Gene transfer to adult human lung tissue ex vivo

The potential of gene therapy for treatment of lung disease remains unrealised. Early model systems often resulted in promising efficiency of gene transfer, only to prove irreproducible in the clinic. While problems such as induction of host immune responses and duration of expression also need to be addressed, it is now widely believed that alternative, relevant models which more accurately reflect gene transfer efficiencies in human lungs are urgently required. We report here on a human lung slice culture system to assess gene transfer to adult lung epithelium. A lacZ-expressing adenovirus (AdCA35lacZ) was used as a reporter vector. A solution of AdCA35lacZ was instilled via bronchioles into resected lung tissue, a route analogous to clinical administration. Following a 1 h incubation, the tissue was inflated with a 0.4% agarose solution, instilled via the same bronchioles. Once solidified, 500 mm slices of the tissue were prepared and cultured for 4 days. b-Galactosidase staining revealed lacZ transgene expression in bronchiolar and alveolar cells of the lung slices throughout the 4 days in culture. This system, which can also be used to study other viral and liposome vectors, could prove to be a useful alternative model for assessing gene delivery to adult human lung epithelium

The Acoustic Peak in the Lyman Alpha Forest

We present the first simulation of the signature of baryonic acoustic oscillations (BAO) in Lyman alpha forest data containing 180,000 mock quasar sight-lines. We use eight large dark-matter only simulations onto which we paint the Lyman alpha field using the fluctuating Gunn-Peterson approximation. We argue that this approach should be sufficient for the mean signature on the scales of interest. Our results indicate that Lyman alpha flux provides a good tracer of the underlying dark matter field on large scales and that redshift space distortions are well described by a simple linear theory prescription. We compare Fourier and configuration space approaches to describing the signal and argue that configuration space statistics provide useful data compression. We also investigate the effect of a fluctuating photo-ionizing background using a simplified model and find that such fluctuations do add smooth power on large scales. The acoustic peak position is, however, unaffected for small amplitude fluctuations (<10%). Larger amplitude fluctuations make the recovery of the BAO signal more difficult and may degrade the achievable significance of the measurement.Comment: 10 pages, 8 figures; v2: minor revision matching version accepted by JCAP (new references, better figures, clarifications

Separable Dual Space Gaussian Pseudo-potentials

We present pseudo-potential coefficients for the first two rows of the periodic table. The pseudo potential is of a novel analytic form, that gives optimal efficiency in numerical calculations using plane waves as basis set. At most 7 coefficients are necessary to specify its analytic form. It is separable and has optimal decay properties in both real and Fourier space. Because of this property, the application of the nonlocal part of the pseudo-potential to a wave-function can be done in an efficient way on a grid in real space. Real space integration is much faster for large systems than ordinary multiplication in Fourier space since it shows only quadratic scaling with respect to the size of the system. We systematically verify the high accuracy of these pseudo-potentials by extensive atomic and molecular test calculations.Comment: 16 pages, 4 postscript figure

Quantum Pumping and Quantized Magnetoresistance in a Hall Bar

We show how a dc current can be generated in a Hall bar without applying a bias voltage. The Hall resistance $R_H$ that corresponds to this pumped current is quantized, just as in the usual integer quantum Hall effect (IQHE). In contrast with the IQHE, however, the longitudinal resistance $R_{xx}$ does not vanish on the plateaus, but equals the Hall resistance. We propose an experimental geometry to measure the pumped current and verify the predicted behavior of $R_H$ and $R_{xx}$.Comment: RevTeX, 3 figure

An Effective-Medium Tight-Binding Model for Silicon

A new method for calculating the total energy of Si systems is presented. The method is based on the effective-medium theory concept of a reference system. Instead of calculating the energy of an atom in the system of interest a reference system is introduced where the local surroundings are similar. The energy of the reference system can be calculated selfconsistently once and for all while the energy difference to the reference system can be obtained approximately. We propose to calculate it using the tight-binding LMTO scheme with the Atomic-Sphere Approximation(ASA) for the potential, and by using the ASA with charge-conserving spheres we are able to treat open system without introducing empty spheres. All steps in the calculational method is {\em ab initio} in the sense that all quantities entering are calculated from first principles without any fitting to experiment. A complete and detailed description of the method is given together with test calculations of the energies of phonons, elastic constants, different structures, surfaces and surface reconstructions. We compare the results to calculations using an empirical tight-binding scheme.Comment: 26 pages (11 uuencoded Postscript figures appended), LaTeX, CAMP-090594-

Electronic structure of the strongly hybridized ferromagnet CeFe2

We report on results from high-energy spectroscopic measurements on CeFe2, a system of particular interest due to its anomalous ferromagnetism with an unusually low Curie temperature and small magnetization compared to the other rare earth-iron Laves phase compounds. Our experimental results indicate very strong hybridization of the Ce 4f states with the delocalized band states, mainly the Fe 3d states. In the interpretation and analysis of our measured spectra, we have made use of two different theoretical approaches: The first one is based on the Anderson impurity model, with surface contributions explicitly taken into account. The second method consists of band-structure calculations for bulk CeFe2. The analysis based on the Anderson impurity model gives calculated spectra in good agreement with the whole range of measured spectra, and reveals that the Ce 4f -- Fe 3d hybridization is considerably reduced at the surface, resulting in even stronger hybridization in the bulk than previously thought. The band-structure calculations are ab initio full-potential linear muffin-tin orbital calculations within the local-spin-density approximation of the density functional. The Ce 4f electrons were treated as itinerant band electrons. Interestingly, the Ce 4f partial density of states obtained from the band-structure calculations also agree well with the experimental spectra concerning both the 4f peak position and the 4f bandwidth, if the surface effects are properly taken into account. In addition, results, notably the partial spin magnetic moments, from the band-structure calculations are discussed in some detail and compared to experimental findings and earlier calculations.Comment: 10 pages, 8 figures, to appear in Phys. Rev. B in December 200

(Sub)mm Interferometry Applications in Star Formation Research

This contribution gives an overview about various applications of (sub)mm interferometry in star formation research. The topics covered are molecular outflows, accretion disks, fragmentation and chemical properties of low- and high-mass star-forming regions. A short outlook on the capabilities of ALMA is given as well.Comment: 20 pages, 7 figures, in proceedings to "2nd European School on Jets from Young Star: High Angular Resolution Observations". A high-resolution version of the paper can be found at http://www.mpia.de/homes/beuther/papers.htm

An EBSD study of the deformation of service-aged 316 austenitic steel

Electron backscatter diffraction (EBSD) has been used to examine the plastic deformation of an ex-service 316 austenitic stainless steel at 297K and 823K (24 °C and 550 °C)at strain rates 3.5x10-3 to 4 x 10-7 s-1. The distribution of local misorientations was found to depend on the imposed plastic strain following a lognormal distribution at true strains 0.1. At 823 K (550 °C), the distribution of misorientations depended on the applied strain rate. The evolution of lattice misorientations with increasing plastic strain up to 0.23 was quantified using the metrics kernel average misorientation, average intragrain misorientation, and low angle misorientation fraction. For strain rate down to 10-5 s-1 all metrics were insensitive to deformation temperature, mode (tension vs. compression) and orientation of the measurement plane. The strain sensitivity of the different metrics was found to depend on the misorientation ranges considered in their calculation. A simple new metric, proportion of undeformed grains, is proposed for assessing strain in both aged and unaged material. Lattice misorientations build up with strain faster in aged steel than in un-aged material and most of the metrics were sensitive to the effects of thermal aging. Ignoring aging effects leads to significant overestimation of the strains around welds. The EBSD results were compared with nanohardness measurements and good agreement established between the two techniques of assessing plastic strain in aged 316 steel

Machine learning algorithms performed no better than regression models for prognostication in traumatic brain injury

Objective: We aimed to explore the added value of common machine learning (ML) algorithms for prediction of outcome for moderate and severe traumatic brain injury. Study Design and Setting: We performed logistic regression (LR), lasso regression, and ridge regression with key baseline predictors in the IMPACT-II database (15 studies, n = 11,022). ML algorithms included support vector machines, random forests, gradient boosting machines, and artificial neural networks and were trained using the same predictors. To assess generalizability of predictions, we performed internal, internal-external, and external validation on the recent CENTER-TBI study (patients with Glasgow Coma Scale <13, n = 1,554). Both calibration (calibration slope/intercept) and discrimination (area under the curve) was quantified. Results: In the IMPACT-II database, 3,332/11,022 (30%) died and 5,233(48%) had unfavorable outcome (Glasgow Outcome Scale less than 4). In the CENTER-TBI study, 348/1,554(29%) died and 651(54%) had unfavorable outcome. Discrimination and calibration varied widely between the studies and less so between the studied algorithms. The mean area under the curve was 0.82 for mortality and 0.77 for unfavorable outcomes in the CENTER-TBI study. Conclusion: ML algorithms may not outperform traditional regression approaches in a low-dimensional setting for outcome prediction after moderate or severe traumatic brain injury. Similar to regression-based prediction models, ML algorithms should be rigorously validated to ensure applicability to new populations