1,472 research outputs found

    Current trends in chloroplast genome research

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    Chloroplast is an important cellular organelle of autotrophs which has an independent, circular, doublestranded DNA molecule termed as chloroplast genome. The chloroplast DNA (cpDNA) contains essential genes for its maintenance and operation. Several components of the photosystems andproteins involved in biosynthetic pathways are also encoded by the chloroplast genome. Exploring the genetic repository of this organelle is vital due to its conserved nature, small size, persistent gene organization and promising ability for transgenic expression. Therefore, cpDNA sequence information has been instrumental in phylogenetic studies and molecular taxonomy of plants. Chloroplast genome sequencing efforts have being initiated with conventional cloning and chain-termination sequencing technologies. Dedicated databases such as CGDB and GOBASE among others have been established as more and more complete cpDNA sequences are being reported. Presently, elegant molecular biologytechniques including shotgun sequencing, rolling circle amplification (RCA), Amplification, Sequencing and Annotation of Plasteome (ASAP) and Next generation sequencing are being used to accelerate data output. Owing to many fold increase in submission of cpDNA sequences in nucleotide databases, challenges of in-depth data analysis stimulated the emergence of devoted annotation, assembling and phylogenetic software. Recently, reported bioinformatics software for chloroplast genome studiescomprise of DOGMA for annotation, SCAN-SE, ARAGON and PREP suit for RNA analyses and CG viewer for circular map construction/comparative analysis. Faster algorithms for gene-order based phylogenetic reconstruction and bootstrap analysis have attracted the attention of research community. Current trends in sequencing strategies and bioinformatics with reference to chloroplast genomes hold great potential to illuminate more hidden corners of this ancient cell organelle

    Estimation of blood loss during Caesarean section: an audit

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    Objective: To evaluate the blood ordering practice and blood transfusion for Caesarean sections at our institution and to compare the estimated blood loss between anaesthetists and obstetricians.Methods: A review of 126 patients undergoing both elective and emergency Caesarean section was undertaken in 2002. Information collected included the number of blood units cross-matched preoperatively, type of surgery (emergency or elective), type of anaesthesia, parity of the patient, estimated blood loss by both anaesthetists and obstetricians, intraoperative and postoperative transfusion within 48 hours and pre and post operative haemoglobin (Hb) and haemocrit (Hct).Results: A total of 215 units were cross-matched for 126 patients undergoing Caesarean section delivery. A small amount (9.5%) were transfused intraoperatively and 5.5% postoperatively. The average blood loss estimated by anaesthetists was 498 +/- 176 ml and that by obstetricians was 592 +/- 222 ml. The calculated blood loss based on patients blood volume and drop in Hct was 787 +/- 519 ml. The cross-match transfusion ratio was 9.7.CONCLUSION: Only 13% of our patients needed blood transfusion. The mean blood loss was estimated to be more by the obstetricians as compared to the anaesthetists. We recommend that the practice of routine cross-match practice prior to Caesarean section should be re-looked by institutions practicing obstetric anaesthesia

    An open-source software framework for the integrated simulation of structures in fire

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    The traditional methods to understand the development of elevated temperature in a structure, and also the associated structural response, are not representative of realistic fire scenarios. To provide a more accurate and realistic reflection of the fire development, the current paper develops a generic middleware which interfaces between the computational fluid dynamics (CFD) software Fire Dynamics Simulator (FDS) and the finite element (FE) analysis software OpenSees. This framework enables a fully integrated simulation of a realistic fire scenario including the heat transfer through the structure and the resulting thermo-mechanical response. The proposed framework is open-source and freely available and therefore can be used and further developed by researchers and practicing engineers and customised to their requirements. This paper shows validation against two sets of experimental results and one real fire incident. A number of different types of thermal boundary conditions such as gas temperatures and heat fluxes, are obtained from the CFD analysis and are then used in the subsequent heat transfer and thermo-mechanical analysis. The primary advantage of this computational tool is that it provides consultants and designers with the means to undertake large-scale projects requiring performance-based fire engineering solutions

    Comparative genomics of an endophytic Pseudomonas putida isolated from mango orchard.

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    This is the final version of the article. Available from the publisher via the DOI in this record.We analyzed the genome sequence of an endophytic bacterial strain Pseudomonas putida TJI51 isolated from mango bark tissues. Next generation DNA sequencing and short read de novo assembly generated the 5,805,096 bp draft genome of P. putida TJI51. Out of 6,036 protein coding genes in P. putida TJI51 sequences, 4,367 (72%) were annotated with functional specifications, while the remaining encoded hypothetical proteins. Comparative genome sequence analysis revealed that the P. putida TJI51genome contains several regions, not identified in so far sequenced P. putida genomes. Some of these regions were predicted to encode enzymes, including acetylornithine deacetylase, betaine aldehyde dehydrogenase, aldehyde dehydrogenase, benzoylformate decarboxylase, hydroxyacylglutathione hydrolase, and uroporphyrinogen decarboxylase. The genome of P. putida TJI51 contained three nonribosomal peptide synthetase gene clusters. Genome sequence analysis of P. putidaTJI51 identified this bacterium as an endophytic resident. The endophytic fitness might be linked with alginate, which facilitates bacterial colonization in plant tissues. Genome sequence analysis shed light on the presence of a diverse spectrum of metabolic activities and adaptation of this isolate to various niches.This research was financially supported by the Higher Education Commission, Islamabad Pakistan

    Instant dynamic response measurements for crack monitoring in metallic beams

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    This paper investigates the interdependencies of the modal behaviour of a cantilever beam, its dynamic response and crack growth. A methodology is proposed that can predict crack growth in a metallic beam using only its dynamic response. Analytical and numerical relationships are formulated between the fundamental mode and crack growth using the existing literature and finite element analysis (FEA) software, respectively. A relationship between the dynamic response and the modal behaviour is formulated empirically. All three relationships are used to predict crack growth and propagation. The load conditions are considered the same in all of the experiments for both model development and model validation. The predicted crack growth is compared with the visual observations. The overall error is within acceptable limits in all comparisons. The results obtained demonstrate the possibility of diagnosing crack growth in metallic beams at any instant within the operational conditions and environment

    Active Clones: Source Code Clones at Runtime

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    Code cloning is a common programming practice, and there have been aconsiderable amount of research that investigated the implications of code clones onsoftware maintenance using static analysis. However, little has been done to investigatethe runtime implications of code cloning. In this paper we investigate sourcecode clones at runtime, referring to clones as ‘active clones’ if they are invokedwhen a software system is in use. For example, if a particular use u of a systemresults in a clone c being invoked, we say that clone c is active with respect to useu. From this definition and given a set of uses fu1;u2; :::g and clones fc1;c2; :::gwe are able to identify the extent clones are active at runtime and analyze activeclone resource use (e.g., CPU time) and define and calculate a set of active clonemetrics to provide insights into source code cloning implications at runtime. We developeda hybrid static and dynamic analysis technique for detecting and analysingactive clones, and conducted an empirical study on five software systems (HSQLDB,JHotDraw, RText, jEdit and UniCentaoPOS) to validate our approach. We found asmall portion of clones are active during a typical use of a software system, and thatactive clones have the potential for guiding a software developer’s code inspectionactivity during a software maintenance task

    Enhanced Version of Multi-algorithm Genetically Adaptive for Multiobjective optimization

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    Abstract: Multi-objective EAs (MOEAs) are well established population-based techniques for solving various search and optimization problems. MOEAs employ different evolutionary operators to evolve populations of solutions for approximating the set of optimal solutions of the problem at hand in a single simulation run. Different evolutionary operators suite different problems. The use of multiple operators with a self-adaptive capability can further improve the performance of existing MOEAs. This paper suggests an enhanced version of a genetically adaptive multi-algorithm for multi-objective (AMAL-GAM) optimisation which includes differential evolution (DE), particle swarm optimization (PSO), simulated binary crossover (SBX), Pareto archive evolution strategy (PAES) and simplex crossover (SPX) for population evolution during the course of optimization. We examine the performance of this enhanced version of AMALGAM experimentally over two different test suites, the ZDT test problems and the test instances designed recently for the special session on MOEA?s competition at the Congress of Evolutionary Computing of 2009 (CEC?09). The suggested algorithm has found better approximate solutions on most test problems in terms of inverted generational distance (IGD) as the metric indicator. - See more at: http://thesai.org/Publications/ViewPaper?Volume=6&Issue=12&Code=ijacsa&SerialNo=37#sthash.lxkuyzEf.dpu
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