Search results for: functional mutations

Authors: Zhenqiu Liu

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Visualizing the heterogeneity within cell-populations for single-cell RNA-seq data is crucial for studying the functional diversity of a cell. However, because of the high level of noises, outlier, and dropouts, it is very challenging to measure the cell-to-cell similarity (distance), visualize and cluster the data in a low-dimension. Minimum volume embedding (MVE) projects the data into a lower-dimensional space and is a promising tool for data visualization. However, it is computationally inefficient to solve a semi-definite programming (SDP) when the sample size is large. Therefore, it is not applicable to single-cell RNA-seq data with thousands of samples. In this paper, we develop an efficient algorithm with an accelerated proximal gradient method and visualize the single-cell RNA-seq data efficiently. We demonstrate that the proposed approach separates known subpopulations more accurately in single-cell data sets than other existing dimension reduction methods.

Keywords: single-cell RNA-seq, minimum volume embedding, visualization, accelerated proximal gradient method

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Authors: Mahsa Mafi

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Encapsulation of Micrococcus Luteus (M. Luteus) in polymeric composites has been employed for the bioremediation, sequestration of metals and for the biodegradation of chemical pollutants and toxic components in waste water. Polymer composites in the form of nonwovens of nanofibers, or core/shell particles can provide a bacterial friendly environment for transfer of nutrients and metabolisms, with the least leakage of bacteria. M. Luteus is encapsulated in a hydrophilic core of poly (vinyl alcohol), following by synthesis or coating of a proper shell as a support to maintain the chemical and mechanical strength. The biological activity of bacteria is confirmed by Live/Dead analysis and agar plate tests. SEM and TEM analysis were utilized for morphological studies of polymer composites. As a result of the successful encapsulation of the alive bacteria in polymers, longer storage time in their functional state were achieved.

Keywords: Polymer composites, Bacteria encapsulation, Bioremediation, Waste water treatment

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Authors: Eric Chabrol, Sidonia B.G. Eckle, Renate de Boer, James McCluskey, Jamie Rossjohn, Mirjam H.M. Heemskerk, Stephanie Gras

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αβ and γδ T-cells are disparate T-cell lineages that, via their use of either αβ or γδ T-cell antigen receptors (TCRs) respectively, can respond to distinct antigens. Here we characterise a new population of human T-cells, term δβ T-cells, that express TCRs comprising a TCR-δ variable gene fused to a Joining-α/Constant-α domain, paired with an array of TCR-β chains. We characterised the cellular, functional, biophysical and structural characteristic feature of this new T-cells population that reveal some new insight into TCR diversity. We provide molecular bases of how δβ T-cells can recognise viral peptide presented by Human Leukocyte Antigen (HLA) molecule. Our findings highlight how components from αβ and γδTCR gene loci can recombine to confer antigen specificity thus expanding our understanding of T-cell biology and TCR diversity.

Keywords: new delta-beta TCR, HLA, viral peptide, structural immunology

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Authors: Brahim Bahloul, Khatir Babesse, Azzedine Dkhira, Yacine Bahloul, Dalila Hammoutene

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In this paper, we investigate with ab initio calculations some structural and optoelectronic properties of Li₂S compound. The structural and electronic properties of the Li₂S antifluorite structure have been studied by first-principles calculations within the density functional theory (DFT), whereas the optical properties have been obtained using empirical relationships such as the modified Moss relation. Our calculated lattice parameters are in good agreement with the experimental data and other theoretical calculations. The electronic band structures and density of states were obtained. The anti-fluorite Li₂S present an indirect band gap of 3.388 eV at equilibrium. The top of the valence bands reflects the p electronic character for both structures. The calculated energy gaps and optical constants are in good agreement with experimental measurements.

Keywords: Ab initio calculations, antifluorite, electronic properties, optical properties

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Authors: Chee Wee Gan, Anthony Herr Cheun Ng, Yee Shan Wong, Subbu Venkatraman, Lynne Hsueh Yee Lim

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Otitis media with effusion (OME) is the leading cause of hearing loss in children worldwide. Surgery to insert grommet tube into the eardrum is usually indicated for OME unresponsive to antimicrobial therapy. It is the most common surgery for children. However, current commercially available grommet tubes are non-bioresorbable, not drug-treated, with unpredictable duration of retention on the eardrum to ventilate middle ear. Their functionality is impaired when clogged or chronically infected, requiring additional surgery to remove/reinsert grommet tubes. We envisaged that a novel fully bioresorbable grommet tube with sustained antibiotic release technology could address these drawbacks. In this study, drug-loaded bioresorbable poly(L-lactide-co-ε-caprolactone)(PLC) copolymer grommet tubes were fabricated by microinjection moulding technique. In vitro drug release and degradation model of PLC tubes were studied. Antibacterial property was evaluated by incubating PLC tubes with P. aeruginosa broth. Surface morphology was analyzed using scanning electron microscopy. A preliminary animal study was conducted using guinea pigs as an in vivo model to evaluate PLC tubes with and without drug, with commercial Mini Shah grommet tube as comparison. Our in vitro data showed sustained drug release over 3 months. All PLC tubes revealed exponential degradation profiles over time. Modeling predicted loss of tube functionality in water to be approximately 14 weeks and 17 weeks for PLC with and without drug, respectively. Generally, PLC tubes had less bacteria adherence, which were attributed to the much smoother tube surfaces compared to Mini Shah. Antibiotic from PLC tube further made bacteria adherence on surface negligible. They showed neither inflammation nor otorrhea after 18 weeks post-insertion in the eardrums of guinea pigs, but had demonstrated severe degree of bioresorption. Histology confirmed the new PLC tubes were biocompatible. Analyses on the PLC tubes in the eardrums showed bioresorption profiles close to our in vitro degradation models. The bioresorbable antibiotic-loaded grommet tubes showed good predictability in functionality. The smooth surface and sustained release technology reduced the risk of tube infection. Tube functional duration of 18 weeks allowed sufficient ventilation period to treat OME. Our ongoing studies include modifying the surface properties with protein coating, optimizing the drug dosage in the tubes to enhance their performances, evaluating their functional outcome on hearing after full resoption of grommet tube and healing of eardrums, and developing animal model with OME to further validate our in vitro models.

Keywords: bioresorbable polymer, drug release, grommet tube, guinea pigs, otitis media with effusion

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Authors: Tanghourte Mohamed, Ouassou Nazih, El Mesky Mohammed, Znini Mohamed, Mabrouk El Houssine

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In the present study, a distinct organic inhibitor, namely 2,2'-(piperazine-1,4-diyl)bis(N-(4-bromophenyl)acetamide) (PBRA), was synthesized and characterized using ¹H, ¹³C NMR, and IR spectroscopy. Subsequently, the inhibition effect of PBRA on the corrosion of carbon steel in 1 M HCl was studied using electrochemical measurements such as potentiodynamic polarization (PDP) and electrochemical impedance spectroscopy (EIS). The results showed that the inhibition efficiency increased with concentration, reaching 87% at 10-³M. Furthermore, PBRA remained effective at temperatures ranging from 298 to 328 K. The adsorption of the inhibitor onto carbon steel was well described by the Langmuir adsorption isotherm. Additionally, a correlation between the molecular structure and quantum chemistry indices was established using density functional theory (DFT).

Keywords: synthesis, corrosion, inhibition, piperazine, efficacy, isotherm, acetamide

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Authors: A.Zitouni, S.Bentata, B.Bouadjemi, T.Lantri, W. Benstaali, Z.Aziz, S.Cherid, A. Sefir

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Using the first-principles method, we investigate the structural, electronic, and magnetic properties of the diluted magnetic semiconductors CdCoTe and CdMnTe in the zinc blende phase with 12.5% of Cr. The calculations are performed by a developed full potential augmented plane wave (FP-L/APW) method within the spin density functional theory (DFT). As exchange–correlation potential, we used the new generalized gradient approximation GGA. Structural properties are determined from the total energy calculations and we found that these compounds are stable in the ferromagnetic phase. We discuss the electronic structures, total and partial densities of states and local moments. Finally, CdCoTe and CdMnTe in the zinc-blend phase show the half-metallic ferromagnetic nature and are expected to be potential materials for spintronic devices.

Keywords: DFT, GGA, band structures, half-metallic, spintronics

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Authors: R. Sharma, J. K. Bhatnagar, Poonam, R. C. Sharma

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Metal–air batteries have been designed and developed as an essential source of electric power to propel automobiles, make electronic equipment functional, and use them as the source of power in remote areas and space. High energy and power density, lightweight, easy recharge capabilities, and low cost are essential features of these batteries. Both primary and rechargeable magnesium air batteries are highly promising. Our focus will be on the basics of electrode reaction kinetics of Mg–air cell in this paper. Design and development of Mg or Mg alloys as anode materials, design and composition of air cathode, and promising electrolytes for Mg–air batteries have been reviewed. A brief note on the possible and proposed improvements in design and functionality is also incorporated. This article may serve as the primary and premier document in the critical research area of Mg-air battery systems.

Keywords: air cathode, battery design, magnesium air battery, magnesium anode, rechargeable magnesium air battery

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Authors: Liz Jackson

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Fear is usually considered as a basic emotion. In society, it is normally cast as undesirable, but also as partly unavoidable. Fear can be said to underlie courage or be required for courage, or it can be understood as its foil. Fear is not normally promoted (intentionally) in education, or treated as something that should be cultivated in schools or in society. However, fear is a basic, to some extent unavoidable emotion, related to truly fearsome things in the world. Fear is also understood to underlie anxiety. Fear is seen as basically disruptive to education, while from a psychological view it is an ordinary state. that cannot be avoided altogether. Despite calls to diminish this negative and mixed feeling in education and society, it can be regarded as socially and personally valuable, and psychologically functional in some situations. One should not take for granted the goodness of fear. However, it can be productive to explore its moral worth, and uses and abuses. Such uncomfortable feelings and experiences can be cultivated and explored via educational and other societal influences, in ways that can benefit a person and their relations with others in the world, while they can also be detrimental.

Keywords: virtue ethics, philosophy of education, moral philosophy, fear

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Authors: Sobiya George, Anna Dora Gudmundsdottir

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The 2-hydroxychalcones form an important group of organic compounds not only because of their pharmacological properties but also because they are intermediates in the biosynthesis of flavanones. We studied the photoreactivity of 2-hydroxychalcone derivatives in aprotic solvent acetonitrile and found that their photochemistry is concentration-dependent. Irradiation of 2-hydroxychalcone derivatives with 365 nm light emitting diode (LED) in dilute concentration selectively forms flavanones, whereas, at higher concentrations, an additional photoproduct is observed. However, the application of the continuous photo-flow method resulted in the selective formation of flavanones even at higher concentrations. To understand the reaction mechanism and explain the concentration-dependent photoreactivity of 2-hydroxychalcones, we preformed trapping studies with tris(trimethylsilyl)silane, nanosecond laser flash photolysis, and time dependent-density functional theory (TD-DFT) calculations.

Keywords: flavanones, hydroxychalcones, laser flash photolysis, TD-DFT calculations

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Authors: Federico Herrera, Valle Gomez García de Soria, Itxaso Portero Sainz, Carlos Fernández Arandojo, Mercedes Royg, Ana Marcos Jimenez, Anna Kreutzman, Cecilia MuñozCalleja

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Introduction: Graft-versus-host disease (GVHD) still remains the major complication associated with allogeneic stem cell transplantation (SCT). The pathogenesis involves migration of donor naïve T-cells into recipient secondary lymphoid organs. Two molecules are important in this process: CD62L and CCR7, which are characteristically expressed in naïve/central memory T-cells. With this background, we aimed to study the influence of CCR7 and CD62L on donor lymphocytes in the development and severity of GVHD. Material and methods: This single center study included 98 donor-recipient pairs. Samples were collected prospectively from the apheresis product and phenotyped by flow cytometry. CCR7 and CD62L expression in CD4+ and CD8+ T-cells were compared between patients who developed acute (n=40) or chronic GVHD (n=33) and those who did not (n=38). Results: The patients who developed acute GVHD were transplanted with a higher percentage of CCR7+CD4+ T-cells (p = 0.05) compared to the no GVHD group. These results were confirmed when these patients were divided in degrees according to the severity of the disease; the more severe disease, the higher percentage of CCR7+CD4+ T-cells. Conversely, chronic GVHD patients received a higher percentage of CCR7+CD8+ T-cells (p=0.02) in comparison to those who did not develop the complication. These data were also confirmed when patients were subdivided in degrees of the disease severity. A multivariable analysis confirmed that percentage of CCR7+CD4+ T-cells is a predictive factor of acute GVHD whereas the percentage of CCR7+CD8+ T-cells is a predictive factor of chronic GVHD. In vitro functional assays (migration and activation assays) supported the idea of CCR7+ T-cells were involved in the development of GVHD. As low levels of CD62L expression were detected in all apheresis products, we tested the hypothesis that CD62L was shed during apheresis procedure. Comparing CD62L surface levels in T-cells from the same donor immediately before collecting the apheresis product, and the final apheresis product we found that this process down-regulated CD62L in both CD4+ and CD8+ T cells (p=0.008). Interestingly, when CD62L levels were analysed in days 30 or 60 after engraftment, they recovered to baseline (p=0.008). However, to investigate the relation between CD62L expression and the development of GVHD in the recipient samples after the engraftment, no differences were observed comparing patients with GVHD to those who did not develop the disease. Discussion: Our prospective study indicates that the CCR7+ T-cells from the donor, which include naïve and central memory T-cells, contain the alloreactive cells with a high ability to mediate GVHD (in the case of both migration and activation). Therefore we suggest that the proportion and functional properties of CCR7+CD4+ and CCR7+CD8+ T-cells in the apheresis could act as a predictive biomarker to both acute and chronic GVHD respectively. Importantly, our study precludes that CD62L is lost in the apheresis and therefore it is not a reliable biomarker for the development of GVHD.

Keywords: CCR7, CD62L, GVHD, SCT

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Authors: Prat Yotyawilai, Taratip Suwannasart

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Business Process Model and Notation (BPMN) is more important in the business process and creating functional models, and is a standard for OMG, which becomes popular in various organizations and in education. Researches related to software testing based on models are prominent. Although most researches use the UML model in software testing, not many researches use the BPMN Model in creating test cases. Therefore, this research proposes a design of a tool for generating test cases from the BPMN. The model is analyzed and the details of the various components are extracted before creating a flow graph. Both details of components and the flow graph are used in generating test cases.

Keywords: software testing, test case, BPMN, flow graph

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Authors: Supriyono Supriyono, Sumardiyono Sumardiyono, Peni Pujiastuti, Dian Indriana Hapsari

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Crude palm oil (CPO) is a vegetable oil that came from a palm tree bunch. The productivity of the oil is 12 ton/hectare/year. Thus palm oil tree was known as highest vegetable oil yield. It was grown across Equatorial County, especially in Malaysia and Indonesia. The greenish-red color on CPO was come from carotenoid. Carotenoid is one of the antioxidants that could be extracted. Carotenoid could be used as functional food and other purposes. Another antioxidant that also found in CPO is tocopherol. The aim of the research work is to find antioxidant activity on CPO comparing to the synthetic antioxidant that available in a market. In this research work, antioxidant was extracted by a mixture of acetone and n.hexane, while the activity of the antioxidant extract was determined by DPPH method. Antioxidant activity of the extracted compound about 46% compared to pure tocopherol. While the solvent mixture compose by 90% acetone and 10% n. hexane meet the best on the antioxidant activity.

Keywords: antioxidant, beta carotene, crude palm oil, DPPH, tocopherol

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Authors: Sudheer Dhume, T. Prasad

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There are distinct signs of Business Education losing its sheen. It is more so in developing countries. One of the reasons is the value addition at the end of 2 year MBA program is not matching with the requirements of present times and expectations of the students. In this backdrop, Pedagogy Innovation has become prerequisite for making our MBA programs relevant and useful. This paper is the description and analysis of innovative Action Learning pedagogical approach adopted by a group of faculty members at NITIE Mumbai. It not only promotes multidisciplinary research but also enhances integration of the functional areas skillsets in the students. The paper discusses the theoretical bases of this pedagogy and evaluates the effectiveness of it vis-à-vis conventional pedagogical tools. The evaluation research using Bloom’s taxonomy framework showed that this blended method of Business Education is much superior as compared to conventional pedagogy.

Keywords: action learning, blooms taxonomy, business education, innovation, pedagogy

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Authors: Amir Mohammad Parvini, Amir Masoud Rahimi

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Currently, most parts of the world have shifted from traditional roundabouts to modern roundabouts with respect to the role of roundabouts in reducing accidents, increasing safety, lowering the maintenance costs compared to traffic circles with their improper functional and safety experiences. In this study, field data collected from a current traditional roundabout was analyzed by the software AIMSUN and the obtained numbers were recorded. The modern roundabout was designed by changes in the traditional one, considering the geometric standards listed in regulations. Then, the modern roundabout was analyzed by applying a heterogeneous traffic by a micro-simulation software SIDRA (5.1). The function, capacity, and safety of the roundabout were analyzed assuming the superiority of modern roundabouts and acceptable LOS. The obtained results indicate that the function, capacity, and safety of modern roundabouts are better than traditional ones.

Keywords: traditional roundabout, traffic circles, modern roundabout, AIMSUN, SIDRA

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Authors: Vijaya Kumar, Vidayasagar Pagilla, Abraham Joshua, Rakshith Kedambadi, Prasanna Mithra

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Background: Post stroke rehabilitation are aimed to accelerate for optimal sensorimotor recovery, functional gain and to reduce long-term dependency. Intensive physical therapy interventions can enhance this recovery as experience-dependent neural plastic changes either directly act at cortical neural networks or at distal peripheral level (muscular components). Neuromuscular Electrical Stimulation (NMES), a traditional bottom-up approach, mirror therapy (MT), a relatively new top down approach have found to be an effective adjuvant treatment methods for lower extremity motor and functional recovery in stroke rehabilitation. However there is a scarcity of evidence to compare their therapeutic gain in stroke recovery.Aim: To compare the efficacy of neuromuscular electrical stimulation (NMES) and mirror therapy (MT) in very early phase of post stroke rehabilitation addressed to lower extremity motor recovery and balance. Design: observer blinded Randomized Clinical Trial. Setting: Neurorehabilitation Unit, Department of Physical Therapy, Tertiary Care Hospitals. Subjects: 32 acute stroke subjects with first episode of unilateral stroke with hemiparesis, referred for rehabilitation (onset < 3 weeks), Brunnstorm lower extremity recovery stages ≥3 and MMSE score more than 24 were randomized into two group [Group A-NMES and Group B-MT]. Interventions: Both the groups received eclectic approach to remediate lower extremity recovery which includes treatment components of Roods, Bobath and Motor learning approaches for 30 minutes a day for 6 days. Following which Group A (N=16) received 30 minutes of surface NMES training for six major paretic muscle groups (gluteus maximus and medius,quadriceps, hamstrings, tibialis anterior and gastrocnemius). Group B (N=16) was administered with 30 minutes of mirror therapy sessions to facilitate lower extremity motor recovery. Outcome measures: Lower extremity motor recovery, balance and activities of daily life (ADLs) were measured by Fugyl Meyer Assessment (FMA-LE), Berg Balance Scale (BBS), Barthel Index (BI) before and after intervention. Results: Pre Post analysis of either group across the time revealed statistically significant improvement (p < 0.001) for all the outcome variables for the either group. All parameters of NMES had greater change scores compared to MT group as follows: FMA-LE (25.12±3.01 vs. 23.31±2.38), BBS (35.12±4.61 vs. 34.68±5.42) and BI (40.00±10.32 vs. 37.18±7.73). Between the groups comparison of pre post values showed no significance with FMA-LE (p=0.09), BBS (p=0.80) and BI (p=0.39) respectively. Conclusion: Though either groups had significant improvement (pre to post intervention), none of them were superior to other in lower extremity motor recovery and balance among acute stroke subjects. We conclude that eclectic approach is an effective treatment irrespective of NMES or MT as an adjunct.

Keywords: balance, motor recovery, mirror therapy, neuromuscular electrical stimulation, stroke

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Authors: A. Nusrath Unissa, Sameer Hassan, Luke Elizabeth Hanna

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Altered drug binding may be an important factor in isoniazid (INH) resistance, rather than major changes in the enzyme’s activity as a catalase or peroxidase (KatG). The identification of structural or functional defects in the mutant KatGs responsible for INH resistance remains as an area to be explored. In this connection, the differences in the binding affinity between wild-type (WT) and mutants of KatG were investigated, through the generation of three mutants of KatG, Ser315Thr [S315T], Ser315Asn [S315N], Ser315Arg [S315R] and a WT [S315]) with the help of software-MODELLER. The mutants were docked with INH using the software-GOLD. The affinity is lower for WT than mutant, suggesting the tight binding of INH with the mutant protein compared to WT type. These models provide the in silico evidence for the binding interaction of KatG with INH and implicate the basis for rationalization of INH resistance in naturally occurring KatG mutant strains of Mycobacterium tuberculosis.

Keywords: Mycobacterium tuberculosis, KatG, INH resistance, mutants, modelling, docking

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Authors: Marina Stramarkou, Sofia Papadaki, Konstantina Kyriakopoulou, Magdalini Krokida

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Nowadays, microalgae represent the diverse branch of microorganism that is used not only in fish farming, but also in food, cosmetics, pharmaceuticals and biofuel production as they can produce a wide range of unique functional ingredients. In the present work, a remarkable microalga Chlorella vulgaris (CV) was selected as a raw material for the recovery of multifunctional extracts. First of all, the drying of raw biomass was examined with freeze-drying showing the best behavior. Ultrasonic-assisted extraction (UAE) using different solvents was applied under the specific optimized conditions. In case of raw biomass, ethanol was the suitable solvent, whereas on dried samples water performed better. The total carotenoid, β-carotene, chlorophyll and protein content in the raw materials, extracts and extraction residues was determined using UV-Vis spectrometry. The microalgae biomass and the extracts were evaluated regarding their antiradical activity using the DPPH method.

Keywords: antioxidant activity, pigments, proteins, ultrasound assisted extraction

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Authors: Magno Enrique Mendoza Meza

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This paper deals with the comparison of three control techniques: the hysteresis on-off control (HyOOC), the hybrid on-off control (HOOC) and the simple Structured Treatment Interruptions (sSTI). These techniques are applied to the mathematical model developed by Kirschner and Webb. To compare these techniques we use a cost functional that minimize the wild-type virus population and the mutant virus population, but the main objective is to minimize the systemic cost of treatment and maximize levels of healthy CD4+ T cells. HyOOC, HOOC, and sSTI are applied to the drug therapies using a reverse transcriptase and protease inhibitors; simulations show that these controls maintain the uninfected cells in a small, bounded neighborhood of a pre-specified level. The controller HyOOC and HOOC are designed by appropriate choice of virtual equilibrium points.

Keywords: virus dynamics, on-off control, hysteresis, multi-drug therapies

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Authors: O. R. Raimi, A. Lateef

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Inoculum developments of A. niger were used for inoculation of medium for submerged fermentation and solid state fermentation. The filtrate obtained were used as sources of the extra-cellular enzymes. The FTase activities and the course of pH in submerged fermentation ranged from 7.53-24.42µ/ml and 4.4-4.8 respectively. The maximum FTase activity was obtained at 48 hours fermentation. In solid state fermentation, FTase activities ranged from 2.41-27.77µ/ml. Using ripe plantain peel and kola nut pod respectively. Both substrates supported the growth of the fungus, producing profuse growth during fermentation. In the control experiment (using kolanut pod) that lack supplementation, appreciable FTase activity of 16.92µ/ml was obtained. The optimum temperature range was 600C. it was also active at broad pH range of 1-9 with optimum obtain at pH of 5.0. FTase was stable within the range of investigated pH showing more than 60% activities. FTase can be used in the production of fructooligosaccharide, a functional food.

Keywords: Aspergillus niger, solid state fermentation, kola nut pods, Fructosyltransferase (FTase)

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Authors: Mintesinot Teshome Mengsha

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Reinforced concrete structural walls are provided in structures to decrease horizontal displacements under seismic loads. The cyclic lateral load resistance capacity of a structural wall is controlled by two parameters, the strength and the ductility; it is better to have the shear strength somewhat greater than the compression to prevent shear failure, which is brittle, sudden and of serious consequence. Due to architectural and functional reasons, small openings are provided in this important structural part. The main objective of this study is to investigate the finite element of RC structural walls with small openings subjected to cyclic load using the finite element approach. The experimental results in terms of load capacity, failure mode, crack pattern, flexural strength, shear strength, and deformation capacity.

Keywords: ABAQUS, finite element method, small openings, reinforced concrete structural walls

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Authors: Leonard Lipovich, Pattaraporn Thepsuwan, Anton-Scott Goustin, Juan Cai, Donghong Ju, James B. Brown

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Two-thirds of human genes do not encode any known proteins. Aside from long non-coding RNA (lncRNA) genes with recently-discovered functions, the ~40,000 non-protein-coding human genes remain poorly understood, and a role for their transcripts as de-facto unconventional messenger RNAs has not been formally excluded. Ribosome profiling (Riboseq) predicts translational potential, but without independent evidence of proteins from lncRNA open reading frames (ORFs), ribosome binding of lncRNAs does not prove translation. Previously, we mass-spectrometrically documented translation of specific lncRNAs in human K562 and GM12878 cells. We now examined lncRNA translation in human MCF7 cells, integrating strand-specific Illumina RNAseq, Riboseq, and deep mass spectrometry in biological quadruplicates performed at two core facilities (BGI, China; City of Hope, USA). We excluded known-protein matches. UCSC Genome Browser-assisted manual annotation of imperfect (tryptic-digest-peptides)-to-(lncRNA-three-frame-translations) alignments revealed three peptides hypothetically explicable by 'stop-to-nonstop' in-frame replacement of stop codons by amino acids in two ORFs of the lncRNA MMP24-AS1. To search for this phenomenon genomewide, we designed and implemented a novel pipeline, matching tryptic-digest spectra to wildcard-instead-of-stop versions of repeat-masked, six-frame, whole-genome translations. Along with singleton putative stop-to-nonstop events affecting four other lncRNAs, we identified 24 additional peptides with stop-to-nonstop in-frame substitutions from multiple positive-strand MMP24-AS1 ORFs. Only UAG and UGA, never UAA, stop codons were impacted. All MMP24-AS1-matching spectra met the same significance thresholds as high-confidence known-protein signatures. Targeted resequencing of MMP24-AS1 genomic DNA and cDNA from the same samples did not reveal any mutations, polymorphisms, or sequencing-detectable RNA editing. This unprecedented apparent gene-specific violation of the genetic code highlights the importance of matching peptides to whole-genome, not known-genes-only, ORFs in mass-spectrometry workflows, and suggests a new mechanism enhancing the combinatorial complexity of the proteome. Funding: NIH Director’s New Innovator Award 1DP2-CA196375 to LL.

Keywords: genetic code, lncRNA, long non-coding RNA, mass spectrometry, proteogenomics, ribo-seq, ribosome, RNAseq

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Authors: Firdaousse Laincer, Rahima Laribi, Abderazak Tamendjari, Rovellini Venturini

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Phenolic compounds present in olive oil have received much attention in recent years due to their beneficial functional and nutritional effects. Phenolic composition, antibacterial activity of phenolic extracts of olive oil varieties from Algeria were investigated. The analysis of polyphenols was performed by Folin-Ciocalteu and HPLC. As a result, many phenolic compounds were identified and quantified by using HPLC; derivatives of oleuropein and ligstroside, hydroxytyrosol, tyrosol, flavonoids, and lignans reporting unique and characteristic phenolic profile. These phenolic fractions also differentiate the total antibacterial activity. Among the bacteria tested, S. aureus and, to a lesser extent, B. subtilis showed the highest sensitivity; the MIC varied from 0.6 to 1.6 mg•mL-1 and 1.2 to 1.8 mg•mL-1, respectively. The results obtained denote that Algerian olive oils may constitute a good source of healthy compounds, phenolics compounds, in the diet, suggesting that their consumption could be useful in the prevention of diseases.

Keywords: antibacterial activity, olive oil, phenols, HPLC

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Authors: Rohin Sharma, Sumantu Chaulagain

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This paper presents calculations of total energy of InGaN alloy carried out in a disordered quasirandom structure for a triclinic super cell. This structure replicates the disorder and composition effect in the alloy. First principle calculations within the density functional theory with the local density approximation approach is employed to accurately determine total energy of the system. Lattice constants and band gaps associated with the ground states are then estimated for different concentration ratios of the alloy. We provide precise results of quasirandom structures of the alloy and their lattice constants with the total energy and band gap energy of the system for the range of seven different composition ratios and their respective lattice parameters.

Keywords: DFT, ground state, LDA, quasicrystal, triclinic super cell

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Authors: N. Hasbullah, K. A. Sekak

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The sulfonated poly (ether ether ketone) SPEEK nanofiber membrane were successfully electrospun for Polymer Electrolyte Membrane (PEM) in Proton Exchange Membrane Fuel Cell (PEMFC) and their nanosized properties were investigated. The poly (ether ether ketone) PEEK victrex® grade 90p was sulfonated with concentrated sulfuric acid (95-98% w/w) at room temperature for 60 hours sulfonation times. The degree sulfonation of SPEEK are 70% was determined by H1 NMR and the functional groups of the SPEEK were characterize using FTIR. Then, the SPEEK nanofiber membrane were prepared via electrospinning method using DMAC as a solvent. The SPEEK sample were successfully electrospun using predetermine set up. FESEM show the electrospun fiber mat surface and confirmed the nanostructure membrane cell.

Keywords: polymer electrolyte membrane (PEM), sulfonated poly (ether ether ketone) (SPEEK), degree sulfonation, Electrospinning, Nanofibers

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Authors: Kunal Shah, Swati Patel

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Many real world problems involve data which can be considered as multi-label data streams. Efficient methods exist for multi-label classification in non streaming scenarios. However, learning in evolving streaming scenarios is more challenging, as the learners must be able to adapt to change using limited time and memory. Classification is used to predict class of unseen instance as accurate as possible. Multi label classification is a variant of single label classification where set of labels associated with single instance. Multi label classification is used by modern applications, such as text classification, functional genomics, image classification, music categorization etc. This paper introduces the task of multi-label classification, methods for multi-label classification and evolution measure for multi-label classification. Also, comparative analysis of multi label classification methods on the basis of theoretical study, and then on the basis of simulation was done on various data sets.

Keywords: binary relevance, concept drift, data stream mining, MLSC, multiple window with buffer

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Authors: N. Mahmoudi, B. Guedim

Abstract:

Composite materials have important assets compared to traditional materials. They bring many functional advantages: lightness, mechanical resistance and chemical, etc. In the present study we examine the effect of a circular central notch and a precrack on the tensile fracture of two woven composite materials. The tensile tests were applied to a standardized specimen, notched and a precracked (orientation of the crack 0°, 45°, and 90°). These tensile tests were elaborated according to an experimental planning design of the type 23.31 requiring 24 experiments with three repetitions. By the analysis of regression, we obtained a mathematical model describing the maximum load according to the influential parameters (hole diameter, precrack length, angle of a precrack orientation). The specimens precracked at 90° have a better behavior than those having a precrack at 45° and still better than those having of the precracks oriented at 0°. In addition the maximum load is inversely proportional to the notch size.

Keywords: polymer matrix, glasses, fracture, precracks

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Authors: Ahlad Neti, Elisa Arch, Martha Hall

Abstract:

Studies have shown that individuals who use Ankle-Foot-Orthoses (AFOs) have a high level of dissatisfaction regarding their current AFOs. Studies point to the focus on technical design with little attention given to the user perspective as a source of AFO designs that leave users dissatisfied. To design a new AFO that satisfies users and thereby improves their quality of life, the reasons for their dissatisfaction and their wants and needs for an improved AFO design must be identified. There has been little research into the user perspective on AFO use and desired improvements, so the relationship between AFO design and satisfaction in daily use must be assessed to develop appropriate metrics and constraints prior to designing a novel AFO. To assess the user perspective on AFO design, structured interviews were conducted with 7 individuals (average age of 64.29±8.81 years) who use AFOs. All interviews were transcribed and coded to identify common themes using Grounded Theory Method in NVivo 12. Qualitative analysis of these results identified sources of user dissatisfaction such as heaviness, bulk, and uncomfortable material and overall needs and wants for an AFO. Beyond the user perspective, certain objective factors must be considered in the construction of metrics and constraints to ensure that the AFO fulfills its medical purpose. These more objective metrics are rooted in a common medical device market and technical standards. Given the large body of research concerning these standards, these objective metrics and constraints were derived through a literature review. Through these two methods, a comprehensive list of metrics and constraints accounting for both the user perspective on AFO design and the AFO’s medical purpose was compiled. These metrics and constraints will establish the framework for designing a new AFO that carries out its medical purpose while also improving the user experience. The metrics can be categorized into several overarching areas for AFO improvement. Categories of user perspective related metrics include comfort, discreteness, aesthetics, ease of use, and compatibility with clothing. Categories of medical purpose related metrics include biomechanical functionality, durability, and affordability. These metrics were used to guide an iterative prototyping process. Six concepts were ideated and compared using system-level analysis. From these six concepts, two concepts – the piano wire model and the segmented model – were selected to move forward into prototyping. Evaluation of non-functional prototypes of the piano wire and segmented models determined that the piano wire model better fulfilled the metrics by offering increased stability, longer durability, fewer points for failure, and a strong enough core component to allow a sock to cover over the AFO while maintaining the overall structure. As such, the piano wire AFO has moved forward into the functional prototyping phase, and healthy subject testing is being designed and recruited to conduct design validation and verification.

Keywords: ankle-foot orthotic, assistive technology, human centered design, medical devices

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Authors: Daniel Sava, Dragos Gudovan, Iulia Alexandra Gudovan, Ioana Ardelean, Maria Sonmez, Denisa Ficai, Laurentia Alexandrescu, Ecaterina Andronescu

Abstract:

Graphene and graphene oxide have been intensively studied due to the very good properties, which are intrinsic to the material or come from the easy doping of those with other functional groups. Graphene and graphene oxide have known a broad band of useful applications, in electronic devices, drug delivery systems, medical devices, sensors and opto-electronics, coating materials, sorbents of different agents for environmental applications, etc. The board range of applications does not come only from the use of graphene or graphene oxide alone, or by its prior functionalization with different moieties, but also it is a building block and an important component in many composite devices, its addition coming with new functionalities on the final composite or strengthening the ones that are already existent on the parent product. An attempt to improve the mechanical properties of polyamide elastomers by compounding with graphene oxide in the parent polymer composition was attempted. The addition of the graphene oxide contributes to the properties of the final product, improving the hardness and aging resistance. Graphene oxide has a lower hardness and textile strength, and if the amount of graphene oxide in the final product is not correctly estimated, it can lead to mechanical properties which are comparable to the starting material or even worse, the graphene oxide agglomerates becoming a tearing point in the final material if the amount added is too high (in a value greater than 3% towards the parent material measured in mass percentages). Two different types of tests were done on the obtained materials, the hardness standard test and the tensile strength standard test, and they were made on the obtained materials before and after the aging process. For the aging process, an accelerated aging was used in order to simulate the effect of natural aging over a long period of time. The accelerated aging was made in extreme heat. For all materials, FT-IR spectra were recorded using FT-IR spectroscopy. From the FT-IR spectra only the bands corresponding to the polyamide were intense, while the characteristic bands for graphene oxide were very small in comparison due to the very small amounts introduced in the final composite along with the low absorptivity of the graphene backbone and limited number of functional groups. In conclusion, some compositions showed very promising results, both in tensile strength test and in hardness tests. The best ratio of graphene to elastomer was between 0.6 and 0.8%, this addition extending the life of the product. Acknowledgements: The present work was possible due to the EU-funding grant POSCCE-A2O2.2.1-2013-1, Project No. 638/12.03.2014, code SMIS-CSNR 48652. The financial contribution received from the national project ‘New nanostructured polymeric composites for centre pivot liners, centre plate and other components for the railway industry (RONERANANOSTRUCT)’, No: 18 PTE (PN-III-P2-2.1-PTE-2016-0146) is also acknowledged.

Keywords: graphene, graphene oxide, mechanical properties, dopping effect

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Authors: Arjmand Khaliq, Pemra Sohaib

Abstract:

In this paper smart grid technologies which converts conventional grid into smart grid has been discussed. Integration of advanced technologies including two way communication, advanced control system, sensors, smart metering system and other provide opportunity to make conventional grid a intelligent and automatic system which is named as smart grid. This paper gives the concept of smart grid and functional characteristics of smart grid technology, summed up the research progress in Pakistan and abroad and the significance of developing smart grid. Based on the analysis of the smart grid, smart grid technologies will result a reliable and energy efficient power system in the future. On the other hand smart grid technologies have been reviewed in this paper highlighting the key technologies of smart grid, and points out the problems and challenges in the realization of smart grid.

Keywords: energy, power system reliability, power system monitoring and control, sensor, smart grid, two-way communication

Procedia PDF Downloads 397