Systems medicine and integrated care to combat chronic noncommunicable diseases

We propose an innovative, integrated, cost-effective health system to combat major non-communicable diseases (NCDs), including cardiovascular, chronic respiratory, metabolic, rheumatologic and neurologic disorders and cancers, which together are the predominant health problem of the 21st century. This proposed holistic strategy involves comprehensive patient-centered integrated care and multi-scale, multi-modal and multi-level systems approaches to tackle NCDs as a common group of diseases. Rather than studying each disease individually, it will take into account their intertwined gene-environment, socio-economic interactions and co-morbidities that lead to individual-specific complex phenotypes. It will implement a road map for predictive, preventive, personalized and participatory (P4) medicine based on a robust and extensive knowledge management infrastructure that contains individual patient information. It will be supported by strategic partnerships involving all stakeholders, including general practitioners associated with patient-centered care. This systems medicine strategy, which will take a holistic approach to disease, is designed to allow the results to be used globally, taking into account the needs and specificities of local economies and health systems.

MULTISCALE EXAMINATION AND MODELING OF ELECTRON TRANSPORT IN NANOSCALE MATERIALS AND DEVICES

For half a century the integrated circuits (ICs) that make up the heart of electronic devices have been steadily improving by shrinking at an exponential rate. However, as the current crop of ICs get smaller and the insulating layers involved become thinner, electrons leak through due to quantum mechanical tunneling. This is one of several issues which will bring an end to this incredible streak of exponential improvement of this type of transistor device, after which future improvements will have to come from employing fundamentally different transistor architecture rather than fine tuning and miniaturizing the metal-oxide-semiconductor field effect transistors (MOSFETs) in use today. Several new transistor designs, some designed and built here at Michigan Tech, involve electrons tunneling their way through arrays of nanoparticles. We use a multi-scale approach to model these devices and study their behavior. For investigating the tunneling characteristics of the individual junctions, we use a first-principles approach to model conduction between sub-nanometer gold particles. To estimate the change in energy due to the movement of individual electrons, we use the finite element method to calculate electrostatic capacitances. The kinetic Monte Carlo method allows us to use our knowledge of these details to simulate the dynamics of an entire device— sometimes consisting of hundreds of individual particles—and watch as a device ‘turns on’ and starts conducting an electric current. Scanning tunneling microscopy (STM) and the closely related scanning tunneling spectroscopy (STS) are a family of powerful experimental techniques that allow for the probing and imaging of surfaces and molecules at atomic resolution. However, interpretation of the results often requires comparison with theoretical and computational models. We have developed a new method for calculating STM topographs and STS spectra. This method combines an established method for approximating the geometric variation of the electronic density of states, with a modern method for calculating spin-dependent tunneling currents, offering a unique balance between accuracy and accessibility.

Cortical local and long-range synchronization interplay in human absence seizure initiation

Brain activity relies on transient, fluctuating interactions between segregated neuronal populations. Synchronization within a single and between distributed neuronal clusters reflects the dynamics of these cooperative patterns. Thus absence epilepsy can be used as a model for integrated, large-scale investigation of the emergence of pathological collective dynamics in the brain. Indeed, spike-wave discharges (SWD) of an absence seizure are thought to reflect abnormal cortical hypersynchronization. In this paper, we address two questions: how and where do SWD arise in the human brain? Therefore, we explored the spatio-temporal dynamics of interactions within and between widely distributed cortical sites using magneto-encephalographic recordings of spontaneous absence seizures. We then extracted, from their time-frequency analysis, local synchronization of cortical sources and long-range synchronization linking distant sites. Our analyses revealed a reproducible sequence of 1) long-range desynchronization, 2) increased local synchronization and 3) increased long-range synchronization. Although both local and long-range synchronization displayed different spatio-temporal profiles, their cortical projection within an initiation time window overlap and reveal a multifocal fronto-central network. These observations contradict the classical view of sudden generalized synchronous activities in absence epilepsy. Furthermore, they suggest that brain states transition may rely on multi-scale processes involving both local and distant interactions.

Integrated Segmentation of Brain Tumor Images for Radiotherapy and Neurosurgery

Image-based modeling of tumor growth combines methods from cancer simulation and medical imaging. In this context, we present a novel approach to adapt a healthy brain atlas to MR images of tumor patients. In order to establish correspondence between a healthy atlas and a pathologic patient image, tumor growth modeling in combination with registration algorithms is employed. In a first step, the tumor is grown in the atlas based on a new multi-scale, multi-physics model including growth simulation from the cellular level up to the biomechanical level, accounting for cell proliferation and tissue deformations. Large-scale deformations are handled with an Eulerian approach for finite element computations, which can operate directly on the image voxel mesh. Subsequently, dense correspondence between the modified atlas and patient image is established using nonrigid registration. The method offers opportunities in atlasbased segmentation of tumor-bearing brain images as well as for improved patient-specific simulation and prognosis of tumor progression.

There is more than "more is up": Hand and foot responses reverse the vertical association of number magnitudes

Recent research in cognitive sciences shows a growing interest in spatial-numerical associations. The horizontal SNARC (spatial-numerical association of response codes) effect is defined by faster left-sided responses to small numbers and faster right-sided responses to large numbers in a parity judgment task. In this study we investigated whether there is also a SNARC effect for upper and lower responses. The grounded cognition approach suggests that the universal experience of "more is up" serves as a robust frame of reference for vertical number representation. In line with this view, lower hand responses to small numbers were faster than to large numbers (Experiment 1). Interestingly, the vertical SNARC effect reversed when the lower responses were given by foot instead of the hand (Experiments 2, 3, and 4). We found faster upper (hand) responses to small numbers and faster lower (foot) responses to large numbers. Additional experiments showed that spatial factors cannot account for the reversal of the vertical SNARC effect (Experiments 4 and 5). Our results question the view of "more is up" as a robust frame of reference for spatial-numerical associations. We discuss our results within a hierarchical framework of numerical cognition and point to a possible link between effectors and number representation.

Experimental validation of a nonlinear μ FE model based on cohesive-frictional plasticity for trabecular bone

Trabecular bone is a porous mineralized tissue playing a major load bearing role in the human body. Prediction of age-related and disease-related fractures and the behavior of bone implant systems needs a thorough understanding of its structure-mechanical property relationships, which can be obtained using microcomputed tomography-based finite element modeling. In this study, a nonlinear model for trabecular bone as a cohesive-frictional material was implemented in a large-scale computational framework and validated by comparison of μFE simulations with experimental tests in uniaxial tension and compression. A good correspondence of stiffness and yield points between simulations and experiments was found for a wide range of bone volume fraction and degree of anisotropy in both tension and compression using a non-calibrated, average set of material parameters. These results demonstrate the ability of the model to capture the effects leading to failure of bone for three anatomical sites and several donors, which may be used to determine the apparent behavior of trabecular bone and its evolution with age, disease, and treatment in the future.

Computational fluid dynamics modelling in cardiovascular medicine.

This paper reviews the methods, benefits and challenges associated with the adoption and translation of computational fluid dynamics (CFD) modelling within cardiovascular medicine. CFD, a specialist area of mathematics and a branch of fluid mechanics, is used routinely in a diverse range of safety-critical engineering systems, which increasingly is being applied to the cardiovascular system. By facilitating rapid, economical, low-risk prototyping, CFD modelling has already revolutionised research and development of devices such as stents, valve prostheses, and ventricular assist devices. Combined with cardiovascular imaging, CFD simulation enables detailed characterisation of complex physiological pressure and flow fields and the computation of metrics which cannot be directly measured, for example, wall shear stress. CFD models are now being translated into clinical tools for physicians to use across the spectrum of coronary, valvular, congenital, myocardial and peripheral vascular diseases. CFD modelling is apposite for minimally-invasive patient assessment. Patient-specific (incorporating data unique to the individual) and multi-scale (combining models of different length- and time-scales) modelling enables individualised risk prediction and virtual treatment planning. This represents a significant departure from traditional dependence upon registry-based, population-averaged data. Model integration is progressively moving towards 'digital patient' or 'virtual physiological human' representations. When combined with population-scale numerical models, these models have the potential to reduce the cost, time and risk associated with clinical trials. The adoption of CFD modelling signals a new era in cardiovascular medicine. While potentially highly beneficial, a number of academic and commercial groups are addressing the associated methodological, regulatory, education- and service-related challenges.

Importance of Nuclear Data Uncertainties in Criticality Calculations

To study the propagation of the uncertainty from basic data across different scale and physics phenomena -> through complex coupled multi-physics and multi-scale simulations

Computational methods to create and analyze a digital gene expression atlas of embryo development from microscopy images

Abstract The creation of atlases, or digital models where information from different subjects can be combined, is a field of increasing interest in biomedical imaging. When a single image does not contain enough information to appropriately describe the organism under study, it is then necessary to acquire images of several individuals, each of them containing complementary data with respect to the rest of the components in the cohort. This approach allows creating digital prototypes, ranging from anatomical atlases of human patients and organs, obtained for instance from Magnetic Resonance Imaging, to gene expression cartographies of embryo development, typically achieved from Light Microscopy. Within such context, in this PhD Thesis we propose, develop and validate new dedicated image processing methodologies that, based on image registration techniques, bring information from multiple individuals into alignment within a single digital atlas model. We also elaborate a dedicated software visualization platform to explore the resulting wealth of multi-dimensional data and novel analysis algo-rithms to automatically mine the generated resource in search of bio¬logical insights. In particular, this work focuses on gene expression data from developing zebrafish embryos imaged at the cellular resolution level with Two-Photon Laser Scanning Microscopy. Disposing of quantitative measurements relating multiple gene expressions to cell position and their evolution in time is a fundamental prerequisite to understand embryogenesis multi-scale processes. However, the number of gene expressions that can be simultaneously stained in one acquisition is limited due to optical and labeling constraints. These limitations motivate the implementation of atlasing strategies that can recreate a virtual gene expression multiplex. The developed computational tools have been tested in two different scenarios. The first one is the early zebrafish embryogenesis where the resulting atlas constitutes a link between the phenotype and the genotype at the cellular level. The second one is the late zebrafish brain where the resulting atlas allows studies relating gene expression to brain regionalization and neurogenesis. The proposed computational frameworks have been adapted to the requirements of both scenarios, such as the integration of partial views of the embryo into a whole embryo model with cellular resolution or the registration of anatom¬ical traits with deformable transformation models non-dependent on any specific labeling. The software implementation of the atlas generation tool (Match-IT) and the visualization platform (Atlas-IT) together with the gene expression atlas resources developed in this Thesis are to be made freely available to the scientific community. Lastly, a novel proof-of-concept experiment integrates for the first time 3D gene expression atlas resources with cell lineages extracted from live embryos, opening up the door to correlate genetic and cellular spatio-temporal dynamics. La creación de atlas, o modelos digitales, donde la información de distintos sujetos puede ser combinada, es un campo de creciente interés en imagen biomédica. Cuando una sola imagen no contiene suficientes datos como para describir apropiadamente el organismo objeto de estudio, se hace necesario adquirir imágenes de varios individuos, cada una de las cuales contiene información complementaria respecto al resto de componentes del grupo. De este modo, es posible crear prototipos digitales, que pueden ir desde atlas anatómicos de órganos y pacientes humanos, adquiridos por ejemplo mediante Resonancia Magnética, hasta cartografías de la expresión genética del desarrollo de embrionario, típicamente adquiridas mediante Microscopía Optica. Dentro de este contexto, en esta Tesis Doctoral se introducen, desarrollan y validan nuevos métodos de procesado de imagen que, basándose en técnicas de registro de imagen, son capaces de alinear imágenes y datos provenientes de múltiples individuos en un solo atlas digital. Además, se ha elaborado una plataforma de visualization específicamente diseñada para explorar la gran cantidad de datos, caracterizados por su multi-dimensionalidad, que resulta de estos métodos. Asimismo, se han propuesto novedosos algoritmos de análisis y minería de datos que permiten inspeccionar automáticamente los atlas generados en busca de conclusiones biológicas significativas. En particular, este trabajo se centra en datos de expresión genética del desarrollo embrionario del pez cebra, adquiridos mediante Microscopía dos fotones con resolución celular. Disponer de medidas cuantitativas que relacionen estas expresiones genéticas con las posiciones celulares y su evolución en el tiempo es un prerrequisito fundamental para comprender los procesos multi-escala característicos de la morfogénesis. Sin embargo, el número de expresiones genéticos que pueden ser simultáneamente etiquetados en una sola adquisición es reducido debido a limitaciones tanto ópticas como del etiquetado. Estas limitaciones requieren la implementación de estrategias de creación de atlas que puedan recrear un multiplexado virtual de expresiones genéticas. Las herramientas computacionales desarrolladas han sido validadas en dos escenarios distintos. El primer escenario es el desarrollo embrionario temprano del pez cebra, donde el atlas resultante permite constituir un vínculo, a nivel celular, entre el fenotipo y el genotipo de este organismo modelo. El segundo escenario corresponde a estadios tardíos del desarrollo del cerebro del pez cebra, donde el atlas resultante permite relacionar expresiones genéticas con la regionalización del cerebro y la formación de neuronas. La plataforma computacional desarrollada ha sido adaptada a los requisitos y retos planteados en ambos escenarios, como la integración, a resolución celular, de vistas parciales dentro de un modelo consistente en un embrión completo, o el alineamiento entre estructuras de referencia anatómica equivalentes, logrado mediante el uso de modelos de transformación deformables que no requieren ningún marcador específico. Está previsto poner a disposición de la comunidad científica tanto la herramienta de generación de atlas (Match-IT), como su plataforma de visualización (Atlas-IT), así como las bases de datos de expresión genética creadas a partir de estas herramientas. Por último, dentro de la presente Tesis Doctoral, se ha incluido una prueba conceptual innovadora que permite integrar los mencionados atlas de expresión genética tridimensionales dentro del linaje celular extraído de una adquisición in vivo de un embrión. Esta prueba conceptual abre la puerta a la posibilidad de correlar, por primera vez, las dinámicas espacio-temporales de genes y células.

1H HR MAS NMR metabolomic and non-destructive 2D NMR relaxometry to assess internal quality in apples.

NMR can be considered a multi-scale multidimensional technology in the sense that it provides both spatial insight at macroscopic (MRI) or microscopic level (relaxometry), together with chemical characterization (HR-MAS). In this study 296 apples (from 4 cultivars) were MRI screened (20 slices per fruit) among which 7 fruits were used for metabolomic study by 1H HR MAS in order to assess various chemical shifts: malic acid, sucrose, glucose, fructose and ethanol. On the first season, tissue samples were taken from the sound and affected apples (near the core, centre and outer part of the mesocarp) belonging to sound and affected locations, while on the second season, tissue samples were focused on the comparison between sound and affected tissue. Beside, MRI and 2D non-destructive relaxometry (on whole fruits, and localized tissue) where performed on 72 and 12 apples respectively in order to compare features at macroscopic (tissue) and microscopic (subcellular) level. HR MAS shows higher content of ?-glucose, ?-glucose, malic acid and aromatic compounds in watercore affected tissues from both seasons, while sound tissue reflects higher sucrose. Microscopic (subcellular) degradation of tissue varies according to disorder development and is in good accordance with macroscopic characterization with MRI.

Arquitectura antidesertización. Fluidez, biodiversidad, hidrofilia y transpirabilidad

La escasez de recursos, la desertización creciente y el previsible calentamiento global forman un escenario físico sin precedentes que urge la revisión de las relaciones entre arquitectura y agua en la urbanización de los paisajes secos, donde la aridez es el factor limitante principal. Cuestionar la idea de escasez, la de residuo o la de confort es el punto de partida para analizar la hidrología urbana. La condición ubicua y dinámica del agua, sus continuos cambios de estado y las implicaciones energéticas y ambientales involucradas argumentan a favor de un entendimiento integral, holístico, que aborda el diseño en relación a lo paisajístico, lo infraestructural y lo ambiental como un único ámbito de investigación, planteado en términos no solo de materia o de escasez, sino de energía. Este trabajo se interesa por el rol de la arquitectura en este proyecto conjunto, integral, del espacio físico con el ciclo hidrológico donde lo orgánico, lo geológico y lo atmosférico están ligados, y donde las categorías de lo hidrológico y lo hidráulico se confunden. Las profundas implicaciones culturales en la construcción de la naturaleza urbana y en la relación con el cuerpo humano adquieren especial notoriedad en los modelos de paisaje y de espacio público adoptados, importados desde las geografías húmedas, y en la estigmatización del agua desde los presupuestos del higienismo decimonónico, que conduce al hidrofugado general de una ciudad aséptica y estéril, que se extiende hasta las envolventes de fachadas estancas y los interiores blancos y satinados. La búsqueda de referentes salta la modernidad hacia contextos de baja energía como el oasis tradicional de las tierras áridas, que concilia la formación de un ecosistema productivo con la climatización de un espacio público exterior, o los ambientes aislados de la investigación aeroespacial, con ciclos cerrados de materia. Las condiciones del ciclo del agua, como la vinculación con el suelo y el territorio, la capacidad de disolver, de mezclarse y de lavar, su volumen variable y su papel como termorregulador señalan el interés que características físicas como la fluidez, la biodiversidad, la hidrofilia y la transpirabilidad tienen para una arquitectura con competencias hidráulicas y un espacio urbano transparente a los procesos del agua. La morfología y localización, la elección de escalas, jerarquías y relaciones entre espacios y la reformulación de los sistemas constructivos aparecen como herramientas y categorías propias desde las que proponer mejores respuestas a problemas como la deshidratación, la erosión y la contaminación. Una urbanización permeable e hidrófila que absorba el agua como un recurso valioso, nuevos ensamblajes para la bioquímica urbana (que introduzcan una idea de limpieza más próxima a fertilidad que a la desinfección), y el diseño de las condiciones atmosféricas a través de una arquitectura transpirable, que se empapa y rezuma frescor, son las claves de este nuevo proyecto. La ciudad se piensa como una síntesis multiescalar de espacios hidráulicos que aporta mayor resiliencia frente a la desertificación y las condiciones climáticas extremas, y mayor visibilidad en la escena pública al agua y a las inevitables conexiones entre ecología y economía. Pero también es una oportunidad para revisar las categorías disciplinares, para renovar las consistencias materiales, las calidades ambientales y las relaciones entre el cuerpo y el espacio. ABSTRACT The shortage of resources, foreseeable global warming and increasing desertification create an unprecedented prospect that question the existing relationships between water and architecture, in the urbanization of the arid lands. The awareness of the huge volumes of water that pierce unnoticed through urban space, their impact on the landscape as well as on environmental qualities, promote a design field where cultural, social and political considerations intersect, related to the body and the physical experience of space within the built environment. Fluidity and ubiquity, solution ability, variability and cyclical processes are characteristic of water as material, directly related with the fields of potential, chemical and thermal energy and the reality of its mass, as it occupies a changing volume in space. These are also the imposing cross sections that water introduces into the project, that argue in favor of a comprehensive and holistic understanding, of addressing design in relationship to landscape, infrastructure and environmental issues as a one single area of research. This work attempts to investigate how architecture, with its specific tools, can partake in the design of water cycle in the space, linking the organic, geological, and atmospheric, blurring the lines between hydrology and hydraulic. It aims to identify issues, within the continuous query associated with water, that deal with the architectural project and may have here better results. The deep cultural implications in the construction of urban nature and the relationship with the body, acquire special notoriety in the models of landscape and public space adopted, imported from humid geographies. Also in the stigmatization of water from the premises of nineteenth- century hygienics, which lead to the entire waterproofing of an aseptic and sterile city, to the sealed facades and white and polished interiors. The search for alternative references goes beyond modernity towards a mindset of low energy, as the traditional oasis of arid lands, which aims to reconcile the formation of a productive ecosystem with the conditioning of an outdoor public space, or the controlled environments of aerospace research, with closed cycles of matter. Fluidity, biodiversity, hydrophilicity and breathability are characteristic of an architecture with hydraulic competences. The distributing phenomenon of water, its necessary connectivity to the ground and to small cycles in the ecosystems, shows strong affinities with an infrastructural architecture, as an alternative to large-scale centralized networks. Its volume has approximated to the dimensions of the built space, promoting a new found condition of coexistence. A permeable and hydrophilic urbanization absorbs water as a valuable resource; new assemblies for urban biochemistry introduce an idea of sanitation closer to fertility than to disinfection; a breathable architecture that soaks and exudes freshness design the atmospheric conditions: these are the essential components of this new project. The city is understood as a synthesis of multi-scale hydraulic spaces that provides greater resilience against desertification and increases the visibility of water and the linkages between ecology and economy in the public scene. It is also an opportunity to review the disciplinary categories of architecture, the material consistencies, the environmental qualities and the relationship between body and space.

Analysis of Contributions to NO2 Ambient Air Quality Levels in Madrid City (Spain) through Modeling. Implications for the Development of Policies and Air Quality Monitoring

As environmental standards become more stringent (e.g. European Directive 2008/50/EC), more reliable and sophisticated modeling tools are needed to simulate measures and plans that may effectively tackle air quality exceedances, common in large cities across Europe, particularly for NO2. Modeling air quality in urban areas is rather complex since observed concentration values are a consequence of the interaction of multiple sources and processes that involve a wide range of spatial and temporal scales. Besides a consistent and robust multi-scale modeling system, comprehensive and flexible emission inventories are needed. This paper discusses the application of the WRF-SMOKE-CMAQ system to the Madrid city (Spain) to assess the contribution of the main emitting sectors in the region. A detailed emission inventory was compiled for this purpose. This inventory relies on bottom-up methods for the most important sources. It is coupled with the regional traffic model and it makes use of an extensive database of industrial, commercial and residential combustion plants. Less relevant sources are downscaled from national or regional inventories. This paper reports the methodology and main results of the source apportionment study performed to understand the origin of pollution (main sectors and geographical areas) and define clear targets for the abatement strategy. Finally the structure of the air quality monitoring is analyzed and discussed to identify options to improve the monitoring strategy not only in the Madrid city but the whole metropolitan area.