Search results for: distribute amplification technique

Authors: Noureddine Litim

Abstract:

This work is to theoretical and numerical studying the real analysis of the seismic response of the soil with an Elasto-plastic behavior. To perform this analysis, we used different core drilling performed at the tunnel T4 in El Horace section of the highway east-west. The two-dimensional model (2d) was established by the code of finite element plaxis to estimate the displacement amplification and accelerations caused by the seismic wave in the different core drilling and compared with the factor of acceleration given by the RPA (2003) in the area studying. Estimate the displacement amplification and accelerations caused by the seismic wave.

Keywords: seismic response, deposition of soil, plaxis, elasto-plastic

Procedia PDF Downloads 67

Authors: Fathul Mubin, Budi E. Nurcahya

Abstract:

In 2006, a large earthquake ever occurred in the province of Yogyakarta, which caused considerable damage. This is the basis need to investigate the seismic vulnerability index in around of the earthquake zone. This research is called microzonation of earthquake hazard. This research has been conducted at the site and surrounding of Prambanan Temple, includes homes and civil buildings. The reason this research needs to be done because in the event of an earthquake in 2006, there was damage to the temples at Prambanan temple complex and its surroundings. In this research, data collection carried out for 60 minutes using three component seismograph measurements at 165 points with spacing of 1000 meters. The data recorded in time function were analyzed using the spectral ratio method, known as the Horizontal to Vertical Spectral Ratio (HVSR). Results from this analysis are dominant frequency (Fg) and maximum amplification factor (Ag) are used to obtain seismic vulnerability index. The results of research showed the dominant frequency range from 0.5 to 30 Hz and the amplification is in interval from 0.5 to 9. Interval value for seismic vulnerability index is 0.1 to 50. Based on distribution maps of seismic vulnerability index and impact of buildings damage seemed for suitability. For further research, it needs to survey to the east (klaten) and south (Bantul, DIY) to determine a full distribution maps of seismic vulnerability index.

Keywords: amplification factor, dominant frequency, microzonation analysis, seismic vulnerability index

Procedia PDF Downloads 169

Authors: Gurmail Singh

Abstract:

Effective supply chain is the main priority of every organization which is the outcome of strategic corporate investments with deliberate management action. Value-driven supply chain is defined through development, procurement and by configuring the appropriate resources, metrics and processes. However, responsiveness of the supply chain can be improved by proper coordination. So the Bullwhip effect (BWE) and Net stock amplification (NSAmp) values were anticipated and used for the control of inventory in organizations by both discrete wavelet transform-Artificial neural network (DWT-ANN) and Adaptive Network-based fuzzy inference system (ANFIS). This work presents a comparative methodology of forecasting for the customers demand which is non linear in nature for a multilevel supply chain structure using hybrid techniques such as Artificial intelligence techniques including Artificial neural networks (ANN) and Adaptive Network-based fuzzy inference system (ANFIS) and Discrete wavelet theory (DWT). The productiveness of these forecasting models are shown by computing the data from real world problems for Bullwhip effect and Net stock amplification. The results showed that these parameters were comparatively less in case of discrete wavelet transform-Artificial neural network (DWT-ANN) model and using Adaptive network-based fuzzy inference system (ANFIS).

Keywords: bullwhip effect, hybrid techniques, net stock amplification, supply chain flexibility

Procedia PDF Downloads 97

Authors: Donatien Niragira

Abstract:

The progress of technology creates new expectations for patients. The world of deafness is no exception. In recent years, there have been considerable advances in the field of technologies aimed at assisting failing hearing. According to the usual medical vocabulary, hearing aids are actually orthotics. They do not replace an organ but compensate for a functional impairment. The Amplifier Hearing amplification is useful for a large number of people with hearing loss. Hearing aids restore speech audibility. However, their benefits vary depending on the quality of residual hearing. The hearing aid is not a "cure" for deafness. It cannot correct all affected hearing abilities. It should be considered as an aid to communication. The urge to judge from the audiogram alone should be resisted here, as audiometry only indicates the ability to detect non-verbal sounds. To prevent hearing aids from ending up in the drawer, it is important to ensure that the patient's disability situations justify the use of this type of orthosis. If the problems of receptive Pre-fitting counseling are crucial: the person with hearing loss must be informed of the advantages and disadvantages of amplification in his or her case. Their expectations must be realistic. They also need to be aware that the adaptation process requires a good deal of patience and perseverance. They should be informed about the various models and types of hearing aids, including all the aesthetic, functional and financial considerations. If the person's motivation "survives" pre-fitting counseling, we are in the presence of a good candidate for amplification. In addition to its relevance, it shows that the results found in this study significantly improve the quality of audibility in the patient, from where this technology must be made accessible everywhere in the world.

Keywords: auditives protheses, hearing, aids, no medicaly treatable deafnes

Procedia PDF Downloads 21

Authors: Rani Danavath, V. B. Narsimha

Abstract:

Cloud computing is emerging as a new paradigm of large scale distributed computing. Cloud computing is a model for enabling ubiquitous, convenient, on-demand network access to a shared pool of configurable computing resources (e.g., three service models, and four deployment networks, servers, storage, applications, and services) that can be rapidly provisioned and released with minimal management effort or service provider interaction. This cloud model is composed of five essential characteristics models. Load balancing is one of the main challenges in cloud computing, which is required to distribute the dynamic workload across multiple nodes, to ensure that no single node is overloaded. It helps in optimal utilization of resources, enhancing the performance of the system. The goal of the load balancing is to minimize the resource consumption and carbon emission rate, that is the direct need of cloud computing. This determined the need of new metrics energy consumption and carbon emission for energy-efficiency load balancing techniques in cloud computing. Existing load balancing techniques mainly focuses on reducing overhead, services, response time and improving performance etc. In this paper we introduced a Technique for energy-efficiency, but none of the techniques have considered the energy consumption and carbon emission. Therefore, our proposed work will go towards energy – efficiency. So this energy-efficiency load balancing technique can be used to improve the performance of cloud computing by balancing the workload across all the nodes in the cloud with the minimum resource utilization, in turn, reducing energy consumption, and carbon emission to an extent, which will help to achieve green computing.

Keywords: cloud computing, distributed computing, energy efficiency, green computing, load balancing, energy consumption, carbon emission

Procedia PDF Downloads 419

Authors: Yash M. Gupta, Kittisak Buddhachat, Surin Peyachoknagul, Somjit Homchan

Abstract:

The house cricket, Acheta domesticus is one of the commonly found species of field crickets. Although it is very commonly used as food and feed, the genomic information of house cricket is still missing for genetic investigation. DNA sequencing technology has evolved over the decades, and it has also revolutionized the molecular marker development for genetic analysis. In the present study, we have sequenced the whole genome of A. domesticus using illumina platform based HiSeq X Ten sequencing technology for searching simple sequence repeats (SSRs) in DNA to develop polymorphic microsatellite markers for population genetic analysis. A total of 112,157 SSRs with primer pairs were identified, 91 randomly selected SSRs used to check DNA amplification, of which nine primers were polymorphic. These microsatellite markers have shown cross-amplification with other three species of crickets which are Gryllus bimaculatus, Gryllus testaceus and Brachytrupes portentosus. These nine polymorphic microsatellite markers were used to check genetic variation for forty-five individuals of A. domesticus, Phitsanulok population, Thailand. For nine loci, the number of alleles was ranging from 5 to 15. The observed heterozygosity was ranged from 0.4091 to 0.7556. These microsatellite markers will facilitate population genetic analysis for future studies of A. domesticus populations. Moreover, the transferability of these SSR makers would also enable researchers to conduct genetic studies for other closely related species.

Keywords: cross-amplification, microsatellite markers, observed heterozygosity, population genetic, simple sequence repeats

Procedia PDF Downloads 115

Authors: Ting-Ying Su, Meng-Shiou Lee, Shyang-Chwen Sheu

Abstract:

Garlic is used commonly as a seasoning around the world. But some people suffer from allergy to garlic. Garlic may also cause burning of mouth, stomach, and throat. In some Buddhist traditions, consuming garlic is not allowed. The objective of this study is to develop a LAMP based method for detection of garlic in food. We designed specific primers targeted on ITS1-5.8S rRNA-ITS2 sequence of garlic DNA. The LAMP assay was performed using a set of four different primers F3, B3, FIP and BIP at 60˚C in less than 60 mins. Results showed that the primer was not cross-reactive to other commonly used spice including Chinese leek, Chinese onion, green onion, onion, pepper, basil, parsley, pepper and ginger. As low as 2% of garlic DNA could be detected. Garlic still could be detected by developed LAMP after boiled at 100˚C for 80 minutes and autoclaved at 121˚C for 60 minutes. Commercial products labeled with garlic ingredient could be identified by the developed method.

Keywords: garlic, loop-mediated isothermal amplification, processing, DNA

Procedia PDF Downloads 267

Authors: Mina Kalantarzadeh, Claire Lockie-Williams, Caroline Howard

Abstract:

DNA barcoding is increasingly used for identification of medicinal plants worldwide. In the last decade, a large number of DNA barcodes have been generated, and their application in species identification explored. The success of DNA barcoding process relies on the accuracy of the results from polymerase chain reaction (PCR) amplification step which could be negatively affected due to a presence of inhibitors or degraded DNA in herbal samples. An established DNA reference material can be used to support molecular characterisation protocols and prove system suitability, for fast and accurate identification of plant species. The present study describes the use of a novel reference material, the trnH-psbA British Pharmacopoeia Nucleic Acid Reference Material (trnH-psbA BPNARM), which was produced to aid in the identification of Ocimum tenuiflorum L., a widely used herb. During DNA barcoding of O. tenuiflorum, PCR amplifications of isolated DNA produced inconsistent results, suggesting an issue with either the method or DNA quality of the tested samples. The trnH-psbA BPNARM was produced and tested to check for the issues caused during PCR amplification. It was added to the plant material as control DNA before extraction and was co-extracted and amplified by PCR. PCR analyses revealed that the amplification was not as successful as expected which suggested that the amplification is affected by presence of inhibitors co-extracted from plant materials. Various potential issues were assessed during DNA extraction and optimisations were made accordingly. A DNA barcoding protocol for O. tenuiflorum was published in the British Pharmacopoeia 2016, which included the reference sequence. The trnH-psbA BPNARM accelerated degradation test which investigates the stability of the reference material over time demonstrated that it has been stable when stored at 56 °C for a year. Using this protocol and trnH-psbA reference material provides a fast and accurate method for identification of O. tenuiflorum. The optimisations of the DNA extraction using the trnH-psbA BPNARM provided a signposting method which can assist in overcoming common problems encountered when using molecular methods with medicinal plants.

Keywords: degradation, DNA extraction, nucleic acid reference material, trnH-psbA

Procedia PDF Downloads 174

Authors: Niragira Donatien

Abstract:

The progress of technology creates new expectations for patients. The world of deafness is no exception. In recent years, there have been considerable advances in the field of technologies aimed at assisting failing hearing. According to the usual medical vocabulary, hearing aids are actually orthotics. They do not replace an organ but compensate for a functional impairment. The amplifier hearing amplification is useful for a large number of people with hearing loss. Hearing aids restore speech audibility. However, their benefits vary depending on the quality of residual hearing. The hearing aid is not a "cure" for deafness. It cannot correct all affected hearing abilities. It should be considered as an aid to communicate who the best candidates for hearing aids are. The urge to judge from the audiogram alone should be resisted here, as audiometry only indicates the ability to detect non-verbal sounds. To prevent hearing aids from ending up in the drawer, it is important to ensure that the patient's disability situations justify the use of this type of orthosis. If the problems of receptive pre-fitting counselling are crucial, the person with hearing loss must be informed of the advantages and disadvantages of amplification in his or her case. Their expectations must be realistic. They also need to be aware that the adaptation process requires a good deal of patience and perseverance. They should be informed about the various models and types of hearing aids, including all the aesthetic, functional, and financial considerations. If the person's motivation "survives" pre-fitting counselling, we are in the presence of a good candidate for amplification. In addition to its relevance, hearing aids raise other questions: Should one or both ears be fitted? In short, all these questions show that the results found in this study significantly improve the quality of audibility in the patient, from where this technology must be made accessible everywhere in the world. So we want to progress with the technology.

Keywords: audiology, influence, hearing, madicaly, treatable

Procedia PDF Downloads 22

Authors: M. Vivodík, Ž. Balážová, Z. Gálová

Abstract:

The aim of this work was to detect genetic variability among the set of 40 castor genotypes using 8 RAPD markers. Amplification of genomic DNA of 40 genotypes, using RAPD analysis, yielded in 66 fragments, with an average of 8.25 polymorphic fragments per primer. Number of amplified fragments ranged from 3 to 13, with the size of amplicons ranging from 100 to 1200 bp. Values of the polymorphic information content (PIC) value ranged from 0.556 to 0.895 with an average of 0.784 and diversity index (DI) value ranged from 0.621 to 0.896 with an average of 0.798. The dendrogram based on hierarchical cluster analysis using UPGMA algorithm was prepared and analyzed genotypes were grouped into two main clusters and only two genotypes could not be distinguished. Knowledge on the genetic diversity of castor can be used for future breeding programs for increased oil production for industrial uses.

Keywords: dendrogram, polymorphism, RAPD technique, Ricinus communis L.

Procedia PDF Downloads 441

Authors: M. Fares, S. Mameri, I. Abdlani, K. Negara

Abstract:

Neutron detectors in general, proportional counters gas filling based isotope 3He in particular are going to be essential for monitoring and control of certain nuclear facilities, monitoring of experimentation around neutron beams and channels nuclear research reactors, radiation protection instruments and other tools multifaceted exploration and testing of materials, etc. This work consists of a measurement campaign features two Proportional Counters 3He (3He: LND252/USA CP, CP prototype: 3He LND/DDM). This is to make a comparison study of a CP 3He LND252/USA reference one hand, and in the context of routine periodic monitoring of the characteristics of the detectors for controlling the operation especially for laboratory prototypes. In this paper, we have described the different characteristics of the detectors and the experimental protocols used. Tables of measures have been developed and the different curves were plotted. The experimental campaign at stake: 2 PC 3He were thus characterized: Their characteristics (sensitivity, energy pulse height distribution spectra, gas amplification etc.) Were identified: 01 PC 3He 1'' Type: prototype DEDIN/DDM, 01 PC 3He 1'' Type: LND252/USA.

Keywords: PC 3He, sensitivity, pulse height distribution spectra, gas amplification

Procedia PDF Downloads 412

Authors: A. Delimitsou, C. Gouedard, E. Konstanta, A. Koletis, S. Patera, E. Manou, K. Spaho, S. Murray

Abstract:

Background: There remains a lack of International Standard Control Reference materials for Next Generation Sequencing-based approaches or device calibration. We have designed and validated dsDNA biomimetic reference materials for targeted such approaches incorporating proprietary motifs (patent pending) for device/test calibration. They enable internal single-sample calibration, alleviating sample comparisons to pooled historical population-based data assembly or statistical modelling approaches. We have validated such an approach for BRCA Copy Number Variation analytics using iQRS™-CNVSUITE versus Mixed Ligation-dependent Probe Amplification. Methods: Standard BRCA Copy Number Variation analysis was compared between mixed ligation-dependent probe amplification and next generation sequencing using a cohort of 198 breast/ovarian cancer patients. Next generation sequencing based copy number variation analysis of samples spiked with iQRS™ dsDNA biomimetics were analysed using proprietary CNVSUITE software. Mixed ligation-dependent probe amplification analyses were performed on an ABI-3130 Sequencer and analysed with Coffalyser software. Results: Concordance of BRCA – copy number variation events for mixed ligation-dependent probe amplification and CNVSUITE indicated an overall sensitivity of 99.88% and specificity of 100% for iQRS™-CNVSUITE. The negative predictive value of iQRS-CNVSUITE™ for BRCA was 100%, allowing for accurate exclusion of any event. The positive predictive value was 99.88%, with no discrepancy between mixed ligation-dependent probe amplification and iQRS™-CNVSUITE. For device calibration purposes, precision was 100%, spiking of patient DNA demonstrated linearity to 1% (±2.5%) and range from 100 copies. Traditional training was supplemented by predefining the calibrator to sample cut-off (lock-down) for amplicon gain or loss based upon a relative ratio threshold, following training of iQRS™-CNVSUITE using spiked iQRS™ calibrator and control mocks. BRCA copy number variation analysis using iQRS™-CNVSUITE™ was successfully validated and ISO15189 accredited and now enters CE-IVD performance evaluation. Conclusions: The inclusion of a reference control competitor (iQRS™ dsDNA mimetic) to next generation sequencing-based sequencing offers a more robust sample-independent approach for the assessment of copy number variation events compared to mixed ligation-dependent probe amplification. The approach simplifies data analyses, improves independent sample data analyses, and allows for direct comparison to an internal reference control for sample-specific quantification. Our iQRS™ biomimetic reference materials allow for single sample copy number variation analytics and further decentralisation of diagnostics to single patient sample assessment.

Keywords: validation, diagnostics, oncology, copy number variation, reference material, calibration

Procedia PDF Downloads 45

Authors: Taru Singh, Shukla Das, V. G. Ramachandran

Abstract:

Objectives: To develop SYBR green based real-time PCR assay to detect carbapenemases (NDM, IMP) genes in E. coli. Methods: A total of 40 E. coli from stool samples were tested. Six were previously characterized as resistant to carbapenems and documented by PCR. The remaining 34 isolates previously tested susceptible to carbapenems and were negative for these genes. Bacterial RNA was extracted using manual method. The real-time PCR was performed using the Light Cycler III 480 instrument (Roche) and specific primers for each carbapenemase target were used. Results: Each one of the two carbapenemase gene tested presented a different melting curve after PCR amplification. The melting temperature (Tm) analysis of the amplicons identified was as follows: blaIMP type (Tm 82.18°C), blaNDM-1 (Tm 78.8°C). No amplification was detected among the negative samples. The results showed 100% concordance with the genotypes previously identified. Conclusions: The new assay was able to detect the presence of two different carbapenemase gene type by real-time PCR.

Keywords: resistance, b-lactamases, E. coli, real-time PCR

Procedia PDF Downloads 383

Authors: Tauhidur Rahman, Kasturi Bhuyan

Abstract:

In the present paper, Ground Response Analysis at the Rukni irrigation project has been thoroughly investigated. Surface level seismic hazard is mainly used by the practical Engineers for designing the important structures. Surface level seismic hazard can be obtained accounting the soil factor. Structures on soft soil will show more ground shaking than the structure located on a hard soil. The Surface level ground motion depends on the type of soil. Density and shear wave velocity is different for different types of soil. The intensity of the soil amplification depends on the density and shear wave velocity of the soil. Rukni irrigation project is located in the North Eastern region of India, near the Dauki fault (550 Km length) which has already produced earthquakes of magnitude (Mw= 8.5) in the past. There is a probability of a similar type of earthquake occuring in the future. There are several faults also located around the project site. There are 765 recorded strong ground motion time histories available for the region. These data are used to determine the soil amplification factor by incorporation of the engineering properties of soil. With this in view, three of soil bore holes have been studied at the project site up to a depth of 30 m. It has been observed that in Soil bore hole 1, the shear wave velocity vary from 99.44 m/s to 239.28 m/s. For Soil Bore Hole No 2 and 3, shear wave velocity vary from 93.24 m/s to 241.39 m/s and 93.24m/s to 243.01 m/s. In the present work, surface level seismic hazard at the project site has been calculated based on the Probabilistic seismic hazard approach accounting the soil factor.

Keywords: Ground Response Analysis, shear wave velocity, soil amplification, surface level seismic hazard

Procedia PDF Downloads 531

Authors: Boitumelo Setlhare, Mduduzi P. Mokoena, Ademola O. Olaniran

Abstract:

Agricultural and industrial activities have led to increasing production of xenobiotics such as 2,4-dichlorophenol (2,4-DCP), a derivative of 2,4-dichlorophenoxyacetic acid (2,4-D), which is a widely used herbicide. Bioremediation offers an efficient, cost-effective and environmentally friendly method for degradation of the compound through the activities of the various microbial enzymes involved in the catabolic pathway. The aim of this study was to isolate and characterize bacterial isolate indigenous to contaminated sites in Durban, South Africa for 2,4-DCP degradation. One bacterium capable of utilizing 2,4-DCP as sole carbon source was isolated using culture enrichment technique and identified as Pseudomonas chlororaphis strain UFB2 via PCR amplification and analysis of 16S rRNA gene sequence. This isolate was able to degrade up to 75.11% of 2,4-DCP in batch cultures within 10 days, with the degradation rate constant of 0.14 mg/l/d. Phylogenetic analysis revealed the relatedness of this bacterial isolate to other Pseudomonas sp. previously characterized for chlorophenol degradation. PCR amplification of the catabolic genes involved in 2,4-DCP degradation revealed the presence of the correct amplicons for phenol hydroxylase (600 bp), catechol 1,2-dioxygenase (214 bp), muconate isomerase (851 bp), cis-dienelactone hydrolase (577 bp), and trans-dienelactone hydrolase (491 bp) genes. Enzyme assays revealed activity as high as 21840 mU/mg, 15630 mU/mg, 2340 mU/mg and 1490 mU/mg obtained for phenol hydroxylase, catechol 1,2-dioxygenase, cis-dienelactone hydroxylase and trans-dienelactone hydroxylase, respectively. The absence of catechol 2,3-dioxygenase gene and the corresponding enzyme in this isolate suggests that the organism followed ortho-pathway for 2,4-DCP degradation. Furthermore, the absence of malaycetate reductase genes showed that the bacterium may not be able to completely mineralize 2,4-DCP. Further studies are required to optimize 2,4-DCP degradation by this isolate as well as to elucidate the mechanism of 2,4-DCP degradation.

Keywords: biodegradation, catechol 1, 2-dioxygenase, 2, 4-dichlorophenol, phenol hydroxylase, Pseudomonas chlororaphis

Procedia PDF Downloads 224

Authors: Irina Mizeva, Elena Potapova, Viktor Dremin, Mikhail Mezentsev, Valeri Shupletsov

Abstract:

The local tissue perfusion is regulated by the microvascular tone which is under the control of a number of physiological mechanisms. Laser Doppler flowmetry (LDF) together with wavelet analyses is the most commonly used technique to study the regulatory mechanisms of cutaneous microcirculation. External factors such as temperature, local pressure of the probe on the skin, etc. influence on the blood flow characteristics and are used as physiological tests to evaluate microvascular regulatory mechanisms. Local probe pressure influences on the microcirculation parameters measured by optical methods: diffuse reflectance spectroscopy, fluorescence spectroscopy, and LDF. Therefore, further study of probe pressure effects can be useful to improve the reliability of optical measurement. During pressure tests variation of the mean perfusion measured by means of LDF usually is estimated. An additional information concerning the physiological mechanisms of the vascular tone regulation system in response to local pressure can be obtained using spectral analyses of LDF samples. The aim of the present work was to develop protocol and algorithm of data processing appropriate for study physiological response to the local pressure test. Involving 6 subjects (20±2 years) and providing 5 measurements for every subject we estimated intersubject and-inter group variability of response of both averaged and oscillating parts of the LDF sample on external surface pressure. The final purpose of the work was to find special features which further can be used in wider clinic studies. The cutaneous perfusion measurements were carried out by LAKK-02 (SPE LAZMA Ltd., Russia), the skin loading was provided by the originally designed device which allows one to distribute the pressure around the LDF probe. The probe was installed on the dorsal part of the distal finger of the index figure. We collected measurements continuously for one hour and varied loading from 0 to 180mmHg stepwise with a step duration of 10 minutes. Further, we post-processed the samples using the wavelet transform and traced the energy of oscillations in five frequency bands over time. Weak loading leads to pressure-induced vasodilation, so one should take into account that the perfusion measured under pressure conditions will be overestimated. On the other hand, we revealed a decrease in endothelial associated fluctuations. Further loading (88 mmHg) induces amplification of pulsations in all frequency bands. We assume that such loading leads to a higher number of closed capillaries, higher input of arterioles in the LDF signal and as a consequence more vivid oscillations which mainly are formed in arterioles. External pressure higher than 144 mmHg leads to the decrease of oscillating components, after removing the loading very rapid restore of the tissue perfusion takes place. In this work, we have demonstrated that local skin loading influence on the microcirculation parameters measured by optic technique; this should be taken into account while developing portable electronic devices. The proposed protocol of local loading allows one to evaluate PIV as far as to trace dynamic of blood flow oscillations. This study was supported by the Russian Science Foundation under project N 18-15-00201.

Keywords: blood microcirculation, laser Doppler flowmetry, pressure-induced vasodilation, wavelet analyses blood

Procedia PDF Downloads 120

Authors: Irina S. Kolesnikova, Alexander A. Dolskiy, Natalya A. Lemskaya, Yulia V. Maksimova, Asia R. Shorina, Alena S. Telepova, Alexander S. Graphodatsky, Dmitry V. Yudkin

Abstract:

A cytogenetic and molecular genetic study of the family with a male child who had mental retardation and autistic features revealed an abnormal chromosome 13 bearing an enlarged p-arm with amplified ribosomal DNA (rDNA) in a boy and his father. Cytogenetic analysis using standard G-banding and FISH with labeled rDNA probes revealed an abnormal chromosome 13 with an enlarged p-arms due to rDNA amplification in a male child, who had clinically confirmed mental retardation and an autistic behavior. This chromosome is evidently inherited from the father, who has morphologically the same chromosome, but is healthy. The karyotype of the mother was normal. Ag-NOR staining showed brightly stained large whole-p-arm nucleolus organizer regions (NORs) in a child and normal-sized NORs in his father with 13p+-NOR-amount mosaicism. qRT-PCR with specific primers showed highly increased levels of 18S, 28S and 5,8 S ribosomal RNA (rRNA) in the patient’s blood samples compared to a normal healthy control donor. Both patient’s father and mother had no elevated levels of rRNAs expression. Thus, in this case, rRNA level seems to correlate with mental retardation in familial individuals with 13p+. Our findings of rRNA overexpression in a patient with mental retardation and his parents may show a possible link between the karyotype (p-arm enlargement due to rDNA amplification), rDNA functionality (rRNA overexpression), functional changes in the brain and mental retardation. The study is supported by Russian Science Foundation Grant 15-15-10001.

Keywords: mental retardation, ribosomal DNA–rDNA, ribosomal RNA–rRNA, nucleolus organizer region–NOR, chromosome 13

Procedia PDF Downloads 230

Authors: M. Omer Faruk, A. M. A. M. Zonaed Siddiki, M. Fazal Karim, Md. Masuduzzaman, S. Chowdhury, Md. Shafiqul Islam, M. Alamgir Hossain

Abstract:

The dog tapeworms Echinococcus granulosus develop hydatid cysts in various organs in human and domestic animals worldwide including Bangladesh. The aim of this study was to identify and characterize the genotype of E. granulosus isolated from cattle using 12S rRNA and Cytochrome oxidase 1 (COX 1) genes. A total of 43 hydatid cyst samples were collected from 390 examined cattle samples derived from slaughterhouses. Among them, three cysts were fertile. Genomic DNA was extracted from germinal membrane and/or protoscoleces followed by PCR amplification of mitochondrial 12S rRNA and Cytochrome oxidase 1 gene fragments. The sequence data revealed existence of G1 (64.28%) and possible G3 (21.43%) genotypes for the first time in Bangladesh. The study indicates that common sheep strain G1 is the dominant subtype of E. granulosus in Chittagong region of Bangladesh. This will increase our understanding of the epidemiology of hydatidosis in the southern part of the country and will be useful to plan suitable control measures in the long run.

Keywords: Echinococcus granulosus, Cox1, 12S rRNA, molecular characterization, Bangladesh

Procedia PDF Downloads 309

Authors: Meimei Shi

Abstract:

Objectives: The identification of endangered species, especially simultaneous detection of multiple species in complex samples, plays a critical role in alleged wildlife crime incidents and prevents illegal trade. This study was to develop a multi-locus DNA metabarcoding method for endangered animal species identification. Methods: Several pairs of universal primers were designed according to the mitochondria conserved gene regions. Experimental mixtures were artificially prepared by mixing well-defined species, including endangered species, e.g., forest musk, bear, tiger, pangolin, and sika deer. The artificial samples were prepared with 1-16 well-characterized species at 1% to 100% DNA concentrations. After multiplex-PCR amplification and parameter modification, the amplified products were analyzed by capillary electrophoresis and used for NGS library preparation. The DNA metabarcoding was carried out based on Illumina MiSeq amplicon sequencing. The data was processed with quality trimming, reads filtering, and OTU clustering; representative sequences were blasted using BLASTn. Results: According to the parameter modification and multiplex-PCR amplification results, five primer sets targeting COI, Cytb, 12S, and 16S, respectively, were selected as the NGS library amplification primer panel. High-throughput sequencing data analysis showed that the established multi-locus DNA metabarcoding method was sensitive and could accurately identify all species in artificial mixtures, including endangered animal species Moschus berezovskii, Ursus thibetanus, Panthera tigris, Manis pentadactyla, Cervus nippon at 1% (DNA concentration). In conclusion, the established species identification method provides technical support for customs and forensic scientists to prevent the illegal trade of endangered animals and their products.

Keywords: DNA metabarcoding, endangered animal species, mitochondria nucleic acid, multi-locus

Procedia PDF Downloads 87

Authors: Muhammad Fiaz Qamar, Uzma Mehreen, Muhammad Arfan Zaman, Kazim Ali

Abstract:

Ovine Theileriosis is a world-wide concern, especially in tropical and subtropical areas, due to having tick abundance that has received less awareness in different developed and developing areas due to less worth of sheep, low to the middle level of infection in different small ruminants herd. Across Asia, the prevalence reports have been conducted to provide equivalent calculation of flock and animal level prevalence of Theileriosisin animals. It is a challenge for veterinarians to timely diagnosis & control of Theileriosis and famers because of the nature of the organism and inadequacy of restricted plans to control. All most work is based upon the development of such a technique which should be farmer-friendly, less expensive, and easy to perform into the field. By the timely diagnosis of this disease will decrease the irrational use of the drugs, and other plan was to determine the prevalence of Theileriosis in District Jhang by using the conventional method, PCR and qPCR, and LAMP. We quantify the molecular epidemiology of T.lestoquardiin sheep from Jhang districts, Punjab, Pakistan. In this study, we concluded that the overall prevalence of Theileriosis was (32/350*100= 9.1%) in sheep by using Giemsa staining technique, whereas (48/350*100= 13%) is observed by using PCR technique (56/350*100=16%) in qPCR and the LAMP technique have shown up to this much prevalence percentage (60/350*100= 17.1%). The specificity and sensitivity also calculated in comparison with the PCR and LAMP technique. Means more positive results have been shown when the diagnosis has been done with the help of LAMP. And there is little bit of difference between the positive results of PCR and qPCR, and the least positive animals was by using Giemsa staining technique/conventional method. If we talk about the specificity and sensitivity of the LAMP as compared to PCR, The cross tabulation shows that the results of sensitivity of LAMP counted was 94.4%, and specificity of LAMP counted was 78%. Advances in scientific field must be upon reality based ideas which can lessen the gaps and hurdles in the way of scientific research; the lamp is one of such techniques which have done wonders in adding value and helping human at large. It is such a great biological diagnostic tools and has helped a lot in the proper diagnosis and treatment of certain diseases. Other methods for diagnosis, such as culture techniques and serological techniques, have exposed humans with great danger. However, with the help of molecular diagnostic technique like LAMP, exposure to such pathogens is being avoided in the current era Most prompt and tentative diagnosis can be made using LAMP. Other techniques like PCR has many disadvantages when compared to LAMP as PCR is a relatively expensive, time consuming, and very complicated procedure while LAMP is relatively cheap, easy to perform, less time consuming, and more accurate. LAMP technique has removed hurdles in the way of scientific research and molecular diagnostics, making it approachable to poor and developing countries.

Keywords: distribution, thelaria, LAMP, primer sequences, PCR

Procedia PDF Downloads 78

Authors: Cecile Meier, Drago Diaz Aleman, Itahisa Perez Conesa, Jose Luis Saorin Perez, Jorge De La Torre Cantero

Abstract:

In this work, two ways of creating small-sized metal sculptures are proposed: the first by means of microcasting and the second by electroforming from models printed in 3D using an FDM (Fused Deposition Modeling‎) printer or using a DLP (Digital Light Processing) printer. It is viable to replace the wax in the processes of the artistic foundry with 3D printed objects. In this technique, the digital models are manufactured with resin using a low-cost 3D FDM printer in polylactic acid (PLA). This material is used, because its properties make it a viable substitute to wax, within the processes of artistic casting with the technique of lost wax through Ceramic Shell casting. This technique consists of covering a sculpture of wax or in this case PLA with several layers of thermoresistant material. This material is heated to melt the PLA, obtaining an empty mold that is later filled with the molten metal. It is verified that the PLA models reduce the cost and time compared with the hand modeling of the wax. In addition, one can manufacture parts with 3D printing that are not possible to create with manual techniques. However, the sculptures created with this technique have a size limit. The problem is that when printed pieces with PLA are very small, they lose detail, and the laminar texture hides the shape of the piece. DLP type printer allows obtaining more detailed and smaller pieces than the FDM. Such small models are quite difficult and complex to melt using the lost wax technique of Ceramic Shell casting. But, as an alternative, there are microcasting and electroforming, which are specialized in creating small metal pieces such as jewelry ones. The microcasting is a variant of the lost wax that consists of introducing the model in a cylinder in which the refractory material is also poured. The molds are heated in an oven to melt the model and cook them. Finally, the metal is poured into the still hot cylinders that rotate in a machine at high speed to properly distribute all the metal. Because microcasting requires expensive material and machinery to melt a piece of metal, electroforming is an alternative for this process. The electroforming uses models in different materials; for this study, micro-sculptures printed in 3D are used. These are subjected to an electroforming bath that covers the pieces with a very thin layer of metal. This work will investigate the recommended size to use 3D printers, both with PLA and resin and first tests are being done to validate use the electroforming process of microsculptures, which are printed in resin using a DLP printer.

Keywords: sculptures, DLP 3D printer, microcasting, electroforming, fused deposition modeling

Procedia PDF Downloads 108

Authors: Babak Rezavand

Abstract:

Pneumocystis carinii pneumonia (PCP) is one of the main causes of morbidity and mortality among immunocompromised and HIV-positive patients and remained one of the most important common opportunistic infections in these individuals in the world. Pneumocystis infection has been reported in many mammals. The aim of this study was to determine the Pneumocystis infection in wild rats as natural reservoirs of this organism in Tehran city, Iran. Fifty three rats (Rattus rattus) were live trapped in different areas of Tehran city, Iran. After isolation of their lung tissues and homogenization in sterile conditions, DNA was extracted. DNAs from all of the Pneumocystis species were amplified by pAZ102-H and pAZ102-E primers, and Nested PCR was performed using pAZ102-X and pAZ102-W primers from the initial PCR product for all the species of Pneumocystis. Amplification of the genome revealed the presence of Pneumocystis in the lungs of 17 rats (32%) through a PCR product with a bandwidth of 346 bp. In the Nested PCR amplification, from the PCR product of 53 rats, 64.2% of the samples were positive with a bandwidth of 261bp. Pneumocystis SPP infestation is highly prevalent among wild rats in Tehran city, indicating the existence of infection in the natural ecosystem of these rodents. As a host, rat plays an important role in the transmission of the microorganism in the world.

Keywords: pneumocystis SPP, rattus rattus, nested PCR, Tehran

Procedia PDF Downloads 179

Authors: Mudawamah Mudawamah, Muhammad Z. Fadli, Gatot Ciptadi, Aulanni’am

Abstract:

Canary breeders have spread throughout Indonesian regions for the low-middle society and become an income source for them. The interesting phenomenon of the canary market is the feather colours become one of determining factor for the price. The advantages of this research were contributed to the molecular database as a base of selection and mating for the Indonesia canary breeder. The research method was experiment with the genome obtained from canary blood isolation. The genome did the PCR amplification with PMEL marker followed by sequencing. Canaries were used 24 heads of light and dark colour feathers. Research data analyses used BioEdit and Network 4.6.0.0 software. The results showed that all samples were amplification with PMEL gene with 500 bp fragment length. In base sequence of 40 was found Cytosine(C) in the light colour canaries, while the dark colour canaries was obtained Thymine (T) in same base sequence. Sequence results had 286-415 bp fragment and 10 haplotypes. The conclusions were the PMEL gene (gene of white pigment) was likely to be used PMEL gene to detect molecular genetic variation of dark and light colour feather.

Keywords: canary, haplotype, PMEL, sequence

Procedia PDF Downloads 206

Authors: H. K. Ratre, M. Roy, S. Roy, M. S. Parmar, V. Bhagat

Abstract:

Mastitis is a common problem of dairy industries. Reduction in milk production and an irreparable damage to the udder associated with the disease are common causes of culling of dairy cows. Milk from infected animals is not suitable for drinking and for making different milk products. So, it has a major economic importance in dairy cattle. The aims of this study were to investigate the bacteriological panorama in milk from udder quarters with subclinical mastitis and to carried out for the molecular characterization of the major isolated organisms, from subclinical mastitis-affected cows in and around Durg and Rajnandgaon district of Chhattisgarh. Isolation and identification of bacteria from the milk samples of subclinical mastitis-affected cows were done by standard and routine culture procedures. A total of 78 isolates were obtained from cows and among the various bacteria isolated, Staphylococcus spp. occupied prime position with occurrence rate of 51.282%. However, other bacteria isolated includeStreptococcus spp. (20.512%), Micrococcus spp. (14.102%), E. coli (8.974%), Klebsiela spp. (2.564%), Salmonella spp. (1.282%) and Proteus spp. (1.282%). Staphylococcus spp. was isolated as the major causative agent of subclinical mastitis in the studied area. Molecular characterization of Staphylococus aureusisolates was done for genetic expression of the virulence genes like ‘nuc’ encoding thermonucleaseexoenzyme, coa and spa by PCR amplification of the respective genes in 25 Staphylococcus isolates. In the present study, 15 isolates (77.27%) out of 20 coagulase positive isolates were found to be genotypically positive for ‘nuc’ where as 20 isolates (52.63%) out of 38 CNS expressed the presence of the same virulence gene. In the present study, three Staphylococcus isolates were found to be genotypically positive for coa gene. The Amplification of the coa gene yielded two different products of 627, 710 bp. The amplification of the gene segment encoding the IgG binding region of protein A (spa) revealed a size of 220 and 253bp in twostaphylococcus isolates. The X-region binding of the spa gene produced an amplicon of 315 bp in one Staphylococcal isolates. Staphylococcus aureus was found to be major isolate (51.28%) responsible for causing subclinical mastitis in cows which also showed expression of virulence genesnuc, coa and spa.

Keywords: mastitis, bacteria, characterization, expression, gene

Procedia PDF Downloads 189

Authors: Munawar Malik, Muntaha Ahmad, Khalil Ullah Khan

Abstract:

Linguistic abilities in students with hearing impairment yet remain a concern for educationists. The emerging technological support and provisions in recent era vows to have addressed the situation and claims significant contribution in terms of linguistic repertoire. Being a descriptive and quantitative paradigm of study, the purpose of this research set forth was to assess linguistic competencies of students with hearing impairment in English language. The goals were further broken down to identify level of reading abilities in the subject population. The population involved students with HI studying at higher secondary level in Lahore. Simple random sampling technique was used to choose a sample of fifty students. A purposive curriculum-based assessment was designed in line with accelerated learning program by Punjab Government, to assess Linguistic competence among the sample. Further to it, an Informal Reading Inventory (IRI) corresponding to reading levels was also developed by researchers duly validated and piloted before the final use. Descriptive and inferential statistics were utilized to reach to the findings. Spearman’s correlation was used to find out relationship between degree of hearing loss, grade level, gender and type of amplification device. Independent sample t-test was used to compare means among groups. Major findings of the study revealed that students with hearing impairment exhibit significant deviation from the mean scores when compared in terms of grades, severity and amplification device. The study divulged that respective students with HI have yet failed to qualify an independent level of reading according to their grades as majority falls at frustration level of word recognition and passage comprehension. The poorer performance can be attributed to lower linguistic competence as it shows in the frustration levels of reading, writing and comprehension. The correlation analysis did reflect an improved performance grade wise, however scores could only correspond to frustration level and independent levels was never achieved. Reported achievements at instructional level of subject population may further to linguistic skills if practiced purposively.

Keywords: linguistic competence, hearing impairment, reading levels, educationist

Procedia PDF Downloads 23

Authors: Ellen Bryant, Virginia Behmer, Rebecca Garbed, Jeanette O’Quin, Dana Howard

Abstract:

As it currently stands, veterinary care in the United States is not accessible to everyone, and veterinarians regularly face cases of clients who are unable to provide necessary care to their animals regardless of the client’s desire to do so. There is currently limited research into how veterinarians address these issues of access to care. It is apparent that veterinarians regularly utilize funding or offer discounted services to treat cases that otherwise would go without care. With need currently exceeding the amount of funds and services available, veterinarians are tasked with deciding which cases are most deserving of assistance. This mixed methods study distributed a survey to companion animal veterinarians practicing in the United States to identify current trends in how these professionals apply principles of distributive justice in the scope of veterinary medicine. Ethical frameworks identified in human bioethics research into distributive justice were presented, along with demographic questions, to identify relationships between veterinarian priorities and the scope of their practice/respective roles/geographic region. By surveying veterinarians across a wide range of specialties, practice types, and clientele this study was able to assess how priorities and opinions shift based on external factors as well as among the respondents themselves. Participants were asked not only to choose how to distribute aid between different clients and case scenarios, but also asked directly which is the best way to distribute aid when need exceeds the resources available.

Keywords: access to veterinary care, bioethics, decision-making, distributive justice, subsidized care

Procedia PDF Downloads 36

Authors: Dawit Gebreegzabher Hagos, Yazezew Kebede Kiro, Mahmud Abdulkader, Henk H. D. F. Schallig, Dawit Wolday

Abstract:

Rapid and accurate visceral leishmaniasis (VL) diagnosis is needed to initiate prompt treatment to reduce morbidity and mortality. Here, we evaluated the performance of loop-mediated isothermal amplification (LAMP) assay for the diagnosis of VL from blood in an endemic area in Ethiopia. LAMP was positive in 117/122 confirmed VL cases and negative in 149/152 controls, resulting in a sensitivity of 95.9% (95% CI: 90.69–98.66) and a specificity of 98.0% (95% CI: 94.34–99.59), respectively. The sensitivity of the LAMP assay was 95.0% (95% CI: 88.61–98.34) in HIV-negatives and 100% (95% CI: 85.18–100.0) in HIV-positives. Compared with microscopy, LAMP detected 82/87 (94.3%, 95% CI: 87.10–98.11) of the microscopy1 cases and was negative in 11/27 (40.7%, 95% CI: 22.39–61.20) of the microscopy2 cases. Compared with the rK39 serology, LAMP detected 113/120 (94.2%, 95% CI: 88.35–97.62) of the rK391 cases and was negative in 149/154 (96.8%, 95% CI: 92.59–98.94) of the rK392 cases. However, when compared with microscopy only, rK39 detected 83/87 (95.4%, 95% CI: 88.64–98.73) of the microscopy1 cases and negative in only 12/27 (44.4%, 95% CI: 25.48–64.67) of the microscopy– cases. There was an excellent agreement between rK39 and LAMP (Kappa 5 0.91, 95% CI: 0.86–0.96). Furthermore, an algorithm using rK39 followed by LAMP would yield a sensitivity of 99.2% (95%CI: 95.52–99.89) and a specificity of 98.0% (95% CI: 94.34–99.59). The findings demonstrate that the LAMP assay is an accurate and rapid molecular assay for VL diagnosis, including in HIV-1 co-infected patients, in an endemic setting.

Keywords: visceral leishmaniasis, HIV, diagnosis, LAMP, Ethiopia

Procedia PDF Downloads 62

Authors: Peter Antwi Buah, Yingbin Zhang, Jianxian He, Chenlin Xiang, Delali Atsu Y. Bakah

Abstract:

Near-fault ground motions with velocity pulses are considered to cause significant damage to structures or slopes compared to ordinary ground motions without velocity pulses. The double pulsed pulse-like ground motion is as well known to be stronger than the single pulse. This study has numerically justified this perspective by studying the dynamic response of a homogeneous rock slope subjected to four pulse-like and two non-pulse-like ground motions using the Fast Lagrangian Analysis of Continua in 3 Dimensions (FLAC3D) software. Two of the pulse-like ground motions just have a single pulse. The results show that near-fault ground motions with velocity pulses can cause a higher dynamic response than regular ground motions. The amplification of the peak ground acceleration (PGA) in horizontal direction increases with the increase of the slope elevation. The seismic response of the slope under double pulse ground motion is stronger than that of the single pulse ground motion. The PGV amplification factor under the effect of the non-pulse-like records is also smaller than those under the pulse-like records. The velocity pulse strengthens the earthquake damage to the slope, which results in producing a more strong dynamic response.

Keywords: velocity pulses, dynamic response, PGV magnification effect, elevation effect, double pulse

Procedia PDF Downloads 125

Authors: Aditi Viswanathan, Shree Ranjani, Aruna Govada

Abstract:

With data sizes constantly expanding, and with classical machine learning algorithms that analyze such data requiring larger and larger amounts of computation time and storage space, the need to distribute computation and memory requirements among several computers has become apparent. Although substantial work has been done in developing distributed binary SVM algorithms and multi-class SVM algorithms individually, the field of multi-class distributed SVMs remains largely unexplored. This research seeks to develop an algorithm that implements the Support Vector Machine over a multi-class data set and is efficient in a distributed environment. For this, we recursively choose the best binary split of a set of classes using a greedy technique. Much like the divide and conquer approach. Our algorithm has shown better computation time during the testing phase than the traditional sequential SVM methods (One vs. One, One vs. Rest) and out-performs them as the size of the data set grows. This approach also classifies the data with higher accuracy than the traditional multi-class algorithms.

Keywords: distributed algorithm, MapReduce, multi-class, support vector machine

Procedia PDF Downloads 367

Authors: Suharni Mohamad Suharni Mohamad, Nurul Izzati Hamzan Nurul Izzati Hamzan, Norhayu Abdul Rahman Norhayu Abdul Rahman, Siti Suraiya Md Noor Siti Suraiya Md Noor

Abstract:

Human papillomavirus (HPV) is an important risk factor for development of oral cancer. HPV16 is the most common type found in HPV-positive squamous cell carcinoma. In the present study, we established a real-time loop-mediated isothermal amplification (real-time LAMP) for detection of HPV16. A set of six primers was specially designed to recognize eight distinct sequences of HPV16-E6. Detection and quantification was achieved by real-time monitoring using a real-time turbidimeter based on threshold time required for turbidity in the LAMP reaction. LAMP reagents (MgSO4, dNTPs, Bst polymerase concentrations) and various incubation times and temperatures were optimized. The sensitivity was determined using 10-fold serial dilutions of HPV16 standard strain. The specificity of was evaluated using other HPV genotypes. The optimized method was established with specifically designed primers by real-time detection in approximately 30 min at 65°C. The limit of detection of HPV16 using the LAMP assay was 10 pg/ml that could be detected in 30 min. The LAMP assay was 10 times more sensitive than the conventional PCR in detecting HPV16. No cross-reactivity with other HPV genotypes was observed. This quantitative real-time LAMP assay may improve diagnostic potential for the detection and quantification of HPV16 in clinical samples and epidemiological studies due to its rapidity, simplicity, high sensitivity and specificity. This assay will be further evaluated with HPV DNAs of saliva from patients with oral squamous cell carcinoma. Acknowledgement: This study was financially supported by the ScienceFund Grant, Ministry of Science, Technology and Innovation (305/PPSG/6113219).

Keywords: Oral Squamous Cell Carcinoma (OSCC), Human Papillomavirus 16 (HPV16), Loop-Mediated Isothermal Amplification (LAMP), rapid detection

Procedia PDF Downloads 377