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37 results for “extraction optimization”
AiNU data for Physics-based material parameters extraction from perovskite experiments via Bayesian optimization
<p>This file contains the AiNU data used for the article entitled by <em>Physics-based material parameters extraction from perovskite experiments via Bayesian optimization</em> (https://arxiv.org/abs/2402.11101).</p>
Figure 4 in Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases
Figure 4. Identification of PCR inhibitors in 18 biological samples positive for Aspergillus. Graph A: Ct values obtained from pure and diluted DNA samples (dilution rate 1/20). Graph B: Ct values obtained with 20 copies of a plasmid DNA systematically added to the same biological samples (undiluted and diluted) and a negative control sample (NC).
Figure 2 in Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases
Figure 2. Influence of proteinase K digestion (56 °C overnight) on DNA extraction. Graph A shows the Ct values obtained by quantifying THP1 cell DNA derived from direct extraction with the NucliSENS easyMAG system and extraction performed on the same quantity of cells following overnight (ON) digestion with Proteinase K. Graph B shows Leishmania quantification after extraction with the NucliSENS easyMAG system both with and without PK and quantification after extraction using a QIAamp DNA Mini kit after ON digestion with PK.
Figure 7 in Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases
Figure 7. Variation of the ratio between kinetoplastic DNA and nuclear DNA extraction with various Leishmania quantities in the presence of 103 THP1 cells.
Figure 5 in Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases
Figure 5. Yield of DNA extraction from Leishmania and THP1 cells using the NucliSENS easyMAG system.
Figure 3 in Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases
Figure 3. Results of the extraction experiments performed on yeast (Candida albicans) and filamentous fungi (Aspergillus fumigatus). A presents the kinetics of the extraction process after vortexing and glass-bead treatment. B shows the differences in DNA quantity obtained from fungal cells using the FastPrep system (with) compared to the same process without grinding.
Figure 6 in Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases
Figure 6. Influence of the quantity of human cells (THP1 cells) on Leishmania quantification at various concentrations of host cells and parasites.
Fig. 2 in Protocol Optimization For Genomic Dna Extraction And Rapd-Pcr Of Alien Ponto-Caspian Amphipod Pontogammarus Robustoides
Fig. 2. RAPD fingerprints results from different samples of Pontogammarus robustoides with primers OPA-02 (1-12 runners- different samples of Pontogammarus robustoides; K- control) using RAPD-PCR 10 × Taq buffer with KCl.
Fig. 3. Agarose gel image Fig. 4 in Optimization Of Dna Extraction Protocol For Dna Isolation From Air-Dried Collection Material For Further Phylogenetic Analysis (Coleoptera: Carabidae)
Fig. 3. Agarose gel image Fig. 4. Agarose gel image (successful PCR amplification) (failed PCR amplification) M: marker (bp) M: marker (bp) A1: Agonum fuliginosum Panzer, 1809 A: Agonum fuliginosum Panzer, 1809 A2: Agonum thoreyi Dejean, 1828 O: Omophron aequale aequale Morawitz, 1863 O: Omophron aequale aequale Morawitz, 1863 N: Notiophilus semistriatus Say, 1823 N: Notiophilus semistriatus Say, 1823 Nk: negative control. Nk: negative control.
Fig. 1 in Optimization Of Dna Extraction Protocol For Dna Isolation From Air-Dried Collection Material For Further Phylogenetic Analysis (Coleoptera: Carabidae)
Fig. 1. Photo of Omophron aequale jacobsoni Fig. 2. Photo of Omophron aequale jacobsoni Semenov, 1922 before incubation. Semenov, 1922 after 16 h (56°C) incubation time in tissue lysis buffer with proteinase K.
Figure 6. (a1), (a2), (a3), (a4), (a5), (a6), (a7) and (a8) watermarked image is degraded respectively through JPEG2000 compression, JPEG compression, median filtering, adding Salt&Pepper noise, rotating, center cropping, surrounding cropping and scaling. (b1), (b2), (b3), (b4), (b5), (b6), (b7) and (b8) The corresponding extracted watermarks.-Discrete Wavelet Transform Method: A New Optimized Robust Digital Image Watermarking Scheme
<p>This paper has described a scheme for digital watermarking of still images based on discrete<br> wavelet transform. In the proposed method, the embedded logo watermark can be extracted without<br> access to the original image. It has been confirmed that the proposed watermarking method is able<br> to extract the embedded logo watermark from the watermarked images that have degraded through<br> compression, filtering, cropping and scaling. Although this algorithm is not robust against rotation,<br> it can completely extract the watermark from watermarked images that lose about 35% of their<br> areas by cropping attack.</p>
Figure 1. (a) Original watermark (b) extracted watermarks after compression(c) merged watermark-Discrete Wavelet Transform Method: A New Optimized Robust Digital Image Watermarking Scheme
<p>Therefore, each bit of the logo watermark is stored in one coefficient of a sub-block to keep<br> the capacity of watermarking fixed.<br> When a region of the watermarked image is destroyed; the whole watermark can be<br> extracted using other regions of the watermarked image by merging extracted watermarks. Figure 1<br> shows result of merging logo watermarks that were extracted from a compressed (with JPEG2000<br> algorithm) watermarked image.</p>
Optimization of nuclei isolation for high-molecular weight DNA extraction of wild plants
<p><strong>Optimization of nuclei isolation for high-molecular weight DNA extraction from wild plants</strong></p> <p><strong>Authors</strong></p> <p>Irene Martínez-García<sup>1</sup>; Martina Degli Alberti<sup>2</sup>; Aureliano, Bombarely<sup>2</sup>; Mario Xavier Ruiz-González<sup>1</sup>; Santiago Vilanova<sup>1</sup>; Silvia Manrique<sup>1</sup></p> <p> </p> <p><strong>Affiliations</strong></p> <p>1 Instituto Universitario para la Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universidad Politécnica de Valencia (UPV), Camino de Vera s/n 46022, Valencia, Spain) 2 Instituto de Biología Molecular y Celular de Plantas (IBMCP) Primo-Yufera, Consejo Superior de Investigaciones Científicas (CSIC)- Universidad Politécnica de Valencia (UPV), Camino de Vera s/n 46022, Valencia, Spain)</p> <p> </p> <p><strong>Abstract</strong></p> <p>Obtaining high-quality, high-molecular-weight (HMW) DNA is mandatory for constructing reference genomes, yet it remains a significant challenge, particularly for non-model plant species. Many plants contain polysaccharides and secondary metabolites such as polyphenols and tannins, which hinder DNA extraction. Exposure to multiple environmental stresses along their lives exacerbate this issue in wild plants collected from nature, as they may synthesize additional compounds that impair DNA extraction.</p> <p>This study investigates the efficacy of various DNA extraction protocols on four recalcitrant plant species—<em>Pistacia lentiscus</em>, <em>Phyllirea angustifolia</em>, <em>Sarcocornia fruticosa</em>, and <em>Limbarda crithmoides</em>—each possessing unique traits complicating DNA extraction (e.g., succulence, lignification, coloration). Samples were collected from El Saler (Valencia), and multiple protocols for nuclei isolation and DNA extraction were tested. The results were systematically evaluated to compile a comprehensive best practices guide, aiding researchers in selecting optimal methods tailored to their species of interest. This guide serves as a valuable resource for future endeavours in genome research, facilitating advancements in understanding and conservation efforts for diverse plant species.</p> <p>Funding: </p> <p>This work was supported by Erasmus+ Program (to MD), Programa María Zambrano 2021 (to SM and MXRG, UPV Ministerio de Universidades, Plan de Recuperación, Transformación y Resiliencia - Financiado por la Unión Europea – NextGenerationEU) and Catalan Initiative For the Earth Biogenome Project (Call1A-2023 to SM and call 2-2023 to AB and SM) and Primeros Proyectos UPV (PAID-06-22 to MXRG).</p>
Figure 1 in Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases
Figure 1. Study design.
Fig.1 in Protocol Optimization For Genomic Dna Extraction And Rapd-Pcr Of Alien Ponto-Caspian Amphipod Pontogammarus Robustoides
Fig.1. Localities of sampling sities in the Latvian reservoirs.
Data from: Drop it all: Extraction-free detection of non-indigenous marine species through optimized direct-droplet digital PCR
<p>Molecular biosecurity surveillance programs increasingly use environmental DNA (eDNA) for detecting marine non-indigenous species (NIS). However, the current molecular detection workflow is cumbersome, prone to errors and delays, and is limited in providing knowledge about eDNA beyond the spatial and temporal extent of the sampling. These limitations can hinder management efforts and restrict the "opportunity window" for a rapid response to new marine NIS incursions. Emerging innovative field-deployable digital droplet PCR (ddPCR) systems offer improved workflow efficiency by autonomously analyzing targeted free-floating extra-cellular eDNA (free-eDNA) signals. Despite their potential, these systems have not been tested in marine environments. Thus, an aquarium study was conducted with three distinct marine NIS: <span>the Mediterranean fanworm <em>Sabella spallanzanii</em>, the ascidian clubbed tunicate <em>Styela clava</em>, and the brown bryozoan <em>Bugula neritina</em></span> to evaluate the detectability of free-eDNA in seawater. The detectability of targeted free-eDNA was assessed by directly analyzing aquarium water samples using an optimized species-specific ddPCR assay, without filtration or DNA extraction, so-called, "direct-ddPCR". The results demonstrated the consistent detection of <em>Sabella spallanzanii</em> and <em>Bugula neritina</em> free-eDNA when these organisms were present in high abundance. Once organisms were removed, the free-eDNA signal exponentially declined, noting that free-eDNA persisted between 24-72 hours. Results indicate that organism biomass, specimen characteristics (e.g., stress and viability), and species-specific biological differences may influence free-eDNA detectability. These results are critical for implementing <em>in-situ</em> nucleic acid automated continuous sensing systems for marine biosurveillance, enabling point-of-need detection and <span>rapid management response to biosecurity threats. </span></p>
Drop it all: Extraction-free detection of non-indigenous marine species through optimized direct-droplet digital PCR
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Optimizing DNA extraction protocols for the diet analysis of a baleen whale (Eubalaena australis)
Open the record for dataset details and reuse information.
Programs and data used for Extracting latent variables from forecast ensembles and advancements in similarity metric utilizing optimal transport
<p>This is compiled from the program and output data using in Nishizawa (2024).</p> <p> </p> <p>Nishizawa, 2024: Extracting latent variables from forecast ensembles and advancements in similarity metric utilizing optimal transport. submitted to JGR: Machine Learning and Computation.</p>
Estimated Oxygen Extraction Versus Dynamic Parameters for Perioperative Hemodynamic Optimization
ClinicalTrials.gov study NCT04053595. IPD Sharing: Not stated. Countries: 1. Publications: 1.
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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)
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DANDI Archive for NWB datasets
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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.