Optimization of a customized simultaneous algebraic reconstruction technique algorithm for phase-contrast breast computed tomography.

Objective.To introduce the optimization of a customized GPU-based simultaneous algebraic reconstruction technique (cSART) in the field of phase-contrast breast computed tomography (bCT). The presented algorithm features a 3D bilateral regularization filter that can be tuned to yield optimal performance for clinical image visualization and tissues segmentation.Approach.Acquisitions of a dedicated test object and a breast specimen were performed at Elettra, the Italian synchrotron radiation (SR) facility (Trieste, Italy) using a large area CdTe single-photon counting detector. Tomographic images were obtained at 5 mGy of mean glandular dose, with a 32 keV monochromatic x-ray beam in the free-space propagation mode. Three independent algorithms parameters were optimized by using contrast-to-noise ratio (CNR), spatial resolution, and noise texture metrics. The results obtained with the cSART algorithm were compared with conventional SART and filtered back projection (FBP) reconstructions. Image segmentation was performed both with gray scale-based and supervised machine-learning approaches.Main results.Compared to conventional FBP reconstructions, results indicate that the proposed algorithm can yield images with a higher CNR (by 35% or more), retaining a high spatial resolution while preserving their textural properties. Alternatively, at the cost of an increased image 'patchiness', the cSART can be tuned to achieve a high-quality tissue segmentation, suggesting the possibility of performing an accurate glandularity estimation potentially of use in the realization of realistic 3D breast models starting from low radiation dose images.Significance.The study indicates that dedicated iterative reconstruction techniques could provide significant advantages in phase-contrast bCT imaging. The proposed algorithm offers great flexibility in terms of image reconstruction optimization, either toward diagnostic evaluation or image segmentation.

Alignment of Nonspherical Active Particles in Chaotic Flows.

We study the orientation statistics of spheroidal, axisymmetric microswimmers, with shapes ranging from disks to rods, swimming in chaotic, moderately turbulent flows. Numerical simulations show that rodlike active particles preferentially align with the flow velocity. To explain the underlying mechanism, we solve a statistical model via the perturbation theory. We show that such an alignment is caused by correlations of fluid velocity and its gradients along particle paths combined with fore-aft symmetry breaking due to both swimming and particle nonsphericity. Remarkably, the discovered alignment is found to be a robust kinematical effect, independent of the underlying flow evolution. We discuss its possible relevance for aquatic ecology.

Validation of a questionnaire about knowledge and perception of biological risk among biomedical students of Sapienza University of Rome.

BACKGROUND ADN AIM: Healthcare workers and Biomedical students are continuously exposed to biological risk in their clinical practice. The objective of this study was to evaluate the validity and reliability of an Italian questionnaire on the knowledge and perception of biological risk in Biomedical students at the beginning of their professional training. MATERIALS AND METHODS: An electronic questionnaire was administered to students attending the second semester of the first year of Biomedical Courses at Sapienza University of Rome. The questionnaire consists of 40 questions divided into five sections collecting sociodemographic data, health status and level of knowledge and perception of biological risk. The statistical analysis was performed with Statistical Package for Social Sciences (SPSS) version 25. RESULTS: A total of 309 individuals answered the online questionnaire, with a response rate of 83.5%. The analysis of internal consistency was performed by two dichotomous variables that measured the knowledge level on hygiene behaviour and gloves use. The analysis showed a standardized Cronbach's alpha equal to 0.765, corresponding to a good reliability. A better reliability was found out among physiotherapy and medical students, with a Cronbach's alpha equal to 0.944 and 0.881, respectively. Regarding vaccines, 97.7% of the sample was given a Hepatitis B vaccination and 98.7% of students consider vaccinations essential for healthcare workers. CONCLUSIONS: Results of Cronbach's alpha showed a good reliability of the questionnaire. First-year Biomedical students may be exposed to occupational biological risk mainly because of their inexperience. A training educational path should be implemented in order to acquire competences, knowledge, attitudes and practical skills, correct behaviors and a personal and professional responsibility.

Rotational radiotherapy of breast cancer with polyenergetic kilovoltage X-ray beams: An experimental and Monte Carlo phantom study.

PURPOSE: We investigated the feasibility of kilovoltage rotational radiotherapy for breast cancer (kV-EBRT) via Monte Carlo simulations and measurements on phantoms. METHODS: We derived the dose distributions for X-ray beams at 150 kV, 300 kVp and 320 kV irradiating breast cylindrical phantoms of 14 cm diameter, mimicking the pendant breast. Simulations were based on the Geant4 toolkit. The point-like X-ray source was rotated either over a full circle or on a limited arc around the phantom. We studied the influence on the surface dose of the distance between the tumor lesion to the skin, of the irradiation protocol (full scan or partial scan) and of the X-ray tube current modulation. RESULTS: Rotational kV-EBRT permitted a periphery-to-center dose ratio from 13% to 9% in homogeneous breast phantoms. Dose distributions in phantoms with off-center simulated lesions, showed a skin-to-tumor dose ratio of 16% and 34% for lesions at 3.25 and 5.25 cm from cylinder axis, respectively. Simulation of the X-ray tube current modulation during the rotation, permits to reach a dose ratio of 20% for the lesion located at 5.25 cm from phantom axis. CONCLUSIONS: We showed the possibility of using low-energy X-ray spectra for kV-EBRT with collimated beams, for obtaining a periphery-to-center dose ratio in the same order of conventional accelerator based megavoltage radiotherapy, when the irradiated area is localized in the center of the breast. For tumors localized near the breast border, we showed that the tube current modulation can be a good solution in order to reduce the skin-to-tumor dose ratio.

Investigation of the refractive index decrement of 3D printing materials for manufacturing breast phantoms for phase contrast imaging.

3D breast modelling for 2D and 3D breast x-ray imaging would benefit from the availability of digital and physical phantoms that reproduce accurately the complexity of the breast anatomy. While a number of groups have produced digital phantoms with increasing level of complexity, physical phantoms reproducing that software approach have been scarcely developed. One possibility is offered by 3D printing technology. This implies the assessment of the energy dependent absorption index ß of 3D printing materials for absorption based imaging, as well as the assessment of the refractive index decrement, δ, of the printing material, for phase contrast imaging studies, at the energies of interest for breast imaging. In this work we set-up a procedure and performed a series of measurements (at 30, 45 and 60 keV, at the European Synchrotron Radiation Facility) for assessing the relative value of δ with respect to that of breast tissues, for twelve 3D printing materials. The method included propagation based phase contrast 2D imaging and retrieval of the estimated phase shift map, using the Paganin's algorithm. Breast glandular, adipose and skin tissues were used as reference materials of known ratio δ/ß. A percentage difference Δδ was introduced to assess the suitability of the printing materials as tissue substitutes. The accuracy of the method (about 4%) was assessed based on the properties of PMMA and Nylon, acting as gold standard. Results show that, for the above photon energies, ABS is a good substitute for adipose tissue, Hybrid as a substitute of the glandular tissue and PET-G for simulating the skin. We plan to realize a breast phantom manufactured by fused deposition modelling (FDM) technology using ABS, Hybrid and PET-G as substitutes of the glandular and skin tissue and a second phantom by stereolithography (SLA) technology with the resins Flex, Tough and Black.

Normalized glandular dose coefficients in mammography, digital breast tomosynthesis and dedicated breast CT.

PURPOSE: To provide mean glandular dose (MGD) estimates via Monte Carlo (MC) simulations as a function of the breast models and scan parameters in mammography, digital breast tomosynthesis (DBT) and dedicated breast CT (BCT). METHODS: The MC code was based on GEANT4 toolkit. The simulated compressed breast was either a cylinder with a semi-circular section or ad hoc shaped for oblique view (MLO). In DBT we studied the influence of breast models and exam parameters on the T-factors (i.e. the conversion factor for the calculation of the MGD in DBT from that for a 0-degree projection), and in BCT we investigated the influence on the MGD estimates of the ion chamber volume used for the air kerma measurements. RESULTS: In mammography, a model representative of a breast undergoing an MLO view exam did not produce substantial differences (0.4%) in MGD estimates, when compared to a conventional cranio-caudal (CC) view breast model. The beam half value layer did not present a significant influence on T-factors in DBT (<0.8%), while the skin model presented significant influence on MGD estimates (up to 3.3% at 30 degrees scan angle), increasing for larger scan angles. We derived a correction factor for taking into account the different ion chamber volume used in MGD estimates in BCT. CONCLUSIONS: A series of MC code modules for MGD estimates in 2D and 3D breast imaging have been developed in order to take into account the most recent advances in breast models.

Homogeneous vs. patient specific breast models for Monte Carlo evaluation of mean glandular dose in mammography.

PURPOSE: To compare, via Monte Carlo simulations, homogeneous and non-homogenous breast models adopted for mean glandular dose (MGD) estimates in mammography vs. patient specific digital breast phantoms. METHODS: We developed a GEANT4 Monte Carlo code simulating four homogenous cylindrical breast models featured as follows: (1) semi-cylindrical section enveloped in a 5-mm adipose layer; (2) semi-elliptical section with a 4-mm thick skin; (3) semi-cylindrical section with a 1.45-mm skin layer; (4) semi-cylindrical section in a 1.45-mm skin layer and 2-mm subcutaneous adipose layer. Twenty patient specific digital breast phantoms produced from a dedicated CT scanner were assumed as reference in the comparison. We simulated two spectra produced from two anode/filter combinations. An additional digital breast phantom was produced via BreastSimulator software. RESULTS: With reference to the results for patient-specific breast phantoms and for W/Al spectra, models #1 and #3 showed higher MGD values by about 1% (ranges [-33%; +28%] and [-31%; +30%], respectively), while for model #4 it was 2% lower (range [-34%; +26%]) and for model #2 -11% (range [-39%; +14%]), on average. On the other hand, for W/Rh spectra, models #1 and #4 showed lower MGD values by 2% and 1%, while for model #2 and #3 it was 14% and 8% lower, respectively (ranges [-43%; +13%] and [-41%; +21%]). The simulation with the digital breast phantom produced with BreastSimulator showed a MGD overestimation of +33%. CONCLUSIONS: The homogeneous breast models led to maximum MGD underestimation and overestimation of 43% and 28%, respectively, when compared to patient specific breast phantoms derived from clinical CT scans.

Point-particle method to compute diffusion-limited cellular uptake.

We present an efficient point-particle approach to simulate reaction-diffusion processes of spherical absorbing particles in the diffusion-limited regime, as simple models of cellular uptake. The exact solution for a single absorber is used to calibrate the method, linking the numerical parameters to the physical particle radius and uptake rate. We study the configurations of multiple absorbers of increasing complexity to examine the performance of the method by comparing our simulations with available exact analytical or numerical results. We demonstrate the potential of the method to resolve the complex diffusive interactions, here quantified by the Sherwood number, measuring the uptake rate in terms of that of isolated absorbers. We implement the method in a pseudospectral solver that can be generalized to include fluid motion and fluid-particle interactions. As a test case of the presence of a flow, we consider the uptake rate by a particle in a linear shear flow. Overall, our method represents a powerful and flexible computational tool that can be employed to investigate many complex situations in biology, chemistry, and related sciences.

Evaluation of the BreastSimulator software platform for breast tomography.

The aim of this work was the evaluation of the software BreastSimulator, a breast x-ray imaging simulation software, as a tool for the creation of 3D uncompressed breast digital models and for the simulation and the optimization of computed tomography (CT) scanners dedicated to the breast. Eight 3D digital breast phantoms were created with glandular fractions in the range 10%-35%. The models are characterised by different sizes and modelled realistic anatomical features. X-ray CT projections were simulated for a dedicated cone-beam CT scanner and reconstructed with the FDK algorithm. X-ray projection images were simulated for 5 mono-energetic (27, 32, 35, 43 and 51 keV) and 3 poly-energetic x-ray spectra typically employed in current CT scanners dedicated to the breast (49, 60, or 80 kVp). Clinical CT images acquired from two different clinical breast CT scanners were used for comparison purposes. The quantitative evaluation included calculation of the power-law exponent, ß, from simulated and real breast tomograms, based on the power spectrum fitted with a function of the spatial frequency, f, of the form S(f) = α/f ß . The breast models were validated by comparison against clinical breast CT and published data. We found that the calculated ß coefficients were close to that of clinical CT data from a dedicated breast CT scanner and reported data in the literature. In evaluating the software package BreastSimulator to generate breast models suitable for use with breast CT imaging, we found that the breast phantoms produced with the software tool can reproduce the anatomical structure of real breasts, as evaluated by calculating the ß exponent from the power spectral analysis of simulated images. As such, this research tool might contribute considerably to the further development, testing and optimisation of breast CT imaging techniques.

Scale-dependent colocalization in a population of gyrotactic swimmers.

We study the small scale clustering of gyrotactic swimmers transported by a turbulent flow, when the intrinsic variability of the swimming parameters within the population is considered. By means of extensive numerical simulations, we find that the variety of the population introduces a characteristic scale R^{*} in its spatial distribution. At scales smaller than R^{*} the swimmers are homogeneously distributed, while at larger scales an inhomogeneous distribution is observed with a fractal dimension close to what observed for a monodisperse population characterized by mean parameters. The scale R^{*} depends on the dispersion of the population and it is found to scale linearly with the standard deviation both for a bimodal and for a Gaussian distribution. Our numerical results, which extend recent findings for a monodisperse population, indicate that in principle it is possible to observe small scale, fractal clustering in a laboratory experiment with gyrotactic cells.

Irreversibility of the two-dimensional enstrophy cascade.

We study the time irreversibility of the direct cascade in two-dimensional turbulence by looking at the time derivative of the square vorticity along Lagrangian trajectories, a quantity called metenstrophy. By means of extensive direct numerical simulations we measure the time irreversibility from the asymmetry of the probability density function of the metenstrophy and we find that it increases with the Reynolds number of the cascade, similarly to what is found in three-dimensional turbulence. A detailed analysis of the different contributions to the enstrophy budget reveals a remarkable difference with respect to what is observed for the energy cascade, in particular the role of the statistics of the forcing to determine the degree of irreversibility.

Imaging performance of phase-contrast breast computed tomography with synchrotron radiation and a CdTe photon-counting detector.

PURPOSE: Within the SYRMA-CT collaboration based at the ELETTRA synchrotron radiation (SR) facility the authors investigated the imaging performance of the phase-contrast computed tomography (CT) system dedicated to monochromatic in vivo 3D imaging of the female breast, for breast cancer diagnosis. METHODS: Test objects were imaged at 38keV using monochromatic SR and a high-resolution CdTe photon-counting detector. Signal and noise performance were evaluated using modulation transfer function (MTF) and noise power spectrum. The analysis was performed on the images obtained with the application of a phase retrieval algorithm as well as on those obtained without phase retrieval. The contrast to noise ratio (CNR) and the capability of detecting test microcalcification clusters and soft masses were investigated. RESULTS: For a voxel size of (60µm)(3), images without phase retrieval showed higher spatial resolution (6.7mm(-1) at 10% MTF) than corresponding images with phase retrieval (2.5mm(-1)). Phase retrieval produced a reduction of the noise level and an increase of the CNR by more than one order of magnitude, compared to raw phase-contrast images. Microcalcifications with a diameter down to 130µm could be detected in both types of images. CONCLUSIONS: The investigation on test objects indicates that breast CT with a monochromatic SR source is technically feasible in terms of spatial resolution, image noise and contrast, for in vivo 3D imaging with a dose comparable to that of two-view mammography. Images obtained with the phase retrieval algorithm showed the best performance in the trade-off between spatial resolution and image noise.

Towards breast tomography with synchrotron radiation at Elettra: first images.

The aim of the SYRMA-CT collaboration is to set-up the first clinical trial of phase-contrast breast CT with synchrotron radiation (SR). In order to combine high image quality and low delivered dose a number of innovative elements are merged: a CdTe single photon counting detector, state-of-the-art CT reconstruction and phase retrieval algorithms. To facilitate an accurate exam optimization, a Monte Carlo model was developed for dose calculation using GEANT4. In this study, high isotropic spatial resolution (120 µm)(3) CT scans of objects with dimensions and attenuation similar to a human breast were acquired, delivering mean glandular doses in the range of those delivered in clinical breast CT (5-25 mGy). Due to the spatial coherence of the SR beam and the long distance between sample and detector, the images contain, not only absorption, but also phase information from the samples. The application of a phase-retrieval procedure increases the contrast-to-noise ratio of the tomographic images, while the contrast remains almost constant. After applying the simultaneous algebraic reconstruction technique to low-dose phase-retrieved data sets (about 5 mGy) with a reduced number of projections, the spatial resolution was found to be equal to filtered back projection utilizing a four fold higher dose, while the contrast-to-noise ratio was reduced by 30%. These first results indicate the feasibility of clinical breast CT with SR.

Energy dependent calibration of XR-QA2 radiochromic film with monochromatic and polychromatic x-ray beams.

PURPOSE: This work investigates the energy response and dose-response curve determinations for XR-QA2 radiochromic film dosimetry system used for synchrotron radiation work and for quality assurance in diagnostic radiology, in the range of effective energies 18-46.5 keV. METHODS: Pieces of XR-QA2 films were irradiated, in a plane transverse to the beam axis, with a monochromatic beam of energy in the range 18-40 keV at the ELETTRA synchrotron radiation facility (Trieste, Italy) and with a polychromatic beam from a laboratory x-ray tube operated at 80, 100, and 120 kV. The film calibration curve was expressed as air kerma (measured free-in-air with an ionization chamber) versus the net optical reflectance change (netΔR) derived from the red channel of the RGB scanned film image. Four functional relationships (rational, linear exponential, power, and logarithm) were tested to evaluate the best curve for fitting the calibration data. The adequacy of the various fitting functions was tested by using the uncertainty analysis and by assessing the average of the absolute air kerma error calculated as the difference between calculated and delivered air kerma. The sensitivity of the film was evaluated as the ratio of the change in net reflectance to the corresponding air kerma. RESULTS: The sensitivity of XR-QA2 films increased in the energy range 18-39 keV, with a maximum variation of about 170%, and decreased in the energy range 38-46.5 keV. The present results confirmed and extended previous findings by this and other groups, as regards the dose response of the radiochromic film XR-QA2 to monochromatic and polychromatic x-ray beams, respectively. CONCLUSIONS: The XR-QA2 radiochromic film response showed a strong dependence on beam energy for both monochromatic and polychromatic beams in the range of half value layer values from 0.55 to 6.1 mm Al and corresponding effective energies from 18 to 46.5 keV. In this range, the film response varied by 170%, from a minimum sensitivity of 0.0127 to a maximum sensitivity of 0.0219 at 10 mGy air kerma in air. The more suitable function for air kerma calibration of the XR-QA2 radiochromic film was the power function. A significant batch-to-batch variation, up to 55%, in film response at 120 kV (46.5 keV effective energy) was observed in comparison with published data.

Glandular dose in breast computed tomography with synchrotron radiation.

The purpose of this work is to provide an evaluation of the mean glandular dose (MGD) for breast computed tomography (CT) with synchrotron radiation in an axial scanning configuration with a partial or total organ volume irradiation, for the in vivo program of breast CT ongoing at the ELETTRA facility (Trieste, Italy). A Geant4 Monte Carlo code was implemented, simulating the photon irradiation from a synchrotron radiation source in the energetic range from 8 to 50 keV with 1 keV intervals, to evaluate the MGD. The code was validated with literature data, in terms of mammographic normalized glandular dose coefficients (DgN) and with ad hoc experimental data, in terms of computed tomography dose index (CTDI). Simulated cylindrical phantoms of different sizes (diameter at phantom base 8, 10, 12, 14 or 16 cm, axial length 1.5 times the radius) and glandular fraction by weight (0%, 14.3%, 25%, 50%, 75% and 100%) were implemented into the code. The validation of the code shows an excellent agreement both with previously published work and in terms of DgN and CDTI measurements. The implemented simulations show a dependence of the glandular dose estimate on the vertical dimension of the irradiated zone when a partial organ irradiation was implemented. Specific normalized coefficients for calculating the MGD to the whole breast or to the single irradiated slice were reported.

Energy response of GR-200A thermoluminescence dosemeters to 60Co and to monoenergetic synchrotron radiation in the energy range 28-40 keV.

The response of LiF:Mg,Cu,P thermoluminescence dosemeters (type GR-200A) to monoenergetic radiation of energy 28, 35, 38 and 40 keV was evaluated with respect to irradiation with a calibrated (60)Co gamma-ray source. High-precision measurements of the relative air kerma response performed at the SYRMEP beamline of the ELETTRA synchrotron radiation facility (Trieste, Italy) showed a significant deviation of the average response to low-energy X-rays from that to (60)Co, with an over-response from 6 % (at 28 keV) to 22 % (at 40 keV). These data are not consistent with literature data for these dosemeters, where model predictions gave deviation from unity of the relative air kerma response of about 10 %. The authors conclude for the need of additional determinations of the low-energy relative response of GR-200A dosemeters, covering a wider range of monoenergetic energies sampled at a fine energy step, as planned in future experiments by their group at the ELETTRA facility.

Anomalous diffusion in confined turbulent convection.

Turbulent convection in quasi-one-dimensional geometry is studied by means of high-resolution direct numerical simulations within the framework of Rayleigh-Taylor turbulence. Geometrical confinement has dramatic effects on the dynamics of the turbulent flow, inducing a transition from superdiffusive to subdiffusive evolution of the mixing layer and arresting the growth of kinetic energy. A nonlinear diffusion model is shown to reproduce accurately the above phenomenology. The model is used to predict, without free parameters, the spatiotemporal evolution of the heat flux profile and the dependence of the Nusselt number on the Rayleigh number.

Control of particle clustering in turbulence by polymer additives.

We study the clustering properties of inertial particles in a turbulent viscoelastic fluid. The investigation is carried out by means of direct numerical simulations of turbulence in the Oldroyd-B model. The effects of polymers on the small-scale properties of homogeneous turbulence are considered in relation with their consequences on clustering of particles, both lighter and heavier than the carrying fluid. We show that, depending on particle and flow parameters, polymers can either increase or decrease clustering.

Shell model for quasi-two-dimensional turbulence.

We discuss the possibility to introduce geometrical constraints in shell models of turbulence in order to mimic the turbulent dynamics that takes place in fluid layers with large aspect ratio. By using a scale-dependent set of coupling parameters, we are able to resolve both scales larger and smaller than a geometrical dimension of the flow. The proposed model is able to resolve with high accuracy the split energy cascade phenomenon recently observed in such flows, and allows us to investigate in detail the scaling properties of turbulent convection confined in narrow convective cells.

Nonlinear diffusion model for Rayleigh-Taylor mixing.

The complex evolution of turbulent mixing in Rayleigh-Taylor convection is studied in terms of eddy diffusivity models for the mean temperature profile. It is found that a nonlinear model, derived within the general framework of Prandtl mixing theory, reproduces accurately the evolution of turbulent profiles obtained from numerical simulations. Our model allows us to give very precise predictions for the turbulent heat flux and for the Nusselt number in the ultimate state regime of thermal convection.