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Dataset results
231 results for “dye”
Input files for molecular dynamics simulations of holo CaM tagged with Alexa Fluor 488 and Texas Red dyes using Amber20
<p>Here we share the input files for molecular dynamics simulations of holo CaM tagged with Alexa Fluor 488 and Texas Red dyes using Amber20, as well as the TrESP charges used in TrESP-MMPol electronic coupling calculations of FRET properties. Links to the TrADA tool used to derive TrESP charges and the Trespcoup software used to compute electronic couplings for FRET are indicated below:</p> <div> <div> <div> <p>Cupellini, L., Jurinovich, S., & Mennucci, B. (2024). TraDA - Transition Density Analyzer. Zenodo. https://doi.org/10.5281/zenodo.10966411</p> <p>Cupellini, L., Lipparini, F., & Cignoni, E. (2024). trespcoup - Software to compute TrEsp couplings. Zenodo. https://doi.org/10.5281/zenodo.10966391</p> </div> </div> </div>
Squaraine dyes for single-component shortwave infrared-sensitive photodiodes and upconversion photodetectors
Open the record for dataset details and reuse information.
Interplay between a heptamethine cyanine dye sensitizer (IR806) and lanthanide upconversion nanoparticles
<p><strong>This folder contains all raw data underlying the results presented in a manuscript, submitted to </strong><strong><em>Angewandte Chemie</em></strong><strong>, and entitled:</strong></p> <p><strong>Interplay between a heptamethine cyanine dye sensitizer (IR806) and lanthanide upconversion nanoparticles</strong></p> <p><strong>Authored by:</strong></p> <p>Haichun Liu<sup>1</sup>, Abhilash Kulkarni<sup>1</sup>, Uliana Kostiv<sup>1</sup>, Elin Sandberg<sup>1</sup>, Anbharasi Lakshmanan<sup>1</sup>, Georgios A. Sotiriou<sup>2</sup>, Jerker Widengren<sup>1,*</sup></p> <p><em><sup>1</sup></em><em> Department of Applied Physics, KTH Royal Institute of Technology, Roslagstullsbacken 21, SE-106 91, Stockholm, Sweden</em></p> <p><em><sup>2</sup></em><em>Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77, Stockholm, Sweden</em></p> <p>Corresponding author:</p> <p>*<u>jwideng@kth.se</u></p> <p><strong>The data files containing raw data and results of the analysis are grouped according to the different figures in the manuscript where the extracted results are presented.</strong></p> <p><strong>ABSTRACT</strong></p> <p><span>Lanthanide-doped upconversion nanoparticles (UCNPs) have attractive emission properties but suffer from weak light-absorbing capacities and thereby relatively low brightnesses. This motivates using strongly absorbing dye molecules as antennas and sensitizers. However, despite much effort, understanding of this dye-UCNP interplay is still limited. Major sensitization mechanisms are still under discussion, largely because there is a lack of effective means to observe key factors such as dark state transitions within the dyes. Here, we established a combined spectroscopic procedure to systematically investigate the photophysics behind the dye-UCNP interaction, embracing fluorescence-based transient-state excitation-modulation, lifetime and correlation spectroscopy, and spectrofluorometry/spectrophotometry. With this procedure we studied the heptamethine cyanine dye IR806, a typical UCNP sensitizer, established its photophysical model, deciphered its photophysics in UCL-sensitization-related environments and could identify energy transfer from the IR806 singlet excited state to Yb<sup>3+</sup> (UCNP sensitizer ion) as the dominant sensitization mechanism. Our studies suggest that IR806 can form non-emissive H-aggregates at the nanoparticle surfaces, which can be dissociated after certain light excitation duration (typically>100µs). Moreover, buildup of a non-fluorescent, photo-redox state of IR806 after longer irradiation times (10–100ms) can deleteriously affect its UCL sensitization, inferring an optimal excitation duration for dye-sensitized UCNPs, relevant for e.g. optical imaging applications.</span></p>
DNA-PAINT Dye Analysis Study
<p>Localization Microscopy Datasets from this publication: https://dx.doi.org/10.1038/s41592-024-02374-8. Archive contains all relevant .hdf5 datasets.</p>
3D Real-Time Single Particle Tracking using two-photon fluorescence from bright dye-based organic nanoparticles
<p>Data set, and attached ReadMe files related to the production of the figures in the article "3D Real-Time Single Particle Tracking using two-photon fluorescence from bright dye-based organic nanoparticles" by Emperauger et al.</p> <p> </p> <p>The ReadMe files explaining how each data file is organised, the data are in txt format, organised by figure and sub-figures and compressed. </p>
"Fruity" Dye-based Fluorescent Nanoparticles (dFONs): A Fully Organic Counterpart of Alloy and Core-Shell Metallic Nanoparticles. Tuning Topology to Maximize Nano-interfacial Promoted Fluorescence Enhancement
<p>Data set related to the production of the figures in the article "“Fruity” Dye-based Fluorescent Nanoparticles (dFONs): A Fully Organic Counterpart of Alloy and Core-Shell Metallic Nanoparticles. Tuning Topology to Maximize Nano-interfacial Promoted Fluorescence Enhancement" by Kurek et al.</p> <p> </p> <p>The data are in txt, lif and opju format, organised by figure and sub-figures and compressed. </p>
Structural modulation of π-conjugated linkers in D-π-A dyes based on Triphenylamine dicyanovinylene framework to explore the NLO properties
<p>A donor-π-acceptor type series of Triphenylamine-dicyanovinylene based chromophores (<b>DPMN1-DPMN11</b>) was designed theoretically by the structural tailoring of π-linkers to exploit changes in the optical properties and their NLO behaviour. Density functional theory (DFT) computations were employed to understand the electronic structures, absorption spectra, charge transfer phenomena and the influence of these structural modifications on NLO properties. Interestingly, all investigated chromophores exhibited lower band gap (2.22-2.60 <i>eV</i>) with broad absorption spectra in the visible region, reflecting the remarkable NLO response. Furthermore, natural Bond Orbital (NBO) findings revealed a strong push-pull mechanism in <b>DPMN1-DPMN11 </b>as donor and π-conjugates exhibited positive, while all acceptors showed negative values. Examination of electronic transitions from donor to acceptor moieties via π-conjugated linkers revealed greater linear (<<i>α</i>>=526.536-641.756 <i>a.u</i>) and non-linear (<i>β</i><sub>tot</sub> =51313.8-314412.661 <i>a.u</i>) response. It was noted that the chromophores containing imidazole in 2<sup>nd</sup> p-linker expressed greater hyperpolarizability when compared with the ones containing pyrrole. This study reveals that by controlling the type of π-spacers, interesting metal-free NLO materials can be designed, which can be valuable for the hi-tech NLO applications.</p>
NMR FID for Novel benzothiophene-based fluorescent dye exhibiting a large Stokes shift
<p>FID NMR data for the manuscript "Novel benzothiophene-based fluorescent dye exhibiting a large Stokes shift" published in Synlett</p>
Dataset to manuscript "Trans-cis isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells" accepted for publication in Nucleic Acids Research
<p><strong>This folder contains all raw data underlying the results presented in a manuscript, accepted for publication in Nucleic Acids Research, and entitled:</strong></p> <p> </p> <p><strong><em>Trans</em></strong><strong>-<em>cis</em> isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells </strong></p> <p> </p> <p><strong>Authored by:</strong></p> <p>Akira Kitamura<sup>2,*</sup>, Johan Tornmalm<sup>1,*</sup>, Baris Demirbay<sup>1</sup>, Joachim Piguet<sup>1</sup>, Masataka Kinjo<sup>2</sup>, Jerker Widengren<sup>1+</sup></p> <p> </p> <p><sup>1</sup> Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology (KTH), Stockholm, Sweden</p> <p><sup>2</sup> Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan</p> <p><sup>* </sup>Contributed equally</p> <p><sup>+</sup> To whom correspondence should be addressed. Email: jwideng@kth.se. Tel: +46-8-7907813</p> <p> </p> <p><strong>The data files are grouped into the different techniques used to generate them, and refer to the figures/tables in the manuscript where the extracted results are presented. </strong></p> <p> </p> <p><strong>ABSTRACT</strong></p> <p>Guanine (G)-rich nucleic acids are prone to assemble into four-stranded structures, so-called G-quadruplexes. Abnormal GGGGCC repeat elongations, and in particular their folding states, are associated with amyotrophic lateral sclerosis and frontotemporal dementia. Due to methodological constraints however, most studies of G quadruplex structures are restricted to <em>in vitro</em> conditions. Evidence of how GGGGCC repeats form into G-quadruplexes <em>in vivo</em> is sparse. We devised a readout strategy, exploiting the sensitivity of <em>trans</em>-<em>cis</em> isomerization of cyanine dyes to local viscosity and sterical constraints. Thereby, folding states of cyanine-labeled RNA, and in particular G-quadruplexes, can be identified in a sensitive manner. The isomerization kinetics, monitored via fluorescence blinking generated upon transitions between a fluorescent <em>trans</em> isomer and a non-fluorescent <em>cis</em> isomer, was first characterized for RNA with GGGGCC repeats in aqueous solution using fluorescence correlation spectroscopy and transient state (TRAST) monitoring. With TRAST, monitoring the isomerization kinetics from how the average fluorescence intensity varies with laser excitation modulation characteristics, we could then detect folding states of fluorescently tagged RNA introduced into live cells.</p>
Carbon Dye Tattooing of Biopsied Axillary Node in Breast Cancer
ClinicalTrials.gov study NCT03640819. IPD Sharing: Not stated. Countries: 1. Publications: 2.
ICG and Blue Dye Guided Sentinel Lymph Node Biopsy in Patients Underwent Neoadjuvant Therapy
ClinicalTrials.gov study NCT02869815. IPD Sharing: UNDECIDED. Countries: 1. Publications: 3.
Safety and Efficacy of Different Onset Times of Treatment With Pulsed Dye Laser on Improvement of Surgical Scars
ClinicalTrials.gov study NCT00506363. IPD Sharing: Not stated. Countries: 1. Publications: 7.
Treatment of Port Wine Stains Using Pulsed Dye Laser, Erbium Yag Laser and Topical Sirolimus
ClinicalTrials.gov study NCT02214706. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Study of the Effects of the Pulsed-dye Laser at 585nm and 595nm to Treat Post-operative Scars on Suture-removal Day
ClinicalTrials.gov study NCT00482144. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Sentinel Lymph Node Biopsy Using Peritumoral Injection With Blue Dye Confirmation
ClinicalTrials.gov study NCT00575744. IPD Sharing: Not stated. Countries: 1. Publications: 10.
The Use of Dye-less Cystoscopy in Assessing Urinary Tract Integrity During Hysterectomy
ClinicalTrials.gov study NCT05190939. IPD Sharing: NO. Countries: 1. Publications: 18.
SLN Mapping and ICG Dye for Vulvar Cancer
ClinicalTrials.gov study NCT06035068. IPD Sharing: NO. Countries: 1. Publications: 4.
A Dye for the Detection of Cancer of the Tongue and Mouth
ClinicalTrials.gov study NCT03085147. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Potassium Titanyl Phosphate Laser Versus Pulsed Dye Laser for Rosacea - a Prospective Study
ClinicalTrials.gov study NCT05771298. IPD Sharing: NO. Countries: 1. Publications: 8.
Myocardial Salvage and Contrast Dye Induced Nephropathy Reduction by N-Acetylcystein
ClinicalTrials.gov study NCT00463749. IPD Sharing: Not stated. Countries: 1. Publications: 7.
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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)
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.