Search results for: horizontal gene transfer

Authors: M. Bakhtaoui, L. Merahi

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The reliability of the filtered HVBK model is now investigated via some large eddy simulations of freely decaying isotropic superfluid turbulence. For homogeneous turbulence at very high Reynolds numbers, comparison of the terms in the spectral kinetic energy budget equation indicates, in the energy-containing range, that the production and energy transfer effects become significant except for dissipation. In the inertial range, where the two fluids are perfectly locked, the mutual friction maybe neglected with respect to other terms. Also the LES results for the other terms of the energy balance are presented.

Keywords: superfluid turbulence, HVBK, energy budget, Large Eddy Simulation

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Authors: Kyi Pyar Zaw, Zin Mar Kyu

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Character recognition is the process of converting a text image file into editable and searchable text file. Feature Extraction is the heart of any character recognition system. The character recognition rate may be low or high depending on the extracted features. In the proposed paper, 25 features for one character are used in character recognition. Basically, there are three steps of character recognition such as character segmentation, feature extraction and classification. In segmentation step, horizontal cropping method is used for line segmentation and vertical cropping method is used for character segmentation. In the Feature extraction step, features are extracted in two ways. The first way is that the 8 features are extracted from the entire input character using eight direction chain code frequency extraction. The second way is that the input character is divided into 16 blocks. For each block, although 8 feature values are obtained through eight-direction chain code frequency extraction method, we define the sum of these 8 feature values as a feature for one block. Therefore, 16 features are extracted from that 16 blocks in the second way. We use the number of holes feature to cluster the similar characters. We can recognize the almost Myanmar common characters with various font sizes by using these features. All these 25 features are used in both training part and testing part. In the classification step, the characters are classified by matching the all features of input character with already trained features of characters.

Keywords: chain code frequency, character recognition, feature extraction, features matching, segmentation

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Authors: Shreya Srivastava, Sagnik Dey

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Aerosol direct radiative forcing (ADRF) refers to the alteration of the Earth's energy balance from the scattering and absorption of solar radiation by aerosol particles. India experiences substantial ADRF due to high aerosol loading from various sources. These aerosols' radiative impact depends on their physical characteristics (such as size, shape, and composition) and atmospheric distribution. Quantifying ADRF is crucial for understanding aerosols’ impact on the regional climate and the Earth's radiative budget. In this study, we have taken radiation data from Clouds and the Earth’s Radiant Energy System (CERES, spatial resolution=1ox1o) for 22 years (2000-2021) over the Indian subcontinent. Except for a few locations, the short-wave DARF exhibits aerosol cooling at the TOA (values ranging from +2.5 W/m2 to -22.5W/m2). Cooling due to aerosols is more pronounced in the absence of clouds. Being an aerosol hotspot, higher negative ADRF is observed over the Indo-Gangetic Plain (IGP). Aerosol Forcing Efficiency (AFE) shows a decreasing seasonal trend in winter (DJF) over the entire study region while an increasing trend over IGP and western south India during the post-monsoon season (SON) in clear-sky conditions. Analysing atmospheric heating and AOD trends, we found that only the aerosol loading is not governing the change in atmospheric heating but also the aerosol composition and/or their vertical profile. We used a Multi-angle Imaging Spectro-Radiometer (MISR) Level-2 Version 23 aerosol products to look into aerosol composition. MISR incorporates 74 aerosol mixtures in its retrieval algorithm based on size, shape, and absorbing properties. This aerosol mixture information was used for analysing long-term changes in aerosol composition and dominating aerosol species corresponding to the aerosol forcing value. Further, ADRF derived from this method is compared with around 35 studies across India, where a plane parallel Radiative transfer model was used, and the model inputs were taken from the OPAC (Optical Properties of Aerosols and Clouds) utilizing only limited aerosol parameter measurements. The result shows a large overestimation of TOA warming by the latter (i.e., Model-based method).

Keywords: aerosol radiative forcing (ARF), aerosol composition, MISR, CERES, SBDART

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Authors: Cristina Galván-Fernández

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Students differentiate the different contexts of their lives as well as employment, hobbies or studies. In higher education is needed to transfer the experiential knowledge to theory and viceversa. However, is difficult to achieve than students use their personal experiences and social readings for get the learning evidences. In an experience with 178 education students from Chile and Spain we have used an e-portfolio system and a methodology for 4 years with the aims of help them to: 1) self-regulate their learning process and 2) use social networks and professional experiences for make the learning evidences. These two objectives have been controlled by interviews to the same students in different moments and two questionnaires. The results of this study show that students recognize the ownership of their learning and progress in planning and reflection of their own learning.

Keywords: competences, e-portfolio, higher education, self-regulation

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Authors: Monika Florczak-Wator

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The model of positive obligations of the state concerning the protection of the rights of an individual was created within the jurisdiction of the German Federal Constitutional Court in the 1970s. That model assumes that the state should protect an individual against infringement of their fundamental rights by another individual. It is based on the idea concerning the modification of the function and duties of the state towards an individual and society. Initially the state was perceived as the main infringer of the fundamental rights of an individual formulating the individual’s obligations of negative nature (obligation of noninterference), however, at present the state is perceived as a guarantor and protector of the fundamental rights of an individual of positive nature (obligation of protection). Examination of the chosen judicial decisions of that court will enable us to determine what the obligation of protection is specifically about, when it is updated and whether it is accompanied by claims of an individual requesting the state to take actions protecting their fundamental rights against infringement by the private entities. The comparative perspective for the German model of positive obligations of the state will be an analogous model present in the jurisdiction of the European Court of Human Rights. It is justified to include it in the research as the Convention, similarly to the constitution, focuses on the protection of an individual against the infringement of their rights by the state and both models have been developed within the jurisdiction for several dozens of years. Analysis of the provisions of the Constitution of the Republic of Poland as well as judgements of the Polish Constitutional Tribunal will allow for the presentation of the application the model of the protective duties of the state in Poland.

Keywords: human rights, horizontal relationships, constitution, state protection

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Authors: Raveendranath Veeramani, Parkash Chand, H. Y. Suma, A. Umamageswari

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Background and Aims: The aim of this study was to evaluate students’ perception of Integrated Learning Program[ILP]. Settings and Design: A questionnaire was used to survey and evaluate the perceptions of 1styear MBBS students at the Department of Anatomy at our medical college in India. Materials and Methods: The first MBBS Students of Anatomy were involved in the ILP on the Liver and extra hepatic biliary apparatus integrating the Departments of Anatomy, Biochemistry and Hepato-biliary Surgery. The evaluation of the ILP was done by two sets of short questionnaire that had ten items using the Likert five-point grading scale. The data involved both the students’ responses and their grading. Results: A majority of students felt that the ILP was better in as compared to the traditional lecture method of teaching.The integrated teaching method was better at fulfilling learning objectives (128 students, 83%), enabled better understanding (students, 94%), were more interesting (140 students, 90%), ensured that they could score better in exams (115 students, 77%) and involved greater interaction (100 students, 66%), as compared to traditional teaching methods. Most of the students (142 students, 95%) opined that more such sessions should be organized in the future. Conclusions: Responses from students show that the integrated learning session should be incorporated even at first phase of MBBS for selected topics so as to create interest in the medical sciences at the entry level and to make them understand the importance of basic science.

Keywords: integrated learning, students response, vertical integration, horizontal integration

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Authors: Si Abdallah Mayouf

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In this work, the effects of the wavy surface on free convection heat transfer boundary layer flow between two parallel wavy plates have been studied numerically. The two plates are considered at a constant temperature. The equations and the boundary conditions are discretized by the finite difference scheme and solved numerically using the Gauss-Seidel algorithm. The important parameters in this problem are the amplitude of the wavy surfaces and the distance between the two wavy plates. Results are presented as velocity profiles, temperature profiles and local Nusselt number according to the important parameters.

Keywords: free convection, wavy surface, parallel plates, fluid dynamics

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Authors: Eylem Güzel, Mustafa Gülen

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Historical structures are the most important symbols of a country that link the past with the future. In order to transfer them in their present conditions to the next generations, maintaining these historical structures are one of our main tasks. Seismic performance of historical structures damaged by the earthquake effects can be enhanced by repair and retrofitting applications. However, repair and retrofitting applications of historical structures are more complicated compared with the traditional structures. For this reason, they need much more attention in repair and retrofitting applications to preserve the spirit of historical structures. In this study, the present condition of selected historical structures built up in Van city that has a very rich historical heritage is given and the necessity of repair and retrofitting applications of historical structures are debated in detail.

Keywords: historical structures, repair, retrofitting, Van city

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Authors: Noshaba Dilbar, Aisha Tahir, Amer Jamil

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During the last decade, DNA barcoding proved to be an authentic tool for discovery and identification of plants. In the present study, DNA barcoding of two species, Fagonia arabica and Fagonia indica was done for differentiation by using matK region. matK gene is considered as a universal barcode because of its easy alignment and high discrimination ability. In this study, matK yielded 100% sequencing results. The sequences from both plants were aligned at clustal W and observed that there is no nucleotide variation and polymorphism among both sequences. This was further analysed by BLAST which showed the similar sequences from different plants belonging to same family but didn’t find sequence of both species. Considering this, the resulted sequence was submitted by the name of Fagonia arabica with accession number KM276890. In the end, we analysed the results from BOLD which gave us the final conclusion that both plants are same as their matK sequences are 100% identical. In literature, both Fagonia indica and Fagonia arabica names are used for this plant but there is no clear differentiation has been observed in these plants. Results evaluate that Fagonia indica and Fagonia arabica are the alternative names of same plant.

Keywords: DNA barcoding, Fagonia arabica, Fagonia indica, matK

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Authors: A. R. Alesaadi

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Flexible AC transmission system (FACTS) devices have an important rule on expended electrical transmission networks. These devices can provide control of one or more AC transmission system parameters to enhance controllability and increase power transfer capability. In this paper the effect of these devices on reliability of electrical networks is studied and it is shown that using of FACTS devices can improve the reliability of power networks and power quality in electrical networks, significantly.

Keywords: FACTS devices, power networks, power quality, STATCOM

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Authors: Agung Sugeng Widodo

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Water boiling system (WBS) using conventional gas stove (CGS) is relatively inefficient unless its mechanism being considered. In this study, an addition of ceramic stove cover (CSC) to a CGS and the gap between CSC and pan have been assessed. Parameters as energy produced by fuel, CSC temperature and water temperature were used to analyze the performance of a CGS. The gaps were varied by 1 – 7 mm in a step of 1 mm. The results showed that a CSC able to increase the performance of a CGS significantly. In certain fuel rate of 0.75 l/m, the efficiency of a CGS obtained in a gap of 4 mm. The best efficiency obtained in this study was 46.4 % due to the optimum condition that achieved simultaneously in convection and radiation heat transfer processes of the heating system. CSC also indicated a good characteristic for covering heat release at the initially of WBS.

Keywords: WBS, CSC, CGS, efficiency, gap

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Authors: Zahir Bakiri, Saci Nacefa

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In this paper a comparison in made between two models, with and without dispersion term, and focused on the characterization of the movement of the sludge blanket in the secondary sedimentation tank using the solid flux theory and the velocity settling. This allowed us develop a one-dimensional models, with and without dispersion based on a thorough experimental study carried out in situ and the application of online data which are the mass load flow, transfer concentration, and influent characteristic. On the other hand, in the proposed model, the new settling velocity law (double-exponential function) used is based on the Vesilind function.

Keywords: wastewater, activated sludge, sedimentation, settling velocity, settling models

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Authors: C. F. Ocoleanu, A. I. Dolan, G. Cividjian, S. Teodorescu

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In this paper we make a temperature investigations in two type of superposed crimped connections using experimental determinations. All the samples use 8 copper wire 7.1 x 3 mm2 crimped by two methods: the first method uses one crimp indents and the second is a proposed method with two crimp indents. The ferrule is a parallel one. We study the influence of number and position of crimp indents. The samples are heated in A.C. current at different current values until steady state heating regime. After obtaining of temperature values, we compare them and present the conclusion.

Keywords: crimped connections, experimental determinations, temperature, heat transfer

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Authors: Mahdi Hamzehei, Seyyed Amin Hakim, Nahid Taherian

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Fins play an important role in increasing the efficiency of compact shell and tube heat exchangers by increasing heat transfer. The objective of this paper is to determine the optimum fin wave angle, as one of the geometric parameters affecting the efficiency of the heat exchangers. To this end, finite volume method is used to model and simulate the flow in heat exchanger. In this study, computational fluid dynamics simulations of wave channel are done. The results show that the wave angle affects the temperature output of the heat exchanger.

Keywords: fin wave angle, tube, intercooler, optimum, performance

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Authors: Vojko Kilar, Boris Azinović, David Koren

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Recently, an increasing trend of passive and low-energy buildings transferring form non earthquake-prone to earthquake-prone regions has thrown out the question about the seismic safety of such buildings. The paper describes the most commonly used thermal insulating materials and the special details, which could be critical from the point of view of earthquake resistance. The most critical appeared to be the cases of buildings founded on the RC foundation slab lying on a thermal insulation (TI) layer made of extruded polystyrene (XPS). It was pointed out that in such cases the seismic response of such buildings might differ to response of their fixed based counterparts. The main parameters that need special designers’ attention are: the building’s lateral top displacement, the ductility demand of the superstructure, the foundation friction coefficient demand, the maximum compressive stress in the TI layer and the percentage of the uplifted foundation. The analyses have shown that the potentially negative influences of inserting the TI under the foundation slab could be expected only for slender high-rise buildings subjected to severe earthquakes. Oppositely it was demonstrated for the foundation friction coefficient demand which could exceed the capacity value yet in the case of low-rise buildings subjected to moderate earthquakes. Some suggestions to prevent the horizontal shifts are also given.

Keywords: earthquake response, extruded polystyrene (XPS), low-energy buildings, foundations on thermal insulation layer

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Authors: J. A. Gbadeyan, R. A. Kareem

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In this paper, we investigated the effects of unsteady internal heat generation of a two-step exothermic reactive hydromagnetic fluid flow under different chemical kinetics namely: Sensitized, Arrhenius and Bimolecular kinetics through an isothermal wall temperature channel. The resultant modeled nonlinear partial differential equations were simplified and solved using a combined Laplace-Differential Transform Method (LDTM). The solutions obtained were discussed and presented graphically to show the salient features of the fluid flow and heat transfer characteristics.

Keywords: unsteady, reactive, hydromagnetic, couette ow, exothermi creactio

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Authors: Jiwuer Jilili, Ulrich Eckern, Udo Schwingenschlogl

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We present first principles results for the electronic, magnetic, and optical properties of the BiFeO3 /La2/3Sr1/3MnO3 heterostructure as obtained by spin polarized calculations using density functional theory. The electronic states of the heterostructure are compared to those of the bulk compounds. Structural relaxation turns out to have only a minor impact on the chemical bonding, even though the oxygen octahedra in La2/3Sr1/3MnO3 develop some distortions due to the interface strain. While a small charge transfer affects the heterointerfaces, our results demonstrate that the half-metallic character of La2/3Sr1/3MnO3 is fully maintained.

Keywords: BiFeO3, La2/3Sr1/3MnO3, superlattice, half-metallicity

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Authors: Waseem Al Talalwah, Shorok Al Dorazi, Roger Soames

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Persistent sciatic artery is a rare anatomical vascular variation resulting from a lack of regression of the embryonic dorsal axial artery. The axial artery is the main artery supplying the lower limb during development in the first trimester. The current research includes 206 sciatic artery cases in 171 patients between 1864 and 2012. It aims to identify the risk factor of sciatic artery aneurysm in congenital limb anomalies. Sciatic artery aneurysm was diagnosed incidentally in amniotic band syndrome (ABS) existing with no congenital anomaly in 0.7% or with double knee in 0.7%, with the tibia in 0.7% and with hemihypertrophy or soft tissue hypertrophy in 1.4%. Therefore, the current study indicates a relationship the same gene responsible for the congenital limb deformities may be responsible for non-regression of the sciatic artery. Furthermore, pediatricians should refer cases of congenital limb anomalies for vascular evaluation prior to corrective surgical intervention.

Keywords: amniotic band syndrome, congenital limb deformities, double knee, sciatic artery, sciatic artery aneurysm , soft tissue hypertrophy

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Authors: Jamal S. M. Sabir, Edward C. Theriot, Schonna R. Manning, Abdulrahman L. Al-Malki, Mohammad, Mumdooh J. Sabir, Dwight K. Romanovicz, Nahid H. Hajrah, Robert K. Jansen, Matt P. Ashworth

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The diatom Phaeodactylum tricornutum has been used as a model for cell biologists and ecologists for over a century. We have incorporated several new raphid pennates into a three-gene phylogenetic dataset (SSU, rbcL, psbC), and recover Gomphonemopsis sp. as sister to P. tricornutum with 100% BS support. This is the first time a close relative has been identified for P. tricornutum with robust statistical support. We test and reject a succession of hypotheses for other relatives. Our molecular data are statistically significantly incongruent with placement of either or both species among the Cymbellales, an order of diatoms with which both have been associated. We believe that further resolution of the phylogenetic position of P. tricornutum will rely more on increased taxon sampling than increased genetic sampling. Gomphonemopsis is a benthic diatom, and its phylogenetic relationship with P. tricornutum is congruent with the hypothesis that P. tricornutum is a benthic diatom with specific adaptations that lead to active recruitment into the plankton. We hypothesize that other benthic diatoms are likely to have similar adaptations and are not merely passively recruited into the plankton.

Keywords: benthic, diatoms; ecology, Phaeodactylum tricornutum, phylogeny, tychoplankton

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Authors: Fehmi Bouguezzi

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This paper studies optimal licensing regimes in a linear Hotelling model where firms are located at the end points of the city and where the transportation cost is not linear but quadratic. We study for that a more general cost function and we try to compare the findings with the results of the linear cost. We find the same optimal licensing regimes. A per unit royalty is optimal when innovation is not drastic and no licensing is better when innovation is drastic. We also find that no licensing is always better than fixed fee licensing.

Keywords: Hotelling model, technology transfer, patent licensing, quadratic transportation cost

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Authors: Amal G. Kurian

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The use of mathematical modeling has seen a considerable boost in recent times with the development of many advanced algorithms and mathematical modeling capabilities. The advantages this method has over other methods are that they are much closer to standard physics theories and thus represent a better theoretical model. They take lesser solving time and have the ability to change various parameters for optimization, which is a big advantage, especially in automotive industry. This thesis work focuses on a thorough investigation of the effects of vehicle speed and road roughness on a heavy commercial vehicle ride and structural dynamic responses. Since commercial vehicles are kept in operation continuously for longer periods of time, it is important to study effects of various physical conditions on the vehicle and its user. For this purpose, various experimental as well as simulation methodologies, are adopted ranging from experimental transfer path analysis to various road scenario simulations. To effectively investigate and eliminate several causes of unwanted responses, an efficient and robust technique is needed. Carrying forward this motivation, the present work focuses on the development of a mathematical model of a 4-axle configuration heavy commercial vehicle (HCV) capable of calculating responses of the vehicle on different road PSD inputs and vehicle speeds. Outputs from the model will include response transfer functions and PSDs and wheel forces experienced. A MATLAB code will be developed to implement the objectives in a robust and flexible manner which can be exploited further in a study of responses due to various suspension parameters, loading conditions as well as vehicle dimensions. The thesis work resulted in quantifying the effect of various physical conditions on ride comfort of the vehicle. An increase in discomfort is seen with velocity increase; also the effect of road profiles has a considerable effect on comfort of the driver. Details of dominant modes at each frequency are analysed and mentioned in work. The reduction in ride height or deflection of tire and suspension with loading along with load on each axle is analysed and it is seen that the front axle supports a greater portion of vehicle weight while more of payload weight comes on fourth and third axles. The deflection of the vehicle is seen to be well inside acceptable limits.

Keywords: mathematical modeling, HCV, suspension, ride analysis

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Authors: Isari Pairoa, Proud Arunrangsiwed

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Celebrity and brand mascot endorsement have been explored for more than three decades. Both endorsers can effectively transfer their reputation to corporate image and can influence the customers to purchase the product. However, there was little known about the mediators between the level of endorsement and its effect on buying behavior. The objective of the current study is to identify the gab of the previous studies and to seek possible mediators. It was found that consumer’s memory and identification are the mediators, of source credibility and endorsement effect. A future study should confirm the model of endorsement, which was established in the current study.

Keywords: product endorsement, memory, identification theory, source credibility, unintentional effect

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Authors: Fereshteh Pourmohammad, Mehdi Zare

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The city of Karaj, having a population of 2.2 millions (est. 2022) is located in the South West of Alborz Mountain Belt in Northern Iran. The region is known to be a highly active seismic zone. This study is focused on the geological and seismological analyses within a radius of 200 km from the center of Karaj. There are identified five seismic zones and seven linear seismic sources. The maximum magnitude was calculated for the seismic zones. Scine tghe seismicity catalog is incomplete, we have used a parametric-historic algorithm and the Kijko and Sellevoll (1992) method was used to calculate seismicity parameters, and the return periods and the probability frequency of recurrence of the earthquake magnitude in each zone obtained for 475-years return period. According to the calculations, the highest and lowest earthquake magnitudes of 7.6 and 6.2 were respectively obtained in Zones 1 and 4. This result is a new and extremely important in view point of earthquake risk in a densely population city. The maximum strong horizontal ground motion for the 475-years return period 0.42g and for 2475-year return period 0.70g also the maximum strong vertical ground motion for 475-years return period 0.25g and 2475-years return period 0.44g was calculated using attenuation relationships. These acceleration levels are new, and are obtained to be about 25% higher than presented values in the Iranian building code.

Keywords: seismic zones, ground motion, return period, hazard analysis

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Authors: Tatiana Butkova, Nikolai Kibrik, Kristina Malsagova, Alexander Izotov, Alexander Stepanov, Anna Kaysheva

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Relevance. The genetic risk of developing schizophrenia is determined by two factors: single nucleotide polymorphisms and gene copy number variations. The search for serological markers for early diagnosis of schizophrenia is driven by the fact that the first five years of the disease are accompanied by significant biological, psychological, and social changes. It is during this period that pathological processes are most amenable to correction. The aim of this study was to analyze single nucleotide polymorphisms (SNPs) that are hypothesized to potentially influence the onset and development of the endogenous process. Materials and Methods It was analyzed 73 single nucleotide polymorphism variants. The study included 48 patients undergoing inpatient treatment at "Psychiatric Clinical Hospital No. 1" in Moscow, comprising 23 females and 25 males. Inclusion criteria: - Patients aged 18 and above. - Diagnosis according to ICD-10: F20.0, F20.2, F20.8, F21.8, F25.1, F25.2. - Voluntary informed consent from patients. Exclusion criteria included: - The presence of concurrent somatic or neurological pathology, neuroinfections, epilepsy, organic central nervous system damage of any etiology, and regular use of medication. - Substance abuse and alcohol dependence. - Women who were pregnant or breastfeeding. Clinical and psychopathological assessment was complemented by psychometric evaluation using the PANSS scale at the beginning and end of treatment. The duration of observation during therapy was 4-6 weeks. Total DNA extraction was performed using QIAamp DNA. Blood samples were processed on Illumina HiScan and genotyped for 652,297 markers on the Infinium Global Chips Screening Array-24v2.0 using the IMPUTE2 program with parameters Ne=20,000 and k=90. Additional filtration was performed based on INFO>0.5 and genotype probability>0.5. Quality control of the obtained DNA was conducted using agarose gel electrophoresis, with each tested sample having a volume of 100 µL. Results. It was observed that several SNPs exhibited gender dependence. We identified groups of single nucleotide polymorphisms with a membership of 80% or more in either the female or male gender. These SNPs included rs2661319, rs2842030, rs4606, rs11868035, rs518147, rs5993883, and rs6269.Another noteworthy finding was the limited combination of SNPs sufficient to manifest clinical symptoms leading to hospitalization. Among all 48 patients, each of whom was analyzed for deviations in 73 SNPs, it was discovered that the combination of involved SNPs in the manifestation of pronounced clinical symptoms of schizophrenia was 19±3 out of 73 possible. In study, the frequency of occurrence of single nucleotide polymorphisms also varied. The most frequently observed SNPs were rs4849127 (in 90% of cases), rs1150226 (86%), rs1414334 (75%), rs10170310 (73%), rs2857657, and rs4436578 (71%). Conclusion. Thus, the results of this study provide additional evidence that these genes may be associated with the development of schizophrenia spectrum disorders. However, it's impossible cannot rule out the hypothesis that these polymorphisms may be in linkage disequilibrium with other functionally significant polymorphisms that may actually be involved in schizophrenia spectrum disorders. It has been shown that missense SNPs by themselves are likely not causative of the disease but are in strong linkage disequilibrium with non-functional SNPs that may indeed contribute to disease predisposition.

Keywords: gene polymorphisms, genotyping, single nucleotide polymorphisms, schizophrenia.

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Authors: Arpit Rai

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In this work, we propose PatchMix, a semi-supervised method for pre-training visual representations. PatchMix mixes patches of two images and then solves an auxiliary task of predicting the label of each patch in the mixed image. Our experiments on the CIFAR-10, 100 and the SVHN dataset show that the representations learned by this method encodes useful information for transfer to new tasks and outperform the baseline Residual Network encoders by on CIFAR 10 by 12% on ResNet 101 and 2% on ResNet-56, by 4% on CIFAR-100 on ResNet101 and by 6% on SVHN dataset on the ResNet-101 baseline model.

Keywords: self-supervised learning, representation learning, computer vision, generalization

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Authors: Apichai Sawisit, Sirima Suvarnakuta Jantama, Sunthorn Kanchanatawee, Lonnie O. Ingram, Kaemwich Jantama

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Escherichia coli KJ122 was engineered to produce succinate from glucose using the wild type GalP for glucose uptake instead of the native phosphotransferase system (ptsI mutation). This strain ferments 10% (w/v) xylose poorly. Mutants were selected by serial transfers in AM1 mineral salts medium with 10% (w/v) xylose. Evolved mutants exhibited a similar improvement, co-fermentation of an equal mixture of xylose and glucose. One of these, AS1600a, produced 84.26±1.37 g/L succinate, equivalent to that produced by the parent (KJ122) strain from 10% glucose (85.46±1.78 g/L). AS1600a was sequenced and found to contain a mutation in galactose permease (GalP, G236D). Expressing the galP* mutation gene in KJ122ΔgalP resembled the xylose utilization phenotype of the mutant AS1600a. The strain AS1600a and KJ122ΔgalP (pLOI5746; galP*) also co-fermented a mixture of glucose, xylose, arabinose, and galactose in sugarcane bagasse hydrolysate for succinate production.

Keywords: xylose, furfural, succinat, sugarcane bagasse, E. coli

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Authors: John N. Idenyi, Hadimundeen Abdallah, Abigeal D. Adeyemi, Jonathan C. Eya

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Gut microbiomes play a significant role in the growth, metabolism, and health of fish. However, we know very little about the interactive effects of variations in dietary composition and temperature on rainbow trout gut microbiota. Exactly 288 rainbow trout weighing 45.6g ± 0.05 (average ± SD) were fed four isocaloric, isolipidic, and isonitrogenous diets comprising 40% crude protein and 20% crude lipid and formulated as 100 % animal-based protein (AP) and a blend of 50 fish oil (FO)/50 camelina oil (CO), 100 % AP and100 % CO, 100 % plant-based protein (PP) and a blend of 50FO/50CO or 100 % PP and 100 % CO in 14 or 18°C for 150 days. Gut content was analyzed using 16S rRNA gene and shotgun sequencing. The most abundant phyla identified regardless of diet were Tenericutes, Firmicutes, Proteobacteria, Spirochaetes, Bacteroidetes, and Actinobacteria, while Aeromonadaceae and Enterobacteriaceae were dominant families in 18°C. Moreover, gut microbes were dominated by genes relating to an amino acid, carbohydrate, fat, and energy metabolisms and influenced by temperature. The shared functional profiles for all the diets suggest that plant protein sources in combination with CO could be as good as the fish meal with 50/50 FO & CO in rainbow trout farming.

Keywords: aquafeed, aquaculture, microbiome, rainbow trout

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Authors: E. L. Albuquerque, U. L. Fulco, G. S. Ourique

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The focus of this work is on the numerical investigation of the charge transport properties of the de novo-designed alpha3 polypeptide, as well as in its variants, all of them probed by gene engineering. The theoretical framework makes use of a tight-binding model Hamiltonian, together with ab-initio calculations within quantum chemistry simulation. The alpha3 polypeptide is a 21-residue with three repeats of the seven-residue amino acid sequence Leu-Glu-Thr-Leu-Ala-Lys-Ala, forming an alpha–helical bundle structure. Its variants are obtained by Ala→Gln substitution at the e (5th) and g (7th) position, respectively, of the alpha3 polypeptide amino acid sequence. Using transmission electron microscopy and atomic force microscopy, it was observed that the alpha3 polypeptide and one of its variant do have the ability to form fibrous assemblies, while the other does not. Our main aim is to investigate whether or not the biased alpha3 polypeptide and its variants can be also identified by quantum charge transport measurements through current-voltage (IxV) curves as a pattern to characterize their fibrous assemblies. It was observed that each peptide has a characteristic current pattern, which may be distinguished by charge transport measurements, suggesting that it might be a useful tool for the development of biosensors.

Keywords: charge transport properties, electronic transmittance, current-voltage characteristics, biological sensor

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Authors: Ricardo Alberto Chiong Zevallos, Eduardo Moraes Rego Reis

Abstract:

Pancreatic adenocarcinoma (PDAC) patients have a less than 10% 5-year survival rate. PDAC has no defined diagnostic and prognostic biomarkers. Gemcitabine is the first-line drug in PDAC and several other cancers. Long non-coding RNAs (lncRNAs) contribute to the tumorigenesis and are potential biomarkers for PDAC. Although lncRNAs aren’t translated into proteins, they have important functions. LncRNAs can decoy or recruit proteins from the epigenetic machinery, act as microRNA sponges, participate in protein translocation through different cellular compartments, and even promote chemoresistance. The chromatin remodeling enzyme EZH2 is a histone methyltransferase that catalyzes the methylation of histone 3 at lysine 27, silencing local expression. EZH2 is ambivalent, it can also activate gene expression independently of its histone methyltransferase activity. EZH2 is overexpressed in several cancers and interacts with lncRNAs, being recruited to a specific locus. EZH2 can be recruited to activate an oncogene or silence a tumor suppressor. The lncRNAs misregulation in cancer can result in the differential recruitment of EZH2 and in a distinct epigenetic landscape, promoting chemoresistance. The relevance of the EZH2-lncRNAs interaction to chemoresistant PDAC was assessed by Real Time quantitative PCR (RT-qPCR) and RNA Immunoprecipitation (RIP) experiments with naïve and gemcitabine-resistant PDAC cells. The expression of several lncRNAs and EZH2 gene targets was evaluated contrasting naïve and resistant cells. Selection of candidate genes was made by bioinformatic analysis and literature curation. Indeed, the resistant cell line showed higher expression of chemoresistant-associated lncRNAs and protein coding genes. RIP detected lncRNAs interacting with EZH2 with varying intensity levels in the cell lines. During RIP, the nuclear fraction of the cells was incubated with an antibody for EZH2 and with magnetic beads. The RNA precipitated with the beads-antibody-EZH2 complex was isolated and reverse transcribed. The presence of candidate lncRNAs was detected by RT-qPCR, and the enrichment was calculated relative to INPUT (total lysate control sample collected before RIP). The enrichment levels varied across the several lncRNAs and cell lines. The EZH2-lncRNA interaction might be responsible for the regulation of chemoresistance-associated genes in multiple cancers. The relevance of the lncRNA-EZH2 interaction to PDAC was assessed by siRNA knockdown of a lncRNA, followed by the analysis of the EZH2 target expression by RT-qPCR. The chromatin immunoprecipitation (ChIP) of EZH2 and H3K27me3 followed by RT-qPCR with primers for EZH2 targets also assess the specificity of the EZH2 recruitment by the lncRNA. This is the first report of the interaction of EZH2 and lncRNAs HOTTIP and PVT1 in chemoresistant PDAC. HOTTIP and PVT1 were described as promoting chemoresistance in several cancers, but the role of EZH2 is not clarified. For the first time, the lncRNA LINC01133 was detected in a chemoresistant cancer. The interaction of EZH2 with LINC02577, LINC00920, LINC00941, and LINC01559 have never been reported in any context. The novel lncRNAs-EZH2 interactions regulate chemoresistant-associated genes in PDAC and might be relevant to other cancers. Therapies targeting EZH2 alone weren’t successful, and a combinatorial approach also targeting the lncRNAs interacting with it might be key to overcome chemoresistance in several cancers.

Keywords: epigenetics, chemoresistance, long non-coding RNAs, pancreatic cancer, histone modification

Procedia PDF Downloads 66

Authors: Adenike Adesanya, Nonthaphat Wong, Xiang-Yun Lan, Shea Ping Yip, Chien-Ling Huang

Abstract:

Background: The most challenging mutation of the oncokinase BCR-ABL protein T315I, which is commonly known as the “gatekeeper” mutation and is notorious for its strong resistance to almost all tyrosine kinase inhibitors (TKIs), especially imatinib. Therefore, this study aims to identify T315I-dependent downstream microRNA (miRNA) pathways associated with drug resistance in chronic myeloid leukemia (CML) for prognostic and therapeutic purposes. Methods: T315I-carrying K562 cell clones (K562-T315I) were generated by the CRISPR-Cas9 system. Imatinib-treated K562-T315I cells were subjected to small RNA library preparation and next-generation sequencing. Putative lncRNA-miRNA-mRNA networks were analyzed with (i) DESeq2 to extract differentially expressed miRNAs, using Padj value of 0.05 as cut-off, (ii) STarMir to obtain potential miRNA response element (MRE) binding sites of selected miRNAs on lncRNA H19, (iii) miRDB, miRTarbase, and TargetScan to predict mRNA targets of selected miRNAs, (iv) IntaRNA to obtain putative interactions between H19 and the predicted mRNAs, (v) Cytoscape to visualize putative networks, and (vi) several pathway analysis platforms – Enrichr, PANTHER and ShinyGO for pathway enrichment analysis. Moreover, mitochondria isolation and transcript quantification were adopted to determine the new mechanism involved in T315I-mediated resistance of CML treatment. Results: Verification of the CRISPR-mediated mutagenesis with digital droplet PCR detected the mutation abundance of ≥80%. Further validation showed the viability of ≥90% by cell viability assay, and intense phosphorylated CRKL protein band being detected with no observable change for BCR-ABL and c-ABL protein expressions by Western blot. As reported by several investigations into hematological malignancies, we determined a 7-fold increase of H19 expression in K562-T315I cells. After imatinib treatment, a 9-fold increment was observed. DESeq2 revealed 171 miRNAs were differentially expressed K562-T315I, 112 out of these miRNAs were identified to have MRE binding regions on H19, and 26 out of the 112 miRNAs were significantly downregulated. Adopting the seed-sequence analysis of these identified miRNAs, we obtained 167 mRNAs. 6 hub miRNAs (hsa-let-7b-5p, hsa-let-7e-5p, hsa-miR-125a-5p, hsa-miR-129-5p, and hsa-miR-372-3p) and 25 predicted genes were identified after constructing hub miRNA-target gene network. These targets demonstrated putative interactions with H19 lncRNA and were mostly enriched in pathways related to cell proliferation, senescence, gene silencing, and pluripotency of stem cells. Further experimental findings have also shown the up-regulation of mitochondrial transcript and lncRNA MALAT1 contributing to the lncRNA-miRNA-mRNA networks induced by BCR-ABL T315I mutation. Conclusions: Our results have indicated that lncRNA-miRNA regulators play a crucial role not only in leukemogenesis but also in drug resistance, considering the significant dysregulation and interactions in the K562-T315I cell model generated by CRISPR-Cas9. In silico analysis has further shown that lncRNAs H19 and MALAT1 bear several complementary miRNA sites. This implies that they could serve as a sponge, hence sequestering the activity of the target miRNAs.

Keywords: chronic myeloid leukemia, imatinib resistance, lncRNA-miRNA-mRNA, T315I mutation

Procedia PDF Downloads 129