Search results for: docking station

Authors: Chakrit Chotamonsak

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This study was analyzed changes in temperature and precipitation extremes in northern Thailand for the period 1981-2011.The study includes an analysis of the average and trends of changes in temperature and precipitation using 22 climate indices, related to the intensity, frequency and duration of extreme climate events. The results showed that the averaged trend of maximum, minimum and mean temperature is likely to increase over the study area in rate of 0.5, 0.9 and 0.7 °C in last 30 years. Changes in temperature at nighttime, then rising at a rate higher daytime is resulting to decline of diurnal temperature range throughout the area. Trend of changes in average precipitation during the year 1981-2011 is expected to increase at an average rate of 21%. The intensity of extreme temperature events is increasing almost all station. In particular, the changes of the night were unusually hot has intensified throughout the region. In some provinces such as Chiang Mai and Lampang are likely be faced with the severity of hot days and hot nights in increasing rate. Frequency of extreme temperature events are likely to increase each station, especially hot days, and hot nights are increasing at a rate of 2.38 and 3.58 days per decade. Changes in the cold days and cold nights are declining at a rate of 0.82 and 3.03 days per decade. The duration of extreme temperature events is expected to increase the events hot in every station. An average of 17.8 days per decade for the number of consecutive cold winter nights likely shortens the rate of 2.90 days per decade. The analysis of the precipitation indices reveals the intensity of extreme precipitation is increasing almost across the region. The intensify expressed the heavy rain in one day (Rx1day) and very heavy rain accumulated in 5 days (RX5day) which is likely to increase, and very heavy rainfall is likely to increase in intensity. Frequency of extreme precipitation events is likely to increase over the station. The average frequency of heavy precipitation events increased xxx days per decade. The duration of extreme precipitation events, such as the consecutive dry days are likely to reduce the numbers almost all station while the consecutive wet days tends to increase and decrease at different numbers in different areas.

Keywords: climate extreme, temperature extreme, precipitation extreme, Northern Thailand

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Authors: Ilham S. M. Elsayed

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The purpose of this study is to investigate Alahsa Governorate status and its vulnerability to generate urban heat islands. Alahsa Governorate is a famous oasis in the Arabic Peninsula including several oil centers. Extensive literature review was done to collect previous relative data on the urban heat island of Alahsa Governorate. Data used for the purpose of this research were collected from authorized bodies who control weather station networks over Alahsa Governorate, Eastern Province, Saudi Arabia. Although, the number of weather station networks within the region is very limited and the analysis using GIS software and its techniques is difficult and limited, the data analyzed confirm an increase in temperature for more than 2 °C from 2004 to 2014. Such increase is considerable whenever human health and comfort are the concern. The increase of temperature within one decade confirms the availability of urban heat islands. The study concludes that, Alahsa Governorate is vulnerable to create urban heat islands and more attention should be drawn to strategic planning of the governorate that is developing with a high pace and considerable increasing levels of urbanization.

Keywords: Alahsa Governorate, population density, Urban Heat Island, weather station

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Authors: Gagan Dhawan

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Mycobacterium tuberculosis was described as ‘captain of death’ with an inherent property of multiple drug resistance majorly caused by the competent mechanism of efflux pumps. In this study, various open source tools combining chemo-informatics with bioinformatics were used for efficient in-silico drug designing. The efflux pump, Rv1218c, belonging to the ABC transporter superfamily, which is predicted to be a tetronasin-transporter in M. tuberculosis was targeted. Recent studies have shown that Rv1218c forms a complex with two more efflux pumps (Rv1219c and Rv1217c) to provide multidrug resistance to the bacterium. The 3D structure of the protein was modeled (as the structure was unavailable in the previously collected databases on this gene). The TMHMM analysis of this protein in TubercuList has shown that this protein is present in the outer membrane of the bacterium. Virtual screening of compounds from various publically available chemical libraries was performed on the M. tuberculosis protein using various open source tools. These ligands were further assessed where various physicochemical properties were evaluated and analyzed. On comparison of different physicochemical properties, toxicity and docking, the ligand 2-(hydroxymethyl)-6-[4, 5, 6-trihydroxy-2-(hydroxymethyl) tetrahydropyran-3-yl] oxy-tetrahydropyran-3, 4, 5-triol was found to be best suited for further studies.

Keywords: drug resistance, efflux pump, molecular docking, virtual screening

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Authors: Nicole C. Valdez, Vincent L. Borromeo, Conrad C. Chong, Ahmad F. Mazahery

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Breast cancer is the most prevalent cancer worldwide, where the majority of cases are estrogen-receptor positive and involve 2 receptor proteins. The binding of estrogen to estrogen receptor alpha (ERα) promotes breast cancer growth, while it's binding to estrogen-receptor beta (ERβ) inhibits tumor growth. While natural products have been a promising source of chemotherapeutic agents, the challenge remains in finding a bioactive compound that specifically targets cancer cells, minimizing side effects on normal cells. Flavonoids are natural products that act as phytoestrogens and induce the same response as estrogen. They are able to compete with estrogen for binding to ERα; however, it has a higher binding affinity for ERβ. Their abundance in nature and low toxicity make them a potential candidate for breast cancer treatment. This study aimed to determine which particular flavonoids can specifically recognize ERβ and potentially be used for breast cancer treatment through molecular docking. A total of 206 flavonoids comprised of 97 isoflavones and 109 flavanones were collected from ZINC15, while the 3D structures of ERβ and ERα were obtained from Protein Data Bank. These flavonoid subclasses were chosen as they bind more strongly to ERs due to their chemical structure. The structures of the flavonoid ligands were converted using Open Babel, while the estrogen receptor protein structures were prepared using Autodock MGL Tools. The optimal binding site was found using BIOVIA Discovery Studio Visualizer before docking all flavonoids on both ERβ and ERα through Autodock Vina. Genistein is a flavonoid that exhibits anticancer effects by binding to ERβ, so its binding affinity was used as a baseline. Eriodictyol and 4”,6”-Di-O-Galloylprunin both exceeded genistein’s binding affinity for ERβ and was lower than its binding affinity for ERα. Of the two, eriodictyol was pursued due to its antitumor properties on a lung cancer cell line and on glioma cells. It is able to arrest the cell cycle at the G2/M phase by inhibiting the mTOR/PI3k/Akt cascade and is able to induce apoptosis via the PI3K/Akt/NF-kB pathway. Protein pathway and gene analysis were also conducted using ChEMBL and PANTHER and it was shown that eriodictyol might induce anticancer effects through the ROS1, CA7, KMO, and KDM1A genes which are involved in cell proliferation in breast cancer, non-small cell lung cancer, and other diseases. The high binding affinity of eriodictyol to ERβ, as well as its potential affected genes and antitumor effects, therefore, make it a candidate for the development of new breast cancer treatment. Verification through in vitro experiments such as checking the upregulation and downregulation of genes through qPCR and checking cell cycle arrest using a flow cytometry assay is recommended.

Keywords: breast cancer, estrogen receptor, flavonoid, molecular docking

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Authors: Amer Ali, Jessica Cecchinelli, Antonis Charalambous

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Cycling is one of the most environmentally friendly, economic and healthy modes of transport but it needs more efficient cycle infrastructure and more effective safety measures. This paper represents an investigation into the performance and operation of the London Cycle Hire Scheme which started to operate in July 2010 using 5,000 cycles and 315 docking stations and currently has more than 10,000 cycles and over 700 docking stations across London which are available 24/7, 365 days a year. The study, which was conducted during the second half of 2014, consists of two parts; namely, the longitudinal review of the hire scheme between its introduction in 2010 and November 2014, and a field survey in November 2014 in the form of face-face interviews of the users of the cycle scheme to ascertain the existing limitations and difficulties experienced by those users and how it could be improved in terms of capability and safety. The study also includes a correlation between the usage of the cycle scheme and the corresponding weather conditions. The main findings are that on average the number of users (hiring frequency) had increased from just over two millions hires in 2010 to just less than ten millions in 2014. The field survey showed that 80% of the users are satisfied with the performance of the scheme whilst 50% of the users raised concern about the safety level of using the available cycle routes and infrastructure. The study also revealed that a high percentage of the cycle trips were relatively short (less than 30 minutes). Although the weather condition had some effect on cycling, the cost of using the cycle scheme and the main events in London had more effect on the number of cycle hires. The key conclusions are that despite the safety concern and the lack of infrastructure for continuous routes there was an encouraging number of people who opted for cycling as a clean, affordable, and healthy mode of transport. There is a need to expand the scheme by providing more cycles and docking stations and to support that by more well-designed and maintained cycle routes. More details about the development of London Cycle Hire Scheme during the last five years, its performance and the key issues revealed by the surveyed users will be reported in the full version of the paper.

Keywords: cycling mode of transport, london cycle hire scheme, safety, environmental and health benefits, user satisfaction

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Authors: Harminder Kaur, Manpreet Kaur, Akanksha Kapila, Reenu

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Schiff base with general formula H₂L was derived from condensation of o-vanillin and 3-nitro-o-phenylenediamine. This Schiff base was used for the synthesis of organotin(IV) complexes with general formula R₂SnL [R=Phenyl or n-octyl] using equimolar quantities. Elemental analysis UV-Vis, FTIR, and multinuclear spectroscopic techniques (¹H, ¹³C, and ¹¹⁹Sn) NMR were carried out for the characterization of the synthesized complexes. These complexes were coloured and soluble in polar solvents. Computational studies have been performed to obtain the details of the geometry and electronic structures of ligand as well as complexes. Geometry of the ligands and complexes have been optimized at the level of Density Functional Theory with B3LYP/6-311G (d,p) and B3LYP/MPW1PW91 respectively followed by vibrational frequency analysis using Gaussian 09. Observed ¹¹⁹Sn NMR chemical shifts of one of the synthesized complexes showed tetrahedral geometry around Tin atom which is also confirmed by DFT. HOMO-LUMO energy distribution was calculated. FTIR, ¹HNMR and ¹³CNMR spectra were also obtained theoretically using DFT. Further IRC calculations were employed to determine the transition state for the reaction and to get the theoretical information about the reaction pathway. Moreover, molecular docking studies can be explored to ensure the anticancer activity of the newly synthesized organotin(IV) complexes.

Keywords: DFT, molecular docking, organotin(IV) complexes, o-vanillin, 3-nitro-o-phenylenediamine

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Authors: Tao Yin, Zeqiang Zhang, Wei Liang, Yanqing Zeng, Yu Zhang

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To accelerate the remanufacturing process of electronic waste products, this study designs a partial disassembly line with the multi-robotic station to effectively dispose of excessive wastes. The multi-robotic partial disassembly line is a technical upgrade to the existing manual disassembly line. Balancing optimization can make the disassembly line smoother and more efficient. For partial disassembly line balancing with the multi-robotic station (PDLBMRS), a mixed-integer programming model (MIPM) considering the robotic efficiency differences is established to minimize cycle time, energy consumption and hazard index and to calculate their optimal global values. Besides, an enhanced NSGA-II algorithm (HNSGA-II) is proposed to optimize PDLBMRS efficiently. Finally, MIPM and HNSGA-II are applied to an actual mixed disassembly case of two types of computers, the comparison of the results solved by GUROBI and HNSGA-II verifies the correctness of the model and excellent performance of the algorithm, and the obtained Pareto solution set provides multiple options for decision-makers.

Keywords: waste disposal, disassembly line balancing, multi-robot station, robotic efficiency difference, HNSGA-II

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Authors: Laxman Budhathoki, Lal Bahadur Shrestha, K. C. Laxman

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Hundreds of people are being lost their life by flood disaster in Nepal every year. Community-based disaster management committee has formed to formulate the disaster management plan including the component of EWS like EWS tower, rain gauge station, flood gauge station, culverts, boats, ropes, life jackets, a communication mechanism, emergency shelter, Spur, dykes, dam, evacuation route, emergency dry food management etc. Now EWS become a successful tool to decrease the human casualty from 13 to 0 every year in Rapti River of Chitwan District.

Keywords: disaster risk reduction, early warning system, flood, participatory approach

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Authors: Mohamed Moussaoui, Mouna Baassi, Soukayna Baammi, Hatim Soufi, Mohammed Salah, Rachid Daoud, Achraf EL Allali, Mohammed Elalaoui Belghiti, Said Belaaouad

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The present study aims to investigate the quantitative structure-activity relationship (QSAR) of a series of Thiazole derivatives reported as anticancer agents (hepatocellular carcinoma), using principally the electronic descriptors calculated by the density functional theory (DFT) method and by applying the multiple linear regression method. The developed model showed good statistical parameters (R²= 0.725, R²ₐ𝒹ⱼ= 0.653, MSE = 0.060, R²ₜₑₛₜ= 0.827, Q²𝒸ᵥ = 0.536). The energy of the highest occupied molecular orbital (EHOMO) orbital, electronic energy (TE), shape coefficient (I), number of rotatable bonds (NROT), and index of refraction (n) were revealed to be the main descriptors influencing the anti-cancer activity. Additional Thiazole derivatives were then designed and their activities and pharmacokinetic properties were predicted using the validated QSAR model. These designed molecules underwent evaluation through molecular docking (MD) and molecular dynamic (MD) simulations, with binding affinity calculated using the MMPBSA script according to a 100 ns simulation trajectory. This process aimed to study both their affinity and stability towards Cyclin-Dependent Kinase 2 (CDK2), a target protein for cancer disease treatment. The research concluded by identifying four CDK2 inhibitors - A1, A3, A5, and A6 - displaying satisfactory pharmacokinetic properties. MDs results indicated that the designed compound A5 remained stable in the active center of the CDK2 protein, suggesting its potential as an effective inhibitor for the treatment of hepatocellular carcinoma. The findings of this study could contribute significantly to the development of effective CDK2 inhibitors.

Keywords: QSAR, ADMET, Thiazole, anticancer, molecular docking, molecular dynamic simulations, MMPBSA calculation

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Authors: Hamidreza Qaderi

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Beauty is a part of our life and we as Muslims cannot ignore it. Furthermore, Islam did not ignore. God in Quran has used words that mean beauty many times. Zain «زین» and its synonyms are some of that words that are used 46 times in a different meaning of beauty. Some of them are mentioned to worldly beauty and not acceptable beauty and other of them are mentioned to the Moral beauty. In this article, the meaning of Zain 'beauty' in Surah Al Aaraf (The Heights) is explained and described. In fact, there are specific signs about beauty in the 31 and 32 verses of this Surah in which the station of beauty can determine. For clarification of this issue, the analytic philosophy method is used to express the relation between this word and aesthetics and beauty in this article. The results of this research show that the beauty is an important issue in Islam as much as God order to Muslims to be beautiful when they want to pray.

Keywords: beauty, Quran, al zinah, Zain

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Authors: Chien Chin-Wen

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Collaborative teaching has different teaching models and station teaching is one type of collaborative teaching. Station teaching is not commonly practiced in elementary school English education and introduced in language teacher education programs in Taiwan. In station teaching, each teacher takes a small part of instructional content, working with a small number of students. Students rotate between stations where they receive the assignments and instruction from different teachers. The teachers provide the same content to each group, but the instructional method can vary based upon the needs of each group of students. This study explores thirty-four Taiwanese pre-service elementary school English teachers’ knowledge about station teaching and their competence demonstrated in designing activities for and delivering of station teaching in an English remedial education to six sixth graders in a local elementary school in northern Taiwan. The participants simultaneously enrolled in this Elementary School English Teaching Materials and Methods class, a part of an elementary school teacher education program in a northern Taiwan city. The instructor (Jennifer, pseudonym) in this Elementary School English Teaching Materials and Methods class collaborated with an English teacher (Olivia, pseudonym) in Maureen Elementary School (pseudonym), an urban elementary school in a northwestern Taiwan city. Of Olivia’s students, four male and two female sixth graders needed to have remedial English education. Olivia chose these six elementary school students because they were in the lowest 5 % of their class in terms of their English proficiency. The thirty-four pre-service English teachers signed up for and took turns in teaching these six sixth graders every Thursday afternoon from four to five o’clock for twelve weeks. While three participants signed up as a team and taught these six sixth graders, the last team consisted of only two pre-service teachers. Each team designed a 40-minute lesson plan on the given language focus (words, sentence patterns, dialogue, phonics) of the assigned unit. Data in this study included the KWLA chart, activity designs, and semi-structured interviews. Data collection lasted for four months, from September to December 2014. Data were analyzed as follows. First, all the notes were read and marked with appropriate codes (e.g., I don’t know, co-teaching etc.). Second, tentative categories were labeled (e.g., before, after, process, future implication, etc.). Finally, the data were sorted into topics that reflected the research questions on the basis of their relevance. This study has the following major findings. First of all, the majority of participants knew nothing about station teaching at the beginning of the study. After taking the course Elementary School English Teaching Materials and Methods and after designing and delivering the station teaching in an English remedial education program to six sixth graders, they learned that station teaching is co-teaching, and that it includes activity designs for different stations and students’ rotating from station to station. They demonstrated knowledge and skills in activity designs for vocabulary, sentence patterns, dialogue, and phonics. Moreover, they learned to interact with individual learners and guided them step by step in learning vocabulary, sentence patterns, dialogue, and phonics. However, they were still incompetent in classroom management, time management, English, and designing diverse and meaningful activities for elementary school students at different English proficiency levels. Hence, language teacher education programs are recommended to integrate station teaching to help pre-service teachers be equipped with eight knowledge and competences, including linguistic knowledge, content knowledge, general pedagogical knowledge, curriculum knowledge, knowledge of learners and their characteristics, pedagogical content knowledge, knowledge of education content, and knowledge of education’s ends and purposes.

Keywords: co-teaching, competence, knowledge, pre-service teachers, station teaching

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Authors: Cherak Imen, Sellami Mehdi

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The Atlas cedar, Cedrus atlantica, is endemic to the mountains of North Africa. This is one of the most valuable softwood, both economically, ecologically, aesthetically and culturally. In Algeria, the cedar forests currently have worrying symptoms of decline which therefore require special monitoring. Fungal endophytes are involved in various diseases of the Atlas cedar. They attack all organs on which they cause many symptoms. These microflora live in complex interaction with plants. In this study, we identified a total of 09 mycotaxons collected needles Cedarwood at three stations with different degrees of decline (Talmet, Boumerzoug and Tuggurt) in the National Park Belezma (Batna, Algeria). The study conducted on a total of 12 trees were identified 08 mycoendophytes in Talmet station, 04 species in the Boumerzoug station and 03 in Tuggurt station. The total species richness mycoendophytes depending on the types of cedar forests showed that the largest diversity was recorded at the cedar forest healthy, Alternaria is the most common type in all stations. This work should be completed by further detailed studies to identify other endophyte species and better know its interactions with the Atlas cedar.

Keywords: Cedrus atlantica, endophytic fungi, microflora, mycotaxons, mycoendophyte

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Authors: Tripti Mishra, Shipra Shukla, Sanjeev Meena, , Ruchi Singh, Mahesh Pal, D. K. Upreti, Dipak Datta

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Roccella montagnei belongs to lichen family Roccelleceae growing luxuriantly along the coastal regions of India. As Roccella has been shown to be bioactive, we prepared methanolic extract and assessed its anticancer potential. The methanolic extract showed significant in vitro cytotoxic activity against four human cancer cell lines such as Colon (DLD-1, SW-620), Breast (MCF-7), Head and Neck (FaDu). This prompted us to isolate bioactive compounds through column chromatography. Two compounds Roccellic acid and Everninic acid have been isolated, out of which Everninic acid is reported for the first time. Both the compounds have been tested for in vitro cytotoxic activity in which Roccellic acid showed strong anticancer activity as compared to the Everninic acid. CDK-10 (Cyclin-dependent kinase) contributes to proliferation of cancer cells, and aberrant activity of these kinases has been reported in a wide variety of human cancers. These kinases, therefore, constitute biomarkers of proliferation and attractive pharmacological targets for the development of anticancer therapeutics. Therefore both the isolated compounds were tested for in silico molecular docking study against CDK-10 isomer enzyme to support the cytotoxic activity.

Keywords: cytotoxic activity, everninic acid, roccellic acid, R. montagnei

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Authors: Sanja O. Podunavac-Kuzmanović, Lidija R. Jevrić, Strahinja Z. Kovačević

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In last decade, metal-organic complexes have captured intensive attention because of their wide range of biological activities such as antibacterial, antifungal, anticancerous, antimicrobial and antiHIV. Therefore, it is of great importance for the development of coordination chemistry to explore the assembly of functional organic ligands with metal ion and to investigate the relationship between the structure and property. In view of our studies, we reasoned that benzimidazoles complexed to metal ions could act as a potent antibacterial agents. Thus, we have bioassayed the inhibitory potency of benzimidazoles and their metal salts (Co or Ni) against Gram negative bacteria Escherichia coli. In order to validate our in vitro study, we performed in silico studies using molecular docking software’s. The investigated compounds and their metal complexes (Co, Ni) showed good antibacterial activity against Escherichia coli. In silico docking studies of the synthesized compounds suggested that complexed benzimidazoles have a greater binding affinity and enhanced antibacterial activity in comparison with noncomplexed ligands. In view of their enhanced inhibitory properties we propose that the studied complexes can be used as potential pharmaceuticals. This study is financially supported by COST action CM1306 and the project No. 114-451-347/2015-02, financially supported by the Provincial Secretariat for Science and Technological Development of Vojvodina.

Keywords: benzimidazoles, complexes, antibacterial, Escherichia coli, metal

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Authors: S. Roy, R. Rekha, K. Sriram, G. Subhadra, R. Johana

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Cardiovascular disease remains a leading cause of death in most industrialized countries. Many chemical drugs are available in the market which targets different receptor proteins related to cardiovascular diseases. Of late the traditional herbal drugs are safer when compared to chemical drugs because of its side effects. However, many herbal remedies used in treating cardiovascular diseases have not undergone scientific assessment to prove its pharmacological activities. There are many natural compounds, nature derived and Natural product mimic compounds are available which are in the market as approved drug. In the most of the cases drug activity at the molecular level are not known. Here we have categorized those compounds with our experimental compounds in different classes based on the structural similarity and physicochemical properties, using a tool, Chemmine and has attempted to understand the mechanism of the action of a experimental compound, which are clustered with Simvastatin, Lovastatin, Mevastatin and Pravastatin. Target protein molecule for Simvastatin, Lovastatin, Mevastatin and Pravastatin is HMG-CoA reductase, so we concluded that the experimental compound may be able to bind to the same target. Molecular docking and atomic interaction studies with simvastatin and our experimental compound were compared. A pharmacophore modeling was done based on the experimental compound and HMG-CoA reductase inhibitor.

Keywords: molecular docking, physicochemical properties, pharmacophore modeling structural similarity, pravastatin

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Authors: Wen-Shyong Tzou, Chih-Ching Huang, Chin-Hwa Hu, Ying-Tsang Lo, Tun-Wen Pai, Chia-Yin Chiang, Chung-Hao Li, Hong-Jyuan Jian

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Plasmin plays an important role in the human circulatory system owing to its catalytic ability of fibrinolysis. The immediate injection of plasmin in patients of strokes has intrigued many scientists to design vectors that can transport plasmin to the desired location in human body. Here we predict the structure of human plasmin and investigate the interaction of plasmin with the gold-nanoparticle. Because the crystal structure of plasminogen has been solved, we deleted N-terminal domain (Pan-apple domain) of plasminogen and generate a mimic of the active form of this enzyme (plasmin). We conducted a simulated annealing process on plasmin and discovered a very large conformation occurs. Kringle domains 1, 4 and 5 had been observed to leave its original location relative to the main body of the enzyme and the original doughnut shape of this enzyme has been transformed to a V-shaped by opening its two arms. This observation of conformational change is consistent with the experimental results of neutron scattering and centrifugation. We subsequently docked the plasmin on the simulated gold surface to predict their interaction. The V-shaped plasmin could utilize its Kringle domain and catalytic domain to contact the gold surface. Our findings not only reveal the flexibility of plasmin structure but also provide a guide for the design of a plasmin-gold nanoparticle.

Keywords: docking, gold nanoparticle, molecular simulation, plasmin

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Authors: Janneth Gonzalez, Marco Avila, George Barreto

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GRP78 participates in multiple functions in the cell during normal and pathological conditions, controlling calcium homeostasis, protein folding and unfolded protein response. GRP78 is located in the endoplasmic reticulum, but it can change its location under stress, hypoxic and apoptotic conditions. NF-κB represents the keystone of the inflammatory process and regulates the transcription of several genes related with apoptosis, differentiation, and cell growth. The possible relationship between GRP78-NF-κB could support and explain several mechanisms that may regulate a variety of cell functions, especially following brain injuries. Although several reports show interactions between NF-κB and heat shock proteins family members, there is a lack of information on how GRP78 may be interacting with NF-κB, and possibly regulating its downstream activation. Therefore, we assessed the computational predictions of the GRP78 (Chain A) and NF-κB complex (IkB alpha and p65) protein-protein interactions. The interaction interface of the docking model showed that the amino acids ASN 47, GLU 215, GLY 403 of GRP78 and THR 54, ASN 182 and HIS 184 of NF-κB are key residues involved in the docking. The electrostatic field between GRP78-NF-κB interfaces and molecular dynamic simulations support the possible interaction between the proteins. In conclusion, this work shed some light in the possible GRP78-NF-κB complex indicating key residues in this crosstalk, which may be used as an input for better drug design strategy targeting NF-κB downstream signaling as a new therapeutic approach following brain injuries.

Keywords: computational biology, protein interactions, Grp78, bioinformatics, molecular dynamics

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Authors: Sakina Fatima, Joseph-Patrick W. E. Clarke, Patricia A. Thibault, Subha Kalyaanamoorthy, Michael Levin, Aravindhan Ganesan

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Heteronuclear ribonucleoprotein (hnRNPA1 or A1) is associated with the pathology of different diseases, including neurological disorders and cancers. In particular, the aggregation and dysfunction of A1 have been identified as a critical driver for neurodegeneration (NDG) in Multiple Sclerosis (MS). Structurally, A1 includes a low-complexity domain (LCD) and two RNA-recognition motifs (RRMs), and their interdomain coordination may play a crucial role in A1 aggregation. Previous studies propose that RNA-inhibitors or nucleoside analogs that bind to RRMs can potentially prevent A1 self-association. Therefore, molecular-level understanding of the structures, dynamics, and nucleotide interactions with A1 RRMs can be useful for developing therapeutics for NDG in MS. In this work, a combination of computational modelling and biochemical experiments were employed to analyze a set of RNA-A1 RRM complexes. Initially, the atomistic models of RNA-RRM complexes were constructed by modifying known crystal structures (e.g., PDBs: 4YOE and 5MPG), and through molecular docking calculations. The complexes were optimized using molecular dynamics simulations (200-400 ns), and their binding free energies were computed. The binding affinities of the selected complexes were validated using a thermal shift assay. Further, the most important molecular interactions that contributed to the overall stability of the RNA-A1 RRM complexes were deduced. The results highlight that adenine and guanine are the most suitable nucleotides for high-affinity binding with A1. These insights will be useful in the rational design of nucleotide-analogs for targeting A1 RRMs.

Keywords: hnRNPA1, molecular docking, molecular dynamics, RNA-binding proteins

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Authors: Aliyu Damri

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This study analyzed the emergence of WhatsApp and how employees at the Federal Radio Corporation of Nigeria, Kaduna defined the concept base on their vast broadcasting experiences for over five decades and application of the phenomenon to the radio station. It also analyzed the nature, patterns, dimensions, features, challenges as well as the effects of WhatsApp as a social networking site with specific interest on the radio outlet. Also, the study identified how the radio organization responded to the challenges in an attempt to adapt to the new pattern of broadcasting characterized by many technological transformations. The study further explained in details such skills journalists need to function optimally using WhatsApp as well as the impacts of the WhatsApp on radio broadcasting. It used a combination of published materials, focus group discussion, in depth interviews and participant observation on the activities of the radio stations to address the research questions. The data generated provided insight to better understand the challenges posed to FRCN Kaduna as a result of WhatsApp application and how FRCN Kaduna responded to the challenges. It also provided information on the skills journalists need to function optimally in using WhatsApp application in the radio station. The interview and focus group discussion’s transcripts and the published materials were analyzed along thematic pattern related to the research questions in the study. The dominant response relied heavily on change in the radio station’s organizational and technical integration of newsrooms, the use of a multiskilled workforce, application of a flexible and user-friendly technology in all aspects of production, expansion of the station’s services in to new media such as internet and mobile phones as well as sharing of ideas across different units in the radio outfit.

Keywords: broadcasting, challenge, northern Nigeria, radio, WhatsApp application

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Authors: Tayyibah Khanam, Mohammad Saad Alam, Sanchari Deb, Yasser Rafat

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Electric vehicles are considered as viable replacements to gasoline cars since they help in reducing harmful emissions and stimulate power generation through renewable energy sources, hence contributing to sustainability. However, one of the significant obstacles in the mass deployment of electric vehicles is the charging time anxiety among users and, thus, the subsequent large waiting times for available chargers at charging stations. Data analytics, on the other hand, has revolutionized the decision-making tasks of management and operating systems since its arrival. In this paper, we attempt to optimize the choice of EV charging stations for users in their vicinity by minimizing the time taken to reach the charging stations and the waiting times for available chargers. Time taken to travel to the charging station is calculated by the Google Maps API and the waiting times are predicted by polynomial regression of the historical data stored. The proposed framework utilizes real-time data and historical data from all operating charging stations in the city and assists the user in finding the best suitable charging station for their current situation and can be implemented in a mobile phone application. The algorithm successfully predicts the most optimal choice of a charging station and the minimum required time for various sample data sets.

Keywords: charging data, electric vehicles, machine learning, waiting times

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Authors: Xuyang Song, Jun Yin

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The smart card has been an extremely universal tool in public transit. It collects a large amount of data on buses, urban railway transit, and ferries and provides possibilities for passenger profiling. This paper combines offline analysis of passenger profiling and real-time prediction to propose a method that can accurately predict the destination station in real-time when passengers tag on. Firstly, this article constructs a static database of user travel characteristics after identifying passenger travel patterns based on the Density-Based Spatial Clustering of Applications with Noise (DBSCAN). The dual travel passenger habits are identified: OD travel habits and D station travel habits. Then a rapid real-time prediction algorithm based on Transit Passenger Profiling is proposed, which can predict the destination of in-board passengers. This article combines offline learning with online prediction, providing a technical foundation for real-time passenger flow prediction, monitoring and simulation, and short-term passenger behavior and demand prediction. This technology facilitates the efficient and real-time acquisition of passengers' travel destinations and demand. The last, an actual case was simulated and demonstrated feasibility and efficiency.

Keywords: travel behavior, destination prediction, public transit, passenger profiling

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Authors: A. Youseef

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One of the most aims of IEEE 802.16 (WiMAX) is to present high-speed wireless access to cover wide range coverage. The base station (BS) and the subscriber station (SS) are the main parts of WiMAX. WiMAX uses either Point-to-Multipoint (PMP) or mesh topologies. In the PMP mode, the SSs connect to the BS to gain access to the network. However, in the mesh mode, the SSs connect to each other to gain access to the BS. The main components of QoS management in the 802.16 standard are the admission control, buffer management, and packet scheduling. There are several researches proposed to create an efficient packet scheduling schemes. Therefore, we use QualNet 5.0.2 to study the performance of different scheduling schemes, such as WFQ, SCFQ, RR, and SP when the numbers of SSs increase. We find that when the number of SSs increases, the average jitter and average end-to-end delay is increased and the throughput is reduced.

Keywords: WiMAX, scheduling scheme, QoS, QualNet

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Authors: H. Parveen Begam, M. A. Maluk Mohamed

Abstract:

Mobile Grid Computing is an environment that allows sharing and coordinated use of diverse resources in dynamic, heterogeneous and distributed environment using different types of electronic portable devices. In a grid environment the security issues are like authentication, authorization, message protection and delegation handled by GSI (Grid Security Infrastructure). Proving better security between mobile devices and grid infrastructure is a major issue, because of the open nature of wireless networks, heterogeneous and distributed environments. In a mobile grid environment, the individual computing devices may be resource-limited in isolation, as an aggregated sum, they have the potential to play a vital role within the mobile grid environment. Some adaptive methodology or solution is needed to solve the issues like authentication of a base station, security of information flowing between a mobile user and a base station, prevention of attacks within a base station, hand-over of authentication information, communication cost of establishing a session key between mobile user and base station, computing complexity of achieving authenticity and security. The sharing of resources of the devices can be achieved only through the trusted relationships between the mobile hosts (MHs). Before accessing the grid service, the mobile devices should be proven authentic. This paper proposes the dynamic certificate based mutual authentication protocol between two mobile hosts in a mobile grid environment. The certificate generation process is done by CA (Certificate Authority) for all the authenticated MHs. Security (because of validity period of the certificate) and dynamicity (transmission time) can be achieved through the secure service certificates. Authentication protocol is built on communication services to provide cryptographically secured mechanisms for verifying the identity of users and resources.

Keywords: mobile grid computing, certificate authority (CA), SSL/TLS protocol, secured service certificates

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Authors: Minjeong Kim, Seungchul Lee, Iman Janghorban Esfahani, Jeong Tai Kim, ChangKyoo Yoo

Abstract:

A trajectory of set-point of ventilation control systems plays an important role for efficient ventilation inside subway stations since it affects the level of indoor air pollutants and ventilation energy consumption. To maintain indoor air quality (IAQ) at a comfortable range with lower ventilation energy consumption, the optimal trajectory of the ventilation control system needs to be determined. The concentration of air pollutants inside the station shows a diurnal variation in accordance with the variations in the number of passengers and subway frequency. To consider the diurnal variation of IAQ, an iterative dynamic programming (IDP) that searches for a piecewise control policy by separating whole duration into several stages is used. When outdoor air is contaminated by pollutants, it enters the subway station through the ventilation system, which results in the deteriorated IAQ and adverse effects on passenger health. In this study, to consider the influence of outdoor air quality (OAQ), a new performance index of the IDP with the passenger health risk and OAQ is proposed. This study was carried out for an underground subway station at Seoul Metro, Korea. The optimal set-points of the ventilation control system are determined every 3 hours, then, the ventilation controller adjusts the ventilation fan speed according to the optimal set-point changes. Compared to manual ventilation system which is operated irrespective of the OAQ, the IDP-based ventilation control system saves 3.7% of the energy consumption. Compared to the fixed set-point controller which is operated irrespective of the IAQ diurnal variation, the IDP-based controller shows better performance with a 2% decrease in energy consumption, maintaining the comfortable IAQ range inside the station.

Keywords: indoor air quality, iterative dynamic algorithm, outdoor air information, ventilation control system

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Authors: Redvan Ghasemlounia, Elham Ansari, Hikmet Kerem Cigizoglu

Abstract:

Hydrological modeling in arid and semi-arid regions is very important. Iran has many regions with these climate conditions such as Chaharmahal and Bakhtiari province that needs lots of attention with an appropriate management. Forecasting of hydrological parameters and estimation of hydrological events of catchments, provide important information that used for design, management and operation of water resources such as river systems, and dams, widely. Discharge in rivers is one of these parameters. This study presents the application and comparison of some estimation methods such as Feed-Forward Back Propagation Neural Network (FFBPNN), Multi Linear Regression (MLR), Gene Expression Programming (GEP) and Bayesian Network (BN) to predict the daily flow discharge of the Soolegan River, located at Chaharmahal and Bakhtiari province, in Iran. In this study, Soolegan, station was considered. This Station is located in Soolegan River at 51° 14՜ Latitude 31° 38՜ longitude at North Karoon basin. The Soolegan station is 2086 meters higher than sea level. The data used in this study are daily discharge and daily precipitation of Soolegan station. Feed Forward Back Propagation Neural Network(FFBPNN), Multi Linear Regression (MLR), Gene Expression Programming (GEP) and Bayesian Network (BN) models were developed using the same input parameters for Soolegan's daily discharge estimation. The results of estimation models were compared with observed discharge values to evaluate performance of the developed models. Results of all methods were compared and shown in tables and charts.

Keywords: ANN, multi linear regression, Bayesian network, forecasting, discharge, gene expression programming

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Authors: Abdulla Rahil, Rupert Gammon, Neil Brown

Abstract:

The rapid growth of renewable energy sources and their integration into the grid have been motivated by the depletion of fossil fuels and environmental issues. Unfortunately, the grid is unable to cope with the predicted growth of renewable energy which would lead to its instability. To solve this problem, energy storage devices could be used. Electrolytic hydrogen production from an electrolyser is considered a promising option since it is a clean energy source (zero emissions). Choosing flexible operation of an electrolyser (producing hydrogen during the off-peak electricity period and stopping at other times) could bring about many benefits like reducing the cost of hydrogen and helping to balance the electric systems. This paper investigates the price of hydrogen during flexible operation compared with continuous operation, while serving the customer (hydrogen filling station) without interruption. The optimization algorithm is applied to investigate the hydrogen station in both cases (flexible and continuous operation). Three different scenarios are tested to see whether the off-peak electricity price could enhance the reduction of the hydrogen cost. These scenarios are: Standard tariff (1 tier system) during the day (assumed 12 p/kWh) while still satisfying the demand for hydrogen; using off-peak electricity at a lower price (assumed 5 p/kWh) and shutting down the electrolyser at other times; using lower price electricity at off-peak times and high price electricity at other times. This study looks at Derna city, which is located on the coast of the Mediterranean Sea (32° 46′ 0 N, 22° 38′ 0 E) with a high potential for wind resource. Hourly wind speed data which were collected over 24½ years from 1990 to 2014 were in addition to data on hourly radiation and hourly electricity demand collected over a one-year period, together with the petrol station data.

Keywords: hydrogen filling station off-peak electricity, renewable energy, off-peak electricity, electrolytic hydrogen

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Authors: Lu Yang, Keng Po Lai

Abstract:

Metformin, a well-known clinical drug against diabetes, is found with potential anti-diabetic and anti-obese benefits, as reported in increasing evidences. However, the current clinical and experimental investigations are not to reveal the detailed mechanisms of metformin-anti-obesity/hypertension. We have used the bioinformatics strategy, including network pharmacology and molecular docking methodology, to uncover the key targets and pathways of bioactive compounds against clinical disorders, such as cancers, coronavirus disease. Thus, in this report, the in-silico approach was utilized to identify the hug targets, pharmacological function, and mechanism of metformin against obesity and hypertension. The networking analysis identified 154 differentially expressed genes of obesity and hypertension, 21 interaction genes, and 6 hug genes of metformin treating hypertensive obesity. As a result, the molecular docking findings indicated the potent binding capability of metformin with the key proteins, including interleukin 6 (IL-6) and chemokine (C-C motif) Ligand 2 (CCL2), in hypertensive obesity. The metformin-exerted anti-hypertensive obesity action involved in metabolic regulation, inflammatory reaction. And the anti-hypertensive obesity mechanisms of metformin were revealed, including regulation of inflammatory and immunological signaling pathways for metabolic homeostasis in tissue and microenvironmental melioration in blood pressure. In conclusion, our identified findings with bioinformatics analysis have demonstrated the detailed hug and pharmacological targets, biological functions, and signaling pathways of metformin treating hypertensive obesity.

Keywords: metformin, obesity, hypertension, bioinformatics findings

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Authors: Nidhi Chadha, A. K. Tiwari, Marilyn D. Milton, Anil K. Mishra

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Translocator protein (18 kDa) TSPO is highly expressed during microglia activation in neuroinflammation. Although a number of PET ligands have been developed for the visualization of activated microglia, one of the advantageous approaches is to develop potential optical imaging (OI) probe. Our study involves computational screening, synthesis and evaluation of TSPO ligand through various imaging modalities namely PET/SPECT/Optical. The initial computational screening involves pharmacophore modeling from the library designing having oxo-benzooxazol-3-yl-N-phenyl-acetamide groups and synthesis for visualization of efficacy of these compounds as multimodal imaging probes. Structure modeling of monomer, Ala147Thr mutated, parallel and anti-parallel TSPO dimers was performed and docking analysis was performed for distinct binding sites. Computational analysis showed pattern of variable binding profile of known diagnostic ligands and NBMP via interactions with conserved residues along with TSPO’s natural polymorphism of Ala147→Thr, which showed alteration in the binding affinity due to considerable changes in tertiary structure. Preliminary in vitro binding studies shows binding affinity in the range of 1-5 nm and selectivity was also certified by blocking studies. In summary, this skeleton was found to be potential probe for TSPO imaging due to ease in synthesis, appropriate lipophilicity and reach to specific region of brain.

Keywords: TSPO, molecular modeling, imaging, docking

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Authors: Syed Asif Hassan, Tabrej Khan

Abstract:

Multiple sclerosis (MS) is a chronic demyelinating autoimmune disorder, of the central nervous system (CNS). In the present scenario, the current therapies either do not halt the progression of the disease or have side effects which limit the usage of current Disease Modifying Therapies (DMTs) for a longer period of time. Therefore, keeping the current treatment failure schema, we are focusing on screening novel analogues of the available DMTs that specifically bind and inhibit the Sphingosine1-phosphate receptor1 (S1PR1) thereby hindering the lymphocyte propagation toward CNS. The novel drug-like analogs molecule will decrease the frequency of relapses (recurrence of the symptoms associated with MS) with higher efficacy and lower toxicity to human system. In this study, an integrated approach involving ligand-based virtual screening protocol (Ultrafast Shape Recognition with CREDO Atom Types (USRCAT)) to identify the non-toxic drug like analogs of the approved DMTs were employed. The potency of the drug-like analog molecules to cross the Blood Brain Barrier (BBB) was estimated. Besides, molecular docking and simulation using Auto Dock Vina 1.1.2 and GOLD 3.01 were performed using the X-ray crystal structure of Mtb LprG protein to calculate the affinity and specificity of the analogs with the given LprG protein. The docking results were further confirmed by DSX (DrugScore eXtented), a robust program to evaluate the binding energy of ligands bound to the ligand binding domain of the Mtb LprG lipoprotein. The ligand, which has a higher hypothetical affinity, also has greater negative value. Further, the non-specific ligands were screened out using the structural filter proposed by Baell and Holloway. Based on the USRCAT, Lipinski’s values, toxicity and BBB analysis, the drug-like analogs of fingolimod and BG-12 showed that RTL and CHEMBL1771640, respectively are non-toxic and permeable to BBB. The successful docking and DSX analysis showed that RTL and CHEMBL1771640 could bind to the binding pocket of S1PR1 receptor protein of human with greater affinity than as compared to their parent compound (Fingolimod). In this study, we also found that all the drug-like analogs of the standard MS drugs passed the Bell and Holloway filter.

Keywords: antagonist, binding affinity, chemotherapeutics, drug-like, multiple sclerosis, S1PR1 receptor protein

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Authors: Homa Hedayat

Abstract:

Public spaces have been a central concern of urban planners for centuries but have been neglected for a long time. In the modernist planning, the focus has been on the requirements of cars rather than the needs and expectations of pedestrians, and therefore, cities have lost many qualities. Urban public space is a space within the city area which is accessible to all people and is the ground for their activity. People’s public life occurs in urban public spaces in a complex set of forms and functions. These spaces must facilitate diverse behavior, uses, and activities such as shopping, walking, conversation, entertainment, relaxation or even passing the time during festivities and events. One of the public spaces is the surrounding space of public transportation stations. Subway stations, although potentially encompass many different groups of people accommodate few social interactions. Making the surrounding areas of subway stations pedestrian-oriented, potentially increases the socialization capacity. The Sadeghieh Subway Station can be considered as the most important subway station in Tehran, which on the one hand is the rail port of Tehran's western entrance, and on the other is the port for railway journeys inside the city. The main concern of this study is to assess the success or failure of the interventions made by the municipality for changing the surrounding area of the Sadeghieh Subway Station into a pedestrian-oriented space and examine the amount of the area's improvement into a desirable space. The method used in this study is surveying, in which the data were collected using a questionnaire and interview. The study's population is all people who use Sadeghieh Subway, and the sample size for the study was 140 subjects. Using parametric one-sample t-test, we found improvement in factors such as transportation, security, pedestrian infrastructure, vitality and climate comfort. However, there was no improvement in mix use, recreational activity, readability.

Keywords: public space, public transportation stations, pedestrian-oriented space, socialization

Procedia PDF Downloads 203