Search results for: antigenic variants

Authors: Andrey Kashcheev, Victor Sytnikov, Mikhail Dubinin, Elena Filipeva, Dmitriy Sorokin

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Various variants of technical solutions aimed at improving the reliability of power supply to consumers of 110 kV substation are considered. For each technical solution, the results of calculation and analysis of electrical modes and short-circuit currents in the electrical network are presented. The estimation of electric energy consumption for losses within the boundaries of substation reconstruction was carried out in accordance with the methodology for determining the standards of technological losses of electricity during its transmission through electric networks. The assessment of the technical and economic feasibility of the use of HTS CL compared with the complex reconstruction of the 110 kV substation was carried out. It is shown that the use of high-temperature superconducting AC cable lines is a possible alternative to traditional technical solutions used in the reconstruction of substations.

Keywords: superconductivity, cable lines, superconducting cable, AC cable, feasibility

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Authors: Pablo Kubo, Cassio Paiva, Adelino Ferreira

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The main objective of this research study is to present the results of the influence of shock absorber condition, from a truck front suspension, on the vertical dynamic load applied on the pavement. For the measurements, it has been used a durability test track located in Brazil. The shock absorber conditions were new, used and failed with a constant load of 6 tons on the front suspension, the maximum allowed load for front axle according to Brazilian legislation. By applying relative damage concept, it is possible to conclude that the variation on the shock absorber conditions will significantly affect the load applied on the pavement. Although, it is recommended to repeat the same methodology in order to analyze the influence on the variation of the quarter car model variants.

Keywords: damage, shock absorber, vertical dynamic load, absorber

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Authors: Marie-Elise Beydon, Daniel Sacristan, Isabel Ruppen

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MB02 (Alymsys®) is a candidate biosimilar to bevacizumab, which was developed against the reference product (RP) Avastin® sourced from both the European Union (EU) and United States (US). MB02 has been extensively characterized comparatively to Avastin® at a physicochemical and biological level using sensitive orthogonal state-of-the-art analytical methods. MB02 has been demonstrated similar to the RP with regard to its primary and higher-order structure, post- and co-translational profiles such as glycosylation, charge, and size variants. Specific focus has been put on the characterization of Fab-related activities, such as binding to VEGF A 165, which directly reflect the bevacizumab mechanism of action. Fc-related functionality was also investigated, including binding to FcRn, which is indicative of antibodies' half-life. The data generated during the analytical similarity assessment demonstrate the high analytical similarity of MB02 to its RP.

Keywords: analytical similarity, bevacizumab, biosimilar, MB02

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Authors: Siti Nadiah Nuwawi, Roshidah Hassan

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Dialect is one of the language variants emerge due to certain factors. One of the distinctive dialects spoken by people in Malaysia is the one spoken by those who reside in the inland area of the East Peninsular Malaysia; Hulu Terengganu, which is known as Ulu Terengganu Malay dialect. This dialect is unique since it possesses ancient elements in its phonology elements, which makes it is hard to be understood by people who come from other states. There is dearth of acoustic studies of the dialect in which this paper aims to attain by describing the quality of the monophthongs found in the dialect instrumentally based on their first and second formant values. The hertz values are observed and recorded from the waveforms and spectrograms depicted in PRAAT version 6.0.43 software. The findings show that Ulu Terengganu Malay speakers produced ten monophthongs namely /ɛ/, /e/, /a/, /ɐ/, /ɞ/, /ɔ/, /i/, /o/, /ɵ/ and /ɘ/ which applauds a few monophthongs suggested by past researchers which were based on auditory impression namely /ɛ/, /e/, /a/, ɔ/, and /i/. It also discovers the other five monophthongs of the dialect which are unknown before namely /ɐ/, /ɞ/, /o/, /ɵ/ and /ɘ/.

Keywords: acoustic analysis, dialect, formant values, monophthongs, Ulu Terengganu Malay

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Authors: Monika Malik, Pooja Arora, Ruchi Sachdeva, Vishnampettai G. Ramachandran, Rahul Pal

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Apoptotic debris is believed to be the antigenic trigger in lupus. Whether such debris and autoantibodies induced in lupus-prone mice which specifically recognize its constituents can mediate differential effects on innate and humoral responses in such mice was assessed. The influence of apoptotic blebs and apoptotic cell-reactive monoclonal antibodies on phenotypic markers expressed on bone marrow-derived dendritic cells (BMDCs) and secreted cytokines were evaluated. Sera from lupus-prone and healthy mice immunized with the antibodies were analyzed for anti-self reactivity. Apoptotic blebs, as well as somatically-mutated IgG and non-mutated IgM apoptotic-cell reactive monoclonal antibodies, induced the preferential maturation of BMDCs derived from lupus-prone mice relative to BMDCs derived from healthy mice; antibody specificity and cell genotype both influenced the secretion of inflammatory cytokines. Immunization of lupus-prone mice with IgM and IgG antibodies led to hypergammaglobulinemia; elicited antibodies were self-reactive, and exhibited enhanced recognition of lupus-associated autoantigens (dsDNA, Ro60, RNP68, and Sm) in comparison with adjuvant-induced sera. While ‘natural’ IgM antibodies are believed to contribute to immune homeostasis, this study reveals that apoptotic cell-reactive IgM antibodies can promote inflammation and drive anti-self responses in lupus. Only in lupus-prone mice did immunization with IgG auto-antibodies enhance the kinetics of humoral anti-self responses, resulting in advanced-onset glomerulosclerosis. This study reveals that preferential innate and humoral recognition of the products of cell death in an autoimmune milieu influences the indices associated with lupus pathology.

Keywords: antigen spreading, apoptotic cell-reactive pathogenic IgG, and IgM autoantibodies, glomerulosclerosis, lupus

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Authors: Jean-Pierre Lomaliza, Kwang-Seok Moon, Hanhoon Park

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It is well-known that Ramer Douglas Peucker (RDP) algorithm greatly depends on the method of choosing starting points. Therefore, this paper focuses on finding such starting points that will optimize the results of RDP algorithm. Specifically, this paper proposes a curve approximation algorithm that finds flat points, called essential points, of an input curve, divides the curve into corner-like sub-curves using the essential points, and applies the RDP algorithm to the sub-curves. The number of essential points play a role on optimizing the approximation results by balancing the degree of shape information loss and the amount of data reduction. Through experiments with curves of various types and complexities of shape, we compared the performance of the proposed algorithm with three other methods, i.e., the RDP algorithm itself and its variants. As a result, the proposed algorithm outperformed the others in term of maintaining the original shapes of the input curve, which is important in various applications like pattern recognition.

Keywords: curve approximation, essential point, RDP algorithm

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Authors: Stefan Bradu, Daniel Siegel, Jameson Loyal, Andrea Leaf, Alana Kurtti, Usha Alapati, Jared Jagdeo

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Compared with all other variants of nodular melanoma, patients with polypoid nodular melanoma have the lowest 5-year survival rate. The pathophysiology and management of polypoid melanoma are scarcely reported in the literature. Although surgical excision is the cornerstone of melanoma management, treatment of polypoid melanoma is complicated by several negative prognostic factors, including early metastasis. This report demonstrates the successful treatment of a rapidly developing red nodular polypoid melanoma with metastasis using surgery and adjuvant nivolumab in a SARS-CoV-2-positive patient who delayed seeking care due to the COVID-19 pandemic. In addition to detailing the successful treatment approach, the immunosuppressive effects of SARS-2-CoV and its possible contribution to the rapid progression of polypoid melanoma are discussed. This case highlights the complex challenges of melanoma diagnosis and management during the COVID-19 pandemic.

Keywords: covid-19, dermatology, immunotherapy, melanoma, nivolumab

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Authors: Chirawat Wattanapanich, Hong Wei

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This study presents new gait representations for improving gait recognition accuracy on cross gait appearances, such as normal walking, wearing a coat and carrying a bag. Based on the Gait Energy Image (GEI), two ideas are implemented to generate new gait representations. One is to append lower knee regions to the original GEI, and the other is to apply convolutional operations to the GEI and its variants. A set of new gait representations are created and used for training multi-class Support Vector Machines (SVMs). Tests are conducted on the CASIA dataset B. Various combinations of the gait representations with different convolutional kernel size and different numbers of kernels used in the convolutional processes are examined. Both the entire images as features and reduced dimensional features by Principal Component Analysis (PCA) are tested in gait recognition. Interestingly, both new techniques, appending the lower knee regions to the original GEI and convolutional GEI, can significantly contribute to the performance improvement in the gait recognition. The experimental results have shown that the average recognition rate can be improved from 75.65% to 87.50%.

Keywords: convolutional image, lower knee, gait

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Authors: Sungzoon Cho, Hye Jin Lee, Sungwhan Jeon, Dongyoung Min, Sungwon Lyu

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Major public corporations worldwide use conference calls to report their quarterly earnings. These 'earnings' conference calls allow for questions from stock analysts. We investigated if it is possible to identify sentiment from the call script and use it to predict stock price movement. We analyzed call scripts from six companies, two each from Korea, China and Indonesia during six years 2011Q1 – 2017Q2. Random forest with Frequency-based sentiment scores using Loughran MacDonald Dictionary did better than control model with only financial indicators. When the stock prices went up 20 days from earnings release, our model predicted correctly 77% of time. When the model predicted 'up,' actual stock prices went up 65% of time. This preliminary result encourages us to investigate advanced sentiment scoring methodologies such as topic modeling, auto-encoder, and word2vec variants.

Keywords: earnings call script, random forest, sentiment analysis, stock price prediction

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Authors: Manik Sharma

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Understanding the anatomy and normal anatomical variations of the lower limb arterial system is undeniably important not only to understand the pathology involving the vessels of the lower limb but also as a part of endovascular intervention and surgical planning in cases that demand them as a part of treatment. There have been very few cases of duplication of SFA cited in the literature, close to six worldwide and this being the seventh case in the world and first to be reported in the Indian population. We incidentally came across this normal variant during US lower limb (US-LL) duplex scan in a patient with claudicating pain in bilateral lower limbs hence suspected of having peripheral vascular disease. It was confirmed on CT-Peripheral Angiography (CT-PA), which was done successively.

Keywords: peripheral vascular disease, claudicating pain, normal anatomical variants, endovascular intervention, duplication, CT-peripheral angiography, duplex scan, Iohexol

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Authors: Mustapha Kamel Mihoubi, Hocine Dahmani

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Over recent years much progress has been achieved in the fields of numerical modeling shoreline processes: waves, currents, waves and current. However, there are still some problems in the existing models to link the on the first, the hydrodynamics of waves and currents and secondly, the sediment transport processes and due to the variability in time, space and interaction and the simultaneous action of wave-current near the shore. This paper is the establishment of a numerical modeling to forecast the sediment transport from development scenarios of harbor structure. It is established on the basis of a numerical simulation of a water-sediment model via a 2D model using a set of codes calculation MIKE 21-DHI software. This is to examine the effect of the sediment transport drivers following the dominant incident wave in the direction to pass input harbor work under different variants planning studies to find the technical and economic limitations to the sediment transport and protection of the harbor structure optimum solution.

Keywords: swell, current, radiation, stress, mesh, mike21, sediment

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Authors: Edlira Donefski, Tina Donefski, Lorenc Ekonomi

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Edgeworth Approximation, Bootstrap, and Monte Carlo Simulations have considerable impacts on achieving certain results related to different problems taken into study. In our paper, we have treated a financial case related to the effect that has the components of a cash-flow of one of the most successful businesses in the world, as the financial activity, operational activity, and investment activity to the cash and cash equivalents at the end of the three-months period. To have a better view of this case, we have created a vector autoregression model, and after that, we have generated the impulse responses in the terms of asymptotic analysis (Edgeworth Approximation), Monte Carlo Simulations, and residual bootstrap based on the standard errors of every series created. The generated results consisted of the common tendencies for the three methods applied that consequently verified the advantage of the three methods in the optimization of the model that contains many variants.

Keywords: autoregression, bootstrap, edgeworth expansion, Monte Carlo method

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Authors: Liang Liu, Xiaopeng Luo

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In this paper, we propose an accelerated stochastic gradient method with momentum. The momentum term is the weighted average of generated gradients, and the weights decay inverse proportionally with the iteration times. Stochastic gradient descent with momentum (SGDM) uses weights that decay exponentially with the iteration times to generate the momentum term. Using exponential decay weights, variants of SGDM with inexplicable and complicated formats have been proposed to achieve better performance. However, the momentum update rules of our method are as simple as that of SGDM. We provide theoretical convergence analyses, which show both the exponential decay weights and our inverse proportional decay weights can limit the variance of the parameter moving directly to a region. Experimental results show that our method works well with many practical problems and outperforms SGDM.

Keywords: exponential decay rate weight, gradient descent, inverse proportional decay rate weight, momentum

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Authors: Minhal Abidi, Moinuddin

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Diabetes mellitus (DM) induced metabolic abnormalities causes oxidative stress which leads to the pathogenesis of complications associated with diabetes like retinopathy, nephropathy periodontitis etc. Combination of glycation and oxidation 'glycoxidation' occurs when oxidative reactions affect the early state of glycation products. Low density lipoprotein (LDL) is prone to glycoxidative attack by sugars and methylglyoxal (MGO) being a strong glycating agent may have severe impact on its structure and consequent role in diabetes. Pro-inflammatory cytokines like IL1β and TNFα produced by the action of gram negative bacteria in periodontits (PD) can in turn lead to insulin resistance. This work discusses modifications to LDL as a result of glycoxidation. The changes in the protein molecule have been characterized by various physicochemical techniques and the immunogenicity of the modified molecules was also evaluated as they presented neo-epitopes. Binding of antibodies present in diabetes patients to the native and glycated LDL has been evaluated. Role of modified epitopes in the generation of antibodies in diabetes and periodontitis has been discussed. The structural perturbations induced in LDL were analyzed by UV–Vis, fluorescence, circular dichroism and FTIR spectroscopy, molecular docking studies, thermal denaturation studies, Thioflavin T assay, isothermal titration calorimetry, comet assay. MALDI-TOF, ketoamine moieties, carbonyl content and HMF content were also quantitated in native and glycated LDL. IL1β and TNFα levels were also measured in the type 2 DM and PD patients. We report increased carbonyl content, ketoamine moieties and HMF content in glycated LDL as compared to native analogue. The results substantiate that in hyperglycemic state MGO modification of LDL causes structural perturbations making the protein antigenic which could obstruct normal physiological functions and might contribute in the development of secondary complications in diabetic patients like periodontitis.

Keywords: advanced glycation end products, diabetes mellitus, glycation, glycoxidation, low density lipoprotein, periodontitis

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Authors: Anna Sikharulidze, Gia Sirbiladze

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For the evaluation of unreliability levels of movement on the closed routes in the vehicle routing problem, the fuzzy operators family is constructed. The interactions between routing factors in extreme conditions on the roads are considered. A multi-criteria decision-making model (MCDM) is constructed. Constructed aggregations are based on the Choquet integral and the associated probability class of a fuzzy measure. Propositions on the correctness of the extension are proved. Connections between the operators and the compositions of dual triangular norms are described. The conjugate connections between the constructed operators are shown. Operators reflect interactions among all the combinations of the factors in the fuzzy MCDM process. Several variants of constructed operators are used in the decision-making problem regarding the assessment of unreliability and possibility levels of movement on closed routes.

Keywords: vehicle routing problem, associated probabilities of a fuzzy measure, choquet integral, fuzzy aggregation operator

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Authors: Lu Zhao, Nadir Farhi, Yeltsin Valero, Zoi Christoforou, Nadia Haddadou

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In this paper, a long short-term memory (LSTM) neural network model is proposed to replicate simultaneously car-following and lane-changing behaviors in road networks. By combining two kinds of LSTM layers and three input designs of the neural network, six variants of the LSTM model have been created. These models were trained and tested on the NGSIM 101 dataset, and the results were evaluated in terms of longitudinal speed and lateral position, respectively. Then, we compared the LSTM model with a classical car-following model (the intelligent driving model (IDM)) in the part of speed decision. In addition, the LSTM model is compared with a model using classical neural networks. After the comparison, the LSTM model demonstrates higher accuracy than the physical model IDM in terms of car-following behavior and displays better performance with regard to both car-following and lane-changing behavior compared to the classical neural network model.

Keywords: traffic modeling, neural networks, LSTM, car-following, lane-change

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Authors: Ferzat Anka

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Many types of problems can be solved using traditional analytical methods. However, these methods take a long time and cause inefficient use of resources. In particular, different approaches may be required in solving complex and global engineering problems that we frequently encounter in real life. The bigger and more complex a problem, the harder it is to solve. Such problems are called Nondeterministic Polynomial time (NP-hard) in the literature. The main reasons for recommending different metaheuristic algorithms for various problems are the use of simple concepts, the use of simple mathematical equations and structures, the use of non-derivative mechanisms, the avoidance of local optima, and their fast convergence. They are also flexible, as they can be applied to different problems without very specific modifications. Thanks to these features, it can be easily embedded even in many hardware devices. Accordingly, this approach can also be used in trend application areas such as IoT, big data, and parallel structures. Indeed, the metaheuristic approaches are algorithms that return near-optimal results for solving large-scale optimization problems. This study is focused on the new metaheuristic method that has been merged with the chaotic approach. It is based on the chaos theorem and helps relevant algorithms to improve the diversity of the population and fast convergence. This approach is based on Chimp Optimization Algorithm (ChOA), that is a recently introduced metaheuristic algorithm inspired by nature. This algorithm identified four types of chimpanzee groups: attacker, barrier, chaser, and driver, and proposed a suitable mathematical model for them based on the various intelligence and sexual motivations of chimpanzees. However, this algorithm is not more successful in the convergence rate and escaping of the local optimum trap in solving high-dimensional problems. Although it and some of its variants use some strategies to overcome these problems, it is observed that it is not sufficient. Therefore, in this study, a newly expanded variant is described. In the algorithm called Ex-ChOA, hybrid models are proposed for position updates of search agents, and a dynamic switching mechanism is provided for transition phases. This flexible structure solves the slow convergence problem of ChOA and improves its accuracy in multidimensional problems. Therefore, it tries to achieve success in solving global, complex, and constrained problems. The main contribution of this study is 1) It improves the accuracy and solves the slow convergence problem of the ChOA. 2) It proposes new hybrid movement strategy models for position updates of search agents. 3) It provides success in solving global, complex, and constrained problems. 4) It provides a dynamic switching mechanism between phases. The performance of the Ex-ChOA algorithm is analyzed on a total of 8 benchmark functions, as well as a total of 2 classical and constrained engineering problems. The proposed algorithm is compared with the ChoA, and several well-known variants (Weighted-ChoA, Enhanced-ChoA) are used. In addition, an Improved algorithm from the Grey Wolf Optimizer (I-GWO) method is chosen for comparison since the working model is similar. The obtained results depict that the proposed algorithm performs better or equivalently to the compared algorithms.

Keywords: optimization, metaheuristic, chimp optimization algorithm, engineering constrained problems

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Authors: Ghada Esheba, Fatimah Alturkistani, Arwa Obaid, Ahdab Bashehab, Moayad Alturkistani

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Introduction: Craniopharyngiomas (CPs) are rare epithelial tumors located mainly in the sellar/parasellar region. CPs have been classified histopathologically, genetically, clinically and prognostically into two distinctive subtypes: adamantinomatous and papillary variants. Aim: To examine the pattern of expression of both the β-catenin and epidermal growth factor receptor (EGFR) in surgically resected samples of adamantinomatous CP, and to asses for the possibility of using anti-EGFR in the management of ACP patients. Materials and methods: β-catenin and EGFR immunostaining was performed on paraffin-embedded tissue sections of 18 ACP cases. Result: 17 out of 18 cases (94%) of ACP exhibited strong nuclear/cytoplasmic expression of β-catenin, 15 (83%) of APC cases were positive for EGFR. Conclusion: Nuclear accumulation of β-catenin is a diagnostic hallmark of ACP. EGFR positivity in most cases of ACP could qualify the use of anti-EGFR therapy. 

Keywords: craniopharyngioma, adamantinomatous, papillary, epidermal growth factor receptor, B-catenin

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Authors: Bothinah Altaf, Gary Montague, Elaine B. Martin

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This study involves the modeling and monitoring of an ammonia synthesis fixed-bed reactor using partial least squares (PLS) and its variants. The process exhibits complex dynamic behavior due to the presence of heat recycling and feed quench. One limitation of static PLS model in this situation is that it does not take account of the process dynamics and hence dynamic PLS was used. Although it showed, superior performance to static PLS in terms of prediction, the monitoring scheme was inappropriate hence adaptive PLS was considered. A limitation of adaptive PLS is that non-conforming observations also contribute to the model, therefore, a new adaptive approach was developed, robust adaptive dynamic PLS. This approach updates a dynamic PLS model and is robust to non-representative data. The developed methodology showed a clear improvement over existing approaches in terms of the modeling of the reactor and the detection of faults.

Keywords: ammonia synthesis fixed-bed reactor, dynamic partial least squares modeling, recursive partial least squares, robust modeling

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Authors: D. R. Apoorva

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Ichthyosis follicularis, alopecia, and photophobia (IFAP) syndrome is a rare oculocutaneous disorder of genetic origin. This disorder results from mutations in the membrane-bound transcription factor protease site, two genes that impair cholesterol homeostasis, and the ability to cope with endoplasmic reticulum stress. We report a rare case of IFAP syndrome with an atypical presentation, and it was interesting to note that the child had patchy non-scarring alopecia over the scalp along with unilateral madarosis. To our best knowledge, this unique presentation has not been described earlier. The child presented with photophobia and unilateral ptosis. The child also had short stature and intellectual disability. Skin histopathology was nonspecific and consisted of dilated hair follicles with keratin plugs extending above the skin surface. This rare oculocutaneous disorder requires proper documentation so that identification of its variants may be possible in the future. Early recognition of atypical presentations can help in preventing cardiovascular complications, which remain the major cause of death.

Keywords: alopecia, photophobia, ichthyosis follicularis, IFAP syndrome

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Authors: H. Sakamoto, Y. Nakagawara, S. Oguri

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Drought stress is a critical environmental factor that adversely affects crop productivity and quality. Because of their immobile nature, plants have evolved mechanisms to sense and respond to drought stress. We identified a novel locus of Arabidopsis, designated DRA1 (drought responsive ankyrin 1), whose disruption leads to increased drought stress tolerance. DRA1 encodes a transmembrane protein with an ankyrin repeat motif that has been implicated in diverse cellular processes such as signal transduction. RT-PCR analysis revealed that there were at least two splicing variants of DRA1 transcripts in wild type plants. In response to drought stress, the levels of DRA1 transcripts retaining second and third introns were increased, whereas these introns were removed under unstressed conditions. These results suggest that DRA1 protein may negatively regulate plant drought tolerance and that the expression of DRA1 is regulated in response to drought stress by alternative splicing.

Keywords: alternative splicing, ankyrin repeat, Arabidopsis, drought tolerance

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Authors: Nguyen Cao Nguyen, Krasimir I. Ivanov, Penka S. Zapryanova

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The present study was carried out to investigate the interaction of foliar applied zinc with other elements in Phyllanthus amarus plants. The plant samples for our experiment were collected from Lam Dong province, Vietnam. Seven suspension solutions of nanosized zinc hydroxide nitrate (Zn₅(OH)₈(NO₃)₂·2H₂O) with different Zn concentration were used. Fertilization and irrigation were the same for all variants. The Zn content and the content of selected micro (Cu, Fe, Mn) and macro (Ca, Mg, P and K) nutrients in plant roots, and stems and leaves were determined. It was concluded that the zinc content of plant roots varies narrowly, with no significant impact of ZnHN fertilization. The same trend can be seen in the content of Cu, Mn, and macronutrients. The zinc content of plant stems and leaves varies within wide limits, with the significant impact of ZnHN fertilization. The trends in the content of Cu, Mn, and macronutrients are kept the same as in the root, whereas the iron trends to increase its content at increasing the zinc content.

Keywords: Phyllanthus amarus, Zinc, Micro and macro elements, foliar fertilizer

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Authors: Liana Lortkipanidze, Nino Amirezashvili, Nino Javashvili

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The purpose of the grammatical dictionary is to provide information on the morphological and syntactic characteristics of the basic word in the dictionary entry. The electronic grammatical dictionaries are used as a tool of automated morphological analysis for texts processing. The Georgian Grammatical Dictionary should contain grammatical information for each word: part of speech, type of declension/conjugation, grammatical forms of the word (paradigm), alternative variants of basic word/lemma. In this paper, we present the system for compiling the Georgian Grammatical Dictionary automatically. We propose dictionary-based methods for extending grammatical lexicons. The input lexicon contains only a few number of words with identical grammatical features. The extension is based on similarity measures between features of words; more precisely, we add words to the extended lexicons, which are similar to those, which are already in the grammatical dictionary. Our dictionaries are corpora-based, and for the compiling, we introduce the method for lemmatization of unknown words, i.e., words of which neither full form nor lemma is in the grammatical dictionary.

Keywords: acquisition of lexicon, Georgian grammatical dictionary, lemmatization rules, morphological processor

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Authors: Hazha Hidayat, Shayma Ibrahim

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Folate metabolism plays a crucial role in the normal development of the neonatal central nervous system. It is regulated by MTHFR gene polymorphism. Any factors, which will affect this metabolism either by hereditary or gene mutation will lead to many mental disorders. The purpose of this study was to investigate whether MTHFR gene mutation contributes to the development of mental retardation and CP combined with mental retardation in Erbil city. DNA was isolated from the peripheral blood samples of 40 cases suffering from mental retardation (MR) and CP combined with MR were recruited, sequence the 4, 6, 7, 8 exons of the MTHFR gene were done to identify the variants. Exons were amplified by PCR technique and then sequenced according to Sanger method to show the differences with MTHFR reference sequences. We observed (14) mutations in 4, 6, 7, 8 exons in the MTHFR gene associated with Cerebral Palsy combined with mental retardation included deletion, insertion, Substitution. The current study provides additional evidence that multiple variations in the MTHFR gene are associated with mental retardation and Cerebral Palsy.

Keywords: methylenetetrahydrofolate reductase (MTHFR) gene, SNPs, homocysteine, sequencing

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Authors: Juraj Camaj, Anna Dolinayova, Jana Lalinska, Miroslav Bariak

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Planning of infrastructure and processes in logistic center within the frame of various kinds of logistic hubs and technological activities in them represent quite complex problem. The main goal is to design appropriate layout, which enables to realize expected operation on the desired levels. The simulation software represents progressive contemporary experimental technique, which can support complex processes of infrastructure planning and all of activities on it. It means that simulation experiments, reflecting various planned infrastructure variants, investigate and verify their eligibilities in relation with corresponding expected operation. The inducted approach enables to make qualified decisions about infrastructure investments or measures, which derive benefit from simulation-based verifications. The paper represents simulation software for simulation infrastructural layout and technological activities in marshalling yard, intermodal terminal, warehouse and combination between them as the parts of logistic center.

Keywords: marshalling yard, intermodal terminal, warehouse, transport technology, simulation

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Authors: Kefaya Qaddoum

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Most of greenhouse growers desire a determined amount of yields in order to accurately meet market requirements. The purpose of this paper is to model a simple but often satisfactory supervised classification method. The original naive Bayes have a serious weakness, which is producing redundant predictors. In this paper, utilized regularization technique was used to obtain a computationally efficient classifier based on naive Bayes. The suggested construction, utilized L1-penalty, is capable of clearing redundant predictors, where a modification of the LARS algorithm is devised to solve this problem, making this method applicable to a wide range of data. In the experimental section, a study conducted to examine the effect of redundant and irrelevant predictors, and test the method on WSG data set for tomato yields, where there are many more predictors than data, and the urge need to predict weekly yield is the goal of this approach. Finally, the modified approach is compared with several naive Bayes variants and other classification algorithms (SVM and kNN), and is shown to be fairly good.

Keywords: tomato yield prediction, naive Bayes, redundancy, WSG

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Authors: Arpit Kumar Shrivastava, Subrat Kumar, Rajani Kanta Mohapatra, Priyadarshi Soumyaranjan Sahu

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Computational approaches to predict structure, function and other biological characteristics of proteins are becoming more common in comparison to the traditional methods in drug discovery. Cryptosporidiosis is a major zoonotic diarrheal disease particularly in children, which is caused primarily by Cryptosporidium hominis and Cryptosporidium parvum. Currently, there are no vaccines for cryptosporidiosis and recommended drugs are not effective. With the availability of complete genome sequence of C. hominis, new targets have been recognized for the development of effective and better drugs and/or vaccines. We identified a unique hypothetical epitopic protein in C. hominis genome through BLASTP analysis. A 3D model of the hypothetical protein was generated using I-Tasser server through threading methodology. The quality of the model was validated through Ramachandran plot by PROCHECK server. The functional annotation of the hypothetical protein through DALI server revealed structural similarity with human Transportin 3. Phylogenetic analysis for this hypothetical protein also showed C. hominis hypothetical protein (CUV04613) was the closely related to human transportin 3 protein. The 3D protein model is further subjected to virtual screening study with inhibitors from the Zinc Database by using Dock Blaster software. Docking study reported N-(3-chlorobenzyl) ethane-1,2-diamine as the best inhibitor in terms of docking score. Docking analysis elucidated that Leu 525, Ile 526, Glu 528, Glu 529 are critical residues for ligand–receptor interactions. The molecular dynamic simulation was done to access the reliability of the binding pose of inhibitor and protein complex using GROMACS software at 10ns time point. Trajectories were analyzed at each 2.5 ns time interval, among which, H-bond with LEU-525 and GLY- 530 are significantly present in MD trajectories. Furthermore, antigenic determinants of the protein were determined with the help of DNA Star software. Our study findings showed a great potential in order to provide insights in the development of new drug(s) or vaccine(s) for control as well as prevention of cryptosporidiosis among humans and animals.

Keywords: cryptosporidium hominis, hypothetical protein, molecular docking, molecular dynamics simulation

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Authors: Ananya Gupta, Sangeeta Bhaskar

Abstract:

Mycobacterium indicus pranii (MIP) is a saprophytic mycobacterium. It is a predecessor of M. avium complex (MAC). Whole genome analysis and growth kinetics studies have placed MIP in between pathogenic and non-pathogenic species. It shares significant antigenic repertoire with M. tuberculosis and have unique immunomodulatory properties. MIP provides better protection than BCG against pulmonary tuberculosis in animal models. Immunization with MIP by aerosol route provides significantly higher protection as compared to immunization by subcutaneous (s.c.) route. However, mechanism behind differential protection has not been studied. In this study, using mice model we have evaluated and compared the M.tb specific immune response in lung compartments (airway lumen / lung interstitium) as well as spleen following MIP immunization via nasal (i.n.) and s.c. route. MIP i.n. vaccination resulted in increased seeding of memory T cells (CD4+ and CD8+ T-cells) in the airway lumen. Frequency of CD4+ T cells expressing Th1 migratory marker (CXCR3) and activation marker (CD69) were also high in airway lumen of MIP i.n. group. Significantly high ex vivo secretion of cytokines- IFN-, IL-12, IL-17 and TNF- from cells of airway luminal spaces provides evidence of antigen-specific lung immune response, besides generating systemic immunity comparable to MIP s.c. group. Analysis of T cell response on per cell basis revealed that antigen specific T-cells of MIP i.n. group were functionally superior as higher percentage of these cells simultaneously secreted IFN-gamma, IL-2 and TNF-alpha cytokines as compared to MIP s.c. group. T-cells secreting more than one of the cytokines simultaneously are believed to have robust effector response and crucial for protection, compared with single cytokine secreting T-cells. Adoptive transfer of airway luminal T-cells from MIP i.n. group into trachea of naive B6 mice revealed that MIP induced CD8 T-cells play crucial role in providing long term protection. Thus the study demonstrates that MIP intranasal vaccination induces M.tb specific memory T-cells in the airway lumen that results in an early and robust recall response against M.tb infection.

Keywords: airway lumen, Mycobacterium indicus pranii, Th1 migratory markers, vaccination

Procedia PDF Downloads 159

Authors: Boris Melnikov, Ye Zhang, Dmitrii Chaikovskii

Abstract:

We continue to consider one of the cybernetic methods in computational biology related to the study of DNA chains. Namely, we are considering the problem of reconstructing the not fully filled distance matrix of DNA chains. When applied in a programming context, it is revealed that with a modern computer of average capabilities, creating even a small-sized distance matrix for mitochondrial DNA sequences is quite time-consuming with standard algorithms. As the size of the matrix grows larger, the computational effort required increases significantly, potentially spanning several weeks to months of non-stop computer processing. Hence, calculating the distance matrix on conventional computers is hardly feasible, and supercomputers are usually not available. Therefore, we started publishing our variants of the algorithms for calculating the distance between two DNA chains; then, we published algorithms for restoring partially filled matrices, i.e., the inverse problem of matrix processing. In this paper, we propose an algorithm for restoring the distance matrix for DNA chains, and the primary focus is on enhancing the algorithms that shape the greedy function within the branches and boundaries method framework.

Keywords: DNA chains, distance matrix, optimization problem, restoring algorithm, greedy algorithm, heuristics

Procedia PDF Downloads 67

Authors: Huma Balouch

Abstract:

Menochilus sexmaculatus commonly known as six spotted zig zag ladybird, is an aphidophagus and the most misidentified Coccinellids due to the occurrence of numerous color variants. The correct identification of Menochilus sexmaculatus and its strains is necessary to implement the use of biological control. In the present study phenotypic and genotypic polymorphism was investigated in Menochilus sexmaculatus collected from Punjab, NWFP and Sindh provinces of Pakistan. Six different morphs of the species were distinguished by analyzing its Elytral color and spot pattern and then Polymerase Chain Reaction was used to generate random amplification of polymorphic DNA (RAPD) from six different types of Menochilus sexmaculatus. Forty primers (OPA & OPC Kit) were used to perform RAPD PCR on six different types of Menochilus sexmaculatus of which, seven primers revealed different patterns related to the Menochilus sexmaculatus types. These seven primers (OPA-04, OPA-09, OPA-18, OPC-04, OPC-12, OPC-15 and OPC-18) produced 111 clear polymorphic bands and 6 scorable strain specific markers. The cluster analysis applied to RAPD data showed high polymorphism among six types and it can be concluded that these six types are six polymorphic strains of the same species.

Keywords: Menochilus sexmaculatus, aphidophagus, coccinellids, phenotypic and genotypic polymorphism, RAPD-PCR, strain specific markers

Procedia PDF Downloads 460