Tracking the invasion of breast cancer cells in paper-based 3D cultures by OCT motility analysis

3D paper-based cultures (PBCs) are easy-to-use and provide a biologically representative microenvironment. By stacking a sheet of cell-laden paper below sheets containing cell-free hydrogel, we form an assay capable of segmenting cells by the distance they invaded from the original cell-seeded layer. These invasion assays are limited to end-point analyses with fluorescence-based readouts due to the highly scattering nature of the paper scaffolds. Here we demonstrate that optical coherence tomography (OCT) can distinguish living cells from the surrounding extracellular matrix (ECM) or paper fibers based upon their intracellular motility amplitude (M). M is computed from fluctuation statistics of the sample, rejects shot noise, and is invariant to OCT signal attenuation. Using OCT motility analysis, we tracked the invasion of breast cancer cells over a 3-day period in 4-layer PBCs (160-300 μm thick) in situ. The cell population distributions determined with OCT are highly correlated with those obtained by fluorescence imaging, with an intraclass correlation coefficient (ICC) of 0.903. The ability of OCT motility analysis to visualize live cells and quantify cell distributions in PBC assays in situ and longitudinally provides a novel means for understanding how chemical gradients within the tumor microenvironment affect cellular invasion

Molecular characterization of slow leaf-rusting resistance in wheat

Slow leaf-rusting resistance in wheat (Triticum aestivum L) is gaining acceptance as a breeding objective because of its durability in comparison with race-specific resistance. CI 13227 was previously reported to provide the highest level of slow leaf-rusting resistance. The objective of this study was to characterize the slow leaf-rusting resistance conferred by CI 13227 using molecular markers. A population of recombinant inbred lines (RILs) derived from CI 13227/Suwon 92 was evaluated for final severity (FS), area under disease progress curve (AUDPC), infection rate (IR), and infection duration (ID) of leaf rust. Four hundred fifty-nine amplified fragment length polymorphism (AFLP) markers and 28 simple sequence repeat (SSR) markers were analyzed in the population. Two quantitative trait loci (QTL), designated as QLr.osu-2B and QLr.osu-7BL, were consistently associated with AUDPC, FS, and IR of leaf rust, caused by Puccinia triticina (previously P. recondita Rob. Ex Desm. f. sp. tritici). The percentages of phenotypic variance explained by each QTL varied with experiments and traits, ranging from 13.4 to 18.8% for AUDPC, 12.5 to 20.8% for FS, and 12.9 to 16.1% for IR. The third QTL for leaf rust ID, designated as QLrid.osu-2DS, was located on chromo- some 2DS and explained 26.4 and 21.47% of the phenotypic variance in 1994 and 1995, respectively. Both the QTL and correlation analysis indicate reasonable progress in leaf-rusting resistance by selecting for final severity. SSR markers closely associated with QLr.osu-2B or QLr.osu-7BL have potential to be used in marker-assisted selection (MAS) for durable leaf rust resistant cultivars.Peer reviewedPlant and Soil SciencesEntomology and Plant Patholog

Susy Hierarchies and Affine Algebras

We review some basic features of the Lie-algebraic classification of W-algebras and related integrable hierarchies in 1+1 dimensions, pointing out the role of affine Lie algebras. We emphasize that the supersymmetric extensions of the above construction possibly lead, though some questions are still opened, to the classification of supersymmetric hierarchies based on ``generic'' supersymmetric affine Lie algebras. Here the word generic is used to make clear that well-known procedures, as those introduced by Inami and Kanno, are too restricted and do not lead to the full spectrum of supersymmetric integrable hierarchies one can construct. A particular attention is devoted to the large-N supersymmetric extensions (here N=4). The attention paid by large-N theories being due to the fact that they arise as dimensional reduction of N=1 models, and moreover that they realize an ``unification'' of known hierarchies.Comment: 11 pages, LaTex, uses lamuphys.sty: talk given at the UIC ``Supersymmetry and Integrable Systems Workshop'', Chicago, June 12-14 199

A Better Way to Reconstruct Dark Energy Models ?

To reconstruct dark energy models the redshift $z_{eq}$, marking the end of radiation era and the beginning of matter-dominated era, can play a role as important as $z_{t}$, the redshift at which deceleration parameter experiences a signature flip. To implement the idea we propose a variable equation of state for matter that can bring a smooth transition from radiation to matter-dominated era in a single model. A popular $\Lambda \propto \rho$ dark energy model is chosen for demonstration but found to be unacceptable. An alternative $\Lambda \propto \rho a^{3}$ model is proposed and found to be more close to observation.Comment: 17 pages, 5 figures Accepted for publication in `Astrophysics and Space Science

Recent Advances in Understanding Particle Acceleration Processes in Solar Flares

We review basic theoretical concepts in particle acceleration, with particular emphasis on processes likely to occur in regions of magnetic reconnection. Several new developments are discussed, including detailed studies of reconnection in three-dimensional magnetic field configurations (e.g., current sheets, collapsing traps, separatrix regions) and stochastic acceleration in a turbulent environment. Fluid, test-particle, and particle-in-cell approaches are used and results compared. While these studies show considerable promise in accounting for the various observational manifestations of solar flares, they are limited by a number of factors, mostly relating to available computational power. Not the least of these issues is the need to explicitly incorporate the electrodynamic feedback of the accelerated particles themselves on the environment in which they are accelerated. A brief prognosis for future advancement is offered.Comment: This is a chapter in a monograph on the physics of solar flares, inspired by RHESSI observations. The individual articles are to appear in Space Science Reviews (2011

Signatures of the slow solar wind streams from active regions in the inner corona

Some of local sources of the slow solar wind can be associated with spectroscopically detected plasma outflows at edges of active regions accompanied with specific signatures in the inner corona. The EUV telescopes (e.g. SPIRIT/CORONAS-F, TESIS/CORONAS-Photon and SWAP/PROBA2) sometimes observed extended ray-like structures seen at the limb above active regions in 1MK iron emission lines and described as "coronal rays". To verify the relationship between coronal rays and plasma outflows, we analyze an isolated active region (AR) adjacent to small coronal hole (CH) observed by different EUV instruments in the end of July - beginning of August 2009. On August 1 EIS revealed in the AR two compact outflows with the Doppler velocities V =10-30 km/s accompanied with fan loops diverging from their regions. At the limb the ARCH interface region produced coronal rays observed by EUVI/STEREO-A on July 31 as well as by TESIS on August 7. The rays were co-aligned with open magnetic field lines expanded to the streamer stalks. Using the DEM analysis, it was found that the fan loops diverged from the outflow regions had the dominant temperature of ~1 MK, which is similar to that of the outgoing plasma streams. Parameters of the solar wind measured by STEREO-B, ACE, WIND, STEREO-A were conformed with identification of the ARCH as a source region at the Wang-Sheeley-Arge map of derived coronal holes for CR 2086. The results of the study support the suggestion that coronal rays can represent signatures of outflows from ARs propagating in the inner corona along open field lines into the heliosphere.Comment: Accepted for publication in Solar Physics; 31 Pages; 13 Figure

Functional diversity of chemokines and chemokine receptors in response to viral infection of the central nervous system.

Encounters with neurotropic viruses result in varied outcomes ranging from encephalitis, paralytic poliomyelitis or other serious consequences to relatively benign infection. One of the principal factors that control the outcome of infection is the localized tissue response and subsequent immune response directed against the invading toxic agent. It is the role of the immune system to contain and control the spread of virus infection in the central nervous system (CNS), and paradoxically, this response may also be pathologic. Chemokines are potent proinflammatory molecules whose expression within virally infected tissues is often associated with protection and/or pathology which correlates with migration and accumulation of immune cells. Indeed, studies with a neurotropic murine coronavirus, mouse hepatitis virus (MHV), have provided important insight into the functional roles of chemokines and chemokine receptors in participating in various aspects of host defense as well as disease development within the CNS. This chapter will highlight recent discoveries that have provided insight into the diverse biologic roles of chemokines and their receptors in coordinating immune responses following viral infection of the CNS

Origins of the Ambient Solar Wind: Implications for Space Weather

The Sun's outer atmosphere is heated to temperatures of millions of degrees, and solar plasma flows out into interplanetary space at supersonic speeds. This paper reviews our current understanding of these interrelated problems: coronal heating and the acceleration of the ambient solar wind. We also discuss where the community stands in its ability to forecast how variations in the solar wind (i.e., fast and slow wind streams) impact the Earth. Although the last few decades have seen significant progress in observations and modeling, we still do not have a complete understanding of the relevant physical processes, nor do we have a quantitatively precise census of which coronal structures contribute to specific types of solar wind. Fast streams are known to be connected to the central regions of large coronal holes. Slow streams, however, appear to come from a wide range of sources, including streamers, pseudostreamers, coronal loops, active regions, and coronal hole boundaries. Complicating our understanding even more is the fact that processes such as turbulence, stream-stream interactions, and Coulomb collisions can make it difficult to unambiguously map a parcel measured at 1 AU back down to its coronal source. We also review recent progress -- in theoretical modeling, observational data analysis, and forecasting techniques that sit at the interface between data and theory -- that gives us hope that the above problems are indeed solvable.Comment: Accepted for publication in Space Science Reviews. Special issue connected with a 2016 ISSI workshop on "The Scientific Foundations of Space Weather." 44 pages, 9 figure

Modeling the Subsurface Structure of Sunspots

While sunspots are easily observed at the solar surface, determining their subsurface structure is not trivial. There are two main hypotheses for the subsurface structure of sunspots: the monolithic model and the cluster model. Local helioseismology is the only means by which we can investigate subphotospheric structure. However, as current linear inversion techniques do not yet allow helioseismology to probe the internal structure with sufficient confidence to distinguish between the monolith and cluster models, the development of physically realistic sunspot models are a priority for helioseismologists. This is because they are not only important indicators of the variety of physical effects that may influence helioseismic inferences in active regions, but they also enable detailed assessments of the validity of helioseismic interpretations through numerical forward modeling. In this paper, we provide a critical review of the existing sunspot models and an overview of numerical methods employed to model wave propagation through model sunspots. We then carry out an helioseismic analysis of the sunspot in Active Region 9787 and address the serious inconsistencies uncovered by \citeauthor{gizonetal2009}~(\citeyear{gizonetal2009,gizonetal2009a}). We find that this sunspot is most probably associated with a shallow, positive wave-speed perturbation (unlike the traditional two-layer model) and that travel-time measurements are consistent with a horizontal outflow in the surrounding moat.Comment: 73 pages, 19 figures, accepted by Solar Physic

Multiwavelength studies of MHD waves in the solar chromosphere: An overview of recent results

The chromosphere is a thin layer of the solar atmosphere that bridges the relatively cool photosphere and the intensely heated transition region and corona. Compressible and incompressible waves propagating through the chromosphere can supply significant amounts of energy to the interface region and corona. In recent years an abundance of high-resolution observations from state-of-the-art facilities have provided new and exciting ways of disentangling the characteristics of oscillatory phenomena propagating through the dynamic chromosphere. Coupled with rapid advancements in magnetohydrodynamic wave theory, we are now in an ideal position to thoroughly investigate the role waves play in supplying energy to sustain chromospheric and coronal heating. Here, we review the recent progress made in characterising, categorising and interpreting oscillations manifesting in the solar chromosphere, with an impetus placed on their intrinsic energetics.Comment: 48 pages, 25 figures, accepted into Space Science Review