Search results for: somatic sequence mutations

Authors: Zouhair Issa Ahmed, Ahmed Abdulrasool Ahmed, Falah Hassan Abdulsada

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This paper presents a layout of a factory using Pro-Model simulation by choosing the best layout that gives the highest productivity and least work in process. The general problem is to find the best sequence in which jobs pass between the machines which are compatible with the technological constraints and optimal with respect to some performance criteria. The best simulation with Pro-Model program increased productivity and reduced work in process by balancing lines of production compared with the current layout of factory when productivity increased from 45 products to 180 products through 720 hours.

Keywords: scheduling, Pro-Model, simulation, balancing lines of production, layout planning, WIP

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Authors: Thi Thao Ninh, Yuri Trusov, José Ramón Botella

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Heterotrimeric G proteins, comprised of three subunits, α, β and γ, are involved in signal transduction pathways that mediate a vast number of processes across the eukaryotic kingdom. 23 Gα subunits are present in humans whereas most plant genomes encode for only one canonical Gα. The disparity observed between Arabidopsis, rice, and maize Gα-deficient mutant phenotypes suggest that Gα functions have diversified between eudicots and monocots during evolution. Alternatively, since the only Gα mutations available in dicots have been produced in Arabidopsis, the possibility exists that this species might be an exception to the rule. In order to test this hypothesis, we studied the G protein α subunit (TGA1) in tomato. Four tga1 knockout lines were generated in tomato cultivar Moneymaker using CRISPR/Cas9. The tga1 mutants exhibit a number of auxin-related phenotypes including changes in leaf shape, reduced plant height, fruit size and number of seeds per fruit. In addition, tga1 mutants have increased sensitivity to abscisic acid during seed germination, reduced sensitivity to exogenous auxin during adventitious root formation from cotyledons and excised hypocotyl explants. Our results suggest that Gα mutant phenotypes in tomato are very similar to those observed in monocots, i.e. rice and maize, and cast doubts about the validity of using Arabidopsis as a model system for plant G protein studies.

Keywords: auxin-related phenotypes, CRISPR/Cas9, G protein α subunit, heterotrimeric G proteins, tomato

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Authors: J. T. Manhire

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A tax authority wants to take actions it knows will foster the greatest degree of voluntary taxpayer compliance to reduce the “tax gap.” This paper suggests that even if a tax authority could attain a state of complete knowledge, there are constraints on whether and to what extent such actions would result in reducing the macro-level tax gap. These limits are not merely a consequence of finite agency resources. They are inherent in the system itself. To show that this is one possible interpretation of the tax gap data, the paper formulates known results in a different way by analyzing tax compliance as a population with a single covariate. This leads to a standard use of the logistic map to analyze the dynamics of non-compliance growth or decay over a sequence of periods. This formulation gives the same results as the tax gap studies performed over the past fifty years in the U.S. given the published margins of error. Limitations and recommendations for future work are discussed, along with some implications for tax policy.

Keywords: income tax, logistic map, tax compliance, tax law

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Authors: O. Abusaeeda, J. P. O. Evans, D. Downes

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We demonstrate the synthesis of intermediary views within a sequence of X-ray images that exhibit depth from motion or kinetic depth effect in a visual display. Each synthetic image replaces the requirement for a linear X-ray detector array during the image acquisition process. Scale invariant feature transform, SIFT, in combination with epipolar morphing is employed to produce synthetic imagery. Comparison between synthetic and ground truth images is reported to quantify the performance of the approach. Our work is a key aspect in the development of a 3D imaging modality for the screening of luggage at airport checkpoints. This programme of research is in collaboration with the UK Home Office and the US Dept. of Homeland Security.

Keywords: X-ray, kinetic depth, KDE, view synthesis

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Authors: Selisha A. Sooklal, Phelelani Mpangase, Shaun Aron, Karl Rumbold

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Organically bound fluorine (C-F bond) is extremely rare in nature. Despite this, the first fluorinated secondary metabolite, fluoroacetate, was isolated from the plant Dichapetalum cymosum (commonly known as Gifblaar). However, the enzyme responsible for fluorination (fluorinase) in Gifblaar was never isolated and very little progress has been achieved in understanding this process in higher plants. Fluorinated compounds have vast applications in the pharmaceutical, agrochemical and fine chemicals industries. Consequently, an enzyme capable of catalysing a C-F bond has great potential as a biocatalyst in the industry considering that the field of fluorination is virtually synthetic. As with any biocatalyst, a range of these enzymes are required. Therefore, it is imperative to expand the exploration for novel fluorinases. This study aimed to gain molecular insights into secondary metabolite biosynthesis in Gifblaar using a high-throughput sequencing-based approach. Mechanical wounding studies were performed using Gifblaar leaf tissue in order to induce expression of the fluorinase. The transcriptome of the wounded and unwounded plant was then sequenced on the Illumina HiSeq platform. A total of 26.4 million short sequence reads were assembled into 77 845 transcripts using Trinity. Overall, 68.6 % of transcripts were annotated with gene identities using public databases (SwissProt, TrEMBL, GO, COG, Pfam, EC) with an E-value threshold of 1E-05. Sequences exhibited the greatest homology to the model plant, Arabidopsis thaliana (27 %). A total of 244 annotated transcripts were found to be differentially expressed between the wounded and unwounded plant. In addition, secondary metabolic pathways present in Gifblaar were successfully reconstructed using Pathway tools. Due to lack of genetic information for plant fluorinases, a transcript failed to be annotated as a fluorinating enzyme. Thus, a local database containing the 5 existing bacterial fluorinases was created. Fifteen transcripts having homology to partial regions of existing fluorinases were found. In efforts to obtain the full coding sequence of the Gifblaar fluorinase, primers were designed targeting the regions of homology and genome walking will be performed to amplify the unknown regions. This is the first genetic data available for Gifblaar. It has provided novel insights into the mechanisms of metabolite biosynthesis and will allow for the discovery of the first eukaryotic fluorinase.

Keywords: biocatalyst, fluorinase, gifblaar, transcriptome

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Authors: Awais Asif

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This article investigates fixed point theorems of Chatterjea type F-contraction in the setting of F-metric space. We relax the conditions of F-contraction and define modified F-contraction for two mappings. The study provides fixed point results for both single-valued and multivalued mappings. The results are further extended to common fixed point theorems for two mappings. Moreover, to discuss the applicability of our results, an application is provided, which shows the role of our results in finding the solution to functional equations in dynamic programming. Our results generalize and extend the existing results in the literature.

Keywords: Chatterjea type F-contraction, F-cauchy sequence, F-convergent, multi valued mappings

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Authors: Clesse C., Lighezzolo-Alnot J., De Lavergne S.

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Considered as the most common surgical procedure worldwide, episiotomy can be defined as an incision around the vulva performed to enlarge it, in the aim of preventing the traumatic rupture of the perineum during childbirth. Rather mediatized, this practice raises many questions in the field of mental health, relayed by different users and health professionals. Today, is topicality is moderately hectic since many queries about the prophylactic exercise of episiotomy are subject to a relative consensus, particularly since WHO advocated in 1996 that only 10% of childbirths should involve an episiotomy. This indicator appeared after the publication of numerous results from randomized clinical trials. Unfortunately, these papers seem mostly centered about somatic impacts of episiotomy. From the side of psychological studies, they mostly integrate a major clinical methodological bias, especially considering that every primiparous woman is identical to the others face to the experience of parturition. In the aim to fill this lack of knowledge, we developed a longitudinal research starting in the 7th month of pregnancy and ending one year after delivery. We are studying in a comparative way different possible psychological consequences inherent to the use of episiotomy. To do this, we use a standardized methodology which combines semi-structured clinical interviews (IRMAG, IRMAN ...), free clinical interviews, a projective test (Rorschach) and five questionnaires (QIC, EPDS, CPQ WOMBLSQ4, SF36). Therefore, we can comprehend with shrewdness the question of psychic impacts of episiotomy in a qualitative and quantitative way by comparing it to other obstetric interventions. In this paper, we will present the first results obtained about a population of twenty-two primiparous women by focusing on body image, sexuality, quality of life, depressive affects, post-traumatic stress disorder and investment of the maternal role. Finally, we will consider the different implications and perspectives of this research which could improve the public health policies in the field of perinatal care.

Keywords: assessment, episiotomy, mental health, psychical impacts

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Authors: Jing-Fung Lin, Jer-Jia Sheu

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In this study, an approach has been developed for the noise reduction of a muffler. The transmission loss (TL) in the muffler is maximized by the use of a double-chamber muffler, and a baffle with a hole is inserted between chambers. Taguchi method is used to optimize the design for the acoustical performance of the muffler. The TL performance is evaluated by COMSOL software. The excellent parameter combination for the maximum TL is attained as high as 35.30 dB in a wide frequency range from 10 Hz to 1400 Hz. The influence sequence of four parameters on TL is determined by the range analysis. The effects of length and expansion ratio of the first chamber on TL performance for the excellent program were discussed. Comparisons of the TL results from different designs are made.

Keywords: acoustics, baffle, chamber, muffler, Taguchi method, transmission loss

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Authors: Shahbaz Ahmed

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This study is conducted to demonstrate the knowledge of intentional learning and incidental learning. Hypothesis of this experiment is intentional learning is better than incidental learning, participants were demonstrated and were asked to learn the 10 nonsense syllables in a specific sequence from the colored cards in the end they were asked to recall the background color of each card instead of nonsense syllables. Independent variables of the experiment are the colored cards containing nonsense syllables which are to be memorized by the participants, dependent variables are the number of correct responses made by the participant. The findings of the experiment concluded that intentional learning is better than incidental learning, hence hypothesis is proved.

Keywords: intentional learning, incidental learning, non-sense syllable cards, score sheets

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Authors: Yali Zheng, Peipei Luo, Shinan Chen, Jiasheng Hao, Hong Cheng

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Most of traditional visual indoor navigation algorithms and methods only consider the localization in ordinary daytime, while we focus on the indoor re-localization in low light in the paper. As RGB images are degraded in low light, less discriminative infrared and depth image pairs are taken, as the input, by RGB-D cameras, the most similar candidates, as the output, are searched from databases which is built in the bag-of-word framework. Epipolar constraints can be used to relocalize the query infrared and depth image sequence. We evaluate our method in two datasets captured by Kinect2. The results demonstrate very promising re-localization results for indoor navigation system in low light environments.

Keywords: indoor navigation, low light, RGB-D camera, vision based

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Authors: Yi-Chun Huang, Kuan-Yun Chen, Chuang-Hung Lin

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Urban Green Belt and Blue is a part of the city landscape, it is an important constituent element of the urban environment and appearance. The Hsinchu East Gate Moat is situated in the center of the city, which not only has a wealth of historical and cultural resources, but also combines the Green Belt and the Blue Belt qualities at the same time. The Moat runs more than a thousand meters through the vital Green Belt and the Blue Belt in downtown, and each section is presented in different qualities of moat from south to north. The water area and the green belt of surroundings are presented linear and banded spread. The water body and the rich diverse river banks form an urban green belt of rich layers. The watercourse with green belt design lets users have connections with blue belts in different ways; therefore, the integration of Hsinchu East Gate and moat have become one of the unique urban landscapes in Taiwan. The study is based on the fact-finding case of Hsinchu East Gate Moat where situated in northern Taiwan, to research the impact between the SVF variation of the city and spatial sequence of Urban Green Belt and Blue landscape and visual analysis by constituent cross-section, and then comparing the influence of different leaf area index – the variable ecological factors to the degree of enclosure. We proceed to survey the landscape design of open space, to measure existing structural features of the plant canopy which contain the height of plants and branches, the crown diameter, breast-height diameter through access to diagram of Geographic Information Systems (GIS) and on-the-spot actual measurement. The north and south districts of blue green belt areas are divided 20 meters into a unit from East Gate Roundabout as the epicenter, and to set up a survey points to measure the SVF above the survey points; then we proceed to quantitative analysis from the data to calculate open landscape degree of enclosure. The results can be reference for the composition of future river landscape and the practical operation for dynamic space planning of blue and green belt landscape.

Keywords: sky view factor, degree of enclosure, spatial sequence, leaf area indices

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Authors: Zerrin Orbak, Busra Demir

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Osteopetrosis is a rare genetic disease characterized by impaired bone resorption and increased bone sclerosis. Clinical presentation is very different in osteopetrosis. It can be asymptomatic or can be seen with typical symptoms. Here, a case of osteopetrosis was presented when evaluated for nystagmus. She was 10 months old. Parents were second-degree relatives. On physical examination, pigeon chest deformity and horizontal nystagmus were observed. There was a failure of thrive but no fracture. The cardiovascular examination was normal. Cranial, vertebral and long bone roentgenograms revealed characteristic deformities of osteopetrosis and diffuse sclerosis. The diagnosis was confirmed by genetic testing. A Homozygous mutation was detected in the TNFRSF11A gene (c.508A>G p.(Arg170Gly)). RANKL is encoded by the tumor necrosis factor ligand superfamily member 11 (TNFSF11) gene, and the binding to its receptor RANK, encoded by the TNFRSF11A gene, determines the activation of the downstream pathway that drives osteoclast differentiation and activation (51). The complete absence of osteoclasts is the key feature of the osteoclast-poor form of osteopetrosis (46). Patients are characterized by the absence of TRAP-positive osteoclasts in bone biopsies. The osteoclast-poor subtype of osteopetrosis caused by mutations in TNFSF11 gene is ultra-rare in humans. Clinical presentation is usually severe, with onset in early infancy or in fetal life. But here, a case was presented with horizontal nystagmus. A case presented with horizontal nystagmus, which was evaluated by neurology and diagnosed incidentally, was shared.

Keywords: osteopetrosis, nystagmus, bone, osteoclast-poor

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Authors: Carmel Sofer, Dan Vilenchik, Ron Dotsch, Galia Avidan

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Studies investigating emotional facial expressions typically reveal consensus among observes regarding the meaning of basic expressions, whose number ranges between 6 to 15 emotional states. Given this limited number of discrete expressions, how is it that the human vocabulary of emotional states is so rich? The present study argues that perceivers use sequences of these discrete expressions as the basis for a much richer vocabulary of emotional states. Such mechanisms, in which a relatively small number of basic components is expanded to a much larger number of possible combinations of meanings, exist in other human communications modalities, such as spoken language and music. In these modalities, letters and notes, which serve as basic components of spoken language and music respectively, are temporally linked, resulting in the richness of expressions. In the current study, in each trial participants were presented with sequences of two images containing facial expression in different combinations sampled out of the eight static basic expressions (total 64; 8X8). In each trial, using single word participants were required to judge the 'state of mind' portrayed by the person whose face was presented. Utilizing word embedding methods (Global Vectors for Word Representation), employed in the field of Natural Language Processing, and relying on machine learning computational methods, it was found that the perceived meanings of the sequences of facial expressions were a weighted average of the single expressions comprising them, resulting in 22 new emotional states, in addition to the eight, classic basic expressions. An interaction between the first and the second expression in each sequence indicated that every single facial expression modulated the effect of the other facial expression thus leading to a different interpretation ascribed to the sequence as a whole. These findings suggest that the vocabulary of emotional states conveyed by facial expressions is not restricted to the (small) number of discrete facial expressions. Rather, the vocabulary is rich, as it results from combinations of these expressions. In addition, present research suggests that using word embedding in social perception studies, can be a powerful, accurate and efficient tool, to capture explicit and implicit perceptions and intentions. Acknowledgment: The study was supported by a grant from the Ministry of Defense in Israel to GA and CS. CS is also supported by the ABC initiative in Ben-Gurion University of the Negev.

Keywords: Glove, face perception, facial expression perception. , facial expression production, machine learning, word embedding, word2vec

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Authors: Bimali Sanjeevani Weerakoon, Toshiaki Osuga, Takehisa Konishi

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Magnetic Resonance Imaging Contrast Agents (MRI-CM) are significant in the clinical and biological imaging as they have the ability to alter the normal tissue contrast, thereby affecting the signal intensity to enhance the visibility and detectability of images. Superparamagnetic Iron Oxide (SPIO) nanoparticles, coated with dextran or carboxydextran are currently available for clinical MR imaging of the liver. Most SPIO contrast agents are T2 shortening agents and Resovist (Ferucarbotran) is one of a clinically tested, organ-specific, SPIO agent which has a low molecular carboxydextran coating. The enhancement effect of Resovist depends on its relaxivity which in turn depends on factors like magnetic field strength, concentrations, nanoparticle properties, pH and temperature. Therefore, this study was conducted to investigate the impact of field strength and different contrast concentrations on enhancement effects of Resovist. The study explored the MRI signal intensity of Resovist in the physiological range of plasma from T2-weighted spin echo sequence at three magnetic field strengths: 0.47 T (r1=15, r2=101), 1.5 T (r1=7.4, r2=95), and 3 T (r1=3.3, r2=160) and the range of contrast concentrations by a mathematical simulation. Relaxivities of r1 and r2 (L mmol-1 Sec-1) were obtained from a previous study and the selected concentrations were 0.05, 0.06, 0.07, 0.08, 0.09, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 2.0, and 3.0 mmol/L. T2-weighted images were simulated using TR/TE ratio as 2000 ms /100 ms. According to the reference literature, with increasing magnetic field strengths, the r1 relaxivity tends to decrease while the r2 did not show any systematic relationship with the selected field strengths. In parallel, this study results revealed that the signal intensity of Resovist at lower concentrations tends to increase than the higher concentrations. The highest reported signal intensity was observed in the low field strength of 0.47 T. The maximum signal intensities for 0.47 T, 1.5 T and 3 T were found at the concentration levels of 0.05, 0.06 and 0.05 mmol/L, respectively. Furthermore, it was revealed that, the concentrations higher than the above, the signal intensity was decreased exponentially. An inverse relationship can be found between the field strength and T2 relaxation time, whereas, the field strength was increased, T2 relaxation time was decreased accordingly. However, resulted T2 relaxation time was not significantly different between 0.47 T and 1.5 T in this study. Moreover, a linear correlation of transverse relaxation rates (1/T2, s–1) with the concentrations of Resovist can be observed. According to these results, it can conclude that the concentration of SPIO nanoparticle contrast agents and the field strengths of MRI are two important parameters which can affect the signal intensity of T2-weighted SE sequence. Therefore, when MR imaging those two parameters should be considered prudently.

Keywords: Concentration, resovist, field strength, relaxivity, signal intensity

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Authors: Akeem Akinboro, Bala Alhaj Kegun

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Haemoglobinopathy is a genetic disorder that has the potentiality to cause death of individuals in whom both the alpha (α) and beta (β) globin chains of the haemoglobin molecule are defective due to mutations in their genes. The haemoglobin genotype variants among some residents of Niger state, Nigeria, were determined using the secondary data available at Bida, Minna and Kotangora general hospitals of the state. A total of 1,639 data, representing 434, 655 and 550, collected from the outside patients who visited the medical laboratory units of the three general hospitals, respectively, over five years period (2015-2020) were analyzed into gene frequency, sex and age to determine their haemoglobin genotypes status. More males (51.6 – 58.7%) than females (41.3 – 48.4%) visited the three hospitals during the period covered and most of the patients were between 11 - 20 years old. The frequency of HbA allele in the human population was 0.72, 0.65, 0.68 for Bida, Minna and Kotangora, respectively, while it was 0.25, 0.29 and 0.28 for HbS allele. The HbC allele was prevalent at 0.03, 0.06 and 0.05 among the human population in Bida, Minna and Kotangora cities of Niger state. In overall, the prevalence of HbA, HbS and HbC alleles in Niger state of Nigeria was 0.68, 0.28 and 0.05. Minna being the capital city of Niger state and the most populous among the three cities in the state seems to have influx of more people who are carriers of abnormal haemoglobin genotypes which has resulted to higher frequency of HbS and HbC than those of the other two cities in this study. These results show that the pattern of haemoglobin genotypes frequency of Kontagora could be a prediction for the whole of Niger state. It is therefore necessary and important to take screening of blood for haemoglobin genotype serious among intending couples to prevent and reduce the possibility of having increase in the number of people with abnormal haemoglobin genotypes in the state.

Keywords: haemoglobin, genotype, niger state, gene frequency, general hospitals

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Authors: Pushpendra Kumar, Sanjeev Kumar, R. Balasubramanian

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Estimation of optical flow from a sequence of images using variational methods is one of the most successful approach. Discontinuity between different motions is one of the challenging problem in flow estimation. In this paper, we design a new anisotropic diffusion operator, which is able to provide smooth flow over a region and efficiently preserve discontinuity in optical flow. This operator is designed on the basis of intensity differences of the pixels and isotropic operator using exponential function. The combination of these are used to control the propagation of flow. Experimental results on the different datasets verify the robustness and accuracy of the algorithm and also validate the effect of anisotropic operator in the discontinuity preserving.

Keywords: optical flow, variational methods, computer vision, anisotropic operator

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Authors: Ladznar S. Laja, Rosalio G. Artes, Jr.

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This paper introduced a graph polynomial relating convexity concepts. A graph polynomial is a polynomial representing a graph given some parameters. On the other hand, a subgraph H of a graph G is said to be convex in G if for every pair of vertices in H, every shortest path with these end-vertices lies entirely in H. We define the convex subgraph polynomial of a graph G to be the generating function of the sequence of the numbers of convex subgraphs of G of cardinalities ranging from zero to the order of G. This graph polynomial is monic since G itself is convex. The convex index which counts the number of convex subgraphs of G of all orders is just the evaluation of this polynomial at 1. Relationships relating algebraic properties of convex subgraphs polynomial with graph theoretic concepts are established.

Keywords: convex subgraph, convex index, generating function, polynomial ring

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Authors: Zhan Haiyang, Zhang Lei, Ning Juan

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This paper presents a configuration software solution in Linux, which is used for the control of space environment simulator. After introducing the structure and basic principle, it is said that the developing of QT software frame and the dynamic data exchanging between PLC and computer. The OPC driver in Linux is also developed. This driver realizes many-to-many communication between hardware devices and SCADA software. Moreover, an algorithm named “Scan PRI” is put forward. This algorithm is much more optimizable and efficient compared with "Scan in sequence" in Windows. This software has been used in practical project. It has a good control effect and can achieve the expected goal.

Keywords: Linux OS, configuration software, OPC Server driver, MYSQL database

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Authors: Aniekan Peter, ECS Naidu, Edidiong Akang, U. Offor, R. Kalhapure, A. A. Chuturgoon, T. Govender, O. O. Azu

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Introduction: Nano-drugs are novel innovations in the management of human immunodeficiency virus (HIV) pandemic, especially resistant strains of the virus in their sanctuary sites: testis and the brain. There are safety concerns to be addressed to achieve the full potential of this new drug delivery system. Aim of study: Our study was designed to investigate toxicity profile of Tenofovir Nanoparticle (TDF-N) synthesized by University of Kwazulu-Natal (UKZN) Nano-team for prevention and treatment of HIV infection. Methodology: Ten adult male Sprague-Dawley rats maintained at the Animal House of the Biomedical Resources Unit UKZN were used for the study. The animals were weighed and divided into two groups of 5 animal each. Control animals (A) were administered with normal saline. Therapeutic dose (4.3 mg/kg) of TDF-N was administered to group B. At the end of four weeks, animals were weighed and sacrificed. Liver and kidney were removed fixed in formal saline, processed and stained using H/E, PAS and MT stains for light microscopy. Serum was obtained for renal function test (RFT), liver function test (LFT) and full blood count (FBC) using appropriate analysers. Cellular measurements were done using ImageJ and Leica software 2.0. Data were analysed using graph pad 6, values < 0.05 were significant. Results: We reported no histological alterations in the liver, kidney, FBC, LFT and RFT between the TDF-N animals and saline control. There were no significant differences in weight, organo-somatic index and histological measurements in the treatment group when compared with saline control. Conclusion/recommendations: TDF-N is not toxic to the liver, kidney and blood cells in our study. More studies using human subjects is recommended.

Keywords: tenofovir nanoparticles, liver, kidney, blood cells

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Authors: Kurniawan Adha, Wan Ismail Wan Yusoff, Luluan Almanna Lubis

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Preventing hazardous events during oil and gas operation is an important contribution of accurate pore pressure data. The availability of pore pressure data also contribute in reducing the operation cost. Suggested methods in pore pressure estimation were mostly complex by the many assumptions and hypothesis used. Basic properties which may have significant impact on estimation model are somehow being neglected. To date, most of pore pressure determinations are estimated by data model analysis and rarely include laboratory analysis, stratigraphy study or core check measurement. Basically, this study developed a model that might be applied to investigate the changes of pore pressure and effective stress due to hydrocarbon production. In general, this paper focused velocity model effect of pore pressure and effective stress changes due to hydrocarbon production with illustrated by changes in saturation. The core samples from Miri field from Sarawak Malaysia ware used in this study, where the formation consists of sandstone reservoir. The study area is divided into sixteen (16) layers and encompassed six facies (A-F) from the outcrop that is used for stratigraphy sequence model. The experimental work was firstly involving data collection through field study and developing stratigraphy sequence model based on outcrop study. Porosity and permeability measurements were then performed after samples were cut into 1.5 inch diameter core samples. Next, velocity was analyzed using SONIC OYO and AutoLab 500. Three (3) scenarios of saturation were also conducted to exhibit the production history of the samples used. Results from this study show the alterations of velocity for different saturation with different actions of effective stress and pore pressure. It was observed that sample with water saturation has the highest velocity while dry sample has the lowest value. In comparison with oil to samples with oil saturation, water saturated sample still leads with the highest value since water has higher fluid density than oil. Furthermore, water saturated sample exhibits velocity derived parameters, such as poisson’s ratio and P-wave velocity over S-wave velocity (Vp/Vs) The result shows that pore pressure value ware reduced due to the decreasing of fluid content. The decreasing of pore pressure result may soften the elastic mineral frame and have tendency to possess high velocity. The alteration of pore pressure by the changes in fluid content or saturation resulted in alteration of velocity value that has proportionate trend with the effective stress.

Keywords: pore pressure, effective stress, production, miri formation

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Authors: Simon Espigolé, Igor Shalyminov, Helen Hastie

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Deep machine learning techniques including deep neural networks (DNN) have been used to model language and dialogue for conversational agents to perform tasks, such as giving technical support and also for general chit-chat. They have been shown to be capable of generating long, diverse and coherent sentences in end-to-end dialogue systems and natural language generation. However, these systems tend to imitate the training data and will only generate the concepts and language within the scope of what they have been trained on. This work explores how deep neural networks can be used in a task that would normally require human creativity, whereby the human would read the movie description and/or watch the movie and come up with a compelling, interesting movie title. This task differs from simple summarization in that the movie title may not necessarily be derivable from the content or semantics of the movie description. Here, we train a type of DNN called a sequence-to-sequence model (seq2seq) that takes as input a short textual movie description and some information on e.g. genre of the movie. It then learns to output a movie title. The idea is that the DNN will learn certain techniques and approaches that the human movie titler may deploy that may not be immediately obvious to the human-eye. To give an example of a generated movie title, for the movie synopsis: ‘A hitman concludes his legacy with one more job, only to discover he may be the one getting hit.’; the original, true title is ‘The Driver’ and the one generated by the model is ‘The Masquerade’. A human evaluation was conducted where the DNN output was compared to the true human-generated title, as well as a number of baselines, on three 5-point Likert scales: ‘creativity’, ‘naturalness’ and ‘suitability’. Subjects were also asked which of the two systems they preferred. The scores of the DNN model were comparable to the scores of the human-generated movie title, with means m=3.11, m=3.12, respectively. There is room for improvement in these models as they were rated significantly less ‘natural’ and ‘suitable’ when compared to the human title. In addition, the human-generated title was preferred overall 58% of the time when pitted against the DNN model. These results, however, are encouraging given the comparison with a highly-considered, well-crafted human-generated movie title. Movie titles go through a rigorous process of assessment by experts and focus groups, who have watched the movie. This process is in place due to the large amount of money at stake and the importance of creating an effective title that captures the audiences’ attention. Our work shows progress towards automating this process, which in turn may lead to a better understanding of creativity itself.

Keywords: creativity, deep machine learning, natural language generation, movies

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Authors: Amer A. Hasan, Mehri Igci, Ersin Borazan, Rozhgar A. Khailany, Emine Bayraktar, Ahmet Arslan

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Gastric cancer (GC) has high morbidity and fatality rate in various countries and is still one of the most frequent and deadly diseases. Novel mitogenic and motogenic Gastrokine1 (GKN1) and Gastrokine 2 (GKN2) genes that are highly expressed in the normal stomach epithelium and plays an important role in maintaining the integrity and homeostasis of stomach mucosal epithelial cells. Significant loss of copy number and mRNA transcript of GKN1 and GKN2 gene expression were frequently observed in all types of gastric cancer. In this study, 47 paired samples that were grouped according to the types of gastric cancer and the clinical characteristics of the patients, including gender and average of age were investigated with gene expression analysis and mutation screening by monetering RT-PCR, SSCP and nucleotide sequencing techniques. Both GKN1 and GKN2 genes were observed significantly reduced found by (Wilcoxon signed rank test; p<0.05). As a result of gene screening, no mutation (no different genotype) was detected. It is considered that gene mutations are not the cause of inactivation of gastrokines. In conclusion, the mRNA expression level of GKN1 and GKN2 genes statistically was decreased regardless the gender, age or cancer type of patients. Reduced of gastrokine genes seems to occur at the initial steps of cancer development. In order to understand the investigation between gastric cancer and diagnostic biomarker; further analysis is necessary.

Keywords: gastric cancer, diagnostic biomarker, nucleotide sequencing, semi-quantitative RT-PCR

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Authors: Lize Tibiriçá, Ronnie Lee, Samantha Behbahani

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Fibromyalgia (FM) is a musculoskeletal disorder affecting men and women of different ages and cultures. The cause of this disorder is unknown; however, studies suggest an etiology that involves biological and psychosocial factors. Few studies have shown that a personality type such as neuroticism is associated with chronic pain conditions. Past research has explored whether patients with FM present with a specific personality trait. However, studies have used different methods (i.e. Minnesota Multiphasic Personality Inventory (MMPI), Sociotropy and Autonomy Scale (SAS) and Dysfunctional Attitude Scale (DAS), Tridimensional Personality Questionnaire or Temperament and Character Inventory (TCI), Karolinska scale of personality, Big Five Inventory or NEO Personality Inventory) to explore the connection between FM and a personality type. They have identified personality types that present similar characteristics but vary in the name (i.e. high harm avoidance and low novelty seeking, psychasthenia/muscular tension/somatic anxiety, neuroticism). Although Zuckerman-Kuhlman Personality Questionnaire and the Big Five Inventory differ in terms of content and structure, both of them identify neuroticism as the personality type of FM patients, and the former also identifies these patients as having a low sociability personality trait. Previous research also shows a trend of sociotropic personality style with FM patients that also suffer from Major Depressive Disorder. Participants in these studies were, for the most part, adult female and researchers have recognized that as a limitation and whether their findings can be generalized to men and younger patients with FM. Furthermore, most studies reviewed were conducted in Europe (i.e. Spain) and had a cross-sectional design. Future research should replicate past studies in different countries and consider conducting a longitudinal study. Although it is suspected that FM course is modulated by FM patients’ personality, it is not known whether individuals with similar personalities will develop FM. This review sought to explain the differences and similarities between the personality types identified. Limitations in the studies reviewed were addressed, and considerations for future research and treatment were discussed.

Keywords: chronic pain, fibromyalgia, neuroticism, personality type

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Authors: R. R. Billones, N. Lukkahatai, L. N. Saligan

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Mindfulness based interventions (MBIs) have been used in medically unexplained symptoms (MUS). This systematic review describes the literature investigating the general effect of MBIs on MUS and identifies the effects of specific MBIs on specific MUS conditions. The preferred reporting items for systematic reviews and meta-analysis guidelines (PRISMA) and the modified Oxford quality scoring system (JADAD) were applied to the review, yielding an initial 1,556 articles. The search engines included PubMed, ScienceDirect, Web of Science, Scopus, EMBASE, and PsychINFO using the search terms: mindfulness, or mediations, or mindful or MBCT or MBSR and medically unexplained symptoms or MUS or fibromyalgia or FMS. A total of 24 articles were included in the final systematic review. MBIs showed large effects on socialization skills for chronic fatigue syndrome (d=0.65), anger in fibromyalgia (d=0.61), improvement of somatic symptoms (d=1.6) and sleep (d=1.12) for painful conditions, physical health for chronic back pain (d=0.51), and disease intensity for irritable bowel disease/syndrome (d=1.13). A manualized MBI that applies the four fundamental elements present in all types of interventions were critical to efficacy. These elements were psycho-education sessions specific to better understand the medical symptoms, the practice of awareness, the non-judgmental observance of the experience at the moment, and the compassion to ones’ self. The effectiveness of different mindfulness interventions necessitates giving attention to improve the gaps that were identified related to home-based practice monitoring, competency training of mindfulness teachers, and sound psychometric properties to measure the mindfulness practice.

Keywords: mindfulness-based interventions, medically unexplained symptoms, mindfulness-based cognitive therapy, mindfulness-based stress reduction, fibromyalgia, irritable bowel syndrome

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Authors: Jeongyeob Hong, Myeonghoon Park, Taeson Yoon

Abstract:

After the advent of Achaeans which utilize different metabolism pathway and contain conspicuously different cellular structure, they have been recognized as possible materials for developing quality of human beings. Among diverse Achaeans, in this paper, we compared 16s RNA Sequences of four different species of Thermococcus: Achaeans genus specialized in sulfur-dealing metabolism. Four Species, Barophilus, Kodakarensis, Hydrothermalis, and Onnurineus, live near the hydrothermal vent that emits extreme amount of sulfur and heat. By comparing ribosomal sequences of aforementioned four species, we found similarities in their sequences and expressed protein, enabling us to expect that certain ribosomal sequence or proteins are vital for their survival. Apriori algorithms and Decision Tree were used. for comparison.

Keywords: Achaeans, Thermococcus, apriori algorithm, decision tree

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Authors: Yildiray Keskin, Omer Acan, Murat Akkus

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In this paper, the solution of fractional diffusion equations is presented by means of the reduced differential transform method. Fractional partial differential equations have special importance in engineering and sciences. Application of reduced differential transform method to this problem shows the rapid convergence of the sequence constructed by this method to the exact solution. The numerical results show that the approach is easy to implement and accurate when applied to fractional diffusion equations. The method introduces a promising tool for solving many fractional partial differential equations.

Keywords: fractional diffusion equations, Caputo fractional derivative, reduced differential transform method, partial

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Authors: Busra Mutlu Ipek, Merve Mutlu, Ahmet Mutlu

Abstract:

Novel coronavirus COVID-19, which has recently influenced the world, poses a great threat to humanity. In order to overcome this challenging situation, scientists are working on developing effective vaccine against coronavirus. Many experts and researchers have also produced articles and done studies on this highly important subject. In this direction, this special topic was chosen for article to make a contribution to this area. The purpose of this article is to perform RNA sequence analysis of selected virus forms in the Coronaviridae family and predict/classify SARS-CoV-2 (COVID-19) from other selected complete genomes in coronaviridae family using proposed Artificial Neural Network(ANN) algorithm.

Keywords: Coronaviridae family, COVID-19, RNA sequencing, ANN, neural network

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Authors: Mouad Zouina, Benaceur Outtaj

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The proposed work falls within the context of improving data security for m-commerce systems. In this context we have placed under the light some flaws encountered in HTTPS the most used m-commerce protocol, particularly the man in the middle attack, shortly MITM. The man in the middle attack is an active listening attack. The idea of this attack is to target the handshake phase of the HTTPS protocol which is the transition from a non-secure connection to a secure connection in our case HTTP to HTTPS. This paper proposes a solution to fix those flaws based on the upgrade of HSTS standard handshake sequence using the DNSSEC standard.

Keywords: m-commerce, HTTPS, HSTS, DNSSEC, MITM bootstrap vulnerability

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Authors: Shalu Jain, Anju Bansal, Anup Kumar, Sunita Saxena

Abstract:

Objectives: The novel TMPRSS2:ERG gene fusion is a common somatic event in prostate cancer that in some studies is linked with a more aggressive disease phenotype. Thus, this study aims to determine whether clinical variables are associated with the presence of TMPRSS2:ERG-fusion gene transcript in Indian patients of prostate cancer. Methods: We evaluated the clinical variables with presence and absence of TMPRSS2:ERG gene fusion in prostate cancer and BPH association of clinical patients. Patients referred for prostate biopsy because of abnormal DRE or/and elevated sPSA were enrolled for this prospective clinical study. TMPRSS2:ERG mRNA copies in samples were quantified using a Taqman chemistry by real time PCR assay in prostate biopsy samples (N=42). The T2:ERG assay detects the gene fusion mRNA isoform TMPRSS2 exon1 to ERG exon4. Results: Histopathology report has confirmed 25 cases as prostate cancer adenocarcinoma (PCa) and 17 patients as benign prostate hyperplasia (BPH). Out of 25 PCa cases, 16 (64%) were T2: ERG fusion positive. All 17 BPH controls were fusion negative. The T2:ERG fusion transcript was exclusively specific for prostate cancer as no case of BPH was detected having T2:ERG fusion, showing 100% specificity. The positive predictive value of fusion marker for prostate cancer is thus 100% and the negative predictive value is 65.3%. The T2:ERG fusion marker is significantly associated with clinical variables like no. of positive cores in prostate biopsy, Gleason score, serum PSA, perineural invasion, perivascular invasion and periprostatic fat involvement. Conclusions: Prostate cancer is a heterogeneous disease that may be defined by molecular subtypes such as the TMPRSS2:ERG fusion. In the present prospective study, the T2:ERG quantitative assay demonstrated high specificity for predicting biopsy outcome; sensitivity was similar to the prevalence of T2:ERG gene fusions in prostate tumors. These data suggest that further improvement in diagnostic accuracy could be achieved using a nomogram that combines T2:ERG with other markers and risk factors for prostate cancer.

Keywords: prostate cancer, genetic rearrangement, TMPRSS2:ERG fusion, clinical variables

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Authors: Hunmin Jung, Michael Hawkins, Seongmin Lee

Abstract:

The exocyclic amines of nucleobases can undergo deamination by various DNA damaging agents such as reactive oxygen species, nitric oxide, and water. The deamination of guanine and adenine generates the promutagenic xanthine and hypoxanthine, respectively. The exocyclic amines of bases in DNA are hydrogen bond donors, while the carbonyl moiety generated by the base deamination acts as hydrogen bond acceptors, which can alter base pairing properties of the purines. Xanthine is known to base pair with both cytosine and thymine, while hypoxanthine predominantly pairs with cytosine to promote A to G mutations. Despite the known promutagenicity of the major deaminated purines, structures of DNA polymerase bypassing these lesions have not been reported. To gain insights into the deaminated-induced mutagenesis, we solved crystal structures of human DNA polymerase η (polη) catalyzing across xanthine and hypoxanthine. In the catalytic site of polη, the deaminated guanine (i.e., xanthine) forms three Watson-Crick-like hydrogen bonds with an incoming dCTP, indicating the O2-enol tautomer of xanthine involves in the base pairing. The formation of the enol tautomer appears to be promoted by the minor groove contact by Gln38 of polη. When hypoxanthine is at the templating position, the deaminated adenine uses its O6-keto tautomer to form two Watson-Crick hydrogen bonds with an incoming dCTP, providing the structural basis for the high promutagenicity of hypoxanthine.

Keywords: DNA damage, DNA polymerase, deamination, mutagenesis, tautomerization, translesion synthesis

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