Search results for: molecular modelling

Authors: Colin O’Hare, Zili Zho, Thomas Sneddon

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The Australian superannuation system has received high praise for its participation rates and level of funding in retirement yet it is only 25 years old. In recent years, with increasing longevity and persistent lower rates of investment return, how adequate will the funds accumulated through a superannuation system be? In this paper we take Australia as a case study and build a stochastic model of accumulation and decummulation of funds and determine the expected number of years a fund may last an individual in retirement.

Keywords: component, mortality, stochastic models, superannuation

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Authors: Alma Khasenovna Zhakina, Arnt Oxana Vasilievna, Vasilets Evgeny Petrovich

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The aim of this project is to develop methods for obtaining new molecularly imprinted polymers from coal waste to study their structure, structural and morphological features and properties. Recently, the development of molecularly imprinted polymers has become one of the hot topics for researchers. Modern research indicates the broad prospects of rapidly developing molecular imprinting technologies for creating a new generation of sorption materials. The attractiveness of this area of research lies in the fact that the use of imprinted polymers is not limited to scientific research; they are already being introduced in the chemical, pharmaceutical and biotechnological industries, primarily at the stages of purification of the final product. For the use of molecularly imprinted polymers in the development of sorption material, their ability to selectively remove pollutants, including trace concentrations, is of fundamental importance, and the exceptional stability of polymeric materials under harsh conditions makes it possible to simplify the process of water purification as a whole. The scientific and technical effect is associated with the development of technologies for the production of new molecularly imprinted polymers, the establishment of optimal conditions for their production and the creation of effective imprinted sorbents on their basis for wastewater treatment from heavy metals. The social effect is due to the fact that the use of coal waste as a feedstock for the production of imprinted sorbents will make it possible in the future to create new industries with additional jobs and obtain competitive multi-purpose products. The economic and multiplier effect is associated with the low cost of the final product due to the involvement of local coal waste in the production, reduction of transport, customs and other costs.

Keywords: imprinted polymers, coal waste, polymerization, template, customized sorbents

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Authors: Doaa Hashad, Amany Elyamany, Perihan Salem

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Introduction: Hepatitis C virus infection (HCV) constitutes a serious dilemma that has an impact on the health of millions of Egyptians. Hepatitis C virus related hepatocellular carcinoma (HCV-HCC) is a crucial consequence of HCV that represents the third cause of cancer-related deaths worldwide. Aim of the study: assess the use of mitochondrial DNA (mtDNA) content as a non-invasive molecular biomarker in hepatitis c virus related hepatocellular carcinoma (HCV-HCC). Methods: A total of 135 participants were enrolled in the study. Volunteers were assigned to one of three groups equally; a group of HCV related cirrhosis (HCV-cirrhosis), a group of HCV-HCC and a control group of age- and sex- matched healthy volunteers with no evidence of liver disease. mtDNA was determined using a quantitative real-time PCR technique. Results: mtDNA content was lowest in HCV-HCC cases. No statistically significant difference was observed between the group of HCV-cirrhosis and the control group as regards mtDNA level. HCC patients with multi-centric hepatic lesions had significantly lower mtDNA content. On using receiver operating characteristic curve analysis, a cutoff of 34 was assigned for mtDNA content to distinguish between HCV-HCC and HCV-cirrhosis patients who are not yet complicated by malignancy. Lower mtDNA was associated with greater HCC risk on using healthy controls, HCV-cirrhosis, or combining both groups as a reference group. Conclusions: mtDNA content might constitute a non-invasive molecular biomarker that reflects tumor burden in HCV-HCC cases and could be used as a predictor of HCC risk in patients of HCV-cirrhosis. In addition, the non significant difference of mtDNA level between HCV-cirrhosis patients and healthy controls could eliminate the grey zone created by the use of AFP in some cirrhotic patients.

Keywords: DNA copy number, HCC, HCV, mitochondrial

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Authors: Mansur Hamma-Adama, Tahar Kouider

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Construction Industry has been evolving since the development of Building Information Modelling (BIM). This technological process is unstoppable; it is out to the market with remarkable case studies of solving the long industry’s history of fragmentation. This industry has been changing over time; United States has recorded the most significant development in construction digitalization, Australia, United Kingdom and some other developed nations are also amongst promoters of BIM process and its development. Recently, a developing country like China and Malaysia are keying into the industry’s digital shift, while very little move is seen in South Africa whose development is considered higher and perhaps leader in the digital transition amongst the African countries. To authors’ best knowledge, Nigerian construction industry has never engaged in BIM discussions hence has no attention at national level. Consequently, Nigeria has no “Noteworthy BIM publications.” Decision makers and key stakeholders need to be informed on the current trend of the industry’s development (BIM in specific) and the opportunities of adopting this digitalization trend in relation to the identified challenges. BIM concept can be traced mostly in Architectural practices than engineering practices in Nigeria. A superficial BIM practice is found to be at organisational level only and operating a model based - “BIM stage 1.” Research to adopting this innovation has received very little attention. This piece of work is literature review based, aimed at exploring BIM in Nigeria and its prospects. The exploration reveals limitations in the literature availability as to extensive research in the development of BIM in the country. Numerous challenges were noticed including building collapse, inefficiencies, cost overrun and late project delivery. BIM has potentials to overcome the above challenges and even beyond. Low level of BIM adoption with reasonable level of awareness is noticed. However, lack of policy and guideline as well as serious lack of experts in the field are amongst the major barriers to BIM adoption. The industry needs to embrace BIM to possibly compete with its global counterpart.

Keywords: adoption, BIM, CAD, construction industry, Nigeria, opportunities

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Authors: Said Echchakoui

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This paper aims to investigate how experiential value added by the salesperson mediates the relationship between perceived salesperson source characteristics and his performance. Structural equation modelling was employed to assess the proposed research model empirically. The empirical results revealed that the three dimensions of experiential value economic benefit, service productivity and enjoyable interaction, mediated the relationship between perceived salesperson source characteristics and his performance. Managerial implications are addressed.

Keywords: sales force, experiential added value, customer perceived value, performance

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Authors: Sukanya Devi Ramachandran, Vaishnavi Muralidharan, Kavya Chandrasekaran

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Polycaprolactone is polymer belonging to the polyester family that has noticeable characteristics of biodegradability and biocompatibility which is essential for medical applications. Polycaprolactone is produced by the ring opening polymerization of the monomer epsilon-Caprolactone (ε-CL) which is a closed ester, comprising of seven-membered ring. This process is normally catalysed by metallic components such as stannous octoate. It is difficult to remove the catalysts after the reaction, and they are also toxic to the human body. An alternate route of using enzymes as catalysts is being employed to reduce the toxicity. Lipase enzyme is a subclass of esterase that can easily attack the ester bonds of ε-CL. This research paper throws light on the extraction of lipase from germinating sunflower seeds and the activity of the biocatalyst in the polymerization of ε-CL. Germinating Sunflower seeds were crushed with fine sand in phosphate buffer of pH 6.5 into a fine paste which was centrifuged at 5000rpm for 10 minutes. The clear solution of the enzyme was tested for activity at various pH ranging from 5 to 7 and temperature ranging from 40oC to 70oC. The enzyme was active at pH6.0 and at 600C temperature. Polymerization of ε-CL was done using toluene as solvent with the catalysis of lipase enzyme, after which chloroform was added to terminate the reaction and was washed in cold methanol to obtain the polymer. The polymerization was done by varying the time from 72 hours to 6 days and tested for the molecular weight and the conversion of the monomer. The molecular weight obtained at 6 days is comparably higher. This method will be very effective, economical and eco-friendly to produce as the enzyme used can be regenerated as such at the end of the reaction and can be reused. The obtained polymers can be used for drug delivery and other medical applications.

Keywords: lipase, monomer, polycaprolactone, polymerization

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Authors: Haffaf Hafid

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Hypergraphs, after being used to model the structural organization of System of Sytems (SoS) at macroscopic level, has recent trends towards generalizing this powerful representation at different stages of complex system modelling. In this paper, we first describe different applications of hypergraph theory, and step by step, introduce multilevel modeling of SoS by means of integrating Constraint Programming Langages (CSP) dealing with engineering system reconfiguration strategy. As an application, we give an A.C.T Terminal controlled by a set of Intelligent Automated Vehicle.

Keywords: hypergraph model, structural analysis, bipartite graph, monitoring, system of systems, reconfiguration analysis, hypernetwork

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Authors: Evanka Madan, Madhu Puri, Dan Zilberstein, Rohini Muthuswami, Rentala Madhubala

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The extensive interaction between the host and pathogen metabolic networks decidedly shapes the outcome of infection. Utilization of arginine by the host and pathogen is critical for determining the outcome of pathogenic infection. Infections with L. donovani, an intracellular parasite, will lead to an extensive competition of arginine between the host and the parasite donovani infection. One of the major amino acid (AA) sensing signaling pathways in mammalian cells are the mammalian target of rapamycin complex I (mTORC1) pathway. mTORC1, as a sensor of nutrient, controls numerous metabolic pathways. Arginine is critical for mTORC1 activation. SLC38A9 is the arginine sensor for the mTORC1, being activated during arginine sufficiency. L. donovani transport arginine via a high-affinity transporter (LdAAP3) that is rapidly up-regulated by arginine deficiency response (ADR) in intracellular amastigotes. This study, to author’s best knowledge, investigates the interaction between two arginine sensing systems that act in the same compartment, the lysosome. One is important for macrophage defense, and the other is essential for pathogen virulence. We hypothesize that the latter modulates lysosome arginine to prevent host defense response. The work presented here identifies an upstream regulatory role of LdAAP3 in regulating the expression of SLC38A9-mTORC1 pathway, and consequently, their function in L. donovani infected THP-1 cells cultured in 0.1 mM and 1.5 mM arginine. It was found that in physiological levels of arginine (0.1 mM), infecting THP-1 with Leishmania leads to increased levels of SLC38A9 and mTORC1 via an increase in the expression of RagA. However, the reversal was observed with LdAAP3 mutants, reflecting the positive regulatory role of LdAAP3 on the host SLC38A9. At the molecular level, upon infection, mTORC1 and RagA were found to be activated at the surface of phagolysosomes which was found to form a complex with phagolysosomal localized SLC38A9. To reveal the relevance of SLC38A9 under physiological levels of arginine, endogenous SLC38A9 was depleted and a substantial reduction in the expression of host mTORC1, its downstream active substrate, p-P70S6K1 and parasite LdAAP3, was observed, thereby showing that silencing SLC38A9 suppresses ADR. In brief, to author’s best knowledge, these results reveal an upstream regulatory role of LdAAP3 in manipulating SLC38A9 arginine sensing in host macrophages. Our study indicates that intra-macrophage survival of L. donovani depends on the availability and transport of extracellular arginine. An understanding of the sensing pathway of both parasite and host will open a new perspective on the molecular mechanism of host-parasite interaction and consequently, as a treatment for Leishmaniasis.

Keywords: arginine sensing, LdAAP3, L. donovani, mTORC1, SLC38A9, THP-1

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Authors: Shuba Anastasiia, Kuchmenko Tatiana, Umarkhanov Ruslan

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The development of new sensitive coatings for sensors is one of the key directions in the development of sensor technologies. Recently, there has been a trend towards the creation of multicomponent coatings for sensors, which make it possible to increase the sensitivity, and specificity, and improve the performance properties of sensors. When analyzing samples with a complex matrix of biological origin, the inclusion of micelles of bioactive substances (amino and nucleic acids, peptides, proteins) in the composition of the sensor coating can also increase useful analytical information. The purpose of this work is to evaluate the analytical characteristics of composite coatings of piezoelectric quartz sensors based on medium-molecular viscous sorbents with incorporated micellar casein concentrate during the sorption of vapors of volatile organic compounds. The sorption properties of the coatings were studied by piezoelectric quartz microbalance. Macromolecular compounds (dicyclohexyl-18-crown-6, triton X-100, lanolin, micellar casein concentrate) were used as sorbents. Highly volatile organic compounds of various classes (alcohols, acids, aldehydes, esters) and water were selected as test substances. It has been established that composite coatings of sensors with the inclusion of micellar casein are more stable and selective to vapors of highly volatile compounds than to water vapors. The method and technique of forming a composite coating using molecular viscous sorbents do not affect the kinetic features of VOC sorption. When casein micelles are used, the features of kinetic sorption depend on the matrix of the coating.

Keywords: piezoquartz sensor, viscous sorbents, micellar casein, coating, volatile compounds

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Authors: Yuriy A. Knirel

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Enteric bacteria Escherichia coli is the predominant facultative anaerobe of the colonic flora, and some specific serotypes are associated with enteritis, hemorrhagic colitis, and hemolytic uremic syndrome. Shigella spp. are human pathogens that cause diarrhea and bacillary dysentery (shigellosis). They are in effect E. coli with a specific mode of pathogenicity. Strains of Salmonella enterica are responsible for a food-borne infection (salmonellosis), and specific serotypes cause typhoid fever and paratyphoid fever. All these bacteria are closely related in respect to structure and genetics of the lipopolysaccharide, including the O-polysaccharide part (O‑antigen). Being exposed to the bacterial cell surface, the O antigen is subject to intense selection by the host immune system and bacteriophages giving rise to diverse O‑antigen forms and providing the basis for typing of bacteria. The O-antigen forms of many bacteria are unique, but some are structurally and genetically related to others. The sequenced O-antigen gene clusters between conserved galF and gnd genes were analyzed taking into account the O-antigen structures established by us and others for all S. enterica and Shigella and most E. coli O-serogroups. Multiple genetic mechanisms of diversification of the O-antigen forms, such as lateral gene transfer and mutations, were elucidated and are summarized in the present paper. They include acquisition or inactivation of genes for sugar synthesis or transfer or recombination of O-antigen gene clusters or their parts. The data obtained contribute to our understanding of the origins of the O‑antigen diversity, shed light on molecular evolutionary relationships between the O-antigens of enteric bacteria, and open a way for studies of the role of gene polymorphism in pathogenicity.

Keywords: enteric bacteria, O-antigen gene cluster, polysaccharide biosynthesis, polysaccharide structure

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Authors: Rajaa Filali, Mohamed Bouhdadi

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This paper presents an incremental formal development of the Wireless Transaction Protocol (WTP) in Event-B. WTP is part of the Wireless Application Protocol (WAP) architectures and provides a reliable request-response service. To model and verify the protocol, we use the formal technique Event-B which provides an accessible and rigorous development method. This interaction between modelling and proving reduces the complexity and helps to eliminate misunderstandings, inconsistencies, and specification gaps. As result, verification of WTP allows us to find some deficiencies in the current specification.

Keywords: event-B, wireless transaction protocol, proof obligation, refinement, Rodin, ProB

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Authors: Timothy Kayode Samson, Adedoyin Isola Lawal

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The past five years have shown a sharp increase in public interest in the crypto market, with its market capitalization growing from $100 billion in June 2017 to $2158.42 billion on April 5, 2022. Despite the outrageous nature of the volatility of cryptocurrencies, the use of skewed error innovation distributions in modelling the volatility behaviour of these digital currencies has not been given much research attention. Hence, this study models the volatility of 5 largest cryptocurrencies by market capitalization (Bitcoin, Ethereum, Tether, Binance coin, and USD Coin) using four variants of GARCH models (GJR-GARCH, sGARCH, EGARCH, and APARCH) estimated using three skewed error innovation distributions (skewed normal, skewed student- t and skewed generalized error innovation distributions). Daily closing prices of these currencies were obtained from Yahoo Finance website. Finding reveals that the Binance coin reported higher mean returns compared to other digital currencies, while the skewness indicates that the Binance coin, Tether, and USD coin increased more than they decreased in values within the period of study. For both Bitcoin and Ethereum, negative skewness was obtained, meaning that within the period of study, the returns of these currencies decreased more than they increased in value. Returns from these cryptocurrencies were found to be stationary but not normality distributed with evidence of the ARCH effect. The skewness parameters in all best forecasting models were all significant (p<.05), justifying of use of skewed error innovation distributions with a fatter tail than normal, Student-t, and generalized error innovation distributions. For Binance coin, EGARCH-sstd outperformed other volatility models, while for Bitcoin, Ethereum, Tether, and USD coin, the best forecasting models were EGARCH-sstd, APARCH-sstd, EGARCH-sged, and GJR-GARCH-sstd, respectively. This suggests the superiority of skewed Student t- distribution and skewed generalized error distribution over the skewed normal distribution.

Keywords: skewed generalized error distribution, skewed normal distribution, skewed student t- distribution, APARCH, EGARCH, sGARCH, GJR-GARCH

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Authors: Lukas Ded

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Studying the tissue structure and histogenesis in the natural, 3D context is challenging but highly beneficial process. Contrary to classical approach of the physical tissue sectioning and subsequent imaging, it enables to study the relationships of individual cellular and histological structures in their native context. Recent developments in the tissue clearing approaches and microscopic volume imaging/data processing enable the application of these methods also in the areas of developmental and reproductive biology. Here, using the CLARITY tissue procedure and 3D confocal volume imaging we optimized the protocol for clearing, staining and imaging of the mice seminiferous tubules isolated from the testes without cardiac perfusion procedure. Our approach enables the high magnification and fine resolution axial imaging of the whole diameter of the seminiferous tubules with possible unlimited lateral length imaging. Hence, the large continuous pieces of the seminiferous tubule can be scanned and digitally reconstructed for the study of the single tubule seminiferous stages using nuclear dyes. Furthermore, the application of the antibodies and various molecular dyes can be used for molecular labeling of individual cellular and subcellular structures and resulting 3D images can highly increase our understanding of the spatiotemporal aspects of the seminiferous tubules development and sperm ultrastructure formation. Finally, our newly developed algorithms for 3D data processing enable the massive parallel processing of the large amount of individual cell and tissue fluorescent signatures and building the robust spermatogenic models under physiological and pathological conditions.

Keywords: CLARITY, spermatogenesis, testis, tissue clearing, volume imaging

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Authors: Wen-Jay Lee, Kuo-Ning Chiang

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The graphene binding with silicon substrate has apparently Schottky barriers property, which can be used in the application of solar cell and light source. Because graphene has only one atom layer, the atomistic structure of graphene binding with the silicon surface plays an important role to affect the properties of graphene. In this work, temperature effect on the morphology of graphene sheet attached on different crystal planes of silicon substrates are investigated by Molecular dynamics (MD) (LAMMPS, developed by Sandia National Laboratories). The results show that the covered graphene sheet would cause the structural deformation of the surface Si atoms of stubtrate. To achieve a stable state in the binding process, the surface Si atoms would adjust their position and fit the honeycomb structure of graphene after the graphene attaches to the Si surface. The height contour of graphene on different plane of silicon surfaces presents different pattern, leading the local residual stress at the interface. Due to the high density of dangling bond on the Si (111)7x7 surface, the surface of Si(111)7x7 is not matching with the graphene so well in contrast with Si(100)2x1and Si(111)2x1. Si(111)7x7 is found that only partial silicon adatoms are rearranged on surface after the attachment when the temperature is lower than 200K, As the temperature gradually increases, the deformation of surface structure becomes significant, as well as the residue stress. With increasing temperature till the 815K, the graphene sheet begins to destroy and mixes with the silicon atoms. For the Si(100)2x1 and Si(111)2x1, the silicon surface structure keep its structural arrangement with a higher temperature. With increasing temperature, the residual stress gradually decrease till a critical temperatures. When the temperature is higher than the critical temperature, the residual stress gradually increases and the structural deformation is found on the surface of the Si substrates.

Keywords: molecular dynamics, graphene, silicon, Schottky barriers, interface

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Authors: Sara Przetocka, Krzysztof Żak, Grzegorz Dubin, Tadeusz Holak

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Toll-like receptors (TLRs) play central role in the innate immune response and inflammation by recognizing pathogen-associated molecular patterns (PAMPs). A fundamental basis of TLR signalling is dependent upon the recruitment and association of adaptor molecules that contain the structurally conserved Toll/interleukin-1 receptor (TIR) domain. MyD88 (myeloid differentiation primary response gene 88) is the universal adaptor for TLRs and cooperates with Mal (MyD88 adapter-like protein, also known as TIRAP) in TLR4 response which is predominantly used in inflammation, host defence and carcinogenesis. Up to date two possible models of MyD88, Mal and TLR4 interactions have been proposed. The aim of our studies is to confirm or abolish presented models and accomplish the full structural characterisation of TIR domains interaction. Using molecular cloning methods we obtained several construct of MyD88 and Mal TIR domain with GST or 6xHis tag. Gel filtration method as well as pull-down analysis confirmed that recombinant TIR domains from MyD88 and Mal are binding in complexes. To examine whether obtained complexes are homo- or heterodimers we carried out cross-linking reaction of TIR domains with BS3 compound combined with mass spectrometry. To investigate which amino acid residues are involved in this interaction the NMR titration experiments were performed. 15N MyD88-TIR solution was complemented with non-labelled Mal-TIR. The results undoubtedly indicate that MyD88-TIR interact with Mal-TIR. Moreover 2D spectra demonstrated that simultaneously Mal-TIR self-dimerization occurs which is necessary to create proper scaffold for Mal-TIR and MyD88-TIR interaction. Final step of this study will be crystallization of MyD88 and Mal TIR domains complex. This crystal structure and characterisation of its interface will have an impact in understanding the TLR signalling pathway and possibly will be used in development of new anti-cancer treatment.

Keywords: cancer, MyD88, TIR domains, Toll-like receptors

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Authors: Taek Hwan Lee, Moon Ho Do, Lalita Subedi, Young Un Park, Sun Yeou Kim

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Natural and artificial toxic substances namely neurotoxins induce the bitter effect in the nervous system termed as neurotoxicity. It can modulate the normal functioning of the nervous system either hyperactivate it or damage homeostasis of neuronal system. Neurotoxins induced toxicity ultimately kills the neuron. The present study investigated the neuroprotective effects of germinated Dolichos lablab on 6-hydroxydopamine (6-OHDA)-induced neurotoxicity using SH-SY5Y neuroblastoma cells. Germination is a process of plant growth from a seed. Sprouting of a seedling from a seed induced many molecular changes in the seed in order to prepare it for further growth. Because of these molecular and chemical changes, the neuroprotective effect of Dolichos lablab is higher in the germinated form than in the normal condition. SH-SY5Y cells were treated with Dolichos lablab extract (50, 100 g/ml) followed by 6-OHDA (25M) induced toxicity. Cell Viability was measured to check the cell survival against 6-OHDA induced toxicity using MTT assay. Dolichos lablab showed a neuroprotective effect against 6-OHDA induced neuronal cell death in neuroblastoma cell at a higher concentration of 100g/ml however the effect is much better even at the lower concentration after germination 50g/ml. Cell survival was increased dramatically after 15 h of germination and increased with time of germination in concentration dependent manner. Trigonelline as a representative compound was validated in germinated Dolichos lablab by HPLC analysis that might enhance the neuroprotective effect of Dolichos lablab. This result suggests that Dolichos lablab possess neuroprotective effect in neuroblastoma cells against 6-OHDA however its activity was more potent in the germinated form.

Keywords: dolichos lablab, germination, neuroprotection, trigonelline

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Authors: Vagolu S. Krishna, Shan Zheng, Estharla M. Rekha, Luke W. Guddat, Dharmarajan Sriram

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Tuberculosis (TB) remains a major threat to human health. This due to the fact that current drug treatments are less than optimal as well as the rising occurrence of multi drug-resistant and extensively drug-resistant strains of the etiological agent, Mycobacterium tuberculosis (Mt). Given the wide-spread significance of this disease, we have undertaken a design and evaluation program to discover new anti-TB drug leads. Here, our attention is focused on ketol-acid reductoisomerase (KARI), the second enzyme in the branched-chain amino acid biosynthesis pathway. Importantly, this enzyme is present in bacteria but not in humans, making it an attractive proposition for drug discovery. In the present work, we used high-throughput virtual screening to identify seventeen potential inhibitors of KARI using the Birla Institute of Technology and Science in-house database. Compounds were selected based on high docking scores, which were assigned as the result of favourable interactions between the compound and the active site of KARI. The Ki values for two leads, compounds 14 and 16 are 3.71 and 3.06 µM, respectively for Mt KARI. To assess the mode of binding, 100 ns molecular dynamics simulations for these two compounds in association with Mt KARI were performed and showed that the complex was stable with an average RMSD of less than 2.5 Å for all atoms. Compound 16 showed an MIC of 2.06 ± 0.91 µM and a 1.9 fold logarithmic reduction in the growth of Mt in an infected macrophage model. The two compounds exhibited low toxicity against murine macrophage RAW 264.7 cell lines. Thus, both compounds are promising candidates for development as an anti-TB drug leads.

Keywords: ketol-acid reductoisomerase, macrophage, molecular docking and dynamics, tuberculosis

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Authors: Leelavinothan Pari , Ayyasamy Rathinam

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Diabetes mellitus (DM) is a major and growing public health problem throughout the world. Pterocarpus marsupium (Roxb.) (Family: Fabaceae) is widely used as a traditional medicine to treat various diseases including diabetes. However, the molecular mechanism of Pterocarpus marsupium has not been investigated so far. Two fractions (2.5% and 5%) of extract from the medicinal plant, Pterocarpus marsupium (PME) were conducted in a dose dependent manner in streptozotocin (45 mg/kg b.w.) induced type 2 diabetic rats. Each fraction of PME was administered to diabetic rats intragastrically at a dose of 50, 100 and 200 mg/kg b.w for 45 days. The effective dose 200 mg/kg b.w of 5% fraction was more pronounced in reducing the levels of blood glucose (95.65 mg/dL) and glycosylated hemoglobin (HbA1c) (0.41 mg/g Hb), and increasing the plasma insulin (16.20 µU/mL) level. Moreover, PME (200 mg/kg b.w) significantly ameliorated lipid peroxidation products (thiobarbituric reactive substances, lipid hydroperoxides) enzymatic (superoxide dismutase, catalase and glutathione peroxidase) and non-enzymatic antioxidants (Vitamin C, Vitamin E and reduced glutathione) levels. The altered activities of the key enzymes of lipid metabolism along with the lipid profile in diabetic rats were significantly reverted to near normal levels by the administration of PME 5% 200 mg/kg b.w fraction. PME (200 mg/kg b.w) has the ability to reduce the inflammatory cytokines, such as TNF-α, IL-6 mRNA, as well as protein expression and apoptotic marker, such as caspase-3 enzyme in diabetic hepatic tissue. The above biochemical findings were also supported by histological studies such as improvement in pancreas and liver. Pterocarpus marsupium could effectively reduce the hyperglycemia, oxidative-stress, inflammation and hyperlipedimea in diabetic rats; hence it could be a useful drug in the management of diabetes without any side effects.

Keywords: diabetes mellitus, streptozotocin, Pterocarpus marsupium, lipid peroxidation, Antioxidants, inflammatory cytokines

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Authors: Alexandra K. Diem, Giles Richardson, Roxana O. Carare, Neil W. Bressloff

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Alzheimer's disease (AD) is the most common form of dementia and although it has been researched for over 100 years, there is still no cure or preventive medication. Its onset and progression is closely related to the accumulation of the neuronal metabolite Aβ. This raises the question of how metabolites and waste products are eliminated from the brain as the brain does not have a traditional lymphatic system. In recent years the rapid uptake of Aβ into cerebral artery walls and its clearance along those arteries towards the lymph nodes in the neck has been suggested and confirmed in mice studies, which has led to the hypothesis that interstitial fluid (ISF), in the basement membranes in the walls of cerebral arteries, provides the pathways for the lymphatic drainage of Aβ. This mechanism, however, requires a net reverse flow of ISF inside the blood vessel wall compared to the blood flow and the driving forces for such a mechanism remain unknown. While possible driving mechanisms have been studied using mathematical models in the past, a mechanism for net reverse flow has not been discovered yet. Here, we aim to address the question of the driving force of this reverse lymphatic drainage of Aβ (also called perivascular drainage) by using multi-scale numerical and analytical modelling. The numerical simulation software COMSOL Multiphysics 4.4 is used to develop a fluid-structure interaction model of a cerebral artery, which models blood flow and displacements in the artery wall due to blood pressure changes. An analytical model of a layer of basement membrane inside the wall governs the flow of ISF and, therefore, solute drainage based on the pressure changes and wall displacements obtained from the cerebral artery model. The findings suggest that an active role in facilitating a reverse flow is played by the components of the basement membrane and that stiffening of the artery wall during age is a major risk factor for the impairment of brain lymphatics. Additionally, our model supports the hypothesis of a close association between cerebrovascular diseases and the failure of perivascular drainage.

Keywords: Alzheimer's disease, artery wall mechanics, cerebral blood flow, cerebral lymphatics

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Authors: Fiffy Hanisdah Saikim, Bruce Prideaux

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One of the aims of wildlife tourism is to educate visitors about the threats facing wildlife, in general, and the actions needed to protect the environment and maintain biodiversity. Annually, millions of tourists visit natural areas and zoos primarily to view flagship species such as rhinos and elephants. Venues rely on the inherent charisma of these species to increase visitation and anchor conservation efforts. Expected visitor outcomes from the use of flagships include raised levels of awareness and pro-conservation behaviors. However, the role of flagships in wildlife tourism has been criticized for not delivering conservation benefits for species of interest or biodiversity and producing negative site impacts. Furthermore, little is known about how the connection to a species influences conservation behaviors. This paper addresses this gap in knowledge by extending previous work exploring wildlife tourism to include the emotional connection formed with wildlife species and pro-conservation behaviors for individual species and biodiversity. This paper represents a substantial contribution to the field because (a) it incorporates the role of the experience in understanding how tourists connect with a species and how this connection influences pro-conservation behaviors; and (b) is the first attempt to operationalize Conservation Caring as a measure of tourists’ connection with a species. Existing studies have investigated how specific elements, such as interpretation or species’ morphology may influence programmatic goals or awareness. However, awareness is a poor measure of an emotional connection with an animal. Furthermore, there has not been work done to address the holistic nature of the wildlife viewing experience, and its subsequent influence on behaviors. Results based on the structural equation modelling, support the validity of Conservation Caring as a factor; the ability of wildlife tourism to influence Conservation Caring; and that this connection is a strong predictor of conservation awareness behaviors. These findings suggest wildlife tourism can deliver conservation outcomes. The studies in this paper also provide a valuable framework for structuring wildlife tourism experiences to align with flagship related conservation outcomes, and exploring a wider assemblage of species as potential flagships.

Keywords: wildlife tourism, conservation caring, conservation awareness, structural equation modelling

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Authors: Varsha Shinde, Belle Damodara Shenoy

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Tarballs are crude oil remnants found in oceans after long term weathering process and are a global concern since several decades as potential marine pollutant. Being complicated in structure microbial remediation of tarballs in natural environment is a slow process. They are rich in high molecular weight alkanes and poly aromatic hydrocarbons which are resistant to microbial attack and other environmental factors, therefore remain in environment for long time. However, it has been found that many bacteria and fungi inhabit on tarballs for nutrients and shelter. Many of them are supposed to be oil degraders, while others are supposed to be getting benefited by byproducts formed during hydrocarbon metabolism. Thus tarballs are forming special interesting ecological niche of microbes. This work aimed to study diversity of bacteria and fungi from tarballs and to see their potential application in crude oil degradation. The samples of tarballs were collected from Betul beach of south Goa (India). Different methods were used to isolate culturable fraction of bacteria and fungi from it. Those were sequenced for 16S rRNA gene and ITS for molecular level identification. The 16S rRNA gene sequence analysis revealed the presence of 13 bacterial genera/clades (Alcanivorax, Brevibacterium, Bacillus, Cellulomonas, Enterobacter, Klebsiella, Marinobacter, Nitratireductor, Pantoea, Pseudomonas, Pseudoxanthomonas, Tistrella and Vibrio), while the ITS sequence analysis placed the fungi in 8 diverse genera/ clades (Aspergillus, Byssochlamys, Monascus, Paecilomyces, Penicillium, Scytalidium/ Xylogone, Talaromyces and Trichoderma). All bacterial isolates were screened for oil degradation capacity. Potential strains were subjected to crude oil degradation experiment for quantification. Results were analyzed by GC-MS-MS.

Keywords: bacteria, biodegradation, crude oil, diversity, fungi, tarballs

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Authors: Hillary Mwongyera

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The Semliki basin has become a frontier for petroleum exploration in recent years. Exploration efforts have resulted into extensive seismic data acquisition and drilling of three wells namely; Turaco 1, Turaco 2 and Turaco 3. A petrophysical analysis of the Turaco 1 well was carried out to identify two reservoir zones on which AVO modeling was performed. A combination of seismic modeling and rock physics modeling was applied during reservoir characterization and monitoring to determine variations of seismic responses with amplitude characteristics. AVO intercept gradient analysis applied on AVO synthetic CDP gathers classified AVO anomalies associated with both reservoir zones as Class 1 AVO anomalies. Fluid replacement modeling was carried out on both reservoir zones using homogeneous mixing and patchy saturation patterns to determine effects of fluid substitution on rock property interactions. For both homogeneous mixing and saturation patterns, density (ρ) showed an increasing trend with increasing brine substitution while Shear wave velocity (Vs) decreased with increasing brine substitution. A study of compressional wave velocity (Vp) with increasing brine substitution for both homogeneous mixing and patchy saturation gave quite interesting results. During patchy saturation, Vp increased with increasing brine substitution. During homogeneous mixing however, Vp showed a slightly decreasing trend with increasing brine substitution but increased tremendously towards and at full brine saturation. A sensitivity analysis carried out showed that density was a very sensitive rock property responding to brine saturation except at full brine saturation during homogeneous mixing where Vp showed greater sensitivity with brine saturation. Rock physics modeling was performed to predict diagnostics of reservoir quality using an inverse deterministic approach which showed low shale content and a high degree of shale stiffness within reservoir zones.

Keywords: Amplitude Versus Offset (AVO), fluid replacement modelling, reservoir characterization, AVO attributes, rock physics modelling, reservoir monitoring

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Authors: Dinuka Herath, Shelley Harrington

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This paper prompts debate about whether disorganization can be positioned as a mechanism that facilitates the creation and enactment of important dynamic capabilities within an organization. This particular article is a conceptual exploration of the link between dynamic capabilities and disorganization and presents the case for agent-based modelling as a viable methodological tool which can be used to explore this link. Dynamic capabilities are those capabilities that an organization needs to sustain competitive advantage in complex environments. Disorganization is the process of breaking down restrictive organizational structures and routines that commonly reside in organizations in order to increase organizational performance. In the 20th century, disorganization was largely viewed as an undesirable phenomenon within an organization. However, the concept of disorganization has been revitalized and garnered research interest in the recent years due to studies which demonstrate some of the advantages of disorganization to an organization. Furthermore, recent Agent-based simulation studies have shown the capability of disorganization to be managed and argue for disorganization to be viewed as an enabler of organizational productivity. Given the natural state of disorganization and resulting fear this can create, this paper argues that instead of trying to ‘correct’ disorganization, it should be actively encouraged to have functional purpose. The study of dynamic capabilities emerged as a result of heightened dynamism and consequentially the very nature of dynamism denotes a level of fluidity and flexibility, something which this paper argues many organizations do not truly foster due to a constrained commitment to organization and order. We argue in this paper that the very state of disorganization is a state that should be encouraged to develop dynamic capabilities needed to not only deal with the complexities of the modern business environment but also to sustain competitive success. The significance of this paper stems from the fact that both dynamic capabilities and disorganization are two concepts that are gaining prominence in their respective academic genres. Despite the attention each concept has received individually, no conceptual link has been established to depict how they actually interact with each other. We argue that the link between these two concepts present a novel way of looking at organizational performance. By doing so, we explore the potential of these two concepts working in tandem in order to increase organizational productivity which has significant implications for both academics and practitioners alike.

Keywords: agent-based modelling, disorganization, dynamic capabilities, performance

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Authors: Benmoussa Dennai, H. Benslimane, A. Helmaoui

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Photo voltaic conversion is the direct conversion of electromagnetic energy into electrical energy continuously. This electromagnetic energy is the most solar radiation. In this work we performed a computer modelling using AMPS 1D optimization of hetero-junction solar cells GaInP/GaAs configuration for p/ n. We studied the influence of the thickness the base layer in the cell offers on the open circuit voltage, the short circuit current and efficiency.

Keywords: optimization, photovoltaic cell, GaInP / GaAs AMPS-1D, hetetro-junction

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Authors: Francesca Fermi, Paola Astegiano, Angelo Martino, Stephanie Heitel, Michael Krail

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In order to achieve the targeted emission reductions for the decarbonisation of the European economy by 2050, fundamental contributions are required from both energy and transport sectors. The objective of this paper is to analyse the impacts of a largescale diffusion of e-vehicles, either battery-based or fuel cells, together with the implementation of transport policies aiming at decreasing the use of motorised private modes in order to achieve greenhouse gas emission reduction goals, in the context of a future high share of renewable energy. The analysis of the impacts and challenges of future scenarios on transport sector is performed with the ASTRA (ASsessment of TRAnsport Strategies) model. ASTRA is a strategic system-dynamic model at European scale (EU28 countries, Switzerland and Norway), consisting of different sub-modules related to specific aspects: the transport system (e.g. passenger trips, tonnes moved), the vehicle fleet (composition and evolution of technologies), the demographic system, the economic system, the environmental system (energy consumption, emissions). A key feature of ASTRA is that the modules are linked together: changes in one system are transmitted to other systems and can feed-back to the original source of variation. Thanks to its multidimensional structure, ASTRA is capable to simulate a wide range of impacts stemming from the application of transport policy measures: the model addresses direct impacts as well as second-level and third-level impacts. The simulation of the different scenarios is performed within the REFLEX project, where the ASTRA model is employed in combination with several energy models in a comprehensive Modelling System. From the transport sector perspective, some of the impacts are driven by the trend of electricity price estimated from the energy modelling system. Nevertheless, the major drivers to a low carbon transport sector are policies related to increased fuel efficiency of conventional drivetrain technologies, improvement of demand management (e.g. increase of public transport and car sharing services/usage) and diffusion of environmentally friendly vehicles (e.g. electric vehicles). The final modelling results of the REFLEX project will be available from October 2018. The analysis of the impacts and challenges of future scenarios is performed in terms of transport, environmental and social indicators. The diffusion of e-vehicles produces a consistent reduction of future greenhouse gas emissions, although the decarbonisation target can be achieved only with the contribution of complementary transport policies on demand management and supporting the deployment of low-emission alternative energy for non-road transport modes. The paper explores the implications through time of transport policy measures on mobility and environment, underlying to what extent they can contribute to a decarbonisation of the transport sector. Acknowledgements: The results refer to the REFLEX project which has received grants from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 691685.

Keywords: decarbonisation, greenhouse gas emissions, e-mobility, transport policies, energy

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Authors: Dong Zhao

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Even though the recent claim of room temperature superconductivity by LK-99 was confirmed an unsuccessful attempt, this work reawakened people’s century striving to get applicable superconductors with Tc of room temperature or higher and under ambient pressure. One of the efforts was focusing on exploring the thorium salts. This is because certain thorium compounds revealed an unusual property of having both high electrical conductivity and diamagnetism or the so-called “coexistence of high electrical conductivity and diamagnetism.” It is well known that this property of the coexistence of high electrical conductivity and diamagnetism is held by superconductors because of the electron pairings. Consequently, the likelihood for these thorium compounds to have superconducting properties becomes great. However, as a surprise, these thorium salts possess this property at room temperature and atmosphere pressure. This gives rise to solid evidence for these thorium compounds to be room-temperature superconductors without a need for external pressure. Among these thorium compound superconductors claimed in that work, thorium di-iodide (ThI₂) is a unique one and has received comprehensive discussion. ThI₂ was synthesized and structurally analyzed by the single crystal diffraction method in the 1960s. Its special property of coexistence of high electrical conductivity and diamagnetism was revealed. Because of this unique property, a special molecular configuration was sketched. Except for an ordinary oxidation of +2 for the thorium cation, the thorium’s oxidation state in ThI₂ is +4. According to the experimental results, ThI₂‘s actual molecular configuration was determined as an unusual one of [Th4+(e-)2](I-)2. This means that the ThI₂ salt’s cation is composed of a [Th4+(e-)2]2+ cation core. In other words, the cation of ThI₂ is constructed by combining an oxidation state +4 of the thorium atom and a pair of electrons or an electron lone pair located on the thorium atom. This combination of the thorium atom and the electron lone pair leads to an oxidation state +2 for the [Th4+(e-)2]2+ cation core. This special construction of the thorium cation is very distinctive, which is believed to be the factor that grants ThI₂ the room temperature superconductivity. Actually, the key for ThI₂ to become a room-temperature superconductor is this characteristic electron lone pair residing on the thorium atom along with the formation of a network constructed by the thorium atoms. This network specializes in a way that allows the electron lone pairs to hop over it and, thus, to generate the supercurrent. This work will discuss, in detail, the special electrical and magnetic properties of ThI₂ as well as its structural features at ambient conditions. The exploration of how the electron pairing in combination with the structurally specialized network works together to bring ThI₂ into a superconducting state. From the experimental results, strong evidence has definitely pointed out that the ThI₂ should be a superconductor, at least at room temperature and under atmosphere pressure.

Keywords: co-existence of high electrical conductivity and diamagnetism, electron lone pair, room temperature superconductor, special molecular configuration of thorium di-iodide ThI₂

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Authors: Monika Kallubai, Shreya Dubey, Rajagopal Subramanyam

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Our study is all about the biological interactions of synthesized 5β-dihydrocortisol (Dhc) and 5β-dihydrocortisol acetate (DhcA) molecules with carrier protein Human Serum Albumin (HSA). The cytotoxic study was performed on breast cancer cell line (MCF-7) normal human embryonic kidney cell line (HEK293), the IC50 values for MCF-7 cells were 28 and 25 µM, respectively, whereas no toxicity in terms of cell viability was observed with HEK293 cell line. The further experiment proved that Dhc and DhcA induced 35.6% and 37.7% early apoptotic cells and 2.5%, 2.9% late apoptotic cells respectively. Morphological observation of cell death through TUNEL assay revealed that Dhc and DhcA induced apoptosis in MCF-7 cells. The complexes of HSA–Dhc and HSA–DhcA were observed as static quenching, and the binding constants (K) was 4.7±0.03×104 M-1 and 3.9±0.05×104 M-1, and their binding free energies were found to be -6.4 and -6.16 kcal/mol, respectively. The displacement studies confirmed that lidocaine 1.4±0.05×104 M-1 replaced Dhc, and phenylbutazone 1.5±0.05×104 M-1 replaced by DhcA, which explains domain I and domain II are the binding sites for Dhc and DhcA. Further, CD results revealed that the secondary structure of HSA was altered in the presence of Dhc and DhcA. Furthermore, the atomic force microscopy and transmission electron microscopy showed that the dimensions like height and molecular sizes of the HSA–Dhc and HSA–DhcA complex were larger compared to HSA alone. Detailed analysis through molecular dynamics simulations also supported the greater stability of HSA–Dhc and HSA–DhcA complexes, and root-mean-square-fluctuation interpreted the binding site of Dhc as domain IB and domain IIA for DhcA. This information is valuable for the further development of steroid derivatives with improved pharmacological significance as novel anti-cancer drugs.

Keywords: apoptosis, dihydrocortisol, fluorescence quenching, protein conformations

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Authors: Y. Kavanagh, N. O'Hara, R. Palmer, P. Lowe, D. Rafferty

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Physical Physics is a physics education methodology for games programfmes that integrates physical activity with movement tracking and modelling. It significantly enhances the learning experience and it is effective in illustrating how physics is core in games design and programming, while allowing students to be active participants and take ownership of the learning process. It has been successfully piloted with undergraduate students studying Games Development.

Keywords: activity, enhanced learning, game development, physics

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Authors: Jiajia Yao, GuanLin Wu, Fang liu, JunShuai Xue, JinCheng Zhang, Yue Hao

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Due to its outstanding material properties like high thermal conductivity and ultra-wide bandgap, Aluminum nitride (AlN) has the promising potential to provide high breakdown voltage and high output power among III-nitrides for various applications in electronics and optoelectronics. This work presents material growth and characterization of strained channel Aluminum nitride/Gallium nitride (AlN/GaN) heterostructures grown by plasma-assisted molecular beam epitaxy (PA-MBE) on AlN-on-sapphire templates. To improve the crystal quality and manifest the ability of the PA-MBE approach, a thick AlN buffer with a thickness of 180 nm is first grown on AlN template, which acts as a back-barrier to enhance the breakdown characteristic and isolates the leakage path existing in the interface between AlN epilayer and AlN template, as well as improve the heat dissipation. The grown AlN buffer features a root-mean-square roughness of 0.2 nm over a scanned area of 2×2 µm2 measured by atomic force microscopy (AFM), and exhibits full-width at half-maximum of 95 and 407 arcsec for the (002) and (102) plane the X-ray rocking curve, respectively, tested by high resolution x-ray diffraction (HR-XRD). With a thin and strained GaN channel, the electron mobility of 294 cm2 /Vs. with a carrier concentration of 2.82×1013 cm-2 at room temperature is achieved in AlN/GaN double-channel heterostructures, and the depletion capacitance is as low as 14 pF resolved by the capacitance-voltage, which indicates the promising opportunities for future applications in next-generation high temperature, high-frequency and high-power electronics with a further increased electron mobility by optimization of heterointerface quality.

Keywords: AlN/GaN, HEMT, MBE, homoepitaxy

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Authors: Lopamudra Ray, Malla Padma, Dibya Bhol, Samir Ranjan Mishra, A. N. Panda, Gurdeep Rastogi, T. K. Adhya, Ajit Kumar Pattnaik, Mrutyunjay Suar, Vishakha Raina

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Chilika Lake is the largest coastal estuarine brackish water lagoon in Asia situated on the east coast of India and is a designated Ramsar site. In the current study, several chitinolytic microorganisms were isolated and screened by appearance of clearance zone on 0.5% colloidal chitin agar plate. A strain designated as RC 1830 displayed maximum colloidal chitin degradation by release of 112 μmol/ml/min of N-acetyl D-glucosamine (GlcNAc) in 48h. The strain was taxonomically identified by polyphasic approach based on a range of phenotypic and genotypic properties and was found to be a novel species named Streptomyces chilikensis RC1830. The organism was halophilic (12% NaCl w/v), alkalophilic (pH10) and was capable of hydrolyzing chitin, starch, cellulose, gelatin, casein, tributyrin and tween 80. The partial purification of chitinase enzymes from RC1830 was performed by DEAE Sephacel anion exchange chromatography which revealed the presence of a very low molecular weight chitinase(10.5kD) which may be a probable chitobiosidase enzyme. The study reports the presence of a low MW chitinase (10.5kD) and a chitin decaetylase from a novel Streptomyces strain RC1830 isolated from Chilika Lake. Previously chitinases less than 20.5kD have not been reported from any other Streptomyces species. The enzymes was characterized with respect to optimum pH, temperature, and substrate specificity and temperature stability.

Keywords: chitinases, chitobiosidase, Chilika Lake, India

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