Search results for: biomolecular sequence synthesis

Authors: Mandeep Singh Azad.Dibyendu Chakraborty, Vikas Vohra

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Introduction: Poonch is one of the remotest districts of the Jammu and Kashmir (UT) and situated on international borders. This native poultry population in these areas is quite hardy and thrives well in adverse climatic conditions. Till date, no local breed from this area (Jammu Province) has been characterized thus present study was undertaken with the main objectives of molecular characterization of ChB6 gene in local native chicken of Poonch region located at international borders between India and Pakistan. The chicken B-cell marker (ChB6) gene has been proposed as a candidate gene in regulating B-cell development. Material and Method: RNA was isolated by Blood RNA Purification Kit (HiPura) and Trizol method from whole blood samples. Positive PCR products with size 1110 bp were selected for further purification, sequencing and analysis. The amplified PCR product was sequenced by Sangers dideoxy chain termination method. The obtained sequence of ChB6 gene of Poonchi chicken were compared by MEGAX software. BioEdit software was used to construct phylogenic tree, and Neighbor Joining method was used to infer evolutionary history. In order to compute evolutionary distance Maximum Composite Likelihood method was used. Results: The positively amplified samples of ChB6 genes were then subjected to Sanger sequencing with “Primer Walking. The sequences were then analyzed using MEGA X and BioEdit software. The sequence results were compared with other reported sequence from different breed of chicken and with other species obtained from the NCBI (National Center for Biotechnology Information). ClustalW method using MEGA X software was used for multiple sequence alignment. The sequence results of ChB6 gene of Poonchi chicken was compared with Centrocercus urophasianus, G. gallus mRNA for B6.1 protein, G. gallus mRNA for B6.2, G. gallus mRNA for B6.3, Gallus gallus B6.1, Halichoeres bivittatus, Miniopterus fuliginosus Ferringtonia patagonica, Tympanuchus phasianellus. The genetic distances were 0.2720, 0.0000, 0.0245, 0.0212, 0.0147, 1.6461, 2.2394, 2.0070 and 0.2363 for ChB6 gene of Poonchi chicken sequence with other sequences in the present study respectively. Sequencing results showed variations between different species. It was observed that AT content were higher then GC content for ChB6 gene. The lower AT content suggests less thermostable. It was observed that there was no sequence difference within the Poonchi population for ChB6 gene. The high homology within chicken population indicates the conservation of ChB6 gene. The maximum difference was observed with Miniopterus fuliginosus (Eastern bent-wing bat) followed by Ferringtonia patagonica and Halichoeres bivittatus. Conclusion: Genetic variation is the essential component for genetic improvement. The results of immune related gene Chb6 shows between population genetic variability. Therefore, further association studies of this gene with some prevalent diseases in large population would be helpful to identify disease resistant/ susceptible genotypes in the indigenous chicken population.

Keywords: ChB6, sequencing, ClustalW, genetic distance, poonchi chicken, SNP

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Authors: Ana Jurkeviciute, Larisa Grigorieva, Ksenia Moskvinа

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Oil shale alkylresorcinols are formed as a by-product in oil shale processing. They are unique raw material for chemical industry. Polycondensation resins obtaining is one of the worthwhile directions of oil shale alkylresorcinols use. These resins are widely applied in many branches of industry such as wood-working, metallurgic, tire, rubber products, construction etc. Possibility of resins obtaining using overall alkylresorcinols will allow to cheapen finished products on their base and to widen the range of resins offered on the market. Synthesis of polycondensation resins on the basis of alkylresorcinols was conducted by several methods in the process of investigations. In the formulations a part of resorcinol was replaced by fractions of oil shale alkylresorcinols containing different amount of 5-methylresorcinol (40-80 mass %). Some resins were modified by aromatic alkene at the stage of synthesis. Thermal stability and degradation behavior of resins were investigated by thermogravimetric analysis (TGA) method both in an inert nitrogen environment and in an oxidative environment of air. TGA integral curves were obtained and processed in dynamic mode for interval of temperatures from 25 to 830 °C. Rate of temperature rise was 5°C/min, gas flow rate - 50 ml/min. Resins power for carbonization was evaluated by carbon residue. Physical-chemical parameters of the resins were determined. Content of resorcinol and 5-methylresorcinol not reacted in the process of synthesis were determined by gas chromatography method.

Keywords: resorcinol, oil shale alkylresorcinols, aromatic alkene, polycondensation resins, modified resins

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Authors: Kyaw Zin Htut

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In this article, the synthesis of the efficiency of intelligent diagnostic system in the aircraft measuring devices is described. The technology developments of the diagnostic system are considered based on the model errors of the gyro instruments, which are used to measure the parameters of the aircraft. The synthesis of the diagnostic intelligent system is considered on the example of the problem of assessment and forecasting errors of the gyroscope devices on the onboard aircraft. The result of the system is to detect of faults of the aircraft measuring devices as well as the analysis of the measuring equipment to improve the efficiency of its work.

Keywords: diagnostic, dynamic system, errors of gyro instruments, model errors, assessment, prognosis

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Authors: Mohamed Arbi Khlifi, Badr M. Alshammari

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This paper discusses the general methods to saturation in the steady-state, two axis (d & q) frame models of synchronous machines. In particular, the important role of the magnetic coupling between the d-q axes (cross-magnetizing phenomenon), is demonstrated. For that purpose, distinct methods of saturation modeling of dumper synchronous machine with cross-saturation are identified, and detailed models synthesis in d-q axes. A number of models are given in the final developed form. The procedure and the novel models are verified by a critical application to prove the validity of the method and the equivalence between all developed models is reported. Advantages of some of the models over the existing ones and their applicability are discussed.

Keywords: cross-magnetizing, models synthesis, synchronous machine, saturated modeling, state-space vectors

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Authors: Ayed S. Al-Shihri, Abul Kalam, Abdullah G. Al-Sehemi, Gaohui Du, Tokeer Ahmad, Ahmad Irfan

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We report here the synthesis of nickel oxide (NiO) nanoparticles by microwave-assisted method, using a common precipitating agent followed by calcination in air at 400°C. The effect of the microwave and pH on the crystallite size, morphology, structure, energy band gap and surface area of NiO have been investigated by means of powder X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), high resolution transmission electron microscopy (HRTEM), Fourier transform infrared spectroscopy (FTIR), ultraviolet visible spectroscopy (UV-vis) and BET surface area studies. X-ray diffraction studies showed the formation of monophasic and highly crystalline cubic NiO. TEM analysis led to decrease the average grain size of NiO nanoparticles from 16.5 nm to 14 nm on increasing the amount of NaOH. FTIR studies also confirm the formation of NiO nanoparticles. It was observed that on increasing the volume of NaOH, the optical band gap energy (2.85 eV to 2.95 eV) and specific surface area (33.1 to 39.8 m2/g) increases, however the average particles size decreases (16.5 nm to 14 nm). This method may be extended to large scale synthesis of other metal oxides nanoparticles and the present study could be used for the potential applications in water treatment and many other fields.

Keywords: BET surface area analysis, electron microscopy, optical properties, X-ray techniques

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Authors: Sakshi Gupta, Anupam Agrawal, Ekta Singla

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An exoskeleton design for rehabilitation purpose encounters many challenges, including ergonomically acceptable wearing technology, architectural design human-motion compatibility, actuation type, human-robot interaction, etc. In this paper, a passive architecture for upper limb exoskeleton is proposed for assisting in rehabilitation tasks. Kinematic modelling is detailed for task-based kinematic synthesis of the wearable exoskeleton for self-feeding tasks. The exoskeleton architecture possesses expansion and torsional springs which are able to store and redistribute energy over the human arm joints. The elastic characteristics of the springs have been optimized to minimize the mechanical work of the human arm joints. The concept of hybrid combination of a 4-bar parallelogram linkage and a serial linkage were chosen, where the 4-bar parallelogram linkage with expansion spring acts as a rigid structure which is used to provide the rotational degree-of-freedom (DOF) required for lowering and raising of the arm. The single linkage with torsional spring allows for the rotational DOF required for elbow movement. The focus of the paper is kinematic modelling, analysis and task-based synthesis framework for the proposed architecture, keeping in considerations the essential tasks of self-feeding and self-exercising during rehabilitation of partially healthy person. Rehabilitation of primary functional movements (activities of daily life, i.e., ADL) is routine activities that people tend to every day such as cleaning, dressing, feeding. We are focusing on the feeding process to make people independent in respect of the feeding tasks. The tasks are focused to post-surgery patients under rehabilitation with less than 40% weakness. The challenges addressed in work are ensuring to emulate the natural movement of the human arm. Human motion data is extracted through motion-sensors for targeted tasks of feeding and specific exercises. Task-based synthesis procedure framework will be discussed for the proposed architecture. The results include the simulation of the architectural concept for tracking the human-arm movements while displaying the kinematic and static study parameters for standard human weight. D-H parameters are used for kinematic modelling of the hybrid-mechanism, and the model is used while performing task-based optimal synthesis utilizing evolutionary algorithm.

Keywords: passive mechanism, task-based synthesis, emulating human-motion, exoskeleton

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Authors: Lin Cheng, Zijiang Yang

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Program synthesis is the task to automatically generate programs based on user specification. In this paper, we present a framework that synthesizes programs from flow charts that serve as accurate and intuitive specification. In order doing so, we propose a deep neural network called GRCNN that recognizes graph structure from its image. GRCNN is trained end-to-end, which can predict edge and node information of the flow chart simultaneously. Experiments show that the accuracy rate to synthesize a program is 66.4%, and the accuracy rates to recognize edge and node are 94.1% and 67.9%, respectively. On average, it takes about 60 milliseconds to synthesize a program.

Keywords: program synthesis, flow chart, specification, graph recognition, CNN

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Authors: Taha Ahmed Özbey, Sedat Nazlıbilek, Alparslan Çağrı Yapıcı

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Combline cavity filters have gained significant attention in recent years due to their exceptional narrowband characteristics, high unloaded Q, remarkable out-of-band rejection, and versatile post-manufacturing tuning capabilities. These filters play a vital role in various wireless communication systems, radar applications, and other advanced technologies where stringent frequency selectivity and superior performance are required. This paper represents combined cavity filter design and implementation by coupling matrix synthesis. Limited filter length, 50 dB out-of-band rejection, and agile design were aimed. To do so, CAD tools and intuitive methods were used.

Keywords: cavity, band pass filter, cavity combline filter, coupling matrix synthesis

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Authors: Carolin Anna Joy, Rohith K. R, Rehin Sulay, Parvathy Santhoshkumar, G.Anil Kumar, Vibin Ipe Thomas

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Ullmann coupling reactions are gaining great relevance owing to their contribution in the synthesis of biologically and pharmaceutically important compounds. Palladium and many other heavy metals have proven their excellent ability in coupling reaction, but the toxicity matters. The first-row transition metal also possess toxicity, except in the case of iron and manganese. The suitability of manganese as a catalyst is achieving great interest in oxidation, reduction, C-H activation, coupling reaction etc. In this presentation, we discuss the thermo chemistry of ligand free manganese catalyzed C-O coupling reaction between phenol and aryl halide for the synthesis of biaryl ethers using Density functional theory techniques. The mechanism involves an oxidative addition-reductive elimination step. The transition state for both the step had been studied and confirmed using Intrinsic Reaction Coordinate (IRC) calculation. The barrier height for the reaction had also been calculated from the rate determining step. The possibility of other mechanistic way had also been studied. To achieve further insight into the mechanism, substrate having various functional groups is considered in our study to direct their effect on the feasibility of the reaction.

Keywords: Density functional theory, Molecular Modeling, ligand free, biaryl ethers, Ullmann coupling

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Authors: Parvesh Singh, Vipan Kumar, Vishu Mehra

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Quinoline-4-ones represent an important class of heterocyclic scaffolds that have attracted significant interest due to their various biological and pharmacological activities. This heterocyclic unit also constitutes an integral component in drugs used for the treatment of neurodegenerative diseases, sleep disorders and in antibiotics viz. norfloxacin and ciprofloxacin. The synthetic accessibility and possibility of fictionalization at varied positions in quinoline-4-ones exemplifies an elegant platform for the designing of combinatorial libraries of functionally enriched scaffolds with a range of pharmacological profles. They are also considered to be attractive precursors for the synthesis of medicinally imperative molecules such as non-steroidal androgen receptor antagonists, antimalarial drug Chloroquine and martinellines with antibacterial activity. 2-Aryl-2,3-dihydroquinolin-4(1H)-ones are present in many natural and non-natural compounds and are considered to be the aza-analogs of favanones. The β-lactam class of antibiotics is generally recognized to be a cornerstone of human health care due to the unparalleled clinical efficacy and safety of this type of antibacterial compound. In addition to their biological relevance as potential antibiotics, β-lactams have also acquired a prominent place in organic chemistry as synthons and provide highly efficient routes to a variety of non-protein amino acids, such as oligopeptides, peptidomimetics, nitrogen-heterocycles, as well as biologically active natural and unnatural products of medicinal interest such as indolizidine alkaloids, paclitaxel, docetaxel, taxoids, cyptophycins, lankacidins, etc. A straight forward route toward the synthesis of quinoline-4-ones via the triflic acid assisted Fries rearrangement of N-aryl-βlactams has been reported by Tepe and co-workers. The ring expansion observed in this case was solely attributed to the inherent ring strain in β-lactam ring because -lactam failed to undergo rearrangement under reaction conditions. Theabovementioned protocol has been recently extended by our group for the synthesis of benzo[b]-azocinon-6-ones via a tandem Michael addition–Fries rearrangement of sorbyl anilides as well as for the single-pot synthesis of 2-aryl-quinolin-4(3H)-ones through the Fries rearrangement of 3-dienyl-βlactams. In continuation with our synthetic endeavours with the β-lactam ring and in view of the lack of convenient approaches for the synthesis of C-3 functionalized quinolin-4(1H)-ones, the present work describes the single-pot synthesis of C-3 functionalized quinolin-4(1H)-ones via the trific acid promoted Fries rearrangement of C-3 vinyl/isopropenyl substituted β-lactams. In addition, DFT calculations and MD simulations were performed to investigate the stability profles of synthetic compounds.

Keywords: dihydroquinoline, fries rearrangement, azetidin-2-ones, quinoline-4-ones

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Authors: Durata Haciu, Berti Manisa, Ozgur Birer

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ZnO nanoparticles have been synthesized by ultrasonic irradiation from simple linear alcohols and water/ethanolic mixtures, at 50 oC. By changing the composition of the solvent, the shape could be altered. While no product was obtained from methanolic solutions, in ethanol, sheet like lamellar structures prevail.n-propanol and n-butanol resulted in needle like structures. The morphology of ZnO could be thus tailored in a simple way, by varying the solvent, under ultrasonic irradiation, in a relatively less time consuming method. Variation of the morphology and size of Zn also provides a means for modulating the band-gap. Although the chemical effects of ultrasound do not come from direct interaction with molecular species, the high energy derived from acoustic cavitation creates a unique interaction of energy and matter with great potential for synthesis.

Keywords: ultrasound, ZnO, linear alcohols, morphology

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Authors: Yu Zhang, Il Kim

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Polypeptides with defined peptide sequences illustrate the power of remarkable applications in drug delivery, tissue engineering, sensing and catalysis. Especially the cyclic polypeptides, the distinctive topological architecture imparts many characteristic properties comparing to linear polypeptides. Here, a facile and highly efficient strategy for the synthesis of linear and cyclic polypeptides is reported using N-heterocyclic carbenes (NHCs)-mediated ring-opening polymerization (ROP) of α-amino acid N-carboxyanhydrides (NCA) in the presence or absence of primary amine initiator. The polymerization proceeds rapidly in a quasi-living manner, allowing access to linear and cyclic polypeptides of well-defined chain length and narrow polydispersity, as evidenced by nuclear magnetic resonance spectrum (1H NMR and 13C NMR spectra) and size exclusion chromatography (SEC) analysis. The cyclic architecture of the polypeptides was further verified by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectra (MALDI-TOF MS) and electrospray ionization (ESI) mass spectra, as well as viscosity studies. This approach can also simplify workup procedures and make bulk scale synthesis possible, which thereby opens avenues for practical uses in diverse areas, opening up the new generation of polypeptide synthesis.

Keywords: α-amino acid N-carboxyanhydrides, living polymerization, polypeptides, N-heterocyclic carbenes, ring-opening polymerization

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Authors: Ali Zazi, Ouiza Cherifi

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Natural gas currently represents a raw material of choice for the manufacture of a wide range of chemical products via synthesis gas, among the routes of transformation of methane into synthesis gas The reaction of the oxidation of methane by gas vapor 'water. This work focuses on the study of the effect of cerieum on the nickel-based catalyst supported by silica for the methane vapor reforming reaction, with a variation of certain parameters of the reaction. The reaction temperature, the H₂O / CH₄ ratio and the flow rate of the reaction mixture (CH₄-H₂O). Two catalysts were prepared by impregnation of Degussa silica with a solution of nickel nitrates and a solution of cerium nitrates [Ni (NO₃) 2 6H₂O and Ce (NO₃) 3 6H₂O] so as to obtain the 1.5% nickel concentrations. For both catalysts and plus 1% cerium for the second catalyst. These Catalysts have been characterized by physical and chemical analysis techniques: BET technique, Atomic Absorption, IR Spectroscopy, X-ray diffraction. These characterizations indicated that the nitrates had impregnated the silica. And that the NiO and Ce₂O3 phases are present and Ni°(after reaction). The BET surface of the silica decreases without being affected. The catalytic tests carried out on the two catalysts for the steam reforming reactions show that the addition of cerium to the nickel improves the catalytic performances of the nickel. And that these performances also depend on the parameters of the reaction, namely the temperature, the rate of the reaction mixture, and the ratio (H₂O / CH₄).

Keywords: heterogeneous catalysis, steam reforming, Methane, Nickel, Cerium, synthesis gas, hydrogen

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Authors: M. D. H. Beg, John O. Akindoyo, Suriati Ghazali, Nitthiyah Jeyaratnam

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Over the period of time, several approaches have been undertaken to mitigate the challenges associated with bone regeneration. This includes but not limited to xenografts, allografts, autografts as well as artificial substitutions like bioceramics, synthetic cements and metals. The former three techniques often come along with peculiar limitation and problems such as morbidity, availability, disease transmission, collateral site damage or absolute rejection by the body as the case may be. Synthetic routes remain the only feasible alternative option for treatment of bone defects. Hydroxyapatite (HA) is very compatible and suitable for this application. However, most of the common methods for HA synthesis are either expensive, complicated or environmentally unfriendly. Interestingly, extraction of HA from bio-wastes have been perceived not only to be cost effective, but also environment friendly. In this research, HA was synthesized from bio-waste: namely bovine bones through three different methods which are hydrothermal chemical processes, ultrasound assisted synthesis and ordinary calcination techniques. Structure and property analysis of the HA was carried out through different characterization techniques such as TGA, FTIR, and XRD. All the methods applied were able to produce HA with similar compositional properties to biomaterials found in human calcified tissues. Calcination process was however observed to be more efficient as it eliminated all the organic components from the produced HA. The HA synthesized is unique for its minimal cost and environmental friendliness. It is also perceived to be suitable for tissue and bone engineering applications.

Keywords: hydroxyapatite, bone, calcination, biowaste

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Authors: Raymond Olayinka

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The last three decades have witnessed myriads of definitions of knowledge management proposed by researchers and industry practitioners. Despite the magnitude of research and available literature on knowledge management, there is yet to be a consensus on what constitutes a good definition. There exists an in-exhaustive list of definitions which can appear confusing, conflicting and overlapping. What is even more daunting is the lack of common terminology in describing knowledge management processes and the inconsistency in the sequence in which the processes take. Whilst newbies to knowledge management research would struggle to make sense of knowledge management definitions, industry practitioners would struggle with their applicability. Against this backdrop, this study aimed to re-evaluate knowledge management definitions and terminologies. The objectives were threefold: (1) to conduct a critical review of an existing body of work around knowledge management concepts and definitions (2) to analyse and synthesise findings (3) to present conclusions and recommendations. The methodology for this study centres around the review of the literature and secondary data sources. A total of 48 knowledge management processes were found and extracted from various definitions (e.g. ‘identify’, ‘capture’, ‘codify’, ‘store’…). A taxonomy of the processes was created based on the commonality of the entities. The 48 processes were classified under 8 headings which were further converged into 3 main headings namely ‘acquire’, ‘exploit’ and ‘evaluate’, of which all definitions therefore hinge. The study concludes that in the multitude of knowledge management definitions, there is a consistent pattern to which the processes are organised and should be utilised. The contribution of this study is in the synthesis of previous work by various authors and the presentation of a more holistic approach to knowledge management definitions and terminologies.

Keywords: knowledge management definitions, knowledge management terminologies, knowledge management processes, literature review

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Authors: Reshu Saxena, R. K. Tripathi

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HIV-1 transmission and spread involves significant host-virus interaction. Potential targets for prevention of HIV-1 lies at the site of mucosal barriers. Thus a better understanding of how HIV-1 infects target cells at such sites and lead their invasion is required, with prime focus on the host determinants regulating HIV-1 spread. HIV-1 Nef is important for viral infectivity and pathogenicity. It promotes HIV-1 replication, facilitating immune evasion by interacting with various host factors and altering cellular pathways via multiple protein-protein interactions. In this study nef was sequenced from HIV-1 patients, and showed specific mutations revealing sequence variability in nef. To explore the difference in Nef functionality based on sequence variability we have studied the effects of HIV-1 Nef in human SupT1 T cell line and (THP-1) monocyte-macrophage cell lines through proteomics approach. 2D-Gel Electrophoresis in control and Nef-transfected SupT1 cells demonstrated several differentially expressed proteins with significant modulation of alpha-enolase. Through further studies, effects of Nef on alpha-enolase regulation were found to be cell lineage-specific, being stimulatory in macrophages/monocytes, inhibitory in T cells and without effect in HEK-293 cells. Cell migration and invasion studies were employed to determine biological function affected by Nef mediated regulation of alpha-enolase. Cell invasion was enhanced in THP-1 cells but was inhibited in SupT1 cells by wildtype nef. In addition, the modulation of enolase and cell invasion remained unaffected by a unique nef variant. These results indicated that regulation of alpha-enolase expression and invasive property of host cells by Nef is sequence specific, suggesting involvement of a particular motif of Nef. To precisely determine this site, we designed a heptapeptide including the suggested alpha-enolase regulating sequence of nef and a nef mutant with deletion of this site. Macrophages/monocytes being the major cells affected by HIV-1 at mucosal barriers, were particularly investigated by the nef mutant and peptide. Both the nef mutant and heptapeptide led to inhibition of enhanced enolase expression and increased invasiveness in THP-1 cells. Together, these findings suggest a possible mechanism of host invasion by HIV-1 through Nef mediated regulation of alpha-enolase and identifies a potential therapeutic target for HIV-1 entry at mucosal barriers.

Keywords: HIV-1 Nef, nef variants, host-virus interaction, tissue invasion

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Authors: Rajkumar Ghosh

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The Out-of-Sequence Thrust (OOST) is a common phenomenon in collisional tectonic settings like the Himalayas. These OOSTs are activated in different locations at different time frames. These OOST are linked with the multiple Himalayan Thrusts. Apart from minimal documentation in geological mapping for OOST, there exists a lack of field data to establish OOST in the field. This work has considered three thrusts from NW Himalaya in Himachal Pradesh with published data from other sources, allowing a re-examination for correlation of OOST. For the Sutlej section, the approach has been to do fieldwork and microstructural studies. The information related to the cross-cut signature of S/C- and relative time relation could help to predict the nature of OOST. The activation timing, along with the basis of identification of OOST in Higher Himalayan, was documented in various literature. Compilation of the Grain Boundary Migration (GBM) associated temperature range (400–750 °C) was documented from microstructural studies along the Jhakri-Chaura section. No such significant temperature variation across thrusts was observed. Strain variation paths using S Ʌ C angle measurement were carried out along the Jeori-Wangtu transect to distinguish overprinting structures for OOSTs. Near the Chaura Thrust (CT), angular variation of S Ʌ C was documented, and it varies within a range of 15° - 28 °. Along the NH22 (National Highway, 22), all tectonic units of the orogen are exposed in NW Himalaya, INDIA. But there are inherent difficulties in finding field evidence of OOST, largely due to the lack of adequate surface morphology, including topography and drainage pattern.

Keywords: out-of-sequence thrust (OOST), main central thrust (MCT), south tibetan detachment system (STDS), jhakri thrust (JT), sarahan thrust (ST), chaura thrust (CT), higher himalaya (HH), greater himalayan crystalline (GHC)

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Authors: An Chengrui, Yin Zi, Wu Bingbing, Ma Yuanzhu, Jin Kaixiu, Chen Xiao, Ouyang Hongwei

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Single cell RNA sequence (scRNA-seq) is one of the effective tools to study transcriptomics of biological processes. Recently, similarity measurement of cells is Euclidian distance or its derivatives. However, the process of scRNA-seq is a multi-variate Bernoulli event model, thus we hypothesize that it would be more efficient when the divergence between cells is valued with relative entropy than Euclidian distance. In this study, we compared the performances of Euclidian distance, Spearman correlation distance and Relative Entropy using scRNA-seq data of the early, medial and late stage of limb development generated in our lab. Relative Entropy is better than other methods according to cluster potential test. Furthermore, we developed KL-SNE, an algorithm modifying t-SNE whose definition of divergence between cells Euclidian distance to Kullback–Leibler divergence. Results showed that KL-SNE was more effective to dissect cell heterogeneity than t-SNE, indicating the better performance of relative entropy than Euclidian distance. Specifically, the chondrocyte expressing Comp was clustered together with KL-SNE but not with t-SNE. Surprisingly, cells in early stage were surrounded by cells in medial stage in the processing of KL-SNE while medial cells neighbored to late stage with the process of t-SNE. This results parallel to Heatmap which showed cells in medial stage were more heterogenic than cells in other stages. In addition, we also found that results of KL-SNE tend to follow Gaussian distribution compared with those of the t-SNE, which could also be verified with the analysis of scRNA-seq data from another study on human embryo development. Therefore, it is also an effective way to convert non-Gaussian distribution to Gaussian distribution and facilitate the subsequent statistic possesses. Thus, relative entropy is potentially a better way to determine the divergence of cells in scRNA-seq data analysis.

Keywords: Single cell RNA sequence, Similarity measurement, Relative Entropy, KL-SNE, t-SNE

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Authors: Ujjawal Kumar Bhagat, Kamaluddin, Rama Krishna Peddinti

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The Huisgen’s 1,3-dipolar [3+2] cycloaddition of organic azides and alkynes often give the mixtures of both the regioisomers 1,4- and 1,5- disubstituted 1,2,3-triazoles. Later, in presence of metal salts (click chemistry) such as copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) was used for the synthesis of 1,4-disubstituted 1,2,3-triazoles as a sole products regioselectively. Also, the ‘click reactions’ of Ruthenium-catalyzed azides-alkynes cycloaddition (RuAAC) is used for the synthesis of 1,5-disubstituted 1,2,3-triazoles as a single isomer. The synthesis of 1,4- and 1.5-disubstituted 1,2,3-triazoles has become the gold standard of ‘click chemistry’ due to its reliability, specificity, and biocompatibility. The 1,4- and 1,5-disubstituted 1,2,3-triazoles have emerged as one of the most powerful entities in the varieties of biological properties like antibacterial, antitubercular, antitumor, antifungal and antiprotozoal activities. Some of the 1,4,5-trisubstituted 1,2,3-triazoles exhibit Hsp90 inhibiting properties. The 1,4-disubstituted 1,2,3-triazoles also play a big role in the area of material sciences. The triazole-derived oligomeric, polymeric structures are the potential materials for the preparation of organic optoelectronics, silicon elastomers and unimolecular block copolymers. By the virtue of hydrogen bonding and dipole interactions, the 1,2,3-triazole moiety readily associates with the biological targets. Since, the 4-aryl-1H-1,2,3-triazoles are stable entities, they are chemically robust and very less reactive. In this regard, the addition of 4-aryl-1H-1,2,3-triazoles as nucleophiles to α,β-unsaturated carbonyls and nucleophilic substitution with the epoxides constitutes a powerful and challenging synthetic approach for the generation of disubstituted 1,2,3-triazoles. Herein, we have developed aza-Michael addition of 4-aryl-1H-1,2,3-triazoles to 2-cycloalken-1-ones in the presence of an organic base (DABCO) in acetonotrile solvent leading to the formation of disubstituted 1,2,3-triazoles. The reaction provides 1,4-disubstituted triazoles, 3-(4-aryl-1H-1,2,3-triazol-1-yl)cycloalkanones in major amount along with 1,5-disubstituted 1,2,3-triazoles, minor regioisomers with excellent combined chemical yields (upto99%). The nucleophilic behavior of 4-aryl-1H-1,2,3-triazoles was also tested in the ring opening of meso-epoxides in the presence of organic bases (DABCO/Et3N) in acetonotrile solvent furnishing the two regioisomers1,4- and 1,5-disubstituted 1,2,3-triazoles. Thus, the novelty of this methodology is synthesis of diversified disubstituted 1,2,3-triazoles under metal free condition.The results will be presented in detail.

Keywords: aza-Michael addition, cycloalkenones, epoxides, triazoles

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Authors: S. M. Kulkarni, D. S. Bormane, S. L. Nalbalwar

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The rapid development in the technology have dramatic impact on the medical health care field. Medical data base obtained with latest machines like CT Machine, MRI scanner requires large amount of memory storage and also it requires large bandwidth for transmission of data in telemedicine applications. Thus, there is need for video compression. As the database of medical images contain number of frames (slices), hence while coding of these images there is need of motion estimation. Motion estimation finds out movement of objects in an image sequence and gets motion vectors which represents estimated motion of object in the frame. In order to reduce temporal redundancy between successive frames of video sequence, motion compensation is preformed. In this paper three step search (TSS) block matching algorithm is implemented on different types of video sequences. It is shown that three step search algorithm produces better quality performance and less computational time compared with exhaustive full search algorithm.

Keywords: block matching, exhaustive search motion estimation, three step search, video compression

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Authors: İsmail Çeli̇k, Gülgün Ayhan-Kılcıgi̇l, Arzu Onay-Beşi̇kçi̇

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In this study, some 2-(2-phenyl/substitutedphenyl)- lH-benzo[d]'imidazol-l-yl)-N'-(alkylthiosemicarbazide were designed and prepared. Firstly, 2-phenyl/ suhstitutedphenyl-lH-Benzo[d]imidazole was prepared via oxidative condensation of o-phenylenediamine, benzaldehyde and sodium metabisulfite. Treatment of the benzimidazole compound with ethyl chloroacetate in KOH/DMSO gave the ester compound ethyl 2-(2-substitutedphenyl)-1H-benzo[d]imidazol-l-yl)acetate. Hydrazine hydrate and the ester in ethanol were refluxed for 4 h to give 2-(2-phenyl/substitutedphenyl)-1H-benzo[d]imidazol-l-yl)acetohydrazide. Thiosemicarbazides were obtained by condensing acyl hydrazide with the alkylisothiocyanate in ethanol. Following the structure elucidation, benzimidazole compounds were tested for their EGFR kinase inhibitory activities by using ADP-GloTM Kinase Assay.

Keywords: benzimidazole, EGFR kinase inhibitor, synthesis, thiosemicarbazide

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Authors: Wisam H. Benamer, Ehab A. Elfallah, Mohamed A. Elshaari, Farag A. Elshaari

Abstract:

A challenge for laboratories is to provide bacterial identification and antibiotic sensitivity results within a short time. Hence, advancement in the required technology is desirable to improve timing, accuracy and quality. Even with the current advances in methods used for both phenotypic and genotypic identification of bacteria the need is there to develop method(s) that enhance the outcome of bacteriology laboratories in accuracy and time. The hypothesis introduced here is based on the assumption that the chromosome of any bacteria contains unique sequences that can be used for its identification and typing. The outcome of a pilot study designed to test this hypothesis is reported in this manuscript. Methods: The complete chromosome sequences of several bacterial species were downloaded to use as search targets for unique sequences. Visual basic and SQL server (2014) were used to generate a complete set of 18-base long primers, a process started with reverse translation of randomly chosen 6 amino acids to limit the number of the generated primers. In addition, the software used to scan the downloaded chromosomes using the generated primers for similarities was designed, and the resulting hits were classified according to the number of similar chromosomal sequences, i.e., unique or otherwise. Results: All primers that had identical/similar sequences in the selected genome sequence(s) were classified according to the number of hits in the chromosomes search. Those that were identical to a single site on a single bacterial chromosome were referred to as unique. On the other hand, most generated primers sequences were identical to multiple sites on a single or multiple chromosomes. Following scanning, the generated primers were classified based on ability to differentiate between medically important bacterial and the initial results looks promising. Conclusion: A simple strategy that started by generating primers was introduced; the primers were used to screen bacterial genomes for match. Primer(s) that were uniquely identical to specific DNA sequence on a specific bacterial chromosome were selected. The identified unique sequence can be used in different molecular diagnostic techniques, possibly to identify bacteria. In addition, a single primer that can identify multiple sites in a single chromosome can be exploited for region or genome identification. Although genomes sequences draft of isolates of organism DNA enable high throughput primer design using alignment strategy, and this enhances diagnostic performance in comparison to traditional molecular assays. In this method the generated primers can be used to identify an organism before the draft sequence is completed. In addition, the generated primers can be used to build a bank for easy access of the primers that can be used to identify bacteria.

Keywords: bacteria chromosome, bacterial identification, sequence, primer generation

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Authors: Abdelaziz Ghrib, Samir Hattali, Mouloud Ghrib, Mohamed Lamine Aouissia, David Ruch

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In the present study, the solid solutions with a chemical composition of Zr0.8Y0.2-xLaxO2 (x=0, 0.1, 0.2) were synthesized via two routes, by hydrothermal method using NaOH as precipitating agent at 230°C for 15h and by the sol–gel process using citric acid as complexing agent. Compounds have been characterized by powder X-ray diffraction (XRD), Scanning Electron Microscopy (SEM), Thermo gravimetric Analysis (TGA) and Differential Thermal Analysis (DTA) techniques for appropriate characterization of the distinct thermal events occurring during synthesis. All the compounds crystallize in cubic fluorite structure, as indicated by X-ray diffraction studie. The microstructure of oxides synthesized by sol-gel showed porosity that increased with the lanthanum La3+ contents compared to hydrothermal method which gives a single crystal oxide.

Keywords: oxide, hydrothermal, rare earth, solubility, sol-gel, ternary mixture

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Authors: G. Sava, I. Popa, T. Sava, A. Ion, M. Ilie, C. Manailescu, A. Robu

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At the RoAMS laboratory in Bucharest we have looked for a head-to-head meeting between AMS radiocarbon dating and dendrochronology dating, aiming to point out and explain any differences or similarities that might appear between their output results. As a subject of this investigation, we have fixed our attention on a sequence of tree rings spanning on a period of 700 years, starting with 1000 AD. The samples were collected from the northern Romanian territory within Moldavia region, and were provided by the ‘Marin Dracea - National Institute for Research and Development in Forestry’. All the 23 single ring wood samples were radiocarbon dated using alpha-cellulose extraction, followed by graphitization in an AGE3 installation. A wiggle matching procedure was applied to reduce the radiocarbon uncertainties for the calibrated ages. The results showed a good agreement on 3 out of 4 wood cores, the age-shifting of one of the wood cores being interpreted as an uncertain dendrochronology matching, which was further corrected.

Keywords: wiggle matching, tree-ring radiocarbon dating, dendrochronology, AMS radiocarbon dating, radiocarbon dating in Romania

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Authors: Amgad Rezk, Heba Ahmed, Leslie Yeo

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Ultrasound presents a powerful means for material synthesis. In this talk, we showcase a new field demonstrating the possibility for harnessing sound energy sources at considerably higher frequencies (10 MHz to 1 GHz) compared to conventional ultrasound (kHz and up to ~2 MHz) for crystalising and manipulating a variety of nanoscale materials. At these frequencies, cavitation—which underpins most sonochemical processes—is largely absent, suggesting that altogether fundamentally different mechanisms are at dominant. Examples include the crystallization of highly oriented structures, quasi-2D metal-organic frameworks and nanocomposites. These fascinating examples reveal how the highly nonlinear electromechanical coupling associated with high-frequency surface vibration gives rise to molecular ordering and assembly on the nano and microscale.

Keywords: high-frequency acoustics, microfluidics, crystallisation, composite nanomaterials

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Authors: Pesaru Vigneshwar Reddy, Parvathaneni Pavan

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Green organic chemistry which is the latest and one of the most researched topics now-a- days has been in demand since 1990’s. Majority of the research in green organic chemistry chemicals are some of the important starting materials for greater number of major chemical industries. The production of organic chemicals has raw materials (or) reagents for other application is major sector of manufacturing polymers, pharmaceuticals, pesticides, paints, artificial fibers, food additives etc. organic synthesis on a large scale compound to the labratory scale, involves the use of energy, basic chemical ingredients from the petro chemical sectors, catalyst and after the end of the reaction, seperation, purification, storage, packing distribution etc. During these processes there are many problems of health and safety for workers in addition to the environmental problems caused there by use and deposition as waste. Green chemistry with its 12 principles would like to see changes in conventional way that were used for decades to make synthetic organic chemical and the use of less toxic starting materials. Green chemistry would like to increase the efficiency of synthetic methods, to use less toxic solvents, reduce the stage of synthetic routes and minimize waste as far as practically possible. In this way, organic synthesis will be part of the effort for sustainable development Green chemistry is also interested for research and alternatives innovations on many practical aspects of organic synthesis in the university and research labaratory of institutions. By changing the methodologies of organic synthesis, health and safety will be advanced in the small scale laboratory level but also will be extended to the industrial large scale production a process through new techniques. The three key developments in green chemistry include the use of super critical carbondioxide as green solvent, aqueous hydrogen peroxide as an oxidising agent and use of hydrogen in asymmetric synthesis. It also focuses on replacing traditional methods of heating with that of modern methods of heating like microwaves traditions, so that carbon foot print should reduces as far as possible. Another beneficiary of this green chemistry is that it will reduce environmental pollution through the use of less toxic reagents, minimizing of waste and more bio-degradable biproducts. In this present paper some of the basic principles, approaches, and early achievements of green chemistry has a branch of chemistry that studies the laws of passing of chemical reactions is also considered, with the summarization of green chemistry principles. A discussion about E-factor, old and new synthesis of ibuprofen, microwave techniques, and some of the recent advancements also considered.

Keywords: energy, e-factor, carbon foot print, micro-wave, sono-chemistry, advancement

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Authors: Tareg M. Elsunaki, Suleiman A. Arafa, Mohamed A. Abd-Alla

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New interesting thermal stable polyesters containing 1-methyl-4-piperidone moiety in the main chain have been synthesized. These polyesters were synthesized by interfacial polycondensation technique of 3,5-bis(4-hydroxybenzylidene)-1-methyl-4-piperidone (I) and 3,5-bis(4-hydroxy-3-methoxy benzyli-dene)-1-methyl-4-piperidone (II) with terphthaloyl, isophthaloyl, 4,4'-diphenic, adipoyl and sebacoyl dichlorides. The yield and the values of the reduced viscosity of the produced polyesters were found to be affected by the type of an organic phase. In order to characterize these polymers, the necessary model compounds (A), (B) were prepared from (I), (II) respectively and benzoyl chloride. The structure of monomers (I), (II), model compounds and resulting polyesters were confirmed by IR, elemental analysis and 1HNMR spectroscopy. The various characteristic of the resulting polymers including solubility, thermal properties, viscosity and X-ray analysis were also studied.

Keywords: synthesis, characterization, new polyesters, chemistry

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Authors: Jong-Ho Moon, Dong-Ho Lee, Hyunuk Kim, Young Cheol Park, Jong-Seop Lee, Jae-deok Jeon, Hyung-Keun Lee

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A novel membrane reactor process for DMC synthesis from carbon dioxide has been developing in Korea Institute of Energy Research. The scheme of direct synthesis of DMC from CO₂ and Methanol is 'CO₂ + 2MeOH ↔ DMC + H₂O'. Among them, reactants are CO₂ and MeOH, product is DMC, and byproduct is H₂O (water). According to Le Chatelier’s principle, removing byproduct (water) can shift the reaction equilibrium to the right (DMC production). The main purpose of this process is removing water during the reaction. For efficient in situ water removal (dehydration) and DMC separation, zeolite 4A membranes with very small pore diameter and hydrophilicity were introduced. In this study, pervaporation performances of binary and ternary DMC / methanol / water mixtures were evaluated.

Keywords: dimehtyl carbonate, methanol, water, zeolite membrane, pervaporation

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Authors: Elena Pozdnyakova

Abstract:

“Government Relations” is a field of knowledge presently taught at the majority of universities around the globe. English as the default language can become the language of teaching since the issues discussed are both global and national in character. However for this field of knowledge key concepts and their word representations in English don’t often coincide with those in other languages. International master’s degree students abroad as well as students, taught the course in English at their national universities, are exposed to difficulties, connected with correct conceptualizing of terminology of GR in British and American academic traditions. The study was carried out during the GR English language course elaboration (pilot research: 2013 -2015) at Moscow State Institute of Foreign Relations (University), Russian Federation. Within this period, English language instructors designed and elaborated the three-semester course of GR. Methodologically the course design was based on elaboration model with the special focus on conceptual elaboration sequence and theoretical elaboration sequence. The course designers faced difficulties in concept selection and theoretical elaboration sequence. To improve the results and eliminate the problems with concept selection, a new, corpus-based approach was worked out. The computer-based tool WordSmith 6.0 was used with the aim to build a model of key concept selection. The corpus of GR English texts consisted of 1 million words (the study corpus). The approach was based on measuring effect size, i.e. the percent difference of the frequency of a word in the study corpus when compared to that in the reference corpus. The results obtained proved significant improvement in the process of concept selection. The corpus-based model also facilitated theoretical elaboration of teaching materials.

Keywords: corpus-based study, English as the default language, key concepts, measuring effect size, model of key concept selection

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Authors: Hassina Harkat, Samiha Taybe, Salima Loucif, Valérie Beneteau, Patrick Pale

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Indole and its derivatives have attracted great interest because of their importance in the synthetic organic and medicinal chemistry. They are widely used as anti hypertension, anti tubercular, anticancer activity, antiviral, Alzheimer's disease, antioxidant properties, and free radical induced lipid peroxidation. Many drugs and natural products contain indole moiety, such as the vinca alkaloids, fungal metabolites and marine natural products. Generally applicable synthetic methods for indole moiety involve ring closure to form the pyrrole. Indole derivatives can also be accessed by further functionalization of the indole nucleus. Therefore we report a mild and efficient protocol for the synthesis of analogues of indole catalyzed via zeolithe USY doped with CuI under solvent-free conditions.

Keywords: indole, zeolithe, USY-CuI, heterogeneous catalysis

Procedia PDF Downloads 563