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MS 32

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Most cited protocols related to «MS 32»

1
Cardiac Function Assessment in UK Biobank
The full CMR protocol in the UK Biobank has been described in detail elsewhere [9 (link)]. In brief, all CMR examinations were performed in Cheadle, United Kingdom, on a clinical wide bore 1.5 Tesla scanner (MAGNETOM Aera, Syngo Platform VD13A, Siemens Healthcare, Erlangen, Germany).
Assessment of cardiac function was performed based on combination of several cine series: long axis cines (horizontal long axis – HLA, vertical long axis – VLA, and left ventricular outflow tract –LVOT cines, both sagittal and coronal) and a complete short axis stack covering the left ventricle (LV) and right ventricle (RV) were acquired at one slice per breath hold. All acquisitions used balanced steady-state free precession (bSSFP) with typical parameters (subject to standard radiographer changes to planning), as follows: TR/TE = 2.6.1.1 ms, flip angle 80°, Grappa factor 2, voxel size 1.8 mm × 1.8 mm × 8 mm (6 mm for long axis). The actual temporal resolution of 32 ms was interpolated to 50 phases per cardiac cycle (~20 ms). No signal or image filtering was applied besides distortion correction.
Petersen S.E., Aung N., Sanghvi M.M., Zemrak F., Fung K., Paiva J.M., Francis J.M., Khanji M.Y., Lukaschuk E., Lee A.M., Carapella V., Kim Y.J., Leeson P., Piechnik S.K, & Neubauer S. (2017). Reference ranges for cardiac structure and function using cardiovascular magnetic resonance (CMR) in Caucasians from the UK Biobank population cohort. Journal of Cardiovascular Magnetic Resonance, 19, 18.
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Publication 2017
Epistropheus Heart Left Ventricles MS 32 Physical Examination Ventricles, Right
2
Quantifying Functional Connectivity in EEG Signals

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Publication 2013
Electricity Joints MS 32
3
Optimized Adiabatic HSQC NMR Characterization
NMR spectra from the gel-samples were acquired on a 750 MHz (DMX-750) Bruker Biospin (Rheinstetten, Germany) instrument equipped with an inverse (proton coils closest to the sample) gradient 5 mm TXI 1H/13C/15N cryoprobe. The central DMSO solvent peak was used as internal reference (δC 39.5, δH 2.49 ppm). The 13C–1H correlation experiment was an adiabatic HSQC experiment (Bruker standard pulse sequence ‘hsqcetgpsisp.2’; phase-sensitive gradient-edited-2D HSQC using adiabatic pulses for inversion and refocusing)109 (link) typically had the following parameters for the plant cell wall samples: spectra were acquired from 11 to −1 ppm in F2 (1H) using 1078 data points for an acquisition time (AQ) of 60 ms, an interscan delay (D1) of 750 ms, 196 to −23 ppm in F1 (13C) using 480 increments (F1 acquisition time 5.78 ms) of 16 scans, with a total acquisition time of 6 h. The same version of the adiabatic HSQC experiment (hsqcetgpsisp.2)was used on a Bruker 500 MHz (DMX-500) NMR with a cryogenically cooled 5 mm gradient cryoprobe with inverse geometry, and the parameter set was more effectively optimized for gel-samples: spectra were acquired from 10 to 0 ppm in F2 (1H) using 1000 data points for an acquisition time (AQ) of 100 ms, an interscan delay (D1) of 500 ms, 200 to 0 ppm in F1 (13C) using 320 increments (F1 acquisition time 6.36 ms) of 100 scans, with a total acquisition time of 5 h 34 m. The number of scans can, of course, be adjusted as usual depending on the signal-to-noise required from a sample. We also used a Bruker Avance 360 MHz instrument equipped with an inverse (proton coils closest to the sample) gradient 5 mm 1H/broadband gradient probe for structural elucidation and assignment authentication for the model compounds. The standard Bruker implementations of the traditional suite of 1D and 2D (gradient-selected, 1H-detected, e.g., COSY, HMQC/HSQC, HSQC-TOCSY, HMBC) NMR experiments were used. Normal HMQC (inv4gptp) experiments at 360 MHz were used for model compounds and had the following parameters: spectra were acquired from 10 to 0 ppm in F2 (1H) using 1400 data points for an acquisition time of ≤200 ms, 200 to 0 ppm in F1 (13C) using 128 (or 256) increments (F1 acquisition time 35.3 ms) of 32 scans, with a total acquisition time of 1 h 23 min. Processing used typical matched Gaussian apodization in F2 and a squared cosine-bell in F1. Interactive integrations of contours in 2D HSQC/HMQC plots were carried out using Bruker’s TopSpin 2.5 software, as was all data processing.
Kim H, & Ralph J. (2009). Solution-state 2D NMR of ball-milled plant cell wall gels in DMSO-d6/pyridine-d5. Organic & biomolecular chemistry, 8(3), 576-591.
Publication 2009
HMQC Inversion, Chromosome MS 32 Plant Cells Protons Pulse Rate Pulses Radionuclide Imaging Solvents Sulfoxide, Dimethyl
4
Quantitative Phantom and In Vivo MRI Evaluation
Data for quantitative evaluation were acquired on a Siemens Avanto (Siemens AG Medical Solutions, Erlangen, Germany) 1.5 T scanner using a phased array coil. Phantom experiments were performed with an SPGR sequence, using an echo-train with monopolar readout: FOV = 36.0 cm × 14.3 cm; bandwidth = 977 Hz/pixel; matrix size = 256 × 102, 8 and 32 TEs with spacing 2.23 ms and initial TE 1.43 ms. Separate acquisitions were used, in order to obtain moderate SNR (SNR≈30) and high SNR (SNR≈90). The moderate SNR acquisition was performed with flip angle 8° and TR 500 ms, and the high SNR acquisition was performed with flip angle 25° and TR 2000 ms. These long TR values were chosen in order to avoid T1 bias (15 (link)), which results in a bias under 1% for the T1 values of water and oil measured in the phantom (953 ms and 207 ms, respectively) (15 (link)). This choice of acquisition parameters was made purposefully to isolate the desired component (signal modeling) from the other complicating factors involved in fat quantification.
The phantom data were acquired using a Monte-Carlo strategy. In order to perform a quantitative evaluation of bias and standard deviation for the different fitting models, each 8-echo acquisition was performed 128 times. This allows us to derive statistics from the estimated parameters on a voxel-by-voxel basis. Therefore, the phantom experiments correspond closely to the analytical and simulation-based results.
Additionally, data for measuring T1 and T2 were acquired on the phantom from the same slice. For the T1 measurements, an inversion-recovery sequence was used with an echo-train with monopolar readout. This allowed water/fat separation at each inversion time (which ranged from 100 ms to 1000 ms). For the T2 measurements, a spin-echo sequence was used with TEs ranging from 11 to 200 ms.
In vivo imaging was performed on a healthy normal volunteer under a research protocol approved by our Institutional Review Board, with written informed consent. Data were obtained using an ECG-triggered SPGR sequence, acquiring 8 echoes with spacing 2.11 ms and initial TE 1.47 ms. Other parameters are: FOV = 40.0 cm ×40.0 cm; bandwidth = 977 Hz/pixel; TR = 18.03 ms; flip angle = 10°; matrix size = 256 × 156 with 13 views per segment. These imaging parameters result in < 4% bias in fat amplitude estimation in the liver, given typical relaxation parameters of fat and liver water at 1.5T (37 (link)). For low FFs, this bias results in very small systematic errors in FF estimation: for instance, if the true FF is 3.00%, a 4% positive bias in fat signal amplitude relative to water will lead to a 3.12% estimated FF in the absence of noise (i.e., an error typically well below the noise level). An additional in vivo dataset with 16 echoes was obtained to calibrate the relative amplitudes of the fat peaks in vivo.
All images were reconstructed using SNR-scaled reconstruction (23 (link)). This allows convenient evaluation of SNR at each voxel. Multi-coil data was combined prior to water/fat separation using the eigenvector filter method described in Ref. (38) (link).
Hernando D., Liang Z.P, & Kellman P. (2010). Chemical Shift-Based Water/Fat Separation: A Comparison of Signal Models. Magnetic resonance in medicine : official journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine, 64(3), 811-822.
Publication 2010
ECHO protocol Ethics Committees, Research Healthy Volunteers Inversion, Chromosome Liver MS 32 Reconstructive Surgical Procedures
5
Imaging Zebrafish Larval Neural Responses
5 and 6dpf AB/nacre larval zebrafish expressing GCaMP2, GCaMP3 or GCaMP5G under the elavl3 promoter were paralyzed by immersing them in 1 mg/ml solution of bungarotoxin dissolved in E3 fish embryo water and were subsequently embedded in 2% low melting point agarose in a 35 mm Petri dish. They were placed in a custom 2-photon microscope and imaged using a Mai Tai HP Ti-Sapphire laser tuned to 950 nm. The visual stimulus used for the experiment consisted of a light dot (0.5 mm × 0.5 mm) projected, using an amber (590 nm) LED mounted into a miniature LCOS projector, onto an opal glass screen directly underneath the larvae. Stimulus light was filtered with a narrow bandpass filter, and each fish was run through one stimulus set with the laser off to detect stimulus bleed-through, which was always negligible. The dot appeared to the left or right of the larva and moved on a straight line at a speed of 3 mm/s until it disappeared on the opposite side. The larva was located halfway along the dot’s trajectory and perpendicular to it, with the point of closest approach of the dot being 0.5 mm rostral to the larva.
The experimental protocol consisted of 1 min dark, followed by a presentation every 30 s of the moving dot, alternating between left to right and right to left. There were ten such presentations (five in each direction). The experiment concluded with 1 min dark, and therefore lasted 7 min in total. Individual frames were captured at 138.32 ms per frame (7.23 Hz), using a quad-interlaced scan pattern that ensured that each cell was sampled evenly at 4 times this frame rate.
Data analysis: Movies were assessed for x-y drift during the experiment (usually < 1 pixel), and a sub-pixel translation correction was applied using MATLAB software (David Heeger, NYU). Neuronal somata were detected based on their dark nuclei. Mean images were smoothed with a Gaussian, and local minima were detected. These were classified as cell nuclei if the ratio of the brightness 3 pixels from the center was more than 3.5 the brightness 1 pixel from the center, i.e. they look like a bright ring around a dark centre, and they were sufficiently bright (>17,500 photons detected per experiment). Fluorescence was then averaged over a 7×7 pixel square. Baseline fluorescence (F) was defined as the average fluorescence in the 50 frames immediately preceding each left-right stimulus.
Akerboom J., Chen T.W., Wardill T.J., Tian L., Marvin J.S., Mutlu S., Calderón N.C., Esposti F., Borghuis B.G., Sun X.R., Gordus A., Orger M.B., Portugues R., Engert F., Macklin J.J., Filosa A., Aggarwal A., Kerr R.A., Takagi R., Kracun S., Shigetomi E., Khakh B.S., Baier H., Lagnado L., Wang S.S., Bargmann C.I., Kimmel B.E., Jayaraman V., Svoboda K., Kim D.S., Schreiter E.R, & Looger L.L. (2012). Optimization of a GCaMP Calcium Indicator for Neural Activity Imaging. The Journal of Neuroscience, 32(40), 13819-13840.
Publication 2012
Amber Bungarotoxins Carisoprodol Cell Nucleus Cells Embryo Fishes Fluorescence GCaMP2 Hyperostosis, Diffuse Idiopathic Skeletal Larva Light Microscopy MS 32 Nacre Radionuclide Imaging Reading Frames Sapphire Sepharose VPDA protocol Zebrafish

Most recents protocols related to «MS 32»

1
Quantifying α-Sarcoglycan in Extracellular Vesicles
To assess α-sarcoglycan protein levels, Western blotting was performed as described above for CD63, and the membranes were incubated with anti-α-sarcoglycan antibody (Santa Cruz, SC-271321) (1:1000 dilution). To further determine the number of EVs that are positive for α-sarcoglycan, we used fluorescence correlation spectroscopy (FCS). FCS is a powerful technique that can quantitatively evaluate picomolar concentrations, with sensitivity that can be up to a single-molecule level [33 (link), 34 (link)]. Specifically, an anti-α-sarcoglycan antibody was used (Santa Cruz, SC-271321). The antibody was first labeled with CF488 dye using antibody labeling kits (Mix-n-Stain, Biotium) following the manufacturer’s antibody labeling protocol. Fifty ng/mL CF488 labeled antibody was added to each EV sample and allowed to incubate for 60 min at room temperature. The vesicles were purified from free dye using a 5000-molecular weight cutoff size exclusion column (PD Minitrap G25, GE Healthcare) as described previously [35 (link)]. Briefly, the binding of fluorescently labeled anti-α-sarcoglycan antibody to EVs was confirmed via FCS based on their diffusion times. All FCS measurements were done as reported previously by Fu et al. [36 (link)]. Briefly, 40 μL of fluorescently labeled EVs were placed onto a coverslip mounted on an Olympus IX83 microscope equipped with a PicoQuant PicoHarp 300 time-correlated single photon counting (TCSPC) system. We employed a 488-nm laser (50 μW) to excite the fluorescent labels, and a 60× water immersion objective was used to focus this laser beam into the sample solution. Two avalanche photodiodes (APDs) were used for photon detection, and the signal was directed to a PicoHarp 300 TCSPC module controller. All measurements were performed 30 μm above the glass surface in the sample solution. For the unconjugated fluorophore, the fitted autocorrelation functions (ACF) yield a diffusion time (τD) of 0.21 ± 0.02 ms. A longer diffusion time of 2.5 ± 0.2 ms was observed for the CF-488-labeled anti-α-sarcoglycan antibody. The immunolabeled (anti-α-sarcoglycan-CF488 antibody) EVs exhibited a diffusion time of 32 ± 5 ms. In order to calculate the average number of immunolabeled (anti-α-sarcoglycan-CF488 antibody) EVs within the focal volume, the FCS focal volume was first calibrated using commercially available 0.1-μm tetra speck beads with a known diffusion constant and concentration. The number of vesicles per mL of solution was determined using NTA, and the number of labeled vesicles per mL was determined using FCS and the calibrated size of the focal volume.
Ismaeel A., Van Pelt D.W., Hettinger Z.R., Fu X., Richards C.I., Butterfield T.A., Petrocelli J.J., Vechetti I.J., Confides A.L., Drummond M.J, & Dupont-Versteegden E.E. (2023). Extracellular vesicle distribution and localization in skeletal muscle at rest and following disuse atrophy. Skeletal Muscle, 13, 6.
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Publication 2023
Antibodies, Anti-Idiotypic Avalanches Diffusion Fluorescence Spectroscopy Hypersensitivity Immunoglobulins Microscopy MS 32 Proteins Sarcoglycans Stains Submersion Technique, Dilution Tetragonopterus Tissue, Membrane
2
Quantitative Analysis of O-Glycans via PGC-LC-MS/MS
The O-glycan samples were then reconstituted in 20 μl of MQ water, and 2 μl were injected for analysis. Analysis was performed using a PGC nano-LC Ultimate 3000 UHPLC system (Thermo Fisher Scientific) coupled to an amaZon ETD speed ion trap (Bruker Daltonics). The samples were loaded using 100% buffer A (10 mM ABC) at a loading flow of 6 μl/min on a custom-made trap column (size 30 × 0.32 mm) packed with 5 μm particle size PGC stationary phase from Hypercarb PGC analytical column (size 100 × 4.6 mm, 5 μm particle size; Thermo Fisher Scientific). Afterward, the O-glycans were separated at a 0.6 μl/min flow rate on a custom-made PGC column (100 × 0.1 mm, 3 μm particle size obtained from Thermo Fisher Scientific) by applying a linear gradient from 1% to 50% buffer B (MeCN, 10 mM ABC) over 73 min. During the procedures, a constant column temperature of 45 °C was maintained. To continue, the LC system was coupled to an amaZon ETD speed electrospray ionization (ESI) ion trap MS using the CaptiveSpray source (Bruker Daltonics) with an applied capillary voltage of 1000 V in negative-ionization mode. The drying gas (N2) flow rate was set to 3 l/min, and the temperature was set at 280 ˚C. The nebulizer gas pressure was kept at 3 psi. The nanoBooster bottle (Bruker Daltonics) was filled with methanol, as a dopant solvent (34 (link)). MS spectra were acquired in enhanced mode within a mass to charge ratio (m/z) range of 380 to 1850. The maximum acquisition time was set to 200 ms, the ion charge control (ICC) to 40,000, and the target mass of smart parameter setting was set to m/z 900. MS/MS spectra were generated by collision-induced dissociation of the three most abundant precursors, applying an isolation width of 3 Thomson. In addition, ICC was set to 150,000, and the fragmentation cutoff was set to 27% with a 100% fragmentation amplitude using the Enhanced SmartFrag option (30–120% in 32 ms). To integrate area under the curve for each individual glycan isomer, extracted ion chromatograms of the first three isotopes were used in Bruker Compass DataAnalysis software (version 5.0). Peaks were manually picked and integrated. Total area normalization was employed for relative quantification of O-glycan species. Identification of O-glycan species was performed by comparison with PGC retention time, MS/MS spectra, and the BSM standard.
Madunić K., Luijkx Y.M., Mayboroda O.A., Janssen G.M., van Veelen P.A., Strijbis K., Wennekes T., Lageveen-Kammeijer G.S, & Wuhrer M. (2023). O-Glycomic and Proteomic Signatures of Spontaneous and Butyrate-Stimulated Colorectal Cancer Cell Line Differentiation. Molecular & Cellular Proteomics : MCP, 22(3), 100501.
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Publication 2023
Buffers Capillaries isolation Isomerism Isotopes Methanol MS 32 Nebulizers Polysaccharides Pressure Retention (Psychology) Solvents Tandem Mass Spectrometry
3
Peptide Profiling of Cerebrospinal Fluid

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Publication 2023
acetonitrile Biopharmaceuticals Buffers DNA Library formic acid isolation MS 32 MS 54 Peptides Proteome Radionuclide Imaging Tandem Mass Spectrometry
4
Repetitive Transcranial Magnetic Stimulation for Neuromodulation
Across the experiment, stimulation intensity varied and was determined by the resting motor threshold (RMT), which is defined as the minimum intensity of TMS applied to the M1 region. It could evoke electromyography (EMG) with an amplitude of >50 μV peak-to-peak in the hands' relaxed first dorsal interosseous muscle in more than five out of 10 pulses. The researchers were trained to use the coil surface which was positioned at a tangent angle of 45° to the scalp (42 (link)) over the left PPC of the patient to perform rTMS interventions. The rTMS pulses were delivered using an NTK-TMS-II300 stimulator with an IIB502 97-mm figure-of-eight coil (surface A sents active pulses, while surface B sents sham pulses). There were two identical surfaces in this coil; one output rTMS-active pluses, and the other output rTMS-sham pluses (Brain Modulation Technology Development CO, LDT, JiangXi, CHN). A biphasic waveform with a pulse width of ~0.32 ms would be produced.
During the active stage of rTMS treatment, patients received 10 consecutive sessions (one session daily) of stimulation. They were seated in a semi-reclined position on either an ABS bed or a wheelchair, and each session lasted 20 min with a frequency of 10 Hz, delivered over the left PPC (train duration: 1s; inter-train interval: 5s; 200 effective stimulation series; 2,000 pulses at 90% of RMT). An EEG cap marked with the international 10–20 positioning system was used to identify the P3 (left PPc) stimulation site. The rTMS treatment was administered in accordance with safety guidelines (43 (link)) (Figure 1B).
During the sham stage of rTMS, patients received 10 consecutive sessions (one session daily) of stimulation. The sham coil was designed to mimic the appearance of the active coil; however, it did not produce a magnetic field and delivered only noise and vibration to mimic the feedback of the active coil. The sham coil was used to control for the placebo effect (44 (link)).
Xu C., Wu W., Zheng X., Liang Q., Huang X., Zhong H., Xiao Q., Lan Y., Bai Y, & Xie Q. (2023). Repetitive transcranial magnetic stimulation over the posterior parietal cortex improves functional recovery in nonresponsive patients: A crossover, randomized, double-blind, sham-controlled study. Frontiers in Neurology, 14, 1059789.
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Publication 2023
Brain Electromyography Magnetic Fields MS 32 Muscle, Back Patients Pulse Rate Pulses Safety Scalp Sitting Transcranial Magnetic Stimulation, Repetitive Vibration Wheelchair
5
CMR Ventricular Function Imaging Protocol
The CMR examination included standard functional imaging using a high spatial and temporal resolution and breath-held balanced steady-state precession (bSSFP) cine sequence [15 (link),16 (link)] with the following acquisition parameters: 58° flip angle, rate-3 parallel imaging, matrix size 256 × 192, pixel size 1.6 mm × 1.6 mm, slice thickness 6 mm, BW 977 Hz/Px, TE/TR 1.4 ms/3.3 ms echo spacing, and a temporal resolution of 32.5 ms. All cine imaging included the entire LV from base to apex using short-axis slices.
Markousis-Mavrogenis G., Belegrinos A., Giannakopoulou A., Papavasiliou A., Koulouri V., Marketos N., Patsilinakou E., Lazarioti F., Bacopoulou F., Mavragani C.P., Chrousos G.P, & Mavrogeni S.I. (2023). Cardiovascular Magnetic Resonance Demonstrates Myocardial Inflammation of Differing Etiologies and Acuities in Patients with Genetic and Inflammatory Myopathies. Journal of Clinical Medicine, 12(4), 1575.
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Publication 2023
ECHO protocol Epistropheus MS 32 Tandem Mass Spectrometry

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