Search results for: high temperature tribology

Authors: Sonja Djilas, Gordana Ćetković, Jasna Čanadanović-Brunet, Vesna Tumbas Šaponjac, Slađana Stajčić, Jelena Vulić, Milica Vinčić

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In recent years, interest in food rich in bioactive compounds, such as polyphenols, increased the advantages of the functional food products. Bioactive components help to maintain health and prevention of diseases such as cancer, cardiovascular and many other degenerative diseases. Recent research has shown that the fruit pomace, a byproduct generated from the production of juice, can be a potential source of valuable bioactive compounds. The use of fruit industrial waste in the processing of functional foods represents an important new step for the food industry. Sour cherries have considerable nutritional, medicinal, dietetic and technological value. According to the production volume of cherries, Serbia ranks seventh in the world, with a share of 7% of the total production. The use of sour cherry pomace has so far been limited to animal feed, even though it can be potentially a good source of polyphenols. For this study, local variety of sour cherry cv. ‘Feketićka’ was chosen for its more intensive taste and deeper red color, indicating high anthocyanin content. The contents of total polyphenols, flavonoids and anthocyanins, as well as radical scavenging activity on DPPH radicals and reducing power of sour cherry juice and pomace were compared using spectrophotometrical assays. According to the results obtained, 66.91% of total polyphenols, 46.77% of flavonoids, 46.77% of total anthocyanins and 47.88% of anthocyanin monomers from sour cherry fruits have been transferred to juice. On the other hand, 29.85% of total polyphenols, 33.09% of flavonoids, 53.23% of total anthocyanins and 52.12% of anthocyanin monomers remained in pomace. Regarding radical scavenging activity, 65.51% of Trolox equivalents from sour cherries were exported to juice, while 34.49% was left in pomace. However, reducing power of sour cherry juice was much stronger than pomace (91.28% and 8.72% of Trolox equivalents from sour cherry fruits, respectively). Based on our results it can be concluded that sour cherry pomace is still a rich source of natural antioxidants, especially anthocyanins with coloring capacity, therefore it can be used for dietary supplements development and food fortification.

Keywords: antioxidants, polyphenols, pomace, sour cherry

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Authors: Hillary Mwongyera

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The Semliki basin has become a frontier for petroleum exploration in recent years. Exploration efforts have resulted into extensive seismic data acquisition and drilling of three wells namely; Turaco 1, Turaco 2 and Turaco 3. A petrophysical analysis of the Turaco 1 well was carried out to identify two reservoir zones on which AVO modeling was performed. A combination of seismic modeling and rock physics modeling was applied during reservoir characterization and monitoring to determine variations of seismic responses with amplitude characteristics. AVO intercept gradient analysis applied on AVO synthetic CDP gathers classified AVO anomalies associated with both reservoir zones as Class 1 AVO anomalies. Fluid replacement modeling was carried out on both reservoir zones using homogeneous mixing and patchy saturation patterns to determine effects of fluid substitution on rock property interactions. For both homogeneous mixing and saturation patterns, density (ρ) showed an increasing trend with increasing brine substitution while Shear wave velocity (Vs) decreased with increasing brine substitution. A study of compressional wave velocity (Vp) with increasing brine substitution for both homogeneous mixing and patchy saturation gave quite interesting results. During patchy saturation, Vp increased with increasing brine substitution. During homogeneous mixing however, Vp showed a slightly decreasing trend with increasing brine substitution but increased tremendously towards and at full brine saturation. A sensitivity analysis carried out showed that density was a very sensitive rock property responding to brine saturation except at full brine saturation during homogeneous mixing where Vp showed greater sensitivity with brine saturation. Rock physics modeling was performed to predict diagnostics of reservoir quality using an inverse deterministic approach which showed low shale content and a high degree of shale stiffness within reservoir zones.

Keywords: Amplitude Versus Offset (AVO), fluid replacement modelling, reservoir characterization, AVO attributes, rock physics modelling, reservoir monitoring

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Authors: Afrouz Yousefi, Mohtada Sadrzadeh

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The widespread presence of poly- and perfluoroalkyl substances (PFAS) poses a significant concern due to their ability to accumulate in living organisms and their persistence in the environment, thanks to their robust carbon-fluorine (C-F) bonds, which require substantial energy to break (485 kJ/mol). The prevalence of toxic PFAS compounds can be highly detrimental to ecosystems, wildlife, and human health. Ongoing efforts are dedicated to investigating methods for fully breaking down and eliminating PFAS from the environment. Among the various techniques employed, advanced oxidation processes have shown promise in completely breaking down emerging contaminants in wastewater. However, the drawback lies in the relatively slow reaction rates of these processes and the substantial energy input required, which currently impedes their widespread commercial adoption. We developed a hybrid process, comprising electro-Fenton as an advanced oxidation process and membrane distillation, to simultaneously degrade organic PFAS pollutants and extract pure water from the mixture. In this study, environmentally persistent perfluorooctanoic acid (PFOA), as an emerging contaminant, was used to study the effectiveness of the electro-Fenton/membrane distillation hybrid system. The PFOA degradation studies were conducted in two modes: electro-Fenton and electro-Fenton coupled with membrane distillation. High-performance liquid chromatography with ultraviolet detection (HPLC-UV), ion-chromatography (measuring fluoride ion concentration), total organic carbon (TOC) decay, mineralization current efficiency (MCE), and specific energy consumption (SEC) were evaluated for a single EF and hybrid EF-MD processes. In contrast to a single EF reaction, TOC decay improved significantly in the EF-MD process. Overall, the MCE of hybrid processes surpassed 100% while it remained under 50% for a single EF reaction. Calculations of specific energy consumption (SEC) demonstrated a substantial decrease of nearly one-third in energy usage when integrating the EF reaction with the MD process.

Keywords: water treatment, PFAS, membrane distillation, electro-Fenton, advanced oxidation

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Authors: Timma Reddy, Srikonda Ramesh

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India has been traditionally vulnerable to natural disasters such as Floods, droughts, cyclones, earthquakes and landslides. It has become a recurrent phenomenon as observed in last five decades. The survey indicates that about 60% of the landmass is prone to earthquakes of various intensities; over 40 million hectares is prone to floods; about 8% of the total area is prone to cyclones and 68% of the area is susceptible to drought. Climate change is likely to be perceived through experience of extreme weather events. There is growing societal concern about climate change, given the potential impacts of associated natural hazards such as cyclones, flooding, earthquakes, landslides etc, hence it is essential and crucial to strengthening our settlements to respond to such calamities. So, the research paper focus is to analyze the effective planning strategy/mechanism to integrate disaster mitigation measures in coastal regions in general and Capital Region of Andhra Pradesh in particular. The basic hypothesis is to govern the appropriate special planning considerations would facilitate to have organized way of protective life and properties from natural disasters. And further to integrate the infrastructure planning with conscious direction would provide an effective mitigations measures. It has been planned and analyzed to Vijayawada city with conscious land use planning with reference to space syntax trajectory in accordance to required social infrastructure such as health facilities, institution areas and recreational and other open spaces. It has been identified that the geographically ideal location with reference to the population densities based on GIS tools the properness strategies can be effectively integrated to protect the life and to save the properties by means of reducing the damage/impact of natural disasters in general earth quake/cyclones or floods in particularly.

Keywords: modular, trajectories, social infrastructure, evidence based syntax, drills and equipments, GIS, geographical micro zoning, high resolution satellite image

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Authors: Khadija Refouh

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Culture bound-expressions have been a bottleneck for Natural Language Processing (NLP) and comprehension, especially in the case of machine translation (MT). In the last decade, the field of machine translation has greatly advanced. Neural machine translation NMT has recently achieved considerable development in the quality of translation that outperformed previous traditional translation systems in many language pairs. Neural machine translation NMT is an Artificial Intelligence AI and deep neural networks applied to language processing. Despite this development, there remain some serious challenges that face neural machine translation NMT when translating culture bounded-expressions, especially for low resources language pairs such as Arabic-English and Arabic-French, which is not the case with well-established language pairs such as English-French. Machine translation of opaque idioms from English into French are likely to be more accurate than translating them from English into Arabic. For example, Google Translate Application translated the sentence “What a bad weather! It runs cats and dogs.” to “يا له من طقس سيء! تمطر القطط والكلاب” into the target language Arabic which is an inaccurate literal translation. The translation of the same sentence into the target language French was “Quel mauvais temps! Il pleut des cordes.” where Google Translate Application used the accurate French corresponding idioms. This paper aims to perform NMT experiments towards better translation of opaque idioms using high quality clean multilingual corpus. This Corpus will be collected analytically from human generated idiom translation. AutoML translation, a Google Neural Machine Translation Platform, is used as a custom translation model to improve the translation of opaque idioms. The automatic evaluation of the custom model will be compared to the Google NMT using Bilingual Evaluation Understudy Score BLEU. BLEU is an algorithm for evaluating the quality of text which has been machine-translated from one natural language to another. Human evaluation is integrated to test the reliability of the Blue Score. The researcher will examine syntactical, lexical, and semantic features using Halliday's functional theory.

Keywords: multilingual corpora, natural language processing (NLP), neural machine translation (NMT), opaque idioms

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Authors: John Masani Nduko, Joseph Wafula Matofari

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Many spontaneously fermented milk products are produced in Kenya, where they are integral to the human diet and play a central role in enhancing food security and income generation via small-scale enterprises. Fermentation enhances product properties such as taste, aroma, shelf-life, safety, texture, and nutritional value. Some of these products have demonstrated therapeutic and probiotic effects although recent reports have linked some to death, biotoxin infections, and esophageal cancer. These products are mostly processed from poor quality raw materials under unhygienic conditions resulting to inconsistent product quality and limited shelf-lives. Though very popular, research on their processing technologies is low, and none of the products has been produced under controlled conditions using starter cultures. To modernize the processing technologies for these products, our study aims at describing the microbiology and biochemistry of a representative Kenyan spontaneously fermented milk product, Mursik using modern biotechnology (DNA sequencing) and their chemical composition. Moreover, co-creation processes reflecting stakeholders’ experiences on traditional fermented milk production technologies and utilization, ideals and senses of value, which will allow the generation of products based on common ground for rapid progress will be discussed. Knowledge of the value of clean starting raw material will be emphasized, the need for the definition of fermentation parameters highlighted, and standard equipment employment to attain controlled fermentation discussed. This presentation will review the available information regarding traditional fermented milk (Mursik) and highlight our current research work on the application of molecular approaches (metagenomics) for the valorization of Mursik production process through starter culture/ probiotic strains isolation and identification, and quality and safety aspects of the product. The importance of the research and future research areas on the same subject will also be highlighted.

Keywords: lactic acid bacteria, high throughput biotechnology, spontaneous fermentation, Mursik

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Authors: Rekha M. Y., Punith Kumar, Anshul Kamboj, Chandan Srivastava

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Coatings plays an important role in providing protection for a substrate and in improving the surface quality. Graphene/graphene oxide (GO) using in coating systems provides an environmental friendly solution towards protection against corrosion. Issues such as, lack of scale, high cost, low quality limits the practical application of graphene/GO as corrosion resistant coating material. One other way to employ these materials for corrosion protection is to incorporate them into coatings that are conventionally used for corrosion protection. Due to the extraordinary properties of graphene/GO, it has been demonstrated that the coatings containing graphene/GO are more corrosion resistant than pure metal/alloy coatings. In the present work, Cr-graphene and SnZn-GO composite coatings were investigated in enhancing the corrosion resistant property when compared to pure Cr coating and pure SnZn coating respectively. All the coatings were electrodeposited over mild-steel substrate. Graphene and GO were synthesized by electrochemical exfoliation method and modified Hummers’ method respectively. In Cr coatings, the microstructural study revealed that the addition of formic acid in the coatings reduced the number of cracks in the coatings. Further addition of graphene in Cr coating enhanced the Cr coating’s morphology. Chemically synthesized ZnO nanoparticles were also embedded in the as-deposited Cr and Cr-graphene coatings to enhance the adhesion of the coating, to improve the surface finish and to increase the corrosion resistant property of the coatings. Diffraction analysis revealed that the addition of graphene also altered the texture of the Cr coatings. In SnZn alloy coatings, the morphological and topographical characterization revealed that the relative smoothness and compactness of the coatings increased with increase in the addition of GO in the coatings. The microstructural investigation revealed large-scale segregation of Zn-rich and Sn-rich phases in the pure SnZn coating. However, in SnZn-GO composite coating the uniform distribution of Zn phase in the Sn-rich matrix was observed. This distribution caused the early and uniform formation of ZnO, which is the corrosion product, yielding better corrosion resistance for the SnZn-GO composite coatings as compared to pure SnZn coating. A significant improvement in corrosion resistance in terms of reduction in corrosion current and corrosion rate and increase in the polarization resistance was observed in Cr coating containing graphene and in SnZn coatings containing GO.

Keywords: coatings, corrosion, electrodeposition, graphene, graphene-oxide

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Authors: Bela Siska Afrida, Wisnu Barlianto, Desy Wulandari, Ery Olivianto

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Background: Allergic asthma, caused by IgE-mediated allergic reactions, remains a global health issue with high morbidity and mortality rates. Immunotherapy is the only etiology-based approach to treating asthma, but no standard biomarkers have been established to evaluate the therapy’s effectiveness. This study aims to determine the correlation between the ratios of serum levels of HDM-specific IgE/total IgE and Asthma Control Test (ACT) score as a biomarker of the response to immunotherapy in pediatric allergic asthma patients. Patient and Methods: This retrospective cohort study involved 26 pediatric allergic asthma patients who underwent HDM-specific subcutaneous immunotherapy for 14 weeks at the Pediatric Allergy Immunology Outpatient Clinic at Saiful Anwar General Hospital, Malang. Serum levels of HDM-Specific IgE and Total IgE were measured before and after immunotherapy using Chemiluminescence Immunoassay and Enzyme-linked Immunosorbent Assay (ELISA) method. Changes in asthma control were assessed using the ACT score. The Wilcoxon Signed Ranked Test and Spearman correlation test were used for data analysis. Results: There were 14 boys and 12 girls with a mean age of 6.48 ± 2.54 years. The study showed a significant decrease in serum HMD-specific levels before immunotherapy [9.88 ± 5.74 kuA/L] compared to those of 14 weeks after immunotherapy [4.51 ± 3.98 kuA/L], p = 0.000. Serum Total IgE levels significant decrease before immunotherapy [207.6 ± 120.8IU/ml] compared to those of 14 weeks after immunotherapy [109.83 ± 189.39 IU/mL], p = 0.000. The ratios of serum HDM-specific IgE/total IgE levels significant decrease before immunotherapy [0.063 ± 0.05] compared to those of 14 weeks after immunotherapy [0.041 ± 0.039], p = 0.012. There was also a significant increase in ACT scores before and after immunotherapy (each 15.5 ± 1.79 and 20.96 ± 2.049, p = 0.000). The correlation test showed a weak negative correlation between the ratios of HDM-specific IgE/total IgE levels and ACT score (p = 0.034 and r = -0.29). Conclusion: In conclusion, this study showed that a decrease in HDM-specific IgE levels, total IgE levels, and HDM-specific IgE/total IgE ratios, and an increase in ACT score, was observed after 14 weeks of HDM-specific subcutaneous immunotherapy. The weak negative correlation between the HDM-specific IgE/total IgE ratio and the ACT score suggests that this ratio can serve as a potential biomarker of the effectiveness of immunotherapy in treating pediatric allergic asthma patients.

Keywords: HDM-specific IgE/total IgE ratio, ACT score, immunotherapy, allergic asthma

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Authors: Lokvendra S. Budania, Yogesh K Gaude, Vamsidhar Chamala

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Introduction: Congenitally corrected transposition of great arteries (CCTGA) is a complex congenital heart disease where there are both atrioventricular and ventriculoarterial discordances, usually accompanied by other cardiovascular malformations. Case Report: A 24-year-old primigravida known case of CCTGA at 37 weeks of gestation was referred to our hospital for safe delivery. Her electrocardiogram showed HR-40/pm, echocardiography showed Ejection Fraction of 65% and CCTGA. Temporary pacemaker was inserted by cardiologist in catheterization laboratory, before giving trial of labour in view of complete heart block. She was planned for normal delivery, but emergency Caesarean section was planned due to non-reassuring foetal Cardiotocography Pre-op vitals showed PR-50 bpm with temporary pacemaker, Blood pressure-110/70 mmHg, SpO2-99% on room air. Nil per oral was inadequate. Patency of two peripheral IV cannula checked and left radial arterial line secured. Epidural Anaesthesia was planned, and catheter was placed at L2-L3. Test dose was given, Anaesthesia was provided with 5ml + 5ml of 2% Lignocaine with 25 mcg Fentanyl and further 2.5Ml of 0.5% Bupivacaine was given to achieve a sensory level of T6. Cesarean section was performed and baby was delivered. Cautery was avoided during this procedure. IV Oxytocin (15U) was added to 500 mL of ringer’s lactate. Hypotension was treated with phenylephrine boluses. Patient was shifted to post-operative care unit and later to high dependency unit for monitoring. Post op vitals remained stable. Temporary pacemaker was removed after 24 hours of surgery. Her post-operative period was uneventful and discharged from hospital. Conclusion: Rare congenital cardiac disorders require detail knowledge of pathophysiology and associated comorbidities with the disease. Meticulously planned and carefully titrated neuraxial techniques will be beneficial for such cases.

Keywords: congenitally corrected transposition of great arteries, complete heart block, emergency LSCS, epidural anaesthesia

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Authors: Gabriela Lucas Sanchez

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The contemporary housing industry is dominated by tract houses, which prioritize uniformity and cost-efficiency over environmental and ecological considerations. However, as the world faces the growing challenges of climate change and resource depletion, there is an urgent need to rethink the residential paradigm. This essay explores how regenerative practices can be integrated into standard residential designs to create a shift that reduces the environmental impact of housing and actively contributes to ecological health. Passive sustainable practices, such as passive solar design, natural ventilation, and the use of energy-efficient materials, aim to maximize resource use efficiency, minimize waste, and create healthy living environments. Regenerative practices, on the other hand, go beyond sustainability to work in harmony with natural systems, actively restoring and enriching the environment. Integrating these two approaches can redefine the residential paradigm, creating homes that reduce harm and positively impact the local ecosystem. The essay begins by exploring the principles and benefits of passive sustainable practices, discussing how they can reduce energy consumption and improve indoor environmental quality in standardized housing. Passive sustainability minimizes energy consumption through strategic design choices, such as optimizing building orientation, utilizing natural ventilation, and incorporating high-performance insulation and glazing. However, while sustainability efforts have been important steps in the right direction, a more holistic, regenerative approach is needed to address the root causes of environmental degradation. Regenerative development and design seek to go beyond simply reducing negative impacts, instead aiming to create built environments that actively contribute to restoring and enhancing natural systems. This shift in perspective is critical, as it recognizes the interdependence between human settlements and the natural world and the potential for buildings to serve as catalysts for positive change.

Keywords: passive sustainability, regenerative architecture, residential architecture, community

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Authors: Atiya Khan

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Recent research on the condition of school education in India has reaffirmed the importance of quality teacher professional development, especially in light of the rapid changes in teaching methods, learning theories, curriculum, and major shifts in information and technology that education systems are experiencing around the world. However, the quality of programs of teacher professional development in India is often uneven, in some cases non-existing. The educational authorities in India have long recognized this and have developed a range of programs to assist in-service teacher education. But, these programs have been mostly inadequate at improving the quality of teachers in India. Policy literature and reports indicate that the unevenness of these programs and more generally the lack of quality teacher professional development in India are due to factors such as a large number of teachers, budgetary constraints, top-down decision making, teacher overload, lack of infrastructure, and little or no follow-up. The disparity between the government stated goals for quality teacher professional development in India and its inability to meet the learning needs of teachers suggests that new interventions are needed. The realization that globalization has brought about an increase in the social, cultural, political and economic interconnectedness between countries has also given rise to transnational opportunities for education systems, such as India’s, aiming to build their capacity to support teacher professional development. Moreover, new developments in communication technologies seem to present a plausible means of achieving high-quality professional development for teachers through the creation of social learning spaces, such as transnational learning networks. This case study investigates the potential of one such transnational learning network to support the quality of teacher professional development in India, namely the Australia-Asia BRIDGE School Partnerships Project. It explores the participation of some fifteen teachers and their principals from BRIDGE participating schools in Delhi region of India; focusing on their professional development expectations from the BRIDGE program and account for their experiences in the program, in order to determine the program’s potential for the professional development of teachers in this study.

Keywords: case study, Australia-Asia BRIDGE Project, teacher professional development, transnational learning networks

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Authors: B. González-Yebra, B. Flores-Nieto, P. Aguilar-Salinas, M. Preciado Puga, A. L. González Yebra

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The monitoring of populations occupationally exposed to organic solvents has been an important issue for several shoe factories for years since the International Agency for Research on Cancer (IARC) has advised on the potential carcinogenic risk of chemicals related to occupations. In order to detect if exposition to organic solvents used in some Mexican shoe factories contributes to oral carcinogenesis, we performed monitoring in three factories. Occupational exposure was determined by using monitors 3M. Organic solvents were assessed by gas chromatography. Then, we recruited 30 shoe workers (30.2 ± 8.4 years) and 10 unexposed subjects (43.3 ± 11.2 years) for the micronuclei (MN) test and immunodetection of some cancer biomarkers (ki-67, p16, caspase-3) in scraped oral epithelial cells. Monitored solvents detected were acetone, benzene, hexane, methyl ethyl ketone, and toluene in acceptable levels according to Official Mexican Norm. We found by MN test higher incidence of nuclear abnormalities (karyorrhexis, pycnosis, karyolysis, condensed chromatin, and macronuclei) in the exposed group than the non-exposed group. On the other hand, we found, a negative expression for Ki-67 and p16 in exfoliated epithelial cells from exposed and non-exposed to organic solvents subjects. Only caspase-3 shown positive patter of expression in 9/30 (30%) exposed subjects, and we detected high karyolysis incidence in caspase-3 subjects (p = 0.021). The absence of expression of proliferation markers p16 and ki-67 and presence of apoptosis marker caspase-3 are indicating the absence of malignancy in oral epithelial cells and low risk for oral cancer. It is a fact that the MN test is a very effective method to detect nuclear abnormalities in exfoliated buccal cells from subjects that have been exposed to organic solvents in the shoe industry. However, in order to improve this tool and predict cancer risk is it is mandatory to implement complementary tests as other biomarkers that can help to detect malignancy in individuals occupationally exposed.

Keywords: biomarkers, oral cancer, organic solvents, shoe industries

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Authors: Dar-Bin Shieh, Gwo-Bin Lee, Chen-Ming Chang, Chen Sheng Yeh, Chih-Chia Huang, Tsung-Ju Li

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Mitochondrial defects have a significant impact in many human diseases and aging associated phenotypes. The pathogenic mitochondrial DNA (mtDNA) mutations are diverse and usually present as heteroplasmic. mtDNA 4977bps deletion is one of the common mtDNA defects, and the ratio of mutated versus normal copy is significantly associated with clinical symptoms thus their quantitative detection has become an important unmet needs for advanced disease diagnosis and therapeutic guidelines. This study revealed a Micro-electro-mechanical-system (MEMS) enabled automatic microfluidic chip that only required minimal sample. The system integrated multiple laboratory operation steps into a Lab-on-a-Chip for high-sensitive and prompt measurement. The entire process including magnetic nanoparticle based mtDNA extraction in chip, mutation selective photonic DNA cleavage, and nanoparticle accelerated photonic quantitative polymerase chain reaction (qPCR). All subsystems were packed inside a miniature three-dimensional micro structured system and operated in an automatic manner. Integration of magnetic beads with microfluidic transportation could promptly extract and enrich the specific mtDNA. The near infrared responsive magnetic nanoparticles enabled micro-PCR to be operated by pulse-width-modulation controlled laser pulsing to amplify the desired mtDNA while quantified by fluorescence intensity captured by a complementary metal oxide system array detector. The proportions of pathogenic mtDNA in total DNA were thus obtained. Micro capillary electrophoresis module was used to analyze the amplicone products. In conclusion, this study demonstrated a new magnetophotonic based qPCR MEMS system that successfully detects and quantify specific disease related DNA mutations thus provides a promising future for rapid diagnosis of mitochondria diseases.

Keywords: mitochondrial DNA, micro-electro-mechanical-system, magnetophotonics, PCR

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Authors: Julio Jesus Salazar, Max Jesus De Lama

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The challenges of water management are aggravated by global change, which implies high complexity and associated uncertainty; water management is difficult because water networks cross domains (natural, societal, and political), scales (space, time, jurisdictional, institutional, knowledge, etc.) and levels (area: patches to global; knowledge: a specific case to generalized principles). In this context, we need to apply natural and non-natural measures to manage water and soil. The Basin Management Methodology considers multifunctional measures of natural water retention and erosion control and soil formation to protect water resources and address the challenges related to the recovery or conservation of the ecosystem, as well as natural characteristics of water bodies, to improve the quantitative status of water bodies and reduce vulnerability to floods and droughts. This method of water management focuses on the positive impacts of the chemical and ecological status of water bodies, restoration of the functioning of the ecosystem and its natural services; thus, contributing to both adaptation and mitigation of climate change. This methodology was applied in 7 interventions in the sub-basin of the Shullcas River in Huancayo-Junín-Peru, obtaining great benefits in the framework of the participation of alliances of actors and integrated planning scenarios. To implement the methodology in the sub-basin of the Shullcas River, a process called Climate Smart Territories (CST) was used; with which the variables were characterized in a highly complex space. The diagnosis was then worked using risk management and adaptation to climate change. Finally, it was concluded with the selection of alternatives and projects of this type. Therefore, the CST approach and process face the challenges of climate change through integrated, systematic, interdisciplinary and collective responses at different scales that fit the needs of ecosystems and their services that are vital to human well-being. This methodology is now replicated at the level of the Mantaro river basin, improving with other initiatives that lead to the model of a resilient basin.

Keywords: climate-smart territories, climate change, ecosystem services, natural measures, Climate Smart Territories (CST) approach

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Authors: Ahmed Makhoukh

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Quality assurance (QA) has recently become a common practice, which is endorsed by most Higher Education (HE) institutions worldwide, due to the pressure of internal and external forces. One of the aims of this quality movement is to make the contribution of university education to socio-economic development highly significant. This entails that graduates are currently required have a high-quality profile, i.e., to be competent and master the 21st-century skills needed in the labor market. This wave of change, mostly imposed by globalization, has the effect that university education should be learner-centered in order to satisfy the different needs of students and meet the expectations of other stakeholders. Such a shift of focus on the student learning outcomes has led HE institutions to reconsider their strategic planning, their mission, the curriculum, the pedagogical competence of the academic staff, among other elements. To ensure that the overall institutional performance is on the right way, a QA system should be established to assume this task of checking regularly the extent to which the set of standards of evaluation are strictly respected as expected. This operation of QA has the advantage of proving the accountability of the institution, gaining the trust of the public with transparency and enjoying an international recognition. This is the case of Doha Institute (DI) for Graduate Studies, in Qatar, the object of the present study. The significance of this contribution is to show that the conception of quality has changed in this digital age, and the need to integrate a department responsible for QA in every HE institution to ensure educational quality, enhance learners and achieve academic leadership. Thus, to undertake the issue of QA in DI for Graduate Studies, an elite university (in the academic sense) that focuses on a small and selected number of students, a qualitative method will be adopted in the description and analysis of the data (document analysis). In an attempt to investigate the extent to which QA is achieved in Doha Institute for Graduate Studies, three broad indicators will be evaluated (input, process and learning outcomes). This investigation will be carried out in line with the UK Quality Code for Higher Education represented by Quality Assurance Agency (QAA).

Keywords: accreditation, higher education, quality, quality assurance, standards

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Authors: Govindan Sudha, Mathumitha Subramaniam, Alamelu Govindasamy, Sasikala Gunasekaran

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The aim of this study was to investigate the protective effect of Hypsizygus ulmarius polysaccharides (HUP) on reducing oxidative stress, cognitive impairment and neurotoxicity in D-galactose induced aging mice. Mice were subcutaneously injected with D-galactose (150 mg/kg per day) for 6 weeks and were administered HUP simultaneously. Aged mice receiving vitamin E (100 mg/kg) served as positive control. Chronic administration of D-galactose significantly impaired cognitive performance oxidative defence and mitochondrial enzymes activities as compared to control group. The results showed that HUP (200 and 400 mg/kg) treatment significantly improved the learning and memory ability in Morris water maze test. Biochemical examination revealed that HUP significantly increased the decreased activities of superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), glutathione reductase (GR), glutathione-S-transferase (GST), mitochondrial enzymes-NADH dehydrogenase, malate dehydrogenase (MDH), isocitrate dehydrogenase (ICDH), Na+K+, Ca2+, Mg2+ATPase activities, elevated the lowered total anti-oxidation capability (TAOC), glutathione (GSH), vitamin C and decreased the raised acetylcholinesterase (AChE) activities, malondialdehyde (MDA), hydroperoxide (HPO), protein carbonyls (PCO), advanced oxidation protein products (AOPP) levels in brain of aging mice induced by D-gal in a dose-dependent manner. In conclusion, present study highlights the potential role of HUP against D-galactose induced cognitive impairment, biochemical and mitochondrial dysfunction in mice. In vitro studies on the effect of HUP on scavenging DPPH, ABTS, DMPD, OH radicals, reducing power, B-carotene bleaching and lipid peroxidation inhibition confirmed the free radical scavenging and antioxidant activity of HUP. The results suggest that HUP possesses anti-aging efficacy and may have potential in treatment of neurodegenerative diseases.

Keywords: aging, antioxidants, mushroom, neurotoxicity

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Authors: Dimakatso B. Gumede, Nicolette N. Houreld

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Diabetic foot ulcers (DFUs) are a complication of diabetes mellitus (DM), a metabolic disease caused by insulin resistance or insufficiency, resulting in hyperglycaemia and low-grade chronic inflammation. Current therapies for treating DFUs include wound debridement, glycaemic control, and wound dressing. However, these therapies are moderately effective as there is a recurrence of these ulcers and an increased risk of lower limb amputations. Photobiomodulation (PBM), which is the application of non-invasive low-level light for wound healing at the spectrum of 660-1000 nm, has shown great promise in accelerating the healing of chronic wounds. However, its underlying mechanisms are not clearly defined. Studies have indicated that PBM induces wound healing via the activation of signaling pathways that are involved in tissue repair, such as the transforming growth factor-β (TGF-β). However, other signaling pathways, such as the WNT/β-catenin pathway, which is also critical for wound repair, have not been investigated. This study aimed to elucidate if PBM at 660 nm and a fluence of 5 J/cm² activates the WNT/β-catenin signaling pathway for wound healing in a diabetic cellular model. Human dermal fibroblasts (WS1) were continuously cultured high-glucose (26.5 mM D-glucose) environment to create a diabetic cellular model. A central scratch was created in the diabetic model to ‘wound’ the cells. The diabetic wounded (DW) cells were thereafter irradiated at 660 nm and a fluence of 5 J/cm². Cell migration, gene expression and protein assays were conducted at 24- and 48-h post-PBM. The results showed that PBM at 660 nm and a fluence of 5 J/cm² significantly increased cell migration in diabetic wounded cells at 24-h post-PBM. The expression of CTNNB1, ACTA2, COL1A1 and COL3A1 genes was also increased in DW cells post-PBM. Furthermore, there was increased cytoplasmic accumulation and nuclear localization of β-catenin at 24 h post-PBM. The findings in this study demonstrate that PBM activates the WNT/β-catenin signaling pathway by inducing the accumulation of β-catenin in diabetic wounded cells, leading to increased cell migration and expression of wound repair markers. These results thus indicate that PBM has the potential to improve wound healing in diabetic ulcers via activation of the WNT/β-catenin signaling pathway.

Keywords: wound healing, diabetic ulcers, photobiomodulation, WNT/β-catenin, signalling pathway

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Authors: Rolivhuwa Bishop Ramagoma1*, Lynn Cairncross1, , Saartjie Roux1

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According to the world health organisation, colon cancer is among the most common cancers diagnosed in both men and women. Specifically, it is the second leading cause of cancer related deaths accounting for over 860 000 deaths worldwide in 2018. Currently, chemotherapy has become an essential component of most cancer treatments. Despite progress in cancer drug development over the previous years, traditional chemotherapeutic drugs still have low selectivity for targeting tumour tissues and are frequently constrained by dose-limiting toxicity. The creation of nanoscale delivery vehicles capable of directly directing treatment into cancer cells has recently caught the interest of researchers. Herein, the development of peptide-functionalized polyethylene glycol gold nanoparticles (Peptide-PEG-AuNPs) as a cellular probe and delivery agent is described, with the higher aim to develop a specific diagnostic prototype and assess their specificity not only against cell lines but primary human cells as well. Gold nanoparticles (AuNPs) were synthesized and stabilized through chemical conjugation. The synthesized AuNPs were characterized, stability in physiological solutions was assessed, their cytotoxicity against colon carcinoma and non-carcinoma skin fibroblasts was also studied. Furthermore, genetic effect through real-time polymerase chain reaction (RT-PCR), localization and uptake, peptide specificity were also determined. In this study, different peptide-AuNPs were found to have preferential toxicity at higher concentrations, as revealed by cell viability assays, however, all AuNPs presented immaculate stability for over 3 months following the method of synthesis. The final obtained peptide-PEG-AuNP conjugates showed good biocompatibility in the presence of high ionic solutions and biological media and good cellular uptake. Formulation of colon cancer specific targeting peptide was successful, additionally, the genes/pathways affected by the treatments were determined through RT-PCR. Primary cells study is still on going with promising results thus far.

Keywords: nanotechnology, cancer, diagnosis, therapeutics, gold nanoparticles.

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Authors: Ahmad B. Habieb, Gabriele Milani, Tavio Tavio, Federico Milani

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Housings in developing countries have often inadequate seismic protection, particularly for masonry. People choose this type of structure since the cost and application are relatively cheap. Seismic protection of masonry remains an interesting issue among researchers. In this study, we develop a low-cost seismic isolation system for masonry using fiber reinforced elastomeric isolators. The elastomer proposed consists of few layers of rubber pads and fiber lamina, making it lower in cost comparing to the conventional isolators. We present a finite element (FE) analysis to predict the behavior of the low cost rubber isolators undergoing moderate deformations. The FE model of the elastomer involves a hyperelastic material property for the rubber pad. We adopt a Yeoh hyperelasticity model and estimate its coefficients through the available experimental data. Having the shear behavior of the elastomers, we apply that isolation system onto small masonry housing. To attach the isolators on the building, we model the shear behavior of the isolation system by means of a damped nonlinear spring model. By this attempt, the FE analysis becomes computationally inexpensive. Several ground motion data are applied to observe its sensitivity. Roof acceleration and tensile damage of walls become the parameters to evaluate the performance of the isolators. In this study, a concrete damage plasticity model is used to model masonry in the nonlinear range. This tool is available in the standard package of Abaqus FE software. Finally, the results show that the low-cost isolators proposed are capable of reducing roof acceleration and damage level of masonry housing. Through this study, we are also capable of monitoring the shear deformation of isolators during seismic motion. It is useful to determine whether the isolator is applicable. According to the results, the deformations of isolators on the benchmark one story building are relatively small.

Keywords: masonry, low cost elastomeric isolator, finite element analysis, hyperelasticity, damped non-linear spring, concrete damage plasticity

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Authors: Sasiwan Tassana-iem, Sumattana Glangkarn

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Diabetic nephropathy is a major complication in diabetic patients whom as the glomerular filtration rate falls. The affects their quality of life and results in loss of money for kidney replacement therapy costs. There is an existing intervention, but the prevalence remains high, thus this research aims to study lessons learned in implementing programs to delay diabetic nephropathy management in primary health care. Method: The target settings are, 24 sub-district health promoting hospital in Sakon Nakhon province. Participants included the health care professionals, head of the sub-district health promoting hospital and the person responsible for managing diabetic nephropathy in each hospital (n= 50). There are 400 patients with diabetes mellitus in an area. Data were collected using questionnaires, patient records data, interviews and focus groups and analyzed by statistics and content analysis. Result: Reflection of participants that the interventions to delay diabetic nephropathy management in each area, the Ministry of Public Health has a policy to screen and manage this disease. The implementing programs aimed to provide health education, innovative teaching media used in communication to educate. Patients and caregivers had misunderstanding about the actual causes and prevention of this disease and how to apply knowledge suitable for daily life. Conclusion: The obstacles to the success of the implementing programs to delay diabetic nephropathy management in primary health care were most importantly, the patient needs self-care and should be evaluated for health literacy. This is crucial to promote health literacy; to access and understand health information as well to decide their health-related choices based on health information which will promote and maintain a good health. This preliminary research confirms that situation of diabetic nephropathy still exists. The results of this study will lead to the development of delay in diabetic nephropathy implementation among patients in the province studied.

Keywords: diabetic nephropathy, chronic kidney disease, primary health care, implementation

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Authors: Suharni Mohamad Suharni Mohamad, Nurul Izzati Hamzan Nurul Izzati Hamzan, Norhayu Abdul Rahman Norhayu Abdul Rahman, Siti Suraiya Md Noor Siti Suraiya Md Noor

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Human papillomavirus (HPV) is an important risk factor for development of oral cancer. HPV16 is the most common type found in HPV-positive squamous cell carcinoma. In the present study, we established a real-time loop-mediated isothermal amplification (real-time LAMP) for detection of HPV16. A set of six primers was specially designed to recognize eight distinct sequences of HPV16-E6. Detection and quantification was achieved by real-time monitoring using a real-time turbidimeter based on threshold time required for turbidity in the LAMP reaction. LAMP reagents (MgSO4, dNTPs, Bst polymerase concentrations) and various incubation times and temperatures were optimized. The sensitivity was determined using 10-fold serial dilutions of HPV16 standard strain. The specificity of was evaluated using other HPV genotypes. The optimized method was established with specifically designed primers by real-time detection in approximately 30 min at 65°C. The limit of detection of HPV16 using the LAMP assay was 10 pg/ml that could be detected in 30 min. The LAMP assay was 10 times more sensitive than the conventional PCR in detecting HPV16. No cross-reactivity with other HPV genotypes was observed. This quantitative real-time LAMP assay may improve diagnostic potential for the detection and quantification of HPV16 in clinical samples and epidemiological studies due to its rapidity, simplicity, high sensitivity and specificity. This assay will be further evaluated with HPV DNAs of saliva from patients with oral squamous cell carcinoma. Acknowledgement: This study was financially supported by the ScienceFund Grant, Ministry of Science, Technology and Innovation (305/PPSG/6113219).

Keywords: Oral Squamous Cell Carcinoma (OSCC), Human Papillomavirus 16 (HPV16), Loop-Mediated Isothermal Amplification (LAMP), rapid detection

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Authors: A. H. Nanher, N. P. Singh, Shashidhar Yadav, Sachin Tyagi

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Agricultural production system is an outcome of a complex interaction of seed, soil, water and agro-chemicals (including fertilizers). Therefore, judicious management of all the inputs is essential for the sustainability of such a complex system. Precision agriculture gives farmers the ability to use crop inputs more effectively including fertilizers, pesticides, tillage and irrigation water. More effective use of inputs means greater crop yield and/or quality, without polluting the environment the focus on enhancing the productivity during the Green Revolution coupled with total disregard of proper management of inputs and without considering the ecological impacts, has resulted into environmental degradation. To evaluate a new approach for site-specific nutrient management (SSNM). Large variation in initial soil fertility characteristics and indigenous supply of N, P, and K was observed among Field- and season-specific NPK applications were calculated by accounting for the indigenous nutrient supply, yield targets, and nutrient demand as a function of the interactions between N, P, and K. Nitrogen applications were fine-tuned based on season-specific rules and field-specific monitoring of crop N status. The performance of SSNM did not differ significantly between high-yielding and low-yielding climatic seasons, but improved over time with larger benefits observed in the second year Future, strategies for nutrient management in intensive rice systems must become more site-specific and dynamic to manage spatially and temporally variable resources based on a quantitative understanding of the congruence between nutrient supply and crop demand. The SSNM concept has demonstrated promising agronomic and economic potential. It can be used for managing plant nutrients at any scale, i.e., ranging from a general recommendation for homogenous management of a larger domain to true management of between-field variability. Assessment of pest profiles in FFP and SSNM plots suggests that SSNM may also reduce pest incidence, particularly diseases that are often associated with excessive N use or unbalanced plant nutrition.

Keywords: nutrient, pesticide, crop, yield

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Authors: Manjusha Choudhary

Abstract:

Objective: Cassia occidentalis Linn. belongs to Family Caesalpiniaceae is a common weed scattered from the foothills of Himalayas to West Bengal, South India, Burma, and Sri Lanka. It is used widely in folklore medicine in India as laxative, expectorant, analgesic, anti-malarial, hepatoprotective, relaxant, anti-inflammatory and antidiabetic. The present study was carried out to investigate the hypoglycaemic and hypolipidemic activities of ethanolic extract of Cassia occidentalis stem bark. Methods: Stem bark extract of Cassia occidentalis (SBCO) was administered orally at 250 and 500 mg/kg doses to normal and streptozotocin (STZ) induced type-2 diabetic mice. Various parameters like fasting blood glucose (FBG) level, serum cholesterol, high density lipoprotein (HDL) cholesterol, triglycerides (TG), total protein, urea, creatinine, serum glutamate oxaloacetate transaminase (SGOT), serum glutamate pyruvate transaminase (SGPT) levels and physical parameters like change in body weight, food intake, water intake were performed for the evaluation of antidiabetic effects. Results: Both the doses of extract caused a marked decrease in FBG levels in STZ induced type 2 diabetic mice. Administration of SBCO led to the decrease in the blood glucose, food intake, water intake, organ weight, SGOT, SGPT levels with significant value and increased the levels of TG, HDL cholesterol, creatinine, cholesterol, total protein with a significant value (p < 0.05-0.01). The decrease in body weight induced by STZ was restored to normal with a significant value (p < 0.01) at both doses. Conclusion: Present study reveals that SBCO possess potent hypoglycaemic and hypolipidemic activities and supports the folklore use of the stem bark of plant as antidiabetic agent.

Keywords: Cassia occidentalis, diabetes, folklore, herbs, hypoglycemia, streptozotocin

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Authors: Jason Terry

Abstract:

Beginning in the mid-nineteenth century, hymns in the Anglo-American tradition often ended with the congregation singing ‘amen,’ most commonly set to a plagal cadence. While the popularity of this tradition is well-known still today, this research presents the origins of this custom. In 1861, Hymns Ancient & Modern deepened this convention by concluding each of its hymns with a published plagal-amen cadence. Subsequently, hymnals from a variety of denominations throughout Europe and the United States heavily adopted this practice. By the middle of the twentieth century the number of participants singing this cadence had suspiciously declined; however, it was not until the 1990s that the plagal-amen cadence all but disappeared from hymnals. Today, it is rare for songs to conclude with the plagal-amen cadence, although instrumentalists have continued to regularly play a plagal cadence underneath the singers’ sustained finalis. After examining a variety of music theory treatises, eighteenth-century newspaper articles, manuscripts & hymnals from the last five centuries, and conducting interviews with a number of scholars around the world, this study presents the context of the plagal-amen cadence through its history. The association of ‘amen’ and the plagal cadence was already being discussed during the late eighteenth century, and the plagal-amen cadence only grew in attractiveness from that time forward, most notably in the nineteenth and twentieth centuries. Throughout this research, the music of Thomas Tallis, primarily through his Preces and Responses, is reasonably shown to be the basis for the high status of the plagal-amen cadence in nineteenth- and twentieth-century society. Tallis’s immediate influence was felt among his contemporary English composers as well as posterity, all of whom were well-aware of his compositional styles and techniques. More importantly, however, was the revival of his music in nineteenth-century England, which had a greater impact on the plagal-amen tradition. With his historical title as the father of English cathedral music, Tallis was favored by the supporters of the Oxford Movement. Thus, with society’s view of Tallis, the simple IV–I cadence he chose to pair with ‘amen’ attained a much greater worth in the history of Western music. A musical device such as the once-revered plagal-amen cadence deserves to be studied and understood in a more factual light than has thus far been available to contemporary scholars.

Keywords: amen cadence, Plagal-amen cadence, singing hymns with amen, Thomas Tallis

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Authors: Robert Cazar, Nathaly Maza

Abstract:

Energy drinks and sports drinks are quite popular among young adults and teenagers worldwide. Some concerns regarding their health effects – particularly those of the energy drinks - have been raised based on scientific findings. Differentiating between these two types of drinks by means of their chemical properties seems to be an instructive task. Chemometrics provides the most appropriate strategy to do so. In this study, a discrimination analysis of the energy and sports drinks has been carried out applying chemometric methods. A set of eleven samples of available commercial brands of drinks – seven energy drinks and four sports drinks – were collected. Each sample was characterized by eight chemical variables (carbohydrates, energy, sugar, sodium, pH, degrees Brix, density, and citric acid). The data set was standardized and examined by exploratory chemometric techniques such as clustering and principal component analysis. As a preliminary step, a variable selection was carried out by inspecting the variable correlation matrix. It was detected that some variables are redundant, so they can be safely removed, leaving only five variables that are sufficient for this analysis. They are sugar, sodium, pH, density, and citric acid. Then, a hierarchical clustering `employing the average – linkage criterion and using the Euclidian distance metrics was performed. It perfectly separates the two types of drinks since the resultant dendogram, cut at the 25% similarity level, assorts the samples in two well defined groups, one of them containing the energy drinks and the other one the sports drinks. Further assurance of the complete discrimination is provided by the principal component analysis. The projection of the data set on the first two principal components – which retain the 71% of the data information – permits to visualize the distribution of the samples in the two groups identified in the clustering stage. Since the first principal component is the discriminating one, the inspection of its loadings consents to characterize such groups. The energy drinks group possesses medium to high values of density, citric acid, and sugar. The sports drinks group, on the other hand, exhibits low values of those variables. In conclusion, the application of chemometric methods on a data set that features some chemical properties of a number of energy and sports drinks provides an accurate, dependable way to discriminate between these two types of beverages.

Keywords: chemometrics, clustering, energy drinks, principal component analysis, sports drinks

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Authors: Fumiya Sugino, Naohiro Nakamura, Yuji Miyazu

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In earthquake resistant design of buildings, evaluation of vibration characteristics is important. In recent years, due to the increment of super high-rise buildings, the evaluation of response is important for not only the first mode but also higher modes. The knowledge of vibration characteristics in buildings is mostly limited to the first mode and the knowledge of higher modes is still insufficient. In this paper, using earthquake observation records of a SRC building by applying frequency filter to ARX model, characteristics of first and second modes were studied. First, we studied the change of the eigen frequency and the damping ratio during the 3.11 earthquake. The eigen frequency gradually decreases from the time of earthquake occurrence, and it is almost stable after about 150 seconds have passed. At this time, the decreasing rates of the 1st and 2nd eigen frequencies are both about 0.7. Although the damping ratio has more large error than the eigen frequency, both the 1st and 2nd damping ratio are 3 to 5%. Also, there is a strong correlation between the 1st and 2nd eigen frequency, and the regression line is y=3.17x. In the damping ratio, the regression line is y=0.90x. Therefore 1st and 2nd damping ratios are approximately the same degree. Next, we study the eigen frequency and damping ratio from 1998 after 3.11 earthquakes, the final year is 2014. In all the considered earthquakes, they are connected in order of occurrence respectively. The eigen frequency slowly declined from immediately after completion, and tend to stabilize after several years. Although it has declined greatly after the 3.11 earthquake. Both the decresing rate of the 1st and 2nd eigen frequencies until about 7 years later are about 0.8. For the damping ratio, both the 1st and 2nd are about 1 to 6%. After the 3.11 earthquake, the 1st increases by about 1% and the 2nd increases by less than 1%. For the eigen frequency, there is a strong correlation between the 1st and 2nd, and the regression line is y=3.17x. For the damping ratio, the regression line is y=1.01x. Therefore, it can be said that the 1st and 2nd damping ratio is approximately the same degree. Based on the above results, changes in eigen frequency and damping ratio are summarized as follows. In the long-term study of the eigen frequency, both the 1st and 2nd gradually declined from immediately after completion, and tended to stabilize after a few years. Further it declined after the 3.11 earthquake. In addition, there is a strong correlation between the 1st and 2nd, and the declining time and the decreasing rate are the same degree. In the long-term study of the damping ratio, both the 1st and 2nd are about 1 to 6%. After the 3.11 earthquake, the 1st increases by about 1%, the 2nd increases by less than 1%. Also, the 1st and 2nd are approximately the same degree.

Keywords: eigenfrequency, damping ratio, ARX model, earthquake observation records

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Authors: E. Syngelaki, C. C. F. Schinkel, S. Klatt, E. Hörandl

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Environmental influence can alter the conditions for plant development and can trigger changes in epigenetic variation. Thus, the exposure to abiotic environmental stress can lead to different DNA methylation profiles and may have evolutionary consequences for adaptation. Epigenetic control mechanisms may further influence mode of reproduction. The alpine species R. kuepferi has diploid and tetraploid cytotypes, that are mostly sexual and facultative apomicts, respectively. Hence, it is a suitable model system for studying the correlations of mode of reproduction, ploidy, and environmental stress. Diploid and tetraploid individuals were placed in two climate chambers and treated with low (+7°C day/+2°C night, -1°C cold shocks for three nights per week) and warm (control) temperatures (+15°C day/+10°C night). Subsequently, methylation sensitive-Amplified Fragment-Length Polymorphism (AFPL) markers were used to screen genome-wide methylation alterations triggered by stress treatments. The dataset was analyzed for four groups regarding treatment (cold/warm) and ploidy level (diploid/tetraploid), and also separately for full methylated, hemi-methylated and unmethylated sites. Patterns of epigenetic variation suggested that diploids differed significantly in their profiles from tetraploids independent from treatment, while treatments did not differ significantly within cytotypes. Furthermore, diploids are more differentiated than the tetraploids in overall methylation profiles of both treatments. This observation is in accordance with the increased frequency of apomictic seed formation in diploids and maintenance of facultative apomixis in tetraploids during the experiment. Global analysis of molecular variance showed higher epigenetic variation within groups than among them, while locus-by-locus analysis of molecular variance showed a high number (54.7%) of significantly differentiated un-methylated loci. To summarise, epigenetic variation seems to depend on ploidy level, and in diploids may be correlated to changes in mode of reproduction. However, further studies are needed to elucidate the mechanism and possible functional significance of these correlations.

Keywords: apomixis, cold stress, DNA methylation, Ranunculus kuepferi

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Authors: Mpho Mokoatle, Darlington Mapiye, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

Abstract:

Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on $k$-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0%, 80.5%, 80.5%, 63.6%, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms.

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Darlington Mapiye, Mpho Mokoatle, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

Abstract:

Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on k-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0 %, 80.5 %, 80.5 %, 63.6 %, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Farzaneh Badinlou, Reza Kormi-Nouri, Monika Knopf, Kamal Kharazi

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Research into long-term memory has demonstrated that the richness of the knowledge base cues in memory tasks improves retrieval process, which in turn influences learning and memory performance. The present research investigated the idea that adding cues connected to knowledge can affect memory performance in the context of action memory in children. In action memory studies, participants are instructed to learn a series of verb–object phrases as verbal learning and experience-based learning (learning by doing and learning by observation). It is well established that executing action phrases is a more memorable way to learn than verbally repeating the phrases, a finding called enactment effect. In the present study, a total of 410 students from four grade groups—2nd, 4th, 6th, and 8th—participated in this study. During the study, participants listened to verbal action phrases (VTs), performed the phrases (SPTs: subject-performed tasks), and observed the experimenter perform the phrases (EPTs: experimenter-performed tasks). During the test phase, cued recall test was administered. Semantic relational cues (i.e., well-integrated vs. poorly integrated items) were manipulated in the present study. In that, the participants were presented two lists of action phrases with high semantic integration between verb and noun, e.g., “write with the pen” and with low semantic integration between verb and noun, e.g., “pick up the glass”. Results revealed that experience-based learning had a better results than verbal learning for both well-integrated and poorly integrated items, though manipulations of semantic relational cues can moderate the enactment effect. In addition, children of different grade groups outperformed for well- than poorly integrated items, in flavour of older children. The results were discussed in relation to the effect of knowledge-based information in facilitating retrieval process in children.

Keywords: action memory, enactment effect, knowledge-based cues, school-aged children, semantic relational cues

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