Search results for: molecular profiles

Authors: Narges Arsanious Kamel Arsanious

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A descriptive statistical analysis of the data showed that the most important factor evoking negative attitudes among teachers is student behavior. It have been presented as useful models for understanding the risk factors and protective factors associated with the emergence of autistic traits. Although these ‘syndrome’ forms of autism reach clinical thresholds, they appear to be distinctly different from the idiopathic or ‘non-syndrome’ autism phenotype. Most teachers reported that kindergartens did not prepare them for the educational needs of children with autism, particularly in relation to non-verbal skills. The study is important and points the way for improving teacher inclusion education in Thailand. Inclusive education for students with autism is still in its infancy in Thailand. Although the number of autistic children in schools has increased significantly since the Thai government introduced the Education Regulations for Persons with Disabilities Act in 2008, there is a general lack of services for autistic students and their families. This quantitative study used the Teaching Skills and Readiness Scale for Students with Autism (APTSAS) to test the attitudes and readiness of 110 elementary school teachers when teaching students with autism in general education classrooms. To uncover the true nature of these co morbidities, it is necessary to expand the definition of autism to include the cognitive features of the disorder, and then apply this expanded conceptualization to examine patterns of autistic syndromes. This study used various established eye-tracking paradigms to assess the visual and attention performance of children with DS and FXS who meet the autism thresholds defined in the Social Communication Questionnaire. To study whether the autistic profiles of these children are associated with visual orientation difficulties (sticky attention), decreased social attention, and increased visual search performance, all of which are hallmarks of the idiopathic autistic child phenotype. Data will be collected from children with DS and FXS, aged 6 to 10 years, and two control groups matched for age and intellectual ability (i.e., children with idiopathic autism). In order to enable a comparison of visual attention profiles, cross-sectional analyzes of developmental trajectories are carried out. Significant differences in the visual-attentive processes underlying the presentation of autism in children with FXS and DS have been suggested, supporting the concept of syndrome specificity. The study provides insights into the complex heterogeneity associated with autism syndrome symptoms and autism itself, with clinical implications for the utility of autism intervention programs in DS and FXS populations.

Keywords: attitude, autism, teachers, sports activities, movement skills, motor skills

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Authors: Sharon N. Nuñal, May Flor S. Muegue, Nizzy Hope N. Cartago, Raymund B. Parcon, Sheina B. Logronio

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The antioxidant and anti-inflammatory potentials of Perna Viridis, Modiolus philippinarum, and Mytella charruana found in the Philippines were assessed. Mussel protein samples were hydrolyzed using trypsin, maturase, alcalase and pepsin at 1% and 2% concentrations and then fractionated through membrane filtration (<10 kDa and <30 kDa). Antioxidant assays showed that pepsin hydrolysate at 2% enzyme concentration exhibited the maximum activities for both 2,2-Diphenyl-1-picrylhydrazyl (DPPH) Radical Scavenging Activity (155-176 µM TE/mg protein) and 2,2-azinobis-(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) radical scavenging (67-68 µM TE/mg protein) assays while trypsin hydrolysate dominated the Ferric Reducing Antioxidant Power (FRAP) for the three mussel species. Lower molecular weight peptide fractions at <10 kDa exhibited better antioxidant activities than the higher molecular weight fractions. The anti-inflammatory activities of M. philippinarum and M. charruana showed comparable protein denaturation inhibition potentials with the highest in P. Viridis samples (98.93%). The 5-Lipoxygenase (5-LOX) inhibitory activities of mussel samples showed no significant difference with inhibition exceeding 70%. P. Viridis demonstrated the highest inhibition against Cyclooxygenase-2 (COX-2) at 56.19%, while the rest showed comparable activities. This study showed that the three mussel species are potential sources of bioactive peptides and lipids with antioxidant and anti-inflammatory properties.

Keywords: anti-inflammatory, antioxidant, bioactive properties, mussel

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Authors: Mohammad Hashemi, John Herbert

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Quantifying and measuring Quality of Experience (QoE) are important and difficult concerns in Human Computer Interaction (HCI). Quality of Service (QoS) and the actual User Interface (UI) of the application are both important contributors to the QoE of a user. This paper describes a framework that measures accurately the way a user uses the UI in order to model users' behaviours and profiles. It monitors the use of the mouse and use of UI elements with accurate time measurement. It does this in real-time and does so unobtrusively and efficiently allowing the user to work as normal with the application. This real-time accurate measurement of the user's interaction provides valuable data and insight into the use of the UI, and is also the basis for analysis of the user's QoE.

Keywords: user modelling, user interface experience, quality of experience, user experience, human and computer interaction

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Authors: Aoxue Yang, Weili Tian, Haikun Liu

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Brain tumor stem cells (BTSCs) are resistant to therapy and give rise to recurrent tumors. These rare and elusive cells are likely to disseminate during cancer progression, and some may enter dormancy, remaining viable but not increasing. The identification of dormant BTSCs is thus necessary to design effective therapies for glioblastoma (GBM) patients. Glucocorticoids (GCs) are used to treat GBM-associated edema. However, glucocorticoids participate in the physiological response to psychosocial stress, linked to poor cancer prognosis. This raises concern that glucocorticoids affect the tumor and BTSCs. Identifying markers specifically expressed by brain tumor stem cells (BTSCs) may enable specific therapies that spare their regular tissue-resident counterparts. By ribosome profiling analysis, we have identified that glycerol-3-phosphate dehydrogenase 1 (GPD1) is expressed by dormant BTSCs but not by NSCs. Through different stress-induced experiments in vitro, we found that only dexamethasone (DEXA) can significantly increase the expression of GPD1 in NSCs. Adversely, mifepristone (MIFE) which is classified as glucocorticoid receptors antagonists, could decrease GPD1 protein level and weaken the proliferation and stemness in BTSCs. Furthermore, DEXA can induce GPD1 expression in tumor-bearing mice brains and shorten animal survival, whereas MIFE has a distinct adverse effect that prolonged mice lifespan. Knocking out GR in NSC can block the upregulation of GPD1 inducing by DEXA, and we find the specific sequences on GPD1 promotor combined with GR, thus improving the efficiency of GPD1 transcription from CHIP-Seq. Moreover, GR and GPD1 are highly co-stained on GBM sections obtained from patients and mice. All these findings confirmed that GR could regulate GPD1 and loss of GPD1 Impairs Multiple Pathways Important for BTSCs Maintenance GPD1 is also a critical enzyme regulating glycolysis and lipid synthesis. We observed that DEXA and MIFE could change the metabolic profiles of BTSCs by regulating GPD1 to shift the transition of cell dormancy. Our transcriptome and lipidomics analysis demonstrated that cell cycle signaling and phosphoglycerides synthesis pathways contributed a lot to the inhibition of GPD1 caused by MIFE. In conclusion, our findings raise concern that treatment of GBM with GCs may compromise the efficacy of chemotherapy and contribute to BTSC dormancy. Inhibition of GR can dramatically reduce GPD1 and extend the survival duration of GBM-bearing mice. The molecular link between GPD1 and GR may give us an attractive therapeutic target for glioblastoma.

Keywords: cancer stem cell, dormancy, glioblastoma, glycerol-3-phosphate dehydrogenase 1, glucocorticoid receptor, dexamethasone, RNA-sequencing, phosphoglycerides

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Authors: Ruzanna Muradyan

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Medical data mining is a crucial field in contemporary healthcare that offers cutting-edge tactics with enormous potential to transform patient care. This abstract examines how sophisticated data mining techniques could transform the healthcare industry, with a special focus on how they might improve patient outcomes. Healthcare data repositories have dynamically evolved, producing a rich tapestry of different, multi-dimensional information that includes genetic profiles, lifestyle markers, electronic health records, and more. By utilizing data mining techniques inside this vast library, a variety of prospects for precision medicine, predictive analytics, and insight production become visible. Predictive modeling for illness prediction, risk stratification, and therapy efficacy evaluations are important points of focus. Healthcare providers may use this abundance of data to tailor treatment plans, identify high-risk patient populations, and forecast disease trajectories by applying machine learning algorithms and predictive analytics. Better patient outcomes, more efficient use of resources, and early treatments are made possible by this proactive strategy. Furthermore, data mining techniques act as catalysts to reveal complex relationships between apparently unrelated data pieces, providing enhanced insights into the cause of disease, genetic susceptibilities, and environmental factors. Healthcare practitioners can get practical insights that guide disease prevention, customized patient counseling, and focused therapies by analyzing these associations. The abstract explores the problems and ethical issues that come with using data mining techniques in the healthcare industry. In order to properly use these approaches, it is essential to find a balance between data privacy, security issues, and the interpretability of complex models. Finally, this abstract demonstrates the revolutionary power of modern data mining methodologies in transforming the healthcare sector. Healthcare practitioners and researchers can uncover unique insights, enhance clinical decision-making, and ultimately elevate patient care to unprecedented levels of precision and efficacy by employing cutting-edge methodologies.

Keywords: data mining, healthcare, patient care, predictive analytics, precision medicine, electronic health records, machine learning, predictive modeling, disease prognosis, risk stratification, treatment efficacy, genetic profiles, precision health

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Authors: N. Dahraoui, M. Boulakroune, D. Benatia

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In this paper, the improvement by deconvolution of the depth resolution in Secondary Ion Mass Spectrometry (SIMS) analysis is considered. Indeed, we have developed a new Tikhonov-Miller deconvolution algorithm where a priori model of the solution is included. This is a denoisy and pre-deconvoluted signal obtained from: firstly, by the application of wavelet shrinkage algorithm, secondly by the introduction of the obtained denoisy signal in an iterative deconvolution algorithm. In particular, we have focused the light on the effect of the iterations number on the evolution of the deconvoluted signals. The SIMS profiles are multilayers of Boron in Silicon matrix.

Keywords: DRF, in-depth resolution, multiresolution deconvolution, SIMS, wavelet shrinkage

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Authors: M. Acin-Albiac, P. Filannino, R. Coda, Carlo G. Rizzello, M. Gobbetti, R. Di Cagno

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Demand for smart management of large amounts of agro-food by-products has become an area of major environmental and economic importance worldwide. Brewers' spent grain (BSG), the most abundant by-product generated in the beer-brewing process, represents an example of valuable raw material and source of health-promoting compounds. To the date, the valorization of BSG as a food ingredient has been limited due to poor technological and sensory properties. Tailored bioprocessing through lactic acid bacteria (LAB) fermentation is a versatile and sustainable means for the exploitation of food industry by-products. Indigestible carbohydrates (e.g., hemicelluloses and celluloses), high phenolic content, and mostly lignin make of BSG a hostile environment for microbial survival. Hence, the selection of tailored starters is required for successful fermentation. Our study investigated the metabolic strategies of Leuconostoc pseudomesenteroides and Lactobacillus plantarum strains to exploit BSG as a food ingredient. Two distinctive BSG samples from different breweries (Italian IT- and Finish FL-BSG) were microbially and chemically characterized. Growth kinetics, organic acid profiles, and the evolution of phenolic profiles during the fermentation in two BSG model media were determined. The results were further complemented with gene expression targeting genes involved in the degradation cellulose, hemicelluloses building blocks, and the metabolism of anti-nutritional factors. Overall, the results were LAB genus dependent showing distinctive metabolic capabilities. Leuc. pseudomesenteroides DSM 20193 may degrade BSG xylans while sucrose metabolism could be furtherly exploited for extracellular polymeric substances (EPS) production to enhance BSG pro-technological properties. Although L. plantarum strains may follow the same metabolic strategies during BSG fermentation, the mode of action to pursue such strategies was strain-dependent. L. plantarum PU1 showed a great preference for β-galactans compared to strain WCFS1, while the preference for arabinose occurred at different metabolic phases. Phenolic compounds profiling highlighted a novel metabolic route for lignin metabolism. These findings will allow an improvement of understanding of how lactic acid bacteria transform BSG into economically valuable food ingredients.

Keywords: brewery by-product valorization, metabolism of plant phenolics, metabolism of lactic acid bacteria, gene expression

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Authors: Jyoti Sharma

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Although notion of giftedness is a reality, yet it swings along the pendulum of equality and excellence. At times, nurturance of gifted abilities becomes a struggle of better catchment of resources and facilities. Those from affluent setup are blessed with better support system whereas gifted children from disadvantaged group suffer from submissive upbringing. In developing countries like India, with diverse demographic profiles, socio-cultural diversity and economic disparity, the very concept of equality in education face severe challenge. The present paper presents the dichotomy of ideology of equality and excellence in education practices. It highlights the need of wider vision, better policy making and decentralized implementation services to allow gifted children to enjoy what they are; dream what they can be; and promote what they will be.

Keywords: gifted, disadvantaged, education safety net, India

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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: L. Torchane

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This study is devoted to defining the optimal conditions for the nitriding of pure iron at atmospheric pressure by using NH3-Ar-C3H8 gas mixtures. After studying the mechanisms of phase formation and mass transfer at the gas-solid interface, a mathematical model is developed in order to predict the nitrogen transfer rate in the solid, the ε-carbonitride layer growth rate and the nitrogen and carbon concentration profiles. In order to validate the model and to show its possibilities, it is compared with thermogravimetric experiments, analyses and metallurgical observations (X-ray diffraction, optical microscopy and electron microprobe analysis). Results obtained allow us to demonstrate the sound correlation between the experimental results and the theoretical predictions.

Keywords: gaseous nitrocarburizing, kinetic model, diffusion, layer growth kinetic

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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: Marianne Miguet, Gaël Plantard, Yves Jaeger, Vincent Goetz

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The contamination of groundwater is a major concern. A common pollutant, the perchloroethylene, is the target contaminant. Water treatment process as Granular Activated Carbons are very efficient but requires pilot-scale testing to determine the full-scale GAC performance. First, the batch mode was used to get a reliable experimental method to estimate the adsorption capacity of a common volatile compound is settled. The Langmuir model is acceptable to fit the isotherms. Dynamic tests were performed with three columns and different operating conditions. A database of concentration profiles and breakthroughs were obtained. The resolution of the set of differential equations is acceptable to fit the dynamics tests and could be used for a full-scale adsorber.

Keywords: activated carbon, groundwater, perchloroethylene, full-scale

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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: 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: Maisa Haj-Tas, Jehad Alaraifi

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The significance of the study: This retrospective study examined the speech and language profiles of patients who received clinical services at the University of Jordan Hearing and Speech Clinic (UJ-HSC) from 2009 to 2014. The UJ-HSC clinic is located in the capital Amman and was established in the late 1990s. It is the first hearing and speech clinic in Jordan and one of first speech and hearing clinics in the Middle East. This clinic provides services to an annual average of 2000 patients who are diagnosed with different communication disorders. Examining the speech and language profiles of patients in this clinic could provide an insight about the most common disorders seen in patients who attend similar clinics in Jordan. It could also provide information about community awareness of the role of speech therapists in the management of speech and language disorders. Methodology: The researchers examined the clinical records of 1140 patients (797 males and 343 females) who received clinical services at the UJ-HSC between the years 2009 and 2014 for the purpose of data analysis for this study. The main variables examined in the study were disorder type and gender. Participants were divided into four age groups: children, adolescents, adults, and older adults. The examined disorders were classified as either speech disorders, language disorders, or dysphagia (i.e., swallowing problems). The disorders were further classified as childhood language impairments, articulation disorders, stuttering, cluttering, voice disorders, aphasia, and dysphagia. Results: The results indicated that the prevalence for language disorders was the highest (50.7%) followed by speech disorders (48.3%), and dysphagia (0.9%). The majority of patients who were seen at the JU-HSC were diagnosed with childhood language impairments (47.3%) followed consecutively by articulation disorders (21.1%), stuttering (16.3%), voice disorders (12.1%), aphasia (2.2%), dysphagia (0.9%), and cluttering (0.2%). As for gender, the majority of patients seen at the clinic were males in all disorders except for voice disorders and cluttering. Discussion: The results of the present study indicate that the majority of examined patients were diagnosed with childhood language impairments. Based on this result, the researchers suggest that there seems to be a high prevalence of childhood language impairments among children in Jordan compared to other types of speech and language disorders. The researchers also suggest that there is a need for further examination of the actual prevalence data on speech and language disorders in Jordan. The fact that many of the children seen at the UJ-HSC were brought to the clinic either as a result of parental concern or teacher referral indicates that there seems to an increased awareness among parents and teachers about the services speech pathologists can provide about assessment and treatment of childhood speech and language disorders. The small percentage of other disorders (i.e., stuttering, cluttering, dysphasia, aphasia, and voice disorders) seen at the UJ-HSC may indicate a little awareness by the local community about the role of speech pathologists in the assessment and treatment of these disorders.

Keywords: clinic, disorders, language, profile, speech

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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: Sara Atibi, Azzeddine Atibi, Salim Ahmed, Khadija El Kababi

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The concept of chemical bonding is fundamental in chemistry education, ubiquitous in school curricula, and essential to numerous topics in the field. Mastery of this concept enables students to predict and explain the physical and chemical properties of substances. However, chemical bonding is often regarded as one of the most complex concepts for secondary and higher education students to comprehend, due to the underlying complex theory and the use of abstract models. Teachers also encounter significant challenges in conveying this concept effectively. This study aims to identify the difficulties and alternative conceptions faced by Moroccan secondary school students in learning about chemical bonding, as well as the pedagogical strategies employed by teachers to overcome these obstacles. A survey was conducted involving 150 Moroccan secondary school physical science teachers, using a structured questionnaire comprising closed, open-ended, and multiple-choice questions. The results reveal frequent student misconceptions, such as the octet rule, molecular geometry, and molecular polarity. Contributing factors to these misconceptions include the abstract nature of the concepts, the use of models, and teachers' difficulties in explaining certain aspects of chemical bonding. The study proposes improvements for teaching chemical bonding, such as integrating information and communication technologies (ICT), diversifying pedagogical tools, and considering students' pre-existing conceptions. These recommendations aim to assist teachers, curriculum developers, and textbook authors in making chemistry more accessible and in addressing students' misconceptions.

Keywords: chemical bonding, alternative conceptions, chemistry education, pedagogical strategies

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Authors: M. G. Murtaza, E. E. Tzirtzilakis, M. Ferdows

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The mixed convective flow of MHD incompressible, steady boundary layer in heat transfer over a curved stretching sheet due to temperature dependent thermal conductivity is studied. We use curvilinear coordinate system in order to describe the governing flow equations. Finite difference solutions with central differencing have been used to solve the transform governing equations. Numerical results for the flow velocity and temperature profiles are presented as a function of the non-dimensional curvature radius. Skin friction coefficient and local Nusselt number at the surface of the curved sheet are discussed as well.

Keywords: curved stretching sheet, finite difference method, MHD, variable thermal conductivity

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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: 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: Csaba Tóth, Éva Lakatos, László Pethő, Seoyoung Cho

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The temperature effect on asphalt pavement structure is a crucial factor at the design stage. In this paper, by applying the German guidelines for temperature along the asphalt depth is estimated. The aim is to consider temperature profiles in different seasons in numerical modelling. The model is built with an elastic and isotropic solid element with 19 subdivisions of asphalt layers to reflect the temperature variation. Comparison with the simple three-layer pavement system (asphalt layers, base, and subgrade layers) will be followed to see the difference in result without temperature variation along with the depth. Finally, the fatigue life calculation was checked to prove the validity of the methodology of considering the temperature in the numerical modelling.

Keywords: temperature profile, flexible pavement modeling, finite element method, temperature modeling

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Authors: Oindrila Nath, S. Sridharan

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Long-term (2002-2012) temperature and ozone measurements by Sounding of Atmosphere by Broadband Emission Radiometry (SABER) instrument onboard Thermosphere, Ionosphere, Mesosphere Energetics and Dynamics (TIMED) satellite zonally averaged over 10°N-15°N are used to study their long-term changes and their responses to solar cycle, quasi-biennial oscillation and El Nino Southern Oscillation. The region is selected to provide more accurate long-term trends and variabilities, which were not possible earlier with lidar measurements over Gadanki (13.5°N, 79.2°E), which are limited to cloud-free nights, whereas continuous data sets of SABER temperature and ozone are available. Regression analysis of temperature shows a cooling trend of 0.5K/decade in the stratosphere and that of 3K/decade in the mesosphere. Ozone shows a statistically significant decreasing trend of 1.3 ppmv per decade in the mesosphere although there is a small positive trend in stratosphere at 25 km. Other than this no significant ozone trend is observed in stratosphere. Negative ozone-QBO response (0.02ppmv/QBO), positive ozone-solar cycle (0.91ppmv/100SFU) and negative response to ENSO (0.51ppmv/SOI) have been found more in mesosphere whereas positive ozone response to ENSO (0.23ppmv/SOI) is pronounced in stratosphere (20-30 km). The temperature response to solar cycle is more positive (3.74K/100SFU) in the upper mesosphere and its response to ENSO is negative around 80 km and positive around 90-100 km and its response to QBO is insignificant at most of the heights. Composite monthly mean of ozone volume mixing ratio shows maximum values during pre-monsoon and post-monsoon season in middle stratosphere (25-30 km) and in upper mesosphere (85-95 km) around 10 ppmv. Composite monthly mean of temperature shows semi-annual variation with large values (~250-260 K) in equinox months and less values in solstice months in upper stratosphere and lower mesosphere (40-55 km) whereas the SAO becomes weaker above 55 km. The semi-annual variation again appears at 80-90 km, with large values in spring equinox and winter months. In the upper mesosphere (90-100 km), less temperature (~170-190 K) prevails in all the months except during September, when the temperature is slightly more. The height profiles of amplitudes of semi-annual and annual oscillations in ozone show maximum values of 6 ppmv and 2.5 ppmv respectively in upper mesosphere (80-100 km), whereas SAO and AO in temperature show maximum values of 5.8 K and 4.6 K in lower and middle mesosphere around 60-85 km. The phase profiles of both SAO and AO show downward progressions. These results are being compared with long-term lidar temperature measurements over Gadanki (13.5°N, 79.2°E) and the results obtained will be presented during the meeting.

Keywords: trends, QBO, solar cycle, ENSO, ozone, temperature

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Authors: Dong Zhao

Abstract:

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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