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Fulltext Investigating meta-approaches for reconstructing gene networks in a mammalian cellular context

Nazri A, Lio P

PLoS One, 2012;7(1):e28713.
PMID: 22253694 DOI: 10.1371/journal.pone.0028713

The output of state-of-the-art reverse-engineering methods for biological networks is often based on the fitting of a mathematical model to the data. Typically, different datasets do not give single consistent network predictions but rather an ensemble of inconsistent networks inferred under the same reverse-engineering method that are only consistent with the specific experimentally measured data. Here, we focus on an alternative approach for combining the information contained within such an ensemble of inconsistent gene networks called meta-analysis, to make more accurate predictions and to estimate the reliability of these predictions. We review two existing meta-analysis approaches; the Fisher transformation combined coefficient test (FTCCT) and Fisher's inverse combined probability test (FICPT); and compare their performance with five well-known methods, ARACNe, Context Likelihood or Relatedness network (CLR), Maximum Relevance Minimum Redundancy (MRNET), Relevance Network (RN) and Bayesian Network (BN). We conducted in-depth numerical ensemble simulations and demonstrated for biological expression data that the meta-analysis approaches consistently outperformed the best gene regulatory network inference (GRNI) methods in the literature. Furthermore, the meta-analysis approaches have a low computational complexity. We conclude that the meta-analysis approaches are a powerful tool for integrating different datasets to give more accurate and reliable predictions for biological networks.
Fulltext The study of seating pressure on car seat between two national cars

Mohd Hidayat, A.R., Nurul Ain, M., Mohd Nazri, A., Mohd Hairizal, O., Mohammad Khalid, W., Tan, W.H., et al.

Malaysian Journal of Public Health Medicine, 2018;18(102):135-141.
MyJurnal

The main objective of this research is to compare the seating pressure during the driving session between two
different types of national cars. The objective of this research is to conduct object pressure distribution study on
two different types of car seat using CONFORMat (model 5330) with system model CER2, compare and analyse the
results based on object pressure between both car seat. Twelve respondents participated a driving session with
TekscanCONFORMat (model 5330) setup using the same route for both national car. We select two types of national
cars equipped with automatic transmission for this research. The seat pressure on the subject along the journey is
recorded using TekscanCONFORMat Research 7.60 software. Later, comparison made with respect to the seat
pressure experiencedby twelve respondents. The results shows different values of backand seat pressure recorded
among the twelve subjects. Lastly, the results are analysedand discussed at the end of this paper. Model B seat
design has better ability to distribute evenly the pressure to both seat and back. However, results for Model A
showed the pressure is more concentrated on the seat area.
Fulltext PENYEK: Automated brown planthopper detection from imperfect sticky pad images using deep convolutional neural network

Nazri A, Mazlan N, Muharam F

PLoS One, 2018;13(12):e0208501.
PMID: 30571683 DOI: 10.1371/journal.pone.0208501

Rice is a staple food in Asia and it contributes significantly to the Gross Domestic Product (GDP) of Malaysia and other developing countries. Brown Planthopper (BPH) causes high levels of economic loss in Malaysia. Identification of BPH presence and monitoring of its abundance has been conducted manually by experts and is time-consuming, fatiguing and tedious. Automated detection of BPH has been proposed by many studies to overcome human fallibility. However, all studies regarding automated recognition of BPH are investigated based on intact specimen although most of the specimens are imperfect, with missing parts have distorted shapes. The automated recognition of an imperfect insect image is more difficult than recognition of the intact specimen. This study proposes an automated, deep-learning-based detection pipeline, PENYEK, to identify BPH pest in images taken from a readily available sticky pad, constructed by clipping plastic sheets onto steel plates and spraying with glue. This study explores the effectiveness of a convolutional neural network (CNN) architecture, VGG16, in classifying insects as BPH or benign based on grayscale images constructed from Euclidean Distance Maps (EDM). The pipeline identified imperfect images of BPH with an accuracy of 95% using deep-learning's hyperparameters: softmax, a mini-batch of 30 and an initial learning rate of 0.0001.
Complete heart block in young adult with acute rheumatic fever

Nor Hidayah ZA, Azerin O, Mohd Nazri A

Med J Malaysia, 2018 10;73(5):323-325.
PMID: 30350813 MyJurnal

Acute Rheumatic fever (ARF) is commonly associated with ECG abnormalities particularly atrioventricular block. However, third degree atrioventricular block or complete heart block is a rare manifestation. Most cases occurred in children. We reported a 25 year old man who developed complete heart block during an acute episode of ARF. He presented to hospital with five days history of fever, malaise and migrating arthralgia, followed by pleuritic chest pain. One day after admission his electrocardiogram (ECG) revealed complete heart block. Transthoracic echocardiography showed good left ventricular function with thickened, mild mitral regurgitation with minimal pericardial effusion. ASOT titer was positive with elevated white blood count and acute phase reactant. A temporary pacemaker was inserted in view of symptomatic bradycardia. The complete heart block resolved after medical therapy. He was successfully treated with penicillin, steroid and aspirin. He was discharged well with oral penicillin. The rarity of this presentation is highlighted.
Fulltext 3-Dimensional facial expression recognition in human using multi-points warping

Agbolade O, Nazri A, Yaakob R, Ghani AA, Cheah YK

BMC Bioinformatics, 2019 Dec 02;20(1):619.
PMID: 31791234 DOI: 10.1186/s12859-019-3153-2

BACKGROUND: Expression in H-sapiens plays a remarkable role when it comes to social communication. The identification of this expression by human beings is relatively easy and accurate. However, achieving the same result in 3D by machine remains a challenge in computer vision. This is due to the current challenges facing facial data acquisition in 3D; such as lack of homology and complex mathematical analysis for facial point digitization. This study proposes facial expression recognition in human with the application of Multi-points Warping for 3D facial landmark by building a template mesh as a reference object. This template mesh is thereby applied to each of the target mesh on Stirling/ESRC and Bosphorus datasets. The semi-landmarks are allowed to slide along tangents to the curves and surfaces until the bending energy between a template and a target form is minimal and localization error is assessed using Procrustes ANOVA. By using Principal Component Analysis (PCA) for feature selection, classification is done using Linear Discriminant Analysis (LDA).
RESULT: The localization error is validated on the two datasets with superior performance over the state-of-the-art methods and variation in the expression is visualized using Principal Components (PCs). The deformations show various expression regions in the faces. The results indicate that Sad expression has the lowest recognition accuracy on both datasets. The classifier achieved a recognition accuracy of 99.58 and 99.32% on Stirling/ESRC and Bosphorus, respectively.
CONCLUSION: The results demonstrate that the method is robust and in agreement with the state-of-the-art results.
Fulltext Morphometric approach to 3D soft-tissue craniofacial analysis and classification of ethnicity, sex, and age

Agbolade O, Nazri A, Yaakob R, Ghani AA, Cheah YK

PLoS One, 2020;15(4):e0228402.
PMID: 32271782 DOI: 10.1371/journal.pone.0228402

BACKGROUND: The application of three-dimensional scan models offers a useful resource for studying craniofacial variation. The complex mathematical analysis for facial point acquisition in three-dimensional models has made many craniofacial assessments laborious.
METHOD: This study investigates three-dimensional (3D) soft-tissue craniofacial variation, with relation to ethnicity, sex and age variables in British and Irish white Europeans. This utilizes a geometric morphometric approach on a subsampled dataset comprising 292 scans, taken from a Liverpool-York Head Model database. Shape variation and analysis of each variable are tested using 20 anchor anatomical landmarks and 480 sliding semi-landmarks.
RESULTS: Significant ethnicity, sex, and age differences are observed for measurement covering major aspects of the craniofacial shape. The ethnicity shows subtle significant differences compared to sex and age; even though it presents the lowest classification accuracy. The magnitude of dimorphism in sex is revealed in the facial, nasal and crania measurement. Significant shape differences are also seen at each age group, with some distinct dimorphic features present in the age groups.
CONCLUSIONS: The patterns of shape variation show that white British individuals have a more rounded head shape, whereas white Irish individuals have a narrower head shape. White British persons also demonstrate higher classification accuracy. Regarding sex patterns, males are relatively larger than females, especially in the mouth and nasal regions. Females presented with higher classification accuracy than males. The differences in the chin, mouth, nose, crania, and forehead emerge from different growth rates between the groups. Classification accuracy is best for children and senior adult age groups.
Fulltext Investigation of age-related facial variation among Angelman syndrome patients

Agbolade O, Nazri A, Yaakob R, Ghani AA, Cheah YK

Sci Rep, 2021 10 21;11(1):20767.
PMID: 34675349 DOI: 10.1038/s41598-021-99944-z

Angelman syndrome (AS) is one of the common genetic disorders that could emerge either from a 15q11-q13 deletion or paternal uniparental disomy (UPD) or imprinting or UBE3A mutations. AS comes with various behavioral and phenotypic variability, but the acquisition of subjects for experiment and automating the landmarking process to characterize facial morphology for Angelman syndrome variation investigation are common challenges. By automatically detecting and annotating subject faces, we collected 83 landmarks and 10 anthropometric linear distances were measured from 17 selected anatomical landmarks to account for shape variability. Statistical analyses were performed on the extracted data to investigate facial variation in each age group. There is a correspondence in the results achieved by relative warp (RW) of the principal component (PC) and the thin-plate spline (TPS) interpolation. The group is highly discriminated and the pattern of shape variability is higher in children than other groups when judged by the anthropometric measurement and principal component.
Fulltext A novel investigation of the effect of iterations in sliding semi-landmarks for 3D human facial images

Nazri A, Agbolade O, Yaakob R, Ghani AA, Cheah YK

BMC Bioinformatics, 2020 May 24;21(1):208.
PMID: 32448182 DOI: 10.1186/s12859-020-3497-7

BACKGROUND: Landmark-based approaches of two- or three-dimensional coordinates are the most widely used in geometric morphometrics (GM). As human face hosts the organs that act as the central interface for identification, more landmarks are needed to characterize biological shape variation. Because the use of few anatomical landmarks may not be sufficient for variability of some biological patterns and form, sliding semi-landmarks are required to quantify complex shape.
RESULTS: This study investigates the effect of iterations in sliding semi-landmarks and their results on the predictive ability in GM analyses of soft-tissue in 3D human face. Principal Component Analysis (PCA) is used for feature selection and the gender are predicted using Linear Discriminant Analysis (LDA) to test the effect of each relaxation state. The results show that the classification accuracy is affected by the number of iterations but not in progressive pattern. Also, there is stability at 12 relaxation state with highest accuracy of 96.43% and an unchanging decline after the 12 relaxation state.
CONCLUSIONS: The results indicate that there is a particular number of iteration or cycle where the sliding becomes optimally relaxed. This means the higher the number of iterations is not necessarily the higher the accuracy.
Fulltext Vancomycin-resistant Enterococcus faecium of multi locus sequence type 18 in Malaysia

Poh LW, Rukman AW, Cheah YK, Norital Z, Nazri AM, Mariana NS

Med J Malaysia, 2012 Dec;67(6):639-40.
PMID: 23770967 MyJurnal

Vancomycin-resistant Enterococcus faecium (VREF) in human infections mostly belong to the high-risk, epidemic, clonal complex-17 (CC17) group. Treatment limitation and high conjugation frequency makes it dominant in hospitals worldwide. We investigated positive cultures by Pulse-field gel electrophoresis (PFGE), multi locus sequence typing (MLST). DNA of two strains (A2 and C) appeared to be clonally related by PFGE. Three strains were of ST 18 type (A1, B and C) and strain A2 is of a new ST 596. This ST 18 type strain found in our study is crucial and is believed to be the first in Malaysia.
Fulltext Landmark-based homologous multi-point warping approach to 3D facial recognition using multiple datasets

Agbolade O, Nazri A, Yaakob R, Ghani AAA, Cheah YK

PeerJ Comput Sci, 2020;6:e249.
PMID: 33816901 DOI: 10.7717/peerj-cs.249

Over the years, neuroscientists and psychophysicists have been asking whether data acquisition for facial analysis should be performed holistically or with local feature analysis. This has led to various advanced methods of face recognition being proposed, and especially techniques using facial landmarks. The current facial landmark methods in 3D involve a mathematically complex and time-consuming workflow involving semi-landmark sliding tasks. This paper proposes a homologous multi-point warping for 3D facial landmarking, which is verified experimentally on each of the target objects in a given dataset using 500 landmarks (16 anatomical fixed points and 484 sliding semi-landmarks). This is achieved by building a template mesh as a reference object and applying this template to each of the targets in three datasets using an artificial deformation approach. The semi-landmarks are subjected to sliding along tangents to the curves or surfaces until the bending energy between a template and a target form is minimal. The results indicate that our method can be used to investigate shape variation for multiple datasets when implemented on three databases (Stirling, FRGC and Bosphorus).