Search results for: small whole genome sequencing

Authors: Francis Ojo Ologunagba, Monday Olatunbosun Ale, Lewis A. Olutayo

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The economic successes of commercial development of agricultural product processing depend upon the adaptability of each processing stage to mechanization. In maize processing, one of its post-harvest operations that is still facing a major challenge is dehusking. Therefore, a maize dehusking machine that could replace the prevalent traditional method of dehusking maize in developing countries, especially Nigeria was designed, constructed and tested at the Department of Agricultural and Bio-Environmental Engineering Technology, Rufus Giwa Polytechnic, Owo. The basic features of the machine are feeding unit (hopper), housing frame, dehusking unit, drive mechanism and discharge outlets. The machine was tested with maize of 50mm average diameter at 13% moisture content and 2.5mm machine roller clearance. Test results showed appreciable performance with the dehusking efficiency of 92% and throughput capacity of 200 Kg/hr at a machine speed of 400rpm. The estimated production cost of the machine at the time of construction is forty-five thousand, one hundred and eighty nairas (₦45,180) excluding the cost of the electric motor. It is therefore recommended for small and medium-scale maize farmers and processors in Nigeria.

Keywords: construction, dehusking, design, efficiency, maize

Procedia PDF Downloads 286

Authors: Justin Pargeter, Metin Eren

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Lithic miniaturization, the systematic production and use of small tools from small cores, was a consequential development in Pleistocene lithic technology. The bipolar reduction is an important, but often overlooked and misidentified, strategy for lithic miniaturization. This experiment addresses the role of axial bipolar reduction in processes of lithic miniaturization. The experiments answer two questions: what benefits does axial bipolar reduction provide, and can we distinguish axial bipolar reduction from freehand reduction? Our experiments demonstrate the numerous advantages of bipolar reduction in contexts of lithic miniaturization. Bipolar reduction produces more cutting edge per gram and is more economical than freehand reduction. Our cutting edge to mass values exceeds even those obtained with pressure blade production on high-quality obsidian. The experimental results show that bipolar reduction produces cutting edge quicker and is more efficient than freehand reduction. We show that bipolar reduction can be distinguished from freehand reduction with a high degree of confidence using the quantitative criteria in these experiments. These observations overturn long-held perceptions about bipolar reduction. We conclude by discussing the role of bipolar reduction in lithic miniaturization and Stone Age economics more broadly.

Keywords: lithic miniaturization, bipolar reduction, late Pleistocene, Southern Africa

Procedia PDF Downloads 693

Authors: Hanadi Al-Mubaraki, Michael Busler

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Both in the developed and developing countries as well as Gulf Cooperation Council (GCC), the small and medium-sized enterprises (SMEs) proven to be main drivers of jobs creation and tools to accelerate economic development and economic diversification. This paper seeks to investigate and identify the strengths and weakness of SME as a veritable tool in economic development. A survey method was used to gather data from 171 SME from Gulf Cooperation Council (GCC). The research methodology uses a quantitative approach (survey) while data were collected with a structured questionnaire and analyzed with several descriptive statistics. The results of the study, therefore, will present sets of the strengths of SME in GCC such as 1) government supported local products (59%), 2) promoting SME local products rather than international products (47%), 3) reduce the legal and administrative procedures of SME establishment (46%) and weakness of SME in GCC such as: 1) lack of funding during the initial phase of the project (46%), 2) lack of liquidity during project continuity (39%), and 3) strong competition in the domestic and global market (38%). The study findings will be guidelines for academia and practitioners such as governments, policymakers, funded organizations, universities and strategic institutions for successful implementation.

Keywords: SME, economic development, GCC, strengths and weaknesses

Procedia PDF Downloads 124

Authors: An-an Chiu, Shaio Yan Huang, Ling-Na Chen, Wei-Hua Lin

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Research has primarily focused on listed companies, less is done regarding small and medium-sized enterprises. Under the authorities' support, Taipei Exchange (TPEx) started Go Incubation Board for Startup and Acceleration Firms (GISA) in January 2014. This platform is designed to help small-sized innovative companies grow and to enter the capital market in the future. This research yield insight into earnings management activities around seasoned equity offerings (SEO) based on Taiwan’s GISA firms and the effectiveness of external corporate governance. Data for the study come from the GISA Market Observation Post System from January 2014 to December 2016. The result finds that GISA firms prone to upward accrual-based earnings management during SEO to avoid long-term negative consequences. Especially, firms with paid-in capital more than NT$ 30 million, higher fundraising amounts, or smaller-sized firms, tend to increase discretionary accruals. Finally, consistent with prior literature, CPA firms effectively serve as the role of external corporate governances on mitigating earnings management.

Keywords: GISA, earnings　management, CPA, seasoned equity offerings

Procedia PDF Downloads 114

Authors: Abdelsabour G. A. Khaled, Ahmed W. A. Abdalla And Sabry Y. M. Mahmoud

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Banana plants showing typical mosaic and yellow stripes on leaves as symptoms were collected from Assiut Governorate in Egypt. The causal agent was identified as Cucumber mosaic virus (CMV) on the basis of symptoms, transmission, serology, transmission electron microscopy and reverse transcription polymerase chain reaction (RT-PCR). Coat protein (CP) gene was amplified using gene specific primers for coat protein (CP), followed by cloning into desired cloning vector for sequencing. In this study the CMV was transmitted into propagation host either by aphid or mechanically. The transmission was confirmed through Direct Antigen Coating Enzyme Linked Immuno Sorbent Assay (DAC-ELISA). Analysis of the 120 deduced amino acid sequence of the coat protein gene revealed that the EG-A strain of CMV shared from 97.50 to 98.33% with those strains belonging to subgroup IA. The cluster analysis grouped the Egyptian isolate with strains Fny and Ri8 belonging sub-group IA. It appears that there occurs a high incidence of CMV infecting banana belonging to IA subgroup in most parts of Egypt.

Keywords: banana, CMV, transmission, CP gene, RT-PCR

Procedia PDF Downloads 318

Authors: Rashad Al-Hindi

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The aims of the study were to isolate and identify potential probiotic lactic acid bacteria due to their therapeutic and food preservation importance. Sixty-three suspected lactic acid bacteria (LAB) strains were isolated from thirteen different raw milk and fermented milk product samples of various animal origins manufactured indigenously in the Kingdom of Saudi Arabia using de Man, Rogosa and Sharpe (MRS) agar medium and various incubation conditions. The identification of forty-six selected LAB strains was performed using molecular methods (16S rDNA gene sequencing). The LAB counts in certain samples were higher under microaerobic incubation conditions than under anaerobic conditions. The identified LAB belonged to the following genera: Enterococcus (16 strains), Lactobacillus (9 strains), Weissella (10 strains), Streptococcus (8 strains) and Lactococcus (3 strains), constituting 34.78%, 19.57%, 21.74%, 17.39% and 6.52% of the suspected isolates, respectively. This study noted that the raw milk and traditional fermented milk products of Saudi Arabia, especially stirred yogurt (Laban) made from camel milk, could be rich in LAB. The obtained LAB strains in this study will be tested for their probiotic potentials in another ongoing study.

Keywords: dairy, LAB, probiotic, Saudi Arabia

Procedia PDF Downloads 262

Authors: Junting Xiang, Jörg Uwe Schlüter, Fei Duan

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The miniaturization of gas turbines promises many advantages. Miniature gas turbines can be used for local power generation or the propulsion of small aircraft, such as UAV and MAV. However, experience shows that the miniaturization of conventional gas turbines, which are optimized at their current large size, leads to a substantial loss of efficiency and performance at smaller scales. This may be due to a number of factors, such as the Reynolds-number effect, the increased heat transfer, and manufacturing tolerances. In the present work, we focus on computational investigations of the Reynolds number effect and the wall heat transfer on the performance of axial compressor during its size change. The NASA stage 35 compressors are selected as the configuration in this study and Computational Fluid Dynamics (CFD) is used to carry out the miniaturization process and simulations. We perform parameter studies on the effect of Reynolds number and wall thermal conditions. Our results indicate a decrease of efficiency, if the compressor is miniaturized based on its original geometry due to the increase of viscous effects. The increased heat transfer through wall has only a small effect and will actually benefit compressor performance based on our study.

Keywords: axial compressor, CFD, heat transfer, miniature gas turbines, Reynolds number

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Authors: M. Arabghahestani, A. Darwish Ahmad, N. K. Akafuah

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In this work, small-scale experiments of fire whirl were conducted to study the spinning fire phenomenon and to gain comprehensive understandings of fire tornadoes and the factors that affect their behavior. High speed imaging was used to track the flames at both temporal and spatial scales. This allowed us to better understand the role of the near-ground height in creating a boundary layer flow profile that, in turn contributes to formation of vortices around the fire, and consequent fire whirls. Based on the results obtained from these observations, we were able to spot the differences in the fuel burning rate of the fire itself as a function of a newly defined specific non-dimensional near-ground height. Based on our observations, there is a cutoff non-dimensional height, beyond which a normal fire can be turned into a fire whirl. Additionally, the results showed that the fire burning rate decreases by moving the fire to a height higher than the ground level. These effects were justified by the interactions between vortices formed by, the back pressure and the boundary layer velocity profile, and the vortices generated by the fire itself.

Keywords: boundary layer profile, fire whirls, near-ground height, vortex interactions

Procedia PDF Downloads 139

Authors: Elena Cangelosi, Wayne Beyea

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This research expands the resilience planning literature by exploring the barriers and enablers to climate and health adaptation planning for small urban, coastal Great Lakes communities. With funding from the United States Centers for Disease Control and Prevention (CDC) Climate Ready City and States Initiative, this research took place during a 3-year pilot intervention project which integrates urban planning and public health. The project used the CDC’s Building Resilience Against Climate Effects (BRACE) framework to prevent or reduce the human health impacts from climate change in Marquette County, Michigan. Using a deliberation with the analysis planning process, interviews, focus groups, and community meetings with over 25 stakeholder groups and over 100 participants identified the area’s climate-related health concerns and adaptation interventions to address those concerns. Marquette County, on the shores of Lake Superior, the largest of the Great Lakes, was selected for the project based on their existing adaptive capacity and proactive approach to climate adaptation planning. With Marquette County as the context, this study fills a gap in the adaptation literature, which currently heavily emphasizes large-urban or agriculturally-based rural areas, and largely neglects small urban areas. This research builds on the qualitative case-study, survey, and interview approach established by previous researchers on contextual barriers and enablers for adaptation planning. This research uses a case study approach, including surveys and interviews of public officials, to identify the barriers and enablers for climate and health adaptation planning for small-urban areas within a large, non-agricultural, Great Lakes county. The researchers hypothesize that the barriers and enablers will, in some cases, overlap those found in other contexts, but in many cases, will be unique to a rural setting. The study reveals that funding, staff capacity, and communication across a large, rural geography act as the main barriers, while strong networks and collaboration, interested leaders, and community interest through a strong human-land connection act as the primary enablers. Challenges unique to rural areas are revealed, including weak opportunities for grant funding, large geographical distances, communication challenges with an aging and remote population, and the out-migration of education residents. Enablers that may be unique to rural contexts include strong collaborative relationships across jurisdictions for regional work and strong connections between residents and the land. As the factors that enable and prevent climate change planning are highly contextual, understanding, and appropriately addressing the unique factors at play for small-urban communities is key for effective planning in those areas. By identifying and addressing the barriers and enablers to climate and health adaptation planning for small-urban, coastal areas, this study can help Great Lakes communities appropriately build resilience to the adverse impacts of climate change. In addition, this research expands the breadth of research and understanding of the challenges and opportunities planners confront in the face of climate change.

Keywords: climate adaptation and resilience, climate change adaptation, climate change and urban resilience, governance and urban resilience

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Authors: M. Kazou, A. Gavriil, O. Kalagkatsi, T. Paschos, E. Tsakalidou

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Kopanisti cheese is a Greek soft Protected Designation of Origin (PDO) cheese made of raw cow, sheep or goat milk, or mixtures of them, with similar organoleptic characteristics to that of Roquefort cheese. Traditional manufacturing of Kopanisti cheese is limited in small-scale dairies, without the addition of starter cultures. Instead, an amount of over-mature Kopanisti cheese, called Mana Kopanisti, is used to initiate ripening. Therefore, the selection of proper starter cultures and the understanding of the contribution of various microbial groups to its overall quality is crucial for the production of a high-quality final product with standardized organoleptic and physicochemical characteristics. Taking the above into account, the aim of the present study was the investigation of Kopanisti cheese microbiota and its role in cheese quality. For this purpose, four different types of Kopanisti were produced in triplicates, all with pasteurized cow milk, with the addition of (A) the typical mesophilic species Lactococcus lactis and Lactobacillus paracasei used as starters in the production of soft spread cheeses, (B) strains of Lactobacillus acidipiscis and Lactobacillus rennini previously isolated from Kopanisti and Mana Kopanisti, (C) all the species from (A) and (B) as inoculum, and finally (D) the species from (A) and Mana Kopanisti. Physicochemical and microbiological analysis was performed for milk and cheese samples during ripening. Enumeration was performed for major groups of lactic acid bacteria (LAB), total mesophilic bacteria, yeasts as well as hygiene indicator microorganisms. Bacterial isolates from all the different LAB groups, apart from enterococci, alongside yeasts isolates, were initially grouped using repetitive sequence-based polymerase chain reaction (rep-PCR) and then identified at the species level using 16S rRNA gene and internal transcribed spacer (ITS) DNA region sequencing, respectively. Sensory evaluation was also performed for final cheese samples at the end of the ripening period (35 days). Based on the results of the classical microbiological analysis, the average counts of the total mesophilic bacteria and LAB, apart from enterococci, ranged between 7 and 10 log colony forming unit (CFU) g⁻¹, phychrotrophic bacteria, and yeast extract glucose chloramphenicol (YGC) isolates between 4 and 8 log CFU g⁻¹, while coliforms and enterococci up to 2 log CFU g⁻¹ throughout ripening in cheese samples A, C and D. In contrast, in cheese sample B, the average counts of the total mesophilic bacteria and LAB, apart from enterococci, phychrotrophic bacteria, and YGC isolates ranged between 0 and 10 log CFU g⁻¹ and coliforms and enterococci up to 2 log CFU g⁻¹. Although the microbial counts were not that different among samples, identification of the bacterial and yeasts isolates revealed the complex microbial community structure present in each cheese sample. Differences in the physicochemical characteristics among the cheese samples were also observed, with pH ranging from 4.3 to 5.3 and moisture from 49.6 to 58.0 % in the final cheese products. Interestingly, the sensory evaluation also revealed differences among samples, with cheese sample B ranking first based on the total score. Overall, the combination of these analyses highlighted the impact of different starter cultures on the Kopanisti microbiota as well as on the physicochemical and sensory characteristics of the final product.

Keywords: Kopanisti cheese, microbiota, classical microbiological analysis, physicochemical analysis

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Authors: Belayneh Matebie, Michael Melese

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The study focuses on addressing the challenges in classifying and ensuring the quality of Eragrostis Teff, a small and round grain that is the smallest cereal grain. Employing a traditional classification method is challenging because of its small size and the similarity of its environmental characteristics. To overcome this, this study employs a machine learning approach to develop a source and quality classification system for Teff cereal. Data is collected from various production areas in the Amhara regions, considering two types of cereal (high and low quality) across eight classes. A total of 5,920 images are collected, with 740 images for each class. Image enhancement techniques, including scaling, data augmentation, histogram equalization, and noise removal, are applied to preprocess the data. Convolutional Neural Network (CNN) is then used to extract relevant features and reduce dimensionality. The dataset is split into 80% for training and 20% for testing. Different classifiers, including FVGG16, FINCV3, QSCTC, EMQSCTC, SVM, and RF, are employed for classification, achieving accuracy rates ranging from 86.91% to 97.72%. The ensemble of FVGG16, FINCV3, and QSCTC using the Max-Voting approach outperforms individual algorithms.

Keywords: Teff, ensemble learning, max-voting, CNN, SVM, RF

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Authors: Xingxin Wu, Fenli Shao, Tao Tan, Yang Tan, Yang Sun, Qiang Xu

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Psoriasis is a chronic inflammatory skin disease that affects about 2% of the world's population. IL-23 signaling plays a key role in the pathogenesis of psoriasis. Control of IL-23 release by small molecule compounds during developing psoriasis has not been well established. Here, we show that compound 1, a small molecule nature product, protected mice from imiquimod-induced psoriasis with improved skin lesions, reduced skin thickness, and reduced IL-23 mRNA expression in the skin tissue. FACS results showed compound 1 reduced the number of dendritic cells in the skin. Interestingly, compound 1 was not able to ameliorate IL-23-induced psoriasis-like skin inflammation in mice. Further, compound 1 inhibited MyD88-dependent IL-23 mRNA expression induced by LPS, CpG and imiquimod in BMDC cells, but not MyD88-independent CD80 and CD86 expression induced by LPS. The methods included real-time PCR, western blot, H & E staining, FACS and ELISA et al. In conclusion, compound 1 regulates MyD88-dependent signaling to control IL-23 release in dendritic cells, which improves imiquimod-induced psoriasis.

Keywords: dendritic cells, IL-23, toll-like receptor signaling, psoriasis

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Authors: C. I. Boshoff, S. Steenkamp-Jonker

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Cystic echinococcosis (CE), caused by Echinococcus granulosus is an important parasitic infection in livestock worldwide, with severe zoonotic potential. It is important to understand the variability of Echinococcus granulosus, as genotype variations may influence lifecycle patterns, development rate, and transmission. Cystic Echinococcus samples were collected from domestic animals in Eastern Cape Province, South Africa. A molecular study was performed on 14 hydatid cysts obtained from caprine, ovine and bovine livers in order to determine the Echinococcus granulosus strain present in these hosts. The sequencing of the mitochondrial cytochrome C oxidase subunit I (coxI) gene of the hydatid cysts produced sequences of 400 bp for each sample analysed. These sequences were aligned with those present in GenBank and a phylogenetic tree was constructed. Based on coxI genotype the isolates could be grouped into E. granulosus sensu stricto. The findings of the study represent a pilot molecular study on Echinococcus from domestic animals undertaken in South Africa.

Keywords: Echinococcus granulosus, genotypes, livestock, South Africa

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Authors: Rumbidzai Sipiwe Zimvumi

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The study aimed to identify the top management team attributes for ambidexterity in small and medium-sized enterprises by utilizing the upper echelons theory. The conventional opinion holds that an organization's ability to pursue both exploitative and explorative innovation methods at the same time is reflected in its ambidexterity. Top-level managers are critical to this matrix because they forecast and explain strategic choices that guarantee success by improving organizational performance. Since the focus of the study was on the unique characteristics of TMTs that can facilitate ambidexterity, the primary goal was to comprehend how TMTs in SMEs can better manage ambidexterity. The study used document analysis to collect information on ambidexterity and TMT traits. Finding, choosing, assessing, and synthesizing data from peer-reviewed publications allowed for the review and evaluation of papers. The fact that SMEs will perform better if they can achieve a balance between exploration and exploitation cannot be overstated. Unfortunately, exploitation is the main priority for most SMEs. The results showed that some of the noteworthy TMT traits that support ambidexterity in SMEs are age diversity, shared responsibility, leadership impact, psychological safety, and self-confidence. It has been shown that most SMEs confront significant obstacles in recruiting people, including formalizing their management and assembling executive teams with seniority. Small and medium-sized enterprises (SMEs) are often held by families or people who neglect to keep their personal lives apart from the firm, which eliminates the opportunity for management and staff to take the initiative. This helps to explain why exploitative strategies, which preserve present success, are used rather than explorative strategies, which open new economic opportunities and dimensions. It is evident that psychological safety deteriorates, and creativity is hindered in the process. The study makes the case that TMTs who are motivated to become ambidextrous can exist. According to the report, small- and medium-sized business owners should value the opinions of all parties involved and provide their managers and regular staff the freedom to think creatively and in a safe environment. TMTs who experience psychological safety are more likely to be inventive, creative, and productive. A team's collective perception that it is acceptable to take chances, voice opinions and concerns, ask questions, and own up to mistakes without fear of unfavorable outcomes is known as team psychological safety. Thus, traits like age diversity, leadership influence, learning agility, psychological safety, and self-assurance are critical to the success of SMEs. As a solution to ensuring ambidexterity is attained, the study suggests a clear separation of ownership and control, the adoption of technology to stimulate creativity, team spirit and excitement, shared accountability, and good management of diversity. Among the suggestions for the SME's success are resource allocation and important collaborations.

Keywords: navigating, ambidexterity, top management team, small and medium enterprises

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Authors: Yongrong Li, Ralf Domroes

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Due to significant energy savings, enablement of higher machining speed as well as environmentally friendly features, Minimum Quantity Lubrication (MQL) has been used for many machining processes efficiently. However, in the deep hole drilling field (small tool diameter D < 5 mm) and long tool (length L > 25xD) it is always a bottle neck for a single channel MQL system. The single channel MQL, based on the Venturi principle, faces a lack of enough oil quantity caused by dropped pressure difference during the deep hole drilling process. In this paper, a system concept based on a bypass design has explored its possibility to dynamically reach the required pressure difference between the air inlet and the inside of aerosol generator, so that the deep hole drilling demanded volume of oil can be generated and delivered to tool tips. The system concept has been investigated in static and dynamic laboratory testing. In the static test, the oil volume with and without bypass control were measured. This shows an oil quantity increasing potential up to 1000%. A spray pattern test has demonstrated the differences of aerosol particle size, aerosol distribution and reaction time between single channel and bypass controlled single channel MQL systems. A dynamic trial machining test of deep hole drilling (drill tool D=4.5mm, L= 40xD) has been carried out with the proposed system on a difficult machining material AlSi7Mg. The tool wear along a 100 meter drilling was tracked and analyzed. The result shows that the single channel MQL with a bypass control can overcome the limitation and enhance deep hole drilling with a small tool. The optimized combination of inlet air pressure and bypass control results in a high quality oil delivery to tool tips with a uniform and continuous aerosol flow.

Keywords: deep hole drilling, green production, Minimum Quantity Lubrication (MQL), near dry machining

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Authors: Noshaba Dilbar, Aisha Tahir, Amer Jamil

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During the last decade, DNA barcoding proved to be an authentic tool for discovery and identification of plants. In the present study, DNA barcoding of two species, Fagonia arabica and Fagonia indica was done for differentiation by using matK region. matK gene is considered as a universal barcode because of its easy alignment and high discrimination ability. In this study, matK yielded 100% sequencing results. The sequences from both plants were aligned at clustal W and observed that there is no nucleotide variation and polymorphism among both sequences. This was further analysed by BLAST which showed the similar sequences from different plants belonging to same family but didn’t find sequence of both species. Considering this, the resulted sequence was submitted by the name of Fagonia arabica with accession number KM276890. In the end, we analysed the results from BOLD which gave us the final conclusion that both plants are same as their matK sequences are 100% identical. In literature, both Fagonia indica and Fagonia arabica names are used for this plant but there is no clear differentiation has been observed in these plants. Results evaluate that Fagonia indica and Fagonia arabica are the alternative names of same plant.

Keywords: DNA barcoding, Fagonia arabica, Fagonia indica, matK

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Authors: Aika Umemuro, Mitsuru Sato, Mizuki Narita, Saya Hori, Saya Sakurai, Tomomi Nakayama, Ayano Nakazawa, Toshihiro Ogura

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Mammography requires the detection of very small calcifications, and physicians search for microcalcifications by magnifying the images as they read them. The mouse is necessary to zoom in on the images, but this can be tiring and distracting when many images are read in a single day. Therefore, an image magnification system combining an eye-detector and a simple electroencephalograph (EEG) scanner was devised, and its operability was evaluated. Two experiments were conducted in this study: the measurement of eye-detection error using an eye-detector and the measurement of the time required for image magnification using a simple EEG scanner. Eye-detector validation showed that the mean distance of eye-detection error ranged from 0.64 cm to 2.17 cm, with an overall mean of 1.24 ± 0.81 cm for the observers. The results showed that the eye detection error was small enough for the magnified area of the mammographic image. The average time required for point magnification in the verification of the simple EEG scanner ranged from 5.85 to 16.73 seconds, and individual differences were observed. The reason for this may be that the size of the simple EEG scanner used was not adjustable, so it did not fit well for some subjects. The use of a simple EEG scanner with size adjustment would solve this problem. Therefore, the image magnification system using the eye-detector and the simple EEG scanner is useful.

Keywords: EEG scanner, eye-detector, mammography, observers

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Authors: Fern Baedyananda, Arkom Chaiwongkot, Somchai Niruthisard, Nakarin Kitkumthorn, Parvapan Bhattarakosol

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High-risk human papillomavirus (HPV) infections cause transformation of the host cells by down-regulating and inhibiting host regulatory proteins such as p53 and pRb by overexpressing the viral oncoproteins E6 and E7. However, the E1 protein which is the only enzyme encoded by HPV has also been shown to cause DNA instability leading to the integration of the virus into the host genome and triggering carcinogenic events. A 63bp duplication in the E1 helicase region has been detected in European patients. However, the clinical prognosis of these patients is still controversial. This study was performed to determine the presence of the HPV-16 E1 63bp duplication in patient cervical samples in Thai women and determine the sequence of the variant in the Thai population. Detection of the HPV-16 E1 duplication in the helicase region was performed in 90 patient cell samples across normal, cervical intraepithelial neoplasia I-III, and squamous cervical carcinoma stages by PCR. The PCR products were purified and sequenced to determine the presence of duplication variants.The variant form was found in 10% of all CIN 1 patients. In this study, the presence of the 63 bp duplication variant in the Thai population was found to be present and was further characterized. Interestingly, all samples that exhibited the variant form of HPV-16 E1 were classified as CIN I. Presence of the variant, constricted to mild dysplasia signifies the importance of HPV-16 E1 in carcinogenesis.

Keywords: carcinogenesis, cervical cancer, human papillomavirus, HPV-16 E1

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Authors: Tamanda Kamwendo

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The concept of benefit sharing has been a prominent global debate in the world, gaining traction in human research ethics. Despite its prevalence, the concept of benefit sharing is not without controversy over its meaning and justification. This is due to the fact that it lacks a broadly accepted definition and many proponents discuss benefit sharing by arguing for its necessity rather than engaging in critical intellectual engagement with technical issues such as what it implies. What is clear in the literature is that the underlying premise of benefit-sharing is that research involving underprivileged and marginalized people is currently unjust and inequitable because these people are denied access to these gains; thus, benefit-sharing arrangements are required for these research projects to be just and equitable. This paper, therefore, investigates the discourses and justifications behind the concept of benefit sharing to human participants, particularly when dealing with human genomics research. Furthermore, considering that benefit sharing is generally viewed as a transaction between research organizations and research participants, it raises ethical concerns concerning the commodification of human material and undermines the sanctity of the human genome. This is predicated on the idea that research sponsors would be compelled to deliver a minimum set of possible benefits to research participants and communities in exchange for their involvement in the study. There is, therefore, need to protect benefit-sharing practices in international health research by developing a governance legal framework. A legal framework of benefit sharing will also dispel the issue of commodification of human material where human genomic research is done.

Keywords: benefit sharing, human participants, human genomic research, ethical concerns

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Authors: S. Vanker, A. Aaver, A. Roio, L. Nuut

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To be sure about the effective and less effective/ineffective approaches to course instruction, we hold the opinion that the faculty members need regular feedback from their students in order to be aware of how well or unwell their teaching styles have worked when instructing the courses. It can be confirmed without a slightest hesitation that undergraduate students’ motivated-ness can be sustained when continually improving the quality of teaching and properly sequencing the academic courses both, in the curricula and timetables. At Estonian Aviation Academy, four different forms of feedback are used: Lecture monitoring, questionnaires for all students, study information system subject monitoring and direct feedback received by the lecturer. Questionnaires for all students are arranged once during a study year and separately for the first year and senior students. The results are discussed in academic departments together with student representatives, analyzed with the teaching staff and, if needed, improvements are suggested. In addition, a monitoring system is planned where a lecturer acts in both roles – as an observer and as the lecturer. This will foster better exchange of experience and through this help to make the whole study process more interesting.

Keywords: learner motivation, feedback, student support, undergraduate education

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Authors: Hassan Wajid

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We will commend accommodating an environmentally friendly architectural proposal that is extremely common/usual but whose features will make it a sustainable space. In this experiment, the natural and artificial built space is being proposed in such a way that deals with Environmental, Ecological, and Economic Criteria under different climatic conditions. Moreover, the criteria against ecology-environment-economics reflect in the different modules which are being experimented with and analyzed by multiple research groups. The ecological, environmental, and economic services are provided used as units of production side by side, resulting in local job creation and saving resources, for instance, conservation of rainwater, soil formation or protection, less energy consumption to achieve Net Zero, and a stable climate as a whole. The synthesized results from the collected data suggest several aspects to consider when designing buildings for beginning the design process under the supervision of instructors/directors who are responsible for developing curricula and sustainable goals. Hence, the results of the research and the suggestions will benefit the sustainable design through multiple results, heat analysis of different small modules, and comparisons. As a result, it is depleted as the resources are either consumed or the pollution contaminates the resources.

Keywords: optimization, ecology, environment, sustainable solution

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Authors: Amina Oukennou, Zitouni Beidouri, Otmane Bouksour

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Small to Medium-sized enterprises are a very important component of the economy. They are present in the whole industries all over the world. They are considered as the engine for future growth in the economy. Project management is an economical international factor impacting all types of enterprises including the SMEs. This paper has the aim of measuring the weight of using projects and project management in Moroccan SMEs in comparison with the large companies. The study is based on interviews with experts: project managers, managers, directors, and consultants. They were asked questions measuring the weight of using projects, the level of using project management, and the resources employed. Eighteen Moroccan companies from a range of industries and sizes were consulted. All the companies consider projects as a key element in their strategy. Most of them affirm the great usefulness of the approach 'project', especially for the external activities. The main differences lie in the duration and the size of used projects. Despite the commonly shared idea about the importance of the project management, the interviewed persons believe that the project management knowledge has the same importance or less than the technical knowledge. All the companies affirm the need for a simpler version of project management. The content varies from one company to another.

Keywords: project dimension, project management, small to medium-sized entreprise, Morocco

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Authors: Lamis Naddaf, Yuval Tabach

Abstract:

In this research, we identified the missense genetic variants that have the potential to enhance resistance against cancer. Such field has not been widely explored, as researchers tend to investigate mutations that cause diseases, in response to the suffering of patients, rather than those mutations that protect from them. In conjunction with the genomic revolution, and the advances in genetic engineering and synthetic biology, identifying the protective variants will increase the power of genotype-phenotype predictions and can have significant implications on improved risk estimation, diagnostics, prognosis and even for personalized therapy and drug discovery. To approach our goal, we systematically investigated the sites of the coding genomes and picked up the alleles that showed a correlation with the species’ cancer resistance. We predicted 250 protecting variants (PVs) with a 0.01 false discovery rate and more than 20 thousand PVs with a 0.25 false discovery rate. Cancer resistance in Mammals and reptiles was significantly predicted by the number of PVs a species has. Moreover, Genes enriched with the protecting variants are enriched in pathways relevant to tumor suppression like pathways of Hedgehog signaling and silencing, which its improper activation is associated with the most common form of cancer malignancy. We also showed that the PVs are more abundant in healthy people compared to cancer patients within different human races.

Keywords: comparative genomics, machine learning, cancer resistance, cancer-protecting alleles

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Authors: P. Chihomvu, P. Stegmann, M. Pillay

Abstract:

Pollution of the Klip River has caused microorganisms inhabiting it to develop protective survival mechanisms. This study isolated and characterized the heavy metal resistant bacteria in the Klip River. Water and sediment samples were collected from six sites along the course of the river. The pH, turbidity, salinity, temperature and dissolved oxygen were measured in-situ. The concentrations of six heavy metals (Cd, Cu, Fe, Ni, Pb, and Zn) of the water samples were determined by atomic absorption spectroscopy. Biochemical and antibiotic profiles of the isolates were assessed using the API 20E® and Kirby Bauer Method. Growth studies were carried out using spectrophotometric methods. The isolates were identified using 16SrDNA sequencing. The uppermost part of the Klip River with the lowest pH had the highest levels of heavy metals. Turbidity, salinity and specific conductivity increased measurably at Site 4 (Henley on Klip Weir). MIC tests showed that 16 isolates exhibited high iron and lead resistance. Antibiotic susceptibility tests revealed that the isolates exhibited multi-tolerances to drugs such as tetracycline, ampicillin, and amoxicillin.

Keywords: Klip River, heavy metals, resistance, 16SrDNA

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Authors: Maddalena Arigoni, Maria Luisa Ratto, Raffaele A. Calogero, Luca Alessandri

Abstract:

The presence of tumor heterogeneity, where distinct cancer cells exhibit diverse morphological and phenotypic profiles, including gene expression, metabolism, and proliferation, poses challenges for molecular prognostic markers and patient classification for targeted therapies. Understanding the causes and progression of cancer requires research efforts aimed at characterizing heterogeneity, which can be facilitated by evolving single-cell sequencing technologies. However, analyzing single-cell data necessitates computational methods that often lack objective validation. Therefore, the establishment of benchmarking datasets is necessary to provide a controlled environment for validating bioinformatics tools in the field of single-cell oncology. Benchmarking bioinformatics tools for single-cell experiments can be costly due to the high expense involved. Therefore, datasets used for benchmarking are typically sourced from publicly available experiments, which often lack a comprehensive cell annotation. This limitation can affect the accuracy and effectiveness of such experiments as benchmarking tools. To address this issue, we introduce omics benchmark experiments designed to evaluate bioinformatics tools to depict the heterogeneity in single-cell tumor experiments. We conducted single-cell RNA sequencing on six lung cancer tumor cell lines that display resistant clones upon treatment of EGFR mutated tumors and are characterized by driver genes, namely ROS1, ALK, HER2, MET, KRAS, and BRAF. These driver genes are associated with downstream networks controlled by EGFR mutations, such as JAK-STAT, PI3K-AKT-mTOR, and MEK-ERK. The experiment also featured an EGFR-mutated cell line. Using 10XGenomics platform with cellplex technology, we analyzed the seven cell lines together with a pseudo-immunological microenvironment consisting of PBMC cells labeled with the Biolegend TotalSeq™-B Human Universal Cocktail (CITEseq). This technology allowed for independent labeling of each cell line and single-cell analysis of the pooled seven cell lines and the pseudo-microenvironment. The data generated from the aforementioned experiments are available as part of an online tool, which allows users to define cell heterogeneity and generates count tables as an output. The tool provides the cell line derivation for each cell and cell annotations for the pseudo-microenvironment based on CITEseq data by an experienced immunologist. Additionally, we created a range of pseudo-tumor tissues using different ratios of the aforementioned cells embedded in matrigel. These tissues were analyzed using 10XGenomics (FFPE samples) and Curio Bioscience (fresh frozen samples) platforms for spatial transcriptomics, further expanding the scope of our benchmark experiments. The benchmark experiments we conducted provide a unique opportunity to evaluate the performance of bioinformatics tools for detecting and characterizing tumor heterogeneity at the single-cell level. Overall, our experiments provide a controlled and standardized environment for assessing the accuracy and robustness of bioinformatics tools for studying tumor heterogeneity at the single-cell level, which can ultimately lead to more precise and effective cancer diagnosis and treatment.

Keywords: single cell omics, benchmark, spatial transcriptomics, CITEseq

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Authors: Mohammad Muhebbullah Ibne Hoque, Zheng Jun, Wang Guoying

Abstract:

Salinity stress is one of the most important abiotic factors contributing to crop growth and yield loss. Exploring the genetic basis is necessary to develop maize varieties with salinity tolerance. In order to discover the inherent basis for salinity tolerance traits in maize, 121 polymorphic SSR markers were used to analyze 163 F2 individuals derived from a single cross of inbred line B73 (a salt susceptible inbred line) and CZ-7 (a salt tolerant inbred line). A linkage map was constructed and the map covered 1195.2 cM of maize genome with an average distance of 9.88 cM between marker loci. Ten salt tolerance traits at seedling stage were evaluated for QTL analysis in maize seedlings. A total of 41 QTLs associated with seedling shoot and root traits were detected, with 16 and 25 QTLs under non-salinity and salinity condition, respectively. And only 4 major stable QTLs were detected in two environments. The detected QTLs were distributed on chromosomes 1, 2, 4, 5, 6, 7, 8, 9, and chromosome 10. Phenotypic variability for the identified QTLs for all the traits was in the range from 6.27 to 21.97%. Fourteen QTLs with more than 10% contributions were observed. Our results and the markers associated with the major QTL detected in this study have the potential application for genetic improvement of salt tolerance in maize through marker-assisted selection.

Keywords: salt tolerance, seedling stage, root shoot traits, quantitative trait loci, simple sequence repeat, maize

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Authors: Thilina Ranaweera, Enes Makalic, John L. Hopper, Adrian Bickerstaffe

Abstract:

Data are the primary asset of biomedical researchers, and the engine for both discovery and research translation. As the volume and complexity of research datasets increase, especially with new technologies such as large single nucleotide polymorphism (SNP) chips, so too does the requirement for software to manage, process and analyze the data. Researchers often need to execute complicated queries and conduct complex analyzes of large-scale datasets. Existing tools to analyze such data, and other types of high-dimensional data, unfortunately suffer from one or more major problems. They typically require a high level of computing expertise, are too simplistic (i.e., do not fit realistic models that allow for complex interactions), are limited by computing power, do not exploit the computing power of large-scale parallel architectures (e.g. supercomputers, GPU clusters etc.), or are limited in the types of analysis available, compounded by the fact that integrating new analysis methods is not straightforward. Solutions to these problems, such as those developed and implemented on parallel architectures, are currently available to only a relatively small portion of medical researchers with access and know-how. The past decade has seen a rapid expansion of data management systems for the medical domain. Much attention has been given to systems that manage phenotype datasets generated by medical studies. The introduction of heterogeneous genomic data for research subjects that reside in these systems has highlighted the need for substantial improvements in software architecture. To address this problem, we have developed SPARK, an enabling and translational system for medical research, leveraging existing high performance computing resources, and analysis techniques currently available or being developed. It builds these into The Ark, an open-source web-based system designed to manage medical data. SPARK provides a next-generation biomedical data management solution that is based upon a novel Micro-Service architecture and Big Data technologies. The system serves to demonstrate the applicability of Micro-Service architectures for the development of high performance computing applications. When applied to high-dimensional medical datasets such as genomic data, relational data management approaches with normalized data structures suffer from unfeasibly high execution times for basic operations such as insert (i.e. importing a GWAS dataset) and the queries that are typical of the genomics research domain. SPARK resolves these problems by incorporating non-relational NoSQL databases that have been driven by the emergence of Big Data. SPARK provides researchers across the world with user-friendly access to state-of-the-art data management and analysis tools while eliminating the need for high-level informatics and programming skills. The system will benefit health and medical research by eliminating the burden of large-scale data management, querying, cleaning, and analysis. SPARK represents a major advancement in genome research technologies, vastly reducing the burden of working with genomic datasets, and enabling cutting edge analysis approaches that have previously been out of reach for many medical researchers.

Keywords: biomedical research, genomics, information systems, software

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Authors: Ghazi Chabchoub, Mouna Feki, Mohamed Abid, Hammadi Ayadi

Abstract:

Autoimmune thyroid diseases (AITDs), including Graves’ disease (GD) and Hashimoto’s thyroiditis (HT), are inherited as complex traits. Genetic factors associated with AITDs have been tentatively identified by candidate gene and genome scanning approaches. We analysed three intragenic microsatellite markers in the thyroid hormone receptor associated protein 2 gene (THRAP2), mapped near D12S79 marker, which have a potential role in immune function and inflammation [THRAP2-1(TG)n, THRAP2-2 (AC)n and THRAP2-3 (AC)n]. Our study population concerned 12 patients affected with AITDs belonging to a multiplex Tunisian family with high prevalence of AITDs. Fluorescent genotyping was carried out on ABI 3100 sequencers (Applied Biosystems USA) with the use of GENESCAN for semi-automated fragment sizing and GENOTYPER peak-calling software. Statistical analysis was performed using the non parametric Lod score (NPL) by Merlin software. Merlin outputs non-parametric NPLall (Z) and LOD scores and their corresponding asymptotic P values. The analysis for three intragenic markers in the THRAP2 gene revealed strong evidence for linkage (NPL=3.68, P=0.00012). Our results suggested the possible role of THRAP2 gene in AITDs susceptibility in this family.

Keywords: autoimmunity, autoimmune disease, genetic, linkage analysis

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Authors: Lamis Naddaf, Yuval Tabach

Abstract:

We identified missense genetic variants with the potential to enhance resistance against cancer. Such a field has not been widely explored as researchers tend to investigate the mutations that cause diseases, in response to the suffering of patients, rather than those mutations that protect from them. In conjunction with the genomic revolution and the advances in genetic engineering and synthetic biology, identifying the protective variants will increase the power of genotype-phenotype predictions and have significant implications for improved risk estimation, diagnostics, prognosis, and even personalized therapy and drug discovery. To approach our goal, we systematically investigated the sites of the coding genomes and selected the alleles that showed a correlation with the species’ cancer resistance. Interestingly, we found several amino acids that are more generally preferred (like the Proline) or avoided (like the Cysteine) by the resistant species. Furthermore, Cancer resistance in mammals and reptiles is significantly predicted by the number of the predicted protecting variants (PVs) a species has. Moreover, PVs-enriched-genes are enriched in pathways relevant to tumor suppression. For example, they are enriched in the Hedgehog signaling and silencing pathways, which its improper activation is associated with the most common form of cancer malignancy. We also showed that the PVs are mostly more abundant in healthy people compared to cancer patients within different human races.

Keywords: cancer resistance, protecting variant, naked mole rat, comparative genomics

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Authors: Guohua Tu, Zhi Fu, Zhiwei Hu, Neil D Sandham, Jianqiang Chen

Abstract:

Tripping of boundary-layers from laminar to turbulent flow, which may be necessary in specific practical applications, requires high amplitude disturbances to be introduced into the boundary layers without large drag penalties. As a possible improvement on fixed trip devices, a technique based on vortex shedding for enhancing supersonic flow transition is demonstrated in the present paper for a Mach 1.5 boundary layer. The compressible Navier-Stokes equations are solved directly using a high-order (fifth-order in space and third-order in time) finite difference method for small-scale cylinders suspended transversely near the wall. For cylinders with proper diameter and mount location, asymmetry vortices shed within the boundary layer are capable of tripping laminar-turbulent transition. Full three-dimensional simulations showed that transition was enhanced. A parametric study of the size and mounting location of the cylinder is carried out to identify the most effective setup. It is also found that the vortex shedding can be suppressed by some factors such as wall effect.

Keywords: boundary layer instability, boundary layer transition, vortex shedding, supersonic flows, flow control

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