MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data

MAPPFinder is a tool that creates a global gene-expression profile across all areas of biology by integrating the annotations of the Gene Ontology (GO) Project with the free software package GenMAPP . The results are displayed in a searchable browser, allowing the user to rapidly identify GO terms with over-represented numbers of gene-expression changes. Clicking on GO terms generates GenMAPP graphical files where gene relationships can be explored, annotated, and files can be freely exchanged

A Century of Cosmology

In the century since Einstein's anno mirabilis of 1905, our concept of the Universe has expanded from Kapteyn's flattened disk of stars only 10 kpc across to an observed horizon about 30 Gpc across that is only a tiny fraction of an immensely large inflated bubble. The expansion of our knowledge about the Universe, both in the types of data and the sheer quantity of data, has been just as dramatic. This talk will summarize this century of progress and our current understanding of the cosmos.Comment: Talk presented at the "Relativistic Astrophysics and Cosmology - Einstein's Legacy" meeting in Munich, Nov 2005. Proceedings will be published in the Springer-Verlag "ESO Astrophysics Symposia" series. 10 pages Latex with 2 figure

Automatic estimation of harmonic tension by distributed representation of chords

The buildup and release of a sense of tension is one of the most essential aspects of the process of listening to music. A veridical computational model of perceived musical tension would be an important ingredient for many music informatics applications. The present paper presents a new approach to modelling harmonic tension based on a distributed representation of chords. The starting hypothesis is that harmonic tension as perceived by human listeners is related, among other things, to the expectedness of harmonic units (chords) in their local harmonic context. We train a word2vec-type neural network to learn a vector space that captures contextual similarity and expectedness, and define a quantitative measure of harmonic tension on top of this. To assess the veridicality of the model, we compare its outputs on a number of well-defined chord classes and cadential contexts to results from pertinent empirical studies in music psychology. Statistical analysis shows that the model's predictions conform very well with empirical evidence obtained from human listeners.Comment: 12 pages, 4 figures. To appear in Proceedings of the 13th International Symposium on Computer Music Multidisciplinary Research (CMMR), Porto, Portuga

GenMAPP 2: New features and resources for pathway analysis

BACKGROUND: Microarray technologies have evolved rapidly, enabling biologists to quantify genome-wide levels of gene expression, alternative splicing, and sequence variations for a variety of species. Analyzing and displaying these data present a significant challenge. Pathway-based approaches for analyzing microarray data have proven useful for presenting data and for generating testable hypotheses. RESULTS: To address the growing needs of the microarray community we have released version 2 of Gene Map Annotator and Pathway Profiler (GenMAPP), a new GenMAPP database schema, and integrated resources for pathway analysis. We have redesigned the GenMAPP database to support multiple gene annotations and species as well as custom species database creation for a potentially unlimited number of species. We have expanded our pathway resources by utilizing homology information to translate pathway content between species and extending existing pathways with data derived from conserved protein interactions and coexpression. We have implemented a new mode of data visualization to support analysis of complex data, including time-course, single nucleotide polymorphism (SNP), and splicing. GenMAPP version 2 also offers innovative ways to display and share data by incorporating HTML export of analyses for entire sets of pathways as organized web pages. CONCLUSION: GenMAPP version 2 provides a means to rapidly interrogate complex experimental data for pathway-level changes in a diverse range of organisms

Nanohertz Frequency Determination for the Gravity Probe B HF SQUID Signal

In this paper, we present a method to measure the frequency and the frequency change rate of a digital signal. This method consists of three consecutive algorithms: frequency interpolation, phase differencing, and a third algorithm specifically designed and tested by the authors. The succession of these three algorithms allowed a 5 parts in 10^10 resolution in frequency determination. The algorithm developed by the authors can be applied to a sampled scalar signal such that a model linking the harmonics of its main frequency to the underlying physical phenomenon is available. This method was developed in the framework of the Gravity Probe B (GP-B) mission. It was applied to the High Frequency (HF) component of GP-B's Superconducting QUantum Interference Device (SQUID) signal, whose main frequency fz is close to the spin frequency of the gyroscopes used in the experiment. A 30 nHz resolution in signal frequency and a 0.1 pHz/sec resolution in its decay rate were achieved out of a succession of 1.86 second-long stretches of signal sampled at 2200 Hz. This paper describes the underlying theory of the frequency measurement method as well as its application to GP-B's HF science signal.Comment: The following article has been submitted to Review of Scientific Instruments. After it is published, it will be found at (http://rsi.aip.org/

Diel variations of H2O2 in Greenland: A discussion of the cause and effect relationship

Atmospheric hydrogen peroxide (H2O2) measurements at Summit, Greenland, in May–June, 1993 exhibited a diel variation, with afternoon highs typically 1–2 parts per billion by volume (ppbv) and nighttime lows about 0.5 ppbv lower. This variation closely followed that for temperature; specific humidity exhibited the same general trend. During a 17-day snowfall-free period, surface snow was accumulating H2O2, apparently from nighttime cocondensation of H2O and H2O2. Previous photochemical modeling (Neftel et al., 1995) suggests that daytime H2O2 should be about 1 ppbv, significantly lower than our measured values. Previous equilibrium partitioning measurements between ice and gas phase (Conklin et al., 1993) suggest that air in equilibrium with H2O2 concentrations measured in surface snow (15–18 μM) should have an H2O2 concentration 2–3 times what we measured 0.2–3.5 m above the snow surface. A simple eddy diffusion model, with vertical eddy diffusion coefficients calculated from balloon soundings, suggested that atmospheric H2O2 concentrations should be affected by any H2O2 degassed from surface snow. However, field measurements showed the absence of either high concentrations of H2O2 or a measurable concentration gradient between inlets 0.2 and 3 m above the snow. A surface resistance to degassing, that is, slow release of H2O2 from the ice matrix, is a plausible explanation for the differences between observations and modeled atmospheric profiles. Degassing of H2O2 at a rate below our detection limit would still influence measured atmospheric concentrations and help explain the difference between measurements and photochemical modeling. The cumulative evidence suggests that surface snow adjusts slowly to drops in atmospheric H2O2 concentration, over timescales of at least weeks. The H2O2 losses previously observed in pits sampled over more than 1 year are thought to have occurred later in the summer or fall, after the May–July field season