Convolution-based free-form deformation for multimodal groupwise registration

Producción CientíficaRecently, an efficient implementation of convolution-based free form deformations (FFD) has been proposed for both groupwise 3D monomodal and 2D pairwise multimodal registrations. However, there is still an unmet need in the field for groupwise -D multimodal registration with L > 2. In this correspondence, we address this need and present a solution for achieving accurate registration using two popular metrics: Renyi entropy and PCA2.Ministerio de Economía, Industria y Competitividad (TEC2017-82408-R and PID2020-115339RB-I00)ESAOTE Ltd. (18IQBM

p75NTR antagonists attenuate photoreceptor cell loss in murine models of retinitis pigmentosa

ProNGF signaling through p75NTR has been associated with neurodegenerative disorders. Retinitis pigmentosa (RP) comprises a group of inherited retinal dystrophies that causes progressive photoreceptor cell degeneration and death, at a rate dependent on the genetic mutation. There are more than 300 mutations causing RP, and this is a challenge to therapy. Our study was designed to explore a common mechanism for p75NTR in the progression of RP, and assess its potential value as a therapeutic target. The proNGF/p75NTR system is present in the dystrophic retina of the rd10 RP mouse model. Compared with wild-type (WT) retina, the levels of unprocessed proNGF were increased in the rd10 retina at early degenerative stages, before the peak of photoreceptor cell death. Conversely, processed NGF levels were similar in rd10 and WT retinas. ProNGF remained elevated throughout the period of photoreceptor cell loss, correlating with increased expression of α2-macroglobulin, an inhibitor of proNGF processing. The neuroprotective effect of blocking p75NTR was assessed in organotypic retinal cultures from rd10 and RhoP mouse models. Retinal explants treated with p75NTR antagonists showed significantly reduced photoreceptor cell death, as determined by the terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) assay and by preservation of the thickness of the outer nuclear layer (ONL), where photoreceptor nuclei are located. This effect was accompanied by decreased retinal-reactive gliosis and reduced TNFα secretion. Use of p75NTR antagonist THX-B (1,3-diisopropyl-1-[2-(1,3-dimethyl-2,6-dioxo-1,2,3,6-tetrahydro-purin-7-yl)-acetyl]-urea) in vivo in the rd10 and RhoP mouse models, by a single intravitreal or subconjunctival injection, afforded neuroprotection to photoreceptor cells, with preservation of the ONL. This study demonstrates a role of the p75NTR/proNGF axis in the progression of RP, and validates these proteins as therapeutic targets in two different RP models, suggesting utility irrespective of etiology.Fil: Platón-Corchado, María. Consejo Superior de Investigaciones Científicas; EspañaFil: Barcelona, Pablo Federico. Mc Gill University. Lady Davis Research Intitute; Canadá. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; ArgentinaFil: Jmaeff, Sean. Mc Gill University. Lady Davis Research Intitute; CanadáFil: Marchena, Miguel. Consejo Superior de Investigaciones Científicas; EspañaFil: Hernández-Pinto, Alberto M.. Consejo Superior de Investigaciones Científicas; EspañaFil: Hernández-Sánchez, Catalina. Consejo Superior de Investigaciones Científicas; EspañaFil: Saragovi, H. Uri. Mc Gill University. Lady Davis Research Intitute; CanadáFil: de la Rosa, Enrique J. Centro de Investigaciones Biológicas; Españ

Efficient convolution-based pairwise elastic image registration on three multimodal similarity metrics

Producción CientíficaThis paper proposes a complete convolutional formulation for 2D multimodal pairwise image registration problems based on free-form deformations. We have reformulated in terms of discrete 1D convolutions the evaluation of spatial transformations, the regularization term, and their gradients for three different multimodal registration metrics, namely, normalized cross correlation, mutual information, and normalized mutual information. A sufficient condition on the metric gradient is provided for further extension to other metrics. The proposed approach has been tested, as a proof of concept, on contrast-enhanced first-pass perfusion cardiac magnetic resonance images. Execution times have been compared with the corresponding execution times of the classical tensor product formulation, both on CPU and GPU. The speed-up achieved by using convolutions instead of tensor products depends on the image size and the number of control points considered, the larger those magnitudes, the greater the execution time reduction. Furthermore, the speed-up will be more significant when gradient operations constitute the major bottleneck in the optimization process.Ministerio de Economía, Industria y Competitividad (grants TEC2017-82408-R and PID2020-115339RB-I00)ESAOTE Ltd (grant 18IQBM

Fast 4D elastic group-wise image registration. Convolutional interpolation revisited

Background and Objective:This paper proposes a new and highly efficient implementation of 3D+t groupwise registration based on the free-form deformation paradigm. Methods:Deformation is posed as a cascade of 1D convolutions, achieving great reduction in execution time for evaluation of transformations and gradients. Results:The proposed method has been applied to 4D cardiac MRI and 4D thoracic CT monomodal datasets. Results show an average runtime reduction above 90%, both in CPU and GPU executions, compared with the classical tensor product formulation. Conclusions:Our implementation, although fully developed for the metric sum of squared differences, can be extended to other metrics and its adaptation to multiresolution strategies is straightforward. Therefore, it can be extremely useful to speed up image registration procedures in different applications where high dimensional data are involved.MEC-TEC2017-82408-

Tendencias de la fanerógama marina Cymodocea nodosa (Magnoliophyta) en las Islas Canarias: cambios poblacionales en las dos últimas décadas

Seagrass meadows perform essential ecosystem functions and services. Though the meadows are globally deteriorating, numerous regressions remain unreported as a result of data fragmentation. Cymodocea nodosa is the most important seagrass in shallow coastal waters of the Canary Islands. No study has so far investigated temporal population trends at the entire archipelago scale. Using data collected in the past 23 years by local companies, public authorities and research groups, the population trends of Cymodocea nodosa were analysed over the past two decades at the scales of islands, island sectors and meadows. During this period, a prevalence of negative trends was revealed for three seagrass demographic descriptors (seagrass shoot density, coverage and leaf length) at the three scales, evidencing an overall deterioration in seagrass meadow integrity. These results suggest the need to develop correct management strategies to guarantee the conservation of this seagrass and the meadows it creates.Las praderas de fanerógamas marinas suministran funciones y servicios esenciales para los ecosistemas. A pesar de que dichas praderas están globalmente deteriorándose, numerosas regresiones son aún desconocidas como resultado de la falta de datos. Cymodocea nodosa es la fanerógama marina más importante en aguas someras de las costas del Archipiélago Canario. No obstante, ningún estudio ha analizado las tendencias temporales de sus poblaciones a escala de todo el archipiélago. Utilizando datos recogidos durante los últimos 23 años por empresas, administraciones públicas y grupos de investigación, se analizaron las tendencias de las poblaciones de Cymodocea nodosa durante las últimas dos décadas en el Archipiélago Canario a la escala de islas, sectores insulares y praderas individuales. A lo largo de este periodo, se observa una prevalencia de tendencias negativas para tres descriptores demográficos (densidad de haces, cobertura y longitud de hoja), evidenciando un deterioro general en la integridad de las praderas. Estos resultados sugieren la necesidad de desarrollar estrategias de gestión correctas para garantizar la conservación de las praderas constituidas por esta planta marina

Control formal a través de la Geometría y la Representación: fundamentos históricos

Junta de Andalucía-Consejería de Política TerritorialEscuela Técnica Superior de Arquitectura de la Universidad de SevillaExcm. Ayuntamiento de SevillaColegio Oficial de Arquitectos de Andalucía Occidenta

Presencia de paratuberculosis en rumiantes en el estado de Zacatecas a través de estudio histopatológico

This study aimed to determine the presence of histopathological lesions suggestive of Mycobacterium avium subspecies paratuberculosis in ruminants with clinical field manifestations of paratuberculosis in the Mexican state of Zacatecas. Sixteen sheep, five goats, and four cattle from the municipalities of Morelos, Enrique Estrada, Jerez de García Salinas, Víctor Rosales, Fresnillo, Saín Alto, and Tepetongo were examined. The animals ranged in age from 5 weeks to 4 years. At necropsy, representative samples were taken from organs such as the small intestine, ileocecal valve, and mesenteric lymph nodes, for the routine histological technique of hematoxylin and eosin (HE). Subsequently, the Ziehl-Neelsen (ZN) technique was performed. It was observed that 56% of the animals were positive for acid-fast bacilli (AFB), compatible with Mycobacterium avium subspecies paratuberculosis. Eighty percent of the cases came from goats and 62.5% from sheep. 58.3% of females of both species showed lesions suggestive of paratuberculosis, and there was no significant difference in males. The lesions observed in the intestine were: proliferative enteritis in 78.6% of the cases, in the jejunum, enteritis, and necrosis in 21.4% of the cases, in the ileum, proliferative enteritis in 100% of the cases and 57.1% of lymph nodes were lymphadenomegalic and 50% of the cases in of the cases contained an inflammatory infiltrate in. In the state of Zacatecas, there is complete lack of studies that have detected the presence of paratuberculosis in any species, despite its economic and health importance.El presente estudio tuvo como objetivo determinar la presencia de lesiones histopatológicas sugestivas de Mycobacterium avium subespecie paratuberculosis en rumiantes con manifestaciones clínicas de campo de paratuberculosis en el estado mexicano de Zacatecas. Se examinaron 16 ovinos, 5 caprinos y 4 bovinos de los municipios de Morelos, Enrique Estrada, Jerez de García Salinas, Víctor Rosales, Fresnillo, Saín Alto y Tepetongo. La edad de los animales osciló entre 5 semanas y 4 años. En la necropsia se tomaron muestras representativas de órganos tales como intestino delgado, válvula ileocecal y ganglios linfáticos mesentéricos, para la técnica histológica de rutina de hematoxilina y eosina (HE). Posteriormente, se realizó la tinción de Ziehl-Neelsen (ZN). Se observó que el 56% de los animales eran positivos para bacilos ácido-alcohol resistentes (BAAR), compatibles con Mycobacterium avium subespecie paratuberculosis. El 80% de casos procedían de cabras y el 62.5% de ovejas. El 58.3% de las hembras de ambas especies presentaban lesiones sugestivas de paratuberculosis, y no había diferencias significativas en los machos. Las lesiones observadas en el intestino fueron: enteritis proliferativa en el 78.6% de los casos, en el yeyuno, enteritis y necrosis en el 21.4% de los casos, en el íleon, enteritis proliferativa en el 100% de los casos y el 57.1% de los ganglios linfáticos eran linfadenomegálicos y el 50% de los casos contenían un infiltrado inflamatorio. En el estado de Zacatecas se carece por completo de estudios que hayan detectado la presencia de paratuberculosis en alguna especie, a pesar de su importancia económica y sanitaria

UroMark-a urinary biomarker assay for the detection of bladder cancer.

BACKGROUND: Bladder cancer (BC) is one of the most common cancers in the western world and ranks as the most expensive to manage, due to the need for cystoscopic examination. BC shows frequent changes in DNA methylation, and several studies have shown the potential utility of urinary biomarkers by detecting epigenetic alterations in voided urine. The aim of this study is to develop a targeted bisulfite next-generation sequencing assay to diagnose BC from urine with high sensitivity and specificity. RESULTS: We defined a 150 CpG loci biomarker panel from a cohort of 86 muscle-invasive bladder cancers and 30 normal urothelium. Based on this panel, we developed the UroMark assay, a next-generation bisulphite sequencing assay and analysis pipeline for the detection of bladder cancer from urinary sediment DNA. The 150 loci UroMark assay was validated in an independent cohort (n = 274, non-cancer (n = 167) and bladder cancer (n = 107)) voided urine samples with an AUC of 97%. The UroMark classifier sensitivity of 98%, specificity of 97% and NPV of 97% for the detection of primary BC was compared to non-BC urine. CONCLUSIONS: Epigenetic urinary biomarkers for detection of BC have the potential to revolutionise the management of this disease. In this proof of concept study, we show the development and utility of a novel high-throughput, next-generation sequencing-based biomarker for the detection of BC-specific epigenetic alterations in urine

Fibronectin rescues estrogen receptor α from lysosomal degradation in breast cancer cells

Estrogen receptor α (ERα) is expressed in tissues as diverse as brains and mammary glands. In breast cancer, ERα is a key regulator of tumor progression. Therefore, understanding what activates ERα is critical for cancer treatment in particular and cell biology in general. Using biochemical approaches and superresolution microscopy, we show that estrogen drives membrane ERα into endosomes in breast cancer cells and that its fate is determined by the presence of fibronectin (FN) in the extracellular matrix; it is trafficked to lysosomes in the absence of FN and avoids the lysosomal compartment in its presence. In this context, FN prolongs ERα half-life and strengthens its transcriptional activity. We show that ERα is associated with β1-integrin at the membrane, and this integrin follows the same endocytosis and subcellular trafficking pathway triggered by estrogen. Moreover, ERα+ vesicles are present within human breast tissues, and colocalization with β1-integrin is detected primarily in tumors. Our work unravels a key, clinically relevant mechanism of microenvironmental regulation of ERα signaling.Fil: Sampayo, Rocío Guadalupe. Universidad Nacional de San Martin. Instituto de Nanosistemas; Argentina. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Oncología "Ángel H. Roffo"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Toscani, Andrés Martin. Universidad Nacional de Luján; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Rubashkin, Matthew G.. University of California; Estados UnidosFil: Thi, Kate. Lawrence Berkeley National Laboratory; Estados UnidosFil: Masullo, Luciano Andrés. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Física de Buenos Aires; ArgentinaFil: Violi, Ianina Lucila. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Investigaciones en Bionanociencias "Elizabeth Jares Erijman"; ArgentinaFil: Lakins, Jonathon N.. University of California; Estados UnidosFil: Caceres, Alfredo Oscar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; ArgentinaFil: Hines, William C.. Lawrence Berkeley National Laboratory; Estados UnidosFil: Coluccio Leskow, Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina. Universidad Nacional de Luján; ArgentinaFil: Stefani, Fernando Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Física de Buenos Aires; ArgentinaFil: Chialvo, Dante Renato. Universidad de Buenos Aires; Argentina. Universidad Nacional de San Martín. Escuela de Ciencia y Tecnología. Centro Internacional de Estudios Avanzados; ArgentinaFil: Bissell, Mina J.. Lawrence Berkeley National Laboratory; Estados UnidosFil: Weaver, Valerie M.. University of California; Estados UnidosFil: Simian, Marina. Universidad Nacional de San Martin. Instituto de Nanosistemas; Argentina. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Oncología "Ángel H. Roffo"; Argentin

El dossier copia/sur: problemas económicos, políticos, e ideológicos del copyright (derecho de autor) en el sur global

In 2005, a group of scholars and activists, mostly from the global South, created the Copy/South Research Group to analyse, criticise, and confront the oppressive nature of current global copyright regimes, such as those defended by the World Intellectual Property Organisation, and similar ones around the globe. In May 2006, 22 of us, including 15 people from the global South, published THE COPY/SOUTH DOSSIER: Issues in the economics, politics, and ideology of copyright in the global South. The aim of the Dossier was to open up a critical and radical debate on the real impact of copyright laws and how they affect the daily lives of people living in more than 150 developing countries of the global South. We also highlighted issues that are not unique to the Global South, but also affect both sides of the North-South divide. This publication of more than 50 articles was addressed to researchers, educators, librarians, musicians, activists, organizations concerned about access to knowledge, and all of those who want to learn more about the oppressive global role of copyright laws and, in particular, their largely negative role in the developing countries of the global South. Given the democratic objectives of the Copy/South Research Group, the Dossier was not restricted by copyright. Therefore, it has been accessed openly and freely in both electronic and paper formats by thousands of readers from around the world in English. But English is not spoken by all citizens in the global South. With this in mind, the entire 200-page Dossier was translated into Spanish in late 2007 by an enthusiastic team of voluntary translators from Argentina, Bolivia, Cuba, Mexico, Spain, and Venezuela. As for this Spanish version, made with the support of the Intellectual Property Automous Service (SAPI), from the Bolivarian Republic of Venezuela, we must acknowledge the prior SAPI's General Director Eduardo Samán for promoting the making of this translation. Besides the general revision of Gerardo Cárdenas and his labor as main translator, some other volunteers translated or revised important sections of the Spanish edition: María Jesús Morillo (Spain), Oscar Pérez Peña and Gilda Gil (Cuba), Edgardo Civallero (Argentina) and Rafael Carreño (Venezuela), who coordinated the process of translation in 2007. Also it is worth to mention the additional colaboration of Ana Lía López (Bolivia), Richard Castro, Rafael Bellota and Carmen Chirinos (Venezuela), Zapopan Muela and Gonzalo Lara (Mexico), and Lilian Álvarez (Cuba). But what is still more extraordinary about this Spanish translation is that it was completely coordinated and edited by the Servicio Autonomo de la Propiedad Intelectual (SAPI) of the democratic government of the Venezuelan Bolivarian Republic. The Dossier provides “useful material to introduce this topic to teachers and students” and does a good job of “summarizing a complex and conflicting situation” for developing countries, Jumersi La Rosa, SAPI’s new director, said last week in announcing the release of the Spanish edition. She has written a special new introduction for the Spanish-language edition. The Copy South Research Group is very pleased that the radical message of resistance found in the Dossier can now be read by thousands of Spanish-language speakers who are questioning the current copyright regime and who hopefully will be ignited by the ideas in the Dossier to take up the fight against oppressive regimes based on copyright. You can get a copy of the Dossier in Spanish and English by downloading it, free of charge, at http://www.copysouth.org . We also still have a limited number of printed and bound copies of the English-language version of the Dossier. If you would to be mailed a copy of the English-language version, which contains eight posters, send us an e-mail ([email protected]) and include your full postal details. COPY/SOUTH RESEARCH GROUP, 28 April 2008