponds to a diffuser with 73.1%. Then, the nozzle and combustion chamber are respectively 68.6% and 51.5%. The lowest exergy efficiency is related to compressor with 4%. After that, the afterburner is ranked second with 11.6%. Also, the values of entropy produced and the efficiency of the second law before optimization were 1176.99 and 479 w/k respectively and the same values after optimization were 1129 and 51.4 w/k respectively which is identified. After the optimization process, the amount of entropy produced is reduced and the efficiency of the second law of thermodynamics has increased.<br> </p>
The ESCAPE project: Energy-efficient Scalable Algorithms for Weather Prediction at Exascale
<p>Data and figures presented in the paper "The ESCAPE project: Energy-efficient scalable algorithms for weather prediction at exascale". The discussion paper is available at: https://doi.org/10.5194/gmd-2018-304</p>
Dataset [Study on Algorithms in Election Campaigns: Analysis with IRaMuteQ]
<p>This is the raw data behind the publication:</p> <p>Carvalho, P. R; Ramos, M. G.; Schneider, M. A. F. Study on algorithms in election campaigns: analysis with Iramuteq. XX ENANCIB 2019.</p> <p>The present work reports the exploratory empirical research carried out in <strong>the Scopus database</strong> with the objective of identifying, quantifying and analyzing the scientific production of the topic algorithms in politics in electoral campaigns, <strong>from 2008 to 2018,</strong> by means of Scientometric techniques. In addition, the Content Analysis of abstracts of the articles collected through Iramuteq, open source and free software. The methodological proposal refers to the construction of a textual corpus composed of <strong>150 articles </strong>retrieved, following analyzes such as: pre-analysis of the material; data mining; simple statistical analysis; Descending Hierarchical Classification; Factorial Correspondence Analysis; similitude analysis; and frequency analysis with word cloud visualization. The result of the study demonstrated the efficiency of the chosen keywords in the retrieval of information. In addition, we identified the convergence and repetition of themes of the articles represented by the text segments.</p> <p>Link: <a href="https://brapci.inf.br/index.php/res/v/122943">https://brapci.inf.br/index.php/res/v/122943</a></p>
Human sequence alignment data set used for analysis of SPDI algorithm and tools
<p>Collection of alignment segments produced on October 30, 2019. The ADS currently consists of over 2,680,000 pairwise alignment segments generated from over 350,000 distinct input sequences. </p> <ul> <li> <p>Old assembly to current Genome Reference Consortium (GRC) <a href="http://f1000.com/work/citation?ids=111899&pre=&suf=&sa=0">(Church et al., 2011)</a> primary assemblies (e.g. GRCh36(hg18) or GRCh37(hg19) with GRCh38(hg38))</p> </li> </ul> <ul> <li> <p>Patches, alternative loci, or pseudoautosomal regions (PAR) to GRC primary assembly</p> </li> <li> <p>RefSeq <a href="http://f1000.com/work/citation?ids=2599029&pre=&suf=&sa=0">(O’Leary et al., 2016)</a> and select GenBank <a href="http://f1000.com/work/citation?ids=6183037&pre=&suf=&sa=0">(Benson et al., 2018)</a> transcripts to selected RefSeq genomic regions, also known as RefSeqGene (NG), a member of the Locus Reference Genome (LRG) collaboration <a href="http://f1000.com/work/citation?ids=3225699&pre=&suf=&sa=0">(Dalgleish et al., 2010)</a>.</p> </li> <li> <p>Current RefSeq transcripts (NM/NR/XM/XR) and RefSeq genomic regions (NG) to the latest Assembly</p> </li> <li> <p>Previous versions of NG and RefSeq transcripts (NM/NR) to GRC primary assembly</p> </li> </ul>
Compilation of data used to implement floodplain DEM algorithm in the Logone Floodplain
<p>This document describes the dataset that was used in the article submitted to Geophysical Research Letters by Shastry and Durand entitled "Water Surface Elevation Constraints in a Data Assimilation Scheme to Infer Floodplain Topography: A Case Study in the Logone Floodplain". The dataset is distributed as a NetCDF file containing the Digital Elevation Models at different stages of the algorithm described in the article, and a set of excel files describing the location coordinates of flood boundaries used in the study.</p> <p><strong>Description of Files</strong></p> <p><strong>Excel files</strong><br> Each excel file provides the location coordinates of flood boundaries on a particular day; the date is mentioned in the file name as YYYYMMDD. Each Sheet is each excel file corresponds to a unique flooded region on the particular day. The first column corresponds to Northing and the second Easting. The coordinates are in the WGS 1984 UTM Zone 33 N coordinate system. </p> <p><strong>NetCDF file</strong><br> This file contains Digital Elevation Models (DEMs) at various stages of the algorithm. The various stages are described below.<br> 1. The Prior DEM: Multi-Error-Removed Improved-Terrain (MERIT) DEM (Yamazaki et al., 2017; http://hydro.iis.u-tokyo.ac.jp/~yamadai/MERIT_DEM/) of the Logone Floodplain in Cameroon upscaled to 500 m.<br> 2. Ensemble of particle DEMs: Spatially correlated errors added to the prior DEM to produce an ensemble of 50 particles.<br> 3. Channel smoothed ensemble of particles: The elevations of the river network smoothed in the ensemble of particles in 2.<br> 4. Flood boundary smoothed ensemble of particles: The elevations along flood boundaries provided in the excel files smoothed in the ensemble mentioned in 3.<br> 5. Water surface constrained ensemble: A water surface constraint is applied to the ensemble in 4 to produce the ensemble that goes into the particle batch smoother described in the article.</p> <p><strong>Reference:</strong></p> <p>Yamazaki, D., Ikeshima, D., Tawatari, R., Yamaguchi, T., O’Loughlin, F., Neal, J. C., Bates, P. D. (2017). A high-accuracy map of global terrain elevations. <em>Geophysical Research Letters</em>, 44 (11), 5844–5853. doi: 10.1002/2017GL072874</p>
Model outputs for "Multi-grid algorithm for passive tracer transport in NEMO ocean circulation model"
<p>Model outputs used to write "Multi-grid algorithm for passive tracer transport in NEMO ocean circulation model" publication.</p>
Reconstructing 10-km-resolution direct normal irradiance dataset through a hybrid algorithm
<p>The 41-year (1982-2022) daily DNI dataset (CHDNI) reconstructed in this study has been uploaded, and stored in netcdf format. The one-year dataset comprises daily DNI estimates for either 365 or 366 days, with individual data files separately organized by year. Each daily file is stored in mat format and labeled as "pred_xxxxxyymm," where ‘xxxx' denotes the year, ‘yy' represents the month, and ‘mm' stands for the day. The geographical scope of CHDNI dataset spans from 3°N to 54°N in latitude and from 72°E to 136°E in longitude. The mat matrix, encapsulating the data, is configured with dimensions of 361 rows and 641 columns, measured in W/m2.</p> <p>If you want to use the CHDNI dataset for related scientific research, please contact us (Email: WHU_wjy@whu.edu.cn).</p> <ul> <li>Wu J, Niu J, Qi Q, Gueymard CA, Wang L, Qin W, et al. Reconstructing 10-km-resolution direct normal irradiance dataset through a hybrid algorithm. Renewable and Sustainable Energy Reviews 2024; 204: 114805.</li> </ul>
Supplementary data for: Graphene Microelectrode Arrays, 4D Structured Illumination Microscopy, and a Machine Learning Spike Sorting Algorithm Permit the Analysis of Ultrastructural Neuronal Changes During Neuronal Signalling in a Model of Niemann-Pick Disease Type C
<p>Supplementary example data for the work presented in "<em>Graphene Microelectrode Arrays, 4D Structured Illumination Microscopy, and a Machine Learning Spike Sorting Algorithm Permit the Analysis of Ultrastructural Neuronal Changes During Neuronal Signalling in a Model of Niemann-Pick Disease Type C</em>". </p> <p><strong>Abstract: </strong></p> <p>Simultaneously recording network activity and ultrastructural changes of the synapse is essential for advancing our understanding of the basis of neuronal functions. However, the rapid millisecond-scale fluctuations in neuronal activity and the subtle sub-diffraction resolution changes of synaptic morphology pose significant challenges to this endeavour. Here, we use specially designed graphene microelectrode arrays (G-MEAs), which are compatible with high spatial resolution imaging across various scales as well as permit high temporal resolution electrophysiological recordings to address these challenges. Furthermore, alongside G-MEAs, we have developed an easy-to-implement machine learning algorithm to efficiently process the large datasets collected from MEA recordings. We demonstrate that the combined use of G-MEAs, machine learning (ML) spike analysis, and four-dimensional (4D) structured illumination microscopy (SIM) enables monitoring the impact of disease progression on hippocampal neurons which have been treated with an intracellular cholesterol transport inhibitor mimicking Niemann-Pick disease type C (NPC), and show that synaptic boutons, compared to untreated controls, significantly increase in size, leading to a loss in neuronal signalling capacity.</p> <p> </p>
Pregnancy-related diagnosis codelist developed for the ConcePTION pregnancy algorithm
<p><span>The IMI ConcePTION project aims to build an ecosystem to generate Real World Evidence to address the information gap in medication safety in pregnancy. </span></p> <p><span>The ConcePTION pregnancy algorithm was developed as part of the IMI ConcePTION project and aimed at identifying a comprehensive list of pregnancies experienced by the population in European healthcare data sources. To achieve this, the ConcePTION pregnancy algorithm was designed to retrieve any record implying a pregnancy at record date from multiple data provenance, for instance, records of birth registries, congenital anomalies register, hospital admission and discharge, primary care. </span></p> <p><span>The diagnosis code list named “PrA_Codelist” was developed and integrated into the ConcePTION pregnancy algorithm to identify records with a diagnostic code implying that the person is experiencing an ongoing or an end of pregnancy.</span></p>
Interpretation of inherited risk signals using genetic algorithms
<p>This tarball contains the pre-processed data in .Rda files and code in .Rmd file required to execute the genetic algorithm model and compile figures in this study.</p>
Supporting information for: The Time Requirements for Primary Care Consultations: Initial Sick Child Visits in Low- and Middle-income Countries Using the Integrated Management of Childhood Illness (IMCI) Clinical Algorithm
<p>Few studies have examined the time required for primary care consultations; none have focused on sick child visits in low- and middle-income countries (LMICs). This project begins to fill that gap by providing evidence-based estimates of the time needed for initial visits with under-five infants and children at public or not-for-profit facilities in countries using the Integrated Management of Childhood Illness (IMCI) clinical algorithm.</p> <p>Estimates of the mean expected duration of IMCI consultations require (a) classification profiles, i.e., tabulations of the gold standard health issues presented by patients less than 5 years old; (b) lists of the tasks included in applicable versions of the IMCI algorithm and the conditions that elicit them, and (c) an estimate of the time needed to perform tasks with no pre-defined minimum duration. The latter requires, in addition to classification profiles, information on rates of task performance and the mean observed duration of consultations.</p> <p>The IMCI clinical algorithm and the research surrounding it provide unusually rich sources of such information. Developed in the mid 1990s by the World Health Organization and the United Nations Children’s Fund, the IMCI algorithm seeks to reduce child mortality in LMICs by improving the technical quality of primary care services. For infants less than 2 months old, the algorithm focuses on bacterial infections, feeding problems, low weight, and, in some versions, jaundice. For children 2-59 months old, the foci include acute respiratory infections, especially pneumonia; diarrhea; fevers, especially malaria and measles; malnutrition, and anemia. Immunization status is a concern for both age groups. The algorithm provides a scheme to classify the health issues with which infants and children present, an array of tasks providers may be expected perform, and criteria by which tasks are elicited. Research on the design and utility of the algorithm, its effects on provider performance, and related topics furnishes data on the prevalence of gold standard IMCI classifications in a variety of patient populations. In some cases, it also enables one to calculate the time required to perform tasks.</p> <p>I found such information by searching MEDLINE, the database of the International Network for Rational Use of Medicines, the websites of the WHO and its regional offices, GOOGLE, and GOOGLE SCHOLAR using search terms such as ‘Integrated Management of Childhood Illness’, ‘observational’, ‘prospective’, ‘classification’, ‘clinical signs’, ‘health facility survey’, and ‘validity’. I also reviewed studies that cited a qualified study and, conversely, material included in the bibliographies of qualified studies.</p> <p>The supplemental information files contain the following:</p> <p>WORKBOOK S1_STUDIES USED</p> <p>Lists features of, and sources for, the studies used to construct classification profiles and to estimate the time required to perform the average task with no predefined minimum duration. With 2 exceptions (see below, DATA S1 and DATA S2), all the studies have been published or are readily available on the internet. None of the data can be used to identify individuals.</p> <p>DATA S1_REPORT OF THE HEALTH FACILITY SURVEY IN BOTSWANA, 2007-08 and DATA S2_REPORT OF THE HEALTH FACILITY SURVEY IN TANZANIA, 2003</p> <p>PDF files of Health Facility Survey reports that were found on the internet but have since been taken down.</p> <p>DATA S3_BURKINA FASO CHART BOOKLET, 2015</p> <p>PDF provided <span>Drs. Sophie Sarrassat (London School of Hygiene and Tropical Medicine) and Serge M. A. Somda (Université Nazi BONI).</span></p> <p>WORKBOOK S2_CLASSIFICATION PROFILES: INFANTS; WORKBOOK S3_CLASSIFICATION PROFILES: CHILDREN IN UPPER MIDDLE-INCOME COUNTRIES; WORKBOOK S4_CLASSIFICATION PROFILES: CHILDREN IN LOWER MIDDLE-INCOME COUNTRIES (I); WORKBOOK S5_CLASSIFICATION PROFILES: CHILDREN IN LOWER MIDDLE-INCOME COUNTRIES (II), and WORKBOOK S6_CLASSIFICATION PROFILES: CHILDREN IN LOW INCOME COUNTRIES </p> <p>The design of the worksheets in these workbooks is described in TEXT S1_NOTES OF THE CONSTRUCTION OF CLASSIFICATION PROFILES (see below).</p> <p>WORKBOOK S7_IMCI CLINICAL TASKS</p> <p>Lists the clinical tasks provided by relevant IMCI algorithms for the care of infants and children. Consists of 6 worksheets covering mandatory tasks, conditional assessments, and treatment and counseling tasks for infants and children.</p> <p>WORKBOOK S8_MINUTES PER TASK WITH NO MINIMUM DURATION</p> <p>Provides estimate of the mean time required to perform a task with no minimum duration for each of 7 populations for which the required data are available, corrected, where necessary, for the effect of an observer on the rate and pace of task performance. Also provides a geometric mean for all 7 populations.</p> <p>TEXT S1_NOTES ON METHODOLOGY</p> <p>WORD document describing the steps involved in estimating the expected durations of consultations.</p> <p>TEXT S2_NOTES OF THE CONSTRUCTION OF CLASSIFICATION PROFILES</p> <p>WORD document describing the steps involved in constructing each profile, problems encountered, and how they were solved.</p> <p>TEXT S3_NOTES ON THE IDENTIFICATION OF IMCI CLINICAL TASKS</p> <p>WORD document describing the standards used in identifying clinical tasks in IMCI algorithms.</p> <p>TEXT S4_NOTES ON THE ESTIMATION OF MINUTES PER TASK WITH NO MINIMUM DURATION</p> <p>WORD document describing the steps involved in estimating the mean time required to perform a task with no predefined minimum duration, problems encountered, and how they were solved.</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.