Search results for: whole genome single nucleotide polymorphisms

Authors: Jaemin Kim, Ilsun Pang, Yongrae Cho, Kwanghun Kim, Sungsun Baik

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Manufacturing cost reduction is becoming more important due to excessive oversupply of Single crystalline ingot in recent solar market. Many companies are carrying out extensive research to grow more than one Single crystalline ingot in one batch to reduce manufacturing cost. However what most companies are finding difficult in this process is the effect on ingot due to increasing levels of impurities. Every ingot leaves a certain amount of melt after it is fully grown. This is the impurity that lowers the ingot quality. This impurity increase in the batch after second, third and more are grown subsequently in one batch. In order to solve this problem, the experiment to remove the residual melt in high temperature of hot zone was performed and succeeded. Theoretical average metal concentration of second ingot by new method was calculated and compared to it by conventional method.

Keywords: single crystal, solar cell, metal impurity, Ingot

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Authors: J. C. Moctezuma, V. Breña-Medina, Jose Luis Nunez-Yanez, Joseph P. McGeehan

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In this work we make a bifurcation analysis for a single compartment representation of Traub model, one of the most important conductance-based models. The analysis focus in two principal parameters: current and leakage conductance. Study of stable and unstable solutions are explored; also Hop-bifurcation and frequency interpretation when current varies is examined. This study allows having control of neuron dynamics and neuron response when these parameters change. Analysis like this is particularly important for several applications such as: tuning parameters in learning process, neuron excitability tests, measure bursting properties of the neuron, etc. Finally, a hardware implementation results were developed to corroborate these results.

Keywords: Traub model, Pinsky-Rinzel model, Hopf bifurcation, single-compartment models, bifurcation analysis, neuron modeling

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Authors: Roya Bakhtiar, Alireza Abdolmohammadi, Hadi Hajarian, Zahra Nikousefat, Davood, Kalantar-Neyestanaki

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The objective of the present study was to determine the polymorphism in the leptin (332G>A) and its association with biometric traits in Sanjabi sheep. For this purpose, blood samples from 96 rams were taken, and tail length, width tail, circumference tail, body length, body width, and height were simultaneously recorded. PCR was performed using specific primer to amplify 463 bp fragment including exon 3 of leptin gene, and PCR products were digested by Cail restriction enzymes. The 332G>A (at 332th nucleotide of exon 3 leptin gene) that caused an amino acid change from Arg to Gln was detected by Cail (CAGNNNCTG) endonuclease, as the endonuclease cannot cut this region if G nucleotide is located in this position. Three genotypes including GG (463), GA (463, 360and 103 bp) and GG (360 bp and 103 bp) were identified after digestion by enzyme. The estimated frequencies of three genotypes including GG, GA, and AA for 332G>A locus were 0.68, 0.29 and 0.03 and those were 0.18 and 0.82 for A and G alleles, respectively. In the current study, chi-square test indicated that 332G>A positions did not deviate from the Hardy–Weinberg (HW) equilibrium. The most important reason to show HW equation was that samples used in this study belong to three large local herds with a traditional breeding system having random mating and without selection. Shannon index amount was calculated which represent an average genetic variation in Sanjabi rams. Also, heterozygosity estimated by Nei index indicated that genetic diversity of mutation in the leptin gene is moderate. Leptin gene polymorphism in the 332G>A had significant effect on body length (P<0.05) trait, and individuals with GA genotype had significantly the higher body length compared to other individuals. Although animals with GA genotype had higher body width, this difference was not statistically significant (P>0.05). This non-synonymous SNP resulted in different amino acid changes at codon positions111(R/Q). As leptin activity is localized, at least in part, in domains between amino acid residues 106-1406, it is speculated that the detected SNP at position 332 may affect the activity of leptin and may lead to different biological functions. Based to our results, due to significant effect of leptin gene polymorphism on body size traits, this gene may be used a candidate gene for improving these traits.

Keywords: body size, Leptin gene, PCR-RFLP, Sanjabi sheep

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Authors: Leander Van Neste, Kirk Wojno

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The innate immune system reacts to foreign insult in several unique ways, one of which is phagocytosis of perceived threats such as cancer, bacteria, and viruses. The goal of this study was to look for evidence of phagocytosed RNA from tumor cells in circulating monocytes. While all monocytes possess phagocytic capabilities, the non-classical CD14+/FCGR3A+ monocytes and the intermediate CD14++/FCGR3A+ monocytes most actively remove threatening ‘external’ cellular materials. Purified CD14-positive monocyte samples from fourteen patients recently diagnosed with clinically localized prostate cancer (PCa) were investigated by single-cell RNA sequencing using the 10X Genomics protocol followed by paired-end sequencing on Illumina’s NovaSeq. Similarly, samples were processed and used as controls, i.e., one patient underwent biopsy but was found not to harbor prostate cancer (benign), three young, healthy men, and three men previously diagnosed with prostate cancer that recently underwent (curative) radical prostatectomy (post-RP). Sequencing data were mapped using 10X Genomics’ CellRanger software and viable cells were subsequently identified using CellBender, removing technical artifacts such as doublets and non-cellular RNA. Next, data analysis was performed in R, using the Seurat package. Because the main goal was to identify differences between PCa patients and ‘control’ patients, rather than exploring differences between individual subjects, the individual Seurat objects of all 21 patients were merged into one Seurat object per Seurat’s recommendation. Finally, the single-cell dataset was normalized as a whole prior to further analysis. Cell identity was assessed using the SingleR and cell dex packages. The Monaco Immune Data was selected as the reference dataset, consisting of bulk RNA-seq data of sorted human immune cells. The Monaco classification was supplemented with normalized PCa data obtained from The Cancer Genome Atlas (TCGA), which consists of bulk RNA sequencing data from 499 prostate tumor tissues (including 1 metastatic) and 52 (adjacent) normal prostate tissues. SingleR was subsequently run on the combined immune cell and PCa datasets. As expected, the vast majority of cells were labeled as having a monocytic origin (~90%), with the most noticeable difference being the larger number of intermediate monocytes in the PCa patients (13.6% versus 7.1%; p<.001). In men harboring PCa, 0.60% of all purified monocytes were classified as harboring PCa signals when the TCGA data were included. This was 3-fold, 7.5-fold, and 4-fold higher compared to post-RP, benign, and young men, respectively (all p<.001). In addition, with 7.91%, the number of unclassified cells, i.e., cells with pruned labels due to high uncertainty of the assigned label, was also highest in men with PCa, compared to 3.51%, 2.67%, and 5.51% of cells in post-RP, benign, and young men, respectively (all p<.001). It can be postulated that actively phagocytosing cells are hardest to classify due to their dual immune cell and foreign cell nature. Hence, the higher number of unclassified cells and intermediate monocytes in PCa patients might reflect higher phagocytic activity due to tumor burden. This also illustrates that small numbers (~1%) of circulating peripheral blood monocytes that have interacted with tumor cells might still possess detectable phagocytosed tumor RNA.

Keywords: circulating monocytes, phagocytic cells, prostate cancer, tumor immune response

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Authors: Komal Saeed

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Introduction: Rhinoplasty is considered one of the challenging aesthetic procedures. Psychosocial concerns motivate the urge for aesthetic procedures especially rhinoplasty. Males who fall in this category are designated as single, immature, male, over expectant and narcissistic (SIMON) in literature. As of yet, there is no term that depicts females showing similar characteristics. The purpose of this study is to evaluate the incidence of body dysmorphic disorder (BDD) in females seeking rhinoplasty and to introduce a term for such individuals. Materials and Methods: A prospective, questionnaire based, qualitative study was conducted in the Department Of Plastic Surgery between March 2018 and March 2020. 110 female candidates seeking aesthetic rhinoplasty were included in the study. BDD was evaluated using the Dysmorphic Concerns Questionnaire, DCQ. Data were analyzed using SPSS version 25 software and correlation between the groups was evaluated. Results: Out of 110 female subjects, 77.3% (n=85) were single, 16.4% (n=18) were married and 6.4% (n=7) were divorced. BDD was found in 41.8% (n=46) of the candidates, majority being single (n=41, 89.1%) and having educational status above diploma (n=39, 84.8%). There was a statistically higher percentage of young adults between 24 and 28 years (n=33, 71.7%) having BDD (p= 0.0001). Conclusion: Considering the high frequency of BDD among females seeking rhinoplasty, a standardized term ‘SIFON’ is introduced to describe such individuals who are S; single, I; immature, F; female, O; over expectant, N; narcissistic as apposed to SIMON in males. These individuals perceive aesthetic procedures as a solution to their body dissatisfaction. Therefore, preoperative counseling seems necessary to avoid unsatisfactory outcomes secondary to mental health.

Keywords: aesthetic rhinoplasty, body dismorphic disorder, single, immature, obsessive

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Authors: Ahmet Calik

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In present study, the effect of adherend geometry on the tensile strength of adhesively single lap aluminum structures joint, bonded was numerically studied using by three dimensional finite element model. Six joint model were investigated. Analyses were performed in ANSYS commercial software. The results shows that the adherends shape has the highest effect on peel and shear stresses.

Keywords: adhesive, adherend, single lap joints, finite element

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Authors: A. Abdikian

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Using the linearized quantum hydrodynamic model (QHD) and by considering the role of quantum parameter (Bohm’s potential) and electron exchange-correlation potential in conjunction with Maxwell’s equations, electromagnetic wave propagation in a single-walled carbon nanotubes was studied. The electronic excitations are described. By solving the mentioned equations with appropriate boundary conditions and by assuming the low-frequency electromagnetic waves, two general expressions of dispersion relations are derived for the transverse magnetic (TM) and transverse electric (TE) modes, respectively. The dispersion relations are analyzed numerically and it was found that the dependency of dispersion curves with the exchange-correlation effects (which have been ignored in previous works) in the low frequency would be limited. Moreover, it has been realized that asymptotic behaviors of the TE and TM modes are similar in single wall carbon nanotubes (SWCNTs). The results show that by adding the function of electron exchange-correlation potential lead to the phenomena and make to extend the validity range of QHD model. The results can be important in the study of collective phenomena in nanostructures.

Keywords: transverse magnetic, transverse electric, quantum hydrodynamic model, electron exchange-correlation potential, single-wall carbon nanotubes

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Authors: Guillaume Schuchardt, Solenn Berson, Gerard Perrier

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Multi-junction solar cell configurations, where two sub-cells with complementary absorption are stacked and connected in series, offer an exciting approach to tackle the single junction limitations of organic solar cells and improve their power conversion efficiency. However, the augmentation of the number of layers has, as a consequence, to increase the risk of reducing the lifetime of the cell due to the ageing phenomena present at the interfaces. In this work, we study the intrinsic degradation mechanisms, under continuous illumination AM1.5G, inert atmosphere and room temperature, in single and tandem organic solar cells using Impedance Spectroscopy, IV Curves, External Quantum Efficiency, Steady-State Photocarrier Grating, Scanning Kelvin Probe and UV-Visible light.

Keywords: single and tandem organic solar cells, intrinsic degradation mechanisms, characterization: SKP, EQE, SSPG, UV-Visible, Impedance Spectroscopy, optical simulation

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Authors: Jung-En Kuan, Whei-Fen Wu

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In this study, a symbiotic bacteria from yellow mealworm's (Tenebrio molitor) mid-gut was isolated with characteristics of growth on minimal-tributyrin medium. After a PCR-amplification of its 16s rDNA, the resultant nucleotide sequences were then analyzed by schemes of the phylogeny trees. Accordingly, it was designated as Pseudomonas nitroreducens D-01. Next, by searching the lipolytic enzymes in its protein data bank, one of those potential lipolytic α/β hydrolases was identified, again using PCR-amplification and nucleotide-sequencing methods. To construct an expression of this lipolytic gene in plasmids, the target-gene primers were then designed, carrying the C-terminal his-tag sequences. Using the vector pET21a, a recombinant lipolytic hydrolase D gene with his-tag nucleotides was successfully cloned into it, of which the lipolytic D gene is under a control of the T7 promoter. After transformation of the resultant plasmids into Eescherichia coli BL21 (DE3), an IPTG inducer was used for the induction of the recombinant proteins. The protein products were then purified by metal-ion affinity column, and the purified proteins were found capable of forming a clear zone on tributyrin agar plate. Shortly, its enzyme activities were determined by degradation of p-nitrophenyl ester(s), and the substantial yellow end-product, p-nitrophenol, was measured at O.D.405 nm. Specifically, this lipolytic enzyme efficiently targets p-nitrophenyl butyrate. As well, it shows the most reactive activities at 40°C, pH 8 in potassium phosphate buffer. In thermal stability assays, the activities of this enzyme dramatically drop when the temperature is above 50°C. In metal ion assays, MgCl₂ and NH₄Cl induce the enzyme activities while MnSO₄, NiSO₄, CaCl₂, ZnSO₄, CoCl₂, CuSO₄, FeSO₄, and FeCl₃ reduce its activities. Besides, NaCl has no effects on its enzyme activities. Most organic solvents decrease the activities of this enzyme, such as hexane, methanol, ethanol, acetone, isopropanol, chloroform, and ethyl acetate. However, its enzyme activities increase when DMSO exists. All the surfactants like Triton X-100, Tween 80, Tween 20, and Brij35 decrease its lipolytic activities. Using Lineweaver-Burk double reciprocal methods, the function of the enzyme kinetics were determined such as Km = 0.488 (mM), Vmax = 0.0644 (mM/min), and kcat = 3.01x10³ (s⁻¹), as well the total efficiency of kcat/Km is 6.17 x10³ (mM⁻¹/s⁻¹). Afterwards, based on the phylogenetic analyses, this lipolytic protein is classified to type IV lipase by its homologous conserved region in this lipase family.

Keywords: enzyme, esterase, lipotic hydrolase, type IV

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Authors: Tomokazu Shirai, Akihiko Kondo

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Technologies of metabolic engineering or synthetic biology are essential for effective microbial bioproduction. It is especially important to develop an in silico tool for designing a metabolic pathway producing an unnatural and valuable chemical such as fossil materials of fuel or plastics. We here demonstrated two in silico tools for designing novel metabolic pathways: BioProV and HyMeP. Furthermore, we succeeded in creating an artificial metabolic pathway by enzyme engineering.

Keywords: bioinformatics, metabolic engineering, synthetic biology, genome scale model

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Authors: S. Ghorbani, N. I. Polushin

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In this study, an approach to identify factors affecting on surface roughness in a machining process is presented. This study is based on 81 data about surface roughness over a wide range of cutting tools (conventional, cutting tool with holes, cutting tool with composite material), workpiece materials (AISI 1045 Steel, AA2024 aluminum alloy, A48-class30 gray cast iron), spindle speed (630-1000 rpm), feed rate (0.05-0.075 mm/rev), depth of cut (0.05-0.15 mm) and tool overhang (41-65 mm). A single decision tree (SDT) analysis was done to identify factors for predicting a model of surface roughness, and the CART algorithm was employed for building and evaluating regression tree. Results show that a single decision tree is better than traditional regression models with higher rate and forecast accuracy and strong value.

Keywords: cutting condition, surface roughness, decision tree, CART algorithm

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Authors: Shagufta Jabeen, Faez Jesse Firdaus Abdullah, Zunita Zakaria, Nurulfiza Mat Isa, Yung Chie Tan, Wai Yan Yee, Abdul Rahman Omar

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Pasteurella multocida is associated with acute, as well as, chronic infections in avian and bovine such as pasteurellosis and hemorrhagic septicemia (HS) in cattle and buffaloes. Iron is one of the most important nutrients for pathogenic bacteria including Pasteurella and acts as a cofactor or prosthetic group in several essential enzymes and is needed for amino acid, pyrimidine, and DNA biosynthesis. In our recent study, we showed that 2% of Pasteurella multocida serotype A strain PMTB2.1 encode for iron regulating genes (Accession number CP007205.1). Genome sequencing of other Pasteurella multocida serotypes namely PM70 and HB01 also indicated up to 2.5% of the respective genome encode for iron regulating genes, suggesting that Pasteurella multocida genome comprises of multiple systems for iron uptake. Since P. multocida PMTB2.1 has more than 40 CDs out of 2097 CDs (approximately 2%), encode for iron-regulated. The gene expression profiling of four iron-regulating genes namely fbpb, yfea, fece and fur were characterized under iron-restricted environment. The P. multocida strain PMTB2.1 was grown in broth with and without iron chelating agent and samples were collected at different time points. Relative mRNA expression profile of these genes was determined using Taqman probe based real-time PCR assay. The data analysis, normalization with two house-keeping genes and the quantification of fold changes were carried out using Bio-Rad CFX manager software version 3.1. Results of this study reflect that iron reduced environment has significant effect on expression profile of iron regulating genes (p < 0.05) when compared to control (normal broth) and all evaluated genes act differently with response to iron reduction in media. The highest relative fold change of fece gene was observed at early stage of treatment indicating that PMTB2.1 may utilize its periplasmic protein at early stage to acquire iron. Furthermore, down-regulation expression of fece with the elevated expression of other genes at later time points suggests that PMTB2.1 control their iron requirements in response to iron availability by down-regulating the expression of iron proteins. Moreover, significantly high relative fold change (p ≤ 0.05) of fbpb gene is probably associated with the ability of P. multocida to directly use host iron complex such as hem, hemoglobin. In addition, the significant increase (p ≤ 0.05) in fbpb and yfea expressions also reflects the utilization of multiple iron systems in P. multocida strain PMTB2.1. The findings of this study are very much important as relative scarcity of free iron within hosts creates a major barrier to microbial growth inside host and utilization of outer-membrane proteins system in iron acquisition probably occurred at early stage of infection with P. multocida. In conclusion, the presence and utilization of multiple iron system in P. multocida strain PMTB2.1 revealed the importance of iron in the survival of P. multocida.

Keywords: iron-related genes, real-time PCR, gene expression profiling, fold changes

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Authors: Faheem Shahzad Baloch, Muhammad Azhar Nadeem, Muhammad Amjad Nawaz, Ephrem Habyarimana, Gonul Comertpay, Tolga Karakoy, Rustu Hatipoglu, Mehmet Zahit Yeken, Vahdettin Ciftci

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Turkey is considered a bridge between Europe, Asia, and Africa and possibly played an important role in the distribution of many crops including common bean. Hundreds of common bean landraces can be found in Turkey, particularly in farmers’ fields, and they consistently contribute to the overall production. To investigate the existing genetic diversity and hybridization events between the Andean and Mesoamerican gene pools in the Turkish common bean, 188 common bean accessions (182 landraces and 6 modern cultivars as controls) were collected from 19 different Turkish geographic regions. These accessions were characterized using phenotypic data (growth habit and seed weight), geographic provenance, 12557 high-quality whole-genome DArTseq markers, and 3767 novel DArTseq loci were also identified. The clustering algorithms resolved the Turkish common bean landrace germplasm into the two recognized gene pools, the Mesoamerican and Andean gene pools. Hybridization events were observed in both gene pools (14.36% of the accessions) but mostly in the Mesoamerican (7.97% of the accessions), and was low relative to previous European studies. The lower level of hybridization witnessed the existence of Turkish common bean germplasm in its original form as compared to Europe. Mesoamerican gene pool reflected a higher level of diversity, while the Andean gene pool was predominant (56.91% of the accessions), but genetically less diverse and phenotypically more pure, reflecting farmers greater preference for the Andean gene pool. We also found some genetically distinct landraces and overall, a meaningful level of genetic variability which can be used by the scientific community in breeding efforts to develop superior common bean strains.

Keywords: bean germplasm, DArTseq markers, genotyping by sequencing, Turkey, whole genome diversity

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Authors: Adel Alblihy, Reem Ali, Mashael Algethami, Ahmed Shoqafi, Michael S. Toss, Juliette Brownlie, Natalie J. Tatum, Ian Hickson, Paloma Ordonez Moran, Anna Grabowska, Jennie N. Jeyapalan, Nigel P. Mongan, Emad A. Rakha, Srinivasan Madhusudan

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Platinum resistance is a clinical challenge in ovarian cancer. Platinating agents induce DNA damage which activate Mre11 nuclease directed DNA damage signalling and response (DDR). Upregulation of DDR may promote chemotherapy resistance. Here we have comprehensively evaluated Mre11 in epithelial ovarian cancers. In clinical cohort that received platinum- based chemotherapy (n=331), Mre11 protein overexpression was associated with aggressive phenotype and poor progression free survival (PFS) (p=0.002). In the ovarian cancer genome atlas (TCGA) cohort (n=498), Mre11 gene amplification was observed in a subset of serous tumours (5%) which correlated highly with Mre11 mRNA levels (p<0.0001). Altered Mre11 levels was linked with genome wide alterations that can influence platinum sensitivity. At the transcriptomic level (n=1259), Mre11 overexpression was associated with poor PFS (p=0.003). ROC analysis showed an area under the curve (AUC) of 0.642 for response to platinum-based chemotherapy. Pre-clinically, Mre11 depletion by gene knock down or blockade by small molecule inhibitor (Mirin) reversed platinum resistance in ovarian cancer cells and in 3D spheroid models. Importantly, Mre11 inhibition was synthetically lethal in platinum sensitive XRCC1 deficient ovarian cancer cells and 3D-spheroids. Selective cytotoxicity was associated with DNA double strand break (DSB) accumulation, S-phase cell cycle arrest and increased apoptosis. We conclude that pharmaceutical development of Mre11 inhibitors is a viable clinical strategy for platinum sensitization and synthetic lethality in ovarian cancer.

Keywords: MRE11; XRCC1, ovarian cancer, platinum sensitization, synthetic lethality

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Authors: Adrià Arbués-Sangüesa, Coloma Ballester, Gloria Haro

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Tracking sports players is a widely challenging scenario, specially in single-feed videos recorded in tight courts, where cluttering and occlusions cannot be avoided. This paper presents an analysis of several geometric and semantic visual features to detect and track basketball players. An ablation study is carried out and then used to remark that a robust tracker can be built with Deep Learning features, without the need of extracting contextual ones, such as proximity or color similarity, nor applying camera stabilization techniques. The presented tracker consists of: (1) a detection step, which uses a pretrained deep learning model to estimate the players pose, followed by (2) a tracking step, which leverages pose and semantic information from the output of a convolutional layer in a VGG network. Its performance is analyzed in terms of MOTA over a basketball dataset with more than 10k instances.

Keywords: basketball, deep learning, feature extraction, single-camera, tracking

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Authors: Hasmayadi Abdul Majid, Yuzman Yusoff, Noor Shelida Salleh

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This paper presents the development of a single-ended 38.5 kS/s 10-bit programmable reference SAR ADC which is realized in MIMOS’s 0.35 µm CMOS process. The design uses a resistive DAC, a dynamic comparator with pre-amplifier and a SAR digital logic to create 10 effective bits ADC. A programmable reference circuitry allows the ADC to operate with different input range from 0.6 V to 2.1 V. A single ended 38.5 kS/s 10-bit programmable reference SAR ADC was proposed and implemented in a 0.35 µm CMOS technology and consumed less than 7.5 mW power with a 3 V supply.

Keywords: successive approximation register analog-to-digital converter, SAR ADC, resistive DAC, programmable reference

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Authors: Rahul Ganpat Mapari, D. G. Wakde

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In this paper, a proposed approach to improve the power factor of single-phase rectifiers and to regulate the output voltage against the change in grid voltage and load is presented. This converter topology is evaluated on the basis of performance and its salient features like simplicity, low cost and high performance are discussed to analyze its applicability. The proposed control strategy is bridgeless, transformer-less and output current sensor-less and consists of only two Bi-directional IGBTs and two diodes. The voltage regulation is achieved by a simple voltage divider to communicate to a controller to control the duty cycles of PWM. A control technique and operational procedure are also developed, both theoretically and experimentally. The experimental results clearly verify the theoretical analysis from the prototype connected to grid unity.

Keywords: Active Rectifier (AC-DC), power factor, single phase, voltage regulation

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Authors: Masoud Safarishaal

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Detecting the location of pole-to-earth faults is essential for the safe operation of the electrical system of the railroad. This paper aims to use a combination of evolutionary algorithms and neural networks to increase the accuracy of single pole-to-earth fault detection and location on the Tehran railroad power supply system. As a result, the Imperialist Competitive Algorithm (ICA) and Particle Swarm Optimization (PSO) are used to train the neural network to improve the accuracy and convergence of the learning process. Due to the system's nonlinearity, fault detection is an ideal application for the proposed method, where the 600 Hz harmonic ripple method is used in this paper for fault detection. The substations were simulated by considering various situations in feeding the circuit, the transformer, and typical Tehran metro parameters that have developed the silicon rectifier. Required data for the network learning process has been gathered from simulation results. The 600Hz component value will change with the change of the location of a single pole to the earth's fault. Therefore, 600Hz components are used as inputs of the neural network when fault location is the output of the network system. The simulation results show that the proposed methods can accurately predict the fault location.

Keywords: single pole-to-pole fault, Tehran railway, ICA, PSO, artificial neural network

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Authors: Nicole Ramlachan, Samuel Mark West

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Lung cancer is the leading cause of cancer-associated deaths in North America, with the vast majority being non-small cell lung cancer (NSCLC), with a five-year survival rate of only 24%. Non-invasive discovery of biomarkers associated with early-diagnosis of NSCLC can enable precision oncology efforts using liquid biopsy-based multiomics profiling of plasma. Although tissue biopsies are currently the gold standard for tumor profiling, this method presents many limitations since these are invasive, risky, and sometimes hard to obtain as well as only giving a limited tumor profile. Blood-based tests provides a less-invasive, more robust approach to interrogate both tumor- and non-tumor-derived signals. We intend to examine 30 stage III-IV NSCLC patients pre-surgery and collect plasma samples.Cell-free DNA (cfDNA) will be extracted from plasma, and next-generation sequencing (NGS) performed. Through the analysis of tumor-specific alterations, including single nucleotide variants (SNVs), insertions, deletions, copy number variations (CNVs), and methylation alterations, we intend to identify tumor-derived DNA—ctDNA among the total pool of cfDNA. This would generate data to be used as an accurate form of cancer genotyping for diagnostic purposes. Using liquid biopsies offer opportunities to improve the surveillance of cancer patients during treatment and would supplement current diagnosis and tumor profiling strategies previously not readily available in Trinidad and Tobago. It would be useful and advantageous to use this in diagnosis and tumour profiling as well as to monitor cancer patients, providing early information regarding disease evolution and treatment efficacy, and reorient treatment strategies in, timethereby improving clinical oncology outcomes.

Keywords: genomics, multiomics, clinical genetics, genotyping, oncology, diagnostics

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Authors: In-Hwan Baek

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Valsartan is a potent and highly selective antagonist of the angiotensin II type 1 receptor, and is widely used for the treatment of hypertension. The aim of this study was to investigate the pharmacokinetic properties of the valsartan in dogs following oral administration of a single dose using quantitative modeling approaches. Forty beagle dogs were randomly divided into two group. Group A (n=20) was administered a single oral dose of valsartan 80 mg (Diovan® 80 mg), and group B (n=20) was administered a single oral dose of valsartan 160 mg (Diovan® 160 mg) in the morning after an overnight fast. Blood samples were collected into heparinized tubes before and at 0.5, 1, 1.5, 2, 2.5, 3, 4, 6, 8, 12 and 24 h following oral administration. The plasma concentrations of the valsartan were determined using LC-MS/MS. Non-compartmental pharmacokinetic analyses were performed using WinNonlin Standard Edition software, and modeling approaches were performed using maximum-likelihood estimation via the expectation maximization (MLEM) algorithm with sampling using ADAPT 5 software. After a single dose of valsartan 80 mg, the mean value of maximum concentration (Cmax) was 2.68 ± 1.17 μg/mL at 1.83 ± 1.27 h. The area under the plasma concentration-versus-time curve from time zero to the last measurable concentration (AUC24h) value was 13.21 ± 6.88 μg·h/mL. After dosing with valsartan 160 mg, the mean Cmax was 4.13 ± 1.49 μg/mL at 1.80 ± 1.53 h, the AUC24h was 26.02 ± 12.07 μg·h/mL. The Cmax and AUC values increased in proportion to the increment in valsartan dose, while the pharmacokinetic parameters of elimination rate constant, half-life, apparent of total clearance, and apparent of volume of distribution were not significantly different between the doses. Valsartan pharmacokinetic analysis fits a one-compartment model with first-order absorption and elimination following a single dose of valsartan 80 mg and 160 mg. In addition, high inter-individual variability was identified in the absorption rate constant. In conclusion, valsartan displays the dose-dependent pharmacokinetics in dogs, and Subsequent quantitative modeling approaches provided detailed pharmacokinetic information of valsartan. The current findings provide useful information in dogs that will aid future development of improved formulations or fixed-dose combinations.

Keywords: dose-dependent, modeling, pharmacokinetics, valsartan

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Authors: Mona Mohamed Shawkt Ragab, Heba Mohamed Darwish

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Context: Comfort properties of garments are crucial for the wearer, and with the increasing demand for cotton fabric, there is a need to explore alternative fabrics that can offer similar or superior comfort properties. This study focuses on comparing the comfort properties of tencel/cotton single jersey fabric and cotton single jersey fabric, with the aim of identifying fabrics that are more suitable for summer clothes. Research Aim: The aim of this study is to evaluate the comfort properties of tencel/cotton single jersey fabric and cotton single jersey fabric, with the goal of identifying fabrics that can serve as alternatives to cotton, considering their comfort properties for summer clothing. Methodology: An experimental, analytical approach was employed in this study. Two circular knitting machines were used to produce the fabrics, one with a 24 inches gauge and the other with a 28 inches gauge. Both fabrics were knitted with three different loop lengths (3.05 mm, 2.9 mm, and 2.6 mm) to obtain loose, medium, and tight fabrics for evaluation. Various comfort properties, including air permeability, water vapor permeability, wickability, and thermal resistance, were measured for both fabric types. Findings: The study found a significant difference in comfort properties between tencel/cotton single jersey fabric and cotton single jersey fabric. Tencel/cotton fabric exhibited higher air permeability, water vapor permeability, and wickability compared to cotton fabric. These findings suggest that tencel fabric is more suitable for summer clothes due to its superior ventilation and absorption properties. Theoretical Importance: This study contributes to the exploration of alternative fabrics to cotton by evaluating their comfort properties. By identifying fabrics that offer better comfort properties than cotton, particularly in terms of water usage, the study provides valuable insights into sustainable fabric choices for the fashion industry. Data Collection and Analysis Procedures: The comfort properties of the fabrics were measured using appropriate testing methods. Paired comparison t-tests were conducted to determine the significant differences between tencel/cotton fabric and cotton fabric in the measured properties. Correlation coefficients were also calculated to examine the relationships between the factors under study. Question Addressed: The study addresses the question of whether tencel/cotton single jersey fabric can serve as an alternative to cotton fabric for summer clothes, considering their comfort properties. Conclusion: The study concludes that tencel/cotton single jersey fabric offers superior comfort properties compared to cotton single jersey fabric, making it a suitable alternative for summer clothes. The findings also highlight the importance of considering fabric properties, such as air permeability, water vapor permeability, and wickability, when selecting materials for garments to enhance wearer comfort. This research contributes to the search for sustainable alternatives to cotton and provides valuable insights for the fashion industry in making informed fabric choices.

Keywords: comfort properties, cotton fabric, tencel fabric, single jersey

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

Abstract:

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: Scott A. Ochsner, Christopher M. Watkins, Apollo McOwiti, David L. Steffen Lauren B. Becnel, Neil J. McKenna

Abstract:

Understanding signaling by nuclear receptors (NRs) requires an appreciation of their cognate ligand- and tissue-specific transcriptomes. While target gene regulation data are abundant in this field, they reside in hundreds of discrete publications in formats refractory to routine query and analysis and, accordingly, their full value to the NR signaling community has not been realized. One of the mandates of the Nuclear Receptor Signaling Atlas (NURSA) is to facilitate access of the community to existing public datasets. Pursuant to this mandate we are developing a freely-accessible community web resource, Transcriptomine, to bring together the sum total of available expression array and RNA-Seq data points generated by the field in a single location. Transcriptomine currently contains over 25,000,000 gene fold change datapoints from over 1200 contrasts relevant to over 100 NRs, ligands and coregulators in over 200 tissues and cell lines. Transcriptomine is designed to accommodate a spectrum of end users ranging from the bench researcher to those with advanced bioinformatic training. Visualization tools allow users to build custom charts to compare and contrast patterns of gene regulation across different tissues and in response to different ligands. Our resource affords an entirely new paradigm for leveraging gene expression data in the NR signaling field, empowering users to query gene fold changes across diverse regulatory molecules, tissues and cell lines, target genes, biological functions and disease associations, and that would otherwise be prohibitive in terms of time and effort. Transcriptomine will be regularly updated with gene lists from future genome-wide expression array and expression-sequencing datasets in the NR signaling field.

Keywords: target gene database, informatics, gene expression, transcriptomics

Procedia PDF Downloads 253

Authors: Jo, Eui Chang, Shin, Heekang, Mun, A. Young , Kim, Hong Kyu

Abstract:

Regarding change on population and family structure in Korea after the 1980s, there has been a rapid change of low fertility, graying and increase of single household that cannot be found in any other parts of the world. With the result of total population residence by the National Statistical Office, Korea will hold 52,160,065 people in 2030 and reduction is predicted and from 2025 people above the age of 65 will take 20% of the total population, which means the entry of a super aging society. Also, average number in a family will be 2.71 in 2015 and decrease to 2.33 in 2035. On the other hand, proportion of single and two person household will be 53.7% in 2015 and it will increase up to 68.4% in 2035. Old population will increase greatly, single and two person household will take 2/3 of the total households. Delphi research was processed in 3 steps on 40 professionals about the importance and changing factors of residential environment of apartment followed by the change of population structure. For interior plan, space variety, variability, safety, convenient installation, eco-friendly installation, and IT installation were important factors for construction plan, plan on aged and single households, convenient installation, safety installation, eco-friendly installation for subdivision plan, education/child care facility, parks/gymnasium facility, community facility, and accessibility of transportation were predicted as important factors.

Keywords: change of population structure, super-graying, change of residential environment of apartment, single household, interior plan, construction plan, subdivision plan, Delphi research

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Authors: Wanatchapong Kongkaew

Abstract:

This paper proposes an application of probabilistic technique, namely Gaussian process regression, for estimating an optimal sequence of the single machine with total weighted tardiness (SMTWT) scheduling problem. In this work, the Gaussian process regression (GPR) model is utilized to predict an optimal sequence of the SMTWT problem, and its solution is improved by using an iterated local search based on simulated annealing scheme, called GPRISA algorithm. The results show that the proposed GPRISA method achieves a very good performance and a reasonable trade-off between solution quality and time consumption. Moreover, in the comparison of deviation from the best-known solution, the proposed mechanism noticeably outperforms the recently existing approaches.

Keywords: Gaussian process regression, iterated local search, simulated annealing, single machine total weighted tardiness

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Authors: R. Pilafkan, M. Kaffash Irzarahimi, S. F. Asbaghian Namin

Abstract:

The biaxial buckling behavior of single-layered graphene sheets (SLGSs) is studied in the present work. To consider the size-effects in the analysis, Eringen’s nonlocal elasticity equations are incorporated into classical plate theory (CLPT). A Generalized Differential Quadrature Method (GDQM) approach is utilized and numerical solutions for the critical buckling loads are obtained. Then, molecular dynamics (MD) simulations are performed for a series of zigzag SLGSs with different side-lengths and with various boundary conditions, the results of which are matched with those obtained by the nonlocal plate model to numerical the appropriate values of nonlocal parameter relevant to each type of boundary conditions.

Keywords: biaxial buckling, single-layered graphene sheets, nonlocal elasticity, molecular dynamics simulation, classical plate theory

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Authors: Fatih Suleyman Taskincan, Ahmet Karaarslan

Abstract:

In this article, the study and analysis of Single Ended Primary Inductance Converter (SEPIC) are presented for battery charging applications that will be used in military applications. The usage of this kind of converters come from its advantage of non-reverse polarity at outputs. As capacitors charge and discharge through inductance, peak current does not occur on capacitors. Therefore, the efficiency will be high compared to buck-boost converters. In this study, the converter (SEPIC) is designed to be operated with Internal Model Controller (IMC). The traditional controllers like Proportional Integral Controller are not preferred as its linearity behavior. Hence IMC is designed for this converter. This controller is a model-based control and provides more robustness and better set point monitoring. Moreover, it can be used for an unstable process where the conventional controller cannot handle the dynamic operation. Matlab/Simulink environment is used to simulate the converter and its controller, then, the results are shown and discussed.

Keywords: DC/DC converter, single ended primary inductance converter, SEPIC, internal model controller, IMC, switched mode power supply

Procedia PDF Downloads 603

Authors: Kaomud Tyagi, Rajasree Chakraborty, Shantanu Kundu, Devkant Singha, Kailash Chandra, Vikas Kumar

Abstract:

The melon thrips, Thrips palmi is a serious pest of a wide range of agriculture crops and also act as vectors for plant viruses (genus Tospovirus, family Bunyaviridae). More molecular data on this species is required to understand the cryptic speciation and evolutionary affiliations. Mitochondrial genomes have been widely used in phylogenetic and evolutionary studies in insect. So far, mitogenomes of five thrips species (Anaphothrips obscurus, Frankliniella intonsa, Frankliniella occidentalis, Scirtothrips dorsalis and Thrips imaginis) is available in the GenBank database. In this study, we sequenced the first complete mitogenome T. palmi and compared it with available thrips mitogenomes. We assembled the mitogenome from the whole genome sequencing data generated using Illumina Hiseq2500. Annotation was performed using MITOS web-server to estimate the location of protein coding genes (PCGs), transfer RNA (tRNAs), ribosomal RNAs (rRNAs) and their secondary structures. The boundaries of PCGs and rRNAs was confirmed manually in NCBI. Phylogenetic analyses were performed using the 13 PCGs data using maximum likelihood (ML) in PAUP, and Bayesian inference (BI) in MrBayes 3.2. The complete mitogenome of T. palmi was 15,333 base pairs (bp), which was greater than the genomes of A. obscurus (14,890bp), F. intonsa (15,215 bp), F. occidentalis (14,889 bp) and S. dorsalis South Asia strain (SA1) (14,283 bp), but smaller than the genomes of T. imaginis (15,407 bp) and S. dorsalis East Asia strain (EA1) (15,343bp). Like in other thrips species, the mitochondrial genome of T. palmi was represented by 37 genes, including 13 PCGs, large and small ribosomal RNA (rrnL and rrnS) genes, 22 transfer RNA (tRNAs) genes (with one extra gene for trn-Serine) and two A+T-rich control regions (CR1 and CR2). Thirty one genes were observed on heavy (H) strand and six genes on the light (L) strand. The six tRNA genes (trnG,trnK, trnY, trnW, trnF, and trnH) were found to be conserved in all thrips species mitogenomes in their locations relative to a protein-coding or rRNA gene upstream or downstream. The gene arrangements of T. palmi is very close to T. imaginis except the rearrangements in tRNAs genes: trnR (arginine), and trnE (glutamic acid) were found to be located between cox3 and CR2 in T. imaginis which were translocated between atp6 and CR1 in T. palmi; trnL1 (Leucine) and trnS1(Serine) were located between atp6 and CR1 in T. imaginis which were translocated between cox3 and CR2 in T. palmi. The location of CR1 upstream of nad5 gene was suggested to be ancestral condition of the thrips species in subfamily Thripinae, was also observed in T. palmi. Both the Maximum likelihood (ML) and Bayesian Inference (BI) phylogenetic trees generated resulted in similar topologies. The T. palmi was clustered with T. imaginis. We concluded that more molecular data on the diverse thrips species from different hierarchical level is needed, to understand the phylogenetic and evolutionary relationships among them.

Keywords: thrips, comparative mitogenomics, gene rearrangements, phylogenetic analysis

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Authors: Benny Benyamin Nasution, Rahmat Widia Sembiring, Abdul Rahman Dalimunthe, Nursiah Mustari, Nisfan Bahri, Berta br Ginting, Riadil Akhir Lubis, Rita Tavip Megawati, Indri Dithisari

Abstract:

The earth coordinate system is an important part of an attempt for earthquake forecasting, such as the one using Single Layer Hierarchical Graph Neuron (SLHGN). However, there are a number of problems that need to be worked out before the coordinate system can be utilized for the forecaster. One example of those is that SLHGN requires that the focused area of an earthquake must be constructed in a grid-like form. In fact, within the current earth coordinate system, the same longitude-difference would produce different distances. This can be observed at the distance on the Equator compared to distance at both poles. To deal with such a problem, a coordinate system has been developed, so that it can be used to support the ongoing earthquake forecasting using SLHGN. Two important issues have been developed in this system: 1) each location is not represented through two-value (longitude and latitude), but only a single value, 2) the conversion of the earth coordinate system to the x-y cartesian system requires no angular formulas, which is therefore fast. The accuracy and the performance have not been measured yet, since earthquake data is difficult to obtain. However, the characteristics of the SLHGN results show a very promising answer.

Keywords: hierarchical graph neuron, multidimensional hierarchical graph neuron, single layer hierarchical graph neuron, natural disaster forecasting, earthquake forecasting, earth coordinate system

Procedia PDF Downloads 196

Authors: Jun Hong Lee

Abstract:

Background: Many dementia patients complain insomnia and depressive mood, and hypnotics and antidepressants are being prescribed. As prevalence of dementia is increasing, insomnia and depressive mood are becoming more important. Objective: We evaluated insomnia and depression in outpatients of dementia center. Patients and Methods/Material and Methods: We reviewed medical records of the patients who visited outpatients clinic of NHIS Ilsan Hospital Dementia Center during 2016. Results: Total 716 patients are included; Subjective Memory Impairment (SMI) : 143 patients (20%), non-amnestic Mild Cognitive Impairment (MCI): single domain 70 (10%), multiple domain 34 (5%), amnestic MCI: single domain 74 (10%), multiple domain 159 (22%), Early onset Alzheimer´s disease (AD): 9 (1%), AD 121 (17%), Vascular dementia: 62 (9%), Mixed dementia 44 (6%). Hypnotics and antidepressants are prescribed as follows; SMI : hypnotics 14 patients (10%), antidepressants 27 (19%), non-amnestic MCI: single domain hypnotics 9 (13%), antidepressants 12 (17%), multiple domain hypnotics 4 (12%), antidepressants 6 (18%), amnestic MCI: single domain hypnotics 10 (14%), antidepressants 16 (22%), multiple domain hypnotics 22 (14%), antidepressants 24 (15%), Early onset Alzheimer´s disease (AD): hypnotics 1 (11%), antidepressants 2 (22%), AD: hypnotics 10 (8%), antidepressants 36 (30%), Vascular dementia: hypnotics 8 (13%), antidepressants 20 (32%), Mixed dementia: hypnotics 4 (9%), antidepressants 17 (39%). Conclusion: Among the outpatients of Dementia Center, MCI and SMI are majorities, and the number of MCI patients are almost half. Depression is more prevalent in AD, and Vascular dementia than MCI and SMI, and about 22% of patients are being prescribed by antidepressants and 11% by hypnotics.

Keywords: insomnia, depression, dementia, antidepressants, hypnotics

Procedia PDF Downloads 143