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The authors examine a proposed means for correcting potential bias in calculating transition probabilities in land-cover and land-use research models. After presenting empirical sensitivity analysis results, the authors conclude that their regression-analysis methods avoid bias.

Author(s): International Human Genome Sequencing Consortium; Whitehead Institute for Biomedical Research, Center for Genome Research:; Eric S. Lander [1]; Lauren M. Linton [1]; Bruce Birren [1]; Chad Nusbaum [1]; Michael [...]

Abstract Recently, we have identified a randomized quartet phylogeny algorithm that has O(nlogn) runtime with high probability, which is asymptotically optimal. Our algorithm has high probability of returning the correct phylogeny when quartet errors are independent and occur with known probability, and when the algorithm uses a guide tree on O(loglogn) taxa that is correct with high probability. In practice, none of these assumptions is correct: quartet errors are positively correlated and occur with unknown probability, and the guide tree is often error prone. Here, we bring our work out of the purely theoretical setting. We present a variety of extensions which, while only slowing the algorithm down by a constant factor, make its performance nearly comparable to that of Neighbour Joining , which requires Θ(n3) runtime in existing implementations. Our results suggest a new direction for quartet-based phylogenetic reconstruction that may yield striking speed improvements at minimal accuracy cost. An early prototype implementation of our software is available at http://www.cs.uwaterloo.ca/jmtruszk/qtree.tar.gz.

Abstract Background Illumina paired-end reads are used to analyse microbial communities by targeting amplicons of the 16S rRNA gene. Publicly available tools are needed to assemble overlapping paired-end reads while correcting mismatches and uncalled bases; many errors could be corrected to obtain higher sequence yields using quality information. Results PANDAseq assembles paired-end reads rapidly and with the correction of most errors. Uncertain error corrections come from reads with many low-quality bases identified by upstream processing. Benchmarks were done using real error masks on simulated data, a pure source template, and a pooled template of genomic DNA from known organisms. PANDAseq assembled reads more rapidly and with reduced error incorporation compared to alternative methods. Conclusions PANDAseq rapidly assembles sequences and scales to billions of paired-end reads. Assembly of control libraries showed a 4-50% increase in the number of assembled sequences over naïve assembly with negligible loss of "good" sequence.

Abstract Background Identifying recombinations in HIV is important for studying the epidemiology of the virus and aids in the design of potential vaccines and treatments. The previous widely-used tool for this task uses the Viterbi algorithm in a hidden Markov model to model recombinant sequences. Results We apply a new decoding algorithm for this HMM that improves prediction accuracy. Exactly locating breakpoints is usually impossible, since different subtypes are highly conserved in some sequence regions. Our algorithm identifies these sites up to a certain error tolerance. Our new algorithm is more accurate in predicting the location of recombination breakpoints. Our implementation of the algorithm is available at http://www.cs.uwaterloo.ca/~jmtruszk/jphmm_balls.tar.gz. Conclusions By explicitly accounting for uncertainty in breakpoint positions, our algorithm offers more reliable predictions of recombination breakpoints in HIV-1. We also document a new domain of use for our new decoding approach in HMMs.

Abstract Background Multiple genome alignment is an important problem in bioinformatics. An important subproblem used by many multiple alignment approaches is that of aligning two multiple alignments. Many popular alignment algorithms for DNA use the sum-of-pairs heuristic, where the score of a multiple alignment is the sum of its induced pairwise alignment scores. However, the biological meaning of the sum-of-pairs of pairs heuristic is not obvious. Additionally, many algorithms based on the sum-of-pairs heuristic are complicated and slow, compared to pairwise alignment algorithms. An alternative approach to aligning alignments is to first infer ancestral sequences for each alignment, and then align the two ancestral sequences. In addition to being fast, this method has a clear biological basis that takes into account the evolution implied by an underlying phylogenetic tree. In this study we explore the accuracy of aligning alignments by ancestral sequence alignment. We examine the use of both maximum likelihood and parsimony to infer ancestral sequences. Additionally, we investigate the effect on accuracy of allowing ambiguity in our ancestral sequences. Results We use synthetic sequence data that we generate by simulating evolution on a phylogenetic tree. We use two different types of phylogenetic trees: trees with a period of rapid growth followed by a period of slow growth, and trees with a period of slow growth followed by a period of rapid growth. We examine the alignment accuracy of four ancestral sequence reconstruction and alignment methods: parsimony, maximum likelihood, ambiguous parsimony, and ambiguous maximum likelihood. Additionally, we compare against the alignment accuracy of two sum-of-pairs algorithms: ClustalW and the heuristic of Ma, Zhang, and Wang. Conclusion We find that allowing ambiguity in ancestral sequences does not lead to better multiple alignments. Regardless of whether we use parsimony or maximum likelihood, the success of aligning ancestral sequences containing ambiguity is very sensitive to the choice of gap open cost. Surprisingly, we find that using maximum likelihood to infer ancestral sequences results in less accurate alignments than when using parsimony to infer ancestral sequences. Finally, we find that the sum-of-pairs methods produce better alignments than all of the ancestral alignment methods.

We describe the use of the Fréchet mean and variance in the Billera–Holmes–Vogtmann (BHV) treespace to summarize and explore the diversity of a set of phylogenetic trees. We show that the Fréchet mean is comparable to other summary methods, and, despite its stickiness property, is more likely to be binary than the majority-rule consensus tree. We show that the Fréchet variance is faster and more precise than commonly used variance measures. The Fréchet mean and variance are more theoretically justified, and more robust, than previous estimates of this type and can be estimated reasonably efficiently, providing a foundation for building more advanced statistical methods and leading to applications such as mean hypothesis testing and outlier detection. [ABSTRACT FROM AUTHOR]

BACKGROUND: Land surface temperature (LST) and percent surface imperviousness (SI), both derived from satellite imagery, have been used to characterize the urban heat island effect, a phenomenon in which urban areas are warmer than non-urban areas. OBJECTIVES: We aimed to assess the correlations between LSTs and SI images with actual temperature readings from a ground-based network of outdoor monitors. METHODS: We evaluated the relationships among a) LST calculated from a 2009 summertime satellite image of the Detroit metropolitan region, Michigan; b) SI from the 2006 National Land Cover Data Set; and c) ground-based temperature measurements monitored during the same time period at 19 residences throughout the Detroit metropolitan region. Associations between these ground-based temperatures and the average LSTs and SI at different radii around the point of the ground-based temperature measurement were evaluated at different time intervals. Spearman correlation coefficients and corresponding p-values were calculated. RESULTS: Satellite-derived LST and SI values were significantly correlated with 24-hr average and August monthly average ground temperatures at all but two of the radii examined (100 m for LST and 0 m for SI). Correlations were also significant for temperatures measured between 0400 and 0500 hours for SI, except at 0 m, but not LST. Statistically significant correlations ranging from 0.49 to 0.91 were observed between LST and SI. CONCLUSIONS: Both SI and LST could be used to better understand spatial variation in heat exposures over longer time frames but are less useful for estimating shorter-term, actual temperature exposures, which can be useful for public health preparedness during extreme heat events. KEY WORDS: epidemiology, ground truthing, heat, Landsat satellite, land surface temperature, remote sensing, surface imperviousness, temperature, urban areas. Environ Health Perspect 121:925-931 (2013). http://dx.doi.org/10.1289/ehp.1206176 [Online 7 June 2013], Introduction Use of thermal remote sensing and advanced spatial modeling are emerging trends in environmental epidemiology and public health. Geospatial technologies provide a valuable resource to assist public health practitioners [...]

Further development of process-based spatial models is needed to facilitate explanation in landscape ecology. We discuss the dual modeling goals of prediction and explanation and identify challenges faced in explaining landscape patterns. These challenges are especially acute in attempts to explain patterns that result from complex adaptive systems. We compare examples of two process models used to describe landscape changes in Yellowstone National Park as a consequence of predator-prey interactions. Generative landscape science is offered as a complementary approach to explanation, combining models of candidate processes that are believed to give rise to observed patterns with empirical observations.