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Isolation and Characterization of SARS-CoV-2 in Kenya

American Journal of Molecular Biology 2024年第2期14卷 66-83页

作者： Albina Makio Robinson Mugasiali Irekwa Matthew Mutinda Munyao Caroline Wangui Njoroge Peter Kipkemboi Rotich Tonny Teya Nyandwaro Joanne Jepkemei Yego Anne Wanjiru Mwangi james Hungo kimotho Ronald Tanui Vincent Rutto Samson Muuo Nzou Center for Traditional Medicine and Drug Research Kenya Medical Research Institute Nairobi Kenya Center for Microbiology Research Kenya Medical Research Institute Nairobi Kenya Production Department Kenya Medical Research Institute Nairobi Kenya Department of Biochemistry and Microbiology Rhodes University Grahamstown South Africa Center for Virus Research Kenya Medical Research Institute Nairobi Kenya

The discovery of Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) in Wuhan, Hubei province, China, in December 2019 raised global health warnings. Quickly, in 2020, the virus crossed borders and infected individuals across the world, evolving into the COVID-19 pandemic. Notably, early signs of the virus’s existence were observed in various countries before the initial outbreak in Wuhan. As of 12th of April, the respiratory disease had infected over 762 million people worldwide, with over 6.8 million deaths recorded. This has led scientists to focus their efforts on understanding the virus to develop effective means to diagnose, treat, prevent, and control this pandemic. One of the areas of focus is the isolation of this virus, which plays a crucial role in understanding the viral dynamics in the laboratory. In this study, we report the isolation and detection of locally circulating SARS-CoV-2 in Kenya. The isolates were cultured on Vero Cercopithecus cell line (CCL-81) cells, RNA extraction was conducted from the supernatants, and reverse transcriptase-polymerase chain reaction (RT-PCR). Genome sequencing was done to profile the strains phylogenetically and identify novel and previously reported mutations. Vero CCL-81 cells were able to support the growth of SARS-CoV-2 in vitro, and mutations were detected from the two isolates sequenced (001 and 002). Genome sequencing revealed the circulation of two isolates that share a close relationship with the Benin isolate with the D614G common mutation identified along the S protein. These virus isolates will be expanded and made available to the Kenya Ministry of Health and other research institutions to advance SARS-CoV-2 research in Kenya and the region.

关键词： SARS-CoV-2 COVID-19 Whole Genome Sequencing Phylogenetic Analysis Nucleotide Substitutions Amino Acid Changes

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Observer-Based Disturbance Accommodation Control Strategy for Useful Lifetime Control and Structural Load Mitigation of Wind Turbines

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Journal of Power and Energy Engineering 2022年第7期10卷 31-55页

作者： Rutendo Goboza Jackson Githu Njiri james Kuria kimotho Department of Mechatronic Engineering Pan African University Institute for Basic Sciences Technology and Innovation Nairobi Kenya Department of Mechatronic Engineering Jomo Kenyatta University of Agriculture and Technology Nairobi Kenya Department of Mechanical Engineering Jomo Kenyatta University of Agriculture and Technology Nairobi Kenya

Wind turbines undergo degradation due to various factors which induce stress, thereby leading to fatigue damage to various wind turbine components. In addition, the current increase in demand for electrical power has led to the development of large wind turbines, which result in increased structural loads, therefore, increasing the possibility of early failure due to fatigue load. This paper proposes a proportional integral observer (PI-Observer) based disturbance accommodation controller (DAC) with individual pitch control (IPC) for load mitigation to reduce components’ damage and ensure the wind turbine is operational for the expected lifetime. The results indicate a reduction in blades’ bending moments with a standard deviation of 15.9%, which positively impacts several other wind turbine subsystems. Therefore, the lifetime control strategy demonstrates effective structural load mitigation without compromise on power generation, thus, achieving a nominal lifetime control to inhibit premature failure.

关键词： Disturbance Accommodation Control Individual Pitch Control Lifetime Control Structural Load Mitigation

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Experimental Study of the Motion Modes of a Planar Mechanical System with Multi-Clearance Revolute Joints

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Open Journal of Applied Sciences 2023年第11期13卷 2014-2031页

作者： Kifatsoa Kolani Mutuku Muvengei Joshua Ngoret james kimotho Department of Mechanical and Mechatronics Engineering Pan African University Institute for Basic Sciences Technology and Innovation Nairobi Kenya College of Engineering and Technology (COETEC) Jomo Kenyatta University of Agriculture and Technology Nairobi Kenya

Clearances in joints of a mechanical multibody system can induce impulsive forces, leading to vibrations that compromise the system’s reliability, stability, and lifespan. Through dynamic analysis, designers can investigate the effects of the clearances on the dynamics of the multibody system. A revolute joint with clearance exhibits three motions which are;free-flight, impact and continuous contact motion modes. Therefore, a multibody system with n-number of revolute clearance joints will exhibit 3n motion modes which are a combination of the three motions in each joint. This study investigates experimentally the nine motion modes in a mechanical system with two revolute clearance joints. A slider crank mechanism has been used as the demonstrative example. We observed that the experimental curve exhibits a greater impact compared to the simulation curve. In conclusion, this experimental investigation offers valuable insights into the dynamics of planar mechanical systems with multiple clearance revolute joints. Utilizing a slider-crank mechanism for data acquisition, the study successfully confirmed seven out of nine motion modes previously identified in numerical research. The missing modes are attributed to inherent complexities in real-world systems, such as journal-bearing misalignment.

关键词： Slider Crank Mechanism Dynamic Responses Revolute Clearance Joints Motion Modes

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Performance Simulation of a Modified Geothermal Grain Dryer Based at Menengai Well 3 in Kenya

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World Journal of Engineering and Technology 2022年第1期10卷 59-87页

作者： Levi Kulundu Hiram Ndiritu Gareth Kituu james kimotho Mechanical Engineering Department Pan African University Institute for Basic Sciences Technology and Innovation Nairobi Kenya College of Engineering and Technology Jomo Kenyatta University of Agriculture and Technology Nairobi Kenya

Geothermal energy can be effectively utilized for grain drying to reduce carbon emissions and also cut operational costs associated with conventional methods. The main challenges encountered in the use of the geothermal grain dryer, such as in Menengai, Kenya, include uneven grain drying and long throughput times. Grains near the hot air inlet dry at a faster rate compared to those near the exhaust end. Therefore, the grains must be recirculated within the dryer to achieve uniform moisture distribution. Grain recirculation is energy-intensive as it utilizes electricity running the elevator motors in addition to the suction pump. A Computational Fluid Dynamics (CFD) model was developed to study the airflow pattern and its impact on drying of maize. The model was simulated in ANSYS 21 and validated using experimental data. Finite volume discretization method was employed for meshing. Pressure-based segregated solver was used in the Computational Fluid Dynamics (CFD) simulation. Also, K-Omega turbulent model was used for enhancing wall treatment. The findings indicate that non-uniform hot air distribution across the grain buffer section causes uneven drying. Introducing filleted flow-guides results in a relatively uniform velocity, temperature, and turbulence kinetic energy distribution across the dryer. The average velocity and temperature magnitudes in lower compartments increased by 153.3% and 0.25% respectively for the improved dryer. In the upper compartments, the velocity and temperature increase were 176.5% and 0.22% respectively.

关键词： Filleted Flow-Guides Flow Distribution Geothermal Grain Dryer Computational Fluid Dynamics

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Fusion of Model-Based and Data Driven Based Fault Diagnostic Methods for Railway Vehicle Suspension

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Journal of Intelligent Learning Systems and Applications 2020年第3期12卷 51-81页

作者： Abdulai Ayirebi Ankrah james Kuria kimotho Onesmus Mutuku Muvengei Department of Mechanical Engineering PAUSTI Nairobi Kenya Department of Mechanical Engineering JKUAT Nairobi Kenya

Transportation of freight and passengers by train is one of the oldest types of transport, and has now taken root in most of the developing countries especially in Africa. Recently, with the advent and development of high-speed trains, continuous monitoring of the railway vehicle suspension is of significant importance. For this reason, railway vehicles should be monitored continuously to avoid catastrophic events, ensure comfort, safety, and also improved performance while reducing life cycle costs. The suspension system is a very important part of the railway vehicle which supports the car-body and the bogie, isolates the forces generated by the track unevenness at the wheels and also controls the attitude of the car-body with respect to the track surface for ride comfort. Its reliability is directly related to the vehicle safety. The railway vehicle suspension often develops faults;worn springs and dampers in the primary and secondary suspension. To avoid a complete system failure, early detection of fault in the suspension of trains is of high importance. The main contribution of the research work is the prediction of faulty regimes of a railway vehicle suspension based on a hybrid model. The hybrid model framework is in four folds;first, modeling of vehicle suspension system to generate vertical acceleration of the railway vehicle, parameter estimation or identification was performed to obtain the nominal parameter values of the vehicle suspension system based on the measured data in the second fold, furthermore, a supervised machine learning model was built to predict faulty and healthy state of the suspension system components (damage scenarios) based on support vector machine (SVM) and lastly, the development of a new SVM model with the damage scenarios to predict faults on the test data. The level of degradation at which the spring and damp

关键词： Railway Vehicle Suspension System Hybird Model Fault Detection Support Vector Machine

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Performance Improvement of Truck Assembly Line through Modeling and Simulation Using Arena Software

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Open Journal of Optimization 2021年第3期10卷 88-100页

作者： Bi-Foua Tanguy Emmanuel Lorou Peter N. Muchiri Patrick Kuloba james K. kimotho Department of Mechanical Engineering Pan African University of Basic Science Technology and Innovation Nairobi Kenya Department of Mechanical Engineering Dedan Kimathi University of Technology Nyeri Kenya Department of Mechanical Engineering Jomo Kenyatta University of Agriculture and Technology Nairobi Kenya

Due to global completion in the automotive industry, productivity improvement is vital in these industries. In automotive assembly lines, productivity loses are attributed to bottlenecks, long processing time in workstations and underutilization of resources. The purpose of this research is to evaluate the performance of the production system, analyze the bottlenecks in different parts of the workstation, their capacity and constraints. Also, develop different scenarios for improvement. To achieve this objective, a simulation model was developed using Arena Software to analyze bottlenecks in each workstation. The analysis was based on the queue in the system to identify the longest queue in workstations. After analysis of the assembly line, the result showed that the longest waiting time observed is cab preparation and drop, bumper, engine subassembly fitment of soundproof with respective numbers 14.4, 13.97, 13.00, 13.70 minutes, with respective average number waiting of 24.87%, 17.57%, 25.91% and 23.39%. Using different scenarios for the improvement of the production line showed that the waiting time observed in-cab preparation and drop, bumper, engine subassembly, fitment of soundproof has greatly reduced for the two workstations added and three operators respectively from 14.4 to 3.97 and 3.1, from 13.97 to 3.77 and 2.48, from 13.00 to 4.21 and 3.83, from 13.70 to 0.00 and 2.37 minutes, with respective average number waiting from 24.87% to 5% and 2%, from 17.57% to 5% and 0.9%, from 25.91% to 5% and 4%, and from 23.39% to 0.00% and 3%. To conclude the research study was able to demonstrate the modelling approach using simulation for analysis of a production line assembly. The contribution of this research was so enormous, this study has improved the output production up to 144%.

关键词： Simulation Arena Productivity Automotive Industry

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Identification and Characterization of Hepatitis B Virus Immune Escape Mutants in Kenya

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American Journal of Molecular Biology 2023年第1期13卷 1-17页

作者： Rhoda Elizabeth King james kimotho Rosaline Macharia Faith Njoki Ndung’u Samson Muuo Nzou Robinson Mugasiali Irekwa Department of Molecular Biology and Biotechnology Institute for Basic Sciences Technology and Innovation Pan African University Nairobi Kenya Department of Innovation Technology and Transfer Kenya Medical Research Institute Nairobi Kenya Department of Biochemistry University of Nairobi Nairobi Kenya Department for Microbiology Research Kenya Medical Research Institute Nairobi Kenya

Hepatitis B Virus (HBV) infections affect about 400 million people globally and cause about 1.4 million deaths annually. The virus displays high levels of genetic variations/mutations, some of which are immune escape mutants. The prevalence of HBV infection in Kenya is high at about 8%. This study aimed at identifying and characterizing HBV immune escape mutants in Kenya. From 547 HBV sequences available in Kenya in NCBI, and HBVdb databases in July 2021, 120 full sequences were retrieved. The S gene sequences at position 1-225, which included the “a” determinant region of the gene were analyzed using various bioinformatics tools such as Bioedit software, and Emboss Cons. The clinical significance was flagged from the search of peer-reviewed journals. Forty-six HBV-positive blood donor samples were obtained from the Kenya National Blood Transfusion Services without personal identifiers, DNA extracted, and sequenced targeting positions 1 to 520 of S genes. Mutations were similarly identified from seventeen sequences after cleaning and analysis. Out of 120 sequences that were extracted from databases and analyzed, 79 different mutations were identified. Fifteen of them were of clinical importance with an occurrence frequency of at least 5% were obtained. The majority (64.6%, n = 51), with S207N and A194V being most dominant, could result in immune escape and reduced HBsAg detection signals while 24.1% (n = 19) could result in immune escape/reduced HBsAg detection signals and high probability of hepatocellular carcinoma. Most likely to occur on the amino acids Alanine, Lysine, Serine, Asparagine, and Valine in decreasing order. The most dominant genotype was found to be Genotype A (N = 10), while four sequences were Genotype D. In contrast to the in-silico studies, the sequences from HBV samples from blood donors did not demonstrate the presence of S207N and A194V mutations and all the genotypes were type A1. Only two (13.3%) samples showed the same mutations of sK122R

关键词： Hepatitis B Virus Mutations Hepatitis B Surface Antigen Gene Genotype

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Interaction between climatic, environmental, and demographic factors on cholera outbreaks in Kenya

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Infectious Diseases of Poverty 2014年第1期3卷 338-346页

作者： james D Stoltzfus Jane Y Carter Muge Akpinar-Elci Martin Matu Victoria kimotho Mark J Giganti Daniel Langat Omur Cinar Elci School of Medicine Department of Public Health and Preventive MedicineSt.George’s University(SGU)West IndiesGrenada African Medical and Research Foundation(AMREF) NairobiKenya. Center for Global Health College of Health SciencesOld Dominion UniversityNorfolkVAUSA

Background:Cholera remains an important public health concern in developing countries including Kenya where 11,769 cases and 274 deaths were reported in 2009 according to the World Health Organization(WHO).This ecological study investigates the impact of various climatic,environmental,and demographic variables on the spatial distribution of cholera cases in ***:District-level data was gathered from Kenya’s Division of Disease Surveillance and Response,the Meteorological Department,and the National Bureau of *** data included the entire population of Kenya from 1999 to ***:Multivariate analyses showed that districts had an increased risk of cholera outbreaks when a greater proportion of the population lived more than five kilometers from a health facility(RR:1.025 per 1%increase;95%CI:1.010,1.039),bordered a body of water(RR:5.5;95%CI:2.472,12.404),experienced increased rainfall from October to December(RR:1.003 per 1 mm increase;95%CI:1.001,1.005),and experienced decreased rainfall from April to June(RR:0.996 per 1 mm increase;95%CI:0.992,0.999).There was no detectable association between cholera and population density,poverty,availability of piped water,waste disposal methods,rainfall from January to March,or rainfall from July to ***:Bordering a large body of water,lack of health facilities nearby,and changes in rainfall were significantly associated with an increased risk of cholera in Kenya.

关键词： Cholera Education Health infrastructure Population density Poverty Rainfall Waste disposal Water supply

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