Cross-species hybridisation of pig RNA to human nylon microarrays

BACKGROUND: The objective of this research was to investigate the reproducibility of cross-species microarray hybridisation. Comparisons between same- and cross-species hybridisations were also made. Nine hybridisations between a single pig skeletal muscle RNA sample and three human cDNA nylon microarrays were completed. Three replicate hybridisations of two different amounts of pig RNA, and of human skeletal muscle RNA were completed on three additional microarrays. RESULTS: Reproducibility of microarray hybridisations of pig cDNA to human microarrays was high, as determined by Spearman and Pearson correlation coefficients and a Kappa statistic. Variability among replicate hybridisations was similar for human and pig data, indicating the reproducibility of results were not compromised in cross-species hybridisations. The concordance between data generated from hybridisations using pig and human skeletal muscle RNA was high, further supporting the use of human microarrays for the analysis of gene expression in the pig. No systematic effect of stripping and re-using nylon microarrays was found, and variability across microarrays was minimal. CONCLUSION: The majority of genes generated highly reproducible data in cross-species microarray hybridisations, although approximately 6% were identified as highly variable. Experimental designs that include at least three replicate hybridisations for each experimental treatment will enable the variability of individual genes to be considered appropriately. The use of cross-species microarray analysis looks promising. However, additional validation is needed to determine the specificity of cross-species hybridisations, and the validity of results

Icosahedral multi-component model sets

A quasiperiodic packing Q of interpenetrating copies of C, most of them only partially occupied, can be defined in terms of the strip projection method for any icosahedral cluster C. We show that in the case when the coordinates of the vectors of C belong to the quadratic field Q[\sqrt{5}] the dimension of the superspace can be reduced, namely, Q can be re-defined as a multi-component model set by using a 6-dimensional superspace.Comment: 7 pages, LaTeX2e in IOP styl

Limit-(quasi)periodic point sets as quasicrystals with p-adic internal spaces

Model sets (or cut and project sets) provide a familiar and commonly used method of constructing and studying nonperiodic point sets. Here we extend this method to situations where the internal spaces are no longer Euclidean, but instead spaces with p-adic topologies or even with mixed Euclidean/p-adic topologies. We show that a number of well known tilings precisely fit this form, including the chair tiling and the Robinson square tilings. Thus the scope of the cut and project formalism is considerably larger than is usually supposed. Applying the powerful consequences of model sets we derive the diffractive nature of these tilings.Comment: 11 pages, 2 figures; dedicated to Peter Kramer on the occasion of his 65th birthda

Growth and structure of Slovenia's scientific collaboration network

We study the evolution of Slovenia's scientific collaboration network from 1960 till present with a yearly resolution. For each year the network was constructed from publication records of Slovene scientists, whereby two were connected if, up to the given year inclusive, they have coauthored at least one paper together. Starting with no more than 30 scientists with an average of 1.5 collaborators in the year 1960, the network to date consists of 7380 individuals that, on average, have 10.7 collaborators. We show that, in spite of the broad myriad of research fields covered, the networks form "small worlds" and that indeed the average path between any pair of scientists scales logarithmically with size after the largest component becomes large enough. Moreover, we show that the network growth is governed by near-liner preferential attachment, giving rise to a log-normal distribution of collaborators per author, and that the average starting year is roughly inversely proportional to the number of collaborators eventually acquired. Understandably, not all that became active early have till now gathered many collaborators. We also give results for the clustering coefficient and the diameter of the network over time, and compare our conclusions with those reported previously.Comment: 10 pages, 3 figures; accepted for publication in Journal of Informetrics [related work available at http://arxiv.org/abs/1003.1018 and http://www.matjazperc.com/sicris/stats.html

ER stress in antigen‐presenting cells promotes NKT cell activation through endogenous neutral lipids

CD1d-restricted invariant natural killer T (iNKT) cells constitute a common glycolipid-reactive innate-like T-cell subset with a broad impact on innate and adaptive immunity. While several microbial glycolipids are known to activate iNKT cells, the cellular mechanisms leading to endogenous CD1d-dependent glycolipid responses remain largely unclear. Here, we show that endoplasmic reticulum (ER) stress in APCs is a potent inducer of CD1d-dependent iNKT cell autoreactivity. This pathway relies on the presence of two transducers of the unfolded protein response: inositol-requiring enzyme-1a (IRE1α) and protein kinase R-like ER kinase (PERK). Surprisingly, the neutral but not the polar lipids generated within APCs undergoing ER stress are capable of activating iNKT cells. These data reveal that ER stress is an important mechanism to elicit endogenous CD1d-restricted iNKT cell responses through induction of distinct classes of neutral lipids

Central extensions of the families of quasi-unitary Lie algebras

The most general possible central extensions of two whole families of Lie algebras, which can be obtained by contracting the special pseudo-unitary algebras su(p,q) of the Cartan series A_l and the pseudo-unitary algebras u(p,q), are completely determined and classified for arbitrary p,q. In addition to the su(p,q) and u({p,q}) algebras, whose second cohomology group is well known to be trivial, each family includes many non-semisimple algebras; their central extensions, which are explicitly given, can be classified into three types as far as their properties under contraction are involved. A closed expression for the dimension of the second cohomology group of any member of these families of algebras is given.Comment: 23 pages. Latex2e fil

Graded contractions of bilinear invariant forms of Lie algebras

We introduce a new construction of bilinear invariant forms on Lie algebras, based on the method of graded contractions. The general method is described and the $\Bbb Z_2$-, $\Bbb Z_3$-, and $\Bbb Z_2\otimes\Bbb Z_2$-contractions are found. The results can be applied to all Lie algebras and superalgebras (finite or infinite dimensional) which admit the chosen gradings. We consider some examples: contractions of the Killing form, toroidal contractions of $su(3)$, and we briefly discuss the limit to new WZW actions.Comment: 15 page

The function of remote sensing in support of environmental policy

Limited awareness of environmental remote sensing’s potential ability to support environmental policy development constrains the technology’s utilization. This paper reviews the potential of earth observation from the perspective of environmental policy. A literature review of “remote sensing and policy” revealed that while the number of publications in this field increased almost twice as rapidly as that of remote sensing literature as a whole (15.3 versus 8.8% yr−1), there is apparently little academic interest in the societal contribution of environmental remote sensing. This is because none of the more than 300 peer reviewed papers described actual policy support. This paper describes and discusses the potential, actual support, and limitations of earth observation with respect to supporting the various stages of environmental policy development. Examples are given of the use of remote sensing in problem identification and policy formulation, policy implementation, and policy control and evaluation. While initially, remote sensing contributed primarily to the identification of environmental problems and policy implementation, more recently, interest expanded to applications in policy control and evaluation. The paper concludes that the potential of earth observation to control and evaluate, and thus assess the efficiency and effectiveness of policy, offers the possibility of strengthening governance

Possible contractions of quantum orthogonal groups

Possible contractions of quantum orthogonal groups which correspond to different choices of primitive elements of Hopf algebra are considered and all allowed contractions in Cayley--Klein scheme are obtained. Quantum deformations of kinematical groups have been investigated and have shown that quantum analog of (complex) Galilei group G(1,3) do not exist in our scheme.Comment: 10 pages, Latex. Report given at XXIII Int. Colloquium on Group Theoretical Methods in Physics, July 31- August 5, 2000, Dubna (Russia