Alignments with non-overlapping moves, inversions and tandem duplications in O ( n 4) time

Sequence alignment is a central problem in bioinformatics. The classical dynamic programming algorithm aligns two sequences by optimizing over possible insertions, deletions and substitutions. However, other evolutionary events can be observed, such as inversions, tandem duplications or moves (transpositions). It has been established that the extension of the problem to move operations is NP-complete. Previous work has shown that an extension restricted to non-overlapping inversions can be solved in O(n 3) with a restricted scoring scheme. In this paper, we show that the alignment problem extended to non-overlapping moves can be solved in O(n 5) for general scoring schemes, O(n 4log n) for concave scoring schemes and O(n 4) for restricted scoring schemes. Furthermore, we show that the alignment problem extended to non-overlapping moves, inversions and tandem duplications can be solved with the same time complexities. Finally, an example of an alignment with non-overlapping moves is provide

SWPS3 – fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and ×86/SSE2

<p>Abstract</p> <p>Background</p> <p>We present swps3, a vectorized implementation of the Smith-Waterman local alignment algorithm optimized for both the Cell/BE and ×86 architectures. The paper describes swps3 and compares its performances with several other implementations.</p> <p>Findings</p> <p>Our benchmarking results show that swps3 is currently the fastest implementation of a vectorized Smith-Waterman on the Cell/BE, outperforming the only other known implementation by a factor of at least 4: on a Playstation 3, it achieves up to 8.0 billion cell-updates per second (GCUPS). Using the SSE2 instruction set, a quad-core Intel Pentium can reach 15.7 GCUPS. We also show that swps3 on this CPU is faster than a recent GPU implementation. Finally, we note that under some circumstances, alignments are computed at roughly the same speed as BLAST, a heuristic method.</p> <p>Conclusion</p> <p>The Cell/BE can be a powerful platform to align biological sequences. Besides, the performance gap between exact and heuristic methods has almost disappeared, especially for long protein sequences.</p

Particle-Based Sampling and Meshing of Surfaces in Multimaterial Volumes

Methods that faithfully and robustly capture the geometry of complex material interfaces in labeled volume data are important for generating realistic and accurate visualizations and simulations of real-world objects. The generation of such multimaterial models from measured data poses two unique challenges: first, the surfaces must be well-sampled with regular, efficient tessellations that are consistent across material boundaries; and second, the resulting meshes must respect the nonmanifold geometry of the multimaterial interfaces. This paper proposes a strategy for sampling and meshing multimaterial volumes using dynamic particle systems, including a novel, differentiable representation of the material junctions that allows the particle system to explicitly sample corners, edges, and surfaces of material intersections. The distributions of particles are controlled by fundamental sampling constraints, allowing Delaunay-based meshing algorithms to reliably extract watertight meshes of consistently high-quality.Engineering and Applied Science

Volume MLS Ray Casting

The method of Moving Least Squares (MLS) is a popular framework for reconstructing continuous functions from scattered data due to its rich mathematical properties and well-understood theoretical foundations. This paper applies MLS to volume rendering, providing a unified mathematical framework for ray casting of scalar data stored over regular as well as irregular grids. We use the MLS reconstruction to render smooth isosurfaces and to compute accurate derivatives for high-quality shading effects. We also present a novel, adaptive preintegration scheme to improve the efficiency of the ray casting algorithm by reducing the overall number of function evaluations, and an efficient implementation of our framework exploiting modern graphics hardware. The resulting system enables high-quality volume integration and shaded isosurface rendering for regular and irregular volume data.Engineering and Applied Science

Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference

Phylogenetic inference is generally performed on the basis of multiple sequence alignments (MSA). Because errors in an alignment can lead to errors in tree estimation, there is a strong interest in identifying and removing unreliable parts of the alignment. In recent years several automated filtering approaches have been proposed, but despite their popularity, a systematic and comprehensive comparison of different alignment filtering methods on real data has been lacking. Here, we extend and apply recently introduced phylogenetic tests of alignment accuracy on a large number of gene families and contrast the performance of unfiltered versus filtered alignments in the context of single-gene phylogeny reconstruction. Based on multiple genome-wide empirical and simulated data sets, we show that the trees obtained from filtered MSAs are on average worse than those obtained from unfiltered MSAs. Furthermore, alignment filtering often leads to an increase in the proportion of well-supported branches that are actually wrong. We confirm that our findings hold for a wide range of parameters and methods. Although our results suggest that light filtering (up to 20% of alignment positions) has little impact on tree accuracy and may save some computation time, contrary to widespread practice, we do not generally recommend the use of current alignment filtering methods for phylogenetic inference. By providing a way to rigorously and systematically measure the impact of filtering on alignments, the methodology set forth here will guide the development of better filtering algorithms

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference

Phylogenetic inference is generally performed on the basis of multiple sequence alignments (MSA). Because errors in an alignment can lead to errors in tree estimation, there is a strong interest in identifying and removing unreliable parts of the alignment. In recent years several automated filtering approaches have been proposed, but despite their popularity, a systematic and comprehensive comparison of different alignment filtering methods on real data has been lacking. Here, we extend and apply recently introduced phylogenetic tests of alignment accuracy on a large number of gene families and contrast the performance of unfiltered versus filtered alignments in the context of single-gene phylogeny reconstruction. Based on multiple genome-wide empirical and simulated data sets, we show that the trees obtained from filtered MSAs are on average worse than those obtained from unfiltered MSAs. Furthermore, alignment filtering often leads to an increase in the proportion of well-supported branches that are actually wrong. We confirm that our findings hold for a wide range of parameters and methods. Although our results suggest that light filtering (up to 20% of alignment positions) has little impact on tree accuracy and may save some computation time, contrary to widespread practice, we do not generally recommend the use of current alignment filtering methods for phylogenetic inference. By providing a way to rigorously and systematically measure the impact of filtering on alignments, the methodology set forth here will guide the development of better filtering algorithm

Stratification of cumulative antibiograms in hospitals for hospital unit, specimen type, isolate sequence and duration of hospital stay

Background Empirical antibiotic therapy is based on patients' characteristics and antimicrobial susceptibility data. Hospital-wide cumulative antibiograms may not sufficiently support informed decision-making for optimal treatment of hospitalized patients. Methods We studied different approaches to analysing antimicrobial susceptibility rates (SRs) of all diagnostic bacterial isolates collected from patients hospitalized between July 2005 and June 2007 at the University Hospital in Zurich, Switzerland. We compared stratification for unit-specific, specimen type-specific (blood, urinary, respiratory versus all specimens) and isolate sequence-specific (first, follow-up versus all isolates) data with hospital-wide cumulative antibiograms, and studied changes of mean SR during the course of hospitalization. Results A total of 16 281 isolates (7965 first, 1201 follow-up and 7115 repeat isolates) were tested. We found relevant differences in SRs across different hospital departments. Mean SRs of Escherichia coli to ciprofloxacin ranged between 64.5% and 95.1% in various departments, and mean SRs of Pseudomonas aeruginosa to imipenem and meropenem ranged from 54.2% to 100% and 80.4% to 100%, respectively. Compared with hospital cumulative antibiograms, lower SRs were observed in intensive care unit specimens, follow-up isolates and isolates causing nosocomial infections (except for Staphylococcus aureus). Decreasing SRs were observed in first isolates of coagulase-negative staphylococci with increasing interval between hospital admission and specimen collection. Isolates from different anatomical sites showed variations in SRs. Conclusions We recommend the reporting of unit-specific rather than hospital-wide cumulative antibiograms. Decreasing antimicrobial susceptibility during hospitalization and variations in SRs in isolates from different anatomical sites should be taken into account when selecting empirical antibiotic treatmen

Correlation between case mix index and antibiotic use in hospitals

Background To compare the quantitative antibiotic use between hospitals or hospital units and to explore differences, adjustment for severity of illness of hospitalized patients is essential. The case mix index (CMI) is an economic surrogate marker (i.e. the total cost weights of all inpatients per a defined time period divided by the number of admissions) to describe the average patients' morbidity of individual hospitals. We aimed to investigate the correlation between CMI and hospital antibiotic use. Methods We used weighted linear regression analysis to evaluate the correlation between in-hospital antibiotic use in 2006 and CMI of 18 departments of the tertiary care University Hospital Zurich and of 10 primary and 2 secondary acute care hospitals in the Canton of Zurich in Switzerland. Results Antibiotic use varied substantially between different departments of the university hospital [defined daily doses (DDD)/100 bed-days, 68.04; range, 20.97-323.37] and between primary and secondary care hospitals (range of DDD/100 bed-days, 15.45-57.05). Antibiotic use of university hospital departments and the different hospitals, respectively, correlated with CMI when calculated in DDD/100 bed-days [coefficient of determination (R2), 0.57 (P = 0.0002) and 0.46 (P = 0.0065)], as well as when calculated in DDD/100 admissions [R2, 0.48 (P = 0.0008) and 0.85 (P < 0.0001), respectively]. Conclusions Antibiotic use correlated with CMI across various specialties of a university hospital and across different acute care hospitals. For benchmarking antibiotic use within and across hospitals, adjustment for CMI may be a useful tool in order to take into account the differences in hospital category and patients' morbiditie

Basic study on the evaluation of thermoplastic polymers as hot-melt adhesives for mixed-substrate joining

A selection of 22 low-melting polymers was thermally and rheologically evaluated to be used as hot-melt adhesives in mixed-substrate joining samples. The choice of polymers was based on the published melting point. It was required to include a broad variety of different polymers backbones to study the influence of the different polymers comprehensively. A tool-box of widely applicable tests was developed to judge if a thermoplastic polymer is suitable for a hot-melt adhesive application. Melting temperature (onset, peak and offset temperature) and melting enthalpy were determined using standardized methods. Rheological methods were used to characterize the shear rate dependence and the flow behavior at the application temperature. The wetting behavior of the polymers was evaluated with contact angle measurements. The adhesive strength of the most promising candidates was analyzed using the Lumi Frac-adhesion method including the failure pattern

O331 Patterns of viral suppression on cART as predictors of uncontrolled viremia after starting a new antiretroviral after 1 January 2003

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