Compressing DNA sequence databases with coil

Background: Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip) compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results: We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST) data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion: coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work

Chandra Observation of the Radio Source / X-ray Gas Interaction in the Cooling Flow Cluster Abell 2052

We present a Chandra observation of Abell 2052, a cooling flow cluster with a central cD that hosts the complex radio source 3C 317. The data reveal ``holes'' in the X-ray emission that are coincident with the radio lobes. The holes are surrounded by bright ``shells'' of X-ray emission. The data are consistent with the radio source displacing and compressing, and at the same time being confined by, the X-ray gas. The compression of the X-ray shells appears to have been relatively gentle and, at most, slightly transonic. The pressure in the X-ray gas (the shells and surrounding cooler gas) is approximately an order of magnitude higher than the minimum pressure derived for the radio source, suggesting that an additional source of pressure is needed to support the radio plasma. The compression of the X-ray shells has speeded up the cooling of the shells, and optical emission line filaments are found coincident with the brightest regions of the shells.Comment: accepted for publication in ApJ Letters; for high-resolution color figures, see http://www.astro.virginia.edu/~elb6n/abell2052.htm

Transcriptional repression by ApiAP2 factors is central to chronic toxoplasmosis

Tachyzoite to bradyzoite development in Toxoplasma is marked by major changes in gene expression resulting in a parasite that expresses a new repertoire of surface antigens hidden inside a modified parasitophorous vacuole called the tissue cyst. The factors that control this important life cycle transition are not well understood. Here we describe an important transcriptional repressor mechanism controlling bradyzoite differentiation that operates in the tachyzoite stage. The ApiAP2 factor, AP2IV-4, is a nuclear factor dynamically expressed in late S phase through mitosis/cytokinesis of the tachyzoite cell cycle. Remarkably, deletion of the AP2IV-4 locus resulted in the expression of a subset of bradyzoite-specific proteins in replicating tachyzoites that included tissue cyst wall components BPK1, MCP4, CST1 and the surface antigen SRS9. In the murine animal model, the mis-timing of bradyzoite antigens in tachyzoites lacking AP2IV-4 caused a potent inflammatory monocyte immune response that effectively eliminated this parasite and prevented tissue cyst formation in mouse brain tissue. Altogether, these results indicate that suppression of bradyzoite antigens by AP2IV-4 during acute infection is required for Toxoplasma to successfully establish a chronic infection in the immune-competent host

Self-healing elastomer system

A composite material includes an elastomer matrix, a set of first capsules containing a polymerizer, and a set of second capsules containing a corresponding activator for the polymerizer. The polymerizer may be a polymerizer for an elastomer. The composite material may be prepared by combining a first set of capsules containing a polymerizer, a second set of capsules containing a corresponding activator for the polymerizer, and a matrix precursor, and then solidifying the matrix precursor to form an elastomeric matrix

Gene Set Enrichment Analysis (GSEA) of Toxoplasma gondii expression datasets links cell cycle progression and the bradyzoite developmental program

BACKGROUND: Large amounts of microarray expression data have been generated for the Apicomplexan parasite Toxoplasma gondii in an effort to identify genes critical for virulence or developmental transitions. However, researchers’ ability to analyze this data is limited by the large number of unannotated genes, including many that appear to be conserved hypothetical proteins restricted to Apicomplexa. Further, differential expression of individual genes is not always informative and often relies on investigators to draw big-picture inferences without the benefit of context. We hypothesized that customization of gene set enrichment analysis (GSEA) to T. gondii would enable us to rigorously test whether groups of genes serving a common biological function are co-regulated during the developmental transition to the latent bradyzoite form. RESULTS: Using publicly available T. gondii expression microarray data, we created Toxoplasma gene sets related to bradyzoite differentiation, oocyst sporulation, and the cell cycle. We supplemented these with lists of genes derived from community annotation efforts that identified contents of the parasite-specific organelles, rhoptries, micronemes, dense granules, and the apicoplast. Finally, we created gene sets based on metabolic pathways annotated in the KEGG database and Gene Ontology terms associated with gene annotations available at http://www.toxodb.org. These gene sets were used to perform GSEA analysis using two sets of published T. gondii expression data that characterized T. gondii stress response and differentiation to the latent bradyzoite form. CONCLUSIONS: GSEA provides evidence that cell cycle regulation and bradyzoite differentiation are coupled. Δgcn5A mutants unable to induce bradyzoite-associated genes in response to alkaline stress have different patterns of cell cycle and bradyzoite gene expression from stressed wild-type parasites. Extracellular tachyzoites resemble a transitional state that differs in gene expression from both replicating intracellular tachyzoites and in vitro bradyzoites by expressing genes that are enriched in bradyzoites as well as genes that are associated with the G1 phase of the cell cycle. The gene sets we have created are readily modified to reflect ongoing research and will aid researchers’ ability to use a knowledge-based approach to data analysis facilitating the development of new insights into the intricate biology of Toxoplasma gondii. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-515) contains supplementary material, which is available to authorized users

Infrared Surface Brightness Fluctuations of the Coma Elliptical NGC 4874 and the Value of the Hubble Constant

We have used the Keck I Telescope to measure K-band surface brightness fluctuations (SBFs) of NGC 4874, the dominant elliptical galaxy in the Coma cluster. We use deep HST WFPC2 optical imaging to account for the contamination due to faint globular clusters and improved analysis techniques to derive measurements of the SBF apparent magnitude. Using a new SBF calibration which accounts for the dependence of K-band SBFs on the integrated color of the stellar population, we measure a distance modulus of 34.99+/-0.21 mag (100+/-10 Mpc) for the Coma cluster. The resulting value of the Hubble constant is 71+/-8 km/s/Mpc, not including any systematic error in the HST Cepheid distance scale.Comment: ApJ Letters, in press. Uses emulateapj5.st

Anomaly Detection in Paleoclimate Records using Permutation Entropy

Permutation entropy techniques can be useful in identifying anomalies in paleoclimate data records, including noise, outliers, and post-processing issues. We demonstrate this using weighted and unweighted permutation entropy of water-isotope records in a deep polar ice core. In one region of these isotope records, our previous calculations revealed an abrupt change in the complexity of the traces: specifically, in the amount of new information that appeared at every time step. We conjectured that this effect was due to noise introduced by an older laboratory instrument. In this paper, we validate that conjecture by re-analyzing a section of the ice core using a more-advanced version of the laboratory instrument. The anomalous noise levels are absent from the permutation entropy traces of the new data. In other sections of the core, we show that permutation entropy techniques can be used to identify anomalies in the raw data that are not associated with climatic or glaciological processes, but rather effects occurring during field work, laboratory analysis, or data post-processing. These examples make it clear that permutation entropy is a useful forensic tool for identifying sections of data that require targeted re-analysis---and can even be useful in guiding that analysis.Comment: 15 pages, 7 figure

Designing for Schadenfreude (or, how to express well-being and see if you're boring people)

This position paper presents two studies of content not normally expressed in status updates—well-being and status feedback—and considers how they may be processed, valued and used for potential quality-of-life benefits in terms of personal and social reflection and awareness. Do I Tweet Good? (poor grammar intentional) is a site investigating more nuanced forms of status feedback than current microblogging sites allow, towards understanding self-identity, reflection, and online perception. Healthii is a tool for sharing physical and emotional well-being via status updates, investigating concepts of self-reflection and social awareness. Together, these projects consider furthering the value of microblogging on two fronts: 1) refining the online personal/social networking experience, and 2) using the status update for enhancing the personal/social experience in the offline world, and considering how to leverage that online/offline split. We offer results from two different methods of study and target groups—one co-workers in an academic setting, the other followers on Twitter—to consider how microblogging can become more than just a communication medium if it facilitates these types of reflective practice