Search results for: single nucleotide polymorphisms

Authors: Jongho Park, Junwon Lee, Byeonghyun Choi, Kicheol Lee, Dongwook Kim

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The typically-used oil sand plant foundations are driven pile or drilled shaft. With more strict environmental regulations world widely, it became more important to completely remove the foundation during the stage of plant demolition. However, it is difficult to remove driven piles or drilled shafts that are installed at a deeper and stronger depth to gain more bearing pile capacity. The helical pile can be easily removed after its use and recycled; therefore it is suitable for oil sand plant foundation. This study analyzes the behavior of helical piles in sands. Axial pile load tests were carried out the varying spacing of helix plates (helices), rotation speed and weight of axial loading during pile installation. From the experiments, optimal helix plate spacing, rotation speed, axial loading during installation were determined. In addition, the behavior of helical pile groups was examined varying pile spacing. Finally, the behavior of single helical piles and that of group helical piles were compared.

Keywords: oil sand plant, pile load test, helical pile, group helical pile, behavior

Procedia PDF Downloads 159

Authors: Chien-Kuo Chiu

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In the displacement-based seismic design and evaluation, equivalent linearization method is one of the approximation methods to estimate the maximum inelastic displacement response of a system. In this study, the accuracy of two equivalent linearization methods are investigated. The investigation consists of three soil condition in Taiwan (Taipei Basin 1, 2, and 3) and five different heights of building (H_r= 10, 20, 30, 40, and 50 m). The first method is the Taiwan equivalent linearization method (TELM) which was proposed based on Japanese equivalent linear method considering the modification factor, α_T= 0.85. On the basis of Lin and Miranda study, the second method is proposed with some modification considering Taiwan soil conditions. From this study, it is shown that Taiwanese equivalent linearization method gives better estimation compared to the modified Lin and Miranda method (MLM). The error index for the Taiwanese equivalent linearization method are 16%, 13%, and 12% for Taipei Basin 1, 2, and 3, respectively. Furthermore, a ductility demand spectrum of single-degree-of-freedom (SDOF) system is presented in this study as a guide for engineers to estimate the ductility demand of a structure.

Keywords: displacement-based design, ductility demand spectrum, equivalent linearization method, RC buildings, single-degree-of-freedom

Procedia PDF Downloads 158

Authors: Alieh Farshbaf, Tayyeb Bahrami

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Introduction: Cc-chemokine receptor-5 (CCR5) is known as a main co-receptor in human immunodeficiency virus type-1 (HIV-1) infection. Many studies showed 32bp deletion (Δ32) in CCR5 gene, provide natural resistance to HIV-1 infection in homozygous individuals. Inducing the resistance mechanism by CCR5 in HIV-1 infected patients eliminated many problems of highly-active-anti retroviral therapy (HAART) drugs like as low safety, side-effects and virus rebounding from latent reservoirs. New treatments solved some restrictions that are based on gene modification and cell therapy. Literature review: The stories of the “Berlin and Boston patients” showed autologous hematopoietic stem cells transplantation (HSCT) could provide effective cure of HIV-1 infected patients. Furthermore, gene modification by zinc finger nuclease (ZFN) demonstrated another successful result again. Despite the other studies for gene therapy by ∆32 genotype, there is another mutation -CCR5 ∆32/m303- that provides HIV-1 resistant. It is a heterozygote genotype for ∆32 and T→A point mutation at nucleotide 303. These results approved the key role of CCR5 gene. Conclusion: Recent studies showed immune gene therapy and cell therapy could provide effective cure for refractory disease like as HIV. Eradication of HIV-1 from immune system was not observed by HAART, because of reloading virus genome from latent reservoirs after stopping them. It is showed that CCR5 could induce natural resistant to HIV-1 infection by the new approaches based on stem cell transplantation and gene modifying.

Keywords: CCR5, HIV-1, stem cell, immune gene therapy, gene modification

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Authors: Atheer Al-Nuaimi, Harry Evdorides

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Daily, many individuals die or get harmed on streets around the globe, which requires more particular solutions for transport safety issues. International road assessment program (iRAP) is one of the models that are considering many variables which influence road user’s safety. In iRAP, roads have been partitioned into five-star ratings from 1 star (the most reduced level) to 5 star (the most noteworthy level). These levels are calculated from risk factors which represent the effect of the geometric and traffic conditions on rod safety. The result of iRAP philosophy are the countermeasures that can be utilized to enhance safety levels and lessen fatalities numbers. These countermeasures can be utilized independently as a single treatment or in combination with other countermeasures for a section or an entire road. There is a general understanding that the efficiency of a countermeasure is liable to reduction when it is used in combination with various countermeasures. That is, crash diminishment estimations of single countermeasures cannot be summed easily. In the iRAP model, the fatalities estimations are calculated using a specific methodology. However, this methodology suffers overestimations. Therefore, this study has developed a calibration method to estimate fatalities numbers more accurately.

Keywords: crash risk factors, international road assessment program, low-income countries, road safety

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Authors: Jinseon Song, Yongwan Park

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In this paper, propose method that can user’s position that based on database is built from single camera. Previous positioning calculate distance by arrival-time of signal like GPS (Global Positioning System), RF(Radio Frequency). However, these previous method have weakness because these have large error range according to signal interference. Method for solution estimate position by camera sensor. But, signal camera is difficult to obtain relative position data and stereo camera is difficult to provide real-time position data because of a lot of image data, too. First of all, in this research we build image database at space that able to provide positioning service with single camera. Next, we judge similarity through image matching of database image and transmission image from user. Finally, we decide position of user through position of most similar database image. For verification of propose method, we experiment at real-environment like indoor and outdoor. Propose method is wide positioning range and this method can verify not only position of user but also direction.

Keywords: positioning, distance, camera, features, SURF(Speed-Up Robust Features), database, estimation

Procedia PDF Downloads 342

Authors: Rabindranath Bag, Surjeet Singh

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Materials in which the electrons are strongly correlated provide some of the most challenging and exciting problems in condensed matter physics today. After the discovery of high critical temperature superconductivity in layered or two-dimensional copper oxides, many physicists got attention in cuprates and it led to an upsurge of interest in the synthesis and physical properties of copper-oxide based material. The quest to understand superconducting mechanism in high-temperature cuprates, drew physicist’s attention to somewhat simpler compounds consisting of spin-chains or one-dimensional lattice of coupled spins. Low-dimensional quantum magnets are of huge contemporary interest in basic sciences as well emerging technologies such as quantum computing and quantum information theory, and heat management in microelectronic devices. Spin ladder is an example of quasi one-dimensional quantum magnets which provides a bridge between one and two dimensional materials. One of the examples of quasi one-dimensional spin-ladder compounds is Sr14Cu24O41, which exhibits a lot of interesting and exciting physical phenomena in low dimensional systems. Very recently, the ladder compound Sr14Cu24O41 was shown to exhibit long-distance quantum entanglement crucial to quantum information theory. Also, it is well known that hole-compensation in this material results in very high (metal-like) anisotropic thermal conductivity at room temperature. These observations suggest that Sr14Cu24O41 is a potential multifunctional material which invites further detailed investigations. To investigate these properties one must needs a large and high quality of single crystal. But these systems are showing incongruently melting behavior, which brings many difficulties to grow a large and quality of single crystals. Hence, we are using TSFZ (Travelling Solvent Floating Zone) method to grow the high quality of single crystals of the low dimensional magnets. Apart from this, it has unique crystal structure (alternating stacks of plane containing edge-sharing CuO2 chains, and the plane containing two-leg Cu2O3 ladder with intermediate Sr layers along the b- axis), which is also incommensurate in nature. It exhibits abundant physical phenomenon such as spin dimerization, crystallization of charge holes and charge density wave. The maximum focus of research so far involved in introducing defects on A-site (Sr). However, apart from the A-site (Sr) doping, there are only few studies in which the B-site (Cu) doping of polycrystalline Sr14Cu24O41 have been discussed and the reason behind this is the possibility of two doping sites for Cu (CuO2 chain and Cu2O3 ladder). Therefore, in our present work, the crystals (pristine and Cu-site doped) were grown by using TSFZ method by tuning the growth parameters. The Laue diffraction images, optical polarized microscopy and Scanning Electron Microscopy (SEM) images confirm the quality of the grown crystals. Here, we report the single crystal growth, magnetic and transport properties of Sr14Cu24O41 and its lightly doped variants (magnetic and non-magnetic) containing less than 1% of Co, Ni, Al and Zn impurities. Since, any real system will have some amount of weak disorder, our studies on these ladder compounds with controlled dilute disorder would be significant in the present context.

Keywords: low-dimensional quantum magnets, single crystal, spin-ladder, TSFZ technique

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Authors: Ahdieh Alijani, Mina Zarrabi, Abdollah Jamshidi, Jamshid Razmyar

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Avian intestinal spirochetosis (AIS) is caused by spiral-shaped Gram-negative Brachyspira spp. in poultry and is known as a cause of diarrhea, low egg production and increased the occurrence of dirty eggs in layer hens. In this study the presence of some Brachyspira spp. was investigated in laying hens. A total of 100 cloacal swab samples were individually collected from 20 laying hen flocks showing fecal egg staining in northeastern Iran. By culture and morphologic examination, 41 samples (41%) from 20 flocks were positive but by using genus–specific PCR only 37 (37%) samples were confirmed as Brachyspira spp. Using species-specific primers, single colonization was identified in 18 samples associated with B. pilosicoli (48.6%) while single colonization with B. intermedia was found in only two samples (5.4%). Simultaneous colonization by B. intermedia and B. murdochii was detected in 3 samples (8.1%). B. pilosicoli was the most prevalent species in concurrent colonization in 11 cases (29.7%). Finally, co-colonization by B. intermedia and B. innocens was identified in 3 samples (8.1%). The results of this study show the colonization of different species of Brachyspira with the dominance of B. pilosicoli in layer hens. In simultaneous colonization with pathogenic and non-pathogenic species the symptoms of intestinal spirochetosis were reduced, suggesting a competitive role in preventing and reducing the colonization of pathogenic species.

Keywords: intestinal spirochetosis, Brachyspira, laying hen, PCR

Procedia PDF Downloads 535

Authors: Zoran Herceg, Višnja Stulić, Anet Režek Jambrak, Tomislava Vukušić

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Electrical discharge plasma is a new non-thermal processing technique which is used for the inactivation of contaminating and hazardous microbes in liquids. Plasma is a source of different antimicrobial species including UV photons, charged particles, and reactive species such as superoxide, hydroxyl radicals, nitric oxide and ozone. Escherichia coli was studied as foodborne pathogen. The aim of this work was to examine inactivation effects of electrical discharge plasma treatment on the Escherichia coli MG 1655 in pure culture. Two types of plasma configuration and polarity were used. First configuration was with titanium wire as high voltage needle and another with medical stainless steel needle used to form bubbles in treated volume and titanium wire as high voltage needle. Model solution samples were inoculated with Escerichia coli MG 1655 and treated by electrical discharge plasma at treatment time of 5 and 10 min, and frequency of 60, 90 and 120 Hz. With the first configuration after 5 minutes of treatment at frequency of 120 Hz the inactivation rate was 1.3 log₁₀ reduction and after 10 minutes of treatment the inactivation rate was 3.0 log₁₀ reduction. At the frequency of 90 Hz after 10 minutes inactivation rate was 1.3 log₁₀ reduction. With the second configuration after 5 minutes of treatment at frequency of 120 Hz the inactivation rate was 1.2 log₁₀ reduction and after 10 minutes of treatment the inactivation rate was also 3.0 log₁₀ reduction. In this work it was also examined the formation of biofilm, nucleotide and protein leakage at 260/280 nm, before and after treatment and recuperation of treated samples. Further optimization of method is needed to understand mechanism of inactivation.

Keywords: electrical discharge plasma, escherichia coli MG 1655, inactivation, point-to-plate electrode configuration

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Authors: Z. Ž. Lazarević, Č. Jovalekić, V. N. Ivanovski, N. Ž. Romčević

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Nickel-zinc ferrite, Ni0.5Zn0.5Fe2O4 was prepared by mechanochemical route in a planetary ball mill starting from mixture of the appropriate quantities of the Ni(OH)2, Zn(OH)2 and Fe(OH)3 hydroxide powders. In order to monitor the progress of chemical reaction and confirm phase formation, powder samples obtained after 5 h and 10 h of milling were characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM), IR, Raman and Mössbauer spectroscopy. It is shown that the soft mechanochemical method, i.e. mechanochemical activation of hydroxides, produces high quality single phase Ni0.5Zn0.5Fe2O4 samples in much more efficient way. From the IR spectroscopy of single phase samples it is obvious that energy of modes depends on the ratio of cations. It is obvious that all samples have more than 5 Raman active modes predicted by group theory in the normal spinel structure. Deconvolution of measured spectra allows one to conclude that all complex bands in the spectra are made of individual peaks with the intensities that vary from spectrum to spectrum. The deconvolution of Raman spectra alows to separate contributions of different cations to a particular type of vibration and to estimate the degree of inversion.

Keywords: ferrite, X-ray diffraction, infrared spectroscopy, Raman spectroscopy, Mössbauer spectroscopy

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Authors: Salim H. Al Salmani, Kevin Tansey, Mohammed S. Ozigis

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The study of the growth of built-up areas and settlement expansion is a major exercise that city managers seek to undertake to establish previous and current developmental trends. This is to ensure that there is an equal match of settlement expansion needs to the appropriate levels of services and infrastructure required. This research aims at demonstrating the potential of satellite image processing technique, harnessing the utility of single feature probability-object based image analysis technique in assessing the urban growth dynamics of the Muscat Governorate in Oman for the period 1990, 2002 and 2013. This need is fueled by the continuous expansion of the Muscat Governorate beyond predicted levels of infrastructural provision. Landsat Images of the years 1990, 2002 and 2013 were downloaded and preprocessed to forestall appropriate radiometric and geometric standards. A novel approach of probability filtering of the target feature segment was implemented to derive the spatial extent of the final Built-Up Area of the Muscat governorate for the three years period. This however proved to be a useful technique as high accuracy assessment results of 55%, 70%, and 71% were recorded for the Urban Landcover of 1990, 2002 and 2013 respectively. Furthermore, the Normalized Differential Built – Up Index for the various images were derived and used to consolidate the results of the SFP-OBIA through a linear regression model and visual comparison. The result obtained showed various hotspots where urbanization have sporadically taken place. Specifically, settlement in the districts (Wilayat) of AL-Amarat, Muscat, and Qurayyat experienced tremendous change between 1990 and 2002, while the districts (Wilayat) of AL-Seeb, Bawshar, and Muttrah experienced more sporadic changes between 2002 and 2013.

Keywords: urban growth, single feature probability, object based image analysis, landcover change

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Authors: Daina Jonkus, Solvita Petrovska, Dace Smiltina, Lasma Cielava

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The beta-lactoglobulin and kappa-casein are milk proteins which are important for milk composition. Cows with beta-lactoglobulin and kappa-casein gene BB genotypes have highest milk crude protein and fat content. The aim of the study was to determinate the frequencies of milk protein gene polymorphisms in local Latvian Brown (LB) cows breed and analyze the influence of beta-lactoglobulin and kappa-casein genotypes to milk productivity traits. 102 cows’ genotypes of milk protein genes were detected using Polymerase Chain Reaction and Restriction Fragment Length Polymorphism (PCR-RFLP) and electrophoresis on 3% agarose gel. For beta-lactoglobulin were observed 2 types of alleles A and B and for kappa-casein 3 types: A, B and E. Highest frequency in beta-lactoglobulin gene was observed for B allele – 0.926. Molecular analysis of beta-lactoglobulin gene shows 86.3% of individuals are homozygous by B allele and animals are with genotypes BB and 12.7% of individuals are heterozygous with genotypes AB. The highest milk yield 4711.7 kg was for 1st lactation cows with AB genotypes, whereas the highest milk protein content (3.35%) and fat content (4.46 %) was for BB genotypes. Analysis of the kappa-casein locus showed a prevalence of the A allele – 0.750. The genetic variant of B was characterized by a low frequency – 0.240. Moreover, the frequency of E occurred in the LB cows’ population with very low frequency – 0.010. 54.9 % of cows are homozygous with genotypes AA, and only 4.9 % are homozygous with genotypes BB. 32.8 % of individuals are heterozygous with genotypes AB, and 2.0 % are with AE. The highest milk productivity was for 1st lactation cows with AB genotypes: milk yield 4620.3 kg, milk protein content 3.39% and fat content 4.53 %. According to the results, in local Latvian brown there are only 2.9% of cows are with BB-BB genotypes, which is related to milk coagulation ability and affected cheese production yield. Acknowledgment: the investigation is supported by VPP 2014-2017 AgroBioRes Project No. 3 LIVESTOCK.

Keywords: beta-lactoglobulin, cows, genotype frequencies, kappa-casein

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Authors: Devendra Gupta, S. P. Ambesh, P. K Singh

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Introduction: Minimally invasive coronary artery bypass grafting (MICABG) is a less invasive method of performing surgical revascularization. Minimally invasive direct coronary artery bypass (MIDCAB) provides many anesthetic challenges including one lung ventilation (OLV), managing myocardial ischemia, and pain. We present an early and midterm result of the use of this technique with OLV. Method: We enrolled 62 patients for analysis operated between 2008 and 2012. Patients were anesthetized and left endobronchial tube was placed. During the procedure left lung was isolated and one lung ventilation was maintained through right lung. Operation was performed utilizing off pump technique of coronary artery bypass grafting through a minimal invasive incision. Left internal mammary artery graft was done for single vessel disease and radial artery was utilized for other grafts if required. Postoperative ventilation was done with single lumen endotracheal tube. Median follow-up is 2.5 years (6 months to 4 years). Results: Median age was 58.5 years (41-77) and all were male. Single vessel disease was present in 36, double vessel in 24 and triple vessel disease in 2 patients. All the patients had normal left ventricular size and function. In 2 cases difficulty were encounter in placement of endobronchial tube. In 1 case cuff of endobronchial tube was ruptured during intubation. High airway pressure was developed on OLV in 1 case and surgery was accomplished with two lung anesthesia with low tidal volume. Mean postoperative ventilation time was 14.4 hour (11-22). There was no perioperative and 30 day mortality. Conversion to median sternotomy to complete the operation was done in 3.23% (2 out of 62 patients). One patient had acute myocardial infarction postoperatively and there were no deaths during follow-up. Conclusion: MICABG is a safe and effective method of revascularization with OLV in low risk candidates for coronary artery bypass grafting.

Keywords: MIDCABG, one lung ventilation, coronary artery bypass grafting, endobronchial tube

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Authors: Sameer N. Goyal, Chandragauda R. Patil

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Oleanolic acid (3/3-hydroxy-olea-12-en-28-oic acid) and its isomer, Ursolic acid (38-hydroxy-urs-12-en-28-oic acid) are triterpenoids compounds which exist widely in plant kingdom in the free acid form or as glycosidic triterpenoids saponins. The aim of the study is to evaluate intravenously administered oleanolic acid and ursolic acid in doxorubicin induced cardiotoxicity. Cardiotoxicity was induced in albino wistar rat with single intravenous injection of doxorubicin at dose of 67.75mg/kg i.v for 48 hrs at 12 hrs interval following doxorubicin administration in the same model cardioprotective effect of amifostine (90 mg/kg i.v, single dose prior 30 min before doxorubicin administration) was evaluated as standard treatment. Induction of cardiotoxicity was confirmed by rise in cardiac markers in serum such as CK–MB, LDH and also by electrocardiographically. The doxorubicin treated group significantly increased in QT interval, serum CK-MB, serum LDH, SGOT, SGPT and antioxidant parameter. Both the treatment group showed significant protective effect on Hemodynamic, electrocardiographic, biochemical, and antioxidant parameters. The oleanolic acid showed slight protective effect in histological lesions in doxorubicin induced cardiotoxicity. Hence, the results indicate that Oleanolic acid has more cardioprotective potential than ursolic acid against doxorubicin induced cardiotoxicity in rats.

Keywords: cardioprotection, doxorubicin, oleanolic acid, ursolic acid

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Authors: V. Nagaraju, G. Murali, Nagarjunavarma Ganna, Atluri Pavan Kalyan, N. Sree Sai Ganesh, V. S. V. S. Badrinath

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The present work focuses on the development of a mathematical model for the yield obtained by single slope solar still incorporated with cylindrical pipes filled with sand. The mathematical results obtained were validated with the experimental results for the 3 cm of water level at the basin. The mathematical model and results obtained with the experimental investigation are within 11% of deviation. The theoretical model to predict the yield obtained due to the capillary effect was proposed first. And then, to predict the total yield obtained, the thermal effect model was integrated with the capillary effect model. With the obtained results, it is understood that the yield obtained is more in the case of solar stills with sand-filled cylindrical pipes when compared to solar stills without sand-filled cylindrical pipes. And later model was used for predicting yield for 1 cm and 2 cm of water levels at the basin. And it is observed that the maximum yield was obtained for a 1 cm water level at the basin. It means solar still produces better yield with the lower depth of water level at the basin; this may be because of the availability of more space in the sand for evaporation.

Keywords: solar still, cylindrical pipes, still efficiency, mathematical modeling, capillary effect model, yield, solar desalination

Procedia PDF Downloads 116

Authors: T. Wejrzanowski, M. Grybczuk, E. Tymicki, K. J. Kurzydlowski

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In the present study numerical simulations silicon carbide single crystal growth process in Physical Vapor Transport reactor are addressed. Silicon Carbide is a perspective material for many applications in modern electronics. One of the main challenges for wider applications of SiC is high price of high quality mono crystals. Improvement of silicon carbide manufacturing process has a significant influence on the product price. Better understanding of crystal growth allows for optimization of the process, and it can be achieved by numerical simulations. In this work Virtual Reactor software was used to simulate the process. Predicted geometrical properties of the final product and information about phenomena occurring inside process reactor were obtained. The latter is especially valuable because reactor chamber is inaccessible during the process due to high temperature inside the reactor (over 2000˚C). Obtained data was used for improvement of the process and reactor geometry. Resultant crystal quality was also predicted basing on crystallization front shape evolution and threading dislocation paths. Obtained results were confronted with experimental data and the results are in good agreement.

Keywords: Finite Volume Method, semiconductors, Physical Vapor Transport, silicon carbide

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Authors: D. E. Egirani, J. E. Andrews, A. R. Baker

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This study investigates sorption of Cu and Zn contained in natural mine wastewater, using mixed mineral systems in sulfidic-anoxic condition. The mine wastewater was obtained from disused mine workings at Cwmheidol in Wales, United Kingdom. These contaminants flow into water courses. These water courses include River Rheidol. In this River fishing activities exist. In an attempt to reduce Cu-Zn levels of fish intake in the watercourses, single mineral systems and 1:1 mixed mineral systems of clay and goethite were tested with the mine waste water for copper and zinc removal at variable pH. Modelling of hydroxyl complexes was carried out using phreeqc method. Reactions using batch mode technique was conducted at room temperature. There was significant differences in the behaviour of copper and zinc removal using mixed mineral systems when compared  to single mineral systems. All mixed mineral systems sorb more Cu than Zn when tested with mine wastewater.

Keywords: Cu- Zn, hydroxyl complexes, kinetics, mixed mineral systems, reactivity

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Authors: Maxime Merheb, Rachel Matar

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Retrieving ancient DNA sequences which in return permit the entire genome sequencing from fossils have extraordinarily improved in recent years, thanks to sequencing technology and other methodological advances. In any case, the quest to search for ancient DNA is still obstructed by the damage inflicted on DNA which accumulates after the death of a living organism. We can characterize this damage into three main categories: (i) Physical abnormalities such as strand breaks which lead to the presence of short DNA fragments. (ii) Modified bases (mainly cytosine deamination) which cause errors in the sequence due to an incorporation of a false nucleotide during DNA amplification. (iii) DNA modifications referred to as blocking lesions, will halt the PCR extension which in return will also affect the amplification and sequencing process. We can clearly see that the issues arising from breakage and coding errors were significantly decreased in recent years. Fast sequencing of short DNA fragments was empowered by platforms for high-throughput sequencing, most of the coding errors were uncovered to be the consequences of cytosine deamination which can be easily removed from the DNA using enzymatic treatment. The methodology to repair DNA sequences is still in development, it can be basically explained by the process of reintroducing cytosine rather than uracil. This technique is thus restricted to amplified DNA molecules. To eliminate any type of damage (particularly those that block PCR) is a process still pending the complete repair methodologies; DNA detection right after extraction is highly needed. Before using any resources into extensive, unreasonable and uncertain repair techniques, it is vital to distinguish between two possible hypotheses; (i) DNA is none existent to be amplified to begin with therefore completely un-repairable, (ii) the DNA is refractory to PCR and it is worth to be repaired and amplified. Hence, it is extremely important to develop a non-enzymatic technique to detect the most degraded DNA.

Keywords: ancient DNA, DNA barcodong, enzymatic repair, PCR

Procedia PDF Downloads 398

Authors: Xiaoming Jiang, Jinqiao Shi, Qingfeng Tan, Wentao Zhang, Xuebin Wang, Muqian Chen

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Nowadays, big companies such as Google, Microsoft, which have adequate proxy servers, have perfectly implemented their web crawlers for a certain website in parallel. But due to lack of expensive proxy servers, it is still a puzzle for researchers to crawl large amounts of information from a single website in parallel. In this case, it is a good choice for researchers to use free public proxy servers which are crawled from the Internet. In order to improve efficiency of web crawler, the following two issues should be considered primarily: (1) Tasks may fail owing to the instability of free proxy servers; (2) A proxy server will be blocked if it visits a single website frequently. In this paper, we propose Proxisch, an optimization approach of large-scale unstable proxy servers scheduling, which allow anyone with extremely low cost to run a web crawler efficiently. Proxisch is designed to work efficiently by making maximum use of reliable proxy servers. To solve second problem, it establishes a frequency control mechanism which can ensure the visiting frequency of any chosen proxy server below the website’s limit. The results show that our approach performs better than the other scheduling algorithms.

Keywords: proxy server, priority queue, optimization algorithm, distributed web crawling

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Authors: Mostafa Jafarian Abyaneh, Khashayar Jafari, Vahab Toufigh

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The cost of experiments on different types of concrete has raised the demand for prediction of their behavior with numerical analysis. In this research, an advanced numerical model has been presented to predict the complete elastic-plastic behavior of polymer concrete (PC), high-strength concrete (HSC), high performance concrete (HPC) along with different steel fiber contents under uniaxial compression. The accuracy of the numerical response was satisfactory as compared to other conventional simple models such as Mohr-Coulomb and Drucker-Prager. In order to predict the complete elastic-plastic behavior of specimens including softening behavior, disturbed state concept (DSC) was implemented by nonlinear finite element analysis (NFEA) and hierarchical single surface (HISS) failure criterion, which is a failure surface without any singularity.

Keywords: disturbed state concept (DSC), hierarchical single surface (HISS) failure criterion, high performance concrete (HPC), high-strength concrete (HSC), nonlinear finite element analysis (NFEA), polymer concrete (PC), steel fibers, uniaxial compression test

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Authors: Lavinia Ruta, Ileana Farcasanu

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The yeast surface display (YSD) technique enables the expression of proteins on yeast cell surfaces, facilitating the identification and isolation of proteins with targeted binding properties, such as nanobodies. Nanobodies, derived from camelid species, are single-domain antibody fragments renowned for their high affinity and specificity towards target proteins, making them valuable in research and potentially in therapeutics. Their advantages include a compact size (~15 kDa), robust stability, and the ability to target challenging epitopes. The project endeavors to establish and validate a platform for producing Green Fluorescent Protein (GFP) and mCherry nanobodies using the yeast surface display method. mCherry, a prevalent red fluorescent protein sourced from coral species, is commonly utilized as a genetic marker in biological studies due to its vibrant red fluorescence. The GFP-nanobody, a single variable domain of heavy-chain antibodies (VHH), exhibits specific binding to GFP, offering a potent means for isolating and engineering fluorescent protein fusions across various biological research domains. Both GFP and mCherry nanobodies find specific utility in cellular imaging and protein analysis applications.

Keywords: YSD, nanobodies, GFP, Saccharomyces cerevisiae

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Authors: Rinku Maji, Joydeep Chakrabortty, Stephen F. King

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The grand unified theory (GUT) rationales the arbitrariness of the standard model (SM) and explains many enigmas of nature at the outset of a single gauge group. The GUTs predict the proton decay and, the spontaneous symmetry breaking (SSB) of the higher symmetry group may lead to the formation of topological defects, which are indispensable in the context of the cosmological observations. The Super-Kamiokande (Super-K) experiment sets sacrosanct bounds on the partial lifetime (τ) of the proton decay for different channels, e.g., τ(p → e+ π0) > 1.6×10³⁴ years which is the most relevant channel to test the viability of the nonsupersymmetric GUTs. The GUTs based on the gauge groups SO(10) and E(6) are broken to the SM spontaneously through one and two intermediate gauge symmetries with the manifestation of the left-right symmetry at least at a single intermediate stage and the proton lifetime for these breaking chains has been computed. The impact of the threshold corrections, as a consequence of integrating out the heavy fields at the breaking scale alter the running of the gauge couplings, which eventually, are found to keep many GUTs off the Super-K bound. The possible topological defects arising in the course of SSB at different breaking scales for all breaking chains have been studied.

Keywords: grand unified theories, proton decay, threshold correction, topological defects

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Authors: Suprabha Islam, Sifat Ullah Tanzil

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During past few decades, being amazed by the excellent silent flight of owl, scientists have been trying to demystify the unique features of its wing feathers. Our present study is dedicated to taking our understanding further on this phenomenon. In this present study, a numerical investigation was performed to analyze how the shape of the leading-edge serration at owl wing feathers effects the flow-induced noise generation. For the analysis, an owl inspired single feather wing model was prepared for both with and without serrations at the leading edge. The serration profiles were taken at different positions of the vane length for a single feather. The broadband noise was studied to quantify the local contribution to the total acoustic power generated by the flow, where the results clearly showed the effect of serrations in reducing the noise generation. It was also clearly visible that the shape of the serration has a very strong influence on noise generation. The frequency spectrum of noise was also analyzed and a strong relation was found between the shape of the serration and the noise generation. It showed that the noise suppression is strongly influenced by the height to length ratio of the serration. With the increase in height to length ratio, the noise suppression is enhanced further.

Keywords: aeroacoustics, aerodynamic, biomimetics, serrations

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Authors: A. Ferasat, S. Rostampour Yasouri

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Seasonal flu is a highly contagious infection caused by influenza viruses. These viruses undergo genetic changes that result in new epidemics across the globe. Medical attention is crucial in severe cases, particularly for the elderly, frail, and those with chronic illnesses, as their immune systems are often weaker. The purpose of this study was to detect new subtypes of the influenza A virus rapidly using a specific RT-PCR method based on the HA gene (hemagglutinin). In the winter and spring of 2022_2023, 120 embryonated egg samples were cultured, suspected of seasonal influenza. RNA synthesis, followed by cDNA synthesis, was performed. Finally, the PCR technique was applied using a pair of specific primers designed based on the HA gene. The PCR product was identified after purification, and the nucleotide sequence of purified PCR products was compared with the sequences in the gene bank. The results showed a high similarity between the sequence of the positive samples isolated from the patients and the sequence of the new strains isolated in recent years. This RT-PCR technique is entirely specific in this study, enabling the detection and multiplication of influenza and its subspecies from clinical samples. The RT-PCR technique based on the HA gene, along with sequencing, is a fast, specific, and sensitive diagnostic method for those infected with influenza viruses and its new subtypes. Rapid molecular diagnosis of influenza is essential for suspected people to control and prevent the spread of the disease to others. It also prevents the occurrence of secondary (sometimes fatal) pneumonia that results from influenza and pathogenic bacteria. The critical role of rapid diagnosis of new strains of influenza is to prepare a drug vaccine against the latest viruses that did not exist in the community last year and are entirely new viruses.

Keywords: influenza, molecular diagnosis, patients, RT-PCR technique

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Authors: Madhurima Poddar, Vinay Sharma, Shaikh M. Mobin, Rajneesh Misra

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Three 1,8-naphthalimide (NPI) substituted 4,4-difluoroboradiaza-s-indacene (BODIPY) dyads were synthesized via Pd-catalyzed Sonogashira cross-coupling reaction of ethynyl substituted NPI with the meso-, β- and α-halogenated BODIPYs, respectively. The photophysical and electrochemical data reveals considerable electronic communication between the BODIPY and NPI moieties. The electronic absorption spectrum reveals that the substitution of NPI at α position of BODIPY exhibit better electronic communication between the NPI and the BODIPY units. The electronic structures of all the dyads exhibit planar geometries which are in a good correlation with the structures obtained from single crystal X-ray diffraction. The crystal structures of the dyads exhibit interesting supramolecular interactions. The dyads show good cytocompatibility with the potential of multicolor live-cell imaging; making them excellent candidates for biological applications. The work provides an important strategy of screening the substitution pattern at different position of BODIPYs which will be useful for the design of BODIPY based organic molecules for various optoelectronic applications as well as bio-imaging.

Keywords: bio-imaging studies, cross-coupling, cyclic voltammetry, density functional calculations, fluorescence spectra, single crystal XRD, UV/Vis spectroscopy

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Authors: M. Mohemmed Sha Mohamed Kunju, Abdalla A. Al-Ameen Abdurahman, T. Manesh Thankappan, A. Mohamed Mustaq Ahmed Hameed

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Web service composition is an effective approach to complete the web based tasks with desired quality. A single web service with limited functionality is inadequate to execute a specific task with series of action. So, it is very much required to combine multiple web services with different functionalities to reach the target. Also, it will become more and more challenging, when these services are from different providers with identical functionalities and varying QoS, so while composing the web services, the overall QoS is considered to be the major factor. Also, it is not true that the expected QoS is always attained when the task is completed. A single web service in the composed chain may affect the overall performance of the task. So care should be taken in different aspects such as functionality of the service, while composition. Dynamic and automatic service composition is one of the main option available. But to achieve the actual functionality of the task, quality of the individual web services are also important. Normally the QoS of the individual service can be evaluated by using the non-functional parameters such as response time, throughput, reliability, availability, etc. At the same time, the QoS is not needed to be at the same level for all the composed services. So this paper proposes a framework that allows composing the services in terms of QoS by setting the appropriate weight to the non-functional parameters of each individual web service involved in the task. Experimental results show that the importance given to the non-functional parameter while composition will definitely improve the performance of the web services.

Keywords: composition, non-functional parameters, quality of service, web service

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Authors: Sumeeta Khurana, Kirti Megha, Amit Gupta, Rakesh Sehgal

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Background: Amoebic keratitis is a painful vision threatening infection caused by a free living pathogenic amoeba Acanthamoeba. It can be misdiagnosed and very difficult to treat if not suspected early. The epidemiology of Acanthamoeba genotypes causing infection in our geographical area is not yet known to the best of our knowledge. Objective: To characterize Acanthamoeba isolates from amoebic keratitis patients. Methods: A total of 19 isolates obtained from patients with amoebic keratitis presenting to the Advanced Eye Centre at Postgraduate Institute of Medical Education and Research, a tertiary care centre of North India over a period of last 10 years were included. Their corneal scrapings, lens solution and lens case (in case of lens wearer) were collected for microscopic examination, culture and molecular diagnosis. All the isolates were maintained in the Non Nutrient agar culture medium overlaid with E.coli and 13 strains were axenised and maintained in modified Peptone Yeast Dextrose Agar. Identification of Acanthamoeba genotypes was based on amplification of diagnostic fragment 3 (DF3) region of the 18srRNA gene followed by sequencing. Nucleotide similarity search was performed by BLAST search of sequenced amplicons in GenBank database (http//www.ncbi.nlm.nih.gov/blast). Multiple Sequence alignments were determined by using CLUSTAL X. Results: Nine out of 19 Acanthamoeba isolates were found to belong to Genotype T4 followed by 6 isolates of genotype T11, 3 T5 and 1 T3 genotype. Conclusion: T4 is the predominant Acanthamoeba genotype in our geographical area. Further studies should focus on differences in pathogenicity of these genotypes and their clinical significance.

Keywords: Acanthamoeba, free living amoeba, keratitis, genotype, ocular

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Authors: Apoorva Vinod, Archana Mathur, Snehanshu Saha

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Though there exists a plethora of Activation Functions (AFs) used in single and multiple hidden layer Neural Networks (NN), their behavior always raised curiosity, whether used in combination or singly. The popular AFs –Sigmoid, ReLU, and Tanh–have performed prominently well for shallow and deep architectures. Most of the time, AFs are used singly in multi-layered NN, and, to the best of our knowledge, their performance is never studied and analyzed deeply when used in combination. In this manuscript, we experiment with multi-layered NN architecture (both on shallow and deep architectures; Convolutional NN and VGG16) and investigate how well the network responds to using two different AFs (Sigmoid-Tanh, Tanh-ReLU, ReLU-Sigmoid) used alternately against a traditional, single (Sigmoid-Sigmoid, Tanh-Tanh, ReLUReLU) combination. Our results show that using two different AFs, the network achieves better accuracy, substantially lower loss, and faster convergence on 4 computer vision (CV) and 15 Non-CV (NCV) datasets. When using different AFs, not only was the accuracy greater by 6-7%, but we also accomplished convergence twice as fast. We present a case study to investigate the probability of networks suffering vanishing and exploding gradients when using two different AFs. Additionally, we theoretically showed that a composition of two or more AFs satisfies Universal Approximation Theorem (UAT).

Keywords: activation function, universal approximation function, neural networks, convergence

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Authors: Trupti Chavan, Ramachandra Guda, Kameshwar Rao

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The lack of data is a pain problem in medical image analysis using a convolutional neural network (CNN). This work uses various spatial transformation techniques to address the medical image augmentation issue for knee detection and localization using an enhanced single shot detector (SSD) network. The spatial transforms like a negative, histogram equalization, power law, sharpening, averaging, gaussian blurring, etc. help to generate more samples, serve as pre-processing methods, and highlight the features of interest. The experimentation is done on the OpenKnee dataset which is a collection of knee images from the openly available online sources. The CNN called enhanced single shot detector (SSD) is utilized for the detection and localization of the knee joint from a given X-ray image. It is an enhanced version of the famous SSD network and is modified in such a way that it will reduce the number of prediction boxes at the output side. It consists of a classification network (VGGNET) and an auxiliary detection network. The performance is measured in mean average precision (mAP), and 99.96% mAP is achieved using the proposed enhanced SSD with spatial transformations. It is also seen that the localization boundary is comparatively more refined and closer to the ground truth in spatial augmentation and gives better detection and localization of knee joints.

Keywords: data augmentation, enhanced SSD, knee detection and localization, medical image analysis, openKnee, Spatial transformations

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Authors: Norma Binti Alias, Che Rahim Che The, Norfarizan Mohd Said, Sakinah Abdul Hanan, Akhtar Ali

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This paper discusses on the transportation of magnetic drug targeting through blood within vessels, tissues and cells. There are three integrated mathematical models to be discussed and analyze the concentration of drug and blood flow through magnetic nanoparticles. The cell therapy brought advancement in the field of nanotechnology to fight against the tumors. The systematic therapeutic effect of Single Cells can reduce the growth of cancer tissue. The process of this nanoscale phenomena system is able to measure and to model, by identifying some parameters and applying fundamental principles of mathematical modeling and simulation. The mathematical modeling of single cell growth depends on three types of cell densities such as proliferative, quiescent and necrotic cells. The aim of this paper is to enhance the simulation of three types of models. The first model represents the transport of drugs by coupled partial differential equations (PDEs) with 3D parabolic type in a cylindrical coordinate system. This model is integrated by Non-Newtonian flow equations, leading to blood liquid flow as the medium for transportation system and the magnetic force on the magnetic nanoparticles. The interaction between the magnetic force on drug with magnetic properties produces induced currents and the applied magnetic field yields forces with tend to move slowly the movement of blood and bring the drug to the cancer cells. The devices of nanoscale allow the drug to discharge the blood vessels and even spread out through the tissue and access to the cancer cells. The second model is the transport of drug nanoparticles from the vascular system to a single cell. The treatment of the vascular system encounters some parameter identification such as magnetic nanoparticle targeted delivery, blood flow, momentum transport, density and viscosity for drug and blood medium, intensity of magnetic fields and the radius of the capillary. Based on two discretization techniques, finite difference method (FDM) and finite element method (FEM), the set of integrated models are transformed into a series of grid points to get a large system of equations. The third model is a single cell density model involving the three sets of first order PDEs equations for proliferating, quiescent and necrotic cells change over time and space in Cartesian coordinate which regulates under different rates of nutrients consumptions. The model presents the proliferative and quiescent cell growth depends on some parameter changes and the necrotic cells emerged as the tumor core. Some numerical schemes for solving the system of equations are compared and analyzed. Simulation and computation of the discretized model are supported by Matlab and C programming languages on a single processing unit. Some numerical results and analysis of the algorithms are presented in terms of informative presentation of tables, multiple graph and multidimensional visualization. As a conclusion, the integrated of three types mathematical modeling and the comparison of numerical performance indicates that the superior tool and analysis for solving the complete set of magnetic drug delivery system which give significant effects on the growth of the targeted cancer cell.

Keywords: mathematical modeling, visualization, PDE models, magnetic nanoparticle drug delivery model, drug release model, single cell effects, avascular tumor growth, numerical analysis

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Authors: Mengying Wang, Dongjing Liu, Holger Schwender, Ping Wang, Hongping Zhu, Tao Wu, Terri H Beaty

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Background: Maternal smoking is a recognized risk factor for nonsyndromic cleft lip with or without cleft palate (NSCL/P). It has been reported that the effect of maternal smoking on oral clefts is mediated through genes that influence nicotine dependence. The polymorphisms of cholinergic receptor nicotinic alpha (CHRNA) and beta (CHRNB) subunits genes have previously shown strong associations with nicotine dependence. Here, we attempted to investigate whether the above genes are associated with clefting risk through testing for potential gene-gene (G×G) and gene-environment (G×E) interaction. Methods: We selected 120 markers in 14 genes associated with nicotine dependence to conduct transmission disequilibrium tests among 806 Chinese NSCL/P case-parent trios ascertained in an international consortium which conducted a genome-wide association study (GWAS) of oral clefts. We applied Cordell’s method using “TRIO” package in R to explore G×G as well as G×E interaction involving environmental tobacco smoke (ETS) based on conditional logistic regression model. Results: while no SNP showed significant association with NSCL/P after Bonferroni correction, we found signals for G×G interaction between 10 pairs of SNPs in CHRNA3, CHRNA5, and CHRNB4 (p<10-8), among which the most significant interaction was found between RS3743077 (CHRNA3) and RS11636753 (CHRNB4, p<8.2×10-12). Linkage disequilibrium (LD) analysis revealed only low level of LD between these markers. However, there were no significant results for G×ETS interaction. Conclusion: This study fails to detect association between nicotine dependence genes and NSCL/P, but illustrates the importance of taking into account potential G×G interaction for genetic association analysis in NSCL/P. This study also suggests nicotine dependence genes should be considered as important candidate genes for NSCL/P in future studies.

Keywords: Gene-Gene Interaction, Maternal Smoking, Nicotine Dependence, Non-Syndromic Cleft Lip with or without Cleft Palate

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