Genetic analysis of east and west coast populations of Penaeus monodon from India based on random amplified polymorphic DNA

The east and west coast populations of wild Penaeus monodon in India were genetically characterized by RAPD analysis using six highly polymorphic primers reported earlier. The average genetic similarities within populations, based on profiles generated by all the six primers, were 0.828 and 0.851 for the east and west coast populations, respectively, values with individual primers ranging from 0.744 to 0.889. The average genetic similarity between populations across all the primers was 0.774. The number of bands found to be polymorphic were 38 (51.35%) and 37 (50.68%) in the east and west coast populations, respectively. Primer 5 yielded the highest level of polymorphism (63.63%) in the east coast population whereas primer 3 yielded the lowest level of polymorphism (36.36%) in the west coast population. The study reveals the existence of genetic variation in P. monodon stocks providing scope for genetic improvement through selective breeding. It also provides baseline data for future work on population structure analysis of P. monodon.

Mutation analysis of a large Chinese pedigree with congenital preaxial polydactyly

Mutations in the long-range limb-specific cis-regulator (ZRS) could cause ectopic shh gene expression and are responsible for preaxial polydactyly (PPD). In this study, we analyzed a large Chinese isolated autosomal dominant PPD pedigree. By fine mapping

Analysis of mitochondrial DNA variants in Japanese patients with schizophrenia

To test the hypothesis that mitochondrial DNA (mtDNA) variants contribute to the susceptibility to schizophrenia, we sequenced the entire mtDNAs from 93 Japanese schizophrenic patients. Three non-synonymous homoplasmic variants in subunit six of the ATP s

Sequencing, annotation and comparative analysis of nine BACs of giant panda (Ailuropoda melanoleuca)

A 10-fold BAC library for giant panda was constructed and nine BACs were selected to generate finish sequences. These BACs could be used as a validation resource for the de novo assembly accuracy of the whole genome shotgun sequencing reads of giant panda newly generated by the Illumina GA sequencing technology. Complete sanger sequencing, assembly, annotation and comparative analysis were carried out on the selected BACs of a joint length 878 kb. Homologue search and de novo prediction methods were used to annotate genes and repeats. Twelve protein coding genes were predicted, seven of which could be functionally annotated. The seven genes have an average gene size of about 41 kb, an average coding size of about 1.2 kb and an average exon number of 6 per gene. Besides, seven tRNA genes were found. About 27 percent of the BAC sequence is composed of repeats. A phylogenetic tree was constructed using neighbor-join algorithm across five species, including giant panda, human, dog, cat and mouse, which reconfirms dog as the most related species to giant panda. Our results provide detailed sequence and structure information for new genes and repeats of giant panda, which will be helpful for further studies on the giant panda.

The evolution of YidC/Oxa/Alb3 family in the three domains of life: a phylogenomic analysis

Background: YidC/Oxa/Alb3 family includes a group of conserved translocases that are essential for protein insertion into inner membranes of bacteria and mitochondria, and thylakoid membranes of chloroplasts. Because mitochondria and chloroplasts are of b

Analysis of CFRP strap-strengthened reinforced concrete beams using the modified compression field theory (MCFT)

External, prestressed carbon fiber reinforced polymer (CFRP) straps can be used to enhance the shear strength of existing reinforced concrete beams. In order to effectively design a strengthening system, a rational predictive theory is required. The current work investigates the ability of the modified compression field theory (MCFT) to predict the behavior of rectangular strap strengthened beams where the discrete CFRP strap forces are approximated as a uniform vertical stress. An unstrengthened control beam and two strengthened beams were tested to verify the predictions. The experimental results suggest that the MCFT could predict the general response of a strengthened beam with a uniform strap spacing < 0.9d. However, whereas the strengthened beams failed in shear, the MCFT predicted flexural failures. It is proposed that a different compression softening model or the inclusion of a crack width limit is required to reflect the onset of shear failures in the strengthened beams.

Cardioviral RNA structure logo analysis: entropy, correlations, and prediction

In recent years, there has been an increased number of sequenced RNAs leading to the development of new RNA databases. Thus, predicting RNA structure from multiple alignments is an important issue to understand its function. Since RNA secondary structures are often conserved in evolution, developing methods to identify covariate sites in an alignment can be essential for discovering structural elements. Structure Logo is a technique established on the basis of entropy and mutual information measured to analyze RNA sequences from an alignment. We proposed an efficient Structure Logo approach to analyze conservations and correlations in a set of Cardioviral RNA sequences. The entropy and mutual information content were measured to examine the conservations and correlations, respectively. The conserved secondary structure motifs were predicted on the basis of the conservation and correlation analyses. Our predictive motifs were similar to the ones observed in the viral RNA structure database, and the correlations between bases also corresponded to the secondary structure in the database.

The analysis of impact forces in randomly vibrating elastic systems

This work is concerned with the characteristics of the impact force produced when two randomly vibrating elastic bodies collide with each other, or when a single randomly vibrating elastic body collides with a stop. The impact condition includes a non-linear spring, which may represent, for example, a Hertzian contact, and in the case of a single body, closed form approximate expressions are derived for the duration and magnitude of the impact force and for the maximum deceleration at the impact point. For the case of two impacting bodies, a set of algebraic equations are derived which can be solved numerically to yield the quantities of interest. The approach is applied to a beam impacting a stop, a plate impacting a stop, and to two impacting beams, and in each case a comparison is made with detailed numerical simulations. Aspects of the statistics of impact velocity are also considered, including the probability that the impact velocity will exceed a specified value within a certain time. © 2012 Elsevier Ltd. All rights reserved.

Analysis of asphalt concrete permeability data using representative pore size

The permeability of asphalt concrete has been the subject of much study by pavement engineers over the last decade. The work undertaken has tended to focus on high air voids as the primary indicator of permeable asphalt concrete. This paper presents a simple approach for understanding the parameters that affect permeability. Principles explained by Taylor in 1956 in channel theory work for soils are used to derive a new parameter-representative pore size. Representative pore size is related to the air voids in the compacted mix and the D75 of the asphalt mix grading curve. Collected Superpave permeability data from published literature and data collected by the writers at the Queensland Department of Transport and Main Roads is shown to be better correlated with representative pore size than air voids, reducing the scatter considerably. Using the database of collected field and laboratory permeability values an equation is proposed that pavement engineers can use to estimate the permeability of in-place pavements. © 2011 ASCE.

Management and Analysis of Unstructured Construction Data Types

Compared with structured data sources that are usually stored and analyzed in spreadsheets, relational databases, and single data tables, unstructured construction data sources such as text documents, site images, web pages, and project schedules have been less intensively studied due to additional challenges in data preparation, representation, and analysis. In this paper, our vision for data management and mining addressing such challenges are presented, together with related research results from previous work, as well as our recent developments of data mining on text-based, web-based, image-based, and network-based construction databases.

Data Analysis on Complicated Construction Data Sources: Vision, Research, and Recent Developments

Compared with construction data sources that are usually stored and analyzed in spreadsheets and single data tables, data sources with more complicated structures, such as text documents, site images, web pages, and project schedules have been less intensively studied due to additional challenges in data preparation, representation, and analysis. In this paper, our definition and vision for advanced data analysis addressing such challenges are presented, together with related research results from previous work, as well as our recent developments of data analysis on text-based, image-based, web-based, and network-based construction sources. It is shown in this paper that particular data preparation, representation, and analysis operations should be identified, and integrated with careful problem investigations and scientific validation measures in order to provide general frameworks in support of information search and knowledge discovery from such information-abundant data sources.

Stall warning by blade pressure signature analysis

At low mass flow rates axial compressors suffer from flow instabilities leading to stall and surge. The inception process of these instabilities has been widely researched in the past - primarily with the aim of predicting or averting stall onset. In recent times, attention has shifted to conditions well before stall and has focussed on the level of irregularity in the blade passing signature in the rotor tip region. In general, this irregularity increases in intensity as the flow rate through the compressor is reduced. Attempts have been made to develop stall warning/avoidance procedures based on the level of the flow irregularity, but little effort has been made to characterise the irregularity, or to understand its underlying causes. Work on this project has revealed for the first time that the increase in irregularity in the blade passing signature is highly dependent on both tip-clearance and eccentricity. In a compressor with small, uniform, tip-clearance, the increase in blade passing irregularity which accompanies a reduction in flow rate will be modest. If the tip-clearance is enlarged, however, there will be a sharp rise in irregularity at all circumferential locations. In a compressor with eccentric tip-clearance, the increase in irregularity will only occur in the part of the annulus where the tip-clearance is largest, regardless of the average clearance level. In this paper, some attention is also given to the question of whether this irregularity observed in the pre-stall flow field is due to random turbulence, or to some form of coherent flow structure. Detailed flow measurements reveal that the latter is the case. From these findings, it is clear that a stall warning system based on blade passing signature irregularity will not be viable in an aero-engine where tip-clearance size and eccentricity change during each flight cycle and over the life of the compressor. Copyright © 2011 by ASME.

Biofluid behaviour in 3D microchannel systems: Numerical analysis and design development of 3D microchannel biochip separators

This paper describes the design and development cycle of a 3D biochip separator and the modelling analysis of flow behaviour in the biochip microchannel features. The focus is on identifying the difference between 2D and 3D implementations as well as developing basic forms of 3D microfluidic separators. Five variants, based around the device are proposed and analysed. These include three variations of the branch channels (circular, rectangular, disc) and two variations of the main channel (solid and concentric). Ignoring the initial transient behaviour and assuming steady state flow has been established, the efficiencies of the flow between the main and side channels for the different designs are analysed and compared with regard to relevant biomicrofluidic laws or effects (bifurcation law, Fahraeus effect, cell-free phenomenon, bending channel effect and laminar flow behaviour). The modelling results identify flow features in microchannels, a constriction and bifurcations and show detailed differences in flow fields between the various designs. The manufacturing process using injection moulding for the initial base case design is also presented and discussed. The work reported here is supported as part of the UK funded 3D-MINTEGRATION project. © 2010 IEEE.

Factor analysis based VTS discriminative adaptive training

Vector Taylor Series (VTS) model based compensation is a powerful approach for noise robust speech recognition. An important extension to this approach is VTS adaptive training (VAT), which allows canonical models to be estimated on diverse noise-degraded training data. These canonical model can be estimated using EM-based approaches, allowing simple extensions to discriminative VAT (DVAT). However to ensure a diagonal corrupted speech covariance matrix the Jacobian (loading matrix) relating the noise and clean speech is diagonalised. In this work an approach for yielding optimal diagonal loading matrices based on minimising the expected KL-divergence between the diagonal loading matrix and "correct" distributions is proposed. The performance of DVAT using the standard and optimal diagonalisation was evaluated on both in-car collected data and the Aurora4 task. © 2012 IEEE.

Stall Warning by Blade Pressure Signature Analysis

At low mass flow rates, axial compressors suffer from flow instabilities leading to stall and surge. The inception process of these instabilities has been widely researched in the past---primarily with the aim of predicting or averting stall onset. In recent times, attention has shifted to conditions well before stall and has focused on the level of irregularity in the blade passing signature in the rotor tip region. In general, the irregularity increases in intensity as the flow rate through the compressor is reduced. Attempts have been made to develop stall warning/avoidance procedures based on the level of flow irregularity, but little effort has been made to characterize the irregularity itself, or to understand its underlying cause. Work on this project has revealed for the first time that the increase in irregularity in the blade passing signature is highly dependent on both tip-clearance size and eccentricity. In a compressor with small, uniform, tip-clearance, the increase in blade passing irregularity that accompanies a reduction in flow rate will be modest. If the tip-clearance is enlarged, however, there will be a sharp rise in irregularity at all circumferential locations. In a compressor with eccentric tip-clearance, the increase in irregularity will only occur in the part of the annulus where the tip-clearance is largest, regardless of the average clearance level. In this paper, some attention is also given to the question of whether the irregularity observed in the prestall flow field is due to random turbulence or to some form of coherent flow structure. Detailed flow measurements reveal that the latter is the case. From these findings, it is clear that a stall warning system based on blade passing signature irregularity would be difficult to implement in an aero-engine where tip-clearance size and eccentricity change during each flight cycle and over the life of the compressor. © 2013 American Society of Mechanical Engineers.