Dataset Information

Quantitative Comparison of Conventional and t-SNE-guided Gating Analyses.

ABSTRACT: Dimensionality reduction using the t-Distributed Stochastic Neighbor Embedding (t-SNE) algorithm has emerged as a popular tool for visualizing high-parameter single-cell data. While this approach has obvious potential for data visualization it remains unclear how t-SNE analysis compares to conventional manual hand-gating in stratifying and quantitating the frequency of diverse immune cell populations. We applied a comprehensive 38-parameter mass cytometry panel to human blood and compared the frequencies of 28 immune cell subsets using both conventional bivariate and t-SNE-guided manual gating. t-SNE analysis was capable of stratifying every general cellular lineage and most sub-lineages with high correlation between conventional and t-SNE-guided cell frequency calculations. However, specific immune cell subsets delineated by the manual gating of continuous variables were not fully separated in t-SNE space thus causing discrepancies in subset identification and quantification between these analytical approaches. Overall, these studies highlight the consistency between t-SNE and conventional hand-gating in stratifying general immune cell lineages while demonstrating that particular cell subsets defined by conventional manual gating may be intermingled in t-SNE space.

SUBMITTER: Toghi Eshghi S

PROVIDER: S-EPMC6560168 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Quantitative Comparison of Conventional and t-SNE-guided Gating Analyses.

Toghi Eshghi Shadi S Au-Yeung Amelia A Takahashi Chikara C Bolen Christopher R CR Nyachienga Maclean N MN Lear Sean P SP Green Cherie C Mathews W Rodney WR O'Gorman William E WE

Frontiers in immunology 20190605

Dimensionality reduction using the t-Distributed Stochastic Neighbor Embedding (t-SNE) algorithm has emerged as a popular tool for visualizing high-parameter single-cell data. While this approach has obvious potential for data visualization it remains unclear how t-SNE analysis compares to conventional manual hand-gating in stratifying and quantitating the frequency of diverse immune cell populations. We applied a comprehensive 38-parameter mass cytometry panel to human blood and compared the fr ...[more]

PMID: 31231371

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Project description:PurposeAs Doppler ultrasound has been proven to be an effective tool to predict and compress the optimal pulsing windows, we evaluated the effective dose and diagnostic accuracy of coronary CT angiography (CTA) incorporating Doppler-guided prospective electrocardiograph (ECG) gating, which presets pulsing windows according to Doppler analysis, in patients with a heart rate >65 bpm.Materials and methods119 patients with a heart rate >65 bpm who were scheduled for invasive coronary angiography were prospectively studied, and patients were randomly divided into traditional prospective (n?=?61) and Doppler-guided prospective (n?=?58) ECG gating groups. The exposure window of traditional prospective ECG gating was set at 30%-80% of the cardiac cycle. For the Doppler group, the length of diastasis was analyzed by Doppler. For lengths greater than 90 ms, the pulsing window was preset during diastole (during 60%-80%); otherwise, the optimal pulsing intervals were moved from diastole to systole (during 30%-50%).ResultsThe mean heart rates of the traditional ECG and the Doppler-guided group during CT scanning were 75.0±7.7 bpm (range, 66-96 bpm) and 76.5±5.4 bpm (range: 66-105 bpm), respectively. The results indicated that whereas the image quality showed no significant difference between the traditional and Doppler groups (P?=?0.42), the radiation dose of the Doppler group was significantly lower than that of the traditional group (5.2±3.4 mSv vs. 9.3±4.5 mSv, P<0.001). The sensitivities of CTA applying traditional and Doppler-guided prospective ECG gating to diagnose stenosis on a segment level were 95.5% and 94.3%, respectively; specificities 98.0% and 97.1%, respectively; positive predictive values 90.7% and 88.2%, respectively; negative predictive values 99.0% and 98.7%, respectively. There was no statistical difference in concordance between the traditional and Doppler groups (P?=?0.22).ConclusionDoppler-guided prospective ECG gating represents an improved method in patients with a high heart rate to reduce effective radiation doses, while maintaining high diagnostic accuracy.

Project description:Orientia tsutsugamushi is the causative agent of scrub typhus. For the diagnosis of scrub typhus, we investigated the performances of conventional PCR (C-PCR), nested PCR (N-PCR), and real-time quantitative PCR (Q-PCR) targeting the O. tsutsugamushi-specific 47-kDa gene. To compare the detection sensitivities of the three techniques, we used two template systems that used plasmid DNA (plasmid detection sensitivity), including a partial region of the 47-kDa gene, and genomic DNA (genomic detection sensitivity) from a buffy coat sample of a single patient. The plasmid detection sensitivities of C-PCR, N-PCR, and Q-PCR were 5 × 10(4) copies/?l, 5 copies/?l, and 50 copies/?l, respectively. The results of C-PCR, N-PCR, and Q-PCR performed with undiluted genomic DNA were negative, positive, and positive, respectively. The genomic detection sensitivities of N-PCR and Q-PCR were 64-fold and 16-fold (crossing point [Cp], 37.7; 426 copies/?l), respectively. For relative quantification of O. tsutsugamushi bacteria per volume of whole blood, we performed real-time DNA PCR analysis of the human GAPDH gene, along with the O. tsutsugamushi 47-kDa gene. At a 16-fold dilution, the copy number and genomic equivalent (GE) of GAPDH were 1.1 × 10(5) copies/?l (Cp, 22.64) and 5.5 × 10(4) GEs/?l, respectively. Therefore, the relative concentration of O. tsutsugamushi at a 16-fold dilution was 0.0078 organism/one white blood cell (WBC) and 117 organisms/?l of whole blood, because the WBC count of the patient was 1.5 × 10(4) cells/?l of whole blood. The sensitivities of C-PCR, N-PCR, and Q-PCR performed with blood samples taken from patients within 4 weeks of onset of fever were 7.3% (95% confidence interval [CI], 1.6 to 19.9), 85.4% (95% CI, 70.8 to 94.4), and 82.9% (95% CI, 67.9 to 92.8), respectively. All evaluated assays were 100% specific for O. tsutsugamushi. In conclusion, given its combined sensitivity, specificity, and speed, Q-PCR is the preferred assay for the diagnosis of scrub typhus.

Project description:PURPOSE:On-board magnetic resonance imaging (MRI) greatly enhances real-time target tracking capability during radiotherapy treatments. However, multislice and volumetric MRI techniques are frame rate limited and introduce unacceptable latency between the target moving out of position and the beam being turned off. We present a technique to estimate continuous volumetric tissue motion using motion models built from a repeated acquisition of a stack of MR slices. Applications including multislice target visualization and out-of-slice motion estimation during MRI-guided radiotherapy are demonstrated. METHODS:Eight healthy volunteer studies were performed using a 0.35 T MRI-guided radiotherapy system. Images were acquired at three frames per second in an interleaved fashion across ten adjacent sagittal slice positions covering 4.5 cm using a balanced steady-state-free precession sequence. A previously published five-dimensional (5D) linear motion model used for MRI-guided radiotherapy gating was extended to include multiple slices. This model utilizes an external respiratory bellows signal recorded during imaging to simultaneously estimate motion across all imaged slices. For comparison to an image-based approach, the manifold learning technique local linear embedding (LLE) was used to derive a respiratory surrogate for motion modeling. Manifolds for every slice were aligned during LLE in a group-wise fashion, enabling motion estimation outside the current imaged slice using a motion model, a process which we denote as mSGA. Additionally, a method is developed to evaluate out-of-slice motion estimates. The multislice motion model was evaluated in a single slice with each newly acquired image using a leave-one-out approach. Model-generated gating decision accuracy and beam-on positive predictive value (PPV) are reported along with the median and 95th percentile distance between model and ground truth target centroids. RESULTS:The average model gating decision accuracy and PPV across all volunteer studies was 93.7% and 92.8% using the 5D model, and 96.8% and 96.1% using the mSGA model, respectively. The median and 95th percentile distance between model and ground truth target centroids was 0.91 and 2.90 mm, respectively, using the 5D model and 0.58 and 1.49 mm using the mSGA model, averaged over all eight subjects. The mSGA motion model provided a statistically significant improvement across all evaluation metrics compared to the external surrogate-based 5D model. CONCLUSION:The proposed techniques for out-of-slice target motion estimation demonstrated accuracy likely sufficient for clinical use. Results indicate the mSGA model may provide higher accuracy, however, the external surrogate-based model allows for unbiased in vivo accuracy evaluation.

Project description:PURPOSE:To develop and validate a technique for radiation therapy gating using slow (?1 frame per second) magnetic resonance imaging (MRI) and a motion model. Proposed uses of the technique include radiation therapy gating using T2-weighted images and conducting additional imaging studies during gated treatments. METHODS AND MATERIALS:The technique uses a physiologically guided breathing motion model to interpolate deformed target position between 2-dimensional (2D) MRI images acquired every 1 to 3 seconds. The model is parameterized by a 1-dimensional respiratory bellows surrogate and is continuously updated with the most recently acquired 2D images. A phantom and 8 volunteers were imaged with a 0.35T MRI-guided radiation therapy system. A balanced steady-state free precession sequence with a 2D frame rate of 3 frames per second was used to evaluate the technique. The accuracy and beam-on positive predictive value (PPV) of the model-based gating decisions were evaluated using the gating decisions derived from imaging as a ground truth. A T2-weighted gating offline proof-of-concept study using a half-Fourier, single-shot, turbo-spin echo sequence is reported. RESULTS:Model-interpolated gating accuracy, beam-on PPV, and median absolute distances between model and image-tracked target centroids were, on average, 98.3%, 98.4%, and 0.33 mm, respectively, in the balanced steady-state free precession phantom studies and 93.7%, 92.1%, and 0.86 mm, respectively, in the volunteer studies. T2 model-interpolated gating in 6 volunteers yielded an average accuracy and PPV of 94.3% and 92.5%, respectively, and the mean absolute median distance between modeled and imaged target centroids was 0.86 mm. CONCLUSIONS:This work demonstrates the concept of model-interpolated gating for MRI-guided radiation therapy. The technique was found to be potentially sufficiently accurate for clinical use. Further development is needed to accommodate out-of-plane motion and the use of an internal MR-based respiratory surrogate.

Dataset Information

Quantitative Comparison of Conventional and t-SNE-guided Gating Analyses.

Publications

Quantitative Comparison of Conventional and t-SNE-guided Gating Analyses.

Similar Datasets

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