Approximate Bayesian techniques for inference in stochastic dynamical systems

This thesis is concerned with approximate inference in dynamical systems, from a variational Bayesian perspective. When modelling real world dynamical systems, stochastic differential equations appear as a natural choice, mainly because of their ability to model the noise of the system by adding a variant of some stochastic process to the deterministic dynamics. Hence, inference in such processes has drawn much attention. Here two new extended frameworks are derived and presented that are based on basis function expansions and local polynomial approximations of a recently proposed variational Bayesian algorithm. It is shown that the new extensions converge to the original variational algorithm and can be used for state estimation (smoothing). However, the main focus is on estimating the (hyper-) parameters of these systems (i.e. drift parameters and diffusion coefficients). The new methods are numerically validated on a range of different systems which vary in dimensionality and non-linearity. These are the Ornstein-Uhlenbeck process, for which the exact likelihood can be computed analytically, the univariate and highly non-linear, stochastic double well and the multivariate chaotic stochastic Lorenz '63 (3-dimensional model). The algorithms are also applied to the 40 dimensional stochastic Lorenz '96 system. In this investigation these new approaches are compared with a variety of other well known methods such as the ensemble Kalman filter / smoother, a hybrid Monte Carlo sampler, the dual unscented Kalman filter (for jointly estimating the systems states and model parameters) and full weak-constraint 4D-Var. Empirical analysis of their asymptotic behaviour as a function of observation density or length of time window increases is provided.

Estimating parameters in stochastic systems:a variational Bayesian approach

This work is concerned with approximate inference in dynamical systems, from a variational Bayesian perspective. When modelling real world dynamical systems, stochastic differential equations appear as a natural choice, mainly because of their ability to model the noise of the system by adding a variation of some stochastic process to the deterministic dynamics. Hence, inference in such processes has drawn much attention. Here a new extended framework is derived that is based on a local polynomial approximation of a recently proposed variational Bayesian algorithm. The paper begins by showing that the new extension of this variational algorithm can be used for state estimation (smoothing) and converges to the original algorithm. However, the main focus is on estimating the (hyper-) parameters of these systems (i.e. drift parameters and diffusion coefficients). The new approach is validated on a range of different systems which vary in dimensionality and non-linearity. These are the Ornstein–Uhlenbeck process, the exact likelihood of which can be computed analytically, the univariate and highly non-linear, stochastic double well and the multivariate chaotic stochastic Lorenz ’63 (3D model). As a special case the algorithm is also applied to the 40 dimensional stochastic Lorenz ’96 system. In our investigation we compare this new approach with a variety of other well known methods, such as the hybrid Monte Carlo, dual unscented Kalman filter, full weak-constraint 4D-Var algorithm and analyse empirically their asymptotic behaviour as a function of observation density or length of time window increases. In particular we show that we are able to estimate parameters in both the drift (deterministic) and the diffusion (stochastic) part of the model evolution equations using our new methods.

Synthesis and evaluation of N-(3-oxo-2,3-dihydro-1H-pyrazol-4-yl)-1H-indole-carboxamides as cholecystokinin antagonists

The structure-activity relationship optimization of the pyrazoline template 3a resulted in novel 3-oxo-1,2-diphenyl-2,3-dihydro-1H-pyrazol-4-yl)-indole carboxamides 4a-4e. These non-peptidal CCK ligands have been shown to act as potent CCK 1 ligands in a [125]I-CCK-8 receptor binding assay. The best amides (4c and 4d) of this series displayed an IC50 of 20/25 CCK 1 for the CCK 1 receptor. In a subsequent in-vivo evaluation using various behaviour pharmacological assays, an anxiolytic effect of these novel 3-oxo-1,2-diphenyl-2,3-dihydro-1H-pyrazol-4-yl)-indole carboxamides was found at high doses in the elevated plus-maze. In the despair swimming test, a model for testing antidepressants, an ED50 of 0.33/0.41 mg kg -1 was determined for amide 4c/4d and the antidepressant effect had a magnitude comparable to desimipramine. © 2006 The Authors.

Conceptual Building Information Modelling Framework for Whole‐house Refurbishment based on LCC and LCA

The UK government aims at achieving 80% CO2 emission reduction by 2050 which requires collective efforts across all the UK industry sectors. In particular, the housing sector has a large potential to contribute to achieving the aim because the housing sector alone accounts for 27% of the total UK CO2 emission, and furthermore, 87% of the housing which is responsible for current 27% CO2 emission will still stand in 2050. Therefore, it is essential to improve energy efficiency of existing housing stock built with low energy efficiency standard. In order for this, a whole‐house needs to be refurbished in a sustainable way by considering the life time financial and environmental impacts of a refurbished house. However, the current refurbishment process seems to be challenging to generate a financially and environmentally affordable refurbishment solution due to the highly fragmented nature of refurbishment practice and a lack of knowledge and skills about whole‐house refurbishment in the construction industry. In order to generate an affordable refurbishment solution, diverse information regarding costs and environmental impacts of refurbishment measures and materials should be collected and integrated in right sequences throughout the refurbishment project life cycle among key project stakeholders. Consequently, various researchers increasingly study a way of utilizing Building Information Modelling (BIM) to tackle current problems in the construction industry because BIM can support construction professionals to manage construction projects in a collaborative manner by integrating diverse information, and to determine the best refurbishment solution among various alternatives by calculating the life cycle costs and lifetime CO2 performance of a refurbishment solution. Despite the capability of BIM, the BIM adoption rate is low with 25% in the housing sector and it has been rarely studied about a way of using BIM for housing refurbishment projects. Therefore, this research aims to develop a BIM framework to formulate a financially and environmentally affordable whole‐house refurbishment solution based on the Life Cycle Costing (LCC) and Life Cycle Assessment (LCA) methods simultaneously. In order to achieve the aim, a BIM feasibility study was conducted as a pilot study to examine whether BIM is suitable for housing refurbishment, and a BIM framework was developed based on the grounded theory because there was no precedent research. After the development of a BIM framework, this framework was examined by a hypothetical case study using BIM input data collected from questionnaire survey regarding homeowners’ preferences for housing refurbishment. Finally, validation of the BIM framework was conducted among academics and professionals by providing the BIM framework and a formulated refurbishment solution based on the LCC and LCA studies through the framework. As a result, BIM was identified as suitable for housing refurbishment as a management tool, and it is timely for developing the BIM framework. The BIM framework with seven project stages was developed to formulate an affordable refurbishment solution. Through the case study, the Building Regulation is identified as the most affordable energy efficiency standard which renders the best LCC and LCA results when it is applied for whole‐house refurbishment solution. In addition, the Fabric Energy Efficiency Standard (FEES) is recommended when customers are willing to adopt high energy standard, and the maximum 60% of CO2 emissions can be reduced through whole‐house fabric refurbishment with the FEES. Furthermore, limitations and challenges to fully utilize BIM framework for housing refurbishment were revealed such as a lack of BIM objects with proper cost and environmental information, limited interoperability between different BIM software and limited information of LCC and LCA datasets in BIM system. Finally, the BIM framework was validated as suitable for housing refurbishment projects, and reviewers commented that the framework can be more practical if a specific BIM library for housing refurbishment with proper LCC and LCA datasets is developed. This research is expected to provide a systematic way of formulating a refurbishment solution using BIM, and to become a basis for further research on BIM for the housing sector to resolve the current limitations and challenges. Future research should enhance the BIM framework by developing more detailed process map and develop BIM objects with proper LCC and LCA Information.

Experiments in the dissociative recombination of xenon and krypton

Experiments were conducted using the Time of Flight (TOF) method to identify the final product states of the dissociative recombination reaction of krypton and xenon. In the dissociative recombination (DR) reaction the molecular ion breaks up into product atoms whose velocities can be measured. These velocities can then be used to identify the final product states. The DR of krypton had been studied by Shiu and Biondi using spectrometric techniques. They observed the 5p states. Hardy et al. using TOF techniques had observed the 5s states. Mitchell et al. studied the DR of xenon. They observed the 6p and 5d states of xenon. In this laboratory using the TOF method I have recently identified the 5s, 6p and the 4d final states of the DR of krypton. Then I was able to identify the 5d, 7s, 6d, and 6p′ final product states of the DR of xenon. The study of the DR of these heavy inert gases can shed light on the theory of the DR of heavy polyatomic gases, which is not well developed. ^

Motion correction algorithm of lung tumors for respiratory gated PET images

Respiratory gating in lung PET imaging to compensate for respiratory motion artifacts is a current research issue with broad potential impact on quantitation, diagnosis and clinical management of lung tumors. However, PET images collected at discrete bins can be significantly affected by noise as there are lower activity counts in each gated bin unless the total PET acquisition time is prolonged, so that gating methods should be combined with imaging-based motion correction and registration methods. The aim of this study was to develop and validate a fast and practical solution to the problem of respiratory motion for the detection and accurate quantitation of lung tumors in PET images. This included: (1) developing a computer-assisted algorithm for PET/CT images that automatically segments lung regions in CT images, identifies and localizes lung tumors of PET images; (2) developing and comparing different registration algorithms which processes all the information within the entire respiratory cycle and integrate all the tumor in different gated bins into a single reference bin. Four registration/integration algorithms: Centroid Based, Intensity Based, Rigid Body and Optical Flow registration were compared as well as two registration schemes: Direct Scheme and Successive Scheme. Validation was demonstrated by conducting experiments with the computerized 4D NCAT phantom and with a dynamic lung-chest phantom imaged using a GE PET/CT System. Iterations were conducted on different size simulated tumors and different noise levels. Static tumors without respiratory motion were used as gold standard; quantitative results were compared with respect to tumor activity concentration, cross-correlation coefficient, relative noise level and computation time. Comparing the results of the tumors before and after correction, the tumor activity values and tumor volumes were closer to the static tumors (gold standard). Higher correlation values and lower noise were also achieved after applying the correction algorithms. With this method the compromise between short PET scan time and reduced image noise can be achieved, while quantification and clinical analysis become fast and precise.

Principal component analysis and assessment of language network activation patterns in pediatric epilepsy

This dissertation establishes a novel data-driven method to identify language network activation patterns in pediatric epilepsy through the use of the Principal Component Analysis (PCA) on functional magnetic resonance imaging (fMRI). A total of 122 subjects’ data sets from five different hospitals were included in the study through a web-based repository site designed here at FIU. Research was conducted to evaluate different classification and clustering techniques in identifying hidden activation patterns and their associations with meaningful clinical variables. The results were assessed through agreement analysis with the conventional methods of lateralization index (LI) and visual rating. What is unique in this approach is the new mechanism designed for projecting language network patterns in the PCA-based decisional space. Synthetic activation maps were randomly generated from real data sets to uniquely establish nonlinear decision functions (NDF) which are then used to classify any new fMRI activation map into typical or atypical. The best nonlinear classifier was obtained on a 4D space with a complexity (nonlinearity) degree of 7. Based on the significant association of language dominance and intensities with the top eigenvectors of the PCA decisional space, a new algorithm was deployed to delineate primary cluster members without intensity normalization. In this case, three distinct activations patterns (groups) were identified (averaged kappa with rating 0.65, with LI 0.76) and were characterized by the regions of: (1) the left inferior frontal Gyrus (IFG) and left superior temporal gyrus (STG), considered typical for the language task; (2) the IFG, left mesial frontal lobe, right cerebellum regions, representing a variant left dominant pattern by higher activation; and (3) the right homologues of the first pattern in Broca's and Wernicke's language areas. Interestingly, group 2 was found to reflect a different language compensation mechanism than reorganization. Its high intensity activation suggests a possible remote effect on the right hemisphere focus on traditionally left-lateralized functions. In retrospect, this data-driven method provides new insights into mechanisms for brain compensation/reorganization and neural plasticity in pediatric epilepsy.

Motion Correction Algorithm of Lung Tumors for Respiratory Gated PET Images

Respiratory gating in lung PET imaging to compensate for respiratory motion artifacts is a current research issue with broad potential impact on quantitation, diagnosis and clinical management of lung tumors. However, PET images collected at discrete bins can be significantly affected by noise as there are lower activity counts in each gated bin unless the total PET acquisition time is prolonged, so that gating methods should be combined with imaging-based motion correction and registration methods. The aim of this study was to develop and validate a fast and practical solution to the problem of respiratory motion for the detection and accurate quantitation of lung tumors in PET images. This included: (1) developing a computer-assisted algorithm for PET/CT images that automatically segments lung regions in CT images, identifies and localizes lung tumors of PET images; (2) developing and comparing different registration algorithms which processes all the information within the entire respiratory cycle and integrate all the tumor in different gated bins into a single reference bin. Four registration/integration algorithms: Centroid Based, Intensity Based, Rigid Body and Optical Flow registration were compared as well as two registration schemes: Direct Scheme and Successive Scheme. Validation was demonstrated by conducting experiments with the computerized 4D NCAT phantom and with a dynamic lung-chest phantom imaged using a GE PET/CT System. Iterations were conducted on different size simulated tumors and different noise levels. Static tumors without respiratory motion were used as gold standard; quantitative results were compared with respect to tumor activity concentration, cross-correlation coefficient, relative noise level and computation time. Comparing the results of the tumors before and after correction, the tumor activity values and tumor volumes were closer to the static tumors (gold standard). Higher correlation values and lower noise were also achieved after applying the correction algorithms. With this method the compromise between short PET scan time and reduced image noise can be achieved, while quantification and clinical analysis become fast and precise.

Principal Component Analysis and Assessment of Language Network Activation Patterns in Pediatric Epilepsy

This dissertation establishes a novel data-driven method to identify language network activation patterns in pediatric epilepsy through the use of the Principal Component Analysis (PCA) on functional magnetic resonance imaging (fMRI). A total of 122 subjects’ data sets from five different hospitals were included in the study through a web-based repository site designed here at FIU. Research was conducted to evaluate different classification and clustering techniques in identifying hidden activation patterns and their associations with meaningful clinical variables. The results were assessed through agreement analysis with the conventional methods of lateralization index (LI) and visual rating. What is unique in this approach is the new mechanism designed for projecting language network patterns in the PCA-based decisional space. Synthetic activation maps were randomly generated from real data sets to uniquely establish nonlinear decision functions (NDF) which are then used to classify any new fMRI activation map into typical or atypical. The best nonlinear classifier was obtained on a 4D space with a complexity (nonlinearity) degree of 7. Based on the significant association of language dominance and intensities with the top eigenvectors of the PCA decisional space, a new algorithm was deployed to delineate primary cluster members without intensity normalization. In this case, three distinct activations patterns (groups) were identified (averaged kappa with rating 0.65, with LI 0.76) and were characterized by the regions of: 1) the left inferior frontal Gyrus (IFG) and left superior temporal gyrus (STG), considered typical for the language task; 2) the IFG, left mesial frontal lobe, right cerebellum regions, representing a variant left dominant pattern by higher activation; and 3) the right homologues of the first pattern in Broca's and Wernicke's language areas. Interestingly, group 2 was found to reflect a different language compensation mechanism than reorganization. Its high intensity activation suggests a possible remote effect on the right hemisphere focus on traditionally left-lateralized functions. In retrospect, this data-driven method provides new insights into mechanisms for brain compensation/reorganization and neural plasticity in pediatric epilepsy.

Annotated record of the detailed examination of Mn deposits from the R/V Thomas Washington ROUNDABOUT Cruise stations

The cores described are taken during the R/V Thomas Washington ROUNDABOUT Cruise from May 1988 until March 1989 by the Scripps Institute of Oceanography. A total of 159 cores and dredges were recovered and are available at Scripps Institute of Oceanography for sampling and study.

Annotated record of the detailed examination of Mn deposits from the QUEBRADA (1969) and SIQUEIROS (1974) expeditions around the East Pacific Rise

Basalt samples obtained from the Siqueiros transform fault/fracture zone and the adjacent East Pacific Rise are mostly very fresh oceanic tholeiite and fractionated oceanic tholeiite with Fe+3/ Fe+2 ? 0.25; however, alkali basalts occur in the area as well. The rocks of the tholeiitic suite are ol + pl phyric and ol + pl + cpx phyric basalts, while the alkali basalts are ol and ol + pl phyric. Microprobe analyses of the tholeiitic suite phenocrysts indicate that they are Fo68-Fo86, An58-An75, and augite (Ca34Mg50Fe16). The range of olivine and plagioclase compositions represents the chemical variation of the phenocryst compositions with fractionation. The phenocyrsts in the alkali basalts are Fo81 and An69. The suite of tholeiites comprises a fractionation series characterized by relative enrichment of Fe, Ti, Mn, V, Na, K, and P and depletion of Ca, Al, Mg, Ni, and Cr. The fractionated tholeiites occur on the median ridge (which is a sliver of normal oceanic crust) of the double Siqueiros transform fault, on the western Siqueiros fracture zone, and on the adjoining East Pacific Rise, while the two transform fault troughs contain mostly unfractionated or only slightly fractionated tholeiite. We suggest that the fractionated tholeiites are produced by fractional crystallization of more 'primitive' tholeiitic liquid in a crustal magma chamber below the crest of the East Pacific Rise. This magma chamber may be disrupted by the transform fault troughs, thus explaining the paucity of fractionated tholeiites in the troughs. The alkali basalts are found only on the flanks of a topographic high near the intersection of the northern transform trough with the East Pacific Rise.

Annotated record of the detailed examination of Mn deposits from STYX expedition stations

The cores described in this paper were taken in the tropical central Pacific Ocean by Scripps Institution of Oceanography's R/V Alexander Agassiz on the STYX Expedition of April-September 1968. A total of 132 cores were attempted of which 97 were successful. These cores are available at Scripps for sampling and study.

Analisi preliminare dei risultati di TC perfusionale effettuata su tessuto polmonare sano

Le ultime ricerche in campo oncologico sulle cure antitumorali sono indirizzate verso una categoria definita target therapy. In particolare tra le più promettenti, le terapie antiangiogenetiche, il cui scopo primario è quello di limitare l’apporto di sangue al tumore. In questo contesto la Tomografia Computerizzata (TC) perfusionale rappresenta un’importante tecnica di imaging radiologico in grado, teoricamente, di fornire misure quantitative, che permettano una valutazione, anche precoce, della risposta alle terapie antiangiogenetiche. I principali problemi aperti in questo campo riguardano la standardizzazione dei protocolli di acquisizione e di elaborazione delle sequenze perfusionali, che determinano la scarsa riproducibilità dei risultati intra- ed inter-paziente, non consentendone l’uso nella pratica clinica. In letteratura sono presenti diversi studi riguardanti la perfusione dei tumori polmonari, ma vi sono pochi studi sull’affidabilità dei parametri perfusionali calcolati. Questa Tesi si propone di analizzare, quantificare e confrontare gli errori e l’affidabilità dei parametri perfusionali calcolati attraverso la TC perfusionale. In particolare, vengono generate delle mappe di errore ed effettuati dei confronti di diverse regioni del polmone sano. I risultati ottenuti dall’analisi dei casi reali sono discussi al fine di poter definire dei livelli di affidabilità dei parametri perfusionali e di quantificare gli errori che si commettono nella valutazione dei parametri stessi. Questo studio preliminare consentirà, quindi, un’analisi di riproducibilità, permettendo, inoltre, una normalizzazione dei valori perfusionali calcolati nella lesione, al fine di effettuare analisi intra- ed inter-paziente.

Frequência de microrganismos em conteúdo vulvovaginal de vacas tratadas com dispositivos intravaginais de progesterona

The dissertation was divided in two studies. With the first, aimed to evaluate the occurrence of microorganisms present in the vulvovaginal region of cows that received intravaginal progesterone devices during the fixed-time artificial insemination (FTAI) programs, and correlate the results with pregnancy rates. Samples were collected from vulvovaginal region of 30 beef cows Guzerá and 30 crossbred dairy cows, and also intravaginal devices, randomly. Of the 120 samples of cows, 60 corresponded to the collections of the period prior to the introduction device (D0) and 60 to the subsequent withdrawal of it (D9); it yielded 100% of bacterial growth, whereas, in most samples, it was found more than one isolated. In D0, the most frequent agent was Escherichia coli (52%), and in D9, Proteus spp and E. coli were the most frequent (32% and 28%, respectively). Regarding intravaginal progesterone devices, in D0 were isolated 37 microorganisms, being predominant those of the genus Bacillus (35%); in D9, 41 colony forming units (CFU) were isolated, of which 36.6% corresponded to Proteus spp. For the analysis of the antimicrobial profile, susceptibility testing was performed by diffusion agar disk, and cows that did not became pregnant after FTAI program were selected, as a future treatment. There resistance 100% to penicillin, and sensitivity, approximately, 90% to gentamicin, both isolates obtained from samples of beef cows and obtained of dairy cows. Regarding pregnancy rate, the 30 beef cows, 11 were diagnosed pregnant (36.7%), 4 (36.4%) treated with reused devices and 7 (63.6%) with new devices, which showed more effective. Of the 30 dairy cows, 15 were pregnant (50%), 8 (53.3%) were implanted with reused devices and 7 (46.7%) with new devices, with no significant differences in pregnancy rates. Because it is a research, females were chosen at random, and factors such as body condition, nutritional management and health weren't priority. With the second study, aimed to analyze the similarity between strains, conducted by technical Random Amplified Polymorphic DNA (RAPD -PCR). Presence of E. coli and the absence of pregnancy were selection criteria used. From the results, it was observed that most of the isolates wasn't phylogenetically similar, since they showed lower than 85% similarity. The study stressed the importance of E. coli in vulvovaginal microbiota of cows and the presence of phenotypic and genotypic characters of this bacterium on possible reproductive problems.