Model-based Segmentation and Fusion of 3D Computed Tomography and 3D Ultrasound of the Eye for Radiotherapy Planning

Computed Tomography (CT) represents the standard imaging modality for tumor volume delineation for radiotherapy treatment planning of retinoblastoma despite some inherent limitations. CT scan is very useful in providing information on physical density for dose calculation and morphological volumetric information but presents a low sensitivity in assessing the tumor viability. On the other hand, 3D ultrasound (US) allows a highly accurate definition of the tumor volume thanks to its high spatial resolution but it is not currently integrated in the treatment planning but used only for diagnosis and follow-up. Our ultimate goal is an automatic segmentation of gross tumor volume (GTV) in the 3D US, the segmentation of the organs at risk (OAR) in the CT and the registration of both modalities. In this paper, we present some preliminary results in this direction. We present 3D active contour-based segmentation of the eye ball and the lens in CT images; the presented approach incorporates the prior knowledge of the anatomy by using a 3D geometrical eye model. The automated segmentation results are validated by comparing with manual segmentations. Then, we present two approaches for the fusion of 3D CT and US images: (i) landmark-based transformation, and (ii) object-based transformation that makes use of eye ball contour information on CT and US images.

Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function.

In conducting genome-wide association studies (GWAS), analytical approaches leveraging biological information may further understanding of the pathophysiology of clinical traits. To discover novel associations with estimated glomerular filtration rate (eGFR), a measure of kidney function, we developed a strategy for integrating prior biological knowledge into the existing GWAS data for eGFR from the CKDGen Consortium. Our strategy focuses on single nucleotide polymorphism (SNPs) in genes that are connected by functional evidence, determined by literature mining and gene ontology (GO) hierarchies, to genes near previously validated eGFR associations. It then requires association thresholds consistent with multiple testing, and finally evaluates novel candidates by independent replication. Among the samples of European ancestry, we identified a genome-wide significant SNP in FBXL20 (P = 5.6 × 10(-9)) in meta-analysis of all available data, and additional SNPs at the INHBC, LRP2, PLEKHA1, SLC3A2 and SLC7A6 genes meeting multiple-testing corrected significance for replication and overall P-values of 4.5 × 10(-4)-2.2 × 10(-7). Neither the novel PLEKHA1 nor FBXL20 associations, both further supported by association with eGFR among African Americans and with transcript abundance, would have been implicated by eGFR candidate gene approaches. LRP2, encoding the megalin receptor, was identified through connection with the previously known eGFR gene DAB2 and extends understanding of the megalin system in kidney function. These findings highlight integration of existing genome-wide association data with independent biological knowledge to uncover novel candidate eGFR associations, including candidates lacking known connections to kidney-specific pathways. The strategy may also be applicable to other clinical phenotypes, although more testing will be needed to assess its potential for discovery in general.

Automated analysis of background EEG and reactivity during therapeutic hypothermia in comatose patients after cardiac arrest.

Visual analysis of electroencephalography (EEG) background and reactivity during therapeutic hypothermia provides important outcome information, but is time-consuming and not always consistent between reviewers. Automated EEG analysis may help quantify the brain damage. Forty-six comatose patients in therapeutic hypothermia, after cardiac arrest, were included in the study. EEG background was quantified with burst-suppression ratio (BSR) and approximate entropy, both used to monitor anesthesia. Reactivity was detected through change in the power spectrum of signal before and after stimulation. Automatic results obtained almost perfect agreement (discontinuity) to substantial agreement (background reactivity) with a visual score from EEG-certified neurologists. Burst-suppression ratio was more suited to distinguish continuous EEG background from burst-suppression than approximate entropy in this specific population. Automatic EEG background and reactivity measures were significantly related to good and poor outcome. We conclude that quantitative EEG measurements can provide promising information regarding current state of the patient and clinical outcome, but further work is needed before routine application in a clinical setting.

Realització d'una aplicació de gestió de xarxes per a la xarxa sensefils de Manresa GuifiBages

En els últims anys, la popularitat de les xarxes sensefils (WIFI) ha anat en augment a un ritme incansable. Des de petits aparells instal•lats a les cases amb aquesta tecnologia com a complement dels routers d’accés a internet instal•lats per diverses companyies, fins a empreses fent petits desplegaments per comunicar entre si les seves seus. Al marge d’aquests escenaris, s’ha produït un fenomen social d’acolliment d’aquesta tecnologia a nivell mundial, en forma del que coneixem com a xarxes ciutadanes / xarxes lliures / xarxes socials. Aquestes xarxes han estat possibles gràcies a diverses raons que han fet assequible a col•lectius de persones, tant els aparells com els coneixements necessaris per dur a terme aquestes actuacions. Dintre d’aquest marc, al Bages, concretament a Manresa, es va començar a desenvolupar una d’aquestes xarxes. Les decisions d’aquesta xarxa d’utilitzar exclusivament hardware i software de codi obert, i determinats aspectes tècnics de la xarxa, ha comportat que la xarxa fos incompatible amb algunes de les aplicacions de gestió de xarxes existents desenvolupades per comunicats com gufi.net a Osona. És per això que per garantir el creixement, la supervivència i l’èxit d’aquesta xarxa en el temps, és indispensable poder comptar amb una eina de gestió que s’adigui a les característiques de GuifiBages. L’objectiu principal d’aquest treball és dotar a la xarxa GuifiBages de les eines necessàries per poder gestionar tota la informació referent a l’estructura de la seva xarxa, tant per facilitar l’accés a nous usuaris sense molts coneixements tècnics, com per facilitar nous desplegaments / reparacions / modificacions de la xarxa d’una manera automàtica. Com a conclusió d’aquest treball, podem afirmar que les avantatges que proporciones tecnologies com Plone, faciliten enormement la creació d’aplicacions de gestió de continguts en entorn web. Alhora, l’ús de noves tècniques de programació com AJAX o recursos com els que ofereix Google, permeten desenvolupar aplicacions web que no tenen res a envejar al software tradicional. D’altra banda, voldríem destacar l’ús exclusiu de programari lliure tant en els paquets de software necessaris pel desenvolupament, com en el sistema operatiu i programes dels ordinadors on s’ha dut a terme, demostrant que es poden desenvolupar sistemes de qualitat sense dependre de programari privatiu.

AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context.

SUMMARY: We present a tool designed for visualization of large-scale genetic and genomic data exemplified by results from genome-wide association studies. This software provides an integrated framework to facilitate the interpretation of SNP association studies in genomic context. Gene annotations can be retrieved from Ensembl, linkage disequilibrium data downloaded from HapMap and custom data imported in BED or WIG format. AssociationViewer integrates functionalities that enable the aggregation or intersection of data tracks. It implements an efficient cache system and allows the display of several, very large-scale genomic datasets. AVAILABILITY: The Java code for AssociationViewer is distributed under the GNU General Public Licence and has been tested on Microsoft Windows XP, MacOSX and GNU/Linux operating systems. It is available from the SourceForge repository. This also includes Java webstart, documentation and example datafiles.

Bringing Funds of Family Knowledge to school. The Living Morocco Project (“برغملا شيعلا”)

The purpose of the study, grounded in sociocultural theory, is to describe the funds of knowledge of a Moroccan family living in Catalonia (Spain) in order to document how teachers can use these funds of knowledge to make direct links between students' lives and classroom teaching. The funds of knowledge approach is based on a simple premise: regardless of any socio-economical and sociocultural "deficit" that people may or may not have all families accumulate bodies of beliefs, ideas, skills and abilities based on their experiences (in areas such as their occupation or their religion). The challenge consists in connecting these bodies of educational resources with teaching practice in order to connect the curriculum with students' lives. In doing so, qualitative research can be carried out using several techniques such as self portraits, self-definition tasks, assessment of family artefacts, documenting routines through photographs, or the analysis of a person's significant circle. The results in terms of teaching practices illustrate the variety of ways teachers can make connections between home and school in ways that assist learners in their academic development. In this article, we propose using the term funds of identity to complement the concept of funds of knowledge

Lengua familiar y conocimiento de la lengua escolar en Cataluña al finalizar la Educación Infantil = Home Language and Knowledge of the School Language in Catalonia at the end of Nursery School

La infancia extranjera se escolariza en Cataluña en un programa de cambio de lengua del hogar a la escuela. Las investigaciones afirman que este alumnado tarda un mínimo de seis años en equiparar sus habilidades lingüístico-cognitivas con sus pares autóctonos, no así las habilidades conversacionales, las cuales se adquieren antes de los dos años de residencia. Sin embargo, no existen estudios sobre los efectos de la escolarización en el parvulario del alumnado alófono, así como de su lengua familiar, en relación con la adquisición de la lengua escolar. El artículo es un estudio comparativo de la adquisición del catalán de 567 autóctonos y 434 alófonos, al final del parvulario, en 50 escuelas de Cataluña que escolarizan a alumnado de origen extranjero. Las lenguas del alumnado autóctono son el catalán, el castellano y el bilingüismo catalán-castellano y las lenguas del alumnado alófono son el árabe, el soninké y el castellano. Los factores utilizados más relevantes han sido el nivel socioprofesional y educativo de las familias, el tiempo de residencia y el momento de escolarización del alumnado, el porcentaje de alumnado catalanohablante y de alumnado alófono en el aula y el contexto sociolingüístico del centro escolar. Los resultados muestran que el alumnado autóctono sabe más catalán que el alumnado alófono, pero las diferencias desaparecen respecto a algunos factores, de los cuales los más relevantes son los relacionados con las características del alumnado de las aulas. La lengua familiar del alumnado alófono no incide en sus resultados

Benchmarking for routines and organizational knowledge

We use best practice benchmarking rationales to propose a dynamic research design that accounts for the endogenous components of across-firms heterogeneous routines to study changes in performance and their link to organizational knowledge investments. We thus contribute to the operationalization of management theoretical frameworks based on resources and routines. The research design employs frontier measures that provide industry-level benchmarking in organizational settings, and proposes some new indicators for firm-level strategic benchmarking. A profit-oriented analysis of the U.S. technology industry during 2000-2011 illustrates the usefulness of our design. Findings reveal that industry revival following economic distress comes along with wider gaps between best and worst performers. Second stage analyses show that increasing intangibles stocks is positively associated with fixed target benchmarking, while enhancing R&D spending is linked to local frontier progress. The discussion develops managerial interpretations of the benchmarking measures that are suitable for control mechanisms and reward systems.

Aplicação de um sistema automatizado (ALES - Automated Land Evaluation System) na avaliação das terras das microrregiões de Chapecó e Xanxerê, Oeste Catarinense, para o cultivo de grãos

A avaliação de terras é o processo que permite estimar o uso potencial da terra com base em seus atributos. Grande variedade de modelos analíticos pode ser usada neste processo. No Brasil, os dois sistemas de avaliação das terras mais utilizados são o Sistema de Classificação da Capacidade de Uso da Terra e o Sistema FAO/Brasileiro de Aptidão Agrícola das Terras. Embora difiram em vários aspectos, ambos exigem o cruzamento de inúmeras variáveis ambientais. O ALES (Automated Land Evaluation System) é um programa de computador que permite construir sistemas especialistas para avaliação de terras. As entidades avaliadas pelo ALES são as unidades de mapeamento, as quais podem ser de caráter generalizado ou detalhado. A área objeto desta avaliação é composta pelas microrregiões de Chapecó e Xanxerê, no Oeste catarinense, e engloba 54 municípios. Os dados sobre os solos e sobre as características da paisagem foram obtidos no levantamento de reconhecimento dos solos do Estado, na escala de 1:250.000. O presente estudo desenvolveu o sistema especialista ATOSC (Avaliação das Terras do Oeste de Santa Catarina) e, na sua construção, incluiu-se a definição dos requerimentos dos tipos de utilização da terra, bem como foi feita a subseqüente comparação destes com os atributos de cada unidade de mapeamento. Os tipos de utilização da terra considerados foram: feijão, milho, soja e trigo, em cultivos solteiros, sob condições de sequeiro e de manejo característicos destas culturas no Estado. As informações sobre os recursos naturais compreendem os atributos climáticos, de solos e das condições da paisagem que interferem na produção destas culturas. Para cada tipo de utilização da terra foram especificados, no ATOSC, o código, o nome e seus respectivos requerimentos de uso da terra. Os requerimentos de cada cultura foram definidos por uma combinação específica das características das terras selecionadas, que determina o nível de severidade de cada um deles em relação à cultura. Estabeleceram-se quatro níveis de severidade que indicam aumento do grau de limitação ou diminuição do potencial para determinado tipo de uso da terra, a saber: limitação nula ou ligeira (favorável); limitação moderada (moderadamente favorável), limitação forte (pouco favorável); e limitação muito forte (desfavorável). Na árvore de decisão, componente básico do sistema especialista, são implementadas as regras que permitirão o enquadramento das terras em classes de adequação definidas, baseado na qualidade dos requerimentos de acordo com o tipo de uso. O ATOSC facilitou o processo de comparação entre as características das terras das microrregiões de Chapecó e Xanxerê e os requerimentos de uso considerados, por permitir efetuar automaticamente a avaliação das terras, reduzindo, assim, o tempo gasto neste processo. As terras das microrregiões de Chapecó e Xanxerê foram enquadradas, em sua maior parte, nas classes de adequação pouco favorável (3) e desfavorável (4) para os cultivos considerados. Os principais fatores limitantes identificados nestas microrregiões foram a fertilidade natural e o risco de erosão, para o feijão e o milho, e condições de mecanização e risco de erosão, para a soja e o trigo.