Parallel approach to sliding window sums

Sliding window sums are widely used in bioinformatics applications, including sequence assembly, k-mer generation, hashing and compression. New vector algorithms which utilize the advanced vector extension (AVX) instructions available on modern processors, or the parallel compute units on GPUs and FPGAs, would provide a significant performance boost for the bioinformatics applications. We develop a generic vectorized sliding sum algorithm with speedup for window size w and number of processors P is O(P/w) for a generic sliding sum. For a sum with commutative operator the speedup is improved to O(P/log(w)). When applied to the genomic application of minimizer based k-mer table generation using AVX instructions, we obtain a speedup of over 5X.Comment: 10 pages, 5 figure

Clinician-reported barriers to implementing breast cancer chemoprevention in the UK: A qualitative investigation

Aims: The use of tamoxifen and raloxifene as preventive therapy for women at increased risk of breast cancer was approved by the National Institute for Health and Care Excellence (NICE) in 2013. We undertook a qualitative investigation to investigate the factors affecting the implementation of preventive therapy within the UK. Methods: We recruited general practitioners (GPs) (n = 10) and clinicians working in family history or clinical genetics settings (FHCG clinicians) (n = 15) to participate in semi-structured interviews. Data were coded thematically within the Consolidated Framework for Implementation Research. Results: FHCG clinicians focussed on the perceived lack of benefit of preventive therapy and difficulties interpreting the NICE guidelines. FHCG clinicians felt poorly informed about preventive therapy, and this discouraged patient discussions on the topic. GPs were unfamiliar with the concept of preventive therapy, and were not aware that they may be asked to prescribe it for high-risk women. GPs were reluctant to initiate therapy because it is not licensed, but were willing to continue a prescription if it had been started in secondary or tertiary care. Conclusions: Barriers to implementing preventive therapy within routine clinical practice are common and could be addressed by engaging all stakeholders during the development of policy documents

Objective Ultrasonic Characterization of Welding Defects Using Physically Based Pattern Recognition Techniques

Computer-based methods for analysing ultrasonic data to distinguish between different defect types have been based on a variety of techniques such as adaptive learning [1], artificial intelligence [2] and statistical pattern recognition [3]. The uncertain classification reliability of these techniques when applied to a range of realistic defect types has, however, often been a significant practical limitation to their use

Salivary androgens in adolescence and their value as a marker of puberty: results from the SCAMP cohort

Context: Salivary androgens represent non-invasive biomarkers of puberty that may have utility in clinical and population studies. Objective: To understand normal age-related variation in salivary sex steroids and demonstrate their correlation to pubertal development in young adolescents. Design, Setting, and participants: School-based cohort study of 1,495 adolescents at two time points for collecting saliva samples approximately two years apart. Outcome measures: The saliva samples were analyzed for five androgens (testosterone, androstenedione (A4), 17-hydroxyprogesterone (17-OHP), 11-ketotestosterone (11-KT) and 11β-hydroxyandrostenedione (11-OHA4)) using LC-MS/MS; in addition, salivary dehydroepiandrosterone (DHEA) and oestradiol (OE2) were analyzed by ELISA. Pubertal staging was self-reported using the pubertal development scale (PDS). Results: In 1,236 saliva samples from 903 boys aged between 11-16 years, salivary androgens except DHEA exhibited an increasing trend with an advancing age (ANOVA, p<0.001), with salivary testosterone and A4 concentration showing the strongest correlation (r=0.55, p<0.001 and r=0.48, p<0.001, respectively). In a subgroup analysis of 155 and 63 saliva samples in boys and girls, respectively morning salivary testosterone concentrations showed the highest correlation with composite PDS scores and voice-breaking category from PDS self-report in boys (r=0.75, r=0.67, respectively). In girls, salivary DHEA and OE2 had negligible correlations with age or composite PDS scores. Conclusion: In boys aged 11-16 years, increase in salivary testosterone and A4 is associated with self-reported pubertal progress and represent valid non-invasive biomarkers of puberty in boys

Chimpanzee Autarky

Background: Economists believe that barter is the ultimate cause of social wealth—and even much of our human culture—yet little is known about the evolution and development of such behavior. It is useful to examine the circumstances under which other species will or will not barter to more fully understand the phenomenon. Chimpanzees (Pan troglodytes) are an interesting test case as they are an intelligent species, closely related to humans, and known to participate in reciprocal interactions and token economies with humans, yet they have not spontaneously developed costly barter. Methodology/Principle Findings: Although chimpanzees do engage in noncostly barter, in which otherwise value-less tokens are exchanged for food, this lack of risk is not typical of human barter. Thus, we systematically examined barter in chimpanzees to ascertain under what circumstances chimpanzees will engage in costly barter of commodities, that is, trading food items for other food items with a human experimenter. We found that chimpanzees do barter, relinquishing lower value items to obtain higher value items (and not the reverse). However, they do not trade in all beneficial situations, maintaining possession of less preferred items when the relative gains they stand to make are small. Conclusions/Significance: Two potential explanations for this puzzling behavior are that chimpanzees lack ownership norms, and thus have limited opportunity to benefit from the gains of trade, and that chimpanzees\u27 risk of defection is sufficiently high that large gains must be imminent to justify the risk. Understanding the conditions that support barter in chimpanzees may increase understanding of situations in which humans, too, do not maximize their gains

Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products

We developed a low-cost, high-throughput microbiome profiling method that uses combinatorial sequence tags attached to PCR primers that amplify the rRNA V6 region. Amplified PCR products are sequenced using an Illumina paired-end protocol to generate millions of overlapping reads. Combinatorial sequence tagging can be used to examine hundreds of samples with far fewer primers than is required when sequence tags are incorporated at only a single end. The number of reads generated permitted saturating or near-saturating analysis of samples of the vaginal microbiome. The large number of reads al- lowed an in-depth analysis of errors, and we found that PCR-induced errors composed the vast majority of non-organism derived species variants, an ob- servation that has significant implications for sequence clustering of similar high-throughput data. We show that the short reads are sufficient to assign organisms to the genus or species level in most cases. We suggest that this method will be useful for the deep sequencing of any short nucleotide region that is taxonomically informative; these include the V3, V5 regions of the bac- terial 16S rRNA genes and the eukaryotic V9 region that is gaining popularity for sampling protist diversity.Comment: 28 pages, 13 figure

Diminished temperature and vegetation seasonality over northern high latitudes

Global temperature is increasing, especially over northern lands (>50° N), owing to positive feedbacks1. As this increase is most pronounced in winter, temperature seasonality (ST)—conventionally defined as the difference between summer and winter temperatures—is diminishing over time2, a phenomenon that is analogous to its equatorward decline at an annual scale. The initiation, termination and performance of vegetation photosynthetic activity are tied to threshold temperatures3. Trends in the timing of these thresholds and cumulative temperatures above them may alter vegetation productivity, or modify vegetation seasonality (SV), over time. The relationship between ST and SV is critically examined here with newly improved ground and satellite data sets. The observed diminishment of ST and SV is equivalent to 4° and 7° (5° and 6°) latitudinal shift equatorward during the past 30 years in the Arctic (boreal) region. Analysis of simulations from 17 state-of-the-art climate models4 indicates an additional STdiminishment equivalent to a 20° equatorward shift could occur this century. How SV will change in response to such large projected ST declines and the impact this will have on ecosystem services5 are not well understood. Hence the need for continued monitoring6 of northern lands as their seasonal temperature profiles evolve to resemble thosefurther south.Lopullinen vertaisarvioitu käsikirjoitu

Clustering exact matches of pairwise sequence alignments by weighted linear regression

<p>Abstract</p> <p>Background</p> <p>At intermediate stages of genome assembly projects, when a number of contigs have been generated and their validity needs to be verified, it is desirable to align these contigs to a reference genome when it is available. The interest is not to analyze a detailed alignment between a contig and the reference genome at the base level, but rather to have a rough estimate of where the contig aligns to the reference genome, specifically, by identifying the starting and ending positions of such a region. This information is very useful in ordering the contigs, facilitating post-assembly analysis such as gap closure and resolving repeats. There exist programs, such as BLAST and MUMmer, that can quickly align and identify high similarity segments between two sequences, which, when seen in a dot plot, tend to agglomerate along a diagonal but can also be disrupted by gaps or shifted away from the main diagonal due to mismatches between the contig and the reference. It is a tedious and practically impossible task to visually inspect the dot plot to identify the regions covered by a large number of contigs from sequence assembly projects. A forced global alignment between a contig and the reference is not only time consuming but often meaningless.</p> <p>Results</p> <p>We have developed an algorithm that uses the coordinates of all the exact matches or high similarity local alignments, clusters them with respect to the main diagonal in the dot plot using a weighted linear regression technique, and identifies the starting and ending coordinates of the region of interest.</p> <p>Conclusion</p> <p>This algorithm complements existing pairwise sequence alignment packages by replacing the time-consuming seed extension phase with a weighted linear regression for the alignment seeds. It was experimentally shown that the gain in execution time can be outstanding without compromising the accuracy. This method should be of great utility to sequence assembly and genome comparison projects.</p

GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics

A large number of sensitive homology searches are required for mapping DNA sequence fragments to known protein sequences in public and private databases during metagenomic analysis. BLAST is currently used for this purpose, but its calculation speed is insufficient, especially for analyzing the large quantities of sequence data obtained from a next-generation sequencer. However, faster search tools, such as BLAT, do not have sufficient search sensitivity for metagenomic analysis. Thus, a sensitive and efficient homology search tool is in high demand for this type of analysis.We developed a new, highly efficient homology search algorithm suitable for graphics processing unit (GPU) calculations that was implemented as a GPU system that we called GHOSTM. The system first searches for candidate alignment positions for a sequence from the database using pre-calculated indexes and then calculates local alignments around the candidate positions before calculating alignment scores. We implemented both of these processes on GPUs. The system achieved calculation speeds that were 130 and 407 times faster than BLAST with 1 GPU and 4 GPUs, respectively. The system also showed higher search sensitivity and had a calculation speed that was 4 and 15 times faster than BLAT with 1 GPU and 4 GPUs.We developed a GPU-optimized algorithm to perform sensitive sequence homology searches and implemented the system as GHOSTM. Currently, sequencing technology continues to improve, and sequencers are increasingly producing larger and larger quantities of data. This explosion of sequence data makes computational analysis with contemporary tools more difficult. We developed GHOSTM, which is a cost-efficient tool, and offer this tool as a potential solution to this problem

A Blast Wave from the 1843 Eruption of Eta Carinae

Very massive stars shed much of their mass in violent precursor eruptions as luminous blue variables (LBVs) before reaching their most likely end as supernovae, but the cause of LBV eruptions is unknown. The 19th century eruption of Eta Carinae, the prototype of these events, ejected about 12 solar masses at speeds of 650 km/s, with a kinetic energy of almost 10^50 ergs. Some faster material with speeds up to 1000-2000 km/s had previously been reported but its full distribution was unknown. Here I report observations of much faster material with speeds up to 3500-6000 km/s, reaching farther from the star than the fastest material in earlier reports. This fast material roughly doubles the kinetic energy of the 19th century event, and suggests that it released a blast wave now propagating ahead of the massive ejecta. Thus, Eta Car's outer shell now mimics a low-energy supernova remnant. The eruption has usually been discussed in terms of an extreme wind driven by the star's luminosity, but fast material reported here suggests that it was powered by a deep-seated explosion rivalling a supernova, perhaps triggered by the pulsational pair instability. This may alter interpretations of similar events seen in other galaxies.Comment: 10 pages, 3 color figs, supplementary information. Accepted by Natur