Search results for: Tandem%20mass%20spectrometry

Authors: Agnieszka Danek, Rafał Pokrzywa

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Approximate tandem repeats in a genomic sequence are two or more contiguous, similar copies of a pattern of nucleotides. They are used in DNA mapping, studying molecular evolution mechanisms, forensic analysis and research in diagnosis of inherited diseases. All their functions are still investigated and not well defined, but increasing biological databases together with tools for identification of these repeats may lead to discovery of their specific role or correlation with particular features. This paper presents a new approach for finding approximate tandem repeats in a given sequence, where the similarity between consecutive repeats is measured using the Hamming distance. It is an enhancement of a method for finding exact tandem repeats in DNA sequences based on the Burrows- Wheeler transform.

Keywords: approximate tandem repeats, Burrows-Wheeler transform, Hamming distance, suffix array

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Authors: Chun Wen, Tingzhu Huang

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We present a new numerical method for the computation of the steady-state solution of Markov chains. Theoretical analyses show that the proposed method, with a contraction factor α, converges to the one-dimensional null space of singular linear systems of the form Ax = 0. Numerical experiments are used to illustrate the effectiveness of the proposed method, with applications to a class of interesting models in the domain of tandem queueing networks.

Keywords: Markov chains, tandem queueing networks, convergence, effectiveness.

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Authors: Sue-Yi Chen, Wei-Chun Hsu, Jon-Yiew Gan

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Si-based double-junction tandem solar cells have become a popular research topic because of the advantages of low manufacturing cost and high energy conversion efficiency. However, there is no set of calculations to select the appropriate top cell materials. Therefore, this paper will propose a simple but practical selection method. First of all, we calculate the S-Q limit and explain the reasons for developing tandem solar cells. Secondly, we calculate the theoretical energy conversion efficiency of the double-junction tandem solar cells while combining the commercial monocrystalline Si and materials' practical efficiency to consider the actual situation. Finally, we conservatively conclude that if considering 75% performance of the theoretical energy conversion efficiency of the top cell, the suitable bandgap energy range will fall between 1.38 eV to 2.5 eV. Besides, we also briefly describe some improvements of several proper materials, CZTS, CdSe, Cu2O, ZnTe, and CdS, hoping that future research can select and manufacture high-efficiency Si-based tandem solar cells based on this paper successfully. Most importantly, our calculation method is not limited to silicon solely. If other materials’ performances match or surpass silicon's ability in the future, researchers can also apply this set of deduction processes.

Keywords: High-efficiency solar cells, material selection, Si-based double-junction solar cells, tandem solar cells, photovoltaics.

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Authors: Arash Mir Abdolah Lavasani, Hamidreza Bayat

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Heat transfer from two cam shape cylinder in tandem arrangement had been studied numerically. The distance between the centers of cylinders (L) is allowed to vary to change the longitudinal pitch ratio (L/Deq). The equivalent diameter of the cylinder (Deq) is 27.6 mm and longitudinal pitch ratio varies in range 2<L/Deq<6. The Reynolds number based on equivalent circular cylinder are within 50< Reeq <300. Results show that Nusselt number of second cylinder increases about 5 to 33 times when longitudinal pitch ratio increases from 2 to 6.

Keywords: Cam Shaped, tandem Cylinders, Numerical, Heat Transfer.

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Authors: Amal Ezzidani, Abdelghani Ben Tahar, Mohamed Hanini

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A sequence of finite tandem queue is considered for this study. Each one has a single server, which operates under the egalitarian processor sharing discipline. External customers arrive at each queue according to a renewal input process and having a general service times distribution. Upon completing service, customers leave the current queue and enter to the next. Under mild assumptions, including critical data, we prove the existence and the uniqueness of the fluid solution. For asymptotic behavior, we provide necessary and sufficient conditions for the invariant state and the convergence to this invariant state. In the end, we establish the convergence of a correctly normalized state process to a fluid limit characterized by a system of algebraic and integral equations.

Keywords: Fluid Limit, fluid model, measure valued process, processor sharing, tandem queue.

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Authors: Arash Mir Abdolah Lavasani, Meghdad Ebrahimi Sabet

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In this paper, the 2-D unsteady viscous flow around two cam shaped cylinders in tandem arrangement is numerically simulated in order to study the characteristics of the flow in turbulent regimes. The investigation covers the effects of high subcritical and supercritical Reynolds numbers and L/D ratio on total drag coefficient. The equivalent diameter of cylinders is 27.6 mm The space between center to center of two cam shaped cylinders is define as longitudinal pitch ratio and it varies in range of 1.5< L/D<6. Reynolds number base on equivalent circular cylinder varies in range of 27×103< Re <166×103 Results show that drag coefficient of both cylinders depends on pitch ratio. However, drag coefficient of downstream cylinder is more dependent on the pitch ratio.

Keywords: Cam shaped, tandem, numerical, drag coefficient, turbulent.

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Authors: Arash Mir Abdolah Lavasani, Hamidreza Bayat

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In this paper flow around two cam shaped cylinders had been studied numerically. The equivalent diameter of cylinders is 27.6 mm. The space between center to center of two cam shaped cylinders is define as longitudinal pitch ratio and it varies in range of 2 varies in range of 50 both cylinders depends on pitch ratio. However drag coefficient of downstream cylinder is more dependent on the pitch ratio.

Keywords: Cam shaped, tandem cylinders, numerical, drag coefficient.

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Authors: T. T. Manikandan, Rajeev Sukumaran

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Coral Reefs are very important for the majority of marine ecosystems. But, such vital species are under major threat due to the factors such as ocean acidification, overfishing, and coral bleaching. To conserve the coral reefs, reef restoration activities are carried out across the world. After reef restoration, various parameters have to be monitored in order to ensure the overall effectiveness of the reef restoration. Underwater Wireless Sensor Network (UWSN) based  monitoring is widely adopted for such long monitoring activities. Since monitoring of coral reef restoration activities is time sensitive, the QoS guarantee offered by the network with respect to delay is vital. So this research focuses on the analytical modeling of network layer delay using Stochastic Network Calculus (SNC). The core focus of the proposed model will be on the analysis of stochastic dependencies between the network flow and deriving the stochastic delay bounds for the flows that traverse in tandem in UWSNs. The derived analytical bounds are evaluated for their effectiveness using discrete event simulations.

Keywords: Coral Reef Restoration, SNC, SFA, PMOO, Tandem of Queues, Delay Bound.

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Authors: John R. Rose, James P. Cleveland, Alvin Fox

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Tandem mass spectrometry (MS/MS) is the engine driving high-throughput protein identification. Protein mixtures possibly representing thousands of proteins from multiple species are treated with proteolytic enzymes, cutting the proteins into smaller peptides that are then analyzed generating MS/MS spectra. The task of determining the identity of the peptide from its spectrum is currently the weak point in the process. Current approaches to de novo sequencing are able to compute candidate peptides efficiently. The problem lies in the limitations of current scoring functions. In this paper we introduce the concept of proteome signature. By examining proteins and compiling proteome signatures (amino acid usage) it is possible to characterize likely combinations of amino acids and better distinguish between candidate peptides. Our results strongly support the hypothesis that a scoring function that considers amino acid usage patterns is better able to distinguish between candidate peptides. This in turn leads to higher accuracy in peptide prediction.

Keywords: Tandem mass spectrometry, proteomics, scoring, peptide, de novo, mutual information

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Authors: Ayat Bani Rashaid, Zain Khasawneh, Mazin Alqhazo, Shreen Nusair, Mohammad El-Khateeb, Mahmoud Bashtawi

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Autism Spectrum disorder (ASD) is a psychiatric disorder with unknown etiology that mainly affects children in the first three years of life. Alterations of amino acid levels are believed to contribute to ASD. The levels of six essential amino acids (methionine, histidine, valine, leucine, threonine, and phenylalanine), five conditional amino acids (proline, tyrosine, glutamine, cysteine, and cystine), and five non-essential amino acids (asparagine, aspartic acid, alanine, serine, and glutamic acid) in hair samples of children with ASD (n = 25) were analyzed and compared to corresponding levels in healthy age-matched controls (n = 25). The results showed that the levels of methionine, alanine, and asparagine were significantly lower in the hair samples of ASD group compared to those of the control group (p ≤ 0.05). However, the levels of glutamic acid were significantly higher in the ASD group than the control group (p ≤ 0.05). The current findings could contribute towards further understanding of ASD etiology and provide specialists with a hair amino acid profile utilized as a biomarker for early diagnosis of ASD. Such biomarkers could participate in future developments of therapies that reduce ASD-related symptoms.

Keywords: Autism spectrum disorder, amino acids, liquid chromatography-tandem mass spectrometry, human hair.

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Authors: M. Shiva Prasad, S. R. Atchuta, T. Vijayaraghavan, S. Sakthivel

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The world is in need of efficient energy conversion technologies which are affordable, accessible, and sustainable with eco-friendly nature. Solar energy is one of the cornerstones for the world’s economic growth because of its abundancy with zero carbon pollution. Among the various solar energy conversion technologies, solar thermal technology has attracted a substantial renewed interest due to its diversity and compatibility in various applications. Solar thermal systems employ concentrators, tracking systems and heat engines for electricity generation which lead to high cost and complexity in comparison with photovoltaics; however, it is compatible with distinct thermal energy storage capability and dispatchable electricity which creates a tremendous attraction. Apart from that, employing cost-effective solar selective receiver tube in a concentrating solar thermal (CST) system improves the energy conversion efficiency and directly reduces the cost of technology. In addition, the development of solar receiver tubes by low cost methods which can offer high optical properties and corrosion resistance in an open-air atmosphere would be beneficial for low and medium temperature applications. In this regard, our work opens up an approach which has the potential to achieve cost-effective energy conversion. We have developed a highly selective tandem absorber coating through a facile wet chemical route by a combination of chemical oxidation, sol-gel, and nanoparticle coating methods. The developed tandem absorber coating has gradient refractive index nature on stainless steel (SS 304) and exhibited high optical properties (α ≤ 0.95 & ε ≤ 0.14). The first absorber layer (Cr-Mn-Fe oxides) developed by controlled oxidation of SS 304 in a chemical bath reactor. A second composite layer of ZrO₂-SiO₂ has been applied on the chemically oxidized substrate by So-gel dip coating method to serve as optical enhancing and corrosion resistant layer. Finally, an antireflective layer (MgF₂) has been deposited on the second layer, to achieve > 95% of absorption. The developed tandem layer exhibited good thermal stability up to 250 °C in open air atmospheric condition and superior corrosion resistance (withstands for > 200h in salt spray test (ASTM B117)). After the successful development of a coating with targeted properties at a laboratory scale, a prototype of the 1 m tube has been demonstrated with excellent uniformity and reproducibility. Moreover, it has been validated under standard laboratory test condition as well as in field condition with a comparison of the commercial receiver tube. The presented strategy can be widely adapted to develop highly selective coatings for a variety of CST applications ranging from hot water, solar desalination, and industrial process heat and power generation. The high-performance, cost-effective medium temperature receiver tube technology has attracted many industries, and recently the technology has been transferred to Indian industry.

Keywords: Concentrated solar thermal system, solar selective coating, tandem absorber, ultralow refractive index.

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Authors: Mia Sorensen

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The introduction of haptic elements in a graphic user interfaces are becoming more widespread. Since haptics are being introduced rapidly into computational tools, investigating how these models affect Human-Computer Interaction would help define how to integrate and model new modes of interaction. The interest of this paper is to discuss and investigate the issues surrounding Haptic and Graphic User Interface designs (GUI) as separate systems, as well as understand how these work in tandem. The development of these systems is explored from a psychological perspective, based on how usability is addressed through learning and affordances, defined by J.J. Gibson. Haptic design can be a powerful tool, aiding in intuitive learning. The problems discussed within the text is how can haptic interfaces be integrated within a GUI without the sense of frivolity. Juxtaposing haptics and Graphic user interfaces has issues of motivation; GUI tends to have a performatory process, while Haptic Interfaces use affordances to learn tool use. In a deeper view, it is noted that two modes of perception, foveal and ambient, dictate perception. These two modes were once thought to work in tandem, however it has been discovered that these processes work independently from each other. Foveal modes interpret orientation is space which provide for posture, locomotion, and motor skills with variations of the sensory information, which instructs perceptions of object-task performance. It is contended, here, that object-task performance is a key element in the use of Haptic Interfaces because exploratory learning uses affordances in order to use an object, without meditating an experience cognitively. It is a direct experience that, through iteration, can lead to skill-sets. It is also indicated that object-task performance will not work as efficiently without the use of exploratory or kinesthetic learning practices. Therefore, object-task performance is not as congruently explored in GUI than it is practiced in Haptic interfaces.

Keywords: Affordances, Graphic User Interface, HapticInterfaces, Tool-Use, Object-Naming, Object-Task Performance

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Authors: J.S.C. Prentice

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The RK5GL3 method is a numerical method for solving initial value problems in ordinary differential equations, and is based on a combination of a fifth-order Runge-Kutta method and 3-point Gauss-Legendre quadrature. In this paper we describe an effective local error control algorithm for RK5GL3, which uses local extrapolation with an eighth-order Runge-Kutta method in tandem with RK5GL3, and a Hermite interpolating polynomial for solution estimation at the Gauss-Legendre quadrature nodes.

Keywords: RK5GL3, RKrGLm, Runge-Kutta, Gauss-Legendre, Hermite interpolating polynomial, initial value problem, local error.

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Authors: Yanqi Yang, Chongshan Liao, Cheuk Hin Ho, Susan Bridges

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Aim: To investigate students’ perceptions of using e-models in an inquiry-based curriculum. Approach: 52 second-year dental students completed a pre- and post-test questionnaire relating to their perceptions of e-models and their use in inquiry-based learning. The pre-test occurred prior to any learning with e-models. The follow-up survey was conducted after one year's experience of using e-models. Results: There was no significant difference between the two sets of questionnaires regarding students’ perceptions of the usefulness of e-models and their willingness to use e-models in future inquiry-based learning. Most students preferred using both plaster models and e-models in tandem. Conclusion: Students did not change their attitude towards e-models and most of them agreed or were neutral that e-models are useful in inquiry-based learning. Whilst recognizing the utility of 3D models for learning, students' preference for combining these with solid models has implications for the development of haptic sensibility in an operative discipline.

Keywords: E-models, inquiry-based curriculum, education.

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Authors: Ji Young Song, Soo Jung Hu, Hyunjin Joo, Joung Boon Hwang, Mi Ok Kim, Shin Jung Kang, Dae Hyun Cho

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Multi-residue analysis method for penicillins was developed and validated in bovine muscle, chicken, milk, and flatfish. Detection was based on liquid chromatography tandem mass spectrometry (LC/MS/MS). The developed method was validated for specificity, precision, recovery, and linearity. The analytes were extracted with 80% acetonitrile and clean-up by a single reversed-phase solid-phase extraction step. Six penicillins presented recoveries higher than 76% with the exception of Amoxicillin (59.7%). Relative standard deviations (RSDs) were not more than 10%. LOQs values ranged from 0.1 and to 4.5 ug/kg. The method was applied to 128 real samples. Benzylpenicillin was detected in 15 samples and Cloxacillin was detected in 7 samples. Oxacillin was detected in 2 samples. But the detected levels were under the MRL levels for penicillins in samples.

Keywords: Penicillins, livestock product, Multi-residue analysis, LC/MS/MS

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Authors: Jana Kisková, Dana Gabriková

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Monoamine oxidase A gene (MAOA) is suggested to be a candidate gene implicated in many neuropsychiatric disorders, including autism spectrum disorder (ASD). This meta-analytic review evaluates the relationship between ASD and MAOA markers such as 30 bp variable number tandem repeats in the promoter region (uVNTR) and single nucleotide polymorphisms (SNPs) by using findings from recently published studies. It seems that in Caucasian males, the risk of developing ASD increase with the presence of 4- repeat allele in the promoter region of MAOA gene whereas no differences were found between autistic patients and controls in Egyptian, West Bengal and Korean population. Some studies point to the importance of specific haplotype groups of SNPs and interaction of MAOA with others genes (e. g. FOXP2 or SRY). The results of existing studies are insufficient and further research is needed.

Keywords: Autism spectrum disorder, MAOA, uVNTR, single nucleotide polymorphism.

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Authors: So-young Jung, Bu-chuhl Choe, Gi-young Shin, Jung-hun Kim, Young-zoo Chae

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A sensitive and specific method for quantitative determination of aflatoxins(B1, B2, G1,G2), deoxynivalenol, fumonisin(B1,B2), ochratoxin A, zearalenone, T-2 and HT-2 in roasted and ground grains using liquid chromatography combined with tandem mass spectrometry. A double extraction using a phosphate buffer solution followed by methanol was applied to achieve effective co extraction of 11 mycotoxins. A multitoxin immunoaffinity column for all these mycotoxins was used to clean up the extract. The LODs of mycotoxins were 0.1~6.1 μg/kg, LOQs were 0.3~18.4 μg/kg. Forty seven samples collected from Seoul (Korea) for mycotoxin contamination monitoring. The results showed that the occurrence of zearalenone and deoxynivalenol were frequent. Zearalenone was detected in all samples and deoxynivalenol was detected in 80.9 % samples in the range 0.626 ~ 29.264 μg/kg and N.D ~ 48.332 μg/kg respectively. Fumonisins and ochratoxin A were detected in 46.8% samples and 17 % samples respectively, aflatoxins and T-2/HT-2 toxins were not detected all samples.

Keywords: LC-MS/MS, mycotoxins, roasted and ground grains.

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Authors: Ammar Redza Ahmad Rizal, Shahrina Md Nordin, Mohd Shamsuri Saad, Kamariah Ismail

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Communication is becoming a significant tool to engage stakeholders since half of the century ago. In the recent years, there has been rapid growth of new technology developments. In tandem with such developments, there has been growing emphasis in communication strategies and management especially in determining the level of influence and management strategies among the said stakeholders on particular field. This paper presents a research conceptual framework focusing on stakeholder theories, communication and management strategies to be implied on the engagement of stakeholders of new technology developments of fertilizer industry in Malaysia. Framework espoused in this paper will provide insights into the various stakeholder theories and engagement strategies from different principal necessary for a successful introduction of new technology development in the above stated industry. The proposed framework has theoretical significance in filling the gap of the body of knowledge in the implementation of communication strategies in Malaysian fertilizer industry.

Keywords: Communication Strategies, Fertilizer Industry, New Technology Development, Stakeholders Management.

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Authors: R. Oonsivilai, M. Oonsivilai, J. Sanguemrum, N. Thumsirirat, A. Oonsivilai

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Chaiyaphum Starch Co. Ltd. is one of many starch manufacturers that has introduced machinery to aid in manufacturing. Even though machinery has replaced many elements and is now a significant part in manufacturing processes, problems that must be solved with respect to current process flow to increase efficiency still exist. The paper-s aim is to increase productivity while maintaining desired quality of starch, by redesigning the flipping machine-s mechanical control system which has grossly low functional lifetime. Such problems stem from the mechanical control system-s bearings, as fluids and humidity can access into said bearing directly, in tandem with vibrations from the machine-s function itself. The wheel which is used to sense starch thickness occasionally falls from its shaft, due to high speed rotation during operation, while the shaft may bend from impact when processing dried bread. Redesigning its mechanical control system has increased its efficiency, allowing quality thickness measurement while increasing functional lifetime an additional 62 days.

Keywords: Control system, Machinery, Measurement, Potato starch

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Authors: O. A. Al-Mashaqbeh, A. M. Ghrair, D. Alsafadi, S. S. Dalahmeh, S. L. Bartelt-Hunt, D. D. Snow

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Grab samples were collected in the summer to characterize selected pharmaceuticals and personal care products (PPCPs) in the influent of two wastewater treatment plants (WWTPs) in Jordan. Liquid chromatography tandem mass spectrometry (LC–MS/MS) was utilized to determine the concentrations of 18 compounds of PPCPs. Among all of the PPCPs analyzed, eight compounds were detected in the influent samples (1,7-dimethylxanthine, acetaminophen, caffeine, carbamazepine, cotinine, morphine, sulfamethoxazole and trimethoprim). However, five compounds (amphetamine, cimetidine, diphenhydramine, methylenedioxyamphetamine (MDA) and sulfachloropyridazine) were not detected in collected samples (below the detection limits <0.005 ng/l). Moreover, the results indicated that the highest concentration levels detected in collected samples were caffeine, acetaminophen, 1,7-dimethylxanthine, cotinine and carbamazepine at concentration of 182.5 µg/L, 28.7 µg/l, 7.47 µg/l, 4.67 µg/l and 1.54 µg/L, respectively. In general, most of compounds concentrations measured in wastewater in Jordan are within the range for wastewater previously reported in India wastewater except caffeine.

Keywords: Pharmaceuticals and personal care products, wastewater, Jordan.

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Authors: Miroslava Šidlovská, Ida Petrovičová, Tomáš Pilka, Branislav Kolena

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Phthalates are ubiquitous environmental pollutants well known because of their endocrine disrupting activity in human organism. The aim of our study was, by biological monitoring, investigate exposure to phthalates of Roma ethnicity group i.e. children and adults from 5 families (n=29, average age 11.8 ± 7.6 years) living in western Slovakia. Additionally, we analysed some associations between anthropometric measures, questionnaire data i.e. socio-economic status, eating and drinking habits, practise of personal care products and household conditions in comparison with concentrations of phthalate metabolites. We used for analysis of urine samples high performance liquid chromatography and tandem mass spectrometry (HPLC-MS/MS) to determine concentrations of phthalate metabolites monoethyl phthalate (MEP), mono-n-butyl phthalate (MnBP), mono-iso-butyl phthalate (MiBP), mono(2-ethyl- 5-hydroxyhexyl) phthalate (5OH-MEHP), mono(2-ethyl-5-oxohexyl) phthalate (5oxo-MEHP) and mono(2-etylhexyl) phthalate (MEHP). Our results indicate that ethnicity, lower socioeconomic status and different housing conditions in Roma population can affect urinary concentration of phthalate metabolites.

Keywords: Biomonitoring, ethnicity, human exposure, phthalate metabolites.

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Authors: Azza. S. Naik, S. S. Lele

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Indian subcontinent has a plethora of traditional medicine systems that provide promising solutions to lifestyle disorders in an 'all natural way'. Spices and oilseeds hold prominence in Indian cuisine hence the focus of the current study was to evaluate the bioactive molecules from Linum usitatissinum (LU), Lepidium sativum (LS), Nigella sativa (NS) and Guizotia abyssinica (GA) seeds. The seeds were characterized for functional lipids like omega-3 fatty acid, antioxidant capacity, phenolic compounds, dietary fiber and anti-nutritional factors. Analysis of the seeds revealed LU and LS to be a rich source of α-linolenic acid (41.85 ± 0.33%, 26.71 ± 0.63%), an omega 3 fatty acid (using GCMS). While studying antioxidant potential NS seeds demonstrated highest antioxidant ability (61.68 ± 0.21 TEAC/ 100 gm DW) due to the presence of phenolics and terpenes as assayed by the Mass spectral analysis. When screened for anti-nutritional factor cyanogenic glycoside, LS seeds showed content as high as 1674 ± 54 mg HCN / kg. GA is a probable good source of a stable vegetable oil (SFA: PUFA 1:2.3). The seeds showed diversified bioactive profile and hence further studies to use different bio molecules in tandem for the development of a possible 'nutraceutical cocktail' have been initiated..

Keywords: antioxidants, bioactives, functional lipids and oilseeds

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Authors: Pierre-Marie Basset, Gabriel Reboul, Binh DangVu, Sébastien Mercier

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Rotorcraft provides invaluable services thanks to their Vertical Take-Off and Landing (VTOL), hover and low speed capabilities. Yet their use is still often limited by their cost and environmental impact, especially noise and energy consumption. One of the main brakes to the expansion of the use of rotorcraft for urban missions is the environmental impact. The first main concern for the population is the noise. In order to develop the transversal competency to assess the rotorcraft environmental footprint, a collaboration has been launched between six research departments within ONERA. The progress in terms of models and methods are capitalized into the numerical workshop C.R.E.A.T.I.O.N. “Concepts of Rotorcraft Enhanced Assessment Through Integrated Optimization Network”. A typical mission for which the environmental impact issue is of great relevance has been defined. The first milestone is to perform the pre-sizing of a reference helicopter for this mission. In a second milestone, an alternate rotorcraft concept has been defined: a tandem rotorcraft with optional propulsion. The key design trends are given for the pre-sizing of this rotorcraft aiming at a significant reduction of the global environmental impact while still giving equivalent flight performance and safety with respect to the reference helicopter. The models and methods have been improved for catching sooner and more globally, the relative variations on the environmental impact when changing the rotorcraft architecture, the pre-design variables and the operation parameters.

Keywords: Environmental impact, flight performance, helicopter, rotorcraft pre-sizing.

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Authors: P. Vaattovaara, H. B. Swan, G. B. Jones, E. Deschaseaux, B. Miljevic, A. Laaksonen, Z. D. Ristovski

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In order to investigate the properties of coral reef origin secondary aerosol and especially the contribution of secondary organic aerosol, ethanol affinity to atmospheric nucleation mode particles (diameter<15nm) was measured at the Heron reef marine environment in the South Pacific Ocean during the first coral reef aerosol characterization experiment in May-June 2011 using an ultrafine organic tandem differential mobility analyzer.

Our campaign study at Heron reef showed that the nucleation mode size particles (diameter =10nm) composition contain internally mixed sulfate and oxidized organic components in approximately equal proportion in sunny and still conditions around low tide time, indicating local biogenic sources. The produced secondary compounds and aerosols have potential to contribute to cloud condensation nuclei formation and properties that may affect local low-level cloud formation over the GBR. Additionally, primary marine sea-salt and organic material during windy conditions and anthropogenic/biogenic sources during continental air masses can affect the properties of these particles.

Keywords: Coral reef, DMS, particle composition, secondary organics.

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Authors: T. P. Athira, Gibin Chacko George

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This paper proposes a dual tree complex wavelet transform (DT-CWT) based directional interpolation scheme for noisy images. The problems of denoising and interpolation are modelled as to estimate the noiseless and missing samples under the same framework of optimal estimation. Initially, DT-CWT is used to decompose an input low-resolution noisy image into low and high frequency subbands. The high-frequency subband images are interpolated by linear minimum mean square estimation (LMMSE) based interpolation, which preserves the edges of the interpolated images. For each noisy LR image sample, we compute multiple estimates of it along different directions and then fuse those directional estimates for a more accurate denoised LR image. The estimation parameters calculated in the denoising processing can be readily used to interpolate the missing samples. The inverse DT-CWT is applied on the denoised input and interpolated high frequency subband images to obtain the high resolution image. Compared with the conventional schemes that perform denoising and interpolation in tandem, the proposed DT-CWT based noisy image interpolation method can reduce many noise-caused interpolation artifacts and preserve well the image edge structures. The visual and quantitative results show that the proposed technique outperforms many of the existing denoising and interpolation methods.

Keywords: Dual-tree complex wavelet transform (DT-CWT), denoising, interpolation, optimal estimation, super resolution.

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Authors: Rodrigo Pacheco-Ruiz, Jonathan Adams, Felix Pedrotti

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This paper introduces the applicability of underwater photogrammetric survey within challenging conditions as the main tool to enhance and enrich the process of documenting archaeological excavation through the creation of 4D models. Photogrammetry was being attempted on underwater archaeological sites at least as early as the 1970s’ and today the production of traditional 3D models is becoming a common practice within the discipline. Photogrammetry underwater is more often implemented to record exposed underwater archaeological remains and less so as a dynamic interpretative tool.  Therefore, it tends to be applied in bright environments and when underwater visibility is > 1m, reducing its implementation on most submerged archaeological sites in more turbid conditions. Recent years have seen significant development of better digital photographic sensors and the improvement of optical technology, ideal for darker environments. Such developments, in tandem with powerful processing computing systems, have allowed underwater photogrammetry to be used by this research as a standard recording and interpretative tool. Using multi-source photogrammetry (5, GoPro5 Hero Black cameras) this paper presents the accumulation of daily (4D) underwater surveys carried out in the Early Bronze Age (3,300 BC) to Late Ottoman (17th Century AD) archaeological site of Ropotamo in the Bulgarian Black Sea under challenging conditions (< 0.5m visibility). It proves that underwater photogrammetry can and should be used as one of the main recording methods even in low light and poor underwater conditions as a way to better understand the complexity of the underwater archaeological record.

Keywords: 4D modelling, Black Sea, maritime archaeology, underwater photogrammetry, Bronze Age, low visibility.

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Authors: Adnan A. Ugla, Hassan J. Khaudair, Ahmed R. J. Almusawi

Abstract:

Shaped Metal Deposition (SMD) in additive layered manufacturing technique is a promising alternative to traditional manufacturing used for manufacturing large, expensive metal components with complex geometry in addition to producing free structures by building materials in a layer by layer technique. The present paper is a comprehensive review of the literature and the latest rapid manufacturing technologies of the SMD technique. The aim of this paper is to comprehensively review the most prominent facts that researchers have dealt with in the SMD techniques especially those associated with the cold wire feed. The intent of this study is to review the literature presented on metal deposition processes and their classifications, including SMD process using Wire + Arc Additive Manufacturing (WAAM) which divides into wire + tungsten inert gas (TIG), metal inert gas (MIG), or plasma. This literary research presented covers extensive details on bead geometry, process parameters and heat input or arc energy resulting from the deposition process in both cases MIG and Tandem-MIG in SMD process. Furthermore, SMD may be done using Single Wire-MIG (SW-MIG) welding and SMD using Double Wire-MIG (DW-MIG) welding. The present review shows that the method of deposition of metals when using the DW-MIG process can be considered a distinctive and low-cost method to produce large metal components due to high deposition rates as well as reduce the input of high temperature generated during deposition and reduce the distortions. However, the accuracy and surface finish of the MIG-SMD are less as compared to electron and laser beam.

Keywords: Shaped metal deposition, additive manufacturing, double-wire feed, cold feed wire.

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Authors: Abdulraaof H. Alqaili, Hamad A. Alsoliman

Abstract:

Through progress in pavement design developments, a pavement design method was developed, which is titled the Mechanistic Empirical Pavement Design Guide (MEPDG). Nowadays, the evolution in roads network and highways is observed in Saudi Arabia as a result of increasing in traffic volume. Therefore, the MEPDG currently is implemented for flexible pavement design by the Saudi Ministry of Transportation. Implementation of MEPDG for local pavement design requires the calibration of distress models under the local conditions (traffic, climate, and materials). This paper aims to prepare data for calibration of MEPDG in Central Saudi Arabia. Thus, the first goal is data collection for the design of flexible pavement from the local conditions of the Riyadh region. Since, the modifying of collected data to input data is needed; the main goal of this paper is the analysis of collected data. The data analysis in this paper includes processing each: Trucks Classification, Traffic Growth Factor, Annual Average Daily Truck Traffic (AADTT), Monthly Adjustment Factors (MAFi), Vehicle Class Distribution (VCD), Truck Hourly Distribution Factors, Axle Load Distribution Factors (ALDF), Number of axle types (single, tandem, and tridem) per truck class, cloud cover percent, and road sections selected for the local calibration. Detailed descriptions of input parameters are explained in this paper, which leads to providing of an approach for successful implementation of MEPDG. Local calibration of MEPDG to the conditions of Riyadh region can be performed based on the findings in this paper.

Keywords: Mechanistic-empirical pavement design guide, traffic characteristics, materials properties, climate, Riyadh.

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Authors: Abdellali Kelil, Shengrui Wang, Ryszard Brzezinski

Abstract:

The literature reports a large number of approaches for measuring the similarity between protein sequences. Most of these approaches estimate this similarity using alignment-based techniques that do not necessarily yield biologically plausible results, for two reasons. First, for the case of non-alignable (i.e., not yet definitively aligned and biologically approved) sequences such as multi-domain, circular permutation and tandem repeat protein sequences, alignment-based approaches do not succeed in producing biologically plausible results. This is due to the nature of the alignment, which is based on the matching of subsequences in equivalent positions, while non-alignable proteins often have similar and conserved domains in non-equivalent positions. Second, the alignment-based approaches lead to similarity measures that depend heavily on the parameters set by the user for the alignment (e.g., gap penalties and substitution matrices). For easily alignable protein sequences, it's possible to supply a suitable combination of input parameters that allows such an approach to yield biologically plausible results. However, for difficult-to-align protein sequences, supplying different combinations of input parameters yields different results. Such variable results create ambiguities and complicate the similarity measurement task. To overcome these drawbacks, this paper describes a novel and effective approach for measuring the similarity between protein sequences, called SAF for Substitution and Alignment Free. Without resorting either to the alignment of protein sequences or to substitution relations between amino acids, SAF is able to efficiently detect the significant subsequences that best represent the intrinsic properties of protein sequences, those underlying the chronological dependencies of structural features and biochemical activities of protein sequences. Moreover, by using a new efficient subsequence matching scheme, SAF more efficiently handles protein sequences that contain similar structural features with significant meaning in chronologically non-equivalent positions. To show the effectiveness of SAF, extensive experiments were performed on protein datasets from different databases, and the results were compared with those obtained by several mainstream algorithms.

Keywords: Protein, Similarity, Substitution, Alignment.

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Authors: G. Zuppardi, F. Romano

Abstract:

Technology of thin film deposition is of interest in many engineering fields, from electronic manufacturing to corrosion protective coating. A typical deposition process, like that developed at the University of Eindhoven, considers the deposition of a thin, amorphous film of C:H or of Si:H on the substrate, using the Expanding Thermal arc Plasma technique. In this paper a computing procedure is proposed to simulate the flow field in a deposition chamber similar to that at the University of Eindhoven and a sensitivity analysis is carried out in terms of: precursor mass flow rate, electrical power, supplied to the torch and fluid-dynamic characteristics of the plasma jet, using different nozzles. To this purpose a deposition chamber similar in shape, dimensions and operating parameters to the above mentioned chamber is considered. Furthermore, a method is proposed for a very preliminary evaluation of the film thickness distribution on the substrate. The computing procedure relies on two codes working in tandem; the output from the first code is the input to the second one. The first code simulates the flow field in the torch, where Argon is ionized according to the Saha-s equation, and in the nozzle. The second code simulates the flow field in the chamber. Due to high rarefaction level, this is a (commercial) Direct Simulation Monte Carlo code. Gas is a mixture of 21 chemical species and 24 chemical reactions from Argon plasma and Acetylene are implemented in both codes. The effects of the above mentioned operating parameters are evaluated and discussed by 2-D maps and profiles of some important thermo-fluid-dynamic parameters, as per Mach number, velocity and temperature. Intensity, position and extension of the shock wave are evaluated and the influence of the above mentioned test conditions on the film thickness and uniformity of distribution are also evaluated.

Keywords: Deposition chamber, Direct Simulation Mote Carlo method (DSMC), Plasma chemistry, Rarefied gas dynamics.

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