Doctor of Philosophy

dissertationAlthough Electronic Health Record (EHR) systems have recently achieved widespread adoption in the U.S., our understanding of their impact on care outcomes is still limited. Current literature has produced mixed results due to the use of non-standardized measurements and weak research designs. In this dissertation, 4 studies are conducted to develop a systematic methodology for detecting near real-time performance changes during EHR implementations. It also explores factors that can affect outcomes during a commercial EHR implementation. The first study assesses the current state of the literature on health IT adoption to identify the most commonly reported outcome measures and proposes a taxonomy to classify these measurements. The second study expands the first study by identifying additional measures through semistructured interviews with experienced clinical and administrative leaders from a large care delivery system. We also collect input from national informatics experts who suggested additional relevant measures. The third study is a robust longitudinal analysis including several measures from our larger inventory that were used for monitoring a large-scale commercial EHR implementation and detected patterns of impact and mixed time-sensitive effects across geographically dispersed settings from an integrated care delivery system. The fourth study is a qualitative analysis guided by the quantitative results of the third study. We identified several factors that may have contributed to performance changes detected by our methodology. In summary, this dissertation will help the broader medical and informatics communities by informing what and how to continuously monitor future similar implementations. First, it contributes to the identification of relevant outcomes likely impacted by health IT interventions. Second, it combines these outcome measures with a robust interrupted time-series design, producing a systematic methodology that allows earlier and potentially more precise detection of unexpected effects, and implementation of effective response to mitigate negative impacts. Last, the identification of factors that may impact outcomes during and following an EHR implementation and covariates to measure them will empower researchers in charge of future evaluations, hopefully increasing the understanding of the full impact of health IT interventions

SPH Method Applied to Naval-Hydrodynamic Problems

Common problems in naval hydrodynamic and coastal engineering are the studies of general internal and external flows. Classic methods of solution have to face break down when dealing with large deformations and fragmentations of the air-water interface. The Smoothed Particles Hydrodynamic (SPH) is an innovative numerical method of solution based on Lagrangian Meshless representation of the flow field. We have applied it to the study of some internal (sloshing and dam-break problem) and external flows (breaking and post-breaking evolution of bores propagation toward beaches and bow breaking waves generated by fast slender vessels). [DOI: 10.1685 / CSC06053] About DO

Reynolds number and Shallow Depth Sloshing

The dependence on the Reynolds number of shallow depth sloshing flows inside rectangular tanks subjected to forced harmonic motion is studied in this paper with weakly compressible SPH. We are interested in assessing the in fluenceof viscous effects on the dynamics of shallow depth sloshing flows by using an SPH solver and by comparing with a Navier-Stokes level-set solver results. The goal of trying to model these viscous flows is compromised by the resolution requested due to their Reynolds number, if boundary layer effects are to be modeled. The convenience and feasibility of the implementation of free-slip and no-slip boundary conditions is also discusse

Mimulus sRNAs Are Wound Responsive and Associated with Transgenerationally Plastic Genes but Rarely Both

Organisms alter development in response to environmental cues. Recent studies demonstrate that they can transmit this plasticity to progeny. While the phenotypic and transcriptomic evidence for this “transgenerational plasticity” has accumulated, genetic and developmental mechanisms remain unclear. Plant defenses, gene expression and DNA methylation are modified as an outcome of parental wounding in Mimulus guttatus. Here, we sequenced M. guttatus small RNAs (sRNA) to test their possible role in mediating transgenerational plasticity. We sequenced sRNA populations of leaf-wounded and control plants at 1 h and 72 h after damage and from progeny of wounded and control parents. This allowed us to test three components of an a priori model of sRNA mediated transgenerational plasticity—(1) A subset of sRNAs will be differentially expressed in response to wounding, (2) these will be associated with previously identified differentially expressed genes and differentially methylated regions and (3) changes in sRNA abundance in wounded plants will be predictive of sRNA abundance, DNA methylation, and/or gene expression shifts in the following generation. Supporting (1) and (2), we found significantly different sRNA abundances in wounded leaves; the majority were associated with tRNA fragments (tRFs) rather than small-interfering RNAs (siRNA). However, siRNAs responding to leaf wounding point to Jasmonic Acid mediated responses in this system. We found that different sRNA classes were associated with regions of the genome previously found to be differentially expressed or methylated in progeny of wounded plants. Evidence for (3) was mixed. We found that non-dicer sRNAs with increased abundance in response to wounding tended to be nearby genes with decreased expression in the next generation. Counter to expectations, we did not find that siRNA responses to wounding were associated with gene expression or methylation changes in the next generation and within plant and transgenerational sRNA plasticity were negatively correlated

Development of a 3D Domain-Decomposition strategy for violent head-sea wave-vessel interactions: Challenges

This research activity represents an additional step toward a three-dimensional Domain-Decomposition strategy for violent wave-ship interaction involving water-on-deck and slamming phenomena. The focus is on FPSO ships and on head-sea waves and vessel without forward speed. The compound solver under development aims to couple a global 3D linear seakeeping solver with an inner 3D single-phase (water) Navier-Stokes (NS) method in a region containing the forward portion of the vessel. The NS solver is characterized by a Projection method with a finite-difference scheme on an Eulerian grid. The Level-Set (LS) technique is applied to step in time the free surface and combined with point markers to enforce adequately the body-boundary condition within a hybrid Eulerian-Lagrangian approach. This requires a much finer discretization than the computational grid around the body to preserve its geometrical details in time. As time goes on, the markers move in a Lagrangian fashion and then the LS function is estimated on the Eulerian grid by interpolation from the markers locations. Previous efforts have been documented for instance in Greco et al. (2009)) and Colicchio et al. (2010). Here some of the challenges and the possible solutions for the development of the inner 3D NS solver are discussed. The stress is on the boundary conditions

Confronto di solutori FEM e solutori BEM per lo sloshing in contenitori

Ė stato studiato il fenomeno di sloshing attraverso due diversi algoritmi numerici: il primo consiste in una discretizzazione con elementi finiti dell’equazione di Navier Stokes in formulazione Arbitrary Lagrangian Eulerian, è indicato nel seguito come FEM ed è descritto in [3]; il secondo è basato sulla discretizzazione delle equazioni agli integrali di contorno e delle equazioni di evoluzione della superficie libera ed è indicato come BEM e descritto in [2]. Per verificare la validità dei due codici sono stati confrontati i loro risultati con quelli presenti in letteratura, sia derivanti da altri codici numerici, sia ottenuti come risultati sperimentali. Il confronto è stato effettuato per un’ampia gamma di situazioni, in modo da studiare il comportamento dei due codici al variare delle caratteristiche della sollecitazione e delle dimensioni del dominio

Assessment study of a domain-decomposition strategy for marine applications

Greco et al. (2011) tried to identify the proper numerical choices for the development of a three-dimensional Domain- Decomposition (DD) strategy. It aims to study the violent interaction of FPSO ships with head-sea regular waves. The present work represents a contribution in this direction

A Systematic, Updated Review on the Antidepressant Agomelatine Focusing on its Melatonergic Modulation

To present an updated, comprehensive review on clinical and pre-clinical studies on agomelatine

Nonlinear air-water interface problems through a BEM-Level set domain decomposition

Several water flow problems of practical interest are characterized by fluid regions where the flow evolution is efficiently de- scribed by the potential theory, and other regions where this model is not valid. For instance, confined fluid areas can experience large air-water interface deformations followed by wave breaking and fragmentation phenomena. Limited water portions can be characterized by substantial vorticity generation due to water-water or water-structure interaction. In these cases the surrounding fluid domains can be slightly affected by such events. The ship hydrodynamic field is full of similar circumstances. The water-on-deck problem represents an example. In this case, compact masses of water enter the ship deck and the subsequent motion can result in important loads for the deck superstructures. On a long time scale, water breaking, air entrainement and vorticity generation are expected to occur. The later water-off-deck phase will cause the re-entering of water in the sea surrounding the vessel. As a result, near the vessel the free surface cannot be modeled as a smooth surface. Both the water shipping event and the final water-entry phase can involve substantial induced water loads on the vessel and large movements of the ship. Therefore related phenomena are of great interest for ship hydrodynamics, both from the operability and safety points of view. Due to the large free-surface deformations involved, a nonlinear analysis is needed. Before breaking and/or vortex shedding events, potential flow theory can capture accurately and with computational efficiency the involved flow evolution and predict connected loads and motions. After that, in the water regions where such phenomena occur and develop, this model has to be substituted by more general methods suitable to track the free surface deformations after the breaking, to handle the flow vorticity introduced in the fluid domain and to model the entrapped air. The present research activity is aimed to develop a numerical method able to simulate such ship flows and to adapt itself to the specific analyzed problem for an efficient and suitable solution. This has been done by considering a domain-decomposition strategy (see i.e. Quarteroni and Valli 1999, Campana and Iafrati 2001)