Search results for: gene expression data analysis

Authors: M. Caruffo, P. Navarrete, C. G. Feijoo, L. Sáenz

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Disease prevention through the use of vaccines has been crucial to achieve the current level of production in the salmon industry. However, vaccines have been developed based largely on inactivated bacterial formulations, using the whole pathogen. These formulations have demonstrated excellent efficacy against extracellular bacterial pathogens. However diseases with the greatest economic impacts correspond to intracellular bacterial and viral pathogens, vaccines based on these types of agents have shown a discrete effectiveness. It is for these reasons that the development of subunit vaccines based on defined antigens offers a promising solution. The main problem is that subunit vaccines offer a low immunogenicity, since they lack immunostimulatory elements, so that the development of new adjuvants platforms becomes an important challenge for this type of formulations. We evaluate the effect of a formulation based on proteoliposomes of Vibrio anguillarum administered by immersion as a new adjuvant strategy, allowing efficient stimulation of the innate immune system. Proteoliposomes physicochemical properties were evaluated in its ability to produce an inflammatory process. Using zebrafish (Danio rerio) larvae as a model species and the transgenic line (Tg(mpx: GFP)i114) allowed us to track the neutrophil migration in real time. Additionally we evaluated the gene expression of some molecular markers involved in the development of the innate immune response characterizing the adjuvant capacity of the formulation.

Keywords: adjuvants, vaccine development, zebrafish, innate immunity

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Authors: Prozorkevitch D., Mishurov A., Sokolov K., Karsakov L., Pestrikova L.

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The current body of knowledge about the marine environment and the dynamics of marine ecosystems includes a huge amount of heterogeneous data collected over decades. It generally includes a wide range of hydrological, biological and fishery data. Marine researchers collect these data and analyze how and why the ecosystem changes from past to present. Based on these historical records and linkages between the processes it is possible to predict future changes. Multivariate analysis of trends and their interconnection in the marine ecosystem may be used as an instrument for predicting further ecosystem evolution. A wide range of information about the components of the marine ecosystem for more than 50 years needs to be used to investigate how these arrays can help to predict the future.

Keywords: barents sea ecosystem, abiotic, biotic, data sets, trends, prediction

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Authors: Adji Achmad Rinaldo Fernandes

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SEM analysis is a complex multivariate analysis because it involves a number of exogenous and endogenous variables that are interconnected to form a model. The measurement model is divided into two, namely, the reflective model (reflecting) and the formative model (forming). Before carrying out further tests on SEM, there are assumptions that must be met, namely the linearity assumption, to determine the form of the relationship. There are three modeling approaches to path analysis, including parametric, nonparametric and semiparametric approaches. The aim of this research is to develop semiparametric SEM and obtain the best model. The data used in the research is secondary data as the basis for the process of obtaining simulation data. Simulation data was generated with various sample sizes of 100, 300, and 500. In the semiparametric SEM analysis, the form of the relationship studied was determined, namely linear and quadratic and determined one and two knot points with various levels of error variance (EV=0.5; 1; 5). There are three levels of closeness of relationship for the analysis process in the measurement model consisting of low (0.1-0.3), medium (0.4-0.6) and high (0.7-0.9) levels of closeness. The best model lies in the form of the relationship X1Y1 linear, and. In the measurement model, a characteristic of the reflective model is obtained, namely that the higher the closeness of the relationship, the better the model obtained. The originality of this research is the development of semiparametric SEM, which has not been widely studied by researchers.

Keywords: semiparametric SEM, measurement model, structural model, reflective model, formative model

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Authors: Meng Su

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High-dimensional data analysis often presents challenges in capturing the complex, nonlinear relationships and manifold structures inherent to the data. This article presents a novel approach that leverages the strengths of two powerful techniques, Diffusion Maps and Diffusion Probabilistic Models (DPMs), to address these challenges. By integrating the dimensionality reduction capability of Diffusion Maps with the data modeling ability of DPMs, the proposed method aims to provide a comprehensive solution for analyzing and generating high-dimensional data. The Diffusion Map technique preserves the nonlinear relationships and manifold structure of the data by mapping it to a lower-dimensional space using the eigenvectors of the graph Laplacian matrix. Meanwhile, DPMs capture the dependencies within the data, enabling effective modeling and generation of new data points in the low-dimensional space. The generated data points can then be mapped back to the original high-dimensional space, ensuring consistency with the underlying manifold structure. Through a detailed example implementation, the article demonstrates the potential of the proposed hybrid approach to achieve more accurate and effective modeling and generation of complex, high-dimensional data. Furthermore, it discusses possible applications in various domains, such as image synthesis, time-series forecasting, and anomaly detection, and outlines future research directions for enhancing the scalability, performance, and integration with other machine learning techniques. By combining the strengths of Diffusion Maps and DPMs, this work paves the way for more advanced and robust data analysis methods.

Keywords: diffusion maps, diffusion probabilistic models (DPMs), manifold learning, high-dimensional data analysis

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Authors: Hyun-Woo Cho

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Unexpected events may occur with serious impacts on industrial process. This work utilizes a data representation technique to model and to analyze process data pattern for the purpose of diagnosis. In this work, the use of triangular representation of process data is evaluated using simulation process. Furthermore, the effect of using different pre-treatment techniques based on such as linear or nonlinear reduced spaces was compared. This work extracted the fault pattern in the reduced space, not in the original data space. The results have shown that the non-linear technique based diagnosis method produced more reliable results and outperforms linear method.

Keywords: process monitoring, data analysis, pattern modeling, fault, nonlinear techniques

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Authors: Monika Soni, Shovonlal Bhowmick, Chandra Bhattacharya, Jitendra Sharma, Prafulla Dutta, Jagadish Mahanta

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Aedes aegypti and Aedes albopictus are considered as two major vectors to transmit dengue virus. In North-east India, two states viz. Assam and Arunachal Pradesh are known to be high endemic zone for dengue and Chikungunya viral infection. The taxonomical classification of medically important vectors are important for mapping of actual evolutionary trends and epidemiological studies. However, misidentification of mosquito species in field-collected mosquito specimens could have a negative impact which may affect vector-borne disease control policy. DNA barcoding is a prominent method to record available species, differentiate from new addition and change of population structure. In this study, a combined approach of a morphological and molecular technique of DNA barcoding was adopted to explore sequence variation in mitochondrial cytochrome c oxidase subunit I (COI) gene within dengue vectors. The study has revealed the map distribution of the dengue vector from two states i.e. Assam and Arunachal Pradesh, India. Approximate five hundred mosquito specimens were collected from different parts of two states, and their morphological features were compared with the taxonomic keys. The analysis of detailed taxonomic study revealed identification of two species Aedes aegypti and Aedes albopictus. The species aegypti comprised of 66.6% of the specimen and represented as dominant dengue vector species. The sequences obtained through standard DNA barcoding protocol were compared with public databases, viz. GenBank and BOLD. The sequences of all Aedes albopictus have shown 100% similarity whereas sequence of Aedes aegypti has shown 99.77 - 100% similarity of COI gene with that of different geographically located same species based on BOLD database search. From dengue prevalent different geographical regions fifty-nine sequences were retrieved from NCBI and BOLD databases of the same and related taxa to determine the evolutionary distance model based on the phylogenetic analysis. Neighbor-Joining (NJ) and Maximum Likelihood (ML) phylogenetic tree was constructed in MEGA6.06 software with 1000 bootstrap replicates using Kimura-2-Parameter model. Data were analyzed for sequence divergence and found that intraspecific divergence ranged from 0.0 to 2.0% and interspecific divergence ranged from 11.0 to 12.0%. The transitional and transversional substitutions were tested individually. The sequences were deposited in NCBI: GenBank database. This observation claimed the first DNA barcoding analysis of Aedes mosquitoes from North-eastern states in India and also confirmed the range expansion of two important mosquito species. Overall, this study insight into the molecular ecology of the dengue vectors from North-eastern India which will enhance the understanding to improve the existing entomological surveillance and vector incrimination program.

Keywords: COI, dengue vectors, DNA barcoding, molecular identification, North-east India, phylogenetics

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

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

Keywords: CCR7, CD62L, GVHD, SCT

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Authors: Abdel-Aziz M. Mohamed, Nermeen Coutry

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Lead time is an important measure of supply chain performance. It impacts both customer satisfactions as well as the total cost of inventory. This paper presents the result of a study on the analysis of the customer order lead-time for a multinational company. In the study, the lead time was divided into three stages: order entry, order fulfillment, and order delivery. A sample of size 2,425 order lines from the company records were considered for this study. The sample data includes information regarding customer orders from the time of order entry until order delivery. Data regarding the lead time of each sage for different orders were also provided. Summary statistics on lead time data reveals that about 30% of the orders were delivered after the scheduled due date. The result of the multiple linear regression analysis technique revealed that component type, logistics parameter, order size and the customer type have significant impact on lead time. Data analysis on the stages of lead time indicates that stage 2 consumes over 50% of the lead time. Pareto analysis was made to study the reasons for the customer order delay in each of the 3 stages. Recommendation was given to resolve the problem.

Keywords: lead time reduction, customer satisfaction, service quality, statistical analysis

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Authors: Nancy Ibrahim Abdalla, Abdelaziz Karamalla Gaiballa

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Rangelands in semi-arid areas provide a good source for feeding huge numbers of animals and serving environmental, economic and social importance; therefore, these areas are considered economically very important for the pastoral sector in Sudan. This paper investigates the means of differentiating between different rangelands sites according to soil types using principal component analysis to assist in monitoring and assessment purposes. Three rangeland sites were identified in the study area as flat sandy sites, sand dune site, and hard clay site. Principal component analysis (PCA) was used to reduce the number of factors needed to distinguish between rangeland sites and produce a new set of data including the most useful spectral information to run satellite image processing. It was performed using selected types of data (two vegetation indices, topographic data and vegetation surface reflectance within the three bands of MODIS data). Analysis with PCA indicated that there is a relatively high correspondence between vegetation and soil of the total variance in the data set. The results showed that the use of the principal component analysis (PCA) with the selected variables showed a high difference, reflected in the variance and eigenvalues and it can be used for differentiation between different range sites.

Keywords: principal component analysis, PCA, rangeland sites, semi-arid areas, soil types

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Authors: Irum Matloob, Shoab Ahmad Khan, Fahim Arif

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As Indo-Pak has been the victim of heart diseases since many decades. Many surveys showed that percentage of cardiac patients is increasing in Pakistan day by day, and special attention is needed to pay on this issue. The framework is proposed for performing detailed analysis of ECG survey data which is conducted for measuring prevalence of heart diseases statistics in Pakistan. The ECG survey data is evaluated or filtered by using automated Minnesota codes and only those ECGs are used for further analysis which is fulfilling the standardized conditions mentioned in the Minnesota codes. Then feature selection is performed by applying proposed algorithm based on discernibility matrix, for selecting relevant features from the database. Clustering is performed for exposing natural clusters from the ECG survey data by applying spectral clustering algorithm using fuzzy c means algorithm. The hidden patterns and interesting relationships which have been exposed after this analysis are useful for further detailed analysis and for many other multiple purposes.

Keywords: arrhythmias, centroids, ECG, clustering, discernibility matrix

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Authors: N. Zeinalzadeh, Mahdi Sadeghi

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Enterotoxigenic Escherichia coli (ETEC) is the most common cause of non-inflammatory diarrhea in the developing countries, resulting in approximately 20% of all diarrheal episodes in children in these areas. ST is one of the most important virulence factors and CFA/I is one of the frequent colonization factors that help to process of ETEC infection. ST and CfaB (CFA/I subunit) are among vaccine candidates against ETEC. So, ST because of its small size is not a good immunogenic in the natural form. However to increase its immunogenic potential, here we explored candidate positions for ST insertion in CfaB sequence. After bioinformatics analysis, one of the candidate positions was selected and the chimeric gene (cfaB*st) sequence was synthesized and expressed in E. coli BL21 (DE3). The chimeric recombinant protein was purified with Ni-NTA columns and characterized with western blot analysis. The residue 74-75 of CfaB sequence could be a good candidate position for ST and other epitopes insertion.

Keywords: bioinformatics, CFA/I, enterotoxigenic E. coli, ST toxoid

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Authors: Ugbajah Maryjane

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The study examined the production of grass cutter and the constraints in Anambra state, Nigeria. Specifically, it described socio-economic characteristics of the respondents, determinants of net farm income and constraints to grass cutter production. Multistage and random sampling methods were used to select 50 respondents for this study. Primary data were collected by means of structured questionnaire. Non-parametric and parametric statistical tools including frequency percentage mean ranking counts, cost and returns and returns and multiple regression were deployed for data analysis. Majority 84% produce on small scale, 64 % had formal education 68% had 3-4 years of farming experience hence small scaled production were common. The income (returns) on investment was used as index of profitability, gross margin (#5,972,280), net farm income (#5,327,055.2) net return on investment (2.5) and return on investment 3.1. Net farm income was significantly influence by stock size and years of farming experience. Grass cutter farmers production problem would be ameliorated by the expression of extension education awareness campaigns to discourage unhealthy practices such as indiscriminant bush burning, use of toxic chemicals as baits, and provision of credits to the farmers.

Keywords: socio-economic factors, profitability, awareness, toxic chemicals, credits

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Authors: Masahiro Nochi

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This study explores the process in which a Japanese child with congenital blindness deepens understanding of the condition of being “unable to see” and develops the idea of “blind self,” despite having no direct experience of vision. The rehabilitation activities of a child with a congenital visual impairment that were video-recorded from 1 to 6 years old were analyzed qualitatively. The duration of the video was about 80 hours. The recordings were transcribed verbatim, and the episodes in which the child used the words related to the act of “looking” were extracted. Detailed transcripts were constructed referencing the notations of conversation analysis. Characteristics of interactions in those episodes were identified and compared longitudinally. Results showed that the child used the expression "look" under certain interaction patterns and her body expressions and interaction with adults developed in conjunction with the development of language use. Four stages were identified. At the age of 1, interactions involving “look” began to occur. The child said "Look" in the sequence: the child’s “Look,” an adult’s “I’m looking,” certain performances by the child, and the adult’s words of praise. At the age of 3, the child began to behave in accordance with the spatial attributes of the act of "looking," such as turning her face to the adult’s voice before saying, “Look.” She also began to use the expression “Keep looking,” which seemed to reflect her understanding of the temporality of the act of “looking.” At the age of 4, the use of “Look” or “Keep looking” became three times more frequent. She also started to refer to the act of looking in the future, such as “Come and look at my puppy someday.” At the age of 5, she moved her hands toward the adults when she was holding something she wanted to show them. She seemed to understand that people could see the object more clearly when it was in close priximity. About that time, she began to say “I cannot see” to her mother, which suggested a heightened understanding of her own blindness. The findings indicate that as she grew up, the child came to utilize nonverbal behavior before and after the order "Look" to make the progress of the interaction with adults even more certain. As a result, actions that reflect the characteristics of the sighted person's visual experience were incorporated into the interaction chain. The purpose of "Look," with which she intended to attract the adult's attention at first, changed and became something that requests a confirmation she was unable to make herself. It is considered that such a change in the use of the word as well as interaction with sighted adults reflected her heightened self-awareness as someone who could not do what sighted people could do easily. A blind child can gradually deepen their understanding of their own characteristics of blindness among sighted people around them. The child can also develop “blind self” by learning how to interact with others even without direct visual experiences.

Keywords: blindness, child development, conversation analysis, self-concept

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Authors: Seunghwan Seo, Woo-Seok Lee, Ji-Sun Shin, Young Kyoung Rhee, Chang-Won Cho, Hee-Do Hong, Kyung-Tae Lee

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Doenjang, known as traditional Korean food, is product of a natural mixed fermentation process carried out by lactic acid bacteria (LAB). Lactobacillus sakei K040706 (K040706) has been accepted as the most populous LAB in over ripened doenjang. Recently, we reported the immunostimulatory effects of K040706 in RAW 264.7 macrophages and in a cyclophosphamide-induced mouse model. In this study, we investigated the ameliorative effects of K040706 in a dextran sulfate sodium (DSS)-induced colitis mouse model. We induced colitis using DSS in 5-week-ICR mice over 14 days with or without 0.1, 1 g/kg/day K040706 orally. The body weight, stool consistency, and gross bleeding were recorded for determination of the disease activity index (DAI). At the end of treatment, animals were sacrificed and colonic tissues were collected and subjected to histological experiments and myeloperoxidase (MPO) accumulation, cytokine determination, qRT-PCR and Western blot analysis. Results showed that K040706 significantly attenuated DSS-induced DAI score, shortening of colon length, enlargement of spleen and immune cell infiltrations into colonic tissues. Histological examinations indicated that K040706 suppressed edema, mucosal damage, and the loss of crypts induced by DSS. These results were correlated with the restoration of tight junction protein expression, such as, ZO-1 and occludin in K040706-treated mice. Moreover, K040706 reduced the abnormal secretions and mRNA expressions of pro-inflammatory mediators, such as nitric oxide (NO), tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), and interleukin-6 (IL-6). DSS-induced mRNA expression of intercellular adhesion molecule (ICAM) and vascular cell adhesion molecule (VCAM) in colonic tissues was also downregulated by K040706 treatment. Furthermore, K040706 suppressed the protein and mRNA expression of toll-like receptor 4 (TLR4) and phosphorylation of NF-κB and signal transducer and activator of transcription 3 (STAT3). These results suggest that K040706 has an anti-colitic effect by inhibition of intestinal inflammatory responses in DSS-induced colitic mice.

Keywords: Lactobacillus sakei, NF-κB, STAT3, ulcerative colitis

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Authors: Nkongho Ayuketang Arreyndip, Ebobenow Joseph

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In this paper, temperature extremes are forecast by employing the block maxima method of the generalized extreme value (GEV) distribution to analyse temperature data from the Cameroon Development Corporation (CDC). By considering two sets of data (raw data and simulated data) and two (stationary and non-stationary) models of the GEV distribution, return levels analysis is carried out and it was found that in the stationary model, the return values are constant over time with the raw data, while in the simulated data the return values show an increasing trend with an upper bound. In the non-stationary model, the return levels of both the raw data and simulated data show an increasing trend with an upper bound. This clearly shows that although temperatures in the tropics show a sign of increase in the future, there is a maximum temperature at which there is no exceedance. The results of this paper are very vital in agricultural and environmental research.

Keywords: forecasting, generalized extreme value (GEV), meteorology, return level

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Authors: Sarthak Deshpande, Akshay Patil, Pradip Pandhare, Nikhil Wankhede, Rushali Deshmukh

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Among the highly significant duties for any language most effective is the sentiment analysis, which is also a key area of NLP, that recently made impressive strides. There are several models and datasets available for those tasks in popular and commonly used languages like English, Russian, and Spanish. While sentiment analysis research is performed extensively, however it is lagging behind for the regional languages having few resources such as Hindi, Marathi. Marathi is one of the languages that included in the Indian Constitution’s 8th schedule and is the third most widely spoken language in the country and primarily spoken in the Deccan region, which encompasses Maharashtra and Goa. There isn’t sufficient study on sentiment analysis methods based on Marathi text due to lack of available resources, information. Therefore, this project proposes the use of different ML/NLP models for the analysis of Marathi data from the comments below YouTube content, tweets or Instagram posts. We aim to achieve a short and precise analysis and summary of the related data using our dataset (Dates, names, root words) and lexicons to locate exact information.

Keywords: multilingual sentiment analysis, Marathi, natural language processing, text summarization, lexicon-based approaches

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Authors: Christopher Benedikt Jakob

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Human beings are intrigued by luxury watches for decades. It is fascinating that customers pay an enormous amount of money for specific wristwatch models. It is fascinating that customers of the luxury watch industry accept a yearly price increase. This behavior increases their desirability even more. Luxury watches are perceived as status symbols, but they are additionally accepted as a currency without the disadvantage of currency fluctuations. It is obvious that the symbolic value is more important as the functional value with reference to the buying-reasons as regards luxury watches. Nowadays human beings do not need a wristwatch to read the time. Tablets, notebooks, smartphones, the watch in the car and watches on public places are used to inform people about the current time. This is one of the reasons why there is a trend that people do not wear wristwatches anymore. Due to these facts, this study has the intention to give answers to the question why people invest an enormous amount of money on the consumption of luxury watches and why those watches are seen as a status symbol. The study examines why the luxury watch industry records significant growth rates. The self-expression model is used as an appropriate methodology to find reasons why human beings purchase specific luxury watches. This evaluative approach further discusses if human beings are aware of their current self and their ideal self and how they express them. Furthermore, the research critically evaluates the people’s social self and their ideal social self. One of the goals is to identify if customers know why they like specific luxury watches and dislike others although they have the same quality and cost comparable prices.

Keywords: luxury watch, brand awareness, buying-behaviour, consumer, self-expression

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Authors: Jamal S. M. Sabir, Edward C. Theriot, Schonna R. Manning, Abdulrahman L. Al-Malki, Mohammad, Mumdooh J. Sabir, Dwight K. Romanovicz, Nahid H. Hajrah, Robert K. Jansen, Matt P. Ashworth

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The diatom Phaeodactylum tricornutum has been used as a model for cell biologists and ecologists for over a century. We have incorporated several new raphid pennates into a three-gene phylogenetic dataset (SSU, rbcL, psbC), and recover Gomphonemopsis sp. as sister to P. tricornutum with 100% BS support. This is the first time a close relative has been identified for P. tricornutum with robust statistical support. We test and reject a succession of hypotheses for other relatives. Our molecular data are statistically significantly incongruent with placement of either or both species among the Cymbellales, an order of diatoms with which both have been associated. We believe that further resolution of the phylogenetic position of P. tricornutum will rely more on increased taxon sampling than increased genetic sampling. Gomphonemopsis is a benthic diatom, and its phylogenetic relationship with P. tricornutum is congruent with the hypothesis that P. tricornutum is a benthic diatom with specific adaptations that lead to active recruitment into the plankton. We hypothesize that other benthic diatoms are likely to have similar adaptations and are not merely passively recruited into the plankton.

Keywords: benthic, diatoms; ecology, Phaeodactylum tricornutum, phylogeny, tychoplankton

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Authors: Hamzeh Alipour, Masoumeh Bagheri, Tahereh Karamzadeh, Abbasali Raz, Kourosh Azizi

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Netrin-A, a protein identified for conducting commissural axons, has a similar role in angiogenesis. In addition, studies have shown that one of the netrin-A receptors is expressed in the growing cells of small capillaries. It will be interesting to study this new group of molecules because their role in wound healing will become clearer in the future due to angiogenesis. The greenbottle blowfly Luciliasericata (L. sericata) larvae are increasingly used in maggot therapy of chronic wounds. This aim of this was the identification of moleculareatures of Netrin-A in L. sericata larvae. Larvae were reared under standard maggotarium conditions. The nucleic acid sequence of L. sericataNetrin-A (LSN-A) was then identified using Rapid Amplification of cDNA Ends (RACE) and Rapid Amplification of Genomic Ends (RAGE). Parts of the Netrin-A gene, including the middle, 3′-, and 5′-ends were identified, TA cloned in pTG19 plasmid, and transferred into DH5ɑ Escherichia coli. Each part was sequenced and assembled using SeqMan software. This gene structure was further subjected to in silico analysis. The DNA of LSN-A was identified to be 2407 bp, while its mRNA sequence was recognized as 2115 bp by Oligo0.7 software. It translated the Netrin-A protein with 704 amino acid residues. Its molecular weight is estimated to be 78.6 kDa. The 3-D structure ofNetrin-A drawn by SWISS-MODEL revealed its similarity to the Netrin-1 of humans with 66.8% identity. The LSN-A protein conduces to repair the myelin membrane in neuronal cells. Ultimately, it can be an effective candidate in neural regeneration and wound healing. Furthermore, our next attempt is to deplore recombinant proteins for use in medical sciences.

Keywords: maggot therapy, netrin-A, RACE, RAGE, lucilia sericata

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Authors: Pei-Ying Lo, Jing-Hao Ciou, Kai-Cheng Yang, Jia-Huei Zheng, Shih-Hsiang Huang, Kuen-Chan Lee, Er-Chieh Cho

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As-produced CNTs are insoluble in all organic solvents and aqueous solutions have imposed limitations to the use of CNTs. Therefore, how to debundle carbon nanotubes and to modify them for further uses is an important issue. There are several methods for the dispersion of CNTs in water using covalent attachment of hydrophilic groups to the surface of tubes. These methods, however, alter the electronic structure of the nanotubes by disrupting the network of sp2 hybridized carbons. In order to keep the nanotubes’ intrinsic mechanical and electrical properties intact, non-covalent interactions are increasingly being explored as an alternative route for dispersion. Apart from conventional surfactants such as sodium dodecylsulfate (SDS) or sodium dodecylbenzenesulfonate (SDBS) which are highly effective in dispersing CNTs, biopolymers have received much attention as dispersing agents due to the anticipated biocompatibility of the dispersed CNTs. Also, The pyrenyl group is known to interact strongly with the basal plane of graphene via π-stacking. In this study, a highly re-dispersible biopolymer is reported for the synthesis of pyrene-modified poly-L-lysine (PBPL) and poly(D-Glu, D-Lys) (PGLP). To provide the evidence of the safety of the PBPL/CNT & PGLP/CNT materials we use in this study, H1299 and HCT116 cells were incubated with PBPL/CNT & PGLP/CNT materials for toxicity analysis, MTS assays. The results from MTS assays indicated that no significant cellular toxicity was shown in H1299 and HCT116 cells. Furthermore, the fluorescence marker fluorescein isothiocyanate (FITC) was added to PBPL & PGLP dispersions. From the fluorescent measurements showed that the chemical functionalisation of the PBPL/CNT & PGLP/CNT conjugates with the fluorescence marker were successful. The fluorescent PBPL/CNT & PGLP/CNT conjugates could find application in medical imaging. In the next step, the GFP gene is immobilized onto PBPL/CNT conjugates by introducing electrostatic interaction. GFP-transfected cells that emitted fluorescence were imaged and counted under a fluorescence microscope. Due to the unique biocompatibility of PBPL modified CNTs, the GFP gene could be transported into H1299 cells without using antibodies. The applicability of such soluble and chemically functionalised polypeptide/CNT conjugates in biomedicine is currently investigated. We expect that this polypeptide/CNT system will be a safe and multi-functional nanomedical delivery platform and contribute to future medical therapy.

Keywords: carbon nanotube, nanotoxicology, GFP transfection, polypeptide/CNT hybrids

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Authors: Eugene Stepanov, Arkadi Ponossov

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Many mathematical models used in biological and other applications are ill-posed. The reason for that is the nature of differential equations, where the nonlinearities are assumed to be step functions, which is done to simplify the analysis. Prominent examples are switched systems arising from gene regulatory networks and neural field equations. This simplification leads, however, to theoretical and numerical complications. In the presentation, it is proposed to apply the theory of hybrid feedback controls to regularize the problem. Roughly speaking, one attaches a finite state control (‘automaton’), which follows the trajectories of the original system and governs its dynamics at the points of ill-posedness. The construction of the automaton is based on the classification of the attractors of the specially designed adjoint dynamical system. This ‘hybridization’ is shown to regularize the original switched system and gives rise to efficient hybrid numerical schemes. Several examples are provided in the presentation, which supports the suggested analysis. The method can be of interest in other applied fields, where differential equations contain step-like nonlinearities.

Keywords: hybrid feedback control, ill-posed problems, singular perturbation analysis, step-like nonlinearities

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Authors: Kapil Pandey, Vishnu Goyal

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Spatial and temporal data analysis is very well known in the field of satellite image processing. When spatial data are correlated with time, series analysis it gives the significant results in change detection studies. In this paper the GIS and Remote sensing techniques has been used to find the change detection using time series satellite imagery of Uttarakhand state during the years of 1990-2010. Natural vegetation, urban area, forest cover etc. were chosen as main landuse classes to study. Landuse/ landcover classes within several years were prepared using satellite images. Maximum likelihood supervised classification technique was adopted in this work and finally landuse change index has been generated and graphical models were used to present the changes.

Keywords: GIS, landuse/landcover, spatial and temporal data, remote sensing

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Authors: Ahmed M. Debela, Mayreli Ortiz , Ciara K. O´Sullivan

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The completion of the human genome Project (HGP) has paved the way for mapping the diversity in the overall genome sequence which helps to understand the genetic causes of inherited diseases and susceptibility to drugs or environmental toxins. Arrayed primer extension (APEX) is a microarray based minisequencing strategy for screening disease causing mutations. It is derived from Sanger DNA sequencing and uses fluorescently dideoxynucleotides (ddNTPs) for termination of a growing DNA strand from a primer with its 3´- end designed immediately upstream of a site where single nucleotide polymorphism (SNP) occurs. The use of DNA polymerase offers a very high accuracy and specificity to APEX which in turn happens to be a method of choice for multiplex SNP detection. Coupling the high specificity of this method with the high sensitivity, low cost and compatibility for miniaturization of electrochemical techniques would offer an excellent platform for detection of mutation as well as sequencing of DNA templates. We are developing an electrochemical APEX for the analysis of SNPs found in the MYH7 gene for group of cardiomyopathy patients. ddNTPs were labeled with four different redox active compounds with four distinct potentials. Thiolated oligonucleotide probes were immobilised on gold and glassy carbon substrates which are followed by hybridisation with complementary target DNA just adjacent to the base to be extended by polymerase. Electrochemical interrogation was performed after the incorporation of the redox labelled dedioxynucleotide. The work involved the synthesis and characterisation of the redox labelled ddNTPs, optimisation and characterisation of surface functionalisation strategies and the nucleotide incorporation assays.

Keywords: array based primer extension, labelled ddNTPs, electrochemical, mutations

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Authors: Mazo Kone, Rachida Salah, Harir Noria

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Background and objectives: c-Cbl and Cbl-b are two members of the Cbl family proteins, with a crucial role of downregulation of tyrosine kinase receptors. They act as E3 ubiquitin ligases and are multivalent adaptor proteins, making them important in maintaining homeostasis in the body. This study investigated the expression level in thymus and testis in normal conditions. Methods: The expression level was assessed by immunochemistry of tissue microarrays of normal thymus and testis biopsies. Results: Cbl-b and c-Cbl proteins were found to be highly expressed in normal testis and thymus, indicated as yellowish brown granules in the cytomembrane and cytoplasm compared to controls. The c-Cbl appears to be more highly expressed than the Cbl-b in the thymus, while c-Cbl appears slightly stronger than Cbl-b in the testis. The thymus was found with a higher grade compared to the testis. Conclusion: In this work we concluded, that in normal condition, thymus tissue expresses more Cbl family proteins(c-Cbl and Cbl-b) than the testis tissue in humans.

Keywords: Human C-Cbl proteins, Human Cbl-b protein, Testis, Thymus

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Authors: Sujata Chaturvedi, Ishita Pant, Deepak Kumar Jha, Vinod Kumar Singh Gautam, Chandra Bhushan Tripathi

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Objective: To describe clinical, histopathological and immunohistochemical profile of glioblastoma in patients and to correlate these findings with patient survival. Material and methods: 30 cases of histopathologically diagnosed glioblastomas were included in this study. These cases were analysed in detail for certain clinical and histopathological parameters. Immunohistochemical staining for p53, epidermal growth factor receptor (EGFR), vascular endothelial growth factor (VEGF), mouse double minute 2 homolog (MDM2) and Ki67 was done and scores were calculated. Results of these findings were correlated with patient survival. Results: A retrospective analysis of the histopathology records and clinical case files was done in 30 cases of glioblastoma (WHO grade IV). The mean age of presentation was 50.6 years with a male predilection. The most common involved site was the frontal lobe. Amongst the clinical parameters, age of the patient and extent of surgical resection showed a significant correlation with the patient survival. Histopathological parameters showed no significant correlation with the patient survival, while amongst the immunohistochemical parameters expression of MDM2 showed a significant correlation with the patient survival. Conclusion: In this study incorporating clinical, histopathological and basic panel of immunohistochemistry, age of the patient, extent of the surgical resection and expression of MDM2 showed significant correlation with the patient survival.

Keywords: glioblastoma, p53, EGFR, VEGF, MDM2, Ki67

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Authors: Margarida Franca

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The influence of the ‘cultural turn’ movement and the consequent deconstruction of scientific thought allowed geography and other social sciences to open or deepen their studies based on the analysis of multiple identities, on singularities, on what is particular or what marks the difference between individuals. In the context of postmodernity, the geography of religion has gained a favorable scientific, thematic and methodological focus for the qualitative and subjective interpretation of various religious identities, sacred places, territories of belonging, religious communities, among others. In the context of ‘late modernity’ or ‘net modernity’, sacred places and the definition of a network of sacred territories allow believers to attain the ‘ontological security’. The integration on a religious group or a local community, particularly a religious community, allows human beings to achieve a sense of belonging, familiarity or solidarity and to overcome, in part, some of the risks or fears that society has discovered. The importance of sacred places comes not only from their inherent characteristics (eg transcendent, mystical and mythical, respect, intimacy and abnegation), but also from the possibility of adding and integrating members of the same community, creating bonds of belonging, reference and individual and collective memory. In addition, the formation of different networks of sacred places, with multiple scales and dimensions, allows the human being to identify and structure his times and spaces of daily life. Thus, each individual, due to his unique identity and life and religious paths, creates his own network of sacred places. The territorial expression of religious identity allows to draw a variable and unique geography of sacred places. Through the case study of the practicing Catholic population in the diocese of Coimbra (Portugal), the aim is to study the territorial expression of the religious identity of the different local communities of this city. Through a survey of six parishes in the city, we sought to identify which factors, qualitative or not, define the different territorial expressions on a local, national and international scale, with emphasis on the socioeconomic profile of the population, the religious path of the believers, the religious group they belong to and the external interferences, religious or not. The analysis of these factors allows us to categorize the communities of the city of Coimbra and, for each typology or category, to identify the specific elements that unite the believers to the sacred places, the networks and religious territories that structure the religious practice and experience and also the non-representational landscape that unifies and creates memory. We conclude that an apparently homogeneous group, the Catholic community, incorporates multitemporalities and multiterritorialities that are necessary to understand the history and geography of a whole country and of the Catholic communities in particular.

Keywords: geography of religion, sacred places, territoriality, Catholic Church

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Authors: Rajapaksha Gedara Prasad Tharanga Jayasooriya, Matharage Gayani Dilshara, Yung Hyun Choi, Gi-Young Kim

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Camptothecin (CPT) is a quinolone alkaloid which inhibits DNA topoisomerase I that induces cytotoxicity in a variety of cancer cell lines. We previously showed that CPT effectively inhibited invasion of prostate cancer cells and also combined treatment with subtoxic doses of CPT and TNF-related apoptosis-inducing ligand (TRAIL) potentially enhanced apoptosis in a caspase-dependent manner in hepatoma cancer cells. Here, we found that treatment with CPT caused an irreversible cell cycle arrest in the G2/M phase. CPT-induced cell cycle arrest was associated with a decrease in protein levels of cell division cycle 25C (Cdc25C) and increased the level of cyclin B and p21. The CPT-induced decrease in Cdc25C was blocked in the presence of proteasome inhibitor MG132, thus reversed the cell cycle arrest. In addition to that treatment of CPT-increased phosphorylation of Cdc25C was the resulted of activation of checkpoint kinase 2 (Chk2), which was associated with phosphorylation of ataxia telangiectasia-mutated. Interestingly CPT induced G2/M phase of the cell cycle arrest is reactive oxygen species (ROS) dependent where ROS inhibitors NAC and GSH reversed the CPT-induced cell cycle arrest. These results further confirm by using transient knockdown of nuclear factor-erythroid 2-related factor 2 (Nrf2) since it regulates the production of ROS. Our data reveal that treatment of siNrf2 increased the ROS level as well as further increased the CPT induce G2/M phase cell cycle arrest. Our data also indicate CPT-enhanced cell cycle arrest through the extracellular signal-regulated kinase (ERK) and the c-Jun N-terminal kinase (JNK) pathway. Inhibitors of ERK and JNK more decreased the Cdc25C expression and protein expression of p21 and cyclin B. These findings indicate that Chk2-mediated phosphorylation of Cdc25C plays a major role in G2/M arrest by CPT.

Keywords: camptothecin, cell cycle, checkpoint kinase 2, nuclear factor-erythroid 2-related factor 2, reactive oxygen species

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Authors: Anna Perrone, Federico Martinelli

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Olive fruit is well-known for the high content in secondary metabolites with high interest at nutritional, nutraceutical, antioxidant, and healthy levels. The content of secondary metabolites in olive at harvest may be affected by different water regimes, with significant effects on olive oil composition and quality and, consequently, on its healthy and nutritional features. In this work, a summary of several research studies dealing with the biosynthesis of healthy and nutraceutical metabolites of the secondary metabolism in olive fruit will be reported. The phytochemical findings have been correlated with the expression of key genes involved in polyphenol, terpenoid, and carotenoid biosynthesis and metabolism in response to different development stages and water regimes. Flavonoids were highest in immature fruits, while anthocyanins increased at ripening. In epicarp tissue, this was clearly associated with an up-regulation of the UFGT gene. Olive fruits cultivated under different water regimes were analyzed by metabolomics. This method identified several hundred metabolites in the ripe mesocarp. Among them, 46 were differentially accumulated in the comparison between rain-fed and irrigated conditions. Well-known healthy metabolites were more abundant at a higher level of water regimes. Increased content of polyphenols was observed in the rain-fed fruit; particularly, anthocyanin concentration was higher at ripening. Several secondary metabolites were differentially accumulated between different irrigation conditions. These results showed that these metabolic approaches could be efficiently used to determine the effects of agronomic treatments on olive fruit physiology and, consequently, on nutritional and healthy properties of the obtained extra-virgin olive oil.

Keywords: olea europea, anthocyanins, polyphenols, water regimes

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Authors: Alexis John de Britto

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Studies were performed to select the superior genotypes based on intra-specific variations, caused by phytogeographical, climatic and edaphic parameters of three anti cancer drug yielding mangrove plants such as Acanthus ilicifolius L., Calophyllum inophyllum L. and Excoecaria agallocha L. using ISSR (Inter Simple Sequence Repeats) markers and phytochemical analysis such as preliminary phytochemical tests, TLC, HPTLC, HPLC and antioxidant tests. The plants were collected from five different geographical locations of the East Coast of south India. Genetic heterozygosity, Nei’s gene diversity, Shannon’s information index and Percentage of polymorphism between the populations were calculated using POPGENE software. Cluster analysis was performed using UPGMA algorithm. AMOVA and correlations between genetic diversity and soil factors were analyzed. Combining the molecular and phytochemical variations superior genotypes were selected. Conservation constraints and methods of efficient exploitation of the species are discussed.

Keywords: anti-cancer drug yielding plants, DNA fingerprinting, phytochemical analysis, selection of superior genotypes

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Authors: Maha Z. Rizk, Sami A. Fattah, Heba M. Darwish, Sanaa A. Ali, Mai O. Kadry

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Although it is known that nano-TiO2 and other nanoparticles can induce liver toxicity, the mechanisms and the molecular pathogenesis are still unclear. The present study investigated some biochemical indices of nano-sized Titanium dioxide (TiO2 NPS) toxicity in mice liver and the ameliorative efficacy of individual and combined doses of idebenone, carnosine and vitamin E. Nano-anatase TiO2 (21 nm) was administered as a total oral dose of 2.2 gm/Kg daily for 2 weeks followed by the afore-mentioned antioxidants daily either individually or in combination for 1month. TiO2-NPS induced a significant elevation in serum levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST) and hepatic oxidative stress biomarkers [lipid peroxides (LP), and nitric oxide levels (NOX), while it significantly reduced glutathione reductase (GR), reduced glutathione (GSH) and glutathione peroxidase(GPX) levels. Moreover the quantitative RT-PCR analysis showed that nano-anatase TiO2 can significantly alter the mRNA and protein expressions of the fibrotic factors TGF-B1, VEGFand Smad-2. Histopathological examination of hepatic tissue reinforced the previous biochemical results. Our results also implied that inflammatory responses and liver injury may be involved in nano-anatase TiO2-induced liver toxicity Tumor necrosis factor-α (TNF-α) and Interleukin -6 (IL-6) and increased the percent of DNA damage which was assessed by COMET assay in addition to the apoptotic marker Caspase-3. Moreover mRNA gene expression observed by RT-PCR showed a significant overexpression in nuclear factor relation -2 (Nrf2), nuclear factor kappa beta (NF-Kβ) and the apoptotic factor (bax), and a significant down regulation in the antiapoptotic factor (bcl2) level. In conclusion idebenone, carnosine and vitamin E ameliorated the deviated previously mentioned parameters with variable degrees with the most pronounced role in alleviating the hazardous effect of TiO2 NPS toxicity following the combination regimen.

Keywords: Nano-anatase TiO2, TGF-B1, SMAD-2

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