Search results for: sequencing strategies

Authors: Abeer A. Q. Ahmed, Tracey McKay

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The increasing demand for renewable fuels and chemicals is pressuring manufacturing industry toward finding more sustainable cost-effective resources. Lignocellulose, such as agro-food wastes, is a suitable equivalent to petroleum for fine chemicals and fuels production. The complex structure of lignocellulose, however, requires a variety of enzymes in order to degrade its components into their respective building blocks that can be used further for the production of various value added products. This study aimed to isolate bacterial strain with the ability to produce a variety of lignocellulosic enzymes. One bacterial isolate was identified by 16S rRNA gene sequencing and phylogenetic analysis as Bacillus safensis LCX found to have CMCase, xylanase, manganese peroxidase, lignin peroxidase, and laccase activities. The enzymes production was induced by growing Bacillus safensis LCX in solid state fermentation using wheat straw, wheat bran, and corn stover. The activities of enzymes were determined by specific colorimetric assays. This study presents Bacillus safensis LCX as a promising source for lignocellulosic enzymes. These findings can extend the knowledge on agro-food wastes valorization strategies toward a sustainable production of fuels and chemicals.

Keywords: Bacillus safensis LCX, high valued chemicals, lignocellulosic enzymes, solid state fermentation

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

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

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

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Authors: Getachew Tilahun, Oluwole Makinde, David Malonza

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We propose and analyze a non-linear mathematical model for the transmission dynamics of pneumonia disease in a population of varying size. The deterministic compartmental model is studied using stability theory of differential equations. The effective reproduction number is obtained and also the local and global asymptotically stability conditions for the disease free and as well as for the endemic equilibria are established. The model exhibit a backward bifurcation and the sensitivity indices of the basic reproduction number to the key parameters are determined. Using Pontryagin’s maximum principle, the optimal control problem is formulated with three control strategies; namely disease prevention through education, treatment and screening. The cost effectiveness analysis of the adopted control strategies revealed that the combination of prevention and treatment is the most cost effective intervention strategies to combat the pneumonia pandemic. Numerical simulation is performed and pertinent results are displayed graphically.

Keywords: cost effectiveness analysis, optimal control, pneumonia dynamics, stability analysis, numerical simulation

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Authors: Larry Lai, Evans Leung

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Falun gong is a self-proclaimed religious group that has been under crackdown by Beijing for more than two decades. Diaosi, on the other hand, is an emerging community with members loosely connected on the internet through different online social platforms, centering around the sharing of different hobbies and interests. Diaosi community has been transformed from a potential threat to the Chinese authority for different causes to a pro-government force. This paper seeks to explain the different strategies adopted by the People's Republic of China (PRC) regime in handling these two potential threatening communities. Both communities share some obvious similarities: (1) both have massive nation-wide participation; (2) both have attempted to challenge the PRC's authority through contentious means; (3) both have high level of mobility, online or offline; and (4) both have at first been unnoticed until the threat against the PRC have taken form. But the strategies the PRC endorsed against the communities were, in many ways, different. The question is: if the strategy against Falun Gong has been an effective one, why used other strategies against Diaosi? The authors argue that the main reason for using different strategies lies in the differences between the two communities in terms of (i) the nature of the groups, and (ii) the group dynamics. Lastly, based on this analysis, the authors attempt to explore the possible strategies that the PRC would adopt against the Hong Kong cyber-world political community in light of the latest national security law in Hong Kong.

Keywords: contentious politics, Diaosi, Falun Gong, Hong Kong, People's Republic of China

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Authors: Yash M. Gupta, Kittisak Buddhachat, Surin Peyachoknagul, Somjit Homchan

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The house cricket, Acheta domesticus is one of the commonly found species of field crickets. Although it is very commonly used as food and feed, the genomic information of house cricket is still missing for genetic investigation. DNA sequencing technology has evolved over the decades, and it has also revolutionized the molecular marker development for genetic analysis. In the present study, we have sequenced the whole genome of A. domesticus using illumina platform based HiSeq X Ten sequencing technology for searching simple sequence repeats (SSRs) in DNA to develop polymorphic microsatellite markers for population genetic analysis. A total of 112,157 SSRs with primer pairs were identified, 91 randomly selected SSRs used to check DNA amplification, of which nine primers were polymorphic. These microsatellite markers have shown cross-amplification with other three species of crickets which are Gryllus bimaculatus, Gryllus testaceus and Brachytrupes portentosus. These nine polymorphic microsatellite markers were used to check genetic variation for forty-five individuals of A. domesticus, Phitsanulok population, Thailand. For nine loci, the number of alleles was ranging from 5 to 15. The observed heterozygosity was ranged from 0.4091 to 0.7556. These microsatellite markers will facilitate population genetic analysis for future studies of A. domesticus populations. Moreover, the transferability of these SSR makers would also enable researchers to conduct genetic studies for other closely related species.

Keywords: cross-amplification, microsatellite markers, observed heterozygosity, population genetic, simple sequence repeats

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Authors: Silvia Riva, Ezekiel Chinyio

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Introduction: Workers in different sectors are prone to stress at varying levels. They also respond to stress in different ways. An inspiration was to study stress development amongst workers in a work dangerous setting (Construction Industry) as well as how they cope with specific stress incidences. Objective: The overarching objective of the study was to study and correlate between stress and coping strategies. The research was conducted in an organizational industrial setting, and its findings on the coping actions of construction workers are reported in this article. Methods: An online cross-sectional survey was conducted with 80 participants aged 18-62. These were working for three different construction organizations in the West Midland region of the UK. Their coping actions were assessed using the COPE Inventory (Carver, 2013) instrument while the level of stress was assessed by the Perceived Stress Scale (Cohen, 1994). Results: Out of 80 workers (20 female, 25%, mean age 40.66), positive reinterpretation (M=4.15, SD=2.60) and active coping (M=4.18, SD=2.55) were the two most adaptive strategies reported by the workers while the most frequent maladaptive behavior was mental disengagement (M=3.62, SD=2.25). Among the maladaptive tactics, alcohol and drug abuse was a significant moderator in stress reactions (t=6.12, p=.000). Conclusion: Some maladaptive strategies are adopted by construction workers to cope with stress. So, it could be argued that programs of stress prevention and control in the construction industry have a basis to develop solutions that can improve and strengthen effective interventions when workers are stressed or getting stressed.

Keywords: coping, organization, strategies, stress

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Authors: Ramune Kasperaviciene, Jurgita Motiejuniene, Dalia Venckiene

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Familiarising students with strategies for transferring cultural meanings (intertextual units, culture-specific idioms, culture-specific items, etc.) should be part of a comprehensive translator training programme. The present paper focuses on strategies for transferring such meanings into other languages and explores possibilities for introducing these methods and practice to translation students. The authors (university translation teachers) analyse the means of transferring cultural meanings from English into Lithuanian in a specific travel book, attribute these means to theoretically grounded strategies, and make calculations related to the frequency of adoption of specific strategies; translation students are familiarised with concepts and methods related to transferring cultural meanings and asked to put their theoretical knowledge into practice, i.e. interpret and translate certain culture-specific items from the same source text, and ground their decisions on theory; the comparison of the strategies employed by the professional translator of the source text (as identified by the authors of this study) and by the students is made. As a result, both students and teachers gain valuable experience, and new practices of conducting translation classes for a specific purpose evolve. Conclusions highlight the differences and similarities of non-professional and professional choices, summarise the possibilities for introducing methods of transferring cultural meanings to students, and round up with specific considerations of the impact of theoretical knowledge and the degree of experience on decisions made in the translation process.

Keywords: cultural meanings, culture-specific items, strategies for transferring cultural meanings, translator training

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Authors: S. U. Kunya, S. A. Mohammad

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Construction projects in Nigeria are characterized with risks emanating from delays and accompanying cost-overruns. The aim of the study was to identify and assess factors constraining the utilization of risk management strategies in the execution of public construction project in North-East Nigeria. Data was collected with the aid of a well-structured questionnaire administered to three identified projects in the North-east. Data collected were analysed using the severity index. Findings revealed political involvement, selection of inexperienced contractors and lack of coordinated public sector strategy as the most severe factors constraining the utilization of risk management strategies. The study recommended that: formulation of laws to prevent negative political meddling in construction projects; selection of experienced, risk-informed contractors; and comprehensive risk assessment and planning on all public construction projects.

Keywords: factors, Nigeria, north-east, public projects, risk management, strategies, utilization

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Authors: R. Khoza, K. K. Govender

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The aim of the study was to review and critically evaluate the supply chain management (SCM) strategies and challenges in the private residential construction sector in South Africa. The study was grounded in three theories, namely, theory of constraints, principal-agency theory, and stakeholder theory. A quantitative approach was used to survey 320 private residential construction companies which registered with the National Homebuilders Registration Council (NHBRC) within the Gauteng province. The data from 250 questionnaires returned were analysed using SPSS (Versions 23) and Smart PLS. It became evident that the SCM challenges included lack of trust between the supplier and the organization; lack of adoption of SCM system; lack of a sufficiently skilled SCM workforce; and poor implementation of contract management. The findings also indicate that there is a significant positive relationship between the performance of the private residential construction sector in South Africa and SCM challenges, SCM strategies and SCM processes. A framework is proposed comprising SCM practices and strategies of private residential construction sector in South Africa, which will enable them to enhance performance.

Keywords: management challenges, residential housing, South Africa, supply chain management

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Authors: Danyi Wang, Andrew Schriefer, Dennis O'Rourke, Brajendra Kumar, Yang Liu, Fei Zhong, Juergen Scheuenpflug, Zheng Feng

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Purpose: It has been recognized that the microbiome plays critical roles in disease pathogenesis, including cancer, autoimmune disease, and multiple sclerosis. To develop a clinical-grade assay for exploring microbiome-derived clinical biomarkers across disease areas, a two-phase approach is implemented. 1) Identification of the optimal sample preparation reagents using pre-mixed bacteria and healthy donor stool samples coupled with proprietary Sigma-Aldrich® bioinformatics solution. 2) Exploratory analysis of patient samples for enabling precision medicine. Study Procedure: In phase 1 study, we first compared the 16S sequencing results of two ATCC® microbiome standards (MSA 2002 and MSA 2003) across five different extraction kits (Kit A, B, C, D & E). Both microbiome standards samples were extracted in triplicate across all extraction kits. Following isolation, DNA quantity was determined by Qubit assay. DNA quality was assessed to determine purity and to confirm extracted DNA is of high molecular weight. Bacterial 16S ribosomal ribonucleic acid (rRNA) amplicons were generated via amplification of the V3/V4 hypervariable region of the 16S rRNA. Sequencing was performed using a 2x300 bp paired-end configuration on the Illumina MiSeq. Fastq files were analyzed using the Sigma-Aldrich® Microbiome Platform. The Microbiome Platform is a cloud-based service that offers best-in-class 16S-seq and WGS analysis pipelines and databases. The Platform and its methods have been extensively benchmarked using microbiome standards generated internally by MilliporeSigma and other external providers. Data Summary: The DNA yield using the extraction kit D and E is below the limit of detection (100 pg/µl) of Qubit assay as both extraction kits are intended for samples with low bacterial counts. The pre-mixed bacterial pellets at high concentrations with an input of 2 x106 cells for MSA-2002 and 1 x106 cells from MSA-2003 were not compatible with the kits. Among the remaining 3 extraction kits, kit A produced the greatest yield whereas kit B provided the least yield (Kit-A/MSA-2002: 174.25 ± 34.98; Kit-A/MSA-2003: 179.89 ± 30.18; Kit-B/MSA-2002: 27.86 ± 9.35; Kit-B/MSA-2003: 23.14 ± 6.39; Kit-C/MSA-2002: 55.19 ± 10.18; Kit-C/MSA-2003: 35.80 ± 11.41 (Mean ± SD)). Also, kit A produced the greatest yield, whereas kit B provided the least yield. The PCoA 3D visualization of the Weighted Unifrac beta diversity shows that kits A and C cluster closely together while kit B appears as an outlier. The kit A sequencing samples cluster more closely together than both the other kits. The taxonomic profiles of kit B have lower recall when compared to the known mixture profiles indicating that kit B was inefficient at detecting some of the bacteria. Conclusion: Our data demonstrated that the DNA extraction method impacts DNA concentration, purity, and microbial communities detected by next-generation sequencing analysis. Further microbiome analysis performance comparison of using healthy stool samples is underway; also, colorectal cancer patients' samples will be acquired for further explore the clinical utilities. Collectively, our comprehensive qualification approach, including the evaluation of optimal DNA extraction conditions, the inclusion of positive controls, and the implementation of a robust qualified bioinformatics pipeline, assures accurate characterization of the microbiota in a complex matrix for deciphering the deep biology and enabling precision medicine.

Keywords: 16S rRNA sequencing, analytical validation, bioinformatics pipeline, metagenomics

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Authors: A. Farhad Sadri, B. Ali Farhadi, C. Nasim Shalamzari

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Waste management is a principle of urban and environmental governance. Waste management in Tehran metropolitan requires good strategies for better governance. Using of good urban governance principles together with eight main indexes can be an appropriate base for this aim. One of the reasonable tools in this field is usage of SWOT methods which provides possibility of comparing the opportunities, threats, weaknesses, and strengths by using IFE and EFE matrixes. The results of the above matrixes, respectively 2.533 and 2.403, show that management system of Tehran metropolitan wastes has performed weak regarding to internal factors and has not have good performance regarding using the opportunities and dealing with threats. In this research, prioritizing and describing the real value of each 24 strategies in waste management in Tehran metropolitan have been surveyed considering good governance derived from Quantitative Strategic Planning Management (QSPM) by using Kolomogrof-Smirnoff by 1.549 and significance level of 0.073 in order to define normalization of final values and all of the strategies utilities and Variance Analysis of ANOVA has been calculated for all SWOT strategies. Duncan’s test results regarding four WT, ST, WO, and SO strategies show no significant difference. In addition to mean comparison by Duncan method in this research, LSD (Lowest Significant Difference test) has been used by probability of 5% and finally, 7 strategies and final model of Tehran metropolitan waste management strategy have been defined. Increasing the confidence of people with transparency of budget, developing and improving the legal structure (rule-oriented and law governance, more responsibility about requirements of private sectors, increasing recycling rates and real effective participation of people and NGOs to improve waste management (contribution) and etc, are main available strategies which have been achieved based on good urban governance management principles.

Keywords: waste, strategy, environmental management, urban good governance, SWOT

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Authors: Pauline Logue

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In recent decades, the Irish Department of Education and Skills has pro-actively promoted student-center learning methodologies. Similarly, the National Forum for the Enhancement of Teaching and Learning has advocated such strategies, aligning them with student success. These developments have informed the author’s professional practice as a teacher educator. This qualitative student-perspective study focuses on a review of one pilot initiative in the academic year 2020-2021, namely, the implementation of universal design for learning strategies within teacher education, employing student-centered learning strategies. Findings included: that student-centered strategies enhanced student performance and success overall, with some minor evidence of student resistance. It was concluded that a dialogical review with student teachers on prior learning experiences (from intellectual and affective perspectives) and learning environments (physical, virtual, and emotional) could facilitate greater student ownership of learning. It is recommended to more formally structure such a dialogical review in a future delivery.

Keywords: professional practice, student-centered learning, teacher education, universal design for learning

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Authors: M. Ottenbrite, G. Yilmaz, J. Devenish, M. Kang, H. Dan, M. Lin, C. Lau, C. Carrillo, K. Bessonov, J. Nash, E. Topp, J. Guan

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Consumption of food contaminated by antibiotic-resistant (AR) bacteria may lead to the transmission of AR genes in the gut microbiota and cause AR bacterial infection, a significant public health concern. However, information is limited on if and how background microbes from the food matrix (food microbes) may influence resistance transmission. Thus, we assessed the colonization of a β-lactam resistant Salmonella Heidelberg strain (donor) and a β-lactam susceptible S. Typhimurium strain (recipient) and the transfer of the resistance genes in the mouse gut in the presence or absence of food microbes that were derived from washing freshly-harvested carrots. Mice were pre-treated with streptomycin and then inoculated with both donor and recipient bacteria or recipient only. Fecal shedding of the donor, recipient, and transconjugant bacteria was enumerated using selective culture techniques. Transfer of AR genes was confirmed by whole genome sequencing. Gut microbial composition was determined by 16s rRNA amplicon sequencing. Significantly lower numbers of donors and recipients were shed from mice that were inoculated with food microbes compared to those without food microbe inoculation. S. Typhimurium transconjugants were only recovered from mice without inoculation of food microbes. A significantly higher survival rate was in mice with vs. without inoculation of food microbes. The results suggest that the food microbes may compete with both the donor and recipient Salmonella, limit their growth and reduce transmission of the β-lactam resistance gene in the mouse gut.

Keywords: antibiotic resistance, gene transfer, gut microbiota, Salmonella infection

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Authors: Phichak Phutrakhul

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The purposes of this research were to study concepts and strategies of human resource development in the automotive manufacturers and to articulate the proposals against the government about the human resource development for automotive industry. In the present study, qualitative study was an in-depth interview in which the qualitative data were collected from the executive or the executive of human resource division from five automotive companies - Toyota Motor (Thailand) Co., Ltd., Nissan Motor (Thailand) Co., Ltd., Mitsubishi Motors (Thailand) Co., Ltd., Honda Automobile (Thailand) Co., Ltd., and Suzuki Motor (Thailand) Co., Ltd. Qualitative data analysis was performed by using inter-coder agreement technique. The research findings were as follows: The external factors included the current conditions of the automotive industry, government’s policy related to the automotive industry, technology, labor market and human resource development systems of the country. The internal factors included management, productive management, organizational strategies, leadership, organizational culture and philosophy of human resource development. These factors were affected to the different concept of human resources development -the traditional human resource development and the strategies of human resource development. The organization focuses on human resources as intellectual capital and uses the strategies of human resource development in all development processes. The strategies of human resource development will enhance the ability of human resources in the organization and the country.

Keywords: human resource development strategy, automotive industry, eco-cars, ASEAN

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Authors: Jerry John T. M., Sylas V. P., Shijo Joy

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Hydrogen is the most essential gas that can be used for many purposes. During the production of hydrogen using raw materials like Soil and leftover cooked rice water (kanjivellam), the major by-product formed is water. Soil is collected from three different places in kottayam district: Kallara, Meenachilar, and Athirampuzha. Collected samples are mixed with rice water and tested for traces of hydrogen using a biohydrogen sensor after 72 hours. The result was the presence of hydrogen in all the 3 samples. After streaking, PCR and gel electrophoresis detected the bacteria which produced the hydrogen. RGCB Thiruvananthapuram conducted the sequencing of the PCR resultant. And identified the bacterial strains. Five variants of Bacillus bacteria ( (1) Bacillus cereus strain JTM GenBank: OP278839.1 (2) Bacillus toyonensis strain JTM2 GenBank: OP278841.1 (3) Bacillus anthracis strain JTM_SR2989-3-R_H08 GenBank: OP278960.1 (4) Bacillus thuringiensis strain JRY1 GenBank: OP278976.1 (5) Bacillus anthracis strain JTM_SR2989-3-F_H07 GenBank: OP278959.1 ) are identified and successfully registered in NCBI Gen bank. These Bacillus bacteria are major types of Rhizobacteria that can form spores and can survive in the soil for a long time period under harsh environmental conditions. Also, plant growth is enhanced by PGPR (Plant growth promoting rhizobacteria) through the induction of systemic resistance, antibiosis, and competitive omission. The molecular sequencing was submitted to the NCBI Gen Bank, and the accession numbers were allotted for the bacterial cultures.

Keywords: bio hydrogen production, bacterial bio hydrogen production, plant related to bacillus bacteria., bacillus bacteria study

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Authors: Seyed Reza Aghili, Tahereh Shokohi, Shirin Sadat Hashemi Fesharaki, Mohammad Ali Boroumand, Bahar Salmanian

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Introduction: Intravenous catheter-associated fungal infection as nosocomial infection continue to be a deep problem among hospitalized patients, decreasing quality of life and adding healthcare costs. The capacity of catheters in the spread of candidemia in heart failure patients is obvious. The aim of this study was to evaluate the prevalence and genetic identification of Candida species in heart disorder patients. Material and Methods: This study was conducted in Tehran Hospital of Cardiology Center (Tehran, Iran, 2014) during 1.5 years on the patients hospitalized for at least 7 days and who had central or peripheral vein catheter. Culture of catheters, blood and skin of the location of catheter insertion were applied for detecting Candida colonies in 223 patients. Identification of Candida species was made on the basis of a combination of various phenotypic methods and confirmed by sequencing the ITS1-5.8S-ITS2 region amplified from the genomic DNA using PCR and the NCBI BLAST. Results: Of the 223 patients samples tested, we identified totally 15 Candida isolates obtained from 9 (4.04%) catheter cultures, 3 (1.35%) blood cultures and 2 (0.90%) skin cultures of the catheter insertion areas. On the base of ITS region sequencing, out of nine Candida isolates from catheter, 5(55.6%) C. albicans, 2(22.2%) C. glabrata, 1(11.1%) C. membranifiaciens and 1 (11.1%) C. tropicalis were identified. Among three Candida isolates from blood culture, C. tropicalis, C. carpophila and C. membranifiaciens were identified. Non-candida yeast isolated from one blood culture was Cryptococcus albidus. One case of C. glabrata and one case of Candida albicans were isolated from skin culture of the catheter insertion areas in patients with positive catheter culture. In these patients, ITS region of rDNA sequence showed a similarity between Candida isolated from the skin and catheter. However, the blood samples of these patients were negative for fungal growth. We report two cases of catheter-related candidemia caused by C. membranifiaciens and C. tropicalis on the base of genetic similarity of species isolated from blood and catheter which were treated successfully with intravenous fluconazole and catheter removal. In phenotypic identification methods, we could only identify C. albicans and C. tropicalis and other yeast isolates were diagnosed as Candida sp. Discussion: Although more than 200 species of Candida have been identified, only a few cause diseases in humans. There is some evidence that non-albicans infections are increasing. Many risk factors, including prior antibiotic therapy, use of a central venous catheter, surgery, and parenteral nutrition are considered to be associated with candidemia in hospitalized heart failure patients. Identifying the route of infection in candidemia is difficult. Non-albicans candida as the cause of candidemia is increasing dramatically. By using conventional method, many non-albicans isolates remain unidentified. So, using more sensitive and specific molecular genetic sequencing to clarify the aspects of epidemiology of the unknown candida species infections is essential. The positive blood and catheter cultures for candida isolates and high percentage of similarity of their ITS region of rDNA sequence in these two patients confirmed the diagnosis of intravenous catheter-associated candidemia.

Keywords: catheter-associated infections, heart failure patient, molecular genetic sequencing, ITS region of rDNA, Candidemia

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Authors: Diogo Ribeiro, Teresa Neto, Ricardo Santos, Maria Portela, Alexandra Trincão

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This article describes a set of innovating student recruitment strategies in a 1st cycle course of Civil Engineering, in particular the Civil Engineering Degree from the School of Engineering - Polytechnic of Porto (ISEP-PP). The strategies described were two-fold, targeting, for one, the increment on the number of admissions for the degree’s first year and two, promoting the re-entry of students who, for whatever reason, interrupted their studies. For the first objective, teacher-student binomials were set, whilst for the second, personalized contacts and assistance were provided. The main initiatives were promoted by the team of degree directors and were upheld with the participation and in consonance with the School’s external relations office. These initiatives were put forward as an attempt to minimize the impact of a national and international crisis on the AEC industry when the sustainability of the course was at risk. The implementation of these strategies was assessed on basis of a statistical analysis of the data collected from official sources and by surveys promoted. The results showed that the re-entry boost of former students, attending classes scattered on the three curricular years, secured registrations on some Curricular Units (UC’s) which more than doubled their numbers. Accompanied by a still incipient but regained interest on Civil Engineering it was possible in the short span of three years to reset the number of new students from less than 10 to the currently maximum allowed of 75, and so invert the tendency of an abrupt decline on the total number of students enrolled on the degree.

Keywords: civil engineering, monitoring, performance indicators, strategies, student recruitment

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Authors: Veronika Zivicova, Petr Broz, Zdenek Fik, Alzbeta Mifkova, Jan Plzak, Zdenek Cada, Herbert Kaltner, Jana Fialova Kucerova, Hans-Joachim Gabius, Karel Smetana Jr.

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The possibility to determine genome-wide expression profiles of cells and tissues opens a new level of analysis in the quest to define dysregulation in malignancy and thus identify new tumor markers. Toward this long-term aim, we here address two issues on this level for head and neck cancer specimen: i) defining profiles in different regions, i.e. the tumor, the transition zone and normal control and ii) comparing complete data sets for seven individual patients. Special focus in the flanking immunohistochemical part is given to adhesion/growth-regulatory galectins that upregulate chemo- and cytokine expression in an NF-κB-dependent manner, to these regulators and to markers of differentiation, i.e. keratins. The detailed listing of up- and down-regulations, also available in printed form (1), not only served to unveil new candidates for testing as marker but also let the impact of the tumor in the transition zone become apparent. The extent of interindividual variation raises a strong cautionary note on assuming uniformity of regulatory events, to be noted when considering therapeutic implications. Thus, a combination of test targets (and a network analysis for galectins and their downstream effectors) is (are) advised prior to reaching conclusions on further perspectives.

Keywords: galectins, genome scale sequencing, squamous cell carcinoma, transition zone

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Authors: Sirajoddeen Al-Ameen

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Researchers seek to introduce development leading to technologies that address environmental problems and learn how to interact with stakeholders, managers, and policymakers for appropriate actions. One of the greatest strategies that African countries need to consider in realizing sustainable development is effective, efficient, credible, and lasting environmental sustainability and ensuring that future generations have access to natural resources to live in a better way. Therefore the coordinated set of participatory and continuously improving processes of analysis, capacity, planning, and investment seeks to integrate the social and environmental objectives of society, and this is not given priority in Nigeria. Environmental sustainability is a field where people can understand the natural environment and public works for sustainable development. Sustainable development requires shifts from ordinary ways of doing things to modern ways of executing activities ranging from low to high productivity, the creation and adoption of new strategies, new skills, and knowledge. It ensures a developed world with a secure and healthy environment for all; human beings, animals, and plants alike. This paper is to carry out a review of various literature sources to ascertain the potential strategy of environment and sustainable development reform using the content analysis method to discuss the environmental strategies towards sustainable development in Nigeria. The objective of this paper is to enable Nigerians to understand and have an orientation on how to manage environmental resources and avoid environmental impact on the ecosystem, and also to find sustainable solutions for environmental issues without compromising economic development.

Keywords: development, environment, strategies, sustainable

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Authors: A. Attahiru, Rabi Abdullahi Danjuma, Fatima Bint

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Language and culture are two concepts which are closely related that one affects the other. This paper attempts to examine the definition of language and culture by discussing the relationship between them. The paper further presents some instructional strategies for the teaching of language and culture as well as the influence of culture on language. It also looks at its implication to language education and finally some recommendation and conclusion were drawn.

Keywords: culture, language, relationship, strategies, teaching

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Authors: Vun Yee Thien, Kenneth Francis Rodrigues, Clemente Michael Vui Ling Wong, Wilson Thau Lym Yong

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Transcriptomes associated with the process of photosynthesis have offered insights into the mechanism of gene regulation in terrestrial plants; however, limited information is available as far as macroalgae are concerned. This investigation aims to decipher the underlying mechanisms associated with photosynthesis in the red alga, Kappaphycus alvarezii, by performing a differential expression analysis on a de novo assembled transcriptomes. Comparative analysis of gene expression was designed to examine the alteration of light qualities and its effect on physiological mechanisms in the red alga. High-throughput paired-end RNA-sequencing was applied to profile the transcriptome of K. alvarezii irradiated with different wavelengths of light (blue 492-455 nm, green 577-492 nm and red 780-622 nm) as compared to the full light spectrum, resulted in more than 60 million reads individually and assembled using Trinity and SOAPdenovo-Trans. The transcripts were annotated in the NCBI non-redundant (nr) protein, SwissProt, KEGG and COG databases with a cutoff E-value of 1e-5 and nearly 30% of transcripts were assigned to functional annotation by Blast searches. Differential expression analysis was performed using edgeR. The DEGs were designated to six categories: BL (blue light) regulated, GL (green light) regulated, RL (red light) regulated, BL or GL regulated, BL or RL regulated, GL or RL regulated, and either BL, GL or RL regulated. These DEGs were mapped to terms in KEGG database and compared with the whole transcriptome background to search for genes that regulated by light quality. The outcomes of this study will enhance our understanding of molecular mechanisms underlying light-induced responses in red algae.

Keywords: de novo transcriptome sequencing, differential gene expression, Kappaphycus alvareziired, red alga

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Authors: Huajuan Shi

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Background: The biopsy of the preimplantation embryo may increase the potential risk and concern of embryo viability. Clinically discarded spent embryo medium (SEM) has entered the view of researchers, sparking an interest in noninvasive embryo screening. However, one of the major restrictions is the extremelty low quantity of cf-RNA, which is difficult to efficiently and unbiased amplify cf-RNA using traditional methods. Hence, there is urgently need to an efficient and low bias amplification method which can comprehensively and accurately obtain cf-RNA information to truly reveal the state of SEM cf-RNA. Result: In this present study, we established an agarose PCR amplification system, and has significantly improved the amplification sensitivity and efficiency by ~90 fold and 9.29 %, respectively. We applied agarose to sequencing library preparation (named AG-seq) to quantify and characterize cf-RNA in SEM. The number of detected cf-RNAs (3533 vs 598) and coverage of 3' end were significantly increased, and the noise of low abundance gene detection was reduced. The increasing percentage 5' end adenine and alternative splicing (AS) events of short fragments (< 400 bp) were discovered by AG-seq. Further, the profiles and characterizations of cf-RNA in spent cleavage medium (SCM) and spent blastocyst medium (SBM) indicated that 4‐mer end motifs of cf-RNA fragments could remarkably differentiate different embryo development stages. Significance: This study established an efficient and low-cost SEM amplification and library preparation method. Not only that, we successfully described the characterizations of SEM cf-RNA of preimplantation embryo by using AG-seq, including abundance features fragment lengths. AG-seq facilitates the study of cf-RNA as a noninvasive embryo screening biomarker and opens up potential clinical utilities of trace samples.

Keywords: cell-free RNA, agarose, spent embryo medium, RNA sequencing, non-invasive detection

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Authors: Manzurul Alam, John Griffiths, David Holloway, Megan Paull, Anne Clear

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Background: This paper investigates the nature of risk management practices in non-profit organizations. It is argued here that the risk exposure of these organizations has increased as a result of their entrepreneurial activities. This study explores how a particular non-profit organization formulates its risk strategies in the face funding restrictions. Design/Method/Approach: The study adopts a case study approach to report the results on how a non-profit organization diversifies its activities, tackles risks arising from such activities and improves performance. Results: The findings show that the organization made structural adjustments and leadership changes which helped to adjust their risk strategies. It also reports the organizational processes to deal with risks arising from both related and unrelated diversification strategies. Implications: Any generalization from this case example needs to be taken with caution as there are significant differences between non-profit organizations operating in different sectors. Originality: The paper makes a significant contribution to the non-profit literature by highlighting the diversification strategies along with risk performance.

Keywords: risk management, performance management, non-profit organizations, financial management

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Authors: Athena Pedro, Gina Stockingt

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This study aimed to explore current management strategies used by Grade 1 educators working with learners presenting with Attention Deficit Hyperactivity Disorder (ADHD) symptoms in mainstream schools in the Western Cape. A sample of grade 1 educators were selected for the study. The sample comprised of twelve grades 1 educators from four local schools in the Western Cape. All twelve educators were individually interviewed and discussed the management strategies used in the classroom when working with learner presenting with ADHD symptoms. The data was analysed qualitatively with a focus in identifying, sorting and analyse meaning according to the subjective perception, understanding and behaviour of the grade 1 educators within their context. Furthermore, the social, cultural, political and physical environment of the participants were taken into consideration to explore and interpret the link between these elements. The findings were as follows: many educators felt that they did not receive enough training on Attention Deficit Hyperactivity Disorder, therefore lacking knowledge on how to apply management strategies to address this. Managing a diverse range of learners, lack of resources, lack of parental involvement, lack of assistance in the classroom, as well as distracted and disorganised children posed as challenges for educators working with learners presenting with Attention Deficit Hyperactivity Disorder symptoms.

Keywords: ADHD, Grade 1 educators, Learners, Management strategies

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Authors: Charity Okeke, Elizabeth Venter

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Verbal discipline is one of the most regularly used disciplinary strategies to deal with classroom misconduct in schools globally. This study provides effective verbal discipline strategies to deal with classroom misconduct in primary schools. The study was qualitative research of ten teachers that took place in two South African primary schools. Data were collected through recorded semi-structured face-to-face interviews. The interview recordings were transcribed and analysed using content analysis. Findings from the study show that talking to learners in a calm and polite manner, raising one’s voice occasionally to show seriousness and disapproval of misconduct, engaging misbehaved learners in private talk to understand the reasons behind their unruly actions, verbal praise and rewards are effective in dealing with classroom misconduct. The study recommends that teachers should avoid shouting at learners and talk to them politely to get them to behave well in class. Teachers should avoid embarrassing misbehaving learners in the classroom but engage them privately to understand the reasons behind their unruly activities. Teachers should also use verbal praise and rewards such as well-done stickers to motivate learners to keep behaving well, as reinforcement is very important in the classroom. The study concludes that the verbal disciplining strategies mentioned above are effective in achieving a conducive teaching and learning atmosphere in the classroom.

Keywords: classroom discipline, classroom misconduct, verbal discipline, verbal discipline strategies

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Authors: Shantanu Prakash, Suruchi Shukla, Amita Jain

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Introduction: The hepatitis C virus (HCV) is a major public health problem and a leading cause of chronic liver disease. Injection drug use and individuals receiving blood and blood products are the primary modes of HCV transmission. Our study aims to establish the prevalent genotypes/ subtypes of HCV circulating in Uttar Pradesh, North India, as reported from a tertiary care hospital. Methods: It is a retrospective observational analysis of consecutive 404 HCV RNA positive cases referred to our hospital during September 2014 to April 2017. The study was approved by an institutional ethics committee. Written informed consent was taken from each participant. Clinical and demographic details of these patients were recorded using predesigned questionnaires. All the laboratory testing was carried on stored serum sample of enrolled cases. Genotyping of all 404 strains was done by Sanger’s sequencing of the core region. The phylogenetic analysis of 179 HCV strains with high -quality sequencing data was performed. Results: The distribution of prevalent genotypes/ subtypes as noted in the present study was; Genotype (GT)1a [n-101(25%)], GT1b [n-12(2.9%)], GT1c [1(0.25%)], GT3a [275(68.07%)], GT3b [9(2.2%)], GT3g [2(0.49%)], GT3i [3(0.74%)], and GT4a [1(0.24%)]. HCV genotypes GT2, GT5 and GT6 were not detected from our region. Sequence analysis showed high genotypic variability in HCV GT3. Phylogenetic analysis showed that HCV GT3 and GT1 circulating in our region were related to Indian strains reported earlier. Conclusions: HCV genotypes 3a and 1a are commonest circulating genotypes in Uttar Pradesh (UP), India.

Keywords: Hepatitis C virus, genetic variation, bioinformatics, genotype, HCV

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Authors: S. Hannah Elizabeth, A. Panneerselvam

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Objective: The main objective was to evaluate the degradative properties of Bacillus cereus sp TUHP2 isolated from TNT-Polluted soils in the Vellore District, Tamil Nadu, India. Methods: Among the 3 bacterial genera isolated from different soil samples, one potent TNT degrading strain Bacillus cereus sp TUHP2 was identified. The morphological, physiological and the biochemical properties of the strain Bacillus cereus sp TUHP2 was confirmed by conventional methods and genotypic characterization was carried out using 16S r-DNA partial gene amplification and sequencing. The broken down by products of DNT in the extract was determined by Gas Chromatogram- Mass spectrometry (GC-MS). Supernatant samples from the broth studied at 24 h interval were analyzed by HPLC analysis and the effect on various nutritional and environmental factors were analysed and optimized for the isolate. Results: Out of three isolates one strain TUHP2 were found to have potent efficiency to degrade TNT and revealed the genus Bacillus. 16S rDNA gene sequence analysis showed highest homology (98%) with Bacillus cereus and was assigned as Bacillus cereus sp TUHP2. Based on the energy of the predicted models, the secondary structure predicted by MFE showed the more stable structure with a minimum energy. Products of TNT Transformation showed colour change in the medium during cultivation. TNT derivates such as 2HADNT and 4HADNT were detected by HPLC chromatogram and 2ADNT, 4ADNT by GC/MS analysis. Conclusion: Hence this study presents the clear evidence for the biodegradation process of TNT by strain Bacillus cereus sp TUHP2.

Keywords: bioremediation, biodegradation, biotransformation, sequencing

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Authors: Amir Salamatzade, Marhamet HematPour

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Due to the increasing importance of psychological factors in the incidence and exacerbation of chronic diseases such as multiple sclerosis, the aim of this study was to determine the difference between emotional regulation strategies and psychological symptoms in patients with multiple sclerosis and normal people. The research method was causal-comparative (post-event). The statistical population of this research included all patients with multiple sclerosis referred to the MS Association of Rasht in the first quarter of 2021, approximately 350 people. The study sample also included 120 people (60 patients with multiple sclerosis and 60 normal people) who were selected by the available sampling method and completed the emotional regulation and anxiety, depression, and stress Lavibund and Lavibund (1995) questionnaires. Data were analyzed using an independent t-test and multivariate variance analysis. The results showed that there was a significant difference between the mean of emotional regulation strategies and the components of emotional reassessment and emotional inhibition between the two groups of patients with multiple sclerosis and normal individuals (p < 0.01). There is a significant difference between the mean of psychological symptoms and the components of depression, anxiety, and stress in the two groups of patients with multiple sclerosis and normal individuals. (p < 0.01). Based on this, it can be concluded that patients with multiple sclerosis have lower levels of emotional regulation strategies and higher levels of psychological symptoms than normal individuals.

Keywords: emotional regulation strategies, psychological symptoms, multiple sclerosis, normal Individuals

Procedia PDF Downloads 191

Authors: Fahimeh Palizban, Farshad Noravesh, Amir Hossein Saeidian, Mahya Mehrmohamadi

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In the recent decade, the emergence of liquid biopsy has significantly improved cancer monitoring and detection. Dying cells, including those originating from tumors, shed their DNA into the blood and contribute to a pool of circulating fragments called cell-free DNA. Accordingly, identifying the tissue origin of these DNA fragments from the plasma can result in more accurate and fast disease diagnosis and precise treatment protocols. Open chromatin regions are important epigenetic features of DNA that reflect cell types of origin. Profiling these features by DNase-seq, ATAC-seq, and histone ChIP-seq provides insights into tissue-specific and disease-specific regulatory mechanisms. There have been several studies in the area of cancer liquid biopsy that integrate distinct genomic and epigenomic features for early cancer detection along with tissue of origin detection. However, multimodal analysis requires several types of experiments to cover the genomic and epigenomic aspects of a single sample, which will lead to a huge amount of cost and time. To overcome these limitations, the idea of predicting OCRs from WGS is of particular importance. In this regard, we proposed a computational approach to target the prediction of open chromatin regions as an important epigenetic feature from cell-free DNA whole genome sequence data. To fulfill this objective, local sequencing depth will be fed to our proposed algorithm and the prediction of the most probable open chromatin regions from whole genome sequencing data can be carried out. Our method integrates the signal processing method with sequencing depth data and includes count normalization, Discrete Fourie Transform conversion, graph construction, graph cut optimization by linear programming, and clustering. To validate the proposed method, we compared the output of the clustering (open chromatin region+, open chromatin region-) with previously validated open chromatin regions related to human blood samples of the ATAC-DB database. The percentage of overlap between predicted open chromatin regions and the experimentally validated regions obtained by ATAC-seq in ATAC-DB is greater than 67%, which indicates meaningful prediction. As it is evident, OCRs are mostly located in the transcription start sites (TSS) of the genes. In this regard, we compared the concordance between the predicted OCRs and the human genes TSS regions obtained from refTSS and it showed proper accordance around 52.04% and ~78% with all and the housekeeping genes, respectively. Accurately detecting open chromatin regions from plasma cell-free DNA-seq data is a very challenging computational problem due to the existence of several confounding factors, such as technical and biological variations. Although this approach is in its infancy, there has already been an attempt to apply it, which leads to a tool named OCRDetector with some restrictions like the need for highly depth cfDNA WGS data, prior information about OCRs distribution, and considering multiple features. However, we implemented a graph signal clustering based on a single depth feature in an unsupervised learning manner that resulted in faster performance and decent accuracy. Overall, we tried to investigate the epigenomic pattern of a cell-free DNA sample from a new computational perspective that can be used along with other tools to investigate genetic and epigenetic aspects of a single whole genome sequencing data for efficient liquid biopsy-related analysis.

Keywords: open chromatin regions, cancer, cell-free DNA, epigenomics, graph signal processing, correlation clustering

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Authors: Yu Guang

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“Case studies are the preferred strategy when ‘how’ or ‘why’ questions are being posed.” Therefore, the study is based on two cases: strategy performed in JingNan War and by NIKE. The two samples are chosen as they are of comparability. Data are gathered and PEST and SWOT are used as analysis models to examine their strategic employment in order that the answer to brilliant strategies in variety is found. The niche strategy has been used in the past and present, in the battle fields and business. The homogeneity among diversity is the skill of performing strategies.

Keywords: challenger, homogeneity, managing diversity, niche strategy

Procedia PDF Downloads 504