Parallel optimization of fiber bundle segmentation for massive tractography datasets

We present an optimized algorithm that performs automatic classification of white matter fibers based on a multi-subject bundle atlas. We implemented a parallel algorithm that improves upon its previous version in both execution time and memory usage. Our new version uses the local memory of each processor, which leads to a reduction in execution time. Hence, it allows the analysis of bigger subject and/or atlas datasets. As a result, the segmentation of a subject of 4,145,000 fibers is reduced from about 14 minutes in the previous version to about 6 minutes, yielding an acceleration of 2.34. In addition, the new algorithm reduces the memory consumption of the previous version by a factor of 0.79.Comment: This research has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sk{\l}odowska-Curie Actions H2020-MSCA-RISE-2015 BIRDS GA No. 690941, CONICYT PFCHA/ DOCTORADO NACIONAL/2016-21160342, CONICYT FONDECYT 1161427, CONICYT PIA/Anillo de Investigaci\'on en Ciencia y Tecnolog\'ia ACT172121, CONICYT BASAL FB0008 and from CONICYT Basal FB000

Effect of antibiotic prophylaxis for preventing infectious complications following impacted mandibular third molar surgery. A randomized controlled trial

The objective of this study was to determine the effect of antibiotic prophylaxis in preventing postoperative infections after extraction of impacted mandibular third molars. A Parallel-group, randomized, blind, placebo-controlled trial was performed. 154 patients were randomly allocated to 2 groups; experimental (n=77) receiving 2g amoxicillin 1 hour prior to surgery and control (n=77) receiving placebo. Primary outcome was postoperative infections and secondary outcome was the need for rescue analgesia. 4.5% of patients developed postoperative infections, five patients of the control group (4 alveolar osteitis, 1 surgical site infection) and two of the experimental group (1 alveolar osteitis, 1 surgical site infection). Difference between groups was not statistically significant, RR=0.4 (95%CI 0.08-1.99, ?=0.41) NNTB=26. Rescue analgesia intake was significantly higher in the control group (41 vs 18 patients of experimental group) RR=0.49 (95%CI 0.32-0.75, ?<0.05) NNTB=3. The use of 2g amoxicillin 1 hour before surgery was not effective in significantly reducing the risk of postoperative infections from impacted mandibular third molars extraction, when compared to placebo. Nevertheless, antibiotic prophylaxis was associated with a reduced need for rescue analgesia

Cuerpos humanos de origen arqueológico: Extractivismo y crisis de los depósitos en Chile, el caso del Museo histórico arqueológico de Quillota

In Chile, Bioanthropological remains – human bodies – are immersed in a delicate legal, economic, political, and ethical conundrum. Various legal entities protect national cultural heritage susceptible of being harmed by extractive projects. However, there are a large number of archaeological excavations, legal entities are ineffective, there is a lack of general ethical guidelines for protecting human remains, and the administrations of local museums are precarious. This has led to an imminent collapse of institutions that house bioanthropological remains. This situation, which we call a "museum storage crisis," is discussed based on our experience at the Museo Histórico Arqueológico de Quillota. Toward a more integral management of protected collections of human bones in Chile, we advance the premise that all bioanthropological remains are human beings, and consequently, must be treated ethically.Los restos bioantropológicos -cuerpos humanos- se encuentran inmersos en una problemática legal, económica, política y ética delicada en Chile. Particularmente, distintos recursos legales protegen el patrimonio nacional susceptible de ser impactado por proyectos extractivistas. No obstante, la enorme cantidad de excavaciones arqueológicas, la ineficacia práctica de los recursos legales, la ausencia de lineamientos éticos generales que regulen la protección de los cuerpos humanos en un sentido amplio, sumadas a la precariedad administrativa de los museos locales, han conllevado a un inminente colapso en las instituciones depositarias. Este diagnóstico que calificamos como "crisis de los depósitos" es discutido en base a la experiencia de trabajo del Museo Histórico Arqueológico de Quillota. Con miras a pensar el manejo integral de las colecciones esqueletales resguardadas, se desarrolla la premisa de que todo resto bioantropológico en el museo posee una condición inherente de ser "humano" y, consecuentemente, la necesidad de un trato ético

What do brain endocasts tell us? A comparative analysis of the accuracy of sulcal identification by experts and perspectives in palaeoanthropology

Palaeoneurology is a complex field as the object of study, the brain, does not fossilize. Studies rely therefore on the (brain) endocranial cast (often named endocast), the only available and reliable proxy for brain shape, size and details of surface. However, researchers debate whether or not specific marks found on endocasts correspond reliably to particular sulci and/or gyri of the brain that were imprinted in the braincase. The aim of this study is to measure the accuracy of sulcal identification through an experiment that reproduces the conditions that palaeoneurologists face when working with hominin endocasts. We asked 14 experts to manually identify well-known foldings in a proxy endocast that was obtained from an MRI of an actual in vivo Homo sapiens head. We observe clear differences in the results when comparing the non-corrected labels (the original labels proposed by each expert) with the corrected labels. This result illustrates that trying to reconstruct a sulcus following the very general known shape/position in the literature or from a mean specimen may induce a bias when looking at an endocast and trying to follow the marks observed there. We also observe that the identification of sulci appears to be better in the lower part of the endocast compared to the upper part. The results concerning specific anatomical traits have implications for highly debated topics in palaeoanthropology. Endocranial description of fossil specimens should in the future consider the variation in position and shape of sulci in addition to using models of mean brain shape. Moreover, it is clear from this study that researchers can perceive sulcal imprints with reasonably high accuracy, but their correct identification and labelling remains a challenge, particularly when dealing with extinct species for which we lack direct knowledge of the brain

Heavy Alcohol Exposure Activates Astroglial Hemichannels and Pannexons in the Hippocampus of Adolescent Rats: Effects on Neuroinflammation and Astrocyte Arborization

A mounting body of evidence indicates that adolescents are specially more susceptible to alcohol influence than adults. However, the mechanisms underlying this phenomenon remain poorly understood. Astrocyte-mediated gliotransmission is crucial for hippocampal plasticity and recently, the opening of hemichannels and pannexons has been found to participate in both processes. Here, we evaluated whether adolescent rats exposed to ethanol exhibit changes in the activity of astrocyte hemichannels and pannexons in the hippocampus, as well as alterations in astrocyte arborization and cytokine levels. Adolescent rats were subjected to ethanol (3.0 g/kg) for two successive days at 48-h periods over 14 days. The opening of hemichannels and pannexons was examined in hippocampal slices by dye uptake, whereas hippocampal cytokine levels and astroglial arborization were determined by ELISA and Sholl analysis, respectively. We found that adolescent ethanol exposure increased the opening of connexin 43 (Cx43) hemichannels and pannexin-1 (Panx1) channels in astrocytes. Blockade of p38 mitogen-activated protein kinase (MAPK), inducible nitric oxide synthase (iNOS) and cyclooxygenases (COXs), as well as chelation of intracellular Ca2+, drastically reduced the ethanol-induced channel opening in astrocytes. Importantly, ethanol-induced Cx43 hemichannel and Panx1 channel activity was correlated with increased levels of interleukin-1β (IL-1β), tumor necrosis factor-α (TNF-α), IL-6 in the hippocampus, as well as with profound alterations in astrocyte arbor complexity. Thus, we propose that uncontrolled opening of astrocyte hemichannels and pannexons may contribute not only to the glial dysfunction and neurotoxicity caused by adolescent alcohol consumption, but also to the pathogenesis of alcohol use disorders in the adulthood

Inférence d’un atlas des faisceaux en U intégrant la variabilité des plissements corticaux

Technological breakthroughs in medical imaging have allowed for first time in vivo exploration of the brain of living beings. This has prompted the creation of big projects and large databases for the study of the human brain such as the Human Connectome Project (HCP) or the Human Brain Project (HBP), of which this thesis is a part. Tractography by diffusion MRI (dMRI) has been the first technique to explore the white matter and the major connections of the human brain but there is still a long way to go regarding short-range connections. Even more, the boundary of the division between long and short fibers remains ambiguous and without consensus among the scientific community and further study is imperative. In recent years, some short bundle atlases have been proposed, identifying about a hundred short-range fascicles. However, the main weakness in the development of these atlases is the poor alignment between subjects which consider only the standard Talairach alignment or the diffusion tensor image registration method (DTI-tk). Neither of those approaches take into account correctly the variability of the cortical folding pattern which is closely related to the short-range connections surrounding sulci, commonly known as U-bundles.This thesis work proposes a new framework for the creation of an extended atlas of short-range fiber bundles between 20mm and 85mm length from two massive dMRI tractography datasets : the ARCHI database and the HCP database. 76 subjects of each one have been used to construct two atlases of short-range connections using exactly the same pipeline. This method uses a two-step diffeomorphic inter-subject alignment procedure that combines DISCO and DARTEL approaches. First, DISCO includes information on cortical folding and forces the accurate match of the main sulci that have to be circumvented by the U-bundles. Then, the well-known DARTEL method is applied to refine the registration. The MNI 152 template is also used, in order to provide our results in a common space to facilitate its use in the scientific community.An adaptative hierarchical clustering based on DBSCAN, focused in the extraction of short-range connections is performed then to extract the most reproducible bundles across subjects. This method does not impose restriction on the shape of the bundle clusters and allows the processing of massive tractography datasets in a reasonable time and without the need of high performance computational resources. The results show an increased number of short-range bundles consistently mapped in the general population compared with previous atlases created from the same ARCHI database. This first atlas contains more than 400 bundles. On the other hand, more than 600 bundles were obtained with the massive HCP database endowed with higher spatial resolution. Each of this new atlases contains all the bundles of the existent atlases of short-range connections and much more to explore. And even, for some bundles in the same region and position, different morphologies of them have been differentiated. Those results open a new path to improve our understanding of the relationship between the folding pattern and the U-bundle variability but also the possibility to detect abnormal configurations induced by developmental issues which may lead to mental pathologies such as bipolar depression or schizophrenia.Les progrès technologiques en imagerie médicale ont permis pour la première fois d'explorer in vivo le cerveau des êtres vivants. Cela a conduit à la création de grands projets et de grandes bases de données pour l'étude du cerveau humain comme le Human Connectome Project (HCP) ou le Human Brain Project (HBP), dont cette thèse est issue. La tractographie par IRM de diffussion (dMRI) a été la première technique pour explorer la substance blanche et les principales connexions du cerveau humain, mais il reste encore beaucoup à faire en ce qui concerne les connexions des fibres courtes. D’ailleurs, la frontière entre fibres longues et courtes reste ambiguë et sans consensus au sein de la communauté scientifique et il est impératif de poursuivre les études. Au cours des dernières années, des atlas de faisceaux courts ont été proposés, identifiant une centaine de faisceaux. Cependant, la principale faiblesse dans le développement de ces atlas est un alignement approximatif entre les sujets qui considèrent soit l’espace standard de Talairach ou une méthode fondée sur le recalage des images du tenseur de diffusion (DTI-tk). Aucune de ces approches ne gère correctement la variabilité des motif du plissement cortical qui est étroitement lié aux connexions courtes entourant les sillons, communément appelées faisceaux en U.Ce travail de thèse propose un nouveau cadre pour la création d'un atlas étendu de faisceaux de fibres entre 20mm et 85mm de longueur à partir de deux bases de données de tractographie massives fondées sur l’IRM de diffusion: la base de données ARCHI et la base de données HCP. 76 sujets de chacune ont été utilisés pour construire deux atlas de connexions courtes en utilisant exactement le même pipeline. Cette méthode utilise une procédure d'alignement inter-sujets difféomorphe en deux étapes qui combine les approches DISCO et DARTEL. Premièrement, DISCO inclut l'information du plissement cortical et force l'appariement précis des sillons majeurs qui doivent être contournés par les faisceaux en U. Ensuite, la méthode DARTEL bien connue est appliquée aux fibres pour affiner l'alignement. Le template MNI 152 est utilisé comme cible de la normalisation spatiale, afin de fournir nos résultats dans un espace commun pour faciliter son utilisation dans la communauté scientifique.Un clustering hiérarchique adaptatif et focalisé sur l'extraction des connexions de courte portée est ensuite réalisé pour extraire les faisceaux les plus reproductibles entre les sujets. Cette méthode n’impose pas de restriction sur la forme des clusters de faisceaux obtenus et permet de traiter des bases de données de tractographie massive dans un temps raisonnable et sans utiliser de ressources de calcul de haute performance. Les résultats montrent un nombre accru de faisceaux en U cartographiés de façon reproductible dans la population générale par rapport aux atlas précédents créés auparavant à partir de la même base de données ARCHI. Ce premier atlas contient plus de 400 faisceaux des deux hémisphères. En outre, plus de 600 faisceaux ont été obtenus avec l'énorme base de données HCP de meilleure résolution spatiale. Chacun de ces nouveaux atlas contient tous les faisceaux des atlas existants de connexions courtes et bien plus encore à explorer. Et même, pour certains faisceaux dans la même région et la même position, on observe différentes morphologies. Ces résultats ouvrent une nouvelle voie pour améliorer notre compréhension de la relation entre le plissement cortical et la variabilité des faisceaux en U mais ils visent également la possibilité de détecter des configurations anormales induites par des problèmes de développement qui peuvent conduire à des pathologies mentales telles que la dépression bipolaire ou la schizophrénie

Alzheimer: El Chile olvidado

Memoria para optar al título de PeriodistaChile se encuentra en una etapa de cambios socioculturales, económicos y demográficos, y es justamente en este último punto donde se entrelazan dos situaciones de gran relevancia para el presente y para el futuro del país. Por un lado, la esperanza de vida ha aumentado considerablemente en las últimas décadas, llegando así a los 79 años en promedio. Y, por otra parte, pero en base a la misma idea, el país tiene 2.6 millones de personas en la etapa adulto mayor, lo que equivale al 15% de la población chilena. Si bien existen varias problemáticas a abordar en torno a la tercera edad, existe un tema en específico que requiere de gran atención y urgencia: la enfermedad de Alzheimer. Este diagnóstico, ligado al olvido, a la pérdida de memoria de la persona, se ha convertido en la quinta causa de muerte en Chile y se estima que será la tercera en Estados Unidos. Sin embargo, a pesar de esto, nuestro país todavía no cuenta con las herramientas suficientes para diagnosticar, tratar, cuidar y hacerse cargo de los más de 90 mil enfermos de Alzheimer que hay en Chile. Ni de ellos, ni de sus familias. A través de esta investigación hemos querido dilucidar cuáles son las verdaderas opciones que tiene una persona con Alzheimer en Chile, incluyendo su acceso a costosos medicamentos para retrasar el progreso de la enfermedad, como la posibilidad de un diagnóstico temprano o la opción de ayuda monetaria y psicológica por parte del Estado. En síntesis, 10 distinguir las políticas públicas vigentes –y relacionadas con esta demencia– que existen hoy en Chile

Optimization of RecoBundles for recognition of short white matter bundles

International audienceShort-range connections have been less studied than long-range connectionq, with most of the white matter fibers atlases available containing mainly large connections. Among the short-range connections atlas, two developed by [6] managed to extract more than 400 bundles for one altas ( ARCHI database [8] ) and more than 600 bundles ( HCP database [1] ). However, they have not been used for white matter segmentation because most techniques for white matter segmentation are optimized for long range connections. Here, we optimize the technique implemented in [2] by analysing the atlas via six geometrical parameters and using bundle specific parameters to increase the quality and the number connections extracted

GeoLab: Geometry-based Tractography Parcellation of Superficial White Matter

Superficial white matter (SWM) has been less studied than long-range connections despite being of interest to clinical research, andfew tractography parcellation methods have been adapted to SWM. Here, we propose an efficient geometry-based parcellation method (GeoLab) that allows high-performance segmentation of hundreds of short white matter bundles from a subject. This method has been designed for the SWM atlas of EBRAINS European infrastructure, which is composed of 657 bundles. The atlas projection relies on the precomputed statistics of six bundle-specific geometrical properties of atlas streamlines. In the spirit of RecoBundles, a global and local streamline-based registration (SBR) is used to align the subject to the atlas space. Then, the streamlines are labeled taking into account the six geometrical parameters describing the similarity to the streamlines in the model bundle. Compared to other state-of-the-art methods, GeoLab allows the extraction of more bundles with a higher number of streamlines

"Cómo traer un pedacito de Inglaterra": a descriptive analysis of social representations of English as a foreign language in private language teaching schools in Santiago de Chile

Informe de Seminario para optar al grado de Licenciado en Lengua y Literatura InglesaDurante las últimas décadas, una gran cantidad de institutos privados de idiomas se han establecido como un medio importante para aprender inglés en Chile. Sin embargo, escasa atención se ha puesto a los temas de ideologías lingüísticas y representaciones sociales detrás de estas instituciones. Por lo tanto, el objetivo de este estudio es caracterizar su relación con el inglés como lengua extranjera (ILE) y sus implicaciones sociales, políticas y pedagógicas en el proceso de enseñanza y aprendizaje en dos institutos privados de inglés de Santiago de Chile, Instituto Chileno-Británico de Cultura y Talk Chile. Para esto, 17 participantes fueron seleccionados considerando los tres actores sociales principales de los institutos. En el caso de los profesores y los coordinadores académicos, se hicieron entrevistas semi-estructuradas, mientras que en el caso de los estudiantes se llevaron a cabo dos focus groups. Los resultados muestran que las categorías principales que emergieron de los datos, como ideologías lingüísticas románticas e instrumentales, implicancias pedagógicas y representaciones sociales en publicidad inciden en las creencias de las personas al considerar el inglés como elemental, global y esencial en su vida profesional y diaria.In the last decades, many private language teaching schools (PLTS) have established themselves as a prominent medium for learning English in Chile. Nevertheless, scarce attention has been paid to issues regarding the language ideologies and the social representations behind these institutions. Consequently, the aim of this study is to characterize them concerning English as a Foreign Language (EFL) and its social, political, and pedagogical implications in the process of teaching and learning in two PLTS from Santiago de Chile, Instituto Chileno-Británico de Cultura and Talk Chile. To accomplish this, 17 participants were selected among the three main social actors. Semi-structured interviews were carried out in the case of teachers and academic coordinators, while two focus groups were conducted in the case of the students. Results depict that the main categories, such as romantic and instrumental linguistic ideologies, pedagogical issues and social representations in advertising have an incidence in people’s beliefs when considering English as elemental, global and essential in their professional and daily life