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8,537
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Dataset results
8,537 results for “Openness”
Open Array Custom Real-time quantitative PCR analysis of mouse ileal mucosa
GEO Series GSE121612. Mus musculus. 36 samples. Type: Expression profiling by RT-PCR.
Changes in global open chromatin structure caused by acute deletion of TERT in spermatogonial stem cells
GEO Series GSE145658. Mus musculus. 22 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Phosphorylated nuclear DICER1 promotes open chromatin state and gastric cell fate in lung adenocarcinomas [ATAC-seq]
GEO Series GSE228964. Mus musculus. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Open Array Mouse Inflammation Real-time quantitative PCR analysis of mouse colonic mucosa
GEO Series GSE121616. Mus musculus. 16 samples. Type: Expression profiling by RT-PCR.
G4access identifies G-quadruplexes and their associations with open chromatin and imprinting control regions. Nat Genet (2023). https://doi.org/10.1038/s41588-023-01437-4
GEO Series GSE187007. Drosophila melanogaster; Saccharomyces cerevisiae; Homo sapiens; Mus musculus. 63 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing.
Open Pediatric Cancer (OpenPedCan) Project v15
OpenPedCan is a project led by the Center for Data-Driven Discovery at the Children's Hospital of Philadelphia. Here, we harmonize pan-cancer data using KidsFirst Data Resource Center workflows and harness OpenPBTA analytics workflows to scale and add modules across pediatric cancer datasets. The v11 release of this data has been integrated into the pediatric open targets platform to assist in development and query of the FDA's Relevant Pediatric Molecular Targets List (PMTL) to identify new therapeutics for children with cancer. This is the v15 release of OpenPedCan. For study release details, please see Release Notes
Figure 1 in Open Access and the Future of the Scientific Research
Figure 1. Growth in manuscript submissions to the BioMed Central open access journals.
Dataset for: Efficacy and safety of intravenous ferric carboxymaltose compared with oral iron for the treatment of iron deficiency anaemia in women following childbirth in Tanzania: a parallel, open-label, superiority, randomised controlled phase III trial
<p>These are pseudo-anonymised data from the randomised trial "Efficacy and safety of intravenous ferric carboxymaltose compared with oral iron for the treatment of iron deficiency anaemia in women following childbirth in Tanzania: a parallel, open-label, superiority, randomised controlled phase III trial". There are two datasets, one containing baseline data (one row per participant) and one containing longitudinal data (one row per participant per visit). The data dictionary explains the data available in each dataset. Between October 2015 and March 2017, 230 eligible and consenting women were enrolled from two sites in Tanzania. The trial results are published here: <a href="https://doi.org/10.1016/S2214-109X(20)30448-4">https://doi.org/10.1016/S2214-109X(20)30448-4</a></p>
Dataset related to article "Post-biopsy cell-free DNA from blood: an open window on primary prostate cancer genetics and biology"
<p>This record contains data related to article "Post-biopsy cell-free DNA from blood: an open window on primary prostate cancer genetics and biology".</p> <p>Circulating cell-free DNA (ccfDNA), released from normal and cancerous cells, is a promising biomarker for cancer detection as in neoplastic patients it is enriched in tumor-derived DNA (ctDNA). ctDNA contains cancer-specific mutations and epigenetic modifications, which can have diagnostic/prognostic value. However, in primary tumors, and in particular in localized prostate cancer (PCa), the fraction of ctDNA is very low and conventional strategies to study ccfDNA are unsuccessful. Here we demonstrate that prostate biopsy, by causing multiple injuries to the organ, leads to a significant increase in plasma concentration of ccfDNA (P<0.0024) in primary PCa patients. By calculating the minor allele fraction at patient-specific somatic mutations pre- and post-biopsy, we show that ctDNA is significantly enriched (from 3.9 to 164 fold) after biopsy, representing a transient “molecular window” to access and analyze ctDNA. Moreover, we show that newly released ccfDNA contains a larger fraction of di-, tri- and multi-nucleosome associated DNA fragments. This feature could be exploited to further enrich prostate-derived ccfDNA and to analyze epigenetic markers. Our data represent a proof-of-concept that liquid tumor profiling from peripheral blood performed just after the biopsy procedure can open a “valuable molecular metastatic window” giving access to the tumor genetic asset, thus providing an opportunity for early cancer detection and individual genomic profiling in the view of PCa precision medicine.</p>
Artikel- und Buchpublikationen aus der Soziologie: Open Science, Open Access zu Texten, Open Access zu Forschungsdaten, Open Access zu Forschungssoftware, Altmetrics [full record]
<p>Die Daten umfassen Stichproben an je 100 Journalartikeln und Buchpublikationen aus der Soziologie. Ausgwählt wurden Veröffentlichungen aus deutschsprachigen und nicht-deutschsprachigen Ländern.</p> <p>Für alle Artikel der Stichprobe wurde geprüft,</p> <p>1) ob sie im Gold Open Access verfügbar waren<br> 2) ob sie im Green Open Access verfügbar waren<br> 3) auf welchem Repository-Typ sie (im Falle einer Green Open Access Publikation) verfügbar waren<br> 4) seit wann sie im Green Open Access verfügbar waren<br> 5) ob Forschungsdaten zum Artikel verfügbar waren<br> 6) ob Forschungssoftware zum Artikel verfügbar war<br> 7) wie häufig der Artikel in Google Scholar zitiert wurde<br> 8) wie häufig der Artikel im Web of Science zitiert wurde<br> 9) wie häufig der Artikel in Scopus zitiert wurde<br> 10) wie häufig der Artikel in den Sociological Abstracts zitiert wurde<br> 11) wie viele Mendeley User Counts der Artikel aufwies<br> 12) wie häufig der Artikel getwittert wurde (Datenquelle: Topsy)</p> <p> </p> <p>Für alle Bücher der Stichprobe wurde geprüft,</p> <p>1) ob sie im Gold Open Access verfügbar waren<br> 2) ob sie im Green Open Access verfügbar waren<br> 3) auf welchem Repository-Typ sie (im Falle einer Green Open Access Publikation) verfügbar waren<br> 4) seit wann sie im Green Open Access verfügbar waren<br> 5) wie häufig das Buch in Google Scholar zitiert wurde<br> 6) wie häufig das Buch im Web of Science zitiert wurde (als Cited-Reference-Analyse)<br> 7) wie häufig das Buch in Scopus zitiert wurde<br> 8) wie häufig das Buch in der International Bibliography of the Social Sciences zitiert wurde<br> 9) wie viele Mendeley User Counts das Buch aufwies<br> 10) wie häufig das Buch getwittert wurde (Datenquelle: Topsy)</p> <p><br> Da die Impact-Informationen unter Copyright-Schutz der Datenbank-Anbieter stehen, können diese nicht frei zugänglich gemacht werden. Es existiert jedoch eine offen verfügbare Version dieser Datensammlung, die allerdings keine Impact-Informationen enthält.</p>
Distribution of peer-reviewed and non-peer-reviewed journals by their status as Open Access / Closed Access Journals and Discipline
<p>1) Shares of peer reviewed and non peer reviewed open access journals and closed access journals by discipline (using ulrichs periodicals subject categories)<br> 2) Shares of journals (social sciences, medicine) in german language that are peer reviewed/ non peer reviewed and that are available open access/ closed access (using ulrichs periodicals subject categories)</p> <p> </p>
Share of Open Access Journals among the Sociology Journals with the highest Journal Impact Factors (2002-2012)
<p>An overview on the portion of Open Access journals among the Sociology Journals with the highest JIF scores (2002-2012).</p>
Open Access Status of the 20 Journals with the highest JIF-Scores within the Subject Category General & Internal Medicine
<p>An Overview on the twenty journals with the highest Journal Impact Factors within the Subject Category General & Internal Medicine and their status as Open Access or Closed Access Journals.</p>
Semifluorinated Polymer Membranes by Ring-Opening Metathesis Polymerization during Spin Coating
<p>Date: 18 November, 2024</p> <p> </p> <p>Dataset Title: Semifluorinated Polymer Membranes by Ring-Opening Metathesis Polymerization during Spin Coating</p> <p> </p> <p> </p> <p>Dataset Creators: Arun Srikanth Sridhar</p> <p> </p> <p>Dataset Contact:</p> <p>Arun Srikanth Sridhar: askforarun@gmail.com</p> <p>Prof. Clare McCabe: C.MCCABE@hw.ac.uk</p> <p> </p> <p> </p> <p>Funding: Division of Materials Research (Award #2119575) , Graduate Research Fellowship Program, HWU high performance computing facility (DMOG)</p> <p> </p> <p> </p> <p>Key Points:</p> <p>- Molecular simulations and experiments agree that fluorocarbon side chains align parallel to the surface in the bulk but normal to the surface at the interface. </p> <p>- Molecular simulations show preferential segregations of CF<sub>3</sub> groups over CF<sub>2</sub> and CH<sub>2</sub> groups.</p> <p>- Fractional free volume increases upon flourination</p> <p> </p> <p> </p> <p>Research Overview:</p> <p> </p> <p>Molecular dynamics (MD) simulations were utilised to validate the theoretical and semi-empirical approaches employed and provide molecular level insight to the experientially observed behavior.</p> <p> </p> <p> </p> <p>Methodology:</p> <p>All simulations were conducted in NPT, NVT ensembles using GROMACS 2023.2. MDanalysis, mdtraj, and gromacs utility functions were used for postprocessing atomic trajectories.</p> <p> </p> <p>Files contained here:</p> <p> </p> <p>The PNBFN_SI folder contains two subfolders, PNBFN_signac and thickfilm_signac, a python file, analysis.py and a Jupyter notebook file, final_results.ipynb.</p> <p> </p> <p>Inside the PNBFN_signac folder you will find workspace folder. Each folder inside workspace folder corresponds to a specific polymer system. The information regarding the system is contained in signac_statepoint.json file. </p> <p> </p> <p>Inside any folder within the workspace folder of PNBFN_signac you will find</p> <p>1) all the necessary GROMACS files to reproduce the simulations of bulk polymer systems.</p> <p>2) The bash scripts used to run the simulations (for example 21stepbulk.sh is the script used to create bulk polymer systems ) in the cluster.</p> <p>3) The free volume folders, freevol_300_0_2.8, freevol_300_500000_2.8, freevol_300_100000_2.8 contain the necessary files to reproduce the calculations carried out using pore blazer. Here, 300 refers to the temperature, the second item (0,500000,100000) refers to the time stamp (in ps), the third item 2.8 refers to the probe diameter.</p> <p>4) log files.</p> <p> </p> <p>Inside the thickfilm_signac folder you will find workspace folder. Each folder inside workspace folder corresponds to a specific polymer film system.</p> <p> </p> <p>Inside any folder within the workspace of thickfilm_signac folder you will find</p> <p>1) all the necessary GROMACS files to reproduce the simulations of polymer film systems.</p> <p>2) The bash scripts used to run the simulations (for example 21stepfilm.sh is the script used to create polymer film systems) in the cluster.</p> <p>3) log files</p> <p> </p> <p>analysis.py in PNBFN_signac contains the python codes for running the simulations (generating the bashscripts) and the codes used in post processing.</p> <p> </p> <p>The final_results.ipynb calls the functions in analysis.py and contains the codes for generating the figures in the manuscript. Each code block in final_results.ipynb corresponds to a figure in the manuscript. The code blocks are commented for clarity.</p> <p>Use and Access:</p> <p>To use the signac framework of this project, MOSDEF suite (https://mosdef.org), SIGNAC (<a href="https://signac.io/">https://signac.io</a>) and other python packages need to be installed. These python packages can be found in analysis.py and final_results.ipynb.</p> <p>The trajectories require large disk space and are not provided but the simulations can be easily extended/reproduced using the following commands. Execute these commands within any folder inside workspace to extend the simulations by 1000 ps.</p> <p>gmx convert-tpr -s X.tpr -extend 1000 -o next.tpr</p> <p>gmx mdrun -s next.tpr -cpi X.cpt -noappend </p> <p>where X.tpr is the tpr file (topology file) and X.cpt is the check point file</p> <p> </p> <p>The full signac framework will be made available upon request.</p>
Dataset related to article " Effect of a Mindfulness-Based Intervention for Chronic Migraine and High Frequency Episodic Migraine in Adolescents: A Pilot Single-Arm Open-Label Study"
<p><strong>Data related to the longitudinal single-arm open study on the effect of mindfulness in adolescents with CM and HFEM</strong></p> <p> </p> <p> </p> <p> </p> <p> </p>
A workflow and digital filters for correcting speed and equalisation errors on digitised audio open-reel magnetic tapes - Audio Samples
<p>This repository makes available the audio samples related to the paper:</p> <p>Niccolò Pretto, Nadir Dalla Pozza, Alberto Padoan, Anthony Chmiel, Kurt James Werner, Alessandra Micalizzi, Emery Schubert, Antonio Rodà, Simone Milani and Sergio Canazza, <em>A workflow and digital filters for compensating speed and equalisation errors on digitised audio open-reel magnetic tapes</em>, Journal of the Audio Engineering Society, Special Issue on Audio Filter Design, 2022.</p> <p>The experiment and the three case studies are described in the publication above.</p> <p>This repository contains two main directories (<strong>bold</strong> indicates directory names):</p> <ul> <li> <p><strong>Experiment Samples</strong>: the 10 seconds long samples used in the experiment;</p> </li> <li> <p><strong>Long Samples</strong>: the original 6 minutes long samples, one for each of the identified cases.</p> </li> </ul> <p>Here is the notation of the file naming:</p> <ul> <li> <p>W: recording (writing);</p> </li> <li> <p>R: reproducing;</p> </li> <li> <p>3: 3.75 NAB;</p> </li> <li> <p>7N: 7.5 NAB;</p> </li> <li> <p>7C: 7.5 CCIR;</p> </li> <li> <p>15C: 15 CCIR.</p> </li> </ul> <p>For what concerns the <strong>Experiment Samples</strong> directory, here is the summary of the recording/reproducing standards of the adopted samples and their notation:</p> <ul> <li> <p>SET A: Recording 3.75 NAB (W3) - Reproducing 7.5 CCIR (R7C);</p> </li> <li> <p>SET B: Recording 3.75 NAB (W3) - Reproducing 15 CCIR (R15C);</p> </li> <li> <p>SET C: Recording 7.5 NAB (W7N) - Reproducing 15 CCIR (R15C).</p> </li> </ul> <p>Here are the variants of the samples:</p> <ul> <li> <p>REFERENCE: produced by using the correct equalization standard;</p> </li> <li> <p>ANCHOR: the "Reference" altered with a low-pass filter, with pass band set at 7 kHz for music and 3.5 kHz for speech;</p> </li> <li> <p>INCORRECT: produced by using an intentionally incorrect equalization, created by mismatching the recording and reading curves and resampled to the correct speed;</p> </li> <li> <p>MATLAB: the “Incorrect” variant corrected by means of a Matlab script;</p> </li> <li> <p>API: the “Incorrect” variant corrected by means of an <em>ad hoc</em> web interface adopting Web Audio API, for simulating real-time correction in web applications.</p> </li> </ul> <p>Here is the samples list:</p> <ul> <li> <p>SET A:</p> <ul> <li> <p>Training:</p> <ul> <li> <p>sample4: Richard Wagner - <em>Ride of the Valkyries</em>;</p> </li> </ul> </li> <li> <p>Test:</p> <ul> <li> <p>sample1: Taylor Swift - <em>Shake It Off</em>;</p> </li> <li> <p>sample5: Queen - <em>We Will Rock You</em>;</p> </li> <li> <p>sample8: Bruno Maderna - <em>Continuo</em>;</p> </li> <li> <p>sample9: Luciano Berio - <em>Différences</em>.</p> </li> </ul> </li> </ul> </li> <li> <p>SET B (the track title reflects the name of the file from which the track itself was extracted, from the CLIPS project of the University of Napoli: <a href="http://www.clips.unina.it/en/index.jsp">http://www.clips.unina.it/en/index.jsp</a>):</p> <ul> <li> <p>Training:</p> <ul> <li> <p>sample22: CLIPS project - <em>LP4m18bZ</em>;</p> </li> </ul> </li> <li> <p>Test:</p> <ul> <li> <p>sample15: CLIPS project - <em>LP1f20bZ</em>;</p> </li> <li> <p>sample16: CLIPS project - <em>LP4m20bZ</em>;</p> </li> <li> <p>sample17: CLIPS project - <em>LP1f19bZ</em>;</p> </li> <li> <p>sample18: CLIPS project - <em>LP4m19bZ</em>.</p> </li> </ul> </li> </ul> </li> <li> <p>SET C:</p> <ul> <li> <p>Training:</p> <ul> <li> <p>sample3: Carl Orff - <em>Carmina Burana - O Fortuna</em>;</p> </li> </ul> </li> <li> <p>Test:</p> <ul> <li> <p>sample2: The Weeknd - <em>Save Your Tears</em>;</p> </li> <li> <p>sample6: Eagles - <em>Hotel California</em>;</p> </li> <li> <p>sample10: Bruno Maderna - <em>Musica su Due Dimensioni</em>;</p> </li> <li> <p>sample12: Bruno Maderna - <em>Syntaxis</em>.</p> </li> </ul> </li> </ul> </li> </ul>
Impact of Open Access monographs, dataset for french-speaking countries
Open the record for dataset details and reuse information.
Open Broadcast Media Audio from TV (OpenBMAT)
<p>Open Broadcast Media Audio from TV (OpenBMAT) is an open, annotated dataset for the task of music detection that contains over 27 hours of TV broadcast audio from 4 countries distributed over 1647 one-minute long excerpts. It is designed to encompass several essential features for any music detection dataset and is the first one to include annotations about the loudness of music in relation to other simultaneous non-music sounds. OpenBMAT has been cross-annotated by 3 annotators obtaining high inter-annotator agreement percentages, which validates the annotation methodology and ensures the annotations reliability.</p>
Dataset related to article "Robotic surgery, video-assisted thoracic surgery, and open surgery for early stage lung cancer comparison of costs and outcomes at a single institute"
<p>This record contains raw data related to article "Robotic surgery, video-assisted thoracic surgery, and open surgery for early stage lung cancer comparison of costs and outcomes at a single institute"</p> <p>Background:</p> <p>Robotic surgery is increasingly used to resect lung cancer. However costs are high. We compared costs and outcomes for robotic surgery, video-assisted thoracic surgery (VATS), and open surgery, to treat non-small cell lung cancer (NSCLC).</p> <p>Methods:</p> <p>We retrospectively assessed 103 consecutive patients given lobectomy or segmentectomy for clinical stage I or II NSCLC. Three surgeons could choose VATS or open, the fourth could choose between all three techniques. Between-group differences were assessed by Fisher's exact, two-way analysis of variance (ANOVA), and Wilcoxon-Mann-Whitney test. P values <0.05 were considered significant.</p> <p>Results:</p> <p>Twenty-three patients were treated by robot, 41 by VATS, and 39 by open surgery. Age, physical status, pulmonary function, comorbidities, stage, and perioperative complications did not differ between the groups. Pathological tumor size was greater in the open than VATS and robotic groups (P=0.025). Duration of surgery was 150, 191 and 116 minutes, by robotic, VATS and open approaches, respectively (P<0.001). Significantly more lymph node stations were removed (P<0.001), and median length of stay was shorter (4, 5 and 6 days, respectively; P<0.001) in the robotic than VATS and open groups. Estimated costs were 82%, 68% and 69%, respectively, of the regional health service reimbursement for robotic, VATS and open approaches.</p> <p>Discussion:</p> <p>Robotic surgery for early lung cancer was associated with shorter stay and more extensive lymph node dissection than VATS and open surgery. Duration of surgery was shorter for robotic than VATS. Although the cost of robotic thoracic surgery is high, the hospital makes a profit.</p>
Classifying Open-Source Pre-Trained Models and Datasets for Software Engineering
<p>The replication package for the short paper titled 'Classifying Open-Source Pre-Trained Models and Datasets for Software Engineering' is provided. It includes a README file and accompanying scripts with comprehensive instructions to facilitate the replication of the analysis presented in the paper.</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.