Search results for: amplification ratio

Authors: Kamal, J. P. Narayan

Abstract:

In the present wok the effects of basin-shape-ratio on the frequency content and spectral amplitudes of the basin-generated surface waves and the associated spatial variation of ground motion amplification and differential ground motion in a 3D semi-spherical basin has been studied. A recently developed 3D fourth-order spatial accurate time-domain finite-difference (FD) algorithm based on the parsimonious staggered-grid approximation of the 3D viscoelastic wave equations was used to estimate seismic responses. The simulated results demonstrated the increase of both the frequency content and the spectral amplitudes of the basin-generated surface waves and the duration of ground motion in the basin with the increase of shape-ratio of semi-spherical basin. An increase of the average spectral amplification (ASA), differential ground motion (DGM) and the average aggravation factor (AAF) towards the centre of the semi-spherical basin was obtained.

Keywords: 3D viscoelastic simulation, basin-generated surface waves, basin-shape-ratio effects, average spectral amplification, aggravation factors and differential ground motion

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Authors: Ata Khorami, Mohammad Sharifkhani

Abstract:

In the dynamic comparators, the pre-amplifier amplifies the input differential voltage and when the output Vcm of the pre-amplifier becomes larger than Vth of the latch input transistors, the latch is activated and finalizes the comparison. As a result, the pre-amplification delay is fixed to a value and cannot be set at the minimum required delay, thus, significant power and delay are imposed. In this paper, a novel structure is proposed through which the pre-amplification delay can be set at any low value saving power and time. Simulations show that using the proposed structure, by setting the pre-amplification delay at the minimum required value the power and comparison delay can be reduced by 55% and 100ps respectively.

Keywords: dynamic comparator, low power comparator, analog to digital converter, pre-amplification delay

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Authors: Haoshu Li, Shaolong Wan

Abstract:

The recent focus has been on directional signal amplification of a signal input at one end of a one-dimensional chain and measured at the other end. The amplification rate is given by the end-to-end Green’s functions of the system. In this work, we derive the exact formulas for the end-to-end Green's functions of non-Hermitian single-band systems. While in the bulk region, it is found that the Green's functions are displaced from the prior established integral formula by O(e⁻ᵇᴸ). The results confirm the correspondence between the signal amplification and the non-Hermitian skin effect.

Keywords: non-Hermitian, Green's function, non-Hermitian skin effect, signal amplification

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Authors: Olena Mayboroda, Angel Gonzalez Benito, Jonathan Sabate Del Rio, Marketa Svobodova, Sandra Julich, Herbert Tomaso, Ciara K. O'Sullivan, Ioanis Katakis

Abstract:

DNA amplification is required for most molecular diagnostic applications but conventional PCR has disadvantages for field testing. Isothermal amplification techniques are being developed to respond to this problem. One of them is the Recombinase Polymerase Amplification (RPA) that operates at isothermal conditions without sacrificing specificity and sensitivity in easy-to-use formats. In this work RPA was used for the optical detection of solid-phase amplification of the potential biowarfare agent Yersinia pestis. Thiolated forward primers were immobilized on the surface of maleimide-activated microtitre plates for the quantitative detection of synthetic and genomic DNA, with elongation occurring only in the presence of the specific template DNA and solution phase reverse primers. Quantitative detection was achieved via the use of biotinylated reverse primers and post-amplification addition of streptavidin-HRP conjugate. The overall time of amplification and detection was less than 1 hour at a constant temperature of 37oC. Single-stranded and double-stranded DNA sequences were detected achieving detection limits of 4.04*10-13 M and 3.14*10-16 M, respectively. The system demonstrated high specificity with negligible responses to non-specific targets.

Keywords: recombinase polymerase amplification, Yersinia pestis, solid-phase detection, ELONA

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Authors: Sunghyun Kim, Hong-Gun Park

Abstract:

In the performance-based design (PBD), by using the nonlinear dynamic analysis (NDA), the actual performance of the structure is evaluated. Unlike frame structures, in the wall structures, base shear force which is resulted from the NDA, is greatly amplified than that from the elastic analysis. This shear amplifying effect causes repeated designs which make designer difficult to apply the PBD. Therefore, in this paper, factors which affect shear amplification were studied. For the 20-story wall model, the NDA was performed. From the analysis results, the base shear amplification factor was proposed.

Keywords: performance based design, shear amplification factor, nonlinear dynamic analysis, RC shear wall

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Authors: Belloui Bouzid

Abstract:

In this paper, broadband design of erbium doped fiber amplifier (EDFA) is demonstrated and proved experimentally. High and broad gain is covered in C and L bands. The used technique combines, in one configuration, two double passes with split band structure for the amplification of two traveled signals one for the C band and the other for L band. This new topology is to investigate the trends of high gain and wide amplification at different status of pumping power, input wavelength, and input signal power. The presented paper is to explore the performance of EDFA gain using what it can be called double pass double branch wide band amplification configuration. The obtained results show high gain and wide broadening range of 44.24 dB and 80 nm amplification respectively.

Keywords: erbium doped fiber amplifier, erbium doped fiber laser, optical amplification, fiber laser

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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

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Authors: Haiping Ding, Rongchu Zhu, Zhenxia Song

Abstract:

Local irregular topography has a great impact on earthquake ground motion. For scarp topography, using numerical simulation method, the influence extent and scope of the scarp terrain on scarp's upside and downside ground motion are discussed in case of different vertical incident SV waves. The results show that: (1) The amplification factor of scarp's upside region is greater than that of the free surface, while the amplification factor of scarp's downside part is less than that of the free surface; (2) When the slope angle increases, for x component, amplification factors of the scarp upside also increase, while the downside part decrease with it. For z component, both of the upside and downside amplification factors will increase; (3) When the slope angle changes, the influence scope of scarp's downside part is almost unchanged, but for the upside part, it slightly becomes greater with the increase of slope angle; (4) Due to the existence of the scarp, the z component ground motion appears at the surface. Its amplification factor increases for larger slope angle, and the peaks of the surface responses are related with incident waves. However, the input wave has little effects on the x component amplification factors.

Keywords: scarp topography, ground motion, amplification factor, vertical incident wave

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Authors: Ji Su Kim, Bo Ram Choi, Ju Yeon Cho, Hyukjin Lee

Abstract:

Epidermal growth factor receptor (EGFR) 19 deletion mutation gene is over-expressed in carcinoma patient. EGFR 19 deletion mutation is known as typical biomarker of non-small cell lung cancer (NSCLC), which one section in the coding exon 19 of EGFR is deleted. Therefore, there have been many attempts over the years to detect EGFR 19 deletion mutation for replacing conventional diagnostic method such as PCR and tissue biopsy. We developed a simple and facile detection platform based on Rolling Circle Amplification (RCA), which provides highly amplified products in isothermal amplification of the ligated DNA template. Limit of detection (~50 nM) and a faster detection time (~30 min) could be achieved by introducing RCA.

Keywords: EGFR19, cancer, diagnosis, rolling circle amplification (RCA), hydrogel

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Authors: I. Paeglite, A. Paeglitis

Abstract:

The paper presents a study of dynamic effects obtained from the dynamic load testing of the city highway bridges in Latvia carried out from 2005 to 2012. 9 pre-stressed concrete bridges and 4 composite bridges were considered. 11 of 13 bridges were designed according to the Eurocodes but two according to the previous structural codes used in Latvia (SNIP 2.05.03-84). The dynamic properties of the bridges were obtained by heavy vehicles passing the bridge roadway with different driving speeds and with or without even pavement. The obtained values of the Dynamic amplification factor (DAF) and bridge natural frequency were analyzed and compared to the values of built-in traffic load models provided in Eurocode 1. The actual DAF values for even bridge deck in the most cases are smaller than the value adopted in Eurocode 1. Vehicle speed for uneven pavements significantly influence Dynamic amplification factor values.

Keywords: bridge, dynamic effects, load testing, dynamic amplification factor

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Authors: Mohammad Raihan Mukhlis, M. Abdur Rahman Bhuiyan

Abstract:

Bangladesh is a developing country in which a lot of multi-span simply/continuous supported flyovers are being constructed in its major cities. Being situated in a seismically active region, seismic safety evaluation of flyovers is essential for seismic risk reduction. Effects of site amplification on seismic safety evaluation of flyover piers are the main concern of this study. In this regard, failure mode, lateral strength and displacement ductility of piers of a typical multi-span simply supported flyover have been evaluated by Japan Road Association (JRA) recommended guidelines, with and without considering site amplification. Ultimate flexural strengths of piers have been computed using the pushover analysis results. Shear capacity of piers has been calculated using the guidelines of JRA. Lateral strengths have been determined depending on the failure modes of the piers. Displacement ductility of piers has been computed using yield and ultimate displacements of the piers obtained from the pushover analysis results. Selected earthquake time history is used in seismic safety evaluation of the flyover piers. Finally, the ductility design method is used to conduct the seismic safety evaluation of the piers with and without considering site amplification. From the numerical results, it has been revealed that the effects of site amplification on seismic safety evaluation of bridge structures should be carefully taken into account.

Keywords: displacement ductility, flyover pier, lateral strength, safety evaluation, site amplification

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Authors: George C. Yao, Chao-Yu Tu, Wei-Chung Chen, Fung-Wen Kuo, Yu-Shan Chang

Abstract:

Building structures are subjected to both horizontal and vertical ground motions during earthquakes, but only the horizontal ground motion has been extensively studied and considered in design. Most of the prevailing seismic codes assume the vertical component to be 1/2 to 2/3 of the horizontal one. In order to understand the building responses from vertical ground motions, many earthquakes records are studied in this paper. System identification methods (ARX Model) are used to analyze the strong motions and to find out the characteristics of the vertical amplification factors and the natural frequencies of buildings. Analysis results show that the vertical amplification factors for high-rise buildings and low-rise building are 1.78 and 2.52 respectively, and the average vertical amplification factor of all buildings is about 2. The relationship between the vertical natural frequency and building height was regressed to a suggested formula in this study. The result points out an important message; the taller the building is, the greater chance of resonance of vertical vibration on the building will be.

Keywords: vertical ground motion, vertical amplification factor, natural frequency, component

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Authors: Bo Ram Choi, Ji Su Kim, Juyeon Cho, Hyukjin Lee

Abstract:

Food contaminated by bacteria (E.coli), causes food poisoning, which occurs to many patients worldwide annually. We have introduced an application of rolling circle amplification (RCA) as a versatile biosensor and developed a diagnostic platform composed of capillary tube and microbeads for rapid and easy detection of Escherichia coli (E. coli). When specific mRNA of E.coli is extracted from cell lysis, rolling circle amplification (RCA) of DNA template can be achieved and can be visualized by beads aggregation in capillary tube. In contrast, if there is no bacterial pathogen in sample, no beads aggregation can be seen. This assay is possible to detect visually target gene without specific equipment. It is likely to the development of a genetic kit for point of care testing (POCT) that can detect target gene using microbeads.

Keywords: rolling circle amplification (RCA), Escherichia coli (E. coli), point of care testing (POCT), beads aggregation, capillary tube

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Authors: Kotbi Lakhdar, Hachi Mostefa

Abstract:

We show that a simple transformation between the regular lattices (the square, the triangular, and the honeycomb) belonging to the same dimensionality can explain in a natural way the universality of the critical exponents found in phase transitions and critical phenomena. It suffices that the Hamiltonian and the lattice present similar writing forms. In addition, it appears that if a property can be calculated for a given lattice then it can be extrapolated simply to any other lattice belonging to the same dimensionality. In this study, we have restricted ourselves on the spectral power amplification (SPA), we note that the SPA does not have an effect on the critical exponents but does have an effect by the criticality temperature of the lattice; the generalisation to other lattice could be shown according to the containment principle.

Keywords: ising model, phase transitions, critical temperature, critical exponent, spectral power amplification

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Authors: Lorico D. S. Lapitan Jr., Yihan Xu, Yuan Guo, Dejian Zhou

Abstract:

The ability of ultrasensitive detection of specific genes and discrimination of single nucleotide polymorphisms is important for clinical diagnosis and biomedical research. Herein, we report the development of a new ultrasensitive approach for label-free DNA detection using magnetic nanoparticle (MNP) assisted rapid target capture/separation in combination with signal amplification using poly-enzyme tagged polymer nanobead. The sensor uses an MNP linked capture DNA and a biotin modified signal DNA to sandwich bind the target followed by ligation to provide high single-nucleotide polymorphism discrimination. Only the presence of a perfect match target DNA yields a covalent linkage between the capture and signal DNAs for subsequent conjugation of a neutravidin-modified horseradish peroxidase (HRP) enzyme through the strong biotin-nuetravidin interaction. This converts each captured DNA target into an HRP which can convert millions of copies of a non-fluorescent substrate (amplex red) to a highly fluorescent product (resorufin), for great signal amplification. The use of polymer nanobead each tagged with thousands of copies of HRPs as the signal amplifier greatly improves the signal amplification power, leading to greatly improved sensitivity. We show our biosensing approach can specifically detect an unlabeled DNA target down to 10 aM with a wide dynamic range of 5 orders of magnitude (from 0.001 fM to 100.0 fM). Furthermore, our approach has a high discrimination between a perfectly matched gene and its cancer-related single-base mismatch targets (SNPs): It can positively detect the perfect match DNA target even in the presence of 100 fold excess of co-existing SNPs. This sensing approach also works robustly in clinical relevant media (e.g. 10% human serum) and gives almost the same SNP discrimination ratio as that in clean buffers. Therefore, this ultrasensitive SNP biosensor appears to be well-suited for potential diagnostic applications of genetic diseases.

Keywords: DNA detection, polymer beads, signal amplification, single nucleotide polymorphisms

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Authors: Jyh Jyh Chen, Fu H. Yang, Chen W. Wang, Yu M. Lin

Abstract:

In this work, a reaction chamber is reciprocated among three temperature regions by using an oscillatory thermal cycling machine. Three cartridge heaters are collocated to heat three aluminum blocks in order to achieve PCR requirements in the reaction chamber. The effects of various chamber moving speeds among different temperature regions on the chamber temperature profiles are presented. To solve the evaporation effect of the sample in the PCR experiment, the mineral oil and the cover lid are used. The influences of various extension times on DNA amplification are also demonstrated. The target fragments of the amplification are 385-bp and 420-bp. The results show when the forward speed is set at 6 mm/s and the backward speed is 2.4 mm/s, the temperature required for the experiment can be achieved. It is successful to perform the amplification of DNA fragments in our device.

Keywords: oscillatory, polymerase chain reaction, reaction chamber, thermal cycling machine

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Authors: Huajuan Shi

Abstract:

Background: The biopsy of the preimplantation embryo may increase the potential risk and concern of embryo viability. Clinically discarded spent embryo medium (SEM) has entered the view of researchers, sparking an interest in noninvasive embryo screening. However, one of the major restrictions is the extremelty low quantity of cf-RNA, which is difficult to efficiently and unbiased amplify cf-RNA using traditional methods. Hence, there is urgently need to an efficient and low bias amplification method which can comprehensively and accurately obtain cf-RNA information to truly reveal the state of SEM cf-RNA. Result: In this present study, we established an agarose PCR amplification system, and has significantly improved the amplification sensitivity and efficiency by ~90 fold and 9.29 %, respectively. We applied agarose to sequencing library preparation (named AG-seq) to quantify and characterize cf-RNA in SEM. The number of detected cf-RNAs (3533 vs 598) and coverage of 3' end were significantly increased, and the noise of low abundance gene detection was reduced. The increasing percentage 5' end adenine and alternative splicing (AS) events of short fragments (< 400 bp) were discovered by AG-seq. Further, the profiles and characterizations of cf-RNA in spent cleavage medium (SCM) and spent blastocyst medium (SBM) indicated that 4‐mer end motifs of cf-RNA fragments could remarkably differentiate different embryo development stages. Significance: This study established an efficient and low-cost SEM amplification and library preparation method. Not only that, we successfully described the characterizations of SEM cf-RNA of preimplantation embryo by using AG-seq, including abundance features fragment lengths. AG-seq facilitates the study of cf-RNA as a noninvasive embryo screening biomarker and opens up potential clinical utilities of trace samples.

Keywords: cell-free RNA, agarose, spent embryo medium, RNA sequencing, non-invasive detection

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Authors: Leila Graini

Abstract:

In this paper, we demonstrate basic all-optical functions for 2R regeneration (Re-amplification and Re-shaping) based on self-similar spectral broadening in low normal dispersion and highly nonlinear fiber (ND-HNLF) to regenerate the signal through optical filtering including the transfer function characteristics, and output extinction ratio. Our approach of all-optical 2R regeneration is based on those of Mamyshev. The numerical study reveals the self-similar spectral broadening very effective for 2R all-optical regeneration; the proposed design presents high stability compared to a conventional regenerator using SPM broadening with reduction of the intensity fluctuations and improvement of the extinction ratio.

Keywords: all-optical function, 2R optical regeneration, self-similar broadening, Mamyshev regenerator

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Authors: Omar S. Sharaf

Abstract:

The mitochondrial 12s rRNA (mt-12s rDNA) gene for pig-specific was developed to detect material from pork species in different products collected from Jordanian market. The amplification PCR products of 359 bp and 531 bp were successfully amplified from the cyt b gene of pig the amplification product using mt-12S rDNA gene were successfully produced a single band with a molecular size of 456 bp. In the present work, the PCR amplification of mtDNA of cytochrome b has been shown as a suitable tool for rapid detection of pig DNA. 100 samples from different dairy, gelatin and chocolate based products and 50 samples from baby food formula were collected and tested to a presence of any pig derivatives. It was found that 10% of chocolate based products, 12% of gelatin and 56% from dairy products and 5.2% from baby food formula showed single band from mt-12S rDNA gene.

Keywords: halal food, baby infant formula, chocolate based products, PCR, Jordan

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Authors: Kamal, Dinesh Kumar, J. P. Narayan, Komal Rani

Abstract:

This paper presents the effects of shape of basement topography on the characteristics of the basin-generated surface (BGS) waves and associated average spectral amplification (ASA) in the 3D basins having circular surface area. Seismic responses were computed using a recently developed 3D fourth-order spatial accurate time-domain finite-difference (FD) algorithm based on parsimonious staggered-grid approximation of 3D viscoelastic wave equations. An increase of amplitude amplification and ASA towards the centre of different considered basins was obtained. Further, it may be concluded that ASA in basin very much depends on the impedance contrast, exposure area of basement to the incident wave front, edge-slope, focusing of the BGS-waves and sediment-damping. There is an urgent need of incorporation of a map of differential ground motion (DGM) caused by the BGS-waves as one of the output maps of the seismic microzonation.

Keywords: 3D viscoelastic simulation, basin-generated surface waves, maximum displacement, average spectral amplification

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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

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Authors: Abtin Farokhipanah

Abstract:

In recent years, analysis of structures is based on ductility design in contradictory to strength design in surveying earthquake effects on structures. ASCE07-10 code offers to intensify relative drifts calculated from a linear analysis with Cd which is called (Deflection Amplification Factor) to obtain the real relative drifts which can be calculated using nonlinear analysis. This lateral drift should be limited to the code boundaries. Calculation of this amplification factor for different structures, comparing with ASCE07-10 code and offering the best coefficient are the purposes of this research. Following our target, short and tall building steel structures with various earthquake resistant systems in linear and nonlinear analysis should be surveyed, so these questions will be answered: 1. Does the Response Modification Coefficient (R) have a meaningful relation to Deflection Amplification Factor? 2. Does structure height, seismic zone, response spectrum and similar parameters have an effect on the conversion coefficient of linear analysis to real drift of structure? The procedure has used to conduct this research includes: (a) Study on earthquake resistant systems, (b) Selection of systems and modeling, (c) Analyzing modeled systems using linear and nonlinear methods, (d) Calculating conversion coefficient for each system and (e) Comparing conversion coefficients with the code offered ones and concluding results.

Keywords: ASCE07-10 code, deflection amplification factor, earthquake engineering, lateral displacement of structures, response modification coefficient

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Authors: L. M. Al-Harbi, A. M. Shokry, J. S. M. Sabir, A. Chaudhary, J. Manikandan, K. S. Saini

Abstract:

Breast cancer is the second most common cause of cancer death worldwide and is the most common malignancy among Saudi females. During breast carcinogenesis, a wide-array of cytogenetic changes involving deletions, or amplification, or translocations, of part or whole of chromosome regions have been observed. Because of the limitations of various earlier technologies, newer tools are developed to scan for changes at the genomic level. Recently, Array Comparative Genomic Hybridization (aCGH) technique has been applied for detecting segmental genomic alterations at molecular level. In this study, aCGH was performed on twenty breast cancer tumors and their matching non-tumor (normal) counterparts using the Agilent 2x400K. Several regions were identified to be either amplified or deleted in a tumor-specific manner. Most frequent alterations were amplification of chromosome 1q, chromosome 8q, 20q, and deletions at 16q were also detected. The amplification of genetic events at 1q and 8q were further validated using FISH analysis using probes targeting 1q25 and 8q (MYC gene). The copy number changes at these loci can potentially cause a significant change in the tumor behavior, as deletions in the E-Cadherin (CDH1)-tumor suppressor gene as well as amplification of the oncogenes-Aurora Kinase A. (AURKA) and MYC could make these tumors highly metastatic. This study validates the use of aCGH in Saudi breast cancer patients and sets the foundations necessary for performing larger cohort studies searching for ethnicity-specific biomarkers and gene copy number variations.

Keywords: breast cancer, molecular biology, ecology, environment

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Authors: Huajuan Shi

Abstract:

Background: The biopsy of the preimplantation embryo may increase the potential risk and concern of embryo viability. Clinically discarded spent embryo medium (SEM) has entered the view of researchers, sparking an interest in noninvasive embryo screening. However, one of the major restrictions is the extremelty low quantity of cf-RNA, which is difficult to efficiently and unbiased amplify cf-RNA using traditional methods. Hence, there is urgently need to an efficient and low bias amplification method which can comprehensively and accurately obtain cf-RNA information to truly reveal the state of SEM cf-RNA. Result: In this present study, we established an agarose PCR amplification system, and has significantly improved the amplification sensitivity and efficiency by ~90 fold and 9.29 %, respectively. We applied agarose to sequencing library preparation (named AG-seq) to quantify and characterize cf-RNA in SEM. The number of detected cf-RNAs (3533 vs 598) and coverage of 3' end were significantly increased, and the noise of low abundance gene detection was reduced. The increasing percentage 5' end adenine and alternative splicing (AS) events of short fragments (< 400 bp) were discovered by AG-seq. Further, the profiles and characterizations of cf-RNA in spent cleavage medium (SCM) and spent blastocyst medium (SBM) indicated that 4‐mer end motifs of cf-RNA fragments could remarkably differentiate different embryo development stages. Significance: This study established an efficient and low-cost SEM amplification and library preparation method. Not only that, we successfully described the characterizations of SEM cf-RNA of preimplantation embryo by using AG-seq, including abundance features fragment lengths. AG-seq facilitates the study of cf-RNA as a noninvasive embryo screening biomarker and opens up potential clinical utilities of trace samples.

Keywords: cell-free RNA, agarose, spent embryo medium, RNA sequencing, non-invasive detection

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Authors: Mahdi Rahaie

Abstract:

MicroRNAs are a novel class of small RNAs which regulate gene expression by translational repression or degradation of messenger RNAs. To produce sensitive, simple and cost-effective assays for microRNAs, detection is in urgent demand due to important role of these biomolecules in progression of human disease such as Alzheimer’s, Multiple sclerosis, and some other neurodegenerative diseases. Herein, we report several novel, sensitive and specific microRNA nanobiosensors which were designed based on colorimetric and fluorescence detection of nanoparticles and hybridization chain reaction amplification as an enzyme-free amplification. These new strategies eliminate the need for enzymatic reactions, chemical changes, separation processes and sophisticated equipment whereas less limit of detection with most specify are acceptable. The important features of these methods are high sensitivity and specificity to differentiate between perfectly matched, mismatched and non-complementary target microRNAs and also decent response in the real sample analysis with blood plasma. These nanobiosensors can clinically be used not only for the early detection of neuro diseases but also for every sickness related to miRNAs by direct detection of the plasma microRNAs in real clinical samples, without a need for sample preparation, RNA extraction and/or amplification.

Keywords: hybridization chain reaction, microRNA, nanobiosensor, neurodegenerative diseases

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Authors: Akterono Budiyati, Gita Kusumo, Teguh Putra, Fritzie Rexana, Antonius Kurniawan, Aru Sudoyo, Ahmad Utomo, Andi Utama

Abstract:

The presence of the programmed death ligand-1 (PD-L1) has been used in multiple clinical trials and approved as biomarker for selecting patients more likely to respond to immune checkpoint inhibitors. However, the expression of PD-L1 is regulated in different ways, which leads to a different significance of its presence. Positive PD-L1 within tumors may result from two mechanisms, induced PD-L1 expression by T-cell presence or genetic mechanism that lead to constitutive PD-L1 expression. Amplification of PD-L1 genes was found as one of genetic mechanism which causes an increase in PD-L1 expression. In case of colorectal cancer (CRC), targeting immune checkpoint inhibitor has been recommended for patients with microsatellite instable (MSI). Although the correlation between PD-L1 expression and MSI status has been widely studied, so far the precise mechanism of PD-L1 gene activation in CRC patients, particularly in MSI population have yet to be clarified. In this present study we have profiled 61 archived formalin fixed paraffin embedded CRC specimens of patients from Medistra Hospital, Jakarta admitted in 2010 - 2016. Immunohistochemistry was performed to measure expression of PD-L1 in tumor cells as well as MSI status using antibodies against PD-L1 and MMR (MLH1, MSH2, PMS2 and MSH6), respectively. PD-L1 expression was measured on tumor cells with cut off of 1% whereas loss of nuclear MMR protein expressions in tumor cells but not in normal or stromal cells indicated presence of MSI. Subset of PD-L1 positive patients was then assessed for copy number variations (CNVs) using single Tube TaqMan Copy Number Assays Gene CD247PD-L1. We also observed KRAS mutation to profile possible genetic mechanism leading to the presence or absence of PD-L1 expression. Analysis of 61 CRC patients revealed 15 patients (24%) expressed PD-L1 on their tumor cell membranes. The prevalence of surface membrane PD-L1 was significantly higher in patients with MSI (87%; 7/8) compared to patients with microsatellite stable (MSS) (15%; 8/53) (P=0.001). Although amplification of PD-L1 gene was not found among PD-L1 positive patients, low-level amplification of PD-L1 gene was commonly observed in MSS patients (75%; 6/8) than in MSI patients (43%; 3/7). Additionally, we found 26% of CRC patients harbored KRAS mutations (16/61), so far the distribution of KRAS status did not correlate with PD-L1 expression. Our data suggest genetic mechanism through amplification of PD-L1 seems not to be the mechanism underlying upregulation of PD-L1 expression in CRC patients. However, further studies are warranted to confirm the results.

Keywords: colorectal cancer, gene amplification, microsatellite instable, programmed death ligand-1

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Authors: F. Tahiri, F. Grajçevci

Abstract:

The cities are coping with permanent demands to extend their residential and economical capacity. The new urban zones are sometimes induced to be developed in more vulnerable environments. This study is aimed to identify and mitigate the seismic hazards in the stage of urban planning for new settlements, including the existing urban environments which initially have not considered the seismic hazard. Seismic microzoning shall study the amplification/attenuation of seismic excitations from the bedrock to the ground surface. Modification of the seismic excitation is governed from the site specific ground conditions, presented on ground surface as mean values of the ratio of maximum accelerations at the surface versus acceleration of subsoil media – presented with dynamic amplification factors (DAF). The values shall be used to create the maps with isolines of DAF and then seismic microzoning with expected maximum mean surface acceleration as a product of DAF with maximum accelerations at bedrock. Development of resonant map shall conglomerate the information’s obtained from seismic microzoning in regard to expected predominant ground periods of seismic excitation and periods of vibrations of designed/built structures. These information’s shall be used as indispensible tool in early stages of urban planning to determine the most optimal zones for construction, the constructive materials, structural systems, range of buildings height, etc. so the resonance of soil media with built structures is avoided. The information’s could be used also for assessment of seismic risk and vulnerability-damageability of existing urban environments.

Keywords: vulnerable environment, mitigation, seismic microzoning, resonant map, urban planning

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Authors: Shreyas Srinivas Rangan, Jurgis Porins

Abstract:

The internet traffic has increased exponentially due to the high demand for data rates by the users, and the constantly increasing metro networks and access networks are focused on improving the maximum transmit distance of the long-reach optical networks. One of the common methods to improve the maximum transmit distance of the long-reach optical networks at the component level is to use broadband optical amplifiers. The Erbium Doped Fiber Amplifier (EDFA) provides high amplification with low noise figure but due to the characteristics of EDFA, its operation is limited to C-band and L-band. In contrast, the Raman amplifier exhibits a wide amplification spectrum, and negative noise figure values can be achieved. To obtain such results, high powered pumping sources are required. Operating Raman amplifiers with such high-powered optical sources may cause fire hazards and it may damage the optical system. In this paper, we implement a hybrid optical amplifier configuration. EDFA and Raman amplifiers are used in this hybrid setup to combine the advantages of both EDFA and Raman amplifiers to improve the reach of the system. Using this setup, we analyze the maximum transmit distance of the network by obtaining a correlation diagram between the length of the single-mode fiber (SMF) and the Bit Error Rate (BER). This hybrid amplifier configuration is implemented in a Wavelength Division Multiplexing (WDM) system with a BER of 10⁻⁹ by using NRZ modulation format, and the gain uniformity noise ratio (signal-to-noise ratio (SNR)), the efficiency of the pumping source, and the optical signal gain efficiency of the amplifier are studied experimentally in a mathematical modelling environment. Numerical simulations were implemented in RSoft OptSim simulation software based on the nonlinear Schrödinger equation using the Split-Step method, the Fourier transform, and the Monte Carlo method for estimating BER.

Keywords: Raman amplifier, erbium doped fibre amplifier, bit error rate, hybrid optical amplifiers

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Authors: Rafia Asghar, Abdul Hafeez

Abstract:

This research aims to determine the influence of Fibonacci numbers and golden ratio through textile designs. This study was carried out by collecting a variety of designs from different textile industries. Top textile designers were also interviewed regarding golden ratio and its application on their designs and design execution process. This study revealed that most of the designs fulfilled the golden ratio and the designs that were according to golden ratio were more favorite to the consumers.

Keywords: golden ratio, Fibonacci numbers, textile design, designs

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Authors: N. Benkaci, E. Oubaiche, J.-L. Chatelain, R. Bensalem, K. Abbes

Abstract:

The ambient vibration H/V technique is widely used nowadays in microzonation studies, because of its easy field handling and its low cost, compared to other geophysical methods. However, in presence of complex geology or lateral heterogeneity evidenced by more than one peak frequency in the H/V curve, it is difficult to interpret the results, especially when soil information is lacking. In this work, we focus on the construction site of the Baraki 40000=place stadium, located in the north-east side of the Mitidja basin (Algeria), to identify the seismic wave amplification zones. H/V curve analysis leads to the observation of spatial and time variability of the H/V frequency peaks. The spatial variability allows dividing the studied area into three main zones: (1) one with a predominant frequency around 1,5 Hz showing an important amplification level, (2) the second exhibits two peaks at 1,5 Hz and in the 4 Hz – 10 Hz range, and (3) the third zone is characterized by a plateau between 2 Hz and 3 Hz. These H/V curve categories reveal a consequent lateral heterogeneity dividing the stadium site roughly in the middle. Furthermore, a continuous ambient vibration recording during several weeks allows showing that the first peak at 1,5 Hz in the second zone, completely disappears between 2 am and 4 am, and reaching its maximum amplitude around 12 am. Consequently, the anthropogenic noise source generating these important variations could be the Algiers Rocade Sud highway, located in the maximum amplification azimuth direction of the H/V curves. This work points out that the H/V method is an important tool to perform nano-zonation studies prior to geotechnical and geophysical investigations, and that, in some cases, the H/V technique fails to reveal the resonance frequency in the absence of strong anthropogenic source.

Keywords: ambient vibrations, amplification, fundamental frequency, lateral heterogeneity, site effect

Procedia PDF Downloads 237