Genetic algorithm in ab initio protein structure prediction using low resolution model : a review
- Hoque, Md Tamjidul, Chetty, Madhu, Sattar, Abdul
- Authors: Hoque, Md Tamjidul , Chetty, Madhu , Sattar, Abdul
- Date: 2009
- Type: Text , Book chapter
- Relation: Biomedical Data and Applications p. 317-342
- Full Text:
- Reviewed:
- Description: Proteins are sequences of amino acids bound into a linear chain that adopt a specific folded three-dimensional (3D) shape. This specific folded shape enables proteins to perform specific tasks. The protein structure prediction (PSP) by ab initio or de novo approach is promising amongst various available computational methods and can help to unravel the important relationship between sequence and its corresponding structure. This article presents the ab initio protein structure prediction as a conformational search problem in low resolution model using genetic algorithm. As a review, the essence of twin removal, intelligence in coding, the development and application of domain specific heuristics garnered from the properties of the resulting model and the protein core formation concept discussed are all highly relevant in attempting to secure the best solution.
- Authors: Hoque, Md Tamjidul , Chetty, Madhu , Sattar, Abdul
- Date: 2009
- Type: Text , Book chapter
- Relation: Biomedical Data and Applications p. 317-342
- Full Text:
- Reviewed:
- Description: Proteins are sequences of amino acids bound into a linear chain that adopt a specific folded three-dimensional (3D) shape. This specific folded shape enables proteins to perform specific tasks. The protein structure prediction (PSP) by ab initio or de novo approach is promising amongst various available computational methods and can help to unravel the important relationship between sequence and its corresponding structure. This article presents the ab initio protein structure prediction as a conformational search problem in low resolution model using genetic algorithm. As a review, the essence of twin removal, intelligence in coding, the development and application of domain specific heuristics garnered from the properties of the resulting model and the protein core formation concept discussed are all highly relevant in attempting to secure the best solution.
Extended HP model for protein structure prediction
- Hoque, Md Tamjidul, Chetty, Madhu, Sattar, Abdul
- Authors: Hoque, Md Tamjidul , Chetty, Madhu , Sattar, Abdul
- Date: 2009
- Type: Text , Journal article
- Relation: Computational Biology and Bioinformatics Vol. Jan-Feb 2011, no. (2009 ), p. 234-245
- Full Text: false
- Reviewed:
- Description: This paper presents the impact of twins and the measures for their removal from the population of genetic algorithm (GA) when applied to effective conformational searching. It is conclusively shown that a twin removal strategy for a GA provides considerably enhanced performance when investigating solutions to complex ab initio protein structure prediction (PSP) problems in low-resolution model. Without twin removal, GA crossover and mutation operations can become ineffectual as generations lose their ability to produce significant differences, which can lead to the solution stalling. The paper relaxes the definition of chromosomal twins in the removal strategy to not only encompass identical, but also highly correlated chromosomes within the GA population, with empirical results consistently exhibiting significant improvements solving PSP problems.
DFS based partial pathways in GA for protein structure prediction
- Hoque, Md Tamjidul, Chetty, Madhu, Lewis, Andrew, Sattar, Abdul
- Authors: Hoque, Md Tamjidul , Chetty, Madhu , Lewis, Andrew , Sattar, Abdul
- Date: 2008
- Type: Text , Conference paper
- Relation: Third IAPR International Conference, PRIB 2008
- Full Text:
- Reviewed:
- Description: Nondeterministic conformational search techniques, such as Genetic Algorithms (GAs) are promising for solving protein structure prediction (PSP) problem. The crossover operator of a GA can underpin the formation of potential conformations by exchanging and sharing potential sub-conformations, which is promising for solving PSP. However, the usual nature of an optimum PSP conformation being compact can produce many invalid conformations (by having non-self-avoiding-walk) using crossover. While a crossover-based converging conformation suffers from limited pathways, combining it with depth-first search (DFS) can partially reveal potential pathways. DFS generates random conformations increasingly quickly with increasing length of the protein sequences compared to random-move-only-based conformation generation. Random conformations are frequently applied for maintaining diversity as well as for initialization in many GA variations.
- Authors: Hoque, Md Tamjidul , Chetty, Madhu , Lewis, Andrew , Sattar, Abdul
- Date: 2008
- Type: Text , Conference paper
- Relation: Third IAPR International Conference, PRIB 2008
- Full Text:
- Reviewed:
- Description: Nondeterministic conformational search techniques, such as Genetic Algorithms (GAs) are promising for solving protein structure prediction (PSP) problem. The crossover operator of a GA can underpin the formation of potential conformations by exchanging and sharing potential sub-conformations, which is promising for solving PSP. However, the usual nature of an optimum PSP conformation being compact can produce many invalid conformations (by having non-self-avoiding-walk) using crossover. While a crossover-based converging conformation suffers from limited pathways, combining it with depth-first search (DFS) can partially reveal potential pathways. DFS generates random conformations increasingly quickly with increasing length of the protein sequences compared to random-move-only-based conformation generation. Random conformations are frequently applied for maintaining diversity as well as for initialization in many GA variations.
A novel plasmid-mediated polymyxin resistance determinant (mcr-1.8) in escherichia coli recovered from broiler chickens in Brunei Darussalam
- Momin, Abdul, Liakopoulos, Apostolos, Bean, David, Phee, Lynette, Wareham, David
- Authors: Momin, Abdul , Liakopoulos, Apostolos , Bean, David , Phee, Lynette , Wareham, David
- Date: 2019
- Type: Text , Journal article , Letter
- Relation: Journal of Antimicrobial Chemotherapy Vol. 74, no. 11 (2019), p. 3392-3394
- Full Text:
- Reviewed:
- Description: Sir, MDR Gram-negative bacteria are identified as critical pathogens and their effective treatment increasingly relies on the polymyxins (polymyxin B, colistin), either alone or as part of unorthodox combination therapies.1 The rapid emergence of polymyxin resistance due to mutations/insertions in genes involved in LPS modifications (lpxCAD, pmrA/B, mgrB, phoP/Q, ccrAB) has been reported among individuals exposed to or treated with polymyxins.1Of greater concern are increasing reports of resistance due to the acquisition of phosphoethanolamine (PEtN) transferases, enzymes that catalyse the addition of phosphoethanolamine to lipid A, resulting in lower binding affinity of polymyxins.1 Since the first identification in China,1 multiple gene variants have been reported in diverse bacterial genera recovered from a range of human, retail food, foodproducing animal and environmental sources.2 Here, we report a novel variant of PEtN transferase, designated MCR-1.8, and its genetic context in an MDR Escherichia coli isolate recovered from poultry in Brunei Darussalam.
- Authors: Momin, Abdul , Liakopoulos, Apostolos , Bean, David , Phee, Lynette , Wareham, David
- Date: 2019
- Type: Text , Journal article , Letter
- Relation: Journal of Antimicrobial Chemotherapy Vol. 74, no. 11 (2019), p. 3392-3394
- Full Text:
- Reviewed:
- Description: Sir, MDR Gram-negative bacteria are identified as critical pathogens and their effective treatment increasingly relies on the polymyxins (polymyxin B, colistin), either alone or as part of unorthodox combination therapies.1 The rapid emergence of polymyxin resistance due to mutations/insertions in genes involved in LPS modifications (lpxCAD, pmrA/B, mgrB, phoP/Q, ccrAB) has been reported among individuals exposed to or treated with polymyxins.1Of greater concern are increasing reports of resistance due to the acquisition of phosphoethanolamine (PEtN) transferases, enzymes that catalyse the addition of phosphoethanolamine to lipid A, resulting in lower binding affinity of polymyxins.1 Since the first identification in China,1 multiple gene variants have been reported in diverse bacterial genera recovered from a range of human, retail food, foodproducing animal and environmental sources.2 Here, we report a novel variant of PEtN transferase, designated MCR-1.8, and its genetic context in an MDR Escherichia coli isolate recovered from poultry in Brunei Darussalam.
Serum antinuclear autoantibodies are associated with measures of oxidative stress and lifestyle factors : analysis of LIPIDOGRAM2015 and LIPIDOGEN2015 studies
- Krzemień, Pawel, Kasperczyk, S, Banach, Maciej, Kasperczyk, Aleksandra, Dobrakowski, Michal, Tomasik, Tomasz, Windak, Adam, Mastej, Miroslaw, Catapano, Alberico, Ray, Kausik, Mikhailidis, Dimitri, Toth, Peter, Howard, George, Lip, Gregory, Tomaszewski, Maciej, Charchar, Fadi, Sattar, Naveed, Williams, Bryan, MacDonald, Thomas, Penson, Peter, Jóźwiak, Jacek
- Authors: Krzemień, Pawel , Kasperczyk, S , Banach, Maciej , Kasperczyk, Aleksandra , Dobrakowski, Michal , Tomasik, Tomasz , Windak, Adam , Mastej, Miroslaw , Catapano, Alberico , Ray, Kausik , Mikhailidis, Dimitri , Toth, Peter , Howard, George , Lip, Gregory , Tomaszewski, Maciej , Charchar, Fadi , Sattar, Naveed , Williams, Bryan , MacDonald, Thomas , Penson, Peter , Jóźwiak, Jacek
- Date: 2023
- Type: Text , Journal article
- Relation: Archives of Medical Science Vol. 19, no. 5 (2023), p. 1214-1227
- Full Text:
- Reviewed:
- Description: Introduction: Oxidative stress is one of many factors suspected to promote antinuclear autoantibody (ANA) formation. Reactive oxygen species can induce changes in the antigenic structure of macromolecules, causing the immune system to treat them as “neo-antigens” and start production of autoantibodies. This study was designed to evaluate the relationship between oxidative stress markers, lifestyle factors and the detection of ANA. Material and methods: We examined measures of oxidative stress indices of free-radical damage to lipids and proteins, such as total oxidant status (TOS), concentration of protein thiol groups (PSH), and malondialdehyde (MDA), activity of superoxide dismutase (SOD) in 1731 serum samples. The parameters of the non-enzymatic antioxidant system, such as total antioxidant status (TAS) and uric acid (UA) concentration, were also measured and the oxidative stress index (OSI-index) was calculated. All samples were tested for the presence of ANA using an indirect immunofluorescence assay (IIFA). Results: The presence of ANA in women was associated with lower physical activity (p = 0.036), less frequent smoking (p = 0.007) and drinking of alcohol (p = 0.024) accompanied by significant changes in SOD isoenzymes activity (p < 0.001) and a higher uric acid (UA) concentration (p < 0.001). In ANA positive males we observed lower concentrations of PSH (p = 0.046) and increased concentrations of MDA (p = 0.047). Conclusions: The results indicate that local oxidative stress may be associated with increased probability of ANA formation in a sex-specific manner. © 2021 Termedia & Banach.
- Authors: Krzemień, Pawel , Kasperczyk, S , Banach, Maciej , Kasperczyk, Aleksandra , Dobrakowski, Michal , Tomasik, Tomasz , Windak, Adam , Mastej, Miroslaw , Catapano, Alberico , Ray, Kausik , Mikhailidis, Dimitri , Toth, Peter , Howard, George , Lip, Gregory , Tomaszewski, Maciej , Charchar, Fadi , Sattar, Naveed , Williams, Bryan , MacDonald, Thomas , Penson, Peter , Jóźwiak, Jacek
- Date: 2023
- Type: Text , Journal article
- Relation: Archives of Medical Science Vol. 19, no. 5 (2023), p. 1214-1227
- Full Text:
- Reviewed:
- Description: Introduction: Oxidative stress is one of many factors suspected to promote antinuclear autoantibody (ANA) formation. Reactive oxygen species can induce changes in the antigenic structure of macromolecules, causing the immune system to treat them as “neo-antigens” and start production of autoantibodies. This study was designed to evaluate the relationship between oxidative stress markers, lifestyle factors and the detection of ANA. Material and methods: We examined measures of oxidative stress indices of free-radical damage to lipids and proteins, such as total oxidant status (TOS), concentration of protein thiol groups (PSH), and malondialdehyde (MDA), activity of superoxide dismutase (SOD) in 1731 serum samples. The parameters of the non-enzymatic antioxidant system, such as total antioxidant status (TAS) and uric acid (UA) concentration, were also measured and the oxidative stress index (OSI-index) was calculated. All samples were tested for the presence of ANA using an indirect immunofluorescence assay (IIFA). Results: The presence of ANA in women was associated with lower physical activity (p = 0.036), less frequent smoking (p = 0.007) and drinking of alcohol (p = 0.024) accompanied by significant changes in SOD isoenzymes activity (p < 0.001) and a higher uric acid (UA) concentration (p < 0.001). In ANA positive males we observed lower concentrations of PSH (p = 0.046) and increased concentrations of MDA (p = 0.047). Conclusions: The results indicate that local oxidative stress may be associated with increased probability of ANA formation in a sex-specific manner. © 2021 Termedia & Banach.
Novel 1-Methyl-1H-pyrazole-5-carboxamide derivatives with potent anthelmintic activity
- Le, Thuy, Kundu, Abhijit, Ghoshal, Atanu, Nguyen, Nghi, Preston, Sarah, Jiao, Yaqing, Ruan, Banfeng, Xue, Lian, Huang, Fei, Keiser, Jennifer, Hofmann, Andreas, Chang, Bill, Garcia-Bustos, Jose, Wells, Timothy, Palmer, Michael, Jabbar, Abdul, Gasser, Robin, Baell, Jonathan
- Authors: Le, Thuy , Kundu, Abhijit , Ghoshal, Atanu , Nguyen, Nghi , Preston, Sarah , Jiao, Yaqing , Ruan, Banfeng , Xue, Lian , Huang, Fei , Keiser, Jennifer , Hofmann, Andreas , Chang, Bill , Garcia-Bustos, Jose , Wells, Timothy , Palmer, Michael , Jabbar, Abdul , Gasser, Robin , Baell, Jonathan
- Date: 2019
- Type: Text , Journal article
- Relation: Journal of Medicinal Chemistry Vol. 62, no. 7 (2019), p. 3367-3380
- Full Text: false
- Reviewed:
- Description: A phenotypic screen of two different libraries of small molecules against the motility and development of the parasitic nematode Haemonchus contortus led to the identification of two 1-methyl-1H-pyrazole-5-carboxamide derivatives. Medicinal chemistry optimization targeted modifications of the left-hand side, middle section, and right-hand side of the hybrid structure of these two hits to elucidate the structure-activity relationship (SAR). Initial SAR around these hits allowed for the iterative and directed assembly of a focused set of 30 analogues of their hybrid structure. Compounds 10, 17, 20, and 22 were identified as the most potent compounds, inhibiting the development of the fourth larval (L4) stage of H. contortus at sub-nanomolar potencies while displaying strong selectivity toward the parasite when tested in vitro against the human MCF10A cell line. In addition, compounds 9 and 27 showed promising activity against a panel of other parasitic nematodes, including hookworms and whipworms.
Twin removal in genetic algorithms for protein structure prediction using low-resolution model
- Hoque, Md Tamjidul, Chetty, Madhu, Lewis, Andrew, Sattar, Abdul
- Authors: Hoque, Md Tamjidul , Chetty, Madhu , Lewis, Andrew , Sattar, Abdul
- Date: 2011
- Type: Text , Journal article
- Relation: IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol. 8, no. 1 (2011), p. 234-245
- Full Text: false
- Reviewed:
- Description: This paper presents the impact of twins and the measures for their removal from the population of genetic algorithm (GA) when applied to effective conformational searching. It is conclusively shown that a twin removal strategy for a GA provides considerably enhanced performance when investigating solutions to complex ab initio protein structure prediction (PSP) problems in low-resolution model. Without twin removal, GA crossover and mutation operations can become ineffectual as generations lose their ability to produce significant differences, which can lead to the solution stalling. The paper relaxes the definition of chromosomal twins in the removal strategy to not only encompass identical, but also highly correlated chromosomes within the GA population, with empirical results consistently exhibiting significant improvements solving PSP problems.
- Authors: Mestrom, Sanne
- Date: 2012
- Type: Text , Visual art work
- Full Text:
Analysis of the impact of sex and age on the variation in the prevalence of antinuclear autoantibodies in Polish population : a nationwide observational, cross-sectional study
- Krzemie, Kasperczyk, Sławomir, Banach, Maciej, Kasperczyk, Aleksandra, Dobrakowski, Michał, Tomasik, Tomasz, Windak, Adam, Mastej, Mirosław, Catapano, Alberico, Ray, Kausik, Mikhailidis, Dimitri, Toth, Peter, Howard, George, Lip, Gregory, Tomaszewski, Macie, Charchar, Fadi, Sattar, Naveed, Williams, Bryan, MacDonald, Thomas, Penson, Peter, Al-Shaer, B, Andrusewicz, W., Anusz-Gaszewska, E., Balawajder, P., Bańka, G., Barańska-Skubisz E., Przyczyna, B., Bartkowiak S.
- Authors: Krzemie , Kasperczyk, Sławomir , Banach, Maciej , Kasperczyk, Aleksandra , Dobrakowski, Michał , Tomasik, Tomasz , Windak, Adam , Mastej, Mirosław , Catapano, Alberico , Ray, Kausik , Mikhailidis, Dimitri , Toth, Peter , Howard, George , Lip, Gregory , Tomaszewski, Macie , Charchar, Fadi , Sattar, Naveed , Williams, Bryan , MacDonald, Thomas , Penson, Peter , Al-Shaer, B , Andrusewicz, W. , Anusz-Gaszewska, E. , Balawajder, P. , Bańka, G. , Barańska-Skubisz E. , Przyczyna, B. , Bartkowiak S.
- Date: 2022
- Type: Text , Journal article
- Relation: Rheumatology International Vol. 42, no. 2 (2022), p. 261-271
- Full Text:
- Reviewed:
- Description: The detection of antinuclear autoantibody (ANA) is dependent on many factors and varies between the populations. The aim of the study was first to assess the prevalence of ANA in the Polish adult population depending on age, sex and the cutoff threshold used for the results obtained. Second, we estimated the occurrence of individual types of ANA-staining patterns. We tested 1731 patient samples using commercially available IIFA using two cutoff thresholds of 1:100 and 1:160. We found ANA in 260 participants (15.0%), but the percentage of positive results strongly depended on the cutoff level. For a cutoff threshold 1:100, the positive population was 19.5% and for the 1:160 cutoff threshold, it was 11.7%. The most prevalent ANA-staining pattern was AC-2 Dense Fine speckled (50%), followed by AC-21 Reticular/AMA (14.38%) ANA more common in women (72%); 64% of ANA-positive patients were over 50 years of age. ANA prevalence in the Polish population is at a level observed in other highly developed countries and is more prevalent in women and elderly individuals. To reduce the number of positive results released, we suggest that Polish laboratories should set 1:160 as the cutoff threshold. © 2021, The Author(s). **Please note that there are multiple authors for this article therefore only the name of the first 30 including Federation University Australia affiliate “Fadi Charchar" is provided in this record**
- Authors: Krzemie , Kasperczyk, Sławomir , Banach, Maciej , Kasperczyk, Aleksandra , Dobrakowski, Michał , Tomasik, Tomasz , Windak, Adam , Mastej, Mirosław , Catapano, Alberico , Ray, Kausik , Mikhailidis, Dimitri , Toth, Peter , Howard, George , Lip, Gregory , Tomaszewski, Macie , Charchar, Fadi , Sattar, Naveed , Williams, Bryan , MacDonald, Thomas , Penson, Peter , Al-Shaer, B , Andrusewicz, W. , Anusz-Gaszewska, E. , Balawajder, P. , Bańka, G. , Barańska-Skubisz E. , Przyczyna, B. , Bartkowiak S.
- Date: 2022
- Type: Text , Journal article
- Relation: Rheumatology International Vol. 42, no. 2 (2022), p. 261-271
- Full Text:
- Reviewed:
- Description: The detection of antinuclear autoantibody (ANA) is dependent on many factors and varies between the populations. The aim of the study was first to assess the prevalence of ANA in the Polish adult population depending on age, sex and the cutoff threshold used for the results obtained. Second, we estimated the occurrence of individual types of ANA-staining patterns. We tested 1731 patient samples using commercially available IIFA using two cutoff thresholds of 1:100 and 1:160. We found ANA in 260 participants (15.0%), but the percentage of positive results strongly depended on the cutoff level. For a cutoff threshold 1:100, the positive population was 19.5% and for the 1:160 cutoff threshold, it was 11.7%. The most prevalent ANA-staining pattern was AC-2 Dense Fine speckled (50%), followed by AC-21 Reticular/AMA (14.38%) ANA more common in women (72%); 64% of ANA-positive patients were over 50 years of age. ANA prevalence in the Polish population is at a level observed in other highly developed countries and is more prevalent in women and elderly individuals. To reduce the number of positive results released, we suggest that Polish laboratories should set 1:160 as the cutoff threshold. © 2021, The Author(s). **Please note that there are multiple authors for this article therefore only the name of the first 30 including Federation University Australia affiliate “Fadi Charchar" is provided in this record**
Strategic planning and performance- A study of small enterprises in Bangladesh
- Authors: Moyeen, Abdul
- Date: 2008
- Type: Text , Conference paper
- Relation: 2nd ANZAM Conference
- Full Text: false
- Reviewed:
- Ruan, Banfeng, Zhang, Yuezhou, Tadesse, Solomon, Preston, Sarah, Taki, Aya, Jabbar, Abdul, Hofmann, Andreas, Jiao, Yaqing, Garcia-Bustos, Jose, Harjani, Jitendra, Le, Thuy, Varghese, Swapna, Teguh, Silvia, Xie, Yiyue, Odiba, Jephthah, Hu, Min, Gasser, Robin, Baell, Jonathan
- Authors: Ruan, Banfeng , Zhang, Yuezhou , Tadesse, Solomon , Preston, Sarah , Taki, Aya , Jabbar, Abdul , Hofmann, Andreas , Jiao, Yaqing , Garcia-Bustos, Jose , Harjani, Jitendra , Le, Thuy , Varghese, Swapna , Teguh, Silvia , Xie, Yiyue , Odiba, Jephthah , Hu, Min , Gasser, Robin , Baell, Jonathan
- Date: 2020
- Type: Text , Journal article
- Relation: European Journal of Medicinal Chemistry Vol. 190, no. (2020), p.
- Full Text: false
- Reviewed:
- Description: Parasitic roundworms (nematodes) are significant pathogens of humans and animals and cause substantive socioeconomic losses due to the diseases that they cause. The control of nematodes in livestock animals relies heavily on the use of anthelmintic drugs. However, their extensive use has led to a widespread problem of drug resistance in these worms. Thus, the discovery and development of novel chemical entities for the treatment of parasitic worms of humans and animals is needed. Herein, we describe our medicinal chemistry optimization efforts of a phenotypic hit against Haemonchus contortus based on a pyrrolidine-oxadiazole scaffold. This led to the identification of compounds with potent inhibitory activities (IC50 = 0.78–22.4 μM) on the motility and development of parasitic stages of H. contortus, and which were found to be highly selective in a mammalian cell counter-screen. These compounds could be used as suitable chemical tools for drug target identification or as lead compounds for further optimization. © 2020 Elsevier Masson SAS
Soil moisture, organic carbon, and nitrogen content prediction with hyperspectral data using regression models
- Datta, Dristi, Paul, Manoranjan, Murshed, Manzur, Teng, Shyh Wei, Schmidtke, Leigh
- Authors: Datta, Dristi , Paul, Manoranjan , Murshed, Manzur , Teng, Shyh Wei , Schmidtke, Leigh
- Date: 2022
- Type: Text , Journal article
- Relation: Sensors (Basel, Switzerland) Vol. 22, no. 20 (2022), p.
- Full Text:
- Reviewed:
- Description: Soil moisture, soil organic carbon, and nitrogen content prediction are considered significant fields of study as they are directly related to plant health and food production. Direct estimation of these soil properties with traditional methods, for example, the oven-drying technique and chemical analysis, is a time and resource-consuming approach and can predict only smaller areas. With the significant development of remote sensing and hyperspectral (HS) imaging technologies, soil moisture, carbon, and nitrogen can be estimated over vast areas. This paper presents a generalized approach to predicting three different essential soil contents using a comprehensive study of various machine learning (ML) models by considering the dimensional reduction in feature spaces. In this study, we have used three popular benchmark HS datasets captured in Germany and Sweden. The efficacy of different ML algorithms is evaluated to predict soil content, and significant improvement is obtained when a specific range of bands is selected. The performance of ML models is further improved by applying principal component analysis (PCA), a dimensional reduction method that works with an unsupervised learning method. The effect of soil temperature on soil moisture prediction is evaluated in this study, and the results show that when the soil temperature is considered with the HS band, the soil moisture prediction accuracy does not improve. However, the combined effect of band selection and feature transformation using PCA significantly enhances the prediction accuracy for soil moisture, carbon, and nitrogen content. This study represents a comprehensive analysis of a wide range of established ML regression models using data preprocessing, effective band selection, and data dimension reduction and attempt to understand which feature combinations provide the best accuracy. The outcomes of several ML models are verified with validation techniques and the best- and worst-case scenarios in terms of soil content are noted. The proposed approach outperforms existing estimation techniques.
- Authors: Datta, Dristi , Paul, Manoranjan , Murshed, Manzur , Teng, Shyh Wei , Schmidtke, Leigh
- Date: 2022
- Type: Text , Journal article
- Relation: Sensors (Basel, Switzerland) Vol. 22, no. 20 (2022), p.
- Full Text:
- Reviewed:
- Description: Soil moisture, soil organic carbon, and nitrogen content prediction are considered significant fields of study as they are directly related to plant health and food production. Direct estimation of these soil properties with traditional methods, for example, the oven-drying technique and chemical analysis, is a time and resource-consuming approach and can predict only smaller areas. With the significant development of remote sensing and hyperspectral (HS) imaging technologies, soil moisture, carbon, and nitrogen can be estimated over vast areas. This paper presents a generalized approach to predicting three different essential soil contents using a comprehensive study of various machine learning (ML) models by considering the dimensional reduction in feature spaces. In this study, we have used three popular benchmark HS datasets captured in Germany and Sweden. The efficacy of different ML algorithms is evaluated to predict soil content, and significant improvement is obtained when a specific range of bands is selected. The performance of ML models is further improved by applying principal component analysis (PCA), a dimensional reduction method that works with an unsupervised learning method. The effect of soil temperature on soil moisture prediction is evaluated in this study, and the results show that when the soil temperature is considered with the HS band, the soil moisture prediction accuracy does not improve. However, the combined effect of band selection and feature transformation using PCA significantly enhances the prediction accuracy for soil moisture, carbon, and nitrogen content. This study represents a comprehensive analysis of a wide range of established ML regression models using data preprocessing, effective band selection, and data dimension reduction and attempt to understand which feature combinations provide the best accuracy. The outcomes of several ML models are verified with validation techniques and the best- and worst-case scenarios in terms of soil content are noted. The proposed approach outperforms existing estimation techniques.
Secondary stroke prevention in polish adults: Results from the lipidogram2015 study
- Labuz-Roszak, Beata, Banach, Maciej, Skrzypek, Michal, Windak, Adam, Charchar, Fadi
- Authors: Labuz-Roszak, Beata , Banach, Maciej , Skrzypek, Michal , Windak, Adam , Charchar, Fadi
- Date: 2021
- Type: Text , Journal article
- Relation: Journal of Clinical Medicine Vol. 10, no. 19 (2021), p.
- Full Text:
- Reviewed:
- Description: Background: The purpose of the study was to evaluate secondary stroke prevention in Poland and its association with sociodemographic factors, place of residence, and concomitant cardiovascular risk factors. Material and methods: From all patients in LIPIDOGRAM2015 Study (n = 13,724), 268 subjects had a history of ischaemic stroke and were included. Results: 165 subjects (61.6%) used at least one preventive medication. Oral antiplatelet and anticoagulation agents were used by 116 (43.3%) and 70 (26.1%) patients, respectively. Only 157 (58.6%) participants used lipid-lowering drugs, and 205 (76.5%) were treated with antihypertensive drugs. Coronary heart disease (CHD) and dyslipidaemia were associated with antiplatelet treatment (p = 0.047 and p = 0.012, respectively). A history of atrial fibrillation, CHD, and previous myocardial infarction correlated with anticoagulant treatment (p = 0.001, p = 0.011, and p < 0.0001, respectively). Age, gender, time from stroke onset, place of residence, and level of education were not associated with antiplatelet or anticoagulant treatment. Only 31.7% of patients were engaged in regular physical activity, 62% used appropriate diet, and 13.6% were current smokers. Conclusions: In Poland drugs and lifestyle modification for secondary stroke prevention are not commonly adhered to. Educational programmes for physicians and patients should be developed to improve application of effective secondary prevention of stroke. © 2021 by the authors. **Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Fadi Charchar” is provided in this record**
- Authors: Labuz-Roszak, Beata , Banach, Maciej , Skrzypek, Michal , Windak, Adam , Charchar, Fadi
- Date: 2021
- Type: Text , Journal article
- Relation: Journal of Clinical Medicine Vol. 10, no. 19 (2021), p.
- Full Text:
- Reviewed:
- Description: Background: The purpose of the study was to evaluate secondary stroke prevention in Poland and its association with sociodemographic factors, place of residence, and concomitant cardiovascular risk factors. Material and methods: From all patients in LIPIDOGRAM2015 Study (n = 13,724), 268 subjects had a history of ischaemic stroke and were included. Results: 165 subjects (61.6%) used at least one preventive medication. Oral antiplatelet and anticoagulation agents were used by 116 (43.3%) and 70 (26.1%) patients, respectively. Only 157 (58.6%) participants used lipid-lowering drugs, and 205 (76.5%) were treated with antihypertensive drugs. Coronary heart disease (CHD) and dyslipidaemia were associated with antiplatelet treatment (p = 0.047 and p = 0.012, respectively). A history of atrial fibrillation, CHD, and previous myocardial infarction correlated with anticoagulant treatment (p = 0.001, p = 0.011, and p < 0.0001, respectively). Age, gender, time from stroke onset, place of residence, and level of education were not associated with antiplatelet or anticoagulant treatment. Only 31.7% of patients were engaged in regular physical activity, 62% used appropriate diet, and 13.6% were current smokers. Conclusions: In Poland drugs and lifestyle modification for secondary stroke prevention are not commonly adhered to. Educational programmes for physicians and patients should be developed to improve application of effective secondary prevention of stroke. © 2021 by the authors. **Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Fadi Charchar” is provided in this record**
Fasting triglycerides are positively associated with cardiovascular mortality risk in people with diabetes
- Wang, Yutang, Fang, Yan, Magliano, Dianna, Charchar, Fadi, Sobey, Christopher, Drummond, Grant, Golledge, Jonathan
- Authors: Wang, Yutang , Fang, Yan , Magliano, Dianna , Charchar, Fadi , Sobey, Christopher , Drummond, Grant , Golledge, Jonathan
- Date: 2023
- Type: Text , Journal article
- Relation: Cardiovascular Research Vol. 119, no. 3 (2023), p. 826-834
- Relation: https://purl.org/au-research/grants/nhmrc/1062671
- Full Text:
- Reviewed:
- Description: Aims We investigated the association of fasting triglycerides with cardiovascular disease (CVD) mortality. Methods and results This cohort study included US adults from the National Health and Nutrition Examination Surveys from 1988 to 2014. CVD mortality outcomes were ascertained by linkage to the National Death Index records. Cox proportional hazards models were used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) of triglycerides for CVD mortality. The cohort included 26 570 adult participants, among which 3978 had diabetes. People with higher triglycerides had a higher prevalence of diabetes at baseline. The cohort was followed up for a mean of 12.0 years with 1492 CVD deaths recorded. A 1-natural-log-unit higher triglyceride was associated with a 30% higher multivariate-adjusted risk of CVD mortality in participants with diabetes (HR, 1.30; 95% CI, 1.08–1.56) but not in those without diabetes (HR, 0.95; 95% CI, 0.83–1.07). In participants with diabetes, people with high triglycerides (200–499 mg/dL) had a 44% (HR, 1.44; 95% CI, 1.12–1.85) higher multivariate-adjusted risk of CVD mortality compared with those with normal triglycerides (<150 mg/dL). The findings remained significant when diabetes was defined by fasting glucose levels alone, or after further adjustment for the use of lipid-lowering medications, or after the exclusion of those who took lipid-lowering medications. Conclusion This study demonstrates that fasting triglycerides of
- Authors: Wang, Yutang , Fang, Yan , Magliano, Dianna , Charchar, Fadi , Sobey, Christopher , Drummond, Grant , Golledge, Jonathan
- Date: 2023
- Type: Text , Journal article
- Relation: Cardiovascular Research Vol. 119, no. 3 (2023), p. 826-834
- Relation: https://purl.org/au-research/grants/nhmrc/1062671
- Full Text:
- Reviewed:
- Description: Aims We investigated the association of fasting triglycerides with cardiovascular disease (CVD) mortality. Methods and results This cohort study included US adults from the National Health and Nutrition Examination Surveys from 1988 to 2014. CVD mortality outcomes were ascertained by linkage to the National Death Index records. Cox proportional hazards models were used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) of triglycerides for CVD mortality. The cohort included 26 570 adult participants, among which 3978 had diabetes. People with higher triglycerides had a higher prevalence of diabetes at baseline. The cohort was followed up for a mean of 12.0 years with 1492 CVD deaths recorded. A 1-natural-log-unit higher triglyceride was associated with a 30% higher multivariate-adjusted risk of CVD mortality in participants with diabetes (HR, 1.30; 95% CI, 1.08–1.56) but not in those without diabetes (HR, 0.95; 95% CI, 0.83–1.07). In participants with diabetes, people with high triglycerides (200–499 mg/dL) had a 44% (HR, 1.44; 95% CI, 1.12–1.85) higher multivariate-adjusted risk of CVD mortality compared with those with normal triglycerides (<150 mg/dL). The findings remained significant when diabetes was defined by fasting glucose levels alone, or after further adjustment for the use of lipid-lowering medications, or after the exclusion of those who took lipid-lowering medications. Conclusion This study demonstrates that fasting triglycerides of
Interactive effect of elevated CO2 and drought on physiological traits of Datura stramonium
- Javaid, Muhammad, Florentine, Singarayer, Mahmood, Athar, Wasaya, Allah, Javed, Talha, Sattar, Abdul, Sarwar, Naeem, Kalaji, Hazem, Ahmad, Hafiz, Worbel, Jacek, Ahmed, Mohammed, Telesiński, Arkadiusz, Mojski, Jacek
- Authors: Javaid, Muhammad , Florentine, Singarayer , Mahmood, Athar , Wasaya, Allah , Javed, Talha , Sattar, Abdul , Sarwar, Naeem , Kalaji, Hazem , Ahmad, Hafiz , Worbel, Jacek , Ahmed, Mohammed , Telesiński, Arkadiusz , Mojski, Jacek
- Date: 2022
- Type: Text , Journal article
- Relation: Frontiers in Plant Science Vol. 13, no. (2022), p.
- Full Text:
- Reviewed:
- Description: Rising atmospheric CO2 concentrations are known to influence the response of many plants under drought. This paper aimed to measure the leaf gas exchange, water use efficiency, carboxylation efficiency, and photosystem II (PS II) activity of Datura stramonium under progressive drought conditions, along with ambient conditions of 400 ppm (aCO2) and elevated conditions of 700 ppm (eCO2). Plants of D. stramonium were grown at 400 ppm and 700 ppm under 100 and 60% field capacity in a laboratory growth chamber. For 10 days at two-day intervals, photosynthesis rate, stomatal conductance, transpiration rate, intercellular CO2 concentration, water use efficiency, intrinsic water use efficiency, instantaneous carboxylation efficiency, PSII activity, electron transport rate, and photochemical quenching were measured. While drought stress had generally negative effects on the aforementioned physiological traits of D. stramonium, it was found that eCO2 concentration mitigated the adverse effects of drought and most of the physiological parameters were sustained with increasing drought duration when compared to that with aCO2. D. stramonium, which was grown under drought conditions, was re-watered on day 8 and indicated a partial recovery in all the parameters except maximum fluorescence, with this recovery being higher with eCO2 compared to aCO2. These results suggest that elevated CO2 mitigates the adverse growth effects of drought, thereby enhancing the adaptive mechanism of this weed by improving its water use efficiency. It is concluded that this weed has the potential to take advantage of climate change by increasing its competitiveness with other plants in drought-prone areas, suggesting that it could expand into new localities. Copyright © 2022 Javaid, Florentine, Mahmood, Wasaya, Javed, Sattar, Sarwar, Kalaji, Ahmad, Worbel, Ahmed, Telesiński and Mojski.
- Authors: Javaid, Muhammad , Florentine, Singarayer , Mahmood, Athar , Wasaya, Allah , Javed, Talha , Sattar, Abdul , Sarwar, Naeem , Kalaji, Hazem , Ahmad, Hafiz , Worbel, Jacek , Ahmed, Mohammed , Telesiński, Arkadiusz , Mojski, Jacek
- Date: 2022
- Type: Text , Journal article
- Relation: Frontiers in Plant Science Vol. 13, no. (2022), p.
- Full Text:
- Reviewed:
- Description: Rising atmospheric CO2 concentrations are known to influence the response of many plants under drought. This paper aimed to measure the leaf gas exchange, water use efficiency, carboxylation efficiency, and photosystem II (PS II) activity of Datura stramonium under progressive drought conditions, along with ambient conditions of 400 ppm (aCO2) and elevated conditions of 700 ppm (eCO2). Plants of D. stramonium were grown at 400 ppm and 700 ppm under 100 and 60% field capacity in a laboratory growth chamber. For 10 days at two-day intervals, photosynthesis rate, stomatal conductance, transpiration rate, intercellular CO2 concentration, water use efficiency, intrinsic water use efficiency, instantaneous carboxylation efficiency, PSII activity, electron transport rate, and photochemical quenching were measured. While drought stress had generally negative effects on the aforementioned physiological traits of D. stramonium, it was found that eCO2 concentration mitigated the adverse effects of drought and most of the physiological parameters were sustained with increasing drought duration when compared to that with aCO2. D. stramonium, which was grown under drought conditions, was re-watered on day 8 and indicated a partial recovery in all the parameters except maximum fluorescence, with this recovery being higher with eCO2 compared to aCO2. These results suggest that elevated CO2 mitigates the adverse growth effects of drought, thereby enhancing the adaptive mechanism of this weed by improving its water use efficiency. It is concluded that this weed has the potential to take advantage of climate change by increasing its competitiveness with other plants in drought-prone areas, suggesting that it could expand into new localities. Copyright © 2022 Javaid, Florentine, Mahmood, Wasaya, Javed, Sattar, Sarwar, Kalaji, Ahmad, Worbel, Ahmed, Telesiński and Mojski.
Psychological distress, fear and coping strategies among hong kong people during the COVID-19 pandemic
- Chair, Sek, Chien, Wai, Liu, Ting, Lam, Louisa, Cross, Wendy, Banik, Biswajit, Rahman, Muhammad Aziz
- Authors: Chair, Sek , Chien, Wai , Liu, Ting , Lam, Louisa , Cross, Wendy , Banik, Biswajit , Rahman, Muhammad Aziz
- Date: 2023
- Type: Text , Journal article
- Relation: Current Psychology Vol. 42, no. 3 (2023), p. 2538-2557
- Full Text:
- Reviewed:
- Description: The COVID-19 pandemic contributed to potential adverse effects on the mental health status of a wide range of people. This study aimed to identify factors associated with psychological distress, fear and coping strategies during the COVID-19 pandemic in Hong Kong. A cross-sectional online survey was conducted among general population in Hong Kong. Psychological distress was assessed using the Kessler Psychological Distress Scale; level of fear was evaluated using the Fear of COVID-19 scale; and coping strategies were assessed using the Brief Resilient Coping Scale. Multivariable logistic regression was used to identify key factors associated with these mental health variables. Of the 555 participants, 53.9% experienced moderate to very high levels of psychological distress, 31.2% experienced a high level of fear of COVID-19, and 58.6% showed moderate to high resilient coping. Multivariable logistic regression indicated that living with family members, current alcohol consumption, and higher level of fear were associated with higher levels of psychological distress; perceived stress due to a change in employment condition, being a frontline worker, experiencing ‘moderate to very high’ distress, and healthcare service use to overcome the COVID-19 related stress in past 6 months were associated with a higher level of fear; and perceived better mental health status was associated with a moderate to high resilient coping. This study identified key factors associated with distress, fear and coping strategies during the pandemic in Hong Kong. Mental health support strategies should be provided continuously to prevent the mental impact of the pandemic from turning into long-term illness. © 2021, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
- Authors: Chair, Sek , Chien, Wai , Liu, Ting , Lam, Louisa , Cross, Wendy , Banik, Biswajit , Rahman, Muhammad Aziz
- Date: 2023
- Type: Text , Journal article
- Relation: Current Psychology Vol. 42, no. 3 (2023), p. 2538-2557
- Full Text:
- Reviewed:
- Description: The COVID-19 pandemic contributed to potential adverse effects on the mental health status of a wide range of people. This study aimed to identify factors associated with psychological distress, fear and coping strategies during the COVID-19 pandemic in Hong Kong. A cross-sectional online survey was conducted among general population in Hong Kong. Psychological distress was assessed using the Kessler Psychological Distress Scale; level of fear was evaluated using the Fear of COVID-19 scale; and coping strategies were assessed using the Brief Resilient Coping Scale. Multivariable logistic regression was used to identify key factors associated with these mental health variables. Of the 555 participants, 53.9% experienced moderate to very high levels of psychological distress, 31.2% experienced a high level of fear of COVID-19, and 58.6% showed moderate to high resilient coping. Multivariable logistic regression indicated that living with family members, current alcohol consumption, and higher level of fear were associated with higher levels of psychological distress; perceived stress due to a change in employment condition, being a frontline worker, experiencing ‘moderate to very high’ distress, and healthcare service use to overcome the COVID-19 related stress in past 6 months were associated with a higher level of fear; and perceived better mental health status was associated with a moderate to high resilient coping. This study identified key factors associated with distress, fear and coping strategies during the pandemic in Hong Kong. Mental health support strategies should be provided continuously to prevent the mental impact of the pandemic from turning into long-term illness. © 2021, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
Computationally efficient path planning algorithm for autonomous vehicle
- Debnath, Sanjoy, Omar, Rosli, Abdul Latip, Nor, Bagchi, Susama, Sabudin, Elia, Mumin, Abdul, Soomro, Abdul, Nafea, Marwan, Muhammad, Bashir, Naha, Ranesh
- Authors: Debnath, Sanjoy , Omar, Rosli , Abdul Latip, Nor , Bagchi, Susama , Sabudin, Elia , Mumin, Abdul , Soomro, Abdul , Nafea, Marwan , Muhammad, Bashir , Naha, Ranesh
- Date: 2021
- Type: Text , Journal article
- Relation: Jurnal teknologi Vol. 83, no. 1 (2021), p. 133-143
- Full Text: false
- Reviewed:
- Description: This paper analyses an experimental path planning performance between the Iterative Equilateral Space Oriented Visibility Graph (IESOVG) and conventional Visibility Graph (VG) algorithms in terms of computation time and path length for an autonomous vehicle. IESOVG is a path planning algorithm that was proposed to overcome the limitations of VG which is slow in obstacle-rich environment. The performance assessment was done in several identical scenarios through simulation. The results showed that the proposed IESOVG algorithm was much faster in comparison to VG. In terms of path length, IESOVG was found to have almost similar performance with VG. It was also found that IESOVG was complete as it could find a collision-free path in all scenarios.
Data-analytically derived flexible HbA1c thresholds for type 2 diabetes mellitus diagnostic
- Stranieri, Andrew, Yatsko, Andrew, Jelinek, Herbert, Venkatraman, Sitalakshmi
- Authors: Stranieri, Andrew , Yatsko, Andrew , Jelinek, Herbert , Venkatraman, Sitalakshmi
- Date: 2015
- Type: Text , Journal article
- Relation: Artificial Intelligence Research Vol. 5, no. 1 (2015), p. 111-134
- Full Text:
- Reviewed:
- Description: Glycated haemoglobin (HbA1c) is now more commonly used as an alternative test to the fasting plasma glucose and oral glucose tolerance tests for the identification of Type 2 Diabetes Mellitus (T2DM) because it is easily obtained using the point-of-care technology and represents long-term blood sugar levels. According to WHO guidelines, HbA1c values of 6.5% or above are required for a diagnosis of T2DM. However outcomes of a large number of trials with HbA1c have been inconsistent across the clinical spectrum and further research is required to determine the efficacy of HbA1c testing in identification of T2DM. Medical records from a diabetes screening program in Australia illustrate that many patients could be classified as diabetics if other clinical indicators are included, even though the HbA1c result does not exceed 6.5%. This suggests that a cutoff for the general population of 6.5% may be too simple and miss individuals at risk or with already overt, undiagnosed diabetes. In this study, data mining algorithms have been applied to identify markers that can be used with HbA1c. The results indicate that T2DM is best classified by HbA1c at 6.2% - a cutoff level lower than the currently recommended one, which can be even less, having assumed the threshold flexibility, if additionally to HbA1c being high the rule is conditioned on oxidative stress or inflammation being present, atherogenicity or adiposity being high, or hypertension being diagnosed, etc.
- Authors: Stranieri, Andrew , Yatsko, Andrew , Jelinek, Herbert , Venkatraman, Sitalakshmi
- Date: 2015
- Type: Text , Journal article
- Relation: Artificial Intelligence Research Vol. 5, no. 1 (2015), p. 111-134
- Full Text:
- Reviewed:
- Description: Glycated haemoglobin (HbA1c) is now more commonly used as an alternative test to the fasting plasma glucose and oral glucose tolerance tests for the identification of Type 2 Diabetes Mellitus (T2DM) because it is easily obtained using the point-of-care technology and represents long-term blood sugar levels. According to WHO guidelines, HbA1c values of 6.5% or above are required for a diagnosis of T2DM. However outcomes of a large number of trials with HbA1c have been inconsistent across the clinical spectrum and further research is required to determine the efficacy of HbA1c testing in identification of T2DM. Medical records from a diabetes screening program in Australia illustrate that many patients could be classified as diabetics if other clinical indicators are included, even though the HbA1c result does not exceed 6.5%. This suggests that a cutoff for the general population of 6.5% may be too simple and miss individuals at risk or with already overt, undiagnosed diabetes. In this study, data mining algorithms have been applied to identify markers that can be used with HbA1c. The results indicate that T2DM is best classified by HbA1c at 6.2% - a cutoff level lower than the currently recommended one, which can be even less, having assumed the threshold flexibility, if additionally to HbA1c being high the rule is conditioned on oxidative stress or inflammation being present, atherogenicity or adiposity being high, or hypertension being diagnosed, etc.
Independent directors : experience and value in contrasting economic contexts
- Philippa Wells, Moyeen, Abdul, Ingley, Coral
- Authors: Philippa Wells , Moyeen, Abdul , Ingley, Coral
- Date: 2019
- Type: Text , Book chapter
- Relation: Research Handbook on Boards of Directors p.169-192
- Full Text: false
- Reviewed:
Visual tools for analysing evolution, emergence, and error in data streams
- Hart, Sol, Yearwood, John, Bagirov, Adil
- Authors: Hart, Sol , Yearwood, John , Bagirov, Adil
- Date: 2007
- Type: Text , Conference paper
- Relation: Paper presented at 6th IEEE/ACIS International Conference on Computer and Information Science, ICIS 2007, Melbourne, Victoria : 11th-13th July 2007 p. 987-992
- Full Text:
- Description: The relatively new field of stream mining has necessitated the development of robust drift-aware algorithms that provide accurate, real time, data handling capabilities. Tools are needed to assess and diagnose important trends and investigate drift evolution parameters. In this paper, we present two new and novel visualisation techniques, Pixie and Luna graphs, which incorporate salient group statistics coupled with intuitive visual representations of multidimensional groupings over time. Through the novel representations presented here, spatial interactions between temporal divisions can be diagnosed and overall distribution patterns identified. It provides a means of evaluating in non-constrained capacity, commonly constrained evolutionary problems.
- Description: 2003005432
- Authors: Hart, Sol , Yearwood, John , Bagirov, Adil
- Date: 2007
- Type: Text , Conference paper
- Relation: Paper presented at 6th IEEE/ACIS International Conference on Computer and Information Science, ICIS 2007, Melbourne, Victoria : 11th-13th July 2007 p. 987-992
- Full Text:
- Description: The relatively new field of stream mining has necessitated the development of robust drift-aware algorithms that provide accurate, real time, data handling capabilities. Tools are needed to assess and diagnose important trends and investigate drift evolution parameters. In this paper, we present two new and novel visualisation techniques, Pixie and Luna graphs, which incorporate salient group statistics coupled with intuitive visual representations of multidimensional groupings over time. Through the novel representations presented here, spatial interactions between temporal divisions can be diagnosed and overall distribution patterns identified. It provides a means of evaluating in non-constrained capacity, commonly constrained evolutionary problems.
- Description: 2003005432