Search results for: Whole genome amplification (WGA)

Authors: Markus Reichhartinger, Martin Horn

Abstract:

In this paper, the application of sliding-mode control to a permanent-magnet synchronous motor (PMSM) is presented. The control design is based on a generic mathematical model of the motor. Some dynamics of the motor and of the power amplification stage remain unmodelled. This model uncertainty is estimated in realtime. The estimation is based on the differentiation of measured signals using the ideas of robust exact differentiator (RED). The control law is implemented on an industrial servo drive. Simulations and experimental results are presented and compared to the same control strategy without uncertainty estimation. It turns out that the proposed concept is superior to the same control strategy without uncertainty estimation especially in the case of non-smooth reference signals.

Keywords: sliding-mode control, Permanent-magnet synchronous motor, uncertainty estimation, robust exact differentiator.

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Authors: Robert I. Nigmatulin, Raisa Kh. Bolotnova, Nailya K. Vakhitova, Andrey S. Topolnikov, Svetlana I. Konovalova, Nikolai A. Makhota

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The theoretical investigation is carried out to describe the effect of increase of pressure waves amplitude in clean and bubbly liquid. The goal of the work is to capture the regime of multiple magnification of acoustic and shock waves in the liquid, which enables to get appropriate conditions to enlarge collapses of micro-bubbles. The influence of boundary conditions and frequency of the governing acoustic field is studied for the case of the cylindrical acoustic resonator. It has been observed the formation of standing waves with large amplitude at resonant frequencies. The interaction of the compression wave with gas and vapor bubbles is investigated for the convergent channel. It is shown theoretically that the chemical reactions, which occur inside gas bubbles, provide additional impulse to the wave, that affect strongly on the collapses of the vapor bubbles

Keywords: acoustics, cavitation, detonation, shock waves

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Authors: Hassan H. Abuelhassan, M. Ali Badawi, Abdelrahman A. Elbadawi, Adam A. Elbashir

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In this paper, the effect of the injected current and temperature into the output power of the laser diode module operating at 808nm were applied, studied and discussed. Low power diode laser was employed as a source. The experimental results were demonstrated and then the output power of laser diode module operating at 808nm was clearly changed by the thermal temperature and injected current. The output power increases by the increasing the injected current and temperature. We also showed that the increasing of the injected current results rising in heat, which also, results into decreasing of the laser diode output power during the highest temperature as well. The best ranges of characteristics made by diode module operating at 808nm were carefully handled and determined.

Keywords: Laser diode, light amplification, injected current, output power.

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Authors: Abbas Ali Mahmood Karwi

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For gamma radiation detection, assemblies having scintillation crystals and a photomultiplier tube, also there is a preamplifier connected to the detector because the signals from photomultiplier tube are of small amplitude. After pre-amplification the signals are sent to the amplifier and then to the multichannel analyser. The multichannel analyser sorts all incoming electrical signals according to their amplitudes and sorts the detected photons in channels covering small energy intervals. The energy range of each channel depends on the gain settings of the multichannel analyser and the high voltage across the photomultiplier tube. The exit spectrum data of the two main isotopes studied ,putting data in biomass program ,process it by Matlab program to get the solid holdup image (solid spherical nuclear fuel)

Keywords: Multichannel analyzer, Spectrum, Energies, Fluids holdup, Image

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Authors: Wisam H. Benamer, Ehab A. Elfallah, Mohamed A. Elshaari, Farag A. Elshaari

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A challenge for laboratories is to provide bacterial identification and antibiotic sensitivity results within a short time. Hence, advancement in the required technology is desirable to improve timing, accuracy and quality. Even with the current advances in methods used for both phenotypic and genotypic identification of bacteria the need is there to develop method(s) that enhance the outcome of bacteriology laboratories in accuracy and time. The hypothesis introduced here is based on the assumption that the chromosome of any bacteria contains unique sequences that can be used for its identification and typing. The outcome of a pilot study designed to test this hypothesis is reported in this manuscript. Methods: The complete chromosome sequences of several bacterial species were downloaded to use as search targets for unique sequences. Visual basic and SQL server (2014) were used to generate a complete set of 18-base long primers, a process started with reverse translation of randomly chosen 6 amino acids to limit the number of the generated primers. In addition, the software used to scan the downloaded chromosomes using the generated primers for similarities was designed, and the resulting hits were classified according to the number of similar chromosomal sequences, i.e., unique or otherwise. Results: All primers that had identical/similar sequences in the selected genome sequence(s) were classified according to the number of hits in the chromosomes search. Those that were identical to a single site on a single bacterial chromosome were referred to as unique. On the other hand, most generated primers sequences were identical to multiple sites on a single or multiple chromosomes. Following scanning, the generated primers were classified based on ability to differentiate between medically important bacterial and the initial results looks promising. Conclusion: A simple strategy that started by generating primers was introduced; the primers were used to screen bacterial genomes for match. Primer(s) that were uniquely identical to specific DNA sequence on a specific bacterial chromosome were selected. The identified unique sequence can be used in different molecular diagnostic techniques, possibly to identify bacteria. In addition, a single primer that can identify multiple sites in a single chromosome can be exploited for region or genome identification. Although genomes sequences draft of isolates of organism DNA enable high throughput primer design using alignment strategy, and this enhances diagnostic performance in comparison to traditional molecular assays. In this method the generated primers can be used to identify an organism before the draft sequence is completed. In addition, the generated primers can be used to build a bank for easy access of the primers that can be used to identify bacteria.

Keywords: Bacteria chromosome, bacterial identification, sequence, primer generation.

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Authors: M. R. Aghaebrahimi, S. H. Zahiri, M. Amiri

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The necessity of solving multi dimensional complicated scientific problems beside the necessity of several objective functions optimization are the most motive reason of born of artificial intelligence and heuristic methods. In this paper, we introduce a new method for multiobjective optimization based on learning automata. In the proposed method, search space divides into separate hyper-cubes and each cube is considered as an action. After gathering of all objective functions with separate weights, the cumulative function is considered as the fitness function. By the application of all the cubes to the cumulative function, we calculate the amount of amplification of each action and the algorithm continues its way to find the best solutions. In this Method, a lateral memory is used to gather the significant points of each iteration of the algorithm. Finally, by considering the domination factor, pareto front is estimated. Results of several experiments show the effectiveness of this method in comparison with genetic algorithm based method.

Keywords: Function optimization, Multiobjective optimization, Learning automata.

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Authors: M. Amelsakhi, A. Sohrabi-Bidar, A. Shareghi

Abstract:

One of the most important issues about the structural damages caused by earthquake is the evaluating of the spectral response of the site on which the construction is built. This fact has demonstrated during many earlier earthquakes and many researchers’ reports have concerned with it. According to these reports, features of the site materials and geometry of the ground surface are considered the main factors. This study concentrates on the specific form of topographies like hills. Assessing of spectral responses of different points on the hills and beside demonstrates considerable differences between 1D and 2D methods of geotechnical analyses. A general trend of amplifications on the top of the hills and de-amplifications near the toe of the hills has been appeared within the acceleration, velocity and displacement response spectrums of horizontal motion. Evaluating of spectral responses of different sizes of the hills revealed that as much as the hill-size enlarges differences between spectral responses of 1D and 2D analyses transfers to longer range of periods and becomes wider.

Keywords: Topography effect, Amplification ratio, Response spectrum.

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Authors: M. Michael Gromiha, Y. Yabuki, K. Imai, P. Horton, K. Fukui

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We have developed a database for membrane protein functions, which has more than 3000 experimental data on functionally important amino acid residues in membrane proteins along with sequence, structure and literature information. Further, we have proposed different methods for identifying membrane proteins based on their functions: (i) discrimination of membrane transport proteins from other globular and membrane proteins and classifying them into channels/pores, electrochemical and active transporters, and (ii) β-signal for the insertion of mitochondrial β-barrel outer membrane proteins and potential targets. Our method showed an accuracy of 82% in discriminating transport proteins and 68% to classify them into three different transporters. In addition, we have identified a motif for targeting β-signal and potential candidates for mitochondrial β-barrel membrane proteins. Our methods can be used as effective tools for genome-wide annotations.

Keywords: Membrane proteins, database, transporters, discrimination, β-signal.

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Authors: Jędrzej Minda

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In aviation a very narrow spectrum of control inceptors exists, namely centre-sticks, side-sticks, pedals and yokes. However, new types of aircraft are emerging and with them a need for new inceptors. A manned multicopter created at AGH University of Science and Technology is an aircraft in which the pilot takes a specific orientation in which classical inceptors may be impractical to use. In this paper unique kind of control inceptor is described, which aims to provide a handling quality not unlike standard solutions and provide a firm grip point for the pilot without the risk of involuntary stick movement. Simulations of pilot-inceptor model were performed in order to compare dynamic amplification factors of design described in this paper with classical one. Functional prototype is built on which drone pilots carried out a comfort of use evaluation. This paper provides a general overview of the project, including literature review, reasoning behind components selection and mechanism design finalized by conclusions.

Keywords: Mechanisms, mechatronics, embedded control, serious gaming, rescue missions, rescue robotics.

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Authors: Kelvin Rozier, Vladimir E. Bondarenko

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It is known that an analog Hopfield neural network with time delay can generate the outputs which are similar to the human electroencephalogram. To gain deeper insights into the mechanisms of rhythm generation by the Hopfield neural networks and to study the effects of noise on their activities, we investigated the behaviors of the networks with symmetric and asymmetric interneuron connections. The neural network under the study consists of 10 identical neurons. For symmetric (fully connected) networks all interneuron connections aij = +1; the interneuron connections for asymmetric networks form an upper triangular matrix with non-zero entries aij = +1. The behavior of the network is described by 10 differential equations, which are solved numerically. The results of simulations demonstrate some remarkable properties of a Hopfield neural network, such as linear growth of outputs, dependence of synchronization properties on the connection type, huge amplification of oscillation by the external uniform noise, and the capability of the neural network to transform one type of noise to another.

Keywords: Chaos, Hopfield neural network, noise, synchronization

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Authors: Rajlaxmi Chouhan, Pritee Khanna

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In this manuscript, a wavelet-based blind watermarking scheme has been proposed as a means to provide security to authenticity of a fingerprint. The information used for identification or verification of a fingerprint mainly lies in its minutiae. By robust watermarking of the minutiae in the fingerprint image itself, the useful information can be extracted accurately even if the fingerprint is severely degraded. The minutiae are converted in a binary watermark and embedding these watermarks in the detail regions increases the robustness of watermarking, at little to no additional impact on image quality. It has been experimentally shown that when the minutiae is embedded into wavelet detail coefficients of a fingerprint image in spread spectrum fashion using a pseudorandom sequence, the robustness is observed to have a proportional response while perceptual invisibility has an inversely proportional response to amplification factor “K". The DWT-based technique has been found to be very robust against noises, geometrical distortions filtering and JPEG compression attacks and is also found to give remarkably better performance than DCT-based technique in terms of correlation coefficient and number of erroneous minutiae.

Keywords: Fingerprint watermarking, minutiae, discrete wavelet transform, PN sequence

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Authors: Aaron Aboshio, Jianqioa Ye

Abstract:

In this study, static and dynamic responses of a typical reinforced concrete solid slab, designed to British Standard (BS 8110: 1997) and under self and live loadings for dance halls are reported. Linear perturbation analysis using finite element method was employed for modal, impulse loading and frequency response analyses of the slab under the aforementioned loading condition. Results from the static and dynamic analyses, comprising of the slab fundamental frequencies and mode shapes, dynamic amplification factor, maximum deflection, stress distributions among other valuable outcomes are presented and discussed. These were gauged with the limiting provisions in the design code with a view of justifying valid optimization objective function for the structure that can ensure both adequate strength and economical section for large clear span slabs. This is necessary owing to the continued increase in cost of erecting building structures and the squeeze on public finance globally.

Keywords: Economical design, Finite element method, Modal dynamics, Reinforced concrete, Slab.

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Authors: Ismail, N., Sarijan, S

Abstract:

The phylogenetic analysis using the most conservative portions of 18S rRNA gene revealed the phylogenetic relationship among the two populations where DNA divergence showed that the nucleotides diversity value were -0.00838 for the Tanjung Dawai, Kedah and -0.00708 for the Cherating, Pahang populations respectively. The net nucleotide divergence among populations (Da) was -0.0073 indicating a low polymorphism among the populations studied. Total number of mutations in the Tanjung Dawai, Kedah samples was higher than Cherating, Pahang samples, which are 73 and 59 respectively while shared mutations across the populations were 8, and reveal the evolutionary in the genome of Malaysian T. gigas. The tree topology of both populations inferred using Neigbour-joining method by comparing 1791 bp of partial 18S rRNA sequence revealed that T. gigas haplotypes were clustered into seven clades, suggesting that they are genetically diverse among populations which derived from a common ancestor.

Keywords: Horseshoe crabs, Tachypleus gigas, 18S rRNA genesequences, phylogenetic analysis

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Authors: Yuhong Lu

Abstract:

Graves’ Disease (GD), an autoimmune health condition caused by the over reactiveness of the thyroid, affects about 1 in 200 people worldwide. GD is not caused by one specific single nucleotide polymorphism (SNP) or gene mutation, but rather determined by multiple factors, each differing from each other. Malfunction of the genes in Human Leukocyte Antigen (HLA) family tend to play a major role in autoimmune diseases, but other genes, such as LOC101929163, have functions that still remain ambiguous. Currently, little studies were done to study GD, resulting in inconclusive results. This study serves not only to introduce background knowledge about GD, but also to organize and pinpoint the major SNPs and genes that are potentially related to the occurrence of GD in humans. Collected from multiple sources from genome-wide association studies (GWAS) Central, the potential SNPs related to the causes of GD are included in this study. This study has located the genes that are related to those SNPs and closely examines a selected sample. Using the data from this study, scientists will then be able to focus on the most expressed genes in GD patients and develop a treatment for GD.

Keywords: CTLA4, Graves’ Disease, HLA, single nucleotide polymorphism, SNP.

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Authors: M. Najafi

Abstract:

In the present paper, a large turbo-generator shaft train including a heavy-duty gas turbine engine, a coupling, and a generator is established. The method of analysis is based on finite element simplified model for lateral and torsional vibration calculation. The basic elements of rotor are the shafts and the disks which are represented as circular cross section flexible beams and rigid body elements, respectively. For more accurate results, the gyroscopic effect and bearing dynamics coefficients and function of rotation are taken into account, and for the influence of shear effect, rotor has been modeled in the form of Timoshenko beam. Lateral critical speeds, critical speed map, damped mode shapes, Campbell diagram, zones of instability, amplitudes, phase angles response due to synchronous forces of excitation and amplification factor are calculated. Also, in the present paper, the effect of imbalanced rotor and effects of changing in internal force and temperature are studied.

Keywords: Rotor dynamic analysis, Finite element method, shaft train, Campbell diagram.

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Authors: T.C.Manjunath, Ph.D., Ashok Kusagur, Shruthi Sanjay, Saritha Sindushree, C. Ardil

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This paper deals with the design, development & implementation of a temperature sensor using zigbee. The main aim of the work undertaken in this paper is to sense the temperature and to display the result on the LCD using the zigbee technology. ZigBee operates in the industrial, scientific and medical (ISM) radio bands; 868 MHz in Europe, 915 MHz in the USA and 2.4 GHz in most jurisdictions worldwide. The technology is intended to be simpler and cheaper than other WPANs such as Bluetooth. The most capable ZigBee node type is said to require only about 10 % of the software of a typical Bluetooth or Wireless Internet node, while the simplest nodes are about 2 %. However, actual code sizes are much higher, more like 50 % of the Bluetooth code size. ZigBee chip vendors have announced 128-kilobyte devices. In this work undertaken in the design & development of the temperature sensor, it senses the temperature and after amplification is then fed to the micro controller, this is then connected to the zigbee module, which transmits the data and at the other end the zigbee reads the data and displays on to the LCD. The software developed is highly accurate and works at a very high speed. The method developed shows the effectiveness of the scheme employed.

Keywords: Zigbee, Microcontroller, PIC, Transmitter, Receiver, Synchronous, Blue tooth, Communication.

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Authors: Jafar Ahmadi, Alireza Pour-Aboughadareh

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Wheat is the first and the most important grain of the world and its bakery property is due to glutenin and gliadin qualities. Wheat seed proteins were divided into four groups according to solubility including albumin, globulin, glutenin and prolamin or gliadin. Gliadins are major components of the storage proteins in wheat endosperm. It seems that little information is available about gliadin genes in Iranian wild relatives of wheat. Thus, the aim of this study was the evaluation of the wheat wild relatives collected from different origins of Zagros Mountains in Iran, in terms of coding gliadin genes using specific primers. For this, forty accessions of Triticum boeoticum and Triticum urartu were selected for this study. For each accession, genomic DNA was extracted and PCRs were performed in total volumes of 15 μl. The amplification products were separated on 1.5% agarose gels. In results, for Gli-2A locus three allelic variants were detected by Gli-2As primer pairs. The sizes of PCR products for these alleles were 210, 490 and 700 bp. Only five (13%) and two accessions (5%) produced 700 and 490 bp fragments when their DNA was amplified with the Gli.As.2 primer pairs. However, 93% of the accessions carried allele 210 bp, and only 8% did not any product for this marker. Therefore, these germplasm could be used as rich gene pool to broaden the genetic base of bread wheat.

Keywords: Diploied wheat, gliadin, Triticum boeoticum, Triticum urartu.

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Authors: Boram Kim, Shigeyasu Uno, Kazuo Nakazato

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Continuous-time delta-sigma analog digital converter (ADC) for radio frequency identification (RFID) complementary metal oxide semiconductor (CMOS) biosensor has been reported. This delta-sigma ADC is suitable for digital conversion of biosensor signal because of small process variation, and variable input range. As the input range of continuous-time switched current delta-sigma ADC (Dynamic range : 50 dB) can be limited by using current reference, amplification of biosensor signal is unnecessary. The input range is switched to wide input range mode or narrow input range mode by command of current reference. When the narrow input range mode, the input range becomes ± 0.8 V. The measured power consumption is 5 mW and chip area is 0.31 mm^2 using 1.2 um standard CMOS process. Additionally, automatic input range detecting system is proposed because of RFID biosensor applications.

Keywords: continuous time, delta sigma, A/D converter, RFID, biosensor, CMOS

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Authors: J. Bernasovská, R. Lohajová Behulová, E. Petrejčiková, I. Boroňová, I. Bernasovský

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Y chromosome microdeletions are the most common genetic cause of male infertility and screening for these microdeletions in azoospermic or severely oligospermic men is now standard practice. Analysis of the Y chromosome in men with azoospermia or severe oligozoospermia has resulted in the identification of three regions in the euchromatic part of the long arm of the human Y chromosome (Yq11) that are frequently deleted in men with otherwise unexplained spermatogenic failure. PCR analysis of microdeletions in the AZFa, AZFb and AZFc regions of the human Y chromosome is an important screening tool. The aim of this study was to analyse the type of microdeletions in men with fertility disorders in Slovakia. We evaluated 227 patients with azoospermia and with normal karyotype. All patient samples were analyzed cytogenetically. For PCR amplification of sequence-tagged sites (STS) of the AZFa, AZFb and AZFc regions of the Y chromosome was used Devyser AZF set. Fluorescently labeled primers for all markers in one multiplex PCR reaction were used and for automated visualization and identification of the STS markers we used genetic analyzer ABi 3500xl (Life Technologies). We reported 13 cases of deletions in the AZF region 5,73%. Particular types of deletions were recorded in each region AZFa,b,c .The presence of microdeletions in the AZFc region was the most frequent. The study confirmed that percentage of microdeletions in the AZF region is low in Slovak azoospermic patients, but important from a prognostic view.

Keywords: AZF, male infertility, microdeletions, Y chromosome.

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Authors: Masroor H. S. Bukhari, Z. H. Shah

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The possibility of intrinsic electromagnetic fields within living cells and their resonant self-interaction and interaction with ambient electromagnetic fields is suggested on the basis of a theoretical and experimental study. It is reported that intrinsic electromagnetic fields are produced in the form of radio-frequency and infra-red photons within atoms (which may be coupled or uncoupled) in cellular structures, such as the cell cytoskeleton and plasma membrane. A model is presented for the interaction of these photons among themselves or with atoms under a dipole-dipole coupling, induced by single-photon or two-photon processes. This resonance is manifested by conspicuous field amplification and it is argued that it is possible for these resonant photons to undergo tunnelling in the form of evanescent waves to a short range (of a few nanometers to micrometres). This effect, suggested as a resonant photon tunnelling mechanism in this report, may enable these fields to act as intracellular signal communication devices and as bridges between macromolecules or cellular structures in the cell cytoskeleton, organelles or membrane. A brief overview of an experimental technique and a review of some preliminary results are presented, in the detection of these fields produced in living cell membranes under physiological conditions.

Keywords: bioelectromagnetism, cell membrane, evanescentwaves, photon tunnelling, resonance

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Authors: Mohammad Ahmadinejad, Mohammad Reza Shakibaie, Kyvan Shams, Mohammad Khalili

Abstract:

Legionella pneumophila is involved in more than 95% cases of severe atypical pneumonia. Infection is mainly by inhalation the indoor aerosols through the water-coolant systems. Because some Legionella strains may be viable but not culturable, therefore, Taq polymerase, DNA amplification and semi-nested-PCR were carried out to detect Legionella-specific 16S-rDNA sequence. For this purpose, 1.5 litter of water samples from 77 water-coolant system were collected from four different hospitals, two nursing homes and one student hostel in Kerman city of Iran, each in a brand new plastic bottle during summer season of 2006 (from April to August). The samples were filtered in the sterile condition through the Millipore Membrane Filter. DNA was extracted from membrane and used for PCR to detect Legionella spp. The PCR product was then subjected to semi-nested PCR for detection of L. pneumophila. Out of 77 water samples that were tested by PCR, 30 (39%) were positive for most species of Legionella. However, L. pneumophila was detected from 14 (18.2%) water samples by semi-nested PCR. From the above results it can be concluded that water coolant systems of different hospitals and nursing homes in Kerman city of Iran are highly contaminated with L. pneumophila spp. and pose serious concern. So, we recommend avoiding such type of coolant system in the hospitals and nursing homes.

Keywords: Legionella pneumophila, water-coolant system, semi-nested -PCR.

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Authors: M. Pandi, K. Premalatha

Abstract:

A DNA microarray technology is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. Elucidating the patterns hidden in gene expression data offers a tremendous opportunity for an enhanced understanding of functional genomics. However, the large number of genes and the complexity of biological networks greatly increase the challenges of comprehending and interpreting the resulting mass of data, which often consists of millions of measurements. It is handled by clustering which reveals the natural structures and identifying the interesting patterns in the underlying data. In this paper, gene based clustering in gene expression data is proposed using Cuckoo Search with Differential Evolution (CS-DE). The experiment results are analyzed with gene expression benchmark datasets. The results show that CS-DE outperforms CS in benchmark datasets. To find the validation of the clustering results, this work is tested with one internal and one external cluster validation indexes.

Keywords: DNA, Microarray, genomics, Cuckoo Search, Differential Evolution, Gene expression data, Clustering.

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Authors: A. Galashev

Abstract:

Absorption spectra of infra-red (IR) radiation of the disperse water medium absorbing the most important greenhouse gases: CO2 , N2O , CH4 , C2H2 , C2H6 have been calculated by the molecular dynamics method. Loss of the absorbing ability at the formation of clusters due to a reduction of the number of centers interacting with IR radiation, results in an anti-greenhouse effect. Absorption of O3 molecules by the (H2O)50 cluster is investigated at its interaction with Cl- ions. The splitting of ozone molecule on atoms near to cluster surface was observed. Interaction of water cluster with Cl- ions causes the increase of integrated intensity of emission spectra of IR radiation, and also essential reduction of the similar characteristic of Raman spectrum. Relative integrated intensity of absorption of IR radiation for small water clusters was designed. Dependences of the quantity of weight on altitude for vapor of monomers, clusters, droplets, crystals and mass of all moisture were determined. The anti-greenhouse effect of clusters was defined as the difference of increases of average global temperature of the Earth, caused by absorption of IR radiation by free water molecules forming clusters, and absorption of clusters themselves. The greenhouse effect caused by clusters makes 0.53 K, and the antigreenhouse one is equal to 1.14 K. The increase of concentration of CO2 in the atmosphere does not always correlate with the amplification of greenhouse effect.

Keywords: Greenhouse gases, infrared absorption and Raman spectra, molecular dynamics method, water clusters.

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Authors: Robersy Sánchez, Ricardo Grau

Abstract:

A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D, G, A, U, C}, where the letter D represent one or more hypothetical bases with unspecific pairing. We hypothesized that the high degeneration of a primeval genetic code with five bases and the gradual origin and improvements of a primitive DNA repair system could make possible the transition from the ancient to the modern genetic code. Our results suggest that the Watson-Crick base pairing and the non-specific base pairing of the hypothetical ancestral base D used to define the sum and product operations are enough features to determine the coding constraints of the primeval and the modern genetic code, as well as the transition from the former to the later. Geometrical and algebraic properties of this vector space reveal that the present codon assignment of the standard genetic code could be induced from a primeval codon assignment. Besides, the Fourier spectrum of the extended DNA genome sequences derived from the multiple sequence alignment suggests that the called period-3 property of the present coding DNA sequences could also exist in the ancient coding DNA sequences.

Keywords: Genetic code vector space, primeval genetic code, power spectrum.

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Authors: Fabian Horn, Reinhard Guthke

Abstract:

In molecular biology, microarray technology is widely and successfully utilized to efficiently measure gene activity. If working with less studied organisms, methods to design custom-made microarray probes are available. One design criterion is to select probes with minimal melting temperature variances thus ensuring similar hybridization properties. If the microarray application focuses on the investigation of metabolic pathways, it is not necessary to cover the whole genome. It is more efficient to cover each metabolic pathway with a limited number of genes. Firstly, an approach is presented which minimizes the overall melting temperature variance of selected probes for all genes of interest. Secondly, the approach is extended to include the additional constraints of covering all pathways with a limited number of genes while minimizing the overall variance. The new optimization problem is solved by a bottom-up programming approach which reduces the complexity to make it computationally feasible. The new method is exemplary applied for the selection of microarray probes in order to cover all fungal secondary metabolite gene clusters for Aspergillus terreus.

Keywords: bottom-up approach, gene clusters, melting temperature, metabolic pathway, microarray probe design, probe selection

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Authors: Mizan Ahmed, Srikanth Venkatesan

Abstract:

Geological and tectonic framework indicates that Bangladesh is one of the most seismically active regions in the world. The Bengal Basin is at the junction of three major interacting plates: the Indian, Eurasian, and Burma Plates. Besides there are many active faults within the region, e.g. the large Dauki fault in the north. The country has experienced a number of destructive earthquakes due to the movement of these active faults. Current seismic provisions of Bangladesh are mostly based on earthquake data prior to the 1990. Given the record of earthquakes post 1990, there is a need to revisit the design provisions of the code. This paper compares the base shear demand of three major cities in Bangladesh: Dhaka (the capital city), Sylhet, and Chittagong for earthquake scenarios of magnitudes 7.0MW, 7.5MW, 8.0MW, and 8.5MW using a stochastic model. In particular, the stochastic model allows the flexibility to input region specific parameters such as shear wave velocity profile (that were developed from Global Crustal Model CRUST2.0) and include the effects of attenuation as individual components. Effects of soil amplification were analysed using the Extended Component Attenuation Model (ECAM). Results show that the estimated base shear demand is higher in comparison with code provisions leading to the suggestion of additional seismic design consideration in the study regions.

Keywords: Attenuation, earthquake, ground motion, stochastic, seismic hazard.

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Authors: Yan Ren, Jun Qiao, Xianxia Liu, Pengyan Wang, Qiang Fu, Huijun Shi, Fei Guo, Yuanzhi Wang, Hui Zhang, Jinliang Sheng, Xinli Gu, Xiao-Jun Liu, Chuangfu Chen

Abstract:

As part of national epidemiological survey on bovine viral diarrhea virus (BVDV), a total of 274 dejecta samples were collected from 14 cattle farms in 8 areas of Xinjiang Uygur Autonomous Region in northwestern China. Total RNA was extracted from each sample, and 5--untranslated region (UTR) of BVDV genome was amplified by using two-step reverse transcriptase-polymerase chain reaction (RT-PCR). The PCR products were subsequently sequenced to study the genetic variations of BVDV in these areas. Among the 274 samples, 33 samples were found virus-positive. According to sequence analysis of the PCR products, the 33 samples could be arranged into 16 groups. All the sequences, however, were highly conserved with BVDV Osloss strains. The virus possessed theses sequences belonged to BVDV-1b subtype by phylogenetic analysis. Based on these data, we established a typing tree for BVDV in these areas. Our results suggested that BVDV-1b was a predominant subgenotype in northwestern China and no correlation between the genetic and geographical distances could be observed above the farm level.

Keywords: bovine viral diarrhea virus, molecular epidemiology, phylogenetic analysis.

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Authors: Chih-Hao Chen, Hsing-Chung Lee, Qingdong Ling, Hsiao-Jung Chen, Sun-Chong Wang, Li-Ching Wu, H.C. Lee

Abstract:

Segmentation, filtering out of measurement errors and identification of breakpoints are integral parts of any analysis of microarray data for the detection of copy number variation (CNV). Existing algorithms designed for these tasks have had some successes in the past, but they tend to be O(N2) in either computation time or memory requirement, or both, and the rapid advance of microarray resolution has practically rendered such algorithms useless. Here we propose an algorithm, SAD, that is much faster and much less thirsty for memory – O(N) in both computation time and memory requirement -- and offers higher accuracy. The two key ingredients of SAD are the fundamental assumption in statistics that measurement errors are normally distributed and the mathematical relation that the product of two Gaussians is another Gaussian (function). We have produced a computer program for analyzing CNV based on SAD. In addition to being fast and small it offers two important features: quantitative statistics for predictions and, with only two user-decided parameters, ease of use. Its speed shows little dependence on genomic profile. Running on an average modern computer, it completes CNV analyses for a 262 thousand-probe array in ~1 second and a 1.8 million-probe array in 9 seconds

Keywords: Cancer, pathogenesis, chromosomal aberration, copy number variation, segmentation analysis.

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Authors: Eusebio A. Jiménez-Arévalo, Deifilia Ahuatzi-Chacón, Juvencio Galíndez-Mayer, Cleotilde Juárez-Ramírez, Nora Ruiz-Ordaz

Abstract:

Bendiocarb is a known toxic xenobiotic that presents acute and chronic risks for freshwater invertebrates and estuarine and marine biota; thus, the treatment of water contaminated with the insecticide is of concern. In this paper, a bacterial community with the capacity to grow in bendiocarb as its sole carbon and nitrogen source was isolated by enrichment techniques in batch culture, from samples of a composting plant located in the northeast of Mexico City. Eight cultivable bacteria were isolated from the microbial community, by PCR amplification of 16 rDNA; Pseudoxanthomonas spadix (NC_016147.2, 98%), Ochrobacterium anthropi (NC_009668.1, 97%), Staphylococcus capitis (NZ_CP007601.1, 99%), Bosea thiooxidans. (NZ_LMAR01000067.1, 99%), Pseudomonas denitrificans. (NC_020829.1, 99%), Agromyces sp. (NZ_LMKQ01000001.1, 98%), Bacillus thuringiensis. (NC_022873.1, 97%), Pseudomonas alkylphenolia (NZ_CP009048.1, 98%). NCBI accession numbers and percentage of similarity are indicated in parentheses. These bacteria were regarded as the isolated species for having the best similarity matches. The ability to degrade bendiocarb by the immobilized bacterial community in a packed bed biofilm reactor, using as support volcanic stone fragments (tezontle), was evaluated. The reactor system was operated in batch using mineral salts medium and 30 mg/L of bendiocarb as carbon and nitrogen source. With this system, an overall removal efficiency (η_bend) rounding 90%, was reached.

Keywords: Bendiocarb, biodegradation, biofilm reactor, carbamate insecticide.

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Authors: Liping Jing, Michael K. Ng, Tieyong Zeng

Abstract:

Microarray data profiles gene expression on a whole genome scale, therefore, it provides a good way to study associations between gene expression and occurrence or progression of cancer. More and more researchers realized that microarray data is helpful to predict cancer sample. However, the high dimension of gene expressions is much larger than the sample size, which makes this task very difficult. Therefore, how to identify the significant genes causing cancer becomes emergency and also a hot and hard research topic. Many feature selection algorithms have been proposed in the past focusing on improving cancer predictive accuracy at the expense of ignoring the correlations between the features. In this work, a novel framework (named by SGS) is presented for stable gene selection and efficient cancer prediction . The proposed framework first performs clustering algorithm to find the gene groups where genes in each group have higher correlation coefficient, and then selects the significant genes in each group with Bayesian Lasso and important gene groups with group Lasso, and finally builds prediction model based on the shrinkage gene space with efficient classification algorithm (such as, SVM, 1NN, Regression and etc.). Experiment results on real world data show that the proposed framework often outperforms the existing feature selection and prediction methods, say SAM, IG and Lasso-type prediction model.

Keywords: Gene Selection, Cancer Prediction, Lasso, Clustering, Classification.

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