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Dataset and code for "FK-means: Automatic Atrial Fibrosis Segmentation using Fractal-guided K-means Clustering with Voronoi-Clipping Feature Extraction of Anatomical Structures": FKmeans for fibrosis segmentation
<p>Assessment of left atrial (LA) fibrosis from late gadolinium enhancement (LGE) magnetic resonance imaging (MRI) adds to the management of patients with atrial fibrillation (AF). However, accurate assessment of fibrosis in the LA wall remains challenging. Excluding anatomical structures in the LA proximity using clipping techniques can reduce misclassification of LA fibrosis. A novel FK-means approach for combined automatic clipping and automatic fibrosis segmentation was developed. This approach combines a feature-based Voronoi diagram with a hierarchical 3D K-means fractal-based method. The proposed automatic Voronoi clipping method was applied on LGE MRI data and achieved a Dice score of 0.75, similar as the score obtained by a deep learning method (3D UNet) for clipping (0.74). The automatic fibrosis segmentation method, which utilizes the Voronoi clipping method, achieved a Dice score of 0.76. This outperformed a 3D U-Net method for clipping and fibrosis classification, which had a Dice score of 0.69. Moreover, the proposed automatic fibrosis segmentation method achieved a Dice score of 0.90, using manual clipping of anatomical structures. The findings suggest that the automatic FK-means analysis approach enables reliable LA fibrosis segmentation and that clipping of anatomical structures in the atrial proximity can add to the assessment of atrial fibrosis. </p>
A Polyphenol-Rich Extract of Olive Mill Wastewater Enhances Cancer Chemotherapy Effects, While Mitigating Cardiac Toxicity
<p>Cardiovascular toxicity remains one of the most adverse side effects in cancer patients receiving chemotherapy. Extra-virgin olive oil (EVOO) is rich in cancer preventive polyphenols endowed with anti-inflammatory, anti-oxidant activities which could exert protective effects on heart cells. One very interesting derivative of EVOO preparation is represented by purified extracts from olive mill waste waters (OMWW) rich in polyphenols. Here, we have investigated the anti-cancer activity of a OMWW preparation, named A009, when combined with chemotherapeutics, as well as its potential cardioprotective activities. Mice bearing prostate cancer (PCa) xenografts were treated with cisplatin, alone or in combination with A009. In an <em>in vivo</em> model, we found synergisms of A009 and cisplatin in reduction of prostate cancer tumor weight. Hearts of mice were analyzed, and the mitochondria were studied by transmission electron microscopy. The hearts of mice co-treated with A009 extracts along with cisplatin had reduced mitochondria damage compared to the those treated with chemotherapy alone, indicating a cardioprotective role. To confirm the <em>in vivo</em> results, tumor cell lines and rat cardiomyocytes were treated with cisplatin <em>in vitro</em>, with and without A009. Another frequently used chemotherapeutic agent 5-fluorouracil (5-FU), was also tested in this assay, observing a similar effect. In vitro, the combination of A009 with cisplatin or 5-FU was effective in decreasing prostate and colon cancer cell growth, while it did not further reduce growth of rat cardiomyocytes also treated with cisplatin or 5-FU. A009 cardioprotective effects towards side effects caused by 5-FU chemotherapy were further investigated, using cardiomyocytes freshly isolated from mice pups. A009 mitigated toxicity of 5-FU on primary cultures of mouse cardiomyocytes. Our study demonstrates that the polyphenol rich purified A009 extracts enhance the effect of chemotherapy <em>in vitro</em> and <em>in vivo,</em> but mitigates chemotherpy adverse effects on heart and on isolated cardiomyocytes. Olive mill waste water extracts could therefore represent a potential candidate for cardiovascular prevention in patients undergoing cancer chemotherapy.</p>
On-line Solid Phase Extraction High Performance Liquid Chromatography Method Coupled with Tandem Mass Spectrometry for the Therapeutic Monitoring of Cannabidiol and 7-Hydroxy-cannabidiol in Human Serum and Saliva
<p>This database includes the raw data linked with the paper “On-line Solid Phase Extraction High Performance Liquid Chromatography Method Coupled with Tandem Mass Spectrometry for the Therapeutic Monitoring of Cannabidiol and 7-Hydroxy-cannabidiol in Human Serum and Saliva".</p> <p>Cannabidiol is a novel antiseizure medication approved in Europe and the US for the treatment of seizures associated with Lennox-Gastaut syndrome, Dravet syndrome and tuberous sclerosis complex. We describe in this article a new and simple liquid chromatography-mass spectrometry method (LC-MS/MS) for the determination of cannabidiol and its active metabolite 7-hydroxy-cannabidiol in microvolumes of serum and saliva (50 μL), to be used as a tool for therapeutic drug monitoring (TDM) and pharmacokinetic studies. After on-line solid phase extraction cannabidiol, 7-hydroxy-cannabidiol and the internal standard cannabidiol-d3 are separated on a monolithic C18 column under gradient conditions. Calibration curves are linear within the validated concentration range (10-1000 ng/mL for cannabidiol and 5-500 ng/mL for 7-hydroxy-cannabidiol).</p> <p>The method is accurate (intraday and interday accuracy within 94-112% for cannabidiol, 91-109% for 7-hydroxy-cannabidiol), precise (intraday and interday precision <11.6% for cannabidiol and <11.7% for 7- hydroxy-cannabidiol) and sensitive, with a LOQ of 2.5 ng/mL for cannabidiol and 5 ng/mL for 7-hydroxy-cannabidiol. The stability of the analytes was confirmed under different storage conditions. Extraction recoveries were in the range of 81-129% for cannabidiol and 100-113% for 7-hydroxy-cannabidiol.</p> <p>The applicability of the method to TDM was demonstrated by analysis of human serum and saliva samples obtained from patients with epilepsy treated with cannabidiol.</p>
Comparison of two RNA extraction methods for the molecular detection of SARS-CoV-2 from nasopharyngeal swab samples
<p>The database includes the raw data of the article “Comparison of two RNA Extraction Methods for the Molecular Detection of SARS-CoV-2 from nasopharyngeal swab samples”.</p> <p>Aim of this work was to compare a two commercially available kit for viral RNA extraction from human swab samples that differ mainly for time consuming (9 min. vs 35 min.) in order to improve SARS-CoV-2 diagnostic workflow.</p> <p>The database contains the data obtained by the following evaluations:</p> <p>a) RNA analysis for the evaluation of quality and quantity by nanodrop instrument</p> <p>b) Real Time PCR analysis of SARS-CoV-2 genes and internal control.</p> <p>The two procedures evaluated gave similar analytical results in terms of extracted RNA analysis and Real Time PCR data for gene expression.</p>
20240205 first screening serratia extractions raw data
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MEDED: Magi Entity Description Extraction Dataset
<p>Magi Entity Description Extraction Dataset (MEDED) contains 500,000 (entity, description, source URL) tuples extracted by the <a href="https://magi.com/">Magi</a> system from Chinese webpages on the Internet that are accessible from Mainland China in May 2019.</p> <p>These data are learned automatically and should not be considered to contain any opinion of any human individual including the authors.</p> <p>Main contents of the source URLs can be found in the <a href="https://zenodo.org/record/3242512">Magi Practical Web Article Corpus</a>.</p>
Extracts spotting test
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Green vegetation extracted during planting of crops
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Green vegetation extracted during crop harvesting
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Main policosanol extraction patents.
<p>Main policosanol extraction patents (parameters and yields) by saponification, transesterification, solvent extraction, supercritical CO<sub>2</sub> extraction and ultrasonic extraction. </p> <p> </p>
Antifeedant efficacy of Mentha spicata aqueous extracts on fall armyworm (Spodoptera frugiperda): a preliminary analysis
<p>Fall armyworms (<em>Spodoptera frugiperda</em>) cause massive destruction to crop produce and vegetation worldwide. Over the years, synthetic insecticides have been used to combat the devastating effects of this notorious polyphagous insect pest. Synthetic insecticides are not only expensive, but they are also harmful to the ecosystem. Safer and cost-effective deterrents, such as those derived from natural products, are highly warranted. This study proposes simplified methods for extracting and the examining the antifeedant properties of phytochemicals <em>Mentha spicata </em>aqueous extracts. Moreover, the study explains why the extracts from <em>Mentha spicata </em>can be potent alternatives to commercially available insecticides.</p>
Gluconobacter oxydans Knockout Collection Finds Improved Rare Earth Element Extraction
<p><strong>Datasets for "<em>Gluconobacter oxydans</em> Knockout Collection Finds Improved Rare Earth Element Extraction":</strong></p> <p>Data S1. BLAST2GO output with assigned gene ontologies, InterPro IDs, and BLAST hits represented in Fig. 1A.</p> <p>Data S2. Monte Carlo (MC) estimate of the number of genes represented by at least one mutant per number of mutants collected for simulated and real picking events, used to generate Fig. 1B.</p> <p>Data S3. Complete condensed knockout collection with sequencing and screen results.</p> <p>Data S4. Results of TB and BPB validation assays with proxy wild types.</p> <p>Data S5. Results of direct pH measurements.</p> <p>Data S6. Results of bioleaching assay.</p>
LHA Sentence Alignments Extracted From the Austria Press Agency Corpus
<p>Conference paper: <a href="https://aclanthology.org/2021.ranlp-1.150/">Exploring German Multi-Level Text Simplification</a></p> <p>Sentence alignments extracted with LHA (Nikolov and Hahnloser, 2019) from the Austria Press Agency (<em>Austria Presse Agentur</em>, APA) corpus. It contains alignments from news items between August 2018 and April 2021. There are alignments for CEFR levels A2 and B1 to the original standard German text.</p> <p> </p> <p>Nikola I. Nikolov and Richard Hahnloser. 2019. Large-scale hierarchical alignment for data-driven text rewriting. In Proceedings of the International Conference on Recent Advances in Natural Language Processing (RANLP 2019), pages 844–853, Varna, Bulgaria. INCOMA Ltd.</p>
Systematic Literature Review - Selected Articles Data Extraction
<p>The files included are the following:</p> <p>- CSV with the raw data extracted from abstract + full-text review from the selected articles.</p> <p>- CSV with normalized data according to the article.</p> <p> </p>
Data for "Extraction and Inversion of Coherent Rayleigh Waves from Urban Anthropogenic Noise with Distributed Acoustic Sensing"
<p>Data for "Extraction and Inversion of Coherent Rayleigh Waves from Urban Anthropogenic Noise with Distributed Acoustic Sensing"</p> <p> </p>
Automatic extraction of road boundary and land marking data
<p>This video demonstrates the application of our method in a software tool for automatically constructing road boundaries and lane markings data.</p>
Estrogenic activity of fermented soymilk extracts and soy compounds
GEO Series GSE226627. Homo sapiens. 22 samples. Type: Expression profiling by high throughput sequencing.
Fly_embryos_1-3_hr_150_mM_Salt_Extracted_Chromatin
GEO Series GSE25375. Drosophila melanogaster. 3 samples. Type: Genome binding/occupancy profiling by genome tiling array.
Detection of Human Viruses from wastewater sewage extracts
GEO Series GSE11195. Viruses. 13 samples. Type: Other.
Transcriptomic profiling of human senescent cells upon medicinal intervention with cocoa extract
GEO Series GSE160771. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
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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.