1,720,984 research outputs found
Development and validation of automatic tools for segmentation of white matter hyperintensities
No full textAutomatic methods for segmentation of various tissues and pathologies are critical for systematic studies of the brain to investigate changes that occur in different components of the phenomenon under study. White matter hyperintensities (WMHs) are one of the major components of small-vessel disease in aging and Alzheimer's disease (AD) populations that need to be assessed and monitored to estimate the vascular disease burden. In this thesis, a new fully automatic technique is proposed for segmenting WMHs from multiple contrasts of magnetic resonance (MR) brain images. The proposed segmentation technique uses a machine learning classification scheme by combining a set of intensity and location features obtained from multi-contrast MR sequences, namely T1w, T2w, proton density (PD) and fluid attenuated inversion recovery (FLAIR) images and a linear or nonlinear classifier to detect WMHs. The segmentations are performed in the native space of the optimal contrast (e.g. FLAIR or T2w) to avoid the blurring caused by resampling the images, especially since these images generally have relatively thick slices (3-5 mm). The classifiers are then trained on the training dataset with manually segmented labels. The performance of the classifiers is assessed using Dice Kappa values as the primary outcome measure and through a 10-fold cross validation scheme.Using the developed tool, the WMHs were segmented using different combinations of input image contrasts (i.e. T1w+T2w+PD, T1w+FLAIR, T1w) to assess the performance of the classifiers and the contribution of each of the contrasts in detecting WMHs. The question of interest was whether the WMHs loads obtained from segmentations based only on T1w images can be used as accurate estimates of the actual WMH loads. To assess this, the volumetric correlation of WMH loads in different brain lobes as well as correlation with age and cognitive measures were compared to investigate the effectiveness of each contrast in providing WMH load estimates that are highly correlated with aging and cognitive scores. The assessments revealed that the best Dice Kappa values are obtained while using the optimal FLAIR and T2w/PD contrasts. Classifications based solely on T1w images tend to undersegment the WMHs, only detecting the brightest of these lesions on FLAIR and T2w/PD images. However, the WMH loads obtained from T1w segmentations were still able to provide high correlations with age and cognitive scores. Finally, using the developed tool, baseline WMHs were segmented in an early stage Parkinson's disease (PD) database as well as age matched healthy controls. Using longitudinal clinical assessments and cortical thickness measures, we studied the relationship between baseline WMHs and future cognitive decline and cortical thinning. PD subjects with high WMH loads were found to present with more future cognitive decline and cortical thinning in comparison with (i) PD subjects with low WMH loads and (ii) age matched control subjects with high WMH loads. These findings show that the existence of WMHs affects PD patients differently from controls.Les méthodes de segmentation automatique de différents tissus et pathologies sont primordiales pour l'étude systématique du cerveau afin d'examiner les changements qui se produisent dans différentes composantes du phénomène étudié. Les hyperintensités de la matière blanche (HMB) sont un des éléments caractéristiques de la maladie des petits vaisseaux qui doit être évalué chez les populations vieillissantes ou souffrant de la maladie d'Alzheimer (MA), afin d'estimer les impacts de la maladie vasculaire. La technique de segmentation proposée utilise un procédé de classification par apprentissage automatique, en associant un ensemble de caractéristiques d'intensité et d'emplacement, obtenues à partir de séquences de RM multi-contrastes, à savoir des images T1w, T2w, de densité de protons (DP) et d'inversion-récupération atténuée par un fluide (FLAIR) ainsi qu'un modèle de classification linéaire ou non-linéaire pour détecter les HMB. Les segmentations sont effectuées dans l'espace natif du contraste optimal (FLAIR ou T2w) afin d'éviter le floutage dû au rééchantillonnage des images, en particulier parce que ces images sont en général composées de tranches épaisses (3-5 mm). La performance des modèles de classification est évaluée en utilisant des valeurs de coefficient de Dice comme mesure primaire de sortie et à travers un procédé de validation croisée en 10 étapes. Grâce à l'outil développé, les HMB ont été segmentées en utilisant différentes combinaisons de contraste comme images d'entrée (par exemple T1w+T2w+PD, T1w+FLAIR, T1w) afin d'évaluer la performance des modèles de classification et la contribution de chacun des contrastes pour la détection des HMB. La question soulevée était de déterminer si la charge de HMB obtenue par une segmentation basée seulement sur des images T1w pouvait être utilisées comme estimé précis de la charge réelle d'HMB. Afin de déterminer la réponse à cette question, la corrélation volumétrique de charge d'HMB dans différents lobes du cerveau ainsi que la corrélation avec l'âge et les mesures cognitives ont été comparées pour examiner l'efficacité de chaque contraste à fournir un estimé de la charge d'HMB fortement corrélé avec l'âge et la performance cognitive. Cette évaluation a révélé que les meilleures valeurs de coefficient de Dice sont obtenues lors de l'utilisation des contrastes FLAIR et T2w/PD optimaux. Les classifications basées uniquement sur les images T1w ont tendance à sous-segmenter les HMB, détectant ainsi uniquement les lésions les plus intenses sur les images FLAIR et T2w/PD. Cependant, les charges de HMB obtenues à partir de segmentations sur les images T1w présentaient tout de même une forte corrélation avec l'âge et la performance cognitive. Enfin, en utilisant l'outil développé, les HMB de base ont été segmentées pour un jeu de données collecté pour des patients à un stade peu avancé de la maladie de Parkinson (MP) ainsi que chez des sujets en bonne santé et d'âge équivalent. En utilisant des évaluations cliniques longitudinales et des mesures de l'épaisseur du cortex, nous avons étudié le lien entre les HMB de base et le déclin cognitif à venir et l'amincissement cortical. Les patients atteints de la MP avec des charges de HMB élevées ont présenté des déclins cognitifs et un amincissement cortical plus importants en comparaison (i) des patients atteints de la MP avec des charges d'HMB basses et (ii) des sujets d'âge comparable possédant des charges élevées d'HMB. Ces résultats montrent que l'existence d'HMB affecte les patients atteints de la MP différemment qu'elle ne le fait chez les individus normaux
Simulation of Chemical Reactions Using Stochastic Petri Nets
Full text linkThe recent breakthroughs in biological experiments have enabled the researchers to measure the quantities of different chemicals that build biological units such as cells. This type of information can be used to build models that can explain and predict the behaviour of the system. Such models can later be used to design control mechanisms that can influence the behaviour of the system in a desired way. With the help of medicine and biology researchers, the designed control mechanisms can be translated into drugs that can control or cure major diseases.
Biological systems usually consist of complex networks of biological components that function through various reactions. In order to affect the behaviour of the system efficiently, the chemicals that have the highest influence on the system behaviour have to be found using a sensitivity analysis. Such chemicals, regarded as inputs, will be the targets for drug design (or other control actions).
Various modeling tools have been empolyed to capture the behaviour of biological systems. Perhaps the most widely used models are the ordinary differential equations (ODEs). In this thesis, an alternative model is propposed for the study of the chemical reactions based on stochastic Petri nets, one type of discrete event systems. It is shown that the proposed method can be used to find the changes of the chemical reactants. The advantage of the proposed method is that it is amenable to implementation on computing systems with parallel processors. This in turn reduces the (time) computational complexity (compared with ODE based simulations). The Petri net based simulations are also used to perform sensitivity analysis. The proposed method is illustrated using the Caspase Apoptosis network
White matter hyperintensity maps in aging and neurodegenerative diseases
No full text<div>The files contain voxel-wise white matter hyperintensity (WMH) maps for 11 different neurodegenerative disease cohorts from the <em>Canadian</em> Consortium on Neurodegeneration in Aging (<em>CCNA</em>) COMPASS-ND dataset in the MNI-ICBM152-2009c space.</div>
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<div>For more information regarding the participants and method details, see: </div>
<div>Dadar, M., Mahmoud, S., Zhernovaia, M., Camicioli, R., Maranzano, J., Duchesne, S., & CCNA Group. (2022). White matter hyperintensity distribution differences in aging and neurodegenerative disease cohorts. <em>NeuroImage: Clinical</em>, <em>36</em>, 103204.</div>
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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