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.

Technical Report on the reduced graphene oxide biosynthesis protocol for biological applications

The interest of scientific community on carbon-based smart materials is growing and, especially focus on graphene oxide (GO) and reduced graphene oxide (rGO). An increasing number of bio-applications such as biological applications as bacterial inhibition, drug delivery and photothermal therapy aims the use of GO and rGO. For this reason, the methods used for the synthesis of graphene materials are more important because same of those procedures imply chemical reactions that involve hazardous and toxic reagents. In fact, the biocompatibility and toxicological activity of graphene-related materials is related to the methodologies employed for the synthesis that determine the carbon/oxygen (C/O) ratio of graphene oxide species. In this technical report, we focused on the synthesis of GO by means of that lead to a biocompatible GO form with a lower oxygen content. Thus, the synthesis of rAsGFP-rGO with the green fluorescent protein allowed us to obtain a biocompatible materials, without using hazardous and toxic reagents. This biocompatibility is the most important prerogative for the use of GO in biological activity assays as reported in several publications.

Study and development of UV photodetectors envisaging COMPASS RICH-1 upgrade and applications

COMPASS is an experiment at CERN’s SPS whose goal is to study hadron structure and spectroscopy. The experiment includes a wide acceptance RICH detector, operating since 2001 and subject to a major upgrade of the central region of its photodetectors in 2006. The remaining 75% of the photodetection area are still using MWPCs from the original design, who suffer from limitations in gain due to aging of the photocathodes from ion bombardment and due to ion-induced instabilities. Besides the mentioned limitations, the increased luminosity conditions expected for the upcoming years of the experiment make an upgrade to the remaining detectors pertinent. This upgrade should be accomplished in 2016, using hybrid detectors composed of ThGEMs and MICROMEGAS. This work presents the study, development and characterization of gaseous photon detectors envisaging the foreseen upgrade, and the progress in production and evaluation techniques necessary to reach increasingly larger area detectors with the performances required. It includes reports on the studies performed under particle beam environment of such detectors. MPGD structures can also be used in a variety of other applications, of which nuclear medical imaging is a notorious example. This work includes, additionally, the initial steps in simulating, assembling and characterizing a prototype of a gaseous detector for application as a Compton Camera.

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.

Fibre components and systems for mid-IR applications

Fibre-optic components and systems are used in a wide variety of industrial, medical and communication applications and can be found in use everywhere in the modern world, from the bottom of the ocean to satellites in orbit. The field of fibre optics has seen rapid growth in the past few decades to become an essential enabling technology. However, much more work is needed to develop components and systems that can work at wavelengths in the short-wavelength infrared (SWIR) / mid-IR part of the spectrum (defined in this work as 1.5 – 4.5.

Développement, validation et nouvelles applications d’un modèle d’analyse des modes normaux basé sur la séquence et la structure de protéines

Les protéines existent sous différents états fonctionnels régulés de façon précise par leur environnement afin de maintenir l‘homéostasie de la cellule et de l‘organisme vivant. La prévalence de ces états protéiques est dictée par leur énergie libre de Gibbs alors que la vitesse de transition entre ces états biologiquement pertinents est déterminée par le paysage d‘énergie libre. Ces paramètres sont particulièrement intéressants dans un contexte thérapeutique et biotechnologique, où leur perturbation par la modulation de la séquence protéique par des mutations affecte leur fonction. Bien que des nouvelles approches expérimentales permettent d‘étudier l‘effet de mutations en haut débit pour une protéine, ces méthodes sont laborieuses et ne couvrent qu‘une fraction de l‘ensemble des structures primaires d‘intérêt. L‘utilisation de modèles bio-informatiques permet de tester et générer in silico différentes hypothèses afin d‘orienter les approches expérimentales. Cependant, ces méthodes basées sur la structure se concentrent principalement sur la prédiction de l‘enthalpie d‘un état, alors que plusieurs évidences expérimentales ont démontré l‘importance de la contribution de l‘entropie. De plus, ces approches ignorent l‘importance de l‘espace conformationnel protéique dicté par le paysage énergétique cruciale à son fonctionnement. Une analyse des modes normaux peut être effectuée afin d‘explorer cet espace par l‘approximation que la protéine est dans une conformation d‘équilibre où chaque acide aminé est représenté par une masse régie par un potentiel harmonique. Les approches actuelles ignorent l‘identité des résidus et ne peuvent prédire l‘effet de mutations sur les propriétés dynamiques. Nous avons développé un nouveau modèle appelé ENCoM qui pallie à cette lacune en intégrant de l‘information physique et spécifique sur les contacts entre les atomes des chaînes latérales. Cet ajout permet une meilleure description de changements conformationnels d‘enzymes, la prédiction de l‘effet d‘une mutation allostérique dans la protéine DHFR et également la prédiction de l‘effet de mutations sur la stabilité protéique par une valeur entropique. Comparativement à des approches spécifiquement développées pour cette application, ENCoM est plus constant et prédit mieux l‘effet de mutations stabilisantes. Notre approche a également été en mesure de capturer la pression évolutive qui confère aux protéines d‘organismes thermophiles une thermorésistance accrue.

A flexible bio-inspired hierarchical model for analyzing musical timbre

A flexible and multipurpose bio-inspired hierarchical model for analyzing musical timbre is presented in this paper. Inspired by findings in the fields of neuroscience, computational neuroscience, and psychoacoustics, not only does the model extract spectral and temporal characteristics of a signal, but it also analyzes amplitude modulations on different timescales. It uses a cochlear filter bank to resolve the spectral components of a sound, lateral inhibition to enhance spectral resolution, and a modulation filter bank to extract the global temporal envelope and roughness of the sound from amplitude modulations. The model was evaluated in three applications. First, it was used to simulate subjective data from two roughness experiments. Second, it was used for musical instrument classification using the k-NN algorithm and a Bayesian network. Third, it was applied to find the features that characterize sounds whose timbres were labeled in an audiovisual experiment. The successful application of the proposed model in these diverse tasks revealed its potential in capturing timbral information.

Characterization of nanoparticle mediated laser transfection by femtosecond laser pulses for applications in molecular medicine

Background: In molecular medicine, the manipulation of cells is prerequisite to evaluate genes as therapeutic targets or to transfect cells to develop cell therapeutic strategies. To achieve these purposes it is essential that given transfection techniques are capable of handling high cell numbers in reasonable time spans. To fulfill this demand, an alternative nanoparticle mediated laser transfection method is presented herein. The fs-laser excitation of cell-adhered gold nanoparticles evokes localized membrane permeabilization and enables an inflow of extracellular molecules into cells. Results: The parameters for an efficient and gentle cell manipulation are evaluated in detail. Efficiencies of 90% with a cell viability of 93% were achieved for siRNA transfection. The proof for a molecular medical approach is demonstrated by highly efficient knock down of the oncogene HMGA2 in a rapidly proliferating prostate carcinoma in vitro model using siRNA. Additionally, investigations concerning the initial perforation mechanism are conducted. Next to theoretical simulations, the laser induced effects are experimentally investigated by spectrometric and microscopic analysis. The results indicate that near field effects are the initial mechanism of membrane permeabilization. Conclusion: This methodical approach combined with an automated setup, allows a high throughput targeting of several 100,000 cells within seconds, providing an excellent tool for in vitro applications in molecular medicine. NIR fs lasers are characterized by specific advantages when compared to lasers employing longer (ps/ns) pulses in the visible regime. The NIR fs pulses generate low thermal impact while allowing high penetration depths into tissue. Therefore fs lasers could be used for prospective in vivo applications.

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.

French good practice guidelines for medical and occupational surveillance of the low back pain risk among workers exposed to manual handling of loads

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Haemocompatibility of iron oxide nanoparticles synthesized for theranostic applications: a high-sensitivity microfluidic tool

The poor heating efficiency of the most reported magnetic nanoparticles (MNPs), allied to the lack of comprehensive biocompatibility and haemodynamic studies, hampers the spread of multifunctional nanoparticles as the next generation of therapeutic bio-agents in medicine. The present work reports the synthesis and characterization, with special focus on biological/toxicological compatibility, of superparamagnetic nanoparticles with diameter around 18 nm, suitable for theranostic applications (i.e. simultaneous diagnosis and therapy of cancer). Envisioning more insights into the complex nanoparticle-red blood cells (RBCs) membrane interaction, the deformability of the human RBCs in contact with magnetic nanoparticles (MNPs) was assessed for the first time with a microfluidic extensional approach, and used as an indicator of haematological disorders in comparison with a conventional haematological test, i.e. the haemolysis analysis. Microfluidic results highlight the potential of this microfluidic tool over traditional haemolysis analysis, by detecting small increments in the rigidity of the blood cells, when traditional haemotoxicology analysis showed no significant alteration (haemolysis rates lower than 2 %). The detected rigidity has been predicted to be due to the wrapping of small MNPs by the bilayer membrane of the RBCs, which is directly related to MNPs size, shape and composition. The proposed microfluidic tool adds a new dimension into the field of nanomedicine, allowing to be applied as a highsensitivity technique capable of bringing a better understanding of the biological impact of nanoparticles developed for clinical applications.

Bioactivity, proximate, mineral and volatile profiles along the flowering stages of Opuntia microdasys (Lehm.): defining potential applications

Opuntia spp. flowers have been traditionally used for medical purposes, mostly because of their diversity in bioactive molecules with health promoting properties. The proximate, mineral and volatile compound profiles, together with the cytotoxic and antimicrobial properties were characterized in O. microdasys flowers at different maturity stages, revealing several statistically significant differences. O. microdasys stood out mainly for its high contents of dietary fiber, potassium and camphor, and its high activities against HCT15 cells, Staphylococcus aureus, Aspergillus versicolor and Penicillium funiculosum. The vegetative stage showed the highest cytotoxic and antifungal activities, whilst the full flowering stage was particularly active against bacterial species. The complete dataset has been classified by principal component analysis, achieving clearly identifiable groups for each flowering stage, elucidating also the most distinctive features, and comprehensively profiling each of the assayed stages. The results might be useful to define the best flowering stage considering practical application purposes.

How does the healthcare industry involve users in medical device development? Pointers for UbiHealth

This paper introduces the Multidisciplinary Assessment of Technology Centre for Healthcare (MATCH) and outlines the problem of integrating a user-centred approach for development of medical devices together with the information and communication technology environments in which they are increasingly required to operate. We highlight some of the regulatory requirements that are relevant to user needs consideration in medical device development. Finally, we reveal a range of limitations in the current practice of the medical device industry in the area of user needs capture, based on responses from interviews with MATCH’s industry partners.

Pediatric Nurses’ Information and Applications Related To Ethical Codes

Background: Ethics is defined as the entirety of moral principles that form the basis of individuals’ behavior; it can also be defined as “moral theory” or “theoretical ethics”. Objectives: To determinate information and applications related to ethical codes of pediatric nurses. Patients and Methods: Participants were nurses attending the Neonatal Intensive Care Unit Nursing Course and the Pediatric Nursing Course conducted in Istanbul between September 2011 and December 2012. A total of nurses attending the courses at the specified dates and who agreed to participate in the study were included in the analysis. Data were collected through a questionnaire that we developed in accordance with current literature on nursing ethics. Results: 140 nurses participated in this study. Information and applications were related to ethical codes of nurses including four categories; autonomy, beneficence, nonmaleficence, justice. The principle of confidentiality/keeping secrets. Exactly 64.3% of nurses reported having heard of nursing ethical codes. The best-known ethical code was the principle of justice. Furthermore, while the rates were generally low, some nurses engaged in unethical practices such as patient discrimination and prioritizing acquaintances. Conclusions: We conclude that most nurses working in pediatric clinics act in compliance with ethical codes. We also found that the majority of nurses wanted to learn about ethical codes. For this reason, we recommended that nurses working in clinics and future nurses in training be informed of the appropriate ethical behavior and codes.

Análise de um queimador infravermelho funcionando com combustível híbrido : GLP/Bio-óleo

Biomass is considered the largest renewable energy source that can be used in an environmentally sustainable. From the pyrolysis of biomass is possible to obtain products with higher energy density and better use properties. The liquid resultant of this process is traditionally called bio-oil. The use of infrared burners in industrial applications has many advantages in terms of technical-operational, for example, uniformity in the heat supply in the form of radiation and convection, with a greater control of emissions due to the passage of exhaust gases through a macroporous ceramic bed. This paper presents a commercial infrared burner adapted with an ejector proposed able to burn a hybrid configuration of liquefied petroleum gas (LPG) and bio-oil diluted. The dilution of bio-oil with absolute ethanol aimed to decrease the viscosity of the fluid, and improving the stability and atomization. It was introduced a temperature controller with thermocouple modulating two stages (low heat / high heat), and solenoid valves for fuels supply. The infrared burner has been tested, being the diluted bio-oil atomized, and evaluated its performance by conducting energy balance. The method of thermodynamic analysis to estimate the load was used an aluminum plate located at the exit of combustion gases and the distribution of temperatures measured by thermocouples. The dilution reduced the viscosity of the bio-oil in 75.4% and increased by 11% the lower heating value (LHV) of the same, providing a stable combustion to the burner through the atomizing with compressed air and burns combined with LPG. Injecting the hybrid fuel there was increase in the heat transfer from the plate to the environment in 21.6% and gain useful benefit of 26.7%, due to the improved in the efficiency of the 1st Law of Thermodynamics of infrared burner