Introduction and Expression of a Rabbit β-globin Gene in Mouse Fibroblasts

The cloned chromosomal rabbit ß-globin gene has been introduced into mouse fibroblasts by DNA-mediated gene transfer (transformation). In this report, we examine the expression of the rabbit gene in six independent transformants that contain from 1 to 20 copies of the cloned globin gene. Rabbit globin transcripts were detected in two of these transformants at steady-state concentrations of 5 and 2 copies per cell. The globin transcripts from one cell line are polyadenylylated and migrate as 9S RNA on methylmercury gels. These transcripts reflect correct processing of the two intervening sequences but lack 48 ± 5 nucleotides present at the 5' terminus of rabbit erythrocyte globin mRNA

Representing complex data using localized principal components with application to astronomical data

Often the relation between the variables constituting a multivariate data space might be characterized by one or more of the terms: ``nonlinear'', ``branched'', ``disconnected'', ``bended'', ``curved'', ``heterogeneous'', or, more general, ``complex''. In these cases, simple principal component analysis (PCA) as a tool for dimension reduction can fail badly. Of the many alternative approaches proposed so far, local approximations of PCA are among the most promising. This paper will give a short review of localized versions of PCA, focusing on local principal curves and local partitioning algorithms. Furthermore we discuss projections other than the local principal components. When performing local dimension reduction for regression or classification problems it is important to focus not only on the manifold structure of the covariates, but also on the response variable(s). Local principal components only achieve the former, whereas localized regression approaches concentrate on the latter. Local projection directions derived from the partial least squares (PLS) algorithm offer an interesting trade-off between these two objectives. We apply these methods to several real data sets. In particular, we consider simulated astrophysical data from the future Galactic survey mission Gaia.Comment: 25 pages. In "Principal Manifolds for Data Visualization and Dimension Reduction", A. Gorban, B. Kegl, D. Wunsch, and A. Zinovyev (eds), Lecture Notes in Computational Science and Engineering, Springer, 2007, pp. 180--204, http://www.springer.com/dal/home/generic/search/results?SGWID=1-40109-22-173750210-

Half-metallic antiferromagnets in thiospinels

We have theoretically designed the half-metallic (HM) antiferromagnets (AFMs) in thiospinel systems, $\rm Mn(CrV)S_{4}$ and $\rm Fe_{0.5}Cu_{0.5}(V_{0.5}Ti_{1.5})S_{4}$, based on the electronic structure studies in the local-spin-density approximation (LSDA). We have also explored electronic and magnetic properties of parent spinel compounds of the above systems; $\rm CuV_{2}S_{4}$ and $\rm CuTi_{2}S_{4}$ are found to be HM ferromagnets in their cubic spinel structures, while $\rm MnCr_{2}S_{4}$ is a ferrimagnetic insulator. We have discussed the feasibility of material synthesis of HM-AFM thiospinel systems.Comment: 4 pages, 5 figure

Shape-based peak identification for ChIP-Seq

We present a new algorithm for the identification of bound regions from ChIP-seq experiments. Our method for identifying statistically significant peaks from read coverage is inspired by the notion of persistence in topological data analysis and provides a non-parametric approach that is robust to noise in experiments. Specifically, our method reduces the peak calling problem to the study of tree-based statistics derived from the data. We demonstrate the accuracy of our method on existing datasets, and we show that it can discover previously missed regions and can more clearly discriminate between multiple binding events. The software T-PIC (Tree shape Peak Identification for ChIP-Seq) is available at http://math.berkeley.edu/~vhower/tpic.htmlComment: 12 pages, 6 figure

Efficiency of Energy Conversion in Thermoelectric Nanojunctions

Using first-principles approaches, this study investigated the efficiency of energy conversion in nanojunctions, described by the thermoelectric figure of merit $ZT$. We obtained the qualitative and quantitative descriptions for the dependence of $ZT$ on temperatures and lengths. A characteristic temperature: $T_{0}= \sqrt{\beta/\gamma(l)}$ was observed. When $T\ll T_{0}$, $ZT\propto T^{2}$. When $T\gg T_{0}$, $ZT$ tends to a saturation value. The dependence of $ZT$ on the wire length for the metallic atomic chains is opposite to that for the insulating molecules: for aluminum atomic (conducting) wires, the saturation value of $ZT$ increases as the length increases; while for alkanethiol (insulating) chains, the saturation value of $ZT$ decreases as the length increases. $ZT$ can also be enhanced by choosing low-elasticity bridging materials or creating poor thermal contacts in nanojunctions. The results of this study may be of interest to research attempting to increase the efficiency of energy conversion in nano thermoelectric devices.Comment: 2 figure

Use of near infrared reflectance spectroscopy to predict nitrogen uptake by winter wheat within fields with high variability in organic matter

In this study, the ability to predict N-uptake in winter wheat crops using NIR-spectroscopy on soil samples was evaluated. Soil samples were taken in unfertilized plots in one winter wheat field during three years (1997-1999) and in another winter wheat field nearby in one year (2000). Soil samples were analyzed for organic C content and their NIR-spectra. N-uptake was measured as total N-content in aboveground plant materials at harvest. Models calibrated to predict N-uptake were internally cross validated and validated across years and across fields. Cross-validated calibrations predicted N-uptake with an average error of 12.1 to 15.4 kg N ha-1. The standard deviation divided by this error (RPD) ranged between 1.9 and 2.5. In comparison, the corresponding calibrations based on organic C alone had an error from 11.7 to 28.2 kg N ha-1 and RPDs from 1.3 to 2.5. In three of four annual calibrations within a field, the NIR-based calibrations worked better than the organic C based calibrations. The prediction of N-uptake across years, but within a field, worked slightly better with an organic C based calibration than with a NIR based one, RPD = 1.9 and 1.7 respectively. Across fields, the corresponding difference was large in favour of the NIR-calibration, RPD = 2.5 for the NIR-calibration and 1.5 for the organic C calibration. It was concluded that NIR-spectroscopy integrates information about organic C with other relevant soil components and therefore has a good potential to predict complex functions of soils such as N-mineralization. A relatively good agreement of spectral relationships to parameters related to the N-mineralization of datasets across the world suggests that more general models can be calibrated

Drugs in early clinical development for the treatment of osteosarcoma

Introduction: Osteosarcomas are the main malignant primary bone tumours found in children and young adults. Conventional treatment is based on diagnosis and resection surgery, combined with polychemotherapy. This is a protocol that was established in the 1970s. Unfortunately, this therapeutic approach has reached a plateau of efficacy and the patient survival rate has not improved in the last four decades. New therapeutic approaches are thus required to improve the prognosis for osteosarcoma patients. Areas covered: From the databases available and published scientific literature, the present review gives an overview of the drugs currently in early clinical development for the treatment of osteosarcoma. For each drug, a short description is given of the relevant scientific data supporting its development. Expert opinion: Multidrug targeted approaches are set to emerge, given the heterogeneity of osteosarcoma subtypes and the multitude of therapeutic responses. The key role played by the microenvironment in the disease increases the number of therapeutic targets (such as macrophages or osteoclasts), as well as the master proteins that control cell proliferation or cell death. Ongoing phase I/II trials are important steps, not only for identifying new therapies with greater safety and efficacy, but also for better defining the role played by the microenvironment in the pathogenesis of osteosarcoma

The VMC Survey - VI. Quasars behind the Magellanic system

The number and spatial distribution of confirmed quasi-stellar objects (QSOs) behind the Magellanic system is limited. This undermines their use as astrometric reference objects for different types of studies. We have searched for criteria to identify candidate QSOs using observations from the VISTA survey of the Magellanic Clouds system (VMC) that provides photometry in the YJKs bands and 12 epochs in the Ks band. The (Y-J) versus (J-Ks) diagram has been used to distinguish QSO candidates from Milky Way stars and stars of the Magellanic Clouds. Then, the slope of variation in the Ks band has been used to identify a sample of high confidence candidates. These criteria were developed based on the properties of 117 known QSOs presently observed by the VMC survey. VMC YJKs magnitudes and Ks light-curves of known QSOs behind the Magellanic system are presented. About 75% of them show a slope of variation in Ks>10^-4 mag/day and the shape of the light-curve is in general irregular and without any clear periodicity. The number of QSO candidates found in tiles including the South Ecliptic Pole and the 30 Doradus regions is 22 and 26, respectively, with a ~20% contamination by young stellar objects, planetary nebulae, stars and normal galaxies. By extrapolating the number of QSO candidates to the entire VMC survey area we expect to find about 1200 QSOs behind the LMC, 400 behind the SMC, 200 behind the Bridge and 30 behind the Stream areas, but not all will be suitable for astrometry. Further, the Ks band light-curves can help support investigations of the mechanism responsible for the variations.Comment: 17 pages, 15 figures, replaced with accepted version by Astronomy & Astrophysic

Streaming fragment assignment for real-time analysis of sequencing experiments

We present eXpress, a software package for efficient probabilistic assignment of ambiguously mapping sequenced fragments. eXpress uses a streaming algorithm with linear run time and constant memory use. It can determine abundances of sequenced molecules in real time and can be applied to ChIP-seq, metagenomics and other large-scale sequencing data. We demonstrate its use on RNA-seq data and show that eXpress achieves greater efficiency than other quantification methods