Search results for: genome stability

Authors: M. Baghdasaryan, A. Sukiasyan

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An algorithm for estimating the stable operation conditions of the synchronous motor of the ore mill electric drive is proposed. The stable operation conditions of the synchronous motor are revealed, taking into account the estimation of the q angle change and the technological factors. The stability condition obtained allows to ensure the stable operation of the motor in the synchronous mode, taking into account the nonlinear character of the mill loading. The developed algorithm gives an opportunity to present the undesirable phenomena, arising in the electric drive system. The obtained stability condition can be successfully applied for the optimal control of the electromechanical system of the mill.

Keywords: electric drive, synchronous motor, ore mill, stability, technological factors

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Authors: Faramarz Khoshnoudian

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A seismic stability assessment of the concrete gravity dam was performed. Initially (Phase 1), a linear response spectrum analysis was performed to verify the potential for crack formation. The result shows the possibility of developing cracks in the upstream face of the dam close to the lowest gallery, which were sufficiently long that the dam would not be stable following the earthquake. The results show the dam has potentially inadequate seismic and post-earthquake resistance and recommended an update of the stability analysis.

Keywords: crack propgation, concrete gravity dam, seismic, assesment

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Authors: Carol Yue-En Ong, Angelina Hui-Min Tan, Quan Liu, Paul Chi-Lui Ho

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A public general hospital in Singapore has recently implemented an automated unit-dose machine in their inpatient dispensary, Swisslog, with the objective of reducing human error and improving patient safety. However, a concern in stability arises as tablets are removed from their original packaging (bottled loose tablets/capsules) and are repackaged into individual, clear plastic wrappers as unit doses in the system. Drugs that are light-sensitive and hygroscopic would be more susceptible to degradation as the wrapper does not offer full protection. Hence, this study was carried out to study the stability of haloperidol tablets and phenytoin capsules that are light-sensitive and hygroscopic respectively. Validated HPLC-UV assays were first established for quantification of these two compounds. The medications involved were put in the Swisslog and sampled every week for one month. The collected data was analysed and showed no degradation over time. This study also explored an alternative approach for drug stability determination-Raman spectroscopy. The advantage of Raman spectroscopy is its high time efficiency and non-destructive nature. The results suggest that drug degradation can indeed be detected using Raman microscopy, but further research is needed to establish this approach for quantification or qualification of compounds. NanoRam®, a portable Raman spectrocope was also used alongside Raman microscopy but was unsuccessful in detecting degradation in this study.

Keywords: drug stability, haloperidol, HPLC, phenytoin, raman spectroscopy, Swisslog

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Authors: Sofia Sehli, Zainab El Ouafi, Casey Eddington, Soumaya Jbara, Kasambula Arthur Shem, Islam El Jaddaoui, Ayorinde Afolayan, Olaitan I. Awe, Allissa Dillman, Hassan Ghazal

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The ability to promptly sequence whole genomes at a relatively low cost has revolutionized the way we study the microbiome. Microbiologists are no longer limited to studying what can be grown in a laboratory and instead are given the opportunity to rapidly identify the makeup of microbial communities in a wide variety of environments. Analyzing whole genome sequencing (WGS) data is a complex process that involves multiple moving parts and might be rather unintuitive for scientists that don’t typically work with this type of data. Thus, to help lower the barrier for less-computationally inclined individuals, TAXAPRO was developed at the first Omics Codeathon held virtually by the African Society for Bioinformatics and Computational Biology (ASBCB) in June 2021. TAXAPRO is an advanced metagenomics pipeline that accurately assembles organelle genomes from whole-genome sequencing data. TAXAPRO seamlessly combines WGS analysis tools to create a pipeline that automatically processes raw WGS data and presents organism abundance information in both a tabular and graphical format. TAXAPRO was evaluated using COVID-19 patient gut microbiome data. Analysis performed by TAXAPRO demonstrated a high abundance of Clostridia and Bacteroidia genera and a low abundance of Proteobacteria genera relative to others in the gut microbiome of patients hospitalized with COVID-19, consistent with the original findings derived using a different analysis methodology. This provides crucial evidence that the TAXAPRO workflow dispenses reliable organism abundance information overnight without the hassle of performing the analysis manually.

Keywords: metagenomics, shotgun metagenomic sequence analysis, COVID-19, pipeline, bioinformatics

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Authors: Ahmed M. Debela, Mayreli Ortiz , Ciara K. O´Sullivan

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The completion of the human genome Project (HGP) has paved the way for mapping the diversity in the overall genome sequence which helps to understand the genetic causes of inherited diseases and susceptibility to drugs or environmental toxins. Arrayed primer extension (APEX) is a microarray based minisequencing strategy for screening disease causing mutations. It is derived from Sanger DNA sequencing and uses fluorescently dideoxynucleotides (ddNTPs) for termination of a growing DNA strand from a primer with its 3´- end designed immediately upstream of a site where single nucleotide polymorphism (SNP) occurs. The use of DNA polymerase offers a very high accuracy and specificity to APEX which in turn happens to be a method of choice for multiplex SNP detection. Coupling the high specificity of this method with the high sensitivity, low cost and compatibility for miniaturization of electrochemical techniques would offer an excellent platform for detection of mutation as well as sequencing of DNA templates. We are developing an electrochemical APEX for the analysis of SNPs found in the MYH7 gene for group of cardiomyopathy patients. ddNTPs were labeled with four different redox active compounds with four distinct potentials. Thiolated oligonucleotide probes were immobilised on gold and glassy carbon substrates which are followed by hybridisation with complementary target DNA just adjacent to the base to be extended by polymerase. Electrochemical interrogation was performed after the incorporation of the redox labelled dedioxynucleotide. The work involved the synthesis and characterisation of the redox labelled ddNTPs, optimisation and characterisation of surface functionalisation strategies and the nucleotide incorporation assays.

Keywords: array based primer extension, labelled ddNTPs, electrochemical, mutations

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Authors: Mahmoud A. Mahmoud, Ashraf Osman

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In this study, the different approaches currently followed by design codes to assess the stability of buildings utilizing concrete moment resisting frames structural system are evaluated. For such purpose, a parametric study was performed. It involved analyzing group of concrete moment resisting frames having different slenderness ratios (height/width ratios), designed for different lateral loads to vertical loads ratios and constructed using ordinary reinforced concrete and high strength concrete for stability check and overall buckling using code approaches and computer buckling analysis. The objectives were to examine the influence of such parameters that directly linked to frames’ lateral stiffness on the buildings’ stability and evaluates the code approach in view of buckling analysis results. Based on this study, it was concluded that, the most susceptible buildings to instability and magnification of second order effects are buildings having high aspect ratios (height/width ratio), having low lateral to vertical loads ratio and utilizing construction materials of high strength. In addition, the study showed that the instability limits imposed by codes are mainly mathematical to ensure reliable analysis not a physical ones and that they are in general conservative. Also, it has been shown that the upper limit set by one of the codes that second order moment for structural elements should be limited to 1.4 the first order moment is not justified, instead, the overall story check is more reliable.

Keywords: buckling, lateral stability, p-delta, second order

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Authors: Chamilani Nikapitiya, Mahanama De Zoysa, Jehee Lee

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Most of the bacterial diseases are associated with high mortalities in aquaculture species and causing huge economic losses. Different approaches have been taken to prevent or control of bacterial diseases including use of vaccines, probiotics, chemotherapy, water quality management, etc. Antibiotics are widely applying as chemotherapy to control bacterial diseases, however, it has been shown that frequent use of antibiotics is favored to develop multi-drug resistance bacteria. Therefore, phages and phage encoded lytic proteins are known to be one of the most promising alternatives for antibiotics to avoid the emergence of antibiotic-resistant bacteria. We isolated and characterized the two lytic phages, namely pAh-1 and pAs-1 against pathogenic Aeromonas hydrophila and Aeromonas salmonicida, respectively. Morphological characteristics were analyzed by Transmission electron microscopy (TEM) and host strain specificities were tested with Aeromonas and other closely related bacterial strains. TEM analysis revealed that both pAh-1 and pAsm-1 are composed of an icosahedral head and a segmented tail, and we suggest that, they are new members of Myoviridae family. Genome sizes of isolated phages were estimated by restriction enzyme digestion of genomic DNA using selected endonucleases followed by agarose gel electrophoresis. Estimated genome size of pAh-1 and pAs-1 were approximately 64 Kbp and 120 Kbp, respectively. Both pAh-1 and pAs-1 have shown narrow host specificity. Moreover, protective effects of phage therapy against fish pathogenic A. hydrophila were investigated in zebrafish model. The survival rate was 40% higher when zebrafish received intra-peritoneal injection (i.p.) of pAh-1 were simultaneously challenge A. hydrophila (2 x 106 CFU/fish) compared to that without phage treatment. Overall results suggest that both pAh-1 and pAs-1 can be used as a potential phage therapy to control Aeromonas infections in aquaculture.

Keywords: Aeromonas infections, antibiotic resistance, bacteriophage, bio-control, lytic phage

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Authors: R. C. Tiwari, N. P. Bhandary, D. B. Thapa Chhetri, R. Yatabe

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The research enlightens the various issues of lake expansion and stability of the moraine dam of Imja lake. The Imja lake considered that the world highest altitude lake (5010m from m.s.l.), located in the Khumbu, Sagarmatha region of Nepal (27.90 N and 86.90 E) was reported as one of the fast growing glacier lakes in the Nepal Himalaya. The research explores a common phenomenon of lake expansion and stability issues of moraine dam to justify the necessity of lake lowering efforts if any in future in other glacier lakes in Nepal Himalaya. For this, we have explored the root causes of rapid lake expansion along with crucial factors responsible for the stability of moraine mass. This research helps to understand the structure of moraine dam and the ice, water and moraine interactions to the strength of moraine dam. The nature of permafrost layer and its effects on moraine dam stability is also studied here. The detail Geo-Technical properties of moraine mass of Imja lake gives a clear picture of the strength of the moraine material and their interactions. The stability analysis of the moraine dam under the consideration of strong ground motion of 7.8Mw 2015 Barpak-Gorkha and its major aftershock 7.3Mw Kodari, Sindhupalchowk-Dolakha border, Nepal earthquakes have also been carried out here to understand the necessity of lake lowering efforts. The lake lowering effort was recently done by Nepal Army by constructing an open channel and lowered 3m. And, it is believed that the entire region is now safe due to continuous draining of lake water by 3m. But, this option does not seem adequate to offer a significant risk reduction to downstream communities in this much amount of volume and depth, lowering as in the 75 million cubic meter water impounded with an average depth of 148.9m.

Keywords: finite element method, glacier, moraine, stability

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Authors: Janos Juhasz, Sandor Pongor, Balazs Ligeti

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Next-generation sequencing, especially whole genome shotgun sequencing, is becoming a common approach to gain insight into the microbiomes in a culture-independent way, even in clinical practice. It does not only give us information about the species composition of an environmental sample but opens the possibility to detect antimicrobial resistance and novel, or currently unknown, pathogens. Accurately and reliably detecting the microbial strains is a challenging task. Here we present a sensitive approach for detecting pathogens in metagenomics samples with special regard to detecting novel variants of known pathogens. We have developed a pipeline that uses fast, short read aligner programs (i.e., Bowtie2/BWA) and comprehensive nucleotide databases. Taxonomic binning is based on the lowest common ancestor (LCA) principle; each read is assigned to a taxon, covering the most significantly hit taxa. This approach helps in balancing between sensitivity and running time. The program was tested both on experimental and synthetic data. The results implicate that our method performs as good as the state-of-the-art BLAST-based ones, furthermore, in some cases, it even proves to be better, while running two orders magnitude faster. It is sensitive and capable of identifying taxa being present only in small abundance. Moreover, it needs two orders of magnitude less reads to complete the identification than MetaPhLan2 does. We analyzed an experimental anthrax dataset (B. anthracis strain BA104). The majority of the reads (96.50%) was classified as Bacillus anthracis, a small portion, 1.2%, was classified as other species from the Bacillus genus. We demonstrate that the evaluation of high-throughput sequencing data is feasible in a reasonable time with good classification accuracy.

Keywords: metagenomics, taxonomy binning, pathogens, microbiome, B. anthracis

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Authors: Richard L. Summers

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The advanced computational analysis of biological systems is becoming increasingly dependent upon an understanding of the information-theoretic structure of the materials, energy and interactive processes that comprise those systems. The stability and survival of these living systems are fundamentally contingent upon their ability to acquire and process the meaning of information concerning the physical state of its biological continuum (biocontinuum). The drive for adaptive system reconciliation of a divergence from steady-state within this biocontinuum can be described by an information metric-based formulation of the process for actionable knowledge acquisition that incorporates the axiomatic inference of Kullback-Leibler information minimization driven by survival replicator dynamics. If the mathematical expression of this process is the Lagrangian integrand for any change within the biocontinuum then it can also be considered as an action functional for the living system. In the direct method of Lyapunov, such a summarizing mathematical formulation of global system behavior based on the driving forces of energy currents and constraints within the system can serve as a platform for the analysis of stability. As the system evolves in time in response to biocontinuum perturbations, the summarizing function then conveys information about its overall stability. This stability information portends survival and therefore has absolute existential meaning for the living system. The first derivative of the Lyapunov energy information function will have a negative trajectory toward a system's steady state if the driving force is dissipating. By contrast, system instability leading to system dissolution will have a positive trajectory. The direction and magnitude of the vector for the trajectory then serves as a quantifiable signature of the meaning associated with the living system’s stability information, homeostasis and survival potential.

Keywords: meaning, information, Lyapunov, living systems

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Authors: M. Najafi, F. Rahimi Dehgolan

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In this paper, the dynamic modeling of a single-link flexible beam with a tip mass is given by using Hamilton's principle. The link has been rotational and translational motion and it was assumed that the beam is moving with a harmonic velocity about a constant mean velocity. Non-linearity has been introduced by including the non-linear strain to the analysis. Dynamic model is obtained by Euler-Bernoulli beam assumption and modal expansion method. Also, the effects of rotary inertia, axial force, and associated boundary conditions of the dynamic model were analyzed. Since the complex boundary value problem cannot be solved analytically, the multiple scale method is utilized to obtain an approximate solution. Finally, the effects of several conditions on the differences among the behavior of the non-linear term, mean velocity on natural frequencies and the system stability are discussed.

Keywords: non-linear vibration, stability, axially moving beam, bifurcation, multiple scales method

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Authors: Awatef Chniguir, Tarek Farah, Zouhair Ben Jemaa, Safya Belguith

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Optimal routing allows minimizing energy consumption in wireless sensor networks (WSN). Clustering has proven its effectiveness in organizing WSN by reducing channel contention and packet collision and enhancing network throughput under heavy load. Therefore, nowadays, with the emergence of the Internet of Things, heterogeneity is essential. Stable election protocol (SEP) that has increased the network stability period and lifetime is the first clustering protocol for heterogeneous WSN. SEP and its descendants, namely SEP, Threshold Sensitive SEP (TSEP), Enhanced TSEP (ETSSEP) and Current Energy Allotted TSEP (CEATSEP), were studied. These algorithms’ performance was evaluated based on different metrics, especially first node death (FND), to compare their stability. Simulations were conducted on the MATLAB tool considering two scenarios: The first one demonstrates the fraction variation of advanced nodes by setting the number of total nodes. The second considers the interpretation of the number of nodes while keeping the number of advanced nodes permanent. CEATSEP outperforms its antecedents by increasing stability and, at the same time, keeping a low throughput. It also operates very well in a large-scale network. Consequently, CEATSEP has a useful lifespan and energy efficiency compared to the other routing protocol for heterogeneous WSN.

Keywords: clustering, heterogeneous, stability, scalability, IoT, WSN

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Authors: Jixiang Zhang, Yanhua Wang

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A dynamic of Bertrand duopoly game is analyzed, where players use different production methods and choose their prices with bounded rationality. The equilibriums of the corresponding discrete dynamical systems are investigated. The stability conditions of Nash equilibrium under a local adjustment process are studied. The stability conditions of Nash equilibrium under a local adjustment process are studied. The stability of Nash equilibrium, as some parameters of the model are varied, gives rise to complex dynamics such as cycles of higher order and chaos. On this basis, we discover that an increase of adjustment speed of bounded rational player can make Bertrand market sink into the chaotic state. Finally, the complex dynamics, bifurcations and chaos are displayed by numerical simulation.

Keywords: Bertrand duopoly model, discrete dynamical system, heterogeneous expectations, nash equilibrium

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Authors: David Alejandro Lazo-Vasquez, Jorge Luis Balino

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In the petroleum industry, multiphase flow occurs when oil, gas, and water are transported in the same pipe through large pipeline systems. The flow can take different patterns depending on parameters like fluid velocities, pipe diameter, pipe inclination, and fluid properties. Mainly, intermittent flow is produced by the natural propagation of short and long waves, according to the Kelvin-Helmholtz Stability Theory. To model stratified flow and the onset of intermittent flow, it is crucial to have knowledge of short and long waves behavior. The two-fluid model, frequently employed for characterizing multiphase systems, becomes ill-posed for high liquid and gas velocities and large inclination angles, for short waves can develop infinite growth rates. We are interested in focusing attention on long-wave instability, which leads to the production of roll waves that may grow and result in the transition from stratified flow to intermittent flow. In this study, global and local linear stability analyses for dynamic and kinematic stability criteria predict the regions of stability of the flow for different pipe inclinations and fluid velocities in regularized and non-regularized systems, concurrently. It was possible to distinguish when: wave growth rates are absolutely bounded (stable stratified smooth flow), waves have finite growth rates (unstable stratified wavy flow), and when the equation system becomes elliptic and hyperbolization is needed. In order to bound short wave growth rates and regularize the equation system, we incorporated some lower and higher-order terms like interfacial drag and surface tension, respectively.

Keywords: linear stability analysis, multiphase flow, onset of slugging, two-fluid model regularization

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Authors: B. Mahfoud, A. Bendjagloli

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The effect of an axial magnetic field on the flow produced by co-rotation of the top and bottom disks in a vertical cylindrical heated from below is numerically analyzed. The governing Navier-Stokes, energy, and potential equations are solved by using the finite-volume method. It was observed that the Reynolds number is increased, the axisymmetric basic state loses stability to circular patterns of axisymmetric vortices and spiral waves. In mixed convection case the axisymmetric mode disappears giving an asymmetric mode m=1. It was also found that the primary thresholds Recr corresponding to the modes m=1and 2, increase with increasing of the Hartmann number (Ha). Finally, stability diagrams have been established according to the numerical results of this investigation. These diagrams giving the evolution of the primary thresholds as a function of the Hartmann number for various values of the Richardson number.

Keywords: bifurcation, co-rotating end disks, magnetic field, stability diagrams, vortices

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Authors: Raouf Fareh, Maarouf Saad, Sofiane Khadraoui, Tamer Rabie

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This paper presents a tracking control strategy based on Lyapunov approach for nonholonomic wheeled mobile robot. This control strategy consists of two levels. First, a kinematic controller is developed to adjust the right and left wheel velocities. Using this velocity control law, the stability of the tracking error is guaranteed using Lyapunov approach. This kinematic controller cannot be generated directly by the motors. To overcome this problem, the second level of the controllers, dynamic control, is designed. This dynamic control law is developed based on Lyapunov theory in order to track the desired trajectories of the mobile robot. The stability of the tracking error is proved using Lupunov and Barbalat approaches. Simulation results on a nonholonomic wheeled mobile robot are given to demonstrate the feasibility and effectiveness of the presented approach.

Keywords: mobile robot, trajectory tracking, Lyapunov, stability

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Authors: Umairah Natasya Binti Mohd Omeershffudin, Suresh Kumar

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Klebsiella pneumoniae, a Gram-negative enteric bacterium that causes nosocomial and urinary tract infections. Particular concern is the global emergence of multidrug-resistant (MDR) strains of Klebsiella pneumoniae. Characterization of antibiotic resistance determinants at the genomic level plays a critical role in understanding, and potentially controlling, the spread of multidrug-resistant (MDR) pathogens. In this study, drug-resistant Klebsiella pneumoniae strain 825795-1 was investigated with extensive computational approaches aimed at identifying novel drug targets among hypothetical proteins. We have analyzed 1099 hypothetical proteins available in genome. We have used in-silico genome subtraction methodology to design potential and pathogen-specific drug targets against Klebsiella pneumoniae. We employed bioinformatics tools to subtract the strain-specific paralogous and host-specific homologous sequences from the bacterial proteome. The sorted 645 proteins were further refined to identify the essential genes in the pathogenic bacterium using the database of essential genes (DEG). We found 135 unique essential proteins in the target proteome that could be utilized as novel targets to design newer drugs. Further, we identified 49 cytoplasmic protein as potential drug targets through sub-cellular localization prediction. Further, we investigated these proteins in the DrugBank databases, and 11 of the unique essential proteins showed druggability according to the FDA approved drug bank databases with diverse broad-spectrum property. The results of this study will facilitate discovery of new drugs against Klebsiella pneumoniae.

Keywords: pneumonia, drug target, hypothetical protein, subtractive genomics

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Authors: Vyacheslav Furtak, Merja Roivainen, Olga Mirochnichenko, Majid Laassri, Bella Bidzhieva, Tatiana Zagorodnyaya, Vladimir Chizhikov, Konstantin Chumakov

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Molecular epidemiology and environmental surveillance are parts of a rational strategy to control infectious diseases. They have been widely used in the worldwide campaign to eradicate poliomyelitis, which otherwise would be complicated by the inability to rapidly respond to outbreaks and determine sources of the infection. The conventional scheme involves isolation of viruses from patients and the environment, followed by their identification by nucleotide sequences analysis to determine phylogenetic relationships. This is a tedious and time-consuming process that yields definitive results when it may be too late to implement countermeasures. Because of the difficulty of high-throughput full-genome sequencing, most such studies are conducted by sequencing only capsid genes or their parts. Therefore the important information about the contribution of other parts of the genome and inter- and intra-species recombination to viral evolution is not captured. Here we propose a new approach based on the rapid concentration of sewage samples with tangential flow filtration followed by deep sequencing and reconstruction of nucleotide sequences of viruses present in the samples. The entire nucleic acids content of each sample is sequenced, thus preserving in digital format the complete spectrum of viruses. A set of rapid algorithms was developed to separate deep sequence reads into discrete populations corresponding to each virus and assemble them into full-length consensus contigs, as well as to generate a complete profile of sequence heterogeneities in each of them. This provides an effective approach to study molecular epidemiology and evolution of natural viral populations.

Keywords: poliovirus, eradication, environmental surveillance, laboratory diagnosis

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Authors: M. Ntswane, N. Mbuma, M. Labuschagne, A. Mofokeng, M. Rantso

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Cowpea is an essential legume for the nutrition and health of millions of people in different regions. The production and productivity of the crop are very limited in South Africa due to a lack of adapted and stable genotypes. The improvement of nutritional quality is made possible by manipulating the genes of diverse cowpea genotypes available around the world. Assessing the adaptability and stability of the cowpea mutant genotypes for yield and nutritional quality requires examining them in different environments. The objective of the study was to determine the adaptability and stability of cowpea mutant genotypes under South African conditions and to identify the superior genotypes that combine grain yield components, antioxidants, and nutritional quality. Thirty-one cowpea genotypes were obtained from the Agricultural Research Council grain crops (ARC-GC) and were planted in Glen, Mafikeng, Polokwane, Potchefstroom, Taung, and Vaalharts during the 2021/22 summer cropping season. Significant genotype by location interactions indicated the possibility of genetic improvement of these traits. The genotype plus genotype by environment indicated broad adaptability and stability of mutant genotypes. The principal component analysis identified the association of the genotypes with the traits. Phenotypic correlation analysis showed that Zn and protein content were significant and positively correlated and suggested the possibility of indirect selection of these traits. Results from this study could be used to help plant breeders in making informed decisions and developing nutritionally improved cowpea genotypes with the aim of addressing the challenges of poor nutritional quality.

Keywords: cowpea seeds, adaptability, stability, mineral elements, protein content

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Authors: Kooshan Nayebzadeh, Maryam Enteshari

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In this study, the oxidative stability of soybean oil under different storage temperatures (4 and 25 ˚C) and during 6-month shelf-life was investigated by various analytical methods and headspace-liquid phase microextraction (HS-LPME) coupled to gas chromatography-mass spectrometry (GC-MS). Oxidation changes were monitored by analytical parameters consisted of acid value (AV), peroxide value (PV), p-Anisidine value (p-AV), thiobarbituric acid value (TBA), fatty acids profile, iodine value (IV) and oxidative stability index (OSI). In addition, concentrations of hexanal and heptanal as secondary volatile oxidation compounds were determined by HS-LPME/GC-MS technique. Rate of oxidation in soybean oil which stored at 25 ˚C was so higher. The AV, p-AV, and TBA were gradually increased during 6 months, while the amount of unsaturated fatty acids, IV, and OSI decreased. Other parameters included concentrations of both hexanal and heptanal, and PV exhibited increasing trend during primitive months of storage; then, at the end of third and fourth months a sudden decrement was understood for the concentrations of hexanal and heptanal and the amount of PV, simultaneously. The latter parameters increased again until the end of shelf-time. As a result, the temperature and time were effective factors in oxidative stability of soybean oil. Also intensive correlations were found for soybean oil at 4 ˚C between AV and TBA (r2=0.96), PV and p-AV (r2=0.9), IV and TBA (-r2=0.9), and for soybean oil stored at 4 ˚C between p-AV and TBA (r2=0.99).

Keywords: headspace-liquid phase microextraction, oxidation, shelf-life, soybean oil

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Authors: Shishir Lamichhane, Saurav Dulal, Bibek Gautam, Madan Thapa Magar, Indraman Tamrakar

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Renewable energies such as wind turbines and solar photovoltaic have gained significance as a result of global environmental pollution and energy crises. These sources of energy are converted into electrical energy and delivered to end-users through the utility system. As a result of the widespread use of power electronics-based grid-interfacing technologies to accommodate renewable sources of energy, the prevalence of converters has expanded as well. As a result, the power system's rotating inertia is decreasing, endangering the utility grid's stability. The use of Virtual Synchronous Machine (VSM) technology has been proposed to overcome the grid stability problem due to low rotating inertia. The grid-connected inverter used in VSM can be controlled to emulate inertia, which replicates the external features of a synchronous generator. As a result, the rotating inertia is increased to support the power system's stability. A power angle control strategy is proposed in this paper and its model is simulated in MATLAB/Simulink to study the effects of parameter disturbances on the active power and frequency for a VSM. The system consists of a synchronous generator, which is modeled in such a way that the frequency drops to an unacceptable region during transient conditions due to a lack of inertia when VSM is not used. Then, the suggested model incorporating VSM emulates rotating inertia, injecting a controllable amount of energy into the grid during frequency transients to enhance transient stability.

Keywords: damping constant, inertia–constant, ROCOF, transient stability, distributed sources

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Authors: N. Prabavathy, R. Balasundaraprabhu, S. Shalini, Dhayalan Velauthapillai, S. Prasanna, N. Muthukumarasamy

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Dye sensitized solar cell (DSSC) has become a significant research area due to their fundamental and scientific importance in the area of energy conversion. Synthetic dyes as sensitizer in DSSC are efficient and durable but they are costlier, toxic and have the tendency to degrade. Natural sensitizers contain plant pigments such as anthocyanin, carotenoid, flavonoid, and chlorophyll which promote light absorption as well as injection of charges to the conduction band of TiO2 through the sensitizer. But, the efficiency of natural dyes is not up to the mark mainly due to instability of the pigment such as anthocyanin. The stability issues in vitro are mainly due to the effect of solvents on extraction of anthocyanins and their respective pH. Taking this factor into consideration, in the present work, the anthocyanins were extracted from the flower Caesalpinia pulcherrima (C. pulcherrimma) with various solvents and their respective stability and pH values are discussed. The usage of citric acid as solvent to extract anthocyanin has shown good stability than other solvents. It also helps in enhancing the sensitization properties of anthocyanins with Titanium dioxide (TiO2) nanorods. The IPCE spectra show higher photovoltaic performance for dye sensitized TiO2nanorods using citric acid as solvent. The natural DSSC using citric acid as solvent shows a higher efficiency compared to other solvents. Hence citric acid performs to be a safe solvent for natural DSSC in boosting the photovoltaic performance and maintaining the stability of anthocyanins.

Keywords: Caesalpinia pulcherrima, citric acid, dye sensitized solar cells, TiO₂ nanorods

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Authors: Marija Vitanovа, Igor Gjorgjiev, Viktor Hristovski, Vlado Micov

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Evaluation of stability is very important in the process of definition of optimal structural measures for maintenance of bridge structures and their strengthening. To define optimal measures for their repair and strengthening, it is necessary to evaluate their static and seismic stability. Presented in this paper are methodologies for evaluation of the seismic stability of existing reinforced concrete bridges designed without consideration of seismic effects and checking of structural justification of newly designed bridge structures. All bridges are located in the territory of the Republic of North Macedonia. A total of 26 existing bridges of different structural systems have been analyzed. Visual inspection has been carried out for all bridges, along with the definition of three main damage categories according to which structures have been categorized in respect to the need for their repair and strengthening. Investigations involving testing the quality of the built-in materials have been carried out, and dynamic tests pointing to the dynamic characteristics of the structures have been conducted by use of non-destructive methods of ambient vibration measurements. The conclusions drawn from the performed measurements and tests have been used for the development of accurate mathematical models that have been analyzed for static and dynamic loads. Based on the geometrical characteristics of the cross-sections and the physical characteristics of the built-in materials, interaction diagrams have been constructed. These diagrams along with the obtained section quantities under seismic effects, have been used to obtain the bearing capacity of the cross-sections. The results obtained from the conducted analyses point to the need for the repair of certain structural parts of the bridge structures. They indicate that the stability of the superstructure elements is not critical during a seismic effect, unlike the elements of the sub-structure, whose strengthening is necessary.

Keywords: existing bridges, newly designed bridges, reinforced concrete bridges, stability assessment

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Authors: Siddharth Deshpande, Nihar Masurkar, Vallerinteavide Mavelli Girish, Malan Desai, Chester Drum

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Folding and stabilization of recombinant proteins remain a consistent challenge for industrial and therapeutic applications. Proteins derived from thermophilic bacteria often have superior expression and stability qualities. To develop a generalizable approach to protein folding and stabilization, we tested the hypothesis that wrapping a thermostable exoshell around a protein substrate would aid folding and impart thermostable qualities to the internalized substrate. To test the effect of internalizing a protein within a thermostable exoshell (tES), we tested in vitro folding and stability using green fluorescent protein (GFPuv), horseradish peroxidase (HRP) and renilla luciferase (rLuc). The 8nm interior volume of a thermostable ferritin assembly was engineered to accommodate foreign proteins and either present a positive, neutral or negative interior charge environment. We further engineered the tES complex to reversibly assemble and disassemble with pH titration. Template proteins were expressed as inclusion bodies and an in vitro folding protocol was developed that forced proteins to fold inside a single tES. Functional yield was improved 100-fold, 100-fold and 150-fold with use of tES for GFPuv, HRP and rLuc respectively and was highly dependent on the internal charge environment of the tES. After folding, functional proteins could be released from the tES folding cavity using size exclusion chromatography at pH 5.8. Internalized proteins were tested for improved stability against thermal, organic, urea and guanidine denaturation. Our results demonstrated that thermostable exoshells can efficiently refold and stabilize inactive aggregates into functional proteins.

Keywords: thermostable shell, in vitro folding, stability, functional yield

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Authors: Markus Mazzola, Gunther Schaaf

Abstract:

A vehicle driving with an Adaptive Cruise Control System (ACC) is usually controlled decentrally, based on the information of radar systems and in some publications based on C2X-Communication (CACC) to guarantee stable platoons. In this paper, we present a Model Predictive Control (MPC) design of a centralized, server-based ACC-System, whereby the vehicular platoon is modeled and controlled as a whole. It is then proven that the proposed MPC design guarantees asymptotic stability and hence string stability of the platoon. The Networked MPC design is chosen to be able to integrate system constraints optimally as well as to reduce the effects of communication delay and packet loss. The performance of the proposed controller is then simulated and analyzed in an LTE communication scenario using the LTE/EPC Network Simulator LENA, which is based on the ns-3 network simulator.

Keywords: adaptive cruise control, centralized server, networked model predictive control, string stability

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Authors: Debamitra Chakravorty, Pratap K. Parida

Abstract:

Cold-adapted proteases enhance wash performance in low-temperature laundry resulting in a reduction in energy consumption and wear of textiles and are also used in the dehairing process in leather industries. Unfortunately, the possible drawbacks of using cold-adapted proteases are their instability at higher temperatures. Therefore, proteases with broad temperature stability are required. Unfortunately, wild-type cold-adapted proteases exhibit instability at higher temperatures and thus have low shelf lives. Therefore, attempts to engineer cold-adapted proteases by protein engineering were made previously by directed evolution and random mutagenesis. The lacuna is the time, capital, and labour involved to obtain these variants are very demanding and challenging. Therefore, rational engineering for cold stability without compromising an enzyme's optimum pH and temperature for activity is the current requirement. In this work, mutations were rationally designed with the aid of high throughput computational methodology of network analysis, evolutionary conservation scores, and molecular dynamics simulations for Savinase from Bacillus lentus with the intention of rendering the mutants cold stable without affecting their temperature and pH optimum for activity. Further, an attempt was made to incorporate a mutation in the most stable mutant rationally obtained by this method to introduce oxidative stability in the mutant. Such enzymes are desired in detergents with bleaching agents. In silico analysis by performing 300 ns molecular dynamics simulations at 5 different temperatures revealed that these three mutants were found to be better in cold stability compared to the wild type Savinase from Bacillus lentus. Conclusively, this work shows that cold adaptation without losing optimum temperature and pH stability and additionally stability from oxidative damage can be rationally designed by in silico enzyme engineering. The key findings of this work were first, the in silico data of H5 (cold stable savinase) used as a control in this work, corroborated with its reported wet lab temperature stability data. Secondly, three cold stable mutants of Savinase from Bacillus lentus were rationally identified. Lastly, a mutation which will stabilize savinase against oxidative damage was additionally identified.

Keywords: cold stability, molecular dynamics simulations, protein engineering, rational design

Procedia PDF Downloads 135

Authors: Andrey V. Khromov, Antonida V. Makhotenko, Ekaterina A. Snigir, Svetlana S. Makarova, Natalia O. Kalinina, Valentin V. Makarov, Mikhail E. Taliansky

Abstract:

Due to its simplicity, CRISPR/Cas9 has become widely used and capable of inducing mutations in the genes of organisms of various kingdoms. The aim of this work was to develop applications for the efficient modification of DNA coding sequences of phytoene desaturase (PDS), coilin and vacuolar invertase (Solanum tuberosum) genes, and to develop a new nanoparticles carrier efficient technology to deliver the CRISPR/Cas9 system for editing the plant genome. For each of the genes - coilin, PDS and vacuolar invertase, five single RNA guide (sgRNAs) were synthesized. To determine the most suitable nanoplatform, two types of NP platforms were used: magnetic NPs (MNPS) and gold NPs (AuNPs). To test the penetration efficiency, they were functionalized with fluorescent agents - BSA * FITS and GFP, as well as labeled Cy3 small-sized RNA. To measure the efficiency, a fluorescence and confocal microscopy were used. It was shown that the best of these options were AuNP - both in the case of proteins and in the case of RNA. The next step was to check the possibility of delivering components of the CRISPR/Cas9 system to plant cells for editing target genes. AuNPs were functionalized with a ribonucleoprotein complex consisting of Cas9 and corresponding to target genes sgRNAs, and they were biolistically bombarded to axillary buds and apical meristems of potato plants. After the treatment by the best NP carrier, potato meristems were grown to adult plants. DNA isolated from this plants was sent to a preliminary fragment of the analysis to screen out the non-transformed samples, and then to the NGS. The present work was carried out with the financial support from the Russian Science Foundation (grant No. 16-16-04019).

Keywords: biobombardment, coilin, CRISPR/Cas9, nanoparticles, NPs, PDS, sgRNA, vacuolar invertase

Procedia PDF Downloads 313

Authors: K. Sathishkumar, V. Thiagarasu

Abstract:

Due to recent advances in DNA microarray technology, it is now feasible to obtain gene expression profiles of tissue samples at relatively low costs. Many scientists around the world use the advantage of this gene profiling to characterize complex biological circumstances and diseases. Microarray techniques that are used in genome-wide gene expression and genome mutation analysis help scientists and physicians in understanding of the pathophysiological mechanisms, in diagnoses and prognoses, and choosing treatment plans. DNA microarray technology has now made it possible to simultaneously monitor the expression levels of thousands of genes during important biological processes and across collections of related samples. Elucidating the patterns hidden in gene expression data offers a tremendous opportunity for an enhanced understanding of functional genomics. However, the large number of genes and the complexity of biological networks greatly increase the challenges of comprehending and interpreting the resulting mass of data, which often consists of millions of measurements. A first step toward addressing this challenge is the use of clustering techniques, which is essential in the data mining process to reveal natural structures and identify interesting patterns in the underlying data. This work presents an analysis of several clustering algorithms proposed to deals with the gene expression data effectively. The existing clustering algorithms like Support Vector Machine (SVM), K-means algorithm and evolutionary algorithm etc. are analyzed thoroughly to identify the advantages and limitations. The performance evaluation of the existing algorithms is carried out to determine the best approach. In order to improve the classification performance of the best approach in terms of Accuracy, Convergence Behavior and processing time, a hybrid clustering based optimization approach has been proposed.

Keywords: microarray technology, gene expression data, clustering, gene Selection

Procedia PDF Downloads 323

Authors: A. S. Gorobtsov, A. S. Polyanina, A. E. Andreev

Abstract:

The movement of points feet of the anthropomorphous robot in space occurs along some stable trajectory of a known form. A large number of modifications to the methods of control of biped robots indicate the fundamental complexity of the problem of stability of the program trajectory and, consequently, the stability of the control for the deviation for this trajectory. Existing gait generators use piecewise interpolation of program trajectories. This leads to jumps in the acceleration at the boundaries of sites. Another interpolation can be realized using differential equations with fractional derivatives. In work, the approach to synthesis of generators of program trajectories is considered. The resulting system of nonlinear differential equations describes a smooth trajectory of movement having rectilinear sites. The method is based on the theory of an asymptotic stability of invariant sets. The stability of such systems in the area of localization of oscillatory processes is investigated. The boundary of the area is a bounded closed surface. In the corresponding subspaces of the oscillatory circuits, the resulting stable limit cycles are curves having rectilinear sites. The solution of the problem is carried out by means of synthesis of a set of the continuous smooth controls with feedback. The necessary geometry of closed trajectories of movement is obtained due to the introduction of high-order nonlinearities in the control of stabilization systems. The offered method was used for the generation of trajectories of movement of point’s feet of the anthropomorphous robot. The synthesis of the robot's program movement was carried out by means of the inverse method.

Keywords: control, limits cycle, robot, stability

Procedia PDF Downloads 331

Authors: Seyed Abolhasan Naeini, Elham Ghanbari Alamooti

Abstract:

Static stability of soil slopes using numerical simulation by a finite element code, ABAQUS, has been investigated, and safety factors of the slopes achieved in the case of static load of a 10-storey building. The embankments have the same soil condition but different loading distance from the slope heel. The numerical method for estimating safety factors is 'Strength Reduction Method' (SRM). Mohr-Coulomb criterion used in the numerical simulations. Two steps used for measuring the safety factors of the slopes: first is under gravity loading, and the second is under static loading of a building near the slope heel. These safety factors measured from SRM, are compared with the values from Limit Equilibrium Method, LEM. Results show that there is good agreement between SRM and LEM. Also, it is seen that by increasing the distance from slope heel, safety factors increases.

Keywords: limit equilibrium method, static stability, soil slopes, strength reduction method

Procedia PDF Downloads 162