Parallelization and improvement of beamforming process in synthetic aperture systems for real-time ultrasonic image generation

Tesis inédita de la Universidad Complutense de Madrid, Facultad de Informática, Departamento de Arquitectura de Computadores y Automática, leída el 9-02-2016La ecografía es hoy en día uno de los métodos de visualización más populares para examinar el interior de cuerpos opacos. Su aplicación es especialmente significativa tanto en el campo del diagnóstico médico como en las aplicaciones de evaluación no destructiva en el ámbito industrial, donde se evalúa la integridad de un componente o una estructura. El desarrollo de sistemas ecográficos de alta calidad y con buenas prestaciones se basa en el empleo de sistemas multisensoriales conocidos como arrays que pueden estar compuestos por varias decenas de elementos. El desarrollo de estos dispositivos tiene asociada una elevada complejidad, tanto por el número de sensores y la electrónica necesaria para la adquisición paralela de señales, como por la etapa de procesamiento de los datos adquiridos que debe operar en tiempo real. Esta etapa de procesamiento de señal trabaja con un elevado flujo de datos en paralelo y desarrolla, además de la composición de imagen, otras sofisticadas técnicas de medidas sobre los datos (medida de elasticidad, flujo, etc). En este sentido, el desarrollo de nuevos sistemas de imagen con mayores prestaciones (resolución, rango dinámico, imagen 3D, etc) está fuertemente limitado por el número de canales en la apertura del array. Mientras algunos estudios se han centrado en la reducción activa de sensores (sparse arrays como ejemplo), otros se han centrado en analizar diferentes estrategias de adquisiciónn que, operando con un número reducido de canales electrónicos en paralelo, sean capaz por multiplexación emular el funcionamiento de una apertura plena. A estas últimas técnicas se las agrupa mediante el concepto de Técnicas de Apertura Sintética (SAFT). Su interés radica en que no solo son capaces de reducir los requerimientos hardware del sistema (bajo consumo, portabilidad, coste, etc) sino que además permiten dentro de cierto compromiso la mejora de la calidad de imagen respecto a los sistemas convencionales...Ultrasound is nowadays one of the most popular visualization methods to examine the interior of opaque objects. Its application is particularly significant in the field of medical diagnosis as well as non-destructive evaluation applications in industry. The development of high performance ultrasound imaging systems is based on the use of multisensory systems known as arrays, which may be composed by dozens of elements. The development of these devices has associated a high complexity, due to the number of sensors and electronics needed for the parallel acquisition of signals, and for the processing stage of the acquired data which must operate on real-time. This signal processing stage works with a high data flow in parallel and develops, besides the image composition, other sophisticated measure techniques (measure of elasticity, flow, etc). In this sense, the development of new imaging systems with higher performance (resolution, dynamic range, 3D imaging, etc) is strongly limited by the number of channels in array’s aperture. While some studies have been focused on the reduction of active sensors (i.e. sparse arrays), others have been centered on analysing different acquisition strategies which, operating with reduced number of electronic channels in parallel, are able to emulate by multiplexing the behavior of a full aperture. These latest techniques are grouped under the term known as Synthetic Aperture Techniques (SAFT). Their interest is that they are able to reduce hardware requirements (low power, portability, cost, etc) and also allow to improve the image quality over conventional systems...Depto. de Arquitectura de Computadores y AutomáticaFac. de InformáticaTRUEunpu

Obtención de distancias y posiciones geográficas mediante técnicas de visión artificial

El objetivo de este proyecto ha sido utilizar técnicas de Visión por Computador para desarrollar un sistema capaz de medir distancias a objetos móviles. Para ello, el trabajo se centra en dos de ellas: la visión estereoscopica o binocular (el enfoque clásico) y la visión monocular o metrología. Por tanto, se han desarrollado en primer lugar, algoritmos de identificación de objetos capaces de procesar y extraer aquellas regiones (conocidas como blobs) de la imagen que son de interés. Una vez, conocemos la posición del objeto en la imagen, se calcula por ambos métodos la distancia a la que se encuentra, y además se realiza una conversión a coordenadas geográficas. Por último, se ha analizado la robustez y fiabilidad del sistema en ambas variantes, la precisión de los resultados obtenidos así como el impacto de las condiciones de luz en las distintas situaciones de emsayo. [ABSTRACT] The aim of this project has been using Computer Vision techniques to develop a system capable of calculating measures distances to objets. To this end, this paper focuses on two of them: the stereoscopic or binocular vision (the traditional approach) and the monocular vision or metrology. Therefore, we have developed identification algorithms of objects capable of processing and extracting those regions (Known as blobs) of the image that are of our interest.Once we know exactly the position of rhe object in the image, it is calculated by both methods the distance where it is, and we also do a conversion to geographical coordinates. Finally, it has analyzed the robustness and reliability of the system in the two cases, precision of the results and the impact of rhe lighting conditions in different situations

Uso de hardware gráfico para la aceleración de métodos algebraicos de recontrucción

El objetivo de este proyecto ha sido implementar un algoritmo de reconstrucción algebraica (en paricular SART, Simultaneous Algebraic Reconstruction Technique) y acelerar su ejecución utilizando los recursos paralelos que ponen a disosición del programador las unidades de procesamiento gráfico de hoy en día. Para ello, primero se han desarrollado dos variantes del algoritmo que sólo utilizan la CPU, en las que nos hemos basado para posteriormente portar a la GPU las partes susceptibles de obtener una mejora substancial de velocidad. Por último, se ha analizado en ambas variantes la calidad de la reconstrucciones y el spedup obtenido respecto a las implementaciones en CPU, así como el impacto en la calidad de los diversos parámetros configurables del algoritmo. [ABSTRACT] The aim of our project has been the implementation of an algebraic reconstrution algorithm (known as SART, Simultaneous Algebraic Reconstruction Technique) and improvement of its running time by making use of the massively parallel computational resources which today's graphics processing units provide the programmer with. To this end, two variants of the algorithm have first been developed which are executed entirely on the CPU, and upon whch we have based our subsequent porting to the GPU of those parts having the potencial to enjoy a subsancial increase in speed. Finally, the quality of both variants' reconstructions has been analyzed, along with the speedup obtained over CPU implementations and the impact that various customizable parameters of the algorithm have on image quality

Diseño e implementación de un sistema de imagen ultrasonica 3D

8 páginas. 4 figuras. 1 Tabla -- PACS: 43.35.Zc. -- Comunicación presentada en: 44º Congreso Español de Acústica - TecniAcustica 2013. Encuentro Ibérico de Acústica. EAA European Symposium on Environmental Acoustics and Noise Mapping, Valladolid, 1 - 4, Octubre, 2013[EN] In this paper the design process of an ultrasonic volumetric imaging system based on synthetic aperture focusing technique is presented. Based on minimum redundancy coarray of 2D aperture an d parallel processing techniques for beamforming an experimental system is developed to operate with a 2D array (3Mhz and 11x11 elements).[ES] Este trabajo describe el proceso de diseño e implementación de un sistema de imagen ultrasónica basado en la composición del coarray de mínima redundancia para aperturas 2D. Esta técnica de adquisición en combinación con la generación de imagen por apertura sintética, implementada por GPGPU, permite diseñar un sistema de imagen 3D con un número reducido de recursos. Se presentan resultados experimentales del sistema implementado sobre un equipo de imagen ultrasónica convencional para una apertura bidimensional de 3Mhz y 11x11 elementos.Este trabajo está financiado por el Gobierno de España a partir del Plan Nacional de I+D+i dentro del marco del proyecto DPI2010-19376.Peer reviewe

Value of Early Circulating Tumor Cells Dynamics to Estimate Docetaxel Benefit in Metastatic Castration-Resistant Prostate Cancer (mCRPC) Patients

Biomarcadores; Células tumorales circulantes; DocetaxelBiomarkers; Circulating tumor cells; DocetaxelBiomarcadors; Cèl·lules tumorals circulants; DocetaxelCirculating tumor cell (CTC) enumeration and changes following treatment have been demonstrated to be superior to PSA response in determining mCRPC outcome in patients receiving AR signaling inhibitors but not taxanes. We carried out a pooled analysis of two prospective studies in mCRPC patients treated with docetaxel. CTCs were measured at baseline and 3–6 weeks post treatment initiation. Cox regression models were constructed to compare 6-month radiographical progression-free survival (rPFS), CTCs and PSA changes predicting outcome. Among the subjects, 80 and 52 patients had evaluable baseline and post-treatment CTC counts, respectively. A significant association of higher baseline CTC count with worse overall survival (OS), PFS and time to PSA progression (TTPP) was observed. While CTC response at 3–6 weeks (CTC conversion (from ≥5 to <5 CTCs), CTC30 (≥30% decline in CTC) or CTC0 (decline to 0 CTC)) and 6-month rPFS were significantly associated with OS (all p < 0.005), the association was not significant for PSA30 or PSA50 response. CTC and PSA response were discordant in over 50% of cases, with outcome driven by CTC response in these patients. The c-index values for OS were superior for early CTC changes compared to PSA response endpoints, and similar to 6-month rPFS. Early CTC declines were good predictors of improved outcomes in mCRPC patients treated with docetaxel in this small study, offering a superior and/or earlier estimation of docetaxel benefit in comparison to PSA or rPFS that merits further confirmation in larger studies.The results reported here were generated as part of two academic studies supported by various grants. The funding sources had no role in study design, data analysis, data interpretation or writing of the report. R.L., D.L. and D.O. had full access to all of the data and had final responsibility for the decision to submit for publication. This project represents independent research supported by the National Institute for Health Research (NIHR) Biomedical Research Centre at The Royal Marsden NHS Foundation Trust and the Institute of Cancer Research, London. The views expressed are those of the author(s) and not necessarily those of the NIHR or the Department of Health and Social Care

Cheetah: A Library for Parallel Ultrasound Beamforming in Multi -Core Systems

6 páginas, 2 figuras, 4 tablasDeveloping new imaging methods needs to establish some proofs of concept before implementing them on real -time scenarios. Nowadays, the high computational power reached by multi-core CPUs and GPUs have driven the development of software-based beamformers. Taking this into account, a library for the fast generation of ultrasound images is presented. It is based on Synthetic Aperture Imaging Techniques (SAFT) and it is fast because of the use of parallel computing techniques. Any kind of transducers as well as SAFT techniques can be defined although it includes some pre-built SAFT methods like 2R -SAFT and TFM. Furthermore, 2D and 3D imaging (slicebased or full volume computation) is supported along with the ability to generate both rectangular and angular images. For interpolation, linear and polynomial schemes can be chosen. The versatility of the library is ensured by interfacing it to Matlab, Python and any programming language over different operating systems. On a standard PC equipped with a single NVIDIA Quadro 4000 (256 cores), the library is able to calculate 262,144 pixels in ≈ 105 ms using a linear transducer with 64 elements, and 2,097,152 voxels in ≈ 5 seconds using a matrix transducer with 121 elements when TFM is applied.This work has been supported by the Spanish Government and the University of Alcalá under projects DPI2010- 19376 and CCG2014/EXP -084, respectively.Peer reviewe

Development of an ultrasonic dry-coupling inspection wheel for Online NDI composite application

8 páginas, 5 figuras. 6th International Symposium on NDT in Aerospace, 12-14th November 2014, Madrid, SpainT he application of ultrasonic waves to the inspection of aeronautic compone nts is based on the use of couplants (water, gel, etc...) to facilitate the propagation of the sensi ng wave through the material. Although several solutions have been designed to integrate the use of these couplants and the NDT operations in different stages of component life (from production to in-service operation) its use incre ases the complexity of the process and the cost of the inspection because in some cases special infrastr uctures may become necessary. Some of the research effort developed in the last decades has been a ddressed to reduce the necessity of couplant gel or fluids. In this sense, the development of ultrasonic inspection w heels based on special rubbers with a high degree of humidity has been proposed and is being commercialized nowadays. How ever, its use is not allowed in applications where the condition of completely dry coupling is imperative. Other tools based on air-coupling have been also developed but they mainly operate in through transmission arrange ments and its use is limited to low frequencies. T his work examines a new wheel-based tool which can operate in dry condit ion . It has been developed in the context of the ICARO Project (Innovación en Composites Avanzados y Rear- End Optimizado) to provide a nondestructive inspection solution to be integrated into an Out of Autoclave ( OoA) composite manufacturing process based on electron beam curing technology layer by layer. T he solution requires be able to inspect very thin composite specimens (from 0.5mm) in clean and dry conditions compatibl e with the manufacturing process. T o overcome these conditions, a special inspection wheel prototype has bee n developed that integrates a 5MHz ultrasonic array transducer composed by 128 elements mounted in a particula r wedge. T his aperture operates in pulse-echo and generates an ultrasonic image based on linear scanning beam forming process and a synthetic aperture acquisition procedure known as 2R-SAFT . Inspection results obtained from reference standard of different thic kness are presented. T hese results are compared with conventional immersion UT inspections and show the high potentia l of this inspection wheel for this special applications.Peer reviewe

Prognostic Score and Benefit from Abiraterone in First-line Metastatic, Castration-resistant Prostate Cancer.

Most available prognostic nomograms in metastatic castration-resistant prostate cancer (mCRPC) are derived from datasets not representative of the current treatment landscape. A prognostic nomogram for first-line mCRPC treatment was developed from patients treated in the PREVAIL study. To validate the Armstrong model in the COU-AA-302 trial. A post hoc analysis of mCRPC patients treated in the COU-AA-302 trial was carried out (NCT00887198). The Armstrong prognostic model was applied to patients treated in COU-AA-302. A continuous risk score was derived from coefficients from the original model. Time-dependent area under the curve (tAUC) was used to evaluate the overall predictive ability of the model. Patients were categorized according to the number of risk factors present into those at a low (three or fewer risk factors), intermediate (four to six risk factors), and high (seven to ten risk factors) risk. The association with survival was assessed with Cox regression models. Interaction tests were used to assess the impact of treatment arm in each of the prognostic groups. A total of 1088 patients were analyzed. The risk score was associated with overall survival (OS; tAUC 0.733). Most patients were at a low (49%) or intermediate (41%) risk. Risk category was significantly associated with OS (hazard ratio [HR]: 2.3; 95% confidence interval [CI]: 1.9-2.4; p < 0.001), radiographic progression-free survival (rPFS; HR: 1.7; 95% CI: 1.5-1.8; p < 0.001), and prostate-specific antigen progression-free survival (HR: 1.7; 95% CI: 1.5-1.9; p < 0.001). A significant interaction between risk group and OS (p = 0.007) and rPFS (p = 0.009) was observed. Survival was superior in low-risk patients (HR: 0.73; 95% CI: 0.59-0.89; p = 0.009), but similar in intermediate-risk (HR: 0.97; 95% CI: 0.79-1.21; p = 0.9) and high-risk (HR: 1.35; 95% CI: 0.80-2.28; p = 0.5) patients. Two-year OS rates in abiraterone versus placebo were 82% versus 74% in low-risk, 55% versus 52% in intermediate-risk, and 28% versus 31% in high-risk patients. We validate the prognostic value of the Armstrong risk model in patients treated with first-line androgen receptor signaling inhibitors. Abiraterone provided a greater benefit in low-risk patients with less aggressive disease. Further research is needed to establish the role of Armstrong risk groups for treatment selection in mCRPC patients. In this report, we validated the Armstrong nomogram in the COU-AA-302 trial population. We found a similar prognostic performance to that of the original model. Good-risk patients received the greatest benefit from abiraterone.Authors acknowledge funding support from Ministerio de Economía y Competitividad de España -Instituto de Salud Carlos III: grants CM17-00221 (Rebeca Lozano), CM19/00234 (Casilda Llacer), JR17/00007 (Nuria Romero-Laorden), and JR18/00011 (Elena Castro); Ministerio de Ciencia e Innovación: RYC-2015-18625 (David Olmos); and Prostate Cancer Foundation: Young Investi-gator Award (2014 David Olmos, 2017 Elena Castro).S

Clonal chromosomal mosaicism and loss of chromosome Y in elderly men increase vulnerability for SARS-CoV-2

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) had an estimated overall case fatality ratio of 1.38% (pre-vaccination), being 53% higher in males and increasing exponentially with age. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, we found 133 cases (1.42%) with detectable clonal mosaicism for chromosome alterations (mCA) and 226 males (5.08%) with acquired loss of chromosome Y (LOY). Individuals with clonal mosaic events (mCA and/or LOY) showed a 54% increase in the risk of COVID-19 lethality. LOY is associated with transcriptomic biomarkers of immune dysfunction, pro-coagulation activity and cardiovascular risk. Interferon-induced genes involved in the initial immune response to SARS-CoV-2 are also down-regulated in LOY. Thus, mCA and LOY underlie at least part of the sex-biased severity and mortality of COVID-19 in aging patients. Given its potential therapeutic and prognostic relevance, evaluation of clonal mosaicism should be implemented as biomarker of COVID-19 severity in elderly people. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, individuals with clonal mosaic events (clonal mosaicism for chromosome alterations and/or loss of chromosome Y) showed an increased risk of COVID-19 lethality

Genetic modifiers of radon-induced lung cancer risk: a genome-wide interaction study in former uranium miners

PURPOSE: Radon is a risk factor for lung cancer and uranium miners are more exposed than the general population. A genome-wide interaction analysis was carried out to identify genomic loci, genes or gene sets that modify the susceptibility to lung cancer given occupational exposure to the radioactive gas radon. METHODS: Samples from 28 studies provided by the International Lung Cancer Consortium were pooled with samples of former uranium miners collected by the German Federal Office of Radiation Protection. In total, 15,077 cases and 13,522 controls, all of European ancestries, comprising 463 uranium miners were compared. The DNA of all participants was genotyped with the OncoArray. We fitted single-marker and in multi-marker models and performed an exploratory gene-set analysis to detect cumulative enrichment of significance in sets of genes. RESULTS: We discovered a genome-wide significant interaction of the marker rs12440014 within the gene CHRNB4 (OR = 0.26, 95% CI 0.11-0.60, p = 0.0386 corrected for multiple testing). At least suggestive significant interaction of linkage disequilibrium blocks was observed at the chromosomal regions 18q21.23 (p = 1.2 × 10-6), 5q23.2 (p = 2.5 × 10-6), 1q21.3 (p = 3.2 × 10-6), 10p13 (p = 1.3 × 10-5) and 12p12.1 (p = 7.1 × 10-5). Genes belonging to the Gene Ontology term "DNA dealkylation involved in DNA repair" (GO:0006307; p = 0.0139) or the gene family HGNC:476 "microRNAs" (p = 0.0159) were enriched with LD-blockwise significance. CONCLUSION: The well-established association of the genomic region 15q25 to lung cancer might be influenced by exposure to radon among uranium miners. Furthermore, lung cancer susceptibility is related to the functional capability of DNA damage signaling via ubiquitination processes and repair of radiation-induced double-strand breaks by the single-strand annealing mechanism