Juan David García

Characterization of electron contamination in megavoltage photon beams

The purpose of the present study is to characterize electron contamination in photon beams in different clinical situations. Variations with field size, beam modifier (tray, shaping block) and source-surface distance (SSD) were studied. Percentage depth dose measurements with and without a purging magnet and replacing the air by helium were performed to identify the two electron sources that are clearly differentiated: air and treatment head. Previous analytical methods were used to fit the measured data, exploring the validity of these models. Electrons generated in the treatment head are more energetic and more important for larger field sizes, shorter SSD, and greater depths. This difference is much more noticeable for the 18 MV beam than for the 6 MV beam. If a tray is used as beam modifier, electron contamination increases, but the energy of these electrons is similar to that of electrons coming from the treatment head. Electron contamination could be fitted to a modified exponential curve. For machine modeling in a treatment planning system, setting SSD at 90 cm for input data could reduce errors for most isocentric treatments, because they will be delivered for SSD ranging from 80 to 100 cm. For very small field sizes, air-generated electrons must be considered independently, because of their different energetic spectrum and dosimetric influence.

Automatic segmentation of right ventricle in cardiac cine MR images using a saliency analysis

PURPOSE Accurate measurement of the right ventricle (RV) volume is important for the assessment of the ventricular function and a biomarker of the progression of any cardiovascular disease. However, the high RV variability makes difficult a proper delineation of the myocardium wall. This paper introduces a new automatic method for segmenting the RV volume from short axis cardiac magnetic resonance (MR) images by a salient analysis of temporal and spatial observations. METHODS The RV volume estimation starts by localizing the heart as the region with the most coherent motion during the cardiac cycle. Afterward, the ventricular chambers are identified at the basal level using the isodata algorithm, the right ventricle extracted, and its centroid computed. A series of radial intensity profiles, traced from this centroid, is used to search a salient intensity pattern that models the inner-outer myocardium boundary. This process is iteratively applied toward the apex, using the segmentation of the previous slice as a regularizer. The consecutive 2D segmentations are added together to obtain the final RV endocardium volume that serves to estimate also the epicardium. RESULTS Experiments performed with a public dataset, provided by the RV segmentation challenge in cardiac MRI, demonstrated that this method is highly competitive with respect to the state of the art, obtaining a Dice score of 0.87, and a Hausdorff distance of 7.26 mm while a whole volume was segmented in about 3 s. CONCLUSIONS The proposed method provides an useful delineation of the RV shape using only the spatial and temporal information of the cine MR images. This methodology may be used by the expert to achieve cardiac indicators of the right ventricle function.

Improvement of Bragg peak shift estimation using dimensionality reduction techniques and predictive linear modeling.

With the emergence of clinical prototypes and first patient acquisitions for proton therapy, the research on prompt gamma imaging is aiming at making most use of the prompt gamma data for in vivo estimation of any shift from expected Bragg peak (BP). The simple problem of matching the measured prompt gamma profile of each pencil beam with a reference simulation from the treatment plan is actually made complex by uncertainties which can translate into distortions during treatment. We will illustrate this challenge and demonstrate the robustness of a predictive linear model we proposed for BP shift estimation based on principal component analysis (PCA) method. It considered the first clinical knife-edge slit camera design in use with anthropomorphic phantom CT data. Particularly, 4115 error scenarios were simulated for the learning model. PCA was applied to the training input randomly chosen from 500 scenarios for eliminating data collinearities. A total variance of 99.95% was used for representing the testing input from 3615 scenarios. This model improved the BP shift estimation by an average of 63±19% in a range between -2.5% and 86%, comparing to our previous profile shift (PS) method. The robustness of our method was demonstrated by a comparative study conducted by applying 1000 times Poisson noise to each profile. 67% cases obtained by the learning model had lower prediction errors than those obtained by PS method. The estimation accuracy ranged between 0.31 ± 0.22 mm and 1.84 ± 8.98 mm for the learning model, while for PS method it ranged between 0.3 ± 0.25 mm and 20.71 ± 8.38 mm.

Acute effect of Vagus nerve stimulation parameters on cardiac chronotropic, inotropic, and dromotropic responses.

Vagus nerve stimulation (VNS) is an established therapy for drug-resistant epilepsy and depression, and is considered as a potential therapy for other pathologies, including Heart Failure (HF) or inflammatory diseases. In the case of HF, several experimental studies on animals have shown an improvement in the cardiac function and a reverse remodeling of the cardiac cavity when VNS is applied. However, recent clinical trials have not been able to reproduce the same response in humans. One of the hypothesis to explain this lack of response is related to the way in which stimulation parameters are defined. The combined effect of VNS parameters is still poorly-known, especially in the case of VNS synchronously delivered with cardiac activity. In this paper, we propose a methodology to analyze the acute cardiovascular effects of VNS parameters individually, as well as their interactive effects. A Latin hypercube sampling method was applied to design a uniform experimental plan. Data gathered from this experimental plan was used to produce a Gaussian process regression (GPR) model in order to estimate unobserved VNS sequences. Finally, a Morris screening sensitivity analysis method was applied to each obtained GPR model. Results highlight dominant effects of pulse current, pulse width and number of pulses over frequency and delay and, more importantly, the degree of interactions between these parameters on the most important acute cardiovascular responses. In particular, high interacting effects between current and pulse width were found. Similar sensitivity profiles were observed for chronotropic, dromotropic and inotropic effects. These findings are of primary importance for the future development of closed-loop, personalized neuromodulator technologies.

Detection of the default mode network by an anisotropic analysis.

This document presents a proposal devoted to improve the detection of the default mode network (DMN) in resting state functional magnetic resonance imaging in noisy conditions caused by head movement. The proposed approach is inspired by the hierarchical treatment of information, in particular at the level of the brain basal ganglia. Essentially, the fact that information must be selected and reduced suggests propagation of information in the Central Nervous System (CNS) is anisotropic. Under this hypothesis, the reconstruction of information of activation should follow an anisotropic pattern. In this work, an anisotropic filter is used to recover the DMN that is perturbed by simulated motion artifacts. Results obtained show this approach outperforms the state-of-the-art methods by 5.93% PSNR.

Semantic knowledge for histopathological image analysis: from ontologies to processing portals and deep learning.

This article presents our vision about the next generation of challenges in computational/digital pathology. The key role of the domain ontology, developed in a sustainable manner (i.e. using reference checklists and protocols, as the living semantic repositories), opens the way to effective/sustainable traceability and relevance feedback concerning the use of existing machine learning algorithms, proven to be very performant in the latest digital pathology challenges (i.e. convolutional neural networks). Being able to work in an accessible web-service environment, with strictly controlled issues regarding intellectual property (image and data processing/analysis algorithms) and medical data/image confidentiality is essential for the future. Among the web-services involved in the proposed approach, the living yellow pages in the area of computational pathology seems to be very important in order to reach an operational awareness, validation, and feasibility. This represents a very promising way to go to the next generation of tools, able to bring more guidance to the computer scientists and confidence to the pathologists, towards an effective/efficient daily use. Besides, a consistent feedback and insights will be more likely to emerge in the near future - from these sophisticated machine learning tools - back to the pathologists--, strengthening, therefore, the interaction between the different actors of a sustainable biomedical ecosystem (patients, clinicians, biologists, engineers, scientists etc.). Beside going digital/computational - with virtual slide technology demanding new workflows--, Pathology must prepare for another coming revolution: semantic web technologies now enable the knowledge of experts to be stored in databases, shared through the Internet, and accessible by machines. Traceability, disambiguation of reports, quality monitoring, interoperability between health centers are some of the associated benefits that pathologists were seeking. However, major changes are also to be expected for the relation of human diagnosis to machine based procedures. Improving on a former imaging platform which used a local knowledge base and a reasoning engine to combine image processing modules into higher level tasks, we propose a framework where different actors of the histopathology imaging world can cooperate using web services - exchanging knowledge as well as imaging services - and where the results of such collaborations on diagnostic related tasks can be evaluated in international challenges such as those recently organized for mitosis detection, nuclear atypia, or tissue architecture in the context of cancer grading. This framework is likely to offer an effective context-guidance and traceability to Deep Learning approaches, with an interesting promising perspective given by the multi-task learning (MTL) paradigm, distinguished by its applicability to several different learning algorithms, its non- reliance on specialized architectures and the promising results demonstrated, in particular towards the problem of weak supervision--, an issue found when direct links from pathology terms in reports to corresponding regions within images are missing.

Supporting the potential of quantitative ultrasonic techniques for the evaluation of platelet concentration.

This article describes the results obtained by making use of a non-destructive, non-invasive ultrasonic system for the acoustic characterization of bovine plasma rich in platelets using digital signal processing techniques. This study includes computational methods based on acoustic spectrometry estimation and experimental measurements of the speed of sound in blood plasma from different samples analyzed, using an ultrasonic field with resonance frequency of 5 MHz. The results showed that the measurements on ultrasonic signals can contribute to the hematological predictions based on the linear regression model applied to the relationship between experimental ultrasonic parameters calculated and platelet concentration, indicating a growth rate of 1 m/s for each 0.90 x103 platelet per mm3. On the other hand, the attenuation coefficient presented changes of 20% in the platelet concentration using a resolution of 0.057 dB/cm MHz.

Analysis of sEMG signals using discrete wavelet transform for muscle fatigue detection.

The purpose of the present article is to characterize sEMG signals to determine muscular fatigue levels. To do this, the signal is decomposed using the discrete wavelet transform, which offers noise filtering features, simplicity and efficiency. sEMG signals on the forearm were acquired and analyzed during the execution of cyclic muscular contractions in the presence and absence of fatigue. When the muscle fatigues, the sEMG signal shows a more erratic behavior of the signal as more energy is required to maintain the effort levels.

Statistical shape (ASM) and appearance (AAM) models for the segmentation of the cerebellum in fetal ultrasound.

The cerebellum is an important structure to determine the gestational age of the fetus, moreover most of the abnormalities it presents are related to growth disorders. In this work, we present the results of the segmentation of the fetal cerebellum applying statistical shape and appearance models. Both models were tested on ultrasound images of the fetal brain taken from 23 pregnant women, between 18 and 24 gestational weeks. The accuracy results obtained on 11 ultrasound images show a mean Hausdorff distance of 6.08 mm between the manual segmentation and the segmentation using active shape model, and a mean Hausdorff distance of 7.54 mm between the manual segmentation and the segmentation using active appearance model. The reported results demonstrate that the active shape model is more robust in the segmentation of the fetal cerebellum in ultrasound images.

Characterizing brain patterns in conversion from mild cognitive impairment (MCI) to Alzheimer's disease.

Structural Magnetic Resonance (MR) brain images should provide quantitative information about the stage and progression of Alzheimer’s disease. However, the use of MRI is limited and practically reduced to corroborate a diagnosis already performed with neuropsychological tools. This paper presents an automated strategy for extraction of relevant anatomic patterns related with the conversion from mild cognitive impairment (MCI) to Alzheimer’s disease (AD) using T1-weighted MR images. The process starts by representing each of the possible classes with models generated from a linear combination of volumes. The difference between models allows us to establish which are the regions where relevant patterns might be located. The approach searches patterns in a space of brain sulci, herein approximated by the most representative gradients found in regions of interest defined by the difference between the linear models. This hypothesis is assessed by training a conventional SVM model with the found relevant patterns under a leave-one-out scheme. The resultant AUC was 0.86 for the group of women and 0.61 for the group of men.