ECM at Work

The performance of the elliptic curve method (ECM) for integer factorization plays an important role in the security assessment of RSA-based protocols as a cofactorization tool inside the number field sieve. The efficient arithmetic for Edwards curves found an application by speeding up ECM. We propose techniques based on generating and combining addition-subtracting chains to optimize Edwards ECM in terms of both performance and memory requirements. This makes our approach very suitable for memory-constrained devices such as graphics processing units (GPU). For commonly used ECM parameters we are able to lower the required memory up to a factor 55 compared to the state-of-the-art Edwards ECM approach. Our ECM implementation on a GTX 580 GPU sets a new throughput record, outperforming the best GPU, CPU and FPGA results reported in literature

A Mathematical Model of Liver Cell Aggregation In Vitro

The behavior of mammalian cells within three-dimensional structures is an area of intense biological research and underpins the efforts of tissue engineers to regenerate human tissues for clinical applications. In the particular case of hepatocytes (liver cells), the formation of spheroidal multicellular aggregates has been shown to improve cell viability and functionality compared to traditional monolayer culture techniques. We propose a simple mathematical model for the early stages of this aggregation process, when cell clusters form on the surface of the extracellular matrix (ECM) layer on which they are seeded. We focus on interactions between the cells and the viscoelastic ECM substrate. Governing equations for the cells, culture medium, and ECM are derived using the principles of mass and momentum balance. The model is then reduced to a system of four partial differential equations, which are investigated analytically and numerically. The model predicts that provided cells are seeded at a suitable density, aggregates with clearly defined boundaries and a spatially uniform cell density on the interior will form. While the mechanical properties of the ECM do not appear to have a significant effect, strong cell-ECM interactions can inhibit, or possibly prevent, the formation of aggregates. The paper concludes with a discussion of our key findings and suggestions for future work

Geometric control of myogenic cell fate.

This work combines expertise in stem cell biology and bioengineering to define the system for geometric control of proliferation and differentiation of myogenic progenitor cells. We have created an artificial niche of myogenic progenitor cells, namely, modified extracellular matrix (ECM) substrates with spatially embedded growth or differentiation factors (GF, DF) that predictably direct muscle cell fate in a geometric pattern. Embedded GF and DF signal progenitor cells from specifically defined areas on the ECM successfully competed against culture media for myogenic cell fate determination at a clearly defined boundary. Differentiation of myoblasts into myotubes is induced in growth-promoting medium, myotube formation is delayed in differentiation-promoting medium, and myogenic cells, at different stages of proliferation and differentiation, can be induced to coexist adjacently in identical culture media. This method can be used to identify molecular interactions between cells in different stages of myogenic differentiation, which are likely to be important determinants of tissue repair. The designed ECM niches can be further developed into a vehicle for transplantation of myogenic progenitor cells maintaining their regenerative potential. Additionally, this work may also serve as a general model to engineer synthetic cellular niches to harness the regenerative potential of organ stem cells

Interaction between extracellular matrix molecules and microbial pathogens: evidence for the missing link in autoimmunity with rheumatoid arthritis as a disease model.

Rheumatoid arthritis (RA) is an autoimmune disease characterized by inflammation followed by tissue rebuilding or fibrosis. A failure by the body to regulate inflammation effectively is one of the hallmarks of RA. The interaction between the external environment and the human host plays an important role in the development of autoimmunity. In RA, the observation of anti-cyclic citrullinated peptide antibodies (ACPA) to autoantigens is well recognized. Citrullination is a post-translational modification mediated by peptidyl arginine deiminases, which exist in both mammalian and bacterial forms. Previous studies have shown how proteins expressed in the human extracellular matrix (ECM) acquire properties of damage-associated molecular patterns (DAMPs) in RA and include collagens, tenascin-C, and fibronectin (FN). ECM DAMPs can further potentiate tissue damage in RA. Recent work has shown that citrullination in RA occurs at mucosal sites, including the oral cavity and lung. Mucosal sites have been linked with bacterial infection, e.g., periodontal disease, where exogenous pathogens are implicated in the development of autoimmunity via an infectious trigger. Proteases produced at mucosal sites, both by bacteria and the human host, can induce the release of ECM DAMPs, thereby revealing neoepitopes which can be citrullinated and lead to an autoantibody response with further production of ACPA. In this perspectives article, the evidence for the interplay between the ECM and bacteria at human mucosal surfaces, which can become a focus for citrullination and the development of autoimmunity, is explored. Specific examples, with reference to collagen, fibrinogen, and FN, are discussed

Synergistic growth factor microenvironments

Growth factors (GF) are remarkably powerful signalling molecules that orchestrate developmental biology. GFs are currently used in medjcal applications with limited success but it is clear that if their potential can be harnessed for biomedicine then they could underpin the discipline of regenerative medicine. However, while we understand that biology uses cell-secreted growth factors tethered to the ECM, biologists typically employ GFs in soluble format at high concentrations. When used in vivo, this causes off-target, unwanted effects, which severely limits their use. There is a vast amount of literature dealing with material systems that control the delivery of GFs. However, it was soon observed that GFs could be more effectively presented bound to surfaces from a solid-phase state rather than in soluble form, recapitulating the way the extracellular matrix (ECM) binds GFs. In parallel, evidence was found that within the ECM, GFs can actually work in cooperation with integrins and that this produced ehnaced GF signalling due to the crosstalk between both receptors. Recently this knowledge was used to engineer microenvironments that target simultaneous integrin and GF receptor engagement seeking to maximise GF effects in vitro (e.g. in terms of stem cell differentiation) but also tissue repair in vivo (e.g. bone regeneration and wound healing). This feature article introduces the concept of synergistic GF/integrin signalling and then introduces GF delivery systems that were key in the development of more advanced synergistic growth factor microenvironments

An investigation of the Eigenvalue Calibration Method (ECM) using GASP for non-imaging and imaging detectors

Polarised light from astronomical targets can yield a wealth of information about their source radiation mechanisms, and about the geometry of the scattered light regions. Optical observations, of both the linear and circular polarisation components, have been impeded due to non-optimised instrumentation. The need for suitable observing conditions and the availability of luminous targets are also limiting factors. GASP uses division of amplitude polarimeter (DOAP) (Compain and Drevillon) to measure the four components of the Stokes vector simultaneously, which eliminates the constraints placed upon the need for moving parts during observation, and offers a real-time complete measurement of polarisation. Results from the GASP calibration are presented in this work for both a 1D detector system, and a pixel-by-pixel analysis on a 2D detector system. Following Compain et al. we use the Eigenvalue Calibration Method (ECM) to measure the polarimetric limitations of the instrument for each of the two systems. Consequently, the ECM is able to compensate for systematic errors introduced by the calibration optics, and it also accounts for all optical elements of the polarimeter in the output. Initial laboratory results of the ECM are presented, using APD detectors, where errors of 0.2% and 0.1{\deg} were measured for the degree of linear polarisation and polarisation angle respectively. Channel-to-channel image registration is an important aspect of 2-D polarimetry. We present our calibration results of the measured Mueller matrix of each sample, used by the ECM. A set of Zenith flat-field images were recorded during an observing campaign at the Palomar 200 inch telescope in November 2012. From these we show the polarimetric errors from the spatial polarimetry indicating both the stability and absolute accuracy of GASP.Comment: Accepted for publication in Experimental Astronom

Dendrimer Conjugation Enhances Tumor Penetration and Cell Kill of Doxorubicin in 3D Coculture Lung Cancer Models

Background: Doxorubicin (DOX) is a potent chemotherapeutic widely used for solid tumors (1). Despite high efficacy in 2D cell culture, DOX efficacy does not translate to in vivo lung cancer models (2). Major side effects such as cardiotoxicity may be alleviated with nano-based drug delivery systems (nanoDDS). However, tumor penetration of DOX and DOX-nanoDDS is largely unknown and is an additional barrier to effective clinical therapy (3). Here we describe a nanoDDS capable of enhancing the penetration of DOX. Methods: DOX was conjugated to generation 4 poly(amido-amine) dendrimers through (GFLG) tumor- liable bond. G4SA-GFLG-DOX was synthesized/characterized. spheroids were formed of (A549) lung adenocarcinoma cells and (3T3) fibroblasts. Spheroids were characterized for ECM components with immunohistochemistry. Confocal microscopy was used to evaluate the penetration, internalization, and colocalization of DOX and G4SA-GFLG-DOX. MTT assay and Caspase 3/7 to assess 2D and 3D cytotoxicity. Flow cytometry to determine cells uptake. Results: DOX conjugation to dendrimer resulted in G4SA-GFLG-DOX with ~5.5 DOX, 10±1 nm hydrodynamic diameter, and a -17±3 mV zeta-potential. Spheroids of (A549:3T3) were ECM- rich, developed ECM containing collagen-I, hyaluronan, laminin, and fibronectin. While DOX and G4SA-GFLG-DOX had similar toxicities in 2D model, G4SA-GFLG-DOX demonstrated a 3.1-fold greater penetration into spheroids compared to DOX and correlated to a greater efficacy as measured by caspase 3/7 activity. Also, flow cytometry showed higher uptake of G4SA- GFLG-DOX in cancer cells compared to fibroblasts. Conclusion: The work demonstrates enhanced penetration of DOX, via dendrimer conjugation, into an ECM- rich 3D lung cancer model. The enhanced penetration of G4SA-GFLG-DOX correlated with greater antitumor efficacy. Acknowledgements: We acknowledge partial financial support from the Center for Pharmaceutical Engineering and Sciences - School of Pharmacy at VCU. This study was supported by VCU Quest for Distinction and NSF (DRM #1508363). Microscopy was performed at the VCU Microscopy Facility, supported, in part, by funding from NIH-NCI Cancer Center Support Grant P30 CA016059. RA would like to acknowledge King Faisal University (KFU) and Saudi Arabian Cultural Mission (SACM) for a scholarship.https://scholarscompass.vcu.edu/gradposters/1091/thumbnail.jp

A Generic Renormalization Method in Curved Spaces and at Finite Temperature

Based only on simple principles of renormalization in coordinate space, we derive closed renormalized amplitudes and renormalization group constants at 1- and 2-loop orders for scalar field theories in general backgrounds. This is achieved through a generic renormalization procedure we develop exploiting the central idea behind differential renormalization, which needs as only inputs the propagator and the appropriate laplacian for the backgrounds in question. We work out this generic coordinate space renormalization in some detail, and subsequently back it up with specific calculations for scalar theories both on curved backgrounds, manifestly preserving diffeomorphism invariance, and at finite temperature.Comment: 15pp., REVTeX, UB-ECM-PF 94/1

The mycorrhizas of Europe’s pine forests in the context of nitrogen pollution

Most trees in temperate and boreal ecosystems form obligate associations with ectomycorrhizal (ECM) fungi, but environmental change may alter ECM communities, potentially having major impacts on forest ecosystem functioning. Understanding the potential consequences of environmental change requires knowledge about current ECM fungal distributions, both to provide a baseline against which to measure changes in communities, and to establish the effects of current broad-scale environmental gradients on mycorrhizal biogeography. This study aims to assess the feasibility of a continental-scale survey of ECM fungal communities across a network of long-term forest monitoring plots, and provide insights into the community ecology of these important organisms. Using a spatially hierarchical sampling strategy and molecular identification of the fungi forming ECM root tips, the ECM fungal communities within 12 plots in the UK and Germany were characterised. In combination with measurements of a range of environmental variables at the 12 plots, the data indicate that nitrogen availability is a potentially important determinant of ECM fungal composition and richness across large spatial scales, but that other environmental variables may also act at large scales to influence ECM fungal communities. Evidence is also found to support a role of interspecific competition structuring ECM fungal communities within, but not across, plots, and a complex interplay between environmental gradients, co-occurrence patterns and phylogenetic relatedness is revealed. Within plots, microsatellite analysis indicates that pine roots from adjacent trees overlap, and do not have exclusive below-ground territories. Re-sampling plots, and reciprocal transplantation of pine seedlings between plots, indicates that pine mycorrhizas are stable both over time and on transplanted seedlings. This work increases our knowledge of the belowground ecology of ECM fungi, and highlights the value of identifying mycorrhizal abundance and distribution patterns - effects of global environmental change may already be significantly altering communities of this functionally critical group