CAUSAL INFERENCE WITH A CONTINUOUS TREATMENT AND OUTCOME: ALTERNATIVE ESTIMATORS FOR PARAMETRIC DOSE-RESPONSE FUNCTIONS WITH APPLICATIONS.

Causal inference with a continuous treatment is a relatively under-explored problem. In this dissertation, we adopt the potential outcomes framework. Potential outcomes are responses that would be seen for a unit under all possible treatments. In an observational study where the treatment is continuous, the potential outcomes are an uncountably infinite set indexed by treatment dose. We parameterize this unobservable set as a linear combination of a finite number of basis functions whose coefficients vary across units. This leads to new techniques for estimating the population average dose-response function (ADRF). Some techniques require a model for the treatment assignment given covariates, some require a model for predicting the potential outcomes from covariates, and some require both. We develop these techniques using a framework of estimating functions, compare them to existing methods for continuous treatments, and simulate their performance in a population where the ADRF is linear and the models for the treatment and/or outcomes may be misspecified. We also extend the comparisons to a data set of lottery winners in Massachusetts. Next, we describe the methods and functions in the R package causaldrf using data from the National Medical Expenditure Survey (NMES) and Infant Health and Development Program (IHDP) as examples. Additionally, we analyze the National Growth and Health Study (NGHS) data set and deal with the issue of missing data. Lastly, we discuss future research goals and possible extensions.

Tensor Completion for Multidimensional Inverse Problems with Applications to Magnetic Resonance Relaxometry

This thesis deals with tensor completion for the solution of multidimensional inverse problems. We study the problem of reconstructing an approximately low rank tensor from a small number of noisy linear measurements. New recovery guarantees, numerical algorithms, non-uniform sampling strategies, and parameter selection algorithms are developed. We derive a fixed point continuation algorithm for tensor completion and prove its convergence. A restricted isometry property (RIP) based tensor recovery guarantee is proved. Probabilistic recovery guarantees are obtained for sub-Gaussian measurement operators and for measurements obtained by non-uniform sampling from a Parseval tight frame. We show how tensor completion can be used to solve multidimensional inverse problems arising in NMR relaxometry. Algorithms are developed for regularization parameter selection, including accelerated k-fold cross-validation and generalized cross-validation. These methods are validated on experimental and simulated data. We also derive condition number estimates for nonnegative least squares problems. Tensor recovery promises to significantly accelerate N-dimensional NMR relaxometry and related experiments, enabling previously impractical experiments. Our methods could also be applied to other inverse problems arising in machine learning, image processing, signal processing, computer vision, and other fields.

Spectral graph theory with applications to quantum adiabatic optimization

In this dissertation I draw a connection between quantum adiabatic optimization, spectral graph theory, heat-diffusion, and sub-stochastic processes through the operators that govern these processes and their associated spectra. In particular, we study Hamiltonians which have recently become known as ``stoquastic'' or, equivalently, the generators of sub-stochastic processes. The operators corresponding to these Hamiltonians are of interest in all of the settings mentioned above. I predominantly explore the connection between the spectral gap of an operator, or the difference between the two lowest energies of that operator, and certain equilibrium behavior. In the context of adiabatic optimization, this corresponds to the likelihood of solving the optimization problem of interest. I will provide an instance of an optimization problem that is easy to solve classically, but leaves open the possibility to being difficult adiabatically. Aside from this concrete example, the work in this dissertation is predominantly mathematical and we focus on bounding the spectral gap. Our primary tool for doing this is spectral graph theory, which provides the most natural approach to this task by simply considering Dirichlet eigenvalues of subgraphs of host graphs. I will derive tight bounds for the gap of one-dimensional, hypercube, and general convex subgraphs. The techniques used will also adapt methods recently used by Andrews and Clutterbuck to prove the long-standing ``Fundamental Gap Conjecture''.

Magnetic resonance spectroscopy. Data analysis for clinical applications

This text is taken from the postgraduate thesis, which one of the authors (A.B.) developed for the degree of Medical Physicist in the School on Medical Physics of the University of Florence. The text explores the feasibility of quantitative Magnetic Resonance Spectroscopy as a tool for daily clinical routine use. The results and analysis comes from two types of hyper spectral images: the first set are hyper spectral images coming from a standard phantom (reference images); and hyper spectral images obtained from a group of patients who have undergone MRI examinations at the Santa Maria Nuova Hospital. This interdisciplinary work stems from the IFAC-CNR know how in terms of data analysis and nanomedicine, and the clinical expertise of Radiologists and Medical Physicists. The results reported here, which were the subject of the thesis, are original, unpublished, and represent independent work.

Geometrical Methods in Multivariate Risk Management: Algorithms and Applications

This thesis builds a framework for evaluating downside risk from multivariate data via a special class of risk measures (RM). The peculiarity of the analysis lies in getting rid of strong data distributional assumptions and in orientation towards the most critical data in risk management: those with asymmetries and heavy tails. At the same time, under typical assumptions, such as the ellipticity of the data probability distribution, the conformity with classical methods is shown. The constructed class of RM is a multivariate generalization of the coherent distortion RM, which possess valuable properties for a risk manager. The design of the framework is twofold. The first part contains new computational geometry methods for the high-dimensional data. The developed algorithms demonstrate computability of geometrical concepts used for constructing the RM. These concepts bring visuality and simplify interpretation of the RM. The second part develops models for applying the framework to actual problems. The spectrum of applications varies from robust portfolio selection up to broader spheres, such as stochastic conic optimization with risk constraints or supervised machine learning.

Story Driven Web Applications

Kern der vorliegenden Arbeit ist die Modellierung komplexer Webapplikationen mit dem Story-Driven-Modeling Ansatz.Ziel ist es hierbei,die komplette Applikation allein durch die Spezifikation von Modellen zu entwickeln. Das händische Erstellen von Quelltext ist nicht notwendig. Die vorliegende Arbeit zeigt sowohl den Forschungsweg, der die angestrebte Modellierung von Webapplikationen ermöglicht, als auch die resultierenden Ergebnisse auf. Zur Unterstützung des Entwicklungsprozesses wird weiterhin ein modellgetriebener Softwareentwicklungsprozess vorgestellt, der die Modellierung einer Webapplikation von der Aufnahme der Anforderungen, bis zur abschließenden Erzeugung des Quelltextes durch Codegenerierung aus den spezifizierten Modellen, abdeckt. Für den definierten Prozess wird ferner Werkzeugunterstützung innerhalb der Fujaba Toolsuite bereitgestellt. Im Rahmen der vorliegenden Arbeit wurde die bestehede Toolsuite hierzu um alle zur Prozessunterstützung notwendigen Werkzeuge erweitert. Darüber hinaus wurden im Rahmen der vorliegenden Arbeit die in Fujaba bestehenden Werkzeuge erweitert, um neben den klassischen Möglichkeiten zur Modellierung komplexer Java-Applikationen auch die Erzeugung von Webapplikationen zu ermöglichen. Neben der genauen Beschreibung des Entwicklungsprozesses werden im Rahmen dieser Arbeit die entstehenden Webapplikationen mit ihren spezifischen Eigenschaften genau beschrieben. Zur Erzeugung dieser Applikationen wird neben dem Entwicklungsprozess die Diagrammart der Workflowdiagramme eingeführt und beschrieben. Diese Diagramme dienen der Abbildung des intendierten Userworkflows der Applikation im Rahmen der Anforderungsanalyse und stellen im weiteren Entwicklungsverlauf ein dediziertes Entwicklungsartefakt dar. Basierend auf den Workflowdiagrammen werden sowohl die grafische Benutzerschnittstelle der Webapplikation beschrieben, als auch ein Laufzeitsystem initialisiert, welches basierend auf den im Workflowdiagramm abgebildeten Abläufen die Anwendung steuert. Dieses Laufzeitsystem wurde im Rahmen der vorliegenden Arbeit entwickelt und in der Prozessunterstützung verankert. Alle notwendigen Änderungen und Anpassungen und Erweiterungen an bereits bestehenden Teilen der Fujaba Toolsuite werden unter dem Aspekt der Erstellung clientseitiger Datenmodelle einer Webapplikation genau beschrieben und in Verbindung mit den zu erfüllenden Voraussetzungen erläutert. In diesem Zusammenhang wird ebenfalls beschrieben, wie Graphtransformationen zur Umsetzung von Businesslogik auf der Clientseite einer Webapplikation eingesetzt werden können und auf welche Weise Datenmodelländerungen zwischen unterschiedlichen Clients synchronisiert werden können. Insgesamt zeigt die vorliegende Arbeit einen Weg auf, den bestehenden Ansatz des StoryDriven-Modeling für die Erzeugung von Webapplikationen einzusetzen. Durch die im Rahmen dieser Arbeit beschriebene Herangehensweise werden hierbei gleichzeitig Webbrowser zu einer neuen Klasse von Graphersetzungs-Engines erweitert, indem Graphtransformationen innerhalb der Ajax-Engine des Browsers ausgeliefert und ausgeführt werden.

UT Austin | Portugal Workshop on Nonlinear Mechanics and Applications in Life Sciences

This is a CoLab Workshop organized as an initiative of the UT Austin | Portugal Program to reinforce the Portuguese competences in Nonlinear Mechanics and in complex problems arising from applications to the mathematical modeling and simulations in the Life Sciences. The Workshop provides a place to exchange recent developments, discoveries and progresses in this challenging research field. The main goal is to bring together doctoral candidates, postdoctoral scientists and graduates interested in the field, giving them the opportunity to make scientific interactions and new connections with established experts in the interdisciplinary topics covered by the event. Another important goal of the Workshop is to promote collaboration between members of the different areas of the UT Austin | Portugal community.

On polynomials with given Hilbert function and applications

Using Macaulay's correspondence we study the family of Artinian Gorenstein local algebras with fixed symmetric Hilbert function decomposition. As an application we give a new lower bound for the dimension of cactus varieties of the third Veronese embedding. We discuss the case of cubic surfaces, where interesting phenomena occur.

State of the art and future perspectives on security metrics and their applications

In modern society, security issues of IT Systems are intertwined with interdisciplinary aspects, from social life to sustainability, and threats endanger many aspects of every- one’s daily life. To address the problem, it’s important that the systems that we use guarantee a certain degree of security, but to achieve this, it is necessary to be able to give a measure to the amount of security. Measuring security is not an easy task, but many initiatives, including European regulations, want to make this possible. One method of measuring security is based on the use of security metrics: those are a way of assessing, from various aspects, vulnera- bilities, methods of defense, risks and impacts of successful attacks then also efficacy of reactions, giving precise results using mathematical and statistical techniques. I have done literature research to provide an overview on the meaning, the effects, the problems, the applications and the overall current situation over security metrics, with particular emphasis in giving practical examples. This thesis starts with a summary of the state of the art in the field of security met- rics and application examples to outline the gaps in current literature, the difficulties found in the change of application context, to then advance research questions aimed at fostering the discussion towards the definition of a more complete and applicable view of the subject. Finally, it stresses the lack of security metrics that consider interdisciplinary aspects, giving some potential starting point to develop security metrics that cover all as- pects involved, taking the field to a new level of formal soundness and practical usability.

Problems in physics and mathematics contexts with middle and high school classes: vertical and horizontal comparison

My thesis falls within the framework of physics education and teaching of mathematics. The objective of this report was made possible by using geometrical (in mathematics) and qualitative (in physics) problems. We have prepared four (resp. three) open answer exercises for mathematics (resp. physics). The test batch has been selected across two different school phases: end of the middle school (third year, 8\textsuperscript{th} grade) and beginning of high school (second and third year, 10\textsuperscript{th} and 11\textsuperscript{th} grades respectively). High school students achieved the best results in almost every problem, but 10\textsuperscript{th} grade students got the best overall results. Moreover, a clear tendency to not even try qualitative problems resolution has emerged from the first collection of graphs, regardless of subject and grade. In order to improve students' problem-solving skills, it is worth to invest on vertical learning and spiral curricula. It would make sense to establish a stronger and clearer connection between physics and mathematical knowledge through an interdisciplinary approach.

An Efficient Protocol For The Generation Of Monocyte Derived Dendritic Cells Using Serum-free Media For Clinical Applications In Post Remission Aml Patients.

Protocols for the generation of dendritic cells (DCs) using serum as a supplementation of culture media leads to reactions due to animal proteins and disease transmissions. Several types of serum-free media (SFM), based on good manufacture practices (GMP), have recently been used and seem to be a viable option. The aim of this study was to evaluate the results of the differentiation, maturation, and function of DCs from Acute Myeloid Leukemia patients (AML), generated in SFM and medium supplemented with autologous serum (AS). DCs were analyzed by phenotype characteristics, viability, and functionality. The results showed the possibility of generating viable DCs in all the conditions tested. In patients, the X-VIVO 15 medium was more efficient than the other media tested in the generation of DCs producing IL-12p70 (p=0.05). Moreover, the presence of AS led to a significant increase of IL-10 by DCs as compared with CellGro (p=0.05) and X-Vivo15 (p=0.05) media, both in patients and donors. We concluded that SFM was efficient in the production of DCs for immunotherapy in AML patients. However, the use of AS appears to interfere with the functional capacity of the generated DCs.

Applications Of Visual Evoked Potentials And Fourier-domain Optical Coherence Tomography In Parkinson's Disease: A Controlled Study.

The goal of this cross-sectional observational study was to quantify the pattern-shift visual evoked potentials (VEP) and the thickness as well as the volume of retinal layers using optical coherence tomography (OCT) across a cohort of Parkinson's disease (PD) patients and age-matched controls. Forty-three PD patients and 38 controls were enrolled. All participants underwent a detailed neurological and ophthalmologic evaluation. Idiopathic PD cases were included. Cases with glaucoma or increased intra-ocular pressure were excluded. Patients were assessed by VEP and high-resolution Fourier-domain OCT, which quantified the inner and outer thicknesses of the retinal layers. VEP latencies and the thicknesses of the retinal layers were the main outcome measures. The mean age, with standard deviation (SD), of the PD patients and controls were 63.1 (7.5) and 62.4 (7.2) years, respectively. The patients were predominantly in the initial Hoehn-Yahr (HY) disease stages (34.8% in stage 1 or 1.5, and 55.8 % in stage 2). The VEP latencies and the thicknesses as well as the volumes of the retinal inner and outer layers of the groups were similar. A negative correlation between the retinal thickness and the age was noted in both groups. The thickness of the retinal nerve fibre layer (RNFL) was 102.7 μm in PD patients vs. 104.2 μm in controls. The thicknesses of retinal layers, VEP, and RNFL of PD patients were similar to those of the controls. Despite the use of a representative cohort of PD patients and high-resolution OCT in this study, further studies are required to establish the validity of using OCT and VEP measurements as the anatomic and functional biomarkers for the evaluation of retinal and visual pathways in PD patients.

Microfluidic Paper-based Devices For Bioanalytical Applications.

Paper has become increasingly recognized as a very interesting substrate for the construction of microfluidic devices, with potential application in a variety of areas, including health diagnosis, environmental monitoring, immunoassays and food safety. The aim of this review is to present a short history of analytical systems constructed from paper, summarize the main advantages and disadvantages of fabrication techniques, exploit alternative methods of detection such as colorimetric, electrochemical, photoelectrochemical, chemiluminescence and electrochemiluminescence, as well as to take a closer look at the novel achievements in the field of bioanalysis published during the last 2 years. Finally, the future trends for production of such devices are discussed.

Critical applications of SW 846 US EPA methods to evaluation of marine samples quality

Technical evaluation of analytical data is of extreme relevance considering it can be used for comparisons with environmental quality standards and decision-making as related to the management of disposal of dredged sediments and the evaluation of salt and brackish water quality in accordance with CONAMA 357/05 Resolution. It is, therefore, essential that the project manager discusses the environmental agency's technical requirements with the laboratory contracted for the follow-up of the analysis underway and even with a view to possible re-analysis when anomalous data are identified. The main technical requirements are: (1) method quantitation limits (QLs) should fall below environmental standards; (2) analyses should be carried out in laboratories whose analytical scope is accredited by the National Institute of Metrology (INMETRO) or qualified or accepted by a licensing agency; (3) chain of custody should be provided in order to ensure sample traceability; (4) control charts should be provided to prove method performance; (5) certified reference material analysis or, if that is not available, matrix spike analysis, should be undertaken and (6) chromatograms should be included in the analytical report. Within this context and with a view to helping environmental managers in analytical report evaluation, this work has as objectives the discussion of the limitations of the application of SW 846 US EPA methods to marine samples, the consequences of having data based on method detection limits (MDL) and not sample quantitation limits (SQL), and present possible modifications of the principal method applied by laboratories in order to comply with environmental quality standards.

Nanostructured thin films obtained by electrodeposition over a colloidal crystal template: applications in electrochemical devices

Colloidal particles have been used to template the electrosynthesis of several materials, such as semiconductors, metals and alloys. The method allows good control over the thickness of the resulting material by choosing the appropriate charge applied to the system, and it is able to produce high density deposited materials without shrinkage. These materials are a true model of the template structure and, due to the high surface areas obtained, are very promising for use in electrochemical applications. In the present work, the assembly of monodisperse polystyrene templates was conduced over gold, platinum and glassy carbon substrates in order to show the electrodeposition of an oxide, a conducting polymer and a hybrid inorganic-organic material with applications in the supercapacitor and sensor fields. The performances of the resulting nanostructured films have been compared with the analogue bulk material and the results achieved are depicted in this paper.