Displaying publications 21 - 40 of 291 in total

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  1. Fulltext Antifungal activities of new coumarins
    Al-Amiery AA, Kadhum AA, Mohamad AB
    Molecules, 2012 May 14;17(5):5713-23.
    PMID: 22628043 DOI: 10.3390/molecules17055713
    Newly synthesized coumarins 4-((5-mercapto-4-phenyl-4H-1,2,4-triazol-3-yl)-methoxy)-2H-chromen-2-one and 4-((5-(phenylamino)-1,3,4-thiadiazol-2-yl)-methoxy)-2H-chromen-2-one were tested against selected types of fungi and showed significant activities. DFT calculations of the synthesized coumarins were performed using molecular structures with optimized geometries. Molecular orbital calculations provide a detailed description of the orbitals, including spatial characteristics, nodal patterns, and the contributions of individual atoms.
  2. Fulltext Ligand-based virtual screening using Bayesian inference network and reweighted fragments
    Ahmed A, Abdo A, Salim N
    ScientificWorldJournal, 2012;2012:410914.
    PMID: 22623895 DOI: 10.1100/2012/410914
    Many of the similarity-based virtual screening approaches assume that molecular fragments that are not related to the biological activity carry the same weight as the important ones. This was the reason that led to the use of Bayesian networks as an alternative to existing tools for similarity-based virtual screening. In our recent work, the retrieval performance of the Bayesian inference network (BIN) was observed to improve significantly when molecular fragments were reweighted using the relevance feedback information. In this paper, a set of active reference structures were used to reweight the fragments in the reference structure. In this approach, higher weights were assigned to those fragments that occur more frequently in the set of active reference structures while others were penalized. Simulated virtual screening experiments with MDL Drug Data Report datasets showed that the proposed approach significantly improved the retrieval effectiveness of ligand-based virtual screening, especially when the active molecules being sought had a high degree of structural heterogeneity.
  3. Implementing relevance feedback in ligand-based virtual screening using Bayesian inference network
    Abdo A, Salim N, Ahmed A
    J Biomol Screen, 2011 Oct;16(9):1081-8.
    PMID: 21862688 DOI: 10.1177/1087057111416658
    Recently, the use of the Bayesian network as an alternative to existing tools for similarity-based virtual screening has received noticeable attention from researchers in the chemoinformatics field. The main aim of the Bayesian network model is to improve the retrieval effectiveness of similarity-based virtual screening. To this end, different models of the Bayesian network have been developed. In our previous works, the retrieval performance of the Bayesian network was observed to improve significantly when multiple reference structures or fragment weightings were used. In this article, the authors enhance the Bayesian inference network (BIN) using the relevance feedback information. In this approach, a few high-ranking structures of unknown activity were filtered from the outputs of BIN, based on a single active reference structure, to form a set of active reference structures. This set of active reference structures was used in two distinct techniques for carrying out such BIN searching: reweighting the fragments in the reference structures and group fusion techniques. Simulated virtual screening experiments with three MDL Drug Data Report data sets showed that the proposed techniques provide simple ways of enhancing the cost-effectiveness of ligand-based virtual screening searches, especially for higher diversity data sets.
  4. Evaluation of groundwater and soil pollution in a landfill area using electrical resistivity imaging survey
    Ahmed AM, Sulaiman WN
    Environ Manage, 2001 Nov;28(5):655-63.
    PMID: 11568845
    Landfills are sources of groundwater and soil pollution due to the production of leachate and its migration through refuse. This study was conducted in order to determine the extent of groundwater and soil pollution within and around the landfill of Seri Petaling located in the State of Selangor, Malaysia. The condition of nearby surface water was also determined. An electrical resistivity imaging survey was used to investigate the leachate production within the landfill. Groundwater geochemistry was carried out and chemical analysis of water samples was conducted upstream and downstream of the landfill. Surface water was also analyzed in order to determine its quality. Soil chemical analysis was performed on soil samples taken from different locations within and around the landfill in the vadose zone (unsaturated zone) and below the water table (in the soil saturated zone). The resistivity image along line L-L1 indicated the presence of large zones of decomposed waste bodies saturated with highly conducting leachate. Analysis of trace elements indicated their presence in very low concentrations and did not reflect any sign of heavy metal pollution of ground and surface water or of soil. Major ions represented by Na, K, and Cl were found in anomalous concentrations in the groundwater of the downstream bore hole, where they are 99.1%, 99.2%, and 99.4%, respectively, higher compared to the upstream bore hole. Electrical conductivity (EC) was also found in anomalous concentration downstream. Ca and Mg ions represent the water hardness (which is comparatively high downstream). There is a general trend of pollution towards the downstream area. Sulfates (SO4) and nitrates (NO3) are found in the area in low concentrations, even below the WHO standards for drinking water, but are significantly higher in the surface water compared to the groundwater. Phosphate (PO4) and nitrite (NO2), although present in low levels, are significantly higher at the downstream. There is no significant difference in the amount of fluoride (F) in the different locations. In the soil vadose zone, heavy metals were found to be in their typical normal ranges and within the background concentrations. Soil exchangeable bases were significantly higher in the soil saturated zone compared to the vadose zone, and no significant difference was obtained in the levels of inorganic pollutants. With the exception of Cd, the concentration ranges of all trace elements (Cu, Zn, Cr, Pb, and Ni) of Seri Petaling landfill soils were below the upper limits of baseline concentrations published from different sources.
  5. Fulltext Experimental relationships between surface roughness, irradiation time and photodecomposition rate constant of pvc films doped by polyphosphates
    Yousif, Emad, Ahmed, Dina S., Ahmed, Ahmed A., Hameed, Ayad S., Yusop, Rahimi M., Redwan, Amamer, et al.
    Science Letters, 2018;12(2):19-27.
    MyJurnal
    The photodegradation rate constant and surface morphology of poly(vinyl chloride), upon irradiation with ultraviolet light was investigated in the presence of polyphosphates as photostabilizers. Poly(vinyl chloride) photodegradation rate constant was lower for the films containing polyphosphates compared to the blank film. In addition, the surface morphology of the irradiated poly(vinyl chloride) containing polyphosphates, examined by scanning electron microscopy, indicates that the surface was much smoother compared to the blank film.
  6. Fulltext Condorcet and borda count fusion method for ligand-based virtual screening
    Ahmed A, Saeed F, Salim N, Abdo A
    J Cheminform, 2014;6:19.
    PMID: 24883114 DOI: 10.1186/1758-2946-6-19
    BACKGROUND: It is known that any individual similarity measure will not always give the best recall of active molecule structure for all types of activity classes. Recently, the effectiveness of ligand-based virtual screening approaches can be enhanced by using data fusion. Data fusion can be implemented using two different approaches: group fusion and similarity fusion. Similarity fusion involves searching using multiple similarity measures. The similarity scores, or ranking, for each similarity measure are combined to obtain the final ranking of the compounds in the database.

    RESULTS: The Condorcet fusion method was examined. This approach combines the outputs of similarity searches from eleven association and distance similarity coefficients, and then the winner measure for each class of molecules, based on Condorcet fusion, was chosen to be the best method of searching. The recall of retrieved active molecules at top 5% and significant test are used to evaluate our proposed method. The MDL drug data report (MDDR), maximum unbiased validation (MUV) and Directory of Useful Decoys (DUD) data sets were used for experiments and were represented by 2D fingerprints.

    CONCLUSIONS: Simulated virtual screening experiments with the standard two data sets show that the use of Condorcet fusion provides a very simple way of improving the ligand-based virtual screening, especially when the active molecules being sought have a lowest degree of structural heterogeneity. However, the effectiveness of the Condorcet fusion was increased slightly when structural sets of high diversity activities were being sought.

  7. Epidemiology of soil-transmitted helminthiases in Malaysia
    Ahmed A, Al-Mekhlafi HM, Surin J
    Southeast Asian J. Trop. Med. Public Health, 2011 May;42(3):527-38.
    PMID: 21706930
    We reviewed the epidemiology of STH in Malaysia from the 1970s to 2009. High prevalence rates persist among the rural Aborigines, estate workers and in urban slums and squatter areas. Trichuris trichiura is the most prevalent helminth in Malaysia ranging from 2.1% to 98.2%. Ascaris lumbricoides follows closely with a prevalence rate of 4.6-86.7%, while hookworm is the least prevalent (0-37.0%). A countrywide control program with special emphasis on school-based intervention is highly recommended among aboriginal people.
  8. Fulltext Coronavirus outbreaks: prevention and management recommendations
    Khan Z, Muhammad K, Ahmed A, Rahman H
    Drugs Ther Perspect, 2020 Mar 07.
    PMID: 32218651 DOI: 10.1007/s40267-020-00717-x
  9. Fulltext The crux of Pakistan's prolonged rabies vaccine shortage: A rising mortal threat in the COVID-19 pandemic
    Siddiqui A, Ahmed A, Tanveer M, Arshad A
    J Med Virol, 2021 Sep;93(9):5221-5222.
    PMID: 33851738 DOI: 10.1002/jmv.27024
  10. Workplace Cyberbullying and Interpersonal Deviance: Understanding the Mediating Effect of Silence and Emotional Exhaustion
    Anwar A, Kee DMH, Ahmed A
    Cyberpsychol Behav Soc Netw, 2020 May;23(5):290-296.
    PMID: 32282237 DOI: 10.1089/cyber.2019.0407
    Workplace cyberbullying (WCB) is a new form of hostility in organizations in which information technology is used as a means to bully employees. The objective of this study is to determine the association between WCB and the interpersonal deviance (ID) of victims through parallel mediation through the ineffectual silence of employees and emotional exhaustion (EE). Conservation of resource (COR) theory and affective events theory were used as the study's guiding framework, and data were drawn from 351 white-collar employees who were employed in a variety of industries-such as banking, telecommunications sector, education, health care, insurance, and consultancy-in Lahore, Pakistan. The results show that ineffectual silence negatively mediated the relationship between cyberbullying and deviance, decreasing the level of deviance of employees who used silence as a coping mechanism. EE, however, positively mediated the relationship between cyberbullying and deviance. This means that when employees felt emotionally overwhelmed they retaliated by engaging in deviant behaviors and acting as a bully toward colleagues. Drawing on the COR theory and the affective events theory, the findings show that WCB has an impact on ID. From a practical standpoint, the study reveals that WCB can lead to ID and it also may associate with large financial costs and workplace disruptions. Thus, organizations should establish a culture that prevent employees from engaging in WCB and adopt practices of prevention and intervention because it is not only harmful to the employees but also to the organization.
  11. Fulltext The adoption of deep learning interpretability techniques on diabetic retinopathy analysis: a review
    Lim WX, Chen Z, Ahmed A
    Med Biol Eng Comput, 2022 Mar;60(3):633-642.
    PMID: 35083634 DOI: 10.1007/s11517-021-02487-8
    Diabetic retinopathy (DR) is a chronic eye condition that is rapidly growing due to the prevalence of diabetes. There are challenges such as the dearth of ophthalmologists, healthcare resources, and facilities that are unable to provide patients with appropriate eye screening services. As a result, deep learning (DL) has the potential to play a critical role as a powerful automated diagnostic tool in the field of ophthalmology, particularly in the early detection of DR when compared to traditional detection techniques. The DL models are known as black boxes, despite the fact that they are widely adopted. They make no attempt to explain how the model learns representations or why it makes a particular prediction. Due to the black box design architecture, DL methods make it difficult for intended end-users like ophthalmologists to grasp how the models function, preventing model acceptance for clinical usage. Recently, several studies on the interpretability of DL methods used in DR-related tasks such as DR classification and segmentation have been published. The goal of this paper is to provide a detailed overview of interpretability strategies used in DR-related tasks. This paper also includes the authors' insights and future directions in the field of DR to help the research community overcome research problems.
  12. Errors in accident data, its types, causes and methods of rectification-analysis of the literature
    Ahmed A, Sadullah AFM, Yahya AS
    Accid Anal Prev, 2019 Sep;130:3-21.
    PMID: 28764851 DOI: 10.1016/j.aap.2017.07.018
    Most of the decisions taken to improve road safety are based on accident data, which makes it the back bone of any country's road safety system. Errors in this data will lead to misidentification of black spots and hazardous road segments, projection of false estimates pertinent to accidents and fatality rates, and detection of wrong parameters responsible for accident occurrence, thereby making the entire road safety exercise ineffective. Its extent varies from country to country depending upon various factors. Knowing the type of error in the accident data and the factors causing it enables the application of the correct method for its rectification. Therefore there is a need for a systematic literature review that addresses the topic at a global level. This paper fulfils the above research gap by providing a synthesis of literature for the different types of errors found in the accident data of 46 countries across the six regions of the world. The errors are classified and discussed with respect to each type and analysed with respect to income level; assessment with regard to the magnitude for each type is provided; followed by the different causes that result in their occurrence, and the various methods used to address each type of error. Among high-income countries the extent of error in reporting slight, severe, non-fatal and fatal injury accidents varied between 39-82%, 16-52%, 12-84%, and 0-31% respectively. For middle-income countries the error for the same categories varied between 93-98%, 32.5-96%, 34-99% and 0.5-89.5% respectively. The only four studies available for low-income countries showed that the error in reporting non-fatal and fatal accidents varied between 69-80% and 0-61% respectively. The logistic relation of error in accident data reporting, dichotomised at 50%, indicated that as the income level of a country increases the probability of having less error in accident data also increases. Average error in recording information related to the variables in the categories of location, victim's information, vehicle's information, and environment was 27%, 37%, 16% and 19% respectively. Among the causes identified for errors in accident data reporting, Policing System was found to be the most important. Overall 26 causes of errors in accident data were discussed out of which 12 were related to reporting and 14 were related to recording. "Capture-Recapture" was the most widely used method among the 11 different methods: that can be used for the rectification of under-reporting. There were 12 studies pertinent to the rectification of accident location and almost all of them utilised a Geographical Information System (GIS) platform coupled with a matching algorithm to estimate the correct location. It is recommended that the policing system should be reformed and public awareness should be created to help reduce errors in accident data.
  13. Modeling technical change in climate analysis: evidence from agricultural crop damages
    Ahmed A, Devadason ES, Al-Amin AQ
    Environ Sci Pollut Res Int, 2017 May;24(13):12347-12359.
    PMID: 28357797 DOI: 10.1007/s11356-017-8747-5
    This study accounts for the Hicks neutral technical change in a calibrated model of climate analysis, to identify the optimum level of technical change for addressing climate changes. It demonstrates the reduction to crop damages, the costs to technical change, and the net gains for the adoption of technical change for a climate-sensitive Pakistan economy. The calibrated model assesses the net gains of technical change for the overall economy and at the agriculture-specific level. The study finds that the gains of technical change are overwhelmingly higher than the costs across the agriculture subsectors. The gains and costs following technical change differ substantially for different crops. More importantly, the study finds a cost-effective optimal level of technical change that potentially reduces crop damages to a minimum possible level. The study therefore contends that the climate policy for Pakistan should consider the role of technical change in addressing climate impacts on the agriculture sector.
  14. Implications of climate change damage for agriculture: sectoral evidence from Pakistan
    Ahmed A, Devadason ES, Al-Amin AQ
    Environ Sci Pollut Res Int, 2016 Oct;23(20):20688-20699.
    PMID: 27473615
    This paper gives a projection of the possible damage of climate change on the agriculture sector of Pakistan for the period 2012-2037, based on a dynamic approach, using an environment-related applied computable general equilibrium model (CGE). Climate damage projections depict an upward trend for the period of review and are found to be higher than the global average. Further, the damage to the agricultural sector exceeds that for the overall economy. By sector, climatic damage disproportionately affects the major and minor crops, livestock and fisheries. The largest losses following climate change, relative to the other agricultural sectors, are expected for livestock. The reason for this is the orthodox system of production for livestock, with a low adaptability to negative shocks of climate change. Overall, the findings reveal the high exposure of the agriculture sector to climate damage. In this regard, policymakers in Pakistan should take seriously the effects of climate change on agriculture and consider suitable technology to mitigate those damages.
  15. COP negotiations and Malaysian climate change roadmap: a comparative assessment using a dynamic environmental model
    Ahmed A, Al-Amin AQ, Rasiah R
    Environ Sci Pollut Res Int, 2019 Oct;26(29):30003-30015.
    PMID: 31414393 DOI: 10.1007/s11356-019-06141-7
    This study critically evaluates two COP proposals on Malaysia that have been under consideration to reduce climate damage. A top-down disaggregation framework deploying an "Empirical Regional Downscaling Dynamic Integrated Model of Climate and the Economy" is used to evaluate the local government climate roadmap and Malaysia's emissions reduction agendas under COP21 and subsequently COP22 proposals. The findings show that the costs from climate damage over the period 2010-2110 under the Malaysian Optimal Climate Action scenario will amount to MYR5,483 (US$1589) billion. The commensurate climate damage costs under the COP21 and COP22 scenario would be MYR5, 264 (US$1526) billion. Thus, the effective proposal for reducing climate damage in Malaysia over the period 2010-2110 is the COP22 time-adjusted COP21 proposal but there are a number of macroeconomic cost implications for savings and consumption that policy makers must address before acting.
  16. Fulltext Antioxidant Activities of 4-Methylumbelliferone Derivatives
    Al-Majedy YK, Al-Amiery AA, Kadhum AA, Mohamad AB
    PLoS One, 2016;11(5):e0156625.
    PMID: 27243231 DOI: 10.1371/journal.pone.0156625
    The synthesis of derivatives of 4-Methylumbelliferone (4-MUs), which are structurally interesting antioxidants, was performed in this study. The modification of 4-Methylumbelliferone (4-MU) by different reaction steps was performed to yield the target compounds, the 4-MUs. The 4-MUs were characterized by different spectroscopic techniques (Fourier transform infrared; FT-IR and Nuclear magnetic resonance; NMR) and micro-elemental analysis (CHNS). The in vitro antioxidant activity of the 4-MUs was evaluated in terms of their free radical scavenging activities against 2,2-diphenyl-1-picrylhydrazyl (DPPH), Nitric oxide radical scavenging activity assay, chelating activity and their (FRAP) ferric-reducing antioxidant power, which were compared with a standard antioxidant. Our results reveal that the 4-MUs exhibit excellent radical scavenging activities. The antioxidant mechanisms of the 4-MUs were also studied. Density Function Theory (DFT)-based quantum chemical studies were performed with the basis set at 3-21G. Molecular models of the synthesized compounds were studied to understand the antioxidant activity. The electron levels, namely HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital), for these synthesized antioxidants were also studied.
  17. Fulltext Properties and Applications of Polyvinyl Alcohol, Halloysite Nanotubes and Their Nanocomposites
    Gaaz TS, Sulong AB, Akhtar MN, Kadhum AA, Mohamad AB, Al-Amiery AA
    Molecules, 2015;20(12):22833-47.
    PMID: 26703542 DOI: 10.3390/molecules201219884
    The aim of this review was to analyze/investigate the synthesis, properties, and applications of polyvinyl alcohol-halloysite nanotubes (PVA-HNT), and their nanocomposites. Different polymers with versatile properties are attractive because of their introduction and potential uses in many fields. Synthetic polymers, such as PVA, natural polymers like alginate, starch, chitosan, or any material with these components have prominent status as important and degradable materials with biocompatibility properties. These materials have been developed in the 1980s and are remarkable because of their recyclability and consideration of the natural continuation of their physical and chemical properties. The fabrication of PVA-HNT nanocomposites can be a potential way to address some of PVA's limitations. Such nanocomposites have excellent mechanical properties and thermal stability. PVA-HNT nanocomposites have been reported earlier, but without proper HNT individualization and PVA modifications. The properties of PVA-HNT for medicinal and biomedical use are attracting an increasing amount of attention for medical applications, such as wound dressings, drug delivery, targeted-tissue transportation systems, and soft biomaterial implants. The demand for alternative polymeric medical devices has also increased substantially around the world. This paper reviews individualized HNT addition along with crosslinking of PVA for various biomedical applications that have been previously reported in literature, thereby showing the attainability, modification of characteristics, and goals underlying the blending process with PVA.
  18. Fulltext New coumarin derivative as an eco-friendly inhibitor of corrosion of mild steel in Acid medium
    Al-Amiery AA, Al-Majedy YK, Kadhum AA, Mohamad AB
    Molecules, 2014 Dec 29;20(1):366-83.
    PMID: 25551187 DOI: 10.3390/molecules20010366
    The anticorrosion ability of a synthesized coumarin, namely 2-(coumarin-4-yloxy)acetohydrazide (EFCI), for mild steel (MS) in 1 M hydrochloric acid solution has been studied using a weight loss method. The effect of temperature on the corrosion rate was investigated, and some thermodynamic parameters were calculated. The results indicated that inhibition efficiencies were enhanced with an increase in concentration of inhibitor and decreased with a rise in temperature. The IE value reaches 94.7% at the highest used concentration of the new eco-friendly inhibitor. The adsorption of inhibitor on MS surface was found to obey a Langmuir adsorption isotherm. Scanning electron microscopy (SEM) was performed on inhibited and uninhibited mild steel samples to characterize the surface. The Density Function theory (DFT) was employed for quantum-chemical calculations such as EHOMO (highest occupied molecular orbital energy), ELUMO (lowest unoccupied molecular orbital energy) and μ (dipole moment), and the obtained results were found to be consistent with the experimental findings. The synthesized inhibitor was characterized by Fourier transform infrared (FTIR) and nuclear magnetic resonance (NMR) spectroscopic studies.
  19. Fulltext Enhancement of the wear resistance and microhardness of aluminum alloy by Nd:YaG laser treatment
    Hussein HT, Kadhim A, Al-Amiery AA, Kadhum AA, Mohamad AB
    ScientificWorldJournal, 2014;2014:842062.
    PMID: 25136694 DOI: 10.1155/2014/842062
    Influence of laser treatment on mechanical properties, wear resistance, and Vickers hardness of aluminum alloy was studied. The specimens were treated by using Nd:YaG laser of energy 780 mj, wavelength 512 nm, and duration time 8 ns. The wear behavior of the specimens was studied for all specimens before and after treatment by Nd:YaG laser and the dry wear experiments were carried out by sing pinon-disc technique. The specimens were machined as a disk with diameter of 25 mm and circular groove in depth of 3 mm. All specimens were conducted by scanning electron microscopy (SEM), energy-dispersive X-ray fluorescence analysis (EDS), optical microscopy, and Vickers hardness. The results showed that the dry wear rate was decreased after laser hardening and increased Vickers hardness values by ratio of 2.4:1. The results showed that the values of wear rate for samples having circular grooves are less than samples without grooves after laser treatment.
  20. Fulltext Synthesis and characterization of some new 4-hydroxy-coumarin derivatives
    Al-Majedy YK, Kadhum AA, Al-Amiery AA, Mohamad AB
    Molecules, 2014 Aug 07;19(8):11791-9.
    PMID: 25105917 DOI: 10.3390/molecules190811791
    Some novel coumarins were synthesized starting from 4-hydroxycoumarin and methyl bromoacetate. The structures of the newly obtained compounds were confirmed by elemental analysis, mass, IR and NMR spectra.
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