Embarrassingly Parallel Search

International audienceWe propose the Embarrassingly Parallel Search, a simple and efficient method for solving constraint programming problems in parallel. We split the initial problem into a huge number of independent subproblems and solve them with available workers (i.e., cores of machines). The decomposition into subproblems is computed by selecting a subset of variables and by enumerating the combinations of values of these variables that are not detected inconsistent by the propagation mechanism of a CP Solver. The experiments on satisfaction problems and on optimization problems suggest that generating between thirty and one hundred subproblems per worker leads to a good scalability. We show that our method is quite competitive with the work stealing approach and able to solve some classical problems at the maximum capacity of the multi-core machines. Thanks to it, a user can parallelize the resolution of its problem without modifying the solver or writing any parallel source code and can easily replay the resolution of a problem

SAMSA: a comprehensive metatranscriptome analysis pipeline

BackgroundAlthough metatranscriptomics-the study of diverse microbial population activity based on RNA-seq data-is rapidly growing in popularity, there are limited options for biologists to analyze this type of data. Current approaches for processing metatranscriptomes rely on restricted databases and a dedicated computing cluster, or metagenome-based approaches that have not been fully evaluated for processing metatranscriptomic datasets. We created a new bioinformatics pipeline, designed specifically for metatranscriptome dataset analysis, which runs in conjunction with Metagenome-RAST (MG-RAST) servers. Designed for use by researchers with relatively little bioinformatics experience, SAMSA offers a breakdown of metatranscriptome transcription activity levels by organism or transcript function, and is fully open source. We used this new tool to evaluate best practices for sequencing stool metatranscriptomes.ResultsWorking with the MG-RAST annotation server, we constructed the Simple Annotation of Metatranscriptomes by Sequence Analysis (SAMSA) software package, a complete pipeline for the analysis of gut microbiome data. SAMSA can summarize and evaluate raw annotation results, identifying abundant species and significant functional differences between metatranscriptomes. Using pilot data and simulated subsets, we determined experimental requirements for fecal gut metatranscriptomes. Sequences need to be either long reads (longer than 100 bp) or joined paired-end reads. Each sample needs 40-50 million raw sequences, which can be expected to yield the 5-10 million annotated reads necessary for accurate abundance measures. We also demonstrated that ribosomal RNA depletion does not equally deplete ribosomes from all species within a sample, and remaining rRNA sequences should be discarded. Using publicly available metatranscriptome data in which rRNA was not depleted, we were able to demonstrate that overall organism transcriptional activity can be measured using mRNA counts. We were also able to detect significant differences between control and experimental groups in both organism transcriptional activity and specific cellular functions.ConclusionsBy making this new pipeline publicly available, we have created a powerful new tool for metatranscriptomics research, offering a new method for greater insight into the activity of diverse microbial communities. We further recommend that stool metatranscriptomes be ribodepleted and sequenced in a 100 bp paired end format with a minimum of 40 million reads per sample

Survival of phyllosticta citricarpa, anamorph of the citrus black spot pathogen

Please read the abstract in the section 06resume of this documentDissertation (MSc)--University of Pretoria, 2008.Microbiology and Plant Pathologyunrestricte

Theory Learning with Symmetry Breaking

This paper investigates the use of a Prolog coded SMT solver in tackling a well known constraints problem, namely packing a given set of consecutive squares into a given rectangle, and details the developments in the solver that this motivates. The packing problem has a natural model in the theory of quantifier-free integer difference logic, a theory supported by many SMT solvers. The solver used in this work exploits a data structure consisting of an incremental Floyd-Warshall matrix paired with a watch matrix that monitors the entailment status of integer difference constraints. It is shown how this structure can be used to build unsatisfiable theory cores on the fly, which in turn allows theory learning to be incorporated into the solver. Further, it is shown that a problem-specific and non-standard approach to learning can be taken where symmetry breaking is incorporated into the learning stage, magnifying the effect of learning. It is argued that the declarative framework allows the solver to be used in this white box manner and is a strength of the solver. The approach is experimentally evaluated

Hypertriglyceridaemia in adolescents may have serious complications

Acute pancreatitis is an often-overlooked cause of acute abdominal pain in children and adolescents. Severe hypertriglyceridaemia is an important cause of recurrent acute pancreatitis. Monogenic causes of hypertriglyceridaemia, such as familial chylomicronaemia caused by lipoprotein lipase deficiency, are more frequently encountered in children and adolescents, but remain rare. Polygenic hypertriglyceridaemia is more common, but may require a precipitant before manifesting. With the global increase in obesity and type 2 diabetes, secondary causes of hypertriglyceridaemia in children and adolescents are increasing. We report two cases of severe hypertriglyceridaemia and pancreatitis in adolescent females. Hypertriglyceridaemia improved markedly with restriction of dietary fat. An inhibitor to lipoprotein lipase was found to be the cause in one patient, while in the other limited genetic investigation excluded chylomicronaemia owing to deficiency of lipoprotein lipase, its activators and processing proteins

Entropy-based analysis of the number partitioning problem

In this paper we apply the multicanonical method of statistical physics on the number-partitioning problem (NPP). This problem is a basic NP-hard problem from computer science, and can be formulated as a spin-glass problem. We compute the spectral degeneracy, which gives us information about the number of solutions for a given cost $E$ and cardinality $m$. We also study an extension of this problem for $Q$ partitions. We show that a fundamental difference on the spectral degeneracy of the generalized ($Q>2$) NPP exists, which could explain why it is so difficult to find good solutions for this case. The information obtained with the multicanonical method can be very useful on the construction of new algorithms.Comment: 6 pages, 4 figure

Compression forces used in the Norwegian Breast Cancer Screening Program

Objectives: Compression is used in mammography to reduce breast thickness, which is claimed to improve image quality and reduce radiation dose. In the Norwegian Breast Cancer Screening Program (NBCSP), the recommended range of compression force for full field digital mammography is 11-18 kg (108-177 Newton [N]). This is the first study to investigate the compression force used in the program. Methods: The study included information from 17,951 randomly selected women screened with FFDM at 14 breast centres in the NBCSP, January-March 2014. We investigated the applied compression force on left breast in craniocaudal (CC) and mediolateral oblique (MLO) view for breast centres, mammography machines within the breast centres and for the radiographers. Results: The mean compression force for all mammograms in the study was 116N and ranged from 91 to 147N between the breast centres. The variation in compression force was wider between the breast centres than between mammography machines (range 137-155N) and radiographers (95-143N) within one breast centre. Approximately 59% of the mammograms in the study complied with the recommended range of compression force. Conclusions: A wide variation in applied compression force was observed between the breast centres in the NBCSP. This variation indicates a need for evidence-based recommendations for compression force aimed at optimizing the image quality and individualising breast compression. Advances in knowledge: There was a wide variation in applied compression force between the breast centres in the NBCSP. The variation was wider between the breast centres than between mammography machines and radiographers within one breast centre

Synthesis and Optimization of Reversible Circuits - A Survey

Reversible logic circuits have been historically motivated by theoretical research in low-power electronics as well as practical improvement of bit-manipulation transforms in cryptography and computer graphics. Recently, reversible circuits have attracted interest as components of quantum algorithms, as well as in photonic and nano-computing technologies where some switching devices offer no signal gain. Research in generating reversible logic distinguishes between circuit synthesis, post-synthesis optimization, and technology mapping. In this survey, we review algorithmic paradigms --- search-based, cycle-based, transformation-based, and BDD-based --- as well as specific algorithms for reversible synthesis, both exact and heuristic. We conclude the survey by outlining key open challenges in synthesis of reversible and quantum logic, as well as most common misconceptions.Comment: 34 pages, 15 figures, 2 table