Integrated Machine Learning and Bioinformatics Approaches for Prediction of Cancer-Driving Gene Mutations

Cancer arises from the accumulation of somatic mutations and genetic alterations in cell division checkpoints and apoptosis, this often leads to abnormal tumor proliferation. Proper classification of cancer-linked driver mutations will considerably help our understanding of the molecular dynamics of cancer. In this study, we compared several cancer-specific predictive models for prediction of driver mutations in cancer-linked genes that were validated on canonical data sets of functionally validated mutations and applied to a raw cancer genomics data. By analyzing pathogenicity prediction and conservation scores, we have shown that evolutionary conservation scores play a pivotal role in the classification of cancer drivers and were the most informative features in the driver mutation classification. Through extensive comparative analysis with structure-functional experiments and multicenter mutational calling data from PanCancer Atlas studies, we have demonstrated the robustness of our models and addressed the validity of computational predictions. We evaluated the performance of our models using the standard diagnostic metrics such as sensitivity, specificity, area under the curve and F-measure. To address the interpretability of cancer-specific classification models and obtain novel insights about molecular signatures of driver mutations, we have complemented machine learning predictions with structure-functional analysis of cancer driver mutations in several key tumor suppressor genes and oncogenes. Through the experiments carried out in this study, we found that evolutionary-based features have the strongest signal in the machine learning classification VII of driver mutations and provide orthogonal information to the ensembled-based scores that are prominent in the ranking of feature importance

The Prevalence of Chronic Disease Risk Behaviors and Their Association with Hypertension in Racial/Ethnic Minorities: an Examination of NHANES Data 2015-2016

INTRODUCTION: Insufficient physical activity, poor diet, tobacco use, and excessive alcohol consumption are each associated with the prevalence of chronic diseases such as hypertension. However, the clustering or co-occurrence of these chronic disease risk behaviors with the prevalence of hypertension among different racial/ethnic groups has not been fully investigated. Understanding the significance of this relationship is essential for efforts in prevention, as well as the alleviation of disparities in hypertension. AIM: To examine racial/ethnic differences in the relationship between clustered chronic disease risk behaviors and hypertension. METHODS: Data was obtained from the 2015-2016 National Health and Nutrition Examination Survey. Only participants that identified as Hispanic American, non-Hispanic Black, and non-Hispanic White who were ≥21 years old were eligible. Odds ratios from univariate and multivariate logistic regression were applied to the data to measure the association between risk behaviors and hypertension. RESULTS: Pearson chi-squared test showed non-Hispanic Blacks had a significantly higher prevalence of hypertension (62.9%) than Hispanic Americans (53.6%) and Non-Hispanic Whites (53.7%; P\u3c .001). In those with hypertension, a large proportion (40.2%) presented two risk behaviors; the most frequent combination being lack of sufficient physical activity and poor diet (41.2%). After adjusting for age, poverty income ratio, education, and body mass index; increase in the number of risk behaviors presented an association with increased odds of having hypertension in all racial/ethnic groups. Hispanic Americans were found to have significantly higher odds for having hypertension with an increased number of risk behaviors (1, 2 and 3 risk behaviors). Also, non-Hispanic Blacks were found to have a considerably higher risk for hypertension with increased age and body mass index. With the exception for Non-Hispanic Whites, increased poverty income ratio was associated with decreased odds for having hypertension. DISCUSSION: The findings of this study confirm a positive relationship between multiple risk behaviors and increased odds of having hypertension. Interventions should focus on the prevention of co-occurring risk behaviors and the promotion of healthy lifestyle choices; specifically, in non-Hispanic Blacks and Hispanic Americans to decrease racial/ethnic disparities in hypertension. In addition, to address the context in which these risk behaviors occur, efforts should incorporate social and behavioral change theories and frameworks

Evaluation of when road space prioritisation/infrastructural improvements for paratransit vehicles is warranted: A case study of Mitchells Plain, Cape Town

In many developing countries, the cities have confined or absolute non-availability of modern quality public transport systems, therefore residents of these cities solely rely on non-scheduled, informal, flexible route transportation system referred to as ‘Paratransit’ to move from one point to another. South Africa being a partly developed and partly developing country also have this particular problem in terms of its public transport system. Some 65% of public transport users make use of paratransit services as a day to day means of transport in South Africa. Paratransit is the most commonly used public transport mode in South African cities as it is relatively affordable and highly flexible. However, it is referred to be very unreliable in terms of journey time and passenger’s waiting time at stops mostly, due to time wasted in traffic congestion and at signalised intersections. So, actions are needed to be taken to improve the travel speed, safety and reliability of paratransit vehicles. In 2007, South Africa’s department of transport envisioned some strategies to revitalise public transport system in South Africa whereby one of the strategies is to replace paratransit called Mini-bus taxi in South Africa with scheduled trunk-feeder services. However, this has proven unachievable, due to resistant from the paratransit association. This dissertation aims to investigate under which traffic condition is road prioritisation/infrastructural improvement is warranted for paratransit vehicles in a trunk-feeder hybrid setting. The dissertation also explored how operations of the paratransit feeders service can be improved through infrastructural improvements and prioritisation on road space using the Mitchells Plain public transport interchange as a case study. An agent-based simulation modelling tool is employed to simulate the present trunk-feeder operations at the Mitchells Plain interchange thereby investigating how the passenger travel performance has been impacted by the configuration and operational characteristics of the current trunk-feeder public transport system. The modelling tool mimic an intermodal trunk feeder operation which include: Passengers arrival at the rank and stops to wait for taxi; boarding and alighting of passengers along the feeder’s route; transfers of passengers alighting from the taxi and walking of the passengers through the interchange to connect to their respective available trunk service public transport system. The main aim of this dissertation is to develop and investigate various infrastructure developments to the road network using road space prioritisation that can be implemented and their effect on the overall efficiency of the paratransit feeder’s system. Each of the proposed infrastructural improvements through prioritisation of paratransit vehicles on road space was tested in a normal and congested traffic condition to evaluate their effectiveness on the operational efficiency of paratransit feeder’s service at varying level of traffic congestion. The effect of the various network infrastructure improvements is being tested using the agent-based simulation tool with the main objectives of improving the operational performance of the paratransit feeder’s services which will lead to a more coordinated, integrated and sustainable trunk-feeder public transport system. The result of the model analysis showed that provision of dedicated lanes for paratransit vehicles is the most efficient infrastructural improvement strategy through road space prioritisation, especially in a traffic-congested route

Experimental and numerical investigation of high viscosity oil-based multiphase flows

Multiphase flows are of great interest to a large variety of industries because flows of two or more immiscible liquids are encountered in a diverse range of processes and equipment. However, the advent of high viscosity oil requires more investigations to enhance good design of transportation system and forestall its inherent production difficulties. Experimental and numerical studies were conducted on water-sand, oil-water and oilwater- sand respectively in 1-in ID 5m long horizontal pipe. The densities of CYL680 and CYL1000 oils employed are 917 and 916.2kg/m3 while their viscosities are 1.830 and 3.149Pa.s @ 25oC respectively. The solid-phase concentration ranged from 2.15e-04 to 10%v/v with mean diameter of 150micron and material density of 2650kg/m3. Experimentally, the observed flow patterns are Water Assist Annular (WA-ANN), Dispersed Oil in Water (DOW/OF), Oil Plug in Water (OPW/OF) with oil film on the wall and Water Plug in Oil (WPO). These configurations were obtained through visualisation, trend and the probability density function (PDF) of pressure signals along with the statistical moments. Injection of water to assist high viscosity oil transport reduced the pressure gradient by an order of magnitude. No significant differences were found between the gradients of oil-water and oil-water-sand, however, increase in sand concentration led to increase in the pressure losses in oil-water-sand flow. Numerically, Water Assist Annular (WA-ANN), Dispersed Oil in Water (DOW/OF), Oil Plug in Water (OPW/OF) with oil film on the wall, and Water Plug in Oil (WPO) flow pattern were successfully obtained by imposing a concentric inlet condition at the inlet of the horizontal pipe coupled with a newly developed turbulent kinetic energy budget equation coded as user defined function which was hooked up to the turbulence models. These modifications aided satisfactory predictions

WOMEN IN CONFLICTUAL SITUATIONS IN THE WAR-TORN DARFUR,SUDAN: AN EXPLOSITION

Women in Africa increasingly bear greater burden of conflicts in which they rarely contribute to the outbreak. Historically, the Geneva Convention of 1949 and their Additional Protocol of 1977 acknowledge women as the most vulnerable members of the population and explicitly contain special measures to protect women during armed conflicts. Rape and sexual violence continue at an alarming rate in the ongoing genocide in Darfur. Rapes and other forms of sexual violence are being used as weapons of war to humiliate, punish, control, inflict fear, and displace women and their communities. These acts constitute grave violations of International Human Rights and Humanitarian Law, including war crimes against humanity. It should be noted that African women face shelling, famine, epidemics, forced displacement, detention, torture and execution like other civilians caught up in the maelstrom of war. Mass rapes in Darfur effectively terrorize women, break their will, and destroy the fabric of the society. Rape also has serious economic and social consequences in Darfurian society by making the victims ineligible for marriage and ostracized by the community and the family members. The economic and political implications of war are also noticeable in the way women that are internally displaced ( I D Ps) and refugees are being forced to exchange sexual favors in desperation for goods and services by the Sudanese security forces, including police deployed to protect them. It is pertinent to note that documented cases of rape or sexual violence in war time only represent the tip of the iceberg. In war and also during peace time. the stigma associated with rape and the victim's self-blame mean that the vast majority of cases go unreported. Therefore , sympathetic care and counseling for victims are essential to regain their self-esteem, dignity, and to facilitate their reintegration into society and family life. There should be greater recognition of the scourge of sexual violence, as well as public condemnation, with strict enforcement of existing national and international laws

IMPACT OF TEACHERS’ INCENTIVE ON PERFORMANCE OF PHYSICAL AND HEALTH EDUCATION TEACHERS

Poor academic achievement of pupils in Nigerian primary schools together with its attendant problems has been worrisome to stakeholders in education system such that several factors like teachers’ incentives and other perennial problems has been pointed to as the cause of its occurrence. This study investigates the impact of teachers’ incentive on teachers’ performance in primary schools in Ogun State. A descriptive survey research design and simple random sampling technique was used to select 100 teachers from both private and public schools for the study. A self-developed questionnaire was used to collect data for the study while collected data analyzed using ANOVA statistics. The findings showed that (i) there is significant difference in teachers’ condition of service and teachers performance in primary school (F (1,98) = 10.245, P < 0.05), (ii) there is significant difference between teachers’ fringe benefit and teachers performance (F (1,98) = 8.133, P < 0.05), (iii) the relationship between teachers’ incentive and teachers’ performance in primary school is positive and significant (r = 0.146* at p < 0.05). It was suggested that government should improve welfare packages, condition of service and other benefits of teachers.  Article visualizations