Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

Optimal Bayes Classifiers for Functional Data and Density Ratios

Bayes classifiers for functional data pose a challenge. This is because probability density functions do not exist for functional data. As a consequence, the classical Bayes classifier using density quotients needs to be modified. We propose to use density ratios of projections on a sequence of eigenfunctions that are common to the groups to be classified. The density ratios can then be factored into density ratios of individual functional principal components whence the classification problem is reduced to a sequence of nonparametric one-dimensional density estimates. This is an extension to functional data of some of the very earliest nonparametric Bayes classifiers that were based on simple density ratios in the one-dimensional case. By means of the factorization of the density quotients the curse of dimensionality that would otherwise severely affect Bayes classifiers for functional data can be avoided. We demonstrate that in the case of Gaussian functional data, the proposed functional Bayes classifier reduces to a functional version of the classical quadratic discriminant. A study of the asymptotic behavior of the proposed classifiers in the large sample limit shows that under certain conditions the misclassification rate converges to zero, a phenomenon that has been referred to as "perfect classification". The proposed classifiers also perform favorably in finite sample applications, as we demonstrate in comparisons with other functional classifiers in simulations and various data applications, including wine spectral data, functional magnetic resonance imaging (fMRI) data for attention deficit hyperactivity disorder (ADHD) patients, and yeast gene expression data

Twenty years of P-splines

P-splines first appeared in the limelight twenty years ago. Since then they have become popular in applications and in theoretical work. The combination of a rich B-spline basis and a simple difference penalty lends itself well to a variety of generalizations, because it is based on regression. In effect, P-splines allow the building of a “backbone” for the “mixing and matching” of a variety of additive smooth structure components, while inviting all sorts of extensions: varying-coefficient effects, signal (functional) regressors, two-dimensional surfaces, non-normal responses, quantile (expectile) modelling, among others. Strong connections with mixed models and Bayesian analysis have been established. We give an overview of many of the central developments during the first two decades of P-splines.Peer Reviewe

Twenty years of P-splines

P-splines first appeared in the limelight twenty years ago. Since then they have become popular in applications and in theoretical work. The combination of a rich B-spline basis and a simple difference penalty lends itself well to a variety of generalizations, because it is based on regression. In effect, P-splines allow the building of a “backbone” for the “mixing and matching” of a variety of additive smooth structure components, while inviting all sorts of extensions: varying-coefficient effects, signal (functional) regressors, two-dimensional surfaces, non-normal responses, quantile (expectile) modelling, among others. Strong connections with mixed models and Bayesian analysis have been established. We give an overview of many of the central developments during the first two decades of P-splines

Stream Power and Geomorphic Effects of Flash Floods

Le piene improvvise (flash flood) sono fra i processi naturali pi\uf9 devastanti e sono responsabili di rilevanti e subitanei effetti morfologici, nonch\ue9 della perdita di vite umane e di gravi danni economici. Le piene improvvise sono caratterizzate dalla forte variabilit\ue0 spazio-temporale delle precipitazioni innescanti, cui consegue una forte variabilit\ue0 delle portate e della potenza della corrente. Gli effetti geomorfologici delle piene improvvise dipendono sia dal controllo che l\u2019assetto geologico esercita sulla geometria del canale e sulle caratteristiche del sedimento, sia dall\u2019intensit\ue0 della piena. Gli effetti geomorfologici delle piene improvvise si manifestano attraverso processi sia erosivi che deposizionali che determinano variazioni nell\u2019assetto del canale rispetto alle condizioni antecedenti l\u2019evento. La questione centrale di questa tesi \ue8 valutare perch\ue9 piene improvvise di simile intensit\ue0 producano talvolta effetti morfologici nettamente differenti. L\u2019uso dei valori istantanei massimi di variabili di tipo idraulico, quali la portata, la velocit\ue0, lo sforzo tangenziale e la potenza della corrente, si \ue8 spesso rivelato non conclusivo nel quantificare i cambiamenti morfologici. Questa tesi mira a studiare come fattori quali la geometria del canale, il substrato, l\u2019intensit\ue0 e la durata dell\u2019evento possano interagire e influenzare l\u2019azione morfologia delle piene improvvise. Un\u2019analisi combinata, basata rilievi post-evento e sulla modellazione idrologica, ha consentito di caratterizzare sette importanti eventi di piena improvvisa verificatisi fra il 2007 e il 2014 in diverse regioni dell\u2019Europa centrale e meridionale. Nei bacini mediterranei gli elevati valori delle portate di picco, uniti alla durata relativamente lunga degli eventi, hanno determinato le condizioni favorevoli a significativi impatti geomorfologici. I valori della potenza della corrente sono generalmente coerenti con i cambiamenti morfologici osservati. Inoltre, i canali in roccia mostrano i valori di dispendio energetico pi\uf9 elevati ma senza erosioni apprezzabili, mente ingenti fenomeni di erosione sono stati osservati in canali alluvionali. Gli andamenti dei processi geomorfologici nei canali semi alluvionali richiedono il riconoscimento di situazioni locali che aumentano la resistenza del letto del canale e delle sponde all\u2019erosione, o di condizioni specifiche di un particolare evento. Piene di breve durata causano talvolta abbondante trasporto solido, peraltro non associato a significativi allargamenti del canale nella maggior parte degli alvei semi-alluvionali. Otto corsi d\u2019acqua, individuati fra quelli maggiormente interessati da tre delle piene studiate sono stati scelti per ulteriori analisi e per la modellazione della variazione longitudinale dei valori della potenza della corrente. Funzioni di potenza interpretano adeguatamente l\u2019aumento verso valle delle portate di picco, mentre funzioni quadratiche si sono dimostrate pi\uf9 soddisfacenti delle relazioni esponenziali comunemente utilizzate per rappresentare la variazione longitudinale della pendenza dell\u2019alveo. Le prestazioni dei modelli empirici per la variazione longitudinale della potenza della corrente per unit\ue0 di larghezza dell\u2019alveo (unit stream power) evidenziano il fondamentale controllo esercitato dalla pendenza dell\u2019alveo. La disponibilit\ue0 di immagini satellitari ad elevata risoluzione riprese prima e dopo gli eventi oggetto di studio ha permesso di valutare le modifiche del canale lungo sette di questi canali. Analisi statistiche hanno indicato che le sole variabili idrauliche non sono sufficienti per interpretare il tasso di allargamento del canale, che \ue8 principalmente influenzato dal grado di confinamento del canale stesso. Insieme al confinamento laterale, la potenza della corrente per unit\ue0 di larghezza dell\u2019alveo appare un valido predittore dell\u2019allargamento in alvei ad elevata pendenza, mentre l\u2019energia complessiva della corrente calcolata per l\u2019intero evento fornisce prestazioni migliori nell\u2019interpretare la variabilit\ue0 dell\u2019allargamento dell\u2019alveo in canali a pendenza moderata. L'uso di differenti soglie di resistenza all\u2019erosione per quantificare i cambiamenti geomorfologici degli alvei supporta la conclusione che la determinazione di tali cambiamenti \ue8 molto pi\uf9 difficile della determinazione delle variabili idrauliche coinvolte

Ecological strategies and disturbance response of tropical forest trees: insight from functional trait variation

Tropical forests store 40% of terrestrial carbon, process six times as much carbon as is released through fossil fuel use, and are epicenters of biodiversity. Despite all that we know about tropical forests, there remains much to discover about variation in ecological strategies, differences in the way species acquire limited resources through dissimilarities in construction and allocation patterns. We also know little as to how this variation shapes the resilience of tropical tree communities to disturbance. These forests are increasingly threatened by global change stressors, such as anthropogenic land-use and climate change. Recent advances in ecological literature show that more insight into differences in ecological strategies among tropical forest species can be gained by going beyond species distributions to also examine functional trait variation. Functional traits are morphological and physiological traits that reflect allocation strategies thought to be important determinants of fitness. In the first two chapters of my dissertation, I quantified wood density and anatomical variation at multiple scales, and related this variation to ecological strategies of tropical forest tree species. The last two chapters examined effects of historical disturbance on the composition and temporal dynamics of tropical forest communities. In addition to wood density, other traits studied in these later chapters were maximum height and diameter. Across my dissertation, the scales spanned ranged from intra-individual, intra-specific, interspecific, community and temporal levels, across two tropical forests, the 50 ha CTFS plot in BCI, Panama, and the 5.2 ha long-term forest plots in Kibale National Park, Uganda. With the functional trait approach, my dissertation demonstrated several novel patterns, including 1) linear radial increases in wood density are typical of fast-growth high mortality tropical tree species, while slow-growth low mortality species show a range of radial changes in wood density including non-linear trends 2) greater variation in ecological strategies when wood density is decomposed into anatomical components, with functional consequences for species growth and mortality of saplings but not adult trees, 3) persistence of the effects of selective logging on the taxonomic and structural composition but not functional composition of a tropical forest 45 years after, and 4) inadequacy of classical successional models that assume recovery to pre-disturbance conditions for predicting the effects of selective logging on tropical forest dynamics

Cross-sectional Morphology and Mechanical Loading in Plio-Pleistocene Hominins: Implications for Locomotion and Taxonomy

This study explores locomotion and locomotor variability in Plio-Pleistocene hominins by examining cross-sectional properties and mechanical loading patterns in the proximal and midshaft femur of Paranthropus, fossil Homo sp. and H. erectus. Modern human and Pan models are used for comparative purposes. Cross-sectional properties in the proximal and midshaft femur of fossil hominins are examined to test the hypothesis that members of the same genus should exhibit similar locomotor behavior. In the proximal femur, fossil Homo sp. cluster with modern humans to the exclusion of Paranthropus, and East and South African Paranthropus cluster together. Group differences are primarily due to differences in average bending and torsional strength. KNM-ER 738, which has been allocated to both Paranthropus and Homo, is more similar to paranthropine samples than to modern and fossil Homo. In the midshaft femur, fossil Homo sp. and H. erectus cluster with modern humans. OH 62 (H. habilis), however, forms a cluster by itself. It is unclear if this indicates a non-Homo status or if locomotor behavior was highly variable in early Homo. KNM-ER 1592, which is generally attributed to Paranthropus, clusters with modern and fossil Homo. This either suggests that mechanical loading is comparable between Paranthropus and Homo or that KNM-ER 1592 is misclassified as Paranthropus. KNM-ER 736 and KNM-ER 1807, which have been allocated to both Paranthropus and Homo, cluster with modern and fossil Homo, and therefore cannot be excluded from this genus. Group differences in the midshaft femur are largely due to differences in average bending and torsional strength. Relationships between cross-sectional properties in the proximal and midshaft femur are examined to investigate if mechanical loading patterns in fossil hominin femora suggest human-like locomotion, Pan-like locomotion or intermediate locomotor behavior. The relative amount of cortical bone is elevated in modern humans compared to Pan, and in fossil hominins compared to modern humans. Axial strength is greater relative to average bending and torsional strength in modern humans compared to Pan. Fossil Homo sp. and H. erectus are most similar to modern humans in this regard. OH 62, however, displays the Pan-like pattern. Mechanical loading patterns in Paranthropus are more similar to patterns in modern humans than to patterns in Pan. The relationship between bending strength in the medio-lateral plane relative to bending strength in the antero-posterior plane of the proximal and midshaft femur is not significantly different between modern humans and Pan. Thus, different mechanical demands could potentially yield similarities in diaphyseal shape