A probabilistic deep learning model of inter-fraction anatomical variations in radiotherapy

In radiotherapy, the internal movement of organs between treatment sessions causes errors in the final radiation dose delivery. Motion models can be used to simulate motion patterns and assess anatomical robustness before delivery. Traditionally, such models are based on principal component analysis (PCA) and are either patient-specific (requiring several scans per patient) or population-based, applying the same deformations to all patients. We present a hybrid approach which, based on population data, allows to predict patient-specific inter-fraction variations for an individual patient. We propose a deep learning probabilistic framework that generates deformation vector fields (DVFs) warping a patient's planning computed tomography (CT) into possible patient-specific anatomies. This daily anatomy model (DAM) uses few random variables capturing groups of correlated movements. Given a new planning CT, DAM estimates the joint distribution over the variables, with each sample from the distribution corresponding to a different deformation. We train our model using dataset of 312 CT pairs from 38 prostate cancer patients. For 2 additional patients (22 CTs), we compute the contour overlap between real and generated images, and compare the sampled and ground truth distributions of volume and center of mass changes. With a DICE score of 0.86 and a distance between prostate contours of 1.09 mm, DAM matches and improves upon PCA-based models. The distribution overlap further indicates that DAM's sampled movements match the range and frequency of clinically observed daily changes on repeat CTs. Conditioned only on a planning CT and contours of a new patient without any pre-processing, DAM can accurately predict CTs seen during following treatment sessions, which can be used for anatomically robust treatment planning and robustness evaluation against inter-fraction anatomical changes

An improved nearest neighbor method for the estimation of the gamma photon entry point in monolithic scintillator detectors for PET

Several improvements of the k-nearest neighbor (k-NN) method for the determination of the entry point (x, y) of a gamma photon in a monolithic scintillator PET detector have been investigated with the aim to obtain better spatial resolution and/or to enable faster detector calibration by reducing the amount of required reference data and by allowing for calibrating with a line source. These methods were tested on a dataset measured with a SiPM-array-based monolithic LYSO detector. It appears that 10% to 25% better spatial resolution can be obtained compared to the standard approach. Moreover, some of the improved methods using two orders of magnitude less reference data, yield essentially the same spatial resolution as the standard method, which reduces the time needed for calibration as well as entry point computation. Finally, line source calibration is shown to be possible with some of the methods, yielding better results than the standard method and allowing much faster and easier collection of the reference data.</p

MicroRNA-204-5p modulates mitochondrial biogenesis in C2C12 myotubes and associates with oxidative capacity in humans

Using an unbiased high-throughput microRNA (miRNA)-silencing screen combined with functional readouts for mitochondrial oxidative capacity in C2C12 myocytes, we previously identified 19 miRNAs as putative regulators of skeletal muscle mitochondrial metabolism. In the current study, we highlight miRNA-204-5p, identified from this screen, and further studied its role in the regulation of skeletal muscle mitochondrial function. Following silencing of miRNA-204-5p in C2C12 myotubes, gene and protein expression were assessed using quantitative polymerase chain reaction, microarray analysis, and western blot analysis, while morphological changes were studied by confocal microscopy. In addition, miRNA-204-5p expression was quantified in human skeletal muscle biopsies and associated with in vivo mitochondrial oxidative capacity. Transcript levels of PGC-1α (3.71-fold; p <.01), predicted as an miR-204-5p target, as well as mitochondrial DNA copy number (p <.05) and citrate synthase activity (p =.06) were increased upon miRNA-204-5p silencing in C2C12 myotubes. Silencing of miRNA-204-5p further resulted in morphological changes, induced gene expression of autophagy marker light chain 3 protein b (LC3B; q =.05), and reduced expression of the mitophagy marker FUNDC1 (q =.01). Confocal imaging revealed colocalization between the autophagosome marker LC3B and the mitochondrial marker OxPhos upon miRNA-204-5p silencing. Finally, miRNA-204-5p was differentially expressed in human subjects displaying large variation in oxidative capacity and its expression levels associated with in vivo measures of skeletal muscle mitochondrial function. In summary, silencing of miRNA-204-5p in C2C12 myotubes stimulated mitochondrial biogenesis, impacted on cellular morphology, and altered expression of markers related to autophagy and mitophagy. The association between miRNA-204-5p and in vivo mitochondrial function in human skeletal muscle further identifies miRNA-204-5p as an interesting modulator of skeletal muscle mitochondrial metabolism.</p

Sub-3mm spatial resolution from a large monolithic LaBr3 (Ce) scintillator

Abstract A Compton camera prototype for ion beam range monitoring via prompt (< 1 ns) gamma detection in hadron therapy is being developed and characterized at the Medical Physics Department of LMU Munich. The system consists of a large (50x50x30 mm3) monolithic LaBr3(Ce) scintillation crystal as absorber component to detect the multi-MeV Compton scattered photons, together with a stack of 6 double-sided silicon strip detectors (DSSSD) acting as scatterer component. Key ingredient of the γ-source reconstruction is the determination of the γ-ray interaction position in the scintillator, which is read out by a 256-fold segmented multi-anode photomultiplier tube (PMT). From simulations an angular resolution of about 1.5o for the photon source reconstruction can be expected for the energy range around 3 – 5 MeV, provided that a spatial resolution of 3 mm can be reached in the absorbing scintillator [1]. Therefore, particular effort was dedicated to characterize this latter property as a function of the γ-ray energy. Intense, tightly collimated 137Cs and 60Co photon sources were used for 2D irradiation scans (step size 0.5 mm) as prerequisite for studying the performance of the "k-Nearest-Neighbors" algorithm developed at TU Delft [2] (together with its variant "Categorical Average Pattern", CAP) and extending its applicability into the energy range beyond the original 511 keV. In this paper we present our most recent interaction position analysis in the absorbing scintillator, leading to a considerably improved value for the spatial resolution: systematic studies were performed as a function of the k-NN parameters and the PMT segmentation. A trend of improving spatial resolution with increasing photon energy was confirmed, resulting in the realization of the presently optimum spatial resolution of 2.9(1) mm @1.3 MeV, thus reaching the design specifications of the Compton camera absorber. The specification goal was reached also for a reduced PMT segmentation of 8x8 anode segments (each with 6x6 mm2 active area), thus allowing to reduce the complexity of the signal processing while preserving the performance

Experimental and computational simulation of beta-dose heterogeneity in sediment

Interpreting the spread in equivalent-dose estimates is an important aspect of optically stimulated luminescence (OSL) dating. Ideally, prior to age estimation, an assessment should be made of the likely spread in equivalent dose due to dose-rate heterogeneity in the sediment. Such a procedure would greatly increase the validity of OSL ages, particularly for sediments susceptible to partial bleaching, and for sediments with coarse or poorly sorted grain-size distributions. In this paper we take a step towards a general model of dose-rate heterogeneity by simulating the 40K-derived beta dose to quartz. We present an experimental simulation of the 40K beta dose, and compare the results with a Monte Carlo simulation of the same experiment. The experiment uses artificially produced 24Na to simulate the 40K beta dose to quartz, allowing a large, heterogeneous dose to be administered in a short period of time. The Monte Carlo simulation correctly predicts the shape of the equivalent-dose distribution, but underestimates the spread in dose received by different grains. The experimental set-up provides a new avenue of research into beta-dose heterogeneity

Towards monolithic scintillator based TOF-PET systems: practical methods for detector calibration and operation

Gamma-ray detectors based on thick monolithic scintillator crystals can achieve spatial resolutions  <2 mm full-width-at-half-maximum (FWHM) and coincidence resolving times (CRTs) better than 200 ps FWHM. Moreover, they provide high sensitivity and depth-of-interaction (DOI) information. While these are excellent characteristics for clinical time-of-flight (TOF) positron emission tomography (PET), the application of monolithic scintillators has so far been hampered by the lengthy and complex procedures needed for position- and time-of-interaction estimation. Here, the algorithms previously developed in our group are revised to make the calibration and operation of a large number of monolithic scintillator detectors in a TOF-PET system practical. In particular, the k-nearest neighbor (k-NN) classification method for x,y-position estimation is accelerated with an algorithm that quickly preselects only the most useful reference events, reducing the computation time for position estimation by a factor of ~200 compared to the previously published k-NN 1D method. Also, the procedures for estimating the DOI and time of interaction are revised to enable full detector calibration by means of fan-beam or flood irradiations only. Moreover, a new technique is presented to allow the use of events in which some of the photosensor pixel values and/or timestamps are missing (e.g. due to dead time), so as to further increase system sensitivity. The accelerated methods were tested on a monolithic scintillator detector specifically developed for clinical PET applications, consisting of a 32 mm  ×  32 mm  ×  22 mm LYSO : Ce crystal coupled to a digital photon counter (DPC) array. This resulted in a spatial resolution of 1.7 mm FWHM, an average DOI resolution of 3.7 mm FWHM, and a CRT of 214 ps. Moreover, the possibility of using events missing the information of up to 16 out of 64 photosensor pixels is shown. This results in only a small deterioration of the detector performance

Advances in digital SiPMs and their application in biomedical imaging

Similar to analog silicon photomultipliers (SiPMs), digital SiPMs (dSiPMs) essentially consist of an array of single-photon avalanche photodiodes (SPADs). Instead of a passive quench resistor, however, an active quenching circuit is locally integrated with each SPAD, making the sensor response faster and less sensitive to the gains of the individual SPADs. Moreover, additional circuits for the fully digital acquisition, processing, and readout of optical signals are integrated within the sensor. As a result, dSiPMs offer high photo-detection efficiency, high single-photon time resolution (SPTR), and high uniformity, as well as many practical advantages, such as a very compact form factor, low voltage operation, magnetic field compatibility, high stability of operation, low gain drift, and a high degree of scalability. At the same time, dSiPMs represent a new paradigm in low-level light sensing technology. That is, their fully digital operation makes them true photon counting devices, preserving at least partly the discrete spatio-temporal structure of the information embedded in the optical signal. This means that the operation of dSiPMs can be fully understood only in statistical terms, but also opens up novel possibilities for extracting information from the measured data. So far, the main driver behind the development of dSiPMs has been the detection of scintillation pulses in detectors for time-of-flight (TOF) positron emission tomography (PET). Several types of dSiPM have been developed in recent years. Moreover, first imaging devices based on dSiPMs have been realized by various groups. This review summarizes the main dSiPM concepts and technologies currently under development, provides an overview of the results obtained recently with dSiPMs-based PET and SPECT devices, and presents a critical outlook on the challenges and chances for dSiPMs in future radiomolecular imaging systems