Search results for: amplification

Authors: M. Najafi

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In the present paper, a large turbo-generator shaft train including a heavy-duty gas turbine engine, a coupling, and a generator is established. The method of analysis is based on finite element simplified model for lateral and torsional vibration calculation. The basic elements of rotor are the shafts and the disks which are represented as circular cross section flexible beams and rigid body elements, respectively. For more accurate results, the gyroscopic effect and bearing dynamics coefficients and function of rotation are taken into account, and for the influence of shear effect, rotor has been modeled in the form of Timoshenko beam. Lateral critical speeds, critical speed map, damped mode shapes, Campbell diagram, zones of instability, amplitudes, phase angles response due to synchronous forces of excitation and amplification factor are calculated. Also, in the present paper, the effect of imbalanced rotor and effects of changing in internal force and temperature are studied.

Keywords: rotor dynamic analysis, finite element method, shaft train, Campbell diagram

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Authors: Ankit Tyagi, Reet Kamal Tiwari, Naveen James

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In India, landslides are the most frequently occurring disaster in the regions of the Himalayas and the Western Ghats. The steep slopes and land use in these areas are quite apprehensive. In the recent past, many landslide hazard zonation (LHZ) works have been carried out in the Himalayas. However, the preparation of LHZ maps considering temporal factors such as seismic ground shaking, seismic amplification at surface level, and rainfall are limited. Hence this study presents a comprehensive use of the multi-criteria decision-making (MCDM) method in landslide risk assessment. In this research, we conducted both geospatial and geotechnical analysis to minimize the danger of landslides. Geospatial analysis is performed using high-resolution satellite data to produce landslide causative factors which were given weightage using the MCDM method. The geotechnical analysis includes a slope stability check, which was done to determine the potential landslide slope. The landslide risk map can provide useful information which helps people to understand the risk of living in an area.

Keywords: landslide hazard zonation, PHA, AHP, GIS

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Authors: J. Hidalgo de Quintana, I. Stoner, M. Tackett, G. Doran, C. Rafferty, A. Windemuth, J. Tytell, D. Pregibon

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We have developed the Multiplexed Circulating microRNA assay that allows the detection of up to 68 microRNA targets per sample. The assay combines particle­based multiplexing, using patented Firefly hydrogel particles, with single­ step RT-PCR signal. Thus, the Circulating microRNA assay leverages PCR sensitivity while eliminating the need for separate reverse transcription reactions and mitigating amplification biases introduced by target­-specific qPCR. Furthermore, the ability to multiplex targets in each well eliminates the need to split valuable samples into multiple reactions. Results from the Circulating microRNA assay are interpreted using Firefly Analysis Workbench, which allows visualization, normalization, and export of experimental data. To aid discovery and validation of biomarkers, we have generated fixed panels for Oncology, Cardiology, Neurology, Immunology, and Liver Toxicology. Here we present the data from several studies investigating circulating and tumor microRNA, showcasing the ability of the technology to sensitively and specifically detect microRNA biomarker signatures from fluid specimens.

Keywords: biomarkers, biofluids, miRNA, photolithography, flowcytometry

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Authors: Neil Erick Q. Madariaga, Noel B. Linsangan

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Body Mass Index (BMI) is one of the different ways to monitor the health of a person. It is based on the height and weight of the person. This study aims to compute for the BMI using an Android tablet by obtaining the height of the person by using a camera and measuring the weight of the person by using a weighing scale or load cell. The height of the person was estimated by applying background subtraction to the image captured and applying different processes such as getting the vanishing point and applying Artificial Neural Network. The weight was measured by using Wheatstone bridge load cell configuration and sending the value to the computer by using Gizduino microcontroller and Bluetooth technology after the amplification using AD620 instrumentation amplifier. The application will process the images and read the measured values and show the BMI of the person. The study met all the objectives needed and further studies will be needed to improve the design project.

Keywords: body mass index, artificial neural network, vanishing point, bluetooth, wheatstone bridge load cell

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Authors: Houria Djebar, Amina Saib, Malika Berredjem, Khaoula Bechlem, Mohammed-Reda Djebar

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Reactive oxygen species (ROS) have a high potential to damage almost all types of cellular components of the body, which explains their involvement in the induction and/or amplification of several pathologies. Supplementation of the body by exogenous antioxidants is very useful against these harmful species. In this context, we attempted to evaluate the in vitro and in vivo antioxidant activities of three newly synthesized amidophosphonates (AP1, AP2, and AP3). The results relating to the in vitro tests for DPPH radical scavenging activity shows that these amidophosphonates have a modest antiradical power (ARP) less effectively pronounced compared with an analogue marketed in Algeria: (Dursban) Clorpiryphos ethyl. However, in vivo effects were evaluated on some antioxidant systems (LP intensity, CAT activity and GSH content), or in combination with 2, 2-diphenyl-picrylhydrazyle (DPPH) radical in paramecium tetraurelia used as a complementary system to rapidly elucidate the cytotoxicity. On the basis of the results obtained it can be concluded that amidophosphonates studied exhibited a mild protective effect. The mechanism for how they influenced the antioxidant activities was discussed.

Keywords: Paramecium tetraurelia, amidophosphonates, antioxidant activity, DPPH free radical, in vitro experiments, biochemical parameters

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Authors: Moneesh Thakur, Hridayesh Prasad, Nikitasha Bora, Parimal Roy Choudhary, A. K. Samanta, Sanjeev Kumar

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Canine demodicosis is a common parasitic condition which involves dog skin. Demodicosis in dogs is due the prominent growth of Demodex. Out of various canine Demodex spp., Demodex canis is the most often involved species. Canine demodicosis can occur as either a localized or generalized form of demodicosis severely affect the dogs and in non-treated dogs may cause death. This study was planned with the aim to screen and characterize the 18S rRNA gene of isolated Demodex canis. A total of 1200 dogs were screened during this study period. The skin scrapings of all the suspected dogs were examined under a microscope at 100X magnification for the presence of Demodex canis. The skin scrapings positive for Demodex canis were examined using PCR for confirmation. A total of 35 dogs were confirmed a positive result for D. canis based on 18S rRNA gene amplification by PCR. Further, the 18S rRNA gene of isolated Demodex canis was cloned and sequenced for genome analysis. On the sequence analysis, it was found that isolated sequence (GenBank Accession No. MK177513) had close similarity (99.7%) to that of D. canis genotype of China (Accession No. MG372254).

Keywords: PCR, phylogenetic analysis, cloning and sequening, Demodex canis

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Authors: Rouhollah Radjabi, Mojtaba Zarei, Elham Sanatgar, Hossein Shouhani

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RAPD molecular markers in order to discrimination of the Iranian native Bombyx mori silkworm breeds were used. DNA extraction using phenol - chloroform was and the qualitative and quantitative measurements of extracted DNA and its dilution, the obtained bands on agarose gel 1.5 percent were marked and analyzed. Results showed that the bands are observed between 250-2500 bp and most bands have been observed as Gilani-orange, the lowest bands observed are Khorasani-lemon. Primer 3 with 100% polymorphism with the highest polymorphism and primer 2 with 61.5 polymorphism had the lowest percentage of polymorphism. Cluster analysis of races and placed them in three main groups, races Gilani - orange, Baghdad and Khorasani -pink if the first group, camel's thorn, Herati - yellow race was alone in the second group and Khorasani – lemon was alone in the third group. The greatest similarity between the races, between Khorasani- pink and Baghdad (0.64). RAPD markers have been determined different silkworm races based on various morphological or economic characteristics except geographic origin.

Keywords: silkworm, molecular marker, RAPD, Iran

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Authors: Ganga K. V. Prakhya, V. Karthigeyan

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The paper describes the influences of the fluid and structure interaction in concrete structures that support large oil platforms in the North Sea. The dynamic interaction of the fluid both in 2D and 3D are demonstrated through a Computational Fluid Dynamics analysis in the event of explosion following a gas leak inside of the concrete column. The structural response characteristics of the column in water under dynamic conditions are quite complex involving axial, radial and circumferential modes. Fluid structure interaction (FSI) modelling showed that there are some frequencies of the column in water which are not found for a column in air. For example, it was demonstrated that one of the axial breathing modes can never be simulated without the use of FSI models. The occurrence of a shift in magnitude and time of pressure from explosion following gas leak along the height of the shaft not only excited the modes of vibration involving breathing (axial), bending and squashing (radial) modes but also magnified the forces in the column. FSI models revealed that dynamic effects resulted in dynamic amplification of loads. The results are summarized from a detailed study that was carried out by the first author for the Offshore Safety Division of Health & Safety Executive United Kingdom.

Keywords: concrete, explosion, fluid structure interaction, offshore structures

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Authors: Zhenfeng Xie

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Acute gastroenteritis (AGE) is a common cause of morbidity and mortality in infants and young children worldwide, especially in developing countries. Enterovirus(EVs) have been identified in patients with AGE in many countries around the world, and some studies have revealed that EV infection is associated with gastrointestinal symptoms and plays a role in AGE. As a potential causative pathogen of AGE in humans, continuous detection and identification of EVs in pediatric patients with AGE is needed. In this study, we aimed to investigate the prevalence, seasonal distribution, and molecular characteristics of EVs circulating in pediatric patients with AGE in Thailand from 2019 to 2022. A total of 1422 stool specimens were collected for this study. RT-PCR amplification of the 5'UTR was used to screen for EV positive samples. EV genotyping was determined based on nucleotide sequence and phylogenetic analysis of the VP1 sequences. EV prevalence in pediatric AGE patients was 8.3% (118 out of 1,422). Among these, 35.6% of EV infection cases were caused by species A, followed by species C and B (33.1% and 30.5%, respectively). A total of 26 EV genotypes were identified in this study. Poliovirus 3 and coxsackievirus A2 were the predominant genotypes detected(14% and 13%, respectively). EV was detected all year round with higher prevalence between July and December. In summary, this study reports EV's prevalence and genotype diversity in pediatric patients with AGE in Thailand during 2019-2022.

Keywords: enterovirus, epidemiology, acute gastroenteritis, genotype

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Authors: Tatsuya Otoshi, Masayuki Murata

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With the development and diversification of applications on the Internet, applications that require high responsiveness, such as video streaming, are becoming mainstream. Application responsiveness is not only a matter of communication delay but also a matter of time required to grasp changes in network conditions. The tradeoff between accuracy and measurement time is a challenge in network control. We people make countless decisions all the time, and our decisions seem to resolve tradeoffs between time and accuracy. When making decisions, people are known to make appropriate choices based on relatively small samples. Although there have been various studies on models of human decision-making, a model that integrates various cognitive biases, called ”quantum decision-making,” has recently attracted much attention. However, the modeling of small samples has not been examined much so far. In this paper, we extend the model of quantum decision-making to model decision-making with a small sample. In the proposed model, the state is updated by value-based probability amplitude amplification. By analytically obtaining a lower bound on the number of samples required for decision-making, we show that decision-making with a small number of samples is feasible.

Keywords: quantum decision making, small sample, MPEG-DASH, Grover's algorithm

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Authors: S. Mohamadi, T. Boudina, A. Rouabeh, A. Seridi

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Equivalent linear and non-linear ground response analyses are conducted at many representative sites at the mosque of Algeria, to compare the free field acceleration spectra with local code of practice. Spectral Analysis of Surface Waves (SASW) technique was adopted to measure the in-situ shear wave velocity profile at the representative sites. The seismic movement imposed on the rock is the NS component of Keddara station recorded during the earthquake in Boumerdes 21 May 2003. The site-specific elastic design spectra for each site are determined to further obtain site specific non-linear acceleration spectra. As a case study, the results of site-specific evaluations are presented for two building sites (site of minaret and site of the prayer hall) to demonstrate the influence of local geological conditions on ground response at Algerian sites. A comparison of computed response with the standard code of practice being used currently in Algeria for the seismic zone of Algiers indicated that the design spectra is not able to capture site amplification due to local geological conditions.

Keywords: equivalent linear, non-linear, ground response analysis, design response spectrum

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Authors: Surangrat Srisurapanon, Chatchawal Wongjitrat, Navin Horthongkham, Ruengpung Sutthent

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HBV infection causes a potential serious public health problem. The ability to detect the HBV DNA concentration is of the importance and improved continuously. By using quantitative Polymerase Chain Reaction (qPCR), several factors in standardized; source of material, calibration standard curve and PCR efficiency are inconsistent. Digital PCR (dPCR) is an alternative PCR-based technique for absolute quantification using Poisson's statistics without requiring a standard curve. Therefore, the aim of this study is to compare the data set of HBV DNA generated between dPCR and qPCR methods. All samples were quantified by Abbott’s real time PCR and 54 samples with 2 -6 log10 HBV DNA were selected for comparison with dPCR. Of these 54 samples, there were two outlier samples defined as negative by dPCR. Of these two, samples were defined as negative by dPCR, whereas 52 samples were positive by both the tests. The difference between the two assays was less than 0.25 log IU/mL in 24/52 samples (46%) of paired samples; less than 0.5 log IU/mL in 46/52 samples (88%) and less than 1 log in 50/52 samples (96%). The correlation coefficient was r=0.788 and P-value <0.0001. Comparison to qPCR, data generated by dPCR tend to be the overestimation in the sample with low HBV DNA concentration and underestimated in the sample with high viral load. The variation in DNA by dPCR measurement might be due to the pre-amplification bias, template. Moreover, a minor drawback of dPCR is the large quantity of DNA had to be used when compare to the qPCR. Since the technology is relatively new, the limitations of this assay will be improved.

Keywords: hepatitis B virus, real time PCR, digital PCR, DNA quantification

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Authors: J. Bernasovská, R. Lohajová Behulová, E. Petrejčiková, I. Boroňová, I. Bernasovský

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Y chromosome microdeletions are the most common genetic cause of male infertility and screening for these microdeletions in azoospermic or severely oligospermic men is now standard practice. Analysis of the Y chromosome in men with azoospermia or severe oligozoospermia has resulted in the identification of three regions in the euchromatic part of the long arm of the human Y chromosome (Yq11) that are frequently deleted in men with otherwise unexplained spermatogenic failure. PCR analysis of microdeletions in the AZFa, AZFb and AZFc regions of the human Y chromosome is an important screening tool. The aim of this study was to analyse the type of microdeletions in men with fertility disorders in Slovakia. We evaluated 227 patients with azoospermia and with normal karyotype. All patient samples were analyzed cytogenetically. For PCR amplification of sequence-tagged sites (STS) of the AZFa, AZFb and AZFc regions of the Y chromosome was used Devyser AZF set. Fluorescently labeled primers for all markers in one multiplex PCR reaction were used and for automated visualization and identification of the STS markers we used genetic analyzer ABi 3500xl (Life Technologies). We reported 13 cases of deletions in the AZF region 5,73%. Particular types of deletions were recorded in each region AZFa,b,c .The presence of microdeletions in the AZFc region was the most frequent. The study confirmed that percentage of microdeletions in the AZF region is low in Slovak azoospermic patients, but important from a prognostic view.

Keywords: AZF, male infertility, microdeletions, Y chromosome

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Authors: Mohamed Al-Hazmi, Abdullah Al-Arfaj, Moussa Ihab

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Raw, unpasteurized milk can carry dangerous bacteria such as Salmonella, E. coli, and Listeria, which are responsible for causing numerous foodborne illnesses. The objective of this study was molecular characterization of shiga toxogenic E. coli in raw milk collected from different Egyptian governorates by multiplex PCR. During the period of 25th May to 25th October 2012, a total of 320 bulk-tank milk samples were collected from 10 cow farms located in different Egyptian governorates. Bacteriological examination of milk samples revealed the presence of E. coli organisms in 65 samples (20.3%), serotyping of the E. coli isolates revealed, 35 strains (10.94%) O111, 15 strains (4.69%) O157: H7, 10 strains (3.13%) O128 and 5 strains (1.56%) O119. Multiplex PCR for detection of shiga toxin type 2 and intimin genes revealed positive amplification of 255 bp fragment of shiga toxin type 2 gene and 384 bp fragment of intimin gene from all E. coli serovar O157: H7, while from serovar O111 were 25 (71.43%), 20 (57.14%) and from serovar O128 were 6 (60%), 8 (80%), respectively. The results of multiplex PCR assay are useful for identification of STEC possessing the eaeA and stx2 genes.

Keywords: raw milk, E. coli, multiplex PCR, Shiga toxin type 2, intimin gene

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Authors: Yudi Zhao, Ziyun Zhou, Yueting Yao, Shuying Dai, Zhiling Yan, Longyu Yang, Chuanyin Li, Li Shi, Yufeng Yao

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HPV16 E4 gene plays an important role in viral genome amplification and release. Therefore, a variation of the E4 gene nucleic acid sequence may affect the carcinogenicity of HPV16. In order to understand the relationship between the variation of HPV16 E4 gene and cervical cancer, this study was to amplify and sequence the DNA sequences of E4 genes in 118 HPV16-positive cervical cancer patients and 151 HPV16-positive asymptomatic individuals. After obtaining E4 gene sequences, the phylogenetic trees were constructed by the Neighbor-joining method for gene variation analysis. The results showed that: 1) The distribution of HPV16 variants between the case group and the control group differed greatly (P = 0.015)，and the Asian-American（AA）variant was likely to relate to the occurrence of cervical cancer. 2) DNA sequence analysis showed that there were significant differences in the distribution of 8 variants between the case group and the control group (P < 0.05). And 3) In European (EUR) variant, two variations, C3384T (L18L) and A3449G (P39P), were associated with the initiation and development of cervical cancer. The results suggested that the variation of HPV16 E4 gene may be a contributor affecting the occurrence as well as the development of cervical cancer, and different HPV16 variants may have different carcinogenic capability.

Keywords: cervical cancer, HPV16, E4 gene, variations

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Authors: Wei Yongxiang, Zhu Haoyue, Tang Heng, Yuan Qunwei

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In order to study the preparation method of gear fatigue load spectrum for loaders, the load signal of four typical working conditions of loader is collected. The signal that reflects the law of load change is obtained by preprocessing the original signal. The torque of the drive axle is calculated by using the rain flow counting method. According to the operating time ratio of each working condition, the two-dimensional load spectrum based on the real working conditions of the drive axle of loader is established by the cycle extrapolation and synthesis method. The two-dimensional load spectrum is converted into one-dimensional load spectrum by means of the mean of torque equal damage method. Torque amplification includes the maximum load torque of the main reduction gear. Based on the theory of equal damage, the accelerated cycles are calculated. In this way, the load spectrum of the loading condition of the drive axle is prepared to reflect loading condition of the loader. The load spectrum can provide reference for fatigue life test and life prediction of loader drive axle.

Keywords: load spectrum, axle, torque, rain-flow counting method, extrapolation

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Authors: Shoaib Yousaf

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The main purpose of this research is to the empirical investigation of the bullwhip effect under sensitivity analysis in the two-tier supply chain. The simulation modeling technique has been applied in this research as a research methodology to see the sensitivity analysis of the bullwhip effect in the rice industry of Pakistan. The research comprises two case studies that have been chosen as a sample. The results of this research have confirmed that reduction in production delay reduces the bullwhip effect, which conforms to the time compressing paradigm and the significance of the reduction in production delay to lessen demand amplification. The result of this research also indicates that by increasing the value of time to adjust inventory decreases the bullwhip effect. Furthermore, by decreasing the value of alpha increases the damping effect of the exponential smoother, it is not surprising that it also reduces the bullwhip effect. Moreover, by reducing the value of time to work in progress also reduces the bullwhip effect. This research will help practitioners and operation managers to reduces the major costs of their products in three ways. They can reduce their i) inventory levels, ii) better utilize their capacity and iii) improve their forecasting techniques. However, this study is based on two tier supply chain, while in reality the supply chain has got many tiers. Hence, future work will be extended across more than two-tier supply chains.

Keywords: bullwhip effect, rice industry, supply chain dynamics, simulation, sensitivity analysis

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Authors: Noor Azwa Azreen Binti Abd. Aziz, Muhamad Zaim Bin Mohd Rozi

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Moving towards the 4th Industrial Revolution, artificial intelligence (AI) is now more popular than ever. This subject is gaining significance every day and is continually expanding, often merging with other fields. Instead of merely being passive observers, there are benefits to understanding modern technology by delving into its inner workings. However, in a world teeming with digital information, the impact of AI on the spread of disinformation has garnered significant attention. The dissemination of inaccurate or misleading information is referred to as misinformation, posing a serious threat to democratic society, public debate, and individual decision-making. This article delves deep into the connection between AI and the dissemination of false information, exploring its potential, risks, and ethical issues as AI technology advances. The rise of AI has ushered in a new era in the dissemination of misinformation as AI-driven technologies are increasingly responsible for curating, recommending, and amplifying information on online platforms. While AI holds the potential to enhance the detection and mitigation of misinformation through natural language processing and machine learning, it also raises concerns about the amplification and propagation of false information. AI-powered deepfake technology, for instance, can generate hyper-realistic videos and audio recordings, making it increasingly challenging to discern fact from fiction.

Keywords: artificial intelligence, digital information, disinformation, ethical issues, misinformation

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Authors: Hai Xu, Yiwei Wang, Xi Bao, Bihua Deng, Pengcheng Li, Yu Lu

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T7 phage could be used as a perfect vector for peptides expression and haptens presentation. T7-3GnRH recombinant phage was constructed by inserting three copies of Gonadotrophin Releasing Hormone (GnRH) gene into the multiple cloning site of T7 Select 415-1b phage genome. The positive T7-3GnRH phage was selected by using polymerase chain reaction amplification, and the p10B-3GnRH fusion protein was verified by SDS-PAGE and Western-blotting assay. T7-3GnRH vaccine was made and immunized with 10¹⁰ pfu in 0.2 ml per dose in mice. Blood samples were collected at an interval in weeks, and anti-GnRH antibody and testosterone concentrations were detected by ELISA and radioimmunoassay, respectively. The results show that T7-3GnRH phage particles confer a high immunogenicity to the GnRH-derived epitope. Moreover, the T7-3GnRH vaccine induced higher level of anti-GnRH antibody than ImproVac^®. However, the testosterone concentrations in both immunized groups were at a similar level, and the testis developments were significantly inhibited compared to controls. These findings demonstrated that the anti-GnRH antibody could neutralize the endogenous GnRH to down regulate testosterone level and limit testis development, highlighting the potential value of T7-3GnRH in the immunocastration vaccine research.

Keywords: Gonadotrophin Releasing Hormone (GnRH), Immunocastration, T7 phage, Phage vaccine

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Authors: Alexandra-Monica Toma

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As the internet became a ruling force of society, computer-mediated communication has enriched its methods to convey meaning by combining linguistic means to visual means of expressivity. One of the elements of cyberspace is what we call a meme, a succinct, visually engaging tool used to communicate ideas or emotions, usually in a funny or ironic manner. Coined by Richard Dawkings in the late 1970s to refer to cultural genes, this term now denominates a special type of vernacular language used to share content on the internet. This research aims to analyse the basic mechanism that stands at the basis of meme creation as a blend of innovation and imitation and will approach some of the most widely used image macros remixed to generate new content while also pointing out success strategies. Moreover, this paper discusses whether memes can transcend the light-hearted and playful mood they mirror and become biting and sharp cultural comments. The study also uses the concept of multimodality and stresses how the text interacts with image, discussing three types of relations between the two: symmetry, amplification, and contradiction. We will furthermore show that memes are cultural artifacts and virtual tropes highly dependent on context and societal issues by using a corpus of memes created related to the COVID-19 pandemic.

Keywords: context, computer-mediated communication, memes, multimodality

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Authors: Abhigna Bhatt, Arnab Banerjee

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A periodic system with only a single coupling degree of freedom is called a monocoupled system. Monocoupled systems with mechanisms like mass in the mass system generates effective negative mass, mass connected with rigid links generates inertial amplification, and spring-mass connected with a rigid link generateseffective negative stiffness. In this paper, the representative unit cell is introduced, considering all three mechanisms combined. Further, the dynamic stiffness matrix of the unit cell is constructed, and the dispersion relation is obtained by applying the Bloch theorem. The frequency response function is also calculated for the finite length of periodic unit cells. Moreover, the input displacement signal is given to the finite length of periodic structure and using inverse Fourier transform to visualize the wave propagation in the time domain. This visualization explains the sudden attenuation in metamaterial due to energy dissipation by an embedded resonator at the resonance frequency. The visualization created for wave propagation is found necessary to understand the insights of physics behind the attenuation characteristics of the system.

Keywords: mono coupled system, negative effective mass, negative effective stiffness, inertial amplifier, fourier transform

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Authors: Kalaumari Mayoral-Peña, Ana I. Montejano-Montelongo, Josué Reyes-Muñoz, Gonzalo A. Ortiz-Mancilla, Mayrin Rodríguez-Cruz, Víctor Hernández-Villalobos, Jesús A. Guzmán-López, Santiago García-Jacobo, Iván Licona-Vázquez, Grisel Fierros-Romero, Rosario Flores-Vallejo

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The group B-lactamic antibiotics include some of the most frequently used small drug molecules against bacterial infections. Nevertheless, an alarming decrease in their efficacy has been reported due to the emergence of antibiotic-resistant bacteria. Infections caused by bacteria expressing extended Spectrum B-lactamases (ESBLs) are difficult to treat and account for higher morbidity and mortality rates, delayed recovery, and high economic burden. According to the Global Report on Antimicrobial Resistance Surveillance, it is estimated that mortality due to resistant bacteria will ascend to 10 million cases per year worldwide. These facts highlight the importance of developing low-cost and readily accessible detection methods of drug-resistant ESBLs bacteria to prevent their spread and promote accurate and fast diagnosis. Bacterial detection is commonly done using molecular diagnostic techniques, where PCR stands out for its high performance. However, this technique requires specialized equipment not available everywhere, is time-consuming, and has a high cost. Loop-Mediated Isothermal Amplification (LAMP) is an alternative technique that works at a constant temperature, significantly decreasing the equipment cost. It yields double-stranded DNA of several lengths with repetitions of the target DNA sequence as a product. Although positive and negative results from LAMP can be discriminated by colorimetry, fluorescence, and turbidity, there is still a large room for improvement in the point-of-care implementation. DNA origami is a technique that allows the formation of 3D nanometric structures by folding a large single-stranded DNA (scaffold) into a determined shape with the help of short DNA sequences (staples), which hybridize with the scaffold. This research aimed to generate DNA origami structures using LAMP products as scaffolds to improve the sensitivity to detect ESBLs in point-of-care diagnosis. For this study, the coding sequence of the CTM-X-15 ESBL of E. coli was used to generate the LAMP products. The set of LAMP primers were designed using PrimerExplorerV5. As a result, a target sequence of 200 nucleotides from CTM-X-15 ESBL was obtained. Afterward, eight different DNA origami structures were designed using the target sequence in the SDCadnano and analyzed with CanDo to evaluate the stability of the 3D structures. The designs were constructed minimizing the total number of staples to reduce costs and complexity for point-of-care applications. After analyzing the DNA origami designs, two structures were selected. The first one was a zig-zag flat structure, while the second one was a wall-like shape. Given the sequence repetitions in the scaffold sequence, both were able to be assembled with only 6 different staples each one, ranging between 18 to 80 nucleotides. Simulations of both structures were performed using scaffolds of different sizes yielding stable structures in all the cases. The generation of the LAMP products were tested by colorimetry and electrophoresis. The formation of the DNA structures was analyzed using electrophoresis and colorimetry. The modeling of novel detection methods through bioinformatics tools allows reliable control and prediction of results. To our knowledge, this is the first study that uses LAMP products and DNA-origami in combination to delect ESBL-producing bacterial strains, which represent a promising methodology for diagnosis in the point-of-care.

Keywords: beta-lactamases, antibiotic resistance, DNA origami, isothermal amplification, LAMP technique, molecular diagnosis

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Authors: Sulaiman A. Alrumman, Abd El-Latif Hesham

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Despite medical progress worldwide, dental caries are still widespread. Miswak is derived from the plant arak (Salvadora persica). It is used by Muslim people as a natural product for the cleansing of teeth, to ensure oral and dental hygiene. This study was designed to evaluate the antimicrobial effects of ethanol, methanol, and ethanol/methanol extracts of miswak against three bacterial pathogens of the oral cavity. The pathogens were isolated from the oral cavity of volunteers/patients and were identified on the basis of 16S rRNA gene amplification data. Sequence comparisons were made with 16S rRNA gene sequences available in the GenBank database. The results of sequence alignment and phylogenetic analysis identified the three pathogens as being Staphylococcus aureus strain KKU-020, Enterococcus faecalis strain KKU-021 and Klebsiella pneumoniae strain KKU-022. All miswak extracts showed powerful antimicrobial activity against the three pathogens. The maximum zone of inhibition (40.67±0.88 mm) was observed against E. faecalis with ethanolic extracts whilst methanolic extracts showed the minimum zone of inhibition (10.33±0.88 mm) against K. pneumonia KKU-022. Based on the significant effects of the miswak extracts against the oral cavity pathogens in our study, we recommend that miswak is to be used as a dental hygiene method to prevent tooth caries.

Keywords: antibacterial, miswak, Salvadora persica, oral cavity pathogens

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Authors: Syed M. Shahid, Rozeena Shaikh, Syeda N. Nawab, Abid Azhar

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Diabetes mellitus (DM) is a prevalent non-communicable disease worldwide. DM may lead to many vascular complications like hypertension, nephropathy, retinopathy, neuropathy and foot infections. Pathogenesis of diabetic nephropathy (DN) is implicated by the polymorphisms in genes encoding the specific components of renin angiotensin aldosterone system (RAAS) which include angiotensinogen (AGT), angiotensin-II receptor and angiotensin converting enzyme (ACE) genes. This study was designed to explore the possible association of AG (M268T) polymorphism in the patients of diabetes and nephropathy in Pakistan. Study subjects included 100 controls, 260 diabetic patients without renal insufficiency and 190 diabetic nephropathy patients with persistent albuminuria. Fasting blood samples were collected from all the subjects after getting institutional ethical approval and informed consent. The biochemical estimations, PCR amplification and direct sequencing for the specific region of AGT gene was carried out. A significantly high frequency of TT genotype and T allele of AGT (M268T) was observed in the patients of diabetes with nephropathy as compared to controls and diabetic patients without any known renal impairment. The TT genotype and T allele of AGT (M268T) polymorphism may be considered as a genetic risk factor for the development and progression of nephropathy in diabetes. Further cross sectional population studies would be of help to establish and confirm the observed possible association of AGT gene variations with development of nephropathy in diabetes.

Keywords: RAAS, AGT (M268T), diabetes, nephropathy

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Authors: Prittesh Patel, Ramar Krishnamurthy

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In the present study, nine strains of C. falcatum obtained from different places and cultivars were characterized for sporulation, growth rate, and 18S rRNA gene sequence. All isolates had characteristic fast-growing sparse and fleecy aerial mycelia on potato dextrose agar with sickle shape conidia (length x width: varied from 20.0 X 3.89 to 25.52 X 5.34 μm) and blackish to orange acervuli with setae (length x width: varied from 112.37X 2.78 to 167.66 X 6.73 μm). They could be divided into two groups on the base of morphology; P1, dense mycelia with concentric growth and P2, sparse mycelia with uneven growth. Genomic DNA isolation followed by PCR amplification with ITS1 and ITS4 primer produced ~550bp amplicons for all isolates. Phylogeny generated by 18S rRNA gene sequence confirmed the variation in isolates and mainly grouped into two clusters; cluster 1 contained CoC671 isolates (cfNAV and cfPAR) and Co86002 isolate (cfTIM). Other isolates cfMAD, cfKAM, and cfMAR were grouped into cluster 2. Remaining isolates did not fall into any cluster. Isolate cfGAN, collected from Co86032 was found highly diverse of all the nine isolates. In a nutshell, we found considerable genetic divergence and morphological variation within C. falcatum accessions collected from different areas of south Gujarat, India and these can be used for the breeding program.

Keywords: Colletotrichum falcatum, ITS, morphology, red rot, sugarcane

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Authors: Narayan Gurung, Fawu Wang, Ranjan Kumar Dahal

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Nepal is highly prone to earthquakes and has witnessed at least one major earthquake in 80 to 90 years interval. The Gorkha earthquake, that measured 7.8 RS in magnitude and struck Nepal on 25th April 2015, after 81 years since Mw 8.3 Nepal Bihar earthquake in 1934, was the largest earthquake after Mw 8.3 Nepal Bihar earthquake. In this paper, an attempt has been made to highlight the lessons learnt from the MwW 7.8 Gorkha (Nepal) earthquake. Several types of damage patterns in buildings were observed for reinforced concrete buildings, as well as for unreinforced masonry and adobe houses in the earthquake of 25 April 2015. Many field visits in the affected areas were conducted, and thus, associated failure and damage patterns were identified and analyzed. Damage patterns in non-engineered buildings, middle and high-rise buildings, commercial complexes, administrative buildings, schools and other critical facilities are also included from the affected districts. For most buildings, the construction and structural deficiencies have been identified as the major causes of failure; however, topography, local soil amplification, foundation settlement, liquefaction associated damages and buildings built in hazard-prone areas were also significantly observed for the failure or damages to buildings and hence are reported. Finally, the lessons learnt from Mw 7.8 Gorkha (Nepal) earthquake are presented in order to mitigate impacts of future earthquakes in Nepal.

Keywords: Gorkha earthquake, reinforced concrete structure, Nepal, lesson learnt

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Authors: Katherine Sparks, Christopher Ring

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This study aimed to investigate whether dispositional sport-specific mindfulness moderated the moderation effect of conscious processing on the relationship between anxiety and rowing race performance. Using a sport-specific (Rowing-Specific) Reinvestment Scale (RSRS) to measure state conscious processing, we examined the effects of trait sport-related mindfulness on the conscious processes of rowers under competitive racing pressure at a number of UK regattas. 276 rowers completed a survey post competitive race. The survey included the RSRS, mindfulness, a perceived performance rating scale, demographic and race information to identify and record the rower’s actual race performance. Results from the research demonstrated that high levels of dispositional mindfulness are associated with a superior performance under pressure. In relation to the moderating moderation effect, conscious processing amplifies the detrimental effects of anxiety on performance. However, mindfulness, mindful awareness, and mindful non-judgement all proved to attenuate this amplification effect by moderating the conscious processing moderation on the anxiety-performance relationship. Therefore, this study provides initial support for the speculation that dispositional mindfulness can help prevent the deleterious effects of rowing-specific reinvestment under pressure.

Keywords: mindful, reinvestment, under pressure, performance, rowing

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Authors: Jafar Ahmadi, Alireza Pour-Aboughadareh

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Wheat is the first and the most important grain of the world and its bakery property is due to glutenin and gliadin qualities. Wheat seed proteins were divided into four groups according to solubility. Two groups are albumin and globulin dissolving in water and salt solutions possessing metabolic activities. Two other groups are inactive and non-dissolvable and contain glutelins or glutenins and prolamins or gliadins. Gliadins are major components of the storage proteins in wheat endosperm. Gliadin proteins are separated into three groups based on electrophoretic mobility: α/β-gliadin, γ-gliadin, and ω-gliadin. It seems that little information is available about gliadin genes in Iranian wild relatives of wheat. Thus, the aim of this study was the evaluation of the wheat wild relatives collected from different origins of Zagros Mountains in Iran, involving coding gliadin genes using specific primers. For this, forty accessions of Triticum boeoticum and Triticum urartu were selected. For each accession, genomic DNA was extracted and PCRs were performed in total volumes of 15 μl. The amplification products were separated on 1.5% agarose gels. In results, for Gli-2A locus, three allelic variants were detected by Gli-2As primer pairs. The sizes of PCR products for these alleles were 210, 490 and 700 bp. Only five (13%) and two accessions (5%) produced 700 and 490 bp fragments when their DNA was amplified with the Gli.As.2 primer pairs. However, 37 of the 40 accessions (93%) carried 210 bp allele, and three accessions (8%) did not yield any product for this marker. Therefore, these germplasm could be used as rich gene pool to broaden the genetic base of bread wheat.

Keywords: diploied wheat, gliadin, Triticum boeoticum, Triticum urartu

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Authors: Muna A. Eissawi, Safaa Abed Elfataah, Haytham Hago, Fatima E Abukunna, Ibtisam Amin Goreish, Nahid Gornas

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The study examined and analyzed the genetic diversity of DRB1locus of exon 2 of major histocompatibility complex of Sudanese desert sheep using PCR-RFLP and DNA sequencing. Five hundred samples belonging to five ecotypes of Desert Sudanese sheep (Abrag (Ab), Ashgar (Ash), Hamari (H), Kabashi (K) and Watish (W) were included. Amplification of exon 2 of the DRB1 gene yielded (300bp) amplified product in different ecotypes. Nine different digestion patterns corresponding to Five distinct alleles were observed with Rsa1 digestion. Genotype (ag) was the most common among all ecotypes, with a percentage comprised (40.4 %). The Hardy-Weinberg equilibrium (HWE) test showed that the studied ecotypes have significantly deviated from the theoretical proportions of Rsa1 patterns; probability values of the Chi-square test for HWE for MHC-DRB1 gene in SDS were 0.00 in all ecotypes. The constructed phylogenetic tree revealed the relation of 22 Sudanese isolates with each other and showed the shared sequences with 47 published foreign sequences randomly selected from different geographic regions. The results of this study highlight the effect of heterozygosity of MHC genes of the Desert sheep of Sudan which may clarify some of genetic back ground of their disease resistance and adaptation to environment.

Keywords: desert sheep, MHC, Ovar-DRB1, polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP)

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Authors: Mizan Ahmed, Srikanth Venkatesan

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Geological and tectonic framework indicates that Bangladesh is one of the most seismically active regions in the world. The Bengal Basin is at the junction of three major interacting plates: the Indian, Eurasian, and Burma Plates. Besides there are many active faults within the region, e.g. the large Dauki fault in the north. The country has experienced a number of destructive earthquakes due to the movement of these active faults. Current seismic provisions of Bangladesh are mostly based on earthquake data prior to the 1990. Given the record of earthquakes post 1990, there is a need to revisit the design provisions of the code. This paper compares the base shear demand of three major cities in Bangladesh: Dhaka (the capital city), Sylhet, and Chittagong for earthquake scenarios of magnitudes 7.0MW, 7.5MW, 8.0MW and 8.5MW using a stochastic model. In particular, the stochastic model allows the flexibility to input region specific parameters such as shear wave velocity profile (that were developed from Global Crustal Model CRUST2.0) and include the effects of attenuation as individual components. Effects of soil amplification were analysed using the Extended Component Attenuation Model (ECAM). Results show that the estimated base shear demand is higher in comparison with code provisions leading to the suggestion of additional seismic design consideration in the study regions.

Keywords: attenuation, earthquake, ground motion, Stochastic, seismic hazard

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