Browsing by Author "Castillo-Passi, Carlos"

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    Accurate characterization of dynamic microbial gene expression and growth rate profiles
    (2022) Vidal, Gonzalo; Vidal-Cespedes, Carlos; Silva, Macarena Munoz; Castillo-Passi, Carlos; Feliu, Guillermo Yanez; Federici, Fernan; Rudge, Timothy J.
    Genetic circuits are subject to variability due to cellular and compositional contexts. Cells face changing internal states and environments, the cellular context, to which they sense and respond by changing their gene expression and growth rates. Furthermore, each gene in a genetic circuit operates in a compositional context of genes which may interact with each other and the host cell in complex ways. The context of genetic circuits can, therefore, change gene expression and growth rates, and measuring their dynamics is essential to understanding natural and synthetic regulatory networks that give rise to functional phenotypes. However, reconstruction of microbial gene expression and growth rate profiles from typical noisy measurements of cell populations is difficult due to the effects of noise at low cell densities among other factors. We present here a method for the estimation of dynamic microbial gene expression rates and growth rates from noisy measurement data. Compared to the current state-of-the-art, our method significantly reduced the mean squared error of reconstructions from simulated data of growth and gene expression rates, improving the estimation of timing and magnitude of relevant shapes of profiles. We applied our method to characterize a triple-reporter plasmid library combining multiple transcription units in different compositional and cellular contexts in Escherichia coli. Our analysis reveals cellular and compositional context effects on microbial growth and gene expression rate dynamics and suggests a method for the dynamic ratiometric characterization of constitutive promoters relative to an in vivo reference.
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    Fast and accessible T2 mapping using off-resonance corrected DESPOT2 with application to 3D prostate
    (2024) Coronado, Ronal; Castillo-Passi, Carlos; Besa, Cecilia; Irarrazaval, Pablo
    Purpose: Most T1 and T2 mapping take long acquisitions or needs specialized sequences not widely accessible on clinical scanners. An available solution is DESPOT1/T2 (Driven equilibrium single pulse observation of T1/T2). DESPOT1/T2 uses Spoiled gradient-echo (SPGR) and balanced Steady-State Free Precession (bSSFP) sequences, offering an accessible and reliable way for 3D accelerated T1/T2 mapping. However, bSSFP is prone to offresonance artifacts, limiting the application of DESPOT2 in regions with high susceptibility contrasts, like the prostate. Our proposal, DESPO+, employs the full bSSFP and SPGR models with a dictionary-based method to reconstruct 3D T1/T2 maps in the prostate region without off-resonance banding. Methods: DESPO+ modifies the bSSFP acquisition of the original variable flip angle DESPOT2. DESPO+ uses variable repetition and echo times, employing a dictionary-based method of the full bSSFP and SPGR models to reconstruct T1, T2, and Proton Density (PD) simultaneously. The proposed DESPO+ method underwent testing through simulations, T1/T2 phantoms, and on fourteen healthy subjects. Results: The results reveal a significant reduction in T2 map banding artifacts compared to the original DESPOT2 method. DESPO+ approach reduced T2 errors by up to seven times compared to DESPOT2 in simulations and phantom experiments. We also synthesized in-vivo T1-weighted/T2-weighted images from the acquired maps using a spin-echo model to verify the map's quality when lacking a reference. For in-vivo imaging, the synthesized images closely resemble those from the clinical MRI protocol, reducing scan time by around 50% compared to traditional spin-echo T1-weighted/T2-weighted acquisitions. Conclusion: DESPO+ provides an off-resonance insensitive and clinically available solution, enabling highresolution 3D T1/T2 mapping and synthesized T1-weighted/T2-weighted images for the entire prostate, all achieved within a short scan time of 3.6 min, similar to DESPOT1/T2.
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    Highly efficient image navigator based 3D whole-heart cardiac MRA at 0.55T
    (2024) Castillo-Passi, Carlos; Kunze, Karl P.; Crabb, Michael G.; Munoz, Camila; Fotaki, Anastasia; Neji, Radhouene; Irarrazaval, Pablo; Prieto, Claudia; Botnar, Rene M.
    PurposeTo develop and evaluate a highly efficient free-breathing and contrast-agent-free three-dimensional (3D) whole-heart Cardiac Magnetic Resonance Angiography (CMRA) sequence at 0.55T.MethodsFree-breathing whole-heart CMRA has been previously proposed at 1.5 and 3T. Direct application of this sequence to 0.55T is not possible due to changes in the magnetic properties of the tissues. To enable free-breathing CMRA at 0.55T, pulse sequence design and acquisition parameters of a previously proposed whole-heart CMRA framework are optimized via Bloch simulations. Image navigators (iNAVs) are used to enable nonrigid respiratory motion-correction and 100% respiratory scan efficiency. Patch-based low-rank denoising is employed to accelerate the scan and account for the reduced signal-to-noise ratio at 0.55T. The proposed approach was evaluated on 11 healthy subjects. Image quality was assessed by a clinical expert (1: poor to 5: excellent) for all intrapericardiac structures. Quantitative evaluation was performed by assessing the vessel sharpness of the proximal right coronary artery (RCA).ResultsOptimization resulted in an imaging flip angle of 110 degrees$$ 11{0}<^>{\circ } $$, fat saturation flip angle of 180 degrees$$ 18{0}<^>{\circ } $$, and six k-space lines for iNAV encoding. The relevant cardiac structures and main coronary arteries were visible in all subjects, with excellent image quality (mean 4.9/5.0$$ 4.9/5.0 $$) and minimal artifacts (mean 4.9/5.0$$ 4.9/5.0 $$), with RCA vessel sharpness (50.3%+/- 9.8%$$ 50.3\%\pm 9.8\% $$) comparable to previous studies at 1.5T.ConclusionThe proposed approach enables 3D whole-heart CMRA at 0.55T in a 6-min scan (5.9 +/- 0.7 min$$ 5.9\pm 0.7\;\min $$), providing excellent image quality, minimal artifacts, and comparable vessel sharpness to previous 1.5T studies. Future work will include the evaluation of the proposed approach in patients with cardiovascular disease.