Search results for: Molecular modeling of 17-picolyl and 17-picolinylidene androstane derivatives with anticancer activity

Authors: Xiaoping Su, Gabriel G. Malouf

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Introduction: Breast cancer is a heterogeneous disease that can be classified in 4 subgroups using transcriptional profiling. The role of lncRNA expression in human breast cancer biology, prognosis, and molecular classification remains unknown. Methods and results: Using an integrative comprehensive analysis of lncRNA, mRNA and DNA methylation in 900 breast cancer patients from The Cancer Genome Atlas (TCGA) project, we unraveled the molecular portraits of 1,700 expressed lncRNA. Some of those lncRNAs (i.e, HOTAIR) are previously reported and others are novel (i.e, HOTAIRM1, MAPT-AS1). The lncRNA classification correlated well with the PAM50 classification for basal-like, Her-2 enriched and luminal B subgroups, in contrast to the luminal A subgroup which behaved differently. Importantly, estrogen receptor (ESR1) expression was associated with distinct lncRNA networks in lncRNA clusters III and IV. Gene set enrichment analysis for cis- and trans-acting lncRNA showed enrichment for breast cancer signatures driven by breast cancer master regulators. Almost two third of those lncRNA were marked by enhancer chromatin modifications (i.e., H3K27ac), suggesting that lncRNA expression may result in increased activity of neighboring genes. Differential analysis of gene expression profiling data showed that lncRNA HOTAIRM1 was significantly down-regulated in basal-like subtype, and DNA methylation profiling data showed that lncRNA HOTAIRM1 was highly methylated in basal-like subtype. Thus, our integrative analysis of gene expression and DNA methylation strongly suggested that lncRNA HOTAIRM1 should be a tumor suppressor in basal-like subtype. Conclusion and significance: Our study depicts the first lncRNA molecular portrait of breast cancer and shows that lncRNA HOTAIRM1 might be a novel tumor suppressor.

Keywords: lncRNA profiling, breast cancer, HOTAIRM1, tumor suppressor

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Authors: Abdulmannan Fadel

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Arabinoxylan is a non-starch polysaccharide (NSP), which is one of the most important polysaccharides contained within cereal grains. Wheat endosperm pentosan and rice bran contain a significant amount of arabinoxylan (7% in rice bran and 10-12% in wheat endosperm pentosan). Several methods have been used for arabinoxylan extraction with varying degrees of success e.g. enzymatic and alkaline treatment. Yet, the use of extrusion alone as a pre-treatment to increase the yield and reduce the molecular weight in wheat endosperm pentosan and rice bran has not been investigated. The samples (wheat pentosan and rice bran) were extruded using a Twin-screw extruder at a range of screw speeds (80 and 160 rpm) and barrel temperatures range (80 to 140°C) with a throughput of 30 Kg hr-1 and moisture content of 25%. Arabinoxylans were extracted with water and the extraction yield and molecular weight was determined using size exclusion high-pressure liquid chromatography system. It was found that increasing screw speed from 80 rpm to 160 rpm, did not effect the extraction yield (p < 0.05) of arabinoxylan from either the wheat endosperm pentosan or the rice bran. However, the molecular weight of the extracted arabinoxylans from pentosan was found to decrease with increasing screw speed in wheat endosperm pentosan. These low molecular weight arabinoxylans have been suggested as immunomodulators.

Keywords: arabinoxylans, extrusion, wheat endosperm pentosan, rice bran

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Authors: Chaoran Liu

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Bioactive polysaccharides and polysaccharide-protein complex derived from mushrooms and fungi have a wide range of immunomodulatory activity with low side-effects and have therefore the potential to be developed as an adjuvant in cancer therapies. Mushrooms sclerotium is rich in polysaccharides and the polysaccharides isolated from the sclerotium of Polyporus rhinocerus have shown potent in vivo and in vitro immunomodulatory effects. Macrophages are considered to be an important component of the innate immune response against bacterial infection and cancer. To better understanding the immunomodulatory effects and its underlying mechanisms of sclerotial water-soluble polysaccharides extracted from P. rhinocerus on macrophages, the objectives of this study are to purify the water-soluble novel sclerotial polysaccharides and to characterize the structure and properties as well as to study the detailed molecular mechanisms of the in vitro immunomodulating effects in murine macrophages. The hot water-soluble fraction PRW from the sclerotium of P. rhinocerus was obtained using solvent extraction. PRW was further fractionated by membrane ultrafiltration to a give a fraction (PRW1) with molecular mass less than 50 kDa. PRW1 was characterized to be a polysaccharide-protein complex composed of 45.7% polysaccharide and 44.2% protein. The chemical structure of the carbohydrate moiety of PRW1 was elucidated by GC and FTIR to be mainly beta-D-glucan with trace amount of galactose and mannose. The immunomodulatory effects of PRW1 on murine RAW 264.7 macrophages were demonstrated in terms of the increase in nitric oxide production and cytokine production. Mechanistically, PRW1 initiates ERK phosphorylation to activate macrophages within 15 min and significantly improves the expression level of inducible NOS (iNOS) from 6 h after treatment. In summary, this study indicates that PRW1 is a potent immunomodulatory agent for macrophages and suggests that mushroom sclerotia from Polyporus rhinocerus requires for further investigation in cancer research.

Keywords: Polyporus rhinocerus, mushroom sclerotia, Polysaccharide-Protein Complex, macrophage activation

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Authors: Omar M. Al Aufi, Abdulwahab Noorwali, Ahmed Al Abd, Safia Alattas, Fathya Zahran, Fahd Almutairi

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Cisplatin (CDDP) is a potent anticancer agent used for several tumor types. Thymoquinone (TQ) is a naturally occurring compound drawing great attention as an anticancer and chemomodulator for chemotherapies. Herein, we studied the potential cytotoxicity of thymoquinone, CDDP and their combination against human oral squamous cell carcinoma cells in contrast to normal oral epithelial cells. CDDP similarly killed both head and neck squamous cell carcinoma cells (UMSCC-14C) and normal oral epithelial cells (OEC). TQ alone exerted considerable cytotoxicity against UMSCC-14C cells, while it induced a weaker killing effect against normal oral epithelial cells (OEC). The equitoxic combination of TQ and CDDP showed additive to synergistic interaction against both UMSCC-14C and OEC cells. TQ alone increased apoptotic cell fraction in UMSCC-14C cells as early as after 6 hours. In addition, prolonged exposure of UMSCC-14C to TQ alone resulted in 96.7±1.6% total apoptosis, which was increased after combination with CDDP to 99.3±1.2% in UMSCC-14C cells. On the other hand, TQ induced a marginal increase in the apoptosis in OEC and even decreased the apoptosis induced by CDDP alone. Finally, apoptosis induction results were confirmed by the change in the expression levels of p53, Bcl-2 and Caspase-9 proteins in both UMSCC-14c and OEC cells.

Keywords: thymoquinone, cisplatin, apoptosis, oral squamous cell carcinoma, P53, Caspase-9, Bcl-2

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Authors: Albert Perez-Bellmunt, Eila Rivera, Aida Valls, Berta Estragues, Sara Ortiz, Roberto Seijas, Pedro Alvarez

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INTRODUCTION: Physical and sports activity on a regular basis present numerous health benefits such as the prevention of cardiovascular and metabolic diseases. Also, there is a relation between sport and the psychological or the cognitive process of children and young people. The objective of the present study is to know if the sports practice has any positive influence on the university academic performance. MATERIALS AND METHODS: The level of the physical activity of 220 students of different degrees in health science was evaluated and compared with the academic results (grades). To assess the level of physical and sports activity, the Global Physical Activity Questionnaire (to calculate the sporting level in a general way) and the International Physical Activity Questionnaire (to estimate the physical activity carried out during the days leading up to the academic exams) were used. RESULTS: The students that realized an average level of sports activity the days before the exam obtained better grades than the rest of their classmate and the result was statistically significant. Controversially, if the sports level was analyzed in a general way, no relationship was observed between academic performance and the level of sport realized. CONCLUSION: A moderate physical activity, on the days leading up to an assessment, can be a positive factor for the university academic performance. Despite the fact that a regular sports activity improves many cognitive and physiological processes, the present study did not observe a direct relationship between sport/physical activity and academic performance.

Keywords: academic performance, academic results, global physical activity questionnaire, physical activity questionnaire, sport, sport practice

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Authors: Abdulrahman M. Alhowikan, Nadra E. Elamin, Sarah S. Aldayel, Sara A. AlSiddiqi, Fai S. Alrowais, Laila Y. Al-Ayadhi

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Background: A growing body of research has suggested that physical activities (PA) have important implications for improving the performance of ASD children. They revealed that the physiological, cognitive, psychological, and behavioral functioning had improved after performing some physical activities. Methods: We compared the sedentary behavior and physical activities between children with autism spectrum disorder (n=21) and age-matched control group (n=30), using the ActiGraph GT3X+ for the assessments. Results: Our results revealed that the total time spent in sedentary activity and the total sedentary activity counts were highly significant in the control group compared to the ASD group (p < 0.001, p=0.001, respectively). ASD spent a significantly longer time than the controls engaging on vigorous physical activity (VPA) (p=0.017). The results also indicated that there were no significant differences between both groups for the total counts and time spent in light physical activity (LPA) and moderate physical activity (MPA). Conclusion: The finding highlights the importance of physical activity intervention for ASD children, using accurate and precise measurement tools to record all activities.

Keywords: Autism spectrum disorders, motor skills, physical activity, ActiGraph GT3X+, moderate-to vigorous-intensity physical activity

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Authors: Sasitorn Chetanont

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The objectives of this study are to find out the approaches to promote healthy recreation activities for elderly tourists and develop Bang Nam Phueng Floating Market to be a health tourism attraction. The research methodology was to analyze internal and external situations according to MP-MF and the MC-STEPS principles. As for the results of this study the researcher found that the healthy recreational activities for elderly tourists could be divided in 7 groups; travelling Bang Nam Phueng Floating Market activity, homestay relaxation, arts center platform activity, healthy massage activity, paying homage to a Buddha image activity, herbal joss-stick home activity, making local desserts and food activity.

Keywords: elderly tourists, recreation activities, Bang Nam Phueng Floating Market, health tourism

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Authors: Isaac Yeboah

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Physical activity (PA) is considered the best preventative tool for maintaining physical health and extending lifespan because it offers a range of benefits. However, for people to benefit from physical activity, it must be done at a level that can enhance fitness, health, and overall well-being. Therefore, this study aimed to determine the link between physical activity participation levels and cardiorespiratory fitness (CRF). The study employed the descriptive correlational design. The census sampling technique included all 190 teaching staff from the two senior high schools in the Dormaa East District. An adapted International Physical Activity Questionnaire (IPAQ) and standardized physical fitness tests were used for data collection. Descriptive statistics of frequency counts and percentages were used to answer the research questions, while inferential statistics of Pearson Product Moment Correlation and the independent sample t-test were used to test hypotheses one and two, respectively. A moderately negative (r = -.156) relationship existed between physical activity participation levels and CRF. Female teachers demonstrated a statistically significant value (p = .045) than males. The study concluded that the reported physical activity levels of the teachers did not reflect their CRF. The implication is that either the participants overestimated their physical activity participation levels or the intensity of the activities was not high enough to affect physiological changes. For the teachers' CRF to improve, it was suggested, among other things, that regular physical activity sessions of the appropriate mixes of FITT be organized.

Keywords: physical activity, participation levels, cardiorespiratory fitness, sedentary lifestyle, teachers

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Authors: Mehdi Nematimoez

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Head posture is paramount to retaining gaze and balance in many activities; its control is thus important in many activities. However, little information is available about the effects of head movement restriction on other spine segment kinematics and movement patterns during lifting and lowering tasks. The aim of this study was to examine the effects of head movement restriction on relative angles and their derivatives using the stepwise segmentation approach during lifting and lowering tasks. Ten healthy men lifted and lowered a box using two styles (stoop and squat), with two loads (i.e., 10 and 20% of body weight); they performed these tasks with two instructed head postures (1. Flexing the neck to keep contact between chin and chest over the task cycle; 2. No instruction, free head posture). The spine was divided into five segments, tracked by six cluster markers (C7, T3, T6, T9, T12, and L5). Relative angles between spine segments and their derivatives (first and second) were analyzed by a stepwise segmentation approach to consider the effect of each segment on the whole spine. Accordingly, head posture significantly affected the derivatives of the relative angles and manifested latency in spine segments movement, i.e., cephalad-to-caudad or caudad-to-cephalad patterns. The relative angles for C7-T3 and T3-T6 increased over the cycle of all lifting and lowering tasks; nevertheless, in lower segments increased significantly when the spine moved into upright standing. However, these effects were clearer during lifting than lowering. Conclusively, the neck flexion can unevenly increase the flexion angles of spine segments from cervical to lumbar over lifting and lowering tasks; furthermore, stepwise segmentation reveals potential for assessing the segmental contribution in spine ROM and movement patterns.

Keywords: head movement restriction, spine kinematics, lifting, lowering, stepwise segmentation

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Authors: Qaiser Akram, Ahsan Naeem, Hafiz Muhammad Rizwan, Waqas Ahmad, Rubeena Yasmeen

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Aspergillus has good secretory potential for phytases. Morphologically and microscopically identified Aspergillus terreus (A. terreus) (n=20) were screened for phytase production and non-toxicity. Phytases produced by non-toxigenic A. terreus under optimum conditions were quantified. Phytases of highest producer A. terreus were evaluated for stability after exposure to temperature (35, 55, 75 and 95ºC) and pH (2, 4, 6 and 8). Effect of metal ions (Fe⁺³, Ba⁺², Ca⁺², Cu⁺², Mg⁺², Mn⁺², K⁺¹ and Na⁺¹) was assessed on phytase activity. Log reduction in phytase activity was calculated. The highest activity units of phytase produced by A. terreus were 271.49 ± 8.14 phytase unit / mL (FTU/ mL). The lowest reduction in phytase activity was 50.20 ± 7.36 (18.5%) and 68.22 ± 10.3 FTU/mL (25.13%) at 35ºC and pH 6, respectively for 15 minutes. The highest reduction 259 ± 0.84 (95.5%) and 211.99 ± 4.39 FTU/mL (78.1%) was recorded at 95ºC for 60 minutes and pH 2.0 for 45 minutes exposure, respectively. All metal ions negatively affected phytase activity. Phytase activity was inhibited minimum (45.32 ± 28.54 FTU/mL, 16.69%) by K⁺¹(1 mM) and maximum (231.48 ± 3.68 FTU/mL, 80.8%) by Cu⁺² (10 mM). It was concluded that A. terreus phytase stability and activity was dependent on physio-chemical factors.

Keywords: stability, phytase, aspergillus terreus, physio-chemical factors and metal ions

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Authors: Shwu-Ling Peng, Chiung-Man Tsai, Chia-Jui Weng

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Chronic micro-inflammation is a hallmark of many aging-related neurodegenerative and metabolic syndrome-driven diseases. In high glucose (HG) environment, reactive oxygen species (ROS) is generated and the ROS induced inflammation, cytokines secretion, DNA damage, and cell cycle arrest to lead to cellular senescence. Water chestnut shell (WCS) is a plant hull which containing polyphenolic compounds and showed antioxidant and anticancer activities. Orchid, which containing a natural polysaccharide compound, possesses many physiological activities including anti-inflammatory and neuroprotective effects. These agricultural plants might be able to reduce oxidative stress and inflammation. This study was used HG-induced human normal dermal fibroblasts (HG-HNDFs) as an in vitro model to disclose the effects of water extract of Phalaenopsis orchid flower (WEPF) and ethanol extract of water chestnut shell (EEWCS) on the anti-aging and their underlying molecular mechanisms. The toxicity of extracts on human normal dermal fibroblasts (HNDFs) was determined by MTT method. The senescence of cells was assayed by β-galactosidase (SA-β-gal) kit. ROS and nitrate production was analyzed by Intracellular ROS contents and ELISA, respectively. Western blotting was used to detect the proteins in cells. The results showed that the exposure of HNDFs to HG (30 mM) for 72 h were caused cellular senescence and arrested cells at G0/G1 phase. Indeed, the treatment of HG-HNDFs with WEPF (200 μg/ml) and EEWCS (10 μg/ml) significantly released cell cycle arrest and promoted cell proliferation. The G1/S phase transition regulatory proteins such as protein retinoblastoma (pRb), p53, and p16ᴵᴺᴷ⁴ᵃ depressed by WEPF and EEWCS were also observed. Additionally, the treatment of WEPF and EEWCS increased the activity of HO-1 through upregulating Nrf2 as well as decreased the ROS and NO of HG-HNDFs. Therefore, the senescence marker protein-30 (SMP30) in cells was diminished. In conclusion, the WEPF and EEWCS might inhibit HG-induced aging of HNDFs by reducing oxidative stress and free radicals.

Keywords: agricultural plant extract, anti-aging, high glucose, Phalaenopsis orchid flower, water chestnut shell

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Authors: M. R. Aher, R. B. Laware, G. S. Asane, B. S. Kuchekar

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Objective: Studies have shown that a new combination therapy with Artemisinin derivatives and curcumin is unique, with potential advantages over known ACTs. In present study an attempt was made to prepare microparticulate drug delivery system of Curcumin-Zn complex and evaluate it in combination with artemether for antimalarial activity. Material and method: Curcumin Zn complex was prepared and encapsulated using sodium alginate. Microparticles thus obtained are further coated with various enteric polymers at different coating thickness to control the release. Microparticles are evaluated for encapsulation efficiency, drug loading and in vitro drug release. Roentgenographic Studies was conducted in rabbits with BaSO 4 tagged formulation. Optimized formulation was screened for antimalarial activity using P. berghei-infected mice survival test and % paracetemia inhibition, alone (three oral dose of 5mg/day) and in combination with arthemether (i.p. 500, 1000 and 1500µg). Curcumin-Zn(II) was estimated in serum after oral administration to rats by using spectroflurometry. Result: Microparticles coated with Cellulose acetate phthalate showed most satisfactory and controlled release with 479 min time for 60% drug release. X-ray images taken at different time intervals confirmed the retention of formulation in GI tract. Estimation of curcumin in serum by spectroflurometry showed that drug concentration is maintained in the blood for longer time with tmax of 6 hours. The survival time (40 days post treatment) of mice infected with P. berghei was compared to survival after treatment with either Curcumin-Zn(II) microparticles artemether combination, curcumin-Zn complex and artemether. Oral administration of Curcumin-Zn(II)-artemether prolonged the survival of P.berghei-infected mice. All the mice treated with Curcumin-Zn(II) microparticles (5mg/day) artemether (1000µg) survived for more than 40 days and recovered with no detectable parasitemia. Administration of Curcumin-Zn(II) artemether combination reduced the parasitemia in mice by more than 90% compared to that in control mice for the first 3 days after treatment. Conclusion: Antimalarial activity of the curcumin Zn-artemether combination was more pronounced than mono therapy. A single dose of 1000µg of artemether in curcumin-Zn combination gives complete protection in P. berghei-infected mice. This may reduce the chances of drug resistance in malaria management.

Keywords: formulation, microparticulate drug delivery, antimalarial, pharmaceutics

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Authors: Kanda Wongwailikhit

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Copper (I) oxide microparticles with the morphology of cubic and hollow sphere were synthesized with the assistance of a surfactant as the shape controller. Both particles were then subjected to a study of the catalytic activity and the results of shape effects of catalysts on rate of catalytic reaction was observed. The decolorizing reaction of crystal violet and sodium hydroxide was chosen and the decrease of reactant with respect to time was measured using a spectrophotometer. The result revealed that morphology of the crystal had no effect on the catalytic activity for the crystal violet reaction but contributed to total surface area predominantly.

Keywords: copper (I) oxide, catalytic activity, crystal violet

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Authors: F. Clara Fang, Hernan Castaneda

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The Connecticut Department of Transportation (ConnDOT) has constructed four roundabouts in the State of Connecticut within the past ten years. VISSIM traffic simulation software was utilized to analyze these roundabouts during their design phase. The queue length and level of service observed in the field appear to be better than predicted by the VISSIM model. The objectives of this project are to: identify VISSIM input variables most critical to accurate modeling; recommend VISSIM calibration factors; and, provide other recommendations for roundabout traffic operations modeling. Traffic data were collected at these roundabouts using Miovision Technologies. Cameras were set up to capture vehicle circulating activity and entry behavior for two weekdays. A large sample size of filed data was analyzed to achieve accurate and statistically significant results. The data extracted from the videos include: vehicle circulating speed; critical gap estimated by Maximum Likelihood Method; peak hour volume; follow-up headway; travel time; and, vehicle queue length. A VISSIM simulation of existing roundabouts was built to compare both queue length and travel time predicted from simulation with measured in the field. The research investigated a variety of simulation parameters as calibration factors for describing driver behaviors at roundabouts. Among them, critical gap is the most effective calibration variable in roundabout simulation. It has a significant impact to queue length, particularly when the volume is higher. The results will improve the design of future roundabouts in Connecticut and provide decision makers with insights on the relationship between various choices and future performance.

Keywords: driver critical gap, roundabout analysis, simulation, VISSIM modeling

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Authors: Elizabeth O. Odewale, Sachithra T. Wanasinghe, Aaron S. Rury

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Cavity polaritons form when molecular excitons strongly couple to photons in carefully constructed optical cavities. These polaritons, which are hybrid light-matter states possessing a unique combination of photonic and excitonic properties, present the opportunity to manipulate the properties of various semiconductor materials. The systematic manipulation of materials through polariton formation could potentially improve the functionalities of many optoelectronic devices such as lasers, light-emitting diodes, photon-based quantum computers, and solar cells. However, the prospects of leveraging polariton formation for novel devices and device operation depend on more complete connections between the properties of molecular chromophores, and the hybrid light-matter states they form, which remains an outstanding scientific goal. Specifically, for most optoelectronic applications, it is paramount to understand how polariton formation affects the spectra of light absorbed by molecules coupled strongly to cavity photons. An essential feature of a polariton state is its dispersive energy, which occurs due to the enhanced spatial delocalization of the polaritons relative to bare molecules. To leverage the spatial delocalization of cavity polaritons, angle-resolved photoluminescence excitation spectroscopy was employed in characterizing light emission from the polaritonic states. Using lasers of appropriate energies, the polariton branches were resonantly excited to understand how molecular light absorption changes under different strong light-matter coupling conditions. Since an excited state has a finite lifetime, the photon absorbed by the polariton decays non-radiatively into lower-lying molecular states, from which radiative relaxation to the ground state occurs. The resulting fluorescence is collected across several angles of excitation incidence. By modeling the behavior of the light emission observed from the lower-lying molecular state and combining this result with the output of angle-resolved transmission measurements, inferences are drawn about how the behavior of molecules changes when they form polaritons. These results show how the intrinsic properties of molecules, such as the excitonic lifetime, affect the rate at which the polaritonic states relax. While it is true that the lifetime of the photon mediates the rate of relaxation in a cavity, the results from this study provide evidence that the lifetime of the molecular exciton also limits the rate of polariton relaxation.

Keywords: flourescece, molecules in cavityies, optical cavity, photoluminescence excitation, spectroscopy, strong coupling

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Authors: Sumit Kumar, Sunil Kumar, Chandan Deep Singh

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This paper presents modeling and simulation of flexible robot in an underwater environment. The underwater environment completely contrasts with ground or space environment. The robot in an underwater situation is subjected to various dynamic forces like buoyancy forces, hydrostatic and hydrodynamic forces. The underwater robot is modeled as Rayleigh beam. The developed model further allows estimating the deflection of tip in two directions. The complete dynamics of the underwater robot is analyzed, which is the main focus of this investigation. The control of robot trajectory is not discussed in this paper. Simulation is performed using Symbol Shakti software.

Keywords: bond graph modeling, dynamics. modeling, rayleigh beam, underwater robot

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Authors: Gamze Uslu, Sebnem Baydere, Alper K. Demir

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In this study, data loss tolerance of Support Vector Machines (SVM) based activity recognition model and multi activity classification performance when data are received over a lossy wireless sensor network is examined. Initially, the classification algorithm we use is evaluated in terms of resilience to random data loss with 3D acceleration sensor data for sitting, lying, walking and standing actions. The results show that the proposed classification method can recognize these activities successfully despite high data loss. Secondly, the effect of differentiated quality of service performance on activity recognition success is measured with activity data acquired from a multi hop wireless sensor network, which introduces high data loss. The effect of number of nodes on the reliability and multi activity classification success is demonstrated in simulation environment. To the best of our knowledge, the effect of data loss in a wireless sensor network on activity detection success rate of an SVM based classification algorithm has not been studied before.

Keywords: activity recognition, support vector machines, acceleration sensor, wireless sensor networks, packet loss

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Authors: Hafiz Md. HasanBabu, Khandaker Mohammad Mohi Uddin, Md. IstiakJaman Ami, Rahat Hossain Faisal

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Computing in biomolecular programming performs through the different types of reactions. Proteins and nucleic acids are used to store the information generated by biomolecular programming. DNA (Deoxyribose Nucleic Acid) can be used to build a molecular computing system and operating system for its predictable molecular behavior property. The DNA device has clear advantages over conventional devices when applied to problems that can be divided into separate, non-sequential tasks. The reason is that DNA strands can hold so much data in memory and conduct multiple operations at once, thus solving decomposable problems much faster. Programmable Logic Array, abbreviated as PLA is a programmable device having programmable AND operations and OR operations. In this paper, a DNA PLA is designed by different molecular operations using DNA molecules with the proposed algorithms. The molecular PLA could take advantage of DNA's physical properties to store information and perform calculations. These include extremely dense information storage, enormous parallelism, and extraordinary energy efficiency.

Keywords: biological systems, DNA computing, parallel computing, programmable logic array, PLA, DNA

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Authors: Smriti, Ajeet Kumar

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We present a variant of the Irving-Kirkwood procedure to obtain the microscopic expressions of the cross-section averaged continuum fields such as internal force and moment in one-dimensional nanostructures in the non-equilibrium setting. In one-dimensional continuum theories for slender bodies, we deal with quantities such as mass, linear momentum, angular momentum, and strain energy densities, all defined per unit length. These quantities are obtained by integrating the corresponding pointwise (per unit volume) quantities over the cross-section of the slender body. However, no well-defined cross-section exists for these nanostructures at finite temperature. We thus define the cross-section of a nanorod to be an infinite plane which is fixed in space even when time progresses and defines the above continuum quantities by integrating the pointwise microscopic quantities over this infinite plane. The method yields explicit expressions of both the potential and kinetic parts of the above quantities. We further specialize in these expressions for helically repeating one-dimensional nanostructures in order to use them in molecular dynamics study of extension, torsion, and bending of such nanostructures. As, the Irving-Kirkwood procedure does not yield expressions of stiffnesses, we resort to a thermodynamic equilibrium approach to obtain the expressions of axial force, twisting moment, bending moment, and the associated stiffnesses by taking the first and second derivatives of the Helmholtz free energy with respect to conjugate strain measures. The equilibrium approach yields expressions independent of kinetic terms. We then establish the equivalence of the expressions obtained using the two approaches. The derived expressions are used to understand the extension, torsion, and bending of single-walled carbon nanotubes at non-zero temperatures.

Keywords: thermoelasticity, molecular dynamics, one dimensional nanostructures, nanotube buckling

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Authors: N. S. Vassilieva-Vashakmadze, R. A. Gakhokidze, I. M. Khachatryan

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In the first part of the paper it is shown that both the depolarization of the cytoplasmic membrane of rods observed in invertebrates and hyperpolarization characteristic of vertebrates on the light may activate the functioning of ion (Na+) channels of cytoplasmic membrane of rods and thus provide the emergence of nerve impulse and its transfer to the neighboring neuron etc. In the second part, using the quantum mechanical program for modeling of the molecular processes, we got a clear picture demonstrating the effect of charged phosphate groups on the protein components of α-helical subunits of the visual rhodopsin receptor. The analysis shows that the phosphorylation of terminal amino acid of seventh α-helical subunits of the visual rhodopsin causes a redistribution of electron density on the atoms, i.e. polarization of subunits, also the changing the configuration of the nuclear subsystem, which corresponds to the deformation process in the molecule. Based on the use of models it can be concluded that this system has an internal relationship between polarization and deformation processes that indicates on the allosteric effect. The allosteric effect is based on quantum-mechanical principle of the self-consistency of the molecules.

Keywords: membrane potential, ion channels, visual rhodopsin, allosteric effect

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Authors: Vigen Barkhudaryan

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The influence of external effects (γ-, UV–radiations, high temperature) in presence of air oxygen on structural transformations of low-density polyethylene (LDPE) have been investigated dependent on the polymers’ thickness, the intensity and the dose of external actions. The methods of viscosimetry, light scattering, turbidimetry and gelation measuring were used for this purpose. The comparison of influence of external effects on LDPE shows, that the destruction and cross-linking processes of macromolecules proceed simultaneously with all kinds of external effects. A remarkable growth of average molecular mass of LDPE along with the irradiation doses and heat treatment exposure growth was established. It was linear for the mass average molecular mass and at the initial doses is mainly the result of the increase of the macromolecular branching. As a result, the macromolecular hydrodynamic volumes have been changed, and therefore the dependence of viscosity average molecular mass on the doses was going through the minimum at initial doses. A significant change of molecular mass, sizes and shape of macromolecules of LDPE occurs under the influence of external effects. The influence is limited only by diffusion of oxygen during -irradiation and heat treatment. At UV–irradiation the influence is limited both by diffusion of oxygen and penetration of radiation. Consequently, the molecular transformations are deeper and evident in case of -irradiation, as soon as the polymer is transformed in a whole volume. It was also established, that the mechanism of molecular transformations in polymers from the surface layer distinctly differs from those of the sample deeper layer. A comparison of the results of these investigations allows us to conclude, that the mechanisms of influence of investigated external effects on polyethylene are similar.

Keywords: cross-linking, destruction, high temperature, LDPE, γ-radiations, UV-radiations

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Authors: Asho Ali

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Tuberculosis is a disease of grave concern which infects one-third of the global population. The high incidence of tuberculosis is further compounded by the increasing emergence of drug resistant strains including multi drug resistant (MDR). Global incidence MDR-TB is ~4%. Molecular epidemiological studies, based on the assumption that patients infected with clustered strains are epidemiologically linked, have helped understand the transmission dynamics of disease. It has also helped to investigate the basis of variation in Mycobacterium tuberculosis (MTB) strains, differences in transmission, and severity of disease or drug resistance mechanisms from across the globe. This has helped in developing strategies for the treatment and prevention of the disease including MDR.

Keywords: Mycobcaterium tuberculosis, molecular epidemiology, drug resistance, disease

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Authors: K. Karapetyan, F. Tkhruni, A. Aghajanyan, T. S. Balabekyan, L. Arstamyan

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Introduction: Globalization of the food supply has created the conditions favorable for the emergence and spread of food-borne and especially dangerous pathogens (EDP) in developing countries. The fresh-cut fruit and vegetable industry is searching for alternatives to replace chemical treatments with biopreservative approaches that ensure the safety of the processed foods product. Antimicrobial compounds of lactic acid bacteria (LAB) possess bactericidal or bacteriostatic activity against intestinal pathogens, spoilage organisms and food-borne pathogens such as Listeria monocytogenes, Staphylococcus aureus and Salmonella. Endemic strains of LAB were isolated. The strains, showing broad spectrum of antimicrobial activity against food spoiling microorganisms, were selected. The genotyping by 16S rRNA sequencing, GS-PCR, RAPD PCR methods showed that they were presented by Lactobacillus rhamnosus109, L.plantarum 65, L.plantarum 66 and Enterococcus faecium 64 species. LAB are deposited in "Microbial Depository Center" (MDC) SPC "Armbiotechnology". Methods: LAB strains were isolated from different dairy products from rural households from the highland regions of Armenia. Serially diluted samples were spread on MRS (Merck, Germany) and hydrolyzed milk agar (1,2 % w/v). Single colonies from each LAB were individually inoculated in liquid MRS medium and incubated at 37oC for 24 hours. Culture broth with biomass was centrifuged at 10,000 g during 20 min for obtaining of cell free culture broth (CFC). The antimicrobial substances from CFC broth were purified by the combination of adsorption-desorption and ion-exchange chromatography methods. Separation of bacteriocins was performed using a HPLC method on "Avex ODS" C18 column. Mass analysis of peptides recorded on the device API 4000 in the electron ionization mode. The spot-on-lawn method on the test culture plated in the solid medium was applied. The antimicrobial activity is expressed in arbitrary units (AU/ml). Results. Purification of CFC broth of LAB allowed to obtain partially purified antimicrobial preparations which contains bacteriocins with broad spectrum of antimicrobial activity. Investigation of their main biochemical properties shown, that inhibitory activity of preparations is partially reduced after treatment with proteinase K, trypsin, pepsin, suggesting a proteinaceous nature of bacteriocin-like substances containing in CFC broth. Preparations preserved their activity after heat treatment (50-121 oC, 20 min) and were stable in the pH range 3–8. The results of SDS PAAG electrophoresis show that L.plantarum 66 and Ent.faecium 64 strains have one bacteriocin (BCN) with maximal antimicrobial activity with approximate molecular weight 2.0-3.0 kDa. From L.rhamnosus 109 two BCNs were obtained. Mass spectral analysis indicates that these bacteriocins have peptide bonds and molecular weight of BCN 1 and BCN 2 are approximately 1.5 kDa and 700 Da. Discussion: Thus, our experimental data shown, that isolated endemic strains of LAB are able to produce bacteriocins with high and different inhibitory activity against broad spectrum of microorganisms of different taxonomic group, such as Salmonella sp., Esherichia coli, Bacillus sp., L.monocytogenes, Proteus mirabilis, Staph. aureus, Ps. aeruginosa. Obtained results proved the perspectives for use of endemic strains in the preservation of foodstuffs. Acknowledgments: This work was realized with financial support of the Project Global Initiatives for Preliferation Prevention (GIPP) T2- 298, ISTC A-1866.

Keywords: antimicrobial activity, bacteriocins, endemic strains, food safety

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Authors: Bin Wang, Yong Xu, Honggang Qu, Rongmei Liu, Zhenji Gao

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Today's mining industry is advancing gradually toward digital and visual direction. The three dimensional visualization geological modeling of mine is the digital characterization of mineral deposit, and is one of the key technology of digital mine. The three-dimensional geological modeling is a technology that combines the geological spatial information management, geological interpretation, geological spatial analysis and prediction, geostatistical analysis, entity content analysis and graphic visualization in three-dimensional environment with computer technology, and is used in geological analysis. In this paper, the three-dimensional geological modeling of an iron mine through the use of Surpac is constructed, and the weight difference of the estimation methods between distance power inverse ratio method and ordinary kriging is studied, and the ore body volume and reserves are simulated and calculated by using these two methods. Compared with the actual mine reserves, its result is relatively accurate, so it provided scientific bases for mine resource assessment, reserve calculation, mining design and so on.

Keywords: three-dimensional geological modeling, geological database, geostatistics, block model

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Authors: Apisaraporn Baicharoen, Prapasiri Pongprayoon

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Betaine aldehyde dehydrogenase 2 (BADH2) is an enzyme that inhibits the accumulation of 2-acetyl-1-pyrroline (2AP), a potent flavor compound in rice fragrance. BADH2 contains three domains (NAD-binding, substrate-binding, and oligomerization domains). It catalyzes the oxidation of amino aldehydes. The lack of BADH2 results in the formation of 2AP and consequently an increase in rice fragrance. To date, inadequate data on BADH2 structure and function are available. An insight into the nature of BADH2 can serve as one of key starting points for the production of high quality fragrant rice. In this study, we therefore constructed the homology model of BADH2 and employed 500-ns Molecular Dynamics simulations (MD) to primarily understand the structural and dynamic properties of BADH2. Initially, Ramachandran plot confirms the good quality of modeled protein structure. Principle Component Analysis (PCA) was also calculated to capture the protein dynamics. Among 3 domains, the results show that NAD binding site is found to be more flexible. Moreover, interactions from key amino acids (N162, E260, C294, and Y419) that are crucial for function are investigated.

Keywords: betaine aldehyde dehydrogenase 2, fragrant rice, homology modeling, molecular dynamics simulations

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Authors: Karakhalis N. B.

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This study aimed to determine the prevalence of heparin resistance among cardiac surgical pediatric and neonatal patients and identify associated risk factors. Materials and Methods: The study included 306 pediatric and neonatal patients undergoing on-pump cardiac surgery. Patients whose activated clotting time (ACT) targets were achieved after the first administration of heparin formed the 1st group (n=280); the 2nd group (n=26) included patients with heparin resistance. The initial assessment of the haemostasiological profile included determining the PT, aPPT, FG, AT III activity, and INR. Intraoperative control of heparinization was carried out with a definition of ACT using a kaolin activator. A weight-associated protocol at the rate of 300 U/kg with target values of ACT >480 sec was used for intraoperative heparinization. Results: The heparin resistance was verified in 8.5% of patients included in the study. Repeated heparin administration at the maximum dose of≥600 U/kg is required in 80.77% of cases. Despite additional heparinization, 19.23% of patients had FFP infusion. There was reduced antithrombin activity in the heparin resistance group (p=0.01). Most patients with heparin resistance (57.7%) were pretreated with low molecular weight heparins during the preoperative period. Conclusion: Determining the initial level of antithrombin activity can predict the risk of developing heparin resistance. The factor analysis verified hidden risk factors for heparin resistance to the heparin pretreatment, chronic hypoxia, and chronic heart failure.

Keywords: congenital heart disease, heparin, antithrombin, activated clotting time, heparin resistance

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Authors: Salem El-Tohami Ashoor

Abstract:

A novel new vanadium (IV) complexes incorporating the chelating diamido cyclopentadienyl {ArN(CH2)3NAr)}2-((ηn-Cp)Cp)} (Ar = 2,6-Pri2C6H3)(Cp = C5H5 and n = 1,2,3,4 and 5) have been studied with calculation of the properties of species involved in various of cyclopentadienyl reaction. These were carried out under investigation of density functional theory (DFT) calculation, and comparing together. Other methods, explicitly including electron correlation, are necessary for more accurate calculations; MB3LYP (Becke) (Lee–Yang–Parr) level of theory often being used to obtain more exact results. These complexes were estimated of electronic energy for molecular system, because it accounts for all electron correlation interactions. The optimised of [V(ArN(CH2)3NAr)2Cl(η5-Cp)] (Ar = 2,6-Pri2C6H3 and Cp= C5H5) was found to be thermally more stable than others of vanadium cyclopentadienyl. In the meantime the complex [V(ArN(CH2)3NAr)2Cl(η1-Cp)] (Ar = 2,6-Pri2C6H3 and Cp= C5H5) which is showed a low thermal stability in case of the just one carbon of cyclopentadienyl can be insertion with vanadium metal centre. By using Dewar-Chatt-Duncanson model, as a basis of the molecular orbital (MO) analysis and showed the highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital LUMO.

Keywords: vanadium (IV) cyclopentadienyl complexes, DFT, MO, HOMO, LUMO

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Authors: Kuni Vergauwen, Ivan P. J. Huijnen, Astrid Depuydt, Jasmine Van Regenmortel, Mira Meeus

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A lower activity level and imbalanced activity pattern are frequently observed in persons with chronic fatigue syndrome (CFS) / myalgic encephalomyelitis (ME) due to debilitating fatigue and post-exertional malaise (PEM). Identification of measurement instruments to evaluate the activity level and pattern is therefore important. The objective is to identify measurement instruments suited to evaluate the activity level and/or pattern in patients with CFS/ME and review their psychometric properties. A systematic literature search was performed in the electronic databases PubMed and Web of Science until 12 October 2016. Articles including relevant measurement instruments were identified and included for further analysis. The psychometric properties of relevant measurement instruments were extracted from the included articles and rated based on the COnsensus-based Standards for the selection of health Measurement INstruments (COSMIN) checklist. The review was performed and reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. A total of 49 articles and 15 unique measurement instruments were found, but only three instruments were evaluated in patients with CFS/ME: the Chronic Fatigue Syndrome-Activity Questionnaire (CFS-AQ), Activity Pattern Interview (API) and International Physical Activity Questionnaire-Short Form (IPAQ-SF), three self-report instruments measuring the physical activity level. The IPAQ-SF, CFS-AQ and API are all equally capable of evaluating the physical activity level, but none of the three measurement instruments are optimal to use. No studies about the psychometric properties of activity monitors in patients with CFS/ME were found, although they are often used as the gold standard to measure the physical activity pattern. More research is needed to evaluate the psychometric properties of existing instruments, including the use of activity monitors.

Keywords: chronic fatigue syndrome, data collection, physical activity, psychometrics

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Authors: Shigeyuki Haruyama, Ken Kaminishi, Junji Kaneko, Tadayuki Kyoutani, Siti Ruhana Omar, Oke Oktavianty

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This study is used as a definition method to the value and function in manufacturing sector. In concurrence of discussion about present condition of modeling method, until now definition of 1D-CAE is ambiguity and not conceptual. Across all the physics fields, those methods are defined with the formulation of differential algebraic equation which only applied time derivation and simulation. At the same time, we propose semi-acausal modeling concept and differential algebraic equation method as a newly modeling method which the efficiency has been verified through the comparison of numerical analysis result between the semi-acausal modeling calculation and FEM theory calculation.

Keywords: system model, physical models, empirical models, conservation law, differential algebraic equation, object-oriented

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Authors: Kinza Khan, Dad Muhmmad, Asif Saleem, Nadia Mukhtar, Tahir Yaqub

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Ethomedicines are more commonly used in underdeveloped and developing countries. These medicines are sometimes more potent in controlling microbial infections than conventional medicines. Medicinal plants have been common practice to cure many diseases for centuries. Murraya koenigii is one of these plants and is commonly used in South Asian countries as a flavoring agent in food. To evaluate its anti-microbial activity, six different bacterial strains (Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, Salmonella typhi, Bacillus cereus and Klebsiella pneumonia were used. N-hexane extract of Murraya koenigii leaves shows maximum activity against Bacillus cereus. Acetone extract of Murraya koenigii shoots showed more efficient activity against Pseudomonas aeruginosa Dichloromethane extracts showed maximum activity against Bacillus cereus. Ethanol extract exhibited maximum activity against Pseudomonas aeruginosa and Klebsiella pneumoniae. The methanol extract of Murraya koenigii shoots displayed maximum antibacterial activity against Bacillus cereus. Antifungal activity Ethanol extract was more effective against Candida albicans.

Keywords: ethnomedicines, bacteria, fungi, murraya koenigii, antimicrobial activity

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