Polygenic Risk Score in African populations: progress and challenges.

Polygenic Risk Score (PRS) analysis is a method that predicts the genetic risk of an individual towards targeted traits. Even when there are no significant markers, it gives evidence of a genetic effect beyond the results of Genome-Wide Association Studies (GWAS). Moreover, it selects  single nucleotide polymorphisms (SNPs) that  contribute to the disease with low effect size  making it more precise at individual level risk prediction. PRS  analysis addresses the shortfall of GWAS by taking into account the SNPs/alleles with  low effect size but play an indispensable role to the observed phenotypic/trait variance.  PRS analysis has  applications that investigate the genetic basis of several traits, which includes rare diseases. However, the accuracy of PRS analysis depends on the genomic data of the underlying population. For instance, several studies  show   that obtaining higher prediction power of PRS analysis is challenging for non-Europeans. In this manuscript, we review the conventional PRS methods and their application to sub-Saharan African communities. We conclude that  lack of sufficient GWAS data and tools is  the limiting factor of applying PRS analysis to sub-Saharan populations.   We recommend developing Africa-specific PRS methods and tools for estimating and analyzing  African population data   for clinical  evaluation of PRSs of interest and predicting  rare diseases.

Large-scale radio propagation path loss measurements and predictions in the VHF and UHF bands.

For decades now, a lot of radio wave path loss propagation models have been developed for predictions across different environmental terrains. Amongst these models, empirical models are practically the most popular due to their ease of application. However, their prediction accuracies are not as high as required. Therefore, extensive path loss measurement data are needed to develop novel measurement-oriented path loss models with suitable correction factors for varied frequency, capturing both local terrain and clutter information, this have been found to be relatively expensive. In this paper, a large-scale radio propagation path loss measurement campaign was conducted across the VHF and UHF frequencies. A multi-transmitter propagation set-up was employed to measure the strengths of radio signals from seven broadcasting transmitters (operating at 89.30, 103.5, 203.25, 479.25, 615.25, 559.25 and 695.25 MHz respectively) at various locations covering a distance of 145.5 km within Nigerian urban environments. The measurement procedure deployed ensured that the data obtained strictly reflect the shadowing effects on radio signal propagation by filtering out the small-scale fading components. The paper also, examines the feasibilities of applying Kriging method to predict distanced-based path losses in the VHF and UHF bands. This method was introduced to minimize the cost of measurements, analysis and predictions of path losses in built-up propagation environments.

Trends and patterns of broadband Internet access speed in a Nigerian university campus: A robust data exploration.

Efficient broadband Internet access is required for optimal productivity in smart campuses. Besides access to broadband Internet, delivery of high speed and good Quality of Service (QoS) are pivotal to achieving a sustainable development in the area of education. In this data article, trends and patterns of the speed of broadband Internet provided in a Nigerian private university campus are largely explored. Data transmission speed and data reception speed were monitored and recorded on daily basis at Covenant University, Nigeria for a period of twelve months (January-December, 2017). The continuous data collection and logging were performed at the Network Operating Center (NOC) of the university using SolarWinds Orion software. Descriptive statistics, correlation and regression analyses, Probability Density Functions (PDFs), Cumulative Distribution Functions (CDFs), Analysis of Variance (ANOVA) test, and multiple comparison post-hoc test are performed using MATLAB 2016a. Extensive statistical visualizations of the results obtained are presented in tables, graphs, and plots. Availability of these data will help network administrators to determine optimal network latency towards efficient deployment of high-speed broadband communication networks in smart campuses.

Exploration of daily Internet data traffic generated in a smart university campus.

In this data article, a robust data exploration is performed on daily Internet data traffic generated in a smart university campus for a period of twelve consecutive (12) months (January-December, 2017). For each day of the one-year study period, Internet data download traffic and Internet data upload traffic at Covenant University, Nigeria were monitored and properly logged using required application software namely: FreeRADIUS; Radius Manager Web application; and Mikrotik Hotspot Manager. A comprehensive dataset with detailed information is provided as supplementary material to this data article for easy research utility and validation. For each month, descriptive statistics of daily Internet data download traffic and daily Internet data upload traffic are presented in tables. Boxplot representations and time series plots are provided to show the trends of data download and upload traffic volume within the smart campus throughout the 12-month period. Frequency distributions of the dataset are illustrated using histograms. In addition, correlation and regression analyses are performed and the results are presented using a scatter plot. Probability Density Functions (PDFs) and Cumulative Distribution Functions (CDFs) of the dataset are also computed. Furthermore, Analysis of Variance (ANOVA) and multiple post-hoc tests are conducted to understand the statistical difference(s) in the Internet traffic volume, if any, across the 12-month period. The robust data exploration provided in this data article will help Internet Service Providers (ISPs) and network administrators in smart campuses to develop empirical model for optimal Quality of Service (QoS), Internet traffic forecasting, and budgeting.

Improved Classification of Lung Cancer Using Radial Basis Function Neural Network with Affine Transforms of Voss Representation.

Lung cancer is one of the diseases responsible for a large number of cancer related death cases worldwide. The recommended standard for screening and early detection of lung cancer is the low dose computed tomography. However, many patients diagnosed die within one year, which makes it essential to find alternative approaches for screening and early detection of lung cancer. We present computational methods that can be implemented in a functional multi-genomic system for classification, screening and early detection of lung cancer victims. Samples of top ten biomarker genes previously reported to have the highest frequency of lung cancer mutations and sequences of normal biomarker genes were respectively collected from the COSMIC and NCBI databases to validate the computational methods. Experiments were performed based on the combinations of Z-curve and tetrahedron affine transforms, Histogram of Oriented Gradient (HOG), Multilayer perceptron and Gaussian Radial Basis Function (RBF) neural networks to obtain an appropriate combination of computational methods to achieve improved classification of lung cancer biomarker genes. Results show that a combination of affine transforms of Voss representation, HOG genomic features and Gaussian RBF neural network perceptibly improves classification accuracy, specificity and sensitivity of lung cancer biomarker genes as well as achieving low mean square error.

Lung cancer prediction using neural network ensemble with histogram of oriented gradient genomic features.

This paper reports an experimental comparison of artificial neural network (ANN) and support vector machine (SVM) ensembles and their "nonensemble" variants for lung cancer prediction. These machine learning classifiers were trained to predict lung cancer using samples of patient nucleotides with mutations in the epidermal growth factor receptor, Kirsten rat sarcoma viral oncogene, and tumor suppressor p53 genomes collected as biomarkers from the IGDB.NSCLC corpus. The Voss DNA encoding was used to map the nucleotide sequences of mutated and normal genomes to obtain the equivalent numerical genomic sequences for training the selected classifiers. The histogram of oriented gradient (HOG) and local binary pattern (LBP) state-of-the-art feature extraction schemes were applied to extract representative genomic features from the encoded sequences of nucleotides. The ANN ensemble and HOG best fit the training dataset of this study with an accuracy of 95.90% and mean square error of 0.0159. The result of the ANN ensemble and HOG genomic features is promising for automated screening and early detection of lung cancer. This will hopefully assist pathologists in administering targeted molecular therapy and offering counsel to early stage lung cancer patients and persons in at risk populations.