Active Contour-Based Segmentation of Head and Neck with Adaptive Atlas Selection

This paper presents automated segmentation of structuresin the Head and Neck (H\&N) region, using an activecontour-based joint registration and segmentation model.A new atlas selection strategy is also used. Segmentationis performed based on the dense deformation fieldcomputed from the registration of selected structures inthe atlas image that have distinct boundaries, onto thepatient's image. This approach results in robustsegmentation of the structures of interest, even in thepresence of tumors, or anatomical differences between theatlas and the patient image. For each patient, an atlasimage is selected from the available atlas-database,based on the similarity metric value, computed afterperforming an affine registration between each image inthe atlas-database and the patient's image. Unlike manyof the previous approaches in the literature, thesimilarity metric is not computed over the entire imageregion; rather, it is computed only in the regions ofsoft tissue structures to be segmented. Qualitative andquantitative evaluation of the results is presented.

Validation of tissue modelization and classification techniques in T1-weighted MR brain images

We propose a deep study on tissue modelization andclassification Techniques on T1-weighted MR images. Threeapproaches have been taken into account to perform thisvalidation study. Two of them are based on FiniteGaussian Mixture (FGM) model. The first one consists onlyin pure gaussian distributions (FGM-EM). The second oneuses a different model for partial volume (PV) (FGM-GA).The third one is based on a Hidden Markov Random Field(HMRF) model. All methods have been tested on a DigitalBrain Phantom image considered as the ground truth. Noiseand intensity non-uniformities have been added tosimulate real image conditions. Also the effect of ananisotropic filter is considered. Results demonstratethat methods relying in both intensity and spatialinformation are in general more robust to noise andinhomogeneities. However, in some cases there is nosignificant differences between all presented methods.

Intensified chemotherapy with ACVBP plus rituximab versus standard CHOP plus rituximab for the treatment of diffuse large B-cell lymphoma (LNH03-2B): an open-label randomised phase 3 trial.

BACKGROUND: The outcome of diffuse large B-cell lymphoma has been substantially improved by the addition of the anti-CD20 monoclonal antibody rituximab to chemotherapy regimens. We aimed to assess, in patients aged 18-59 years, the potential survival benefit provided by a dose-intensive immunochemotherapy regimen plus rituximab compared with standard treatment plus rituximab. METHODS: We did an open-label randomised trial comparing dose-intensive rituximab, doxorubicin, cyclophosphamide, vindesine, bleomycin, and prednisone (R-ACVBP) with subsequent consolidation versus standard rituximab, doxorubicin, cyclophosphamide, vincristine, and prednisone (R-CHOP). Random assignment was done with a computer-assisted randomisation-allocation sequence with a block size of four. Patients were aged 18-59 years with untreated diffuse large B-cell lymphoma and an age-adjusted international prognostic index equal to 1. Our primary endpoint was event-free survival. Our analyses of efficacy and safety were of the intention-to-treat population. This study is registered with ClinicalTrials.gov, number NCT00140595. FINDINGS: One patient withdrew consent before treatment and 54 did not complete treatment. After a median follow-up of 44 months, our 3-year estimate of event-free survival was 81% (95% CI 75-86) in the R-ACVBP group and 67% (59-73) in the R-CHOP group (hazard ratio [HR] 0·56, 95% CI 0·38-0·83; p=0·0035). 3-year estimates of progression-free survival (87% [95% CI, 81-91] vs 73% [66-79]; HR 0·48 [0·30-0·76]; p=0·0015) and overall survival (92% [87-95] vs 84% [77-89]; HR 0·44 [0·28-0·81]; p=0·0071) were also increased in the R-ACVBP group. 82 (42%) of 196 patients in the R-ACVBP group experienced a serious adverse event compared with 28 (15%) of 183 in the R-CHOP group. Grade 3-4 haematological toxic effects were more common in the R-ACVBP group, with a higher proportion of patients experiencing a febrile neutropenic episode (38% [75 of 196] vs 9% [16 of 183]). INTERPRETATION: Compared with standard R-CHOP, intensified immunochemotherapy with R-ACVBP significantly improves survival of patients aged 18-59 years with diffuse large B-cell lymphoma with low-intermediate risk according to the International Prognostic Index. Haematological toxic effects of the intensive regimen were raised but manageable. FUNDING: Groupe d'Etudes des Lymphomes de l'Adulte and Amgen.

A statistical shape model of the human second cervical vertebra.

PURPOSE: Statistical shape and appearance models play an important role in reducing the segmentation processing time of a vertebra and in improving results for 3D model development. Here, we describe the different steps in generating a statistical shape model (SSM) of the second cervical vertebra (C2) and provide the shape model for general use by the scientific community. The main difficulties in its construction are the morphological complexity of the C2 and its variability in the population. METHODS: The input dataset is composed of manually segmented anonymized patient computerized tomography (CT) scans. The alignment of the different datasets is done with the procrustes alignment on surface models, and then, the registration is cast as a model-fitting problem using a Gaussian process. A principal component analysis (PCA)-based model is generated which includes the variability of the C2. RESULTS: The SSM was generated using 92 CT scans. The resulting SSM was evaluated for specificity, compactness and generalization ability. The SSM of the C2 is freely available to the scientific community in Slicer (an open source software for image analysis and scientific visualization) with a module created to visualize the SSM using Statismo, a framework for statistical shape modeling. CONCLUSION: The SSM of the vertebra allows the shape variability of the C2 to be represented. Moreover, the SSM will enable semi-automatic segmentation and 3D model generation of the vertebra, which would greatly benefit surgery planning.

Efficient total variation algorithm for fetal MRI reconstruction

Fetal MRI reconstruction aims at finding a high-resolution image given a small set of low-resolution images. It is usually modeled as an inverse problem where the regularization term plays a central role in the reconstruction quality. Literature has considered several regularization terms s.a. Dirichlet/Laplacian energy [1], Total Variation (TV)based energies [2,3] and more recently non-local means [4]. Although TV energies are quite attractive because of their ability in edge preservation, standard explicit steepest gradient techniques have been applied to optimize fetal-based TV energies. The main contribution of this work lies in the introduction of a well-posed TV algorithm from the point of view of convex optimization. Specifically, our proposed TV optimization algorithm for fetal reconstruction is optimal w.r.t. the asymptotic and iterative convergence speeds O(1/n(2)) and O(1/root epsilon), while existing techniques are in O(1/n) and O(1/epsilon). We apply our algorithm to (1) clinical newborn data, considered as ground truth, and (2) clinical fetal acquisitions. Our algorithm compares favorably with the literature in terms of speed and accuracy.

St. Petersburg Court Chant and the Tradition of Eastern Slavic Church Singing

The present study examines the repertory of liturgical chant known as St. Petersburg Court Chant which emerged within the Imperial Court of St. Petersburg, Russia, and appeared in print in a number of revisions during the course of the 19th century, eventually to spread throughout the Russian Empire and even abroad. The study seeks answers to questions on the essence and composition of Court Chant, its history and liturgical background, and most importantly, its musical relationship to other repertories of Eastern Slavic chant. The research questions emerge from previous literary accounts of Court Chant (summarized in the Introduction), which have tended to be inaccurate and generally not based on critical research. The study is divided into eight main chapters. Chapter 1 provides a survey of the history of Eastern Slavic chant and the Imperial Court Chapel of St. Petersburg until 1917, with special emphasis on the history of singing traditional chant in polyphony, the status of the Court Chapel as a government authority, and its endeavours in publishing church music. Chapter 2 deals with the liturgical background of Eastern chant, the chant genres, and main repertories of Eastern Slavic chant. Chapter 3 concentrates on chant sources: it introduces the musical notations utilised, after which a typology of chant books is presented. The discussion continues with a survey of the sources of Court Chant and their content, the specimens selected for closer analysis, the comparative materials from other repertories, and ends with a commentary on some chant sources that have been excluded. The comparative sources include a specimen from around the beginning of the 12th century, a few manuscripts from the 17th century, and printed and manuscript chant books from the early 18th to early 20th century, covering the geographical area that delimits to the western Ukraine, Astrakhan, Nizhny Novgorod, and the Solovetsky Monastery. Chapter 4 presents the approach and methods used in the subsequent analytical comparisons. After a survey of the pitch organization of Eastern Slavic chant, the customary harmonization strategy of traditional chant polyphony is examined, according to which a method for meaningful analysis of the harmony is proposed. The method is based on the observation that the harmonic framework of chant polyphony derives from the standard pitch collection of monodic chant known as the Church Gamut, specific pitches of which form eight harmonic regions that behave like the usual tonalities of major and harmonic minor. Because of the considerable quantity of comparative chant forms, computer-assisted statistical methods are applied to the analysis of chant melodies. The primary chant forms and their respective comparative forms have been pre-processed into reduced chant prototypes and divided into redactions. The analyses are carried out by measuring the formal dissimilarities of the primary chant forms of the Court Chant repertory against each comparative form, and also by measuring the reciprocal dissimilarities of all chant versions in a redaction, the results of which are subjected to agglomerative hierarchical clustering in order to find out how the chant forms relate to each other. The dissimilarities are determined by applying a metric dissimilarity function that is based on the Levenshtein Distance. Chapter 5 provides the melodic and harmonic analyses of generic chants (chants used for multiple texts of different lengths), i.e., chants for stichera samoglasny and troparia, Chapter 6 of pseudo-generic chants (chants that are used for multiple texts but with certain restrictions), i.e., chants for heirmoi, prokeimena, and three other hymns, and Chapter 7 of non-generic chants, covering nine chants that in the Court repertory are not shared by multiple texts. The results are summarized and evaluated in Chapter 8. Accordingly, it can be established that, contrary to previous conceptions, melodically, Court Chant is in effect a full part of the wider Eastern Slavic chant tradition. Even if it is somewhat detached from the chant versions of the Synodal square-note chant books and the local tradition of Moscow, it is particularly close to chant forms of East Ukraine and some vernacular repertories from Russia. Respectively, the harmonization strategies of Court Chant do not show significant individuality in comparison with those of the available polyphonic comparative sources, the main difference being the part-writing, which generally conforms to western common practice standard, whereas the deviations from this tend to be more significant in other analysed repertories of polyphonic chant. Thus, insofar as the subsequent prevalence of Court Chant is not based on its forceful dissemination by authorities (as suggested in previous literature but for which little tangible evidence could be found in Chapter 1), in the present author’s interpretation, Court Chant attained its dominance principally because musically it was considered sufficiently traditional, and as a chant body supported by the government, was conveniently available in print in serviceable harmonizations.

PTEN expression in patients with carcinoma of the cervix and its association with p53, Ki-67 and CD31

PURPOSE: To investigate protein expression and mutations in phosphatase and tensin homolog (PTEN) in patients with stage IB cervical squamous cell carcinoma (CSCC) and the association with clinical-pathologic features, tumor p53 expression, cell proliferation and angiogenesis.METHODS:Women with stage IB CSCC (n=20 - Study Group) and uterine myoma (n=20 - Control Group), aged 49.1±1.7 years (mean±standard deviation, range 27-78 years), were prospectively evaluated. Patients with cervical cancer were submitted to Piver-Rutledge class III radical hysterectomy and pelvic lymphadenectomy and patients in the Control Group underwent vaginal hysterectomy. Tissue samples from the procedures were stained with hematoxylin and eosin for histological evaluation. Protein expression was detected by immunohistochemistry. Staining for PTEN, p53, Ki-67 and CD31 was evaluated. The intensity of PTEN immunostaining was estimated by computer-assisted image analysis, based on previously reported protocols. Data were analyzed using the Student's t-test to evaluate significant differences between the groups. Level of significance was set at p<0.05.RESULTS:The PTEN expression intensity was lower in the CSCC group than in the Control (benign cervix) samples (150.5±5.2 versus 204.2±2.6; p<0.001). Our study did not identify any mutations after sequencing all nine PTEN exons. PTEN expression was not associated with tumor expression of p53 (p=0.9), CD31 (p=0.8) or Ki-67 (p=0.3) or clinical-pathologic features in patients with invasive carcinoma of the cervix.CONCLUSIONS: Our findings demonstrate that the PTEN protein expression is significantly diminished in CSCC.

Elever syns på nätet : multimodala texter och autentiska mottagare

This study is based on the notion that all students are likely to have a computer of some kind as their primary tool at school within a few years. The overall aim is to contribute to the knowledge of what this development of computer-assisted multimodal text production and communication on and over the net may entail in a school context. The study has an abductive approach drawing on theory from Media and Communication studies and from Pedagogy - particularly on media peda-gogy, multimodality, storytelling, conversation research and deliberative democracy – and is based on a DBR project in three schools. The empirical data are retrieved from four school classes, school years 4 and 5, with good access to computers and digital cameras. The classes have used the class blogs to tell the blog visitors about their school work and Skype to communicate with other classes in Sweden and Tanzania. A variety of research methods was employed: content analysis of texts, observations with field notes and camera documentation, interviews with individual students, group interviews with teachers and students, and a small survey. The study is essentially qualitative, focusing on students’ different perceptions. A small quantitative study was conducted to determine if any factors and variables could be linked to each other and to enable comparisons of the surveyed group with other research results. The results suggest that more computers at school offer more opportunities for real-life assignments and the chance to secure an authentic audience to the students’ production; primarily the students’ parents and relatives, students in the same class and at other schools. A theoretical analysis model to determine the degree of reality and authenticity in various school assignments was developed. The results also indicate that having access to cameras for documenting various events in the classes and to an authentic audience can create new opportunities for storytelling that have not been practiced previously at school. The documentary photo invites a viewer into the present tense of the image and the location where the picture was taken, whoever took the picture. It is used by the students and here too, a model has been developed to describe this relationship. The study also focuses on the freedom of expression and democracy. One of the more unexpected findings is that the students in the study did not see that they can influence other people’s perceptions or change various power structures through communication on the web, neither in nor outside of school.

Validation of a simple and inexpensive method for the quantitation of infarct in the rat brain

A gravimetric method was evaluated as a simple, sensitive, reproducible, low-cost alternative to quantify the extent of brain infarct after occlusion of the medial cerebral artery in rats. In ether-anesthetized rats, the left medial cerebral artery was occluded for 1, 1.5 or 2 h by inserting a 4-0 nylon monofilament suture into the internal carotid artery. Twenty-four hours later, the brains were processed for histochemical triphenyltetrazolium chloride (TTC) staining and quantitation of the schemic infarct. In each TTC-stained brain section, the ischemic tissue was dissected with a scalpel and fixed in 10% formalin at 0ºC until its total mass could be estimated. The mass (mg) of the ischemic tissue was weighed on an analytical balance and compared to its volume (mm³), estimated either by plethysmometry using platinum electrodes or by computer-assisted image analysis. Infarct size as measured by the weighing method (mg), and reported as a percent (%) of the affected (left) hemisphere, correlated closely with volume (mm³, also reported as %) estimated by computerized image analysis (r = 0.88; P < 0.001; N = 10) or by plethysmography (r = 0.97-0.98; P < 0.0001; N = 41). This degree of correlation was maintained between different experimenters. The method was also sensitive for detecting the effect of different ischemia durations on infarct size (P < 0.005; N = 23), and the effect of drug treatments in reducing the extent of brain damage (P < 0.005; N = 24). The data suggest that, in addition to being simple and low cost, the weighing method is a reliable alternative for quantifying brain infarct in animal models of stroke.

Automatic image-based identification of Saimaa ringed seals

The Saimaa ringed seal is one of the most endangered seals in the world. It is a symbol of Lake Saimaa and a lot of effort have been applied to save it. Traditional methods of seal monitoring include capturing the animals and installing sensors on their bodies. These invasive methods for identifying can be painful and affect the behavior of the animals. Automatic identification of seals using computer vision provides a more humane method for the monitoring. This Master's thesis focuses on automatic image-based identification of the Saimaa ringed seals. This consists of detection and segmentation of a seal in an image, analysis of its ring patterns, and identification of the detected seal based on the features of the ring patterns. The proposed algorithm is evaluated with a dataset of 131 individual seals. Based on the experiments with 363 images, 81\% of the images were successfully segmented automatically. Furthermore, a new approach for interactive identification of Saimaa ringed seals is proposed. The results of this research are a starting point for future research in the topic of seal photo-identification.

Effectiveness of computer training on attentional skills

This paper presents two studies, both examining the efficacy of a computer programme (Captain's Log) in training attentional skills. The population of interest is the traumatically brain injured. Study #1 is a single-case design that offers recommendations for the second, .larger (N=5) inquiry. Study #2 is an eight-week hierarchical treatment programme with a multi-based testing component. Attention, memory, listening comprehension, locus-of-control, self-esteem, visuo-spatial, and general outcome measures are employed within the testing schedule. Results suggest that any improvement was a result of practice effects. With a few single-case exceptions, the participants showed little improvement in the dependent measures.

Elementary computer-mediated online distance education : identification of criteria for successful implementation and practice

This study had three purposes related to the effective implem,entation and practice of computer-mediated online distance education (C-MODE) at the elementary level: (a) To identify a preliminary framework of criteria 'or guidelines for effective implementation and practice, (b) to identify areas ofC-MODE for which criteria or guidelines of effectiveness have not yet been developed, and (c) to develop an implementation and practice criteria questionnaire based on a review of the distance education literature, and to use the questionnaire in an exploratory survey of elementary C-MODE practitioners. Using the survey instrument, the beliefs and attitudes of 16 elementary C'- MODE practitioners about what constitutes effective implementation and practice principles were investigated. Respondents, who included both administrators and instructors, provided information about themselves and the program in which they worked. They rated 101 individual criteria statenlents on a 5 point Likert scale with a \. point range that included the values: 1 (Strongly Disagree), 2 (Disagree), 3 (Neutral or Undecided), 4 (Agree), 5 (Strongly Agree). Respondents also provided qualitative data by commenting on the individual statements, or suggesting other statements they considered important. Eighty-two different statements or guidelines related to the successful implementation and practice of computer-mediated online education at the elementary level were endorsed. Response to a small number of statements differed significantly by gender and years of experience. A new area for investigation, namely, the role ofparents, which has received little attention in the online distance education literature, emerged from the findings. The study also identified a number of other areas within an elementary context where additional research is necessary. These included: (a) differences in the factors that determine learning in a distance education setting and traditional settings, (b) elementary students' ability to function in an online setting, (c) the role and workload of instructors, (d) the importance of effective, timely communication with students and parents, and (e) the use of a variety of media.

The development of a Flanders Interaction Analysis style instrument for use in educational computer mediated communication research

Please consult the paper edition of this thesis to read. It is available on the 5th Floor of the Library at Call Number: Z 9999 E38 D56 1992

Moyens informatiques de restitution en archéologie monumentale : cas du temple de Karnak

L’objectif de notre recherche est l’exploration et l’étude de la question de l’instrumentation informatique des projets de reconstitution archéologiques en architecture monumentale dans le but de proposer de nouveaux moyens. La recherche a pour point de départ une question, à savoir : « Comment, et avec quels moyens informatiques, les projets de reconstitution architecturale pourraient-ils être menés en archéologie? ». Cette question a nécessité, en premier lieu, une étude des différentes approches de restitution qui ont été mises à contribution pour des projets de reconstitution archéologiques, et ceci, à ses différentes phases. Il s’agit de comprendre l’évolution des différentes méthodologies d’approche (épistémologiquement) que les acteurs de ce domaine ont adoptées afin de mettre à contribution les technologies d’information et de communication (TIC) dans le domaine du patrimoine bâti. Cette étude nous a permis de dégager deux principales avenues: une première qui vise exclusivement la « représentation » des résultats des projets et une seconde qui vise la modélisation de ce processus dans le but d’assister l’archéologue dans les différentes phases du projet. Nous démontrons que c’est la deuxième approche qui permet la combinaison et met à la disposition des archéologues une meilleure exploitation des possibilités que l’outil informatique peut et pourra présenter. Cette partie permet de démontrer la nature systémique et complexe de la mise à contribution des TICs dans le domaine de la restitution archéologique. La multitude des acteurs, des conditions techniques, culturelles et autres, des moyens utilisés ainsi que la variété des objectifs envisagés dans les projets de reconstitution archéologiques poussent à explorer une nouvelle approche qui tient compte de cette complexité. Pour atteindre notre objectif de recherche, la poursuite de l’étude de la nature de la démarche archéologique s’impose. Il s’agit de comprendre les liens et les interrelations qui s’établissent entre les différentes unités techniques et intellectuelles en jeu ainsi que les différents modes de réflexions présents dans les projets de reconstitution archéologique du patrimoine bâti. Cette étude met en évidence le rapport direct entre le caractère subjectif de la démarche avec la grande variabilité des approches et des raisonnements mis en œuvre. La recherche est alors exploratoire et propositionnelle pour confronter notamment le caractère systémique et complexe de l’expérience concrète et à travers les publications savantes, les éléments de la réalité connaissable. L’étude des raisonnements archéologiques à travers les publications savantes nous permet de proposer une première typologie de raisonnements étudiés. Chacune de ces typologies reflète une méthodologie d’approche basée sur une organisation d’actions qui peut être consignée dans un ensemble de modules de raisonnements. Cette recherche fait ressortir, des phénomènes et des processus observés, un modèle qui représente les interrelations et les interactions ainsi que les produits spécifiques de ces liaisons complexes. Ce modèle témoigne d’un processus récursif, par essais et erreurs, au cours duquel l’acteur « expérimente » successivement, en fonction des objectifs de l’entreprise et à travers des modules de raisonnements choisis, plusieurs réponses aux questions qui se posent à lui, au titre de la définition du corpus, de la description, de la structuration, de l’interprétation et de la validation des résultats, jusqu’à ce que cette dernière lui paraisse satisfaire aux objectifs de départ. Le modèle établi est validé à travers l’étude de cas du VIIème pylône du temple de Karnak en Égypte. Les résultats obtenus montrent que les modules de raisonnements représentent une solution intéressante pour assister les archéologues dans les projets de reconstitution archéologiques. Ces modules offrent une multiplicité de combinaisons des actions et avantagent ainsi une diversité d’approches et de raisonnements pouvant être mis à contribution pour ces projets tout en maintenant la nature évolutive du système global.

Une approche fréquentielle pratique pour l'échantillonnage adaptatif en espace image

En synthèse d'images réalistes, l'intensité finale d'un pixel est calculée en estimant une intégrale de rendu multi-dimensionnelle. Une large portion de la recherche menée dans ce domaine cherche à trouver de nouvelles techniques afin de réduire le coût de calcul du rendu tout en préservant la fidelité et l'exactitude des images résultantes. En tentant de réduire les coûts de calcul afin d'approcher le rendu en temps réel, certains effets réalistes complexes sont souvent laissés de côté ou remplacés par des astuces ingénieuses mais mathématiquement incorrectes. Afin d'accélerer le rendu, plusieurs avenues de travail ont soit adressé directement le calcul de pixels individuels en améliorant les routines d'intégration numérique sous-jacentes; ou ont cherché à amortir le coût par région d'image en utilisant des méthodes adaptatives basées sur des modèles prédictifs du transport de la lumière. L'objectif de ce mémoire, et de l'article résultant, est de se baser sur une méthode de ce dernier type[Durand2005], et de faire progresser la recherche dans le domaine du rendu réaliste adaptatif rapide utilisant une analyse du transport de la lumière basée sur la théorie de Fourier afin de guider et prioriser le lancer de rayons. Nous proposons une approche d'échantillonnage et de reconstruction adaptative pour le rendu de scènes animées illuminées par cartes d'environnement, permettant la reconstruction d'effets tels que les ombres et les réflexions de tous les niveaux fréquentiels, tout en préservant la cohérence temporelle.