Search results for: simple sequence repeat (SSR)

Authors: Nicholas Mavrogiannis, Francesca Crivellari, Zachary Gagnon

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Development of low-cost, rapid, sensitive and portable biosensing systems are important for the detection and prevention of disease in developing countries, biowarfare/antiterrorism applications, environmental monitoring, point-of-care diagnostic testing and for basic biological research. Currently, the most established commercially available and widespread assays for portable point of care detection and disease testing are paper-based dipstick and lateral flow test strips. These paper-based devices are often small, cheap and simple to operate. The last three decades in particular have seen an emergence in these assays in diagnostic settings for detection of pregnancy, HIV/AIDS, blood glucose, Influenza, urinary protein, cardiovascular disease, respiratory infections and blood chemistries. Such assays are widely available largely because they are inexpensive, lightweight, and portable, are simple to operate, and a few platforms are capable of multiplexed detection for a small number of sample targets. However, there is a critical need for sensitive, quantitative and multiplexed detection capabilities for point-of-care diagnostics and for the detection and prevention of disease in the developing world that cannot be satisfied by current state-of-the-art paper-based assays. For example, applications including the detection of cardiac and cancer biomarkers and biothreat applications require sensitive multiplexed detection of analytes in the nM and pM range, and cannot currently be satisfied with current inexpensive portable platforms due to their lack of sensitivity, quantitative capabilities and often unreliable performance. In this talk, inexpensive label-free biomolecular detection at liquid interfaces using a newly discovered electrokinetic phenomenon known as fluidic dielectrophoresis (fDEP) is demonstrated. The electrokinetic approach involves exploiting the electrical mismatches between two aqueous liquid streams forced to flow side-by-side in a microfluidic T-channel. In this system, one fluid stream is engineered to have a higher conductivity relative to its neighbor which has a higher permittivity. When a “low” frequency (< 1 MHz) alternating current (AC) electrical field is applied normal to this fluidic electrical interface the fluid stream with high conductivity displaces into the low conductive stream. Conversely, when a “high” frequency (20MHz) AC electric field is applied, the high permittivity stream deflects across the microfluidic channel. There is, however, a critical frequency sensitive to the electrical differences between each fluid phase – the fDEP crossover frequency – between these two events where no fluid deflection is observed, and the interface remains fixed when exposed to an external field. To perform biomolecular detection, two streams flow side-by-side in a microfluidic T-channel: one fluid stream with an analyte of choice and an adjacent stream with a specific receptor to the chosen target. The two fluid streams merge and the fDEP crossover frequency is measured at different axial positions down the resulting liquid

Keywords: biodetection, fluidic dielectrophoresis, interfacial polarization, liquid interface

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Authors: Piotr Kacejko, Mariusz Duk, Miroslaw Wendeker

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This paper presents an adaptive controller to track the maximum power point of a photovoltaic modules (PV) under fast irradiation change on the city-bus roof. Photovoltaic systems have been a prominent option as an additional energy source for vehicles. The Municipal Transport Company (MPK) in Lublin has installed photovoltaic panels on its buses roofs. The solar panels turn solar energy into electric energy and are used to load the buses electric equipment. This decreases the buses alternators load, leading to lower fuel consumption and bringing both economic and ecological profits. A DC–DC boost converter is selected as the power conditioning unit to coordinate the operating point of the system. In addition to the conversion efficiency of a photovoltaic panel, the maximum power point tracking (MPPT) method also plays a main role to harvest most energy out of the sun. The MPPT unit on a moving vehicle must keep tracking accuracy high in order to compensate rapid change of irradiation change due to dynamic motion of the vehicle. Maximum power point track controllers should be used to increase efficiency and power output of solar panels under changing environmental factors. There are several different control algorithms in the literature developed for maximum power point tracking. However, energy performances of MPPT algorithms are not clarified for vehicle applications that cause rapid changes of environmental factors. In this study, an adaptive MPPT algorithm is examined at real ambient conditions. PV modules are mounted on a moving city bus designed to test the solar systems on a moving vehicle. Some problems of a PV system associated with a moving vehicle are addressed. The proposed algorithm uses a scanning technique to determine the maximum power delivering capacity of the panel at a given operating condition and controls the PV panel. The aim of control algorithm was matching the impedance of the PV modules by controlling the duty cycle of the internal switch, regardless of changes of the parameters of the object of control and its outer environment. Presented algorithm was capable of reaching the aim of control. The structure of an adaptive controller was simplified on purpose. Since such a simple controller, armed only with an ability to learn, a more complex structure of an algorithm can only improve the result. The presented adaptive control system of the PV system is a general solution and can be used for other types of PV systems of both high and low power. Experimental results obtained from comparison of algorithms by a motion loop are presented and discussed. Experimental results are presented for fast change in irradiation and partial shading conditions. The results obtained clearly show that the proposed method is simple to implement with minimum tracking time and high tracking efficiency proving superior to the proposed method. This work has been financed by the Polish National Centre for Research and Development, PBS, under Grant Agreement No. PBS 2/A6/16/2013.

Keywords: adaptive control, photovoltaic energy, city bus electric load, DC-DC converter

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Authors: Regita P. Permata, Ulfa S. Nuraini

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Traveling Salesman Problem (TSP) is the most studied problem in combinatorial optimization. In simple language, TSP can be described as a problem of finding a minimum distance tour to a city, starting and ending in the same city, and exactly visiting another city. In product distribution, companies often get problems in determining the minimum distance that affects the time allocation. In this research, we aim to apply TSP heuristic methods to simulate nodes as city coordinates in product distribution. The heuristics used are sub tour reversal, nearest neighbor, farthest insertion, cheapest insertion, nearest insertion, and arbitrary insertion. We have done simulation nodes using Euclidean distances to compare the number of cities and processing time, thus we get optimum heuristic method. The results show that the optimum heuristic methods are farthest insertion and nearest insertion. These two methods can be recommended to solve product distribution problems in certain companies.

Keywords: Euclidean, heuristics, simulation, TSP

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Authors: Yakup Sahin, Naim Suleyman Ting, Ismail Aksoy

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In this paper, a single phase soft switched Zero Voltage Transition and Zero Current Transition (ZVT-ZCT) Power Factor Correction (PFC) boost converter is proposed. In the proposed PFC converter, the main switch turns on with ZVT and turns off with ZCT without any additional voltage or current stresses. Auxiliary switch turns on and off with zero current switching (ZCS). Also, the main diode turns on with zero voltage switching (ZVS) and turns off with ZCS. The proposed converter has features like low cost, simple control and structure. The output current and voltage are controlled by the proposed PFC converter in wide line and load range. The theoretical analysis of converter is clarified and the operating steps are given in detail. The simulation results of converter are obtained for 500 W and 100 kHz. It is observed that the semiconductor devices operate with soft switching (SS) perfectly. So, the switching power losses are minimum. Also, the proposed converter has 0.99 power factor with sinusoidal current shape.

Keywords: power factor correction, zero-voltage transition, zero-current transition, soft switching

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Authors: Márcia Afonso, Cristina Fael, Marisa Dinis-Almeida

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Population growth in cities has led to an increase in the infrastructures construction, including buildings and roadways. This aspect leads directly to the soils waterproofing. In turn, changes in precipitation patterns are developing into higher and more frequent intensities. Thus, these two conjugated aspects decrease the rainwater infiltration into soils and increase the volume of surface runoff. The practice of green and sustainable urban solutions has encouraged research in these areas. The porous asphalt pavement, as a green infrastructure, is part of practical solutions set to address urban challenges related to land use and adaptation to climate change. In this field, permeable pavements with porous asphalt mixtures (PA) have several advantages in terms of reducing the runoff generated by the floods. The porous structure of these pavements, compared to a conventional asphalt pavement, allows the rainwater infiltration in the subsoil, and consequently, the water quality improvement. This green infrastructure solution can be applied in cities, particularly in streets or parking lots to mitigate the floods effects. Over the years, the pores of these pavements can be filled by sediment, reducing their function in the rainwater infiltration. Thus, double layer porous asphalt (DLPA) was developed to mitigate the clogging effect and facilitate the water infiltration into the lower layers. This study intends to deepen the knowledge of the performance of DLPA when subjected to clogging. The experimental methodology consisted on four evaluation phases of the DLPA infiltration capacity submitted to three precipitation events (100, 200 and 300 mm/h) in each phase. The evaluation first phase determined the behavior after DLPA construction. In phases two and three, two 500 g/m² clogging cycles were performed, totaling a 1000 g/m² final simulation. Sand with gradation accented in fine particles was used as clogging material. In the last phase, the DLPA was subjected to simple sweeping and vacuuming maintenance. A precipitation simulator, type sprinkler, capable of simulating the real precipitation was developed for this purpose. The main conclusions show that the DLPA has the capacity to drain the water, even after two clogging cycles. The infiltration results of flows lead to an efficient performance of the DPLA in the surface runoff attenuation, since this was not observed in any of the evaluation phases, even at intensities of 200 and 300 mm/h, simulating intense precipitation events. The infiltration capacity under clogging conditions decreased about 7% on average in the three intensities relative to the initial performance that is after construction. However, this was restored when subjected to simple maintenance, recovering the DLPA hydraulic functionality. In summary, the study proved the efficacy of using a DLPA when it retains thicker surface sediments and limits the fine sediments entry to the remaining layers. At the same time, it is guaranteed the rainwater infiltration and the surface runoff reduction and is therefore a viable solution to put into practice in permeable pavements.

Keywords: clogging, double layer porous asphalt, infiltration capacity, rainfall intensity

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Authors: Yi-Lin Chen, Sheng-Jou Hung, Tsunglin Liu

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Adaptive immune system recognizes a wide range of antigens via expressing a large number of structurally distinct T cell and B cell receptor genes. The distinct receptor genes arise from complex rearrangements called V(D)J recombination, and constitute the immune repertoire. A common method of profiling immune repertoire is via amplifying recombined receptor genes using multiple primers and high-throughput sequencing. This multiplex-PCR approach is efficient; however, the resulting repertoire can be distorted because of primer bias. To eliminate primer bias, 5’ RACE is an alternative amplification approach. However, the application of RACE approach is limited by its low efficiency (i.e., the majority of data are non-regular receptor sequences, e.g., containing intronic segments) and lack of the convenient tool for analysis. We propose a computational tool that can correctly identify non-regular receptor sequences in RACE data via aligning receptor sequences against the whole gene instead of only the exon regions as done in all other tools. Using our tool, the remaining regular data allow for an accurate profiling of immune repertoire. In addition, a RACE approach is improved to yield a higher fraction of regular T-cell receptor sequences. Finally, we quantify the degree of primer bias of a multiplex-PCR approach via comparing it to the RACE approach. The results reveal significant differences in frequency of VJ combination by the two approaches. Together, we provide a new experimental and computation pipeline for an unbiased profiling of immune repertoire. As immune repertoire profiling has many applications, e.g., tracing bacterial and viral infection, detection of T cell lymphoma and minimal residual disease, monitoring cancer immunotherapy, etc., our work should benefit scientists who are interested in the applications.

Keywords: immune repertoire, T-cell receptor, 5' RACE, high-throughput sequencing, sequence alignment

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Authors: Neelamshobha Nirala, R. Periyasamy, Awanish Kumar

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Diabetes is a metabolic disorder and with the increase of global prevalence of diabetes, cardiovascular diseases and mortality related to diabetes has also increased. Diabetes causes the increase of arterial stiffness by elusive hormonal and metabolic abnormalities. We used photoplethysmograph (PPG), a simple non-invasive method to study the change in arterial stiffness due to diabetes. Toe PPG signals were taken from 29 diabetic subjects with mean age of (65±8.4) years and 21 non-diabetic subjects of mean age of (49±14) years. Mean duration of diabetes is 12±8 years for diabetic group. Rise-time (RT) and area under rise time (AUR) were calculated from the PPG signal of each subject and Welch’s t-test is used to find the significant difference between two groups. We obtained a significant difference of (p-value) 0.0005 and 0.03 for RT and AUR respectively between diabetic and non-diabetic subjects. Average value of RT and AUR is 0.298±0.003 msec and 14.4±4.2 arbitrary units respectively for diabetic subject compared to 0.277±0.0005 msec and 13.66±2.3 a.u respectively for non-diabetic subjects. In conclusion, this study support that arterial stiffness is increased in diabetes and can be detected early using PPG.

Keywords: area under rise-time, AUR, arterial stiffness, diabetes, photoplethysmograph, PPG, rise-time (RT)

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Authors: N. W. U. D. Chathurani, Shlomo Geva, Vinod Chandran, Proboda Rajapaksha

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Selecting an appropriate image representation is the most important factor in implementing an effective Content-Based Image Retrieval (CBIR) system. This paper presents a multi-feature fusion approach for efficient CBIR, based on the distance distribution of features and relative feature weights at the time of query processing. It is a simple yet effective approach, which is free from the effect of features' dimensions, ranges, internal feature normalization and the distance measure. This approach can easily be adopted in any feature combination to improve retrieval quality. The proposed approach is empirically evaluated using two benchmark datasets for image classification (a subset of the Corel dataset and Oliva and Torralba) and compared with existing approaches. The performance of the proposed approach is confirmed with the significantly improved performance in comparison with the independently evaluated baseline of the previously proposed feature fusion approaches.

Keywords: feature fusion, image retrieval, membership function, normalization

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Authors: Ali Dulla

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This paper introduces a new dataset (and the methodology used to generate it) based on a wide range of historical Arabic documents containing clean data simple and homogeneous-page layouts. The experiments are implemented on printed and handwritten documents obtained respectively from some important libraries such as Qatar Digital Library, the British Library and the Library of Congress. We have gathered and commented on 150 archival document images from different locations and time periods. It is based on different documents from the 17th-19th century. The dataset comprises differing page layouts and degradations that challenge text line segmentation methods. Ground truth is produced using the Aletheia tool by PRImA and stored in an XML representation, in the PAGE (Page Analysis and Ground truth Elements) format. The dataset presented will be easily available to researchers world-wide for research into the obstacles facing various historical Arabic documents such as geometric correction of historical Arabic documents.

Keywords: dataset production, ground truth production, historical documents, arbitrary warping, geometric correction

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Authors: Dalila Hammiche, Lisa Klaai, Sonia Imzi, Amar Boukerrou

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The fight against plastic pollution implies the development of polymers as alternatives to synthetic polymers. Starch is a natural polymer that can easily be plasticized by means of additives. The objective of this work is to develop and characterize biodegradable biofilms based on starch, plasticized by glycerol (20 and 30%). The elaboration of the biofilms was carried out by the casting method under simple conditions. The samples were characterized by infrared spectroscopy analysis with Fourier transform (FTIR), thermogravimetric analysis, and biodegradability test. Infrared spectral analysis showed that the 30% and 20% glycerol films have the same chemical structure and no functional group changes occurred. Thermogravimetric analysis showed that a 30% glycerol film has higher thermal stability than a 20% glycerol film. Biodegradability test showed that the lower the percentage of glycerol, the more easily the biofilm degrades.

Keywords: starch, natural sources, FTIR, thermogravimetric analysis, biodegradability test

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Authors: Elsie L. Echeverri-Carroll

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Entrepreneurial ecosystems have become an important concept to explain the birth and sustainability of technology-based entrepreneurship within regions. However, as a theoretical concept, the temporal evolution of entrepreneurship systems remain underdeveloped, making it difficult to understand their dynamic contributions to entrepreneurs. This paper argues that successful technology-based ecosystems go over three cumulative spawning stages: corporate spawning, entrepreneurial spawning, and community spawning. The importance of corporate incubation in vibrant entrepreneurial ecosystems is well documented in the entrepreneurial literature. Similarly, entrepreneurial spawning processes for venture capital-backed startups are well documented in the financial literature. In contrast, there is little understanding of both the third stage of entrepreneurial spawning (when a community of entrepreneurs become a source of firm spawning) and the temporal sequence in which spawning effects occur in a region. We test this three-stage model of entrepreneurial spawning using data from two large databases on firm births—the Secretary of State (160,000 observations) and the National Establishment Time Series (NEST with 150,000 observations)—and information collected from 60 1½-hour interviews with startup founders and representatives of key entrepreneurial organizations. This temporal model is illustrated with case study of Austin, Texas ranked by the Kauffman Foundation as the number one entrepreneurial city in the United States in 2015 and 2016. The 1½-year study founded by the Kauffman Foundation demonstrates the importance of taken into consideration the temporal contributions of both large and entrepreneurial firms in understanding the factors that contribute to the birth and growth of technology-based entrepreneurial regions. More important, these learnings could offer an important road map for regions that pursue to advance their entrepreneurial ecosystems.

Keywords: entrepreneurial ecosystems, entrepreneurial industrial clusters, high-technology, temporal changes

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Authors: Shaher Bano, Samia Fida, Asif Israr

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The synergistic effect of properties of metals and fibers reinforced laminates has diverted attention of the world towards use of robust composite materials known as fiber-metal laminates in many high performance applications. In this study, modification of an adhesively bonded joint as a single lap joint of carbon fibers based CARALL FML has done to increase interlaminar shear strength of the joint. The effect of different configurations of joint designs such as spews, stepped and modification in adhesive by addition of nano-fillers was studied. Both experimental and simulation results showed that modified joint design have superior properties as maximum force experienced stepped joint was 1.5 times more than the simple lap joint. Addition of carbon nano-tubes as nano-fillers in the adhesive joint increased the maximum force due to crack deflection mechanism.

Keywords: adhesive joint, Carbon Reinforced Aluminium Laminate (CARALL), fiber metal laminates, spews

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Authors: Jeyaseelan Maria Michael

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This study investigated the prevalence of cyberbullying among college female students and its effects on their psychological well-being. The respondents were from the age group of 17 and 18, doing the first-year college in Tamilnadu, India. In this study, 110 participants were selected through simple random sampling. The standardized questionnaire of David Alvare-Garcia’s Cybervictimization Questionnaire for Adolescents (CYVIC) and Ryff’s Psychological Well-Being (PWB) were administered for data collection. CYVIC has four subdomains namely, impersonation, visual-sexual cybervictimization, written-verbal cybervictimization, online exclusion. Ryff’s PWB has six domains namely, autonomy, environmental mastery, personal growth, positive relations with others, purpose in life, and self- acceptance. The collected data were analyzed by SPSS v.23. The results indicate that cyberbullying prevails among college female students (M=1.24, SD= .21). Among the participants, 17 are scored one standard deviation above the mean (1.45). Among the subdomains of the CYVIC, the respondents have the highest score (M=1.40, SD= .38) in written-verbal cybervictimization. Cyber victimization has a significant correlation at the 0.01 level with psychological well-being.

Keywords: college students, cyberbullying, cyber victimization, psychological well-being

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Authors: Alena Semeradtova, Marcel Stofik, Lucie Mareckova, Petr Maly, Ondrej Stanek, Jan Maly

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Recently, novel strategies based on so-called molecular evolution were shown to be effective for the production of various peptide ligand libraries with high affinities to molecular targets of interest comparable or even better than monoclonal antibodies. The major advantage of these peptide scaffolds is mainly their prevailing low molecular weight and simple structure. This study describes a new high-affinity binding molecules based immunesensor using a simple optical system for human serum albumin (HSA) detection as a model molecule. We present a comparison of two variants of recombinant binders based on albumin binding domain of the protein G (ABD) performed on micropatterned glass chip. Binding domains may be tailored to any specific target of interest by molecular evolution. Micropatterened glass chips were prepared using UV-photolithography on chromium sputtered glasses. Glass surface was modified by (3-aminopropyl)trietoxysilane and biotin-PEG-acid using EDC/NHS chemistry. Two variants of high-affinity binding molecules were used to detect target molecule. Firstly, a variant is based on ABD domain fused with TolA chain. This molecule is in vivo biotinylated and each molecule contains one molecule of biotin and one ABD domain. Secondly, the variant is ABD domain based on streptavidin molecule and contains four gaps for biotin and four ABD domains. These high-affinity molecules were immobilized to the chip surface via biotin-streptavidin chemistry. To eliminate nonspecific binding 1% bovine serum albumin (BSA) or 6% fetal bovine serum (FBS) were used in every step. For both variants range of measured concentrations of fluorescently labelled HSA was 0 – 30 µg/ml. As a control, we performed a simultaneous assay without high-affinity binding molecules. Fluorescent signal was measured using inverse fluorescent microscope Olympus IX 70 with COOL LED pE 4000 as a light source, related filters, and camera Retiga 2000R as a detector. The fluorescent signal from non-modified areas was substracted from the signal of the fluorescent areas. Results were presented in graphs showing the dependence of measured grayscale value on the log-scale of HSA concentration. For the TolA variant the limit of detection (LOD) of the optical immunosensor proposed in this study is calculated to be 0,20 µg/ml for HSA detection in 1% BSA and 0,24 µg/ml in 6% FBS. In the case of streptavidin-based molecule, it was 0,04 µg/ml and 0,07 µg/ml respectively. The dynamical range of the immunosensor was possible to estimate just in the case of TolA variant and it was calculated to be 0,49 – 3,75 µg/ml and 0,73-1,88 µg/ml respectively. In the case of the streptavidin-based the variant we didn´t reach the surface saturation even with the 480 ug/ml concentration and the upper value of dynamical range was not estimated. Lower value was calculated to be 0,14 µg/ml and 0,17 µg/ml respectively. Based on the obtained results, it´s clear that both variants are useful for creating the bio-recognizing layer on immunosensors. For this particular system, it is obvious that the variant based on streptavidin molecule is more useful for biosensing on glass planar surfaces. Immunosensors based on this variant would exhibit better limit of detection and wide dynamical range.

Keywords: high affinity binding molecules, human serum albumin, optical immunosensor, protein G, UV-photolitography

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Authors: Natascha C. D'Amico, Enzo Grossi, Giovanni Valbusa, Ala Malasevschi, Gianpiero Cardone, Sergio Papa

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Purpose: To characterize, through a radiomic approach, the nature of areas classified PI-RADS (Prostate Imaging Reporting and Data System) 3/5, recognized in multiparametric prostate magnetic resonance with T2-weighted (T2w), diffusion and perfusion sequences with paramagnetic contrast. Methods and Materials: 24 cases undergoing multiparametric prostate MR and biopsy were admitted to this pilot study. Clinical outcome of the PI-RADS 3/5 was found through biopsy, finding 8 malignant tumours. The analysed images were acquired with a Philips achieva 1.5T machine with a CE- T2-weighted sequence in the axial plane. Semi-automatic tumour segmentation was carried out on MR images using 3DSlicer image analysis software. 45 shape-based, intensity-based and texture-based features were extracted and represented the input for preprocessing. An evolutionary algorithm (a TWIST system based on KNN algorithm) was used to subdivide the dataset into training and testing set and select features yielding the maximal amount of information. After this pre-processing 20 input variables were selected and different machine learning systems were used to develop a predictive model based on a training testing crossover procedure. Results: The best machine learning system (three-layers feed-forward neural network) obtained a global accuracy of 90% ( 80 % sensitivity and 100% specificity ) with a ROC of 0.82. Conclusion: Machine learning systems coupled with radiomics show a promising potential in distinguishing benign from malign tumours in PI-RADS 3/5 areas.

Keywords: machine learning, MR prostate, PI-Rads 3, radiomics

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Authors: Sun-Ki Hong, Yong-Ho Cho, Ki-Seok Kim, Tae-Sam Kang

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Piezoelectric actuator is treated as RC load when it is modeled electrically. For some piezoelectric actuator applications, arbitrary voltage is required to actuate. Especially for unidirectional arbitrary voltage driving like as sine wave, some special inverter with circuit that can charge and discharge the capacitive energy can be used. In this case, the difference between power supply level and the object voltage level for RC load is varied. Because the control gain is constant, the controlled output is not uniform according to the voltage difference. In this paper, for charge and discharge circuit for unidirectional arbitrary voltage driving for piezoelectric actuator, the controller gain is controlled according to the voltage difference. With the proposed simple idea, the load voltage can have controlled smoothly although the voltage difference is varied. The appropriateness is proved from the simulation of the proposed circuit.

Keywords: analog voltage inverter, capacitive load, gain control, dc-dc converter, piezoelectric, voltage waveform

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Authors: Martynova Alina, Lyubov Buzoleva

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Streptococcus pneumoniae is the causative agent of pneumonias and meningitids throught all the world. Having high genetic diversity, this microorganism can cause different clinical forms of pneumococcal infections and microbiologically it is really difficult diagnosed by routine methods. Also, epidemiological surveillance requires more developed methods of molecular typing because the recent method of serotyping doesn't allow to distinguish invasive and non-invasive isolates properly. Non-coding genome of bacteria seems to be the interesting source for seeking of highly distinguishable markers to discriminate the subspecies of such a variable bacteria as Streptococcus pneumoniae. Technically, we proposed scheme of discrimination of S.pneumoniae strains with amplification of non-coding region (SP_1932) with the following restriction with 2 types of enzymes of Alu1 and Mn1. Aim: This research aimed to compare different methods of typing and their application for molecular epidemiology purposes. Methods: we analyzed population of 100 strains of S.pneumoniae isolated from different patients by different molecular epidemiology methods such as pulse-field gel electophoresis (PFGE), restriction polymorphism analysis (RFLP) and multilolocus sequence typing (MLST), and all of them were compared with classic typing method as serotyping. The discriminative power was estimated with Simpson Index (SI). Results: We revealed that the most discriminative typing method is RFLP (SI=0,97, there were distinguished 42 genotypes).PFGE was slightly less discriminative (SI=0,95, we identified 35 genotypes). MLST is still the best reference method (SI=1.0). Classic method of serotyping showed quite weak discriminative power (SI=0,93, 24 genotypes). In addition, sensivity of RFLP was 100%, specificity was 97,09%. Conclusion: the most appropriate method for routine epidemiology surveillance is RFLP with non-coding region of Streptococcsu pneumoniae, then PFGE, though in some cases these results should be obligatory confirmed by MLST.

Keywords: molecular epidemiology typing, non-coding genome, Streptococcus pneumoniae, MLST

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Authors: Mevlüt Burak Dalmış, Kemal Yaman

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In this study, flutter characteristics of cantilever rectangular plate structure under incompressible flow regime are investigated by comparing the results of commercial flutter analysis program ZAERO^© with wind tunnel tests conducted in Ankara Wind Tunnel (ART). A rectangular polycarbonate (PC) plate, 5x125x1000 mm in dimensions, is used for both numerical and experimental investigations. Analysis and test results are very compatible with each other. A comparison between two different solution methods (g and k-method) of ZAERO^© is also done. It is seen that, k-method gives closer result than the other one. However, g-method results are on conservative side and it is better to use conservative results namely g-method results. Even if the modal analysis results are used for the flutter analysis for this simple structure, a modal test should be conducted in order to validate the modal analysis results to have accurate flutter analysis results for more complicated structures.

Keywords: flutter, plate, subsonic flow, wind tunnel

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Authors: Zainul A. Khan, Malik Z. Abdin, Jawaid A. Khan

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Begomoviruses belonging to the family Geminiviridae, have single-stranded circular DNA genomes that are monopartite or bipartite. The large intergenic region (LIR) of the monopartite and common region (CR) of bipartite begomoviruses possess promoter activity in their genomes. In this study, we have characterized novel bidirectional promoters from Cotton leaf curl Burewala virus (CLCuBuV) genome using high-throughput software and analyzed with PlantCARE, PLACE, Cister and PlantPAN databases. The promoters (Rep and CP promoters) were assayed both in stable and transient expression systems in tobacco as well as cotton plants. Rep and CP-based promoters from the LIR sequence of CLCuBuV and 35S promoter of Cauliflower mosaic virus (CaMV) were tagged with β-glucuronidase (GUS) and green fluorescent protein (GFP) reporter genes to check the efficacy of the promoters. Histochemical staining of GUS in transformed tobacco (Nicotiana tabacum cv. Xanthi) leaves showed higher GUS expression driven by CLCuBuV Rep (complimentary sense) promoter as compared to conventional CaMV 35S promoter and CLCuBuV CP (virion sense) promoter, respectively. GUS activity in individual plant cells driven by CLCuBuV Rep, CLCuBuV CP, and CaMV 35S promoter were quantified through fluorometric GUS assay and reverse transcription quantitative real-time PCR (RT-qPCR). The expression level of GUS tagged with CLCuBuV Rep promoter in the transformed tobacco plants was obtained 2 to 4 fold higher than CaMV 35S promoter. When CLCuBuV CP promoter was used, lower expression level was monitored than that by CaMV 35S promoter. The expression of GFP-tagged with CLCuBuV promoters was also investigated through agroinfiltration. The CLCuBuV Rep promoters showed stronger consistent transient expression in the leaves of N. benthamiana, N. tabacum and Gossypium hirsutum plants when compared with CaMV 35S and CLCuBuV CP promoter.

Keywords: Begmovirus, bidirectional promoter, CaMV 35S promoter, GFP, GUS, qPCR

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Authors: Djalal Hamed

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The aim of this paper is to perform an analytic solution of steady state natural convection in a narrow rectangular channel between two vertical parallel MTR-type fuel plates, imposed under a cosine shape heat flux to determine the margin of the nuclear core power at which the natural convection cooling mode can ensure a safe core cooling, where the cladding temperature should not be reach the specific safety limits (90 °C). For this purpose, a simple computer program is developed to determine the principal parameter related to the nuclear core safety such as the temperature distribution in the fuel plate and in the coolant (light water) as a function of the reactor power. Our results are validated throughout a comparison against the results of another published work, which is considered like a reference of this study.

Keywords: buoyancy force, friction force, natural convection, thermal hydraulic analysis, vertical heated rectangular channel

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Authors: Maxim Panov, Evgenia Khairullina, Sergey Ermakov, Oleg Gundobin, Vladimir Kochemirovsky

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The continuous in situ laser-induced catalysis proceeding via generation and growth of nano-sized copper particles was discussed. Also, the simple and lost-cost method for manufacturing of microstructural copper electrodes was proposed. The electrochemical properties of these electrodes were studied by cyclic voltammetry and impedance spectroscopy. The surface of the deposited copper structures (electrodes) was investigated by X-ray photoelectron spectroscopy and atomic force microscopy. These microstructures are highly conductive and porous with a dispersion of pore size ranging from 50 nm to 50 μm. An analytical response of the fabricated copper electrode is 30 times higher than those observed for a pure bulk copper with similar geometric parameters. A study of sensory characteristics for hydrogen peroxide determination showed that the value of Faraday current at the fabricated copper electrode is 2-2.5 orders of magnitude higher than for etalon one.

Keywords: laser-induced deposition, electrochemical electrodes, non-enzymatic sensors, copper

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Authors: Tran Trong Thang, Nguyen Phan Kien, Trinh Quang Duc

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The phased-array ultrasound transducer types are utilities for medical ultrasonography as well as optical imaging. However, their discontinuity characteristic limits the applications due to the artifacts contaminated into the reconstructed images. Because of the effects of the ultrasound pressure field pattern to the echo ultrasonic waves as well as the optical modulated signal, the side lobes of the focused ultrasound beam induced by discontinuity of the phased-array ultrasound transducer might the reason of the artifacts. In this paper, a simple method in approach of numerical simulation was used to investigate the limitation of discontinuity of the elements in phased-array ultrasound transducer and their effects to the ultrasound pressure field. Take into account the change of ultrasound pressure field patterns in the conditions of variation of the pitches between elements of the phased-array ultrasound transducer, the appropriated parameters for phased-array ultrasound transducer design were asserted quantitatively.

Keywords: phased-array ultrasound transducer, sound pressure pattern, discontinuous sound field, numerical visualization

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Authors: Rami El-Hajj Mohamad, Mahmoud Skafi, Ali Massoud Haidar

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Several meteorological parameters were used for the prediction of monthly average daily global solar radiation on horizontal using recurrent neural networks (RNNs). Climatological data and measures, mainly air temperature, humidity, sunshine duration, and wind speed between 1995 and 2007 were used to design and validate a feed forward and recurrent neural network based prediction systems. In this paper we present our reference system based on a feed-forward multilayer perceptron (MLP) as well as the proposed approach based on an RNN model. The obtained results were promising and comparable to those obtained by other existing empirical and neural models. The experimental results showed the advantage of RNNs over simple MLPs when we deal with time series solar radiation predictions based on daily climatological data.

Keywords: recurrent neural networks, global solar radiation, multi-layer perceptron, gradient, root mean square error

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Authors: Victor Prevost, Solene Landerneau, Michel Duhamel, Joel Sternheimer, Olivier Gallet, Pedro Ferrandiz, Marwa Mokni

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The search for homologous proteins is one of the ongoing challenges in biology and bioinformatics. Traditionally, a pair of proteins is thought to be homologous when they originate from the same ancestral protein. In such a case, their sequences share similarities, and advanced scientific research effort is spent to investigate this question. On this basis, we propose the Protein-Wave Alignment Tool (”P-WAT”) developed within the framework of the France Relance 2030 plan. Our work takes into consideration the mass-related wave aspect of protein biosynthesis, by associating specific frequencies to each amino acid according to its mass. Amino acids are then regrouped within their mass category. This way, our algorithm produces specific alignments in addition to those obtained with a common amino acid coding system. For this purpose, we develop the ”P-WAT” original algorithm, able to address large protein databases, with different attributes such as species, protein names, etc. that allow us to align user’s requests with a set of specific protein sequences. The primary intent of this algorithm is to achieve efficient alignments, in this specific conceptual frame, by minimizing execution costs and information loss. Our algorithm identifies sequence similarities by searching for matches of sub-sequences of different sizes, referred to as primers. Our algorithm relies on Boolean operations upon a dot plot matrix to identify primer amino acids common to both proteins which are likely to be part of a significant alignment of peptides. From those primers, dynamic programming-like traceback operations generate alignments and alignment scores based on an adjusted PAM250 matrix.

Keywords: protein, alignment, homologous, Genodic

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Authors: Mona Vijayaran, Gurleen Oberoi, Sanjay Mishra

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Introduction: p190 BCR‐ABL1 in CML is often associated with monocytosis. In the case described here, monocytosis is associated with coexisting p210 BCR‐ABL and CMML clones. Mutation analysis using next‐generation sequence (NGS) in our case showed TET2 and SRSF2 mutations. Aims & Objectives: A 75-year male was evaluated for monocytosis and thrombocytopenia. CBC showed Hb-11.8g/dl, TLC-12,060/cmm, Monocytes-35%, Platelets-39,000/cmm. Materials & Methods: Bone marrow examination showed a hypercellular marrow with myeloid series showing sequential maturation up to neutrophils with 30% monocytes. Immunophenotyping by flow cytometry from bone marrow had 3% blasts. Making chronic myelomonocytic leukemia as the likely diagnosis. NGS for myeloid mutation panel had TET2 (48.9%) and SRSF2 (32.5%) mutations. This report further supported the diagnosis of CMML. To fulfil the WHO diagnostic criteria for CMML, a BCR ABL1 by RQ-PCR was sent. The report came positive for p210 (B3A2, B2A2) Major Transcript (M-BCR) % IS of 38.418. Result: The patient was counselled regarding the unique presentation of the presence of 2 clones- P210 CML and CMML. After discussion with an international faculty with vast experience in CMML. It was decided to start this elderly gentleman on Imatinib 200mg and not on azacytidine, as ASXL1 was not present; hence, his chances of progressing to AML would be less and on the other end, if CML is left untreated then chances of progression to blast phase would always be a possibility. After 3 months on Imatinib his platelet count improved to 80,000 to 90,000/cmm, but his monocytosis persists. His 3rd month BCR-ABL1 IS% is 0.004%. Conclusion: After searching the literature, there were no case reports of a coexisting CML p210 with CMML. This case might be the first case report. p190 BCR ABL1 is often associated with monocytosis. There are few case reports of p210 BCR ABL1 positivity in patients with monocytosis but none with coexisting CMML. This case highlights the need for extensively evaluating patients with monocytosis with next-generation sequencing for myeloid mutation panel and BCR-ABL1 by RT-PCR to correctly diagnose and treat them.

Keywords: CMML, NGS, p190 CML, Imatinib

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Authors: Muizz Sanni-Anibire

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The 21st century has witnessed growing concerns for the protection of built facilities against natural and man-made disasters. Studies in earthquake resistant buildings, fire, and explosion resistant buildings now dominate the arena. To protect people and facilities from the effects of the explosion, reinforced concrete walls have been designed to be blast resistant. Understanding the performance of these walls is a key step in ensuring the safety of built facilities. Blast walls are mostly designed using simple techniques such as single degree of freedom (SDOF) method, despite the increasing use of multi-degree of freedom techniques such as the finite element method. This study is the first stage of a continuous research into the safety and reliability of blast walls. It presents the SDOF approach applied to the analysis of a concrete wall panel under three representative bomb situations. These are motorcycle 50 kg, car 400kg and also van with the capacity of 1500 kg of TNT explosive.

Keywords: blast wall, safety, protection, explosion

Procedia PDF Downloads 253

Authors: Doga Erisik, Ahmet Karaman, Gulfem Alptekin, Ozlem Durmaz Incel

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Augmented reality (AR) is a type of virtual reality aiming to duplicate real world’s environment on a computer’s video feed. The mobile application, which is built for this project (called SARAS), enables annotating real world point of interests (POIs) that are located near mobile user. In this paper, we aim at introducing a robust and simple algorithm for placing labels in an augmented reality system. The system places labels of the POIs on the mobile device screen whose GPS coordinates are given. The proposed algorithm is compared to an existing one in terms of energy consumption and accuracy. The results show that the proposed algorithm gives better results in energy consumption and accuracy while standing still, and acceptably accurate results when driving. The technique provides benefits to AR browsers with its open access algorithm. Going forward, the algorithm will be improved to more rapidly react to position changes while driving.

Keywords: accurate tagging algorithm, augmented reality, localization, location-based AR

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Authors: Alpana Goel, Kawalpreet Kalra

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The study of level structures of deformed nuclei is the most complex topic in nuclear physics. For the description of level structure, a simple model is good enough to bring out the basic features which may then be further refined. The low lying level structures of these nuclei can, therefore, be understood in terms of Two Quasiparticle plus axially symmetric Rotor Model (TQPRM). The formulation of TQPRM for deformed nuclei has been presented. The analysis of available experimental data on two quasiparticle rotational bands of deformed nuclei present unusual features like signature dependence, odd-even staggering, signature inversion and signature reversal in two quasiparticle rotational bands of deformed nuclei. These signature effects are well discussed within the framework of TQPRM. The model is well efficient in reproducing the large odd-even staggering and anomalous features observed in even-even and odd-odd deformed nuclei. The effect of particle-particle and the Coriolis coupling is well established from the model. Detailed description of the model with implications to deformed nuclei is presented in the paper.

Keywords: deformed nuclei, signature effects, signature inversion, signature reversal

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Authors: V. Rashtchi, H. Bizhani, F. R. Tatari

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This paper presents a new online loss minimization for an induction motor drive. Among the many loss minimization algorithms (LMAs) for an induction motor, a particle swarm optimization (PSO) has the advantages of fast response and high accuracy. However, the performance of the PSO and other optimization algorithms depend on the accuracy of the modeling of the motor drive and losses. In the development of the loss model, there is always a trade off between accuracy and complexity. This paper presents a new online optimization to determine an optimum flux level for the efficiency optimization of the vector-controlled induction motor drive. An induction motor (IM) model in d-q coordinates is referenced to the rotor magnetizing current. This transformation results in no leakage inductance on the rotor side, thus the decomposition into d-q components in the steady-state motor model can be utilized in deriving the motor loss model. The suggested algorithm is simple for implementation.

Keywords: induction machine, loss minimization, magnetizing current, particle swarm optimization

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Authors: M. Rehan, H. Mashaly, H. Emam, A. Abou El-Kheir, S. Mowafi

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In this work, we will study a simple highly efficient technique to impart multi functional properties to different fabric substrates by in situ Ag NPs incorporation into fabric matrix. Ag NPs as a coloration and antimicrobial agent were prepared in situ incorporation into fabric matrix (Cotton and Wool) by using trisodium citrate as reducing and stabilizing agent. The Ag NPs treated fabric (Cotton and Wool) showed different color because of localized surface Plasmon resonance (LSPR) property of Ag NPs. The formation of Ag NPs was confirmed by UV/Vis spectra for the supernatant solutions and The Ag NPs treated fabric (Cotton and Wool) were characterized by scanning electron microscopy (SEM) and X-ray photo electron spectroscopy (XPS). The dependence of color properties characterized by colorimetric, fastness and antibacterial properties evaluated by Escherichia coli using counting method and the reaction parameters were studied. The results indicate that, the in situ Ag NPs incorporation into fabric matrix approach can simultaneously impart colorant and antimicrobial properties into different fabric substrates.

Keywords: Ag NPs, coloration, antibacterial, wool, cotton fabric

Procedia PDF Downloads 342