Suitability of a CMV/EGFP cassette to monitor stable expression from human artificial chromosomes but not transient transfer in the cells forming viable clones

Human artificial chromosomes (HACs) were generated by transfer of telomerized PAC constructs containing alpha satellite DNA of various human chromosomes. To monitor which cells took up constructs and subsequently formed stable clones under blasticidin S (BS) selection, a CMV/EGFP expression cassette was inserted into a HAC construct based on chromosome 5 alpha satellite DNA (142 kb). Lipofection into HT1080 cells resulted in a small proportion of cells exhibiting bright green fluorescence on day 1. Areas containing such early green cells were marked, and plates monitored over 2 weeks. In only one out of 41 marked areas, a viable clone developed. In the remaining 40 areas, the green cells ceased division at 1-8 cells. In contrast, outside the marked areas, 16 stable clones formed which did not exhibit green fluorescence during the first cell divisions, but all cells of each became green around day 4 -6. Fluorescence in situ hybridization (FISH) analysis of isolated clonal lines demonstrated low copy HAC formation without integration. We conclude that transient expression of an EGFP marker on HAC DNA is not a suitable means for the identification of the proportion of transfected cells which are capable of forming viable clones. One explanation could be that the high copy number required to consistently detect transient EGFP expression (Schindelhauer and Laner, 2002) impairs viability and clone formation. Copyright (C) 2004 S. Karger AG, Basel

MeV oxygen ion implantation induced compositional intermixing in AlAs/GaAs superlattices

We present in this letter an investigation of compositional intermixing in AlAs/GaAs superlattices induced by 2 MeV oxygen ion implantation. The results are compared with implantation at 500 keV. In addition to Al intermixing in the direct lattice damage region by nuclear collision spikes, as is normally present in low-energy ion implantation, Al interdiffusion has also been found to take place in the subsurface region where MeV ion induced electronic spike damage dominates and a uniform strain field builds up due to defect generation and diffusion. Uniform compositional intermixing of the superlattices results after subsequent thermal annealing when Al interdiffusion is stimulated through recovery of the implantation-induced lattice strain field, the reconstruction and the redistribution of lattice defects, and annealing of lattice damage

Experimental Generation and Observation of Intrinsic Localized Spin Wave Modes in an Antiferromagnet

By driving with a microwave pulse the lowest frequency antiferromagnetic resonance of the quasi 1-D biaxial antiferromagnet (C_2 H_5 NH_3)_2 CuCl_4 into an unstable region intrinsic localized spin waves have been generated and detected in the spin wave gap. These findings are consistent with the prediction that nonlinearity plus lattice discreteness can lead to localized excitations with dimensions comparable to the lattice constant.Comment: 10 pages, 4 figures, accepted for publication in Physical Review Letter

Buckling without bending: a new paradigm in morphogenesis

A curious feature of organ and organoid morphogenesis is that in certain cases, spatial oscillations in the thickness of the growing "film" are out-of-phase with the deformation of the slower-growing "substrate," while in other cases, the oscillations are in-phase. The former cannot be explained by elastic bilayer instability, and contradict the notion that there is a universal mechanism by which brains, intestines, teeth, and other organs develop surface wrinkles and folds. Inspired by the microstructure of the embryonic cerebellum, we develop a new model of 2d morphogenesis in which system-spanning elastic fibers endow the organ with a preferred radius, while a separate fiber network resides in the otherwise fluid-like film at the outer edge of the organ and resists thickness gradients thereof. The tendency of the film to uniformly thicken or thin is described via a "growth potential". Several features of cerebellum, +blebbistatin organoid, and retinal fovea morphogenesis, including out-of-phase behavior and a film thickness amplitude that is comparable to the radius amplitude, are readily explained by our simple analytical model, as may be an observed scale-invariance in the number of folds in the cerebellum. We also study a nonlinear variant of the model, propose further biological and bio-inspired applications, and address how our model is and is not unique to the developing nervous system.Comment: version accepted by Physical Review

Influence of substrate temperature on lattice strain field and phase transition in MeV oxygen ion implanted GaAs crystals

A detailed study of the influence of substrate temperature on the radiation-induced lattice strain field and crystalline-to-amorphous (c-a) phase transition in MeV oxygen ion implanted GaAs crystals has been made using channeling Rutherford backscattering spectroscopy, secondary ion mass spectrometry, and the x-ray rocking curve technique. A comparison has been made between the cases of room temperature (RT) and low temperature (LT) (about 100 K) implantation. A strong in situ dynamic annealing process is found in RT implantation at a moderate beam current, resulting in a uniform positive strain field in the implanted layer. LT implantation introduces a freeze-in effect which impedes the recombination and diffusion of initial radiation-created lattice damage and defects, and in turn drives more efficiently the c-a transition as well as strain saturation and relaxation. The results are interpreted with a spike damage model in which the defect production process is described in terms of the competition between defect generation by nuclear spikes and defects diffusion and recombination stimulated by electronic spikes. It is also suggested that the excess population of vacancies and their complexes is responsible for lattice spacing expansion in ion-implanted GaAs crystals

The Loss Rank Principle for Model Selection

We introduce a new principle for model selection in regression and classification. Many regression models are controlled by some smoothness or flexibility or complexity parameter c, e.g. the number of neighbors to be averaged over in k nearest neighbor (kNN) regression or the polynomial degree in regression with polynomials. Let f_D^c be the (best) regressor of complexity c on data D. A more flexible regressor can fit more data D' well than a more rigid one. If something (here small loss) is easy to achieve it's typically worth less. We define the loss rank of f_D^c as the number of other (fictitious) data D' that are fitted better by f_D'^c than D is fitted by f_D^c. We suggest selecting the model complexity c that has minimal loss rank (LoRP). Unlike most penalized maximum likelihood variants (AIC,BIC,MDL), LoRP only depends on the regression function and loss function. It works without a stochastic noise model, and is directly applicable to any non-parametric regressor, like kNN. In this paper we formalize, discuss, and motivate LoRP, study it for specific regression problems, in particular linear ones, and compare it to other model selection schemes.Comment: 16 page

JDFTx: software for joint density-functional theory

Density-functional theory (DFT) has revolutionized computational prediction of atomic-scale properties from first principles in physics, chemistry and materials science. Continuing development of new methods is necessary for accurate predictions of new classes of materials and properties, and for connecting to nano- and mesoscale properties using coarse-grained theories. JDFTx is a fully-featured open-source electronic DFT software designed specifically to facilitate rapid development of new theories, models and algorithms. Using an algebraic formulation as an abstraction layer, compact C++11 code automatically performs well on diverse hardware including GPUs. This code hosts the development of joint density-functional theory (JDFT) that combines electronic DFT with classical DFT and continuum models of liquids for first-principles calculations of solvated and electrochemical systems. In addition, the modular nature of the code makes it easy to extend and interface with, facilitating the development of multi-scale toolkits that connect to ab initio calculations, e.g. photo-excited carrier dynamics combining electron and phonon calculations with electromagnetic simulations.Comment: 9 pages, 3 figures, 2 code listing

Abelian Duality

We show that on three-dimensional Riemannian manifolds without boundaries and with trivial first real de Rham cohomology group (and in no other dimensions) scalar field theory and Maxwell theory are equivalent: the ratio of the partition functions is given by the Ray-Singer torsion of the manifold. On the level of interaction with external currents, the equivalence persists provided there is a fixed relation between the charges and the currents.Comment: 11 pages, LaTeX, no figures, a reference added, submitted to Phys. Rev.