Development and Optimization of Four-dimensional Magnetic Resonance Imaging (4D-MRI) for Radiation Therapy

A tenet of modern radiotherapy (RT) is to identify the treatment target accurately, following which the high-dose treatment volume may be expanded into the surrounding tissues in order to create the clinical and planning target volumes. Respiratory motion can induce errors in target volume delineation and dose delivery in radiation therapy for thoracic and abdominal cancers. Historically, radiotherapy treatment planning in the thoracic and abdominal regions has used 2D or 3D images acquired under uncoached free-breathing conditions, irrespective of whether the target tumor is moving or not. Once the gross target volume has been delineated, standard margins are commonly added in order to account for motion. However, the generic margins do not usually take the target motion trajectory into consideration. That may lead to under- or over-estimate motion with subsequent risk of missing the target during treatment or irradiating excessive normal tissue. That introduces systematic errors into treatment planning and delivery. In clinical practice, four-dimensional (4D) imaging has been popular in For RT motion management. It provides temporal information about tumor and organ at risk motion, and it permits patient-specific treatment planning. The most common contemporary imaging technique for identifying tumor motion is 4D computed tomography (4D-CT). However, CT has poor soft tissue contrast and it induce ionizing radiation hazard. In the last decade, 4D magnetic resonance imaging (4D-MRI) has become an emerging tool to image respiratory motion, especially in the abdomen, because of the superior soft-tissue contrast. Recently, several 4D-MRI techniques have been proposed, including prospective and retrospective approaches. Nevertheless, 4D-MRI techniques are faced with several challenges: 1) suboptimal and inconsistent tumor contrast with large inter-patient variation; 2) relatively low temporal-spatial resolution; 3) it lacks a reliable respiratory surrogate. In this research work, novel 4D-MRI techniques applying MRI weightings that was not used in existing 4D-MRI techniques, including T2/T1-weighted, T2-weighted and Diffusion-weighted MRI were investigated. A result-driven phase retrospective sorting method was proposed, and it was applied to image space as well as k-space of MR imaging. Novel image-based respiratory surrogates were developed, improved and evaluated.

Comparison of two methods for measuring the pubococcygeal line from sagittal-plane magnetic resonance imaging

Aims The pubococcygeal line (PCL) is an important reference line for determining measures of pelvic organ support on sagittal-plane magnetic resonance imaging (MRI); however, there is no consensus on where to place the posterior point of the PCL. As coccyx movement produced during pelvic floor muscle (PFM) contractions may affect other measures, optimal placement of the posterior point is important. This study compared two methods for measuring the PCL, with different posterior points, on T2-weighted sagittal MRI to determine the effect of coccygeal movement on measures of pelvic organ support in older women. Methods MRI of the pelvis was performed in the midsagittal plane, at rest and during PFM contractions, on 47 community-dwelling women 60 and over. The first PCL was measured to the tip of the coccyx (PCLtip) and the second to the sacrococcygeal joint (PCLjnt). Four measures of pelvic organ support were made using each PCL as the reference line: urethrovesical junction height, uterovaginal junction height, M-line and levator plate angle. Results During the PFM contraction the PCLtip shortened and lifted (P < 0.001); the PCLjnt did not change (P > 0.05). The changes in the four measures of pelvic organ support were smaller when measured relative to the PCLtip as compared to those to the PCLjnt (P < 0.001). Conclusions Coccyx movement affected the length and position of the PCLtip, which resulted in underestimates of the pelvic-organ lift produced by the PFM contraction. Therefore, we recommend that the PCL be measured to the sacrococcygeal joint and not to the tip of the coccyx

Functional Magnetic Resonance Imaging Neurofeedback and Motor training for Parkinson’s Disease: Randomised Trial

Objective: Real-time functional magnetic resonance imaging (rt-fMRI) neurofeedback (NF) uses feedback of the patient’s own brain activity to self-regulate brain networks which in turn could lead to a change in behaviour and clinical symptoms. The objective was to determine the effect of neurofeedback and motor training and motor training (MOT) alone on motor and non-motor functions in Parkinson’s disease (PD) in a 10-week small Phase I randomised controlled trial. Methods: 30 patients with PD (Hoehn & Yahr I-III) and no significant comorbidity took part in the trial with random allocation to two groups. Group 1 (NF: 15 patients) received rt-fMRI-NF with motor training. Group 2 (MOT: 15 patients) received motor training alone. The primary outcome measure was the Movement Disorder Society – Unified Parkinson’s Disease Rating Scale-Motor scale (MDS-UPDRS-MS), administered pre- and post-intervention ‘off-medication’. The secondary outcome measures were the ‘on-medication’ MDS-UPDRS, the Parkinson’s disease Questionnaire-39, and quantitative motor assessments after 4 and 10 weeks. Results: Patients in the NF group were able to upregulate activity in the supplementary motor area by using motor imagery. They improved by an average of 4.5 points on the MDS-UPDRS-MS in the ‘off-medication’ state (95% confidence interval: -2.5 to -6.6), whereas the MOT group improved only by 1.9 points (95% confidence interval +3.2 to -6.8). However, the improvement did not differ significantly between the groups. No adverse events were reported in either group. Interpretation: This Phase I study suggests that NF combined with motor training is safe and improves motor symptoms immediately after treatment, but larger trials are needed to explore its superiority over active control conditions. Clinical Trial website : Unique Identifier: NCT01867827 URL: https://clinicaltrials.gov/ct2/show/NCT01867827?term=NCT01867827&rank=1

Real-time functional magnetic resonance imaging neurofeedback in motor neurorehabilitation

Purpose of review Recent developments in functional magnetic resonance imaging (fMRI) have catalyzed a new field of translational neuroscience. Using fMRI to monitor the aspects of task-related changes in neural activation or brain connectivity, investigators can offer feedback of simple or complex neural signals/patterns back to the participant on a quasireal-time basis [real-time-fMRI-based neurofeedback (rt-fMRI-NF)]. Here, we introduce some background methodology of the new developments in this field and give a perspective on how they may be used in neurorehabilitation in the future. Recent findings The development of rt-fMRI-NF has been used to promote self-regulation of activity in several brain regions and networks. In addition, and unlike other noninvasive techniques, rt-fMRI-NF can access specific subcortical regions and in principle any region that can be monitored using fMRI including the cerebellum, brainstem and spinal cord. In Parkinson’s disease and stroke, rt-fMRI-NF has been demonstrated to alter neural activity after the self-regulation training was completed and to modify specific behaviours. Summary Future exploitation of rt-fMRI-NF could be used to induce neuroplasticity in brain networks that are involved in certain neurological conditions. However, currently, the use of rt-fMRI-NF in randomized, controlled clinical trials is in its infancy.

Vibrational characteristics of brain magnetic resonance elastography

This thesis aims to investigate vibrational characteristics of magnetic resonance elastography (MRE) of the brain. MRE is a promising, non-invasive methodology for the mapping of shear stiffness of the brain. A mechanical actuator shakes the brain and generates shear waves, which are then imaged with a special MRI sequence sensitive to sub-millimeter displacements. This research focuses on exploring the profile of vibrations utilized in brain elastography from the standpoint of ultimately investigating nonlinear behavior of the tissue. The first objective seeks to demonstrate the effects of encoding off-frequency vibrations using standard MRE methodologies. Vibrations of this nature can arise from nonlinearities in the system and contaminate the results of the measurement. The second objective is to probe nonlinearity in the dynamic brain system using MRE. A non-parametric decomposition technique, novel to the MRE field, is introduced and investigated.

Tensor Completion for Multidimensional Inverse Problems with Applications to Magnetic Resonance Relaxometry

This thesis deals with tensor completion for the solution of multidimensional inverse problems. We study the problem of reconstructing an approximately low rank tensor from a small number of noisy linear measurements. New recovery guarantees, numerical algorithms, non-uniform sampling strategies, and parameter selection algorithms are developed. We derive a fixed point continuation algorithm for tensor completion and prove its convergence. A restricted isometry property (RIP) based tensor recovery guarantee is proved. Probabilistic recovery guarantees are obtained for sub-Gaussian measurement operators and for measurements obtained by non-uniform sampling from a Parseval tight frame. We show how tensor completion can be used to solve multidimensional inverse problems arising in NMR relaxometry. Algorithms are developed for regularization parameter selection, including accelerated k-fold cross-validation and generalized cross-validation. These methods are validated on experimental and simulated data. We also derive condition number estimates for nonnegative least squares problems. Tensor recovery promises to significantly accelerate N-dimensional NMR relaxometry and related experiments, enabling previously impractical experiments. Our methods could also be applied to other inverse problems arising in machine learning, image processing, signal processing, computer vision, and other fields.

Magnetic resonance spectroscopy. Data analysis for clinical applications

This text is taken from the postgraduate thesis, which one of the authors (A.B.) developed for the degree of Medical Physicist in the School on Medical Physics of the University of Florence. The text explores the feasibility of quantitative Magnetic Resonance Spectroscopy as a tool for daily clinical routine use. The results and analysis comes from two types of hyper spectral images: the first set are hyper spectral images coming from a standard phantom (reference images); and hyper spectral images obtained from a group of patients who have undergone MRI examinations at the Santa Maria Nuova Hospital. This interdisciplinary work stems from the IFAC-CNR know how in terms of data analysis and nanomedicine, and the clinical expertise of Radiologists and Medical Physicists. The results reported here, which were the subject of the thesis, are original, unpublished, and represent independent work.

Preoperative assessment of deep myometrial and cervical invasion in endometrial carcinoma: comparison of magnetic resonance imaging and histopathologic evaluation

This study aimed to evaluate the accuracy of magnetic resonance imaging (MRI) in the detection of deep myometrial invasion and cervical extension by endometrial carcinoma. This prospective study included 101 patients with histologically documented endometrial carcinoma, between July 1998 and April 2004. The findings of preoperative pelvic MRI were compared with histological diagnosis. From 101 cases studied by pelvic MRI, 43 were classified as deep myometrial invasion (50% of myometrium), where the pathological evaluation confirmed as having deep myometrial invasion. Cervical extension in the MRI study was found in 19 cases. Pathologic study found cervical extension and/or invasion in 31 cases including all cases identified by MRI. The accuracy, sensitivity and specificity of MRI were 95%, 89%, 100%, detecting deep myometrial invasion and 88%, 61%, 100%, detecting cervical invasion, respectively. The high accuracy achieved makes MRI an adequate method for determine the depth of myometrial and cervical invasion in endometrial carcinoma.

Comparison of two methods for measuring the pubococcygeal line from sagittal-plane magnetic resonance imaging

Aims The pubococcygeal line (PCL) is an important reference line for determining measures of pelvic organ support on sagittal-plane magnetic resonance imaging (MRI); however, there is no consensus on where to place the posterior point of the PCL. As coccyx movement produced during pelvic floor muscle (PFM) contractions may affect other measures, optimal placement of the posterior point is important. This study compared two methods for measuring the PCL, with different posterior points, on T2-weighted sagittal MRI to determine the effect of coccygeal movement on measures of pelvic organ support in older women. Methods MRI of the pelvis was performed in the midsagittal plane, at rest and during PFM contractions, on 47 community-dwelling women 60 and over. The first PCL was measured to the tip of the coccyx (PCLtip) and the second to the sacrococcygeal joint (PCLjnt). Four measures of pelvic organ support were made using each PCL as the reference line: urethrovesical junction height, uterovaginal junction height, M-line and levator plate angle. Results During the PFM contraction the PCLtip shortened and lifted (P < 0.001); the PCLjnt did not change (P > 0.05). The changes in the four measures of pelvic organ support were smaller when measured relative to the PCLtip as compared to those to the PCLjnt (P < 0.001). Conclusions Coccyx movement affected the length and position of the PCLtip, which resulted in underestimates of the pelvic-organ lift produced by the PFM contraction. Therefore, we recommend that the PCL be measured to the sacrococcygeal joint and not to the tip of the coccyx

Cerebral misery perfusion diagnosed using hypercapnic blood-oxygenation-level-dependent contrast functional magnetic resonance imaging: a case report

Introduction Cerebral misery perfusion represents a failure of cerebral autoregulation. It is animportant differential diagnosis in post-stroke patients presenting with collapses in the presence of haemodynamically significant cerebrovascular stenosis. This is particularly the case when cortical or internal watershed infarcts are present. When this condition occurs, further investigation should be done immediately. Case presentation A 50-year-old Caucasian man presented with a stroke secondary to complete occlusion of his left internal carotid artery. He went on to suffer recurrent seizures. Neuroimaging demonstrated numerous new watershed-territory cerebral infarcts. No source of arterial thromboembolism was demonstrable. Hypercapnic blood-oxygenation-level-dependent-contrast functional magnetic resonance imaging was used to measure his cerebrovascular reserve capacity. The findings were suggestive of cerebral misery perfusion. Conclusions Blood-oxygenation-level-dependent-contrast functional magnetic resonance imaging allows the inference of cerebral misery perfusion. This procedure is cheaper and more readily available than positron emission tomography imaging, which is the current gold standard diagnostic test. The most evaluated treatment for cerebral misery perfusion is extracranial-intracranial bypass. Although previous trials of this have been unfavourable, the results of new studies involving extracranial-intracranial bypass in high-risk patients identified during cerebral perfusion imaging are awaited. Cerebral misery perfusion is an important and under-recognized condition in which emerging imaging and treatment modalities present the possibility of practical and evidence-based management in the near future. Physicians should thus be aware of this disorder and of recent developments in diagnostic tests that allow its detection.

Nuclear Magnetic Resonance Spectroscopic and Computational Investigations of Chloroperoxidase Catalyzed Regio- and Enantio-Selective Transformations

Chloroperoxidase (CPO) is the most versatile heme-containing enzyme that catalyzes a broad spectrum of reactions. The remarkable feature of this enzyme is the high regio- and enantio-selectivity exhibited in CPO-catalyzed oxidation reactions. The aim of this dissertation is to elucidate the structural basis for regio- and enantio-selective transformations and investigate the application of CPO in biodegradation of synthetic dyes. To unravel the mechanism of CPO-catalyzed regioselective oxidation of indole, the dissertation explored the structure of CPO-indole complex using paramagnetic relaxation and molecular modeling. The distances between the protons of indole and the heme iron revealed that the pyrrole ring of indole is oriented toward the heme with its 2-H pointing directly at the heme iron. This provides the first experimental and theoretical explanation for the "unexpected" regioselectivity of CPO-catalyzed indole oxidation. Furthermore, the residues including Leu 70, Phe 103, Ile 179, Val 182, Glu 183, and Phe 186 were found essential to the substrate binding to CPO. These results will serve as a lighthouse in guiding the design of CPO mutants with tailor-made activities for biotechnological applications. To understand the origin of the enantioselectivity of CPO-catalyzed oxidation reactions, the interactions of CPO with substrates such as 2-(methylthio)thiophene were investigated by nuclear magnetic resonance spectroscopy (NMR) and computational techniques. In particular, the enantioselectivity is partly explained by the binding orientation of substrates. In third facet of this dissertation, a green and efficient system for degradation of synthetic dyes was developed. Several commercial dyes such as orange G were tested in the CPO-H2O2-Cl- system, where degradation of these dyes was found very efficient. The presence of halide ions and acidic pH were found necessary to the decomposition of dyes. Significantly, the results revealed that this degradation of azo dyes involves a ferric hypochlorite intermediate of CPO (Fe-OCl), compound X.

Optimization of Wireless Power Transfer via Magnetic Resonance in Different Media

A wide range of non-destructive testing (NDT) methods for the monitoring the health of concrete structure has been studied for several years. The recent rapid evolution of wireless sensor network (WSN) technologies has resulted in the development of sensing elements that can be embedded in concrete, to monitor the health of infrastructure, collect and report valuable related data. The monitoring system can potentially decrease the high installation time and reduce maintenance cost associated with wired monitoring systems. The monitoring sensors need to operate for a long period of time, but sensors batteries have a finite life span. Hence, novel wireless powering methods must be devised. The optimization of wireless power transfer via Strongly Coupled Magnetic Resonance (SCMR) to sensors embedded in concrete is studied here. First, we analytically derive the optimal geometric parameters for transmission of power in the air. This specifically leads to the identification of the local and global optimization parameters and conditions, it was validated through electromagnetic simulations. Second, the optimum conditions were employed in the model for propagation of energy through plain and reinforced concrete at different humidity conditions, and frequencies with extended Debye's model. This analysis leads to the conclusion that SCMR can be used to efficiently power sensors in plain and reinforced concrete at different humidity levels and depth, also validated through electromagnetic simulations. The optimization of wireless power transmission via SMCR to Wearable and Implantable Medical Device (WIMD) are also explored. The optimum conditions from the analytics were used in the model for propagation of energy through different human tissues. This analysis shows that SCMR can be used to efficiently transfer power to sensors in human tissue without overheating through electromagnetic simulations, as excessive power might result in overheating of the tissue. Standard SCMR is sensitive to misalignment; both 2-loops and 3-loops SCMR with misalignment-insensitive performances are presented. The power transfer efficiencies above 50% was achieved over the complete misalignment range of 0°-90° and dramatically better than typical SCMR with efficiencies less than 10% in extreme misalignment topologies.

The foodomics approach to investigate the impact of the matrix structure on food quality: applications of magnetic resonance spectroscopy, relaxometry and imaging

The aim of this thesis is to explore the possible influence of the food matrix on food quality attributes. Using nuclear magnetic resonance techniques, the matrix-dependent properties of different foods were studied and some useful indices were defined to classify food products based on the matrix behaviour when responding to processing phenomena. Correlations were found between fish freshness indices, assessed by certain geometric parameters linked to the morphology of the animal, i.e. a macroscopic structure, and the degradation of the product structure. The same foodomics approach was also applied to explore the protective effect of modified atmospheres on the stability of fish fillets, which are typically susceptible to oxidation of the polyunsaturated fatty acids incorporated in the meat matrix. Here, freshness is assessed by evaluating the time-dependent change in the fish metabolome, providing an established freshness index, and its relationship to lipid oxidation. In vitro digestion studies, focusing on food products with different matrixes, alone and in combination with other meal components (e.g. seasoning), were conducted to investigate possible interactions between enzymes and food, modulated by matrix structure, which influence digestibility. The interaction between water and the gelatinous matrix of the food, consisting of a network of protein gels incorporating fat droplets, was also studied by means of nuclear magnetic relaxometry, in order to create a prediction tool for the correct classification of authentic and counterfeit food products protected by a quality label. This is one of the first applications of an NMR method focusing on the supramolecular structure of the matrix, rather than the chemical composition, to assess food authenticity. The effect of innovative processing technologies, such as PEF applied to fruit products, has been assessed by magnetic resonance imaging, exploiting information associated with the rehydration kinetics exerted by a modified food structure.