Search results for: molecular topology

Authors: Muhammad Munir, Riffat Mehboob, Samina Naeem, Muhammad Salman, Shehryar Ahmed, Irshad Hussain Qureshi, Tahira Murtaza Cheema, Ashraf Sultan, Akmal Laeeq, Nakhshab Choudhry, Asad Aslam Khan, Fridoon Jawad Ahmad

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A dengue outbreak in Lahore, Pakistan during 2011 was unprecedented in terms of severity and magnitude. This research aims to determine the serotype distribution of dengue virus during this outbreak and classify the patients demographically. 5ml of venous blood was drawn aseptically from 166 patients with dengue-like signs to test for the virus between the months of August to November 2011. The samples were sent to the CDC, Atlanta, Georgia for the purpose of molecular assays to determine their serotype. RT-PCR protocol was performed targeting at the 4 dengue serotypes. Out of 166 cases, dengue infection was detected with RT-PCR in 95 cases, all infected with same serotype DEN-2. 75% of positive cases were males while 25% were females. Most positive patients were in the age range of 16-30 years. 33% positive cases had accompanying bleeding. This is first study during the 2011 dengue epidemic in Lahore that reports DEN-2 as the only prevalent serotype. It also indicates that more infected patients were males, adults, within age range of 16-30 years, peaked in the month of November, Dengue hemorrhagic fever (DHF) is manifested more in females, Ravi town was heavily hit by dengue virus infection.

Keywords: dengue, serotypes, Pakistan, DEN 2, Lahore, demography, serotype distrbution, 2011 epidemic

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Authors: Strahinja Kovačević, Lidija Jevrić, Miloš Kuzmanović, Sanja Podunavac-Kuzmanović

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In this paper, various derivatives of benzimidazole have been evaluated against Gram-negative bacteria Escherichia coli. For all investigated compounds the minimum inhibitory concentration (MIC) was determined. Quantitative structure-activity relationships (QSAR) attempts to find consistent relationships between the variations in the values of molecular properties and the biological activity for a series of compounds so that these rules can be used to evaluate new chemical entities. The correlation between MIC and some absorption, distribution, metabolism and excretion (ADME) parameters was investigated, and the mathematical models for predicting the antibacterial activity of this class of compounds were developed. The quality of the multiple linear regression (MLR) models was validated by the leave-one-out (LOO) technique, as well as by the calculation of the statistical parameters for the developed models and the results are discussed on the basis of the statistical data. The results of this study indicate that ADME parameters have a significant effect on the antibacterial activity of this class of compounds. Principal component analysis (PCA) and agglomerative hierarchical clustering algorithms (HCA) confirmed that the investigated molecules can be classified into groups on the basis of the ADME parameters: Madin-Darby Canine Kidney cell permeability (MDCK), Plasma protein binding (PPB%), human intestinal absorption (HIA%) and human colon carcinoma cell permeability (Caco-2).

Keywords: benzimidazoles, QSAR, ADME, in silico

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Authors: Anupuma Raina, Ajay Parkash

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In forensic investigation, DNA analysis helps in the identification of a particular individual under investigation. A set of Short Tandem Repeats loci are widely used for individualization at a molecular level in forensic testing. STRs with tetrameric repeats of DNA are highly polymorphic and widely used for forensic DNA analysis. Identification of an individual became challenging for forensic examiners after Hematopoietic Stem Cell Transplantation. HSCT is a well-accepted and life-saving treatment to treat malignant and nonmalignant diseases. It involves the administration of healthy donor stem cells to replace the patient’s own unhealthy stem cells. A successful HSCT results in complete donor-derived cells in a patient’s hematopoiesis and hence have the capability to change the genetic makeup of the patient. Although an individual who has undergone HSCT and then committed a crime is a very rare situation, but not impossible. Keeping such a situation in mind, various biological samples like blood, buccal swab, and hair follicle were collected and studied after a certain interval of time after HSCT. Blood was collected from both the patient and the donor before the transplant. The DNA profile of both was analyzed using a short tandem repeat kit for autosomal chromosomes. Among all exhibits studied, only hair follicles were found to be the most suitable biological exhibit, as no donor DNA profile was observed for up to 90 days of study.

Keywords: chimerism, HSCT, STRs analysis, forensic identification

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Authors: Jiajia Yao, Guanlin Wu, Fang Liu, Junshuai Xue, Yue Hao

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As the production process of self-standing GaN substrates evolves, the commercialization of low dislocation density, large-scale, semi-insulating self-standing GaN substrates is gradually becoming a reality. This advancement has given rise to increased interest in GaN materials' homoepitaxial technology. However, at the homoepitaxial interface, there are considerable concentrations of impurity elements, including C, Si, and O, which generate parasitic leakage channels at the re-growth junction. This phenomenon results in leaked HEMTs that prove difficult to switch off, rendering them effectively non-functional. The emergence of leakage channels can also degrade the high-frequency properties and lower the power devices' breakdown voltage. In this study, the uniform epitaxy of AlGaN/GaN heterojunction with high electron mobility was accomplished through the surface treatment of the GaN substrates prior to growth and the design of the AlN isolation layer structure. By employing a procedure combining gallium atom in-situ cleaning and plasma nitridation, the C and O impurity concentrations at the homoepitaxial interface were diminished to the scale of 10¹⁷ cm-³. Additionally, the 1.5 nm nitrogen-rich AlN isolation layer successfully prevented the diffusion of Si impurities into the GaN channel layer. The result was an AlGaN/GaN heterojunction with an electron mobility of 1552 cm²/Vs and an electron density of 1.1 × 10¹³ cm-² at room temperature, obtained on a Fe-doped semi-insulating GaN substrate.

Keywords: MBE, AlGaN/GaN, homogenerous epitaxy, HEMT

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Authors: Innocent Kafodya, Guijun Xian

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This paper presents effects of distilled water, seawater and sustained bending strains of 30% and 50% ultimate strain at room temperature, on the durability of unidirectional pultruded carbon fiber reinforced polymer (CFRP) plates. In this study, dynamic mechanical analyzer (DMA) was used to investigate the synergic effects of the immersions and bending strains on the visco-elastic properties of (CFRP) such as storage modulus, tan delta and glass transition temperature. The study reveals that the storage modulus and glass transition temperature increase while tan delta peak decreases in the initial stage of both immersions due to the progression of curing. The storage modulus and Tg subsequently decrease and tan delta increases due to the matrix plasticization. The blister induced damages in the unstrained seawater samples enhance water uptake and cause more serious degradation of Tg and storage modulus than in water immersion. Increasing sustained bending decreases Tg and storage modulus in a long run for both immersions due to resin matrix cracking and debonding. The combined effects of immersions and strains are not clearly reflected due to the statistical effects of DMA sample sizes and competing processes of molecular reorientation and postcuring.

Keywords: pultruded CFRP plate, bending strain, glass transition temperature, storage modulus, tan delta

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Authors: M. Suwaibah, S. W. Tan, I. Aiini, K. Yusoff, A. R. Omar

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Respiratory diseases are the most important infectious diseases affecting poultry worldwide. One of the avian respiratory virus of global importance causing significant economic losses is Infectious Bronchitis Virus (IBV). The virus causes a wide spectrum disease known as Infectious Bronchitis (IB), affecting not only the respiratory system but also the kidney and the reproductive system, depending on its strain. IB and Newcastle disease are two of the most prevalent diseases affecting poultry in Malaysia. However, a study on the molecular characterization of Malaysian IBV is lacking. In this study, an IBV strain IBS130 which was isolated in 2015 was fully sequenced using next-gene sequencing approach. Sequence analysis of IBS130 based on the complete genome, polyprotein 1ab and S1 genes were compared with other IBV sequences available in Genbank, National Center for Biotechnology Information (NCBI). IBV strain IBS130 is characterised as QX-like strain based on whole genome and S1 gene sequence analysis. Comparisons of the virus with other IBV strains showed that the nucleotide identity ranged from 67% to 99.2%, depending on the region analysed. The similarity in whole genome nucleotide ranging from 84.9% to 90.7% with the least similar was from Singapore strains (84.9%) and highly similar with China QX-like strains. Meanwhile, the similarity in polyprotein 1ab ranging from 85.3% to 89.9% with the least similar to Singapore strains (85.3%) and highly similar with Mass strains from USA.

Keywords: infectious bronchitis virus, phylogenetic analysis, chicken, Malaysia

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Authors: Sam Bahreini, Payam Hayati

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Metal-organic coordination [Cu(L)₄(SCN)₂] was synthesized applying ultrasonic irradiation, and its photocatalytic performance for the degradation of Remdesivir (RS) under sunlight irradiation was systematically explored for the first time in this study. The physicochemical properties of the synthesized photocatalyst were investigated using Fourier-transform infrared (FT-IR), field emission scanning electron microscopy (FE-SEM), powder x-ray diffraction (PXRD), energy-dispersive x-ray (EDX), thermal gravimetric analysis (TGA), diffuse reflectance spectroscopy (DRS) techniques. Systematic examinations were carried out by changing irradiation time, temperature, solution pH value, contact time, RS concentration, and catalyst dosage. The photodegradation kinetic profiles were modeled in pseudo-first order, pseudo-second-order, and intraparticle diffusion models reflected that photodegradation onto [Cu(L)₄(SCN)₂] catalyst follows pseudo-first order kinetic model. The fabricated [Cu(L)₄(SCN)₂] nanostructure bandgap was determined as 2.60 eV utilizing the Kubelka-Munk formula from the diffuse reflectance spectroscopy method. Decreasing chemical oxygen demand (COD) (from 70.5 mgL-1 to 36.4 mgL-1) under optimal conditions well confirmed mineralizing of the RS drug. The values of ΔH° and ΔS° was negative, implying the process of adsorption is spontaneous and more favorable in lower temperatures.

Keywords: Photocatalytic degradation, COVID-19, density functional theory (DFT), molecular electrostatic potential (MEP)

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Authors: Bandar A. Alkhayyal

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Modern supply chains are typically linear, transforming virgin raw materials into products for end consumers, who then discard them after use to landfills or incinerators. Nowadays, there are major efforts underway to create a circular economy to reduce non-renewable resource use and waste. One important aspect of these efforts is the development of Green Supply Chain (GSC) systems which enables a reverse flow of used products from consumers back to manufacturers, where they can be refurbished or remanufactured, to both economic and environmental benefit. This paper develops novel multi-objective optimization models to inform GSC system design at multiple levels: (1) strategic planning of facility location and transportation logistics; (2) tactical planning of optimal pricing; and (3) policy planning to account for potential valuation of GSC emissions. First, physical linear programming was applied to evaluate GSC facility placement by determining the quantities of end-of-life products for transport from candidate collection centers to remanufacturing facilities while satisfying cost and capacity criteria. Second, disassembly and remanufacturing processes have received little attention in industrial engineering and process cost modeling literature. The increasing scale of remanufacturing operations, worth nearly $50 billion annually in the United States alone, have made GSC pricing an important subject of research. A non-linear physical programming model for optimization of pricing policy for remanufactured products that maximizes total profit and minimizes product recovery costs were examined and solved. Finally, a deterministic equilibrium model was used to determine the effects of internalizing a cost of GSC greenhouse gas (GHG) emissions into optimization models. Changes in optimal facility use, transportation logistics, and pricing/profit margins were all investigated against a variable cost of carbon, using case study system created based on actual data from sites in the Boston area. As carbon costs increase, the optimal GSC system undergoes several distinct shifts in topology as it seeks new cost-minimal configurations. A comprehensive study of quantitative evaluation and performance of the model has been done using orthogonal arrays. Results were compared to top-down estimates from economic input-output life cycle assessment (EIO-LCA) models, to contrast remanufacturing GHG emission quantities with those from original equipment manufacturing operations. Introducing a carbon cost of $40/t CO2e increases modeled remanufacturing costs by 2.7% but also increases original equipment costs by 2.3%. The assembled work advances the theoretical modeling of optimal GSC systems and presents a rare case study of remanufactured appliances.

Keywords: circular economy, extended producer responsibility, greenhouse gas emissions, industrial ecology, low carbon logistics, green supply chains

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Authors: Atefeh Omidkhah Kharashtomi, Rasoul Hedayat Nejad, Saeed Bakhtiyari

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Circulation paths and indoor connection network of the building play an important role both in the daily operation of the building and during evacuation in emergency situations. The degree of legibility of the paths for navigation inside the building has a deep connection with the perceptive and cognitive system of human, and the way the surrounding environment is being perceived. Human perception of the space is based on the sensory systems in a three-dimensional environment, and non-linearly, so it is necessary to avoid reducing its representations in architectural design as a two-dimensional and linear issue. Today, the advances in the field of virtual reality (VR) technology have led to various applications, and architecture and building science can benefit greatly from these capabilities. Especially in cases where the design solution requires a detailed and complete understanding of the human perception of the environment and the behavioral response, special attention to VR technologies could be a priority. Way-finding in the indoor circulation network is a proper example for such application. Success in way-finding could be achieved if human perception of the route and the behavioral reaction have been considered in advance and reflected in the architectural design. This paper discusses the VR technology applications for the way-finding improvements in indoor engineering of the building. In a systematic review, with a database consisting of numerous studies, firstly, four categories for VR applications for circulation way-finding have been identified: 1) data collection of key parameters, 2) comparison of the effect of each parameter in virtual environment versus real world (in order to improve the design), 3) comparing experiment results in the application of different VR devices/ methods with each other or with the results of building simulation, and 4) training and planning. Since the costs of technical equipment and knowledge required to use VR tools lead to the limitation of its use for all design projects, priority buildings for the use of VR during design are introduced based on case-studies analysis. The results indicate that VR technology provides opportunities for designers to solve complex buildings design challenges in an effective and efficient manner. Then environmental parameters and the architecture of the circulation routes (indicators such as route configuration, topology, signs, structural and non-structural components, etc.) and the characteristics of each (metrics such as dimensions, proportions, color, transparency, texture, etc.) are classified for the VR way-finding experiments. Then, according to human behavior and reaction in the movement-related issues, the necessity of scenario-based and experiment design for using VR technology to improve the design and receive feedback from the test participants has been described. The parameters related to the scenario design are presented in a flowchart in the form of test design, data determination and interpretation, recording results, analysis, errors, validation and reporting. Also, the experiment environment design is discussed for equipment selection according to the scenario, parameters under study as well as creating the sense of illusion in the terms of place illusion, plausibility and illusion of body ownership.

Keywords: virtual reality (VR), way-finding, indoor, circulation, design

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Authors: Yu-Ling Tsai, Chih-Jung Chang, Chia-Chen Lu, Eric Wu, Chuan-Sheng Lin, Tzu-Lung Lin, Hsin-Chih Lai

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It is urgent that novel anti-obesity measures that are safe, effective and widely available are developed for counteracting the rapidly growing obesity epidemics. In the present study, we show that a probiotic bacterium Parabacteroides goldsteinii screened through culture under the high molecular weight polysaccharides prepared from two iconic medicinal fungi, the Ganoderma lucidum and the Hirsutella sinensis, reduced body weight by ca. 20% in high-fat diet (HFD)-fed mice. The bacterium also decreased intestinal permeability, metabolic endotoxemia, inflammation and insulin resistance. Notably, oral administration of live, but not high temperature-killed, P. goldsteinii to HFD fed mice considerably reduces weight gain and obesity-associated metabolic disorders. A three months feeding of the mice with P. goldsteinii did not show any aberrant side effects, indicating the safety of this bacterium. Transcriptome analysis indicated that P. goldsteinii enhances immunity in resting dendritic cells, but reduces inflammation in lipopolysaccharide (LPS)-induced dendritic cells. On top, Naïve T-cells were skewed towards regulatory T-cells after encountering with dendritic cells (DCs) pretreated with P. goldsteinii. These results indicated P. goldsteinii showed anti-inflammatory effects and can work as a potential probiotic ameliorating obesogenicity and related metabolic syndromes.

Keywords: Parabacteroides goldsteinii, gut microbiome, obesity, immune modulation

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Authors: Livy Febria Tedjamulia, Aas Nurasyiah, Ivana Josephin Purnama, Monika Diah Maharani Kusumastuti, Achmad Ridwan Ariyantoro

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Papua's candy is one of Indonesia’s indigenous consumption consisting of areca nut (Areca catechu), forest betel fruit (Piper aduncum), and CaCO3. This research aims to determine the concentration of tannins in areca nut, alkaloids in areca nut, flavonoids in forest betel fruit; detect their interaction and CaCO3; also toform a standardize consumption recommendation. The research methodwas includingDPPH assay for papua’s candy mixture, which resulted in IC50 value. Data analysis used is mathematical linear regression for each experiment. The test result of alkaloid is a Rf value of 0.773, while concentration of tannin and flavonoidare 0.603 mgGAE/g and 125.402 gQE/g, respectively. The IC50 value shows number of 3.0403, showing high antioxidant capacity.Other antioxidant assays were being studied using literature review, namely trolox and oxygen radical absorbance capacity, to figure out interaction among the bioactive compounds. It turned out that the interaction detected is antagonistic, which means the compound that is joined already has a stable molecular structure so that could reduce free radicals by donating hydrogen atoms. The recommendation consumptions given are 4 areca nuts, 5 forest betels, and 1 gram of lime betel. Therefore, papua's candy has its potential to be developed into functional food.

Keywords: antioxidant, bioactive compounds interaction, free radical, papua’s candy

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Authors: Chuan-Wen Liu, Min-Hsien Liu, Chung-Chieh Tai, Bing-Cheng Kuo, Cheng-Lung Chen, Huazhen Shen

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A recent surge in research on magnetic radar absorbing materials (RAMs) has presented researchers with new opportunities and challenges. This study was performed to gain a better understanding of the wave-absorbing phenomenon of magnetic RAMs. First, we hypothesized that the absorbing phenomenon is dependent on the particle shape. Using the Material Studio program and the micro-dot magnetic dipoles (MDMD) method, we obtained results from magnetic RAMs to support this hypothesis. The total MDMD energy of disk-like iron particles was greater than that of spherical iron particles. In addition, the particulate aggregation phenomenon decreases the wave-absorbance, according to both experiments and computational data. To conclude, this study may be of importance in terms of explaining the wave- absorbing characteristic of magnetic RAMs. Combining molecular dynamics simulation results and the theory of magnetization of magnetic dots, we investigated the magnetic properties of iron materials with different particle shapes and degrees of aggregation under external magnetic fields. The MDMD of the materials under magnetic fields of various strengths were simulated. Our results suggested that disk-like iron particles had a better magnetization than spherical iron particles. This result could be correlated with the magnetic wave- absorbing property of iron material.

Keywords: wave-absorbing property, magnetic material, micro-dot magnetic dipole, particulate aggregation

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Authors: Zhao Yang Liu, Jing Tao

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The Asian long-horned beetle, Anoplophora glabripennis (Motschulsky) (Coleoptera: Cerambycidae: Lamiinae), is a wood-borer and polyphagous xylophages native to Asia and killing healthy trees. As it causes serious danger to trees, the beetle has been paid close attention in the world. However, the genetic markers limited, especially microsatellite. In this study, 24 novel simple sequence repeat (SSR) molecular markers, a powerful tool for genetic diversity studies and linkage map construction, were developed and characterized from whole genome shotgun sequences. We developed SSR loci of 2 to 6 repeated and perfect units including 9895 points, the density of SSRs was found one SSR per 56.57 kb and the abundance of SSR was 0.02/kb, besides 140 types of repeats motifs were found. Half of the 48 pairs SSR primers (containing 4 di-, 7 tri-, 2 tetra- and 11 hexamers SSRs) we selected randomly from 1222 pairs of primers were polymorphism. The number of alleles for these markers in 48 individuals varied from 3 to 21 with an average of 7.71, the number of effective alleles ranged from 1.22 to 9.97 with an average of 3.54. Besides this, the polymorphic information content (PIC) ranged from 0.18 to 0.89 with a mean of 0.65, And Shannon's Information index (I) ranged from 0.46 to 2.62 with an average of 1.44. The results suggest that the method for screening of SSR in the whole genome is feasible and efficient. SSR markers developed in this study can be used for population genetic studies of A. glabripennis. Moreover, they may also be helpful for the development of microsatellites for other Coleoptera.

Keywords: SSR markers, Anoplophora glabripennis, genetic diversity, whole genome

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Authors: Taoufik Bettaieb, Sihem Soufi

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As a bioactive metalloid, silicon (Si) is an essential element for plant growth and development. It also plays a crucial role in enhancing plants’ resilience to different abiotic and biotic stresses. The morpho-physiological, biochemical, and molecular background of Si-mediated stress tolerance in plants were unraveled. Cold stress is a severe abiotic stress response to the decrease of plant growth and yield by affecting various physiological activities in plants. Several approaches have been used to alleviate the adverse effects generated from cold stress exposure, but the cost-effective, environmentally friendly, and defensible approach is the supply of silicon. Silicon has the ability to neutralize the harmful impacts of cold stress. Therefore, based on these hypotheses, this study was designed in order to investigate the morphological and physiological background of silicon effects applied at different concentrations on cold stress mitigation during early growth of a turfgrass, namely Paspalum vaginatum Sw. Results show that silicon applied at different concentrations improved the morphological development of Paspalum subjected to cold stress. It is also effective on the photosynthetic apparatus by maintaining stability the photochemical efficiency. As the primary component of cellular membranes, lipids play a critical function in maintaining the structural integrity of plant cells. Silicon application decreased membrane lipid peroxidation and kept on membrane frontline barrier relatively stable under cold stress.

Keywords: crops, cold stress, silicon, abiotic stress

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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: Ashfaque Hossain Khan, Brian Thomson, Ratan Debnath, Abhishek Motayed, Mulpuri V. Rao

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Though the efforts had been made, the problem of cross-sensitivity for a single metal oxide-based sensor can’t be fully eliminated. In this work, a sensor array has been designed and fabricated comprising of platinum (Pt), copper (Cu), and silver (Ag) decorated TiO2 and ZnO functionalized GaN nanowires using industry-standard top-down fabrication approach. The metal/metal-oxide combinations within the array have been determined from prior molecular simulation study using first principle calculations based on density functional theory (DFT). The gas responses were obtained for both single and mixture of NO2, SO2, ethanol, and H2 in the presence of H2O and O2 gases under UV light at room temperature. Each gas leaves a unique response footprint across the array sensors by which precise discrimination of cross-sensitive gases has been achieved. An unsupervised principal component analysis (PCA) technique has been implemented on the array response. Results indicate that each gas forms a distinct cluster in the score plot for all the target gases and their mixtures, indicating a clear separation among them. In addition, the developed array device consumes very low power because of ultra-violet (UV) assisted sensing as compared to commercially available metal-oxide sensors. The nanowire sensor array, in combination with PCA, is a potential approach for precise real-time gas monitoring applications.

Keywords: cross-sensitivity, gas sensor, principle component analysis (PCA), sensor array

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Authors: Hye Kyung Kim, Myung-Gyou Kim, Kang-Hyun Leem

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It has been reported that deer antler extract has bone-strengthening activity and effectively used in bone diseases therapy. However, little is known about the cellular and molecular mechanism of this effect. The upper section, mid section, and base of the antler has been known to exhibit different biological properties. Present study investigated the effects of these three parts of deer antler extracts on bone formation and resorption. The effects of deer antler extracts (DH) on bone formation were determined by cell proliferation, alkaline phosphatase (ALP) activity, collagen synthesis, and mineralization in human osteoblastic MG-63 cells. The effect on bone resorption was determined by osteoclastogenesis from bone marrow-derived precursor cells driven by RANKL. Ethanol extracts of DH (50 ~ 100 µg/ml) dose-dependently increased cell proliferation, and upper part increased the cell proliferation by 118.4% while mid and base parts increased proliferation by 107.8% and 102.3%, respectively. ALP activity was significantly increased by upper part of the DH treatment. After enhancement of ALP activity, significant augmentation of collagen synthesis and calcification assessed by Sirus red and Alzarin red staining, respectively, was observed in upper part of the DH treatment. The effect of DH on bone resorption was not observed in all three parts of the DH. These results could provide a mechanistic explanation for the bone-strengthening effects of DH.

Keywords: alkaline phosphatase, collagen synthesis, deer antler, osteoblastic MG-63 cells

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Authors: Adewole Tomiwa Adetunji, Francis Bayo Lewu, Richard Mundembe

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Plants require nitrogen (N) to support desired production levels. There is a need for better understanding of N transport mechanism in order to improve N assimilation by plant root. Nitrogen is available to plants in the form of nitrate or ammonium, which are transported into the cell with the aid of various transport proteins. Ammonium transporters (AMTs) play a role in the uptake of ammonium, the form in which N is preferentially absorbed by plants. Solanum tuberosum AMT1 (StAMT1) was amplified, sequenced and characterized using molecular biology and bioinformatics methods. Nucleotide database sequences were used to design 976 base pairs AMT1-specific primers which include forward primer 5’- GCCATCGCCGCCGCCGG-3’ and reverse primer 5’-GGGTCAGATCCATACCCGC-3’. These primers were used to amplify the Solanum tuberosum AMT1 internal regions. Nucleotide sequencing, alignment and phylogenetic analysis assigned StAMT1 to the AMT1 family due to the clade and high similarity it shared with other plant AMT1 genes. The deduced amino acid sequences showed that StAMT1 is 92%, 83% and 76% similar to Solanum lycopersicum LeAMT1.1, Lotus japonicus LjAMT1.1, and Solanum lycopersicum LeAMT1.2 respectively. StAMT1 fragments were shown to correspond to the 5th-10th trans-membrane domains. Residue StAMT1 D15 is predicted to be essential for ammonium transport, while mutations of StAMT1 S76A may further enhance ammonium transport.

Keywords: ammonium transporter, bioinformatics, nitrogen, primers, Solanum tuberosum

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Authors: S. Salah, S. A. El-Masry, H. F. Sheba, R. A. El-Banna, W. Saad

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Background: Familial Mediterranean fever (FMF) has episodic or subclinical inflammation that may lead to a decrease in bone mineral density (BMD). Objective: To assess BMD in Egyptian children with FMF on genetic basis. Subjects and Methods: A cross sectional study included 45 FMF patients and 25 control children of both sexes, with age range between 3-16 years old. The patients were reclassified into 2 groups: Group I (A) 23 cases used colchicines for 1 month or less, and Group I (B) 22 cases used colchicines for more than 6 months. For both patients and control, MEFV mutations were defined using molecular genetics technique and BMD was measured by DXA at 2 sites: proximal femur and the lumber spines. Results: four frequent gene mutations were found in the patient group: E148Q (35.6%), V726A (33.3%), M680I (28.9.0%) and M694V (2.2%). There were also 4 heterozygous gene mutations in 40% of control children. Patients received colchicines treatment for less than 1 month had highly significant lower values of BMD at femur and lumber spines than control children (p<0.05). Patients received colchicines treatment for more than 6 months had improved values of BMD at femur compared to control, but there were still significant differences between them at lumbar spine (p>0.05). There are insignificant effect of type of gene mutation on BMD and the risk of osteopenia among the patients. Conclusion: FMF had significant effect on BMD. However, regular use of colchicines treatment improves this effect mainly at femur.

Keywords: familial mediterranean fever, bone mineral density, genes, children

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Authors: Ananthakrishna L. R., Ramesh D., Kumar Wodeyar, Kotresh A. M., Gururaj P. M.

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Malnad Gidda is the indigenous recognized cattle breed of Shivamogga District of Karnataka state, India is known for its disease resistance to many of the infectious diseases. There are 25 LRR (Leucine Rich Repeats) identified in bovine (Bos indicus) TLR9. The amino acid sequence of LRR is deduced to nucleotide sequence in BLASTx bioinformatic online tools. LRR2 to LRR10 are involved in pathogen recognition and binding in human TLR9 which showed a higher degree of nucleotide variations with respect to disease resistance to various pathogens. Hence, primers were designed to amplify the flanking sequences of LRR2 to LRR10, to discover the nucleotide variations if any, in Malnad Gidda breed of Cattle which is associated with disease resistance. The DNA isolated from peripheral blood mononuclear cells of ten Malnad Gidda cattle. A desired and specific amplification product of 0.8 kb was obtained at an annealing temperature of 56.6ᵒC. All the PCR products were sequenced on both sides by gene-specific primers. The sequences were compared with TLR9 sequence of cross breed cattle obtained from NCBI data bank. The sequence analysis between Malnad Gidda and crossbreed cattle revealed no nucleotide variations in the region LRR2 to LRR9 which shows the conserved in pathogen binding domain (LRR) of TLR9.

Keywords: leucine rich repeats, Malnad Gidda, cross breed, TLR9

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Authors: Zuzana Chaloupková, Zdeňka Marková, Václav Ranc, Radek Zbořil

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Prostate cancer is now one of the most serious oncological diseases in men with an incidence higher than that of all other solid tumors combined. Diagnosis of prostate cancer usually involves detection of related genes or detection of marker proteins, such as PSA. One of the new potential markers is PSMA (prostate specific membrane antigen). PSMA is a unique membrane bound glycoprotein, which is considerably overexpressed on prostate cancer as well as neovasculature of most of the solid tumors. Commonly applied methods for a detection of proteins include techniques based on immunochemical approaches, including ELISA and RIA. Magnetically assisted surface enhanced Raman spectroscopy (MA-SERS) can be considered as an interesting alternative to generally accepted approaches. This work describes a utilization of MA-SERS in a detection of PSMA in human blood. This analytical platform is based on magnetic nanocomposites Fe3O4@Ag, functionalized by a low-molecular selector labeled as JB303. The system allows isolating the marker from the complex sample using application of magnetic force. Detection of PSMA is than performed by SERS effect given by a presence of silver nanoparticles. This system allowed us to analyze PSMA in clinical samples with limits of detection lower than 1 ng/mL.

Keywords: diagnosis, cancer, PSMA, MA-SERS, Ag nanoparticles

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Authors: Peikun Zhang, Chunhua Cui

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Photoelectrochemical (PEC) water splitting provides a promising pathway to convert solar energy into renewable fuels. However, the main and seemingly insurmountable obstacle is that the sluggish kinetics of oxygen evolution reaction (OER) severely jeopardizes the overall efficiency, thus exploring highly active, stable, and appreciable catalysts is urgently requested. Herein a competitive coordination strategy was demonstrated to form a reversible hybrid homo-heterogeneous catalyst for efficient OER in alkaline media. The dynamic process involves an in-situ anchoring of soluble nickel–bipyridine pre-catalyst to a conductive substrate under OER and a re-dissolution course under open circuit potential, induced by the competitive coordination between nickel–bipyridine and nickel-hydroxyls. This catalyst allows to elaborately self-modulate a charge-transfer layer thickness upon the catalytic on-off operation, which affords substantially increased active sites, yet remains light transparency, and sustains the stability of over 200 hours of continuous operation. The integration of this catalyst with exemplified state-of-the-art Ni-sputtered Si photoanode can facilitate a ~250 mV cathodic shift at a current density of 20 mA cm-2. This finding helps the understanding of catalyst from a “dynamic” perspective, which represents a viable alternative to address remaining hurdles toward solar-driven water oxidation.

Keywords: molecular catalyst, oxygen evolution reaction, solar energy, transition metal complex, water splitting

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Authors: Nishal Parbhoo, John B. Dewar, Samantha Gildenhuys

Abstract:

Rotavirus is the major cause of severe gastroenteritis worldwide in children aged 5 and younger. Death rates are high particularly in developing countries. The mature rotavirus is a non-enveloped triple-layered nucleocapsid containing 11 double-stranded RNA segments. Here a global view on the sequence and structure of the three main capsid proteins, VP7, VP6, and VP2 is taken by generating a consensus sequence for each of these rotavirus proteins, for each species obtained from published data of representative rotavirus genotypes from across the world and across species. The degree of conservation between species was represented on homology models for each of the proteins. VP7 shows the highest level of variation with 14 - 45 amino acids showing conservation of less than 60%. These changes are localized to the outer surface which is exposed to antibodies alluding to a possible mechanism in evading the immune system. The middle layer, VP6 shows lower variability with only 14-32 sites having lower than 70% conservation. The inner structural layer made up of VP2 showed the lowest variability with only 1-16 sites having less than 70% conservation across species. The results correlate with proteins’ multiple structural roles. Although the nucleotide sequences vary due to an error-prone replication and lack of proofreading, the corresponding amino acid sequence of VP2, 6 and 7 remains conserved. Sequence conservation maintained for the virus results in stable protein structures, fit for function. This can be exploited in drug design, molecular studies and biotechnological applications.

Keywords: amino acid sequence conservation, capsid protein, protein structure, vaccine candidate

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Authors: Cahit Demetgul, Sahin Bayraktar, Neslihan Beyazit

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Metalloenzymes are enzyme proteins containing metal ions, which are directly bound to the protein or to enzyme-bound nonprotein components. One of the major metalloenzymes that play a key role in oxidation reactions is catechol oxidase, which shows catecholase activity i.e. oxidation of a broad range of catechols to quinones through the four-electron reduction of molecular oxygen to water. Studies on the model compounds mimicking the catecholase activity are very useful and promising for the development of new, more efficient bioinspired catalysts, for in vitro oxidation reactions. In this study, a new tetradentate asymmetrical Schiff-base and its Cu(II) complex were synthesized by condensation of 4-nitro-1,2-phenylenediamine with 6-formyl-7-hydroxy-5-methoxy-2-methylbenzopyran-4-one and by using an appropriate Cu(II) salt, respectively. The prepared compounds were characterized by elemental analysis, FT-IR, NMR, UV-Vis and magnetic susceptibility. The catecholase-mimicking activity of the new Schiff Base Cu(II) complex was performed for the oxidation of 3,5-di-tert-butylcatechol (3,5-DTBC) in methanol at 25 °C, where the electronic spectra were recorded at different time intervals. The yield of the quinone (3,5-DTBQ) was determined from the measured absorbance at 400 nm of the resulting solution. The compatibility of catalytic reaction with Michaelis-Menten kinetics was also investigated. In conclusion, we have found that our new Schiff Base Cu(II) complex presents a significant capacity to catalyze the oxidation reaction of the catechol to o-quinone.

Keywords: catecholase activity, Michaelis-Menten kinetics, Schiff base, transition metals

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Authors: M. J. Pourvaghar, M. E. Bahram

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Obesity and overweight is one of the most common metabolic disorders in industrialized countries and in developing countries. One consequence of pathological obesity is cardiovascular disease and metabolic syndrome. Chemerin is an adipocyne that plays a role in the regulation of the adipocyte function and the metabolism of glucose in the liver and musculoskeletal system. Most likely, chemerin is involved in obesity-related disorders such as type 2 diabetes and cardiovascular disease. Aerobic exercises reduce the level of chemerin and cause macrophage penetration into fat cells and inflammatory factors. Several efforts have been made to clarify the cellular and molecular mechanisms of hypertrophy and muscular atrophy. Myostatin, a new member of the TGF-β family, is a transforming growth factor β that its expression negatively regulates the growth of the skeletal muscle; and the increase of this hormone has been observed in conditions of muscular atrophy. While in response to muscle overload, its levels decrease after the atrophy period, TGF-β is the most important cytokine in the development of skeletal muscle. Myostatin plays an important role in muscle control, and animal and human studies show a negative role of myostatin in the growth of skeletal muscle. Separation of myostatin from Golgi begins on the ninth day of the onset period and continues until birth at all times of muscle growth. Higher levels of myostatin are found in obese people. Resistance training for 10 weeks could reduce levels of plasma myostatin.

Keywords: chemerin, myostatin, obesity, physical activity

Procedia PDF Downloads 279

Authors: Jiahui Song

Abstract:

The application of an electric field can cause poration at cell membranes. This includes the outer plasma membrane, as well as the membranes of intracellular organelles. In order to analyze and predict such electroporation effects, it becomes necessary to first evaluate the electric fields and the transmembrane voltages. This information can then be used to assess changes in the pore formation energy that finally yields the pore distributions and their radii based on the Smolchowski equation. The dynamic pore model can be achieved by including a dynamic aspect and a dependence on the pore population density into the pore formation energy equation. These changes make the pore formation energy E(r) self-adjusting in response to pore formation without causing uncontrolled growth and expansion. By using dynamic membrane tension, membrane electroporation in response to a 180kV/cm trapezoidal pulse with a 10 ns on time and 1.5 ns rise- and fall-times is discussed. Poration is predicted to occur at times beyond the peak at around 9.2 ns. Modeling also yields time-dependent distributions of the membrane pore population after multiple pulses. It shows that the pore distribution shifts to larger values of the radius with multiple pulsing. Molecular dynamics (MD) simulations are also carried out for a fixed field of 0.5 V/nm to demonstrate nanopore formation from a microscopic point of view. The result shows that the pore is predicted to be about 0.9 nm in diameter and somewhat narrower at the central point.

Keywords: high-intensity, nanosecond, dynamics, electroporation

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Authors: Jyoti Singh, Swati Dubey, Mukta Singh, R. P. Singh

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The freshwater microalgae Chlorella sp. is alluring considerable interest as a source for biofuel production due to its fast growth rate and high lipid content. Under nitrogen limited conditions, they can accumulate significant amounts of lipids. Thus, it is important to gain insight into the molecular mechanism of their lipid metabolism. In this study under nitrogen limited conditions, regular pattern of growth characteristics lipid accumulation and gene expression analysis of key regulatory genes of lipid biosynthetic pathway were carried out in microalgae Chlorella sp 3. Our results indicated that under nitrogen limited conditions there is a significant increase in the lipid content and lipid productivity, achieving 44.21±2.64 % and 39.34±0.66 mg/l/d at the end of the cultivation, respectively. Time-course transcript patterns of lipid biosynthesis genes i.e. acetyl coA carboxylase (accD) and diacylglycerol acyltransferase (dgat) showed that during late log phase of microalgae Chlorella sp.3 both the genes were significantly up regulated as compared to early log phase. Moreover, the transcript level of the dgat gene is two-fold higher than the accD gene. The results suggested that both the genes responded sensitively to the nitrogen limited conditions during the late log stage, which proposed their close relevance to lipid biosynthesis. Further, this transcriptome data will be useful for engineering microalgae species by targeting these genes for genetic modification to improve microalgal biofuel quality and production.

Keywords: biofuel, gene, lipid, microalgae

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Authors: Dilip Depan, Austin Simoneaux, William Chirdon, Ahmed Khattab

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In this study, we present a novel approach to synthesize polymer nanocomposites with nanohybrid shish-kebab architecture (NHSK). For this low-density and high density polyethylene (PE) was crystallized on various carbon nano-fillers using a novel and convenient method to prepare high-yield NHSK. Polymer crystals grew epitaxially on carbon nano-fillers using a solution crystallization method. The mixture of polymer and carbon fillers in xylene was flocculated and precipitated in ethanol to improve the product yield. Carbon nanofillers of varying diameter were also used as a nucleating template for polymer crystallization. The morphology of the prepared nanocomposites was characterized scanning electron microscopy (SEM), while differential scanning calorimetry (DSC) was used to quantify the amount of crystalline polymer. Interestingly, whatever the diameter of the carbon nanofiller is, the lamellae of PE is always perpendicular to the long axis of nanofiller. Surface area analysis was performed using BET. Our results indicated that carbon nanofillers of varying diameter can be used to effectively nucleate the crystallization of polymer. The effect of molecular weight and concentration of the polymer was discussed on the basis of chain mobility and crystallization capability of the polymer matrix. Our work shows a facile, rapid, yet high-yield production method to form polymer nanocomposites to reveal application potential of NHSK architecture.

Keywords: carbon nanotubes, polyethylene, nanohybrid shish-kebab, crystallization, morphology

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Authors: Muhammad H. Alu’datt, Inteaz Alli

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This study was conducted to prepare and evaluate the biological properties of protein co-precipitates from flaxseed and soybean. Protein was prepared by NaOH extraction through the mixing of soybean flour (Sf) and flaxseed flour (Ff) or mixtures of soybean extract (Se) and flaxseed extract (Fe). The protein co-precipitates were precipitated by isoelectric (IEP) and isoelectric-heating (IEPH) co-precipitation techniques. Effects of extraction and co-precipitation techniques on co-precipitate yield were investigated. Native-PAGE, SDS-PAGE were used to study the molecular characterization. Content and antioxidant activity of extracted free and bound phenolic compounds were evaluated for protein co-precipitates. Removal of free and bound phenolic compounds from protein co-precipitates showed little effects on the electrophoretic behavior of the proteins or the protein subunits of protein co-precipitates. Results showed that he highest protein contents and yield were obtained in for Sf-Ff/IEP co-precipitate with values of 53.28 and 25.58% respectively as compared to protein isolates and other co-precipitates. Results revealed that the Sf-Ff/IEP showed a higher content of bound phenolic compounds (53.49% from total phenolic content) as compared to free phenolic compounds (46.51% from total phenolic content). Antioxidant activities of extracted bound phenolic compounds with and without heat treatment from Sf-Ff/IEHP were higher as compared to free phenolic compounds extracted from other protein co-precipitates (29.68 and 22.84%, respectively).

Keywords: antioxidant, phenol, protein co-precipitate, yield

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Authors: Rini Rahul, Manoj Kumar

Abstract:

Cadmium (Cd) is a poisonous trace metal, which is responsible for excess reactive oxygen species generation (ROS) in plants, thereby adversely affecting their productivity and commercial potential. Ricinus communis (castor) is an industry-efficient non-edible bioenergy crop used for phytoremediation and re-vegetation. We have determined the total Cd content in castor genotypes and established a relationship between the Cd tolerance mechanism and physiological parameters like chlorophyll fluorescence, the total photosynthetic activity, chlorophyll and carotenoid content as well as ROS generation and malondialdehyde content. This study is an effort to comprehend the interrelation between Cd toxicity (control, 250 µM and 500 µM), proline, various ROS scavenging enzymes (anti-oxidative in nature), nicotianamine synthase (NAS) and Natural resistance-associated macrophage protein (NRAMP) gene. The antioxidant enzyme activity increased for WM hence conferring Cd toxicity in this genotype. RcNRAMP genes showed differential expression in GCH2 and WM genotypes; this can also be one of the reasons for Cd toxicity and sensitivity in WM and GCH2, respectively. The cause of pronounced Cd tolerance in WM leaves can be because of enhanced expression of RcNAS1, RcNAS2 and RcNAS3 genes. Our results demonstrate that there is an interrelation between Cd toxicity (control, 250 µM and 500 µM), proline, various ROS scavenging enzymes (anti-oxidative in nature), NAS and NRAMP gene.

Keywords: ricinus communis, cadmium, reactive oxygen species, nicotianamine synthase, NRAMP, malondialdehyde

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