ITK及其在医学图像分割中的应用

ITK(The Insight Toolkit)是一个开放的、面向对象的类库。它提供了强大的二维医学图像处理功能,主要用于医学图像的预处理、分割及配准。本文主要介绍图像分割的算法以及ITK在图像分割中的应用,并简要介绍一个基于ITK的医学图像处理的实现。

A Skull-Stripping Filter for ITK

Skull-stripping (or brain extraction) is an important pre-processing step in neuroimage analysis. This document describes a skull-stripping filter implemented using the Insight Toolkit ITK, which we named itk::StripTsImageFilter. It is a composite filter based on existing ITK classes. The filter has been implemented with usability, robustness, speed and versatility in mind, rather than accuracy. This makes it useful for many pre-processing tasks in neuroimage analysis. This paper is accompanied by the source code, input data and a testing environment.

Src-induced activation of inducible T cell kinase (ITK) requires phosphatidylinositol 3-kinase activity and the Pleckstrin homology domain of inducible T cell kinase

The Tec family of tyrosine kinases are involved in signals emanating from cytokine receptors, antigen receptors, and other lymphoid cell surface receptors. One family member, ITK (inducible T cell kinase), is involved in T cell activation and can be activated by the T cell receptor and the CD28 cell surface receptor. This stimulation of tyrosine phosphorylation and activation of ITK can be mimicked by the Src family kinase Lck. We have explored the mechanism of this requirement for Src family kinases in the activation of ITK. We found that coexpression of ITK and Src results in increased membrane association, tyrosine phosphorylation and activation of ITK, which could be blocked by inhibitors of the lipid kinase phosphatidylinositol 3-kinase (PI 3-kinase) as well as overexpression of the p85 subunit of PI 3-kinase. Removal of the Pleckstrin homology domain (PH) of ITK resulted in a kinase that could no longer be induced to localize to the membrane or be activated by Src. The PH of ITK was also able to bind inositol phosphates phosphorylated at the D3 position. Membrane targeting of ITK without the PH recovered its ability to be activated by Src. These results suggest that ITK can be activated by a combination of Src and PI 3-kinase.

p56Lck and p59Fyn regulate CD28 binding to phosphatidylinositol 3-kinase, growth factor receptor-bound protein GRB-2, and T cell-specific protein-tyrosine kinase ITK: implications for T-cell costimulation.

T-cell activation requires cooperative signals generated by the T-cell antigen receptor zeta-chain complex (TCR zeta-CD3) and the costimulatory antigen CD28. CD28 interacts with three intracellular proteins-phosphatidylinositol 3-kinase (PI 3-kinase), T cell-specific protein-tyrosine kinase ITK (formerly TSK or EMT), and the complex between growth factor receptor-bound protein 2 and son of sevenless guanine nucleotide exchange protein (GRB-2-SOS). PI 3-kinase and GRB-2 bind to the CD28 phosphotyrosine-based Tyr-Met-Asn-Met motif by means of intrinsic Src-homology 2 (SH2) domains. The requirement for tyrosine phosphorylation of the Tyr-Met-Asn-Met motif for SH2 domain binding implicates an intervening protein-tyrosine kinase in the recruitment of PI 3-kinase and GRB-2 by CD28. Candidate kinases include p56Lck, p59Fyn, zeta-chain-associated 70-kDa protein (ZAP-70), and ITK. In this study, we demonstrate in coexpression studies that p56Lck and p59Fyn phosphorylate CD28 primarily at Tyr-191 of the Tyr-Met-Asn-Met motif, inducing a 3- to 8-fold increase in p85 (subunit of PI 3-kinase) and GRB-2 SH2 binding to CD28. Phosphatase digestion of CD28 eliminated binding. In contrast to Src kinases, ZAP-70 and ITK failed to induce these events. Further, ITK binding to CD28 was dependent on the presence of p56Lck and is thus likely to act downstream of p56Lck/p59Fyn in a signaling cascade. p56Lck is therefore likely to be a central switch in T-cell activation, with the dual function of regulating CD28-mediated costimulation as well as TCR-CD3-CD4 signaling.

Mivhar ketavaṿ shel Yosef Ṿitḳin ... /

With: author's ʻUru aḥim, Tel Aviv [1936 or 1937]

Nonlinear container ship model for the study of parametric roll resonance

Parametric roll is a critical phenomenon for ships, whose onset may cause roll oscillations up to +-40 degrees, leading to very dangerous situations and possibly capsizing. Container ships have been shown to be particularly prone to parametric roll resonance when they are sailing in moderate to heavy head seas. A Matlab/Simulink parametric roll benchmark model for a large container ship has been implemented and validated against a wide set of experimental data. The model is a part of a Matlab/Simulink Toolbox (MSS, 2007). The benchmark implements a 3rd-order nonlinear model where the dynamics of roll is strongly coupled with the heave and pitch dynamics. The implemented model has shown good accuracy in predicting the container ship motions, both in the vertical plane and in the transversal one. Parametric roll has been reproduced for all the data sets in which it happened, and the model provides realistic results which are in good agreement with the model tank experiments.

Extracting Three Dimensional Surface Model of Human Kidney from the Visible Human Data Set using Free Software

Three dimensional digital model of a representative human kidney is needed for a surgical simulator that is capable of simulating a laparoscopic surgery involving kidney. Buying a three dimensional computer model of a representative human kidney, or reconstructing a human kidney from an image sequence using commercial software, both involve (sometimes significant amount of) money. In this paper, author has shown that one can obtain a three dimensional surface model of human kidney by making use of images from the Visible Human Data Set and a few free software packages (ImageJ, ITK-SNAP, and MeshLab in particular). Images from the Visible Human Data Set, and the software packages used here, both do not cost anything. Hence, the practice of extracting the geometry of a representative human kidney for free, as illustrated in the present work, could be a free alternative to the use of expensive commercial software or to the purchase of a digital model.

Avaliação tridimensional da sínfise mandibular em crânios secos e sua associação com diferentes classificações de tipos faciais

O objetivo deste trabalho foi desenvolver um estudo morfológico quantitativo e qualitativo da região da sínfise mandibular (SM), através da construção de modelos tridimensionais (3D) e avaliar o seu grau de associação com diferentes classificações de padrões faciais. Foram avaliados 61 crânios secos humanos de adultos jovens com oclusão normal, com idade entre 18 e 45 anos e dentadura completa. Tomografias computadorizadas de feixe cônico (TCFC) de todos os crânios foram obtidas de forma padronizada. O padrão facial foi determinado por método antropométrico e cefalométrico. Utilizando o critério antropométrico, tomando como referência o índice facial (IF), o padrão facial foi classificado em: euriprósopo (≤84,9), mesoprósopo (85,0 - 89,9) e leptoprósopo (≥90,0). Pelo critério cefalométrico, o plano mandibular (FMA) determinou o padrão facial em curto (≤21,0), médio (21,1 - 29,0) e longo (≥29,1); e o índice de altura facial (IAF) classificou a face em hipodivergente (≥0,750), normal (0,749 - 0,650) e hiperdivergente (≤0,649). A construção de modelos 3D, representativos da região da SM, foi realizada com o auxílio do software ITK-SNAP. Os dentes presentes nesta região, incisivos, caninos e pré-molares inferiores, foram separados do modelo por técnica de segmentação semi-automática, seguida de refinamento manual. Em seguida, foram obtidos modelos 3D somente com o tecido ósseo, possibilitando a mensuraçãodo volume ósseo em mm3 (VOL) e da densidade radiográfica, pela média de intensidade dos voxels (Mvox). No programa Geomagic Studio 10 foi feita uma superposição anatômica dos modelos 3D em bestfit para estabelecer um plano de corte padronizado na linha média. Para cada sínfise foi medida a altura (Alt), a largura (Larg) e calculado o índice de proporção entre altura e largura (PAL). A avaliação da presença de defeitos alveolares foi feita diretamente na mandíbula,obtendo-se a média de todas as alturas ósseas alveolares (AltOss) e a média da dimensão das deiscências presentes (Medef). O índice de correlação intra-classe (ICC) com valores entre 0,923 a 0,994,indicou alta reprodutibilidade e confiabilidade das variáveis medidas. As diferenças entre os grupos, determinados pelas classificações do padrão facial (IF, FMA e IAF), foram avaliadas através da análise de variância (oneway ANOVA) seguida do teste post-hoc de Tukey. O grau de associação entre o padrão facial e as variáveis Vol, Mvox, PAL, Alt, Larg, AltOss e Medef foi avaliado pelo coeficiente de correlação de Pearson com um teste t para r. Os resultados indicaram ausência de diferença ou associação entre o volume, densidade radiográfica e presença de defeitos alveolares da SM e o padrão facial quando determinado pelo IF, FMA e IAF. Verificou-se tendência de SM mais longas nos indivíduos com face alongada, porém a largura não mostrou associação com o padrão facial. Estes resultados sugerem que as classificações utilizadas para determinar o padrão facial não representam satisfatoriamente o caráter 3D da face humana e não estão associadas com a morfologia da SM.

Indigenous traditional technical knowledge of disease cure and prevention through fish consumption

Our knowledge regarding ethno-medico zoology is scanty and scattered. The present work is an endeavour to collect information on indigenous traditional knowledge (ITK) of disease cure through fish consumption, prepare a consolidated report on this aspect and to document our ITK so that in the long run after due verification (by Medical experts), such ITK can be patented. We also suggest for the recognition of the age old tribal medicine and establishment of a national research institute for tribal medicines at suitable place for the welfare of all the human beings.

CD30-positive peripheral T-cell lymphomas share molecular and phenotypic features.

Peripheral T-cell lymphoma, not otherwise specified is a heterogeneous group of aggressive neoplasms with indistinct borders. By gene expression profiling we previously reported unsupervised clusters of peripheral T-cell lymphomas, not otherwise specified correlating with CD30 expression. In this work we extended the analysis of peripheral T-cell lymphoma molecular profiles to prototypical CD30(+) peripheral T-cell lymphomas (anaplastic large cell lymphomas), and validated mRNA expression profiles at the protein level. Existing transcriptomic datasets from peripheral T-cell lymphomas, not otherwise specified and anaplastic large cell lymphomas were reanalyzed. Twenty-one markers were selected for immunohistochemical validation on 80 peripheral T-cell lymphoma samples (not otherwise specified, CD30(+) and CD30(-); anaplastic large cell lymphomas, ALK(+) and ALK(-)), and differences between subgroups were assessed. Clinical follow-up was recorded. Compared to CD30(-) tumors, CD30(+) peripheral T-cell lymphomas, not otherwise specified were significantly enriched in ALK(-) anaplastic large cell lymphoma-related genes. By immunohistochemistry, CD30(+) peripheral T-cell lymphomas, not otherwise specified differed significantly from CD30(-) samples [down-regulated expression of T-cell receptor-associated proximal tyrosine kinases (Lck, Fyn, Itk) and of proteins involved in T-cell differentiation/activation (CD69, ICOS, CD52, NFATc2); upregulation of JunB and MUM1], while overlapping with anaplastic large cell lymphomas. CD30(-) peripheral T-cell lymphomas, not otherwise specified tended to have an inferior clinical outcome compared to the CD30(+) subgroups. In conclusion, we show molecular and phenotypic features common to CD30(+) peripheral T-cell lymphomas, and significant differences between CD30(-) and CD30(+) peripheral T-cell lymphomas, not otherwise specified, suggesting that CD30 expression might delineate two biologically distinct subgroups.

Caractérisation cytogénétique et moléculaire des translocations chromosomiques dans la phase blastique de la leucémie myéloïde chronique

La leucémie myéloïde chronique (LMC) est un modèle d’évolution tumorale dans les cancers humains. Le processus d’évolution de la LMC de la phase chronique (PC) à la phase blastique (PB) est caractérisé par un arrêt de différenciation et l’acquisition de la capacité d’autorenouvellement incontrôlé d’une cellule souche ou d’un progéniteur hématopoïétique. La LMC en PB est associée à la présence d’anomalies génétiques additionnelles à la fusion BCR-ABL1 qui résulte de la translocation chromosomique t(9;22). Contrairement aux patients en PC, les patients en PB de la LMC n’obtiennent pas une réponse moléculaire complète à long terme avec 1’Imatinib mesylate, un inhibiteur de la tyrosine kinase (ITK) BCR-ABL1. De plus, les ITKs de deuxième et troisième générations sont moins efficaces en PB de la LMC lorsque les cellules leucémiques ont acquis une résistance au traitement indépendante des mutations de BCR-ABL1. Les mécanismes moléculaires des voies de signalisation impliquées dans la progression de la LMC en PB ne sont pas entièrement élucidés. Le but de notre travail est de caractériser de nouvelles anomalies génétiques dans la PB de la LMC. Nous avons identifié en cytogénétique, quatre nouvelles translocations chromosomiques : t(1;21)(p36;q22), t(7;17)(p15;q22), t(8;17)(q11;q22) et t(2;12)(q31;p13) dans les cellules leucémiques de patients en PB de la LMC résistants au traitement. En utilisant des techniques d'hybridation in situ en fluorescence, de RT-PCR et de séquençage, nous avons délimité les régions à investiguer au niveau des points de cassure et identifié un réarrangement de plusieurs gènes codant pour des facteurs de transcription importants lors de l’hématopoïèse tels que RUNX1, ETV6, PRDM16 et HOXA. L’altération de ces gènes pourrait expliquer l’arrêt de différenciation et/ou l’acquisition de la capacité d’autorenouvellement caractéristiques de la LMC en PB. Nous avons identifié les fusions RUNX1-PRDM16, MSI2-HOXA, MSI2-SOX17 et ETV6-HOXD11, respectivement associées aux translocations chromosomiques t(1;21), t(7;17), t(8;17) et t(2;12). Ces fusions génèrent différents transcrits alternatifs qui maintiennent et altèrent le cadre ouvert de lecture. L’analyse des séquences des transcrits chimériques identifiés dans ce projet, incluant RUNX1-PRDM16, MSI2-HOXA9, MSI2-HOXA10, MSI2-HOXA11 et ETV6-HOXD11, nous a permis de prédire les domaines fonctionnels potentiellement présents au niveau des protéines chimériques prédites. Les transcrits de fusion qui respectent le cadre ouvert de lecture peuvent générer des domaines fonctionnels des deux partenaires. C’est le cas des deux transcrits identifiés pour la fusion RUNX1-PRDM16 où le domaine de liaison à l’ADN RHD (Runt homology domain) de RUNX1 est fusionné avec la quasi-totalité des domaines de PRDM16. Les transcrits de fusion qui ne respectent pas le cadre ouvert de lecture donnent des formes tronquées des transcrits RUNX1, MSI2 et ETV6. La juxtaposition des régions promotrices de ces derniers en 5’ de leurs partenaires entraîne l’activation de la forme courte oncogénique de PRDM16 dans la t(1;21) ou de différents gènes HOXA/D dans les t(7;17) et t(2;12), ainsi que l’expression aberrante d’un nouveau transcrit alternatif de SOX17 dans la t(8;17). Notre étude nous a permis d’identifier de nouveaux gènes de fusion et/ou une activation de gènes qui pourraient coopérer avec la fusion BCR-ABL1 dans la progression de la LMC et être impliqués dans la résistance au traitement de la LMC en phase avancée. La caractérisation des événements génétiques associés à la transformation blastique de la LMC est essentielle pour l’investigation des voies moléculaires impliquées dans cette phase de la maladie. Investiguer la résistance au traitement de ces patients pourrait aussi contribuer à identifier de nouvelles cibles thérapeutiques dans cette leucémie.

Is Breast Asymmetry Present in Girls with Adolescent Idiopathic Scoliosis?

Study Design Cross-sectional descriptive study. Objectives To characterize breast asymmetry (BA), as defined by breast volume difference, in girls with significant adolescent idiopathic scoliosis (AIS), using magnetic resonance imaging (MRI). Summary and Background BA is a frequent concern among girls with AIS. It is commonly believed that this results from chest wall deformity. Although many women exhibit physiological BA, the prevalence is not known in adolescents and it remains unclear if it is more frequent in AIS. Breasts vary in shape and size and many ways of measuring them have been explored. MRI shows the highest precision at defining breast tissue. Methods Thirty patients were enrolled on the basis of their thoracic curvature, skeletal and breast maturity, without regard to their perception on their BA. MRI acquisitions were performed in prone with a 1.5-Tesla system using a 16-channel breast coil. Segmentation was achieved using the ITK-SNAP 2.4.0 software and subsequently manually refined. Results The mean left breast volume (528.32 ± 205.96 cc) was greater compared with the mean right breast volume (495.18 ± 170.16 cc) with a significant difference between them. The mean BA was found to be 8.32% ± 6.43% (p < .0001). A weak positive correlation was observed between BA and thoracic Cobb angle (0.177, p = .349) as well as thoracic gibbosity angle (0.289, p = .122). The left breast was consistently larger in 65.5% of the patients. Twenty patients (66.7%) displayed BA ≥5%. Conclusions We have described BA in patients with significant AIS using MRI. This method is feasible, objective, and very precise. The majority of patients had a larger left breast, which could compound the apparent BA secondary to trunk rotation. In many cases, BA is present independently of thoracic deformity. This knowledge will assist in counseling AIS patients in regards to their concerns with BA.

Evaluation of major feed resources in crop-livestock mixed farming systems, southern Ethiopia: Indigenous knowledge versus laboratory analysis results

Evaluation of major feed resources was conducted in four crop-livestock mixed farming systems of central southern Ethiopia, with 90 farmers, selected using multi-stage purposive and random sampling methods. Discussions were held with focused groups and key informants for vernacular name identification of feed, followed by feed sampling to analyse chemical composition (CP, ADF and NDF), in-vitro dry matter digestibility (IVDMD), and correlate with indigenous technical knowledge (ITK). Native pastures, crop residues (CR) and multi-purpose trees (MPT) are the major feed resources, demonstrated great variations in seasonality, chemical composition and IVDMD. The average CP, NDF and IVDMD values for grasses were 83.8 (ranged: 62.9–190), 619 (ranged: 357–877) and 572 (ranged: 317–743) g kg^(−1) DM, respectively. Likewise, the average CP, NDF and IVDMD for CR were 58 (ranged: 20–90), 760 (ranged: 340–931) and 461 (ranged: 285–637)g kg^(−1) DM, respectively. Generally, the MPT and non-conventional feeds (NCF, Ensete ventricosum and Ipomoea batatas) possessed higher CP (ranged: 155–164 g kg^(−1) DM) and IVDMD values (611–657 g kg^(−1) DM) while lower NDF (331–387 g kg^(−1) DM) and ADF (321–344 g kg^(−1) DM) values. The MPT and NCF were ranked as the best nutritious feeds by ITK while crop residues were the least. This study indicates that there are remarkable variations within and among forage resources in terms of chemical composition. There were also complementarities between ITK and feed laboratory results, and thus the ITK need to be taken into consideration in evaluation of local feed resources.

Pre-procés i segmentació en imatges d’ultrasons 2D i 3D de la pròstata

Aquest projecte s'ha dut a terme amb el Grup de visió per computador del departament d'Arquitectura i Tecnologia de Computadors (ATC) de la Universitat de Girona. Està enfocat a l'anàlisi d'imatges mèdiques, en concret s'analitzaran imatges de pròstata en relació a desenvolupaments que s'estan realitzant en el grup de visió esmentat. Els objectius fixats per aquest projecte són desenvolupar dos mòduls de processamentm d'imatges els quals afrontaran dos blocs important en el tractament d'imatges, aquests dos mòduls seran un pre-processat d'imatges, que constarà de tres filtres i un bloc de segmentació per tal de cercar la pròstata dintre de les imatges a tractar. En el projecte es treballarà amb el llenguatge de programació C++, concretament amb unes llibreries que es denominen ITK (Insight Toolkit ) i són open source enfocades al tractament d'imatges mèdiques. A part d'aquesta eina s'utilitzaran d'altres com les Qt que és una biblioteca d'eines per crear entorns gràfics

Política exterior de Canadá en el ártico: entre la seguridad nacional y la prosperidad económica (2006-2011)

En el año 2010 el gobierno de Canadá pública su estrategia de política exterior hacia el Ártico, en la cual manifiesta que esta región es una de las principales prioridades del Gobierno de Stephen Harper en materia de política exterior. Así las cosas, a partir de la perspectiva teórica del realismo neoclásico la investigación se enfoca en analizar por qué la seguridad nacional y la prosperidad económica son los principales intereses de este Gobierno en la zona.