Mutual information for examining correlations in DNA

This paper examines two methods for finding whether long-range correlations exist in DNA: a fractal measure and a mutual information technique. We evaluate the performance and implications of these methods in detail. In particular we explore their use comparing DNA sequences from a variety of sources. Using software for performing in silico mutations, we also consider evolutionary events leading to long range correlations and analyse these correlations using the techniques presented. Comparisons are made between these virtual sequences, randomly generated sequences, and real sequences. We also explore correlations in chromosomes from different species.Comment: 8 pages, 3 figure

Who wrote the Letter to the Hebrews? - Data mining for detection of text authorship

© 2005 COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only. Copyright 2005 Society of Photo-Optical Instrumentation Engineers. This paper was published in Smart Structures, Devices, and Systems II, edited by Said F. Al-Sarawi, Proceedings of SPIE Vol. 5649 and is made available as an electronic reprint with permission of SPIE. One print or electronic copy may be made for personal use only. Systematic or multiple reproduction, distribution to multiple locations via electronic or other means, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper are prohibited.This paper explores the authorship of the Letter to the Hebrews using a number of different measures of relationship between different texts of the New Testament. The methods used in the study include file zipping and compression techniques, prediction by the partial matching technique and the word recurrence interval technique. The long term motivation is that the techniques employed in this study may find applicability in future generation web search engines, email authorship identification, detection of plagiarism and terrorist email traffic filtration.Madeleine Sabordo, Shong Y. Chai, Matthew J. Berryman, and Derek Abbot

Methods for Generating Complex Networks with Selected Structural Properties for Simulations: A Review and Tutorial for Neuroscientists

Many simulations of networks in computational neuroscience assume completely homogenous random networks of the Erdös–Rényi type, or regular networks, despite it being recognized for some time that anatomical brain networks are more complex in their connectivity and can, for example, exhibit the “scale-free” and “small-world” properties. We review the most well known algorithms for constructing networks with given non-homogeneous statistical properties and provide simple pseudo-code for reproducing such networks in software simulations. We also review some useful mathematical results and approximations associated with the statistics that describe these network models, including degree distribution, average path length, and clustering coefficient. We demonstrate how such results can be used as partial verification and validation of implementations. Finally, we discuss a sometimes overlooked modeling choice that can be crucially important for the properties of simulated networks: that of network directedness. The most well known network algorithms produce undirected networks, and we emphasize this point by highlighting how simple adaptations can instead produce directed networks

Epiphytic macrolichens in relation to forest management and topography in a western Oregon watershed

This dissertation describes patterns in epiphytic macrolichen community composition, diversity, and biomass across various stand types in the Blue River watershed of western Oregon. It first examines the relative importance of ecological factors such as stand age, remnant tree retention, and topography to lichen communities in the landscape. It then develops models for estimating epiphytic macrolichen biomass and uses these models to assess potential impacts of forest management strategies on future lichen biomass in the watershed. Epiphytic macrolichen communities were sampled in 117 coniferous stands in uplands and riparian areas. Stands were typed by stand age (young, 200 yrs) and by the degree of remnant tree retention (older trees that survived the most recent disturbance). Lichen biomass (oven-dried, kg/ha) was estimated for three functional groups: nitrogen-fixing cyanolichens, forage lichens, and matrix lichens in 63 of the 117 stands. Elevation was the leading factor related to differences in macrolichen communities and biomass. Cyanolichens (dominated by Lobaria oregana) were largely limited to lower elevations and were most abundant in old growth (median 1,377 kg/ha). Lichen community composition changed with stand age. Remnant presence was related only to lichen community differences in young stands. Lichen biomass increased with stand age and with remnant retention. Stands along perennial streams were cyanolichen hotspots compared to uplands. Lichen biomass was unrelated to uplands and riparian areas. Regression models estimating lichen biomass by functional group were developed from topography, stand structure, and lichen communities. The model for cyanolichen biomass had the strongest predictive power (R²= 0.85), whereas models for forage and matrix lichen biomass were less powerful (R² = 0.55 and R² = 0.58, respectively). We estimated cyanolichen and forage lichen biomass in the present watershed and forecasted lichen biomass in 200 yrs for two different management scenarios: the Landscape Plan (LP) and the Northwest Forest Plan (NWFP). Under both scenarios, lichen biomass was predicted to increase substantially from current levels due to increased remnant tree retention and the elimination of clear-cutting. The LP scenario yielded 12% higher forage lichen biomass and 8% higher cyanolichen biomass than the NWFP

Characterization of two complete Isospora mitochondrial genomes from passerine birds: Isospora serinuse in a domestic canary and Isospora manorinae in a yellow-throated miner

The genus term Isospora is now applied specifically to parasites of birds, with the term Cystoisospora preferred for parasites which infect mammals. Isospora is a common parasitic coccidian in birds worldwide, especially in passerine birds, in which it can cause systemic coccidiosis. The complete mitochondrial genome sequences from two recently identified Isospora species; Isospora serinuse in a domestic canary and Isospora manorinae in a yellow-throated miner, were sequenced and compared with those of other closely related coccidian species. The complete mitochondrial genome sequence for Isospora serinuse is 6260. bp in size and 6223. bp for Isospora manorinae. The mitochondrial genomes of Isospora serinuse and Isospora manorinae include three protein-coding genes (COI, COIII and CytB), 19 LSU and 14 SSU rDNA fragments, including one newly identified putative LSU fragment in Isospora sp. The arrangement of coding regions in these two Isospora species were identical to that of available Isospora sp. and Eimeria spp. mitochondrial genomes and the start codon usage for protein coding genes was conservative. Phylogenetic analysis of the mt genome of the two Isospora species based on the three coding regions further support that the monophyletic nature of avian Isospora

Target characterization using decomposition of the time-reversal operator: electromagnetic scattering from small ellipsoids

Decomposition of the time-reversal operator for an array, or equivalently the singular value decomposition of the multistatic response matrix, has been used to improve imaging and localization of targets in complicated media. Typically, each singular value is associated with one scatterer even though it has been shown in several cases that a single scatterer can generate several singular values. In earlier papers Chambers and Berryman [1, 2] showed that a small spherical scatterer can generate up to six singular values depending on the array geometry and sphere composition. It was shown that the existence and characteristics of multiple singular values for each scatterer can, in principle, be used to determine certain properties of the scatterers, e.g. conducting or non-conducting material. In this paper, we extend this analysis to non-spherical targets and show how orientation information about the target may be obtained from the spectrum of singular values. The general properties of the decomposition for small non-spherical dielectric (and possibly conductive) targets in an electromagnetic field are derived and detailed results are obtained for the specific cases of non-magnetic and perfectly conducting needles and disks. It is shown that scatterer orientation can be estimated by tracking the singular values of a linear array as it is rotated around its midpoint