Search results for: modal identification

Authors: Manju Kanu, Subrata Sinha, Surabhi Johari

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Viral proteins of Ebola viruses belong to one of the best studied viruses; however no effective prevention against EBOV has been developed. Epitope-based vaccines provide a new strategy for prophylactic and therapeutic application of pathogen-specific immunity. A critical requirement of this strategy is the identification and selection of T-cell epitopes that act as vaccine targets. This study describes current methodologies for the selection process, with Ebola virus as a model system. Hence great challenge in the field of ebola virus research is to design universal vaccine. A combination of publicly available bioinformatics algorithms and computational tools are used to screen and select antigen sequences as potential T-cell epitopes of supertypes Human Leukocyte Antigen (HLA) alleles. MUSCLE and MOTIF tools were used to find out most conserved peptide sequences of viral proteins. Immunoinformatics tools were used for prediction of immunogenic peptides of viral proteins in zaire strains of Ebola virus. Putative epitopes for viral proteins (VP) were predicted from conserved peptide sequences of VP. Three tools NetCTL 1.2, BIMAS and Syfpeithi were used to predict the Class I putative epitopes while three tools, ProPred, IEDB-SMM-align and NetMHCII 2.2 were used to predict the Class II putative epitopes. B cell epitopes were predicted by BCPREDS 1.0. Immunogenic peptides were identified and selected manually by putative epitopes predicted from online tools individually for both MHC classes. Finally sequences of predicted peptides for both MHC classes were looked for common region which was selected as common immunogenic peptide. The immunogenic peptides were found for viral proteins of Ebola virus: epitopes FLESGAVKY, SSLAKHGEY. These predicted peptides could be promising candidates to be used as target for vaccine design.

Keywords: epitope, b cell, immunogenicity, ebola

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Authors: Abdullah Al-Mamun, Md. Nuruzzaman, Md. Noor Salleh, Muhammad Abu Eusuf, Ahmad Jalal Khan Chowdhury, Mohd. Zaki M. Amin, Norlida Mohd. Dom

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Identification of pollution sources and determination of pollution loads from all areas are very important for sustainable rehabilitation of any contaminated river. Pusu is a small river which, flows through the main campus of International Islamic University Malaysia (IIUM) at Gombak. Poor aesthetics of the river, which is flowing through the entrance of the campus, gives negative impression to the local and international visitors. As such, this study is being conducted to find ways to rehabilitate the river in a sustainable manner. The point and non-point pollution sources of the river basin are identified. Upper part of the 12.6 km2 river basin is covered with secondary forest. However, it is the lower-middle reaches of the river basin which is being cleared for residential development and source of high sediment load. Flow and concentrations of the common pollutants, important for a healthy river, such as Biochemical Oxygen Demand (BOD), Chemical Oxygen Demand (COD), Suspended Solids (SS), Turbidity, pH, Ammoniacal Nitrogen (AN), Total Nitrogen (TN) and Total Phosphorus (TP) are determined. Annual pollution loading to the river was calculated based on the primary and secondary data. Concentrations of SS were high during the rainy day due to contribution from the non-point sources. There are 7 ponds along the river system within the campus, which are severely affected by high sediment load from the land clearing activities. On the other hand, concentrations of other pollutants were high during the non-rainy days. The main sources of point pollution are the hostels, cafeterias, sewage treatment plants located in the campus. Therefore, both pollution sources need to be controlled in order to rehabilitate the river in a sustainable manner.

Keywords: river pollution, rehabilitation, point pollution source, non-point pollution sources, pollution loading

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Authors: Sarah Gaßmeyer, Nadine Hülsemann, Raphael Stoll, Kenji Miyamoto, Robert Kourist

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Enzymatic racemization allows the smooth interconversion of stereocenters under very mild reaction conditions. Racemases find frequent applications in deracemization and dynamic kinetic resolutions. Arylmalonate decarboxylase (AMDase) from Bordetella Bronchiseptica has high structural similarity to amino acid racemases. These cofactor-free racemases are able to break chemically strong CH-bonds under mild conditions. The racemase-like catalytic machinery of mutant G74C conveys it a unique activity in the racemisation of pharmacologically relevant derivates of 2-phenylpropionic acid (profenes), which makes AMDase G74C an interesting object for the mechanistic investigation of cofactor-independent racemases. Structure-guided protein engineering achieved a variant of this unique racemase with 40-fold increased activity in the racemisation of several arylaliphatic carboxylic acids. By saturation–transfer–difference NMR spectroscopy (STD-NMR), substrate binding during catalysis was investigated. All atoms of the substrate showed interactions with the enzyme. STD-NMR measurements revealed distinct nuclear Overhauser effects in experiments with and without molecular conversion. The spectroscopic analysis led to the identification of several amino acid residues whose variation increased the activity of G74C. While single-amino acid exchanges increased the activity moderately, structure-guided saturation mutagenesis yielded a quadruple mutant with a 40 times higher reaction rate. This study presents STD-NMR as versatile tool for the analysis of enzyme-substrate interactions in catalytically competent systems and for the guidance of protein engineering.

Keywords: racemase, rational protein design, STD-NMR, structure guided saturation mutagenesis

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Authors: Adya Uluwita, Fernando Pedrosa, Georgi Georgiev, Christian Bernard, Raoul Masterson

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CERN is an international organisation funded by 23 countries that provide the particle physics community with excellence in particle accelerators and other related facilities. Founded in 1954, CERN has a wide range of accelerators that allow groundbreaking science to be conducted. Accelerators bring particles to high levels of energy and make them collide with each other or with fixed targets, creating specific conditions that are of high interest to physicists. A chain of accelerators is used to ramp up the energy of particles and eventually inject them into the largest and most recent one: the Large Hadron Collider (LHC). Among this chain of machines is, for instance the Proton Synchrotron, which was started in 1959 and is still in operation. These machines, called "injectors”, keep evolving over time, as well as the related infrastructure. Massive decommissioning of obsolete cables started in 2015 at CERN in the frame of the so-called "injectors de-cabling project phase 1". Its goal was to replace aging cables and remove unused ones, freeing space for new cables necessary for upgrades and consolidation campaigns. To proceed with the de-cabling, a project co-ordination team was assembled. The start of this project led to the investigation of legacy cables throughout the organisation. The identification of cables stacked over half a century proved to be arduous. Phase 1 of the injectors de-cabling was implemented for 3 years with success after overcoming some difficulties. Phase 2, started 3 years later, focused on improving safety and structure with the introduction of a quality assurance procedure. This paper discusses the implementation of this quality assurance procedure throughout phase 2 of the project and the transition between the two phases. Over hundreds of kilometres of cable were removed in the injectors complex at CERN from 2015 to 2023.

Keywords: CERN, de-cabling, injectors, quality assurance procedure

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Authors: Ndarusanze Berchmans

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This research work focused on the analysis of the observations of tuberculous meningitis in HIV-positive patients who were treated by the Prince Regent Charles Hospital in Bujumbura. A number of 246 seropositive patients were examined by the laboratory of Prince Regent Charles in the period between 2010 and 2015. We did a retrospective study; we used data from the registers of the laboratories mentioned above; the objective was to approach the epidemiological, biological, clinical, and therapeutic characteristics of tuberculosis meningitis infection: 124 women (50.40% of AIDS patients) and 122 men (49.59% of AIDS patients) were subject to the diagnosis by identification of cerebrospinal fluid (CSF). The average age of the patients was 30 years for this period. The population at risk has an average age of between 34 and 42 years for the years between 2010-2015. From 2010 to 2012, cases of opportunistic diseases (e.g., tuberculous meningitis and Cryptococcus neoformans meningitis), often found in immunocompromised, were observed at a high rate; in this period, there was a disturbance of the rhythm providing antiretroviral drugs to people with AIDS. The rate of the two meningitis (tuberculous meningitis and Cryptococcus neoformans meningitis) remained above 10% to gradually decrease until 2015, with the gradual return of antiretrovirals. This period records an overall average of 25 cases of tuberculous meningitis, or a percentage of 10.16%. For the year 2015, there were 4 cases of tuberculous meningitis out of a total of 35 seropositive examined (11.42%). This year's percentage shows that the number of tuberculous meningitis cases has fallen from the rate in previous years. This is the result of the care given by associations against HIV/AIDS to HIV-positive people. This decrease in cases of tuberculous meningitis is due to the acquisition of antiretrovirals by all HIV-positive people treated by hospitals. For the moment, these hospitals are taking care of many AIDS patients by providing them permanently with antiretrovirals; Besides that, there are many patients who are supported by associations whose activities are directed against HIV/AIDS.

Keywords: Cryptococcus neoformans meningitis, tuberculosis meningitis, neurological complications, epidemiology of meningitis

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Authors: Devinder Kaur Sugga, Ekamdeep Kaur, Jaspreet Kaur, C. Rajesh, Preeti Rajesh, Harsimran Kaur

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Withanolides are steroidal lactones and are highly oxygenated phytoconstituents that can be developed as potential anti-carcinogenic agents. The two main withanolides, namely Withaferin A and Withanolides D, have been extensively studied for their pharmacological activities. Both these withanolides are present in the Withania somnifera (WS) leaves belonging to the family Solanaceae, also known as “Indian ginseng .”In this study effects of WS leaf extract on the MCF7 breast cancer cell line were investigated by performing a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay to evaluate the cytotoxic effects and in vitro wound-healing assay to study the effect on cancer cell migration. Our data suggest WS extracts have cytotoxic effects and are effective anti-migrating agents and thus can be a source of potential candidates for the development of potential agents against metastasis. Thus, it can be a source of potential candidates for the development of potential agents against metastasis. Insight into these results, the in-silico approach to identify the possible protein targets interacting with withanolides was taken. Protein kinase C alpha (PKCα) was among the selected 5 top-ranked target proteins identified by the Swiss Target Prediction tool. PKCα is known to promote the growth and invasion of cancer cells and is being evaluated as a prognostic biomarker and therapeutic target in clinically aggressive tumors. Molecular docking of Withaferin A and Withanolides D was performed using AutoDock Vina. Both the bioactive compounds interacted with PKCα. The targets predicted using this approach will serve as leads for the possible therapeutic potential of withanolides, the bioactive ingredients of WS extracts, as anti-cancer drugs.

Keywords: withania somnifera, withaferin A, withanolides D, PKCα

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Authors: Shayli Varasteh Moradi, Wayne A. Johnston, Dejan Gagoski, Kirill Alexandrov

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The demand for a rapid and more efficient technique to identify protein-protein interaction particularly in the areas of therapeutics and diagnostics development is growing. The method described here is a rapid in vitro protein-protein interaction analysis approach based on AlphaLISA technology combined with Leishmania tarentolae cell-free protein production (LTE) system. Cell-free protein synthesis allows the rapid production of recombinant proteins in a multiplexed format. Among available in vitro expression systems, LTE offers several advantages over other eukaryotic cell-free systems. It is based on a fast growing fermentable organism that is inexpensive in cultivation and lysate production. High integrity of proteins produced in this system and the ability to co-express multiple proteins makes it a desirable method for screening protein interactions. Following the translation of protein pairs in LTE system, the physical interaction between proteins of interests is analysed by AlphaLISA assay. The assay is performed using unpurified in vitro translation reaction and therefore can be readily multiplexed. This approach can be used in various research applications such as epitope mapping, antigen-antibody analysis and protein interaction network mapping. The intra-viral protein interaction network of Zika virus was studied using the developed technique. The viral proteins were co-expressed pair-wise in LTE and all possible interactions among viral proteins were tested using AlphaLISA. The assay resulted to the identification of 54 intra-viral protein-protein interactions from which 19 binary interactions were found to be novel. The presented technique provides a powerful tool for rapid analysis of protein-protein interaction with high sensitivity and throughput.

Keywords: AlphaLISA technology, cell-free protein expression, epitope mapping, Leishmania tarentolae, protein-protein interaction

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Authors: Liane Marcia Freitas Silva, Fernando Augusto Silva Marins, Maria Silene Alexandre Leite

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The adoption of a network structure, like in the supply chains, favors the increase of dependence between companies and, by consequence, their vulnerability. Environment disasters, sociopolitical and economical events, and the dynamics of supply chains elevate the uncertainty of their operation, favoring the occurrence of events that can generate break up in the operations and other undesired consequences. Thus, supply chains are exposed to various risks that can influence the profitability of companies involved, and there are several previous studies that have proposed risk classification models in order to categorize the risks and to manage them. The objective of this paper is to analyze and discuss thirty of these risk classification models by means a theoretical survey. The research method adopted for analyzing and discussion includes three phases: The identification of the types of risks proposed in each one of the thirty models, the grouping of them considering equivalent concepts associated to their definitions, and, the analysis of these risks groups, evaluating their similarities and differences. After these analyses, it was possible to conclude that, in fact, there is more than thirty risks types identified in the literature of Supply Chains, but some of them are identical despite of be used distinct terms to characterize them, because different criteria for risk classification are adopted by researchers. In short, it is observed that some types of risks are identified as risk source for supply chains, such as, demand risk, environmental risk and safety risk. On the other hand, other types of risks are identified by the consequences that they can generate for the supply chains, such as, the reputation risk, the asset depreciation risk and the competitive risk. These results are consequence of the disagreements between researchers on risk classification, mainly about what is risk event and about what is the consequence of risk occurrence. An additional study is in developing in order to clarify how the risks can be generated, and which are the characteristics of the components in a Supply Chain that leads to occurrence of risk.

Keywords: sisks classification, survey, supply chain management, theoretical discussion

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Authors: Zarah M. Bello, Nathan Baddoo, Mariana Lilley, Paul Wernick

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In this paper, we present findings from a multi-part study to evaluate candidate elements reflecting the level of digital capability maturity (DCM) in higher education and the relationship between these elements. We will use these findings to propose a model of DCM for educational institutions. We suggest that the success of learning in higher education is dependent in part on the level of maturity of digital capabilities of institutions as well as the abilities of learners and those who support the learning process. It is therefore important to have a good understanding of the elements that underpin this maturity as well as their impact and interactions in order to better exploit the benefits that technology presents to the modern learning environment and support its continued improvement. Having identified ten candidate elements of digital capability that we believe support the level of a University’s maturity in this area as well as a number of relevant stakeholder roles, we conducted two studies utilizing both quantitative and qualitative research methods. In the first of these studies, 85 electronic questionnaires were completed by various stakeholders in a UK university, with a 100% response rate. We also undertook five in-depth interviews with management stakeholders in the same university. We then utilized statistical analysis to process the survey data and conducted a textual analysis of the interview transcripts. Our findings support our initial identification of candidate elements and support our contention that these elements interact in a multidimensional manner. This multidimensional dynamic suggests that any proposal for improvement in digital capability must reflect the interdependency and cross-sectional relationship of the elements that contribute to DCM. Our results also indicate that the notion of DCM is strongly data-centric and that any proposed maturity model must reflect the role of data in driving maturity and improvement. We present these findings as a key step towards the design of an operationalisable DCM maturity model for universities.

Keywords: digital capability, elements, maturity, maturity framework, university

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Authors: Fabrizio Albion

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In response to the escalating recognition of the need to combat climate change, renewable energy sources (RES), particularly solar energy, have witnessed exponential growth. The intricate nature of agriphotovoltaics, which combines agriculture and solar energy production, demands rapid legislative and technological development, facing various challenges and multifaceted design. This complexity is also represented by its application for orchard cultivation (APVO), which, in the first part of this research, was studied in its environmental, economic, and sociocultural aspects. Insights from literature, case studies, and consultations with experts contributed valuable perspectives, forming a robust foundation for understanding and integrating APVO into rural environments, including those in the South Tyrolean context. For its harmonious integration into the sensitive Alpine landscape, the second part was then dedicated to the development of guidelines, from the identification of the requirements to be defined as APVO to its design flexibilities for being integrated into the context. As a basis for further considerations, the drafting of these guidelines was preceded by a program of interviews conducted to investigate the social perceptions of farmers, citizens and tourists on the potential integration of APVO in the fruit-growing valleys of the province. Conclusive results from the data collected in the first phase are, however, still pending. Due to ongoing experiments and data collection, the current results, although being generally positive, cannot guarantee a definitive exclusion of potential negative impacts on the crop. The guidelines developed should, therefore, be understood as an initial exploration, providing a basis for future updates, also in synergy with the evolution of existing local projects.

Keywords: agriphotovoltaics, Alpin agricultural landscapes, landscape impact assessment, renewable energy

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Authors: X. Han, S. Duan, C. Liu, C. Zhou, W. Zhu, L. Kong

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The ionic imprinting technique refers to the three-dimensional rigid structure with the fixed pore sizes, which was formed by the binding interactions of ions and functional monomers and used ions as the template, it has a high level of recognition to the ionic template. The preparation of monolithic column by the in-situ polymerization need to put the compound of template, functional monomers, cross-linking agent and initiating agent into the solution, dissolve it and inject to the column tube, and then the compound will have a polymerization reaction at a certain temperature, after the synthetic reaction, we washed out the unread template and solution. The monolithic columns are easy to prepare, low consumption and cost-effective with fast mass transfer, besides, they have many chemical functions. But the monolithic columns have some problems in the practical application, such as low-efficiency, quantitative analysis cannot be performed accurately because of the peak shape is wide and has tailing phenomena; the choice of polymerization systems is limited and the lack of theoretical foundations. Thus the optimization of components and preparation methods is an important research direction. During the preparation of ionic imprinted monolithic columns, pore-forming agent can make the polymer generate the porous structure, which can influence the physical properties of polymer, what’ s more, it can directly decide the stability and selectivity of polymerization reaction. The compounds generated in the pre-polymerization reaction could directly decide the identification and screening capabilities of imprinted polymer; thus the choice of pore-forming agent is quite critical in the preparation of imprinted monolithic columns. This article mainly focuses on the research that when using different pore-forming agents, the impact of zinc ion imprinted monolithic column on the enrichment performance of zinc ion.

Keywords: high performance liquid chromatography (HPLC), ionic imprinting, monolithic column, pore-forming agent

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Authors: N. A. Kharisa, I. Wulandari, R. Narendratama, M. I. Faisal, K. Kirana, R. Zipora, I. Arfiansah, I. Suyanto

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Acquisition of geophysical survey with magnetic method has been done in manifestation of geothermalat Candi Umbul, Grabag, Magelang, Central Java Province on 10-12 May 2013. This objective research is interpretation to interpret structural geology that control geothermal system in CandiUmbul area. The research has been finished with area size 1,5 km x 2 km and measurement space of 150 m. And each point of line space survey is 150 m using PPM Geometrics model G-856. Data processing was started with IGRF and diurnal variation correction to get total magnetic field anomaly. Then, advance processing was done until reduction to pole, upward continuation, and residual anomaly. That results become next interpretation in qualitative step. It is known that the biggest object position causes low anomaly located in central of area survey that comes from hot spring manifestation and demagnetization zone that indicates the existence of heat source activity. Then, modeling the anomaly map was used for quantitative interpretation step. The result of modeling is rock layers and geological structure model that can inform about the geothermal system. And further information from quantitative interpretations can be interpreted about lithology susceptibility. And lithology susceptibilities are andesiteas heat source has susceptibility value of (k= 0.00014 emu), basaltic as alteration rock (k= 0.0016 emu), volcanic breccia as reservoir rock (k= 0.0026 emu), andesite porfirtic as cap rock (k= 0.004 emu), lava andesite (k= 0.003 emu), and alluvium (k= 0.0007 emu). The hot spring manifestation is controlled by the normal fault which becomes a weak zone, easily passed by hot water which comes from the geothermal reservoir.

Keywords: geological structure, geothermal system, magnetic, susceptibility

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Authors: Svitlana Antonenko, Gennady Telegeev

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Introductive statement: The development of chronic myeloid leukemia (CML) is caused by Bcr-Abl oncoprotein. Modern treatments with tyrosine kinase inhibitors are greatly complicated by the mutational variability of the Bcr-Abl oncoprotein, which causes drug resistance. Therefore, there is an urgent need to develop new approaches to the treatment of the disease, which will allow modeling the level of Bcr-Abl oncoprotein in the cell. Promising in this direction is the identification of proteases that can selectively promote cellular proteolysis of oncoproteins. The aim of the study was to study the effect of the interaction of Bcr-Abl with deubiquitinase USP1 on the level of oncoprotein in CML cells. Methodology: K562 cells were selected for the experiment. Сells were incubated with ML323 inhibitor for 24 hours. Precipitation of endogenous proteins from K562 cell lysate was performed using anti-Bcr-Abl antibodies. Cell lysates and precipitation results were studied by Western blot. Subcellular localization of proteins was studied by immunofluorescence analysis followed by confocal microscopy. The results were analyzed quantitatively and statistically. Major findings: The Bcr-Abl/USP1 protein complex was detected in CML cells, and it was found that inhibition of USP1 deubiquitinating activity by the compound ML323 leads to disruption of this protein complex and a decrease in the level of Bcr-Abl oncoprotein in cells. The interaction of Bcr-Abl with USP1 may result in deubiquitination of the oncoprotein, which disrupts its proteasomal degradation and leads to the accumulation of CML in cells. Conclusion: We believe that the interaction of oncoprotein with USP1 may be one of the prerequisites that contribute to malignant cell transformation due to the deubiquitination of oncoprotein, which leads to its accumulation and disease progression. A correlation was found between the deubiquitinating activity of USP1 and the level of oncoprotein in CML cells. Thus, we identify deubiquitinase USP1 as a promising therapeutic target for the development of a new strategy for the treatment of CML by modulating the level of Bcr-Abl in the cell.

Keywords: chronic myeloid leukemia, Bcr-Abl, USP1, deubiquitination Bcr-Abl, K562 cell

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Authors: Francisco Miroslav Ulloa-Stanojlovic, Gina Polo, Ricardo Augusto Dias

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In Brazil, there is a high incidence of rabies in herbivores of economic interest (HEI) transmitted by the common vampire bat Desmodus rotundus, the presence of human rabies cases and the huge economic losses in the world's largest cattle industry, it is important to assist the National Program for Control of Rabies in herbivores in Brazil, that aims to reduce the incidence of rabies in HEI populations, mainly through epidemiological surveillance, vaccination of herbivores and control of vampire-bat roosts. Material and Methods: A spatiotemporal retrospective Kulldorff's spatial scan statistic based on a Poisson model and Monte Carlo simulation and an Anselin's Local Moran's I statistic were used to uncover spatial clustering of HEI rabies from 2000 – 2014. Results: Were identify three important clusters with significant year-to-year variation (Figure 1). In 2000, was identified one area of clustering in the North region, specifically in the State of Tocantins. Between the year 2000 and 2004, a cluster centered in the Midwest and Southeast region including the States of Goiás, Minas Gerais, Rio de Janeiro, Espirito Santo and São Paulo was prominent. And finally between 2000 and 2005 was found an important cluster in the North, Midwest and South region. Conclusions: The HEI rabies is endemic in the country, in addition, appears to be significant differences among the States according to their surveillance services, that may be difficulting the control of the disease, also other factors could be influencing in the maintenance of this problem like the lack of information of vampire-bat roosts identification, and limited human resources for realization of field monitoring. A review of the program control by the authorities it’s necessary.

Keywords: Brazil, Desmodus rotundus, herbivores, rabies

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Authors: Oleg Redkin, Olga Bernikova

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Globalization and migrations have made cross-cultural contacts more frequent and intensive. Sometimes, these contacts may lead to misunderstanding between partners of communication and misinterpretations of the verbal messages that some researchers tend to consider as the 'clash of civilizations'. In most cases, reasons for that may be found in cultural and linguistic differences and hence misinterpretations of intentions and behavior. The current research examines factors of verbal and non-verbal communication that should be taken into consideration in verbal and non-verbal contacts. Language is one of the most important manifestations of the cultural code, and it is often considered as one of the special features of a civilization. The Arabic language, in particular, is commonly associated with Islam and the language and the Arab-Muslim civilization. It is one of the most important markers of self-identification for more than 200 million of native speakers. Arabic is the language of the Quran and hence the symbol of religious affiliation for more than one billion Muslims around the globe. Adequate interpretation of Arabic texts requires profound knowledge of its grammar, semantics of its vocabulary. Communicating sides who belong to different cultural groups are guided by different models of behavior and hierarchy of values, besides that the vocabulary each of them uses in the dialogue may convey different semantic realities and vary in connotations. In this context direct, literal translation in most cases cannot adequately convey the original meaning of the original message. Besides that peculiarities and diversities of the extralinguistic information, such as the body language, communicative etiquette, cultural background and religious affiliations may make the dialogue even more difficult. It is very likely that the so called 'clash of civilizations' in most cases is due to misinterpretation of counterpart's means of discourse such as language, cultural codes, and models of behavior rather than lies in basic contradictions between partners of communication. In the process of communication, one has to rely on universal values rather than focus on cultural or religious peculiarities, to take into account current linguistic and extralinguistic context.

Keywords: Arabic, civilization, discourse, language, linguistic

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Authors: Saif Ullah

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Survey of avian fauna of Bara Gali Summer Campus, University of Peshawar in the Hazara District was conducted from April to October, 2013. A total of 21 species belonging to 5 orders and 15 families were recorded. Out of these 6 were resident, 12 were summer visitor and 3 were rare. Order Passeriformes was represented by 16 species which are Certhia himalayana, Megalaima virens, Phylloscopus trochiloides, Garrulax lineatus, Passer rutilans, Corvus macrorhynchos, Hypsipetes leucocephalus, Acridotheres tristis, Delichon dasypus cashmeriensis, Hirundo rustica, Muscicapa thalassina, Saxicola ferrea, Myiophoneus caeruleus, Parus melonolophus, Parus rufonuchalis, Parus monticolus, belonging to 11 families. Two species Dendrocopos himalayansis and Picus squamatus belongs to only 1 family of order Piciformes. Only one species from the remaining 3 orders were recorded i.e. Accipiter virgatus belongs to order Accipitriformes, Upupa epops from order Coraciformes, while order Psittaciformes represented by Psittacula himalayana .The distribution and abundance varied with season and maximum number of species was found during the monsoon season when most of the birds migrate for breeding. Some habits and behaviors like nesting, feeding, breeding and vocalizations were also studied which are very unique from other birds. Among bird species adapted to diverse habitat in the field, Himalayan Jungle Crow, Common Mynas, Bulbuls, Barn Swallows, barbets were prominent. Interesting feature of the avian fauna is familiarity with flora was greatly observed. Human related impacts such as grazing by livestock, removal of shrub cover, disturbance of habitat etc. were also studied.

Keywords: birds, summer visitor, Phylloscopus trochiloides, Parus monticolus

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Authors: Van Huong Do, Simon Walton, German Amaya, Madeline Batsiokis, Sally Catt, Andrew Taylor-Robinson

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Identification of the most suitable stages of bovine in vitro-derived blastocysts (early, expanded and hatching) prior to vitrification is a straightforward process that facilitates the decision as to which blastocyst stage to use for transfer of fresh and vitrified embryos. Research on in vitro evaluation of suitable stages has shown that the more advanced developmental stage of blastocysts is recommended for fresh embryo transfer while the earlier stage is proposed for embryo transfer following vitrification. There is, however, limited information on blastocyst stages using in vivo assessment. Hence, the aim of the present study was to determine the optimal stage of a blastocyst for vitrification and embryo transfer through a two-step procedure of embryo transfer followed by pregnancy testing at 35, 60 and 90 days of pregnancy. 410 good quality oocytes aspirated by the ovum pick-up technique from 8 donor cows were subjected to in vitro embryo production, vitrification and embryo transfer. Good quality embryos were selected, subjected to vitrification and embryo transfer. Subsequently, 77 vitrified embryos at different blastocyst stages were transferred to synchronised recipient cows. The overall cleavage and blastocyst rates of oocytes were 68.8% and 41.7%, respectively. In addition, the fertility and blastocyst production of 6 bulls used for in vitro fertilization was examined and shown to be statistically different (P<0.05). Results of ongoing pregnancy trials conducted at 35 days, 60 days and 90 days will be discussed. However, preliminary data indicate that individual bulls demonstrate distinctly different fertility performance in vitro. Findings from conception rates would provide a useful tool to aid selection of bovine in vitro-derived embryos for vitrification and embryo transfer in commercial settings.

Keywords: blastocyst, embryo transfer, in vitro-derived embryos, ovum pick-up, vitrification

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Authors: Konrad Rejdak, Agnieszka Korchut, Sebastian Szklener, Urszula Skrobas, Justyna Gerlowska, Katarzyna Grabowska-Aleksandrowicz, Dorota Szczesniak-Stanczyk

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Introduction: Neurodegenerative diseases are frequently accompanied by loss and unwanted change in functional independence, social relationships, and economic circumstances. Currently, the achievements of social robots to date is being projected to improve multidimensional quality of life among people with cognitive impairment and others. Objectives: Identification of particular human needs in context of the changes occurring in course of neurodegenerative diseases. Methods: Based on the 110 surveys performed in Medical University of Lublin from medical staff, patients, and caregivers we made prioritization of the users' needs as: high, medium, and low. The issues included in the surveys concerned four aspects: user acceptance, functional requirements, design of the robotic assistant and preferred types of human-robot interaction. Results: We received completed questionnaires: 50 from medical staff, 30 from caregivers and 30 from potential users. Above 90% of the respondents from each of the three groups, accepted robotic assistant as a potential caregiver. High priority functional capability of assistive technology was to handle emergencies in a private home like recognizing life-threatening situations and reminding about medication intake. With reference to design of the robotic assistant, the majority of the respondent would like to have an anthropomorphic appearance with positive emotionally expressive face. The most important type of human-robot interaction was voice-operated system and by touchscreen. Conclusion: The results from our study might contribute to a better understanding of the system and users’ requirements for the development of a service robot intended to support patients with dementia.

Keywords: social robot, dementia, requirements, patients needs

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Authors: Ali Aydin, Mert Sudagidan, Aysen Coban, Alparslan Kadir Devrim

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Pseudomonas spp. (specifically, P. fluorescens and P. fragi) are considered the principal spoilage microorganisms of refrigerated poultry meats. The higher the level psychrophilic spoilage Pseudomonas spp. on carcasses at the end of processing lead to decrease the shelf life of the refrigerated product. The aim of the study was the identification of psychrophilic Pseudomonas spp. having proteolytic and lipolytic activities from poultry meats by 16S rRNA and rpoB gene sequencing, investigation of protease and lipase related genes and determination of proteolytic activity of Pseudomonas spp. In the of isolation procedure, collected chicken meat samples from local markets and slaughterhouses were homogenized and the lysates were incubated on Standard method agar and Skim Milk agar for selection of proteolytic bacteria and tributyrin agar for selection of lipolytic bacteria at +4 °C for 7 days. After detection of proteolytic and lipolytic colonies, the isolates were firstly analyzed by biochemical tests such as Gram staining, catalase and oxidase tests. DNA gene sequencing analysis and comparison with GenBank revealed that 126 strong enzyme Pseudomonas spp. were identified as predominantly P. fluorescens (n=55), P. fragi (n=42), Pseudomonas spp. (n=24), P. cedrina (n=2), P. poae (n=1), P. koreensis (n=1), and P. gessardi (n=1). Additionally, protease related aprX gene was screened in the strains and it was detected in 69/126 strains, whereas, lipase related lipA gene was found in 9 Pseudomonas strains. Protease activity was determined using commercially available protease assay kit and 5 strains showed high protease activity. The results showed that psychrophilic Pseudomonas strains were present in chicken meat samples and they can produce important levels of proteases and lipases for food spoilage to decrease food quality and safety.

Keywords: Pseudomonas, chicken meat, protease, lipase

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Authors: Raya Morag

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This paper proposes a new paradigm for cinema/trauma studies - the trauma of the perpetrator. Canonical trauma research from Freud’s Aetiology of Hysteria to the present has been carried out from the perspective of identification with the victim, as have cinema trauma research and contemporary humanities-based trauma studies, climaxing during the 1990s in widespread interest in the victim vis-à-vis the Holocaust, war, and domestic violence. Breaking over 100 years of repression of the abhorrent and rejected concept of the perpetrator in psychoanalytic-based research proposes an uncanny shift in our conception of psychoanalysis' trajectory from women's 'hysteria' to 'post-traumatic stress disorder'. This new paradigm is driven by the global emergence of new waves of films (2007-2015) representing trauma suffered by perpetrators involved in the new style of war entailing deliberate targeting of non-combatants. Analyzing prominent examples from Israeli post-second Intifada documentaries (e.g., Ari Folman’s Waltz with Bashir), and post post-Iraq (and Afghanistan) War American documentaries (e.g., Errol Morris' Standard Operating Procedure), the paper discusses the limitations of victim trauma by the firm boundaries it (rightly) set in order to defend such victims of nineteenth and especially twentieth-century catastrophes; the epistemological processes needed in order to consider perpetrators’ trauma as an inevitable part of psychiatric-psychological and cultural perspectives on trauma, and, thus, the definition of perpetrators' trauma in contrast to victims'. It also analyzes the perpetrator's figure in order to go beyond the limitation of current trauma theory's relation to the Real, thus transgressing the 'unspeakableness' of the trauma itself. The paper seeks an exploration of what perpetrator trauma teaches us not only as a counter-paradigm to victim trauma, but as a reflection on the complex intertwining of the two paradigms in the twenty-first century collective new war unconscious, and on what psychoanalysis might offer us in the first decade of this terrorized-ethnicized century.

Keywords: American war documentaries, Israeli war documentaries, 'new war', perpetrator trauma

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Authors: L. Piñeiro, N. Cobas, L. Gómez-Limia, S. Martínez, I. Franco

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The swordfish (Xiphias gladius) is a large oceanic fish of high commercial value, which is widely distributed in waters of the world’s oceans. They are considered to be an important source of high quality proteins, vitamins and essential fatty acids, although only half of the population follows the recommendation of nutritionists to consume fish at least twice a week. Swordfish is consumed worldwide because of its low fat content and high protein content. It is generally sold as fresh, frozen, and as pieces or slices. The aim of this study was to evaluate the effect of salting and frying on the composition of the water-soluble vitamins (B₂, B₃, B₉ and B₁₂) and fat-soluble vitamins (A, D, and E) of swordfish. Three loins of swordfish from Pacific Ocean were analyzed. All the fishes had a weight between 50 and 70 kg and were transported to the laboratory frozen (-18 ºC). Before the processing, they were defrosted at 4 ºC. Each loin was sliced and salted in brine. After cleaning the slices, they were divided into portions (10×2 cm) and fried in olive oil. The identification and quantification of vitamins were carried out by high-performance liquid chromatography (HPLC), using methanol and 0.010% trifluoroacetic acid as mobile phases at a flow-rate of 0.7 mL min^-1. The UV-Vis detector was used for the detection of the water- and fat-soluble vitamins (A and D), as well as the fluorescence detector for the detection of the vitamin E. During salting, water and fat-soluble vitamin contents remained constant, observing an evident decrease in the values of vitamin B₂. The diffusion of salt into the interior of the pieces and the loss of constitution water that occur during this stage would be related to this significant decrease. In general, after frying water-soluble and fat-soluble vitamins showed a great thermolability with high percentages of retention with values among 50–100%. Vitamin B₃ is the one that exhibited higher percentages of retention with values close to 100%. However, vitamin B₉ presented the highest losses with a percentage of retention of less than 20%.

Keywords: frying, HPLC, salting, swordfish, vitamins

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Authors: Dharmendra Pratap

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Large Cardamom (Amomum subulatum), family Zingiberaceae is an aromatic spice crop and has rich medicinal value. Large Cardamom is as synonymous to Sikkim as Tea is to Darjeeling. Since Sikkim alone contributes up to 88% of India's large cardamom production which is the world leader by producing over 50% of the global yield. However, the production of large cardamom has declined almost to half since last two decade. The economic losses have been attributed to two viral diseases namely, chirke and Foorkey. Chirke disease is characterized by light and dark green streaks on leaves. The affected leaves exhibit streak mosaic, which gradually coalesce, turn brown and eventually dry up. Excessive sprouting and formation of bushy dwarf clumps at the base of mother plants that gradually die characterize the foorkey disease. In our surveys in Sikkim–Darjeeling hill area during 2012-14, 40-45% of plants were found to be affected with foorkey disease and 10-15% with chirke. Mechanical and aphid transmission study showed banana as an alternate host for both the disease. For molecular identification, total genomic DNA and RNA was isolated from the infected leaf tissues and subjected to Rolling circle amplification (RCA) and RT-PCR respectively. The DNA concatamers produced in the RCA reaction were monomerized by different restriction enzymes and the bands corresponding to ~1 kb genomes were purified and cloned in the respective sites. The nucleotide sequencing results revealed the association of Nanovirus with the foorkey disease of large cardamom. DNA1 showed 74% identity with Replicase gene of FBNYV, DNA2 showed 77% identity with the NSP gene of BBTV and DNA3 showed 74% identity with CP gene of BBTV. The finding suggests the presence of a new species of nanovirus associated with foorkey disease of large cardamom in Sikkim and Darjeeling hills. The details of their epidemiology and other factors would be discussed.

Keywords: RCA, nanovirus, large cardamom, molecular virology and microbiology

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Authors: Ning Li, Jiacheng Zhang, Zheng Yang, Sylvia Kang

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Introduction: Polycystic ovary syndrome (PCOS) is a common physiological symptom in women of reproductive age. Women with PCOS may have infrequent or prolonged menstrual periods and excess male hormone (androgen) levels. Mira analyzes the cycle profiles and the luteinizing hormone (LH) changes in urine, closely related to the fertility level of healthy women and PCOS women. From the difference between the two groups, Mira helps to understand the physiological state of PCOS women and their hormonal changes in the menstrual cycle. Methods: In this study, data from 1496 cycles and information from 342 women belonging to two groups (181 PCOS and 161 Healthy) were collected and analyzed. Women test their luteinizing hormone (LH) in urine daily with Mira fertility test wand and Mira analyzer, from the day after the menstruation to the starting day of the next menstruation. All the collected data meets Mira’s user agreement and users’ identification was removed. The cycle length, LH peak, and other cycle information of the PCOS group were compared with the Healthy group. Results: The average cycle length of PCOS women is 41 days and of the Healthy women is 33 days. 91.4% of cycle length is within 40 days for the Healthy group, while it decreases to 71.9% for the PCOS group. This means PCOS women have a longer menstrual cycle and more variation during the cycle. With more variation, the ovulation prediction becomes more difficult for the PCOS group. The deviation between the LH surge day and the predicted ovulation day, calculated by the starting day of the next menstruation minus 14 days, is greater in the PCOS group compared with the Healthy group. Also, 46.96% of PCOS women have an irregular cycle, and only 19.25% of healthy women show an irregular cycle. Conclusion: PCOS women have longer menstrual cycles and more variation during the menstrual cycles. The traditional ovulation prediction is not suitable for PCOS women.

Keywords: menstrual cycle, PCOS, urinary luteinizing hormone, Mira

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Authors: Nwafia Ifeyinwa Nkeiruka, Nwafia Walter Chukwuma

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Since the early 1980’s fungi have emerged as major causes of human diseases, especially among immunocompromised. The most commonly isolated yeast is Candida albicans and constitutes the 4th most common nosocomial BSI in humans. It is progressive and cumulative and become more complex over time.It can even lead to leaky gut syndrome that causes food and environmental allergies. It is worthy of note that all the available data on oral Candida risk factors in humans were documented essentially using data from studies conducted in other areas, hence there is need for comparative and complementary information from the South eastern part of Nigeria. Method: 200 subjects of all age groups of both sexes were randomly examined,by swabbing their palatine mucosa and dorsal tongue with sterile cotton wool,then cultured into Sabouraud dextrose agar plates supplemented with antibiotics and incubated aerobically at 37 degree for 48 hrs. Identification of Candida albicans was done by germ tubes tests, chlamydospores production on cornmeal agar supplemented with 1% Tween 80.Sugar and nitrogen assimilation test using API 20C Auxanogram and potassium nitrate agar. Results: Out of 30 samples that were positive for candida, 15 (50%) were candida albicans. Using the anova test (P < 0.05) this variation is significant (P = 0016). followed by C. dublinensis 3 (13%), C. tropicalis 3 (10%), C. pseudotropicalis 3 (10%), C, glabrata 2 (7%), C. parapsilosis 2 (7%) and lastly C. krusei 1 (3%).However, 53% of the patients were female while 47% were male. Among the HIV positive isolates.67% were HIV isolates not on drugs while 33% positives isolates were on drugs and the percentages of candida species in these patients were as follows C. albicans were 45% followed by C. glabrata and C.tropicalis which were 17% each, C.parapsilosis, C.dubliensis and C.pseudotropicalis were all 8% each. Conclusion: Oral Candidiasis is a marker of systemic diseases and in some cases, it may be the first clinical presentation. There is need for more intensive clinical and laboratory monitoring and possible early intervention to prevent the reoccurrence and resistance to treatment.

Keywords: oral cavity, Candida species, oral Candidiasis, risk factors

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Authors: Lola Brasseur, Guillaume Caulier, Marie Demeyer, Pascal Gerbaux, Igor Eeckhaut

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Seawater being an ideal dispersing agent, chemical communication stays predominant in marine ecosystems. However, if many molecules acting in chemical heterospecific communication have already been well described in terrestrial ecosystems, only three of these molecules were identified in marine ecosystems. Echinoderms and their symbiotic organisms constitute very good models to study heterospecific chemical communication because each class synthesizes a specific type of molecules and symbioses with echinoderms as hosts are very usual. In this study, the chemical communication that allows the commensal shrimps Tuleariocaris holthuisi Hipeau-Jacquotte, 1965 to live with their host Echinometra mathaei (Blainville, 1825) was investigated. The chemoreception of the shrimp was characterized using olfactometers and it was demonstrated that hosts and synthetic hydroxynaphthoquinones are attractive to the symbiotic shrimps. Hydroxynaphthoquinonic pigments also known as spinochromes are by the way synthesized by sea urchin and involved in all probability in a lot of mechanisms. To our knowledge, this study is the first highlighting the ecological function of naphthoquinones as kairomones. Chemical extractions were also performed on sea urchins in order to analyze and identify their specific hydroxynaphthoquinones using HPLC-ESI-MS. Accurate mass identification and elemental composition have been performed on various organs (gonads, coelomic liquid, digestive system and test) in different morphotypes of Echinometra mathaei for a better understanding of the molecular diversity of these semiochemicals. Moreover, some experiments were performed to investigate the dependence of T. holthuisi for their host. First, the analyses showed that the molecules involved in shrimp pigmentation are the same that the ones involved in E. mathaei, suggesting a potential feeding on the host. Secondly, a substantial shrimp depigmentation and an increase of the mortality rate were demonstrated after the symbionts-host separation which could mean a potential implication of spinochromes in the shrimp metabolism.

Keywords: crustacean, sea urchin, spinochrome, symbiosis

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Authors: Avinash Vellore Sunder, Shikha Shah, Pramod P. Wangikar

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The enzymatic conversion of nitriles to carboxylic acids by nitrilases has gained significance in the green synthesis of several pharmaceutical precursors and fine chemicals. While nitrilases have been characterized from different sources, the industrial application requires the identification of nitrilases that possess higher substrate tolerance, wider specificity and better thermostability, along with the development of an efficient bioprocess for producing large amounts of nitrilase. To produce large amounts of nitrilase, we developed a fed-batch fermentation process on defined media for the high cell density cultivation of E. coli cells expressing the well-studied nitrilase from Alcaligenes fecalis. A DO-stat feeding approach was employed combined with an optimized post-induction strategy to achieve nitrilase titer of 2.5*105 U/l and 78 g/l dry cell weight. We also identified 16 novel nitrilase sequences from genome mining and analysis of substrate binding residues. The nitrilases were expressed in E. coli and their biocatalytic potential was evaluated on a panel of 22 industrially relevant nitrile substrates using high-throughput screening and HPLC analysis. Nine nitrilases were identified to exhibit high activity on structurally diverse nitriles including aliphatic and aromatic dinitriles, heterocyclic, -hydroxy and -keto nitriles. With fed-batch biotransformation, whole-cell Zobelia galactanivorans nitrilase achieved yields of 2.4 M nicotinic acid and 1.8 M isonicotinic acid from 3-cyanopyridine and 4-cyanopyridine respectively within 5 h, while Cupravidus necator nitrilase enantioselectively converted 740 mM mandelonitrile to (R)–mandelic acid. The nitrilase from Achromobacter insolitus could hydrolyze 542 mM iminodiacetonitrile in 1 h. The availability of highly active nitrilases along with bioprocesses for enzyme production expands the toolbox for industrial biocatalysis.

Keywords: biocatalysis, isonicotinic acid, iminodiacetic acid, mandelic acid, nitrilase

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Authors: N. Umasuthan, S. D. N. K. Bathige, W. S. Thulasitha, I. Whang, J. Lee

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The MyD88 is an evolutionarily conserved host-expressed adaptor protein that is essential for proper TLR/ IL1R immune-response signaling. A previously identified complete cDNA (1626 bp) of OfMyD88 comprised an ORF of 867 bp encoding a protein of 288 amino acids (32.9 kDa). The gDNA (3761 bp) of OfMyD88 revealed a quinquepartite genome organization composed of 5 exons (with the sizes of 310, 132, 178, 92 and 155 bp) separated by 4 introns. All the introns displayed splice signals consistent with the consensus GT/AG rule. A bipartite domain structure with two domains namely death domain (24-103) coded by 1st exon, and TIR domain (151-288) coded by last 3 exons were identified through in silico analysis. Moreover, homology modeling of these two domains revealed a similar quaternary folding nature between human and rock bream homologs. A comprehensive comparison of vertebrate MyD88 genes showed that they possess a 5-exonic structure. In this structure, the last three exons were strongly conserved, and this suggests that a rigid structure has been maintained during vertebrate evolution. A cluster of TATA box-like sequences were found 0.25 kb upstream of cDNA starting position. In addition, putative 5'-flanking region of OfMyD88 was predicted to have TFBS implicated with TLR signaling, including copies of NFB1, APRF/ STAT3, Sp1, IRF1 and 2 and Stat1/2. Using qPCR technique, a ubiquitous mRNA expression was detected in liver and blood. Furthermore, a significantly up-regulated transcriptional expression of OfMyD88 was detected in head kidney (12-24 h; >2-fold), spleen (6 h; 1.5-fold), liver (3 h; 1.9-fold) and intestine (24 h; ~2-fold) post-Fla challenge. These data suggest a crucial role for MyD88 in antibacterial immunity of teleosts.

Keywords: MyD88, innate immunity, flagellin, genomic analysis

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Authors: Oluwaseun K. Oyebode, Josiah A. Adeyemo

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Hydrological modelling plays a crucial role in the planning and management of water resources, most especially in water stressed regions where the need to effectively manage the available water resources is of critical importance. However, due to the complex, nonlinear and dynamic behaviour of hydro-climatic interactions, achieving reliable modelling of water resource systems and accurate projection of hydrological parameters are extremely challenging. Although a significant number of modelling techniques (process-based and data-driven) have been developed and adopted in that regard, the field of hydrological modelling is still considered as one that has sluggishly progressed over the past decades. This is majorly as a result of the identification of some degree of uncertainty in the methodologies and results of techniques adopted. In recent times, evolutionary computation (EC) techniques have been developed and introduced in response to the search for efficient and reliable means of providing accurate solutions to hydrological related problems. This paper presents a comprehensive review of the underlying principles, methodological needs and applications of a promising evolutionary computation modelling technique – genetic programming (GP). It examines the specific characteristics of the technique which makes it suitable to solving hydrological modelling problems. It discusses the opportunities inherent in the application of GP in water related-studies such as rainfall estimation, rainfall-runoff modelling, streamflow forecasting, sediment transport modelling, water quality modelling and groundwater modelling among others. Furthermore, the means by which such opportunities could be harnessed in the near future are discussed. In all, a case for total embracement of GP and its variants in hydrological modelling studies is made so as to put in place strategies that would translate into achieving meaningful progress as it relates to modelling of water resource systems, and also positively influence decision-making by relevant stakeholders.

Keywords: computational modelling, evolutionary algorithms, genetic programming, hydrological modelling

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Authors: Omer Livvarcin, Mary Kay Park, Michael Miles

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The current literature includes a few studies that mention the impact of relations between teams, the business environment, and experiences from previous projects. There is, however, limited research that treats the phenomenon of project atmosphere (PA) as a whole. This is especially true of research identifying parameters and sub-parameters, which allow project management (PM) teams to build a project culture that ultimately imbues project success. This study’s findings identify a number of key project atmosphere parameters and sub-parameters that affect project management success. One key parameter identified in the study is a cluster related to cultural concurrence, including artifacts such as policies and mores, values, perceptions, and assumptions. A second cluster centers on motivational concurrence, including such elements as project goals and team-member expectations, moods, morale, motivation, and organizational support. A third parameter cluster relates to experiential concurrence, with a focus on project and organizational memory, previous internal PM experience, and external environmental PM history and experience). A final cluster of parameters is comprised of those falling in the area of relational concurrence, including inter/intragroup relationships, role conflicts, and trust. International and intercultural project management data was collected and analyzed from the following countries: Canada, China, Nigeria, South Korea and Turkey. The cross-cultural nature of the data set suggests increased confidence that the findings will be generalizable across cultures and thus applicable for future international project management success. The intent of the identification of project atmosphere as a critical project management element is that a clear understanding of the dynamics of its sub-parameters upon projects may significantly improve the odds of success of future international and intercultural projects.

Keywords: project management, project atmosphere, cultural concurrence, motivational concurrence, relational concurrence

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Authors: Kai-Yao Huang, Tzong-Yi Lee, Pin-Hao Ho, Tzu-Hao Chang, Cheng-Wei Chang

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Background: Human cytomegalovirus (HCMV) infects much people around the world, and there were many researches mention that many diseases were caused by HCMV. To understand the mechanism of HCMV lead to diseases during infection. We observe a microRNA (miRNA) – miRNA interaction between HCMV and host during infection. We found HCMV miRNA sequence component complementary with host miRNA precursors, and we also found that the host miRNA abundances were decrease in HCMV infection. Hence, we focus on the host miRNA which may target by the other HCMV miRNA to find theirs target mRNAs expression and analysis these mRNAs affect what kind of signaling pathway. Interestingly, we found the affected mRNA play an important role in some diseases related pathways, and these diseases had been annotated by HCMV infection. Results: From our analysis procedure, we found 464 human miRNAs might be targeted by 26 HCMV miRNAs and there were 291 human miRNAs shows the concordant decrease trend during HCMV infection. For case study, we found hcmv-miR-US22-5p may regulate hsa-mir-877 and we analysis the KEGG pathway which built by hsa-mir-877 validate target mRNA. Additionally, through survey KEGG Disease database found that these mRNA co-regulate some disease related pathway for instance cancer, nerve disease. However, there were studies annotated that HCMV infection casuse cancer and Alzheimer. Conclusions: This work supply a different scenario of miRNA target interactions(MTIs). In previous study assume miRNA only target to other mRNA. Here we wonder there is possibility that miRNAs might regulate non-mRNA targets, like other miRNAs. In this study, we not only consider the sequence similarity with HCMV miRNAs and human miRNA precursors but also the expression trend of these miRNAs. Then we analysis the human miRNAs validate target mRNAs and its associated KEGG pathway. Finally, we survey related works to validate our investigation.

Keywords: human cytomegalovirus, HCMV, microRNA, miRNA

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