Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
118
datasets available to search
ShareScore release 0.9.0
Dataset results
118 results for “streamlines”
Meiotic DNA breaks activate a streamlined response that largely avoids protein level changes
GEO Series GSE197022. Saccharomyces cerevisiae. 6 samples. Type: Expression profiling by high throughput sequencing.
A streamlined protocol and analysis pipeline for CUT&RUN chromatin profiling
GEO Series GSE126612. Homo sapiens. 67 samples. Type: Other; Genome binding/occupancy profiling by high throughput sequencing.
A streamlined nanopore-compatible 5PSeq protocol for rapid phenotypic antimicrobial sensitivity testing(Fig1_HT-5PSeq)
GEO Series GSE293523. Lactiplantibacillus plantarum; Bacillus subtilis. 53 samples. Type: Other.
A streamlined nanopore-compatible 5PSeq protocol for rapid phenotypic antimicrobial sensitivity testing (Fig.4_MinION)
GEO Series GSE293528. Clostridioides difficile. 62 samples. Type: Other.
A streamlined nanopore-compatible 5PSeq protocol for rapid phenotypic antimicrobial sensitivity testing (Fig2_s5PSeq)
GEO Series GSE293524. Clostridioides difficile; Enterococcus faecalis; Bacillus subtilis; Staphylococcus aureus. 18 samples. Type: Other.
Trial run of a streamlined locomotive
<u>Source</u>: Europeana <br><u>4DCity URL</u>: <a href="https://4dcity.org/imgupload/1652274662.6092.jpg">https://4dcity.org/imgupload/1652274662.6092.jpg</a> <br><u>Original Image URL</u>: <a href="https://api.europeana.eu/thumbnail/v2/url.json?uri=https%3A%2F%2Fwww.openbeelden.nl%2Fimages%2F682373%2FProefrit_van_een_stroomlijnlocomotief_%25280_31%2529.png&type=VIDEO">https://api.europeana.eu/thumbnail/v2/url.json?uri=https%3A%2F%2Fwww.openbeelden.nl%2Fimages%2F682373%2FProefrit_van_een_stroomlijnlocomotief_%25280_31%2529.png&type=VIDEO</a> <br><br><u>Image-Metadata:</u><br>Filename: 1652274662.6092.jpg<br>Image Dimensions: 360x288<br>Megapixels: 0.10 MP<br>Filesize: 114.90 KB<br>
Streamlined One-wire Logistics Optimize Transcatheter Aortic Valve Replacement
ClinicalTrials.gov study NCT07090811. IPD Sharing: Not stated. Countries: 0. Publications: 0.
STREAMLINE®SURGICAL SYSTEM Compared to iStent Inject W® in Patients With Open-Angle Glaucoma
ClinicalTrials.gov study NCT05280366. IPD Sharing: NO. Countries: 3. Publications: 0.
Project SPEED - Streamlined Protocol for Early Engagement and Delivery of HIV Prevention With Long-acting Injectable Cabotegravir: A Nurse-driven Protocol
ClinicalTrials.gov study NCT07346508. IPD Sharing: NO. Countries: 0. Publications: 0.
BLADE-R: streamlined RNA extraction for molecular diagnostics and high-throughput applications.
GEO Series GSE278095. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing.
A streamlined and comprehensive protocol for the generation and multi-omic analysis of human monocyte-derived macrophages
GEO Series GSE300681. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
A streamlined and comprehensive protocol for the generation and multi-omic analysis of human monocyte-derived macrophages [bulk RNA-Seq]
GEO Series GSE300680. Homo sapiens. 20 samples. Type: Expression profiling by high throughput sequencing.
Streamlined low-input transcriptomics through EASY-RNAseq
GEO Series GSE135290. Mus musculus. 23 samples. Type: Expression profiling by high throughput sequencing.
Streamlined DNA-encoded small molecule library screening and validation for the discovery of novel chemotypes targeting BET proteins (ChIP-seq)
GEO Series GSE225339. Mus musculus. 9 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Streamlined DNA-encoded small molecule library screening and validation for the discovery of novel chemotypes targeting BET proteins (RNA-seq)
GEO Series GSE225342. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Fast, streamlined fluorescence nanoscopy resolves rearrangements of SNARE and cargo proteins in platelets co-incubated with cancer cells.
<p><strong>This folder contains all raw data underlying the results presented in a manuscript, submitted to </strong><strong><em>Journal of Nanobiotechnology</em></strong><strong>, and entitled:</strong></p> <p> </p> <p><strong>Fast, streamlined fluorescence nanoscopy resolves rearrangements of SNARE and cargo proteins in platelets co-incubated with cancer cells.</strong></p> <p> </p> <p><strong>Authored by:</strong></p> <p>Jan Bergstrand<sup>a,+</sup>, Xinyan Miao<sup>a,+</sup>, Chinmaya Venugopal Srambickal<sup>a,+</sup>, Gert Auer<sup>b</sup>, Jerker Widengren<sup>a,*</sup></p> <p><sup>a</sup> Royal Institute of Technology (KTH), Department of Applied Physics, Experimental Biomolecular Physics, Albanova Univ Center, SE-106 91 Stockholm, Sweden</p> <p><sup>b</sup> Karolinska Institutet, Department of Oncology-Pathology, K7, Z1:00, Karolinska University Hospital, 171 76 Stockholm, Sweden</p> <p><sup>* </sup>To whom correspondence should be addressed. E-mail: <a href="mailto:jwideng@kth.se">jwideng@kth.se</a>, Phone: +46-8-7907813</p> <p><sup>+ </sup>These authors contributed equally</p> <p> </p> <p><strong>The data files are grouped into the different </strong><strong>figures where they are presented</strong><strong>.</strong></p> <p> </p> <p><strong>ABSTRACT</strong></p> <p>Background:</p> <p>Increasing evidence suggests that platelets play a central role in cancer progression, with altered storage and selective release from platelets of specific tumor-promoting proteins as a major mechanism. Fluorescence-based super-resolution microscopy (SRM) can resolve nanoscale spatial distribution patterns of such proteins, and how they are altered in platelets upon different activations. Analysing such alterations by SRM thus represents a promising, minimally invasive strategy for platelet-based diagnosis and monitoring of cancer progression. However, broader applicability beyond specialized research labs will require objective, more automated imaging procedures. Moreover, for statistically significant analyses many SRM platelet images are needed, of several different platelet proteins. Such proteins, showing alterations in their distributions upon cancer progression additionally need to be identified.</p> <p>Results:</p> <p>A fast, streamlined and objective procedure for SRM platelet image acquisition, analysis and classification was developed to overcome these limitations. By stimulated emission depletion SRM we imaged nanoscale patterns of six different platelet proteins; four different SNAREs (soluble N-ethylmaleimide factor attachment protein receptors) mediating protein secretion by membrane fusion of storage granules, and two angiogenesis regulating proteins, representing cargo proteins within these granules coupled to tumor progression. By an streamlined procedure, we recorded about 100 SRM images of platelets, for each of these six proteins, and for five different categories of platelets; incubated with cancer cells (MCF-7, MDA-MB-231, EFO-21), non-cancer cells (MCF-10A), or no cells at all. From these images, structural similarity and protein cluster parameters were determined, and probability functions of these parameters were generated for the different platelet categories. By comparing these probability functions between the categories, we could identify nanoscale alterations in the protein distributions, allowing us to classify the platelets into their correct categories, if they were co-incubated with cancer cells, non-cancer cells, or no cells at all.</p> <p>Conclusions:</p> <p>The fast, streamlined and objective acquisition and analysis procedure established in this work confirms the role of SNAREs and angiogenesis-regulating proteins in platelet-mediated cancer progression, provides additional fundamental knowledge on the interplay between tumor cells and platelets, and represent an important step towards using tumor-platelet interactions and redistribution of nanoscale protein patterns in platelets as a basis for cancer diagnostics.</p> <p> </p> <p><strong>Key Words:</strong></p> <p>STED, super-resolution microscopy, platelet, cancer, tumorigenesis, SNARE protein, dictionary learning</p>
Dataset related to article "Multicentric evaluation of a machine learning model to streamline the radiotherapy patient specific quality assurance process"
<p> This record contains raw data related to article “Multicentric evaluation of a machine learning model to streamline the radiotherapy patient specific quality assurance process"</p> <p><em>Purpose:</em> Patient-specific quality assurance (PSQA) is performed to ensure that modulated treatment plans can be delivered as intended, but constitutes a substantial workload that could slow down the radiotherapy process and delay the start of clinical treatments. In this study, we investigated a machine learning (ML) tree-based ensemble model to predict the gamma passing rate (GPR) for volumetric modulated arc therapy (VMAT) plans.</p> <p><em>Materials and Methods:</em> 5622 VMAT plans from multiple treatment sites were selected from a database of Institution 1 and the ML model trained using 19 metrics. PSQA analyses were performed automatically using criteria 3%/1 mm (global normalization, absolute dose, 10% threshold) and 95% action limit. Model’s performance was evaluated on an out-of-sample test set of Institution 1 and on two independent sets of measurements collected at Institution 2 and Institution 3. Mean absolute error (MAE), as well as the model’s sensitivity and specificity, were computed.</p> <p><em>Results:</em> The model obtained a MAE of 2.33%, 2.54% and 3.91% for the three Institutions, with a specificity of 0.90, 0.90 and 0.68, and a sensitivity of 0.61, 0.25, and 0.55, respectively. Small positive median values of the residuals (i.e., the difference between measurements and predictions) were observed for each Institution (0.95%, 1.66%, and 3.42%). Thus, the model’s predictions were, on average, close to the real values and provided a conservative estimation of the GPR.</p> <p><em>Conclusions</em>: ML models can be integrated into clinical practice to streamline the radiotherapy workflow, but they should be center-specific or thoroughly verified within centers before clinical use.</p> <p> </p>
Dataset related to article "Deep learning and atlas-based models to streamline the segmentation workflow of Total Marrow and Lymphoid Irradiation"
<p>This record contains raw data related to article “Deep learning and atlas-based models to streamline the segmentation workflow of Total Marrow and Lymphoid Irradiation"</p> <p>Abstract:</p> <p><strong>Purpose: </strong>To improve the workflow of Total Marrow and Lymphoid Irradiation (TMLI) by enhancing the delineation of organs-at-risk (OARs) and clinical target volume (CTV) using deep learning (DL) and atlas-based (AB) segmentation models.</p> <p><strong>Materials and Methods:</strong> Ninety-five TMLI plans optimized in our institute were analyzed. Two commercial DL software were tested for segmenting 18 OARs. An AB model for lymph node CTV (CTV_LN) delineation was built using 20 TMLI patients. The AB model was evaluated on 20 independent patients and a semi-automatic approach was tested by correcting the automatic contours. The generated OARs and CTV_LN contours were compared to manual contours in terms of topological agreement, dose statistics, and time workload. A clinical decision tree was developed to define a specific contouring strategy for each OAR.</p> <p><strong>Results: </strong>The two DL models achieved a median Dice Similarity Coefficient (DSC) of 0.84 [0.73;0.92] and 0.84 [0.77;0.93] across the OARs. The absolute median dose (Dmedian) difference between manual and the two DL models was 2% [1%;5%] and 1% [0.2%;1%]. The AB model achieved a median DSC of 0.70 [0.66;0.74] for CTV_LN delineation, increasing to 0.94 [0.94;0.95] after manual revision, with minimal Dmedian differences. Since September 2022, our institution has implemented DL and AB models for all TMLI patients, reducing from 5 to 2 hours the time required to complete the entire segmentation process.</p> <p><strong>Conclusion: </strong>DL models can streamline the TMLI contouring process of OARs. Manual revision is still necessary for lymph node delineation using AB models.</p> <p> </p> <p><strong>Statements & Declarations</strong></p> <p><strong>Funding:</strong> This work was funded by the Italian Ministry of Health, grant AuToMI (GR-2019-12370739).</p> <p><strong>Competing Interests:</strong> The authors have no conflict of interests to disclose.</p> <p><strong>Author Contributions:</strong> All authors contributed to the study conception and design. Material preparation, data collection and analysis were performed by D.D., N.L., L.C., R.C.B., D.L., and P.M. The first draft of the manuscript was written by D.D. and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.</p> <p><strong>Ethics approval:</strong> The study was conducted in accordance with the Declaration of Helsinki and approved by the Institutional Ethics Committee of IRCCS Humanitas Research Hospital (ID 2928, 26 January 2021). ClinicalTrials.gov identifier: NCT04976205.</p> <p><strong>Consent to participate: </strong>Informed consent was obtained from all individual participants included in the study.</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.