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Early Detection of Ganoderma Basal Stem Rot of Oil Palms Using Artificial Neural Network Spectral Analysis

Ahmadi P, Muharam FM, Ahmad K, Mansor S, Abu Seman I

Plant Dis, 2017 Jun;101(6):1009-1016.
PMID: 30682927 DOI: 10.1094/PDIS-12-16-1699-RE

Ganoderma boninense is a causal agent of basal stem rot (BSR) and is responsible for a significant portion of oil palm (Elaeis guineensis) losses, which can reach US$500 million a year in Southeast Asia. At the early stage of this disease, infected palms are symptomless, which imposes difficulties in detecting the disease. In spite of the availability of tissue and DNA sampling techniques, there is a particular need for replacing costly field data collection methods for detecting Ganoderma in its early stage with a technique derived from spectroscopic and imagery data. Therefore, this study was carried out to apply the artificial neural network (ANN) analysis technique for discriminating and classifying fungal infections in oil palm trees at an early stage using raw, first, and second derivative spectroradiometer datasets. These were acquired from 1,016 spectral signatures of foliar samples in four disease levels (T1: healthy, T2: mildly-infected, T3: moderately infected, and T4: severely infected). Most of the satisfactory results occurred in the visible range, especially in the green wavelength. The healthy oil palms and those which were infected by Ganoderma at an early stage (T2) were classified satisfactorily with an accuracy of 83.3%, and 100.0% in 540 to 550 nm, respectively, by ANN using first derivative spectral data. The results further indicated that the sensitive frond number modeled by ANN provided the highest accuracy of 100.0% for frond number 9 compared with frond 17. This study showed evidence that employment of ANN can predict the early infection of BSR disease on oil palm with a high degree of accuracy.
Fulltext Evaluating the impacts of land use/land cover changes across topography against land surface temperature in Cameron Highlands

How Jin Aik D, Ismail MH, Muharam FM, Alias MA

PLoS One, 2021;16(5):e0252111.
PMID: 34019599 DOI: 10.1371/journal.pone.0252111

The Cameron Highlands has experienced multiple land encroachment activities and repeated deforestation, leading to extensive land-use and land-cover change (LULCC) during the past six decades. This study aims to determine the LULCC against topography in Cameron Highlands between 2009 and 2019 by using geospatial techniques to analyze Landsat 7 (ETM+) and 8 (OLI/TIRS), ASTER GDEM and MODIS imaging sensors. The results showed a decline of 35.98 km2 in primary forests over ten years across the Cameron Highlands, while agricultural lands and urban areas flourished by a rise of 51.61 km2 and 11.00 km2 respectively. It can be noted that the elevation most affected is between 1000 and 1500 m, across all classes. Further results showed the expansion of both agriculture and urban development onto slopes above 35°, leading to an instability of soil structure. In a comparison of the base years of 2009 with 2019, mean LST results have shown temperatures rising by 7.5°C, while an average between 3 and 4°C across the region is recorded. The results obtained provide new information for government bodies and land planners to coordinate their actions without further jeopardizing the environment of the Cameron Highlands.
Developing a Predictive Model for Plasmodium knowlesi-Susceptible Areas in Malaysia Using Geospatial Data and Artificial Neural Networks

Hod R, Mokhtar SA, Muharam FM, Shamsudin UK, Hisham Hashim J

Asia Pac J Public Health, 2021 Sep 27.
PMID: 34569889 DOI: 10.1177/10105395211048620

Plasmodium knowlesi is an emerging species for malaria in Malaysia, particularly in East Malaysia. This infection contributes to almost half of all malaria cases and deaths in Malaysia and poses a challenge in eradicating malaria. The aim of this study was to develop a predictive model for P. knowlesi susceptibility areas in Sabah, Malaysia, using geospatial data and artificial neural networks (ANNs). Weekly malaria cases from 2013 to 2014 were used to identify the malaria hotspot areas. The association of malaria cases with environmental factors (elevation, water bodies, and population density, and satellite images providing rainfall, land surface temperature, and normalized difference vegetation indices) were statistically determined. The significant environmental factors were used as input for the ANN analysis to predict malaria cases. Finally, the malaria susceptibility index and zones were mapped out. The results suggested integrating geospatial data and ANNs to predict malaria cases, with overall correlation coefficient of 0.70 and overall accuracy of 91.04%. From the malaria susceptibility index and zoning analyses, it was found that areas located along the Crocker Range of Sabah and the East part of Sabah were highly susceptible to P. knowlesi infections. Following this analysis, targetted entomological mapping and malaria control programs can be initiated.
Fulltext Using satellite-measured relative humidity for prediction of Metisa plana's population in oil palm plantations: A comparative assessment of regression and artificial neural network models

Ruslan SA, Muharam FM, Zulkafli Z, Omar D, Zambri MP

PLoS One, 2019;14(10):e0223968.
PMID: 31626637 DOI: 10.1371/journal.pone.0223968

Metisa plana (Walker) is a leaf defoliating pest that is able to cause staggering economical losses to oil palm cultivation. Considering the economic devastation that the pest could bring, an early warning system to predict its outbreak is crucial. The state of art of satellite technologies are now able to derive environmental factors such as relative humidity (RH) that may influence pest population's fluctuations in rapid, harmless, and cost-effective manners. This study examined the relationship between the presence of Metisa plana at different time lags and remote sensing (RS) derived RH by using statistical and machine learning approaches. Metisa plana census data of cumulated larvae instar 1, 2, 3, and 4 were collected biweekly in 2014 and 2015 in an oil palm plantation in Muadzam Shah, Pahang, Malaysia. Relative humidity values derived from Moderate Resolution Imaging Spectroradiometer (MODIS) satellite images were apportioned to 6 time lags; 1 week (T1), 2 weeks (T2), 3 week (T3), 4 weeks (T4), 5 week (T5) and 6 weeks (T6) and paired with the respective census data. Pearson's correlation was carried out to analyse the relationship between Metisa plana and RH at different time lags. Regression analyses and artificial neural network (ANN) were also conducted to develop the best prediction model of Metisa plana's outbreak. The results showed relatively high correlations, positively or negatively, between the presences of Metisa plana with RH ranging from 0.46 to 0.99. ANN was found to be superior to regression models with the adjusted coefficient of determination (R2) between the actual and predicted Metisa plana values ranging from 0.06 to 0.57 versus 0.00 to 0.05. The analysis on the best time lags illustrated that the multiple time lags were more influential on the Metisa plana population than the individual time lags. The best Metisa plana prediction model was derived from T1, T2 and T3 multiple time lags modelled using the ANN algorithm with R2 value of 0.57, errors below 1.14 and accuracies above 93%. Based on the result of this study, the elucidation of Metisa plana's landscape ecology was possible with the utilization of RH as the predictor variable in consideration of the time lag effects of RH on the pest's population.
Fulltext Development of a web-geographical information system application for plotting tuberculosis cases

Mohidem NA, Osman M, Muharam FM, Mohd Elias S, Shaharudin R, Hashim Z

Geospat Health, 2021 Oct 19;16(2).
PMID: 34672178 DOI: 10.4081/gh.2021.980

In the last few decades, public health surveillance has increasingly applied statistical methods to analyze the spatial disease distributions. Nevertheless, contact tracing and follow up control measures for tuberculosis (TB) patients remain challenging because public health officers often lack the programming skills needed to utilize the software appropriately. This study aimed to develop a more user-friendly application by applying the CodeIgniter framework for server development, ArcGIS JavaScript for data display and a web application based on JavaScript and Hypertext Preprocessor to build the server's interface, while a webGIS technology was used for mapping. The performance of this approach was tested based on 3325 TB cases and their sociodemographic data, such as age, gender, race, nationality, country of origin, educational level, employment status, health care worker status, income status, residency status, and smoking status between 1st January 2013 and 31st December 2017 in Gombak, Selangor, Malaysia. These data were collected from the Gombak District Health Office and Rawang Health Clinic. Latitude and longitude of the location for each case was geocoded by uploading spatial data using Google Earth and the main output was an interactive map displaying location of each case. Filters are available for the selection of the various sociodemographic factors of interest. The application developed should assist public health experts to utilize spatial data for the surveillance purposes comprehensively as well as for the drafting of regulations aimed at to reducing mortality and morbidity and thus minimizing the public health impact of the disease.
Fulltext Environment as the risk factor for tuberculosis in Malaysia: a systematic review of the literature

Mohidem NA, Hashim Z, Osman M, Muharam FM, Elias SM, Shaharudin R

Rev Environ Health, 2021 Dec 20;36(4):493-499.
PMID: 34821116 DOI: 10.1515/reveh-2020-0096

OBJECTIVE: To investigate the prevalence and incidence of TB by focusing on its environmental risk factor in Malaysia.
CONTENT: Databases search of Scopus, ScienceDirect, PubMed, Directory of Open Access Journals (DOAJ), Cumulative Index to Nursing and Allied Health Literature (CINAHL) Plus, MyJournal, Biblioteca Regional de Medicina (BIREME), BioMed Central (BMC) Public Health, Medline, Commonwealth Agricultural Bureaux (CAB), EMBASE (Excerpta Medica dataBASE) OVID, and Web of Science (WoS) was performed, which include the article from 1st January 2008 until 31st August 2018 using medical subject heading (MeSH). Articles initially identified were screened for relevance.
SUMMARY: Out of 744 papers screened, nine eligible studies did meet our inclusion criteria. Prison and housing environments were evaluated for TB transmission in living environment, while the other factor was urbanization. However, not all association for these factors were statistically significant, thus assumed to be conflicting or weak to end up with a strong conclusion.
OUTLOOK: Unsustainable indoor environment in high congregate setting and overcrowding remained as a challenge for TB infection in Malaysia. Risk factors for transmission of TB, specifically in high risk areas, should focus on the implementation of specialized program. Further research on health care environment, weather variability, and air pollution are urgently needed to improve the management of TB transmission.
Prediction of tuberculosis cases based on sociodemographic and environmental factors in gombak, Selangor, Malaysia: A comparative assessment of multiple linear regression and artificial neural network models

Mohidem NA, Osman M, Muharam FM, Elias SM, Shaharudin R, Hashim Z

Int J Mycobacteriol, 2021 12 18;10(4):442-456.
PMID: 34916466 DOI: 10.4103/ijmy.ijmy_182_21

Background: Early prediction of tuberculosis (TB) cases is very crucial for its prevention and control. This study aims to predict the number of TB cases in Gombak based on sociodemographic and environmental factors.
Methods: The sociodemographic data of 3325 TB cases from January 2013 to December 2017 in Gombak district were collected from the MyTB web and TB Information System database. Environmental data were obtained from the Department of Environment, Malaysia; Department of Irrigation and Drainage, Malaysia; and Malaysian Metrological Department from July 2012 to December 2017. Multiple linear regression (MLR) and artificial neural network (ANN) were used to develop the prediction model of TB cases. The models that used sociodemographic variables as the input datasets were referred as MLR1 and ANN1, whereas environmental variables were represented as MLR2 and ANN2 and both sociodemographic and environmental variables together were indicated as MLR3 and ANN3.
Results: The ANN was found to be superior to MLR with higher adjusted coefficient of determination (R2) values in predicting TB cases; the ranges were from 0.35 to 0.47 compared to 0.07 to 0.14, respectively. The best TB prediction model, that is, ANN3 was derived from nationality, residency, income status, CO, NO2, SO2, PM10, rainfall, temperature, and atmospheric pressure, with the highest adjusted R2 value of 0.47, errors below 6, and accuracies above 96%.
Conclusions: It is envisaged that the application of the ANN algorithm based on both sociodemographic and environmental factors may enable a more accurate modeling for predicting TB cases.
Fulltext Association of sociodemographic and environmental factors with spatial distribution of tuberculosis cases in Gombak, Selangor, Malaysia

Mohidem NA, Osman M, Hashim Z, Muharam FM, Mohd Elias S, Shaharudin R

PLoS One, 2021;16(6):e0252146.
PMID: 34138899 DOI: 10.1371/journal.pone.0252146

Tuberculosis (TB) cases have increased drastically over the last two decades and it remains as one of the deadliest infectious diseases in Malaysia. This cross-sectional study aimed to establish the spatial distribution of TB cases and its association with the sociodemographic and environmental factors in the Gombak district. The sociodemographic data of 3325 TB cases such as age, gender, race, nationality, country of origin, educational level, employment status, health care worker status, income status, residency, and smoking status from 1st January 2013 to 31st December 2017 in Gombak district were collected from the MyTB web and Tuberculosis Information System (TBIS) database at the Gombak District Health Office and Rawang Health Clinic. Environmental data consisting of air pollution such as air quality index (AQI), carbon monoxide (CO), nitrogen dioxide (NO2), sulphur dioxide (SO2), and particulate matter 10 (PM10,) were obtained from the Department of Environment Malaysia from 1st July 2012 to 31st December 2017; whereas weather data such as rainfall were obtained from the Department of Irrigation and Drainage Malaysia and relative humidity, temperature, wind speed, and atmospheric pressure were obtained from the Malaysia Meteorological Department in the same period. Global Moran's I, kernel density estimation, Getis-Ord Gi* statistics, and heat maps were applied to identify the spatial pattern of TB cases. Ordinary least squares (OLS) and geographically weighted regression (GWR) models were used to determine the spatial association of sociodemographic and environmental factors with the TB cases. Spatial autocorrelation analysis indicated that the cases was clustered (p<0.05) over the five-year period and year 2016 and 2017 while random pattern (p>0.05) was observed from year 2013 to 2015. Kernel density estimation identified the high-density regions while Getis-Ord Gi* statistics observed hotspot locations, whereby consistently located in the southwestern part of the study area. This could be attributed to the overcrowding of inmates in the Sungai Buloh prison located there. Sociodemographic factors such as gender, nationality, employment status, health care worker status, income status, residency, and smoking status as well as; environmental factors such as AQI (lag 1), CO (lag 2), NO2 (lag 2), SO2 (lag 1), PM10 (lag 5), rainfall (lag 2), relative humidity (lag 4), temperature (lag 2), wind speed (lag 4), and atmospheric pressure (lag 6) were associated with TB cases (p<0.05). The GWR model based on the environmental factors i.e. GWR2 was the best model to determine the spatial distribution of TB cases based on the highest R2 value i.e. 0.98. The maps of estimated local coefficients in GWR models confirmed that the effects of sociodemographic and environmental factors on TB cases spatially varied. This study highlighted the importance of spatial analysis to identify areas with a high TB burden based on its associated factors, which further helps in improving targeted surveillance.
Fulltext Relationship between High Temperature and Formation of Chalkiness and Their Effects on Quality of Rice

Nevame AYM, Emon RM, Malek MA, Hasan MM, Alam MA, Muharam FM, et al.

Biomed Res Int, 2018;2018:1653721.
PMID: 30065932 DOI: 10.1155/2018/1653721

Occurrence of chalkiness in rice is attributed to genetic and environmental factors, especially high temperature (HT). The HT induces heat stress, which in turn compromises many grain qualities, especially transparency. Chalkiness in rice is commonly studied together with other quality traits such as amylose content, gel consistency, and protein storage. In addition to the fundamental QTLs, some other QTLs have been identified which accelerate chalkiness occurrence under HT condition. In this review, some of the relatively stable chalkiness, amylose content, and gel consistency related QTLs have been presented well. Genetically, HT effect on chalkiness is explained by the location of certain chalkiness gene in the vicinity of high-temperature-responsive genes. With regard to stable QTL distribution and availability of potential material resources, there is still feasibility to find out novel stable QTLs related to chalkiness under HT condition. A better understanding of those achievements is essential to develop new rice varieties with a reduced chalky grain percentage. Therefore, we propose the pyramiding of relatively stable and nonallelic QTLs controlling low chalkiness endosperm into adaptable rice varieties as pragmatic approach to mitigate HT effect.