Find research datasets worth reusing

restrictedAug 2022View details →

Dataset for paper [Application of Deep Learning in Generating Structured Radiology Reports: A Transformer-Based Technique]

Since radiology reports needed for clinical practice and research are written and stored in free-text narrations, extraction of relative information for further analysis is difficult. In these circumstances, natural language processing (NLP) techniques can facilitate automatic information extraction and transformation of free-text formats to structured data. In recent years, deep learning (DL)-based models have been adapted for NLP experiments with promising results. Despite the significant potential of DL models based on artificial neural networks (ANN) and convolutional neural networks (CNN), the models face some limitations to implement in clinical practice. Transformers, another new DL architecture, have been increasingly applied to improve the process. Therefore, in this study, we propose a transformer-based fine-grained named entity recognition (NER) architecture for clinical information extraction. We collected 88 abdominopelvic sonography reports in free-text formats and annotated them based on our developed information schema. The text-to-text transfer transformer model (T5) and Scifive, a pre-trained domain-specific adaptation of the T5 model, were applied for fine-tuning to extract entities and relations and transform the input into a structured format. Our transformer-based model in this study outperformed previously applied approaches such as ANN and CNN models based on ROUGE-1, ROUGE-2, ROUGE-L, and BLEU scores of 0.816, 0.668, 0.528, and 0.743, respectively, while providing an interpretable structured report.

restrictedcc-by-4.0Jun 2024View details →

Dataset for Automated Unit Test Generation via Chain of Thought Prompt and Reinforcement Learning

This is the replication package including three types datasets: training dataset with CoT prompts, reward dataset for training reward model, rl dataset for optimizing policy model. The training dataset includes filter_test_cot_rule_50k.csv, filter_train_cot_rule_50k.csv, and filter_valid_cot_rule_50k.csv. These three datasets includes multiple fields (i.e., src_fm, intention, plan, elaboration, gpt_test, src_fm_cot_gpt, target, src_fm_fc_ms_ff,src_fm_intention,src_fm_plan,src_fm_elaboration,idx,rule_cot,rule_cot_nlp,combine_cot,src_fm_rule_cot_nlp,src_fm_cot_nlp_gpt,gpt_cot_filter,src_fm_plan_intention). The reward dataset includes test_athena.json, train_athena.json, and valid_athena.json three files. The rl dataset includes three files: filter_test_cot_gpt_rl.csv, filter_train_cot_gpt_rl.csv, filter_valid_cot_gpt_rl.csv. These files include mulitple fields: src_fm,intention,plan,elaboration,gpt_test,src_fm_cot_gpt,target,src_fm_fc_ms_ff,src_fm_intention,src_fm_plan,src_fm_elaboration,gpt_cot_filter.

restrictedNov 2022View details →

Dataset related to article "Left atrial appendage closure with the II generation Ultraseal device: An international registry. The LIGATE study "

This record contains raw data related to article "Left atrial appendage closure with the II generation Ultraseal device: An international registry. The LIGATE study " Abstract Objectives: To assess feasibility and safety of second-generation left atrial appendage closure (LAAC) Ultraseal device in patients with nonvalvular atrial fibrillation (NVAF). Background: LAAC with first-generation Ultraseal device (Cardia, Eagan, Minnesota) has been shown to be a feasible therapeutic option in patients with NVAF. However, there is a paucity of data regarding the novel second-generation Ultraseal device. Methods: All patients with NVAF undergoing second-generation Ultraseal device implantation between February 2018 and September 2020 were included in a multicenter international registry. Periprocedural and post-discharge events were collected through 6-month follow-up. Co-primary efficacy endpoints were device success and technical success while primary safety endpoint was in-hospital major adverse event (MAE) occurrence. Results: A total of 52 patients were included: mean age 75 ± 8, 30.8% women, mean HAS-BLED 3 ± 1. The device was successfully implanted in all patients. Technical success was achieved in 50 patients (96.1%). In-hospital MAEs occurred in three patients (5.8%). The incidence of 6-month all-cause death and major bleeding was 11.6% and 2.1%, respectively. No strokes, transient ischemic attacks, systemic embolisms, or device embolization were reported after discharge. Conclusions: Second-generation Ultraseal device implantation was associated with high success rates and a low incidence of peri-procedural complications. Larger studies with longer follow-up are warranted to further evaluate the safety and the efficacy of this device, especially at long-term follow-up.

restrictedMay 2023View details →

Time-Resolved Plasmon-Assisted Generation of Arbitrary Optical-Vortex Pulses - Dataset

This folder contains raw data and information to reproduce the findings of the article titled 'Time-Resolved Plasmon-Assisted Generation of Arbitrary Optical-Vortex Pulses' . Each folder corresponds to a figure in the article. Raw data is provided for the calculations along with the input file and output log of the calculation. When raw data is too large, it is possible to reproduce the calculation from the provided input file. Calculations are performed with <a href="https://octopus-code.org/documentation/12/">Octopus code</a> , the related version and commit number of the code can be retrieved from output log file provided in calculation folder.

restrictedMar 2020View details →

Dataset related to the article: "Generation of three iPSC lines (IAIi002, IAIi004, IAIi003) from Rubinstein-Taybi syndrome 1 patients carrying CREBBP non sense c.4435G>T, p.(Gly1479) and c.3474G>A, p.(Trp1158) and missense c.4627G>T, p.(Asp1543Tyr) mutations"

This record contains raw data related to the article: "Generation of three iPSC lines (IAIi002, IAIi004, IAIi003) from Rubinstein-Taybi syndrome 1 patients carrying CREBBP non sense c.4435G>T, p.(Gly1479*) and c.3474G>A, p.(Trp1158*) and missense c.4627G>T, p.(Asp1543Tyr) mutations." Abstract: Rubinstein-Taybi syndrome (RSTS) is a neurodevelopmental disorder characterized by growth retardation, skeletal anomalies and intellectual disability, caused by heterozygous mutations in either CREBBP (RSTS1) or EP300 (RSTS2) genes. We characterized 3 iPSC lines generated by Sendai from blood of RSTS1 patients with unique non sense c.4435G > T, p.(Gly1479*), c.3474G > A, p.(Trp1158*) and missense c.4627G > T, p.(Asp1543Tyr) CREBBP mutations. All lines displayed iPSC morphology, pluripotency markers, trilineage differentiation potential, stable karyotype and specific mutations. Western-blot using a CREB- Binding Protein N-terminus antibody demonstrated the same amount of full length protein as control in the missense mutation line and reduced amount in lines with stop mutations.

restrictedMay 2020View details →

Dataset related to the article "Cryoablation of Atrial Fibrillation With the Fourth-Generation Balloon: The First Reported Case"

This record contains raw data related to the article "Cryoablation of Atrial Fibrillation With the Fourth-Generation Balloon: The First Reported Case" ABSTRACT Cryoballoon ablation was developed as a new treatment for pulmonary vein (PV) isolation and has demonstrated high procedural success and comforting long-term clinical outcome. However, some improvements are necessary for real-time visualization of PV signals that appeared important to increase the efficacy and reduce ineffective cryoapplications. We report, for the first time, a cryoablation procedure using the fourth-generation cryoballoon, describing betterment in vein signal recording and acute procedural success.

restrictedOct 2020View details →

Dataset related to the article "A comparison of acute procedural outcomes within four generations of cryoballoon catheters utilized in the real-world multicenter experience of 1STOP"

This record contains raw data related to the article “A comparison of acute procedural outcomes within four generations of cryoballoon catheters utilized in the real-world multicenter experience of 1STOP".   Abstract Introduction: Four generations of the cryoballoon (CB) catheter were retrospectively evaluated in a real-world examination of patients with atrial fibrillation (AF). Methods and results: Four hundred eighty patients (27% female and 60 ± 10 years) suffering from AF, underwent pulmonary vein (PV) ablation with one-of-four generations of the CB catheter. The total cohort was divided into four groups of patients: 120 with first-generation (CB-1); 120 with second-generation (CB-2); 120 with third-generation (CB-3); and 120 with fourth-generation (CB-4). Equal group sizes were achieved by examining the last 120 patients treated in each cohort, attempting to minimize the effect of a learning curve between the generations of CB catheter. Baseline clinical and patient characteristics were similar between the four cohorts, excepting age and the number of tested antiarrhythmic drugs. Procedure, fluoroscopy, and left atrial dwell times were significantly lower in the CB-4 cohort compared to previous generations of the CB catheters, while the acute procedural success rate was comparable across all catheter groups (>99%). Total acute procedural complications were low (2.5%), and acute complications were comparable within the CB-2, CB-3, and CB-4 groups (0.8% reported in each cohort). The rate of time-to-isolation (TTI) visualization increased with later generations of the CB catheters. Conclusions: The novel CB-4 achieved significantly faster procedural ablation times in comparison to the previous generations, while still maintaining a low rate of acute complications. Also, the rate of TTI visualization was observed to be higher with the CB-4 catheter. Further long-term evaluation is necessary, including an assessment of AF recurrence and PV reconnection(s).

restrictedNov 2023View details →

Dataset related to article "Development of Personalized Thrombogenesis and Thrombin Generation Assays to Assess Endothelial Dysfunction in Cardiovascular Diseases"

This record contains raw data related to article "Development of Personalized Thrombogenesis and Thrombin Generation Assays to Assess Endothelial Dysfunction in Cardiovascular Diseases"AbstractThe study of endothelial dysfunction (ED) is crucial to identify the pathogenetic mechanism(s) and provide indications for patient management in cardiovascular diseases. It is currently hindered by the limited availability of patient-specific primary endothelial cells (ECs). Endothelial colony-forming cells (ECFCs) represent an optimal non-invasive tool to overcome this issue. Therefore, we investigated the use of ECFCs as a substrate in thrombogenesis and thrombin generation assay (TGA) to assess ED. Both assays were set up on human umbilical vein endothelial cells (HUVECs) and then tested on ECFCs obtained from healthy donors. To prove the ability of the assays to detect endothelial activation, ECs stimulated with TNFα were compared with unstimulated ECs. EC activation was confirmed by the upregulation of VCAM-1 and Tissue Factor expression. Both assays discriminated between unstimulated and activated HUVECs and ECFCs, as significantly higher platelet deposition and fibrin formation in thrombogenesis assay, and thrombin generation in TGA, were observed when TNFα-activated ECs were used as a substrate. The amount of fibrin and thrombin measured in the two assays were directly correlated. Our results support the combined use of a thrombogenesis assay and TGA performed on patient-derived ECFCs to provide a personalized global assessment of ED relevant to the patient's hemostatic profile.

restrictedMar 2022View details →

Dataset related to article "Current and New Next-Generation Sequencing Approaches to Study Mitochondrial DNA"

Dataset contain raw data relate to article mentioned at title

restrictedcc-by-4.0Jul 2024View details →

Dataset of Attracting hearts, saving lives: How University-School partnerships between Brazil and Spain inspire a new generation of blood donors (BDKQ).

Dataset of the validation of the Blood Donation Knowledge Questionnaire (BDKQ-SPAIN)

restrictedJul 2024View details →

UMD-350MB: Refined MIDI Dataset for Symbolic Music Generation

UMD-350MB The Universal MIDI Dataset 350MB (UMD-350MB) is a proprietary collection of 85,618 MIDI files curated for research and development within our organization. This collection is a subset sampled from a larger dataset developed for pretraining symbolic music models. The field of symbolic music generation is constrained by limited data compared to language models. Publicly available datasets, such as the Lakh MIDI Dataset, offer large collections of MIDI files sourced from the web. While the sheer volume of musical data might appear beneficial, the actual amount of valuable data is less than anticipated, as many songs contain less desirable melodies with erratic and repetitive events. The UMD-350MB employs an attention-based approach to achieve more desirable output generations by focusing on human-reviewed training examples of single-track melodies, chord progressions, leads and arpeggios with an average duration of 8 bars. This was achieved by refining the dataset over 24 months, ensuring consistent quality and tempo alignment. Moreover, the dataset is normalized by setting the timing information to 120 BPM with a tick resolution (PPQ) of 96 and transposing the musical scales to C major and A minor (natural scales). Melody Styles A major portion of the dataset is composed of newly produced private data to represent modern musical styles. <ul> <li>Pop: 1970s to 2020s Pop music</li> <li>EDM: Trance, House, Synthwave, Dance, Arcade</li> <li>Jazz: Bebop, Ballad, Latin-Jazz, Bossa-Jazz, Ragtime</li> <li>Soul: 80s Classic, Neo-Soul, Latin-Soul</li> <li>Urban: Pop, Hip-Hop, Trap, R&B, Afrobeat</li> <li>World: Latin, Bossa Nova, European</li> <li>Other: Film, Cinematic, Game music and piano references</li> </ul> Actual MIDI files are unlabeled for unsupervised training. Dataset Access Please note that this is a closed-source dataset with very limited access. Considerations for access include proposals for data augmentation, chord extraction and other enhancement methods, whether through scripts, algorithmic techniques, manual editing in a DAW or additional processing methods. For inquiries about this dataset, please email us.

restrictedcc-by-4.0Sep 2024View details →

Dataset of AI-generated code and human-written code created by Stack Overflow questions

Open the record for dataset details and reuse information.

restrictedAug 2023View details →

(Tiny) Music Score Generation Dataset

This dataset is a much smaller version of the Music Score Generation Dataset from the thesis on automatic score-to-score music generation

restrictedJan 2022View details →

DATASET RELATED TO ARTICLE "The Alpha-Synuclein RT-QuIC Products Generated by the Olfactory Mucosa of Patients with Parkinson's Disease and Multiple System Atrophy Induce Inflammatory Responses in SH-SY5Y Cells"

RAW DATA RELATED TO ARTICLE AT TITLE

restrictedMar 2022View details →

The datasets generated to plot the Figure 2 to Figure 9.

(1) The Terrestrial Hybrid Repeated Gravity Observation data is applied from Data Sharing Infrastructure of National Earthquake Data Center(http://data.earthquake.cn).Only Chinese language link(https://data.earthquake.cn/datashare/report.shtml?PAGEID=datasourcelist&dt=40280d0453e5add30153e5ee3dc1001f; https://data.earthquake.cn/datashare/report.shtml?PAGEID=datasourcelist&dt=40280d0453e5add30153e5f03dd10022). Data can be requested through the email application form or the offline application form. (2) Earthquake catalog data comes from the end of China Seismic Experimental Site webpage (http://www.cses.ac.cn/sjcp/ggmx/2021/132.shtml). Click on "cata2019". (3) 3He/4He release data is downloaded from the supplementary data of published article. (https://github.com/mzhangrocks/Plateau-Growth) We have cited this article in this paper. (4) The 3-D P- and S-wave community velocity model of the crust and uppermost mantle in southwest China is downloaded from the supplementary data of published article. (https://github.com/liuyingustc/SWChinaCVM),(SWChinaCVM-1.0, DOI:10.12093/02md.02.2019.01.v1). We have cited this article in this paper.

restrictedJul 2022View details →

Archive of the iSALE simulation datasets for Jackson et al. 2022, "Impact generation of holes in the early lunar crust I: scaling relations"

Archive of the iSALE simulation datasets used in Jackson et al. 2022, "Impact generation of holes in the early lunar crust I: scaling relations". This archive contains all necessary information to re-run any of the simulations in the dataset along with plots that can be used to check the outcomes of each simulation.  In addition, it also contains a full compilation of all of the derived data used in Jackson et al. 2022 as well as the analysis scripts used to extract that data from the simulations and the scripts that use the derived data to generate the figures in the manuscript. The archive is provided in a standard compressed (.zip) format.   Detailed description of the contents Note that this description can also be found in the ReadMe file provided with the archive   1) Simulation folders The folder 'simsmain' contains files for the iSALE2D simulations that comprise the primary simulation database. For each simulation we provide: <ul> <li>asteroid.inp - the initialisation file for the simulation that would allow it to be re-run</li> <li>[].dat - a text file containing data derived from the final simulation output.  These values from all simulations are compiled in alldata.csv.  A description of the columns is provided below for alldata.csv</li> <li>[]-Crthickprof.pdf - a figure showing the radial crust thickness profile at the end of the simulation. Light pink shows the cell-by-cell profile, solid red a moving average.</li> <li>[]-Damprof.pdf - a figure showing the radial profile of the mean damage factor (averaged over the depth of the crust at each radial cell) at the end of the simulation.  Light grey shows the cell-by-cell profile, solid black a moving average.</li> <li>[]-TmpDam.dpdf - a figure showing the temperature and damage structure of the entire high-resolution zone at the end of the simulation at 1:1 aspect ratio (i.e. square cells are square in the image).  The boundary of the crust is outlined in black.</li> <li>[]-TmpDam-zoom.pdf - as above, but zoomed in on the central region of interest in the simulation.  This image is stretched to highlight the region of interest (i.e. square cells are not square in the image).</li> <li>[]-temporal.dat - a text file containing data derived from the full simulation time series.  These values from all simulations are compiled in alldata_temporal.csv.  A description of the columns is provided below for alldata_temporal.csv</li> <li>[]-crdepthtime.png - a figure showing the change in the maximum depression of the upper surface of the simulation over time.  This records the excavation and collapse of the initial transient cavity.</li> <li>[]-holeradtime.png - a figure recording the radius of the hole (as measured by the locations at which the crust thickness passes 90 and 95 percent of the initial value) over time.  A final plateau is indicative of the simulation having settled.</li> <li>[]-holevoltime.png - a figure recording the volume of the hole within the 95% crust thickness radius over time.</li> <li>[]-trcavtime.png - a figure recording the volume of the surface depression over time.  This can be quite sensitive to small fluctuations at the edges of the surface depression and does not always plateau.</li> </ul> Within simsmain each sub-folder is named in the format dW_vX_cY_gZ, where d is the diameter of the impactor (in km), v is the impact velocity (in m/s), c is the crust thickness (in km) and g is the grid resolution of the high-resolution zone (in km).  W, X, Y and Z are all in exponential notation with two significant figures (i.e. N.NE+NN). The folder 'simsres' contains files for the additional iSALE2D simulations run for resolution testing purposes.  These files have the same formats and naming conventions as simsmain. The folder 'material' contains the file material.inp, the initialisation file for the material properties which is common to all of the simulations.   2) Analysis scripts The folder 'analysisscripts' contains the Python scripts that were used to generate the files in simsmain and simsres.  There are two scripts, iSALEanalysis_batch.py which generates the end-of-simulation plots and data, and iSALEanalysis_batch_temporal.py which generates the time series plots and data.  The temporal script typically takes around 400 times longer to run than the end-of-simulation script since the former must examine all (usually 800) timesteps, whereas the end-of-simulation script examines only the first and last timestep.   3) Figures The folder 'figures' contains CSV files summarising all of the data derived from the iSALE2D simulations along with plotting scripts that use this derived data to generate the plots in Jackson et al. 2022. ----------- alldata.csv is a compilation of the data in the [].dat files for all 252 simulations in the primary simulation database.  There are 14 columns which in order are: <ol> <li>dimp        - impactor diameter in km</li> <li>vimp        - impact velocity in km/s</li> <li>crd         - initial crust thickness in km</li> <li>tdat        - simulation time (in seconds) at which the data was taken</li> <li>gres        - grid resolution in the high-resolution zone in km</li> <li>rhires      - radius of the high-resolution zone in km</li> <li>r_thincr0_95- radial distance (in km) at which the crust thickness exceeds 95% of the initial value</li> <li>r_thincr0_9 - radial distance (in km) at which the crust thickness exceeds 90% of the initial value</li> <li>r_magcr     - radius (in km) within which there is direct exposure of magma to the surface (i.e. crust thickness is zero)</li> <li>r_frac09    - radial distance (in km) within which the vertically averaged damage factor in the crust exceeds 0.9</li> <li>r_frac08    - radial distance (in km) within which the vertically averaged damage factor in the crust exceeds 0.8</li> <li>r_frac05    - radial distance (in km) within which the vertically averaged damage factor in the crust exceeds 0.5</li> <li>holevolume  - volume (in km^3) of crust excavated from within r_thincr0_95</li> <li>comment2    - impact regime classification, 'partial'= partial penetration, 'complete' = complete penetration, 'cfd' = cratering with full-depth fracturing, 'classical' = classical crater.</li> </ol> ----------- alldata_temporal.csv is a compilation of the data in the []-temporal.dat files for all 252 simulations in the primary simulation database.  There are 20 columns which in order are: <ol> <li>dimp        - impactor diameter in km</li> <li>vimp        - impact velocity in m/s (Note the difference from alldata.csv)</li> <li>crd         - initial crust thickness in km</li> <li>tdat        - simulation time (in seconds) at which the data was taken</li> <li>gres        - grid resolution in the high-resolution zone in km</li> <li>rhires      - radius of the high-resolution zone in km</li> <li>r_thincr0_95- radial distance (in km) at which the crust thickness exceeds 95% of the initial value</li> <li>r_thincr0_9 - radial distance (in km) at which the crust thickness exceeds 90% of the initial value</li> <li>r_magcr     - radius (in km) within which there is direct exposure of magma to the surface (i.e. crust thickness is zero)</li> <li>r_frac09    - radial distance (in km) within which the vertically averaged damage factor in the crust exceeds 0.9</li> <li>r_frac08    - radial distance (in km) within which the vertically averaged damage factor in the crust exceeds 0.8</li> <li>r_frac05    - radial distance (in km) within which the vertically averaged damage factor in the crust exceeds 0.5</li> <li>holevolume  - volume (in km^3) of crust excavated from within r_thincr0_95</li> <li>mcrd        - maximum depth of the transient cavity in km</li> <li>t_mcrd      - simulation time (in seconds) at which transient cavity reaches maximum depth</li> <li>trcav_mcrd  - volume (in km^3) of the transient cavity at the time of maximum depth</li> <li>mtrcav      - maximum volume of the transient cavity</li> <li>t_mtrcav    - simulation time (in seconds) at which transient cavity reaches maximum volume</li> <li>crd_mtrcav  - depth of the transient cavity (in km) at the time of maximum volume</li> <li>comment2    - impact regime classification, 'partial'= partial penetration, 'complete' = complete penetration, 'cfd' = cratering with full-depth fracturing, 'classical' = classical crater.</li> </ol> ----------- restest-rthin.csv and restest-frac.csv are in the same format as alldata.csv and contain the data for the sets of simulations used to test the resolution dependence of r_thin and r_frac respectively. ----------- There are 7 Python plotting scripts: <ol> <li>plotter_main.py - the main plotting script, produces plots that don't fall under another heading</li> <li>plotter_KE.py   - produces plots as a function of impact kinetic energy</li> <li>plotter_temporal.py - produces plots using time series data from alldata_temporal</li> <li>plotter_cox.py  - produces plots comparing our results to those of Bray et al. 2014, Cox et al. 2008, Cox & Bauer 2015 and Miljkovic et al. 2015.  Note that we do not include the CSV files containing the data from those papers since it is not ours to distribute, however they can be easily extracted from the relevant publications.</li> <li>plotter_res.py  - produces resolution comparison plots</li> <li>plotter_pi.py   - produces Pi-scaling plots</li> <li>kplot-sims.py   - produces a plot of the 'k' factor (hole size/impactor mass) for comparison with Perera et al. 2018</li> </ol> All of the plots and fitting summaries produced by the plotting scripts are also included

restrictedMar 2023View details →

Dataset for generating figures 3 and 4 in paper titled "Spectroscopy of a mesospheric ghost", and figure 1 in supplementary information of the same paper.

Dataset for figures 3 and 4 in Passas-Varo et al. (2023): "Spectroscopy of a mesospheric ghost" and figure 1 in the related "Supplementary Information". AllSpectra_20190921_214514.csv contains the dataset of the sequence of spectra for the reported event.  Flux_Ratio_20190921_214514.csv contains the dataset of the line flux to generate figure 4 in the main paper and figure 1 in the supplementary information.  More information on the data of this study is given in the main paper.