Effect of wavelength selection on the accuracy of blood oxygen saturation estimates obtained from photoacoustic images

In photoacoustic tomography (PAT) the image contrast is due to optical absorption, and because of this PAT images are sensitive to changes in blood oxygen saturation (sO2). However, this is not a linear relationship due to the presence of a non-uniform light fluence distribution. In this paper we systematically evaluate the conditions in which an approximate linear inversion scheme–which assumes the internal fluence distribution is unchanged when the absorption coefficient changes–can give accurate estimates of sO2. A numerical phantom of highly vascularised tissue is used to test this assumption. It is shown that using multiple wavelengths over a broad range of the near-infrared spectrum yields inaccurate estimates of oxygenation, while a careful selection of wavelengths in the 620-920nm range is likely to yield more accurate oxygenation values. We demonstrate that a 1D fluence correction obtained by fitting a linear function to the average decay rate in the image can further improve the estimates. However, opting to use these longer wavelengths involves sacrificing signal-to-noise ratio in the image, as the absorption of blood is low in this range. This results in an inherent trade-off between error in the sO2 estimates due to fluence variation and error due to noise. This study shows that the depth to which sO2 can be estimated accurately using a linear approximation is limited in vivo, even with idealised measurements, to at most 3mm. In practice, there will be even greater uncertainties affecting the estimates, e.g., due to bandlimited or partial-view acoustic detection

Radiance Monte-Carlo for application of the radiative transport equation in the inverse problem of diffuse optical tomography

We introduce a new Monte-Carlo technique to estimate the radiance distribution in a medium according to the radiative transport equation (RTE). We demonstrate how to form gradients of the forward model, and thus how to employ this technique as part of the inverse problem in Diffuse Optical Tomography (DOT). Use of the RTE over the more typical application of the diffusion approximation permits accurate modelling in the case of short source-detector separation and regions of low scattering, in addition to providing time-domain information without extra computational effort over continuous-wave solutions

Monte Carlo Methods in Quantitative Photoacoustic Tomography

Quantitative photoacoustic tomography (QPAT) is a hybrid biomedical imaging technique that derives its specificity from the wavelength-dependent absorption of near-infrared/visible laser light, and its sensitivity from ultrasonic waves. This promising technique has the potential to reveal more than just structural information, it can also probe tissue function. Specifically, QPAT has the capability to estimate concentrations of endogenous chromophores, such as the concentrations of oxygenated and deoxygenated haemoglobin (from which blood oxygenation can be calculated), as well as the concentrations of exogenous chromophore, e.g. near-infrared dyes or metallic nanoparticles. This process is complicated by the fact that a photoacoustic image is not directly related to the tissue properties via the absorption coefficient, but is proportional to the wavelength-dependent absorption coefficient times the internal light fluence, which is also wavelength-dependent and is in general unknown. This thesis tackles this issue from two angles; firstly, the question of whether certain experimental conditions allow the impact of the fluence to be neglected by assuming it is constant with wavelength, a `linear inversion', is addressed. It is demonstrated that a linear inversion is appropriate only for certain bands of illumination wavelengths and for limited depth. Where this assumption is not accurate, an alternative approach is proposed, whereby the fluence inside the tissue is modelled using a novel Monte Carlo model of light transport. This model calculates the angle-dependent radiance distribution by storing the field in Fourier harmonics, in 2D, or spherical harmonics, in 3D. This thesis demonstrates that a key advantage of computing the radiance in this way is that it simplifies the computation of functional gradients when the estimation of the absorption and scattering coefficients is cast as a nonlinear least-squares problem. Using this approach, it is demonstrated in 2D that the estimation of the absorption coefficient can be performed to a useful level of accuracy, despite the limited accuracy in reconstruction of the scattering coefficient

Forward and Adjoint Radiance Monte Carlo Models for Quantitative Photoacoustic Imaging

In quantitative photoacoustic imaging, the aim is to recover physiologically relevant tissue parameters such as chromophore concentrations or oxygen saturation. Obtaining accurate estimates is challenging due to the non-linear relationship between the concentrations and the photoacoustic images. Nonlinear least squares inversions designed to tackle this problem require a model of light transport, the most accurate of which is the radiative transfer equation. This paper presents a highly scalable Monte Carlo model of light transport that computes the radiance in 2D using a Fourier basis to discretise in angle. The model was validated against a 2D finite element model of the radiative transfer equation, and was used to compute gradients of an error functional with respect to the absorption and scattering coefficient. It was found that adjoint-based gradient calculations were much more robust to inherent Monte Carlo noise than a finite difference approach. Furthermore, the Fourier angular discretisation allowed very efficient gradient calculations as sums of Fourier coefficients. These advantages, along with the high parallelisability of Monte Carlo models, makes this approach an attractive candidate as a light model for quantitative inversion in photoacoustic imaging

The effect of modern intensive monitoring in obstetrics on infant mortality and the incidence of hypoxia and acidosis

Peer Reviewe

Purification and Reconstitution of the Glutamate Carrier GltT of the Thermophilic Bacterium Bacillus stearothermophilus

An affinity tag consisting of six adjacent histidine residues followed by an enterokinase cleavage site was genetically engineered at the N-terminus of the glutamate transport protein GltT of the thermophilic bacterium Bacillus stearothermophilus. The fusion protein was expressed in Escherichia coli and shown to transport glutamate. The highest levels of expression were observed in E. coli strain DH5α grown on rich medium. The protein could be purified in a single step by Ni2+-NTA affinity chromatography after solubilization of the cytoplasmic membranes with the detergent Triton X100. Purified GltT was reconstituted in an active state in liposomes prepared from E. coli phospholipids. The protein was reconstituted in detergent-treated preformed liposomes, followed by removal of the detergent with polystyrene beads. Active reconstitution was realized with a wide range of Triton X100 concentrations. Neither the presence of glycerol, phospholipids, nor substrates of the transporter was necessary during the purification and reconstitution procedure to keep the enzyme in an active state. In B. stearothermophilus, GltT translocates glutamate in symport with protons or sodium ions. In membrane vesicles derived from E. coli cells expressing GltT, the Na+ ion dependency seems to be lost, suggesting a role for the lipid environment in the cation specificity. In agreement with the last observation, glutamate transport catalyzed by purified GltT reconstituted in E. coli phospholipid is driven by an electrochemical gradient of H+ but not of Na+.

Vehicle Occurrence-based Parking Space Detection

Smart-parking solutions use sensors, cameras, and data analysis to improve parking efficiency and reduce traffic congestion. Computer vision-based methods have been used extensively in recent years to tackle the problem of parking lot management, but most of the works assume that the parking spots are manually labeled, impacting the cost and feasibility of deployment. To fill this gap, this work presents an automatic parking space detection method, which receives a sequence of images of a parking lot and returns a list of coordinates identifying the detected parking spaces. The proposed method employs instance segmentation to identify cars and, using vehicle occurrence, generate a heat map of parking spaces. The results using twelve different subsets from the PKLot and CNRPark-EXT parking lot datasets show that the method achieved an AP25 score up to 95.60\% and AP50 score up to 79.90\%.Comment: Accepted for presentation at the 2023 IEEE International Conference on Systems, Man, and Cybernetics (SMC 2023

Formation of SRP-like particle induces a conformational change in E. coli 4.5S RNA

E. coli P48 protein is homologous to the SRP54 component of the eukaryotic signal recognition particle. In vivo, P48 is associated with 4.5S RNA which shares a homology with eukaryotic SRP RNA. To study the interaction between P48 and 4.5S RNA in vitro, we used 4.5S RNA with fluorescein coupled to the 3'-terminal ribose. Upon binding of P48, the fluorescent 4.5S RNA shows a substantial decrease in fluorescence. Fluorescence quenching as well as anisotropy measurements reveal that the effect is not due to a direct interaction of P48 with the dye. This suggests that the binding of P48 induces a conformational change in 4.5S RNA which affects the structure at the 3' end of the RNA. From equilibrium titrations with fluorescent 4.5S RNA, a dissociation constant of 0.15 microns is obtained for the RNA.protein complex. The formation of the complex is not affected by GTP binding to or hydrolysis by P48

An Efficient Ligation Method in the Making of an in vitro Virus for in vitro Protein Evolution

The “in vitro virus” is a molecular construct to perform evolutionary protein engineering. The “virion (=viral particle)” (mRNA-peptide fusion), is made by bonding a nascent protein with its coding mRNA via puromycin in a test tube for in vitro translation. In this work, the puromycin-linker was attached to mRNA using the Y-ligation, which was a method of two single-strands ligation at the end of a double-stranded stem to make a stem-loop structure. This reaction gave a yield of about 95%. We compared the Y-ligation with two other ligation reactions and showed that the Y-ligation gave the best productivity. An efficient amplification of the in vitro virus with this “viral genome” was demonstrated