A Vacation

We were going to Hawaii for a rest. The doctor had said we needed a short vacation, but that was his idea, not ours

Applying weighted network measures to microarray distance matrices

In recent work we presented a new approach to the analysis of weighted networks, by providing a straightforward generalization of any network measure defined on unweighted networks. This approach is based on the translation of a weighted network into an ensemble of edges, and is particularly suited to the analysis of fully connected weighted networks. Here we apply our method to several such networks including distance matrices, and show that the clustering coefficient, constructed by using the ensemble approach, provides meaningful insights into the systems studied. In the particular case of two data sets from microarray experiments the clustering coefficient identifies a number of biologically significant genes, outperforming existing identification approaches.Comment: Accepted for publication in J. Phys.

Volume 3: Ethnographies of Islam : Ritual Performances and Everyday Practices

This comparative approach to the various uses of the ethnographic method in research about Islam in anthropology and other social sciences is particularly relevant in the current climate. Political discourses and stereotypical media portrayals of Islam as a monolithic civilisation have prevented the emergence of cultural pluralism and individual freedom. This book counters such discourses by showing the diversity and plurality of Muslim societies and by promoting reflection on how the ethnographic method allows the description, representation and analysis of the social and cultural complexity of Muslim societies in the discourse of anthropology.https://ecommons.aku.edu/uk_ismc_series_emc/1006/thumbnail.jp

Groups Whose Universal Theory Is Axiomatizable by Quasi-Identities

Discriminating groups were introduced in [3] with an eye toward applications to the universal theory of various groups. In [6] it was shown that if G is any discriminating group, then the universal theory of G coincides with that of its direct square G x G. In this paper we explore groups G whose universal theory coincides with that of their direct square. These are called square-like groups. We show that the class of square-like groups is first-order axiomatizable and contains the class of discriminating groups as a proper subclass. Further we show that the class of discriminating groups is not first-order axiomatizable

Regulatory networks and connected components of the neutral space

The functioning of a living cell is largely determined by the structure of its regulatory network, comprising non-linear interactions between regulatory genes. An important factor for the stability and evolvability of such regulatory systems is neutrality - typically a large number of alternative network structures give rise to the necessary dynamics. Here we study the discretized regulatory dynamics of the yeast cell cycle [Li et al., PNAS, 2004] and the set of networks capable of reproducing it, which we call functional. Among these, the empirical yeast wildtype network is close to optimal with respect to sparse wiring. Under point mutations, which establish or delete single interactions, the neutral space of functional networks is fragmented into 4.7 * 10^8 components. One of the smaller ones contains the wildtype network. On average, functional networks reachable from the wildtype by mutations are sparser, have higher noise resilience and fewer fixed point attractors as compared with networks outside of this wildtype component.Comment: 6 pages, 5 figure

Super-paramagnetic clustering of yeast gene expression profiles

High-density DNA arrays, used to monitor gene expression at a genomic scale, have produced vast amounts of information which require the development of efficient computational methods to analyze them. The important first step is to extract the fundamental patterns of gene expression inherent in the data. This paper describes the application of a novel clustering algorithm, Super-Paramagnetic Clustering (SPC) to analysis of gene expression profiles that were generated recently during a study of the yeast cell cycle. SPC was used to organize genes into biologically relevant clusters that are suggestive for their co-regulation. Some of the advantages of SPC are its robustness against noise and initialization, a clear signature of cluster formation and splitting, and an unsupervised self-organized determination of the number of clusters at each resolution. Our analysis revealed interesting correlated behavior of several groups of genes which has not been previously identified

Comparison of Fenoterol, Isoproterenol, and Isoetharine with Phenylephrine Aerosol in Asthma

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/97253/1/j.1552-4604.1983.tb02708.x.pd

Relationship between gene co-expression and probe localization on microarray slides

BACKGROUND: Microarray technology allows simultaneous measurement of thousands of genes in a single experiment. This is a potentially useful tool for evaluating co-expression of genes and extraction of useful functional and chromosomal structural information about genes. RESULTS: In this work we studied the association between the co-expression of genes, their location on the chromosome and their location on the microarray slides by analyzing a number of eukaryotic expression datasets, derived from the S. cerevisiae, C. elegans, and D. melanogaster. We find that in several different yeast microarray experiments the distribution of the number of gene pairs with correlated expression profiles as a function of chromosomal spacing is peaked at short separations and has two superimposed periodicities. The longer periodicity has a spacing of 22 genes (~42 Kb), and the shorter periodicity is 2 genes (~4 Kb). CONCLUSION: The relative positioning of DNA probes on microarray slides and source plates introduces subtle but significant correlations between pairs of genes. Careful consideration of this spatial artifact is important for analysis of microarray expression data. It is particularly relevant to recent microarray analyses that suggest that co-expressed genes cluster along chromosomes or are spaced by multiples of a fixed number of genes along the chromosome

The Iterative Signature Algorithm for the analysis of large scale gene expression data

We present a new approach for the analysis of genome-wide expression data. Our method is designed to overcome the limitations of traditional techniques, when applied to large-scale data. Rather than alloting each gene to a single cluster, we assign both genes and conditions to context-dependent and potentially overlapping transcription modules. We provide a rigorous definition of a transcription module as the object to be retrieved from the expression data. An efficient algorithm, that searches for the modules encoded in the data by iteratively refining sets of genes and conditions until they match this definition, is established. Each iteration involves a linear map, induced by the normalized expression matrix, followed by the application of a threshold function. We argue that our method is in fact a generalization of Singular Value Decomposition, which corresponds to the special case where no threshold is applied. We show analytically that for noisy expression data our approach leads to better classification due to the implementation of the threshold. This result is confirmed by numerical analyses based on in-silico expression data. We discuss briefly results obtained by applying our algorithm to expression data from the yeast S. cerevisiae.Comment: Latex, 36 pages, 8 figure

Radiation Induced Stress Relaxation in Silicone and Polyurethane Elastomers

Many different materials are used in the National Ignition Facility, NIF, located at Lawrence Livermore National Laboratory, LLNL. Some of these are exposed to significant doses of ionizing radiation. Two elastomers are of special interest because they are used in sealing applications with long expected lifetimes. These are LPU4, a polyurethane formulated at LLNL, and Dow Corning DC93-500, a silicone RTV elastomer. In 2004 a program to determine the impact of ionizing radiation on the stress relaxation and compression set characteristics of these two elastomers was undertaken. Since the materials are used in continuous compression and must reliably seal, the primary test utilized was a stress relaxation test. This test provides insight into the ability of a seal to remain functional in a static seal. The test determines how much residual force remains after a certain period of time under compression. The temperature and absorbed radiation dose can dramatically impact this property. In this study the only independent environmental variable studied is the effect of radiation at ambient temperatures. Two levels of radiation exposure were studied, 1 MRad, and 10 MRad. One of the independent test parameters is the compression deflection during storage and in this test the value used was 25%. The need for a compression retention mechanism ruled out radiation exposure in the compressed direction since the high atomic number materials for that device would block the radiation. Therefore, an annular ring was chosen for the specimen shape. The procedures are, as closely as possible, based on ASTM D 6147-97. Since the data is readily obtained at the end of the stress relaxation test, the samples were also evaluated for compression set. Compression set is the essentially permanent deformation incurred in a seal after the seal is compressed for some period of time and then unloaded. Though this is indicative of potential sealing reliability, it is not as direct an indicator of seal performance as is stress relaxation. Compression set does not yield any useable, quantified information but is an indicator of viscoelastic deformation with time. The needed thickness measurements were obtained both from the unloading curves and direct measurement in general accordance with ASTM D395-03. The radiation source for this testing was the Co60 gamma source located at Lawrence Livermore National Laboratory (LLNL). This source has an exposure vessel approximately 29.2cm (11.5-inch) tall with an inside diameter of 7.44cm (2.93-inch). Because of the geometry limits, cylindrical symmetry and limited volume, a standard stress relaxation test such as ASTM D 6147-97 could not be utilized and a modified test was developed. An additional constraint imposed by the vertical asymmetry of the radiation dose in the exposure chamber was a limited height with reasonably uniform radiation exposure. The specific dimensions and radiation characteristics of the test cell are in Appendix A