Guidance of collective cell migration by substrate geometry.

Collective behavior refers to the emergence of complex migration patterns over scales larger than those of the individual elements constituting a system. It plays a pivotal role in biological systems in regulating various processes such as gastrulation, morphogenesis and tissue organization. Here, by combining experimental approaches and numerical modeling, we explore the role of cell density ('crowding'), strength of intercellular adhesion ('cohesion') and boundary conditions imposed by extracellular matrix (ECM) proteins ('constraints') in regulating the emergence of collective behavior within epithelial cell sheets. Our results show that the geometrical confinement of cells into well-defined circles induces a persistent, coordinated and synchronized rotation of cells that depends on cell density. The speed of such rotating large-scale movements slows down as the density increases. Furthermore, such collective rotation behavior depends on the size of the micropatterned circles: we observe a rotating motion of the overall cell population in the same direction for sizes of up to 200 μm. The rotating cells move as a solid body, with a uniform angular velocity. Interestingly, this upper limit leads to length scales that are similar to the natural correlation length observed for unconfined epithelial cell sheets. This behavior is strongly altered in cells that present a downregulation of adherens junctions and in cancerous cell types. We anticipate that our system provides a simple and easy approach to investigate collective cell behavior in a well-controlled and systematic manner.

Geometric perspectives on MDO and MDO architectures

Two main perspectives have been developed within the Multidisciplinary Design Optimization (MDO) literature for classifying and comparing MDO architectures: a numerical point of view and a formulation/data flow point of view. Although significant work has been done here, these perspectives have not provided much in the way of a priori information or predictive power about architecture performance. In this report, we outline a new perspective, called the geometric perspective, which we believe will be able to provide such predictive power. Using tools from differential geometry, we take several prominent architectures and describe mathematically how each constructs the space through which it moves. We then consider how the architecture moves through the space which it has constructed. Taken together, these investigations show how each architecture relates to the original feasible design manifold, how the architectures relate to each other, and how each architecture deals with the design coupling inherent to the original system. This in turn lays the groundwork for further theoretical comparisons between and analyses of MDO architectures and their behaviour using tools and techniques derived from differential geometry. © 2012 by the American Institute of Aeronautics and Astronautics, Inc. All rights reserved.

The influence of room geometry on the overturning of smoke owing to a floor fire

The present paper explores the influence of room geometry on the overturning of smoke owing to a centrally located floor fire, and examines the implications on smoke filling times. The focus is on presenting practical design guidelines based on the theoretical predictions of the model of Kaye and Hunt. An engineering platform is developed for the prediction of smoke filling times, and a rational basis is provided by way of which smoke behaviour can be specified for simple room designs. The time taken for smoke to fill a room to a given height is critically affected by the room aspect ratio and the characteristic size of the buoyancy source. At large times, taller (small aspect ratio) rooms are shown to fill with smoke at a faster rate than wide (large aspect ratio) rooms owing to large-scale overturning and engulfing of ambient air during the initial transients. Larger area sources of buoyancy also decrease significantly the smoke filling times, with important implications for fire and smoke safety design. Simplified design curves incorporating the main findings have been developed for use as a tool by practising fire-safety engineers.

Influence of tire geometry on the horn effect

A reciprocal-configuration Boundary Element Method calculation of acoustic radiation characteristics has been implemented for a generic tire geometry. The influence of the geometric parameters on the radiation characteristics has been studied. The degree of amplification of noise sources on the tire belt is strongly affected by the overall tire width. In contrast, the tire radius predominantly influences the pattern of the varying amplification around the belt, rather than its absolute level. Radiusing the tire's 'shoulder' region is potentially beneficial in terms of lowering amplification levels, for a tire of fixed overall width. However, it is less effective than maintaining sharp shoulders and reducing the overall width. Thus, for an acoustically optimal belted tire, the overall width should be as small as possible, even if this leads to a larger diameter. The width should not be increased in order to accommodate a radiused crown region. Copyright © (2012) by the Institute of Noise Control Engineering (INCE).

Vibration decay along deepwater moorings with complex geometry and configuration, as a tool for truncation

This paper is concerned with the difficulties in model testing deepwater structures at reasonable scales. An overview of recent research efforts to tackle this challenge is given first, introducing the concept of line truncation. Passive truncation has traditionally been the preferred method by industry; however, these techniques tend to suffer in capturing accurately line dynamic response and so reproducing peak tensions. In an attempt to improve credibility of model test data the proposed truncation procedure sets up the truncated model, based on line dynamic response rather than quasi-static system stiffness. Vibration decay of transverse elastic waves due to fluid drag forces is assessed and it is found that below a certain length criterion, the transverse vibrational characteristics for each line are inertia driven, hence with respect to these motions the truncated model can assume a linear damper whose coefficient depends on the local line properties and vibration frequency. Initially a simplified taut string model is assumed for which the line is submerged in still water, one end fixed at the bottom the other assumed to follow the vessel response, which can be harmonic or random. A dimensional analysis, supported by exact benchmark numerical solutions, has shown that it is possible to produce a general guideline for the truncation length criterion, which is suitable for any kind of line with any top motion. The focus of this paper is to extend this work to a more complex line configuration of a conventional deepwater mooring line and so enhance the generality of the truncation guideline. The paper will close with an example case study of a spread mooring system, applying this method to create an equivalent numerical model at a reduced depth that replicates exactly the static and dynamic characteristics of the full depth system. Copyright © 2012 by ASME.

Optimization on manifolds: Methods and applications

This paper provides an introduction to the topic of optimization on manifolds. The approach taken uses the language of differential geometry, however,we choose to emphasise the intuition of the concepts and the structures that are important in generating practical numerical algorithms rather than the technical details of the formulation. There are a number of algorithms that can be applied to solve such problems and we discuss the steepest descent and Newton's method in some detail as well as referencing the more important of the other approaches.There are a wide range of potential applications that we are aware of, and we briefly discuss these applications, as well as explaining one or two in more detail. © 2010 Springer -Verlag Berlin Heidelberg.

Identification of differential transcript profiles between mutual crossbred embryos of zebrafish (Danio rerio) and Chinese rare minnow (Gobiocypris rarus) by cDNA-AFLP

The crosstalk between naive nucleus and maternal factors deposited in egg cytoplasm before zygotic genome activation is crucial for early development. In this study, we utilized two laboratory fishes, zebrafish (Danio rerio) and Chinese rare minnow and Chinese rare minnow (Gobiocypris rarus), to obtain mutual crossbred embroys and examine the interaction between nucleus and egg cytoplasm from different species. Although these two types of crossbred embryos originated from common nuclei, various developmental capacities were gained due to different origins of the egg cytoplasm. Using cDNA amplified fragment length polymorphism (cDNA-AFLP), We Compared transcript profiles between the mutual crossbred embryos at two developmental stages (50%- and 90%-epiholy). Three thousand cDNA fragments were generated in four cDNA pools with 64 primer combinations. All differently displayed transcript-derived fragments (TDFs) were screened by (lot blot hybridization, and the selected sequences were further analyzed by semi-quantitative RT-PCR and quantitative real-time RT-PCR. Compared with ZR embryos, 12 genes were up-regulated and 12 were down-regulated in RZ embryos. The gene fragments were sequenced and subjected to BLASTN analysis. The sequences encoded various proteins which functioned at various levels of proliferation, growth, and development. One gene (ZR6), dramatically down-regulated in RZ embryos, was chosen for loss-of-function study; the knockdown of ZR6 gave rise to the phenotype resembling that of RZ embryos. (c) 2008 Elsevier Inc. All rights reserved.

Avian influenza virus infection induces differential expression of genes in chicken kidney

The pathogenic process of highly pathogenic avian influenza virus (HPAIV) infection is poorly understood. To explore the differential expression of kidney genes as a result of HPAIV infection, two cDNA libraries were constructed from uninfected and infected kidneys by suppression subtractive hybridization (SSH). Fifteen genes including IFN-stimulated genes (ISG12), lymphocyte antigen 6 complex locus E gene (LY6E), matrix Gla protein gene (MGP), lysozyme gene, haemopoiesis related membrane protein I gene, KIAA1259, MGC68696, G6pe-prov protein gene (G6PC), MGC4504, alcohol dehydrogenase gene (ADH), glutathione S-transferase gene (GST), sodium-dependent high-affinity dicarboxylate transporter gene (SDCT), Synaptotagmin XV (SytXV) and two novel genes were found significantly up-regulated or dramatically suppressed. Differential expression of these genes was further identified by Northern blot. Functional analysis indicated that the regulation of their expression might contribute to the pathogenic process of HPAIV infection. In contrast, the increased expression of three IFN-stimulated genes named ISG12, LY6E, and haemopoiesis related membrane protein 1 gene might reflect host defense responses. Further study showed that ISG12 protein failed to directly interact with NS1 protein of HPAIV which expressed simultaneously in the organs where HPAIV replication occurred, by use of BacterioMatch two-hybrid system. Therefore, our findings may provide new insights into understanding the molecular mechanism underlying the pathophysiological process of HPAIV infection in chicken. (c) 2007 Elsevier Ltd. All rights reserved.

A differential lyapunov framework for contraction analysis

Lyapunov's second theorem is an essential tool for stability analysis of differential equations. The paper provides an analog theorem for incremental stability analysis by lifting the Lyapunov function to the tangent bundle. The Lyapunov function endows the state-space with a Finsler structure. Incremental stability is inferred from infinitesimal contraction of the Finsler metrics through integration along solutions curves. © 2013 IEEE.

Optimization algorithms and ODE's in MDO

There is a need for a stronger theoretical understanding of Multidisciplinary Design Optimization (MDO) within the field. Having developed a differential geometry framework in response to this need, we consider how standard optimization algorithms can be modeled using systems of ordinary differential equations (ODEs) while also reviewing optimization algorithms which have been derived from ODE solution methods. We then use some of the framework's tools to show how our resultant systems of ODEs can be analyzed and their behaviour quantitatively evaluated. In doing so, we demonstrate the power and scope of our differential geometry framework, we provide new tools for analyzing MDO systems and their behaviour, and we suggest hitherto neglected optimization methods which may prove particularly useful within the MDO context. Copyright © 2013 by ASME.

Unified form language: A domain-specific language for weak formulations of partial differential equations

We present the Unified Form Language (UFL), which is a domain-specific language for representing weak formulations of partial differential equations with a view to numerical approximation. Features of UFL include support for variational forms and functionals, automatic differentiation of forms and expressions, arbitrary function space hierarchies formultifield problems, general differential operators and flexible tensor algebra. With these features, UFL has been used to effortlessly express finite element methods for complex systems of partial differential equations in near-mathematical notation, resulting in compact, intuitive and readable programs. We present in this work the language and its construction. An implementation of UFL is freely available as an open-source software library. The library generates abstract syntax tree representations of variational problems, which are used by other software libraries to generate concrete low-level implementations. Some application examples are presented and libraries that support UFL are highlighted. © 2014 ACM.

Differential expression and dynamic changes of SOX3 during gametogenesis and sex reversal in protogynous hermaphroditic fish

SOX3 has been suggested to play significant roles in gametogenesis and gonad differentiation of vertebrates, but the exact cellular localization evidence is insufficient and controversial. In this study, a protogynous hermaphrodite fish Epinephelus coioides is selected to analyze EcSox3 differential expression and the expression pattern in both processes of oogenesis and spermatogenesis by utilizing the advantages that gonad development undergoes transition from ovary to intersexual gonad and then to testis, and primordial germ cells and different stage cells during oogenesis and spermatogenesis are synchronously observed in the transitional gonads. The detailed and clear immunofluoresence localization indicates that significantly differential expression and dynamic changes of Sox3 occur in the progresses of gametogenesis and sex reversal, and EcSOX3 protein exists in the differentiating primordial germ cells, oogonia, and different stage oocytes of ovaries, and also in the differentiating primordial germ cells and the Sertoli cells of testis. One important finding is that the EcSox3 expression is a significant time point for enterable gametogenesis of primordial germ cells because EcSOX3 is obviously expressed and localized in primordial germ cells. As EcSox3 continues to express, the EcSOX3-positive primordial germ cells develop toward oogonia and then oocytes, whereas when EcSox3 expression is ceased, the EcSOX3-positive primordial germ cells develop toward spermatogonia. Therefore, the current finding of EcSOX3 in the differentiating primordial germ cells again confirms the potential regulatory role in oogenesis and germ cell differentiation. The data further suggest that SOX3, as a transcription factor, might have more important roles in oogenesis than in spermatogenesis.