Deep Model for Improved Operator Function State Assessment

A deep learning framework is presented for engagement assessment using EEG signals. Deep learning is a recently developed machine learning technique and has been applied to many applications. In this paper, we proposed a deep learning strategy for operator function state (OFS) assessment. Fifteen pilots participated in a flight simulation from Seattle to Chicago. During the four-hour simulation, EEG signals were recorded for each pilot. We labeled 20- minute data as engaged and disengaged to fine-tune the deep network and utilized the remaining vast amount of unlabeled data to initialize the network. The trained deep network was then used to assess if a pilot was engaged during the four-hour simulation

Proceedings, MSVSCC 2014

Proceedings of the 8th Annual Modeling, Simulation & Visualization Student Capstone Conference held on April 17, 2014 at VMASC in Suffolk, Virginia

Combining Smart Material Platforms and New Computational Tools to Investigate Cell Motility Behavior and Control

Cell-extracellular matrix (ECM) interactions play a critical role in regulating important biological phenomena, including morphogenesis, tissue repair, and disease states. In vivo, cells are subjected to various mechanical, chemical, and electrical cues to collectively guide their functionality within a specific microenvironment. To better understand the mechanisms regulating cell adhesive, differentiation, and motility dynamics, researchers have developed in vitro platforms to synthetically mimic native tissue responses. While important information about cell-ECM interactions have been revealed using these systems, a knowledge gap currently exists regarding how cell responses in static environments relate to the dynamic cell-ECM interaction behaviors observed in vivo. Advances at the intersection of materials science, biophysics, and cell biology have recently enabled the production of dynamic ECM mimics where cells can be exposed to controlled mechanical, electrical or chemical cues to directly decouple cell-ECM related behaviors from cell-cell or cell-environmental factors. Utilization of these dynamic synthetic biomaterials will enable discovery of novel mechanisms fundamental in tissue development, homeostasis, repair, and disease. In this dissertation, the primary goal was to evaluate how mechanical changes in the ECM regulate cell motility and polarization responses. This was accomplished through two major aims: 1) by developing a modular image processing tool that could be applied in complex synthetic in vitro microenvironments to asses cell motility dynamics, and 2) to utilize that tool to advance understanding of mechanobiology and mechanotransduction processes associated with development, wound healing, and disease progression. Therefore, the first portion of this thesis (Chapters 2 and 3) dealt with proof of concept for our newly developed automated cell tracking system, termed ACTIVE (automated contour-based tracking for in vitro environments), while the second portion of this thesis (Chapter 4-7) addressed applying this system in multiple experimental designs to synthesize new knowledge regarding cell-ECM or cell-cell interactions. In Chapter 1, we introduced why cell-ECM interactions are essential for in vivo processes and highlighted the current state of the literature. In Chapter 2, we demonstrated that ACTIVE could achieve greater than 95% segmentation accuracy at multiple cell densities, while improving two-body cell-cell interaction error by up to 43%. In Chapter 3 we showed that ACTIVE could be applied to reveal subtle differences in fibroblast motility atop static wrinkled or static non-wrinkled surfaces at multiple cell densities. In Chapters 4 and 5, we characterized fibroblast motility and intracellular reorganization atop a dynamic shape memory polymer biomaterial, focusing on the role of the Rho-mediated pathway in the observed responses. We then utilized ACTIVE to identify differences in subpopulation dynamics of monoculture versus co-culture endothelial and smooth muscle cells (Chapter 6). In Chapter 7, we applied ACTIVE to investigate E. coli biofilm formation atop poly(dimethylsiloxane) surfaces with varying stiffness and line patterns. Finally, we presented a summary and future work in Chapter 8. Collectively, this work highlights the capabilities of the newly developed ACTIVE tracking system and demonstrates how to synthesize new information about mechanobiology and mechanotransduction processes using dynamic biomaterial platforms

Numerical modelling of additive manufacturing process for stainless steel tension testing samples

Nowadays additive manufacturing (AM) technologies including 3D printing grow rapidly and they are expected to replace conventional subtractive manufacturing technologies to some extents. During a selective laser melting (SLM) process as one of popular AM technologies for metals, large amount of heats is required to melt metal powders, and this leads to distortions and/or shrinkages of additively manufactured parts. It is useful to predict the 3D printed parts to control unwanted distortions and shrinkages before their 3D printing. This study develops a two-phase numerical modelling and simulation process of AM process for 17-4PH stainless steel and it considers the importance of post-processing and the need for calibration to achieve a high-quality printing at the end. By using this proposed AM modelling and simulation process, optimal process parameters, material properties, and topology can be obtained to ensure a part 3D printed successfully

Quantifying Atherosclerosis: IVUS Imaging For Lumen Border Detection And Plaque Characterization

The importance of atherosclerotic disease in coronary artery has been a subject of study for many researchers in the past decade. In brief, the aim is to understand progression of such a disease, detect plaques at risks (vulnerable plaques), and treat them selectively to prevent mortality and immobility. Consequently, several imaging modalities have been developed and among them intravascular ultrasound (IVUS) has been of particular interest since it provides useful information about tissues microstructures and images with sufficient penetration as well as resolution. In general, the ultimate goal is to provide interventional cardiologists with reliable clinical tools so they can identify vulnerable plaques, make decisions confidently, choose the most appropriate drugs or implant devices (i.e. stent), and stabilize them during catheterization procedures with minimal risk. In this work, we review existing atherosclerotic tissue characterization algorithms including the state-of-the-art virtual histology (VH) framework, which has been implemented in the Volcano (Rancho Cordova, CA) IVUS clinical scanners using 64-elements 20 MHz phased-array transducer. Initially, we intended to extend this technique for data acquired with 40 MHz single-element transducers. For this reason, we started acquiring in vitro IVUS data and studied involved challenges from specimen preparation toward classification. We observed inconsistency among extracted features along with transducer's spectral parameters (i.e. bandwidth, center frequency). This, in addition to infeasibility of construction of reliable training dataset due to heterogeneity of atherosclerotic tissues motivated us to develop an unsupervised texture-based atherosclerotic tissue characterization algorithm. We proposed a two-dimensional multiscale wavelet-based algorithm to expand IVUS backscattered signals and/or grayscale images onto orthogonal symmetric quadrature mirror filters (QMF) such as Lemarie-Battle. At the bottom of decomposition tree, we employed ISODATA to cluster enveloped detected features in an unsupervised fashion and classify atherosclerotic plaque constitutes into fibrotic, lipidic, calcified, and no tissues. For the first time, we studied numbers of factors that were necessary for extension of in vitro derived classifier for in vivo applications such as reliability of classified tissues behind arc of calcified plaques and effects of pressure changes as well as flowing blood on constructed tissue color maps, called prognosis histology (PH) images. The second half of this dissertation is devoted to automatic detection of lumen borders in IVUS grayscale images acquired with high frequency (40 MHz up) transducers where more scattering exhibited within lumen area that makes the problem of interest more challenging. We established our framework on three-dimensional expansion of IVUS sub-volumes onto orthonormal brushlet basis function. The rational behind our framework was presence of incoherent (i.e. blood) versus coherent (i.e. plaque, surrounding fat) textural patterns along pullback direction, which was motivated by what an interventional cardiologist does to locate the lumen border visually by going back and forth among IVUS frames. We studied the feasibility of brushlet analysis through filtering blood speckles and supervised classification of blood versus non-blood regions. Our preliminary study confirmed that the most informative features reside in the innermost cubes, representing low-frequency components in transformed domain. Finally, we explored that tissue responses to IVUS signals are proportionally preserved in brushlet coefficients and it enabled us to classify blood regions in complex brushlet space. Subsequently, we employed surface function actives (SFA) to estimate the lumen borders after regularization. In a comparison study, we quantified our results with two of existing algorithms, employing IVUS grayscale images acquired with 40 MHz and 45 MHz single-element transducers. Overall, our proposed algorithm outperformed and the resulting automated detected borders showed good correlation with manually traced borders by an expert

G-CSC Report 2010

The present report gives a short summary of the research of the Goethe Center for Scientific Computing (G-CSC) of the Goethe University Frankfurt. G-CSC aims at developing and applying methods and tools for modelling and numerical simulation of problems from empirical science and technology. In particular, fast solvers for partial differential equations (i.e. pde) such as robust, parallel, and adaptive multigrid methods and numerical methods for stochastic differential equations are developed. These methods are highly adanvced and allow to solve complex problems.. The G-CSC is organised in departments and interdisciplinary research groups. Departments are localised directly at the G-CSC, while the task of interdisciplinary research groups is to bridge disciplines and to bring scientists form different departments together. Currently, G-CSC consists of the department Simulation and Modelling and the interdisciplinary research group Computational Finance

Book of short Abstracts of the 11th International Symposium on Digital Earth

The Booklet is a collection of accepted short abstracts of the ISDE11 Symposium

Computational methods for high-throughput metabolomics

Hoffmann N. Computational methods for high-throughput metabolomics. Bielefeld: Universität Bielefeld; 2014.The advent of analytical technologies being broadly and routinely applied in biology and biochemistry for the analysis and characterization of small molecules in biological organisms has brought with it the need to process, analyze, compare, and evaluate large amounts of experimental data in a highly automated fashion. The most prominent methods used in these fields are chromatographic methods capable of separating complex mixtures of chemical compounds by properties like size or charge, coupled to mass spectrometry detectors that measure the mass and intensity of a compound's ion or its fragments eluting from the chromatographic separation system. One major problem in these high-throughput applications is the automatic extraction of features quantifying the compounds contained in the measured results and their reliable association among multiple measurements for quantification and statistical analysis. The main goal of this thesis is the creation of scalable and robust methods for highly automated processing of large numbers of samples. Of special importance is the comparison of different samples in order to find similarities and differences in the context of metabolomics, the study of small chemical compounds in biological organisms. We herein describe novel algorithms for retention time alignment of peak and chromatogram data from one- and two-dimensional gas chromatography-mass spectrometry experiments in the application area of metabolomics. We also perform a comprehensive evaluation of each method against other state-of-the-art methods on publicly available datasets with genuine biological backgrounds. In addition to these methods, we also describe the underlying software framework Maltcms and the accompanying graphical user interface Maui, and demonstrate their use on instructive application examples

Neural networks in a multiscale approach for concrete

From a macroscopic point of view, failure within concrete structures is characterized by the initiation and propagation of cracks. In the first part of the thesis, a methodology for macroscopic crack growth simulations for concrete structures using a cohesive discrete crack approach based on the extended finite element method is introduced. Particular attention is turned to the investigation of criteria for crack initiation and crack growth. A drawback of the macroscopic simulation is that the real physical phenomena leading to the nonlinear behavior are only modeled phenomenologically. For concrete, the nonlinear behavior is characterized by the initiation of microcracks which coalesce into macroscopic cracks. In order to obtain a higher resolution of this failure zones, a mesoscale model for concrete is developed that models particles, mortar matrix and the interfacial transition zone (ITZ) explicitly. The essential features are a representation of particles using a prescribed grading curve, a material formulation based on a cohesive approach for the ITZ and a combined model with damage and plasticity for the mortar matrix. Compared to numerical simulations, the response of real structures exhibits a stochastic scatter. This is e.g. due to the intrinsic heterogeneities of the structure. For mesoscale models, these intrinsic heterogeneities are simulated by using a random distribution of particles and by a simulation of spatially variable material parameters using random fields. There are two major problems related to numerical simulations on the mesoscale. First of all, the material parameters for the constitutive description of the materials are often difficult to measure directly. In order to estimate material parameters from macroscopic experiments, a parameter identification procedure based on Bayesian neural networks is developed which is universally applicable to any parameter identification problem in numerical simulations based on experimental results. This approach offers information about the most probable set of material parameters based on experimental data and information about the accuracy of the estimate. Consequently, this approach can be used a priori to determine a set of experiments to be carried out in order to fit the parameters of a numerical model to experimental data. The second problem is the computational effort required for mesoscale simulations of a full macroscopic structure. For this purpose, a coupling between mesoscale and macroscale model is developed. Representative mesoscale simulations are used to train a metamodel that is finally used as a constitutive model in a macroscopic simulation. Special focus is placed on the ability of appropriately simulating unloading.Makroskopisch betrachtet kann das Versagen von Beton durch die Entstehung und das Wachstum von Rissen beschrieben werden. Im ersten Teil der Arbeit wird eine Methode zur Simulation der makroskopischen Rissentwicklung von Beton unter Verwendung von kohäsiven diskreten Rissen basierend auf der erweiterten Finiten Elemente Methode vorgestellt. Besondere Bedeutung liegt dabei auf der Untersuchung von Kriterien zur Rissentstehung und zum Risswachstum. Ein Nachteil von makroskopischen Simulationen liegt in der nur phänomenologischen Berücksichtigung der tatsächlichen Vorgänge. Nichtlineares Verhalten von Beton ist durch die Entstehung von Mikrorissen gekennzeichnet, die bei weiterer Belastung zu makroskopischen Rissen zusammenwachsen. Um die Versagenszone realitätsnah abbilden zu können, wurde ein Mesoskalenmodell von Beton entwickelt, welches Zuschläge, Matrix und Übergangszone zwischen beiden Materialien (ITZ) direkt abbildet. Hauptmerkmal sind die Simulation der Zuschläge nach einer Sieblinie, eine kohäsive Materialformulierung der ITZ und ein kombiniertes Model aus Schädigung und Plastizität für das Matrixmaterial. Im Gegensatz zu numerischen Simulationen ist die Systemantwort reeller Strukturen eine unscharfe Größe. Dies liegt u.a. an Heterogenitäten innerhalb der Struktur, die im Rahmen der Arbeit durch eine zufällige Verteilung der Zuschläge und über räumlich variierende Materialparameter unter Verwendung von Zufallsfeldern simuliert werden. Zwei Hauptprobleme sind bei den Mesoskalensimulationen aufgetreten. Einerseits sind Materialparameter auf der Mesoskala oft schwer zu bestimmen. Deswegen wurde eine Methode basierend auf Bayes neuronalen Netzen entwickelt, die eine Parameteridentifikation unter Verwendung von makroskopischen Versuchen erlaubt. Diese Methode ist aber universell anwendbar auf alle Parameteridentifikationsprobleme in numerischen Simulationen basierend auf experimentellen Daten. Der Ansatz liefert sowohl Informationen über den wahrscheinlichsten Parametersatz des Models zur numerischen Simulation eines Experiments als auch eine Einschätzung der Genauigkeit dieses Schätzers. Die Methode kann auch verwendet werden, um a priori einen Satz von Experimenten auszuwählen der notwendig ist, um die Parameter eines numerischen Modells zu bestimmen. Ein zweites Problem ist der numerische Aufwand von Mesoskalensimulationen für makroskopische Strukturen. Aus diesem Grund wurde eine Kopplungsstrategie zwischen Meso- und Makromodell entwickelt, bei dem repräsentative Simulationen auf der Mesoebene verwendet werden, um ein Metamodell zu generieren, welches dann die Materialformulierung in einer makroskopischen Simulation darstellt. Ein Fokus liegt dabei auf der korrekten Abbildung von Entlastungen