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92 results for “Duplex”
Duplex Underplating, Sediment Dehydration and Quartz Vein Mineralization in the Deep Tremor Source Region
<p>Data for Duplex Underplating, Sediment Dehydration and Quartz Vein Mineralization in the Deep Tremor Source Region</p>
Isomerization pathways of a mismatched base pair of A:8OG in free duplex DNA
<p>plumed.dat --> input file for OPES simulation.</p> <p>str0.pdb ~ str19.pdb --> initial structures for OPES simulation.</p> <p>traj.xtc --> sample output trajectory of OPES simulation.</p>
Fig. 1 in Verification of Natural Marking for Individual Identification Using a Duplex Marking Approach in Ijima's Sea Snakes, (Reptilia: Elapidae).
Fig. 1. Maps showing the location of Zamami Island and the study sites: (a) Urunusachi and (b) Ama.
CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters
<p>CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters</p> <p>Collected and generated data for the paper</p> <p>## Data Tables</p> <p>Off-target score data for the ROC analysis using Haeussler dataset [2].</p> <p>Data from the table below is used to generate the Figure-2, Table-1 and Supplementary Figure-1 in the corresponding paper [1]. Don't forget to cite the corresponding studies as well if you use this table.</p> <ul> <li><strong>Haeussler_mm6_scores.csv.gz</strong>: This table includes the off-targeting scores of 1167036 off-target sequences, computed with CRISPRoff[1], CCTop[3], CFD[4], Cropit[5], Elevation (Elevation-score)[6], MIT[2,7] and VfoldCAS[8] methods. Off-target data has been taken from the Haeussler dataset [2].</li> </ul> <p>Analysis with CIRCLE-seq dataset [9]</p> <p>Data in all the three tables below has been generated to analyze the CIRCLE-seq dataset [9]. This data is further used to generate the Figure-3, Figure-4, and Supplementary Figure-4 in the corresponding paper. Don't forget to cite the corresponding studies as well if you use these tables.</p> <ul> <li> <p><strong>CIRCLEseq_known_off_scores.csv.gz</strong>: This table is used when generating the Figure-3 in the paper. It includes the 7 different off-targeting scores of CIRCLE-seq reported off-target sequences and the read counts from CIRCLE-seq experiments.</p> </li> <li> <p><strong>CIRCLEseq_mm6_off_scores.csv.gz</strong>: This table is used when generating the Figure-4 in the paper. It includes the 7 different off-targeting scores of RIsearch2(v2.1)[10] based off-target predictions for CIRCLE-seq gRNAs.</p> </li> <li> <p><strong>CIRCLEseq_specificities.csv.gz</strong>: This table is used when generating the Supplementary Figure-4 in the supplementary document of the paper. It includes the specificty scores of CIRCLE-seq gRNAs, computed with CRISPRspec[1], MIT[2,7], MIT*[1,2,7] and Elevation (Elevation-aggregate)[6] methods.</p> </li> </ul> <p>Analysis with SITE-seq dataset [11]</p> <p>Data in all the three tables below has been generated to analyze the SITE-seq dataset [11]. This data is further used to generate the Figure-5, Supplementary Figure-2 and Supplementary Figure-3 in the corresponding paper. Don't forget to cite the corresponding studies as well if you use these tables.</p> <ul> <li> <p><strong>SITEseq_known_off_scores.csv.gz</strong>: This table is used when generating the Supplementary Figure-2 in the supplementary document of the paper. It includes the 7 different off-targeting scores of SITE-seq reported off-target sequences and the read counts from SITE-seq experiments.</p> </li> <li> <p><strong>SITEseq_mm6_off_scores.csv.gz</strong>: This table is used when generating the Supplementary Figure-3 in the supplementary document of the paper. It includes the 7 different off-targeting scores of RIsearch2(v2.1) based off-target predictions for SITE-seq gRNAs.</p> </li> <li> <p><strong>SITEseq_specificities.csv.gz</strong>: This table is used when generating the Figure-5 in the paper. It includes the 4 different specificty scores of SITE-seq gRNAs.</p> </li> </ul> <p>Specificity-Efficiency Analysis</p> <p>This data is used to generate the Figure-6 and Supplementary Figure-5 in the corresponding paper. Don't forget to cite the corresponding studies as well if you use these tables.</p> <ul> <li><strong>Doench_Wang_specificity_grps.csv.gz</strong>: This table includes the specificity group of 3802 gRNA/on-target sequences, computed with CRISPRspec and MIT methods. gRNA sequence and modulation frequency data have been taken from the Haeussler dataset [2].</li> </ul> <p>## Citation</p> <p>If you find this data useful for your research, please cite the following works where appropriate:</p> <ol> <li>[Our citation comes here]</li> <li>Haeussler, M., Schonig, K., Eckert, H., Eschstruth, A., Mianne, J., Renaud, J.B., Schneider-Maunoury, S., Shkumatava, A., Teboul, L., Kent, J., Joly, J.S., Concordet, J.P.: Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol. 17(1), 148 (2016). <a href="https://www.ncbi.nlm.nih.gov/pubmed/27380939">PMID 27380939</a></li> <li>Stemmer, M., Thumberger, T., Del Sol Keyer, M., Wittbrodt, J., Mateo, J.L.: CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool. PLoS ONE 10(4), 0124633 (2015). <a href="https://www.ncbi.nlm.nih.gov/pubmed/25909470">PMID 25909470</a></li> <li>Doench, J.G., Fusi, N., Sullender, M., Hegde, M., Vaimberg, E.W., Donovan, K.F., Smith, I., Tothova, Z., Wilen, C., Orchard, R., Virgin, H.W., Listgarten, J., Root, D.E.: Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat. Biotechnol. 34(2), 184–191 (2016). <a href="https://www.ncbi.nlm.nih.gov/pubmed/26780180">PMID 26780180</a></li> <li>Singh, R., Kuscu, C., Quinlan, A., Qi, Y., Adli, M.: Cas9-chromatin binding information enables more accurate CRISPR off-target prediction. Nucleic Acids Res. 43(18), 118 (2015). <a href="https://www.ncbi.nlm.nih.gov/pubmed/26032770">PMID 26032770</a></li> <li>Listgarten, J., Weinstein, M., Kleinstiver, B.P., Sousa, A.A., Joung, J.K., Crawford, J., Gao, K., Hoang, L., Elibol, M., Doench, J.G., Fusi, N.: Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs. Nature Biomedical Engineering 2, 38–47 (2018). <a href="https://www.ncbi.nlm.nih.gov/pubmed/29998038">PMID 29998038</a></li> <li>Hsu, P.D., Scott, D.A., Weinstein, J.A., Ran, F.A., Konermann, S., Agarwala, V., Li, Y., Fine, E.J., Wu, X., Shalem, O., Cradick, T.J., Marraffini, L.A., Bao, G., Zhang, F.: DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol. 31(9), 827–832 (2013). <a href="https://www.ncbi.nlm.nih.gov/pubmed/23873081">PMID 23873081</a></li> <li>Xu, X., Duan, D., Chen, S.J.: CRISPR-Cas9 cleavage efficiency correlates strongly with target-sgRNA folding stability: from physical mechanism to off-target assessment. Sci Rep 7(1), 143 (2017). <a href="https://www.ncbi.nlm.nih.gov/pubmed/28273945">PMID 28273945</a></li> <li>Tsai, S.Q., Nguyen, N.T., Malagon-Lopez, J., Topkar, V.V., Aryee, M.J., Joung, J.K.: CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets. Nat. Methods 14(6), 607–614 (2017). <a href="https://www.ncbi.nlm.nih.gov/pubmed/28459458">PMID 28459458</a></li> <li>Alkan, F., Wenzel, A., Palasca, O., Kerpedjiev, P., Rudebeck, A.F., Stadler, P.F., Hofacker, I.L., Gorodkin, J.: RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets. Nucleic Acids Res. (2017). <a href="https://www.ncbi.nlm.nih.gov/pubmed/28108657">PMID 28108657</a></li> <li>Cameron, P., Fuller, C.K., Donohoue, P.D., Jones, B.N., Thompson, M.S., Carter, M.M., Gradia, S., Vidal, B., Garner, E., Slorach, E.M., Lau, E., Banh, L.M., Lied, A.M., Edwards, L.S., Settle, A.H., Capurso, D., Llaca, V., Deschamps, S., Cigan, M., Young, J.K., May, A.P.: Mapping the genomic landscape of CRISPR-Cas9 cleavage. Nat. Methods 14(6), 600–606 (2017). <a href="https://www.ncbi.nlm.nih.gov/pubmed/28459459">PMID 28459459</a></li> </ol> <p>## Contact</p> <p>ferro@rth.dk gorodkin@rth.dk</p>
Data for the manuscript "Bridged Nucleic Acid ASOs over Locked Nucleic Acid ASOs and their impact on the structure and stability of ASO/RNA duplexes"
<p>The dataset contains: DFT and MD Data for the manuscript "Bridged Nucleic Acid ASOs over Locked Nucleic Acid ASOs and their impact on the structure and stability of ASO/RNA duplexes". </p> <p> </p> <p> </p>
The Long-term Value of Preoperative Duplex Before Surgery for Varicose Veins
ClinicalTrials.gov study NCT01195623. IPD Sharing: Not stated. Countries: 1. Publications: 5.
Pharmacokinetics and Safety of Cefazolin 3gm DUPLEX in Adults
ClinicalTrials.gov study NCT05205486. IPD Sharing: NO. Countries: 1. Publications: 11.
Data from: Effect of pH regulation by microbes on corrosion behaviour of duplex stainless steel 2205 in acidic artificial seawater environment
Open the record for dataset details and reuse information.
FIGURE 83 Uroptychus duplex n in Chirostylidae of the Western and Central Pacific: Uroptychus and a new genus (Crustacea: Decapoda: Anomura)
FIGURE 83 Uroptychus duplex n. sp., holotype, ovigerous female 4.7 mm (MNHN-IU-2011-5923). A, right P2, lateral. B, same, distal part, setae omitted, lateral. C, right P3, lateral. D, same, distal part, lateral. E, right P4, lateral.F, same, distal part, lateral. Scale bars: 1 mm.
PLATE 20. Figures 1–5. Duplex species, male genitalia. 1, 2, D. horakae, slide 6076 and 6079 in Revision of the Micronoctuidae (Lepidoptera: Noctuoidea) Part 3, Taxonomy of the Tactusinae
PLATE 20. Figures 1–5. Duplex species, male genitalia. 1, 2, D. horakae, slide 6076 and 6079, Australia, Northern Territory, Cobourg Peninsula and Australia, Western Australia, Mitchell River; 3, D. edwardsi, slide 6088, Australia, Northern Territory, 27 km S Nhulunbuy; 4, D. pullata, slide 6081, Australia, Northern Territory, Mataranka Homestead; 5, D. cockingi, slide 6084, Australia, New South Wales, 11 km SW Narrabri.
Data set for 5S-Tg Epimer flipping in DNA duplex
<p>Dataset from dynamics simulations and MSM calculations of the 5S,&S-Tg and 5S,&R-Tg epimers in DNA duplex.</p>
Thermal stabilisation of the short DNA duplexes by acridine-4-carboxamide derivatives
<p>The short oligodeoxynucleotide (ODN) probes are suitable for good discrimination of point mutations, however, they suffer from low melting temperatures. In this work, the strategy of using acridine-4-carboxamide intercalators to improve thermal stabilization is investigated. The study of large series of acridines revealed that optimal stabilization is achieved upon decoration of acridine by secondary carboxamide carrying sterically not demanding basic function bound through two-carbon linker. Presence of secondary carboxamides plays a key role in stabilization of the duplex. Two highly active intercalators were attached to short probes (13 or 18 bases; designed as a part of HFE gene) by click chemistry into positions 7 and/or 13 and proved to increase the melting temperate (T<sub>m</sub>) of the duplex by almost 8°C for the best combination. The acridines interact with both single- and double-stranded DNAs with substantially preferred interaction for the latter. The study of interaction suggested higher affinity of the acridines toward the GC- than AT-rich sequences. Good discrimination of two types of point mutations was shown.</p>
Supporting Data for "Disruption of energetic and dynamic base pairing cooperativity in DNA duplexes by an abasic site"
<p>Temperature-jump IR spectroscopy data and coarse-grained molecular dynamics trajectories for three DNA sequences with and without an abasic site.</p>
Impact of a Single Nucleotide Change or Non-Nucleoside Modifications in G-Rich Region on the Quadruplex–Duplex Hybrid Formation
<p>„Impact of a Single Nucleotide Change or Non-Nucleoside Modifications in G-Rich Region on the Quadruplex–Duplex Hybrid Formation”.</p> <p>In article, a method to discriminate between two target RNA sequences that differ by one nucleotide only is presented. The method relies on the formation of alternative structures, i.e., quadruplex–duplex hybrid (QDH) and duplex with dangling ends (Dss), after hybridization of RNA G-rich oligonucleotides with target sequences containing 5′–GGGCUGG–3′ (U<sup>T</sup>) or 5′–GGGCGGG–3′ (G<sup>T</sup>) fragments. Using biophysical methods, the effect of covalently attached G4 ligand on the ability of G-rich oligonucleotides to assemble a G-quadruplex motif was studied. The sequence-guided o-BMVC G4-ligand acted as a quadruplex stabilizer but not duplex. The use of such conjugates (o-BMVC-RNA) creates the possibility of inducing and stabilizing the bimolecular quadruplexes on the G-rich mRNA template in a sequence-specific manner. The formation of QDH or Dss structures is dependent on a single nucleotide change in the target sequence, and the possibility to selectively stabilize the G-quadruplex domain by attaching the G4 ligand may become an attractive alternative therapy for patients with an EGFR-L858R mutation.</p> <p><a href="https://www.mdpi.com/2218-273X/11/8/1236">https://www.mdpi.com/2218-273X/11/8/1236</a>, <a href="https://doi.org/10.3390/biom11081236">https://doi.org/10.3390/biom11081236</a></p> <p>Files are available in original formats: .xlsx, .opi, bruker, MultiGauge raw-image file (.img), JPG file (.jpg), text document (.txt)</p>
Duplex UltraSound afTer Endo Revascularisation - Feasibility Randomised Control Trial (DUSTER)
ClinicalTrials.gov study NCT06702306. IPD Sharing: YES. Countries: 1. Publications: 1.
Transcranial Duplex Scanning and Single Photon Emission Computer Tomography (SPECT) in Parkinsonian Syndromes
ClinicalTrials.gov study NCT00368199. IPD Sharing: YES. Countries: 1. Publications: 4.
Changes of Upper and Lower Limb Blood Flow and Vascular Resistance in Hyperbaric Spinal Anesthesia for Transurethral Resection of the Prostate (TURP) Using Duplex Ultrasonography: Comparison of Normot
ClinicalTrials.gov study NCT01091779. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Computed Tomography Scan Versus Color Duplex Ultrasound for Surveillance of Endovascular Repair of Abdominal Aortic Aneurysm. A Prospective Multicenter Study
ClinicalTrials.gov study NCT01230203. IPD Sharing: Not stated. Countries: 1. Publications: 1.
FOAM-study, Cost Minimization Study Comparing Surgery Versus Duplex Guided Foam Sclerotherapy of Varicose Veins
ClinicalTrials.gov study NCT01103258. IPD Sharing: Not stated. Countries: 1. Publications: 1.
AI-assisted Transcranial Duplex Sonography for Early Detection of Intracerebral Haemorrhage: HYPER-AI-SCAN
ClinicalTrials.gov study NCT07319013. IPD Sharing: NO. Countries: 1. Publications: 1.
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Allen Brain Atlas
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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.
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