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

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

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

Strategies For Effecting Gender Balance And The Position of Nigerian State

The concept of gender was used during the early 1970's as an analytical category to draw a line of demaccation between biological sex differences. The way the differences are UKd to infonn behaviors and competencies are as either "Masculine or feminine". Gender balancing has to do with equality of the sexes in socia~ economic and political issue. A gender hierarchy is part of all societies regardless of their level of technical development and Nigeria is.no exception. There is the need to balance the roles of male and female in the society and Nigeria needs to maintain a positive and effective position in this regard. A clear understanding of the role and responsibilities of men and women is crucial in identifYing areas for effecting gender balance. The position of Nigeria, a country of great diversity of 250 ethnic groups and over 120 million people remains tbatthe males dictate the pace for the society as a whole. There bas always been a missing gap in gender equality or balance in Nigeria though the gap between opportunities for men and Women is narrowing strategies for effecting gender balance in Nigeria are more compelling today than ever

The Internal Migration and Livelihood Strategies of the Benue Children and Youths in Lagos, Ogun and Oyo States in Nigeria Due to Ripple Effects of Global Economic Downturn

Benue state is named after the River Benue, one of Nigeria’s two principal rivers. It is located in the North-Central geo-political zone in Nigeria. It is bordered on the North by Nasarawa state, the East by Taraba state, and the West by Kogi state and in the South by Cross River, Enugu and Ebonyi states. The Cameroonian border is located on the Southeast. As with most central states, Benue is a boiling pot of ethnic groups dominated by the Tiv and Idoma people. Other ethnic groups indigenous to the state include Igede, Etulo and Abakwa. Benue state is a rich agricultural region that produces crops such as yam, rice and cassava, and fruits such as oranges and mangoes, with yam and cassava being the main crop. The state also has a vibrant fishing community. According to the 2006 census the Benue state is home to over 4 million people and has 23 local government areas (LGAs) with the capital located in Makurdi LGA. Most people in Benue State live in rural areas. Farming is the key livelihood activity in Benue State for male heads of household living. Sources of livelihood diversification include agro-processing, trade and crafts, which are linked to access to urban centres and market places. Migration to urban areas or rural areas elsewhere in Nigeria, such as cocoa plantations in the South, is another important livelihood strategy. Households and individuals employ hired labour on their farms if they have the means to do so. Most women do not own land, but are given access to fields by male relatives and in-laws to cultivate their own crops, in addition to their work on the family fields. Compared with men, women have fewer assets and are less likely to cultivate cash crops. Female-headed households rely more on trading and agro-processing to make a Nigerian average income per capita was estimated at US$ 290 in 2001 (UNICEF), and as many as 65% of the people in Benue State were estimated to be living in poverty in 1996 (NCS-data, FOS 1999). Infrastructure and basic services are in a dilapidated state, and public investment in these sectors is limited. Moreover, over the past two decades farming in Benue has actually become more labour-intensive per unit of harvest because of declining soil fertility, poorly functioning input markets and worsening terms of trade. These developments increase the vulnerability of both households and communities, leading to migration of youths in search of good livelihoods in other parts of Nigeria especially Lagos, Ogun and Oyo States. Benue children of less than eighteen and a little over eighteen years work as housemaids, shop attendants and farm workers and other menial jobs in the case studies of Lagos, Ogun and Oyo States of Nigeria. Methodology: A community-based selection of respondents was used in Ikeja, Ota and Ogbomosho, Lagos, Ogun and Oyo States. Twenty-four (24) villages were randomly selected: two in each of the twelve (12) purposeful selected local government areas (LGA). These LGAs represent the variety of livelihoods in Benue State and the main ethnic groups since the Tiv, Idoma and Igede are living in distinct local government areas. Nine (9) selected LGAs are classified as rural and 3 as (peri)-urban. Data collection and analysis: The outline of the study design was developed in close consultation with stakeholders in Lagos, Ogun and Oyo States and resource persons. The research questions were based on a review of other impact studies. Data collection focused on demographic trends, and reasons for migrating, livelihood strategies, and causes of vulnerability. These data were gathered at individual, household and community level, mainly through in-depth interviews and focus group discussion. Field workers who have the knowledge of local languages and also originated from Benue State were selected. They received a two and half-day training on participatory raid appraisal (PRA) and the specific research tools developed for this study. The study took great care to respect confidentiality and all data has been anonymised. At community level, local leaders were introduced to the objectives of the study and asked for their approval and cooperation in carrying out the study. Selected respondents were again informed about the objectives of the study and their oral consent to participate in the study was asked for. In each of the 10 study sites, a five-day qualitative research exercise was carried out between October, 2010 and January 2011. To gather the detailed data required by the study’s goals and questions, a triangulation of people and data collection methods, involving multiple sources of information (observations, interviews, documents, and audiovisual materials) were used People are more available and access to communities is easier. Over 120 respondents were selected for in-depth interviews based on socio-economic background, gender and the extent to which they had been affected by the global economic downturn that has a ripple effect on the Nigeria’s economy. Data were entered and analysed using SPSS. Comparisons were also made for variables between the different ethnic groups and wealth categories. Statistical significance was analysed using Chi-square tests for categorical variables. The results of the qualitative research and household survey were also triangulated. In this article, most findings are reported in an integrated way; data originating from the household survey are presented as percentages

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

The Diaspora and Nigeria-Ghana Relations (1979-2010)

The migration of Africans within West Africa is far from being a recent phenomenon. People moved within and across the ethnic lines before the colonial era, but in recent times the number of African emigrants has risen significantly, especially in the 21st Century. African diasporas within the African continent, especially in the sub-region of West Africa are often overlooked actors in the area of development and integration. Therefore, this study examined the roles of diasporas in Ghana and Nigeria in the areas of development and sub-regional integration in West Africa and how they are enhanced or diminished by the ECOWAS treaty, as a formal institution of development and integration in West Africa. Also, the contributions of African diasporas outside of West-African countries is an issue that has not been well articulated in the foreign policies of Nigeria and Ghana for the purpose of actualising the integration agenda of the ECOWAS. This study adopted a mixed research design, a combination of qualitative and quantitative methods. Up to 357 Nigerians living in Ghana and 211 Ghanaians living in Nigeria participated in the study. The ratio of males to females among Nigerian diasporas was 8 to 1 while the Ghanaian diasporas had a ratio of about 7 to 1. The mean ages of Nigerian diasporas was 24.6 years and Ghanaian diasporas was 45.6 years. Three research questions were raised and answered. The findings revealed that both Nigerian and Ghanaian diasporas contributed to the social, economic, political and cultural development of Ghana and Nigeria respectively. The present state of diaspora linkages between Nigeria and Ghana was found to be supportive of the sub-regional integration agenda of ECOWAS. The findings of hypotheses revealed that Nigerian and Ghanaian diasporas are contributing to the development of their countries of origin and destination. The formal institutional arrangements such as ECOWAS Protocol was found to be operational and aiding the developmental activities of Ghanaian and Nigerian diasporas. The linkages between Ghanaian and Nigerian diasporas and their countries of destination and origin were found to enhance Nigeria and Ghana bilateral relations. It was concluded that the ECOWAS community leaders aimed at a borderless West Africa when they signed the ECOWAS treaty, but the officials entrusted with implementing the policy seem to be self-centered and not community-oriented. This study recommends among others that in order to facilitate diaspora engagement in the development process of Nigeria and Ghana, the Nigerian and Ghanaian governments should strengthen their links with the existing diaspora networks and organisations, such as religious organisations and communities, associations, and venues of engagement created and maintained by the Nigerian and Ghanaian diasporas

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