Investigation of upwind, multigrid, multiblock numerical schemes for three dimensional flows. Volume 1: Runge-Kutta methods for a thin layer Navier-Stokes solver

A state-of-the-art computer code has been developed that incorporates a modified Runge-Kutta time integration scheme, upwind numerical techniques, multigrid acceleration, and multi-block capabilities (RUMM). A three-dimensional thin-layer formulation of the Navier-Stokes equations is employed. For turbulent flow cases, the Baldwin-Lomax algebraic turbulence model is used. Two different upwind techniques are available: van Leer's flux-vector splitting and Roe's flux-difference splitting. Full approximation multi-grid plus implicit residual and corrector smoothing were implemented to enhance the rate of convergence. Multi-block capabilities were developed to provide geometric flexibility. This feature allows the developed computer code to accommodate any grid topology or grid configuration with multiple topologies. The results shown in this dissertation were chosen to validate the computer code and display its geometric flexibility, which is provided by the multi-block structure

Micro-Bioreactor Array for Controlling Cellular Microenvironments

High throughput experiments can be used to spatially and temporally investigate the many factors that regulate cell differentiation. We have developed a micro-bioreactor array (MBA) that is fabricated using soft lithography and contains twelve independent micro-bioreactors perfused with culture medium. The MBA enables cultivation of cells that are either attached to substrates or encapsulated in hydrogels, at variable levels of hydrodynamic shear, and with automated image analysis of the expression of cell differentiation markers. The flow and mass transport in the MBA were characterized by computational fluid dynamic (CFD) modeling. The representative MBA configurations were validated using the C2C12 cell line, primary rat cardiac myocytes and human embryonic stem cells (hESCs) (lines H09 and H13). To illustrate the utility of the MBA for controlled studies of hESCs, we established correlations between the expression of smooth muscle actin and cell density for three different flow configurations

Surface-Patterned Electrode Bioreactor for Electrical Stimulation

We present a microscale cell culture system with an interdigitated microarray of excimer-laser-ablated indium tin oxide electrodes for electrical stimulation of cultured cells. The system has been characterized in a range of geometeries and stimulation regimes via electrochemical impedance spectroscopy and used to culture primary cardiomyocytes and human adipose derived stem cells. Over 6 days of culture with electrical stimulation (2 ms duration, 1 Hz, 180 μm wide electrodes with 200 μm spacing), both cell types exhibited enhanced proliferation, elongation and alignment, and adipose derived stem cells exhibited higher numbers of Connexin-43-composed gap junctions

Dedicated JPSS VIIRS Ocean Color Calibration/Validation Cruise

The NOAA/STAR ocean color team is focused on “end-to-end” production of high quality satellite ocean color products. In situ validation of satellite data is essential to produce the high quality, “fit for purpose” remotely sensed ocean color products that are required and expected by all NOAA line offices, as well as by external (both applied and research) users. In addition to serving the needs of its diverse users within the U.S., NOAA has an ever increasing role in supporting the international ocean color community and is actively engaged in the International Ocean-Colour Coordinating Group (IOCCG). The IOCCG, along with the Committee on Earth Observation Satellites (CEOS) Ocean Colour Radiometry Virtual Constellation (OCR-VC), is developing the International Network for Sensor Inter-comparison and Uncertainty assessment for Ocean Color Radiometry (INSITU-OCR). The INSITU-OCR has identified, amongst other issues, the crucial need for sustained in situ observations for product validation, with longterm measurement programs established and maintained beyond any individual mission. Recently, the NOAA/STAR Ocean Color Team has been making in situ validation measurements continually since the launch in fall 2011 of the Visible Infrared Imaging Radiometer Suite (VIIRS) aboard the Suomi National Polar-orbiting Partnership (SNPP) platform, part of the U.S. Joint Polar Satellite System (JPSS) program. NOAA ship time for the purpose of ocean color validation, however, had never been allocated until the cruise described herein. As the institutional lead for this cruise, NOAA/STAR invited external collaborators based on scientific objectives and existing institutional collaborations. The invited collaborators are all acknowledged professionals in the ocean color remote sensing community. Most of the cruise principal investigators (PIs) are also PIs of the VIIRS Ocean Color Calibration and Validation (Cal/Val) team, including groups from Stennis Space Center/Naval Research Laboratory (SSC/NRL) and the University of Southern Mississippi (USM); City College of New York (CCNY); University of Massachusetts Boston (UMB); University of South Florida (USF); University of Miami (U. Miami); and, the National Institute of Standards and Technology (NIST). These Cal/Val PIs participated directly, sent qualified researchers from their labs/groups, or else contributed specific instruments or equipment. Some of the cruise PIs are not part of the NOAA VIIRS Ocean Color Cal/Val team but were chosen to complement and augment the strengths of the Cal/Val team participants. Outside investigator groups included NASA Goddard Space Flight Center (NASA/GSFC), Lamont-Doherty Earth Observatory at Columbia University (LDEO), and the Joint Research Centre of the European Commission (JRC). This report documents the November 2014 cruise off the U.S. East Coast aboard the NOAA Ship Nancy Foster. This cruise was the first dedicated ocean color validation cruise to be supported by the NOAA Office of Marine and Air Operations (OMAO). A second OMAO-supported cruise aboard the Nancy Foster is being planned for late 2015. We at NOAA/STAR are looking forward to continuing dedicated ocean color validation cruises, supported by OMAO on NOAA vessels, on an annual basis in support of JPSS VIIRS on SNPP, J-1, J-2 and other forthcoming satellite ocean color missions from the U.S as well as other countries. We also look forward to working with the U.S. and the international ocean community for improving our understanding of global ocean optical, biological, and biogeochemical properties.JRC.H.1-Water Resource

Meaning and Function in the Theory of Consumer Choice: Dual Selves in Evolving Networks

Building on the philosophy of Charles Sanders Peirce, recent advances in biosemiotics have resulted into a concise framework for the analysis of signs in living systems. This paper explores the potential for economics and shows how biosemiotics can integrate two different research agendas, each of which are also connected with biological theories, namely neuroeconomics and the theory of networks. I introduce the triadic conceptual framework established by Peirce which distinguishes between object, sign and interpretant and the corresponding causal forces in evolving hierarchical systems. This framework is used to systematize recent results of neuroeconomics in the form of the dual selves approach, following early contributions of James Coleman, partitioning the individual into the acting self and the object self. This distinction implies that there is a fundamental information asymmetry between the two selves. Against this background, the semeiotic process is an information generating and processing dynamics, which is driven by the internal selection of classificatory schemes of actions chosen and the population level dynamics of sign selection, with mimetic behavior as a driver. This can be further analyzed by means of the theory of signal selection. A central insight is that the internal information gap between acting self and object self implies a systematic role of sign processing in social networks for any kind of consumer choice. I exemplify my approach with empirical references to food consumption as a most universal and simple form of consumer choice

JC virus and its possible role in oncogenesis

No abstract.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/34652/1/3_ftp.pd

Mouse Chromosome 11

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46996/1/335_2004_Article_BF00648429.pd

The Helicobacter pylori Genome Project : insights into H. pylori population structure from analysis of a worldwide collection of complete genomes

Helicobacter pylori, a dominant member of the gastric microbiota, shares co-evolutionary history with humans. This has led to the development of genetically distinct H. pylori subpopulations associated with the geographic origin of the host and with differential gastric disease risk. Here, we provide insights into H. pylori population structure as a part of the Helicobacter pylori Genome Project (HpGP), a multi-disciplinary initiative aimed at elucidating H. pylori pathogenesis and identifying new therapeutic targets. We collected 1011 well-characterized clinical strains from 50 countries and generated high-quality genome sequences. We analysed core genome diversity and population structure of the HpGP dataset and 255 worldwide reference genomes to outline the ancestral contribution to Eurasian, African, and American populations. We found evidence of substantial contribution of population hpNorthAsia and subpopulation hspUral in Northern European H. pylori. The genomes of H. pylori isolated from northern and southern Indigenous Americans differed in that bacteria isolated in northern Indigenous communities were more similar to North Asian H. pylori while the southern had higher relatedness to hpEastAsia. Notably, we also found a highly clonal yet geographically dispersed North American subpopulation, which is negative for the cag pathogenicity island, and present in 7% of sequenced US genomes. We expect the HpGP dataset and the corresponding strains to become a major asset for H. pylori genomics